Index: /trunk/src/ListDir.m =================================================================== --- /trunk/src/ListDir.m (revision 2) +++ /trunk/src/ListDir.m (revision 2) @@ -0,0 +1,98 @@ +%'ListDir': scan the structure of the directory tree (for dataview.m) +%------------------------------------------------------------------------ +function [ListDevices,ListRecords,ListXml,List]=ListDir(CurrentPath,ListExperiments,ListDevices_in,ListRecords_in) + +ListRecords={}; +ListDevices={}; +ListXml={}; +irecord_tot=0; +idevice_tot=0; +ixml_tot=0; +for iexp=1:length(ListExperiments) + List.Experiment{iexp}.name=ListExperiments{iexp}; + hdir=dir(fullfile(CurrentPath,ListExperiments{iexp})); + idevice=0; + for isub=1:length(hdir)% scan the sub-directories of the current experiment + if hdir(isub).isdir + name=hdir(isub).name;%name of the current device + if ~isequal(name(1),'.')% subdirectory of the current experiment + [testnew,testselect]=test_select(name,ListDevices,ListDevices_in); + if testselect + idevice=idevice+1; + List.Experiment{iexp}.Device{idevice}.name=name; + if testnew + idevice_tot=idevice_tot+1; + ListDevices{idevice_tot}=name; + end + CurrentDevice=fullfile(CurrentPath,ListExperiments{iexp},name); + hsubxml=dir(fullfile(CurrentDevice,'*.xml'));%look at xml files in the subdirectory of the current device + if isempty(hsubxml) % the subdirectory of the current device contains directories 'Record'' + hsubdir=dir(fullfile(CurrentPath,ListExperiments{iexp},name));%list what is inside the directory 'Device' + irecord=0; + for isubsub=1:length(hsubdir)% subdirectories of the current device + if hsubdir(isubsub).isdir + RecordName=hsubdir(isubsub).name; + if ~isequal(RecordName(1),'.') + [testnew,testselect]=test_select(RecordName,ListRecords,ListRecords_in); + if testselect + if testnew + irecord_tot=irecord_tot+1; + ListRecords{irecord_tot}=RecordName; + end + irecord=irecord+1; + List.Experiment{iexp}.Device{idevice}.Record{irecord}.name=RecordName; + hsubsubxml=dir(fullfile(CurrentDevice,RecordName,'*.xml'));% + for ixml=1:length(hsubsubxml) + XmlName=hsubsubxml(ixml).name; + List.Experiment{iexp}.Device{idevice}.Record{irecord}.xmlfile{ixml}=XmlName; + testnew=test_select(XmlName,ListXml,{}); + if testnew + ixml_tot=ixml_tot+1; + ListXml{ixml_tot}=XmlName; + end + end + end + end + end + end + else + for ixml=1:length(hsubxml) + XmlName=hsubxml(ixml).name; + List.Experiment{iexp}.Device{idevice}.xmlfile{ixml}=XmlName; + testnew=test_select(XmlName,ListXml,{}); + if testnew + ixml_tot=ixml_tot+1; + ListXml{ixml_tot}=XmlName; + end + end + end + end + end + end + end +end + +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% +function [testnew,testselect]=test_select(name,ListDevices,ListDevices_in) +if ~isempty(ListDevices_in) + testnew=0; + testselect=0; + for ilist=1:length(ListDevices_in) + if isequal(name,ListDevices_in{ilist}) + testnew=1; + testselect=1; + break + end + end +else + testnew=1; + testselect=1; +end +if testnew + for ilist=1:length(ListDevices) + if isequal(name,ListDevices{ilist}) + testnew=0; + break + end + end +end Index: /trunk/src/PARAM_LINUX.xml =================================================================== --- /trunk/src/PARAM_LINUX.xml (revision 2) +++ /trunk/src/PARAM_LINUX.xml (revision 2) @@ -0,0 +1,13 @@ + + + /CIVX/bin/civ + /CIVX/bin/civ1 + /CIVX/bin/civ2 + /CIVX/bin/fix_flag + /CIVX/bin/patch_up + /CIVX/bin/interpolation + /CIVX/bin/job_folder/ + 1 + /CIVX/bin/calibration/ccal_fo + /coriolis/bigone/PROJETS/00_DATA_MANAGEMENT/XML_SCHEMAS + Index: /trunk/src/PARAM_WIN.xml =================================================================== --- /trunk/src/PARAM_WIN.xml (revision 2) +++ /trunk/src/PARAM_WIN.xml (revision 2) @@ -0,0 +1,13 @@ + + + /home/gauthier/SVN/civx/civ/civ + \\Papillon\civbin\civx2004\civ1.exe + \\Papillon\civbin\civx2004\civ2.exe + \\Papillon\civbin\civx2004\fix_flag.exe + \\Papillon\civbin\civx2004\patch.exe + + \\Papillon\civbin\job_folder1 + 1 + /CIVX/bin/calibration/ccal_fo + \\Papillon\civbin\XML_SCHEMAS + Index: /trunk/src/RUN_FIX.m =================================================================== --- /trunk/src/RUN_FIX.m (revision 2) +++ /trunk/src/RUN_FIX.m (revision 2) @@ -0,0 +1,145 @@ +%'RUN_FIX': function for fixing velocity fields: +%----------------------------------------------- +% RUN_FIX(filename,field,flagindex,thresh_vecC,thresh_vel,iter,flag_mask,maskname,fileref,fieldref) +% +%filename: name of the netcdf file (used as input and output) +%field: structure specifying the field to fix (field.vel_type='civ1' or 'civ2') +%flagindex: flag specifying which values of vec_f are removed: + % if flagindex(1)=1: vec_f=-2 vectors are removed + % if flagindex(2)=1: vec_f=3 vectors are removed + % if flagindex(3)=1: vec_f=2 vectors are removed (if iter=1) or vec_f=4 vectors are removed (if iter=2) +%iter=1 for civ1 fields and iter=2 for civ2 fields +%thresh_vecC: threshold in the image correlation vec_C +%flag_mask: =1 mask used to remove vectors (0 else) +%maskname: name of the mask image file for fix +%thresh_vel: threshold on velocity, or on the difference with the reference file fileref if exists +%inf_sup=1: remove values smaller than threshold thresh_vel, =2, larger than threshold +%fileref: .nc file name for a reference velocity (='': refrence 0 used) +%fieldref: 'civ1','filter1'...feld used in fileref + +function error=RUN_FIX(filename,field,flagindex,iter,thresh_vecC,flag_mask,maskname,thresh_vel,inf_sup,fileref,fieldref) +error=[]; %default +vel_type{1}=field.vel_type; +Field=read_civxdata(filename,[],field.vel_type); +if isfield(Field,'Txt') + error=Field.Txt; %error in reading + return +end + +if ~isfield(Field,'X') || ~isfield(Field,'Y') || ~isfield(Field,'U') || ~isfield(Field,'V') + error=['input file ' filename ' does not contain vectors in RUN_FIX.m']; %bad input file + return +end +if ~isfield(Field,'C') + Field.C=ones(size(Field.X));%correlation=1 by default +end +if ~isfield(Field,'F') + Field.F=ones(size(Field.X));%warning flag=1 by default +end +if ~isfield(Field,'FF') + Field.FF=zeros(size(Field.X));%fixflag=0 by default +end + +vec_f_unit=abs(Field.F)-10*double(uint16(abs(Field.F)/10)); %unityterm of vec_F in abs value +vec_f_sign=sign(Field.F).*vec_f_unit;% gives the unity digit of vec_f with correct sign +flag1=(flagindex(1)==1)&(vec_f_sign==-2);%removed vectors vec_f=-2 +flag2=(flagindex(2)==1)&(vec_f_sign==3);%removed vectors vec_f=3 +if iter==1 + flag3=(flagindex(3)==1)&(vec_f_sign==2); % Hart vectors +elseif iter==2 + flag3=(flagindex(3)==1)&(vec_f_sign==4); % +end +flag4=(Field.C < thresh_vecC)&(flag1~=1)&(flag2~=1)&(flag3~=1); % =1 for low vec_C vectors not previously removed + +% criterium on velocity values +delta_u=Field.U;%default without ref file +delta_v=Field.V; +if exist('fileref','var') && ~isempty(fileref) + if ~exist(fileref,'file') + error='reference file not found in RUN_FIX.m'; + display(error); + return + end + FieldRef=read_civxdata(fileref,[],fieldref); + if isfield(FieldRef,'FF') + index_true=find(FieldRef.FF==0); + FieldRef.X=FieldRef.X(index_true); + FieldRef.Y=FieldRef.Y(index_true); + FieldRef.U=FieldRef.U(index_true); + FieldRef.V=FieldRef.V(index_true); + end + if ~isfield(FieldRef,'X') || ~isfield(FieldRef,'Y') || ~isfield(FieldRef,'U') || ~isfield(FieldRef,'V') + error='reference file is not a velocity field in RUN_FIX.m '; %bad input file + return + end + if length(FieldRef.X)<=1 + errordlg('reference field with one vector or less in RUN_FIX.m') + return + end + vec_U_ref=griddata_uvmat(FieldRef.X,FieldRef.Y,FieldRef.U,Field.X,Field.Y); %interpolate vectors in the ref field + vec_V_ref=griddata_uvmat(FieldRef.X,FieldRef.Y,FieldRef.V,Field.X,Field.Y); %interpolate vectors in the ref field to the positions of the main field + delta_u=Field.U-vec_U_ref;%take the difference with the interpolated ref field + delta_v=Field.V-vec_V_ref; +end + +thresh_vel_x=thresh_vel; +thresh_vel_y=thresh_vel; +if isequal(inf_sup,1) + flag5=abs(delta_u)thresh_vel_x | abs(delta_v)>thresh_vel_y) &(flag1~=1)&(flag2~=1)&(flag3~=1)&(flag4~=1); +end + + % flag7 introduce a grey mask, matrix M +if isequal (flag_mask,1) + M=imread(maskname); + nxy=size(M); + M=reshape(M,1,nxy(1)*nxy(2)); + rangx0=[0.5 nxy(2)-0.5]; + rangy0=[0.5 nxy(1)-0.5]; + vec_x1=Field.X-Field.U/2;%beginning points + vec_x2=Field.X+Field.U/2;%end points of vectors + vec_y1=Field.Y-Field.V/2;%beginning points + vec_y2=Field.Y+Field.V/2;%end points of vectors + indx=1+round((nxy(2)-1)*(vec_x1-rangx0(1))/(rangx0(2)-rangx0(1)));% image index x at abcissa vec_x + indy=1+round((nxy(1)-1)*(vec_y1-rangy0(1))/(rangy0(2)-rangy0(1)));% image index y at ordinate vec_y + test_in=~(indx < 1 |indy < 1 | indx > nxy(2) |indy > nxy(1)); %=0 out of the mask image, 1 inside + indx=indx.*test_in+(1-test_in); %replace indx by 1 out of the mask range + indy=indy.*test_in+(1-test_in); %replace indy by 1 out of the mask range + ICOMB=((indx-1)*nxy(1)+(nxy(1)+1-indy));%determine the indices in the image reshaped in a Matlab vector + Mvalues=M(ICOMB); + flag7b=((20 < Mvalues) & (Mvalues < 200))| ~test_in'; + indx=1+round((nxy(2)-1)*(vec_x2-rangx0(1))/(rangx0(2)-rangx0(1)));% image index x at abcissa Field.X + indy=1+round((nxy(1)-1)*(vec_y2-rangy0(1))/(rangy0(2)-rangy0(1)));% image index y at ordinate vec_y + test_in=~(indx < 1 |indy < 1 | indx > nxy(2) |indy > nxy(1)); %=0 out of the mask image, 1 inside + indx=indx.*test_in+(1-test_in); %replace indx by 1 out of the mask range + indy=indy.*test_in+(1-test_in); %replace indy by 1 out of the mask range + ICOMB=((indx-1)*nxy(1)+(nxy(1)+1-indy));%determine the indices in the image reshaped in a Matlab vector + Mvalues=M(ICOMB); + flag7e=((Mvalues > 20) & (Mvalues < 200))| ~test_in'; + flag7=(flag7b|flag7e)'; +else + flag7=0; +end +flagmagenta=flag1|flag2|flag3|flag4|flag5|flag7; + +%write fix flags +[errorread,message]=fileattrib(filename); + +if ~isempty(message) && ~isequal(message.UserWrite,1) + msgbox_uvmat('ERROR',['no writting access to ' filename ' (RUN_FIX.m)']); + return +end +nc=netcdf(filename,'write'); %open netcdf file for writing +result=redef(nc); +if isempty(result), errordlg('##Bad redef operation.'),end +if iter==1 + nc.fix=1; +elseif iter==2 + nc.fix2=1; +end +%theDim=nc(field.nb) ;% get the number of velocity vectors +nc{field.fixflag}=ncfloat(field.nb); +fixflag_unit=Field.FF-10*floor(Field.FF/10); %unity term of fix_flag +nc{field.fixflag}(:)=fixflag_unit+10*flagmagenta; +close(nc); Index: /trunk/src/RUN_STLIN.m =================================================================== --- /trunk/src/RUN_STLIN.m (revision 2) +++ /trunk/src/RUN_STLIN.m (revision 2) @@ -0,0 +1,202 @@ +%'RUN_STLIN': combine velocity fields for stereo PIV +% file_A,file_B: input velocity files +%vel_type: string ='civ1' or 'civ2' +function RUN_STLIN(file_A,file_B,vel_type,file_st,nx_patch,ny_patch,thresh_patch,fileAxml,fileBxml) + + [XmlDataA,error]=imadoc2struct(fileAxml); + [XmlDataB,error]=imadoc2struct(fileBxml); + npxA=[]; npyA=[]; pxB=[]; npyB=[]; + if isfield(XmlDataA,'Camera') && isfield(XmlDataB,'Camera') + if isfield(XmlDataA.Camera,'ImageSize')&& isfield(XmlDataB.Camera,'ImageSize') + ImageSizeA=XmlDataA.Camera.ImageSize; + ImageSizeB=XmlDataB.Camera.ImageSize; + if ~isempty(ImageSizeA)&& ~isempty(ImageSizeB) + xindex=findstr(ImageSizeA,'x'); + if length(xindex)>=2 + npxA=str2num(ImageSizeA(1:xindex(1)-1)); + npyA=str2num(ImageSizeA(xindex(1)+1:xindex(2)-1)); + end + xindex=findstr(ImageSizeB,'x'); + if length(xindex)>=2 + npxB=str2num(ImageSizeB(1:xindex(1)-1)); + npyB=str2num(ImageSizeB(xindex(1)+1:xindex(2)-1)); + end + end + end + end + if isempty(npxA) ||isempty(npxB) + warndlg_uvmat('The size of image A needs to be defined in the xml file ImaDoc','ERROR') + return + elseif isempty(npxB) || isempty(npyB) + warndlg_uvmat('The size of image B needs to be defined in the xml file ImaDoc','ERROR') + return + end + if isfield(XmlDataA,'GeometryCalib') + tsaiA=XmlDataA.GeometryCalib; + else + warndlg_uvmat('no geometric calibration available for image A','ERROR') + return + end + if isfield(XmlDataB,'GeometryCalib') + tsaiB=XmlDataB.GeometryCalib; + else + warndlg_uvmat('no geometric calibration available for image B','ERROR') + return + end + + %corners of each image in real coordinates: + cornerA(:,1)=[0 0 npxA npxA]';%x positions + cornerA(:,2)=[0 npyA 0 npyA]';%y positions + cornerB(:,1)=[0 0 npxB npxB]';%x positions + cornerB(:,2)=[0 npyB 0 npyB]';%y positions +[xyA(:,1),xyA(:,2)]=phys_XYZ(tsaiA,cornerA(:,1),cornerA(:,2)); +[xyB(:,1),xyB(:,2)]=phys_XYZ(tsaiB,cornerB(:,1),cornerB(:,2)); + max_x=max(max(xyA(:,1)),max(xyB(:,1)));%maximum on the 4 corners of the the images + min_x=min(min(xyA(:,1)),min(xyB(:,1)));%minimum on the 4 corners of the the images + max_y=max(max(xyA(:,2)),max(xyB(:,2))); + min_y=min(min(xyA(:,2)),min(xyB(:,2))); + array_realx=[min_x:(max_x-min_x)/(nx_patch-1):max_x]; + array_realy=[min_y:(max_y-min_y)/(ny_patch-1):max_y]; + [grid_realx,grid_realy]=meshgrid(array_realx,array_realy); + grid_real(:,1)=reshape(grid_realx,nx_patch*ny_patch,1); + grid_real(:,2)=reshape(grid_realy,nx_patch*ny_patch,1); + grid_real(:,3)=zeros(nx_patch*ny_patch,1); +[grid_imaA(:,1),grid_imaA(:,2)]=px_XYZ(tsaiA,grid_real(:,1),grid_real(:,2)); +[grid_imaB(:,1),grid_imaB(:,2)]=px_XYZ(tsaiB,grid_real(:,1),grid_real(:,2)); + + flagA=grid_imaA(:,1)>0 & grid_imaA(:,1)0 & grid_imaA(:,2)0 & grid_imaB(:,1)0 & grid_imaB(:,2)length(textlu) + blankstr=char(32*ones(1,widthcolumn(jtab)-length(textlu))); + textlu=[textlu blankstr]; + end + if ~isempty(charchain) + textlu=[separator textlu]; + end + charchain=[charchain textlu]; + end + %Tabchar(itab)={charchain}; + Tabchar(itab,1)={charchain}; +end Index: /trunk/src/check_field_structure.m =================================================================== --- /trunk/src/check_field_structure.m (revision 2) +++ /trunk/src/check_field_structure.m (revision 2) @@ -0,0 +1,151 @@ +%'check_field_structure': check the validity of the field struture representation consitant with the netcdf format +%---------------------------------------------------------------------- +% function [DataOut,errormsg]=check_field_structure(Data) +% +% OUTPUT: +% Data: structure reproducing the input structure Data, with the additional elements: +% with fields: +% +% .ListDimName: cell listing the names of the array dimensions +% .DimValue: array dimension values (Matlab vector with the same length as .ListDimName +% .VarDimIndex: cell containing the set of dimension indices (in list .ListDimName) for each variable of .ListVarName +% .VarDimName: cell containing a cell of dimension names (in list .ListDimName) for each variable of .ListVarName +% errormsg: error message which is not empty when the input structure does not have the right form +% +%INPUT: +% Data: structure containing +% (optional) .ListGlobalAttribute: cell listing the names of the global attributes +% .Att_1,Att_2... : values of the global attributes +% (requested) .ListVarName: list of variable names to select (cell array of char strings {'VarName1', 'VarName2',...} ) +% (requested) .VarDimName: list of dimension names for each element of .ListVarName (cell array of string cells) +% (requested) .Var1, .Var2....: variables (Matlab arrays) with names listed in .ListVarName + + +function [DataOut,errormsg]=check_field_structure(Data) +DataOut=[]; %default +errormsg=[]; +if ~isstruct(Data) + errormsg='input field is not a structure'; + return +end +if isfield(Data,'ListVarName') && iscell(Data.ListVarName) + nbfield=numel(Data.ListVarName); +else + errormsg='input field does not contain the list of variables .ListVarNames'; + return +end +%check dimension names +% definition by VarDimIndex (obsolete) +% if ~isfield(Data,'VarDimName') && isfield(Data,'VarDimIndex') && isfield(Data,'ListDimName')%old convention +% for ivar=1:nbfield +% DimCell=Data.VarDimIndex{ivar}; +% if isnumeric(DimCell) +% if DimCell <= numel(Data.ListDimName) +% Data.VarDimName{ivar}=Data.ListDimName(DimCell); +% else +% errormsg='dimension names not defined'; +% return +% end +% else +% errormsg='unrecognized format for .VarDimIndex'; +% end +% end +% end +if ~(isfield(Data,'VarDimName') && iscell(Data.VarDimName)) + errormsg='input field does not contain the list of dimensions .VarDimName'; + return +end +if isfield(Data,'DimValue') + Data=rmfield(Data,'DimValue'); +end +if isfield(Data,'VarDimName') && iscell(Data.VarDimName) + nbdim=0; + if numel(Data.VarDimName)==nbfield + for ivar=1:nbfield + VarName=Data.ListVarName{ivar}; + if ~isfield(Data,VarName) + errormsg=['the listed variable ' VarName ' is not found']; + return + else + eval(['sizvar=size(Data.' VarName ');'])% sizvar = dimension of variable + DimCell=Data.VarDimName{ivar}; + if ischar(DimCell) + DimCell={DimCell}; + elseif ~iscell(DimCell) + errormsg=['wrong format for .VarDimName{' num2str(ivar) ' (must be the cell of dimension names of the variable ' VarName]; + return + end + nbcoord=numel(sizvar); + if numel(DimCell)==0 + errormsg=['empty declared dimension .VarDimName{' num2str(ivar) '} for ' VarName]; + return + elseif numel(DimCell)==1% one dimension declared + if nbcoord==2 + if sizvar(1)==1 + nbcoord=1; + sizvar(1)=sizvar(2); + elseif sizvar(2)==1 + nbcoord=1; + else + errormsg=['1 dimension declared in .VarDimName{' num2str(ivar) '} inconsistent with the nbre of dimensions =2 of the variable ' VarName]; + return + end + else + errormsg=['1 dimension declared in .VarDimName{' num2str(ivar) '} inconsistent with the nbre of dimensions =' num2str(nbcoord) ' of the variable ' VarName]; + return + end + else + if numel(DimCell)>nbcoord + DimCell=DimCell(end-nbcoord+1:end);%first singleton diemnsions omitted, + elseif nbcoord > numel(DimCell) + errormsg=['nbre of declared dimensions in .VarDimName{' num2str(ivar) '} smaller than the nbre of dimensions =' num2str(nbcoord) ' of the variable ' VarName]; + return + end + end + DimIndex=[]; + for idim=1:nbcoord %loop on the coordinates of variable #ivar + DimName=DimCell{idim}; + testprev=0; + for iprev=1:nbdim %check previously listed dimension names + if strcmp(Data.ListDimName{iprev},DimName) + if ~isequal(Data.DimValue(iprev),sizvar(idim)) + if isequal(Data.DimValue(iprev),0) % the dimension has been already detected as a range [min max] + Data.DimValue(idim)=sizvar(idim); %update with actual value + elseif sizvar(idim)==2 && strcmp(DimName,VarName) + %case of a regularly spaced coordinate defined by the first and last values: dimension will be determined later + else + errormsg=['dimension declaration inconsistent with the size =[' num2str(sizvar) '] for ' VarName]; + return + end + end + DimIndex=[DimIndex iprev]; + testprev=1; + break + end + end + if ~testprev % a new dimension is appended to the list + nbdim=nbdim+1; + if sizvar(idim)==2 && strcmp(DimName,VarName) + Data.DimValue(nbdim)=0; %to be updated for a later variable +% Data.VarType{ivar}='range'; + else + Data.DimValue(nbdim)=sizvar(idim); + end + Data.ListDimName{nbdim}=DimName; + DimIndex=[DimIndex nbdim]; + end + end + Data.VarDimIndex{ivar}=DimIndex; + end + end + else + errormsg=' .ListVarNames and .VarDimName have different lengths'; + return + end +else + errormsg='input field does not contain the cell of dimension names .VarDimName for variables'; + return +end +DataOut=Data; + + Index: /trunk/src/check_functions.m =================================================================== --- /trunk/src/check_functions.m (revision 2) +++ /trunk/src/check_functions.m (revision 2) @@ -0,0 +1,117 @@ +%'check_functions': check the path and modification date for all the +% function in the toolbox UVMAT. Called at the opening of uvmat.fig +%---------------------------------------------------------------------- +% function [errormsg,date_str]=check_functions +% +% OUTPUT: +% errormsg: error message listing functions whose paths are not in the directory of uvmat.m +% date_str: date of the most recent modification of a file in the toolbox +% +%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +% Copyright Joel Sommeria, 2008, LEGI / CNRS-UJF-INPG, sommeria@coriolis-legi.org. +%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +% This file is part of the toolbox UVMAT. +% +% UVMAT is free software; you can redistribute it and/or modify +% it under the terms of the GNU General Public License as published by +% the Free Software Foundation; either version 2 of the License, or +% (at your option) any later version. +% +% UVMAT is distributed in the hope that it will be useful, +% but WITHOUT ANY WARRANTY; without even the implied warranty of +% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +% GNU General Public License (file UVMAT/COPYING.txt) for more details. +%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA + +function [errormsg,date_str]=check_functions +errormsg={};%default +list_fct={'calc_field';...% defines fields (velocity, vort, div...) from civx data and calculate them + 'cell2tab';... %transform a Matlab cell in a character array suitable for display in a table + 'check_functions';... + 'civ';... %function associated with the interface 'civ.fig' for PIV and spline interpolation + 'civ.fig';... + 'civ_3D';... function associated with the interface 'civ_3D.fig' for PIV in volume (in progress) + 'civ_3D.fig';... + 'close_fig';...% function activated when a figure is closed + 'copyfields';...%copy fields between two matlab structures + 'delete_object';...%delete a projection object, defined by its index in the Uvmat list or by its graphic handle + 'editxml';...%display and edit xml files using a xls schema + 'editxml.fig';...%interface for editxml + 'find_field_indices';...% group the variables of a nc-formated Matlab structure into 'fields' with common dimensions + 'geometry_calib';...%performs geometric calibration from a set of reference points + 'geometry_calib.fig';...%interface for geometry_calib + 'get_field';...% choose and plot a field from a Netcdf file + 'get_field.fig';...%interface for get_field + 'get_plot_handles';... %provides handles of elements setting the plotting parameters in the uvmat interface + 'griddata_uvmat';...%make 2D linear interpolation using griddata, with input appropriate for both Matlab 6.5 and 7 + 'hist_update';...% update of a current global histogram by inclusion of a new field + 'imadoc2struct';...%convert the image documentation file ImaDoc into a Matlab structure + 'keyboard_callback';... % function activated when a key is pressed on the keyboard + 'ListDir';... scan the structure of the directory tree (for dataview.m) + 'mouse_down';% function activated when the mouse button is pressed on a figure (callback for 'WindowButtonDownFcn') + 'mouse_motion';...% permanently called by mouse motion over a figure (callback for 'WindowButtonMotionFcn') + 'mouse_up';... % function to be activated when the mouse button is released (callback for 'WindowButtonUpFcn') + 'msgbox_uvmat';... associated with GUI msgbox_uvmat.fig to display message boxes, for error, warning or input calls + 'msgbox_uvmat.fig';... + 'name2display';...% extracts the root name and field numbers from an input filename + 'name_generator';...%creates a file name from a root name and indices. + 'nc2struct';...% transform a netcdf file in a corresponding matlab structure + 'peaklock';...% + 'phys';...% transforms fields from image (px) to real world (phys) coordinates using geometric calibration parameters + 'phys_polar';... transform image coordinates (px) to physical ploar coordinates + 'phys_XYZ';...%transforms image (px) to real world (phys) coordinates using geometric calibration parameters + 'px';...% transform fields from physical to px coordinates using geometrical calibration parameters + 'px_XYZ';...% ransform physical to px coordinates using geometrical calibration parameters + 'plot_field';...%displays a vector field and/or scalar or images + 'plot_object';...%draws a projection object (points, line, plane...) + 'proj_field';...%project a field on a projection object (plane, line,...) + 'read_civxdata';...reads civx data from netcdf files + 'read_imatext';...%read .civ files (obsolete, but can be adapted to other text documentation files) + 'read_plot_param';... %read the plotting option parameters on the uvmat interface + 'read_set_object';...%read the data on the set_object interface + 'read_xls';...%read excel files containing the list of the experiments + 'reinit';...% suppress the personal parameter file 'uvmat_perso.mat' + 'RUN_FIX';...% fix velocity fields + 'RUN_STLIN';...% combine 2 displacement fields for stereo PIV + 'series';...% master function for analysis field series, with interface 'series.fig' + 'series.fig';...% interface for 'series' + 'set_col_vec';... + 'set_grid';...% creates a grid for PIV + 'set_grid.fig';...% interface for set_grid + 'set_object.m';...% edit a projection object + 'set_object.fig';...% interface for set_object + 'sub_field';...% combine the two input fields, + 'struct2nc';...% %write fields in netcdf files + 'uvmat';...% master function for file scanning and visualisation of 2D fields + 'uvmat.fig';... %interface for uvmat + 'update_obj';... update the object representation graph and its projection field, record it in the uvmat interface + 'update_waitbar';... update the waitbar display, used for ACTION functions in the GUI 'series' + 'warndlg_uvmat';...% display messages (error, warning, confirmation) , OBSOLETE, use msgbox_uvmat + 'write_plot_param'};%update plotting parameters after plot + dir_fct=which('uvmat');% path to uvmat +[pathuvmat,name,ext]=fileparts(dir_fct); +icount=0; +% loop on the list of functions in the uvmat package + for i=1:length(list_fct) + dir_fct=which(list_fct{i});% path to fct + if isempty(dir_fct) + icount=icount+1; + errormsg{icount}=[list_fct{i} ' not found'];% test for function not found + else + [pth,name,ext]=fileparts(dir_fct); + if ~isequal(pathuvmat,pth) + icount=icount+1; + errormsg{icount}=[dir_fct ' overrides the package UVMAT'];% bad path for the function + end + datfile=dir(dir_fct); + date_str=datfile.date;%string of the date of last modification + datnum(i)=0;%default + char_code=double(date_str);% code of the date characters + special_char=(char_code>127); %non standard Ascii character (e.g. date in french) + if isempty(find(special_char))% standard Ascii character + datnum(i)=datenum(date_str); + end + end +end +errormsg=errormsg'; +date_str=datestr(max(datnum)); Index: /trunk/src/civ.m =================================================================== --- /trunk/src/civ.m (revision 2) +++ /trunk/src/civ.m (revision 2) @@ -0,0 +1,5248 @@ +%'civ': function associated with the interface 'civ.fig' for PIV, spline interpolation and stereo PIV (patch) +%------------------------------------------------------------------------ +% provides an interface for the software CIVx +% function varargout = civ(varargin) +% provides an interface for the software CIVx +% +%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +% Copyright Joel Sommeria, 2008, LEGI / CNRS-UJF-INPG, sommeria@coriolis-legi.org. +%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +% This file is part of the toolbox UVMAT. +% +% UVMAT is free software; you can redistribute it and/or modify +% it under the terms of the GNU General Public License as published by +% the Free Software Foundation; either version 2 of the License, or +% (at your option) any later version. +% +% UVMAT is distributed in the hope that it will be useful, +% but WITHOUT ANY WARRANTY; without even the implied warranty of +% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +% GNU General Public License (file UVMAT/COPYING.txt) for more details. +%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +function varargout = civ(varargin) + +% Last Modified by GUIDE v2.5 29-Oct-2009 19:05:39 +% Begin initialization code - DO NOT EDIT +gui_Singleton = 1; +gui_State = struct('gui_Name', mfilename, ... + 'gui_Singleton', gui_Singleton, ... + 'gui_OpeningFcn', @civ_OpeningFcn, ... + 'gui_OutputFcn', @civ_OutputFcn, ... + 'gui_LayoutFcn', [] , ... + 'gui_Callback', []); +if nargin && ischar(varargin{1}) + gui_State.gui_Callback = str2func(varargin{1}); +end + +if nargout + [varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:}); +else + gui_mainfcn(gui_State, varargin{:}); +end +% End initialization code - DO NOT EDIT + +%-------------------------------------------------------------------------- +% --- Executes just before civ is made visible. +%-------------------------------------------------------------------------- +function civ_OpeningFcn(hObject, eventdata, handles, varargin) +% This function has no output args, see OutputFcn. +% hObject handle to figure +% eventdata reserved - to be defined in a future version of MATLAB +% handles structure with handles and user data (see GUIDATA) +% varargin command line arguments to civ (see VARARGIN) +global test_batch patch_new_exe%=1 if patch processing available +%filebase: root name +%nom_type: nomencalture used ('png_old','_i_j'...) +%list of field numbers to process +%subdir: subdirectory of the opened netcdf file +%ind_opening: operation number advised for beginning (1=civ1,2=fix1,3=patch1,4=civ2,5=fix2,6=patch2), +%ind_a_opening ind_b_opening chosen pair from the opened netcdf file +% Choose default command line output for civ +handles.output = hObject; +% Update handles structure +guidata(hObject, handles); + +%default initial parameters +filebase=''; % root file name ('filebase'.civ) +nom_type=[]; % nomenclature type +ext=[]; +testall=0; +browse=[]; + +%load the initial parameters if the interface is started from uvmat +if ~isempty(varargin)% the interface is opened from uvmat + varcell=varargin{1}; + filebase=varcell{1}; + nom_type_read=varcell{2}; + num1=varcell{3}; + num2=varcell{4}; + num_a=varcell{5}; + num_b=varcell{6}; + subdir=varcell{7}; + ind_opening=varcell{8}; + ext=varcell{11}; +else + num1=1; % set of field i numbers + num2=2; % set of field i numbers + num_a=1; % set of field j numbers (fields a) + num_b=1; % second set of field j numbers (fields b) + subdir='A'; % subdir for the netcdf result files + ind_opening=1; % proposed operation number (1=civ1,2=fix1,3=patch1,4=civ2,5=fix2,6=patch2) +end + +if exist('ext','var') && length(ext)>1 && (~isempty(imformats(ext([2:end])))|... + isequal(ext,'.avi')||isequal(ext,'.AVI'));%if an image file has been opened by uvmat + set(handles.ext_ima,'String',ext) + if exist('nom_type_read','var') + browse.nom_type_ima=nom_type_read; % the image nomenclature is stored + end +elseif isequal(ext,'.nc') + if exist('nom_type_read','var') + browse.nom_type_nc=nom_type_read;% the netcdf nomenclature is stored + end +end +set(handles.displ_filebase,'String',filebase); +set(handles.ImaDoc,'UserData',testall); +set(handles.ImaDoc,'String',ext) + + +% set(handles.ImaDoc,'String',ext) + +%read names of the .exe file to adjust the interface according to +%available prog +%read names of the .exe file +path_uvmat=which('uvmat');% check the path detected for source file uvmat +path_UVMAT=fileparts(path_uvmat); %path to UVMAT +if isunix + syst='LINUX'; + %fid = fopen(fullfile(path_UVMAT,'PARAM_LINUX.txt'),'r');%open the file with civ binary names + xmlfile=fullfile(path_UVMAT,'PARAM_LINUX.xml'); + display(xmlfile) + if exist(xmlfile,'file') + t=xmltree(xmlfile); + sparam=convert(t); + end +else + syst='WIN'; + %fid = fopen(fullfile(path_UVMAT,'PARAM_WIN.txt'),'r');%open the file with civ binary names + xmlfile=fullfile(path_UVMAT,'PARAM_WIN.xml'); + if exist(xmlfile,'file') + t=xmltree(xmlfile); + sparam=convert(t); + end +end +display(syst) +patch_new_exe=''; +% todo_patch=''; +sge=0; + +if isfield(sparam,'PatchNew_exe') + patch_new_exe=sparam.PatchNew_exe; +end +if isfield(sparam,'Todo_path') + todo_path=sparam.Todo_path; +end +if isfield(sparam,'SGE') + sge=str2num(sparam.SGE); +end +name_todo=fullfile(todo_path,'TODO.txt'); +display(name_todo) +test_batch=1; +if ~sge +if isequal(todo_path,'') || isequal(todo_path,[]) + display(['no batch distributed processing available:file path TODO.txt not defined in UVMAT/PARAM_' syst]) + test_batch=0; +end +if exist(name_todo,'file')~=2 + msgbox_uvmat('WARNING',['no batch distributed processing available, queue file ' name_todo ' absent']); + % test_batch=0; % Problems to detect file on linux/nfs filesystems +end +end + + +if test_batch==0 + set(handles.BATCH,'BackgroundColor',[0.831 0.816 0.784])% put the BATCH button in grey (unactivated) +end + +set(handles.subdir_civ1,'String',subdir)%default subdir on which uvmat was working +set(handles.subdir_civ2,'String',subdir)%default subdir on which uvmat was working + +%initiate advised operations +if isequal(ind_opening,[]) + ind_opening=1; % default +end +% set default operation options + enable_civ1(handles,'off') + enable_civ2(handles,'off') + enable_pair1(handles,'on') + enable_fix1(handles,'off') + desable_patch1(handles) + desable_fix2(handles) + desable_patch2(handles) + set(handles.CIV1,'Value',0) + set(handles.FIX1,'Value',0) + set(handles.PATCH1,'Value',0) + set(handles.CIV2,'Value',0) + set(handles.FIX2,'Value',0) + set(handles.PATCH2,'Value',0) + set(handles.frame_subdirciv2,'BackgroundColor',[0.831 0.816 0.784]) +if isequal(ind_opening,1) + set(handles.CIV1,'Value',1) + enable_civ1(handles,'on') +elseif isequal(ind_opening,2) + set(handles.FIX1,'Value',1) + enable_fix1(handles,'on') +elseif isequal(ind_opening,3) + set(handles.PATCH1,'Value',1) + enable_patch1(handles) +elseif isequal(ind_opening,4) + set(handles.CIV2,'Value',1) + enable_civ2(handles,1) +elseif isequal(ind_opening,5) + set(handles.FIX2,'Value',1) + enable_fix2(handles) + set(handles.frame_subdirciv2,'BackgroundColor',[1 1 0]) + set(handles.list_pair_civ2,'Enable','On') + set(handles.list_pair_civ2,'Enable','On') + enable_pair1(handles,'off') +elseif isequal(ind_opening,6) + set(handles.PATCH2,'Value',1) + enable_patch2(handles) + set(handles.frame_subdirciv2,'BackgroundColor',[1 1 0]) + set(handles.list_pair_civ2,'Enable','On') + enable_pair1(handles,'off') +end + +% set the range of fields (1:1 by default) and selected pair +if isempty(num2)|isequal(num2,num1) + num_ref_i=num1; +else + num_ref_i=floor((num1+num2)/2); + browse.incr_pair(1)=num2-num1; + browse.incr_pair(2)=0; +end +if isempty(num_b)|isequal(num_a,num_b) + if isempty(num_a) + num_ref_j=1; + else + num_ref_j=num_a; + end +else + num_ref_j=floor((num_a+num_b)/2); + browse.incr_pair(2)=num_b-num_a; +end +set(handles.first_i,'String',num2str(num_ref_i)); +set(handles.last_i,'String',num2str(num_ref_i)); +set(handles.first_j,'String',num2str(num_ref_j)); +set(handles.last_j,'String',num2str(num_ref_j)); +set(handles.ref_i,'String',num2str(num_ref_i)); +set(handles.ref_j,'String',num2str(num_ref_j)); +set(handles.browse_root,'UserData',browse); +if ~isempty(varargin)% the interface is opened from uvmat + displ_filebase_Callback(hObject, eventdata, handles); +end + +set(handles.waitbar_1,'Position',[0.946 0.877 0.03 0.001]) +set(handles.waitbar_patch1,'Position',[0.946 0.626 0.03 0.001]) +set(handles.waitbar_civ2,'Position',[0.946 0.406 0.03 0.001]) +set(handles.waitbar_patch2,'Position',[0.946 0.187 0.03 0.001]) + + +%-------------------------------------------------------------- +% --- Outputs from this function are returned to the command line. +%----------------------------------------------------------------- +function varargout = civ_OutputFcn(hObject, eventdata, handles) +% varargout cell array for returning output args (see VARARGOUT); +% hObject handle to figure +% eventdata reserved - to be defined in a future version of MATLAB +% handles structure with handles and user data (see GUIDATA) +% Get default command line output from handles structure +varargout{1} = handles.output; + +%------------------------------------------------------------------ +% --- Executes on button press in browse_root. +function browse_root_Callback(hObject, eventdata, handles) +%get the input file properties +filebase=get(handles.displ_filebase,'String'); +oldfile=''; %default +if isempty(filebase)|isequal(filebase,'')%loads the previously stored file name and set it as default in the file_input box + dir_perso=prefdir; + profil_perso=fullfile(dir_perso,'uvmat_perso.mat'); + display(profil_perso) + if exist(profil_perso,'file') + h=load (profil_perso); + if isfield(h,'filebase')&& ischar(h.filebase) + oldfile=h.filebase; + end + if isfield(h,'RootPath') && ischar(h.RootPath) + oldfile=h.RootPath; + end + end + else + oldfile=filebase; + end +testall=get(handles.ImaDoc,'UserData'); +ind_opening=1;%default +browse.incr_pair=[0 0]; %default +if testall + menu={'*.*', 'All Files (*.*)'; '*.xml; *.avi;*.AVI;*.nc','(*.xml,*.avi,*.nc)'; ... + '*.xml', '.xml files';'*.avi;*.AVI', '.avi files';'*.nc','.nc files'}; +else % menu selecting only .civ or .avi files +menu={'*.xml;*.avi;*.AVI;*.nc','(*.xml,*.avi,*.nc)'; ... + '*.xml', '.xml files';'*.avi;*.AVI', '.avi files';'*.nc', '.nc files';... + '*.*', 'All Files (*.*)'}; +end +[FileName, PathName, filtindex] = uigetfile( menu, 'Pick a file',oldfile); +fileinput=[PathName FileName];%complete file name +sizf=size(fileinput); +if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end %stop if fileinput not a character string +[path,name,ext]=fileparts(fileinput); +testeditxml=0; +if isequal(ext,'.xml') + testeditxml=1; + t_browse=xmltree(fileinput); + head_element=get(t_browse,1); + if isfield(head_element,'name')& isequal(head_element.name,'ImaDoc') + testeditxml=0; + end +end +if testeditxml==1 | isequal(ext,'.xls') + heditxml=editxml({fileinput}); + set(heditxml,'Tag','browser') + waitfor(heditxml,'Tag','idle') + if ~ishandle(heditxml) + return + end + attr=findobj(get(heditxml,'children'),'Tag','CurrentAttributes'); + set(handles.browse,'UserData',fileinput)% store for future opening with browser + fileinput=get(attr,'UserData'); + if ~exist(fileinput,'file') + return + end +end + +[RootPath,RootFile,field_count,str2,str_a,str_b,ext,nom_type,subdir]=name2display(fileinput); +filebase=fullfile(RootPath,RootFile); +if isequal(get(handles.compare,'Value'),1) + browse=[];%initialisation +else + browse=get(handles.browse_root,'UserData'); +end +if length(ext)>1 & (~isempty(imformats(ext([2:end])))|... + isequal(ext,'.avi')|isequal(ext,'.AVI'));%if an image file has been opened by uvmat + set(handles.ext_ima,'String',ext) + browse.nom_type_ima=nom_type; + browse.field_count=str2num(field_count); + A=imread(fileinput); + npxy=size(A); + set(handles.ext_ima,'UserData',npxy) +end +set(handles.ImaDoc,'String',ext); + +%%%%% read the state of the selected netcdf file to advise default operation +if isequal(ext,'.nc') + browse.nom_type_nc=nom_type; + ind_opening=2;% propose 'fix' as the default option + Data=nc2struct(fileinput,[]); + if isfield(Data,'absolut_time_T0')%test for civx files + if isfield(Data,'fix') && isequal(Data.fix,1) + ind_opening=3; + end + if isfield(Data,'patch') && isequal(Data.patch,1) + ind_opening=4; + end + if isfield(Data,'civ2') && isequal(Data.civ2,1) + ind_opening=5; + end + if isfield(Data,'fix2') && isequal(Data.fix2,1) + ind_opening=6; + end + testciv=1; %TO SUPPRESS WITH NEW VERSION OF CIVX + else + ind_opening=3; %GUI used only for patch + testciv=0; + end + set(handles.subdir_civ1,'String',subdir);%set the default subdir directories for installing the .nc results + set(handles.subdir_civ2,'String',subdir); + browse.testciv=testciv; + browse.ind_opening=ind_opening; +end +set(handles.displ_filebase,'String',filebase); +set(handles.ImaDoc,'String',ext); +if ~isempty(str2num(field_count)) + ref_i=str2num(field_count); + if ~isempty(str2num(str2)) + ref_i=floor((ref_i+str2num(str2))/2);% reference image number corresponding to the file + browse.incr_pair(1)=str2num(str2)-str2num(field_count); + browse.incr_pair(2)=0; + end + set(handles.first_i,'String',num2str(ref_i)); + set(handles.last_i,'String',num2str(ref_i)); + set(handles.ref_i,'String',num2str(ref_i)); +end +if isempty(str2num(str_a)) + set(handles.ref_j,'String','1'); +else + ref_j=str2num(str_a); + if ~isempty(str2num(str_b)) + ref_j=floor((str2num(str_a)+str2num(str_b))/2); + browse.incr_pair(2)=str2num(str_b)-str2num(str_a); + end + set(handles.first_j,'String',num2str(ref_j)); + set(handles.last_j,'String',num2str(ref_j)); + set(handles.ref_j,'String',num2str(ref_j)); +end + +% set default operation options +enable_civ1(handles,'off') +enable_civ2(handles,'off') +enable_pair1(handles,'on') +enable_fix1(handles,'off') +desable_patch1(handles) +desable_fix2(handles) +desable_patch2(handles) +set(handles.CIV1,'Value',0) +set(handles.FIX1,'Value',0) +set(handles.PATCH1,'Value',0) +set(handles.CIV2,'Value',0) +set(handles.FIX2,'Value',0) +set(handles.PATCH2,'Value',0) +set(handles.frame_subdirciv2,'BackgroundColor',[0.831 0.816 0.784]) +if isequal(ind_opening,1) + set(handles.CIV1,'Value',1) + enable_civ1(handles,'on') +elseif isequal(ind_opening,2) + set(handles.FIX1,'Value',1) + enable_fix1(handles,'on') +elseif isequal(ind_opening,3) + set(handles.PATCH1,'Value',1) + enable_patch1(handles) +elseif isequal(ind_opening,4) + set(handles.CIV2,'Value',1) + enable_civ2(handles,1) +elseif isequal(ind_opening,5) + enable_pair1(handles,'off') + set(handles.FIX2,'Value',1) + enable_fix2(handles) + set(handles.frame_subdirciv2,'BackgroundColor',[1 1 0]) + set(handles.list_pair_civ2,'Enable','On') + set(handles.list_pair_civ2,'Enable','On') +elseif isequal(ind_opening,6) + enable_pair1(handles,'off') + set(handles.PATCH2,'Value',1) + enable_patch2(handles) + set(handles.frame_subdirciv2,'BackgroundColor',[1 1 0]) + set(handles.list_pair_civ2,'Enable','On') +end +set(handles.browse_root,'UserData',browse);% store information from browser +testall=isequal(menu(filtindex,1),{'*.*'}); +set(handles.ImaDoc,'UserData',testall); + +displ_filebase_Callback(hObject, eventdata, handles); + +%------------------------------------------------ + +function ImaDoc_Callback(hObject, eventdata, handles) +displ_filebase_Callback(hObject, eventdata, handles) + +%-------------------------------------------------------------- +%function activated when a new filebase (image series) is introduced +%------------------------------------------------------------ +function displ_filebase_Callback(hObject, eventdata, handles) + +global test_batch +%set(gcf,'Pointer','watch') +set(handles.compare,'Visible','on') +ext_ima=get(handles.ext_ima,'String'); +nom_type_ima=[];%default +field_count=1;%default +nom_type_nc=[]; +npx=[];%default +npy=[]; +time=[]; +TimeUnit=[]; %default +CoordUnit=[];%default +pxcmx_search=[];%default +pxcmy_search=[];%default +filebase=get(handles.displ_filebase,'String'); + +ext=get(handles.ImaDoc,'String'); +browse=get(handles.browse_root,'UserData');%default +if ~isempty(browse) + if isfield(browse,'nom_type_ima') + nom_type_ima=browse.nom_type_ima; + end + if isfield(browse,'field_count') + field_count=browse.field_count; + end +end + +%default first_i and j and increments +first_i=str2num(get(handles.first_i,'String'));%value possibly set by uvmat_Opening +if isempty(first_i)| first_i < 1 + first_i=1; %default first_i +end +last_i=str2num(get(handles.last_i,'String')); +if isempty(last_i)| last_i < first_i + last_i=first_i; %default last_i +end +first_j=str2num(get(handles.first_j,'String')); +if isempty(first_j)| first_j < 1 + first_j=1; %default first_j +end +last_j=str2num(get(handles.last_j,'String')); +if isempty(last_j)| last_j < first_j + last_j=first_j; %default last_j +end +incr_i=str2num(get(handles.incr_i,'String')); +if isempty(incr_i) | incr_i < 1; + set(handles.incr_i,'String','1') %default incr_i +end +incr_j=str2num(get(handles.incr_j,'String')); +if isempty(incr_j) | incr_j < 1; + set(handles.incr_j,'String','1') %default incr_j +end +dt=[];%default +testmode=0;%default +nbfield=[]; %default +nburst=[];%default +pxcmx=1; +pxcmy=1; + + %look for an image documentation file +ext +if ~isequal(ext,'.xml') && ~isequal(ext,'.civ')&& ~isequal(ext,'.avi')&& ~isequal(ext,'.AVI') + if exist([filebase '.xml'],'file') + ext='.xml'; + elseif exist([filebase '.civxml'],'file') + ext='.civxml'; + elseif exist([filebase '.civ'],'file') + ext='.civ'; + elseif exist([filebase '.avi'],'file') + ext='.avi'; + elseif exist([filebase '.AVI'],'file') + ext='.AVI'; + end + set(handles.ImaDoc,'String',ext) +end + +%%%%%%%% read image documentation file %%%%%%%%%%%%%%%%%%%%%%%%%%% + mode=''; %default + set(handles.ImaDoc,'BackgroundColor',[1 1 0]) + drawnow + %read the image documentation file if found +if isequal(ext,'.civxml') | isequal(ext,'.xml')| isequal(ext,'.civ') + set(handles.ref_i,'Visible','On')%use a reference index + set(handles.ref_j,'Visible','On') + set(handles.dt,'Visible','Off') + set(handles.dt_text,'String','ref. ind.') +elseif isequal(ext,'.avi') | isequal(ext,'.AVI') + set(handles.ref_j,'Visible','Off') + set(handles.dt,'Visible','Off') + set(handles.dt_text,'String','ref. ind.') +else + set(handles.ref_i,'Visible','Off') + set(handles.ref_j,'Visible','Off') + set(handles.dt,'Visible','On') + set(handles.dt_text,'String','dt(ms)=') +end +if isequal(ext,'.civxml')%TO ABANDON + [nbfield,nburst,time]=read_civxml([filebase '.civxml']); + mode='pair j1-j2'; + if isempty(nom_type_ima)% dtermine types by default if not already selected by browser or uvmat + nom_type_ima='_i_j'; + end +elseif isequal(ext,'.xml') + [XmlData,warntext]=imadoc2struct([filebase '.xml']); + if isfield(XmlData,'Time') + time=XmlData.Time; + nbfield=size(XmlData.Time,1); + nburst=size(XmlData.Time,2); + end + ext_ima_read=[]; + nom_type_read=[]; + XmlData.Heading + if isfield(XmlData,'Heading')&&isfield(XmlData.Heading','ImageName') + [PP,FF,fc,str2,str_a,str_b,ext_ima_read,nom_type_read]=name2display(XmlData.Heading.ImageName); + end + if isfield(XmlData,'Camera') + if isfield(XmlData.Camera,'TimeUnit') + TimeUnit=XmlData.Camera.TimeUnit; + end + if isfield(XmlData.Camera,'ImageSize') + ImageSize=XmlData.Camera.ImageSize; + if ~isempty(ImageSize)&& ~isempty(ImageSize) + xindex=findstr(ImageSize,'x'); + if length(xindex)>=2 + npx=str2num(ImageSize(1:xindex(1)-1)); + npy=str2num(ImageSize(xindex(1)+1:xindex(2)-1)); + end + end + end + end + pxcmx_search=1; + pxcmy_search=1; + if isfield(XmlData,'GeometryCalib') + tsai=XmlData.GeometryCalib; + if isfield(tsai,'f') & isfield(tsai,'Tz') & isfield(tsai,'dpx') & isfield(tsai,'dpy')& isfield(tsai,'R') + rot2D=tsai.R([1:2],[1,2]); + pxcmx_search=tsai.f * sqrt(det(rot2D))/(tsai.Tz*tsai.dpx); + pxcmy_search=tsai.f * sqrt(det(rot2D))/(tsai.Tz*tsai.dpy); + end + if isfield(tsai,'CoordUnit') + CoordUnit=tsai.CoordUnit; + end + end + if ~isempty(ext_ima_read) && ~isempty(nom_type_read) + if isempty(ext_ima) + ext_ima=ext_ima_read;% define image extension from the xml file if an image has not been opened previously + else %keep the image extension + if ~strcmp(ext_ima_read,ext_ima) + msgbox_uvmat('WARNING',['FirtsImage extension ' ext_ima_read ' announced in the xml file inconsistent with the selected image']) + end + end + nom_type_ima=nom_type_read; + end +elseif isequal(ext,'.civ')% case of .civ image documentation file + [error,time,TimeUnit,mode,npx,npy]=read_imatext([filebase '.civ']); + if error==2, warndlg(['no file ' filebase '.civ']); + elseif error==1, warndlg('inconsistent number of fields in the .civ file'); + end +% ext_ima='.png'; + nom_type_ima='png_old'; +elseif isequal(lower(ext),'.avi') + nom_type_ima='*'; + ext_ima=ext; + set(handles.mode,'String',{'series(Di)'}) + dt=0.04;%default + if exist([filebase ext],'file')==2 + info=aviinfo([filebase ext]);%read infos on the avi movie + dt=1/info.FramesPerSecond;%time interval between successive frames + nbfield=info.NumFrames;%number of frames + end + time=(dt*[0:nbfield-1])';%list of image times + set(handles.dt,'String',num2str(dt*1000));%store the time interval between successive images +end +if isempty(time) + set(handles.ImaDoc,'String',''); %xml file not used for timing +end +set(handles.ImaDoc,'BackgroundColor',[1 1 1]) + +% no image documentation file found: look for a series of existing images or .nc files +if isempty(time) && ~isequal(ext,'.nc') + subdir=get(handles.subdir_civ1,'String'); + incr_pair=[0 0];%default + if isfield(browse,'incr_pair') + incr_pair=browse.incr_pair; + end + nbdetect=0;%test of detected images + field_i=field_count; + idetect=1; + while idetect==1 %look for the maximum file number in the series + field_i=field_i+1; + imagename=name_generator(filebase,field_i,1,ext_ima,nom_type_ima); + if strcmp(nom_type_ima,'none')||strcmp(nom_type_ima,'') + idetect=0; %stop if the same image is repeated (if nom_type='none') + nbdetect=1; + else + idetect=(exist(imagename,'file')==2); + end + %SEE CASE OF NETCDF FILES + nbdetect=nbdetect+(exist(imagename,'file')==2); + end + nb_field=field_i;% last detected field number + field_i=field_count;%look for the minimum file number in the series + idetect=1; + while idetect==1 + field_i=field_i-1; + imagename=name_generator(filebase,field_i,1,ext_ima,nom_type_ima); + if isequal(nom_type_ima,'none')||strcmp(nom_type_ima,'') + idetect=0; %stop if the same image is repeted (if nom_type='none') + nbdetect=1; + else + idetect=(exist(imagename,'file')==2); + end + nbdetect=nbdetect+idetect; + end + first_i=max(field_i+1,1); + %determine the set of times and possible intervals for CIV + dt=(1/1000)*str2num(get(handles.dt,'String')); + time=(dt*[0:nb_field-1])'; + set(handles.mode,'String',{'series(Di)'}) +end +if isequal(nom_type_ima,'none')% no file numbering used + first_i=1; + last_i=1; + first_j=1; + last_j=1; +end +if exist('time','var') + if size(time,1)+size(time,2)>=3 % if there are at least two time values to define dt + nbfield=size(time,1); + nbfield2=size(time,2); + set(handles.displ_filebase,'UserData',time); %store the set of times + if isempty(TimeUnit) + set(handles.dt_unit,'String','e-03'); + set(handles.TimeUnit,'String',''); + else + set(handles.dt_unit,'String',['m' TimeUnit]); + set(handles.TimeUnit,'String',TimeUnit); + end + set(handles.nb_field,'String',num2str(nbfield)); + set(handles.nb_field2,'String',num2str(nbfield2)); + end +end +set(handles.CoordUnit,'String',[CoordUnit '/']) +set(handles.calcul_search,'UserData',[pxcmx_search pxcmy_search]); +% npxy=[npy npx]; +set(handles.ext_ima,'String',ext_ima) +set(handles.first_i,'String',num2str(first_i)); +set(handles.last_i,'String',num2str(last_i));% +set(handles.first_j,'String',num2str(first_j)); +set(handles.last_j,'String',num2str(last_j));% +browse.nom_type_ima=nom_type_ima; +set(handles.browse_root,'UserData',browse)% store the nomenclature type + + %%%%%%%%%%% set the menus of image pairs and default selection for civ %%%%%%%%%%%%%%%%%%% +if isequal(nom_type_ima,'_i')| isequal(nom_type_nc,'_i1-i2')|~exist('nbfield2','var')|(nbfield2==1) + set(handles.mode,'String',{'series(Di)'}) + set(handles.mode,'Value',1) +elseif isequal(nom_type_ima,'png_old')|isequal(nom_type_nc,'netc_old') + set(handles.mode,'String',{'pair j1-j2'}) + set(handles.mode,'Value',1) +elseif (nbfield==1)% simple series in j + set(handles.mode,'String',{'series(Dj)'}) + set(handles.mode,'Value',1) +else + set(handles.mode,'String',{'pair j1-j2';'series(Dj)';'series(Di)'})%multiple choice + if isequal(mode,'volume') + set(handles.mode,'Value',3) + elseif nbfield2 <= 5 + set(handles.mode,'Value',1)% advice 'pair j1-j2' for small bursts + else + set(handles.mode,'Value',2)% advice series Dj for long bursts, not volume + end +end + +%update the subdir +pathdir=fileparts(filebase);%path to the current xml file +listot=dir(pathdir); +idir=0; +listdir={''};%default +for ilist=1:length(listot) + if listot(ilist).isdir + name=listot(ilist).name; + if ~isequal(name,'.') && ~isequal(name,'..') + idir=idir+1; + listdir{idir,1}=listot(ilist).name; + end + end +end +set(handles.list_subdir_civ1,'Value',1) +set(handles.list_subdir_civ2,'Value',1) +set(handles.list_subdir_civ1,'String',['browse...';listdir]) +set(handles.list_subdir_civ2,'String',['browse...';listdir]) +%check wether the current subdir exists: +subdir_civ1=get(handles.subdir_civ1,'String'); +subdir_civ2=get(handles.subdir_civ2,'String'); + +mode_Callback(hObject, eventdata, handles) + +%%%%%% initialize waitbars and RUN button +set(handles.waitbar_1,'Position',[0.946 0.876 0.03 0.001]) +set(handles.waitbar_patch1,'Position',[0.946 0.439 0.03 0.001]) +set(handles.waitbar_civ2,'Position',[0.946 0.219 0.03 0.001]) +set(handles.waitbar_patch2,'Position',[0.946 0.0 0.03 0.001]) +set(handles.RUN, 'Enable','On') +set(handles.RUN,'BackgroundColor',[1 0 0]) +if isequal(test_batch,1)%if batch installation is available + set(handles.BATCH, 'Enable','On') + set(handles.BATCH,'BackgroundColor',[1 0 0]) +end + +%%%%% store the root input filename for future opening +dir_perso=prefdir; +profil_perso=fullfile(prefdir,'uvmat_perso.mat'); +RootPath=fileparts(filebase); +if exist(profil_perso,'file') + save (profil_perso,'RootPath','-append'); %store the root name for future opening of uvmat +else + txt=ver; + Release=txt(1).Release; + relnumb=str2num(Release(3:4)); + if relnumb >= 14 + save (profil_perso,'RootPath','-V6'); %store the root name for future opening of uvmat + else + save (profil_perso,'RootPath'); %store the root name for future opening of uvmat + end +end +% save(profil_perso, 'filebase'); %store the root name for future opening of uvmat +set(gcf,'Pointer','arrow') + +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%???????????? +% --- Executes on button press in mode. +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% +function mode_Callback(hObject, eventdata, handles) +browse=get(handles.browse_root,'UserData'); + +compare_list=get(handles.compare,'String'); +val=get(handles.compare,'Value'); +compare=compare_list{val}; +if strcmp(compare,'displacement') + mode='displacement'; +else + mode_list=get(handles.mode,'String'); + mode_value=get(handles.mode,'Value'); + mode=mode_list{mode_value}; +end +displ_num=[];%default +first_i=str2num(get(handles.first_i,'String')); +% last_i=str2num(get(handles.last_i,'String')); +time=get(handles.displ_filebase,'UserData'); %get the set of times +siztime=size(time); +nbfield=siztime(1); +nbfield2=siztime(2); +indchosen=1; %%first pair selected by default +if isequal(mode,'pair j1-j2')%| isequal(mode,'st_pair j1-j2') + dt=1; + displ=''; + index=0; + numlist_a=[]; + numlist_B=[]; + %get all the time intervals in bursts + displ_dt=1;%default + nbfield2=min(nbfield2,10);%limitate the number of pairs to 10x10 +% if nbfield2<2 +% nbfield2=2, +% end + for numod_a=1:nbfield2-1 %nbfield2 always >=2 for 'pair j1-j2' mode + for numod_b=(numod_a+1):nbfield2 + index=index+1; + numlist_a(index)=numod_a; + numlist_b(index)=numod_b; + if ~isempty(time) + dt(numod_a,numod_b)=time(first_i,numod_b)-time(first_i,numod_a);%first time interval dt + displ_dt(index)=dt(numod_a,numod_b); + else + displ_dt(index)=1; + end + end + end + [dtsort,indsort]=sort(displ_dt); + if ~isempty(numlist_a) + displ_num(1,:)=numlist_a(indsort); + displ_num(2,:)=numlist_b(indsort); + end + displ_num(3,:)=0; + displ_num(4,:)=0; + set(handles.jtext,'Visible','Off') + set(handles.first_j,'Visible','Off') + set(handles.last_j,'Visible','Off') + set(handles.incr_j,'Visible','Off') + set(handles.nb_field2,'Visible','Off') + set(handles.ref_j,'Visible','Off') +elseif isequal(mode,'series(Dj)') %| isequal(mode,'st_series(Dj)') + for index=1:min(nbfield2-1,200) + displ_num(1,index)=-floor(index/2); + displ_num(2,index)=ceil(index/2); + displ_num(3,index)=0; + displ_num(4,index)=0; + end + set(handles.jtext,'Visible','On') + set(handles.first_j,'Visible','On') + set(handles.last_j,'Visible','On') + set(handles.incr_j,'Visible','On') + set(handles.nb_field2,'Visible','On') + set(handles.ref_j,'Visible','On') + if nbfield > 1 + set(handles.itext,'Visible','On') + set(handles.first_i,'Visible','On') + set(handles.last_i,'Visible','On') + set(handles.incr_i,'Visible','On') + set(handles.nb_field,'Visible','On') + set(handles.ref_i,'Visible','On') + else + set(handles.itext,'Visible','Off') + set(handles.first_i,'Visible','Off') + set(handles.last_i,'Visible','Off') + set(handles.incr_i,'Visible','Off') + set(handles.nb_field,'Visible','Off') + set(handles.ref_i,'Visible','Off') + end +elseif isequal(mode,'series(Di)') %| isequal(mode,'st_series(Di)') + for index=1:200%min(nbfield-1,200) + displ_num(1,index)=0; + displ_num(2,index)=0; + displ_num(3,index)=-floor(index/2); + displ_num(4,index)=ceil(index/2); + end + set(handles.itext,'Visible','On') + set(handles.first_i,'Visible','On') + set(handles.last_i,'Visible','On') + set(handles.incr_i,'Visible','On') + set(handles.nb_field,'Visible','On') + set(handles.ref_i,'Visible','On') + if nbfield2 > 1 + set(handles.jtext,'Visible','On') + set(handles.first_j,'Visible','On') + set(handles.last_j,'Visible','On') + set(handles.incr_j,'Visible','On') + set(handles.nb_field2,'Visible','On') + set(handles.ref_j,'Visible','On') + else + set(handles.jtext,'Visible','Off') + set(handles.first_j,'Visible','Off') + set(handles.last_j,'Visible','Off') + set(handles.incr_j,'Visible','Off') + set(handles.nb_field2,'Visible','Off') + set(handles.ref_j,'Visible','Off') + end +elseif isequal(mode,'displacement')%the pairs have the same indices + displ_num(1,1)=0; + displ_num(2,1)=0; + displ_num(3,1)=0; + displ_num(4,1)=0; + if nbfield > 1 + set(handles.itext,'Visible','On') + set(handles.first_i,'Visible','On') + set(handles.last_i,'Visible','On') + set(handles.incr_i,'Visible','On') + set(handles.nb_field,'Visible','On') + set(handles.ref_i,'Visible','On') + else + set(handles.itext,'Visible','Off') + set(handles.first_i,'Visible','Off') + set(handles.last_i,'Visible','Off') + set(handles.incr_i,'Visible','Off') + set(handles.nb_field,'Visible','Off') + set(handles.ref_i,'Visible','Off') + end + if nbfield2 > 1 + set(handles.jtext,'Visible','On') + set(handles.first_j,'Visible','On') + set(handles.last_j,'Visible','On') + set(handles.incr_j,'Visible','On') + set(handles.nb_field2,'Visible','On') + set(handles.ref_j,'Visible','On') + else + set(handles.jtext,'Visible','Off') + set(handles.first_j,'Visible','Off') + set(handles.last_j,'Visible','Off') + set(handles.incr_j,'Visible','Off') + set(handles.nb_field2,'Visible','Off') + set(handles.ref_j,'Visible','Off') + end +end +set(handles.list_pair_civ1,'UserData',displ_num); +find_netcpair_civ1(hObject, eventdata, handles) +find_netcpair_civ2(hObject, eventdata, handles) + +%-------------------------------------------------------------- +% determine the menu for civ1 pairs depending on existing netcdf file at the middle of +% the field series set by first_i, incr, last_i +%---------------------------------------------------------------- +function find_netcpair_civ1(hObject, eventdata, handles) +set(gcf,'Pointer','watch') +%nomenclature types +filebase=get(handles.displ_filebase,'String'); +[filepath,Nme,ext_dir]=fileparts(filebase); +browse=get(handles.browse_root,'UserData'); +compare_list=get(handles.compare,'String'); +val=get(handles.compare,'Value'); +compare=compare_list{val}; +if strcmp(compare,'displacement') + mode='displacement'; +else + mode_list=get(handles.mode,'String'); + mode_value=get(handles.mode,'Value'); + mode=mode_list{mode_value}; +end + +% nomenclature type of the .nc files +nom_type_ima=[];%default +if isfield(browse,'nom_type_ima') + nom_type_ima=browse.nom_type_ima; +end + +%determine nom_type_nc: +nom_type_nc=[];%default +if isfield(browse,'nom_type_nc') + nom_type_nc=browse.nom_type_nc; +end +if isempty(nom_type_nc) + 'TESTciv' + nom_type_ima + [nom_type_nc]=nomtype2pair(nom_type_ima,isequal(mode,'series(Di)'),isequal(mode,'series(Dj)')); +end +browse.nom_type_nc=nom_type_nc; +set(handles.browse_root,'UserData',browse) + +%reads .nc subdirectoy and image numbers from the interface +subdir_civ1=get(handles.subdir_civ1,'String');%subdirectory subdir_civ1 for the netcdf data +first_i=str2num(get(handles.first_i,'String')); +last_i=str2num(get(handles.last_i,'String')); +incr=str2num(get(handles.incr_i,'String')); +num1=first_i:incr:last_i; +if isempty(num1) + set(handles.list_pair_civ1,'String',{''}); + return +end +ref_i=str2num(get(handles.ref_i,'String')); +if isequal(mode,'pair j1-j2')%|isequal(mode,'st_pair j1-j2') + ref_j=0; +else + ref_j=str2num(get(handles.ref_j,'String')); +end +if isequal(get(handles.dt_text,'String'),'dt(ms)=')%simple series(Di) with equal interval + ref_i=floor((first_i+last_i)/2); + ref_j=1; +end +time=get(handles.displ_filebase,'UserData');%get the set of times +if isempty(time) + time=[0 1]; +end +dt_unit=str2num(get(handles.dt,'String'));% used when there is no image documentation file +displ_num=get(handles.list_pair_civ1,'UserData'); + +%eliminate the first pairs inconsistent with the position + if isempty(displ_num) + nbpair=0; + else + nbpair=length(displ_num(1,:));%nbre of displayed pairs + if isequal(mode,'series(Di)') %| isequal(mode,'st_series(Di)') + nbpair=min(2*ref_i-1,nbpair);%limit the number of pairs with positive first index + elseif isequal(mode,'series(Dj)')% | isequal(mode,'st_series(Dj)') + nbpair=min(2*ref_j-1,nbpair);%limit the number of pairs with positive first index + end + end +nbpair=min(200,nbpair);%limit the number of displayed pairs to 200 + +%look for existing processed pairs involving the field at the middle of the series if civ1 will not +% be performed, while the result is needed for next steps. +displ_pair={''}; +select=ones(size(1:nbpair));%default =1 for numbers of displayed pairs +testpair=0; +if get(handles.CIV1,'Value')==0 % + dirname=fullfile(filepath,subdir_civ1,ext_dir); + if ~exist(fullfile(filepath,subdir_civ1,ext_dir),'dir') + msgbox_uvmat('ERROR',['no civ1 file available: subdirectory ' subdir_civ1 ' does not exist']); + set(handles.list_pair_civ1,'String',{}); + return + end + for ipair=1:nbpair + filename=name_generator(filebase,ref_i+displ_num(3,ipair),ref_j+displ_num(1,ipair),'.nc',nom_type_nc,1,... + ref_i+displ_num(4,ipair),ref_j+displ_num(2,ipair),subdir_civ1); + select(ipair)=exist(filename,'file')==2; + end + if ~exist('select','var') || isequal(select,zeros(size(1:nbpair))) + if isfield(browse,'incr_pair') + num_i1=ref_i-floor(browse.incr_pair(1)/2); + num_i2=ref_i+ceil(browse.incr_pair(1)/2); + num_j1=ref_j-floor(browse.incr_pair(2)/2); + num_j2=ref_j+ceil(browse.incr_pair(2)/2); + filename=name_generator(filebase,num_i1,num_j1,'.nc',nom_type_nc,1,num_i2,num_j2,subdir_civ1); + select(1)=exist(filename,'file')==2; + testpair=1; + else + if isequal(mode,'series(Dj)')% | isequal(mode,'st_series(Dj)') + msgbox_uvmat('ERROR',['no civ1 file available for the selected reference index j=' num2str(ref_j) ' and subdirectory ' subdir_civ1]); + else + msgbox_uvmat('ERROR',['no civ1 file available for the selected reference index i=' num2str(ref_i) ' and subdirectory ' subdir_civ1]); + end + set(handles.list_pair_civ1,'String',{''}); + %COMPLETER CAS STEREO + return + end + end +end +if isequal(mode,'series(Di)') %| isequal(mode,'st_series(Di)') + if testpair + displ_pair{1}=['Di= ' num2str(-floor(browse.incr_pair(1)/2)) '|' num2str(ceil(browse.incr_pair(1)/2))]; + elseif ~isequal(get(handles.dt_text,'String'),'dt(ms)=') + for ipair=1:nbpair + if select(ipair) + if size(time,1)>=ref_i+displ_num(4,ipair) && size(time,2)>=ref_j+displ_num(2,ipair) + dt=time(ref_i+displ_num(4,ipair),ref_j+displ_num(2,ipair))-time(ref_i+displ_num(3,ipair),ref_j+displ_num(1,ipair));%time interval dt + displ_pair{ipair}=['Di= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2)) ' :dt= ' num2str(dt*1000)]; + end + else + displ_pair{ipair}='...'; %pair not displayed in the menu + end + end + else + for ipair=1:nbpair + if select(ipair) + displ_pair{ipair}=['Di= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2)) ' :dt= ' num2str(dt_unit*ipair)]; + else + displ_pair{ipair}='...'; %pair not displayed in the menu + end + end + end +elseif isequal(mode,'series(Dj)')%|isequal(mode,'st_series(Dj)')% series on the j index + if testpair + displ_pair{1}=['Dj= ' num2str(-floor(browse.incr_pair(1)/2)) '|' num2str(ceil(browse.incr_pair(1)/2))]; + else + for ipair=1:nbpair + if select(ipair) + if size(time,1)>=ref_i+displ_num(4,ipair) && size(time,2)>=ref_j+displ_num(2,ipair) + dt=time(ref_i+displ_num(4,ipair),ref_j+displ_num(2,ipair))-time(ref_i+displ_num(3,ipair),ref_j+displ_num(1,ipair));%time interval dt + displ_pair{ipair}=['Dj= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2)) ' :dt= ' num2str(dt*1000)]; + end + elseif testpair + displ_pair{1}=['Dj= ' num2str(-floor(browse.incr_pair(2)/2)) '|' num2str(ceil(browse.incr_pair(2)/2))]; + else + displ_pair{ipair}='...'; %pair not displayed in the menu + end + end + end +elseif isequal(mode,'pair j1-j2')%|isequal(mode,'st_pair j1-j2')%case of pairs + for ipair=1:nbpair + if select(ipair) + dt=time(ref_i+displ_num(4,ipair),displ_num(2,ipair))-time(ref_i+displ_num(3,ipair),displ_num(1,ipair));%time interval dt + displ_pair{ipair}=['j= ' num2stra(displ_num(1,ipair),nom_type_ima) '-' num2stra(displ_num(2,ipair),nom_type_ima) ... + ' :dt= ' num2str(dt*1000)]; + else + displ_pair{ipair}='...'; %pair not displayed in the menu + end + end +elseif isequal(mode,'displacement') + displ_pair={'Di=Dj=0'}; +end +set(handles.list_pair_civ1,'String',displ_pair'); +ichoice=min(find(select)); +if (isempty(ichoice) | ichoice < 1); ichoice=1; end; +initial=get(handles.list_pair_civ1,'Value'); +if initial>nbpair |~isequal(select(initial),1) + set(handles.list_pair_civ1,'Value',ichoice);% first valid pair proposed by default in the menu +end +%set(handles.list_pair_civ2,'String',displ_pair'); +initial=get(handles.list_pair_civ2,'Value'); +if initial>length(displ_pair')%|~isequal(select(initial),1) + if ichoice <= length(displ_pair') + set(handles.list_pair_civ2,'Value',ichoice);% same pair proposed by default for civ2 + else + set(handles.list_pair_civ2,'Value',1);% same pair proposed by default for civ2 + end +end +set(handles.list_pair_civ2,'String',displ_pair'); +set(gcf,'Pointer','arrow') +%-------------------------------------------------------------- +% determine the menu for civ2 pairs depending on the existing netcdf file at the +%middle of the series set by first_i, incr, last_i +%-------------------------------------------------------------- +function find_netcpair_civ2(hObject, eventdata, handles) +set(gcf,'Pointer','watch') +%nomenclature types +filebase=get(handles.displ_filebase,'String'); +[filepath,Nme,ext_dir]=fileparts(filebase); +browse=get(handles.browse_root,'UserData'); +compare_list=get(handles.compare,'String'); +val=get(handles.compare,'Value'); +compare=compare_list{val}; +if strcmp(compare,'displacement') + mode='displacement'; +else + mode_list=get(handles.mode,'String'); + mode_value=get(handles.mode,'Value'); + mode=mode_list{mode_value}; +end + +% nomenclature type of the .nc files +nom_type_ima='ima_num';%default +if isfield(browse,'nom_type_ima') + nom_type_ima=browse.nom_type_ima; +end +nom_type_nc='_i1-i2';%default +if isfield(browse,'nom_type_nc') + nom_type_nc=browse.nom_type_nc; +end +if isequal(nom_type_ima,'png_old') | isequal(nom_type_ima,'netc_old')| isequal(nom_type_ima,'raw_SMD')| isequal(nom_type_nc,'netc_old') + nom_type_nc='netc_old';%nom_type for the netcdf files +elseif isequal(nom_type_ima,'none')|isequal(nom_type_nc,'none') + nom_type_nc='none'; +elseif isequal(nom_type_ima,'avi')|isequal(nom_type_ima,'_i')|isequal(nom_type_ima,'ima_num')|isequal(nom_type_nc,'_i1-i2') + nom_type_nc='_i1-i2'; +else + if isequal(mode,'series(Di)')%|isequal(mode,'st_series(Di)') + nom_type_nc='_i1-i2_j'; % PIV in volume + else + nom_type_nc='_i_j1-j2'; + end +end +browse.nom_type_nc=nom_type_nc; +set(handles.browse_root,'UserData',browse) + +%reads .nc subdirectory and image numbers from the interface +subdir_civ1=get(handles.subdir_civ1,'String');%subdirectory subdir_civ1 for the netcdf data +subdir_civ2=get(handles.subdir_civ2,'String');%subdirectory subdir_civ2 for the netcdf data +first_i=str2num(get(handles.first_i,'String')); +last_i=str2num(get(handles.last_i,'String')); +incr=str2num(get(handles.incr_i,'String')); +num1=first_i:incr:last_i; +if isempty(num1) + set(handles.list_pair_civ2,'Value',1); + set(handles.list_pair_civ2,'String',{''}); + return +end +ref_i=str2num(get(handles.ref_i,'String')); +if isequal(mode,'pair j1-j2')%|isequal(mode,'st_pair j1-j2') + ref_j=0; +else + ref_j=str2num(get(handles.ref_j,'String')); +end +if isequal(get(handles.dt_text,'String'),'dt(ms)=')%simple series(Di) with equal interval + ref_i=ceil((first_i+last_i)/2); + ref_j=1; +end +% ref_i=browse.num_ref;%field number initially selected by the browser +time=get(handles.displ_filebase,'UserData'); %get the set of times +if isempty(time) + time=[0 1];%default +end +dt_unit=str2num(get(handles.dt,'String'));% used when there is no image documentation file +displ_num=get(handles.list_pair_civ1,'UserData'); + + +%eliminate the first pairs inconsistent with the position +if isempty(displ_num) + nbpair=0; +else + nbpair=length(displ_num(1,:));%nbre of displayed pairs + if isequal(mode,'series(Di)')% | isequal(mode,'st_series(Di)') + nbpair=min(2*ref_i-1,nbpair);%limit the number of pairs with positive first index + elseif isequal(mode,'series(Dj)')% | isequal(mode,'st_series(Dj)') + nbpair=min(2*ref_j-1,nbpair);%limit the number of pairs with positive first index + end +end +nbpair=min(200,nbpair);%limit the number of displayed pairs to 200 + +%look for existing processed pairs involving the field at the middle of the series if civ1 will not +% be performed, while the result is needed for next steps. +displ_pair={''}; %default +select=ones(size(1:nbpair));%default =1 for numbers of displayed pairs +if get(handles.CIV2,'Value')==0 & get(handles.CIV1,'Value')==0 & get(handles.FIX1,'Value')==0 & get(handles.PATCH1,'Value')==0%&... + if ~exist(fullfile(filepath,subdir_civ2,ext_dir),'dir') + errordlg(['no civ2 file available: subdirectory ' subdir_civ2 ' does not exist']) + set(handles.list_pair_civ2,'Value',1); + set(handles.list_pair_civ2,'String',{''}); + return + end + for ipair=1:nbpair + filename=name_generator(filebase,ref_i+displ_num(3,ipair),ref_j+displ_num(1,ipair),'.nc',nom_type_nc,1,... + ref_i+displ_num(4,ipair),ref_j+displ_num(2,ipair),subdir_civ1); + select(ipair)=exist(filename,'file')==2; + end + if isequal(select,zeros(size(1:nbpair))) + if isfield(browse,'incr_pair') + num_i1=ref_i-floor(browse.incr_pair(1)/2); + num_i2=ref_i+floor((browse.incr_pair(1)+1)/2); + num_j1=ref_j-floor(browse.incr_pair(2)/2); + num_j2=ref_j+floor((browse.incr_pair(2)+1)/2); + filename=name_generator(filebase,num_i1,num_j1,'.nc',nom_type_nc,1,num_i2,num_j2,subdir_civ2); + select(1)=exist(filename,'file')==2; + else + if isequal(mode,'series(Dj)')% | isequal(mode,'st_series(Dj)') + errordlg(['no civ2 file available for the selected reference index j=' num2str(ref_j) ' and subdirectory ' subdir_civ2]) + else + errordlg(['no civ2 file available for the selected reference index i=' num2str(ref_i) ' and subdirectory ' subdir_civ2]) + end + set(handles.list_pair_civ2,'Value',1); + set(handles.list_pair_civ2,'String',{''}); + return + end + end +end +if isequal(mode,'series(Di)') % | isequal(mode,'st_series(Di)') +% if ~isequal(get(handles.dt_text,'String'),'dt(ms)=') + for ipair=1:nbpair + if select(ipair) + if size(time,1)>=ref_i+displ_num(4,ipair) && size(time,2)>=ref_j+displ_num(2,ipair) + dt=time(ref_i+displ_num(4,ipair),ref_j+displ_num(2,ipair))-time(ref_i+displ_num(3,ipair),ref_j+displ_num(1,ipair));%time interval dt + displ_pair{ipair}=['Di= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2)) ' :dt= ' num2str(dt*1000)]; + end + else + displ_pair{ipair}='...'; %pair not displayed in the menu + end + end +% else +% for ipair=1:nbpair +% if select(ipair) +% displ_pair{ipair}=['Di= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2)) ' :dt= ' num2str(dt_unit*ipair)]; +% else +% displ_pair{ipair}='...'; %pair not displayed in the menu +% end +% end +% end +elseif isequal(mode,'series(Dj)') %| isequal(mode,'st_series(Dj)') % series on the j index + for ipair=1:nbpair + if select(ipair) + if size(time,1)>=ref_i+displ_num(4,ipair) && size(time,2)>=ref_j+displ_num(2,ipair) + dt=time(ref_i+displ_num(4,ipair),ref_j+displ_num(2,ipair))-time(ref_i+displ_num(3,ipair),ref_j+displ_num(1,ipair));%time interval dt + displ_pair{ipair}=['Dj= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2)) ' :dt= ' num2str(dt*1000)]; + end + else + displ_pair{ipair}='...'; %pair not displayed in the menu + end + end +elseif isequal(mode,'pair j1-j2')% | isequal(mode,'st_pair j1-j2') %case of pairs + for ipair=1:nbpair + if select(ipair) + dt=time(ref_i+displ_num(4,ipair),displ_num(2,ipair))-time(ref_i+displ_num(3,ipair),displ_num(1,ipair));%time interval dt + displ_pair{ipair}=['j= ' num2stra(displ_num(1,ipair),nom_type_ima) '-' num2stra(displ_num(2,ipair),nom_type_ima) ... + ' :dt= ' num2str(dt*1000)]; + else + displ_pair{ipair}='...'; %pair not displayed in the menu + end + end +elseif isequal(mode,'displacement') + displ_pair={'Di=Dj=0'}; +end +val=get(handles.list_pair_civ2,'Value'); +ichoice=min(find(select)); +if (isempty(ichoice) | ichoice < 1); ichoice=1; end; +if get(handles.CIV2,'Value')==0 & get(handles.CIV1,'Value')==0 & get(handles.FIX1,'Value')==0 & get(handles.PATCH1,'Value')==0 + val=ichoice;% first valid pair proposed by default in the menu +end +if val>length(displ_pair') + set(handles.list_pair_civ2,'Value',1);% first valid pair proposed by default in the menu +else + set(handles.list_pair_civ2,'Value',val); +end +set(handles.list_pair_civ2,'String',displ_pair'); + + +set(gcf,'Pointer','arrow') +%---------------------------------------------------- +% determine the list of index pairs of processing file +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% +function [num1_civ1,num2_civ1,num_a_civ1,num_b_civ1,num1_civ2,num2_civ2,num_a_civ2,num_b_civ2]=... + find_pair_indices(handles,mode) +first_i=str2num(get(handles.first_i,'String')); +last_i=str2num(get(handles.last_i,'String')); +incr=str2num(get(handles.incr_i,'String')); +num1=[first_i:incr:last_i]; +if isequal(get(handles.first_j,'Visible'),'on') + first_j=str2num(get(handles.first_j,'String')); + last_j=str2num(get(handles.last_j,'String')); + incr_j=str2num(get(handles.incr_j,'String')); +else + first_j=1; + last_j=1; + incr_j=1; +end +num_j=[first_j:incr_j:last_j]; +list_civ1=get(handles.list_pair_civ1,'String'); +index_civ1=get(handles.list_pair_civ1,'Value'); +str_civ1=list_civ1{index_civ1}; +if isempty(str_civ1)||isequal(str_civ1,'') + msgbox_uvmat('ERROR','no image pair selected for civ1') + return +end +list_civ2=get(handles.list_pair_civ2,'String'); +index_civ2=get(handles.list_pair_civ2,'Value'); +if index_civ2>length(list_civ2) + list_civ2=list_civ1; + index_civ2=index_civ1; +end +str_civ2=list_civ2{index_civ2}; +if isequal(first_i,[])|isequal(first_j,[]), errordlg('first field number not defined'),... + set(handles.RUN, 'Enable','On'), set(handles.RUN,'BackgroundColor',[1 0 0]),return,end; +if isequal(last_i,[])| isequal(last_j,[]),errordlg('last field number not defined'),... + set(handles.RUN, 'Enable','On'), set(handles.RUN,'BackgroundColor',[1 0 0]),return,end; +if isequal(incr,[])| isequal(incr_j,[]),errordlg('increment in field number not defined'),... + set(handles.RUN, 'Enable','On'), set(handles.RUN,'BackgroundColor',[1 0 0]),return,end; +if last_i < first_i | last_j < first_j , errordlg('last field number must be larger than the first one'),... + set(handles.RUN, 'Enable','On'), set(handles.RUN,'BackgroundColor',[1 0 0]),return,end; +if isequal (mode,'series(Di)')% |isequal(mode,'st_series(Di)') + %recognize the pair civ1 from the display + indsel=find((double(str_civ1)<48)|(double(str_civ1)>57));% character indices of non numerical characters + str_raw=str_civ1(indsel); + indsepar=find(str_raw=='|'); %character index of the separator + d1=str2num(str_civ1([indsel(indsepar-1)+1:indsel(indsepar)-1])); + if indsepar==length(str_raw) + d2=str2num(str_civ1([indsel(indsepar)+1:end])); + else + d2=str2num(str_civ1([indsel(indsepar)+1:indsel(indsepar+1)-1])); + end + num1_civ1=num1-d1;% set of first image numbers + num2_civ1=num1+d2; + num_a_civ1=num_j; + num_b_civ1=num_j; + + %recognize the pair civ2 from the display + indsel=find((double(str_civ2)<48)|(double(str_civ2)>57));% character indices of non numerical characters + str_raw=str_civ2(indsel); + indsepar=find(str_raw=='|'); %character index of the separator + d1=str2num(str_civ2([indsel(indsepar-1)+1:indsel(indsepar)-1])); + if indsepar==length(str_raw) + d2=str2num(str_civ2([indsel(indsepar)+1:end])); + else + d2=str2num(str_civ2([indsel(indsepar)+1:indsel(indsepar+1)-1])); + end + if isempty(d1) + num1_civ2=num1; + else + num1_civ2=num1-d1;% set of first image numbers + end + if isempty(d2) + num2_civ2=num1; + else + num2_civ2=num1+d2; + end + num_a_civ2=num_j; + num_b_civ2=num_j; + + % adjust the first and last field number + lastfield=str2num(get(handles.nb_field,'String')); + if isequal(lastfield,[]) + indsel=find((num1_civ1 >= 1)&(num1_civ2 >= 1)); + else + indsel=find((num2_civ1 <= lastfield)&(num2_civ2 <= lastfield)&(num1_civ1 >= 1)&(num1_civ2 >= 1)); + end + if length(indsel)>=1 + firstind=indsel(1); + lastind=indsel(end); + set(handles.first_i,'String',num2str(num1(firstind)))%update the display of first and last fields + set(handles.last_i,'String',num2str(num1(lastind))) + num1=num1(indsel); + num1_civ1=num1_civ1(indsel); + num1_civ2=num1_civ2(indsel); + num2_civ1=num2_civ1(indsel); + num2_civ2=num2_civ2(indsel); + end +elseif isequal (mode,'series(Dj)')%|isequal (mode,'st_series(Dj)') + lastfield_j=str2num(get(handles.nb_field2,'String')); + num1_civ1=num1;% set of first image numbers + num2_civ1=num1; + num_a_civ1=num_j-floor(index_civ1/2)*ones(size(num_j)); + num_b_civ1=num_j+ceil(index_civ1/2)*ones(size(num_j)); + num1_civ2=num1; + num2_civ2=num1; + num_a_civ2=num_j-floor(index_civ2/2)*ones(size(num_j)); + num_b_civ2=num_j+ceil(index_civ2/2)*ones(size(num_j)); + % adjust the first and last field number + if isequal(lastfield_j,[]) + indsel=find((num_a_civ1 >= 1)&(num_a_civ2 >= 1)); + else + indsel=find((num_b_civ1 <= lastfield_j)&(num_b_civ2 <= lastfield_j)&(num_a_civ1 >= 1)&(num_a_civ2 >= 1)); + end + if length(indsel)>=1 + firstind=indsel(1); + lastind=indsel(end); + set(handles.first_j,'String',num2str(num_j(firstind)))%update the display of first and last fields + set(handles.last_j,'String',num2str(num_j(lastind))) + num_j=num_j(indsel); + num_a_civ1=num_a_civ1(indsel); + num_a_civ2=num_a_civ2(indsel); + num_b_civ1=num_b_civ1(indsel); + num_b_civ2=num_b_civ2(indsel); + end +elseif isequal(mode,'pair j1-j2')% | isequal(mode,'st_pair j1-j2') %case of bursts (png_old or png_2D) + num1_civ1=num1; + num1_civ2=num1; + displ_num=get(handles.list_pair_civ1,'UserData'); + num2_civ1=num1; + num_a_civ1=displ_num(1,index_civ1); + num_b_civ1=displ_num(2,index_civ1); + num2_civ2=num1; + num_a_civ2=displ_num(1,index_civ2); + num_b_civ2=displ_num(2,index_civ2); +elseif isequal(mode,'displacement') + num1_civ1=num1; + num2_civ1=num1; + num_a_civ1=num_j; + num_b_civ1=num_j; + num1_civ2=num1; + num2_civ2=num1; + num_a_civ2=num_j; + num_b_civ2=num_j; +end + + +%------------------------------------------------------------- +% --- Executes on selection change in list_pair_civ1. +function list_pair_civ1_Callback(hObject, eventdata, handles) +%------------------------------------------------------------ +%reproduce by default the chosen pair in the civ2 menu +list_pair=get(handles.list_pair_civ1,'String');%get the menu of image pairs +index_pair=get(handles.list_pair_civ1,'Value'); +displ_num=get(handles.list_pair_civ1,'UserData'); +num_a=displ_num(1,index_pair); +num_b=displ_num(2,index_pair); +list_pair2=get(handles.list_pair_civ2,'String');%get the menu of image pairs +if index_pair<=length(list_pair2) + set(handles.list_pair_civ2,'Value',index_pair); +end + +%update first_i and last_i according to the chosen image pairs +mode_list=get(handles.mode,'String'); +mode_value=get(handles.mode,'Value'); +mode=mode_list{mode_value}; +if isequal(mode,'series(Di)') + first_i=str2num(get(handles.first_i,'String')); + last_i=str2num(get(handles.last_i,'String')); + incr_i=str2num(get(handles.incr_i,'String')); + num1=first_i:incr_i:last_i; + lastfield=str2num(get(handles.nb_field,'String')); + if ~isequal(lastfield,[]) + ind=find((num1-floor(index_pair/2)*ones(size(num1))>0)& ... + (num1+ceil(index_pair/2)*ones(size(num1))<=lastfield)); + num1=num1(ind); + end + set(handles.first_i,'String',num2str(num1(1))); + set(handles.last_i,'String',num2str(num1(end))); +elseif isequal(mode,'series(Dj)') + first_j=str2num(get(handles.first_j,'String')); + last_j=str2num(get(handles.last_j,'String')); + incr_j=str2num(get(handles.incr_j,'String')); + num_j=first_j:incr_j:last_j; + lastfield2=str2num(get(handles.nb_field2,'String')); + if ~isequal(lastfield2,[]) + ind=find((num_j-floor(index_pair/2)*ones(size(num_j))>0)& ... + (num_j+ceil(index_pair/2)*ones(size(num_j))<=lastfield2)); + num1=num_j(ind); + end + set(handles.first_j,'String',num2str(num1(1))); + set(handles.last_j,'String',num2str(num1(end))); +end + +%------------------------------------------------------------------ +% --- Executes on selection change in list_pair_civ2. +function list_pair_civ2_Callback(hObject, eventdata, handles) + +index_pair=get(handles.list_pair_civ2,'Value');%get the selected position index in the menu + +%update first_i and last_i according to the chosen image pairs +mode_list=get(handles.mode,'String'); +mode_value=get(handles.mode,'Value'); +mode=mode_list{mode_value}; +if isequal(mode,'series(Di)') + first_i=str2num(get(handles.first_i,'String')); + last_i=str2num(get(handles.last_i,'String')); + incr_i=str2num(get(handles.incr_i,'String')); + num1=first_i:incr_i:last_i; + lastfield=str2num(get(handles.nb_field,'String')); + if ~isequal(lastfield,[]) + ind=find((num1-floor(index_pair/2)*ones(size(num1))>0)& ... + (num1+ceil(index_pair/2)*ones(size(num1))<=lastfield)); + num1=num1(ind); + end + set(handles.first_i,'String',num2str(num1(1))); + set(handles.last_i,'String',num2str(num1(end))); +elseif isequal(mode,'series(Dj)') + first_j=str2num(get(handles.first_j,'String')); + last_j=str2num(get(handles.last_j,'String')); + incr_j=str2num(get(handles.incr_j,'String')); + num_j=first_j:incr_j:last_j; + lastfield2=str2num(get(handles.nb_field2,'String')); + if ~isequal(lastfield2,[]) + ind=find((num_j-floor(index_pair/2)*ones(size(num_j))>0)& ... + (num_j+ceil(index_pair/2)*ones(size(num_j))<=lastfield2)); + num1=num_j(ind); + end + set(handles.first_j,'String',num2str(num1(1))); + set(handles.last_j,'String',num2str(num1(end))); +end + +%--------------------------------------------------- +% --- Executes on button press in RUN. +%------------------------------------------------------ +function RUN_Callback(hObject, eventdata, handles) +global civ1_exe civ2_exe patch_exe patch_new_exe sge + +compare=get(handles.compare,'Value');%test for usual PIV (compare=1) or displacement (=2) or stereo PIV (=3) +%check the list of operations: +operations={'CIV1','FIX1','PATCH1','CIV2','FIX2','PATCH2'}; +run_flag=1; +box_test(1)=get(handles.CIV1,'Value'); +box_test(2)=get(handles.FIX1,'Value'); +box_test(3)=get(handles.PATCH1,'Value'); +box_test(4)=get(handles.CIV2,'Value'); +box_test(5)=get(handles.FIX2,'Value'); +box_test(6)=get(handles.PATCH2,'Value'); +index=find(box_test==1); +if isempty(index) + msgbox_uvmat('ERROR','no selected operation') + return +end +index_first=min(index); +index_last=max(index); +box_used=box_test([index_first : index_last]); +[box_missing,ind_missing]=min(box_used); +if isequal(box_missing,0) + msgbox_uvmat('ERROR',['missing' cell2mat(operations(ind_missing))]); + return +end + +%root name +filebase=get(handles.displ_filebase,'String'); +if isempty(filebase)||isequal(filebase,'') + msgbox_uvmat('ERROR','no input files') + return +end +%check mask if selecetd +if isequal(get(handles.get_mask_civ1,'Value'),1) + get_mask_civ1_Callback(hObject, eventdata, handles); +end +if isequal(get(handles.get_mask_fix1,'Value'),1) + get_mask_fix1_Callback(hObject, eventdata, handles); +end +if isequal(get(handles.get_mask_civ2,'Value'),1) + get_mask_civ2_Callback(hObject, eventdata, handles); +end +if isequal(get(handles.get_mask_fix2,'Value'),1) + get_mask_fix2_Callback(hObject, eventdata, handles); +end + +%read names of the .exe file +if box_test(1)==1 | box_test(3)==1 | box_test(4)==1 | box_test(6)==1 + path_uvmat=which('uvmat');% check the path detected for source file uvmat + path_UVMAT=fileparts(path_uvmat); %path to UVMAT + if isunix + %fid = fopen(fullfile(path_UVMAT,'PARAM_LINUX.txt'),'r');%open the file with civ binary names + xmlfile=fullfile(path_UVMAT,'PARAM_LINUX.xml'); + if exist(xmlfile,'file') + t=xmltree(xmlfile); + sparam=convert(t); + end + else + %fid = fopen(fullfile(path_UVMAT,'PARAM_WIN.txt'),'r');%open the file with civ binary names + xmlfile=fullfile(path_UVMAT,'PARAM_WIN.xml'); + if exist(xmlfile,'file') + t=xmltree(xmlfile); + sparam=convert(t); + end + end + if isfield(sparam,'Civ1_exe') + civ1_exe=sparam.Civ1_exe; + end + if isfield(sparam,'Civ2_exe') + civ2_exe=sparam.Civ2_exe; + end + if isfield(sparam,'Patch_exe') + patch_exe=sparam.Patch_exe; + end + if isfield(sparam,'Stinterp_exe') + stinterp_exe=sparam.Stinterp_exe; + end + if isfield(sparam,'SGE') + sge=str2num(sparam.SGE); + end + if ~isunix % for windows system, check whether the Matlab working dir is a UBC name + dircur=pwd; + if ~isequal(dircur([2 3]),':\') + msgbox_uvmat('ERROR','move to a Matlab current working directory with a Windows name, e.g. m:/...') + return; + end + end +end + +%initialize the waitbars +set(handles.waitbar_1,'Position',[0.946 0.877 0.03 0.001]) +set(handles.waitbar_patch1,'Position',[0.946 0.626 0.03 0.001]) +set(handles.waitbar_civ2,'Position',[0.946 0.406 0.03 0.001]) +set(handles.waitbar_patch2,'Position',[0.946 0.187 0.03 0.001]) +set(handles.RUN,'BackgroundColor',[0.831 0.816 0.784]) +set(handles.RUN, 'Enable','Off') +drawnow + +% get the list of file names and check the files +display('checking the files...') +[filecell,num1_civ1,num2_civ1,num_a_civ1,num_b_civ1,num1_civ2,num2_civ2,num_a_civ2,num_b_civ2,nom_type_nc,file_ref_fix1,file_ref_fix2]=... + set_civ_filenames(handles,compare,box_test); +display('files OK, processing...') +nbfield=size(num1_civ1,2); +nbslice=size(num1_civ1,1); + +%RUN CIV1 +if box_test(1)==1 + RUN_CIV1(handles,filecell.ima1.civ1,filecell.ima2.civ1,filecell.nc.civ1,num1_civ1,num2_civ1,num_a_civ1,num_b_civ1,nom_type_nc) + if compare==3 + RUN_CIV1(handles,filecell.imaA1.civ1,filecell.imaA2.civ1,filecell.ncA.civ1,num1_civ1,num2_civ1,num_a_civ1,num_b_civ1,nom_type_nc) + end +end + +%RUN FIX1 +if box_test(2)==1 + filebase=get(handles.displ_filebase,'String'); + %names of the civ1 fields + field1.vel_type='civ1'; + field1.nb='nb_vectors'; + field1.X='vec_X'; + field1.Y='vec_Y'; + field1.U='vec_U'; + field1.V='vec_V'; + field1.fixflag='vec_FixFlag'; + flagindex(1)=get(handles.vec_Fmin2, 'Value'); + flagindex(2)=get(handles.vec_F3, 'Value'); + flagindex(3)=get(handles.vec_F2, 'Value'); + thresh_vecC=str2num(get(handles.thresh_vecC,'String'));%threshold on image correlation vec_C + thresh_vel=str2num(get(handles.thresh_vel,'String'));%threshold on velocity modulus + inf_sup=get(handles.inf_sup1,'Value'); + menu=get(handles.field_ref1,'String'); + index=get(handles.field_ref1,'Value'); + if isempty(menu) + fieldchoice=''; + else + fieldchoice=menu{index}; + end + h = waitbar(0,['removing velocity vectors, fix1']);% display a wait bar + test_mask=get(handles.get_mask_fix1,'Value'); + maskdispl=get(handles.mask_fix1,'String'); + maskbase=[get(handles.displ_filebase,'String') '_' maskdispl]; % mask root name + for ifile=1:nbfield + waitbar(ifile/nbfield); %update the waitbar + for j=1:nbslice + if test_mask==0 + maskname='noFile use default'; + maskflag=0; + else + nbslice_mask=str2num(maskdispl(1:end-4)); % + num1_mask=mod(num1_civ1(ifile)-1,nbslice_mask)+1; + maskname=name_generator(maskbase,num1_mask,1,'.png','_i');% mask corresponding to the first image of the pair + maskflag= exist(maskname,'file')==2; + if ~maskflag; + maskname='noFile use default'; + end + end + if ~isempty(file_ref_fix1) + file_ref=file_ref_fix1{ifile,j}; + else + file_ref=''; + end + error=RUN_FIX(filecell.nc.civ1{ifile,j},field1,flagindex,1,thresh_vecC,maskflag,maskname,... + thresh_vel,inf_sup,file_ref,fieldchoice); + + if compare==3 &&(isequal(mode,'pair j1-j2') || isequal(mode,'series(Dj)') || isequal(mode,'series(Di)')) + if test_mask==0 + maskname='noFile use default'; + maskflag=0; + else + maskbase=[get(handles.displ_filebase2,'String') '_' maskdispl]; % mask root name + nbslice_mask=str2num(maskdispl(1:end-4)); % + num1_mask=mod(num1_civ1(ifile)-1,nbslice_mask)+1; + maskname=name_generator(maskbase,num1_mask,1,'.png','_i'); + maskflag= exist(maskname,'file')==2; + if ~maskflag; + maskname='noFile use default'; + end + end + error=RUN_FIX(filecell.ncA.civ1{ifile,j},field1,flagindex,1,thresh_vecC,maskflag,maskname,... + thresh_vel,inf_sup,file_ref,fieldchoice); + if ~isempty(error) + msgbox_uvmat('ERROR',error) + return + end + end + end + end + close(h) +end + +% RUN PATCH1 +if box_test(3)==1 + rho_patch1=str2num(get(handles.rho_patch1,'String')); + if isempty(rho_patch1) + rho_patch1='1000'; + set(handles.rho_patch1,'String','1') + else + rho_patch1=num2str(1000*rho_patch1); + end + nx_patch1=get(handles.nx_patch1,'String'); + if isequal(str2num(nx_patch1),[]) + nx_patch1='50' ;%default + set(handles.nx_patch1,'String','50'); + end + ny_patch1=get(handles.ny_patch1,'String'); + if isequal(str2num(ny_patch1),[]) + ny_patch1='50' ;%default + set(handles.ny_patch1,'String','50'); + end + subdomain_patch1=get(handles.subdomain_patch1,'String'); + thresh_patch1=get(handles.thresh_patch1,'String'); + test_interp=get(handles.test_interp,'Value'); + icount=0; + for ifile=1:nbfield + for j=1:nbslice + icount=icount+1; + barlength=0.188*icount/(nbfield*nbslice); + set(handles.waitbar_patch1,'Position',[0.946 0.627-barlength 0.03 barlength]) + drawnow + if isequal(get(handles.test_stereo1,'Value'),0) + cmd=RUN_PATCH(filecell.nc.civ1{ifile,j},nx_patch1,ny_patch1,rho_patch1,subdomain_patch1,thresh_patch1,test_interp); + s=-1; + if sge + [s,w]=unix(['qrsh -q -fast.q ' cmd]); + end + if s~=0 + display(['!' cmd]) + eval(['!' cmd]); + end + + %stereo case: + elseif isequal(get(handles.test_stereo1,'Value'),1) + if exist('stinterp_exe','var')%Prog Gauthier + cmd=RUN_STINTERP(stinterp_exe,filecell.ncA.civ1{ifile,j},filecell.nc.civ1{ifile,j},filecell.st{ifile,j},... + nx_patch1,ny_patch1,rho_patch1,subdomain_patch1,thresh_patch1,[filebase_A '.xml'],[filebase_B '.xml']); + display(['!' cmd]) + eval(['!' cmd]); + else + RUN_STLIN(filecell.ncA.civ1{ifile,j},filecell.nc.civ1{ifile,j},'civ1',filecell.st{ifile,j},... + str2num(nx_patch1),str2num(ny_patch1),str2num(thresh_patch1),[filebase_A '.xml'],[filebase_B '.xml']); + end + end + if compare==3 && isequal(get(handles.test_stereo1,'Value'),0) + cmd=RUN_PATCH(filecell.ncA.civ1{ifile,j},nx_patch1,ny_patch1,rho_patch1,subdomain_patch1,thresh_patch1,test_interp); + s=-1; + if sge + [s,w]=unix(['qrsh -q -fast.q ' cmd]); + end + if s~=0 + display(['!' cmd]) + eval(['!' cmd]); + end + end + end + end +end + +% CIV2 +if box_test(4)==1 + RUN_CIV2(handles,filecell.ima1.civ2,filecell.ima2.civ2,filecell.nc.civ1,filecell.nc.civ2,num1_civ2,num2_civ2,... + num_a_civ2,num_b_civ2,nom_type_nc) +end + +% FIX2 +if box_test(5)==1 + %names of the civ2 fields + field2.vel_type='civ2'; + field2.nb='nb_vectors2'; + field2.X='vec2_X'; + field2.Y='vec2_Y'; + field2.U='vec2_U'; + field2.V='vec2_V'; + field2.fixflag='vec2_FixFlag'; + flagindex(1)=get(handles.vec_Fmin2_2, 'Value'); + flagindex(2)=get(handles.vec_F3_2, 'Value'); + flagindex(3)=get(handles.vec_F4, 'Value'); + thresh_vec2C=str2num(get(handles.thresh_vec2C,'String'));%threshold on image correlation vec_C + thresh_vel2=str2num(get(handles.thresh_vel2,'String'));%threshold on velocity modulus + inf_sup=get(handles.inf_sup2,'Value'); + menu=get(handles.field_ref2,'String'); + index=get(handles.field_ref2,'Value'); + if isempty(menu) + fieldchoice=''; + else + fieldchoice=menu{index}; + end + h = waitbar(0,['removing velocity vectors, fix2']);% display a wait bar + test_mask=get(handles.get_mask_fix2,'Value'); + maskdispl=get(handles.mask_fix2,'String'); + maskbase=[get(handles.displ_filebase,'String') '_' maskdispl]; % mask root name + for ifile=1:nbfield + waitbar(ifile/nbfield); %update the waitbar + for j=1:nbslice + if test_mask==0 + maskname='noFile use default'; + maskflag=0; + else + nbslice_mask=str2num(maskdispl(1:end-4)); % + num1_mask=mod(num1_civ2(ifile)-1,nbslice_mask)+1; + maskname=name_generator(maskbase,num1_mask,1,'.png','_i'); + maskflag= exist(maskname,'file')==2; + if ~maskflag; + maskname='noFile use default'; + end + end + if ~isempty(file_ref_fix2) + file_ref=file_ref_fix2{ifile,j}; + else + file_ref=''; + end + error=RUN_FIX(filecell.nc.civ2{ifile,j},field2,flagindex,2,thresh_vec2C,maskflag,maskname,... + thresh_vel2,inf_sup,file_ref,fieldchoice); + if ~isempty(error) + msgbox_uvmat('ERROR',error) + return + end + if compare==3 + if test_mask==0 + maskname='noFile use default'; + maskflag=0; + else + maskbase=[get(handles.displ_filebase2,'String') '_' maskdispl]; % mask root name + nbslice_mask=str2num(maskdispl(1:end-4)); % + num1_mask=mod(num1_civ2(ifile)-1,nbslice_mask)+1; + maskname=name_generator(maskbase,num1_mask,1,'.png','_i'); + maskflag= exist(maskname,'file')==2; + if ~maskflag; + maskname='noFile use default'; + end + end + error=RUN_FIX(filecell.ncA.civ2{ifile,j},field2,flagindex,1,thresh_vec2C,maskflag,maskname,... + thresh_vel2,inf_sup,file_ref,fieldchoice); + if ~isempty(error) + msgbox_uvmat('ERROR',error) + return + end + end + end + end + close(h) +end + +%PATCH 2 +if box_test(6)==1 + rho_patch2=str2num(get(handles.rho_patch2,'String')); + if isempty(rho_patch2) + rho_patch2='1000'; + set(handles.rho_patch2,'String','1') + else + rho_patch2=num2str(1000*rho_patch2); + end + nx_patch2=get(handles.nx_patch2,'String'); + ny_patch2=get(handles.ny_patch2,'String'); + thresh_patch2=get(handles.thresh_patch2,'String'); + if isequal(str2num(nx_patch2),[]) + nx_patch2='50' ;%default + set(handles.nx_patch2,'String','50'); + end + if isequal(str2num(ny_patch2),[]) + ny_patch2='50' ;%default + set(handles.ny_patch2,'String','50'); + end + subdomain_patch2=get(handles.subdomain_patch2,'String'); + icount=0; + for ifile=1:nbfield + for j=1:nbslice + icount=icount+1; + barlength=0.188*icount/(nbfield*nbslice); + set(handles.waitbar_patch2,'Position',[0.946 0.188-barlength 0.03 barlength]) + drawnow + if compare~=3 | isequal(get(handles.test_stereo2,'Value'),0) + cmd=RUN_PATCH(filecell.nc.civ2{ifile,j},nx_patch2,ny_patch2,rho_patch2,subdomain_patch2,1,0); + s=-1; + if sge + [s,w]=unix(['qrsh -q -fast.q ' cmd]); + end + if s~=0 + display(['!' cmd]) + eval(['!' cmd]); + end + elseif compare==3 && isequal(get(handles.test_stereo2,'Value'),1) + if exist('stinterp_exe','var')%Prog Gauthier + cmd=RUN_STINTERP(stinterp_exe,filecell.ncA.civ2{ifile,j},filecell.nc.civ2{ifile,j},filecell.st{ifile,j},... + nx_patch2,ny_patch2,rho_patch2,subdomain_patch2,thresh_patch2,[filebase_A '.xml'],[filebase_B '.xml']); + display(['!' cmd]) + eval(['!' cmd]) + else + RUN_STLIN(filecell.ncA.civ2{ifile,j},filecell.nc.civ2{ifile,j},'civ2',filecell.st{ifile,j},... + str2num(nx_patch2),str2num(ny_patch2),str2num(thresh_patch2),[filebase_A '.xml'],[filebase_B '.xml']) + end + end + if compare==3 && isequal(get(handles.test_stereo2,'Value'),0) + cmd=RUN_PATCH(filecell.ncA.civ2{ifile,j},nx_patch2,ny_patch2,rho_patch2,subdomain_patch2,1,0); + s=-1; + if sge + [s,w]=unix(['qrsh -q -fast.q ' cmd]); + end + if s~=0 + display(['!' cmd]) + eval(['!' cmd]); + end + end + end + end +end + +set(handles.RUN, 'Enable','On') +set(handles.RUN,'BackgroundColor',[1 0 0]) + +%save the current interface setting as figure namefig, append .0 to the name if it already exists +if isfield(filecell,'st') + fileresu=filecell.st{1,1}; +elseif isfield(filecell,'nc') + if isfield(filecell.nc,'civ2') + fileresu=filecell.nc.civ2{1,1}; + else + fileresu=filecell.nc.civ1{1,1}; + end +end +[RootPath,RootFile,field_count,str2,str_a,str_b,ext,nom_type,subdir]=name2display(fileresu); +namedoc=fullfile(RootPath,subdir,RootFile); +detect=1; +while detect==1 + namefigfull=[namedoc '.fig']; + hh=dir(namefigfull); + if ~isempty(hh) + detect=1; + namedoc=[namedoc '.0']; + else + detect=0; + end +end +saveas(gcbf,namefigfull);%save the interface with name namefigfull (A CHANGER EN FICHIER .xml) + + +%----------------------------------------------------------- +% --- Executes on button press in BATCH: remote processing +%----------------------------------------------------------- +function BATCH_Callback(hObject, eventdata, handles) +global civ1_exe civ2_exe patch_exe patch_new_exe fix_exe todo_path sge Civ_exe +compare=get(handles.compare,'Value');%test for usual PIV (compare=1) or displacement (=2) or stereo PIV (=3) + +%check the list of operations: +operations={'CIV1','FIX1','PATCH1','CIV2','FIX2','PATCH2'}; +run_flag=1; +box_test(1)=get(handles.CIV1,'Value'); +box_test(2)=get(handles.FIX1,'Value'); +box_test(3)=get(handles.PATCH1,'Value'); +box_test(4)=get(handles.CIV2,'Value'); +box_test(5)=get(handles.FIX2,'Value'); +box_test(6)=get(handles.PATCH2,'Value'); +index=find(box_test==1); +if isempty(index) + msgbox_uvmat('ERROR','no selected operation') + return +end +index_first=min(index); +index_last=max(index); +box_used=box_test([index_first : index_last]); +[box_missing,ind_missing]=min(box_used); +if isequal(box_missing,0) + msgbox_uvmat('ERROR',['missing' cell2mat(operations(ind_missing))]); + return +end + +%root name +filebase=get(handles.displ_filebase,'String'); +if isempty(filebase)||isequal(filebase,'') + msgbox_uvmat('ERROR','no input files') + return +end + +%check mask if selecetd +if isequal(get(handles.get_mask_civ1,'Value'),1) + get_mask_civ1_Callback(hObject, eventdata, handles); +end +if isequal(get(handles.get_mask_fix1,'Value'),1) + get_mask_fix1_Callback(hObject, eventdata, handles); +end +if isequal(get(handles.get_mask_civ2,'Value'),1) + get_mask_civ2_Callback(hObject, eventdata, handles); +end +if isequal(get(handles.get_mask_fix2,'Value'),1) + get_mask_fix2_Callback(hObject, eventdata, handles); +end + +%read names of the .exe file +path_uvmat=which('uvmat');% check the path detected for source file uvmat +path_UVMAT=fileparts(path_uvmat); %path to UVMAT +if isunix + xmlfile=fullfile(path_UVMAT,'PARAM_LINUX.xml'); + if exist(xmlfile,'file') + t=xmltree(xmlfile); + sparam=convert(t); + end +else + xmlfile=fullfile(path_UVMAT,'PARAM_WIN.xml'); + if exist(xmlfile,'file') + t=xmltree(xmlfile); + sparam=convert(t); + end +end +sge=0; +if isfield(sparam,'Civ_exe') + Civ_exe=sparam.Civ_exe; +end +if isfield(sparam,'Civ1_exe') + civ1_exe=sparam.Civ1_exe; +end +if isfield(sparam,'Civ2_exe') + civ2_exe=sparam.Civ2_exe; +end +if isfield(sparam,'Patch_exe') + patch_exe=sparam.Patch_exe; +end + if isfield(sparam,'PatchNew_exe') + patch_new_exe=sparam.PatchNew_exe; + end + if isfield(sparam,'Fix_exe') + fix_exe=sparam.Fix_exe; + end + if isfield(sparam,'Todo_path') + todo_path=sparam.Todo_path; + end +if isfield(sparam,'SGE') + sge=str2num(sparam.SGE); +end + +%choice of batch priority +ind_answer=2; +if sge + [s,w]=unix('qstat -q civ.q|grep job_| wc -l'); %check the waiting list (command unix) + if isequal(s,0) + w(end)=[]; + str_displ={[w ' jobs in the waiting list'];'Select a priority:'}; + str={'urgent';'normal';'low'}; + [ind_answer,v] = listdlg('PromptString',str_displ,... + 'SelectionMode','single',... + 'ListString',str,'ListSize',[200 200],'Name','job priority','InitialValue',3); + if isequal(v,0) % to handle Cancel button and figure close, + return % a better way should be create + end + else + msgbox_uvmat('ERROR','batch system not available') + return + end +end + +%initialize the waitbars +set(handles.waitbar_1,'Position',[0.946 0.876 0.03 0.001]) +set(handles.waitbar_patch1,'Position',[0.946 0.439 0.03 0.001]) +set(handles.waitbar_civ2,'Position',[0.946 0.219 0.03 0.001]) +set(handles.waitbar_patch2,'Position',[0.946 0.0 0.03 0.001]) +set(handles.BATCH, 'Enable','Off') +set(handles.BATCH,'BackgroundColor',[0.831 0.816 0.784]) +drawnow +%get the filename root, nomenclature and numbers + +% for Windows system find the UBC path name if needed +if ~isunix & isequal(todo_path(1:2),'\\') & isequal(filebase(2:3),':\') + cur_dir=pwd; + if ~isequal(cur_dir(2:3),':\') + cd(matlabroot); %move to the Matlab root directory if the current Matlab dir does not allow the dos command or is M: + end + [ss,ww]=dos(['net use ' filebase(1:2)]); + if isequal(ss,0) + rankpath=findstr(ww,'\\'); + if ~isempty(rankpath) + wwrest=ww(rankpath:end); + rankend=min(find(double(wwrest)==10))-1; + filebase=[wwrest(1:rankend) filebase(3:end)]; + set(handles.displ_filebase,'String',filebase); + end + else + msgbox_uvmat('ERROR','for BATCH option, UBC file names, beginning by \\, are needed'); + set(handles.BATCH, 'Enable','On') + set(handles.BATCH,'BackgroundColor',[1 0 0]) + return + end +end + +% set the list of files and check them +display('checking the files...') +[filecell,num1_civ1,num2_civ1,num_a_civ1,num_b_civ1,num1_civ2,num2_civ2,num_a_civ2,num_b_civ2,nom_type_nc,file_ref_fix1,file_ref_fix2]=... + set_civ_filenames(handles,compare,box_test); +display('files OK, processing...') +nbfield=size(num1_civ1,2); +nbslice=size(num1_civ1,1); + +%GET PARAMETERS: + %get civ parameters +if box_test(1)==1 + par_civ1=read_param_civ1(handles,filecell.ima1.civ1{1,1}); +end + +%get fix1 parameters +if box_test(2)==1 + flagindex1(1)=get(handles.vec_Fmin2, 'Value'); + flagindex1(2)=get(handles.vec_F3, 'Value'); + flagindex1(3)=get(handles.vec_F2, 'Value'); + thresh_vecC1=str2num(get(handles.thresh_vecC,'String'));%threshold on image correlation vec_C + thresh_vel1=str2num(get(handles.thresh_vel,'String'));%threshold on velocity modulus + test_mask=get(handles.get_mask_fix1,'Value'); + nbslice_mask=get(handles.mask_fix1,'UserData'); % get the number of slices (= number of masks) + %%%%%%%%%%%%%COMPLETER LE PROGRAMME FIX +% inf_sup=get(handles.inf_sup1,'Value'); +% fileref=get(handles.ref_fix1,'String'); +% refpath=get(handles.ref_fix1,'UserData'); +% fileref=fullfile(refpath,fileref); + menu=get(handles.field_ref1,'String'); + index=get(handles.field_ref1,'Value'); + if isempty(menu) + fieldchoice=''; + else + fieldchoice=menu{index}; + msgbox_uvmat('WARNING','reference field is not used presently with batch, use RUN option') + end +end + + %get patch1 parameters + if box_test(3)==1 + rho_patch1=str2num(get(handles.rho_patch1,'String')); + if isempty(rho_patch1) + rho_patch1='1000'; + set(handles.rho_patch1,'String','1') + else + rho_patch1=num2str(1000*rho_patch1); + end + nx_patch1=get(handles.nx_patch1,'String'); + ny_patch1=get(handles.ny_patch1,'String'); + if isequal(str2num(nx_patch1),[]) + nx_patch1='50' ;%default + set(handles.nx_patch1,'String','50'); + end + if isequal(str2num(ny_patch1),[]) + ny_patch1='50' ;%default + set(handles.ny_patch1,'String','50'); + end + subdomain_patch1=get(handles.subdomain_patch1,'String'); + thresh_patch1=get(handles.thresh_patch1,'String'); + test_interp=get(handles.test_interp,'Value'); + end + + %get civ2 parameters +if box_test(4)==1 + par_civ2=read_param_civ2(handles,cell2mat(filecell.ima1.civ2(1,1))); +end + +%get fix2 parameters +if box_test(5)==1 + flagindex2(1)=get(handles.vec_Fmin2_2, 'Value'); + flagindex2(2)=get(handles.vec_F3_2, 'Value'); + flagindex2(3)=get(handles.vec_F4, 'Value'); + thresh_vec2C=str2num(get(handles.thresh_vec2C,'String'));%threshold on image correlation vec_C + thresh_vel2=str2num(get(handles.thresh_vel2,'String'));%threshold on velocity modulus + test_mask=get(handles.get_mask_fix2,'Value'); + nbslice_mask=get(handles.mask_fix2,'UserData'); % get the number of slices (= number of masks) + %%%%%%%%%%%%%COMPLETER LE PROGRAMME FIX AVEC REF FILE ET OPTION inf_sup=2 +% inf_sup=get(handles.inf_sup2,'Value'); +% ref=get(handles.ref_fix2,'UserData'); + + %%%%%%%%%%%%%%%%%%% +end + + +%get patch2 parameters +if box_test(6)==1 + rho_patch2=str2num(get(handles.rho_patch2,'String')); + if isempty(rho_patch2) + rho_patch2='1000'; + set(handles.rho_patch2,'String','1') + else + rho_patch2=num2str(1000*rho_patch2); + end + nx_patch2=get(handles.nx_patch2,'String'); + ny_patch2=get(handles.ny_patch2,'String'); + if isequal(str2num(nx_patch2),[]) + nx_patch2='50' ;%default + set(handles.nx_patch2,'String','50'); + end + if isequal(str2num(ny_patch2),[]) + ny_patch2='50' ;%default + set(handles.ny_patch2,'String','50'); + end + subdomain_patch2=get(handles.subdomain_patch2,'String'); + thresh_patch2=get(handles.thresh_patch2,'String'); + test_interp=get(handles.test_interp,'Value'); +end + +if ~sge + + %OPEN THE WAIT LIST FOR BATCH PROCESSES + name_lock=fullfile(todo_path,'lock'); %lock file + iwait=0; + while(exist(name_lock) & iwait<15) + pause(1); %wait 1 second + iwait=iwait+1; + end + if iwait==15 + msgbox_uvmat('ERROR',['I''m tired to wait for the lock file, please delete it then click again on BATCH' name_lock ]) + set(handles.BATCH, 'Enable','On') + set(handles.BATCH,'BackgroundColor',[1 0 0]) + return + end + p0=fopen(name_lock,'w'); %create the file name_lock: prevents other users to interfere + name_todo=fullfile(todo_path,'TODO.txt'); + p1=fopen(name_todo,'a'); + if (p1<0) + msgbox_uvmat('ERROR',['error in opening ' name_todo]) + set(handles.BATCH, 'Enable','On') + set(handles.BATCH,'BackgroundColor',[1 0 0]) + return; + end +end + +%MAIN LOOP +% for ifile=1:nbfield +p1text=[];%initiate command text +time=get(handles.displ_filebase,'UserData'); %get the set of times +civAll=get(handles.Experimental,'Value'); % Boolean for new civ excution method +for ifile=1:nbfield + for j=1:nbslice + i_cmd=0; + cmd=''; + if sge + cmd='#!/bin/bash'; + cmd=char({cmd;'#$ -cwd'}); + cmd=char({cmd;'hostname && date'}); + end + if civAll + civAllxml=xmltree;% xml contents, all parameters + civAllCmd=[]; + civAllxml=set(civAllxml,1,'name','CivDoc'); + end +% filecell.nc.civ1 + filename_cmx=cell2mat(filecell.nc.civ1(ifile,j));%output netcdf file + filename_cmx([end-1:end])='cm';%name of cmx file + filename_cmx=[filename_cmx 'x']; + + %CIV1 + if box_test(1)==1 + par_civ1.filename_ima_a=cell2mat(filecell.ima1.civ1(ifile,j)); + % par_civ1.filename_ima_a([end-3:end])=[];%remove .png extension + par_civ1.filename_ima_b=cell2mat(filecell.ima2.civ1(ifile,j)); + % par_civ1.filename_ima_b([end-3:end])=[];%remove .png extension + + namelog=[filename_cmx([1:end-3]) 'log']; + par_civ1.Dt=num2str(time(num2_civ1(ifile),num_b_civ1(j))-time(num1_civ1(ifile),num_a_civ1(j))); + par_civ1.T0=num2str((time(num2_civ1(ifile),num_b_civ1(j))+time(num1_civ1(ifile),num_a_civ1(j)))/2); + par_civ1.term_a=num2stra(num_a_civ1(j),nom_type_nc);%UTILITE? + par_civ1.term_b=num2stra(num_b_civ1(j),nom_type_nc);% + test_mask=get(handles.get_mask_civ1,'Value'); + if test_mask==0 + par_civ1.maskname='noFile use default'; + par_civ1.maskflag='n'; + else + maskdispl=get(handles.mask_civ1,'String'); + maskbase=[filebase '_' maskdispl]; % + nbslice_mask=str2num(maskdispl(1:end-4)); % + num1_mask=mod(num1_civ1(ifile)-1,nbslice_mask)+1; + par_civ1.maskname=name_generator(maskbase,num1_mask,1,'.png','_i'); + if exist(par_civ1.maskname,'file') + par_civ1.maskflag='y'; + else + par_civ1.maskname='noFile use default'; + par_civ1.maskflag='n'; + end + end + + %TESTgrid + test_grid=get(handles.browse_gridciv1,'Value'); + if test_grid + par_civ1.gridflag='y'; + gridname=get(handles.grid_civ1,'String'); + if isequal(gridname(end-3:end),'grid') + nbslice_grid=str2num(gridname(1:end-4)); % + if ~isempty(nbslice_grid) + num1_grid=mod(num1_civ1(ifile)-1,nbslice_grid)+1; + par_civ1.gridname=[filebase '_' name_generator(gridname,num1_grid,1,'.grid','_i')]; + if ~exist(par_civ1.gridname,'file') + msgbox_uvmat('ERROR','grid file absent for civ1') + end + elseif exist(gridname,'file') + par_civ1.gridname=gridname; + else + msgbox_uvmat('ERROR','grid file absent for civ1') + end + end + else + par_civ1.gridname='noFile use default'; + par_civ1.gridflag='n'; + end + %endTESTgrid + + i_cmd=i_cmd+1; + if isequal(civAll,0) + cmd=char({cmd;BATCH_CIV1(filename_cmx([1:end-4]),namelog,par_civ1,handles)}); + else + civAllCmd=[civAllCmd ' civ1 ']; + str=BATCH_CIV1_Unified(filename_cmx([1:end-4]),namelog,par_civ1); + fieldnames=fields(str); + [civAllxml,uid_civ1]=add(civAllxml,1,'element','civ1'); + for ilist=1:length(fieldnames) + val=eval(['str.' fieldnames{ilist}]); + if ischar(val) + [civAllxml,uid_t]=add(civAllxml,uid_civ1,'element',fieldnames{ilist}); + [civAllxml,uid_t2]=add(civAllxml,uid_t,'chardata',val); + end + end + end + end + + % FIX1 + if box_test(2)==1 + test_mask=get(handles.get_mask_fix1,'Value'); + if test_mask==0 + maskname=''; + else + maskdispl=get(handles.mask_fix1,'String'); + nbslice_mask=str2num(maskdispl(1:end-4)); % + num1_mask=mod(num1_civ1(ifile)-1,nbslice_mask)+1; + maskbase=[filebase '_' maskdispl]; + maskname=name_generator(maskbase,num1_mask,1,'.png','_i'); + end + if isequal(civAll,0) + cmd_FIX=[fix_exe ' -f ' filecell.nc.civ1{ifile,j} ' -fi1 ' num2str(flagindex1(1)) ... + ' -fi2 ' num2str(flagindex1(2)) ' -fi3 ' num2str(flagindex1(3)) ... + ' -threshC ' num2str(thresh_vecC1) ' -threshV ' num2str(thresh_vel1) ' -maskName ' maskname]; + cmd=char({cmd ;cmd_FIX}); + else + fix1.inputFileName=filecell.nc.civ1{ifile,j} ; + fix1.fi1=num2str(flagindex1(1)); + fix1.fi2=num2str(flagindex1(2)); + fix1.fi3=num2str(flagindex1(3)); + fix1.threshC=num2str(thresh_vecC1); + fix1.threshV=num2str(thresh_vel1); + fieldnames=fields(fix1); + [civAllxml,uid_fix1]=add(civAllxml,1,'element','fix1'); + for ilist=1:length(fieldnames) + val=eval(['fix1.' fieldnames{ilist}]); + if ischar(val) + [civAllxml,uid_t]=add(civAllxml,uid_fix1,'element',fieldnames{ilist}); + [civAllxml,uid_t2]=add(civAllxml,uid_t,'chardata',val); + end + end + civAllCmd=[civAllCmd ' fix1 ']; + end + end + + %PATCH1 + if box_test(3)==1 + if isequal(civAll,0) + cmd_PATCH=RUN_PATCH(filecell.nc.civ1{ifile,j},nx_patch1,ny_patch1,rho_patch1,subdomain_patch1,thresh_patch1,test_interp); + cmd=char({cmd ;cmd_PATCH}); + else + patch1.inputFileName=filecell.nc.civ1{ifile,j} ; + patch1.nopt=subdomain_patch1; + patch1.maxdiff=thresh_patch1; + patch1.ro=rho_patch1; + test_grid=get(handles.get_gridpatch1,'Value'); + if test_grid + patch1.gridflag='y'; + gridname=get(handles.grid_patch1,'String'); + if isequal(gridname(end-3:end),'grid') + nbslice_grid=str2num(gridname(1:end-4)); % + if ~isempty(nbslice_grid) + num1_grid=mod(num1_civ1(ifile)-1,nbslice_grid)+1; + patch1.gridPatch=[filebase '_' name_generator(gridname,num1_grid,1,'.grid','_i')]; + if ~exist(patch1.gridPatch,'file') + msgbox_uvmat('ERROR','grid file absent for patch1') + end + elseif exist(gridname,'file') + patch1.gridPatch=gridname; + else + msgbox_uvmat('ERROR','grid file absent for patch1') + end + end + else + patch1.gridPatch='n'; + patch1.gridflag='n'; + patch1.m=nx_patch1; + patch1.n=ny_patch1; + end + patch1.convectFlow='n'; + fieldnames=fields(patch1); + [civAllxml,uid_patch1]=add(civAllxml,1,'element','patch1'); + for ilist=1:length(fieldnames) + val=eval(['patch1.' fieldnames{ilist}]); + if ischar(val) + [civAllxml,uid_t]=add(civAllxml,uid_patch1,'element',fieldnames{ilist}); + [civAllxml,uid_t2]=add(civAllxml,uid_t,'chardata',val); + end + end + civAllCmd=[civAllCmd ' patch1 ']; + end + end + + if box_test(4)==1 | box_test(5)==1 | box_test(6)==1 + filename_cmx=filecell.nc.civ2{ifile,j};%output netcdf file + filename_cmx([end-1:end])=[ 'cm'];%name of cmx file + filename_cmx=[filename_cmx 'x']; + end + + if box_test(4)==1 + par_civ2.filename_ima_a=filecell.ima1.civ2{ifile,j}; + %par_civ2.filename_ima_a([end-3:end])=[];%remove .png extension + par_civ2.filename_ima_b=filecell.ima2.civ2{ifile,j}; + %par_civ2.filename_ima_b([end-3:end])=[];%remove .png extension + namelog=[filename_cmx([1:end-3]) 'log']; + par_civ2.Dt=num2str(time(num2_civ2(ifile),num_b_civ2(j))-time(num1_civ2(ifile),num_a_civ2(j))); + par_civ2.T0=num2str((time(num2_civ1(ifile),num_b_civ2(j))+time(num1_civ2(ifile),num_a_civ2(j)))/2); + par_civ2.term_a=num2stra(num_a_civ2(j),nom_type_nc); + par_civ2.term_b=num2stra(num_b_civ2(j),nom_type_nc); + par_civ2.filename_nc1=filecell.nc.civ1{ifile,j}; + par_civ2.filename_nc1([end-2:end])=[]; % remove '.nc' + test_mask=get(handles.get_mask_civ2,'Value'); + if test_mask==0 + par_civ2.maskname='noFile use default'; + par_civ2.maskflag='n'; + else + maskdispl=get(handles.mask_civ2,'String'); + maskbase=[filebase '_' maskdispl]; % + nbslice_mask=str2num(maskdispl(1:end-4)); % + num1_mask=mod(num1_civ2(ifile)-1,nbslice_mask)+1; + par_civ2.maskname=name_generator(maskbase,num1_mask,1,'.png','_i'); + if exist(par_civ2.maskname,'file') + par_civ2.maskflag='y'; + else + par_civ2.maskname='noFile use default'; + par_civ2.maskflag='n'; + end + end + %TESTgrid + test_grid=get(handles.browse_gridciv2,'Value'); + gridname=get(handles.grid_civ2,'String'); + gridflag='y'; + if numel(gridname)>=4 && isequal(gridname(end-3:end),'grid') + nbslice_grid=str2num(gridname(1:end-4)); % + if ~isempty(nbslice_grid) + par_civ2.gridflag='y'; + num1_grid=mod(num1_civ2(ifile)-1,nbslice_grid)+1; + par_civ2.gridname=[filebase '_' name_generator(gridname,num1_grid,1,'.grid','_i')]; + if exist(par_civ2.gridname,'file') + par_civ2.gridflag='y'; + else + par_civ2.gridname='noFile use default'; + par_civ2.gridflag='n'; + end + elseif exist(gridname,'file') + par_civ2.gridflag='y'; + else + par_civ2.gridname='noFile use default'; + par_civ2.gridflag='n'; + end + end + %endTESTgrid + i_cmd=i_cmd+1; + cmd_CIV2=BATCH_CIV2(filename_cmx,namelog,par_civ2); + if isequal(civAll,0) + if(isunix) + cmd=char({cmd ; ['cp -f ' filename_cmx '2 ' filename_cmx]; cmd_CIV2}); + else + cmd=char({cmd ; ['copy /Y ' filename_cmx '2 ' filename_cmx]; cmd_CIV2}); + end + else + civAllCmd=[civAllCmd ' civ2 ']; + str=BATCH_CIV2_Unified(filename_cmx([1:end-4]),namelog,par_civ2); + fieldnames=fields(str); + [civAllxml,uid_civ2]=add(civAllxml,1,'element','civ2'); + for ilist=1:length(fieldnames) + val=eval(['str.' fieldnames{ilist}]); + if ischar(val) + [civAllxml,uid_t]=add(civAllxml,uid_civ2,'element',fieldnames{ilist}); + [civAllxml,uid_t2]=add(civAllxml,uid_t,'chardata',val); + end + end + end + end + + % FIX2 + if box_test(5)==1 + test_mask=get(handles.get_mask_fix2,'Value'); + if test_mask==0 + maskname=''; %no mask used + else + maskdispl=get(handles.mask_fix2,'String'); + maskbase=[filebase '_' maskdispl]; % + nbslice_mask=str2num(maskdispl(1:end-4)); % + num1_mask=mod(num1_civ2(ifile)-1,nbslice_mask)+1; + maskname =name_generator(maskbase,num1_mask,1,'.png','_i'); + end + if isequal(civAll,0) + cmd_FIX=[fix_exe ' -f ' filecell.nc.civ2{ifile,j} ' -fi1 ' num2str(flagindex2(1)) ... + ' -fi2 ' num2str(flagindex2(2)) ' -fi3 ' num2str(flagindex2(3)) ... + ' -threshC ' num2str(thresh_vec2C) ' -threshV ' num2str(thresh_vel2) ' -maskName ' maskname]; + cmd=char({cmd ;cmd_FIX}); + else + fix2.inputFileName=filecell.nc.civ2{ifile,j} ; + fix2.fi1=num2str(flagindex2(1)); + fix2.fi2=num2str(flagindex2(2)); + fix2.fi3=num2str(flagindex2(3)); + fix2.threshC=num2str(thresh_vec2C); + fix2.threshV=num2str(thresh_vel2); + fieldnames=fields(fix2); + [civAllxml,uid_fix2]=add(civAllxml,1,'element','fix2'); + for ilist=1:length(fieldnames) + val=eval(['fix2.' fieldnames{ilist}]); + if ischar(val) + [civAllxml,uid_t]=add(civAllxml,uid_fix2,'element',fieldnames{ilist}); + [civAllxml,uid_t2]=add(civAllxml,uid_t,'chardata',val); + end + end + civAllCmd=[civAllCmd ' fix2 ']; + end + end + + %PATCH2 + if box_test(6)==1 + if isequal(civAll,0) + cmd_PATCH=RUN_PATCH(filecell.nc.civ2{ifile,j},nx_patch2,ny_patch2,rho_patch2,subdomain_patch2,thresh_patch2,test_interp); + cmd=char({cmd; cmd_PATCH}); + else + patch2.inputFileName=filecell.nc.civ1{ifile,j} ; + patch2.nopt=subdomain_patch1; + patch2.maxdiff=thresh_patch1; + patch2.ro=rho_patch1; + test_grid=get(handles.get_gridpatch2,'Value'); + if test_grid + patch2.gridflag='y'; + gridname=get(handles.grid_patch2,'String'); + if isequal(gridname(end-3:end),'grid') + nbslice_grid=str2num(gridname(1:end-4)); % + if ~isempty(nbslice_grid) + num1_grid=mod(num1_civ2(ifile)-1,nbslice_grid)+1; + patch2.gridPatch=[filebase '_' name_generator(gridname,num1_grid,1,'.grid','_i')]; + if ~exist(patch2.gridPatch,'file') + msgbox_uvmat('ERROR','grid file absent for patch2') + end + elseif exist(gridname,'file') + patch2.gridPatch=gridname; + else + msgbox_uvmat('ERROR','grid file absent for patch2') + end + end + else + patch2.gridPatch='n'; + patch2.gridflag='n'; + patch2.m=nx_patch2; + patch2.n=ny_patch2; + end + patch2.convectFlow='n'; + fieldnames=fields(patch2); + [civAllxml,uid_patch2]=add(civAllxml,1,'element','patch2'); + for ilist=1:length(fieldnames) + val=eval(['patch2.' fieldnames{ilist}]); + if ischar(val) + [civAllxml,uid_t]=add(civAllxml,uid_patch2,'element',fieldnames{ilist}); + [civAllxml,uid_t2]=add(civAllxml,uid_t,'chardata',val); + end + end + civAllCmd=[civAllCmd ' patch2 ']; + end + end + if isequal(civAll,1) + civAllxml + save(civAllxml,[filename_cmx([1:end-4]) '.xml']); + cmd=char({cmd;[Civ_exe ' -f ' [filename_cmx([1:end-4]) '.xml'] ' ' civAllCmd]}); + end + + % create the .bat file: + if sge + [Rootbat,Filebat,extbat]=fileparts(filename_cmx); + filename_bat=fullfile(Rootbat,['job_' Filebat extbat]); + else + filename_bat=filename_cmx; + end + filename_bat(end-2:end)='bat'; + + dlmwrite(filename_bat,cmd,'');%write commands in filename_bat + if sge + pvalue=num2str((1-ind_answer)*500); + namelog=[filename_bat '.patch.log']; + ['!qsub -p ' pvalue ' -q civ.q -e ' filename_cmx(1:end-4) '.errors -o ' filename_cmx(1:end-4) '.log' ' ' filename_bat]; + eval( ['!qsub -p ' pvalue ' -q civ.q -e ' filename_cmx(1:end-4) '.errors -o ' filename_cmx(1:end-4) '.log' ' ' filename_bat]); + else + if(isunix) + cmdtodo=['. ' filename_bat ];%removed for Mathieu tests %' && rm -f ' filename_bat] ; + else + cmdtodo=[filename_bat];%removed for Mathieu tests %' && del /F /Q ' filename_bat' ; + end + count= fprintf(p1,'%s\n', cmdtodo); + end + end +end +if ~sge + fclose(p1); + fclose(p0); + delete(name_lock); +end + +set(handles.BATCH, 'Enable','On') +set(handles.BATCH,'BackgroundColor',[1 0 0]) + +%save interface state +if isfield(filecell,'nc') + if isfield(filecell.nc,'civ2') + fileresu=filecell.nc.civ2{1,1}; + else + fileresu=filecell.nc.civ1{1,1}; + end +end +[RootPath,RootFile,field_count,str2,str_a,str_b,ext,nom_type,subdir]=name2display(fileresu); +namedoc=fullfile(RootPath,subdir,RootFile); +detect=1; +while detect==1 + namefigfull=[namedoc '.fig']; + hh=dir(namefigfull); + if ~isempty(hh) + detect=1; + namedoc=[namedoc '.0']; + else + detect=0; + end +end +saveas(gcbf,namefigfull);%save the interface with name namefigfull (A CHANGER EN FICHIER .xml) + + +%---------------------------------------------------------- +%OUTPUT: +% filecell: structure of input and output files +% .ima1.civ1{i,j}, .ima1.civ2{i,j}; set of first image names for correlations, for civ1 and civ2 +% .ima2.civ1{i,j}, .ima2.civ2{i,j} ; set of second image names for correlations +% .imaA1.civ1{i,j}, .ima1.civ2{i,j}; set of first image names for correlations, for civ1 and civ2, with camA in stereo case (then .ima1 corresponds to camB) +% .imaA2.civ1{i,j}, .ima2.civ2{i,j} ; set of second image names for correlations, with camA in stereo case (then .ima1 corresponds to camB) +% .nc.civ1{i,j}, .nc.civ2{i,j}; set of nc files for PIV results +% .ncA.civ1{i,j}, .ncA.civ2{i,j}; set of nc files for PIV results with camA (then .nc corresponds to camB) +% .st{i,j}; set of nc files for the combined stereo fields + +function [filecell,num1_civ1,num2_civ1,num_a_civ1,num_b_civ1,num1_civ2,num2_civ2,num_a_civ2,num_b_civ2,nom_type_nc,file_ref_fix1,file_ref_fix2]=... + set_civ_filenames(handles,compare,box_test) + +%get the filename root, nomenclature and numbers +filebase=get(handles.displ_filebase,'String'); +browse=get(handles.browse_root,'UserData'); +compare_list=get(handles.compare,'String'); +val=get(handles.compare,'Value'); +compare=compare_list{val}; +if strcmp(compare,'displacement') + mode='displacement'; +else + mode_list=get(handles.mode,'String'); + mode_value=get(handles.mode,'Value'); + mode=mode_list{mode_value}; +end +time=get(handles.displ_filebase,'UserData'); %get the set of times +ext_ima=get(handles.ext_ima,'String'); +nom_type_nc=browse.nom_type_nc; +nom_type_ima2=browse.nom_type_ima; +if isequal(nom_type_ima2,[]),nom_type_ima2='ima_num';end; %default +if isequal(nom_type_nc,[]),nom_type_nc='_i1-i2';end; %default +[num1_civ1,num2_civ1,num_a_civ1,num_b_civ1,num1_civ2,num2_civ2,num_a_civ2,num_b_civ2]=... + find_pair_indices(handles,mode); + +%determine the new filebase for 'displacement' mode (comparison of two series) +filebase_B=filebase;% root name of the second field series for stereo +if strcmp(compare,'displacement') || strcmp(compare,'stereo PIV') + test_disp=1; + nom_type_ima1=browse.nom_type_ima_1; %nomenclature type of the second file series + [Path2,Name2]=fileparts(filebase_B); + Path1=Path2; + Name1=get(handles.displ_filebase2,'String');% root name of the first field series for stereo + filebase_A=fullfile(Path1,Name1); + if length(Name1)>6 + Name1=Name1(end-5:end); + end + if length(Name2)>6 + Name2=Name2(end-5:end); + end + filebase_AB=fullfile(Path2,[Name2 '-' Name1]); +else + test_disp=0; + filebase_A=filebase; + nom_type_ima1=nom_type_ima2; + filebase_AB=filebase; +end +if strcmp(compare,'displacement') + filebase_ima1=filebase_A; + filebase_ima2=filebase_B; + filebase_nc=filebase_AB; %root name for the result of civ2 +else + filebase_ima1=filebase_B; + filebase_ima2=filebase_B; + filebase_nc=filebase_B; +end + +%determine reference files for fix: +file_ref_fix1={};%default +file_ref_fix2={}; +nbfield=length(num1_civ1); +nbslice=length(num_a_civ1); +if box_test(2)==1% fix1 performed + ref=get(handles.ref_fix1,'UserData');%read data on the ref file stored by get_ref_fix1_Callback + if ~isempty(ref) + first_i=str2num(get(handles.first_i,'String')); + last_i=str2num(get(handles.last_i,'String')); + incr_i=str2num(get(handles.incr_i,'String')); + first_j=str2num(get(handles.first_j,'String')); + last_j=str2num(get(handles.last_j,'String')); + incr_j=str2num(get(handles.incr_j,'String')); + num_i_ref=[first_i:incr_i:last_i]; + num_j_ref=[first_j:incr_j:last_j]; + if isequal(mode,'displacement') + num_i1=num_i_ref; + num_i2=num_i_ref; + num_j1=num_j_ref; + num_j2=num_j_ref; + elseif isequal(mode,'pair j1-j2')% isequal(mode,'st_pair j1-j2') + num_i1=num_i_ref; + num_i2=num_i1; + num_j1=ref.num_a*ones(size(num_i_ref)); + num_j2=ref.num_b*ones(size(num_i_ref)); + elseif isequal(mode,'series(Di)') % isequal(mode,'st_series(Di)') + delta1=floor((ref.num2-ref.num1)/2); + delta2=ceil((ref.num2-ref.num1)/2); + num_i1=num_i_ref-delta1*ones(size(num_i_ref)); + num_i2=num_i_ref+delta2*ones(size(num_i_ref)); + if isempty(ref.num_a) + ref.num_a=1; + end + num_j1=ref.num_a*ones(size(num_i1)); + num_j2=num_j1; + elseif isequal(mode,'series(Dj)')%| isequal(mode,'st_series(Dj)') + delta1=floor((ref.num_b-ref.num_a)/2); + delta2=ceil((ref.num_b-ref.num_a)/2); + num_i1=ref.num1*ones(size(num_i_ref)); + num_i2=num_i1; + num_j1=num_j_ref-delta1*ones(size(num_j_ref)); + num_j2=num_j_ref+delta2*ones(size(num_j_ref)); + end + for ifile=1:nbfield + for j=1:nbslice + file_ref=name_generator(ref.filebase,num_i1(ifile),num_j1(j),'.nc',ref.nom_type,1,num_i2(ifile),num_j2(j),ref.subdir);% + file_ref_fix1(ifile,j)={file_ref}; + if ~exist(file_ref,'file') + msgbox_uvmat('ERROR',['reference file ' file_ref ' not found for fix1']) + set(handles.RUN, 'Enable','On') + set(handles.RUN,'BackgroundColor',[1 0 0]) + set(handles.BATCH, 'Enable','On') + set(handles.BATCH,'BackgroundColor',[1 0 0]) + return + end + end + end + end +end + +%determine reference files for fix2: +if box_test(5)==1% fix2 performed + ref=get(handles.ref_fix2,'UserData'); + if ~isempty(ref) + first_i=str2num(get(handles.first_i,'String')); + last_i=str2num(get(handles.last_i,'String')); + incr_i=str2num(get(handles.incr_i,'String')); + first_j=str2num(get(handles.first_j,'String')); + last_j=str2num(get(handles.last_j,'String')); + incr_j=str2num(get(handles.incr_j,'String')); + num_i_ref=[first_i:incr_i:last_i]; + num_j_ref=[first_j:incr_j:last_j]; + if isequal(mode,'displacement') + num_i1=num_i_ref; + num_i2=num_i_ref; + num_j1=num_j_ref; + num_j2=num_j_ref; + elseif isequal(mode,'pair j1-j2') + num_i1=num_i_ref; + num_i2=num_i1; + num_j1=ref.num_a; + num_j2=ref.num_b; + elseif isequal(mode,'series(Di)') + delta1=floor((ref.num2-ref.num1)/2); + delta2=ceil((ref.num2-ref.num1)/2); + num_i1=num_i_ref-delta1*ones(size(num_i_ref)); + num_i2=num_i_ref+delta2*ones(size(num_i_ref)); + num_j1=ref.num_a*ones(size(num_i1)); + num_j2=num_j1; + elseif isequal(mode,'series(Dj)') + delta1=floor((ref.num_b-ref.num_a)/2); + delta2=ceil((ref.num_b-ref.num_a)/2); + num_i1=ref.num1*ones(size(num_i_ref)); + num_i2=num_i1; + num_j1=num_j_ref-delta1*ones(size(num_j_ref)); + num_j2=num_j_ref+delta2*ones(size(num_j_ref)); + end + for ifile=1:nbfield + for j=1:nbslice + file_ref=name_generator(ref.filebase,num_i1(ifile),num_j1(j),'.nc',ref.nom_type,1,num_i2(ifile),num_j2(j),ref.subdir);% + file_ref_fix2(ifile,j)={file_ref}; + if ~exist(file_ref,'file') + msgbox_uvmat('ERROR',['reference file ' file_ref ' not found for fix2']) + set(handles.RUN, 'Enable','On') + set(handles.RUN,'BackgroundColor',[1 0 0]) + set(handles.BATCH, 'Enable','On') + set(handles.BATCH,'BackgroundColor',[1 0 0]) + return + end + end + end + end +end + +%check dir +subdir_civ1=get(handles.subdir_civ1,'String');%subdirectory subdir_civ1 for the netcdf output data +subdir_civ2=get(handles.subdir_civ2,'String'); +if isequal(subdir_civ1,''),subdir_civ1='A'; end% put default subdir +if isequal(subdir_civ2,''),subdir_civ2=subdir_civ1; end% put default subdir +currentdir=pwd;%store the current working directory +[Path_ima,Name]=fileparts(filebase);%Path of the image files (.civ) +if ~exist(Path_ima,'dir') + warndlg_uvmat(['path to images ' Path_ima ' not found'],'ERROR') + return +end +cd(Path_ima);%move to the directory of the images: needed to create the result dir by 'mkdir' +dircur=pwd; %current working directory +m2=''; +[erread,message]=fileattrib(Path_ima); +if ~isempty(message) & ~isequal(message.UserWrite,1) + msgbox_uvmat('ERROR',['No writting access to ' Path_ima]) + cd(currentdir); + return +end + +%check the existence of the netcdf and image files involved +% %%%%%%%%%%%% case CIV1 activated %%%%%%%%%%%%% +if box_test(1)==1; + detect=1; + while detect==1 %create a new subdir if the netcdf files already exist + for ifile=1:nbfield; + for j=1:nbslice + filename=name_generator(filebase_nc,num1_civ1(ifile),num_a_civ1(j),'.nc',nom_type_nc,1,num2_civ1(ifile),num_b_civ1(j),subdir_civ1); + detect=exist(filename,'file')==2; + if detect% if a netcdf file already exists + subdir_civ1=[subdir_civ1 '.0']; + subdir_civ2=subdir_civ1; + break + end + filecell.nc.civ1(ifile,j)={filename}; + end + if detect% if a netcdf file already exists + break + end + end + %create the new subdir_civ1 + if ~exist(fullfile(Path_ima,subdir_civ1),'dir') + [m1,m2,m3]=mkdir(subdir_civ1); + if ~isequal(m2,'') + msgbox_uvmat('ERROR', m2) + %msgbox(m2);%error message for directory creation + end + end + if strcmp(compare,'stereo PIV')&&(strcmp(mode,'pair j1-j2')||strcmp(mode,'series(Dj)')||strcmp(mode,'series(Di)'))%check second nc series + for ifile=1:nbfield + for j=1:nbslice + filename=name_generator(filebase_A,num1_civ1(ifile),num_a_civ1(j),'.nc',nom_type_nc,1,num2_civ1(ifile),num_b_civ1(j),subdir_civ1);% + detect=exist(filename,'file')==2; + if detect% if a netcdf file already exists + subdir_civ1=[subdir_civ1 '.0']; + subdir_civ2=subdir_civ1; + break + end + filecell.ncA.civ1(ifile,j)={filename}; + end + if detect% if a netcdf file already exists + break + end + end + %create the new subdir_civ1 + if ~exist(fullfile(Path_ima,subdir_civ1),'dir') + [m1,m2,m3]=mkdir(subdir_civ1); + if ~isequal(m2,'') + msgbox_uvmat('ERROR', m2) + end + end + end + end + % get image names + for ifile=1:nbfield + for j=1:nbslice + filename=name_generator(filebase_ima1, num1_civ1(ifile),num_a_civ1(j),ext_ima,nom_type_ima1); + idetect(j)=exist(filename,'file')==2; + filecell.ima1.civ1(ifile,j)={filename}; %first image + filename=name_generator(filebase_ima2, num2_civ1(ifile),num_b_civ1(j),ext_ima,nom_type_ima2); + idetect_1(j)=exist(filename,'file')==2; + filecell.ima2.civ1(ifile,j)={filename};%second image + end + [idetectmin,indexj]=min(idetect); + if idetectmin==0, + msgbox_uvmat('ERROR',[filecell.ima1.civ1{ifile,indexj} ' not found']) + set(handles.RUN, 'Enable','On') + set(handles.RUN,'BackgroundColor',[1 0 0]) + set(handles.BATCH, 'Enable','On') + set(handles.BATCH,'BackgroundColor',[1 0 0]) + cd(currentdir) + return + end + [idetectmin,indexj]=min(idetect_1); + if idetectmin==0, + msgbox_uvmat('ERROR',[filecell.ima2.civ1{ifile,indexj} ' not found']) + set(handles.RUN, 'Enable','On') + set(handles.RUN,'BackgroundColor',[1 0 0]) + set(handles.BATCH, 'Enable','On') + set(handles.BATCH,'BackgroundColor',[1 0 0]) + cd(currentdir) + return + end + end + if strcmp(compare,'stereo PIV') && (strcmp(mode,'pair j1-j2') || strcmp(mode,'series(Dj)') || strcmp(mode,'series(Di)')) + for ifile=1:nbfield + for j=1:nbslice + filename=name_generator(filebase_A, num1_civ1(ifile),num_a_civ1(j),ext_ima,nom_type_ima1); + idetect(j)=exist(filename,'file')==2; + filecell.imaA1.civ1(ifile,j)={filename} ;%first image + filename=name_generator(filebase_A, num2_civ1(ifile),num_b_civ1(j),ext_ima,nom_type_ima2); + idetect_1(j)=exist(filename,'file')==2; + filecell.imaA2.civ1(ifile,j)={filename};%second image + end + [idetectmin,indexj]=min(idetect); + if idetectmin==0, + msgbox_uvmat('ERROR',[filecell.imaA1.civ1{ifile,indexj} ' not found']) + set(handles.RUN, 'Enable','On') + set(handles.RUN,'BackgroundColor',[1 0 0]) + set(handles.BATCH, 'Enable','On') + set(handles.BATCH,'BackgroundColor',[1 0 0]) + cd(currentdir) + return + end + [idetectmin,indexj]=min(idetect_1); + if idetectmin==0, + msgbox_uvmat('ERROR',[filecell.imaA2.civ1{ifile,indexj} ' not found']) + set(handles.RUN, 'Enable','On') + set(handles.RUN,'BackgroundColor',[1 0 0]) + set(handles.BATCH, 'Enable','On') + set(handles.BATCH,'BackgroundColor',[1 0 0]) + cd(currentdir) + return + end + end + end + + %%%%%%%%%%%%% fix1 or patch1 activated but no civ1 %%%%%%%%%%%%% +elseif (box_test(2)==1 || box_test(3)==1); + for ifile=1:nbfield + for j=1:nbslice + filename=name_generator(filebase_nc,num1_civ1(ifile),num_a_civ1(j),'.nc',... + nom_type_nc,1,num2_civ1(ifile),num_b_civ1(j),subdir_civ1);% + detect=exist(filename,'file')==2; + filecell.nc.civ1(ifile,j)={filename}; + end + end + if strcmp(compare,'stereo PIV') + for ifile=1:nbfield + for j=1:nbslice + filename=name_generator(filebase_A,num1_civ1(ifile),num_a_civ1(j),'.nc',nom_type_nc,1,num2_civ1(ifile),num_b_civ1(j),subdir_civ1);% + filecell.ncA.civ1(ifile,j)={filename}; + if ~exist(filename,'file') + msgbox_uvmat('ERROR',['input file ' filename ' not found']) + set(handles.RUN, 'Enable','On') + set(handles.RUN,'BackgroundColor',[1 0 0]) + set(handles.BATCH, 'Enable','On') + set(handles.BATCH,'BackgroundColor',[1 0 0]) + cd(currentdir) + return + end + end + end + end +end + +%%%%%%%%%%%%% if civ2 performed with pairs different than civ1 %%%%%%%%%%%%% +testdiff=0; +if (box_test(4)==1)&&... + ((get(handles.list_pair_civ1,'Value')~=get(handles.list_pair_civ2,'Value'))||~isequal(subdir_civ2,subdir_civ1)) + testdiff=1; + detect=1; + while detect==1 %create a new subdir if the netcdf files already exist + for ifile=1:nbfield + for j=1:nbslice + filename=name_generator(filebase_nc,num1_civ2(ifile),num_a_civ2(j),'.nc',nom_type_nc,1,num2_civ2(ifile),num_b_civ2(j),subdir_civ2);% + detect=exist(filename,'file')==2; + if detect% if a netcdf file already exists + subdir_civ2=[subdir_civ2 '.0']; + break + end + filecell.nc.civ2(ifile,j)={filename}; + end + if detect% if a netcdf file already exists + break + end + end + %create the new subdir_civ2 + if ~exist(fullfile(Path_ima,subdir_civ2),'dir') + [m1,m2,m3]=mkdir(subdir_civ2); + if ~isequal(m2,'') + msgbox_uvmat('ERROR', m2) + end + end + if strcmp(compare,'stereo PIV')%check second nc series + for ifile=1:nbfield + for j=1:nbslice + filename=name_generator(filebase_A,num1_civ2(ifile),num_a_civ2(j),'.nc',... + nom_type_nc,1,num2_civ2(ifile),num_b_civ1(j),subdir_civ2);% + detect=exist(filename,'file')==2; + if detect% if a netcdf file already exists + subdir_civ2=[subdir_civ2 '.0']; + break + end + filecell.ncA.civ2(ifile,j)={filename}; + end + if detect% if a netcdf file already exists + break + end + end + %create the new subdir_civ1 + if ~exist(fullfile(Path_ima,subdir_civ2),'dir') + [m1,m2,m3]=mkdir(subdir_civ2); + if ~isequal(m2,'') + msgbox_uvmat('ERROR', m2) + %msgbox(m2);%error message for directory creation + end + end + end + end +end +cd(currentdir);%come back to the current working directory + + +%%%%%%%%%%%%% if civ2 results are obtained or used %%%%%%%%%%%%% +if box_test(4)==1 || box_test(5)==1 || box_test(6)==1 %civ2 + %check source netcdf file of civ1 estimates + if box_test(1)==0; %no civ1 performed + for ifile=1:nbfield + for j=1:nbslice + filename=name_generator(filebase_nc,num1_civ1(ifile),num_a_civ1(j),'.nc',... + nom_type_nc,1,num2_civ1(ifile),num_b_civ1(j),subdir_civ1);% + filecell.nc.civ1(ifile,j)={filename};% name of the civ1 file + if ~exist(filename,'file') + msgbox_uvmat('ERROR',['input file ' filename ' not found']) + set(handles.RUN, 'Enable','On') + set(handles.RUN,'BackgroundColor',[1 0 0]) + set(handles.BATCH, 'Enable','On') + set(handles.BATCH,'BackgroundColor',[1 0 0]) + return + end + if ~testdiff % civ2 or patch2 are written in the same file as civ1 + if box_test(4)==0 ; %check the existence of civ2 if it is not calculated + Data=nc2struct(filename,'ListGlobalAttribute','civ2'); + if isempty(Data.civ2)||isequal(Data.civ2,0) + msgbox_uvmat('ERROR',['no civ2 data in ' filename]) + set(handles.RUN, 'Enable','On') + set(handles.RUN,'BackgroundColor',[1 0 0]) + set(handles.BATCH, 'Enable','On') + set(handles.BATCH,'BackgroundColor',[1 0 0]) + return + end + elseif box_test(3)==0; %check the existence of patch if it is not calculated + Data=nc2struct(filename,'ListGlobalAttribute','patch'); + if isempty(Data.patch)||isequal(Data.patch,0) + msgbox_uvmat('ERROR',['no patch data in ' filename]) + set(handles.RUN, 'Enable','On') + set(handles.RUN,'BackgroundColor',[1 0 0]) + set(handles.BATCH, 'Enable','On') + set(handles.BATCH,'BackgroundColor',[1 0 0]) + return + end + end + end + end + end + if strcmp(compare,'stereo PIV') + for ifile=1:nbfield + for j=1:nbslice + filename=name_generator(filebase_A,num1_civ2(ifile),num_a_civ2(j),'.nc',... + nom_type_nc,1,num2_civ2(ifile),num_b_civ2(j),subdir_civ2);% + filecell.ncA.civ2(ifile,j)={filename}; + if ~exist(filename,'file') + msgbox_uvmat('ERROR',['input file ' filename ' not found']) + set(handles.RUN, 'Enable','On') + set(handles.RUN,'BackgroundColor',[1 0 0]) + set(handles.BATCH, 'Enable','On') + set(handles.BATCH,'BackgroundColor',[1 0 0]) + cd(currentdir) + return + end + end + end + end + end + + detect=1; +% while detect==1%creates a new subdir if the netcdf files already contain civ2 data + for ifile=1:nbfield + for j=1:nbslice + filename=name_generator(filebase_nc,num1_civ2(ifile),num_a_civ2(j),'.nc',... + nom_type_nc,1,num2_civ2(ifile),num_b_civ2(j),subdir_civ2); + detect=exist(filename,'file')==2; + filecell.nc.civ2(ifile,j)={filename}; + end + end + %get first image names for civ2 + if box_test(1)==1 & isequal(num1_civ1,num1_civ2) & isequal(num_a_civ1,num_a_civ2) + filecell.ima1.civ2=filecell.ima1.civ1; + elseif box_test(4)==1 + for ifile=1:nbfield + for j=1:nbslice + filename=name_generator(filebase_ima1, num1_civ2(ifile),num_a_civ2(j),ext_ima,nom_type_ima1); + idetect_2(j)=exist(filename,'file')==2; + filecell.ima1.civ2(ifile,j)={filename};%first image + end + [idetectmin,indexj]=min(idetect_2); + if idetectmin==0, + msgbox_uvmat('ERROR',['input image ' filecell.ima1.civ2{ifile,indexj} ' not found']) + set(handles.RUN, 'Enable','On') + set(handles.RUN,'BackgroundColor',[1 0 0]) + set(handles.BATCH, 'Enable','On') + set(handles.BATCH,'BackgroundColor',[1 0 0]) + return + end + end + end + + %get second image names for civ2 + if box_test(1)==1 & isequal(num2_civ1,num2_civ2) & isequal(num_b_civ1,num_b_civ2) + filecell.ima2.civ2=filecell.ima2.civ1; + elseif box_test(4)==1 + for ifile=1:nbfield + for j=1:nbslice + filename=name_generator(filebase_ima2, num2_civ2(ifile),num_b_civ2(j),ext_ima,nom_type_ima2); + idetect_3(j)=exist(filename,'file')==2; + filecell.ima2.civ2(ifile,j)={filename};%first image + end + [idetectmin,indexj]=min(idetect_3); + if idetectmin==0, + msgbox_uvmat('ERROR',['input image ' filecell.ima2.civ2{ifile,indexj} ' not found']) + set(handles.RUN, 'Enable','On') + set(handles.RUN,'BackgroundColor',[1 0 0]) + set(handles.BATCH, 'Enable','On') + set(handles.BATCH,'BackgroundColor',[1 0 0]) + return + end + end + end +end +if (box_test(5)==1 || box_test(6)==1 ) && box_test(4)==0 % need to read an existing netcdf civ2 file + if ~testdiff + filecell.nc.civ2=filecell.nc.civ1;% file already checked + else % check the civ2 files + for ifile=1:nbfield + for j=1:nbslice + filename=name_generator(filebase_nc,num1_civ2(ifile),num_a_civ2(j),'.nc',... + nom_type_nc,1,num2_civ2(ifile),num_b_civ2(j),subdir_civ2);% + filecell.nc.civ2(ifile,j)={filename}; + if ~exist(filename,'file') + msgbox_uvmat('ERROR',['input file ' filename ' not found']) + set(handles.RUN, 'Enable','On') + set(handles.RUN,'BackgroundColor',[1 0 0]) + set(handles.BATCH, 'Enable','On') + set(handles.BATCH,'BackgroundColor',[1 0 0]) + return + else + Data=nc2struct(filename,'ListGlobalAttribute','civ2'); + if isempty(Data.civ2)||isequal(Data.civ2,0) + msgbox_uvmat('ERROR',['no civ2 data in ' filename]) + set(handles.RUN, 'Enable','On') + set(handles.RUN,'BackgroundColor',[1 0 0]) + set(handles.BATCH, 'Enable','On') + set(handles.BATCH,'BackgroundColor',[1 0 0]) + return + end + end + end + end + end +end + +%%%%%%%%%%%%% if stereo fields are calculated by PATCH %%%%%%%%%%%%% +if strcmp(compare,'stereo PIV') + if box_test(3)==1 & isequal(get(handles.test_stereo1,'Value'),1) + for ifile=1:nbfield + for j=1:nbslice + filename=name_generator(filebase_AB,num1_civ1(ifile),num_a_civ1(j),'.nc',... + nom_type_nc,1,num2_civ1(ifile),num_b_civ1(j),subdir_civ1);% + filecell.st(ifile,j)={filename}; + end + end + end + if box_test(6)==1 & isequal(get(handles.test_stereo2,'Value'),1) + for ifile=1:nbfield + for j=1:nbslice + filename=name_generator(filebase_AB,num1_civ2(ifile),num_a_civ2(j),'.nc',... + nom_type_nc,1,num2_civ2(ifile),num_b_civ2(j),subdir_civ2);% + filecell.st(ifile,j)={filename}; + end + end + end +end +set(handles.subdir_civ1,'String',subdir_civ1);%update the edit box +set(handles.subdir_civ2,'String',subdir_civ2);%update the edit box +browse.nom_type_nc=nom_type_nc; +set(handles.browse_root,'UserData',browse); %update the nomenclature type for uvmat + + +%COPY IMAGES TO THE FORMAT .png IF NEEDED +if isequal(nom_type_ima1,'*') + nom_type_imanew='_i'; +else + nom_type_imanew1=nom_type_ima1; +end +if isequal(nom_type_ima2,'*') + nom_type_imanew='_i'; +else + nom_type_imanew2=nom_type_ima2; +end +if ~isequal(ext_ima,'.png') + %npxy=get(handles.ext_ima,'UserData'); +% % if numel(npxy)<2 +% +% filename=name_generator(filebase_ima1,num1_civ1(1),num_a_civ1(1),ext_ima,nom_type_ima1); +% A=imread(filename); +% npxy=size(A); +% % end +% npy=npxy(1); +% npx=npxy(2); + if box_test(1)==1 %if civ1 is performed + h = waitbar(0,['copy images to the .png format for civ1']);% display a wait bar + for ifile=1:nbfield + waitbar(ifile/nbfield); + for j=1:nbslice + filename=name_generator(filebase_ima1,num1_civ1(ifile),num_a_civ1(j),'.png',nom_type_imanew1); + if ~exist(filename,'file') + A=read_image(filecell.ima1.civ1{ifile,j},nom_type_ima2,num1_civ1(ifile)); + imwrite(A,filename,'BitDepth',16); + end + filecell.ima1.civ1(ifile,j)={filename}; + filename=name_generator(filebase_ima2, num2_civ1(ifile),num_b_civ1(j),'.png',nom_type_imanew2); + if ~exist(filename,'file') + A=read_image(filecell.ima2.civ1{ifile,j},nom_type_ima2,num2_civ1(ifile)); + imwrite(A,filename,'BitDepth',16); + end + filecell.ima2.civ1(ifile,j)={filename}; + end + end + close(h) + end + if box_test(4)==1 %if civ2 is performed + h = waitbar(0,['copy images to the .png format for civ2']);% display a wait bar + for ifile=1:nbfield + waitbar(ifile/nbfield); + for j=1:nbslice + filename=name_generator(filebase_ima1,num1_civ2(ifile),num_a_civ2(j),'.png',nom_type_imanew1); + if ~exist(filename,'file') + A=read_image(cell2mat(filecell.ima1.civ2(ifile,j)),nom_type_ima2,num1_civ2(ifile)); + imwrite(A,filename,'BitDepth',16); + end + filecell.ima1.civ2(ifile,j)={filename}; + filename=name_generator(filebase_ima2, num2_civ2(ifile),num_b_civ2(j),'.png',nom_type_imanew2); + if ~exist(filename,'file') + A=read_image(cell2mat(filecell.ima2.civ2(ifile,j)),nom_type_ima2,num2.civ1(ifile)); + imwrite(A,filename,'BitDepth',16); + end + filecell.ima2.civ2(ifile,j)={filename}; + end + end + close(h); + end +end + +%--------------------------------------------------------- +%CIV1 CIV1 CIV1 CIV1 +%---------------------------------------------------------- +function RUN_CIV1(handles,filecell,filecell_1,filecell_nc1,num1,num2,num_a,num_b,nom_type_nc) +%pixels per cm and matrix of the image times, read from the .civ file by uvmat +global civ1_exe sge%name of the executable for civ1 calculation + +%get civ parameters +ibx_val=str2num(get(handles.ibx,'String')); +if isempty(ibx_val) + ibx='21'; set(handles.ibx,'String','21') +else + ibx=num2str(ibx_val); +end +iby_val=str2num(get(handles.iby,'String')); +if isempty(iby_val) + iby='21'; set(handles.iby,'String','21') +else + iby=num2str(iby_val); +end +isx=get(handles.isx,'String'); +if isempty(str2num(isx)), isx='41'; set(handles.isx,'String','41'), end; %default +if str2num(isx)4 && isequal(gridname(end-3:end),'grid') + nbslice_grid=str2num(gridname(1:end-4)); % + if ~isempty(nbslice_grid) + gridflag='y'; + end + elseif exist(gridname,'file') + gridflag='y'; + else + msgbox_uvmat('ERROR',['input grid file ' gridname ' not found']) + return + end +end +if isequal(get(handles.ImaThreshold,'Value'),1) + threshflag='y'; + min_ima=get(handles.MinIma,'String'); + max_ima=get(handles.MaxIma,'String'); +else + threshflag='n'; + min_ima='0'; + max_ima='4096'; +end + %main loop +filebase=get(handles.displ_filebase,'String'); +sizcell=size(filecell); +nbfield=sizcell(1); +nbslice=sizcell(2); +icount=0; +for ifile=1:nbfield + for j=1:nbslice + icount=icount+1; + barlength=0.188*icount/(nbfield*nbslice); + set(handles.waitbar_1,'Position',[0.946 0.877-barlength 0.03 barlength]) + drawnow + filename_ima=cell2mat(filecell(ifile,j)); + filename_ima([end-3:end])=[];%remove .png extension + filename_ima_1=cell2mat(filecell_1(ifile,j)); + filename_ima_1([end-3:end])=[];%remove .png extension + filename_cmx=cell2mat(filecell_nc1(ifile,j));%output netcdf file + filename_cmx([end-1:end])=[ 'cm'];%name of cmx file + filename_cmx=[filename_cmx 'x']; + namelog=[filename_cmx([1:end-3]) 'log']; + if size(time,1)>=num2(ifile) & size(time,2)>=num_b(j) + Dt=num2str(time(num2(ifile),num_b(j))-time(num1(ifile),num_a(j))); + if isequal(Dt,'0') + Dt='1' ;%case of 'displacement' mode + end + T0=num2str((time(num2(ifile),num_b(j))+time(num1(ifile),num_a(j)))/2); + else + Dt='1'; + T0='0'; + end + term_a=num2stra(num_a(j),nom_type_nc);%UTILITE? + term_b=num2stra(num_b(j),nom_type_nc);% + if test_grid && ~isempty(nbslice_grid) + num1_grid=mod(num1(ifile)-1,nbslice_grid)+1 + gridname=[filebase '_' name_generator(gridname,num1_grid,1,'.grid','_i')]; + if ~exist(gridname,'file') + msgbox_uvmat('ERROR',['missing grid file ' gridname]) + return + end + end + test_mask=get(handles.get_mask_civ1,'Value'); + if test_mask==0 + maskname='noFile use default'; + maskflag='n'; + else + maskdispl=get(handles.mask_civ1,'String');%look for mask name in edit box + maskbase=[filebase '_' maskdispl];% + nbslice=str2num(maskdispl(1:end-4)); % + num1_mask=mod(num1(ifile)-1,nbslice)+1; + maskname=name_generator(maskbase,num1_mask,1,'.png','_i'); + if exist(maskname,'file') + maskflag='y'; + else + maskname='noFile use default'; + maskflag='n'; + end + end + textcmx={'############## CMX file';... + ['FirstImage ' filename_ima];... + ['LastImage ' filename_ima_1];... + 'XX' ;... + ['Mask ' maskflag] ;... + ['MaskName ' maskname];... + ['ImageSize ' npx ' ' npy];... %VERIFIER CAS GENERAL ? + ['CorrelationBoxesSize ' ibx ' ' iby];... + ['SearchBoxeSize ' isx ' ' isy];... + ['RO ' rho];... + ['GridSpacing ' dx ' ' dy];... + 'XX 1.0';... + ['Dt_TO ' Dt ' ' T0];... + ['PixCmXY ' pxcmx ' ' pxcmy];... + 'XX 1';... + ['ShiftXY ' shiftx ' ' shifty];... + ['Grid ' gridflag];... + ['GridName ' gridname] ;... + 'XX 85';... + 'XX 1.0';... + 'XX 1.0';... + 'Hart 1';... + 'DecimalShift 0';... + 'Deformation 0';... + 'CorrelationMin 0';... + 'IntensityMin 0';... + ['SeuilImage ' threshflag];... + ['SeuilImageValues ' min_ima ' ' max_ima];... + ['ImageToUse ' term_a ' ' term_b];... % VERIFIER ? + 'ImageUsedBefore null null'}; + textout=char(textcmx); + dlmwrite(filename_cmx,textout,''); + s=-1; + display(['!' civ1_exe ' -f ' filename_cmx ' > ' namelog]) + eval(['!' civ1_exe ' -f ' filename_cmx ' > ' namelog]); +% if sge%dispatch computation on the cluster using interactive queue +% % [s,w] = unix(['qrsh -q fast.q ' civ1_exe ' -f ' filename_cmx ' > ' namelog ' 2>&1' ]); +% end +% if s~=0 +% % ['!' civ1_exe ' -f ' filename_cmx ' > ' namelog] +% % eval(['!' civ1_exe ' -f ' filename_cmx ' > ' namelog]); +% end + end +end + +%--------------------------------------------------------------- +% RUN CIV2 CIV2 CIV2 CIV2 +%----------------------------------------------------------- +function RUN_CIV2(handles,filecell_2,filecell_3,filecell_nc1,filecell_nc2,num1,num2,num_a,num_b,nom_type_nc) +%filecell_2: names of first image +%filecell_3: names of second images +global civ2_exe sge + +%names of the civ2 fields +field.vel_type='civ2'; +field.nb='nb_vectors2'; +field.X='vec2_X'; +field.Y='vec2_Y'; +field.U='vec2_U'; +field.V='vec2_V'; + +%get civ parameters +ibx=get(handles.ibx_civ2,'String'); +iby=get(handles.iby_civ2,'String'); +rho=get(handles.rho_civ2,'String'); +decimal=int2str(get(handles.decimal,'Value')); +deformation=int2str(get(handles.deformation,'Value')); +dx=get(handles.dx_civ2,'String'); +dy=get(handles.dy_civ2,'String'); +if isequal(str2num(dx),[]) + dx='20';%default +end +if isequal(str2num(dy),[]) + dy='20';%default +end + pxcmx='1';%velocity fields are expressed in pixel displacement + pxcmy='1'; +A=imread(cell2mat(filecell_2(1,1)));%read the first image to get the size +sizim=size(A); +npx=num2str(sizim(2)); +npy=num2str(sizim(1)); +time=get(handles.displ_filebase,'UserData'); %get the set of times +filebase=get(handles.displ_filebase,'String'); +%grid +gridname='';%default ='noFile use default' +gridflag='n';%default +test_grid=get(handles.browse_gridciv2,'Value'); +nbslice_grid=[]; +if test_grid + gridname=get(handles.grid_civ2,'String'); + if numel(gridname)>4 && isequal(gridname(end-3:end),'grid') + nbslice_grid=str2num(gridname(1:end-4)); % + if ~isempty(nbslice_grid) + gridflag='y'; + end + elseif exist(gridname,'file') + gridflag='y'; + else + msgbox_uvmat('ERROR',['input grid file ' gridname ' not found']) + return + end +end +sizcell=size(filecell_2); +nbfield=sizcell(1); +nbslice=sizcell(2); + +%main loop +icount=0; +for ifile=1:nbfield + for j=1:nbslice + icount=icount+1; + barlength=0.188*icount/(nbfield*nbslice); + set(handles.waitbar_civ2,'Position',[0.946 0.407-barlength 0.03 barlength]) + drawnow + filename_ima_2=cell2mat(filecell_2(ifile,j)); + filename_ima_2([end-3:end])=[];%remove .png extension + filename_ima_3=cell2mat(filecell_3(ifile,j)); + filename_ima_3([end-3:end])=[];%remove .png extension + filename_cmx=cell2mat(filecell_nc2(ifile,j));%output netcdf file + filename_cmx([end-1:end])=[ 'cm'];%name of cmx file + filename_cmx=[filename_cmx 'x']; + namelog=[filename_cmx([1:end-3]) 'log']; + if size(time,1)>=num2(ifile) & size(time,2)>=num_b(j) + Dt=num2str(time(num2(ifile),num_b(j))-time(num1(ifile),num_a(j))); + if isequal(Dt,'0') + Dt='1' ;%case of 'displacement' mode + end + T0=num2str((time(num2(ifile),num_b(j))+time(num1(ifile),num_a(j)))/2); + else + Dt='1'; + T0='0'; + end + term_a=num2stra(num_a(j),nom_type_nc); + term_b=num2stra(num_b(j),nom_type_nc); + filename_nc1=cell2mat(filecell_nc1(ifile,j)); + filename_nc1([end-2:end])=[]; % remove '.nc' + if test_grid && ~isempty(nbslice_grid) + num1_grid=mod(num1(ifile)-1,nbslice_grid)+1 + gridname=[filebase '_' name_generator(gridname,num1_grid,1,'.grid','_i')]; + if ~exist(gridname,'file') + msgbox_uvmat('ERROR',['missing grid file ' gridname]) + return + end + end + test_mask=get(handles.get_mask_civ2,'Value'); + if test_mask==0 + maskname='noFile use default'; + maskflag='n'; + else + maskdispl=get(handles.mask_civ2,'String'); + maskbase=[filebase '_' maskdispl]; % + nbslice_mask=str2num(maskdispl(1:end-4)); % + num1_mask=mod(num1(ifile)-1,nbslice_mask)+1; + maskname =name_generator(maskbase,num1_mask,1,'.png','_i'); + if ~exist(maskname,'file') + maskflag='y'; + else + maskname='noFile use default'; + maskflag='n'; + end + end + + textcmx={'############## CMX file';... + ['FirstImage ' filename_ima_2];... + ['LastImage ' filename_ima_3];... + 'XX' ;... + ['Mask ' maskflag];... + ['MaskName ' maskname];... + ['ImageSize ' npx ' ' npy];... + ['CorrelationBoxesSize ' ibx ' ' iby];... + ['SearchBoxeSize ' ibx ' ' iby];... + ['RO ' rho];... + ['GridSpacing ' dx ' ' dy];... + 'XX 1.0';... + ['Dt_TO ' Dt ' ' T0];... + ['PixCmXY ' pxcmx ' ' pxcmy];... + 'XX 1';... + ['ShiftXY 0 0'];... + ['Grid ' gridflag];... + ['GridName ' gridname];... + 'XX 85';... + 'XX 1.0';... + 'XX 1.0';... + 'Hart 1';... + ['DecimalShift ' decimal];... + ['Deformation ' deformation];... + 'CorrelationMin 0';... + 'IntensityMin 0';... + 'SeuilImage n';... + 'SeuilImageValues 0 4096';... + ['ImageToUse ' term_a ' ' term_b];... % VERIFIER ? + ['ImageUsedBefore ' filename_nc1]}; + textout=char(textcmx); + dlmwrite(filename_cmx,textout,''); + s=-1; + display(['!' civ2_exe ' -f ' filename_cmx ' > ' namelog]) + eval(['!' civ2_exe ' -f ' filename_cmx ' > ' namelog]); + +% if sge%dispatch computation on the cluster using interactive queue +% [s,w] = unix(['qrsh -q fast.q ' civ2_exe ' -f ' filename_cmx ' > ' namelog ' 2>&1']); +% end +% if s~=0 +% eval(['!' civ2_exe ' -f ' filename_cmx ' > ' namelog]); +% ['!' civ2_exe ' -f ' filename_cmx ' > ' namelog] +% end + end +end +% close(h) + + +%---------------------------------------- +%PATCH +%--------------------------------------- +function cmd_PATCH=RUN_PATCH(filename_nc,nx_patch,ny_patch,rho_patch,subdomain_patch,thresh_value,test_interp) +global patch_exe patch_new_exe + namelog=[filename_nc([1:end-3]) '_patch.log']; + if test_interp==0 + cmd_PATCH=[patch_exe ' -f ' filename_nc ' -m ' nx_patch ' -n ' ny_patch ' -ro ' rho_patch ' -nopt ' subdomain_patch ... + ' > ' namelog ' 2>&1']; % redirect standard output to the log file + else %nouveau programme patch + cmd_PATCH=[patch_new_exe ' -f ' filename_nc ' -m ' nx_patch ' -n ' ny_patch ' -ro ' rho_patch ... + ' -max ' thresh_value ' -nopt ' subdomain_patch ' > ' namelog ' 2>&1']; % redirect standard output to the log file + end + +%---------------------------------------- +%STEREO Interp +%--------------------------------------- +function cmd=RUN_STINTERP(stinterp_exe,filename_A_nc,filename_B_nc,filename_nc,nx_patch,ny_patch,rho_patch,subdomain_patch,thresh_value,xmlA,xmlB) +namelog=[filename_nc([1:end-3]) '_stinterp.log']; +cmd=[stinterp_exe ' -f1 ' filename_A_nc ' -f2 ' filename_B_nc ' -f ' filename_nc ... + ' -m ' nx_patch ' -n ' ny_patch ' -ro ' rho_patch ' -nopt ' subdomain_patch ' -c1 ' xmlA ' -c2 ' xmlB ' -xy x -Nfy 1024 > ' namelog ' 2>&1']; % redirect standard output to the log file + +%---------------------------------------------------- +function first_j_Callback(hObject, eventdata, handles) +last_j_Callback(hObject, eventdata, handles) + +%--------------------------------------------------------- +% --- Executes on button press in CIV1. +function CIV1_Callback(hObject, eventdata, handles) +val=get(handles.CIV1,'Value'); +if isequal(val,1) + enable_civ1(handles,'on') + enable_pair1(handles,'on') +else + enable_civ1(handles,'off') +end +find_netcpair_civ1(hObject, eventdata, handles); + +%------------------------------------------------------ +% --- Executes on button press in FIX1. +function FIX1_Callback(hObject, eventdata, handles) + +enable_fix1(handles,get(handles.FIX1,'Value')) + + +%---------------------------------------------------------------- +% --- Executes on button press in PATCH1. +function PATCH1_Callback(hObject, eventdata, handles) + +if get(handles.PATCH1,'Value')==1 +enable_patch1(handles) +else +desable_patch1(handles) +end + +%---------------------------------------------------------- +% --- Executes on button press in CIV2. +function CIV2_Callback(hObject, eventdata, handles) +state=get(handles.CIV2,'Value'); +enable_civ2(handles,state) +if state + find_netcpair_civ2(hObject, eventdata, handles) + enable_pair1(handles,'on') +end + +%--------------------------------------------------- +% --- Executes on button press in FIX2. +function FIX2_Callback(hObject, eventdata, handles) +if get(handles.FIX2,'Value')==1 + enable_fix2(handles) + if get(handles.CIV2,'Value')==0 + find_netcpair_civ2(hObject, eventdata, handles) % select the available netcdf files + end +else + desable_fix2(handles) +end + + +%------------------------------------------------------- +% --- Executes on button press in PATCH2. +function PATCH2_Callback(hObject, eventdata, handles) +%-------------------------------------------------------- +if get(handles.PATCH2,'Value')==1 + enable_patch2(handles) + if get(handles.CIV2,'Value')==0 + find_netcpair_civ2(hObject, eventdata, handles) % select the available netcdf files + end +else + desable_patch2(handles) +end + + + +%----------------------------------------------------------- +function first_i_Callback(hObject, eventdata, handles) +%------------------------------------------------------ +last_i_Callback(hObject, eventdata, handles) + +%----------------------------------------------------------- +% --- Executes on button press in calcul_search: determine the search range isx,isy +%-------------------------------------------------------- +function calcul_search_Callback(hObject, eventdata, handles) + +%determine pair numbers +list_pair=get(handles.list_pair_civ1,'String');%get the menu of image pairs +index=get(handles.list_pair_civ1,'Value'); +displ_num=get(handles.list_pair_civ1,'UserData'); +time=get(handles.displ_filebase,'UserData'); %get the set of times +pxcm_xy=get(handles.calcul_search,'UserData'); +pxcmx=pxcm_xy(1); +pxcmy=pxcm_xy(2); +mode_list=get(handles.mode,'String'); +mode_value=get(handles.mode,'Value'); +mode=mode_list{mode_value}; +if isequal (mode, 'series(Di)' ) + ref_i=str2num(get(handles.ref_i,'String')); + num1=ref_i-floor(index/2);% first image numbers + num2=ref_i+ceil(index/2); + num_a=1; + num_b=1; +elseif isequal (mode, 'series(Dj)') + num1=1; + num2=1; + ref_j=str2num(get(handles.ref_j,'String')); + num_a=ref_j-floor(index/2);% first image numbers + num_b=ref_j+ceil(index/2); +elseif isequal(mode,'pair j1-j2') %case of bursts (png_old or png_2D) + ref_i=str2num(get(handles.ref_i,'String')); + num1=ref_i; + num2=ref_i; + num_a=displ_num(1,index); + num_b=displ_num(2,index); +end +dt=time(num2,num_b)-time(num1,num_a); +ibx=str2num(get(handles.ibx,'String')); +iby=str2num(get(handles.iby,'String')); +umin=dt*pxcmx*str2num(get(handles.umin,'String')); +umax=dt*pxcmx*str2num(get(handles.umax,'String')); +vmin=dt*pxcmy*str2num(get(handles.vmin,'String')); +vmax=dt*pxcmy*str2num(get(handles.vmax,'String')); +shiftx=round((umin+umax)/2); +shifty=round((vmin+vmax)/2); +isx=(umax+2-shiftx)*2+ibx; +isx=2*ceil(isx/2)+1; +isy=(vmax+2-shifty)*2+iby; +isy=2*ceil(isy/2)+1; +set(handles.shiftx,'String',num2str(shiftx)); +set(handles.shifty,'String',num2str(shifty)); +set(handles.isx,'String',num2str(isx)); +set(handles.isy,'String',num2str(isy)); + + +%--------------------------------------------------------- +% Executes on carriage return on the subdir civ1 edit window +%-------------------------------------------------------- +function subdir_civ1_Callback(hObject, eventdata, handles) +subdir=get(handles.subdir_civ1,'String'); +set(handles.subdir_civ2,'String',subdir); +if get(handles.CIV1,'Value')==0 + find_netcpair_civ1(hObject, eventdata, handles); %update the list of available pairs from netcdf files in the new directory +end + +%--------------------------------------------------------- +% Executes on carriage return on the subdir civ1 edit window +%--------------------------------------------------------- +function subdir_civ2_Callback(hObject, eventdata, handles) +%update the list of available pairs from netcdf files in the new directory +if get(handles.CIV2,'Value')==0 & get(handles.CIV1,'Value')==0 & get(handles.FIX1,'Value')==0 & get(handles.PATCH1,'Value')==0 + find_netcpair_civ2(hObject, eventdata, handles); +end + +%------------------------------------------------------ +% --- Executes on button press in get_mask_civ1. +%------------------------------------------------------ +function get_mask_civ1_Callback(hObject, eventdata, handles) +maskval=get(handles.get_mask_civ1,'Value'); +if isequal(maskval,0) + set(handles.mask_civ1,'String','') +else + mask_displ='no mask'; %default + filebase=get(handles.displ_filebase,'String'); + [ nbslice_mask, flag_mask]=get_mask(filebase,handles); + if isequal(flag_mask,1) + mask_displ=[num2str(nbslice_mask) 'mask']; + elseif get(handles.compare,'Value')>1 & ~isequal(mask_displ,'no mask')% look for the second mask series + common_path=fileparts(filebase); + filebase_a=fullfile(common_path,get(handles.displ_filebase2,'String')); + [nbslice_a, flag_mask_a]=get_mask(filebase_a,handles); + if isequal(flag_mask_a,0) | ~isequal(nbslice_a,nbslice_mask) + mask_displ='no mask'; + end + end + if isequal(mask_displ,'no mask') + set(handles.get_mask_civ1,'Value',0) + set(handles.get_mask_fix1,'Value',0) + set(handles.get_mask_civ2,'Value',0) + set(handles.get_mask_fix2,'Value',0) + else + set(handles.get_mask_fix1,'Value',1) + set(handles.get_mask_fix2,'Value',1) + end + set(handles.mask_civ1,'String',mask_displ) + set(handles.mask_fix1,'String',mask_displ) + set(handles.mask_civ2,'String',mask_displ) + set(handles.mask_fix2,'String',mask_displ) +end + +%-------------------------------------------------------------- +% --- Executes on button press in get_mask_fix1. +function get_mask_fix1_Callback(hObject, eventdata, handles) +maskval=get(handles.get_mask_fix1,'Value'); +if isequal(maskval,0) + set(handles.mask_fix1,'String','') +else +mask_displ='no mask'; %default +filebase=get(handles.displ_filebase,'String'); +[nbslice, flag_mask]=get_mask(filebase,handles); +if isequal(flag_mask,1) + mask_displ=[num2str(nbslice) 'mask']; +elseif get(handles.compare,'Value')>1 & ~isequal(mask_displ,'no mask')% look for the second mask series + filebase_a=get(handles.displ_filebase2,'String'); + [nbslice_a, flag_mask_a]=get_mask(filebase_a,handles); + if isequal(flag_mask_a,0) | ~isequal(nbslice_a,nbslice) + mask_displ='no mask'; + end +end +if isequal(mask_displ,'no mask') + set(handles.get_mask_fix1,'Value',0) + set(handles.get_mask_civ2,'Value',0) + set(handles.get_mask_fix2,'Value',0) +else + %set(handles.get_mask_civ2,'Value',1) + set(handles.get_mask_fix2,'Value',1) +end +set(handles.mask_fix1,'String',mask_displ) +set(handles.mask_civ2,'String',mask_displ) +set(handles.mask_fix2,'String',mask_displ) +end +%----------------------------------------- +% --- Executes on button press in get_mask_civ2. +function get_mask_civ2_Callback(hObject, eventdata, handles) +maskval=get(handles.get_mask_civ2,'Value'); +if isequal(maskval,0) + set(handles.mask_civ2,'String','') +else +mask_displ='no mask'; %default +filebase=get(handles.displ_filebase,'String'); +[nbslice, flag_mask]=get_mask(filebase,handles); +if isequal(flag_mask,1) + mask_displ=[num2str(nbslice) 'mask']; +elseif get(handles.compare,'Value')>1 & ~isequal(mask_displ,'no mask')% look for the second mask series + filebase_a=get(handles.displ_filebase2,'String'); + [nbslice_a, flag_mask_a]=get_mask(filebase_a,handles); + if isequal(flag_mask_a,0) | ~isequal(nbslice_a,nbslice) + mask_displ='no mask'; + end +end +if isequal(mask_displ,'no mask') + set(handles.get_mask_civ2,'Value',0) + set(handles.get_mask_fix2,'Value',0) +else + set(handles.get_mask_fix2,'Value',1) +end +set(handles.mask_civ2,'String',mask_displ) +set(handles.mask_fix2,'String',mask_displ) +end +%------------------------------------- +% --- Executes on button press in get_mask_fix2. +function get_mask_fix2_Callback(hObject, eventdata, handles) +maskval=get(handles.get_mask_fix2,'Value'); +if isequal(maskval,0) + set(handles.mask_fix2,'String','') +else +mask_displ='no mask'; %default +filebase=get(handles.displ_filebase,'String'); +[nbslice, flag_mask]=get_mask(filebase,handles); +if isequal(flag_mask,1) + mask_displ=[num2str(nbslice) 'mask']; +elseif get(handles.compare,'Value')>1 & ~isequal(mask_displ,'no mask')% look for the second mask series + filebase_a=get(handles.displ_filebase2,'String'); + [nbslice_a, flag_mask_a]=get_mask(filebase_a,handles); + if isequal(flag_mask_a,0) | ~isequal(nbslice_a,nbslice) + mask_displ='no mask'; + end +end +if isequal(mask_displ,'no mask') + set(handles.get_mask_fix2,'Value',0) +end +set(handles.mask_fix2,'String',mask_displ) +end + +%--------------------------------------- +function [nbslice, flag_mask]=get_mask(filebase,handles) +%detect mask files, images with appropriate file base +%[filebase '_' xx 'mask'], xx=nbslice +%flag_mask=1 indicates detection + +flag_mask=0;%default +nbslice=1; + +% subdir=get(handles.subdir_civ1,'String'); +[Path,Name]=fileparts(filebase); +currentdir=pwd; +cd(Path);%move in the dir of the root name filebase +maskfiles=dir([Name '_*mask_*.png']);%look for mask files +cd(currentdir);%come back to the current working directory +if isempty(maskfiles) + msgbox_uvmat('ERROR','no mask available, to create it use Tools/Make mask in the upper menu bar of uvmat') +else + flag_mask=1; + maskname=maskfiles(1).name;% take the first mask file in the list + [Path2,Name,ext]=fileparts(maskname); + Namedouble=double(Name); + val=(48>Namedouble)|(Namedouble>57);% select the non-numerical characters + ind_mask=findstr('mask',Name); + i=ind_mask-1; + while val(i)==0 & i>0 + i=i-1; + end + nbslice=str2num(Name(i+1:ind_mask-1)); + if ~isequal(nbslice,[]) & Name(i)=='_' + flag_mask=1; + else + msgbox_uvmat('ERROR',['bad mask file ' Name ext ' found in ' Path2]) + return + nbslice=1; + end +end + +%--------------------------------------- +function [nbslice, flag_mask]=get_grid(filebase,handles) + +flag_mask=0;%default +nbslice=1; +[Path,Name]=fileparts(filebase); +currentdir=pwd; +cd(Path);%move in the dir of the root name filebase +maskfiles=dir([Name '_*grid_*.grid']);%look for mask files +cd(currentdir);%come back to the current working directory +if ~isempty(maskfiles) + flag_mask=1; + maskname=maskfiles(1).name;% take the first mask file in the list + [Path2,Name,ext]=fileparts(maskname); + Namedouble=double(Name); + val=(48>Namedouble)|(Namedouble>57);% select the non-numerical characters + ind_mask=findstr('grid',Name); + i=ind_mask-1; + while val(i)==0 & i>0 + i=i-1; + end + nbslice=str2num(Name(i+1:ind_mask-1)); + if ~isequal(nbslice,[]) & Name(i)=='_' + flag_mask=1; + else + msgbox_uvmat('ERROR',['bad grid file ' Name ext ' found in ' Path2]) + return + nbslice=1; + end +end +%------------------------------ + +function grid_civ1_Callback(hObject, eventdata, handles) +% hObject handle to grid_civ1 (see GCBO) +% eventdata reserved - to be defined in a future version of MATLAB +% handles structure with handles and user data (see GUIDATA) + +% Hints: get(hObject,'String') returns contents of grid_civ1 as text +% str2double(get(hObject,'String')) returns contents of grid_civ1 as a double + + +%----------------------------------------------------------- +% transform numbers to letters +%-------------------------------------------- +function str=num2stra(num,nom_type); +if isequal(nom_type,'png_old') | isequal(nom_type,'netc_old') |isequal(nom_type,'raw_SMD') + str=char(96+num); +elseif isequal(nom_type,'_i')|isequal(nom_type,'_i1-i2')... + |isequal(nom_type,'ima_num')| isequal(nom_type,'avi')| isequal(nom_type,'none') + str=''; +else + str=num2str(num); +end +%--------------------------------------------------- +function mask_civ1_Callback(hObject, eventdata, handles) +set(handles.mask_civ1,'UserData',[]) +set(handles.mask_civ1,'String','') +%---------------------------------------------------- +function mask_civ2_Callback(hObject, eventdata, handles) +set(handles.mask_civ2,'UserData',[]) +set(handles.mask_civ2,'String','') +%---------------------------------------------------- +function mask_fix1_Callback(hObject, eventdata, handles) +set(handles.mask_fix1,'UserData',[]) +set(handles.mask_fix1,'String','') +%---------------------------------------------------- +function mask_fix2_Callback(hObject, eventdata, handles) +set(handles.mask_fix2,'UserData',[]) +set(handles.mask_fix2,'String','') + +%-------------------------------------------------------------------------- +% --- Executes on button press in list_subdir_civ1. +function list_subdir_civ1_Callback(hObject, eventdata, handles) +list_subdir_civ1=get(handles.list_subdir_civ1,'String'); +val=get(handles.list_subdir_civ1,'Value'); +if val>1 + subdir=list_subdir_civ1{val}; + set(handles.subdir_civ1,'String',subdir); + set(handles.list_subdir_civ1,'Value',1); +end + + +%-------------------------------------------------------------------------- +% --- Executes on button press in list_subdir_civ2. +function list_subdir_civ2_Callback(hObject, eventdata, handles) +list_subdir_civ2=get(handles.list_subdir_civ2,'String'); +val=get(handles.list_subdir_civ2,'Value'); +if val>1 + subdir=list_subdir_civ2{val}; + set(handles.subdir_civ2,'String',subdir); + set(handles.list_subdir_civ2,'Value',1); +end + + +%---------------------------------------------- +function last_i_Callback(hObject, eventdata, handles) +first_i=str2num(get(handles.first_i,'String')); +last_i=str2num(get(handles.last_i,'String')); +ref_i=ceil((first_i+last_i)/2); +set(handles.ref_i,'String', num2str(ref_i)) +ref_i_Callback(hObject, eventdata, handles) + +%------------------------------------------------------- +function last_j_Callback(hObject, eventdata, handles) +first_j=str2num(get(handles.first_j,'String')); +last_j=str2num(get(handles.last_j,'String')); +ref_j=ceil((first_j+last_j)/2); +set(handles.ref_j,'String', num2str(ref_j)) +ref_j_Callback(hObject, eventdata, handles) + + +%----------------------------------------------------------- +% --- Executes on button press in browse_gridciv1. +function browse_gridciv1_Callback(hObject, eventdata, handles) +%----------------------------------------------------------- +value=get(handles.browse_gridciv1,'Value'); +testgrid=0; +if value + filebase=get(handles.displ_filebase,'String'); + [nbslice, flag_grid]=get_grid(filebase,handles) + if isequal(flag_grid,1) + filegrid=[num2str(nbslice) 'grid']; + testgrid=1; + else + [FileName, PathName, filterindex] = uigetfile( ... + {'*.grid', ' (*.grid)'; + '*.grid', '.grid files '; ... + '*.*', 'All Files (*.*)'}, ... + 'Pick a file',filebase); + filegrid=fullfile(PathName,FileName); + if ~(isempty(FileName)||isempty(PathName)||isequal(FileName,0)||~exist(filegrid,'file')) + testgrid=1; + end + end +end +if testgrid + set(handles.browse_gridciv2,'Value',1) + set(handles.get_gridpatch1,'Value',1) + set(handles.get_gridpatch2,'Value',1) + set(handles.dx_civ1,'Visible','off'); + set(handles.dy_civ1,'Visible','off'); + set(handles.dx_civ2,'Visible','off'); + set(handles.dy_civ2,'Visible','off'); + set(handles.grid_civ1,'String',filegrid) + set(handles.grid_patch1,'String',filegrid) + set(handles.grid_civ2,'String',filegrid) + set(handles.grid_patch2,'String',filegrid) + else + set(handles.browse_gridciv1,'Value',0); + set(handles.browse_gridciv2,'Value',0); + set(handles.get_gridpatch1,'Value',0) + set(handles.get_gridpatch2,'Value',0) + set(handles.dx_civ1,'Visible','on'); + set(handles.dy_civ1,'Visible','on'); + set(handles.dx_civ2,'Visible','on'); + set(handles.dy_civ2,'Visible','on'); + set(handles.grid_civ1,'String','') + set(handles.grid_patch1,'String','') + set(handles.grid_civ2,'String','') + set(handles.grid_patch2,'String','') +end + +%----------------------------------------------------------- +% --- Executes on button press in browse_gridciv1. +function browse_gridciv2_Callback(hObject, eventdata, handles) +%----------------------------------------------------------- +value=get(handles.browse_gridciv2,'Value'); +if value + filebase=get(handles.displ_filebase,'String'); + [nbslice, flag_grid]=get_grid(filebase,handles) + if isequal(flag_grid,1) + mask_displ=[num2str(nbslice) 'grid']; + set(handles.grid_civ2,'String',mask_displ) + set(handles.dx_civ2,'Visible','off'); + set(handles.dy_civ2,'Visible','off'); + else + [FileName, PathName, filterindex] = uigetfile( ... + {'*.grid', ' (*.grid)'; + '*.grid', '.grid files '; ... + '*.*', 'All Files (*.*)'}, ... + 'Pick a file',filebase); + filegrid=fullfile(PathName,FileName); + if isempty(FileName)|isempty(PathName)|isequal(FileName,0)|~exist(filegrid,'file') + set(handles.browse_gridciv2,'Value',0); + set(handles.grid_civ2,'string',''); + set(handles.dx_civ2,'Visible','on'); + set(handles.dy_civ2,'Visible','on'); + set(handles.grid_civ2,'string',''); + else + set(handles.grid_civ2,'string',filegrid); + set(handles.dx_civ2,'Visible','off'); + set(handles.dy_civ2,'Visible','off'); + set(handles.grid_civ2,'string',filegrid); + end + end +else + set(handles.grid_civ2,'string',''); + set(handles.dx_civ2,'Visible','on'); + set(handles.dy_civ2,'Visible','on'); + set(handles.grid_civ2,'string',''); +end + +% % --- Executes on button press in browse_gridciv2. +% function browse_gridciv2_Callback(hObject, eventdata, handles) +% +% filebase=get(handles.displ_filebase,'String'); +% [FileName, PathName, filterindex] = uigetfile( ... +% {'*.grid', ' (*.grid)'; +% '*.grid', '.grid files '; ... +% '*.*', 'All Files (*.*)'}, ... +% 'Pick a file',filebase); +% filegrid=fullfile(PathName,FileName); +% set(handles.grid_civ2,'string',filegrid); +% set(handles.dx_civ2,'String',' '); +% set(handles.dy_civ2,'String',' '); +% % set(handles.grid_patch2,'string',filegrid); + +% --- Executes on button press in get_gridpatch1. +function get_gridpatch1_Callback(hObject, eventdata, handles) +% hObject handle to get_gridpatch1 (see GCBO) +% eventdata reserved - to be defined in a future version of MATLAB +% handles structure with handles and user data (see GUIDATA) + +filebase=get(handles.displ_filebase,'String'); +[FileName, PathName, filterindex] = uigetfile( ... + {'*.grid', ' (*.grid)'; + '*.grid', '.grid files '; ... + '*.*', 'All Files (*.*)'}, ... + 'Pick a file',filebase); +filegrid=fullfile(PathName,FileName); +set(handles.grid_patch1,'string',filegrid); +% set(handles.grid_patch2,'string',filegrid + +%----------------------------------------------------------------- +% --- Executes on button press in get_gridpatch2. +function get_gridpatch2_Callback(hObject, eventdata, handles) + + +%---------------------------------------------------------- +function enable_civ1(handles,state) +if isequal(state,0) + state='off'; +end +if isequal(state,1) + state='on'; +end +if isequal(state,'on') + set(handles.frame_civ1,'BackgroundColor',[1 1 0]) + set(handles.frame_para_civ1,'BackgroundColor',[1 1 0]) + set(handles.frame_grid_civ1,'BackgroundColor',[1 1 0]) +else + set(handles.frame_civ1,'BackgroundColor',[0.831 0.816 0.784]) + set(handles.frame_para_civ1,'BackgroundColor',[0.831 0.816 0.784]) + set(handles.frame_grid_civ1,'BackgroundColor',[0.831 0.816 0.784]) +end +set(handles.ibx,'Visible',state) +set(handles.iby,'Visible',state) +set(handles.isx,'Visible',state) +set(handles.isy,'Visible',state) +set(handles.shiftx,'Visible',state) +set(handles.shifty,'Visible',state) +set(handles.rho,'Visible',state) +set(handles.dx_civ1,'Visible',state) +set(handles.dy_civ1,'Visible',state) +set(handles.calcul_search,'Visible',state) +set(handles.u_text,'Visible',state) +set(handles.v_text,'Visible',state) +set(handles.min,'Visible',state) +set(handles.max,'Visible',state) +set(handles.umin,'Visible',state) +set(handles.umax,'Visible',state) +set(handles.vmin,'Visible',state) +set(handles.vmax,'Visible',state) +set(handles.grid_civ1,'Visible',state) +set(handles.mask_civ1,'Visible',state) +set(handles.browse_gridciv1,'Visible',state) +set(handles.get_mask_civ1,'Visible',state) +set(handles.parameters,'Visible',state) +set(handles.grid,'Visible',state) +set(handles.dx_civ1,'Visible',state) +set(handles.dy_civ1,'Visible',state) +set(handles.ImaThreshold,'Visible',state) +if isequal(state,'off') + set(handles.MinIma,'Visible','off') + set(handles.MaxIma,'Visible','off') + set(handles.ImaThreshold,'Value',0) +end +set(handles.dx_civ1_title,'Visible',state) +set(handles.dy_civ1_title,'Visible',state) +set(handles.ImaThreshold_title,'Visible',state) +set(handles.ib_title,'Visible',state) +set(handles.is_title,'Visible',state) +set(handles.shift_title,'Visible',state) +set(handles.rho_title,'Visible',state) + +%---------------------------------------------------------- +function enable_fix1(handles,state) +if isequal(state,0) + state='off'; +end +if isequal(state,1) + state='on'; +end +if isequal(state,'on') + set(handles.frame_fix1,'BackgroundColor',[1 1 0]) +else + set(handles.frame_fix1,'BackgroundColor',[0.7 0.7 0.7]) +end +set(handles.REMOVE,'Visible',state) +set(handles.vec_Fmin2,'Visible',state) +set(handles.vec_F2,'Visible',state) +set(handles.vec_F3,'Visible',state) +set(handles.thresh_vecC,'Visible',state) +set(handles.thresh_vecC_title,'Visible',state) +set(handles.thresh_vel,'Visible',state) +set(handles.thresh_vel_text,'Visible',state) +set(handles.mask_fix1,'Visible',state) +set(handles.get_mask_fix1,'Visible',state) +set(handles.get_ref_fix1,'Visible',state) +set(handles.ref_fix1,'Visible',state) +set(handles.inf_sup1,'Visible',state) +set(handles.field_ref1,'Visible',state) + + +%-------------------------------------------------------------- +function enable_patch1(handles) +global patch_new_exe +set(handles.frame_patch1,'BackgroundColor',[1 1 0]) +set(handles.rho_patch1,'Visible','on') +set(handles.rho_text1,'Visible','on') +set(handles.thresh_patch1,'Visible','on') +set(handles.thresh_text1,'Visible','on') +set(handles.subdomain_patch1,'Visible','on') +set(handles.subdomain_text1,'Visible','on') +set(handles.nx_patch1,'Visible','on') +set(handles.ny_patch1,'Visible','on') +set(handles.nx_patch1_title,'Visible','on') +set(handles.ny_patch1_title,'Visible','on') +if (~isequal(patch_new_exe,[]) & ~isequal(patch_new_exe,[])) + set(handles.test_interp,'Visible','on'); +end +set(handles.get_gridpatch1,'Visible','on') +set(handles.grid_patch1,'string','none'); +set(handles.grid_patch1,'Visible','on') + +%-------------------------------------------------------------- +function desable_patch1(handles) +set(handles.frame_patch1,'BackgroundColor',[0.831 0.816 0.784]) +set(handles.rho_patch1,'Visible','off') +set(handles.rho_text1,'Visible','off') +set(handles.thresh_patch1,'Visible','off') +set(handles.thresh_text1,'Visible','off') +set(handles.subdomain_patch1,'Visible','off') +set(handles.subdomain_text1,'Visible','off') +set(handles.nx_patch1,'Visible','off') +set(handles.ny_patch1,'Visible','off') +set(handles.nx_patch1_title,'Visible','off') +set(handles.ny_patch1_title,'Visible','off') +set(handles.test_interp,'Visible','off') +set(handles.get_gridpatch1,'Visible','off') +set(handles.grid_patch1,'Visible','off') + +%---------------------------------------------------------- +function enable_civ2(handles,state) +if isequal(state,0) + state='off'; +end +if isequal(state,1) + state='on'; +end +if isequal(state,'on') + set(handles.frame_civ2,'BackgroundColor',[1 1 0]) + set(handles.frame_para_civ2,'BackgroundColor',[1 1 0]) + set(handles.frame_grid_civ2,'BackgroundColor',[1 1 0]) + set(handles.frame_subdirciv2,'BackgroundColor',[1 1 0]) +else + set(handles.frame_civ2,'BackgroundColor',[0.831 0.816 0.784]) + set(handles.frame_para_civ2,'BackgroundColor',[0.831 0.816 0.784]) + set(handles.frame_grid_civ2,'BackgroundColor',[0.831 0.816 0.784]) + set(handles.frame_subdirciv2,'BackgroundColor',[0.831 0.816 0.784]) +end +set(handles.ibx_civ2,'Visible',state) +set(handles.iby_civ2,'Visible',state) +set(handles.decimal,'Visible',state) +set(handles.deformation,'Visible',state) +set(handles.rho_civ2,'Visible',state) +set(handles.dx_civ2,'Visible',state) +set(handles.dy_civ2,'Visible',state) +set(handles.browse_gridciv2,'Visible',state) +set(handles.get_mask_civ2,'Visible',state) +set(handles.parameters,'Visible',state) +set(handles.grid,'Visible',state) +set(handles.parameters_text,'Visible',state) +set(handles.grid_text,'Visible',state) +set(handles.grid_civ2,'Visible',state) +set(handles.mask_civ2,'Visible',state) +set(handles.dx_civ2_title,'Visible',state) +set(handles.dy_civ2_title,'Visible',state) +set(handles.ibx_civ2_text,'Visible',state) +set(handles.rho_civ2_title,'Visible',state) +set(handles.ImaThreshold2,'Visible',state) +set(handles.ImaThreshold_title2,'Visible',state) +if isequal(state,'off') + set(handles.MinIma2,'Visible','off') + set(handles.MaxIma2,'Visible','off') + set(handles.ImaThreshold2,'Value',0) + if isequal(get(handles.FIX2,'Value'),0) & isequal(get(handles.PATCH2,'Value'),0) + set(handles.list_pair_civ2,'Visible','off') + set(handles.subdir_civ2,'Visible','off') + set(handles.subdir_civ2_text,'Visible','off') + end +else + set(handles.list_pair_civ2,'Visible','on') + set(handles.subdir_civ2,'Visible','on') + set(handles.subdir_civ2_text,'Visible','on') +end + + +%---------------------------------------------------------- +function enable_fix2(handles) +set(handles.frame_fix2,'BackgroundColor',[1 1 0]) +set(handles.REMOVE2,'Visible','on') +set(handles.vec_Fmin2_2,'Visible','on') +set(handles.vec_F4,'Visible','on') +set(handles.vec_F3_2,'Visible','on') +set(handles.thresh_vec2C,'Visible','on') +set(handles.thresh_vec2C_text,'Visible','on') +set(handles.thresh_vel2,'Visible','on') +set(handles.thresh_vel2_text,'Visible','on') +set(handles.mask_fix2,'Visible','on') +set(handles.get_mask_fix2,'Visible','on') +set(handles.list_pair_civ2,'Visible','on') +set(handles.subdir_civ2,'Visible','on') +set(handles.subdir_civ2_text,'Visible','on') +set(handles.get_ref_fix2,'Visible','on') +set(handles.ref_fix2,'Visible','on') +set(handles.inf_sup2,'Visible','on') +set(handles.field_ref2,'Visible','on') + +%---------------------------------------------------------- +function desable_fix2(handles) +set(handles.frame_fix2,'BackgroundColor',[0.831 0.816 0.784]) +set(handles.REMOVE2,'Visible','off') +set(handles.vec_Fmin2_2,'Visible','off') +set(handles.vec_F4,'Visible','off') +set(handles.vec_F3_2,'Visible','off') +set(handles.thresh_vec2C,'Visible','off') +set(handles.thresh_vec2C_text,'Visible','off') +set(handles.thresh_vel2,'Visible','off') +set(handles.thresh_vel2_text,'Visible','off') +set(handles.mask_fix2,'Visible','off') +set(handles.get_mask_fix2,'Visible','off') +set(handles.get_ref_fix2,'Visible','off') +set(handles.ref_fix2,'Visible','off') +set(handles.inf_sup2,'Visible','off') +set(handles.field_ref2,'Visible','off') +if isequal(get(handles.CIV2,'Value'),0) & isequal(get(handles.PATCH2,'Value'),0) + set(handles.list_pair_civ2,'Visible','off') + set(handles.subdir_civ2,'Visible','off') + set(handles.subdir_civ2_text,'Visible','off') +end + +%-------------------------------------------------------------- +function enable_patch2(handles) +set(handles.frame_patch2,'BackgroundColor',[1 1 0]) +%set(handles.rho_patch2,'Visible','on') +set(handles.rho_text2,'Visible','on') +set(handles.thresh_patch2,'Visible','on') +set(handles.thresh_text2,'Visible','on') +set(handles.subdomain_patch2,'Visible','on') +set(handles.subdomain_text2,'Visible','on') +set(handles.nx_patch2,'Visible','on') +set(handles.ny_patch2,'Visible','on') +set(handles.nx_patch2_title,'Visible','on') +set(handles.ny_patch2_title,'Visible','on') +set(handles.get_gridpatch2,'Visible','on') +set(handles.grid_patch2,'Visible','on') +set(handles.list_pair_civ2,'Visible','on') +set(handles.subdir_civ2,'Visible','on') +set(handles.subdir_civ2_text,'Visible','on') + +%-------------------------------------------------------------- +function desable_patch2(handles) +set(handles.frame_patch2,'BackgroundColor',[0.831 0.816 0.784]) +set(handles.rho_patch2,'Visible','off') +set(handles.rho_text2,'Visible','off') +set(handles.thresh_patch2,'Visible','off') +set(handles.thresh_text2,'Visible','off') +set(handles.subdomain_patch2,'Visible','off') +set(handles.subdomain_text2,'Visible','off') +set(handles.nx_patch2,'Visible','off') +set(handles.ny_patch2,'Visible','off') +set(handles.nx_patch2_title,'Visible','off') +set(handles.ny_patch2_title,'Visible','off') +set(handles.get_gridpatch2,'Visible','off') +set(handles.grid_patch2,'Visible','off') +if isequal(get(handles.CIV2,'Value'),0) & isequal(get(handles.FIX2,'Value'),0) + set(handles.list_pair_civ2,'Visible','off') + set(handles.subdir_civ2,'Visible','off') + set(handles.subdir_civ2_text,'Visible','off') +end + +%-------------------------------------------------------------- +function enable_pair1(handles,state) +set(handles.subdir_civ1,'Visible',state) +set(handles.list_subdir_civ1,'Visible',state) +set(handles.SUBDIR_CIV1_txt,'Visible',state) +set(handles.frame_subdirciv1,'Visible',state) +set(handles.list_pair_civ1,'Visible',state) +set(handles.PAIR_txt,'Visible',state) +set(handles.dt_display_txt,'Visible',state) +set(handles.dt_unit,'Visible',state) +set(handles.PAIR_frame,'Visible',state) + +% --- Executes on button press in test_interp. +function test_interp_Callback(hObject, eventdata, handles) +% hObject handle to test_interp (see GCBO) +% eventdata reserved - to be defined in a future version of MATLAB +% handles structure with handles and user data (see GUIDATA) + +% Hint: get(hObject,'Value') returns toggle state of test_interp + + + + + + +%------------------------------------------------ +%Read the parameters for civ1 on the interface +%-------------------------------------------------- +function par=read_param_civ1(handles,file_ima) + +ibx_val=str2num(get(handles.ibx,'String')); +par.ibx=num2str(ibx_val); +iby_val=str2num(get(handles.iby,'String')); +par.iby=num2str(iby_val); +isx=get(handles.isx,'String'); +if isempty(str2num(isx)), isx='41'; set(handles.isx,'String','41'), end; %default +if str2num(isx) filename ( no extension ) + + if isequal(par.Dt,'0') + par.Dt='1' ;%case of 'displacement' mode + end + + textcmx={'############## CMX file';... + ['FirstImage ' par.filename_ima_a];... + ['LastImage ' par.filename_ima_b];... + 'XX' ;... + ['Mask ' par.maskflag] ;... + ['MaskName ' par.maskname];... + ['ImageSize ' par.npx ' ' par.npy];... %VERIFIER CAS GENERAL ? + ['CorrelationBoxesSize ' par.ibx ' ' par.iby];... + ['SearchBoxeSize ' par.isx ' ' par.isy];... + ['RO ' par.rho];... + ['GridSpacing ' par.dx ' ' par.dy];... + 'XX 1.0';... + ['Dt_TO ' par.Dt ' ' par.T0];... + ['PixCmXY ' par.pxcmx ' ' par.pxcmy];... + 'XX 1';... + ['ShiftXY ' par.shiftx ' ' par.shifty];... + ['Grid ' par.gridflag];... + ['GridName ' par.gridname] ;... + 'XX 85';... + 'XX 1.0';... + 'XX 1.0';... + 'Hart 1';... + 'DecimalShift 0';... + 'Deformation 0';... + 'CorrelationMin 0';... + 'IntensityMin 0';... + 'SeuilImage n';... + 'SeuilImageValues 0 4096';... + ['ImageToUse ' par.term_a ' ' par.term_b];... % VERIFIER ? + 'ImageUsedBefore null null'}; + + textout=char(textcmx); + % timeL1=clock; + dlmwrite([filename '.cmx'],textout,''); + % timeL2=clock; + % timciv1=etime(timeL2,timeL1) + if sge + cmd_CIV1=[civ1_exe ' -f ' filename '.cmx' ]; % redirect standard output to the log file + else + cmd_CIV1=[civ1_exe ' -f ' filename_cmx ' > ' namelog ' 2>&1']; % redirect standard output to the log file + end + if(isunix) + [Rootbat,Filebat,extbat]=fileparts(namelog); + ncName=fullfile(Rootbat,[ Filebat '.nc']); + cmd_CIV1=char({cmd_CIV1 ; ['mv ' namelog ' ' namelog '.civ1.log'];['chmod g+w ' ncName]}); + else + cmd_CIV1=char({cmd_CIV1 ; ['copy /Y ' namelog ' ' namelog '.civ1.log']}); + end + +%--------------------------------------------------------- +%CIV1 Unified +%---------------------------------------------------------- +function xml_civ1_parameters=BATCH_CIV1_Unified(filename,namelog,par) +%pixels per cm and matrix of the image times, read from the .civ file by uvmat +global civ1_exe Civ_exe%name of the executable for civ1 calculation + + civ1.image1=par.filename_ima_a; + civ1.image2=par.filename_ima_b; + civ1.imageSize_X=par.npx; + civ1.imageSize_Y=par.npy; + civ1.outputFileName=[filename '.nc']; + civ1.correlationBoxesSize_X=par.ibx; + civ1.correlationBoxesSize_Y=par.iby; + civ1.searchBoxesSize_X=par.isx; + civ1.searchBoxesSize_Y=par.isy; + civ1.globalShift_X=par.shiftx; + civ1.globalShift_Y=par.shifty; + civ1.ro=par.rho; + civ1.hart='y'; + if isequal(par.gridflag,'y') + civ1.grid=par.gridname; + else + civ1.grid='n'; + civ1.gridSpacing_X=par.dx; + civ1.gridSpacing_Y=par.dy; + end + if isequal(par.maskflag,'y') + civ1.mask=par.maskname; + end + civ1.dt=par.Dt; + civ1.unit='pixel'; + civ1.absolut_time_T0=par.T0; + civ1.pixcmx=par.pxcmx; + civ1.pixcmy=par.pxcmy; + civ1.convectFlow='n'; + + xml_civ1_parameters=civ1; + +%--------------------------------------------------------- +%CIV2 Unified +%---------------------------------------------------------- +function civ2=BATCH_CIV2_Unified(filename,namelog,par) +%pixels per cm and matrix of the image times, read from the .civ file by uvmat +global civ2_exe Civ_exe%name of the executable for civ1 calculation + +civ2.image1=par.filename_ima_a; +civ2.image2=par.filename_ima_b; +civ2.imageSize_X=par.npx; +civ2.imageSize_Y=par.npy; +civ2.inputFileName=[par.filename_nc1 '.nc']; +civ2.outputFileName=[filename '.nc']; +civ2.correlationBoxesSize_X=par.ibx; +civ2.correlationBoxesSize_Y=par.iby; +civ2.ro=par.rho; +%civ2.decimalShift=par.decimal; +%civ2.deformation=par.deformation; +if isequal(par.decimal,'1') + civ2.decimalShift='y'; +else + civ2.decimalShift='n'; +end +if isequal(par.deformation,'1') + civ2.deformation='y'; +else + civ2.deformation='n'; +end +if isequal(par.gridflag,'y') + civ2.grid=par.gridname; +else + civ2.grid='n'; + civ2.gridSpacing_X=par.dx; + civ2.gridSpacing_Y=par.dy; +end +civ2.gridSpacing_X='10'; +civ2.gridSpacing_Y='10';%NOTE: faut mettre gridSpacing pourque ca tourne, meme si c'est la grille qui est utilisee +if isequal(par.maskflag,'y') + civ2.mask=par.maskname; +else + civ2.mask='n'; +end +civ2.dt=par.Dt; +civ2.unit='pixel'; +civ2.absolut_time_T0=par.T0; +civ2.pixcmx=par.pxcmx; +civ2.pixcmy=par.pxcmy; +civ2.convectFlow='n'; +civ2.pixcmx=par.pxcmx; +civ2.pixcmy=par.pxcmy; +civ2.convectFlow='n'; + +%--------------------------------------------------------- +%CIV2 CIV2 CIV2 CIV2 +%---------------------------------------------------------- +function cmd_CIV2=BATCH_CIV2(filename_cmx,namelog,par) +%pixels per cm and matrix of the image times, read from the .civ file by uvmat +global civ2_exe sge%name of the executable for civ1 calculation + if isequal(par.Dt,'0') + par.Dt='1' ;%case of 'displacement' mode + end +textcmx={'############## CMX file';... +['FirstImage ' par.filename_ima_a];... +['LastImage ' par.filename_ima_b];... +'XX' ;... +['Mask ' par.maskflag];... +['MaskName ' par.maskname];... +['ImageSize ' par.npx ' ' par.npy];... +['CorrelationBoxesSize ' par.ibx ' ' par.iby];... +['SearchBoxeSize ' par.ibx ' ' par.iby];... +['RO ' par.rho];... +['GridSpacing ' par.dx ' ' par.dy];... +'XX 1.0';... +['Dt_TO ' par.Dt ' ' par.T0];... +['PixCmXY ' par.pxcmx ' ' par.pxcmy];... +'XX 1';... +['ShiftXY 0 0'];... +['Grid ' par.gridflag];... +['GridName ' par.gridname];... +'XX 85';... +'XX 1.0';... +'XX 1.0';... +'Hart 1';... +['DecimalShift ' par.decimal];... +['Deformation ' par.deformation];... +'CorrelationMin 0';... +'IntensityMin 0';... +'SeuilImage n';... +'SeuilImageValues 0 4096';... +['ImageToUse ' par.term_a ' ' par.term_b];... % VERIFIER ? +['ImageUsedBefore ' par.filename_nc1]}; + textout=char(textcmx); + dlmwrite([filename_cmx '2'] ,textout,''); + if sge + cmd_CIV2=[civ2_exe ' -f ' filename_cmx ]; % redirect standard output to the log file + else + cmd_CIV2=[civ2_exe ' -f ' filename_cmx ' > ' namelog ' 2>&1']; % redirect standard output to the log file + end + + +% --- Executes on button press in HELP. +function HELP_Callback(hObject, eventdata, handles) +path_to_uvmat=which ('uvmat');% check the path of uvmat +pathelp=fileparts(path_to_uvmat); +helpfile=fullfile(pathelp,'UVMAT_DOC','uvmat_doc.html'); +if isempty(dir(helpfile)), errordlg('Please put the help file uvmat_doc.html in the directory UVMAT/UVMAT_DOC') +else +web([helpfile '#civ']) +end + + +%---------------------------------------------------------- +%--read images and convert them to the uint16 format used for PIV +function A=read_image(filename,nom_type,npx,npy,num); +%npx, npy are the dimensions needed for the raw SMD images +%num is the view number needed for an avi movie +if isequal(nom_type,'avi') + mov=aviread(filename,num); + A=frame2im(mov(1)); + A=sum(double(A),3); + A=uint16(A); +elseif isequal(nom_type,'raw_SMD') + [fid,message]=fopen(filename,'r'); + B=fread(fid,Inf,'int16',0,'ieee-le');%read 16 bit binary file + A=(reshape(B,npx,npy))'; %remplissage ligne par ligne avec une matrice colonne ? transposer(uB) pour avoir une matrice ligne + A=uint16(A); + fclose(fid); +else + A=imread(filename); + siz=size(A); + if length(siz)==3;%color images + A=sum(double(A),3); + end + A=uint16(A); +end + +%---------------------------------------------------------------- +%Executes on carriage return on the time interval dt +%---------------------------------------------------------------- +function dt_Callback(hObject, eventdata, handles) +%determine the set of times and possible intervals for CIV +% answer=inputdlg('time interval between images?'); + dt=(1/1000)*str2num(get(handles.dt,'String')); + nbfield=str2num(get(handles.nb_field,'String')); %last image number selected in the processing series + time=(dt*[0:nbfield-1])'; +% set(handles.incr_i,'UserData',dt);%store the time interval between successive images + set(handles.displ_filebase,'UserData',time); %store the set of times + for index=1:min(nbfield-1,200) + displ_num(1,index)=1; + displ_num(2,index)=1; + displ_num(3,index)=-floor(index/2); + displ_num(4,index)=ceil(index/2); + end +set(handles.list_pair_civ1,'Value',1); +set(handles.list_pair_civ1,'UserData',displ_num); +set(handles.list_pair_civ2,'Value',1); +%update the list of time intervals +find_netcpair_civ1(hObject, eventdata, handles) +find_netcpair_civ2(hObject, eventdata, handles) + +%------------------------------------------------------- +function ref_i_Callback(hObject, eventdata, handles) +mode_list=get(handles.mode,'String'); +mode_value=get(handles.mode,'Value'); +mode=mode_list{mode_value}; +if isequal(get(handles.CIV1,'Value'),0)| isequal(mode,'series(Di)') + find_netcpair_civ1(hObject, eventdata, handles);% update the menu of pairs depending on the available netcdf files +end +if isequal(mode,'series(Di)') | ...% we do patch2 only + (get(handles.CIV2,'Value')==0 & get(handles.CIV1,'Value')==0 & get(handles.FIX1,'Value')==0 & get(handles.PATCH1,'Value')==0) + find_netcpair_civ2(hObject, eventdata, handles); +end + +%---------------------------------------------------- +function ref_j_Callback(hObject, eventdata, handles) +mode_list=get(handles.mode,'String'); +mode_value=get(handles.mode,'Value'); +mode=mode_list{mode_value}; +if isequal(get(handles.CIV1,'Value'),0)| isequal(mode,'series(Dj)') + find_netcpair_civ1(hObject, eventdata, handles);% update the menu of pairs depending on the available netcdf files +end +if isequal(mode,'series(Dj)') | ... + (get(handles.CIV2,'Value')==0 & get(handles.CIV1,'Value')==0 & get(handles.FIX1,'Value')==0 & get(handles.PATCH1,'Value')==0) + find_netcpair_civ2(hObject, eventdata, handles); +end +%---------------------------------------------------- +% --- Executes on button press in compare. +function compare_Callback(hObject, eventdata, handles) +test=get(handles.compare,'Value'); +if test==2 || test==3 + filebase=get(handles.displ_filebase,'String'); + browse=get(handles.browse_root,'Userdata'); + browse.nom_type_ima1=browse.nom_type_ima; + set(handles.browse_root,'UserData',browse); + set(handles.sub_txt,'Visible','on') + set(handles.displ_filebase2,'Visible','On');%mkes the second file input window visible + mode_store=get(handles.mode,'String');%get the present 'mode' + set(handles.compare,'UserData',mode_store);%store the mode display + set(handles.mode,'Visible','off') + if test==2 + set(handles.mode,'Visible','off') + else + set(handles.mode,'Visible','on') + end + + % open an image file with the browser + ind_opening=1;%default + browse.incr_pair=[0 0]; %default + oldfile=get(handles.displ_filebase,'String'); + menu={'*.xml;*.avi;*.AVI;*.nc','(*.xml,*.avi,*.nc)'; ... + '*.xml', '.xml files';'*.avi;*.AVI', '.avi files';'*.nc', '.nc files';... + '*.*', 'All Files (*.*)'}; + [FileName, PathName, filtindex] = uigetfile( menu, 'Pick a file',oldfile); + fileinput=[PathName FileName];%complete file name + sizf=size(fileinput); + if (~ischar(fileinput)|~isequal(sizf(1),1)),return;end %stop if fileinput not a character string + [path,name,ext]=fileparts(fileinput); + [path1]=fileparts(filebase); + if ~strcmp(path1,path) + msgbox_uvmat('ERROR','The two input image series must be in the same directory') + return + end + set(handles.displ_filebase2,'String',name); + [RootPath,RootFile,field_count,str2,str_a,str_b,xx,nom_type,subdir]=name2display(name); + browse=get(handles.browse_root,'UserData'); + browse.nom_type_ima_1=nom_type; + set(handles.browse_root,'UserData',browse) + + %check image extension + if ~strcmp(ext,get(handles.ext_ima,'String')) + msgbox_uvmat('ERROR','The two input image series must have the same extenion name') + return + end + + %check image size + A=imread(fileinput); + npxy=get(handles.ext_ima,'UserData'); + if ~isequal(npxy(1),size(A,1))|| ~isequal(npxy(2),size(A,2)) + msgbox_uvmat('ERROR','The two input image series must have the same size') + return + end +else + set(handles.mode,'Visible','on') + set(handles.displ_filebase2,'Visible','Off'); + set(handles.sub_txt,'Visible','off') + set(handles.displ_filebase2,'String',[]); + mode_store=get(handles.compare,'UserData'); + set(handles.mode,'String',mode_store) + set(handles.test_stereo1,'Value',0) + set(handles.test_stereo2,'Value',0) +end +mode_Callback(hObject, eventdata, handles) + +%----------------------------------------------------------- +% --- Executes on button press in get_ref_fix1. +function get_ref_fix1_Callback(hObject, eventdata, handles) +filebase=get(handles.displ_filebase,'String'); +[FileName, PathName, filterindex] = uigetfile( ... + {'*.nc', ' (*.nc)'; + '*.nc', 'netcdf files '; ... + '*.*', 'All Files (*.*)'}, ... + 'Pick a file',filebase); + +fileinput=[PathName FileName]; +sizf=size(fileinput); +if (~ischar(fileinput)|~isequal(sizf(1),1)),return;end %stop if fileinput not a character string +%[filebasesub,field_count,str2,str_a,str_b,ref.ext,ref.nom_type,ref.subdir]=name2display(fileinput); +[Path,File,field_count,str2,str_a,str_b,ref.ext,ref.nom_type,ref.subdir]=name2display(fileinput); +%filebase=fullfile(RootPath,RootFile); +% [Pth,FileN]=fileparts(filebasesub); +% Pth=fileparts(Pth); +ref.filebase=fullfile(Path,File); +ref.num_a=stra2num(str_a); +ref.num_b=stra2num(str_b); +ref.num1=str2num(field_count); +ref.num2=str2num(str2); +browse=[];%initialisation +if ~isequal(ref.ext,'.nc') + msgbox_uvmat('ERROR','the reference file must be in netcdf format (*.nc)') + return +end +% [path,name]=fileparts(ref.filebase); +set(handles.ref_fix1,'String',[fullfile(ref.subdir,File) '....nc']); +set(handles.ref_fix1,'UserData',ref) +menu_field{1}='civ1'; +Data=nc2struct(fileinput,[]); +if isfield(Data,'patch') & isequal(Data.patch,1) + menu_field{2}='filter1'; +end +if isfield(Data,'civ2') & isequal(Data.civ2,1) + menu_field{3}='civ2'; +end +if isfield(Data,'patch2') & isequal(Data.patch2,1) + menu_field{4}='filter2'; +end +% [cte_detect,vdt,cte_read]=read_netcdf(fileinput,{'patch','civ2','patch2'}); +% if isequal(cte_detect(1),1) & isequal(cte_read(1),1) +% menu_field{2}='filter1'; +% end +% if isequal(cte_detect(2),1) & isequal(cte_read(2),1) +% menu_field{3}='civ2'; +% end +% if isequal(cte_detect(3),1) & isequal(cte_read(3),1) +% menu_field{4}='filter2'; +% end +set(handles.field_ref1,'String',menu_field); +set(handles.field_ref1,'Value',length(menu_field)); +set(handles.inf_sup1,'Value',2); +set(handles.thresh_vel,'String','1');%default threshold +set(handles.ref_fix1,'Enable','on') + +%--------------------------------------------------------------- +% --- Executes on button press in get_ref_fix2. +function get_ref_fix2_Callback(hObject, eventdata, handles) +if isequal(get(handles.get_ref_fix2,'Value'),1) + filebase=get(handles.displ_filebase,'String'); + [FileName, PathName, filterindex] = uigetfile( ... + {'*.nc', ' (*.nc)'; + '*.nc', 'netcdf files '; ... + '*.*', 'All Files (*.*)'}, ... + 'Pick a file',filebase); + fileinput=[PathName FileName]; + sizf=size(fileinput); + if (~ischar(fileinput)|~isequal(sizf(1),1)),return;end %stop if fileinput not a character string + %[filebasesub,field_count,str2,str_a,str_b,ref.ext,ref.nom_type,ref.subdir]=name2display(fileinput); + [Path,File,field_count,str2,str_a,str_b,ref.ext,ref.nom_type,ref.subdir]=name2display(fileinput); +% [Pth,FileN]=fileparts(filebasesub); +% Pth=fileparts(Pth); + ref.filebase=fullfile(Path,File); + ref.num_a=stra2num(str_a); + ref.num_b=stra2num(str_b); + ref.num1=str2num(field_count); + ref.num2=str2num(str2); + browse=[];%initialisation + if ~isequal(ref.ext,'.nc') + msgbox_uvmat('ERROR','the reference file must be in netcdf format (*.nc)') + return + end +% [path,name]=fileparts(ref.filebase); + set(handles.ref_fix2,'String',[fullfile(ref.subdir,File) '....nc']); + set(handles.ref_fix2,'UserData',ref) + menu_field{1}='civ1'; +% [cte_detect,vdt,cte_read]=read_netcdf(fileinput,{'patch','civ2','patch2'}); + Data=nc2struct(fileinput,[]); + if isfield(Data,'patch') & isequal(Data.patch,1) + menu_field{2}='filter1'; + end + if isfield(Data,'civ2') & isequal(Data.civ2,1) + menu_field{3}='civ2'; + end + if isfield(Data,'patch2') & isequal(Data.patch2,1) + menu_field{4}='filter2'; + end + +% if isequal(cte_detect(1),1) & isequal(cte_read(1),1) +% menu_field{2}='filter1'; +% end +% if isequal(cte_detect(2),1) & isequal(cte_read(2),1) +% menu_field{3}='civ2'; +% end +% if isequal(cte_detect(3),1) & isequal(cte_read(3),1) +% menu_field{4}='filter2'; +% end + set(handles.field_ref2,'String',menu_field); + set(handles.field_ref2,'Value',length(menu_field)); + set(handles.inf_sup2,'Value',2); + set(handles.thresh_vel2,'String','1');%default threshold + set(handles.ref_fix2,'Enable','on') + set(handles.ref_fix2,'Visible','on') + set(handles.field_ref2,'Visible','on') +else + set(handles.ref_fix2,'Visible','off') + set(handles.field_ref2,'Visible','off') +end +%------------------------------------------------------- + +function ref_fix1_Callback(hObject, eventdata, handles) + set(handles.inf_sup1,'Value',1); + set(handles.field_ref1,'Value',1) + set(handles.field_ref1,'String',{' '}) + set(handles.ref_fix1,'UserData',[]); + set(handles.ref_fix1,'String',''); + set(handles.thresh_vel1,'String','0'); + + +%------------------------------------------------------ + +function ref_fix2_Callback(hObject, eventdata, handles) + set(handles.inf_sup2,'Value',1); + set(handles.field_ref2,'Value',1) + set(handles.field_ref2,'String',{' '}) + set(handles.ref_fix2,'UserData',[]); + set(handles.ref_fix2,'String',''); + set(handles.thresh_vel2,'String','0'); + +%-------------------------------------------------------- +% --- Executes on selection change in inf_sup1. +function inf_sup1_Callback(hObject, eventdata, handles) + +%-------------------------------------------------------------------------- + + +% --- Executes on selection change in field_ref. +function field_ref_Callback(hObject, eventdata, handles) + +%------------------------------------------------------------------------- + +% --- Executes on selection change in field_ref2. +function field_ref2_Callback(hObject, eventdata, handles) + +% ----------------------------------------------------------- +% transform letters to numbers +%-------------------------------------------- +function numres=stra2num(str) +numres=double(str)-96; +if double(str) >= 48 & double(str) <= 57 % = 1 for numbers + numres=str2num(str); +end + + +% --- Executes on button press in test_stereo1. +function test_stereo1_Callback(hObject, eventdata, handles) +if isequal(get(handles.test_stereo1,'Value'),0) + set(handles.subdomain_patch1,'Visible','on') + set(handles.rho_patch1,'Visible','on') +else + set(handles.subdomain_patch1,'Visible','off') + set(handles.rho_patch1,'Visible','off') +end + +% --- Executes on button press in test_stereo2. +function test_stereo2_Callback(hObject, eventdata, handles) +if isequal(get(handles.test_stereo2,'Value'),0) + set(handles.subdomain_patch2,'Visible','on') + set(handles.rho_patch2,'Visible','on') +else + set(handles.subdomain_patch2,'Visible','off') + set(handles.rho_patch2,'Visible','off') +end + +% --- Executes on button press in ImaThreshold. +function ImaThreshold_Callback(hObject, eventdata, handles) +if isequal(get(handles.ImaThreshold,'Value'),1) + set(handles.MinIma,'Visible','on') + set(handles.MaxIma,'Visible','on') +else + set(handles.MinIma,'Visible','off') + set(handles.MaxIma,'Visible','off') +end + + +% --- Executes on button press in ImaThreshold2. +function ImaThreshold2_Callback(hObject, eventdata, handles) +if isequal(get(handles.ImaThreshold2,'Value'),1) + set(handles.MinIma2,'Visible','on') + set(handles.MaxIma2,'Visible','on') +else + set(handles.MinIma2,'Visible','off') + set(handles.MaxIma2,'Visible','off') +end + + +% --- Executes on button press in Experimental. +function Experimental_Callback(hObject, eventdata, handles) + + + +function ext_ima_1_Callback(hObject, eventdata, handles) +% hObject handle to ext_ima_1 (see GCBO) +% eventdata reserved - to be defined in a future version of MATLAB +% handles structure with handles and user data (see GUIDATA) + +% Hints: get(hObject,'String') returns contents of ext_ima_1 as text +% str2double(get(hObject,'String')) returns contents of ext_ima_1 as a double + + +% --- Executes during object creation, after setting all properties. +function ext_ima_1_CreateFcn(hObject, eventdata, handles) +% hObject handle to ext_ima_1 (see GCBO) +% eventdata reserved - to be defined in a future version of MATLAB +% handles empty - handles not created until after all CreateFcns called + +% Hint: edit controls usually have a white background on Windows. +% See ISPC and COMPUTER. +if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor')) + set(hObject,'BackgroundColor','white'); +end + + + +function ext_ima_Callback(hObject, eventdata, handles) +% hObject handle to ext_ima (see GCBO) +% eventdata reserved - to be defined in a future version of MATLAB +% handles structure with handles and user data (see GUIDATA) + +% Hints: get(hObject,'String') returns contents of ext_ima as text +% str2double(get(hObject,'String')) returns contents of ext_ima as a double + + +% --- Executes during object creation, after setting all properties. +function ext_ima_CreateFcn(hObject, eventdata, handles) +% hObject handle to ext_ima (see GCBO) +% eventdata reserved - to be defined in a future version of MATLAB +% handles empty - handles not created until after all CreateFcns called + +% Hint: edit controls usually have a white background on Windows. +% See ISPC and COMPUTER. +if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor')) + set(hObject,'BackgroundColor','white'); +end + + Index: /trunk/src/civ_3D.m =================================================================== --- /trunk/src/civ_3D.m (revision 2) +++ /trunk/src/civ_3D.m (revision 2) @@ -0,0 +1,3340 @@ +%'civ_3D': function associated with the interface 'civ_3D.fig' for PIV in volume +%------------------------------------------------------------------------ +% provides an interface for the software CIVx +% function varargout = civ_3D(varargin) +% provides an interface for the software CIVx +% +%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +% Copyright Joel Sommeria, 2008, LEGI / CNRS-UJF-INPG, sommeria@coriolis-legi.org. +%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +% This file is part of the toolbox UVMAT. +% +% UVMAT is free software; you can redistribute it and/or modify +% it under the terms of the GNU General Public License as published by +% the Free Software Foundation; either version 2 of the License, or +% (at your option) any later version. +% +% UVMAT is distributed in the hope that it will be useful, +% but WITHOUT ANY WARRANTY; without even the implied warranty of +% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +% GNU General Public License (file UVMAT/COPYING.txt) for more details. +%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +function varargout = civ_3D(varargin) + +% Last Modified by GUIDE v2.5 25-Feb-2009 23:14:16 +% Begin initialization code - DO NOT EDIT +gui_Singleton = 1; +gui_State = struct('gui_Name', mfilename, ... + 'gui_Singleton', gui_Singleton, ... + 'gui_OpeningFcn', @civ_3D_OpeningFcn, ... + 'gui_OutputFcn', @civ_3D_OutputFcn, ... + 'gui_LayoutFcn', [] , ... + 'gui_Callback', []); +if nargin & isstr(varargin{1}) + gui_State.gui_Callback = str2func(varargin{1}); +end + +if nargout + [varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:}); +else + gui_mainfcn(gui_State, varargin{:}); +end +% End initialization code - DO NOT EDIT + +%-------------------------------------------------------------------------- +% --- Executes just before civ_3D is made visible. +%-------------------------------------------------------------------------- +function civ_3D_OpeningFcn(hObject, eventdata, handles, varargin) +% This function has no output args, see OutputFcn. +% hObject handle to figure +% eventdata reserved - to be defined in a future version of MATLAB +% handles structure with handles and user data (see GUIDATA) +% varargin command line arguments to civ_3D (see VARARGIN) +global test_batch patch_new_exe%=1 if patch processing available +%filebase: root name +%nom_type: nomencalture used ('png_old','_i_j'...) +%list of field numbers to process +%subdir: subdirectory of the opened netcdf file +%ind_opening: operation number advised for beginning (1=civ1,2=fix1,3=patch1,4=civ2,5=fix2,6=patch2), +%ind_a_opening ind_b_opening chosen pair from the opened netcdf file +% Choose default command line output for civ_3D +handles.output = hObject; +% Update handles structure +guidata(hObject, handles); + +%default initial parameters +filebase=''; % root file name ('filebase'.civ_3D) +nom_type=[]; % nomenclature type +ext=[]; +testall=0; +browse=[]; + +%load the initial parameters if the interface is started from uvmat +if ~isempty(varargin)% the interface is opened from uvmat + varcell=varargin{1}; + filebase=varcell{1}; + nom_type_read=varcell{2}; + num1=varcell{3}; + num2=varcell{4}; + num_a=varcell{5}; + num_b=varcell{6}; + subdir=varcell{7}; + ind_opening=varcell{8}; + ind_a_opening=varcell{9}; + ind_b_opening=varcell{10}; + ext=varcell{11}; +else + num1=1; % set of field i numbers + num2=2; % set of field i numbers + num_a=1; % set of field j numbers (fields a) + num_b=1; % second set of field j numbers (fields b) + subdir='A'; % subdir for the netcdf result files + ind_opening=1; % proposed operation number (1=civ1,2=fix1,3=patch1,4=civ2,5=fix2,6=patch2) + ind_a_opening=1; % proposed index in the menu of fields a + ind_b_opening=2; % proposed index in the menu of fields b +end + +if exist('ext','var') & length(ext)>1 & (~isempty(imformats(ext([2:end])))|... + isequal(ext,'.avi')|isequal(ext,'.AVI'));%if an image file has been opened by uvmat + browse.ext_ima=ext; + if exist('nom_type_read','var') + browse.nom_type_ima=nom_type_read; % the image nomenclature is stored + end +elseif isequal(ext,'.nc') + if exist('nom_type_read','var') + browse.nom_type_nc=nom_type_read;% the netcdf nomenclature is stored + end +end +set(handles.displ_filebase,'String',filebase); +set(handles.ImaDoc,'UserData',testall); +set(handles.browse_root,'UserData',browse) +set(handles.ImaDoc,'String',ext) + + +% set(handles.ImaDoc,'String',ext) + +%read names of the .exe file to adjust the interface according to +%available prog +%read names of the .exe file +path_uvmat=which('uvmat');% check the path detected for source file uvmat +path_UVMAT=fileparts(path_uvmat); %path to UVMAT +if isunix + syst='LINUX' + %fid = fopen(fullfile(path_UVMAT,'PARAM_LINUX.txt'),'r');%open the file with civ_3D binary names + xmlfile=fullfile(path_UVMAT,'PARAM_LINUX.xml') + if exist(xmlfile,'file') + t=xmltree(xmlfile); + sparam=convert(t); + end +else + syst='WIN' + %fid = fopen(fullfile(path_UVMAT,'PARAM_WIN.txt'),'r');%open the file with civ_3D binary names + xmlfile=fullfile(path_UVMAT,'PARAM_WIN.xml'); + if exist(xmlfile,'file') + t=xmltree(xmlfile); + sparam=convert(t); + end +end + +patch_new_exe=''; +todo_patch=''; +sge=0; + +if isfield(sparam,'PatchNew_exe') + patch_new_exe=sparam.PatchNew_exe; +end +if isfield(sparam,'Todo_path') + todo_path=sparam.Todo_path +end +if isfield(sparam,'SGE') + sge=str2num(sparam.SGE); +end +name_todo=fullfile(todo_path,'TODO.txt') +test_batch=1; +if ~sge +if isequal(todo_path,'') |isequal(todo_path,[]) + ['no batch distributed processing available:file path TODO.txt not defined in UVMAT/PARAM_' syst] + test_batch=0; +end +if exist(name_todo,'file')~=2 + hwarn=warndlg(['no batch distributed processing available, queue file ' name_todo ' absent']); + % test_batch=0; % Problems to detect file on linux/nfs filesystems +end +end + + +if test_batch==0 + set(handles.BATCH,'BackgroundColor',[0.831 0.816 0.784])% put the BATCH button in grey (unactivated) +end + +set(handles.subdir_civ1,'String',subdir)%default subdir on which uvmat was working +set(handles.subdir_civ2,'String',subdir)%default subdir on which uvmat was working + +%initiate advised operations +if isequal(ind_opening,[]) + ind_opening=1; % default +end +% set default operation options + enable_civ1(handles,'off') + enable_civ2(handles,'off') + desable_fix1(handles) + desable_patch1(handles) + desable_fix2(handles) + desable_patch2(handles) + set(handles.CIV1,'Value',0) + set(handles.FIX1,'Value',0) + set(handles.PATCH1,'Value',0) + set(handles.CIV2,'Value',0) + set(handles.FIX2,'Value',0) + set(handles.PATCH2,'Value',0) + set(handles.frame_subdirciv2,'BackgroundColor',[0.831 0.816 0.784]) +if isequal(ind_opening,1) + set(handles.CIV1,'Value',1) + enable_civ1(handles,'on') +elseif isequal(ind_opening,2) + set(handles.FIX1,'Value',1) + enable_fix1(handles) +elseif isequal(ind_opening,3) + set(handles.PATCH1,'Value',1) + enable_patch1(handles) +elseif isequal(ind_opening,4) + set(handles.CIV2,'Value',1) + enable_civ2(handles,1) +elseif isequal(ind_opening,5) + set(handles.FIX2,'Value',1) + enable_fix2(handles) + set(handles.frame_subdirciv2,'BackgroundColor',[1 1 0]) + set(handles.list_pair_civ2,'Enable','On') + set(handles.list_pair_civ2,'Enable','On') +elseif isequal(ind_opening,6) + set(handles.PATCH2,'Value',1) + enable_patch2(handles) + set(handles.frame_subdirciv2,'BackgroundColor',[1 1 0]) + set(handles.list_pair_civ2,'Enable','On') +end + +% set the range of fields (1:1 by default) and selected pair +if isempty(num2)|isequal(num2,num1) + num_ref_i=num1; +else + num_ref_i=floor((num1+num2)/2); + browse.incr_pair(1)=num2-num1; + browse.incr_pair(2)=0; +end +if isempty(num_b)|isequal(num_a,num_b) + if isempty(num_a) + num_ref_j=1; + else + num_ref_j=num_a; + end +else + num_ref_j=floor((num_a+num_b)/2); + browse.incr_pair(2)=num_b-num_a; +end +set(handles.first_i,'String',num2str(num_ref_i)); +set(handles.last_i,'String',num2str(num_ref_i)); +set(handles.first_j,'String',num2str(num_ref_j)); +set(handles.last_j,'String',num2str(num_ref_j)); +set(handles.ref_i,'String',num2str(num_ref_i)); +set(handles.ref_j,'String',num2str(num_ref_j)); +set(handles.browse_root,'UserData',browse); +if ~isempty(varargin)% the interface is opened from uvmat + displ_filebase_Callback(hObject, eventdata, handles); +end + +set(handles.waitbar_1,'Position',[0.946 0.877 0.03 0.001]) +set(handles.waitbar_patch1,'Position',[0.946 0.626 0.03 0.001]) +set(handles.waitbar_civ2,'Position',[0.946 0.406 0.03 0.001]) +set(handles.waitbar_patch2,'Position',[0.946 0.187 0.03 0.001]) + + +%-------------------------------------------------------------- +% --- Outputs from this function are returned to the command line. +%----------------------------------------------------------------- +function varargout = civ_3D_OutputFcn(hObject, eventdata, handles) +% varargout cell array for returning output args (see VARARGOUT); +% hObject handle to figure +% eventdata reserved - to be defined in a future version of MATLAB +% handles structure with handles and user data (see GUIDATA) +% Get default command line output from handles structure +varargout{1} = handles.output; + +%------------------------------------------------------------------ +% --- Executes on button press in browse_root. +function browse_root_Callback(hObject, eventdata, handles) +%get the input file properties +filebase=get(handles.displ_filebase,'String'); +oldfile=''; %default +if isempty(filebase)|isequal(filebase,'')%loads the previously stored file name and set it as default in the file_input box + dir_perso=prefdir; + profil_perso=fullfile(dir_perso,'uvmat_perso.mat') + if exist(profil_perso,'file') + h=load (profil_perso); + if isfield(h,'filebase')&ischar(h.filebase) + oldfile=h.filebase; + end + if isfield(h,'RootPath')&ischar(h.RootPath) +% oldfile=h.filebase{1} + oldfile=h.RootPath; + end + end + else + oldfile=filebase; + end +testall=get(handles.ImaDoc,'UserData'); +ind_opening=1;%default +browse.incr_pair=[0 0]; %default + +menu={'*.*', 'All Files (*.*)'; '*.xml;*.vol; *.avi;*.AVI','(*.xml,*.civ,*.avi,*.vol)'; ... + '*.xml', '.xml files';'*.civ', '.civ files';... + '*.avi;*.AVI', '.avi files';'*.vol', '.vol files'}; + +[FileName, PathName, filtindex] = uigetfile( menu, 'Pick a file',oldfile); +fileinput=[PathName FileName];%complete file name +sizf=size(fileinput); +if (~ischar(fileinput)|~isequal(sizf(1),1)),return;end %stop if fileinput not a character string +[path,name,ext]=fileparts(fileinput); +testeditxml=0; +if isequal(ext,'.xml') + testeditxml=1; + t_browse=xmltree(fileinput); + head_element=get(t_browse,1); + if isfield(head_element,'name')& isequal(head_element.name,'ImaDoc') + testeditxml=0; + end +end +if testeditxml==1 | isequal(ext,'.xls') + heditxml=editxml({fileinput}); + set(heditxml,'Tag','browser') + waitfor(heditxml,'Tag','idle') + if ~ishandle(heditxml) + return + end + attr=findobj(get(heditxml,'children'),'Tag','CurrentAttributes'); + set(handles.browse,'UserData',fileinput)% store for future opening with browser + fileinput=get(attr,'UserData'); + if ~exist(fileinput,'file') + return + end +end +[RootPath,RootFile,field_count,str2,str_a,str_b,ext,nom_type,subdir]=name2display(fileinput); +filebase=fullfile(RootPath,RootFile); +if isequal(get(handles.compare,'Value'),1) + browse=get(handles.browse_root,'UserData'); +else + browse=[];%initialisation +end +if length(ext)>1 & (~isempty(imformats(ext([2:end])))||... + isequal(lower(ext),'.avi')||isequal(ext,'.vol'));%if an image file has been opened by uvmat + browse.ext_ima=ext; + browse.nom_type_ima=nom_type; + browse.field_count=str2num(field_count); +end +set(handles.ImaDoc,'String',ext); +%%%%% read the state of the selected netcdf file to advise default operation +if isequal(ext,'.nc') + browse.nom_type_nc=nom_type; + ind_opening=2;% propose 'fix' as the default option + Data=nc2struct(fileinput,[]); + if isfield(Data,'fix') & isequal(Data.fix,1) + ind_opening=3; + end + if isfield(Data,'patch') & isequal(Data.patch,1) + ind_opening=4; + end + if isfield(Data,'civ2') & isequal(Data.civ2,1) + ind_opening=5; + end + if isfield(Data,'fix2') & isequal(Data.fix2,1) + ind_opening=6; + end + if isfield(Data,'pixcmx') & isequal(Data,'pixcmy') + browse.pxcmx=Data.pixcmx; + browse.pxcmy=Data.pixcmy; + end + testciv=1; %TO SUPPRESS WITH NEW VERSION OF CIVX + subdir='';%default + if testciv + [Pathbase,Namebase]=fileparts(filebase) + [Pathprev,subdir,extdir]=fileparts(Pathbase) + subdir=[subdir extdir] +% if isequal (subdir,subdir_obs) + filebase=fullfile(Pathprev,Namebase)% move upward to get the base name (corresponding to the .civ_3D file and images) +% end + end + set(handles.subdir_civ1,'String',subdir);%set the default subdir directories for installing the .nc results + set(handles.subdir_civ2,'String',subdir); + browse.testciv=testciv; + browse.ind_opening=ind_opening; +end +set(handles.displ_filebase,'String',filebase); +set(handles.ImaDoc,'String',ext); +if ~isempty(str2num(field_count)) + ref_i=str2num(field_count); + if ~isempty(str2num(str2)) + ref_i=floor((ref_i+str2num(str2))/2);% reference image number corresponding to the file + browse.incr_pair(1)=str2num(str2)-str2num(field_count); + browse.incr_pair(2)=0; + end + set(handles.first_i,'String',num2str(ref_i)); + set(handles.last_i,'String',num2str(ref_i)); + set(handles.ref_i,'String',num2str(ref_i)); +end +if isempty(str2num(str_a)) + set(handles.ref_j,'String','1'); +else + ref_j=str2num(str_a); + if ~isempty(str2num(str_b)) + ref_j=floor((str2num(str_a)+str2num(str_b))/2); + browse.incr_pair(2)=str2num(str_b)-str2num(str_a); + end + set(handles.first_j,'String',num2str(ref_j)); + set(handles.last_j,'String',num2str(ref_j)); + set(handles.ref_j,'String',num2str(ref_j)); +end; +if isequal(ind_opening,1) + set(handles.CIV1,'Value',1) + enable_civ1(handles,'on') +elseif isequal(ind_opening,2) + set(handles.FIX1,'Value',1) + enable_fix1(handles) +elseif isequal(ind_opening,3) + set(handles.PATCH1,'Value',1) + enable_patch1(handles) +elseif isequal(ind_opening,4) + set(handles.CIV2,'Value',1) + enable_civ2(handles,1) +elseif isequal(ind_opening,5) + set(handles.FIX2,'Value',1) + enable_fix2(handles) + set(handles.frame_subdirciv2,'BackgroundColor',[1 1 0]) + set(handles.list_pair_civ2,'Enable','On') + set(handles.list_pair_civ2,'Enable','On') +elseif isequal(ind_opening,6) + set(handles.PATCH2,'Value',1) + enable_patch2(handles) + set(handles.frame_subdirciv2,'BackgroundColor',[1 1 0]) + set(handles.list_pair_civ2,'Enable','On') +end +set(handles.browse_root,'UserData',browse);% store information from browser +testall=isequal(menu(filtindex,1),{'*.*'}); +set(handles.ImaDoc,'UserData',testall); + +displ_filebase_Callback(hObject, eventdata, handles); + +%------------------------------------------------ + +function ImaDoc_Callback(hObject, eventdata, handles) +displ_filebase_Callback(hObject, eventdata, handles) + +%-------------------------------------------------------------- +%function activated when a new filebase (image series) is introduced +%------------------------------------------------------------ +function displ_filebase_Callback(hObject, eventdata, handles) + +global test_batch +set(gcf,'Pointer','watch') +ext_ima=[]; %default +nom_type_ima=[];%default +field_count=1;%default +nom_type_nc=[]; +npx=[];%default +npy=[]; +TimeUnit='s'; %default +CoordUnit='cm';%default +pxcmx_search=[];%default +pxcmy_search=[];%default +filebase=get(handles.displ_filebase,'String'); + +ext=get(handles.ImaDoc,'String'); +browse=get(handles.browse_root,'UserData');%default +if ~isempty(browse) + if isfield(browse,'ext_ima') + ext_ima=browse.ext_ima; + end + if isfield(browse,'nom_type_ima') + nom_type_ima=browse.nom_type_ima; + end + if isfield(browse,'field_count') + field_count=browse.field_count; + end +end + +%default first_i and j and increments +first_i=str2num(get(handles.first_i,'String'));%value possibly set by uvmat_Opening +if isempty(first_i)| first_i < 1 + first_i=1; %default first_i +end +last_i=str2num(get(handles.last_i,'String')); +if isempty(last_i)| last_i < first_i + last_i=first_i; %default last_i +end +first_j=str2num(get(handles.first_j,'String')); +if isempty(first_j)| first_j < 1 + first_j=1; %default first_j +end +last_j=str2num(get(handles.last_j,'String')); +if isempty(last_j)| last_j < first_j + last_j=first_j; %default last_j +end +incr_i=str2num(get(handles.incr_i,'String')); +if isempty(incr_i) | incr_i < 1; + set(handles.incr_i,'String','1') %default incr_i +end +incr_j=str2num(get(handles.incr_j,'String')); +if isempty(incr_j) | incr_j < 1; + set(handles.incr_j,'String','1') %default incr_j +end +dt=[];%default +testmode=0;%default +nbfield=1; %default +if isfield(browse,'pxcmx') & isfield(browse,'pxcmy') + pxcmx=num2str(browse.pxcmx); + pxcmy=num2str(browse.pxcmy); +else + pxcmx=1;%default + pxcmy=1; +end + %look for an image documentation file +if ~isequal(ext,'.xml') & ~ isequal(ext,'.avi')& ~ isequal(ext,'.AVI') + if exist([filebase '.xml'],'file') + ext='.xml'; + set(handles.ImaDoc,'String','.xml') + elseif exist([filebase '.civ_3D'],'file') + ext='.civ_3D'; + set(handles.ImaDoc,'String','.civ_3D') + elseif exist([filebase '.avi'],'file') + ext='.avi'; + set(handles.ImaDoc,'String','.avi') + elseif exist([filebase '.AVI'],'file') + ext='.AVI'; + set(handles.ImaDoc,'String','.AVI') + end +end +%%%%%%%% read image documentation file %%%%%%%%%%%%%%%%%%%%%%%%%%% + mode=''; %default + %read the image documentation file if found +if isequal(ext,'.xml') + set(handles.ref_i,'Visible','On')%use a reference index + set(handles.ref_j,'Visible','On') + set(handles.dt,'Visible','Off') + set(handles.dt_text,'String','ref. ind.') +elseif isequal(ext,'.avi') | isequal(ext,'.AVI') + set(handles.ref_j,'Visible','Off') + set(handles.dt,'Visible','Off') + set(handles.dt_text,'String','ref. ind.') +else + set(handles.ref_i,'Visible','Off') + set(handles.ref_j,'Visible','Off') + set(handles.dt,'Visible','On') + set(handles.dt_text,'String','dt(ms)=') +end + +if isequal(ext,'.xml') + [XmlData,warntext]=imadoc2struct([filebase '.xml']); + if isfield(XmlData,'Heading')&&isfield(XmlData.Heading','ImageName') + [PP,FF,fc,str2,str_a,str_b,ext_ima_read,nom_type_read]=name2display(XmlData.Heading.ImageName); + end + if isfield(XmlData,'Camera') + if isfield(XmlData.Camera,'TimeUnit') + TimeUnit=XmlData.Camera.TimeUnit; + end + if isfield(XmlData.Camera,'ImageSize') + ImageSize=XmlData.Camera.ImageSize; + if ~isempty(ImageSize)&& ~isempty(ImageSize) + xindex=findstr(ImageSize,'x'); + if length(xindex)>=2 + npx=str2num(ImageSize(1:xindex(1)-1)); + npy=str2num(ImageSize(xindex(1)+1:xindex(2)-1)); + end + end + end + end + pxcmx_search=1; + pxcmy_search=1; + if isfield(XmlData,'GeometryCalib') + tsai=XmlData.GeometryCalib; + if isfield(tsai,'f') & isfield(tsai,'Tz') & isfield(tsai,'dpx') & isfield(tsai,'dpy')& isfield(tsai,'R') + rot2D=tsai.R([1:2],[1,2]); + pxcmx_search=tsai.f * sqrt(det(rot2D))/(tsai.Tz*tsai.dpx); + pxcmy_search=tsai.f * sqrt(det(rot2D))/(tsai.Tz*tsai.dpy); + end + if isfield(tsai,'CoordUnit') + CoordUnit=tsai.CoordUnit; + end + end + if isempty(ext_ima_read) + ext_ima='.png';%default + else + ext_ima=ext_ima_read; + end + if isempty(nom_type_read) + nom_type_ima='_i_j'; + warndlg_uvmat('no ImageName defined in ImaDoc/Heading, take _i_j indexing by default','WARNING') + else + nom_type_ima=nom_type_read; + end + +elseif isequal(ext,'.avi')|isequal(ext,'.AVI') + nom_type_ima='avi'; + ext_ima=ext; + set(handles.mode,'String',{'series(Di)'}) + dt=0.04;%default + if exist([filebase ext],'file')==2 + info=aviinfo([filebase ext]);%read infos on the avi movie + dt=1/info.FramesPerSecond;%time interval between successive frames + nbfield=info.NumFrames;%number of frames + end + time=(dt*[0:nbfield-1])';%list of image times + set(handles.dt,'String',num2str(dt*1000));%store the time interval between successive images + + % no image documentation file found: look for a series of existing images or .nc files +elseif ~isequal(ext,'.nc') + subdir=get(handles.subdir_civ1,'String'); + incr_pair=[0 0];%default + if isfield(browse,'incr_pair') + incr_pair=browse.incr_pair; + end + nbdetect=0;%test of detected images + field_i=field_count; + idetect=1; +% imagename='';%default + while idetect==1 %look for the maximum file number in the series + field_i=field_i+1; +% imagename_last=imagename; + [imagename,idetect]=name_generator(filebase,field_i,1,ext_ima,nom_type_ima); + if isequal(nom_type_ima,'none') + idetect=0; %stop if the same image is repeated (if nom_type='none') + nbdetect=1; + end + %SEE CASE OF NETCDF FILES + nbdetect=nbdetect+idetect; + end +% nb_field=field_i-1;% last detected field number + nb_field=field_i;% last detected field number + field_i=field_count;%look for the minimum file number in the series + idetect=1; + while idetect==1 + field_i=field_i-1; + [imagename,idetect]=name_generator(filebase,field_i,1,ext_ima,nom_type_ima); + if isequal(nom_type_ima,'none') + idetect=0; %stop if the same image is repeted (if nom_type='none') + nbdetect=1; + end + nbdetect=nbdetect+idetect; + end + first_i=max(field_i+1,1); + %determine the set of times and possible intervals for CIV_3D + dt=(1/1000)*str2num(get(handles.dt,'String')); + time=(dt*[0:nb_field-1])'; +% set(handles.incr_i,'UserData',dt);%store the time interval +% between successive images + %displ_num:list of possible time intervals for civ_3D calculations + set(handles.mode,'String',{'series(Di)'}) +end +if isequal(nom_type_ima,'none')% no file numbering used + first_i=1; + last_i=1; + first_j=1; + last_j=1; +end +if exist('time','var') + siztime=size(time); + nbfield=siztime(1); + nbfield2=siztime(2); + set(handles.displ_filebase,'UserData',time); %store the set of times + set(handles.dt_unit,'String',['m' TimeUnit]); + set(handles.TimeUnit,'String',TimeUnit); + set(handles.nb_field,'String',num2str(nbfield)); + set(handles.nb_field2,'String',num2str(nbfield2)); +end +set(handles.CoordUnit,'String',[CoordUnit '/']) +set(handles.pxcmx,'String',num2str(pxcmx)); +set(handles.pxcmy,'String',num2str(pxcmy)); +if isempty(pxcmx_search) + set(handles.calcul_search,'UserData',[pxcmx pxcmy]); +else + set(handles.calcul_search,'UserData',[pxcmx_search pxcmy_search]); +end +set(handles.pxcmx,'UserData',npx); +set(handles.pxcmy,'UserData',npy); +set(handles.first_i,'String',num2str(first_i)); +set(handles.last_i,'String',num2str(last_i));% +set(handles.first_j,'String',num2str(first_j)); +set(handles.last_j,'String',num2str(last_j));% +browse.ext_ima=ext_ima; +browse.nom_type_ima=nom_type_ima; +set(handles.browse_root,'UserData',browse)% store the nomenclature type + + %%%%%%%%%%% set the menus of image pairs and default selection for civ_3D %%%%%%%%%%%%%%%%%%% +if isequal(get(handles.compare,'Value'),1) + if isequal(nom_type_ima,'_i')| isequal(nom_type_nc,'_i1-i2')|~exist('nbfield2','var')|(nbfield2==1) + set(handles.mode,'String',{'st_series(Di)';'displacement'}) + set(handles.mode,'Value',1) + elseif (nbfield==1)% simple series in j + set(handles.mode,'String',{'st_series(Dj)';'displacement'}) + set(handles.mode,'Value',1) + else + set(handles.mode,'String',{'st_pair j1-j2';'st_series(Dj)';'st_series(Di)';'displacement'})%multiple choice + if isequal(mode,'volume') + set(handles.mode,'Value',3) + elseif nbfield2 <= 5 + set(handles.mode,'Value',1)% advice 'pair j1-j2' for small bursts + end + end +else + if isequal(nom_type_ima,'_i')| isequal(nom_type_nc,'_i1-i2')|~exist('nbfield2','var')|(nbfield2==1) + set(handles.mode,'String',{'series(Di)'}) + set(handles.mode,'Value',1) + elseif isequal(nom_type_ima,'png_old')|isequal(nom_type_nc,'netc_old') + set(handles.mode,'String',{'pair j1-j2'}) + set(handles.mode,'Value',1) + elseif (nbfield==1)% simple series in j + set(handles.mode,'String',{'series(Dj)'}) + set(handles.mode,'Value',1) + else + set(handles.mode,'String',{'pair j1-j2';'series(Dj)';'series(Di)'})%multiple choice + if isequal(mode,'volume') + set(handles.mode,'Value',3) + elseif nbfield2 <= 5 + set(handles.mode,'Value',1)% advice 'pair j1-j2' for small bursts + else + set(handles.mode,'Value',2)% advice series Dj for long bursts, not volume + end + end +end +mode_Callback(hObject, eventdata, handles) + +%%%%%% initialize waitbars and RUN button +set(handles.waitbar_1,'Position',[0.946 0.876 0.03 0.001]) +set(handles.waitbar_patch1,'Position',[0.946 0.439 0.03 0.001]) +set(handles.waitbar_civ2,'Position',[0.946 0.219 0.03 0.001]) +set(handles.waitbar_patch2,'Position',[0.946 0.0 0.03 0.001]) +set(handles.RUN, 'Enable','On') +set(handles.RUN,'BackgroundColor',[1 0 0]) +if isequal(test_batch,1)%if batch installation is available + set(handles.BATCH, 'Enable','On') + set(handles.BATCH,'BackgroundColor',[1 0 0]) +end + +%%%%% store the root input filename for future opening +dir_perso=prefdir; +profil_perso=fullfile(prefdir,'uvmat_perso.mat'); +RootPath=fileparts(filebase); +if exist(profil_perso,'file') + save (profil_perso,'RootPath','-append'); %store the root name for future opening of uvmat +else + txt=ver; + Release=txt(1).Release; + relnumb=str2num(Release(3:4)); + if relnumb >= 14 + save (profil_perso,'RootPath','-V6'); %store the root name for future opening of uvmat + else + save (profil_perso,'RootPath'); %store the root name for future opening of uvmat + end +end +% save(profil_perso, 'filebase'); %store the root name for future opening of uvmat +set(gcf,'Pointer','arrow') + +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%???????????? +% --- Executes on button press in mode. +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% +function mode_Callback(hObject, eventdata, handles) +browse=get(handles.browse_root,'UserData'); +mode_list=get(handles.mode,'String'); +mode_value=get(handles.mode,'Value'); +mode=mode_list{mode_value}; +displ_num=[];%default +first_i=str2num(get(handles.first_i,'String')); +% last_i=str2num(get(handles.last_i,'String')); +time=get(handles.displ_filebase,'UserData'); %get the set of times +siztime=size(time); +nbfield=siztime(1); +nbfield2=siztime(2); +indchosen=1; %%first pair selected by default +if isequal(mode,'pair j1-j2')| isequal(mode,'st_pair j1-j2') + dt=1; + displ=''; + index=0; + %get all the time intervals in bursts + displ_dt=1;%default + nbfield2=min(nbfield2,10),%limitate the number of pairs to 10x10 +% if nbfield2<2 +% nbfield2=2, +% end + for numod_a=1:nbfield2-1 %nbfield2 always >=2 for 'pair j1-j2' mode + for numod_b=(numod_a+1):nbfield2 + index=index+1; + numlist_a(index)=numod_a; + numlist_b(index)=numod_b; + if ~isempty(time) + dt(numod_a,numod_b)=time(first_i,numod_b)-time(first_i,numod_a);%first time interval dt + displ_dt(index)=dt(numod_a,numod_b); + else + displ_dt(index)=1 + end + end + end + [dtsort,indsort]=sort(displ_dt); + displ_num(1,:)=numlist_a(indsort); + displ_num(2,:)=numlist_b(indsort); + displ_num(3,:)=0; + displ_num(4,:)=0; + set(handles.jtext,'Visible','Off') + set(handles.first_j,'Visible','Off') + set(handles.last_j,'Visible','Off') + set(handles.incr_j,'Visible','Off') + set(handles.nb_field2,'Visible','Off') + set(handles.ref_j,'Visible','Off') +elseif isequal(mode,'series(Dj)') | isequal(mode,'st_series(Dj)') + for index=1:min(nbfield2-1,200) + displ_num(1,index)=-floor(index/2); + displ_num(2,index)=ceil(index/2); + displ_num(3,index)=0; + displ_num(4,index)=0; + end + set(handles.jtext,'Visible','On') + set(handles.first_j,'Visible','On') + set(handles.last_j,'Visible','On') + set(handles.incr_j,'Visible','On') + set(handles.nb_field2,'Visible','On') + set(handles.ref_j,'Visible','On') + if nbfield > 1 + set(handles.itext,'Visible','On') + set(handles.first_i,'Visible','On') + set(handles.last_i,'Visible','On') + set(handles.incr_i,'Visible','On') + set(handles.nb_field,'Visible','On') + set(handles.ref_i,'Visible','On') + else + set(handles.itext,'Visible','Off') + set(handles.first_i,'Visible','Off') + set(handles.last_i,'Visible','Off') + set(handles.incr_i,'Visible','Off') + set(handles.nb_field,'Visible','Off') + set(handles.ref_i,'Visible','Off') + end +elseif isequal(mode,'series(Di)') | isequal(mode,'st_series(Di)') + for index=1:min(nbfield-1,200) + displ_num(1,index)=0; + displ_num(2,index)=0; + displ_num(3,index)=-floor(index/2); + displ_num(4,index)=ceil(index/2); + end + set(handles.itext,'Visible','On') + set(handles.first_i,'Visible','On') + set(handles.last_i,'Visible','On') + set(handles.incr_i,'Visible','On') + set(handles.nb_field,'Visible','On') + set(handles.ref_i,'Visible','On') + if nbfield2 > 1 + set(handles.jtext,'Visible','On') + set(handles.first_j,'Visible','On') + set(handles.last_j,'Visible','On') + set(handles.incr_j,'Visible','On') + set(handles.nb_field2,'Visible','On') + set(handles.ref_j,'Visible','On') + else + set(handles.jtext,'Visible','Off') + set(handles.first_j,'Visible','Off') + set(handles.last_j,'Visible','Off') + set(handles.incr_j,'Visible','Off') + set(handles.nb_field2,'Visible','Off') + set(handles.ref_j,'Visible','Off') + end +elseif isequal(mode,'displacement')%the pairs have the same indices + displ_num(1,1)=0; + displ_num(2,1)=0; + displ_num(3,1)=0; + displ_num(4,1)=0; + if nbfield > 1 + set(handles.itext,'Visible','On') + set(handles.first_i,'Visible','On') + set(handles.last_i,'Visible','On') + set(handles.incr_i,'Visible','On') + set(handles.nb_field,'Visible','On') + set(handles.ref_i,'Visible','On') + else + set(handles.itext,'Visible','Off') + set(handles.first_i,'Visible','Off') + set(handles.last_i,'Visible','Off') + set(handles.incr_i,'Visible','Off') + set(handles.nb_field,'Visible','Off') + set(handles.ref_i,'Visible','Off') + end + if nbfield2 > 1 + set(handles.jtext,'Visible','On') + set(handles.first_j,'Visible','On') + set(handles.last_j,'Visible','On') + set(handles.incr_j,'Visible','On') + set(handles.nb_field2,'Visible','On') + set(handles.ref_j,'Visible','On') + else + set(handles.jtext,'Visible','Off') + set(handles.first_j,'Visible','Off') + set(handles.last_j,'Visible','Off') + set(handles.incr_j,'Visible','Off') + set(handles.nb_field2,'Visible','Off') + set(handles.ref_j,'Visible','Off') + end +end +set(handles.list_pair_civ1,'UserData',displ_num); +find_netcpair_civ1(hObject, eventdata, handles) +find_netcpair_civ2(hObject, eventdata, handles) + +%-------------------------------------------------------------- +% determine the menu for civ1 pairs depending on existing netcdf file at the middle of +% the field series set by first_i, incr, last_i +%---------------------------------------------------------------- +function find_netcpair_civ1(hObject, eventdata, handles) +set(gcf,'Pointer','watch') +%nomenclature types +filebase=get(handles.displ_filebase,'String'); +[filepath,Nme,ext_dir]=fileparts(filebase); +browse=get(handles.browse_root,'UserData'); +mode_list=get(handles.mode,'String'); +mode_value=get(handles.mode,'Value'); +mode=mode_list{mode_value}; +% nomenclature type of the .nc files +nom_type_ima=[];%default +if isfield(browse,'nom_type_ima') + nom_type_ima=browse.nom_type_ima; +end + +%determine nom_type_nc: +nom_type_nc=[];%default +if isfield(browse,'nom_type_nc') + nom_type_nc=browse.nom_type_nc; +end +if isequal(nom_type_ima,'png_old') | isequal(nom_type_nc,'netc_old')| isequal(nom_type_ima,'raw_SMD') + nom_type_nc='netc_old';%nom_type for the netcdf files +elseif isequal(nom_type_ima,'none')|isequal(nom_type_nc,'none') + nom_type_nc='none'; +elseif isequal(nom_type_ima,'avi')|isequal(nom_type_ima,'_i')|isequal(nom_type_ima,'ima_num')|... + isequal(nom_type_nc,'_i1-i2') + nom_type_nc='_i1-i2'; +elseif isequal(nom_type_ima,'_i_j1-j2')||isequal(nom_type_nc,'_i1-i2_j1-j2') + nom_type_nc='_i1-i2_j1-j2'; +else + if isequal(mode,'series(Di)')|isequal(mode,'st_series(Di)') + nom_type_nc='_i1-i2_j'; % PIV in volume + else + nom_type_nc='_i_j1-j2'; + end +end +browse.nom_type_nc=nom_type_nc; +set(handles.browse_root,'UserData',browse) + +%reads .nc subdirectoy and image numbers from the interface +subdir_civ1=get(handles.subdir_civ1,'String');%subdirectory subdir_civ1 for the netcdf data +first_i=str2num(get(handles.first_i,'String')); +last_i=str2num(get(handles.last_i,'String')); +incr=str2num(get(handles.incr_i,'String')); +num1=first_i:incr:last_i; +if isempty(num1) + set(handles.list_pair_civ1,'String',{''}); + return +end +ref_i=str2num(get(handles.ref_i,'String')); +if isequal(mode,'pair j1-j2')|isequal(mode,'st_pair j1-j2') + ref_j=0; +else + ref_j=str2num(get(handles.ref_j,'String')); +end +if isequal(get(handles.dt_text,'String'),'dt(ms)=')%simple series(Di) with equal interval + ref_i=floor((first_i+last_i)/2); + ref_j=1; +end +time=get(handles.displ_filebase,'UserData');%get the set of times +if isempty(time) + time=[0 1]; +end +dt_unit=str2num(get(handles.dt,'String'));% used when there is no image documentation file +displ_num=get(handles.list_pair_civ1,'UserData'); + +%eliminate the first pairs inconsistent with the position +if isempty(displ_num) + nbpair=0; +else + nbpair=length(displ_num(1,:));%nbre of displayed pairs + if isequal(mode,'series(Di)') | isequal(mode,'st_series(Di)') + nbpair=min(2*ref_i-1,nbpair);%limit the number of pairs with positive first index + elseif isequal(mode,'series(Dj)') | isequal(mode,'st_series(Dj)') + nbpair=min(2*ref_j-1,nbpair);%limit the number of pairs with positive first index + end +end +nbpair=min(200,nbpair);%limit the number of displayed pairs to 200 + +%look for existing processed pairs involving the field at the middle of the series if civ1 will not +% be performed, while the result is needed for next steps. +displ_pair={''}; +select=ones(size(1:nbpair));%default =1 for numbers of displayed pairs +testpair=0; +if get(handles.CIV1,'Value')==0 % + dirname=fullfile(filepath,subdir_civ1,ext_dir); + if ~exist(fullfile(filepath,subdir_civ1,ext_dir),'dir') + hwarn=warndlg_uvmat(['no civ1 file available: subdirectory ' subdir_civ1 ' does not exist'],'ERROR'); + set(handles.list_pair_civ1,'String',{}); + return + end + for ipair=1:nbpair + [filename,select(ipair)]=name_generator(filebase,ref_i+displ_num(3,ipair),ref_j+displ_num(1,ipair),'.nc',nom_type_nc,1,... + ref_i+displ_num(4,ipair),ref_j+displ_num(2,ipair),subdir_civ1); + end + if ~exist('select','var') | isequal(select,zeros(size(1:nbpair))) + if isfield(browse,'incr_pair') + num_i1=ref_i-floor(browse.incr_pair(1)/2); + num_i2=ref_i+ceil(browse.incr_pair(1)/2); + num_j1=ref_j-floor(browse.incr_pair(2)/2); + num_j2=ref_j+ceil(browse.incr_pair(2)/2); + [filename,select(1)]=name_generator(filebase,num_i1,num_j1,'.nc',nom_type_nc,1,num_i2,num_j2,subdir_civ1); + testpair=1; + else + if isequal(mode,'series(Dj)') | isequal(mode,'st_series(Dj)') + hwarn=warndlg_uvmat(['no civ1 file available for the selected reference index j=' num2str(ref_j) ' and subdirectory ' subdir_civ1],'ERROR'); + set(hwarn,'WindowStyle','modal'); + else + hwarn=warndlg_uvmat(['no civ1 file available for the selected reference index i=' num2str(ref_i) ' and subdirectory ' subdir_civ1],'ERROR'); + set(hwarn,'WindowStyle','modal'); + end + set(handles.list_pair_civ1,'String',{''}); + %COMPLETER CAS STEREO + return + end + end +end +if isequal(mode,'series(Di)') | isequal(mode,'st_series(Di)') + if testpair + displ_pair{1}=['Di= ' num2str(-floor(browse.incr_pair(1)/2)) '|' num2str(ceil(browse.incr_pair(1)/2))]; + elseif ~isequal(get(handles.dt_text,'String'),'dt(ms)=') + for ipair=1:nbpair + if select(ipair) + dt=time(ref_i+displ_num(4,ipair),ref_j+displ_num(2,ipair))-time(ref_i+displ_num(3,ipair),ref_j+displ_num(1,ipair));%time interval dt + displ_pair{ipair}=['Di= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2)) ' :dt= ' num2str(dt*1000)]; + else + displ_pair{ipair}='...'; %pair not displayed in the menu + end + end + else + for ipair=1:nbpair + if select(ipair) + displ_pair{ipair}=['Di= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2)) ' :dt= ' num2str(dt_unit*ipair)]; + else + displ_pair{ipair}='...'; %pair not displayed in the menu + end + end + end +elseif isequal(mode,'series(Dj)')|isequal(mode,'st_series(Dj)')% series on the j index + if testpair + displ_pair{1}=['Dj= ' num2str(-floor(browse.incr_pair(1)/2)) '|' num2str(ceil(browse.incr_pair(1)/2))]; + else + for ipair=1:nbpair + if select(ipair) + dt=time(ref_i+displ_num(4,ipair),ref_j+displ_num(2,ipair))-time(ref_i+displ_num(3,ipair),ref_j+displ_num(1,ipair));%time interval dt + displ_pair{ipair}=['Dj= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2)) ' :dt= ' num2str(dt*1000)]; + elseif testpair + displ_pair{1}=['Dj= ' num2str(-floor(browse.incr_pair(2)/2)) '|' num2str(ceil(browse.incr_pair(2)/2))]; + else + displ_pair{ipair}='...'; %pair not displayed in the menu + end + end + end +elseif isequal(mode,'pair j1-j2')|isequal(mode,'st_pair j1-j2')%case of pairs + for ipair=1:nbpair + if select(ipair) + dt=time(ref_i+displ_num(4,ipair),displ_num(2,ipair))-time(ref_i+displ_num(3,ipair),displ_num(1,ipair));%time interval dt + displ_pair{ipair}=['j= ' num2stra(displ_num(1,ipair),nom_type_ima) '-' num2stra(displ_num(2,ipair),nom_type_ima) ... + ' :dt= ' num2str(dt*1000)]; + else + displ_pair{ipair}='...'; %pair not displayed in the menu + end + end +elseif isequal(mode,'displacement') + displ_pair={'Di=Dj=0'}; +end +set(handles.list_pair_civ1,'String',displ_pair'); +ichoice=min(find(select)); +if (isempty(ichoice) | ichoice < 1); ichoice=1; end; +initial=get(handles.list_pair_civ1,'Value'); +if initial>nbpair |~isequal(select(initial),1) + set(handles.list_pair_civ1,'Value',ichoice);% first valid pair proposed by default in the menu +end +set(handles.list_pair_civ2,'String',displ_pair'); +initial=get(handles.list_pair_civ2,'Value'); +if initial>nbpair |~isequal(select(initial),1) + set(handles.list_pair_civ2,'Value',ichoice);% same pair proposed by default for civ2 +end +set(gcf,'Pointer','arrow') +%-------------------------------------------------------------- +% determine the menu for civ2 pairs depending on the existing netcdf file at the +%middle of the series set by first_i, incr, last_i +%-------------------------------------------------------------- +function find_netcpair_civ2(hObject, eventdata, handles) +set(gcf,'Pointer','watch') +%nomenclature types +filebase=get(handles.displ_filebase,'String'); +[filepath,Nme,ext_dir]=fileparts(filebase); +browse=get(handles.browse_root,'UserData'); +mode_list=get(handles.mode,'String'); +mode_value=get(handles.mode,'Value'); +mode=mode_list{mode_value}; + +% nomenclature type of the .nc files +nom_type_ima='ima_num';%default +if isfield(browse,'nom_type_ima') + nom_type_ima=browse.nom_type_ima; +end +nom_type_nc='_i1-i2';%default +if isfield(browse,'nom_type_nc') + nom_type_nc=browse.nom_type_nc; +end +if isequal(nom_type_ima,'png_old') | isequal(nom_type_ima,'netc_old')| isequal(nom_type_ima,'raw_SMD')| isequal(nom_type_nc,'netc_old') + nom_type_nc='netc_old';%nom_type for the netcdf files +elseif isequal(nom_type_ima,'none')|isequal(nom_type_nc,'none') + nom_type_nc='none'; +elseif isequal(nom_type_ima,'avi')|isequal(nom_type_ima,'_i')|isequal(nom_type_ima,'ima_num')|isequal(nom_type_nc,'_i1-i2') + nom_type_nc='_i1-i2'; +else + if isequal(mode,'series(Di)')|isequal(mode,'st_series(Di)') + nom_type_nc='_i1-i2_j'; % PIV in volume + else + nom_type_nc='_i_j1-j2'; + end +end +browse.nom_type_nc=nom_type_nc; +set(handles.browse_root,'UserData',browse) + +%reads .nc subdirectory and image numbers from the interface +subdir_civ1=get(handles.subdir_civ1,'String');%subdirectory subdir_civ1 for the netcdf data +subdir_civ2=get(handles.subdir_civ2,'String');%subdirectory subdir_civ2 for the netcdf data +first_i=str2num(get(handles.first_i,'String')); +last_i=str2num(get(handles.last_i,'String')); +incr=str2num(get(handles.incr_i,'String')); +num1=first_i:incr:last_i; +if isempty(num1) + set(handles.list_pair_civ2,'String',{}); + return +end +ref_i=str2num(get(handles.ref_i,'String')); +if isequal(mode,'pair j1-j2')|isequal(mode,'st_pair j1-j2') + ref_j=0; +else + ref_j=str2num(get(handles.ref_j,'String')); +end +if isequal(get(handles.dt_text,'String'),'dt(ms)=')%simple series(Di) with equal interval + ref_i=ceil((first_i+last_i)/2); + ref_j=1; +end +% ref_i=browse.num_ref;%field number initially selected by the browser +time=get(handles.displ_filebase,'UserData'); %get the set of times +if isempty(time) + time=[0 1];%default +end +dt_unit=str2num(get(handles.dt,'String'));% used when there is no image documentation file +displ_num=get(handles.list_pair_civ1,'UserData'); + + +%eliminate the first pairs inconsistent with the position +if isempty(displ_num) + nbpair=0; +else + nbpair=length(displ_num(1,:));%nbre of displayed pairs + if isequal(mode,'series(Di)') | isequal(mode,'st_series(Di)') + nbpair=min(2*ref_i-1,nbpair);%limit the number of pairs with positive first index + elseif isequal(mode,'series(Dj)') | isequal(mode,'st_series(Dj)') + nbpair=min(2*ref_j-1,nbpair);%limit the number of pairs with positive first index + end +end +nbpair=min(200,nbpair);%limit the number of displayed pairs to 200 + +%look for existing processed pairs involving the field at the middle of the series if civ1 will not +% be performed, while the result is needed for next steps. +displ_pair={''}; %default +select=ones(size(1:nbpair));%default =1 for nubers of displayed pairs +if get(handles.CIV2,'Value')==0 & get(handles.CIV1,'Value')==0 & get(handles.FIX1,'Value')==0 & get(handles.PATCH1,'Value')==0%&... + if ~exist(fullfile(filepath,subdir_civ2,ext_dir),'dir') + errordlg(['no civ2 file available: subdirectory ' subdir_civ2 ' does not exist']) + set(handles.list_pair_civ2,'String',{}); + return + end + for ipair=1:nbpair + [filename,select(ipair)]=name_generator(filebase,ref_i+displ_num(3,ipair),ref_j+displ_num(1,ipair),'.nc',nom_type_nc,1,... + ref_i+displ_num(4,ipair),ref_j+displ_num(2,ipair),subdir_civ1); + end + if isequal(select,zeros(size(1:nbpair))) + if isfield(browse,'incr_pair') + num_i1=ref_i-floor(browse.incr_pair(1)/2); + num_i2=ref_i+floor((browse.incr_pair(1)+1)/2); + num_j1=ref_j-floor(browse.incr_pair(2)/2); + num_j2=ref_j+floor((browse.incr_pair(2)+1)/2); + [filename,select(1)]=name_generator(filebase,num_i1,num_j1,'.nc',nom_type_nc,1,num_i2,num_j2,subdir_civ2); + else + if isequal(mode,'series(Dj)') | isequal(mode,'st_series(Dj)') + errordlg(['no civ2 file available for the selected reference index j=' num2str(ref_j) ' and subdirectory ' subdir_civ2]) + else + errordlg(['no civ2 file available for the selected reference index i=' num2str(ref_i) ' and subdirectory ' subdir_civ2]) + end + set(handles.list_pair_civ2,'String',{}); + return + end + end +end +if isequal(mode,'series(Di)') | isequal(mode,'st_series(Di)') + if ~isequal(get(handles.dt_text,'String'),'dt(ms)=') + for ipair=1:nbpair + if select(ipair) + dt=time(ref_i+displ_num(4,ipair),ref_j+displ_num(2,ipair))-time(ref_i+displ_num(3,ipair),ref_j+displ_num(1,ipair));%time interval dt + displ_pair{ipair}=['Di= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2)) ' :dt= ' num2str(dt*1000)]; + else + displ_pair{ipair}='...'; %pair not displayed in the menu + end + end + else + for ipair=1:nbpair + if select(ipair) + displ_pair{ipair}=['Di= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2)) ' :dt= ' num2str(dt_unit*ipair)]; + else + displ_pair{ipair}='...'; %pair not displayed in the menu + end + end + end +elseif isequal(mode,'series(Dj)') | isequal(mode,'st_series(Dj)') % series on the j index + for ipair=1:nbpair + if select(ipair) + dt=time(ref_i+displ_num(4,ipair),ref_j+displ_num(2,ipair))-time(ref_i+displ_num(3,ipair),ref_j+displ_num(1,ipair));%time interval dt + displ_pair{ipair}=['Dj= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2)) ' :dt= ' num2str(dt*1000)]; + else + displ_pair{ipair}='...'; %pair not displayed in the menu + end + end +elseif isequal(mode,'pair j1-j2') | isequal(mode,'st_pair j1-j2') %case of pairs + for ipair=1:nbpair + if select(ipair) + dt=time(ref_i+displ_num(4,ipair),displ_num(2,ipair))-time(ref_i+displ_num(3,ipair),displ_num(1,ipair));%time interval dt + displ_pair{ipair}=['j= ' num2stra(displ_num(1,ipair),nom_type_ima) '-' num2stra(displ_num(2,ipair),nom_type_ima) ... + ' :dt= ' num2str(dt*1000)]; + else + displ_pair{ipair}='...'; %pair not displayed in the menu + end + end +elseif isequal(mode,'displacement') + displ_pair={'Di=Dj=0'}; +end +set(handles.list_pair_civ2,'String',displ_pair'); +ichoice=min(find(select)); +if (isempty(ichoice) | ichoice < 1); ichoice=1; end; +if get(handles.CIV2,'Value')==0 & get(handles.CIV1,'Value')==0 & get(handles.FIX1,'Value')==0 & get(handles.PATCH1,'Value')==0 + set(handles.list_pair_civ2,'Value',ichoice);% first valid pair proposed by default in the menu +end +set(gcf,'Pointer','arrow') +%---------------------------------------------------- +% determine the list of index pairs of processing file +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% +function [num1_civ1,num2_civ1,num_a_civ1,num_b_civ1,num1_civ2,num2_civ2,num_a_civ2,num_b_civ2]=... + find_pair_indices(handles,mode) +first_i=str2num(get(handles.first_i,'String')); +last_i=str2num(get(handles.last_i,'String')); +incr=str2num(get(handles.incr_i,'String')); +first_j=str2num(get(handles.first_j,'String')); +last_j=str2num(get(handles.last_j,'String')); +incr_j=str2num(get(handles.incr_j,'String')); +list_civ1=get(handles.list_pair_civ1,'String'); +index_civ1=get(handles.list_pair_civ1,'Value'); +str_civ1=list_civ1{index_civ1}; +list_civ2=get(handles.list_pair_civ2,'String'); +index_civ2=get(handles.list_pair_civ2,'Value'); +str_civ2=list_civ2{index_civ2}; +if isequal(first_i,[])|isequal(first_j,[]), errordlg('first field number not defined'),... + set(handles.RUN, 'Enable','On'), set(handles.RUN,'BackgroundColor',[1 0 0]),return,end; +if isequal(last_i,[])| isequal(last_j,[]),errordlg('last field number not defined'),... + set(handles.RUN, 'Enable','On'), set(handles.RUN,'BackgroundColor',[1 0 0]),return,end; +if isequal(incr,[])| isequal(incr_j,[]),errordlg('increment in field number not defined'),... + set(handles.RUN, 'Enable','On'), set(handles.RUN,'BackgroundColor',[1 0 0]),return,end; +if last_i < first_i | last_j < first_j , errordlg('last field number must be larger than the first one'),... + set(handles.RUN, 'Enable','On'), set(handles.RUN,'BackgroundColor',[1 0 0]),return,end; +num1=[first_i:incr:last_i]; +num_j=[first_j:incr_j:last_j]; +if isequal (mode,'series(Di)') |isequal(mode,'st_series(Di)') + %recognize the pair civ1 from the display + indsel=find((double(str_civ1)<48)|(double(str_civ1)>57));% character indices of non numerical characters + str_raw=str_civ1(indsel); + indsepar=find(str_raw=='|'); %character index of the separator + d1=str2num(str_civ1([indsel(indsepar-1)+1:indsel(indsepar)-1])); + if indsepar==length(str_raw) + d2=str2num(str_civ1([indsel(indsepar)+1:end])); + else + d2=str2num(str_civ1([indsel(indsepar)+1:indsel(indsepar+1)-1])); + end + %recognize the pair civ2 from the display + num1_civ1=num1-d1;% set of first image numbers + num2_civ1=num1+d2; + num_a_civ1=num_j; + num_b_civ1=num_j; + num1_civ2=num1-floor(index_civ2/2)*ones(size(num1));% set of first image numbers + num2_civ2=num1+ceil(index_civ2/2)*ones(size(num1)); + num1_civ2=num1-d1;% set of first image numbers + num2_civ2=num1+d2; + num_a_civ2=num_j; + num_b_civ2=num_j; + % adjust the first and last field number + lastfield=str2num(get(handles.nb_field,'String')); + if isequal(lastfield,[]) + indsel=find((num1_civ1 >= 1)&(num1_civ2 >= 1)); + else + indsel=find((num2_civ1 <= lastfield)&(num2_civ2 <= lastfield)&(num1_civ1 >= 1)&(num1_civ2 >= 1)); + end + if length(indsel)>=1 + firstind=indsel(1); + lastind=indsel(end); + set(handles.first_i,'String',num2str(num1(firstind)))%update the display of first and last fields + set(handles.last_i,'String',num2str(num1(lastind))) + num1=num1(indsel); + num1_civ1=num1_civ1(indsel); + num1_civ2=num1_civ2(indsel); + num2_civ1=num2_civ1(indsel); + num2_civ2=num2_civ2(indsel); + end +elseif isequal (mode,'series(Dj)')|isequal (mode,'st_series(Dj)') + lastfield_j=str2num(get(handles.nb_field2,'String')); + num1_civ1=num1;% set of first image numbers + num2_civ1=num1; + num_a_civ1=num_j-floor(index_civ1/2)*ones(size(num_j)); + num_b_civ1=num_j+ceil(index_civ1/2)*ones(size(num_j)); + num1_civ2=num1; + num2_civ2=num1; + num_a_civ2=num_j-floor(index_civ2/2)*ones(size(num_j)); + num_b_civ2=num_j+ceil(index_civ2/2)*ones(size(num_j)); + % adjust the first and last field number + if isequal(lastfield_j,[]) + indsel=find((num_a_civ1 >= 1)&(num_a_civ2 >= 1)); + else + indsel=find((num_b_civ1 <= lastfield_j)&(num_b_civ2 <= lastfield_j)&(num_a_civ1 >= 1)&(num_a_civ2 >= 1)); + end + if length(indsel)>=1 + firstind=indsel(1); + lastind=indsel(end); + set(handles.first_j,'String',num2str(num_j(firstind)))%update the display of first and last fields + set(handles.last_j,'String',num2str(num_j(lastind))) + num_j=num_j(indsel); + num_a_civ1=num_a_civ1(indsel); + num_a_civ2=num_a_civ2(indsel); + num_b_civ1=num_b_civ1(indsel); + num_b_civ2=num_b_civ2(indsel); + end +elseif isequal(mode,'pair j1-j2') | isequal(mode,'st_pair j1-j2') %case of bursts (png_old or png_2D) + num1_civ1=num1; + num1_civ2=num1; + displ_num=get(handles.list_pair_civ1,'UserData'); + num2_civ1=num1; + num_a_civ1=displ_num(1,index_civ1); + num_b_civ1=displ_num(2,index_civ1); + num2_civ2=num1; + num_a_civ2=displ_num(1,index_civ2); + num_b_civ2=displ_num(2,index_civ2); +elseif isequal(mode,'displacement') + num1_civ1=num1; + num2_civ1=num1; + num_a_civ1=num_j; + num_b_civ1=num_j; + num1_civ2=num1; + num2_civ2=num1; + num_a_civ2=num_j; + num_b_civ2=num_j; +end + + +%------------------------------------------------------------- +% --- Executes on selection change in list_pair_civ1. +function list_pair_civ1_Callback(hObject, eventdata, handles) +%------------------------------------------------------------ +%reproduce by default the chosen pair in the civ2 menu +list_pair=get(handles.list_pair_civ1,'String');%get the menu of image pairs +index_pair=get(handles.list_pair_civ1,'Value'); +displ_num=get(handles.list_pair_civ1,'UserData'); +num_a=displ_num(1,index_pair); +num_b=displ_num(2,index_pair); +set(handles.list_pair_civ2,'Value',index_pair); + +%update first_i and last_i according to the chosen image pairs +mode_list=get(handles.mode,'String'); +mode_value=get(handles.mode,'Value'); +mode=mode_list{mode_value}; +if isequal(mode,'series(Di)') + first_i=str2num(get(handles.first_i,'String')); + last_i=str2num(get(handles.last_i,'String')); + incr_i=str2num(get(handles.incr_i,'String')); + num1=first_i:incr_i:last_i; + lastfield=str2num(get(handles.nb_field,'String')); + if ~isequal(lastfield,[]) + ind=find((num1-floor(index_pair/2)*ones(size(num1))>0)& ... + (num1+ceil(index_pair/2)*ones(size(num1))<=lastfield)); + num1=num1(ind); + end + set(handles.first_i,'String',num2str(num1(1))); + set(handles.last_i,'String',num2str(num1(end))); +elseif isequal(mode,'series(Dj)') + first_j=str2num(get(handles.first_j,'String')); + last_j=str2num(get(handles.last_j,'String')); + incr_j=str2num(get(handles.incr_j,'String')); + num_j=first_j:incr_j:last_j; + lastfield2=str2num(get(handles.nb_field2,'String')); + if ~isequal(lastfield2,[]) + ind=find((num_j-floor(index_pair/2)*ones(size(num_j))>0)& ... + (num_j+ceil(index_pair/2)*ones(size(num_j))<=lastfield2)); + num1=num_j(ind); + end + set(handles.first_j,'String',num2str(num1(1))); + set(handles.last_j,'String',num2str(num1(end))); +end + +%------------------------------------------------------------------ +% --- Executes on selection change in list_pair_civ2. +function list_pair_civ2_Callback(hObject, eventdata, handles) + +index_pair=get(handles.list_pair_civ2,'Value');%get the selected position index in the menu + +%update first_i and last_i according to the chosen image pairs +mode_list=get(handles.mode,'String'); +mode_value=get(handles.mode,'Value'); +mode=mode_list{mode_value}; +if isequal(mode,'series(Di)') + first_i=str2num(get(handles.first_i,'String')); + last_i=str2num(get(handles.last_i,'String')); + incr_i=str2num(get(handles.incr_i,'String')); + num1=first_i:incr_i:last_i; + lastfield=str2num(get(handles.nb_field,'String')); + if ~isequal(lastfield,[]) + ind=find((num1-floor(index_pair/2)*ones(size(num1))>0)& ... + (num1+ceil(index_pair/2)*ones(size(num1))<=lastfield)); + num1=num1(ind); + end + set(handles.first_i,'String',num2str(num1(1))); + set(handles.last_i,'String',num2str(num1(end))); +elseif isequal(mode,'series(Dj)') + first_j=str2num(get(handles.first_j,'String')); + last_j=str2num(get(handles.last_j,'String')); + incr_j=str2num(get(handles.incr_j,'String')); + num_j=first_j:incr_j:last_j; + lastfield2=str2num(get(handles.nb_field2,'String')); + if ~isequal(lastfield2,[]) + ind=find((num_j-floor(index_pair/2)*ones(size(num_j))>0)& ... + (num_j+ceil(index_pair/2)*ones(size(num_j))<=lastfield)); + num1=num_j(ind); + end + set(handles.first_j,'String',num2str(num1(1))); + set(handles.last_j,'String',num2str(num1(end))); +end + + + + +%----------------------------------------------------------- +% --- Executes on button press in BATCH: remote processing +%----------------------------------------------------------- +function BATCH_Callback(hObject, eventdata, handles) +global civ1_exe civ2_exe patch_exe patch_new_exe fix_exe todo_path sge Civ_exe + +pxcmx=get(handles.pxcmx,'String'); +pxcmy=get(handles.pxcmy,'String'); +npx=get(handles.pxcmx,'UserData'); +npy=get(handles.pxcmy,'UserData'); + +%check the list of operations: +operations={'CIV1','FIX1','PATCH1','CIV2','FIX2','PATCH2'}; +run_flag=1; +box_test(1)=get(handles.CIV1,'Value'); +box_test(2)=get(handles.FIX1,'Value'); +box_test(3)=get(handles.PATCH1,'Value'); +box_test(4)=get(handles.CIV2,'Value'); +box_test(5)=get(handles.FIX2,'Value'); +box_test(6)=get(handles.PATCH2,'Value'); +index=find(box_test==1); +if isempty(index) + errordlg('no selected operation') + set(handles.BATCH, 'Enable','On') + set(handles.BATCH,'BackgroundColor',[1 0 0]) + return +end +index_first=min(index); +index_last=max(index); +box_used=box_test([index_first : index_last]); +[box_missing,ind_missing]=min(box_used); +if isequal(box_missing,0) + errordlg(['missing' cell2mat(operations(ind_missing))]); + set(handles.BATCH, 'Enable','On') + set(handles.BATCH,'BackgroundColor',[1 0 0]) + return +end + +%check mask if selecetd +if isequal(get(handles.get_mask_civ1,'Value'),1) + get_mask_civ1_Callback(hObject, eventdata, handles); +end +if isequal(get(handles.get_mask_fix1,'Value'),1) + get_mask_fix1_Callback(hObject, eventdata, handles); +end +if isequal(get(handles.get_mask_civ2,'Value'),1) + get_mask_civ2_Callback(hObject, eventdata, handles); +end +if isequal(get(handles.get_mask_fix2,'Value'),1) + get_mask_fix2_Callback(hObject, eventdata, handles); +end + + +%read names of the .exe file +path_uvmat=which('uvmat');% check the path detected for source file uvmat +path_UVMAT=fileparts(path_uvmat); %path to UVMAT +if isunix + %fid = fopen(fullfile(path_UVMAT,'PARAM_LINUX.txt'),'r');%open the file with civ_3D binary names + xmlfile=fullfile(path_UVMAT,'PARAM_LINUX.xml'); + if exist(xmlfile,'file') + t=xmltree(xmlfile); + sparam=convert(t); + end +else + %fid = fopen(fullfile(path_UVMAT,'PARAM_WIN.txt'),'r');%open the file with civ_3D binary names + xmlfile=fullfile(path_UVMAT,'PARAM_WIN.xml'); + if exist(xmlfile,'file') + t=xmltree(xmlfile); + sparam=convert(t); + end +end + sge=0; +if isfield(sparam,'Civ_exe') + Civ_exe=sparam.Civ_exe +end +if isfield(sparam,'Civ1_exe') + civ1_exe=sparam.Civ1_exe +end +if isfield(sparam,'Civ2_exe') + civ2_exe=sparam.Civ2_exe +end +if isfield(sparam,'Patch_exe') + patch_exe=sparam.Patch_exe +end +if isfield(sparam,'PatchNew_exe') + patch_new_exe=sparam.PatchNew_exe +end +if isfield(sparam,'Fix_exe') + fix_exe=sparam.Fix_exe +end +if isfield(sparam,'Todo_path') + todo_path=sparam.Todo_path +end +if isfield(sparam,'SGE') + sge=str2num(sparam.SGE) +end +%choice of batch priority +ind_answer=2; +if sge + [s,w]=unix('qstat -q civ_3D.q|grep job_| wc -l'); %check the waiting list (command unix) + if isequal(s,0) + w(end)=[]; + str_displ={[w ' jobs in the waiting list'];'Select a priority:'}; + str={'urgent';'normal';'low'}; + [ind_answer,v] = listdlg('PromptString',str_displ,... + 'SelectionMode','single',... + 'ListString',str,'ListSize',[200 200],'Name','job priority','InitialValue',3); + if isequal(v,0) % to handle Cancel button and figure close, + return % a better way should be create + end + else + warndlg_uvmat('batch system not available','ERROR') + return + end +end +%initialize the waitbars +set(handles.waitbar_1,'Position',[0.946 0.876 0.03 0.001]) +set(handles.waitbar_patch1,'Position',[0.946 0.439 0.03 0.001]) +set(handles.waitbar_civ2,'Position',[0.946 0.219 0.03 0.001]) +set(handles.waitbar_patch2,'Position',[0.946 0.0 0.03 0.001]) +set(handles.BATCH, 'Enable','Off') +set(handles.BATCH,'BackgroundColor',[0.831 0.816 0.784]) + +%get the filename root, nomenclature and numbers +filebase=get(handles.displ_filebase,'String'); +% for Windows system find the UBC path name if needed +if ~isunix & isequal(todo_path(1:2),'\\') & isequal(filebase(2:3),':\') + cur_dir=pwd; + if ~isequal(cur_dir(2:3),':\') + cd(matlabroot); %move to the Matlab root directory if the current Matlab dir does not allow the dos command or is M: + end + [ss,ww]=dos(['net use ' filebase(1:2)]); + if isequal(ss,0) + rankpath=findstr(ww,'\\'); + if ~isempty(rankpath) + wwrest=ww(rankpath:end); + rankend=min(find(double(wwrest)==10))-1; + filebase=[wwrest(1:rankend) filebase(3:end)]; + set(handles.displ_filebase,'String',filebase); + end + else + warndlg_uvmat('for BATCH option, UBC file names, beginning by \\, are needed','ERROR'); + set(handles.BATCH, 'Enable','On') + set(handles.BATCH,'BackgroundColor',[1 0 0]) + return + end +end +browse=get(handles.browse_root,'UserData') +ext_ima=browse.ext_ima; +nom_type_nc='_i1-i2'; +nom_type_ima=browse.nom_type_ima; +% nom_type_nc=browse.nom_type_nc; +% if isequal(nom_type_ima2,[]),nom_type_ima2='ima_num';end; %default +% if isequal(nom_type_nc,[]),nom_type_nc='_i1-i2';end; %default +mode_list=get(handles.mode,'String'); +mode_value=get(handles.mode,'Value'); +mode=mode_list{mode_value}; +time=get(handles.displ_filebase,'UserData'); %get the set of times + +[num1_civ1,num2_civ1,num_a_civ1,num_b_civ1,num1_civ2,num2_civ2,num_a_civ2,num_b_civ2]=... +find_pair_indices(handles,mode); %determine the pairs of processing file + +%check dir +subdir_civ1=get(handles.subdir_civ1,'String');%subdirectory subdir_civ1 for the netcdf output data +subdir_civ2=get(handles.subdir_civ2,'String'); +if isequal(subdir_civ1,''),subdir_civ1='A'; end% put default subdir +if isequal(subdir_civ2,''),subdir_civ2=subdir_civ1; end% put default subdir +currentdir=pwd;%store the current working directory +[Path_ima,Name]=fileparts(filebase);%Path of the image files (.civ_3D) +if ~exist(Path_ima,'dir') + warndlg_uvmat(['path to images ' Path_ima ' not found'],'ERROR') + return +end +cd(Path_ima);%move to the directory of the images +dircur=pwd; %current working directory +m2=''; +[erread,message]=fileattrib(Path_ima); +if ~isempty(message) & ~isequal(message.UserWrite,1) + errordlg(['No writting access to ' Path_ima]) + cd(currentdir) + return +end + +%test for reference file in fix +ref_fix1=get(handles.ref_fix1,'UserData'); +ref_fix2=get(handles.ref_fix2,'UserData'); +if (~isempty(ref_fix1) & box_test(2)==1)|(~isempty(ref_fix2) & box_test(5)==1) + errordlg('reference file not implemented in BATCH mode, use RUN') + set(handles.BATCH, 'Enable','On') + set(handles.BATCH,'BackgroundColor',[1 0 0]) + return +end +nbfield=length(num1_civ1); +nbslice=length(num_a_civ1); + +%check the existence of the netcdf and image files involved +% if box_test(1)==1;%CIV1 activated +detect=1; +while detect==1 %name a new subdir if one of the netcdf files already exists + for ifile=1:nbfield +% for j=1:nbslice + [filename,detect]=name_generator(filebase,num1_civ1(ifile),[],'.nc',... + nom_type_nc,1,num2_civ1(ifile),[],subdir_civ1);% + if detect==1% if a netcdf file already exists + subdir_civ1=[subdir_civ1 '.0']; + subdir_civ2=subdir_civ1; + break + end + filecell_nc1(ifile)={filename}; + if detect==1% if a netcdf file already exists + break + end + end + %create the new subdir_civ1 if it does not exist + if ~exist(fullfile(Path_ima,subdir_civ1),'dir') + [m1,m2,m3]=mkdir(subdir_civ1) + if ~isequal(m2,'') + msgbox(m2);%error message for directory creation + end + end +end +%get image names +for ifile=1:nbfield + [filecell_ima1_civ1{ifile},idetect]=name_generator(filebase, num1_civ1(ifile),[],ext_ima,nom_type_ima);%first image + [filecell_ima2_civ1{ifile},idetect_1]=name_generator(filebase, num2_civ1(ifile),[],ext_ima,nom_type_ima); %second image + if idetect==0 + warndlg_uvmat([filecell_ima1_civ1{ifile} ' not found'],'ERROR') + set(handles.BATCH, 'Enable','On') + set(handles.BATCH,'BackgroundColor',[1 0 0]) + cd(currentdir) + return + end + if idetect_1==0, + errordlg([filecell_ima2_civ1{ifile} ' not found']) + set(handles.BATCH, 'Enable','On') + set(handles.BATCH,'BackgroundColor',[1 0 0]) + cd(currentdir) + return + end +end + +cd(currentdir);%come back to the initial working directory +% if ~isequal(m2,'') +% msgbox(m2);%error message for directory creation +% end +set(handles.subdir_civ1,'String',subdir_civ1);%update the edit box +set(handles.subdir_civ2,'String',subdir_civ2);%update the edit box +browse.nom_type_nc=nom_type_nc; +set(handles.browse_root,'UserData',browse);%update the nomenclature type for uvmat + +%COPY IMAGES TO THE FORMAT .vol IF NEEDED +if isequal(nom_type_ima,'avi') + nom_type_imanew='_i'; +else + nom_type_imanew=nom_type_ima; +end + +if ~isequal(ext_ima,'.vol') + if box_test(1)==1 %if civ1 is performed + h = waitbar(0,['copy images to the .png format for civ1']);% display a wait bar + for ifile=1:nbfield + waitbar(ifile/nbfield); + Atot=[]; + [filename_A,idetect_cur]=name_generator(filebase,num1_civ1(ifile),1,'.png','_i');%A VOIR + for j=1:nbslice + if idetect_cur==0 + A=read_image(cell2mat(filecell_ima1_civ1(ifile,j)),nom_type_ima2,npx,npy,num1_civ1(ifile)); + Atot=[Atot;A]; + %imwrite(A,filename,'BitDepth',16); + end + end + imwrite(Atot,filename_A,'BitDepth',16); + %filecell_ima1_civ1(ifile,j)={filename}; + Atot=[]; + [filename_B,idetect_cur]=name_generator(filebase, num2_civ1(ifile),1,'.png','_i'); + for j=1:nbslice + if idetect_cur==0 + A=read_image(cell2mat(filecell_ima2_civ1(ifile,j)),nom_type_ima2,npx,npy,num2_civ1(ifile)); + Atot=[Atot;A]; +% imwrite(A,filename,'BitDepth',16); + end + %filecell_ima2_civ1(ifile,j)={filename}; + end + imwrite(Atot,filename_B,'BitDepth',16); + end + close(h) + end +end + +if ~sge + %OPEN THE WAIT LIST FOR BATCH PROCESSES + name_lock=fullfile(todo_path,'lock'); %lock file + iwait=0; + while(exist(name_lock) & iwait<15) + pause(1); %wait 1 second + iwait=iwait+1; + end + if iwait==15 + errordlg(['I''m tired to wait for the lock file, please delete it then click again on BATCH' name_lock ]) + set(handles.BATCH, 'Enable','On') + set(handles.BATCH,'BackgroundColor',[1 0 0]) + return + end + p0=fopen(name_lock,'w'); %create the file name_lock: prevents other users to interfere + name_todo=fullfile(todo_path,'TODO.txt'); + p1=fopen(name_todo,'a'); + if (p1<0) + errordlg(['error in opening ' name_todo]) + set(handles.BATCH, 'Enable','On') + set(handles.BATCH,'BackgroundColor',[1 0 0]) + return; + end +end + +for ifile=1:nbfield + i_cmd=0; + cmd=''; + if sge + cmd='#!/bin/bash'; + cmd=char({cmd;'#$ -cwd'}); + cmd=char({cmd;'hostname && date'}); + end + filename_cmx=cell2mat(filecell_nc1(ifile));%output netcdf file + filename_cmx([end-1:end])='cm';%name of cmx file + filename_cmx=[filename_cmx 'x']; + +%CIV1 + if box_test(1)==1 + %GET civ_3D PARAMETERS: + par_civ1=read_param_civ1(handles,cell2mat(filecell_ima1_civ1(1,1))); + p1text=[]; + [par_civ1.path,resu_file,resu_ext]=fileparts(filecell_nc1{ifile}); + par_civ1.volume1=filecell_ima1_civ1{ifile}; + par_civ1.volume2=filecell_ima2_civ1{ifile} + par_civ1.nx=1024; + par_civ1.ny=1024; + par_civ1.nz=par_civ1.gridLimits_Zmax - par_civ1.gridLimits_Zmin; + 'TEST' + par_civ1 + % civAll=get(handles.Experimental,'Value'); % Boolean for new civ excution method + % if isequal(civAll,1) + civAllxml=struct2xml(par_civ1);% xml contents, all parameters + civAllxml=set(civAllxml,1,'name','civ3d3c'); + % save(civAllxml) + par_civ1_3d_xml=fullfile(par_civ1.path,[resu_file '.xml']);%[par_civ1.path '/test_to_change.xml']; + pvalue=num2str((1-ind_answer)*500); + save(civAllxml,par_civ1_3d_xml); + if(isunix && sge) + ['echo /CIVX/bin/MPI/lam-7.1.3_g95/bin/mpirun C /CIVX/bin/civ3d3c -p ' par_civ1_3d_xml '|qsub -p ' pvalue ' -q lam.q -pe lam_loose 16 -e ' par_civ1_3d_xml '.errors -o ' par_civ1_3d_xml '.log' ] + eval ( ['!echo /CIVX/bin/MPI/lam-7.1.3_g95/bin/mpirun C /CIVX/bin/civ3d3c -p ' par_civ1_3d_xml '|qsub -p ' pvalue ' -q lam.q -pe lam_loose 16 -e ' par_civ1_3d_xml '.errors -o ' par_civ1_3d_xml '.log' ]) + else + '3D mode is NOT supported without sge' + end + return + % %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + % fichier xml produit + %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + % A CONTINUER + %civAllxml + civAllCmd=[]; + civAllxml=set(civAllxml,1,'name','civ3d3c'); + namelog=[filename_cmx([1:end-3]) 'log']; + %par_civ1.Dt=num2str(time(num2_civ1(ifile),num_b_civ1(j))-time(num1_civ1(ifile),num_a_civ1(1))); + %par_civ1.T0=num2str((time(num2_civ1(ifile),num_b_civ1(j))+time(num1_civ1(ifile),num_a_civ1(1)))/2); + % test_mask=get(handles.get_mask_civ1,'Value'); + i_cmd=i_cmd+1; +% if isequal(civAll,0) +% cmd=char({cmd;BATCH_CIV1(filename_cmx([1:end-4]),namelog,par_civ1,handles)}); +% else + civAllCmd=[civAllCmd ' civ1 ']; + str=BATCH_CIV1_Unified(filename_cmx([1:end-4]),namelog,par_civ1,handles); + fieldnames=fields(str); + [civAllxml,uid_civ1]=add(civAllxml,1,'element','civ1'); + for ilist=1:length(fieldnames) + val=eval(['str.' fieldnames{ilist}]); + if ischar(val) + [civAllxml,uid_t]=add(civAllxml,uid_civ1,'element',fieldnames{ilist}); + [civAllxml,uid_t2]=add(civAllxml,uid_t,'chardata',val); + end + end +% end + end + if(isunix) + cmd=char({cmd ; ['cp -f ' filename_cmx '2 ' filename_cmx]; cmd_CIV2}); + else + cmd=char({cmd ; ['copy /Y ' filename_cmx '2 ' filename_cmx]; cmd_CIV2}); + end +end + +% if isequal(civAll,1) + save(civAllxml,[filename_cmx([1:end-4]) '.xml']); + cmd=char({cmd;[Civ_exe ' -f ' [filename_cmx([1:end-4]) '.xml'] ' ' civAllCmd]}); + + %save(civAllxml,'/tmp/test.xml'); +% end + + +% create the .bat file: +if sge + [Rootbat,Filebat,extbat]=fileparts(filename_cmx); + filename_bat=fullfile(Rootbat,['job_' Filebat extbat]); +else + filename_bat=filename_cmx; +end +filename_bat(end-2:end)='bat'; + +% pbat=fopen(filename_bat,'w'); %create the file filename_bat +dlmwrite(filename_bat,cmd,'');%write commands in filename_bat +if sge + pvalue=num2str((1-ind_answer)*500); + namelog=[filename_bat '.patch.log']; + ['!qsub -p ' pvalue ' -q civ_3D.q -e ' filename_cmx(1:end-4) '.errors -o ' filename_cmx(1:end-4) '.log' ' ' filename_bat]; + eval( ['!qsub -p ' pvalue ' -q civ_3D.q -e ' filename_cmx(1:end-4) '.errors -o ' filename_cmx(1:end-4) '.log' ' ' filename_bat]); +else + if(isunix) + cmdtodo=['. ' filename_bat ];%removed for Mathieu tests %' && rm -f ' filename_bat] ; + else +% cmdtodo=[filename_bat ' && del /F /Q ' filename_bat]; + cmdtodo=[filename_bat];%removed for Mathieu tests %' && del /F /Q ' filename_bat' ; + end + count= fprintf(p1,'%s\n', cmdtodo); +end +if ~sge + fclose(p1); + fclose(p0); + delete(name_lock); +end +set(handles.BATCH, 'Enable','On') +set(handles.BATCH,'BackgroundColor',[1 0 0]) +%save interface state +[Path,Name]=fileparts(filebase); +namefig=fullfile(Path,subdir_civ2,Name); +detect=1; +while detect==1 + namefigfull=[namefig '.fig']; + hh=dir(namefigfull); + if ~isempty(hh) + detect=1; + namefig=[namefig '.0']; + else + detect=0; + end +end +saveas(gcbf,namefigfull);%save the interface with name namefigfull + + +%---------------------------------------- +%PATCH +%--------------------------------------- +function cmd_PATCH=RUN_PATCH(filename_nc,nx_patch,ny_patch,rho_patch,subdomain_patch,thresh_value,test_interp) +global patch_exe patch_new_exe + namelog=[filename_nc([1:end-3]) '_patch.log']; + if test_interp==0 + cmd_PATCH=[patch_exe ' -f ' filename_nc ' -m ' nx_patch ' -n ' ny_patch ' -ro ' rho_patch ' -nopt ' subdomain_patch ... + ' > ' namelog ' 2>&1'] % redirect standard output to the log file + else %nouveau programme patch + cmd_PATCH=[patch_new_exe ' -f ' filename_nc ' -m ' nx_patch ' -n ' ny_patch ' -ro ' rho_patch ... + ' -max ' thresh_value ' -nopt ' subdomain_patch ' > ' namelog ' 2>&1']; % redirect standard output to the log file + end + + +%---------------------------------------------------- +function first_j_Callback(hObject, eventdata, handles) +last_j_Callback(hObject, eventdata, handles) + +%--------------------------------------------------------- +% --- Executes on button press in CIV1. +function CIV1_Callback(hObject, eventdata, handles) +enable_civ1(handles,get(handles.CIV1,'Value')) +find_netcpair_civ1(hObject, eventdata, handles); + +%------------------------------------------------------ +% --- Executes on button press in FIX1. +function FIX1_Callback(hObject, eventdata, handles) + +if get(handles.FIX1,'Value')==1 +enable_fix1(handles) +else +desable_fix1(handles) +end + +%---------------------------------------------------------------- +% --- Executes on button press in PATCH1. +function PATCH1_Callback(hObject, eventdata, handles) + +if get(handles.PATCH1,'Value')==1 +enable_patch1(handles) +else +desable_patch1(handles) +end + +%---------------------------------------------------------- +% --- Executes on button press in CIV2. +function CIV2_Callback(hObject, eventdata, handles) +state=get(handles.CIV2,'Value'); +enable_civ2(handles,state) +if state + find_netcpair_civ2(hObject, eventdata, handles) +end + +%--------------------------------------------------- +% --- Executes on button press in FIX2. +function FIX2_Callback(hObject, eventdata, handles) +if get(handles.FIX2,'Value')==1 + enable_fix2(handles) + if get(handles.CIV2,'Value')==0 + find_netcpair_civ2(hObject, eventdata, handles) % select the available netcdf files + end +else + desable_fix2(handles) +end + + +%------------------------------------------------------- +% --- Executes on button press in PATCH2. +function PATCH2_Callback(hObject, eventdata, handles) +%-------------------------------------------------------- +if get(handles.PATCH2,'Value')==1 + enable_patch2(handles) + if get(handles.CIV2,'Value')==0 + find_netcpair_civ2(hObject, eventdata, handles) % select the available netcdf files + end +else + desable_patch2(handles) +end + + + +%----------------------------------------------------------- +function first_i_Callback(hObject, eventdata, handles) +%------------------------------------------------------ +last_i_Callback(hObject, eventdata, handles) + +%----------------------------------------------------------- +% --- Executes on button press in calcul_search: determine the search range isx,isy +%-------------------------------------------------------- +function calcul_search_Callback(hObject, eventdata, handles) + +%determine pair numbers +list_pair=get(handles.list_pair_civ1,'String');%get the menu of image pairs +index=get(handles.list_pair_civ1,'Value'); +displ_num=get(handles.list_pair_civ1,'UserData'); +time=get(handles.displ_filebase,'UserData'); %get the set of times +pxcm_xy=get(handles.calcul_search,'UserData') +pxcmx=pxcm_xy(1); +pxcmy=pxcm_xy(2); +mode_list=get(handles.mode,'String'); +mode_value=get(handles.mode,'Value'); +mode=mode_list{mode_value}; +if isequal (mode, 'series(Di)' ) + ref_i=str2num(get(handles.ref_i,'String')); + num1=ref_i-floor(index/2);% first image numbers + num2=ref_i+ceil(index/2); + num_a=1; + num_b=1; +elseif isequal (mode, 'series(Dj)') + num1=1; + num2=1; + ref_j=str2num(get(handles.ref_j,'String')); + num_a=ref_j-floor(index/2);% first image numbers + num_b=ref_j+ceil(index/2); +elseif isequal(mode,'pair j1-j2') %case of bursts (png_old or png_2D) + ref_i=str2num(get(handles.ref_i,'String')); + num1=ref_i; + num2=ref_i; + num_a=displ_num(1,index); + num_b=displ_num(2,index); +end +dt=time(num2,num_b)-time(num1,num_a); +ibx=str2num(get(handles.ibx,'String')); +iby=str2num(get(handles.iby,'String')); +umin=dt*pxcmx*str2num(get(handles.umin,'String')); +umax=dt*pxcmx*str2num(get(handles.umax,'String')); +vmin=dt*pxcmy*str2num(get(handles.vmin,'String')); +vmax=dt*pxcmy*str2num(get(handles.vmax,'String')); +shiftx=round((umin+umax)/2); +shifty=round((vmin+vmax)/2); +isx=(umax+2-shiftx)*2+ibx; +isx=2*ceil(isx/2)+1; +isy=(vmax+2-shifty)*2+iby; +isy=2*ceil(isy/2)+1; +set(handles.shiftx,'String',num2str(shiftx)); +set(handles.shifty,'String',num2str(shifty)); +set(handles.isx,'String',num2str(isx)); +set(handles.isy,'String',num2str(isy)); + + +%--------------------------------------------------------- +% Executes on carriage return on the subdir civ1 edit window +%-------------------------------------------------------- +function subdir_civ1_Callback(hObject, eventdata, handles) +subdir=get(handles.subdir_civ1,'String'); +set(handles.subdir_civ2,'String',subdir); +if get(handles.CIV1,'Value')==0 + find_netcpair_civ1(hObject, eventdata, handles); %update the list of available pairs from netcdf files in the new directory +end + +%--------------------------------------------------------- +% Executes on carriage return on the subdir civ1 edit window +%--------------------------------------------------------- +function subdir_civ2_Callback(hObject, eventdata, handles) +%update the list of available pairs from netcdf files in the new directory +if get(handles.CIV2,'Value')==0 & get(handles.CIV1,'Value')==0 & get(handles.FIX1,'Value')==0 & get(handles.PATCH1,'Value')==0 + find_netcpair_civ2(hObject, eventdata, handles); +end + +%------------------------------------------------------ +% --- Executes on button press in get_mask_civ1. +%------------------------------------------------------ +function get_mask_civ1_Callback(hObject, eventdata, handles) +maskval=get(handles.get_mask_civ1,'Value') +if isequal(maskval,0) + set(handles.mask_civ1,'String','') +else +mask_displ='no mask'; %default +filebase=get(handles.displ_filebase,'String'); +[ nbslice, flag_mask]=get_mask(filebase,handles) +if isequal(flag_mask,1) + mask_displ=[num2str(nbslice) 'mask']; +end +if get(handles.compare,'Value')==1 & ~isequal(mask_displ,'no mask')% look for the second mask series + filebase_a=get(handles.displ_filebase2,'String'); + [nbslice_a, flag_mask_a]=get_mask(filebase_a,handles) + if isequal(flag_mask_a,0) | ~isequal(nbslice_a,nbslice) + mask_displ='no mask'; + end +end +if isequal(mask_displ,'no mask') + set(handles.get_mask_civ1,'Value',0) + set(handles.get_mask_fix1,'Value',0) + set(handles.get_mask_civ2,'Value',0) + set(handles.get_mask_fix2,'Value',0) +else + set(handles.get_mask_fix1,'Value',1) + set(handles.get_mask_civ2,'Value',1) + set(handles.get_mask_fix2,'Value',1) +end +set(handles.mask_civ1,'String',mask_displ) +set(handles.mask_fix1,'String',mask_displ) +set(handles.mask_civ2,'String',mask_displ) +set(handles.mask_fix2,'String',mask_displ) +end +%-------------------------------------------------------------- +% --- Executes on button press in get_mask_fix1. +function get_mask_fix1_Callback(hObject, eventdata, handles) +maskval=get(handles.get_mask_fix1,'Value') +if isequal(maskval,0) + set(handles.mask_fix1,'String','') +else +mask_displ='no mask'; %default +filebase=get(handles.displ_filebase,'String'); +[nbslice, flag_mask]=get_mask(filebase,handles) +if isequal(flag_mask,1) + mask_displ=[num2str(nbslice) 'mask']; +end +if get(handles.compare,'Value')==1 & ~isequal(mask_displ,'no mask')% look for the second mask series + filebase_a=get(handles.displ_filebase2,'String'); + [nbslice_a, flag_mask_a]=get_mask(filebase_a,handles) + if isequal(flag_mask_a,0) | ~isequal(nbslice_a,nbslice) + mask_displ='no mask'; + end +end +if isequal(mask_displ,'no mask') + set(handles.get_mask_fix1,'Value',0) + set(handles.get_mask_civ2,'Value',0) + set(handles.get_mask_fix2,'Value',0) +else + set(handles.get_mask_civ2,'Value',1) + set(handles.get_mask_fix2,'Value',1) +end +set(handles.mask_fix1,'String',mask_displ) +set(handles.mask_civ2,'String',mask_displ) +set(handles.mask_fix2,'String',mask_displ) +end +%----------------------------------------- +% --- Executes on button press in get_mask_civ2. +function get_mask_civ2_Callback(hObject, eventdata, handles) +maskval=get(handles.get_mask_civ2,'Value') +if isequal(maskval,0) + set(handles.mask_civ2,'String','') +else +mask_displ='no mask'; %default +filebase=get(handles.displ_filebase,'String'); +[nbslice, flag_mask]=get_mask(filebase,handles) +if isequal(flag_mask,1) + mask_displ=[num2str(nbslice) 'mask']; +end +if get(handles.compare,'Value')==1 & ~isequal(mask_displ,'no mask')% look for the second mask series + filebase_a=get(handles.displ_filebase2,'String'); + [nbslice_a, flag_mask_a]=get_mask(filebase_a,handles) + if isequal(flag_mask_a,0) | ~isequal(nbslice_a,nbslice) + mask_displ='no mask'; + end +end +if isequal(mask_displ,'no mask') + set(handles.get_mask_civ2,'Value',0) + set(handles.get_mask_fix2,'Value',0) +else + set(handles.get_mask_fix2,'Value',1) +end +set(handles.mask_civ2,'String',mask_displ) +set(handles.mask_fix2,'String',mask_displ) +end +%------------------------------------- +% --- Executes on button press in get_mask_fix2. +function get_mask_fix2_Callback(hObject, eventdata, handles) +maskval=get(handles.get_mask_fix2,'Value') +if isequal(maskval,0) + set(handles.mask_fix2,'String','') +else +mask_displ='no mask'; %default +filebase=get(handles.displ_filebase,'String'); +[nbslice, flag_mask]=get_mask(filebase,handles) +if isequal(flag_mask,1) + mask_displ=[num2str(nbslice) 'mask']; +end +if get(handles.compare,'Value')==1 & ~isequal(mask_displ,'no mask')% look for the second mask series + filebase_a=get(handles.displ_filebase2,'String'); + [nbslice_a, flag_mask_a]=get_mask(filebase_a,handles) + if isequal(flag_mask_a,0) | ~isequal(nbslice_a,nbslice) + mask_displ='no mask'; + end +end +if isequal(mask_displ,'no mask') + set(handles.get_mask_fix2,'Value',0) +end +set(handles.mask_fix2,'String',mask_displ) +end + +%--------------------------------------- +function [nbslice, flag_mask]=get_mask(filebase,handles) +%detect mask files, images with appropriate file base +%[filebase '_' xx 'mask'], xx=nbslice +%flag_mask=1 indicates detection + +flag_mask=0;%default +nbslice=1; + +% subdir=get(handles.subdir_civ1,'String'); +[Path,Name]=fileparts(filebase) +currentdir=pwd; +cd(Path);%move in the dir of the root name filebase +maskfiles=dir([Name '_*mask_*.png'])%look for mask files +cd(currentdir);%come back to the current working directory +if isempty(maskfiles) + browse=get(handles.browse_root,'UserData'); + varargin{1}=''; + [image_name,idetect]=name_generator(filebase,1,1,browse.ext_ima,browse.nom_type_ima);%name of an image + if idetect==1 + varargin{1}=image_name; + end + warndlg_uvmat('no mask available, use TOOL menu in the uvmat interface to create it','ERROR') +% makemask(varargin); %open the makemask interface +else + maskname=maskfiles(1).name;% take the first mask file in the list + [Path2,Name,ext]=fileparts(maskname); + Namedouble=double(Name); + val=(48>Namedouble)|(Namedouble>57);% select the non-numerical characters + ind_mask=findstr('mask',Name); + i=ind_mask-1; + while val(i)==0 & i>0 + i=i-1; + end + nbslice=str2num(Name(i+1:ind_mask-1)); + if ~isequal(nbslice,[]) & Name(i)=='_' + flag_mask=1; + else + errordlg(['bad mask file ' Name ext ' found in ' Path2]) + return + nbslice=1; + end +end +%------------------------------ + + +function grid_civ1_Callback(hObject, eventdata, handles) +% hObject handle to grid_civ1 (see GCBO) +% eventdata reserved - to be defined in a future version of MATLAB +% handles structure with handles and user data (see GUIDATA) + +% Hints: get(hObject,'String') returns contents of grid_civ1 as text +% str2double(get(hObject,'String')) returns contents of grid_civ1 as a double + + +%----------------------------------------------------------- +% transform numbers to letters +%-------------------------------------------- +function str=num2stra(num,nom_type); +if isequal(nom_type,'png_old') | isequal(nom_type,'netc_old') |isequal(nom_type,'raw_SMD') + str=char(96+num); +elseif isequal(nom_type,'_i')|isequal(nom_type,'_i1-i2')... + |isequal(nom_type,'ima_num')| isequal(nom_type,'avi')| isequal(nom_type,'none') + str=''; +else + str=num2str(num); +end +%--------------------------------------------------- +function mask_civ1_Callback(hObject, eventdata, handles) +set(handles.mask_civ1,'UserData',[]) +set(handles.mask_civ1,'String','') +%---------------------------------------------------- +function mask_civ2_Callback(hObject, eventdata, handles) +set(handles.mask_civ2,'UserData',[]) +set(handles.mask_civ2,'String','') +%---------------------------------------------------- +function mask_fix1_Callback(hObject, eventdata, handles) +set(handles.mask_fix1,'UserData',[]) +set(handles.mask_fix1,'String','') +%---------------------------------------------------- +function mask_fix2_Callback(hObject, eventdata, handles) +set(handles.mask_fix2,'UserData',[]) +set(handles.mask_fix2,'String','') + +%-------------------------------------------------------------------------- +% --- Executes on button press in list_subdir_civ1. +function list_subdir_civ1_Callback(hObject, eventdata, handles) + +filebase=get(handles.displ_filebase,'String'); +dirinput = uigetdir(filebase) + set(handles.subdir_civ1,'String',dirinput) + set(handles.subdir_civ2,'String',dirinput) + +displ_filebase_Callback(hObject, eventdata, handles); + + +function rho_civ2_Callback(hObject, eventdata, handles) +% hObject handle to rho_civ2 (see GCBO) +% eventdata reserved - to be defined in a future version of MATLAB +% handles structure with handles and user data (see GUIDATA) + +% Hints: get(hObject,'String') returns contents of rho_civ2 as text +% str2double(get(hObject,'String')) returns contents of rho_civ2 as a double + +%---------------------------------------------- +function last_i_Callback(hObject, eventdata, handles) +first_i=str2num(get(handles.first_i,'String')); +last_i=str2num(get(handles.last_i,'String')); +ref_i=ceil((first_i+last_i)/2); +set(handles.ref_i,'String', num2str(ref_i)) +ref_i_Callback(hObject, eventdata, handles) + +%------------------------------------------------------- +function last_j_Callback(hObject, eventdata, handles) +first_j=str2num(get(handles.first_j,'String')); +last_j=str2num(get(handles.last_j,'String')); +ref_j=ceil((first_j+last_j)/2); +set(handles.ref_j,'String', num2str(ref_j)) +ref_j_Callback(hObject, eventdata, handles) + +%-------------------------------------------------------------------------- +% --- Executes on button press in browse_gridciv1. +function browse_gridciv1_Callback(hObject, eventdata, handles) +value=get(handles.browse_gridciv1,'Value'); +if value + filebase=get(handles.displ_filebase,'String'); + [FileName, PathName, filterindex] = uigetfile( ... + {'*.grid', ' (*.grid)'; + '*.grid', '.grid files '; ... + '*.*', 'All Files (*.*)'}, ... + 'Pick a file',filebase); + filegrid=fullfile(PathName,FileName); + if isempty(FileName)|isempty(PathName)|isequal(FileName,0)|~exist(filegrid,'file') + set(handles.browse_gridciv1,'Value',0); + set(handles.grid_civ1,'string',''); + set(handles.dx_civ1,'Visible','on'); + set(handles.dy_civ1,'Visible','on'); + set(handles.grid_civ2,'string',''); + if get(handles.CIV2,'Value') + set(handles.dx_civ2,'Visible','on'); + set(handles.dy_civ2,'Visible','on'); + end + else + set(handles.grid_civ1,'string',filegrid); + set(handles.dx_civ1,'Visible','off'); + set(handles.dy_civ1,'Visible','off'); + set(handles.grid_civ2,'string',filegrid); + set(handles.dx_civ2,'Visible','off'); + set(handles.dy_civ2,'Visible','off'); +% set(handles.grid_patch1,'string',filegrid); +% set(handles.grid_patch2,'string',filegrid); + end +else + set(handles.grid_civ1,'string',''); + set(handles.dx_civ1,'Visible','on'); + set(handles.dy_civ1,'Visible','on'); + set(handles.grid_civ2,'string',''); + if get(handles.CIV2,'Value') + set(handles.dx_civ2,'Visible','on'); + set(handles.dy_civ2,'Visible','on'); + end +end + + + +function pxcmx_Callback(hObject, eventdata, handles) +% hObject handle to pxcmx (see GCBO) +% eventdata reserved - to be defined in a future version of MATLAB +% handles structure with handles and user data (see GUIDATA) + +% Hints: get(hObject,'String') returns contents of pxcmx as text +% str2double(get(hObject,'String')) returns contents of pxcmx as a double + + + +function pxcmy_Callback(hObject, eventdata, handles) +% hObject handle to pxcmy (see GCBO) +% eventdata reserved - to be defined in a future version of MATLAB +% handles structure with handles and user data (see GUIDATA) + +% Hints: get(hObject,'String') returns contents of pxcmy as text +% str2double(get(hObject,'String')) returns contents of pxcmy as a double + + +% --- Executes on button press in browse_gridciv2. +function browse_gridciv2_Callback(hObject, eventdata, handles) + +filebase=get(handles.displ_filebase,'String'); +[FileName, PathName, filterindex] = uigetfile( ... + {'*.grid', ' (*.grid)'; + '*.grid', '.grid files '; ... + '*.*', 'All Files (*.*)'}, ... + 'Pick a file',filebase); +filegrid=fullfile(PathName,FileName); +set(handles.grid_civ2,'string',filegrid); +set(handles.dx_civ2,'String',' '); +set(handles.dy_civ2,'String',' '); +% set(handles.grid_patch2,'string',filegrid); + +% --- Executes on button press in get_gridpatch1. +function get_gridpatch1_Callback(hObject, eventdata, handles) +% hObject handle to get_gridpatch1 (see GCBO) +% eventdata reserved - to be defined in a future version of MATLAB +% handles structure with handles and user data (see GUIDATA) + +filebase=get(handles.displ_filebase,'String'); +[FileName, PathName, filterindex] = uigetfile( ... + {'*.grid', ' (*.grid)'; + '*.grid', '.grid files '; ... + '*.*', 'All Files (*.*)'}, ... + 'Pick a file',filebase); +filegrid=fullfile(PathName,FileName); +set(handles.grid_patch1,'string',filegrid); +% set(handles.grid_patch2,'string',filegrid + +%----------------------------------------------------------------- +% --- Executes on button press in get_gridpatch2. +function get_gridpatch2_Callback(hObject, eventdata, handles) +% hObject handle to get_gridpatch2 (see GCBO) +% eventdata reserved - to be defined in a future version of MATLAB +% handles structure with handles and user data (see GUIDATA) + + +%---------------------------------------------------------- +function enable_civ1(handles,state) +if isequal(state,0) + state='off'; +end +if isequal(state,1) + state='on'; +end +if isequal(state,'on') + set(handles.frame_civ1,'BackgroundColor',[1 1 0]) + set(handles.frame_para_civ1,'BackgroundColor',[1 1 0]) + set(handles.frame_grid_civ1,'BackgroundColor',[1 1 0]) +else + set(handles.frame_civ1,'BackgroundColor',[0.831 0.816 0.784]) + set(handles.frame_para_civ1,'BackgroundColor',[0.831 0.816 0.784]) + set(handles.frame_grid_civ1,'BackgroundColor',[0.831 0.816 0.784]) +end +set(handles.ibx,'Visible',state) +set(handles.iby,'Visible',state) +set(handles.isx,'Visible',state) +set(handles.isy,'Visible',state) +set(handles.shiftx,'Visible',state) +set(handles.shifty,'Visible',state) +set(handles.rho,'Visible',state) +set(handles.dx_civ1,'Visible',state) +set(handles.dy_civ1,'Visible',state) +set(handles.calcul_search,'Visible',state) +set(handles.u_text,'Visible',state) +set(handles.v_text,'Visible',state) +set(handles.min,'Visible',state) +set(handles.max,'Visible',state) +set(handles.umin,'Visible',state) +set(handles.umax,'Visible',state) +set(handles.vmin,'Visible',state) +set(handles.vmax,'Visible',state) +set(handles.grid_civ1,'Visible',state) +set(handles.mask_civ1,'Visible',state) +set(handles.browse_gridciv1,'Visible',state) +set(handles.get_mask_civ1,'Visible',state) +set(handles.parameters,'Visible',state) +set(handles.grid,'Visible',state) +set(handles.dx_civ1,'Visible',state) +set(handles.dy_civ1,'Visible',state) +set(handles.ImaThreshold,'Visible',state) +if isequal(state,'off') + set(handles.MinIma,'Visible','off') + set(handles.MaxIma,'Visible','off') + set(handles.ImaThreshold,'Value',0) +end +set(handles.dx_civ1_title,'Visible',state) +set(handles.dy_civ1_title,'Visible',state) +set(handles.ImaThreshold_title,'Visible',state) +set(handles.ib_title,'Visible',state) +set(handles.is_title,'Visible',state) +set(handles.shift_title,'Visible',state) +set(handles.rho_title,'Visible',state) + +%---------------------------------------------------------- +function enable_fix1(handles) +set(handles.frame_fix1,'BackgroundColor',[1 1 0]) +set(handles.REMOVE,'Visible','on') +set(handles.vec_Fmin2,'Visible','on') +set(handles.vec_F2,'Visible','on') +set(handles.vec_F3,'Visible','on') +set(handles.thresh_vecC,'Visible','on') +set(handles.thresh_vecC_title,'Visible','on') +set(handles.thresh_vel,'Visible','on') +set(handles.thresh_vel_text,'Visible','on') +set(handles.mask_fix1,'Visible','on') +set(handles.get_mask_fix1,'Visible','on') +set(handles.get_ref_fix1,'Visible','on') +set(handles.ref_fix1,'Visible','on') +set(handles.inf_sup1,'Visible','on') +set(handles.field_ref1,'Visible','on') + +%---------------------------------------------------------- +function desable_fix1(handles) +set(handles.frame_fix1,'BackgroundColor',[0.831 0.816 0.784]) +set(handles.REMOVE,'Visible','off') +set(handles.vec_Fmin2,'Visible','off') +set(handles.vec_F2,'Visible','off') +set(handles.vec_F3,'Visible','off') +set(handles.thresh_vecC,'Visible','off') +set(handles.thresh_vecC_title,'Visible','off') +set(handles.thresh_vel,'Visible','off') +set(handles.thresh_vel_text,'Visible','off') +set(handles.mask_fix1,'Visible','off') +set(handles.get_mask_fix1,'Visible','off') +set(handles.get_ref_fix1,'Visible','off') +set(handles.ref_fix1,'Visible','off') +set(handles.inf_sup1,'Visible','off') +set(handles.field_ref1,'Visible','off') + +%-------------------------------------------------------------- +function enable_patch1(handles) +global patch_new_exe +set(handles.frame_patch1,'BackgroundColor',[1 1 0]) +set(handles.rho_patch1,'Visible','on') +set(handles.rho_text1,'Visible','on') +set(handles.thresh_patch1,'Visible','on') +set(handles.thresh_text1,'Visible','on') +set(handles.subdomain_patch1,'Visible','on') +set(handles.subdomain_text1,'Visible','on') +set(handles.nx_patch1,'Visible','on') +set(handles.ny_patch1,'Visible','on') +set(handles.nx_patch1_title,'Visible','on') +set(handles.ny_patch1_title,'Visible','on') +if (~isequal(patch_new_exe,[]) & ~isequal(patch_new_exe,[])) + set(handles.test_interp,'Visible','on'); +end +set(handles.get_gridpatch1,'Visible','on') +set(handles.grid_patch1,'string','none'); +set(handles.grid_patch1,'Visible','on') + +%-------------------------------------------------------------- +function desable_patch1(handles) +set(handles.frame_patch1,'BackgroundColor',[0.831 0.816 0.784]) +set(handles.rho_patch1,'Visible','off') +set(handles.rho_text1,'Visible','off') +set(handles.thresh_patch1,'Visible','off') +set(handles.thresh_text1,'Visible','off') +set(handles.subdomain_patch1,'Visible','off') +set(handles.subdomain_text1,'Visible','off') +set(handles.nx_patch1,'Visible','off') +set(handles.ny_patch1,'Visible','off') +set(handles.nx_patch1_title,'Visible','off') +set(handles.ny_patch1_title,'Visible','off') +set(handles.test_interp,'Visible','off') +set(handles.get_gridpatch1,'Visible','off') +set(handles.grid_patch1,'Visible','off') + +%---------------------------------------------------------- +function enable_civ2(handles,state) +if isequal(state,0) + state='off'; +end +if isequal(state,1) + state='on'; +end +if isequal(state,'on') + set(handles.frame_civ2,'BackgroundColor',[1 1 0]) + set(handles.frame_para_civ2,'BackgroundColor',[1 1 0]) + set(handles.frame_grid_civ2,'BackgroundColor',[1 1 0]) + set(handles.frame_subdirciv2,'BackgroundColor',[1 1 0]) +else + set(handles.frame_civ2,'BackgroundColor',[0.831 0.816 0.784]) + set(handles.frame_para_civ2,'BackgroundColor',[0.831 0.816 0.784]) + set(handles.frame_grid_civ2,'BackgroundColor',[0.831 0.816 0.784]) + set(handles.frame_subdirciv2,'BackgroundColor',[0.831 0.816 0.784]) +end +set(handles.ibx_civ2,'Visible',state) +set(handles.iby_civ2,'Visible',state) +set(handles.decimal,'Visible',state) +set(handles.deformation,'Visible',state) +set(handles.rho_civ2,'Visible',state) +set(handles.dx_civ2,'Visible',state) +set(handles.dy_civ2,'Visible',state) +set(handles.browse_gridciv2,'Visible',state) +set(handles.get_mask_civ2,'Visible',state) +set(handles.parameters,'Visible',state) +set(handles.grid,'Visible',state) +set(handles.parameters_text,'Visible',state) +set(handles.grid_text,'Visible',state) +set(handles.grid_civ2,'Visible',state) +set(handles.mask_civ2,'Visible',state) +set(handles.dx_civ2_title,'Visible',state) +set(handles.dy_civ2_title,'Visible',state) +set(handles.ibx_civ2_text,'Visible',state) +set(handles.rho_civ2_title,'Visible',state) +set(handles.ImaThreshold2,'Visible',state) +set(handles.ImaThreshold_title2,'Visible',state) +if isequal(state,'off') + set(handles.MinIma2,'Visible','off') + set(handles.MaxIma2,'Visible','off') + set(handles.ImaThreshold2,'Value',0) + if isequal(get(handles.FIX2,'Value'),0) & isequal(get(handles.PATCH2,'Value'),0) + set(handles.list_pair_civ2,'Visible','off') + set(handles.subdir_civ2,'Visible','off') + set(handles.subdir_civ2_text,'Visible','off') + end +else + set(handles.list_pair_civ2,'Visible','on') + set(handles.subdir_civ2,'Visible','on') + set(handles.subdir_civ2_text,'Visible','on') +end + +%---------------------------------------------------------- +% function desable_civ2(handles) +% set(handles.frame_civ2,'BackgroundColor',[0.831 0.816 0.784]) +% set(handles.frame_para_civ2,'BackgroundColor',[0.831 0.816 0.784]) +% set(handles.frame_grid_civ2,'BackgroundColor',[0.831 0.816 0.784]) +% set(handles.ibx_civ2,'Visible','off') +% set(handles.iby_civ2,'Visible','off') +% set(handles.decimal,'Visible','off') +% set(handles.deformation,'Visible','off') +% set(handles.rho_civ2,'Visible','off') +% set(handles.dx_civ2,'Visible','off') +% set(handles.dy_civ2,'Visible','off') +% set(handles.browse_gridciv2,'Visible','off') +% set(handles.get_mask_civ2,'Visible','off') +% set(handles.parameters,'Visible','off') +% set(handles.grid,'Visible','off') +% set(handles.grid,'Visible','on') +% set(handles.parameters_text,'Visible','off') +% set(handles.grid_text,'Visible','off') +% set(handles.grid_civ2,'Visible','off') +% set(handles.mask_civ2,'Visible','off') +% set(handles.dx_civ2_title,'Visible','off') +% set(handles.dy_civ2_title,'Visible','off') +% set(handles.ibx_civ2_text,'Visible','off') +% set(handles.rho_civ2_title,'Visible','off') +% set(handles.frame_subdirciv2,'BackgroundColor',[0.831 0.816 0.784]) +% if isequal(get(handles.FIX2,'Value'),0) & isequal(get(handles.PATCH2,'Value'),0) +% set(handles.list_pair_civ2,'Visible','off') +% set(handles.subdir_civ2,'Visible','off') +% set(handles.subdir_civ2_text,'Visible','off') +% end + +%---------------------------------------------------------- +function enable_fix2(handles) +set(handles.frame_fix2,'BackgroundColor',[1 1 0]) +set(handles.REMOVE2,'Visible','on') +set(handles.vec_Fmin2_2,'Visible','on') +set(handles.vec_F4,'Visible','on') +set(handles.vec_F3_2,'Visible','on') +set(handles.thresh_vec2C,'Visible','on') +set(handles.thresh_vec2C_text,'Visible','on') +set(handles.thresh_vel2,'Visible','on') +set(handles.thresh_vel2_text,'Visible','on') +set(handles.mask_fix2,'Visible','on') +set(handles.get_mask_fix2,'Visible','on') +set(handles.list_pair_civ2,'Visible','on') +set(handles.subdir_civ2,'Visible','on') +set(handles.subdir_civ2_text,'Visible','on') +set(handles.get_ref_fix2,'Visible','on') +set(handles.ref_fix2,'Visible','on') +set(handles.inf_sup2,'Visible','on') +set(handles.field_ref2,'Visible','on') + +%---------------------------------------------------------- +function desable_fix2(handles) +set(handles.frame_fix2,'BackgroundColor',[0.831 0.816 0.784]) +set(handles.REMOVE2,'Visible','off') +set(handles.vec_Fmin2_2,'Visible','off') +set(handles.vec_F4,'Visible','off') +set(handles.vec_F3_2,'Visible','off') +set(handles.thresh_vec2C,'Visible','off') +set(handles.thresh_vec2C_text,'Visible','off') +set(handles.thresh_vel2,'Visible','off') +set(handles.thresh_vel2_text,'Visible','off') +set(handles.mask_fix2,'Visible','off') +set(handles.get_mask_fix2,'Visible','off') +set(handles.get_ref_fix2,'Visible','off') +set(handles.ref_fix2,'Visible','off') +set(handles.inf_sup2,'Visible','off') +set(handles.field_ref2,'Visible','off') +if isequal(get(handles.CIV2,'Value'),0) & isequal(get(handles.PATCH2,'Value'),0) + set(handles.list_pair_civ2,'Visible','off') + set(handles.subdir_civ2,'Visible','off') + set(handles.subdir_civ2_text,'Visible','off') +end + +%-------------------------------------------------------------- +function enable_patch2(handles) +set(handles.frame_patch2,'BackgroundColor',[1 1 0]) +set(handles.rho_patch2,'Visible','on') +set(handles.rho_text2,'Visible','on') +set(handles.thresh_patch2,'Visible','on') +set(handles.thresh_text2,'Visible','on') +set(handles.subdomain_patch2,'Visible','on') +set(handles.subdomain_text2,'Visible','on') +set(handles.nx_patch2,'Visible','on') +set(handles.ny_patch2,'Visible','on') +set(handles.nx_patch2_title,'Visible','on') +set(handles.ny_patch2_title,'Visible','on') +set(handles.get_gridpatch2,'Visible','on') +set(handles.grid_patch2,'Visible','on') +set(handles.list_pair_civ2,'Visible','on') +set(handles.subdir_civ2,'Visible','on') +set(handles.subdir_civ2_text,'Visible','on') + +%-------------------------------------------------------------- +function desable_patch2(handles) +set(handles.frame_patch2,'BackgroundColor',[0.831 0.816 0.784]) +set(handles.rho_patch2,'Visible','off') +set(handles.rho_text2,'Visible','off') +set(handles.thresh_patch2,'Visible','off') +set(handles.thresh_text2,'Visible','off') +set(handles.subdomain_patch2,'Visible','off') +set(handles.subdomain_text2,'Visible','off') +set(handles.nx_patch2,'Visible','off') +set(handles.ny_patch2,'Visible','off') +set(handles.nx_patch2_title,'Visible','off') +set(handles.ny_patch2_title,'Visible','off') +set(handles.get_gridpatch2,'Visible','off') +set(handles.grid_patch2,'Visible','off') +if isequal(get(handles.CIV2,'Value'),0) & isequal(get(handles.FIX2,'Value'),0) + set(handles.list_pair_civ2,'Visible','off') + set(handles.subdir_civ2,'Visible','off') + set(handles.subdir_civ2_text,'Visible','off') +end + +% --- Executes on button press in test_interp. +function test_interp_Callback(hObject, eventdata, handles) + + +%------------------------------------------------ +%Read the parameters for civ1 on the interface +%-------------------------------------------------- +function par=read_param_civ1(handles,file_ima) + +ibx_val=str2num(get(handles.ibx,'String')); +par.correlationBoxesSize_X=num2str(ibx_val); +iby_val=str2num(get(handles.iby,'String')); +par.correlationBoxesSize_Y=num2str(iby_val); +ibz_val=str2num(get(handles.ibz,'String')); +par.correlationBoxesSize_Z=num2str(ibz_val); +isx=get(handles.isx,'String'); +if isempty(str2num(isx)), isx='41'; set(handles.isx,'String','41'), end; %default +maxDisplacement_X=floor((str2num(isx)-ibx_val)/2); +par.maxDisplacement_X=num2str(maxDisplacement_X); +isy=get(handles.isy,'String'); +if isempty(str2num(isy)), isy='41'; set(handles.isy,'String','41'), end; %default +maxDisplacement_Y=floor((str2num(isy)-iby_val)/2); +par.maxDisplacement_Y=num2str(maxDisplacement_Y); +isz=get(handles.isz,'String'); +if isempty(str2num(isz)), isz='41'; set(handles.isz,'String','41'), end; %default +maxDisplacement_Z=floor((str2num(isz)-ibz_val)/2); +par.maxDisplacement_Z=num2str(maxDisplacement_Z); +% par.rho=get(handles.rho,'String'); +par.gridSpacing_X=get(handles.dx_civ1,'String'); +par.gridSpacing_Y=get(handles.dy_civ1,'String'); +par.gridSpacing_Z=get(handles.dz_civ1,'String'); +% Zmin=str2num(get(handles.first_j,'String'))-1; +Zmax=str2num(get(handles.nb_field2,'String')); +par.gridLimits_Xmin=0; +par.gridLimits_Ymin=0; +par.gridLimits_Zmin=0; +% A=imread(file_ima);%read the first image to get the size +%sizim=size(A); +par.gridLimits_Xmax=1024;%num2str(sizim(2)); +par.gridLimits_Ymax=1024;%num2str(sizim(1)); +par.gridLimits_Zmax=Zmax; +par.grid='grille'; +par.grid_division=4; +par.hart=0; +par.ratioHoverZ=1; + +% +% %---------------------------------------------------------------- +% function par=read_param_civ2(handles,file_ima) +% par.ibx=get(handles.ibx_civ2,'String'); +% par.iby=get(handles.iby_civ2,'String'); +% par.rho=get(handles.rho_civ2,'String'); +% par.decimal=int2str(get(handles.decimal,'Value')); +% par.deformation=int2str(get(handles.deformation,'Value')); +% par.dx=get(handles.dx_civ2,'String'); +% par.dy=get(handles.dy_civ2,'String'); +% if isequal(str2num(par.dx),[]) +% if isempty(get(handles.grid_civ2,'String')); +% par.dx='0'; %just read by civ_3D program, not used +% else +% par.dx='20';%default +% set(handles.dx_civ2,'String','20'); +% end +% end +% if isequal(str2num(par.dy),[]) +% if isempty(get(handles.grid_civ2,'String')); +% par.dy='0';%just read by civ_3D program, not used +% else +% par.dy='20';%default +% set(handles.dy_civ2,'String','20'); +% end +% end +% par.pxcmx=get(handles.pxcmx,'String'); +% par.pxcmy=get(handles.pxcmy,'String'); +% if isempty(str2num(par.pxcmx)) |isempty(str2num(par.pxcmy)) +% par.pxcmx='1'; +% par.pxcmy='1'; +% end +% % par.npx=get(handles.pxcmx,'UserData'); +% % par.npy=get(handles.pxcmy,'UserData'); +% A=imread(file_ima);%read the first image to get the size +% sizim=size(A); +% par.npx=num2str(sizim(2)); +% par.npy=num2str(sizim(1)); +% time=get(handles.displ_filebase,'UserData'); %get the set of times +% par.gridname=get(handles.grid_civ2,'String'); +% par.gridflag='y'; +% if isequal(par.gridname,'')| isempty(par.gridname) +% par.gridname='nogrid'; +% par.gridflag='n'; +% end + + +%--------------------------------------------------------- +%CIV1 CIV1 CIV1 CIV1 +%---------------------------------------------------------- +function cmd_CIV1=BATCH_CIV1(filename,namelog,par,handles) +%pixels per cm and matrix of the image times, read from the .civ_3D file by uvmat +global civ1_exe Civ_exe sge%name of the executable for civ1 calculation + +%changes : filename_cmx -> filename ( no extension ) + + if isequal(par.Dt,'0') + par.Dt='1' ;%case of 'displacement' mode + end + + textcmx={'############## CMX file';... + ['FirstImage ' par.filename_ima_a];... + ['LastImage ' par.filename_ima_b];... + 'XX' ;... + ['Mask ' par.maskflag] ;... + ['MaskName ' par.maskname];... + ['ImageSize ' par.npx ' ' par.npy];... %VERIFIER CAS GENERAL ? + ['CorrelationBoxesSize ' par.ibx ' ' par.iby];... + ['SearchBoxeSize ' par.isx ' ' par.isy];... + ['RO ' par.rho];... + ['GridSpacing ' par.dx ' ' par.dy];... + 'XX 1.0';... + ['Dt_TO ' par.Dt ' ' par.T0];... + ['PixCmXY ' par.pxcmx ' ' par.pxcmy];... + 'XX 1';... + ['ShiftXY ' par.shiftx ' ' par.shifty];... + ['Grid ' par.gridflag];... + ['GridName ' par.gridname] ;... + 'XX 85';... + 'XX 1.0';... + 'XX 1.0';... + 'Hart 1';... + 'DecimalShift 0';... + 'Deformation 0';... + 'CorrelationMin 0';... + 'IntensityMin 0';... + 'SeuilImage n';... + 'SeuilImageValues 0 4096';... + ['ImageToUse ' par.term_a ' ' par.term_b];... % VERIFIER ? + 'ImageUsedBefore null null'}; + + textout=char(textcmx); + % timeL1=clock; + dlmwrite([filename '.cmx'],textout,''); + % timeL2=clock; + % timciv1=etime(timeL2,timeL1) + if sge + cmd_CIV1=[civ1_exe ' -f ' filename '.cmx' ]; % redirect standard output to the log file + else + cmd_CIV1=[civ1_exe ' -f ' filename_cmx ' > ' namelog ' 2>&1']; % redirect standard output to the log file + end + if(isunix) + [Rootbat,Filebat,extbat]=fileparts(namelog); + ncName=fullfile(Rootbat,[ Filebat '.nc']); + cmd_CIV1=char({cmd_CIV1 ; ['mv ' namelog ' ' namelog '.civ1.log'];['chmod g+w ' ncName]}); + else + cmd_CIV1=char({cmd_CIV1 ; ['copy /Y ' namelog ' ' namelog '.civ1.log']}); + end + +%--------------------------------------------------------- +%CIV1 Unified +%---------------------------------------------------------- +function xml_civ1_parameters=BATCH_CIV1_Unified(filename,namelog,par,handles) +%pixels per cm and matrix of the image times, read from the .civ_3D file by uvmat +global civ1_exe Civ_exe%name of the executable for civ1 calculation + + civ1.image1=par.filename_ima_a; + civ1.image2=par.filename_ima_b; + civ1.imageSize_X=par.npx; + civ1.imageSize_Y=par.npy; + civ1.outputFileName=[filename '.nc']; + civ1.correlationBoxesSize_X=par.ibx; + civ1.correlationBoxesSize_Y=par.iby; + civ1.searchBoxesSize_X=par.isx; + civ1.searchBoxesSize_Y=par.isy; + civ1.globalShift_X=par.shiftx; + civ1.globalShift_Y=par.shifty; + civ1.ro=par.rho; + civ1.hart='y'; + if isequal(par.gridflag,'y') + civ1.grid=par.gridname; + end + civ1.gridSpacing_X=par.dx; + civ1.gridSpacing_Y=par.dy; + if isequal(par.maskflag,'y') + civ1.mask=par.maskname; + end + civ1.dt=par.Dt; + civ1.unit='pixel'; + civ1.absolut_time_T0=par.T0; + civ1.pixcmx=par.pxcmx; + civ1.pixcmy=par.pxcmy; + civ1.convectFlow='n'; + + xml_civ1_parameters=civ1; + +%--------------------------------------------------------- +%CIV2 CIV2 CIV2 CIV2 +%---------------------------------------------------------- +function cmd_CIV2=BATCH_CIV2(filename_cmx,namelog,par) +%pixels per cm and matrix of the image times, read from the .civ_3D file by uvmat +global civ2_exe sge%name of the executable for civ1 calculation + if isequal(par.Dt,'0') + par.Dt='1' ;%case of 'displacement' mode + end +textcmx={'############## CMX file';... +['FirstImage ' par.filename_ima_a];... +['LastImage ' par.filename_ima_b];... +'XX' ;... +['Mask ' par.maskflag];... +['MaskName ' par.maskname];... +['ImageSize ' par.npx ' ' par.npy];... +['CorrelationBoxesSize ' par.ibx ' ' par.iby];... +['SearchBoxeSize ' par.ibx ' ' par.iby];... +['RO ' par.rho];... +['GridSpacing ' par.dx ' ' par.dy];... +'XX 1.0';... +['Dt_TO ' par.Dt ' ' par.T0];... +['PixCmXY ' par.pxcmx ' ' par.pxcmy];... +'XX 1';... +['ShiftXY 0 0'];... +['Grid ' par.gridflag];... +['GridName ' par.gridname];... +'XX 85';... +'XX 1.0';... +'XX 1.0';... +'Hart 1';... +['DecimalShift ' par.decimal];... +['Deformation ' par.deformation];... +'CorrelationMin 0';... +'IntensityMin 0';... +'SeuilImage n';... +'SeuilImageValues 0 4096';... +['ImageToUse ' par.term_a ' ' par.term_b];... % VERIFIER ? +['ImageUsedBefore ' par.filename_nc1]}; + textout=char(textcmx); + dlmwrite([filename_cmx '2'] ,textout,''); + if sge + cmd_CIV2=[civ2_exe ' -f ' filename_cmx ]; % redirect standard output to the log file + else + cmd_CIV2=[civ2_exe ' -f ' filename_cmx ' > ' namelog ' 2>&1']; % redirect standard output to the log file + end + + +% --- Executes on button press in HELP. +function HELP_Callback(hObject, eventdata, handles) +path_to_uvmat=which ('uvmat');% check the path of uvmat +pathelp=fileparts(path_to_uvmat); +helpfile=fullfile(pathelp,'UVMAT_DOC','uvmat_doc.html'); +if isempty(dir(helpfile)), errordlg('Please put the help file uvmat_doc.html in the directory UVMAT/UVMAT_DOC') +else +web([helpfile '#civ_3D']) +end + + +%---------------------------------------------------------- +%--read images and convert them to the uint16 format used for PIV +function A=read_image(filename,nom_type,npx,npy,num); +%npx, npy are the dimensions needed for the raw SMD images +%num is the view number needed for an avi movie +if isequal(nom_type,'avi') + mov=aviread(filename,num); + A=frame2im(mov(1)); + A=sum(double(A),3); + A=uint16(A); +elseif isequal(nom_type,'raw_SMD') + [fid,message]=fopen(filename,'r'); + B=fread(fid,Inf,'int16',0,'ieee-le');%read 16 bit binary file + A=(reshape(B,npx,npy))'; %remplissage ligne par ligne avec une matrice colonne ? transposer(uB) pour avoir une matrice ligne + A=uint16(A); + fclose(fid); +else + A=imread(filename); + siz=size(A); + if length(siz)==3;%color images + A=sum(double(A),3); + end + A=uint16(A); +end + +%---------------------------------------------------------------- +%Executes on carriage return on the time interval dt +%---------------------------------------------------------------- +function dt_Callback(hObject, eventdata, handles) +%determine the set of times and possible intervals for CIV_3D +% answer=inputdlg('time interval between images?'); + dt=(1/1000)*str2num(get(handles.dt,'String')); + nbfield=str2num(get(handles.nb_field,'String')); %last image number selected in the processing series + time=(dt*[0:nbfield-1])'; +% set(handles.incr_i,'UserData',dt);%store the time interval between successive images + set(handles.displ_filebase,'UserData',time); %store the set of times + for index=1:min(nbfield-1,200) + displ_num(1,index)=1; + displ_num(2,index)=1; + displ_num(3,index)=-floor(index/2); + displ_num(4,index)=ceil(index/2); + end +set(handles.list_pair_civ1,'Value',1); +set(handles.list_pair_civ1,'UserData',displ_num); +set(handles.list_pair_civ2,'Value',1); +%update the list of time intervals +find_netcpair_civ1(hObject, eventdata, handles) +find_netcpair_civ2(hObject, eventdata, handles) + +%------------------------------------------------------- +function ref_i_Callback(hObject, eventdata, handles) +mode_list=get(handles.mode,'String'); +mode_value=get(handles.mode,'Value'); +mode=mode_list{mode_value}; +if isequal(get(handles.CIV1,'Value'),0)| isequal(mode,'series(Di)') + find_netcpair_civ1(hObject, eventdata, handles);% update the menu of pairs depending on the available netcdf files +end +if isequal(mode,'series(Di)') | ...% we do patch2 only + (get(handles.CIV2,'Value')==0 & get(handles.CIV1,'Value')==0 & get(handles.FIX1,'Value')==0 & get(handles.PATCH1,'Value')==0) + find_netcpair_civ2(hObject, eventdata, handles); +end + +%---------------------------------------------------- +function ref_j_Callback(hObject, eventdata, handles) +mode_list=get(handles.mode,'String'); +mode_value=get(handles.mode,'Value'); +mode=mode_list{mode_value}; +if isequal(get(handles.CIV1,'Value'),0)| isequal(mode,'series(Dj)') + find_netcpair_civ1(hObject, eventdata, handles);% update the menu of pairs depending on the available netcdf files +end +if isequal(mode,'series(Dj)') | ... + (get(handles.CIV2,'Value')==0 & get(handles.CIV1,'Value')==0 & get(handles.FIX1,'Value')==0 & get(handles.PATCH1,'Value')==0) + find_netcpair_civ2(hObject, eventdata, handles); +end +%---------------------------------------------------- +% --- Executes on button press in compare. +function compare_Callback(hObject, eventdata, handles) +test=get(handles.compare,'Value'); +if test + filebase=get(handles.displ_filebase,'String'); + browse=get(handles.browse_root,'Userdata'); + browse.nom_type_ima1=browse.nom_type_ima; + set(handles.browse_root,'UserData',browse); + set(handles.displ_filebase2,'Visible','On');%mkes the second file input window visible + set(handles.displ_filebase2,'String',filebase); + mode_store=get(handles.mode,'String');%get the present 'mode' + set(handles.compare,'UserData',mode_store);%store the mode display + set(handles.mode,'Value',1) + set(handles.mode,'String',{'displacement';'st_pair j1-j2'}) +else + set(handles.displ_filebase2,'Visible','Off'); + set(handles.displ_filebase2,'String',[]); + mode_store=get(handles.compare,'UserData'); + set(handles.mode,'String',mode_store) + set(handles.test_stereo1,'Value',0) + set(handles.test_stereo2,'Value',0) +end +mode_Callback(hObject, eventdata, handles) + +%----------------------------------------------------------- +% --- Executes on button press in get_ref_fix1. +function get_ref_fix1_Callback(hObject, eventdata, handles) +filebase=get(handles.displ_filebase,'String'); +[FileName, PathName, filterindex] = uigetfile( ... + {'*.nc', ' (*.nc)'; + '*.nc', 'netcdf files '; ... + '*.*', 'All Files (*.*)'}, ... + 'Pick a file',filebase); + +fileinput=[PathName FileName]; +sizf=size(fileinput); +if (~ischar(fileinput)|~isequal(sizf(1),1)),return;end %stop if fileinput not a character string +%[filebasesub,field_count,str2,str_a,str_b,ref.ext,ref.nom_type,ref.subdir]=name2display(fileinput); +[Path,File,field_count,str2,str_a,str_b,ref.ext,ref.nom_type,ref.subdir]=name2display(fileinput); +%filebase=fullfile(RootPath,RootFile); +% [Pth,FileN]=fileparts(filebasesub); +% Pth=fileparts(Pth); +ref.filebase=fullfile(Path,File); +ref.num_a=stra2num(str_a); +ref.num_b=stra2num(str_b); +ref.num1=str2num(field_count); +ref.num2=str2num(str2); +browse=[];%initialisation +if ~isequal(ref.ext,'.nc') + errordlg('the reference file must be in netcdf format (*.nc)') + return +end +% [path,name]=fileparts(ref.filebase); +set(handles.ref_fix1,'String',[fullfile(ref.subdir,File) '....nc']); +set(handles.ref_fix1,'UserData',ref) +menu_field{1}='civ1'; +Data=nc2struct(fileinput,[]); +if isfield(Data,'patch') & isequal(Data.patch,1) + menu_field{2}='filter1'; +end +if isfield(Data,'civ2') & isequal(Data.civ2,1) + menu_field{3}='civ2'; +end +if isfield(Data,'patch2') & isequal(Data.patch2,1) + menu_field{4}='filter2'; +end +% [cte_detect,vdt,cte_read]=read_netcdf(fileinput,{'patch','civ2','patch2'}); +% if isequal(cte_detect(1),1) & isequal(cte_read(1),1) +% menu_field{2}='filter1'; +% end +% if isequal(cte_detect(2),1) & isequal(cte_read(2),1) +% menu_field{3}='civ2'; +% end +% if isequal(cte_detect(3),1) & isequal(cte_read(3),1) +% menu_field{4}='filter2'; +% end +set(handles.field_ref1,'String',menu_field); +set(handles.field_ref1,'Value',length(menu_field)); +set(handles.inf_sup1,'Value',2); +set(handles.thresh_vel,'String','1');%default threshold +set(handles.ref_fix1,'Enable','on') + +%--------------------------------------------------------------- +% --- Executes on button press in get_ref_fix2. +function get_ref_fix2_Callback(hObject, eventdata, handles) +if isequal(get(handles.get_ref_fix2,'Value'),1) + filebase=get(handles.displ_filebase,'String'); + [FileName, PathName, filterindex] = uigetfile( ... + {'*.nc', ' (*.nc)'; + '*.nc', 'netcdf files '; ... + '*.*', 'All Files (*.*)'}, ... + 'Pick a file',filebase); + fileinput=[PathName FileName]; + sizf=size(fileinput); + if (~ischar(fileinput)|~isequal(sizf(1),1)),return;end %stop if fileinput not a character string + %[filebasesub,field_count,str2,str_a,str_b,ref.ext,ref.nom_type,ref.subdir]=name2display(fileinput); + [Path,File,field_count,str2,str_a,str_b,ref.ext,ref.nom_type,ref.subdir]=name2display(fileinput); +% [Pth,FileN]=fileparts(filebasesub); +% Pth=fileparts(Pth); + ref.filebase=fullfile(Path,File) + ref.num_a=stra2num(str_a); + ref.num_b=stra2num(str_b); + ref.num1=str2num(field_count); + ref.num2=str2num(str2); + browse=[];%initialisation + if ~isequal(ref.ext,'.nc') + errordlg('the reference file must be in netcdf format (*.nc)') + return + end +% [path,name]=fileparts(ref.filebase); + set(handles.ref_fix2,'String',[fullfile(ref.subdir,File) '....nc']); + set(handles.ref_fix2,'UserData',ref) + menu_field{1}='civ1'; +% [cte_detect,vdt,cte_read]=read_netcdf(fileinput,{'patch','civ2','patch2'}); + Data=nc2struct(fileinput,[]); + if isfield(Data,'patch') & isequal(Data.patch,1) + menu_field{2}='filter1'; + end + if isfield(Data,'civ2') & isequal(Data.civ2,1) + menu_field{3}='civ2'; + end + if isfield(Data,'patch2') & isequal(Data.patch2,1) + menu_field{4}='filter2'; + end + +% if isequal(cte_detect(1),1) & isequal(cte_read(1),1) +% menu_field{2}='filter1'; +% end +% if isequal(cte_detect(2),1) & isequal(cte_read(2),1) +% menu_field{3}='civ2'; +% end +% if isequal(cte_detect(3),1) & isequal(cte_read(3),1) +% menu_field{4}='filter2'; +% end + set(handles.field_ref2,'String',menu_field); + set(handles.field_ref2,'Value',length(menu_field)); + set(handles.inf_sup2,'Value',2); + set(handles.thresh_vel2,'String','1');%default threshold + set(handles.ref_fix2,'Enable','on') + set(handles.ref_fix2,'Visible','on') + set(handles.field_ref2,'Visible','on') +else + set(handles.ref_fix2,'Visible','off') + set(handles.field_ref2,'Visible','off') +end +%------------------------------------------------------- + +function ref_fix1_Callback(hObject, eventdata, handles) + set(handles.inf_sup1,'Value',1); + set(handles.field_ref1,'Value',1) + set(handles.field_ref1,'String',{' '}) + set(handles.ref_fix1,'UserData',[]); + set(handles.ref_fix1,'String',''); + set(handles.thresh_vel1,'String','0'); + + +%------------------------------------------------------ + +function ref_fix2_Callback(hObject, eventdata, handles) + set(handles.inf_sup2,'Value',1); + set(handles.field_ref2,'Value',1) + set(handles.field_ref2,'String',{' '}) + set(handles.ref_fix2,'UserData',[]); + set(handles.ref_fix2,'String',''); + set(handles.thresh_vel2,'String','0'); + +%-------------------------------------------------------- +% --- Executes on selection change in inf_sup1. +function inf_sup1_Callback(hObject, eventdata, handles) + +%-------------------------------------------------------------------------- + + +% --- Executes on selection change in field_ref. +function field_ref_Callback(hObject, eventdata, handles) + +%------------------------------------------------------------------------- + +% --- Executes on selection change in field_ref2. +function field_ref2_Callback(hObject, eventdata, handles) + +% ----------------------------------------------------------- +% transform letters to numbers +%-------------------------------------------- +function numres=stra2num(str) +numres=double(str)-96; +if double(str) >= 48 & double(str) <= 57 % = 1 for numbers + numres=str2num(str); +end + + +% --- Executes on button press in test_stereo1. +function test_stereo1_Callback(hObject, eventdata, handles) +if isequal(get(handles.test_stereo1,'Value'),0) + set(handles.subdomain_patch1,'Visible','on') + set(handles.rho_patch1,'Visible','on') +else + set(handles.subdomain_patch1,'Visible','off') + set(handles.rho_patch1,'Visible','off') +end + +% --- Executes on button press in test_stereo2. +function test_stereo2_Callback(hObject, eventdata, handles) +if isequal(get(handles.test_stereo2,'Value'),0) + set(handles.subdomain_patch2,'Visible','on') + set(handles.rho_patch2,'Visible','on') +else + set(handles.subdomain_patch2,'Visible','off') + set(handles.rho_patch2,'Visible','off') +end + +% --- Executes on button press in ImaThreshold. +function ImaThreshold_Callback(hObject, eventdata, handles) +if isequal(get(handles.ImaThreshold,'Value'),1) + set(handles.MinIma,'Visible','on') + set(handles.MaxIma,'Visible','on') +else + set(handles.MinIma,'Visible','off') + set(handles.MaxIma,'Visible','off') +end + + +% --- Executes on button press in ImaThreshold2. +function ImaThreshold2_Callback(hObject, eventdata, handles) +if isequal(get(handles.ImaThreshold2,'Value'),1) + set(handles.MinIma2,'Visible','on') + set(handles.MaxIma2,'Visible','on') +else + set(handles.MinIma2,'Visible','off') + set(handles.MaxIma2,'Visible','off') +end + + + +% --- Executes on button press in Experimental. +function Experimental_Callback(hObject, eventdata, handles) + + + +function ibz_Callback(hObject, eventdata, handles) +% hObject handle to ibz (see GCBO) +% eventdata reserved - to be defined in a future version of MATLAB +% handles structure with handles and user data (see GUIDATA) + +% Hints: get(hObject,'String') returns contents of ibz as text +% str2double(get(hObject,'String')) returns contents of ibz as a double + + +% --- Executes during object creation, after setting all properties. +function ibz_CreateFcn(hObject, eventdata, handles) +% hObject handle to ibz (see GCBO) +% eventdata reserved - to be defined in a future version of MATLAB +% handles empty - handles not created until after all CreateFcns called + +% Hint: edit controls usually have a white background on Windows. +% See ISPC and COMPUTER. +if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor')) + set(hObject,'BackgroundColor','white'); +end + + + +function edit74_Callback(hObject, eventdata, handles) +% hObject handle to edit74 (see GCBO) +% eventdata reserved - to be defined in a future version of MATLAB +% handles structure with handles and user data (see GUIDATA) + +% Hints: get(hObject,'String') returns contents of edit74 as text +% str2double(get(hObject,'String')) returns contents of edit74 as a double + + +% --- Executes during object creation, after setting all properties. +function edit74_CreateFcn(hObject, eventdata, handles) +% hObject handle to edit74 (see GCBO) +% eventdata reserved - to be defined in a future version of MATLAB +% handles empty - handles not created until after all CreateFcns called + +% Hint: edit controls usually have a white background on Windows. +% See ISPC and COMPUTER. +if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor')) + set(hObject,'BackgroundColor','white'); +end + + + +function edit75_Callback(hObject, eventdata, handles) +% hObject handle to edit75 (see GCBO) +% eventdata reserved - to be defined in a future version of MATLAB +% handles structure with handles and user data (see GUIDATA) + +% Hints: get(hObject,'String') returns contents of edit75 as text +% str2double(get(hObject,'String')) returns contents of edit75 as a double + + +% --- Executes during object creation, after setting all properties. +function edit75_CreateFcn(hObject, eventdata, handles) +% hObject handle to edit75 (see GCBO) +% eventdata reserved - to be defined in a future version of MATLAB +% handles empty - handles not created until after all CreateFcns called + +% Hint: edit controls usually have a white background on Windows. +% See ISPC and COMPUTER. +if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor')) + set(hObject,'BackgroundColor','white'); +end + + + +function dz_civ1_Callback(hObject, eventdata, handles) +% hObject handle to dz_civ1 (see GCBO) +% eventdata reserved - to be defined in a future version of MATLAB +% handles structure with handles and user data (see GUIDATA) + +% Hints: get(hObject,'String') returns contents of dz_civ1 as text +% str2double(get(hObject,'String')) returns contents of dz_civ1 as a double + + +% --- Executes during object creation, after setting all properties. +function dz_civ1_CreateFcn(hObject, eventdata, handles) +% hObject handle to dz_civ1 (see GCBO) +% eventdata reserved - to be defined in a future version of MATLAB +% handles empty - handles not created until after all CreateFcns called + +% Hint: edit controls usually have a white background on Windows. +% See ISPC and COMPUTER. +if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor')) + set(hObject,'BackgroundColor','white'); +end + + Index: /trunk/src/close_fig.m =================================================================== --- /trunk/src/close_fig.m (revision 2) +++ /trunk/src/close_fig.m (revision 2) @@ -0,0 +1,12 @@ +%'close_fig': function activated when a figure is closed +%---------------------------------------------------------------- +% function close_fig(ggg,eventdata,hparent,type) +% activated by the command: +%set(hObject,'DeleteFcn',{@close_fig,hparent,type}) +% where hObject is the handle of the figure +% + +function close_fig(ggg,eventdata,hparent,type) +if isequal(type,'zoom') + delete(hparent) % delete the rectangle showing the zoom graph in the parent fig +end Index: /trunk/src/copyfields.m =================================================================== --- /trunk/src/copyfields.m (revision 2) +++ /trunk/src/copyfields.m (revision 2) @@ -0,0 +1,22 @@ +%'copyfields' copy fields between two matlab structures +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% +% OUPUT: +% NewData: resulting structure +% +%INPUT: +% listfields: cell arrays representing the list of field names to be copied +% SourceData: structure containing the source data to copy in NewData +% OldData: (optional) preexisting data structure. + +function NewData=copyfields(listfields,SourceData,OldData) +if ~exist('OldData','var') + OldData=[]; +end +NewData=OldData;%default +for ifield=1:length(listfields) + if isfield(SourceData,listfields{ifield}) & ~isempty(eval(['SourceData.' listfields{ifield}])) + eval(['NewData.' listfields{ifield} '=SourceData.' listfields{ifield} ';']); + elseif isfield(OldData,listfields{ifield}) + NewData=rmfield(NewData,listfields{ifield}); + end +end Index: /trunk/src/dataview.m =================================================================== --- /trunk/src/dataview.m (revision 2) +++ /trunk/src/dataview.m (revision 2) @@ -0,0 +1,513 @@ +%TEST 'dataview': function for scanning directories in a campaign (TEST) +%------------------------------------------------------------------------ +% function varargout = series(varargin) +% associated with the GUI dataview.fig +% +%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +% Copyright Joel Sommeria, 2008, LEGI / CNRS-UJF-INPG, sommeria@coriolis-legi.org. +%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +% This file is part of the toolbox UVMAT. +% +% UVMAT is free software; you can redistribute it and/or modify +% it under the terms of the GNU General Public License as published by +% the Free Software Foundation; either version 2 of the License, or +% (at your option) any later version. +% +% UVMAT is distributed in the hope that it will be useful, +% but WITHOUT ANY WARRANTY; without even the implied warranty of +% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +% GNU General Public License (file UVMAT/COPYING.txt) for more details. +%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA + +function varargout = dataview(varargin) + +% Last Modified by GUIDE v2.5 28-Apr-2009 00:12:36 + +% Begin initialization code - DO NOT EDIT +gui_Singleton = 1; +gui_State = struct('gui_Name', mfilename, ... + 'gui_Singleton', gui_Singleton, ... + 'gui_OpeningFcn', @dataview_OpeningFcn, ... + 'gui_OutputFcn', @dataview_OutputFcn, ... + 'gui_LayoutFcn', [] , ... + 'gui_Callback', []); +if nargin & isstr(varargin{1}) + gui_State.gui_Callback = str2func(varargin{1}); +end + +if nargout + [varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:}); +else + gui_mainfcn(gui_State, varargin{:}); +end +% End initialization code - DO NOT EDIT + + +% --- Executes just before dataview is made visible. +function dataview_OpeningFcn(hObject, eventdata, handles, varargin) + +% Choose default command line output for dataview +handles.output = hObject; + +% Update handles structure +guidata(hObject, handles); + +%---------------------------------------------------------------- +% --- Outputs from this function are returned to the command line. +function varargout = dataview_OutputFcn(hObject, eventdata, handles) + +% Get default command line output from handles structure +varargout{1} = handles.output; + + + +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% +%------------------------------------------------------ +% --- Executes on button press in browser. +function browser_Callback(hObject, eventdata, handles) +%------------------------------------------------------------------------ + +CurrentFile='/coriolis/bigone/PROJETS';%get(handles.RootDirectory,'String'); +set(handles.SubCampaignTest,'Value',0) +CampaignDir=uigetdir(CurrentFile,'Open the Campaign directory'); %file browser +set(handles.RootDirectory,'String',CampaignDir) +RootDirectory_Callback(hObject, eventdata, handles) + +% --- Executes on button press in open_SubCampaign. +function OpenSubCampaign_Callback(hObject, eventdata, handles) +CurrentFile='/coriolis/bigone/PROJETS';%get(handles.RootDirectory,'String'); +set(handles.SubCampaignTest,'Value',1) +CampaignDir=uigetdir(CurrentFile,'Open the Campaign directory'); %file browser +set(handles.RootDirectory,'String',CampaignDir) + +RootDirectory_Callback(hObject, eventdata, handles) + +%------------------------------------------------------------------------ + +function RootDirectory_Callback(hObject, eventdata, handles) +CampaignDir=get(handles.RootDirectory,'String'); +if exist(CampaignDir,'dir') + hdir=dir(CampaignDir); %list files and dirs + idir=0; + for ilist=1:length(hdir) + if hdir(ilist).isdir + dirname=hdir(ilist).name; + if ~isequal(dirname(1),'.')&&~isequal(dirname(1),'0') + idir=idir+1; + ExpName{idir}=hdir(ilist).name; + end + % look for the list of 'devices' + else + %warning for isolated files + end + end + set(handles.ListExperiments,'String',[{'*'};ExpName']) + set(handles.ListExperiments,'Value',1) + ListExperiments_Callback(hObject, eventdata, handles) +else + warndlg_uvmat(['The input ' CampaignDir ' is not a directory'],'ERROR') +end + +%------------------------------------------------------------------------ +% --- Executes on selection change in ListExperiments. + function ListExperiments_Callback(hObject, eventdata, handles) +CurrentPath=get(handles.RootDirectory,'String'); +ListExperiments=get(handles.ListExperiments,'String'); +list_val=get(handles.ListExperiments,'Value'); +if isequal(list_val(1),1) + ListExperiments=ListExperiments(2:end); %choose all experiments + testList=1; + set(handles.ListExperiments,'Value',1) +else + ListExperiments=ListExperiments(list_val);%choose selected experiments + testList=0; +end +set(handles.ListDevices,'Value',1) +set(handles.ListRecords,'Value',1) +set(handles.ListXml,'Value',1) +[ListDevices,ListRecords,ListXml,List]=ListDir(CurrentPath,ListExperiments,{},{}); +set(handles.ListRecords,'String',[{'*'};ListRecords']) +set(handles.ListDevices,'String',[{'*'};ListDevices']) +set(handles.ListXml,'String',[{'*'};ListXml']) +if testList + hh=get(handles.ListExperiments,'parent'); + set(hh,'UserData',List) +end +set(handles.CampaignDoc,'Visible','on') +set(handles.edit_xml,'Visible','on') + +%------------------------------------------------------------------------ +% --- Executes on button press in update_headings. +function ListDevices_Callback(hObject, eventdata, handles) +CurrentPath=get(handles.RootDirectory,'String'); +ListExperiments=get(handles.ListExperiments,'String'); +list_val=get(handles.ListExperiments,'Value'); +if isequal(list_val,1) + ListExperiments=ListExperiments(2:end); +else + ListExperiments=ListExperiments(list_val); +end +set(handles.ListRecords,'Value',1) +set(handles.ListXml,'Value',1) +ListDevices=get(handles.ListDevices,'String'); +list_val=get(handles.ListDevices,'Value'); +if isequal(list_val,1) + ListDevices=ListDevices(2:end); +else + ListDevices=ListDevices(list_val); +end +[ListDevices,ListRecords,ListXml]=ListDir(CurrentPath,ListExperiments,ListDevices,{}); +set(handles.ListRecords,'String',[{'*'};ListRecords']) +set(handles.ListXml,'String',[{'*'};ListXml']) + + +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + + + +%------------------------------------------------------------------------ +% --- Executes on selection change in ListRecords. +function ListRecords_Callback(hObject, eventdata, handles) +Value=get(handles.ListRecords,'Value'); +if isequal(Value(1),1) + set(handles.ListRecords,'Value',1); +end + +%------------------------------------------------------------------------ +% --- Executes on button press in CampaignDoc. +function CampaignDoc_Callback(hObject, eventdata, handles) +%------------------------------------------------------------------------ +answer=msgbox_uvmat('INPUT_Y-N','This function will update the global xml rpresentation of the data set and the Heading of each xml file') +if ~isequal(answer{1},'OK') + return +end +set(handles.ListExperiments,'Value',1) +ListExperiments_Callback(hObject, eventdata, handles)%update the overview of the experiment directories +hh=get(handles.CampaignDoc,'parent'); +List=get(hh,'UserData'); +Currentpath=get(handles.RootDirectory,'String'); +[Currentpath,Campaign,DirExt]=fileparts(Currentpath); +Campaign=[Campaign DirExt]; +t=xmltree; +t=set(t,1,'name','CampaignDoc'); +t = attributes(t,'add',1,'source','directory'); +SubCampaignTest=get(handles.SubCampaignTest,'Value'); +root_uid=1; +if SubCampaignTest + %TO DO open an exoiting xml doc + [t,root_uid]=add(t,1,'element','SubCampaign'); + t =attributes(t,'add',root_uid,'DirName',Campaign); +end +for iexp=1:length(List.Experiment) + set(handles.ListExperiments,'Value',iexp+1) + drawnow + test_mod=0; + [t,uid_exp]=add(t,root_uid,'element','Experiment'); + t = attributes(t,'add',uid_exp,'i',num2str(iexp)); + ExpName=List.Experiment{iexp}.name; + t = attributes(t,'add',uid_exp,'DirName',List.Experiment{iexp}.name); + + if isfield(List.Experiment{iexp},'Device') + for idevice=1:length(List.Experiment{iexp}.Device) + [t,uid_device]=add(t,uid_exp,'element','Device'); + DeviceName=List.Experiment{iexp}.Device{idevice}.name; + t = attributes(t,'add',uid_device,'DirName',List.Experiment{iexp}.Device{idevice}.name); + if isfield(List.Experiment{iexp}.Device{idevice},'xmlfile') + for ixml=1:length(List.Experiment{iexp}.Device{idevice}.xmlfile) + FileName=List.Experiment{iexp}.Device{idevice}.xmlfile{ixml}; + [Title,test]=check_heading(Currentpath,Campaign,ExpName,DeviceName,[],FileName,SubCampaignTest); + if test + [List.Experiment{iexp}.Device{idevice}.xmlfile{ixml} ' , Heading updated'] + end + if isequal(Title,'ImaDoc') + [t,uid_xml]=add(t,uid_device,'element','ImaDoc'); + t = attributes(t,'add',uid_xml,'source','file'); + [t]=add(t,uid_xml,'chardata',List.Experiment{iexp}.Device{idevice}.xmlfile{ixml}); + end + end + elseif isfield(List.Experiment{iexp}.Device{idevice},'Record') + for irecord=1:length(List.Experiment{iexp}.Device{idevice}.Record) + RecordName=List.Experiment{iexp}.Device{idevice}.Record{irecord}.name; + [t,uid_record]=add(t,uid_device,'element','Record'); + t = attributes(t,'add',uid_record,'DirName',RecordName); + if isfield(List.Experiment{iexp}.Device{idevice}.Record{irecord},'xmlfile') + for ixml=1:length(List.Experiment{iexp}.Device{idevice}.Record{irecord}.xmlfile) + FileName=List.Experiment{iexp}.Device{idevice}.Record{irecord}.xmlfile{ixml}; + [Title,test]=check_heading(Currentpath,Campaign,ExpName,DeviceName,RecordName,FileName,SubCampaignTest); + if test + [FileName ' , Heading updated'] + end + [t,uid_xml]=add(t,uid_record,'element','ImaDoc'); + t = attributes(t,'add',uid_xml,'source','file'); + [t]=add(t,uid_xml,'chardata',FileName); + end + end + end + end + end + end +end +set(handles.ListExperiments,'Value',1) +outputdir=get(handles.RootDirectory,'String'); +[path,dirname]=fileparts(outputdir); +outputfile=fullfile(outputdir,[dirname '.xml']); +%campaigndoc(t); +save(t,outputfile) + +%------------------------------------------------------------------------ +% --- Executes on button press in CampaignDoc. +function edit_xml_Callback(hObject, eventdata, handles) +%------------------------------------------------------------------------ +CurrentPath=get(handles.RootDirectory,'String'); +%[CurrentPath,Name,Ext]=fileparts(CurrentDir); +ListExperiments=get(handles.ListExperiments,'String'); +Value=get(handles.ListExperiments,'Value'); +if ~isequal(Value,1) + ListExperiments=ListExperiments(Value); +end +ListDevices=get(handles.ListDevices,'String'); +Value=get(handles.ListDevices,'Value'); +if ~isequal(Value,1) + ListDevices=ListDevices(Value); +end +ListRecords=get(handles.ListRecords,'String'); +Value=get(handles.ListRecords,'Value'); +if ~isequal(Value,1) + ListRecords=ListRecords(Value); +end +[ListDevices,ListRecords,ListXml,List]=ListDir(CurrentPath,ListExperiments,ListDevices,ListRecords); +ListXml=get(handles.ListXml,'String'); +Value=get(handles.ListXml,'Value'); +set(handles.ListXml,'Value',Value(1)); +if isequal(Value(1),1) + warndlg_uvmat('an xml file needs to be selected','ERROR') + return +else + XmlName=ListXml{Value(1)}; +end +for iexp=1:length(List.Experiment) + ExpName=List.Experiment{iexp}.name; + if isfield(List.Experiment{iexp},'Device') + for idevice=1:length(List.Experiment{iexp}.Device) + DeviceName=List.Experiment{iexp}.Device{idevice}.name; + if isfield(List.Experiment{iexp}.Device{idevice},'xmlfile') + for ixml=1:length(List.Experiment{iexp}.Device{idevice}.xmlfile) + FileName=List.Experiment{iexp}.Device{idevice}.xmlfile{ixml} + if isequal(FileName,XmlName) + editxml(fullfile(CurrentPath,ExpName,DeviceName,FileName)); + return + end + end + elseif isfield(List.Experiment{iexp}.Device{idevice},'Record') + for irecord=1:length(List.Experiment{iexp}.Device{idevice}.Record) + RecordName=List.Experiment{iexp}.Device{idevice}.Record{irecord}.name; + if isfield(List.Experiment{iexp}.Device{idevice}.Record{irecord},'xmlfile') + for ixml=1:length(List.Experiment{iexp}.Device{idevice}.Record{irecord}.xmlfile) + FileName=List.Experiment{iexp}.Device{idevice}.Record{irecord}.xmlfile{ixml}; + if isequal(FileName,XmlName) + editxml(fullfile(CurrentPath,ExpName,DeviceName,RecordName,FileName)); + return + end + end + end + end + end + end + end +end + + + +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% +% CurrentPath/Campaign: root directory +function [Title,test_mod]=check_heading(Currentpath,Campaign,Experiment,Device,Record,xmlname,testSubCampaign) + + %Shema for Heading: +% Campaign +% (SubCampaign) +% Experiment +% Device +% (Record) +% ImageName +% DateExp +% old: %Project: suppressed ( changed to Campaign) + %Exp: suppressed (changed to experiment) + %ImaNames: changed to ImageName +if exist('Record','var') && ~isempty(Record) + xmlfullname=fullfile(Currentpath,Campaign,Experiment,Device,Record,xmlname); + testrecord=1; +else + xmlfullname=fullfile(Currentpath,Campaign,Experiment,Device,xmlname); + testrecord=0; +end +if ~exist('testSubCampaign','var') + testSubCampaign=0; +end +if testSubCampaign + SubCampaign=Campaign; + [Currentpath,Campaign,DirExt]=fileparts(Currentpath); + Campaign=[Campaign DirExt]; +end +test_mod=0; %test for the modification of the xml file +t_device=xmltree(xmlfullname); +Title=get(t_device,1,'name'); +uid_child=children(t_device,1); +Heading_old=[]; +uidheading=0; +for ilist=1:length(uid_child) + name=get(t_device,uid_child(ilist),'name'); + if isequal(name,'Heading') + uidheading=uid_child(ilist); + end +end +if uidheading + subt=branch(t_device,uidheading); + Heading_old=convert(subt); +else + return % do not edit xml files without element 'Heading' +end +if ~(isfield(Heading_old,'Campaign')&& isequal(Heading_old.Campaign,Campaign)) + test_mod=1; +end +Heading.Campaign=Campaign; +if testSubCampaign + if ~(isfield(Heading_old,'SubCampaign')&& isequal(Heading_old.SubCampaign,SubCampaign)) + test_mod=1; + end + Heading.SubCampaign=SubCampaign; +end +if ~(isfield(Heading_old,'Experiment')&& isequal(Heading_old.Experiment,Experiment)) + test_mod=1; +end +Heading.Experiment=Experiment; +if ~(isfield(Heading_old,'Device')&& isequal(Heading_old.Device,Device)) + test_mod=1; +end +Heading.Device=Device; +if testrecord + if ~(isfield(Heading_old,'Record')&& isequal(Heading_old.Record,Record)) + test_mod=1; + end + Heading.Record=Record; +end +if isfield(Heading_old,'ImaNames') + test_mod=1; + if ~isempty(Heading_old.ImaNames) + Heading.ImageName=Heading_old.ImaNames; + end +end +if isfield(Heading_old,'ImageName')&& ~isempty(Heading_old.ImageName) + Heading.ImageName=Heading_old.ImageName; +end +if isfield(Heading_old,'DateExp')&& ~isempty(Heading_old.DateExp) + Heading.DateExp=Heading_old.DateExp; +end +if test_mod && uidheading + uid_child=children(t_device,uidheading); + t_device=delete(t_device,uid_child); + t_device=struct2xml(Heading,t_device,uidheading); + backupfile=xmlfullname; + testexist=2; + while testexist==2 + backupfile=[backupfile '~']; + testexist=exist(backupfile,'file'); + end + [success,message]=copyfile(xmlfullname,backupfile);%make backup + if isequal(success,1) + delete(xmlfullname) + else + return + end + save(t_device,xmlfullname) +end + +% --- Executes on button press in HELP. +function HELP_Callback(hObject, eventdata, handles) +path_to_uvmat=which ('uvmat')% check the path of uvmat +pathelp=fileparts(path_to_uvmat); +helpfile=fullfile(pathelp,'UVMAT_DOC','uvmat_doc.html'); +if isempty(dir(helpfile)), errordlg('Please put the help file uvmat_doc.html in the directory UVMAT/UVMAT_DOC') +else +web([helpfile '#dataview']) +end + + + + +% --- Executes on button press in SubCampaignTest. +function SubCampaignTest_Callback(hObject, eventdata, handles) + + +% --- Executes on selection change in ListXml. +function ListXml_Callback(hObject, eventdata, handles) +Value=get(handles.ListXml,'Value'); +if isequal(Value(1),1) + set(handles.ListXml,'Value',1); +end + + +% --- Executes on button press in clean_civ_cmx. +function clean_civ_cmx_Callback(hObject, eventdata, handles) +message='this function will delete all files with extensions .log, .bat, .cmx,.cmx2,.errors in the input directory(ies)'; +answer=msgbox_uvmat('INPUT_Y-N',message); +if ~isequal(answer{1},'OK') + return +end +set(handles.ListExperiments,'Value',1) +ListExperiments_Callback(hObject, eventdata, handles)%update the overview of the experiment directories +hh=get(handles.CampaignDoc,'parent'); +List=get(hh,'UserData'); +Currentpath=get(handles.RootDirectory,'String'); +[Currentpath,Campaign,DirExt]=fileparts(Currentpath); +Campaign=[Campaign DirExt]; +SubCampaignTest=get(handles.SubCampaignTest,'Value'); +nbdelete_tot=0; +for iexp=1:length(List.Experiment) + set(handles.ListExperiments,'Value',iexp+1) + drawnow + test_mod=0; + ExpName=List.Experiment{iexp}.name; + nbdelete=0; + if isfield(List.Experiment{iexp},'Device') + for idevice=1:length(List.Experiment{iexp}.Device) + DeviceName=List.Experiment{iexp}.Device{idevice}.name; + if isfield(List.Experiment{iexp}.Device{idevice},'xmlfile') + currentdir=fullfile(Currentpath,Campaign,ExpName,DeviceName); + hdir=dir(currentdir); %list files and dirs + idir=0; + for ilist=1:length(hdir) + if hdir(ilist).isdir + dirname=hdir(ilist).name; + if ~isequal(dirname(1),'.')&&~isequal(dirname(1),'0') + CivDir=fullfile(currentdir,dirname) + hCivDir=dir(CivDir); + for ilist=1:length(hCivDir) + FileName=hCivDir(ilist).name; + [dd,ff,Ext]=fileparts(FileName); + if isequal(Ext,'.log')||isequal(Ext,'.bat')||isequal(Ext,'.cmx')||isequal(Ext,'.cmx2')|| isequal(Ext,'.errors') + delete(fullfile(CivDir,FileName)) + nbdelete=nbdelete+1; + end + end + end + end + end + elseif isfield(List.Experiment{iexp}.Device{idevice},'Record') + for irecord=1:length(List.Experiment{iexp}.Device{idevice}.Record) + RecordName=List.Experiment{iexp}.Device{idevice}.Record{irecord}.name; + if isfield(List.Experiment{iexp}.Device{idevice}.Record{irecord},'xmlfile') + 'look at subdirectories' + end + end + end + end + end + display([num2str(nbdelete) ' files deleted']) + nbdelete_tot=nbdelete_tot+nbdelete; +end +msgbox_uvmat('CONFIRMATION',['END: ' num2str(nbdelete_tot) ' files deleted by clean_civ_cmx']) +set(handles.ListExperiments,'Value',1) + + + + Index: /trunk/src/datenum_uvmat.m =================================================================== --- /trunk/src/datenum_uvmat.m (revision 2) +++ /trunk/src/datenum_uvmat.m (revision 2) @@ -0,0 +1,602 @@ +%'datenum_uvmat': like the Matlab function datenum.m but gives empty output instead of stopping for input error +%-------------------------------------------------------------------------- +function n = datenum_uvmat(arg1,arg2,arg3,h,min,s) +%DATENUM Serial date number. +% N = DATENUM(V) converts one or more date vectors V into serial date +% numbers N. Input V can be an M-by-6 or M-by-3 matrix containing M full +% or partial date vectors respectively. DATENUM returns a column vector +% of M date numbers. +% +% A date vector contains six elements, specifying year, month, day, hour, +% minute, and second. A partial date vector has three elements, specifying +% year, month, and day. Each element of V must be a positive double +% precision number. A serial date number of 1 corresponds to Jan-1-0000. +% The year 0000 is merely a reference point and is not intended to be +% interpreted as a real year. +% +% N = DATENUM(S,F) converts one or more date strings S to serial date +% numbers N using format string F. S can be a character array where each +% row corresponds to one date string, or one dimensional cell array of +% strings. DATENUM returns a column vector of M date numbers, where M is +% the number of strings in S. +% +% All of the date strings in S must have the same format F, which must be +% composed of date format symbols according to Table 2 in DATESTR help. +% Formats with 'Q' are not accepted by DATENUM. +% +% Certain formats may not contain enough information to compute a date +% number. In those cases, hours, minutes, and seconds default to 0, days +% default to 1, months default to January, and years default to the +% current year. Date strings with two character years are interpreted to +% be within the 100 years centered around the current year. +% +% N = DATENUM(S,F,P) or N = DATENUM(S,P,F) uses the specified format F +% and the pivot year P to determine the date number N, given the date +% string S. The pivot year is the starting year of the 100-year range in +% which a two-character year resides. The default pivot year is the +% current year minus 50 years. +% +% N = DATENUM(Y,MO,D) and N = DATENUM([Y,MO,D]) return the serial date +% numbers for corresponding elements of the Y,MO,D (year,month,day) +% arrays. Y, MO, and D must be arrays of the same size (or any can be a +% scalar). +% +% N = DATENUM(Y,MO,D,H,MI,S) and N = DATENUM([Y,MO,D,H,MI,S]) return the +% serial date numbers for corresponding elements of the Y,MO,D,H,MI,S +% (year,month,day,hour,minute,second) arrays. The six arguments must be +% arrays of the same size (or any can be a scalar). +% +% N = DATENUM(S) converts the string or date vector (as defined by +% DATEVEC) S into a serial date number. If S is a string, it must be in +% one of the date formats 0,1,2,6,13,14,15,16,23 as defined by DATESTR. +% This calling syntax is provided for backward compatibility, and is +% significantly slower than the syntax which specifies the format string. +% If the format is known, the N = DATENUM(S,F) syntax should be used. +% +% N = DATENUM(S,P) converts the date string S, using pivot year P. If the +% format is known, the N = DATENUM(S,F,P) or N = DATENUM(S,P,F) syntax +% should be used. +% +% Note: The vectorized calling syntax can offer significant performance +% improvement for large arrays. +% +% Examples: +% n = datenum('19-May-2000') returns n = 730625. +% n = datenum(2001,12,19) returns n = 731204. +% n = datenum(2001,12,19,18,0,0) returns n = 731204.75. +% n = datenum('19.05.2000','dd.mm.yyyy') returns n = 730625. +% +% See also NOW, DATESTR, DATEVEC, DATETICK. + +% Copyright 1984-2004 The MathWorks, Inc. +% $Revision: 1.24.4.7 $ $Date: 2004/10/27 23:53:57 $ + +if (nargin<1) || (nargin>6) + error('MATLAB:datenumr:Nargin',nargchk(1,6,nargin)); +end + +% parse input arguments +isdatestr = ~isnumeric(arg1); +isdateformat = false; +if nargin == 2 + isdateformat = ischar(arg2); +elseif nargin == 3 + isdateformat = [ischar(arg2),ischar(arg3)]; +end +% try to convert date string or date vector to a date number +try + switch nargin + case 1 + if isdatestr + n = datenummx(datevec(arg1)); + elseif (size(arg1,2)==3) || (size(arg1,2)==6) + n = datenummx(arg1); + else + n = arg1; + end + case 2 + if isdateformat + if ischar(arg1) + arg1 = cellstr(arg1); + end + n = dtstr2dtnummx(arg1,cnv2icudf(arg2)); + else + n = datenummx(datevec(arg1,arg2)); + end + case 3 + if any(isdateformat) + if isdateformat(1) + format = arg2; + pivot = arg3; + elseif isdateformat(2) + format = arg3; + pivot = arg2; + end + if ischar(arg1) + arg1 = cellstr(arg1); + end + icu_dtformat = cnv2icudf(format); + showyr = strfind(icu_dtformat,'y'); + if ~isempty(showyr) + wrtYr = numel(showyr); + checkYr = diff(showyr); + if any(checkYr~=1) + error('MATLAB:datenum:YearFormat','Unrecognized year format'); + end + switch wrtYr + case 4, + icu_dtformat = strrep(icu_dtformat,'yyyy','yy'); + case 3, + icu_dtformat = strrep(icu_dtformat,'yyy','yy'); + end + end + n = dtstr2dtnummx(arg1,icu_dtformat,pivot); + else + n = datenummx(arg1,arg2,arg3); + end + case 6, n = datenummx(arg1,arg2,arg3,h,min,s); + otherwise, error('MATLAB:datenum:Nargin',... + 'Incorrect number of arguments'); + end +catch + err = lasterror; + err.message = sprintf('DATENUM failed.\n%s',err.message); + + if (nargin == 1 && ~isdatestr) + err.identifier = 'MATLAB:datenum:ConvertDateNumber'; + elseif (nargin == 1 && isdatestr) || (isdatestr && any(isdateformat)) + err.identifier = 'MATLAB:datenum:ConvertDateString'; + elseif (nargin > 1) && ~isdatestr && ~any(isdateformat) + err.identifier = 'MATLAB:datenum:ConvertDateVector'; + end + + rethrow(err); +end +end + +function [y,mo,d,h,mi,s] = datevec(t,varargin) +%DATEVEC Date components. +% V = DATEVEC(N) converts one or more date numbers N to date vectors V. N +% can be a scalar, vector, or multidimensional array of positive date +% numbers. DATEVEC returns an M-by-6 matrix containing M date vectors, +% where M is the total number of date numbers in N. +% +% V = DATEVEC(S,F) converts one or more date strings S to date vectors +% V using format string F to interpret the date strings in S. S can be a +% cell array of strings or a character array where each row corresponds +% to one date string. All of the date strings in S must have the same +% format which must be composed of date format symbols according to +% Table 2 in DATESTR help. Formats with 'Q' are not accepted by DATEVEC. +% DATEVEC returns an M-by-6 matrix of date vectors, where M is the number +% of date strings in S. +% +% Certain formats may not contain enough information to compute a date +% vector. In those cases, hours, minutes, and seconds default to 0, days +% default to 1, months default to January, and years default to the +% current year. Date strings with two character years are interpreted to +% be within the 100 years centered around the current year. +% +% V = DATEVEC(S,F,P) or V = DATEVEC(S,P,F) converts the date string S to +% a date vector V, using the pivot year P and the date format F. The +% pivot year is the starting year of the 100-year range in which a +% two-character year resides. The default pivot year is the current year +% minus 50 years. +% +% [Y,MO,D,H,MI,S] = DATEVEC(...) takes any of the two syntaxes shown +% above and returns the components of the date vector as individual +% variables. +% +% V = DATEVEC(S) converts date string S to date vector V. S must be in +% one of the date formats 0,1,2,6,13,14,15,16,23 as defined by DATESTR. +% This calling syntax is provided for backward compatibility, and is +% significantly slower than the syntax which specifies the format string. +% If the format is known, the V = DATEVEC(S,F) syntax should be used. +% +% V = DAVEVEC(S,P) converts the date string S using pivot year P. +% If the format is known, the V = DATEVEC(S,F,P) or V = DATEVEC(S,P,F) +% syntax should be used. +% +% Note 1: If more than one input argument is used, the first argument +% must be a date string or array of date strings. +% +% Note 2: The vectorized calling syntax can offer significant performance +% improvement for large arrays. +% +% Examples +% d = '12/24/1984'; +% t = 725000.00; +% c = datevec(d) or c = datevec(t) produce c = [1984 12 24 0 0 0]. +% [y,m,d,h,mi,s] = datevec(d) returns y=1984, m=12, d=24, h=0, mi=0, s=0. +% c = datevec('5/6/03') produces c = [2003 5 6 0 0 0] until 2054. +% c = datevec('5/6/03',1900) produces c = [1903 5 6 0 0 0]. +% c = datevec('19.05.2000','dd.mm.yyyy') produces c = [2000 5 19 0 0 0]. +% +% See also DATENUM, DATESTR, CLOCK, DATETICK. + +% Copyright 1984-2004 The MathWorks, Inc. +% $Revision: 1.28.4.11 $ $Date: 2004/10/27 23:53:59 $ + +if (nargin<1) || (nargin>3) +% error('MATLAB:datevec:Nargin',nargchk(1,3,nargin)); + return +end + +% parse input arguments +isdatestr = ~isnumeric(t); +isdateformat = false; +if ~isdatestr && nargin > 1 + warning('MATLAB:datevec:Inputs', ... + 'Unless the first input argument is a date string, all subsequent\narguments will be ignored.'); +elseif nargin > 1 + isdateformat = cellfun('isclass',varargin,'char'); + if (nargin == 3) + if ~isdateformat(1) + pivotyear = varargin{1}; + elseif ~isdateformat(2) + pivotyear = varargin{2}; + elseif isdateformat(1) && isdateformat(2) +% error('MATLAB:datevec:DateFormat',... +% 'You specified two date format strings.\nThere can only be one.'); + return + end + elseif (nargin == 2) && ~isdateformat + pivotyear = varargin{1}; + end +end + +if isdatestr && isempty(t) + if nargout <= 1 + y = zeros(0,6); + else + [y,mo,d,h,mi,s] = deal(zeros(0,0)); + end; + warning('MATLAB:datevec:EmptyDate',... + 'Usage of DATEVEC with empty date strings is not supported.\nResults may change in future versions.'); + return; +end + +% branch to appropriate date string parser +if isdatestr + % a date format string was specified + % map date format to ICU date format tokens + if ischar(t) + % convert to cellstring. + t = cellstr(t); + end + icu_dtformat = {}; + if ~any(isdateformat) + format = getformat(t); + if ~isempty(format) + icu_dtformat = cnv2icudf(format); + end + else + icu_dtformat = cnv2icudf(varargin{isdateformat}); + end + if ~isempty(icu_dtformat) + % call ICU MEX function to parse date string to date vector + try + if nargin < 2 || (nargin == 2 && any(isdateformat)) + y = dtstr2dtvecmx(t,icu_dtformat); + else + showyr = findstr(icu_dtformat,'y'); + if ~isempty(showyr) + wrtYr = numel(showyr); + if showyr(end) - showyr(1) >= wrtYr +% error('MATLAB:datevec:YearFormat','Unrecognized year format'); + return + end + switch wrtYr + case 4, + icu_dtformat = strrep(icu_dtformat,'yyyy','yy'); + case 3, + icu_dtformat = strrep(icu_dtformat,'yyy','yy'); + end + end + y = dtstr2dtvecmx(t,icu_dtformat,pivotyear); + end + if nargout > 1 + mo = y(:,2); + d = y(:,3); + h = y(:,4); + mi = y(:,5); + s = y(:,6); + y = y(:,1); + end + catch + err = lasterror; + err.identifier = 'MATLAB:datevec:dtstr2dtvecmx'; + err.message = sprintf(['DATEVEC failed, calling DTSTR2DTVECMX.\n'... + '%s'],err.message); + rethrow(err); + end + else + %last resort!!! + if ischar(t) + m = size(t,1); + else + m = length(t); + end + y = zeros(m,6); + t = lower(t); +% ampmtokens = lower(getampmtokensmx); + amtok = 'am'; %ampmtokens{1}; + amtok0 = 'am'; + pmtok = 'pm';%ampmtokens{2}; + pmtok0 = 'pm'; + M={'jan';'feb';'mar';'apr';'may';'jun';'jul';'aug';'sept';'oct';'nov';'dec'}; + M0=M; +% M = lower(getmonthnames); +% M0 = lower(getmonthnames(0)); % fall-back list of English short month names. + try + for i = 1:m + % Convert date input to date vector + % Initially, the six fields are all unknown. + c(1,1:6) = NaN; + pm = -1; % means am or pm is not in datestr + if ischar(t) + str = t(i,:); + else + str = t{i}; + end + d = [' ' str ' ']; + + % Replace 'a ' or 'am', 'p ' or 'pm' with ': '. + p = max(find(d == amtok(1) | d == pmtok(1) | ... + d == amtok0(1)| d == pmtok0(1))); + if ~isempty(p) + if (d(p+1) == amtok(2) | ... + d(p+1) == amtok0(2)| isspace(d(p+1))) & ... + d(p-1) ~= lower('e') + pm = (d(p) == pmtok(1) | d(p) == pmtok0(1)); + if d(p-1) == ' ' + d(p-1:p+1) = ': '; + else + d(p:p+1) = ': '; + end + end + end + + % Any remaining letters must be in the month field + p = find(isletter(d)); + + % Test length of string to catch a bogus date string. + % Get index of month in list of months of year + % replace with spaces, month name in date string. + % If native month name lookup fails, fall back on + % list of English month names. + if ~isempty(p) && numel(d)>4 + k = min(p); + if d(k+3) == '.', d(k+3) = ' '; end + monthidx = ~cellfun('isempty',strfind(M,d(k:k+2))); + if ~any(monthidx) + monthidx = ~cellfun('isempty',strfind(M0,d(k:k+2))); + if ~any(monthidx) +% error('MATLAB:datevec:MonthOfYear',... +% 'Failed to lookup month of year.'); + return + end + end + c(2) = find(monthidx); + d(p) = char(' '*ones(size(p))); + end + + % Find all nonnumbers. + p = find((d < '0' | d > '9') & (d ~= '.')); + + % Pick off and classify numeric fields, one by one. + % Colons delinate hour, minutes and seconds. + + k = 1; + while k < length(p) + if d(p(k)) ~= ' ' && d(p(k)+1) == '-' + f = str2double(d(p(k)+1:p(k+2)-1)); + k = k+1; + else + f = str2double(d(p(k)+1:p(k+1)-1)); + end + if ~isnan(f) + if d(p(k))==':' || d(p(k+1))==':' + if isnan(c(4)) + c(4) = f; % hour + % Add 12 if pm specified and hour isn't 12 + if pm == 1 && f ~= 12 + c(4) = f+12; + elseif pm == 0 && f == 12 + c(4) = 0; + end + elseif isnan(c(5)) + c(5) = f; % minutes + elseif isnan(c(6)) + c(6) = f; % seconds + else +% error('MATLAB:datevec:NumberOfTimeFields',... +% 'Too many time fields in %s', str); + return + end + elseif isnan(c(2)) + if f > 12 +% error('MATLAB:datevec:IllegalDateField',... +% '%s is too large to be a month.',num2str(f)); + return + end + c(2) = f; % month + elseif isnan(c(3)) + c(3) = f; % date + elseif isnan(c(1)) + if (f >= 0) & (p(k+1)-p(k) == 3) % two char year + if nargin < 2 + clk = clock; + pivotyear = clk(1)-50; %(current year-50 years) + end + % Moving 100 year window centered around current year + c(1) = pivotyear+rem(f+100-rem(pivotyear,100),100); + else + c(1) = f; % year + end + else +% error('MATLAB:datevec:NumberOfDateFields',... +% 'Too many date fields in %s', str); + return + end + end + k = k+1; + end + + if sum(isnan(c)) >= 5 +% error('MATLAB:datevec:ParseDateString',... +% 'Cannot parse date %s', str); + return + end + % If any field has not been specified + if isnan(c(1)), clk = clock; c(1) = clk(1); end + if isnan(c(2)), c(2) = 1; end; + if isnan(c(3)), c(3) = 1; end; + if isnan(c(4)), c(4) = 0; end; + if isnan(c(5)), c(5) = 0; end; + if isnan(c(6)), c(6) = 0; end; + + % Normalize components to correct ranges. + y(i,:) = datevecmx(datenummx(c)); + end + catch + err = lasterror; + err.message = sprintf('Failed to parse date string.\n%s',... + err.message); + rethrow(err); + end + if nargout > 1 + mo = y(:,2); + d = y(:,3); + h = y(:,4); + mi = y(:,5); + s = y(:,6); + y = y(:,1); + end + end +elseif nargout <= 1 + % date number was specified + y = datevecmx(t); +elseif nargout == 3 + % date number was specified and first three date fields for output + [y,mo,d] = datevecmx(t); +else + % date number was specified and all six date fields for output + [y,mo,d,h,mi,s] = datevecmx(t); +end +end +%-------------------------------------------------------------------------- +%-- +function [format] = getformat(str) + format = ''; + formatstr = cell(11,1); + formatstr(1) = {'dd-mmm-yyyy HH:MM:SS'}; + formatstr(2) = {'dd-mmm-yyyy'}; + formatstr(3) = {'mm/dd/yy'}; + formatstr(4) = {'mm/dd'}; + formatstr(5) = {'HH:MM:SS'}; + formatstr(6) = {'HH:MM:SS PM'}; + formatstr(7) = {'HH:MM'}; + formatstr(8) = {'HH:MM PM'}; + formatstr(9) = {'mm/dd/yyyy'}; + formatstr(10) = {'dd-mmm-yyyy HH:MM'}; %used by finance + formatstr(11) = {'dd-mmm-yy'}; %used by finance + + AlphaFormats = [1 1 0 0 0 1 0 1 0 1 1]; + %[1 2 6 8 10 11]; + SlashFormats = [ 0 0 1 1 0 0 0 0 1 0 0]; + %[3 4 9]; + TwoSlashFormats = [ 0 0 1 0 0 0 0 0 1 0 0]; + %[3 9]; + DashFormats = [ 1 1 0 0 0 0 0 0 0 1 1]; + %[1 2 10 11]; + ColonFormats = [1 0 0 0 1 1 1 1 0 1 0]; + %[1 5 6 7 8 10]; + TwoColonFormats = [1 0 0 0 1 1 0 0 0 0 0]; + %[1 5 6]; + SpaceFormats = [1 0 0 0 0 1 0 1 0 1 0]; + %[1 6 8 10]; + + bMask = [ 1 1 1 1 1 1 1 1 1 1 1]; + + if length(str) > 1 + str = str(1,1); + end + str = strtrim(char(str)); + slashes = strfind(str, '/'); + if ~isempty(slashes) + bMask = bMask & SlashFormats; + if (length(slashes) > 0 && slashes(1) == 2) + if (length(slashes) > 1 && slashes(2) == 4) + str = ['0' str(1:slashes(1)) '0' str(slashes(1)+1:end)]; + else + str = ['0' str]; + end + elseif (length(slashes) > 1 && slashes(2) - slashes(1) == 2) + str = [str(1:slashes(1)) '0' str(slashes(1)+1:end)]; + end + if length(slashes) > 1 + bMask = bMask & TwoSlashFormats; + else + bMask = bMask & ~TwoSlashFormats; + end + else + bMask = bMask & ~SlashFormats; + end + + dashes = strfind(str,'-'); + if ~isempty(dashes) + bMask = bMask & DashFormats; + if (length(dashes) > 0 && dashes(1) == 2) + str = ['0' str]; + end + else + bMask = bMask & ~DashFormats; + end + + colons = strfind(str,':'); + if ~isempty(colons) + bMask = bMask & ColonFormats; + if (length(colons) > 0) && (colons(1) == 2) && (length(str) - colons(end) > 3) + str = ['0' str]; + end + if length(colons) > 1 + bMask = bMask & TwoColonFormats; + else + bMask = bMask & ~TwoColonFormats; + end + else + bMask = bMask & ~ColonFormats; + end + + spaces = strfind(str,' '); + if ~isempty(spaces) + bMask = bMask & SpaceFormats; + else + bMask = bMask & ~SpaceFormats; + end + + for i = 1:11 + if bMask(i) + try + str1 = dateformverify(str,char(formatstr(i))); + if (strcmpi(str, strtrim(str1)) == 1) + format = char(formatstr(i)); + break; + end + catch + lasterr(''); + end + if AlphaFormats(i) + try + str1 = dateformverify(str,char(formatstr(i)),'local'); + if (strcmpi(str, strtrim(str1)) == 1) + format = char(formatstr(i)); + break; + end + catch + lasterr(''); + end + end + end + end + end Index: /trunk/src/delete_object.m =================================================================== --- /trunk/src/delete_object.m (revision 2) +++ /trunk/src/delete_object.m (revision 2) @@ -0,0 +1,73 @@ +%'delete_object': delete a projection object, defined by its index in the Uvmat list or by its graphic handle +% +%INPUT: +% hObject: object index (if integer) or handle of the graphic object. If +% hObject is a subobject, the parent object is detected and deleted. + +function delete_object(hObject) + +huvmat=findobj('Name','uvmat');%handles of the uvmat interface +UvData=get(huvmat,'UserData'); +hlist_object=findobj(huvmat,'Tag','list_object');%handles of the object liçst in the uvmat interface +list_str=get(hlist_object,'String');%objet list +ObjectData=[];%default +hdisplay=[]; +if isequal(floor(hObject),hObject) %case of an index + if ~isempty(UvData) & isfield(UvData, 'Object') & length(UvData.Object)>=hObject + if isfield(UvData.Object{hObject},'HandlesDisplay') + hdisplay=UvData.Object{hObject}.HandlesDisplay; + for iview=1:length(hdisplay) + if ishandle(hdisplay(iview)) & ~isequal(hdisplay(iview),0) + ObjectData=get(hdisplay(iview),'UserData'); + if isfield(ObjectData,'SubObject') & ishandle(ObjectData.SubObject) + delete(ObjectData.SubObject); + end + if isfield(ObjectData,'DeformPoint') & ishandle(ObjectData.DeformPoint) + delete(ObjectData.DeformPoint); + end + delete(hdisplay(iview)) + end + ishandle(hdisplay(iview)) + end + end + for iobj=hObject+1:length(UvData.Object) + hdisplay=UvData.Object{iobj}.HandlesDisplay; + for iview=1:length(hdisplay) + if ishandle(hdisplay(iview)) && ~isequal(hdisplay(iview),0) + PlotData=get(hdisplay(iview),'UserData'); + PlotData.IndexObj=iobj-1; + set(hdisplay(iview),'UserData',PlotData); + end + end + end + UvData.Object(hObject)=[]; + list_str(hObject)=[]; + end +elseif ishandle(hObject)%object handle + userdata=get(hObject,'UserData'); + if ishandle(userdata)%the selected line depends on a parent line + hdisplay=userdata;% the parent object becomes the current one + else + hdisplay=hObject;% the selected object becomes the current one + end + PlotData=get(hdisplay,'UserData'); + if isfield(PlotData,'SubObject') & ishandle(PlotData.SubObject) + delete(PlotData.SubObject); + end + if isfield(PlotData,'DeformPoint') & ishandle(PlotData.DeformPoint) + delete(PlotData.DeformPoint); + end + delete(hdisplay); + if isfield(PlotData,'IndexObj') + IndexObj=PlotData.IndexObj; + if isequal(round(IndexObj),IndexObj) & IndexObj>=1 & length(list_str) > IndexObj + if isfield(UvData,'Object')& length(UvData.Object) > IndexObj + UvData.Object(IndexObj)=[]; + end + list_str(IndexObj)=[]; + end + end +end +set(huvmat,'UserData',UvData); +set(hlist_object,'String',list_str) +set(hlist_object,'Value',length(list_str)) Index: /trunk/src/editxml.m =================================================================== --- /trunk/src/editxml.m (revision 2) +++ /trunk/src/editxml.m (revision 2) @@ -0,0 +1,1556 @@ +%'editxml': function for editing xml files using a xml schema (associated with the GUI editxml.fig) +%------------------------------------------------------------------------ +% function heditxml=editxml(inputfile) +% +%OUTPUT: heditxml: graphic handle of the GUI +% +%INPUT: inputfile: name of an xml file +% +%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +% Copyright Joel Sommeria, 2008, LEGI / CNRS-UJF-INPG, sommeria@coriolis-legi.org. +%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +% This file is part of the toolbox UVMAT. +% +% UVMAT is free software; you can redistribute it and/or modify +% it under the terms of the GNU General Public License as published by +% the Free Software Foundation; either version 2 of the License, or +% (at your option) any later version. +% +% UVMAT is distributed in the hope that it will be useful, +% but WITHOUT ANY WARRANTY; without even the implied warranty of +% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +% GNU General Public License (file UVMAT/COPYING.txt) for more details. +%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA + +function varargout = editxml(varargin) + +% Begin initialization code - DO NOT EDIT +gui_Singleton = 1; +gui_State = struct('gui_Name', mfilename, ... + 'gui_Singleton', gui_Singleton, ... + 'gui_OpeningFcn', @editxml_OpeningFcn, ... + 'gui_OutputFcn', @editxml_OutputFcn, ... + 'gui_LayoutFcn', [] , ... + 'gui_Callback', []); +if nargin & isstr(varargin{1}) + gui_State.gui_Callback = str2func(varargin{1}); +end + +if nargout + [varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:}); +else + gui_mainfcn(gui_State, varargin{:}); +end +% End initialization code - DO NOT EDIT + + +% --- Executes just before editxml is made visible. +function editxml_OpeningFcn(hObject, eventdata, handles, varargin) +% This function has no output args, see OutputFcn. +% hObject handle to figure +% eventdata reserved - to be defined in a future version of MATLAB +% handles structure with handles and user data (see GUIDATA) +% varargin command line arguments to editxml (see VARARGIN) + +% set(handles.replicate,'String',['copy';'<---']) +if nargin + CurrentFile=varargin{1} +else + CurrentFile=[]; +end +% if exist('varargin') & length(varargin)>=1 +% CurrentFile=cell2mat(varargin{1}); +% else +% CurrentFile=[]; +% end +% Choose default command line output for editxml +handles.output = hObject; +% set(hObject,'Units','pixel') +if exist(CurrentFile,'file') + [PathName,Nme,FileExt]=fileparts(CurrentFile); + if isequal(FileExt,'.xls') + DataIn.hfig_xls=read_xls(CurrentFile);% DataIn.hfig_xls=handle of the Excel display figure + DataIn.CurrentUid=1; + figpos=get(hObject,'Position');%position of the editxml interface + figposunit=get(hObject,'Units');%unity used to indicate position + newfigpos=[figpos(1)-0.5*figpos(3) figpos(2) figpos(3) figpos(4)]; + set(DataIn.hfig_xls,'Units',figposunit) + set(DataIn.hfig_xls,'Position',newfigpos); %set position of the Excel display figure + set(hObject,'UserData',DataIn) + else + set(handles.CurrentFile,'String',CurrentFile) + CurrentFile_Callback(hObject, eventdata, handles) + end +end +% Update handles structure +guidata(hObject, handles); + +%---------------------------------------------------------------- +% --- Outputs from this function are returned to the command line. +function varargout = editxml_OutputFcn(hObject, eventdata, handles) +% varargout cell array for returning output args (see VARARGOUT); +% hObject handle to figure +% eventdata reserved - to be defined in a future version of MATLAB +% handles structure with handles and user data (see GUIDATA) + +% Get default command line output from handles structure +varargout{1} = handles.output; + + +% --- Executes on selection change in list_element. +function list_element_Callback(hObject, eventdata, handles) +global t xs t_ref +CurrentFile=get(handles.CurrentFile,'String'); +bla=get(hObject,'String'); +ind=get(hObject,'Value'); +list=get(hObject,'UserData'); +NewRootUid=list.uid(ind); +heditxml=get(hObject,'Parent'); +DataIn=get(heditxml,'UserData'); +if ~isempty(xs) + xs_node=list.xs_uid(ind);%xs_node of the subelement #ind + [nodeup,path,xs_element,xs_subelem]=scan_schema(xs,xs_node); + [element,subelem]=get_xml(t,path,xs_element,NewRootUid,xs_subelem); + update_list(handles,path,xs_element,element,NewRootUid,xs_subelem,subelem); + if xs_element.subtest + DataIn.CurrentUid=[DataIn.CurrentUid NewRootUid];%record new current uid + DataIn.xs_CurrentUid=[DataIn.xs_CurrentUid xs_node];%record the new curent schema uid + end + +% %update the import file display +% if isfield(DataIn,'h_ref')&ishandle(DataIn.h_ref) +% tag0_ref=find(t_ref,['/' path '/' xs_element.key]); +% node_ref=list.index(ind); +% if length(tag0_ref)1 + nodeup=DataIn.CurrentUid(end-1); + DataIn.CurrentUid(end)=[]; +else + nodeup=[]; +end +if isempty(xs) + if isempty(nodeup) + test_root=1; + else + DataIn=displ_xml(handles,t,nodeup,DataIn,heditxml); + end +else + xs_nodeup=[]; +% if isfield(DataIn,'xs_UpUid') + if isfield(DataIn,'xs_CurrentUid')&length(DataIn.xs_CurrentUid)>1 +% xs_nodeup=DataIn.xs_UpUid + xs_nodeup=DataIn.xs_CurrentUid(end-1); + DataIn.xs_CurrentUid(end)=[];%uid of the root element in the schema + end + if isempty(xs_nodeup) + test_root=1; + else + [xs_nodeup,path,xs_element,xs_subelem]=scan_schema(xs,xs_nodeup); + [element,subelem]=get_xml(t,path,xs_element,nodeup,xs_subelem); + update_list(handles,path,xs_element,element,nodeup,xs_subelem,subelem); + %update the import file display + if isfield(DataIn,'h_ref')&ishandle(DataIn.h_ref) + [ref_element,ref_subelem]=get_xml(t_ref,path,xs_element,nodeup,xs_subelem); + update_ref_list(DataIn.h_ref,xs_element,ref_element,nodeup,xs_subelem,ref_subelem); + end + end + set(get(hObject,'parent'),'UserData',DataIn); +end +if test_root% we are a the root, + testupfile=0; + DataIn=get(get(hObject,'parent'),'UserData'); + if isfield(DataIn,'UpFile')&~isempty(DataIn.UpFile) + [UpPath,UpName,UpExt]=fileparts(DataIn.UpFile{1}); + if isequal(UpExt,'.xml') + set(handles.CurrentFile,'String',DataIn.UpFile{1}) + CurrentFile_Callback(handles.CurrentFile,[],handles) + testupfile=1; + DataIn.UpFile{1}={}; + end + end + if ~testupfile %open the browser + RootPath=fileparts(CurrentFile); + [FileName, PathName]=uigetfile( ... + {'*.xml', '(*.xml)'; + '*.xml', '.xml files '; ... + '*.*', 'All Files (*.*)'}, ... + 'Pick a file',RootPath); %file browser + fileinput_new=fullfile(PathName,FileName); + set(handles.CurrentFile,'String',fileinput_new) + CurrentFile_Callback(handles.CurrentFile,[],handles) + end +end +set(heditxml,'UserData',DataIn); +%--------------------------------------------------------- +%edit element value +function element_value_Callback(hObject, eventdata, handles) +%---------------------------------------------------------- +global t xs +if isequal(get(handles.element_value,'ForegroundColor'),[0.7 0.7 0.7]) + return% edit element desactivated (grey display) +end +list_enum=get(handles.element_value,'String'); +list_index=get(handles.element_value,'Value'); +if iscell(list_enum) + value=list_enum{list_index}; +else + value=list_enum; +end +heditxml=get(handles.element_value,'Parent'); +DataIn=get(heditxml,'UserData'); +%create the current root element if needed +LengthElement=length(DataIn.CurrentUid); +FilledUid=find(DataIn.CurrentUid~=0); +LengthFilled=FilledUid(end); +for irank=LengthFilled+1:LengthElement + attrib=attributes(xs,'get',DataIn.xs_CurrentUid(irank),1); + [t,DataIn.CurrentUid(irank)]=add(t,DataIn.CurrentUid(irank-1),'element',attrib.val); +end +node_element=get(handles.element_value,'UserData'); +element_key=get(handles.element_key,'String'); +t=set_element(t,DataIn.CurrentUid(end),node_element,element_key,value); + +set(heditxml,'UserData',DataIn) +%update the current listing +[nodeup,path,xs_element,xs_subelem]=scan_schema(xs,DataIn.xs_CurrentUid(end)); +[element,subelem]=get_xml(t,path,xs_element,DataIn.CurrentUid(end),xs_subelem); +element_index=get(handles.list_element,'Value'); +update_list(handles,path,xs_element,element,DataIn.CurrentUid(end),xs_subelem,subelem); +set(handles.list_element,'Value',element_index); + +% +% % --- Executes on button press in inport_file. +% function inport_file_Callback(hObject, eventdata, handles) +% CurrentFile=get(handles.RefFile,'String'); +% if isempty(CurrentFile)|isequal(CurrentFile,'') +% CurrentFile=get(handles.CurrentFile,'String') +% end +% [FileName, PathName]=uigetfile( ... +% {'*.xml', '(*.xml)'; +% '*.xml', '.xml files '; ... +% '*.*', 'All Files (*.*)'}, ... +% 'Pick a file',CurrentFile); %file browser +% fileinput=fullfile(PathName,FileName); +% sizf=size(fileinput); +% if (~ischar(fileinput)|~isequal(sizf(1),1)),return;end% keep only character strings as input file name +% if exist(fileinput,'file') +% set(handles.RefFile,'Visible','on') +% set(handles.replicate,'Visible','on') +% set(handles.RefFile,'String',fileinput) +% RefFile_Callback(handles.RefFile, eventdata, handles) +% end + + +%------------------------------------------------------ +% --- Executes on button press in browser. +function browser_Callback(hObject, eventdata, handles) +%------------------------------------------------------- +heditxml=get(hObject,'parent');%handle of the interface figure +DataIn=get(heditxml,'UserData');%get the current input xml file +CurrentFile=get(handles.CurrentFile,'String'); +DataIn.Schema=[];%schema input file put to [] by default +[FileName, PathName]=uigetfile( ... + {'*.xml;*.xls','(*.xml,*.xls)'; + '*.xml', '.xml files '; ... + '*.xls', '.xls files '; ... + '*.*', 'All Files (*.*)'}, ... + 'Pick a file',CurrentFile); %file browser +CurrentFile=fullfile(PathName,FileName); +sizf=size(CurrentFile); +if (~ischar(CurrentFile)|~isequal(sizf(1),1)),return;end% keep only character strings as input file name +if exist(CurrentFile,'file') +% set(handles.CurrentAttributes,'UserDataIn',PathName); %store the path to the xml file + [CurPath,CurName,CurExt]=fileparts(CurrentFile); + if isequal(CurExt,'.xls') + if isfield(DataIn,'hfig_xls')&ishandle(DataIn.hfig_xls) + [hfig_xls]=read_xls(CurrentFile,DataIn.hfig_xls); + else + [hfig_xls]=read_xls(CurrentFile); + end + figpos=get(heditxml,'Position'); + newfigpos=[figpos(1)-0.25*figpos(3) figpos(2) 0.5*figpos(3) 0.5*figpos(4)]; + set(hfig_xls,'Position',newfigpos) + else + set(handles.CurrentFile,'String',CurrentFile) + CurrentFile_Callback(hObject, eventdata, handles) + end +end + +%------------------------------------ +function CurrentFile_Callback(hObject, eventdata, handles) +global t xs +CurrentFile=get(handles.CurrentFile,'String'); +heditxml=get(handles.CurrentFile,'parent');%handles of the inteface +DataIn=get(heditxml,'UserData'); +t=xmltree(CurrentFile);%open the xml file +head_element=get(t,1); +if ~isfield(head_element,'name') | ~isfield(head_element,'attributes') + warndlg_uvmat('root element of the .xml file not in correct format','ERROR') +end +head_name=head_element.name; +head_attr=head_element.attributes;% attribute of root gives the name of the associated schema +xstest=0; +for iattr=1:length(head_attr) + if isequal(head_attr{iattr}.key,'xmlns:xsi')& isequal(head_attr{iattr}.val,'none')%no schema to read + xs=[]; +% xstest=1; + end + if isequal(head_attr{iattr}.key,'xsi:noNamespaceSchemaLocation') & exist(head_attr{iattr}.val,'file') + DataIn.Schema=head_attr{iattr}.val; + xs=xmltree(DataIn.Schema);%open the associated schema file + xstest=1; + end +end +if xstest==0 %look for the corresponding schema in the directory PARAM_LINUX.xml or PARAM_WIN.xml + head_name=get(t,1,'name'); + %Path to shemas: + path_uvmat=which('editxml');% check the path detected for source file uvmat + path_UVMAT=fileparts(path_uvmat); %path to UVMAT + if isunix + xmlparam=fullfile(path_UVMAT,'PARAM_LINUX.xml') + if exist(xmlparam,'file') + tparam=xmltree(xmlparam); + sparam=convert(tparam); + if isfield(sparam,'SchemaPath') + schemapath=[fullfile(sparam.SchemaPath,head_name) '.xsd'] + end + end +% schemapath=['/coriolis/papillon/data/civbin/XML_SCHEMAS/' head_name '.xsd']%current dir for schema + else + xmlparam=fullfile(path_UVMAT,'PARAM_WIN.xml') + if exist(xmlparam,'file') + tparam=xmltree(xmlparam); + sparam=convert(tparam) + if isfield(sparam,'SchemaPath') + schemapath=[fullfile(sparam.SchemaPath,head_name) '.xsd'] + end + end +% schemapath=['\\Papillon\data\civbin\XML_SCHEMAS\' head_name '.xsd']%current dir for schemas + end + if exist(schemapath,'file') + xs=xmltree(schemapath); + else + warndlg_uvmat(['The xml schema for ' CurrentFile ' is unknown, check the schema path set in the xml file PARAM'],'ERROR') + [FileName, PathName]=uigetfile( ... + {'*.xsd', '(*.xsd)'; + '*.xsd', '.xsd files '; ... + '*.*', 'All Files (*.*)'}, ... + ['Pick a .xsd schema'] ,schemapath); %file browser + if ischar(PathName)&ischar(FileName)& exist(fullfile(PathName,FileName),'file') + DataIn.Schema=fullfile(PathName,FileName); + xs=xmltree(DataIn.Schema);%open the associated schema file + else + xs=[]; + end + end +end +DataIn.CurrentUid=1; +if isempty(xs) + displ_xml(handles,t,1,DataIn,get(hObject,'parent'));%no associated schema, default display of the xml file +% set(handles.inport_file,'Visible','off') +% set(handles.RefFile,'Visible','off') +else + DataIn.xs_CurrentUid=find(xs,'/xs:schema/xs:element');%uid of the root element in the schema + [nodeup,path,xs_element,xs_subelem]=scan_schema(xs,DataIn.xs_CurrentUid);%scan the schema at the root level + [element,subelem]=get_xml(t,path,xs_element,1,xs_subelem);% read the corresponding xml data + update_list(handles,path,xs_element,element,1,xs_subelem,subelem);%update the display of information on the interface + % set(handles.inport_file,'Visible','on') + % set(handles.RefFile,'Visible','on') +end +set(heditxml,'UserData',DataIn);%store the new input xml file name + +%------------------------------------------------------- +% function scan_schema: read the xml schema xs +%-------------------------------------------------------- +%OUTPUT: +%nodeup: parent node of nodeinput +%path: path to nodeinput in the tree +%xs_element: element corresponding to nodeinput + %xs_element.uid, =tag of the element in the schema (=nodeinput) + %xs_element.key: key label of nodeinput + %xs_element.type: type of data contained in the element + %xs_element.annot: annotation of nodeinput + %xs_element.attrib: list of accepted attributes keys for xs_element + %xs_element.enum: enumeration, list of accepted values for nodeinput + %xs_element.subtest: =1 if the element contains subelements in the schema, 0 else + +%xs_subelement(k): subelement #k of xs_element + %xs_subelem(k).node: node number in the schema + %xs_subelem(k).key: key name of the element + %xs_subelem(k).testsub: =1 if element contains subelements, 0 else + %xs_subelem(k).minOccurs: =0 for a non mandatory element, =1 else + %xs_subelem(k).maxOccurs +% +%INPUT: +%xs: schema xml tree +%nodeinput: tag of the current root element in the schema +function [nodeup,path,xs_element,xs_subelem]=scan_schema(xs,nodeinput) +nodeup=[]; +path=[]; +xs_element.key=[]; +xs_element.type=[]; +xs_element.annot=[]; +xs_element.attrib=[]; +xs_element.subtest=0; +xs_element.enum={}; +xs_subelem=[];%default +% get default nodeinput (root of the file) if not defined +if ~exist('nodeinput') | isempty(nodeinput)% we start at the root + node=find(xs,'/xs:schema/xs:element');%description of the root element +else + node=nodeinput; +end +xs_element.uid=node; +%get the key name and element_type of the element +node_content=get(xs,node); +if isempty(node_content),return,end; +if ~isempty(node_content) & isfield(node_content,'attributes') + attrib=node_content.attributes; + for iattr=1:length(attrib) + struct=attrib{iattr}; + if isequal(struct.key,'name') + xs_element.key=struct.val; % read element key name + elseif isequal(struct.key,'type') + xs_element.type=struct.val; % read element key name + end + end +end + +%get the parent node of nodeinput +if ~isempty(node_content) + nodeup=get(xs,node,'parent');%move up to the parent in the tree + if ~isempty(nodeup) + nodeup=get(xs,nodeup(1),'parent');%move up to the parent in the tree + if isequal(nodeup,[]) + %OUVRIR FICHIER AMONT + up=0; + else + nodeup=get(xs,nodeup(1),'parent');%move up to the parent in the tree + end + end +end +%get the path to 'nodeinput' in the schema +up=1; +path=[]; +if ~isempty(nodeup) + attrib=attributes(xs,'get',nodeup,1); + path=attrib.val; + nodeup2=nodeup; + while up==1; + nodeup2=get(xs,nodeup2(1),'parent');%move up to the parent in the tree + nodeup2=get(xs,nodeup2(1),'parent');%move up to the parent in the tree + if isempty(nodeup2) + up=0; + else + nodeup2=get(xs,nodeup2(1),'parent');%move up to the parent in the tree + if isempty(nodeup2) + up=0; + else + attrib=attributes(xs,'get',nodeup2,1); + path=[attrib.val '/' path]; + end + end + end +end + +%explore the subtree in the schema file +node1=children(xs,node); %find the children of the root element +test_sub=0; %no subtree in the .xml file by default +comment=''; +element={}; +minOccurs={}; +maxOccurs={}; +testsub={}; +list_menu={}; +text={}; +if ~isempty(node1) + for i=1:length(node1) + nodename1=get(xs,node1(i),'name'); + node2=children(xs,node1(i)); + if isequal(nodename1,'xs:annotation') + for j=1:length(node2) + nodename2=get(xs,node2(j),'name'); + if isequal(nodename2,'xs:documentation') + node3=children(xs,node2(j)); + xs_element.annot=get(xs,node3,'value');%read annotation + end + end + % pour les elements + elseif isequal(nodename1,'xs:simpleType') + for j=1:length(node2) + nodename2=get(xs,node2(j),'name'); + if isequal(nodename2,'xs:restriction') + node3=children(xs,node2(j)); + for k=1:length(node3) + nodename3=get(xs,node3(k),'name'); + if isequal(nodename3,'xs:enumeration') + node3_content=get(xs,node3(k)); + attr=node3_content.attributes; + for m=1:length(attr) + struct=attr{m}; + if isequal(struct.key,'value') + xs_element.enum{k}=struct.val; % read enumeration + end + end + end + end + end + end + elseif isequal(nodename1,'xs:complexType') + for j=1:length(node2) + nodename2=get(xs,node2(j),'name'); + if isequal(nodename2,'xs:attribute') + node_content=get(xs,node2(j)); + attr=node_content.attributes; + for k=1:length(attr) + struct=attr{k};%read attributes + if isequal(struct.key,'name') + xs_element.attrib=struct.val; %read attributes of main node + end + end + elseif isequal(nodename2,'xs:sequence') + xs_element.subtest=1; + node3=children(xs,node2(j));%nodes of the sequence + for k=1:length(node3) + xs_subelem(k).node=node3(k); + xs_subelem(k).testsub=0;%default + node_content=get(xs,node3(k)); + xs_subelem(k).minOccurs=1; %default + xs_subelem(k).maxOccurs=1; %default +% pref{k}=[]; %default + if isequal(node_content.name,'xs:element') + attr=node_content.attributes; +% attr{:}.key + for l=1:length(attr) + if isequal(attr{l}.key,'name') + xs_subelem(k).key=attr{l}.val;%name of the element + elseif isequal(attr{l}.key, 'minOccurs') + xs_subelem(k).minOccurs=attr{l}.val; + elseif isequal(attr{l}.key, 'maxOccurs') + xs_subelem(k).maxOccurs=attr{l}.val; + end + end + end + node4=children(xs,node3(k)); + for l=1:length(node4) + res=get(xs,node4(l),'name'); + if isequal(res,'xs:complexType')%look whether the element k contains a subtree + node5=children(xs,node4(l)); + for m=1:length(node5) + res2=get(xs,node5(m),'name'); + if isequal(res2,'xs:sequence') + xs_subelem(k).testsub=1; %flag for the existence of a subtree + end + end + end + end + end + + end + end + end + end +end +% look for predefined types +if length(xs_element.type)>=3 & (xs_element.type([1:3])~='xs:') + node_type=find(xs,'/xs:schema/xs:simpleType') + for i=1:length(node_type) + content=get(xs,node_type(i)); + nodeattr=content.attributes; + if ~isempty(nodeattr) & isequal(nodeattr{1}.key,'name') & isequal(nodeattr{1}.val,xs_element.type) + node1=children(xs,node_type(i)); + node2=find(xs,node1,'name','xs:restriction'); +% nodename1=find(xs, + node3=children(xs,node2); + node4=find(xs,node3,'name','xs:enumeration'); + for ienum=1:length(node4) + struct2=get(xs,node4(ienum)); + enumval=struct2.attributes; + xs_element.enum{ienum}=enumval{1}.val; + end + end + end +end + +%-------------------------------------------------------- +%OUTPUT: +%element.val: value of the current element, =[] in the absence of chardata value +%node: node (iud) of the element in t +%element.attr_key{iattr}: attribute key #iattr of the current element +%element.attr_val{iattr}: attribute value #iattr of the current element +%element.attrup: %structure containing the attributes of the element, including the ones unheritated from parent nodes +%subelem(iline).val : value of subelement # iline, concatenated with corresponding attributes +%subelem(iline).xsindex: index k of the subelement #iline in the list xs_subelem of the schema +%subelem(iline).index: index of the subelement #iline inside its xs_subelement, =0 when the xs_subelement is absent in t + +%INPUT: +%t: xml tree +%path: path to the current element in the schema +%xs_element: current element in the schema + %xs_element.key: key label + %xs_element.type: type of data contained in the element + %xs_element.annot: annotation of nodeinput + %xs_element.attrib: list of accepted attributes keys for xs_element + %xs_element.enum: enumeration, list of accepted values + %xs_element.subtest: =1 if the element contains subelements in the schema, 0 else +%index: index of the element, =1 in case of single occurence in xs_element,=0 in case of missing element +%xs_subelem(k): subelement #k of the current element in the schema + %xs_subelem(k).node: node iud of the + %xs_subelem(k).key: key name of the subelement #k in the schema + %xs_subelem(k).testsub: =1 if element contains subelements, 0 else + %xs_subelem(k).minOccurs + %xs_subelem(k).maxOccurs + +function [element,subelem]=get_xml(t,path,xs_element,node,xs_subelem) +element.attr_key='';%default +element.attr_val='';%default +element.val=''; +% element.type=''; +% element.testmanual=testmanual %inheritates the input manual editing flag by default +subelem=[]; %default +attrup=[]; +% node=[]; + +% %find the element properties in the xml file +if node >= 1 + elem_struct=get(t,node); + if ~xs_element.subtest + elem_contents=get(t,elem_struct.contents); + if isempty(elem_contents) + element.val=[]; + else + element.val=elem_contents.value + end + end + if isfield(elem_struct,'attributes') + elem_attr=elem_struct.attributes; + for iattr=1:length(elem_attr) + element.attr_key{iattr}=elem_attr{iattr}.key ; + element.attr_val{iattr}=elem_attr{iattr}.val; +% attrup=setfield(attrup,elem_attr{iattr}.key,elem_attr{iattr}.val); + breakdetect=find(elem_attr{iattr}.key=='/'| elem_attr{iattr}.key==':'| elem_attr{iattr}.key=='.');% find '/' + if isempty(breakdetect) +% comline=['attrup.' elem_attr{iattr}.key '=' elem_attr{iattr}.val ';'] + eval(['attrup.' elem_attr{iattr}.key '=''' elem_attr{iattr}.val ''';']) + end + end + end +end +%get the parent node attributes +up=1; +if node>0 + nodeup=node; + while up==1; + nodeup=get(t,nodeup,'parent');%move up to the parent in the tree + if isempty(nodeup) + up=0; + else + nodeup_content=get(t,nodeup); + attrib=nodeup_content.attributes; + for iattr=1:length(attrib) + key=attrib{iattr}.key; + breakdetect=find(key=='/'| key==':'| key=='.');% find '/' + if ~isfield(attrup,key) & isempty(breakdetect) + eval(['attrup.' key '=''' attrib{iattr}.val ''';']) + end + end + end + end + element.attrup=attrup; +end +%find the subelement properties in the xml file +if xs_element.subtest + iline=0; + for k=1:length(xs_subelem)%node2: list of subelements in the sub-sequence +% attr=attributes(xs,'get',node2(i),1);% +% element=attr.val;%name of the element + tag=find(t,['/' path '/' xs_element.key '/' xs_subelem(k).key]);%look for the corresponding element node in the .xml tree + struct_element=get(t,tag);%get the content of the element + if isempty(struct_element) + iline=iline+1; + subelem(iline).uid=0; + subelem(iline).xsindex=k; + subelem(iline).index=0; +% subelem(iline).testmanual=element.testmanual;% inheritates the manual editing flag by default + if isequal(xs_subelem(k).minOccurs,'0') + subelem(iline).val='[]';%element value not mandatory in the schema + else + subelem(iline).val='[MISSING]';%element value mandatory in the schema + end +% subelem(iline).attrup=attrup; %inheritated attributes + elseif isequal(length(struct_element),1) + contents=get(t,struct_element.contents); + iline=iline+1; + subelem(iline).uid=tag; + subelem(iline).xsindex=k; + subelem(iline).index=1; +% subelem(iline).testmanual=element.testmanual;% + if isfield(contents,'value') & ~isempty(contents.value) + subelem(iline).val=contents.value; + elseif xs_subelem(k).testsub + subelem(iline).val=''; + elseif isequal(xs_subelem(k).minOccurs,0) + subelem(iline).val='[]';%element value not mandatory in the schema + else + subelem(iline).val='[MISSING]';%element value mandatory in the schema + end +% subelem(iline).attrup=attrup; %inheritated attributes + if isfield(struct_element,'attributes') + element_attr=struct_element.attributes; + attr_display=[]; + for iattr=1:length(element_attr) +% attr_display{iline}=[attr_display ' , ' element_attr{iattr}.key ' = ' element_attr{iattr}.val]; + subelem(iline).val=[subelem(iline).val attr_display ' , ' element_attr{iattr}.key ' = ' element_attr{iattr}.val]; +% subelem(iline).attrup=setfield(subelem(iline).attrup,element_attr{iattr}.key,element_attr{iattr}.val); + end + end + else%case of a multiple element + for subindex=1:length(struct_element) + contents=get(t,struct_element{subindex}.contents); + iline=iline+1; + subelem(iline).index=subindex;%index of the element + subelem(iline).xsindex=k; +% subelem(iline).testmanual=element.testmanual;% + if isfield(contents,'value')& ~isempty(contents.value) + subelem(iline).val=contents.value; + elseif xs_subelem(k).testsub + subelem(iline).val=''; + else + subelem(iline).val='[]'; + end +% subelem(iline).attrup=attrup; %inheritated attributes + if isfield(struct_element{subindex},'attributes') + element_attr=struct_element{subindex}.attributes; + attr_display=[]; + for iattr=1:length(element_attr) +% attr_display{iline}=[attr_display ' , ' element_attr{iattr}.key ' = ' element_attr{iattr}.val]; + subelem(iline).val=[subelem(iline).val attr_display ' , ' element_attr{iattr}.key ' = ' element_attr{iattr}.val]; +% subelem(iline).attrup=setfield(subelem(iline).attrup,element_attr{iattr}.key,element_attr{iattr}.val); + end + end + end + end + end +end + +%------------------------------------- +%updates the interface +function update_list(handles,path,xs_element,element,node,xs_subelem,subelem) +%----------------------------- +if xs_element.subtest% we list the sub-elements of root + set(handles.export_list,'Value',1) + set(handles.export_list,'String','')%flush the export list + set(handles.CurrentElement,'String',[path '/' xs_element.key]) +% title_element.key=[path '/' xs_element.key]; +% if ~isempty(path) +% xsnode_index=get(handles.list_element,'UserDataIn'); +% ind=get(handles.list_element,'Value'); +% title_element.index=xsnode_index(2,ind); +% else +% title_element.index=1; +% end +% title_element.xsnode=xs_element.uid; +% title_element.node=node; +% set(handles.CurrentFile,'UserDataIn',title_element)%element corresponding to the title + set(handles.CurrentAnnotation,'String',xs_element.annot) + attr_col=[]; + testedit=0;% cannot edit elements by default + for iattr=1:length(element.attr_key) +% if isequal(element.attr_key{iattr},'source') & isequal(element.attr_val{iattr},'manual') +% testedit=1; +% end + attr_col=strvcat(attr_col,[element.attr_key{iattr} ' = ' element.attr_val{iattr}]); + end + set(handles.CurrentAttributes,'String',attr_col) + pref_col=''; + key_col=''; + equal_sign=''; + val_col=''; + for iline=1:length(subelem) + xsindex=subelem(iline).xsindex; + index(iline)=subelem(iline).index; + subuid=subelem(iline).uid; + if isempty(subuid) + list.uid(iline)=0; + else + list.uid(iline)=subuid; + end + node(iline)=xs_subelem(xsindex).node; +% testmanual(iline)=subelem(iline).testmanual; + ikey=xs_subelem(xsindex).key; + if xs_subelem(xsindex).testsub + ival=[' + ' subelem(iline).val]; + else + ival=[' = ' subelem(iline).val]; + end + key_col=strvcat(key_col,ikey); + val_col=strvcat(val_col,ival); + end + list_element=[key_col val_col]; + set(handles.list_element,'String',list_element) + set(handles.list_element,'Value',1) + list.xs_uid=node; + list.index=index; + set(handles.list_element,'UserData',list) + set(handles.element_attrib,'Visible','off') + set(handles.element_key,'Visible','off') + set(handles.element_value,'Visible','off') +else % we edit an element + + export_list=get(handles.export_list,'String');%export list + testadd=1; + for ilist=1:length(export_list) + if isequal(xs_element.key,export_list{ilist}) + testadd=0; + break + end + end + if testadd + export_list=[export_list;{xs_element.key}]; + ilist=length(export_list); + end + set(handles.export_list,'String',export_list) + if iscell(element.val) + element_val=element.val{1}; + else + element_val=element.val; + end + set(handles.element_value,'String',element_val) + export_val=get(handles.export_list,'UserData'); + export_val{ilist}=element_val; + set(handles.export_list,'UserData',export_val); + set(handles.element_annot,'String',xs_element.annot) + set(handles.element_type,'String',['type: ' xs_element.type]) + attr_col=[]; + testedit=0;% cannot edit element by default + for iattr=1:length(element.attr_key) +% if isequal(element.attr_key{iattr},'source') & isequal(element.attr_val{iattr},'manual') +% testedit=1; +% end + attr_col=strvcat(attr_col,[element.attr_key{iattr} ' = ' element.attr_val{iattr}]); + end + set(handles.element_attrib,'String',attr_col) + set(handles.element_key,'String',xs_element.key) + + + if isempty(xs_element.enum) + set(handles.element_value,'Value',1) + set(handles.element_value,'Style','edit') + else % case of an enumeration of possible values + list_enum=[]; + list_val=[]; + for ienum=1:length(xs_element.enum) + list_enum{ienum,1}=xs_element.enum{ienum}; + if isequal(xs_element.enum{ienum},element_val) + list_val=ienum; + end + end + if isempty(list_val) + list_enum{length(xs_element.enum)+1,1}=['[' element_val ']'];%show the non-valid element between brackets + list_val=length(xs_element.enum)+1; + end + set(handles.element_value,'Style','popupmenu') + set(handles.element_value,'String',list_enum) + set(handles.element_value,'Value',list_val) + end + if isempty(element.val) + testedit=1;%allow element editing if value is missing + end + set(handles.element_attrib,'Visible','On') + set(handles.element_key,'Visible','On') + set(handles.element_value,'Visible','On') +end +set(handles.element_value,'UserData',node) +if ~testedit && isfield(element,'attrup') & isfield(element.attrup,'source')&& ~isequal(element.attrup.source,'manual') + set(handles.element_value,'Enable','inactive') +else + set(handles.element_value,'Enable','on') +end + + +% --- Executes on button press in SAVE. +function SAVE_Callback(hObject, eventdata, handles) +global t +DataIn=get(get(handles.SAVE,'parent'),'UserData'); +CurrentFile=get(handles.CurrentFile,'String'); +if isfield(DataIn,'Schema') +if ~isempty(DataIn.Schema)% update ref to schema + attrxsd=attributes(t,'get',1); + setest=0; + for iattr=1:length(attrxsd) + if isequal(attrxsd{iattr}.key,'xsi:noNamespaceSchemaLocation') + t= attributes(t,'set',1,iattr,'xsi:noNamespaceSchemaLocation',DataIn.Schema); + setest=1; + end + end + if setest==0; + t=attributes(t,'add',1,'xmlns:xsi','http://www.w3.org/2001/XMLSchema-instance'); + t= attributes(t,'add',1,'xsi:noNamespaceSchemaLocation',DataIn.Schema); + end +end +end +copyfile(CurrentFile,[CurrentFile '.bak']); +save(t,CurrentFile); + +%------------------------------------- +% creates and/or set values to an element in t +%t: xml tree +%RootUid: uid of t under which we introduce an element +%node: uid of the element that we correct, if =0, a new element is created +%key: key name of the element +%value: new value of the element +function t=set_element(t,RootUid,node,key,value) +%create the subelement if needed +if isequal(node,0) + [t,node]= add(t,RootUid,'element',key); +end +node_chardata=children(t,node); %corresponding data node +if isempty(node_chardata)%if the data does not exist in t, create it + t=add(t,node,'chardata',value); +elseif isequal(length(node_chardata),1)&isequal(get(t,node_chardata,'type'),'chardata')% update only a simple element with 'chardata' + t=set(t,node_chardata,'value',value);%modify existing data +end +attr=attributes(t,'get',node); +if isempty(attr) + t=attributes(t,'add',node,'source','manual');%indicate a manual eidting +end + +% --- Executes on selection change in element_attr_val. +function element_attr_val_Callback(hObject, eventdata, handles) +% hObject handle to element_attr_val (see GCBO) +% eventdata reserved - to be defined in a future version of MATLAB +% handles structure with handles and user data (see GUIDATA) + +% Hints: contents = get(hObject,'String') returns element_attr_val contents as cell array +% contents{get(hObject,'Value')} returns selected item from element_attr_val + + +% --- Executes on button press in ADD. +function ADD_Callback(hObject, eventdata, handles) +% hObject handle to ADD (see GCBO) +% eventdata reserved - to be defined in a future version of MATLAB +% handles structure with handles and user data (see GUIDATA) + +%---------------------------------------- +%read an xml file without schema +function [Data,testsimple]=displ_xml(handles,t,root_uid,DataIn,heditxml) +Data=DataIn;%default +if ~isfield(Data,'CurrentUid') + Data.CurrentUid=[]; +end +CurrentFile=get(handles.CurrentFile,'String'); + +%display the current element +root_element=get(t,root_uid); +uidparent=root_uid; +if isfield(root_element,'name') + CurrentElement=root_element.name; + while ~isequal(uidparent,1)%while the first level has not been reached + uidparent=parent(t,uidparent); + dirdat=get(t,uidparent); + if isfield(dirdat,'name') + CurrentElement=[dirdat.name '/' CurrentElement]; + end + end + set(handles.CurrentElement,'String',CurrentElement) +end +list_uid=children(t,root_uid); +%case of a single element +testsimple=0; +filedat=[]; +if ~isempty(list_uid) + filedat=get(t,list_uid(1)) + if isfield(filedat,'type') & isequal(filedat.type,'chardata') &isfield(filedat,'value') + testsimple=1;%simple element + end +end + +%attributes of the current element +nbattrib= attributes(t,'length',root_uid); +testopen=0; +attr_col=[]; +for iattr=1:nbattrib + attr= attributes(t,'get',root_uid,iattr); + if isequal(attr.key,'source')% look for 'source' attribute + if isequal(attr.val,'file')%if the source is 'file', look for the path and open it + if isfield(filedat,'type') & isequal(filedat.type,'chardata') &isfield(filedat,'value') + cur_file=filedat.value; + uidparent=root_uid;%initialization + while ~isequal(uidparent,1)%while the first level has not been reached + uidparent=parent(t,uidparent); + dirdat=get(t,uidparent); + if isfield(dirdat,'type') & isequal(dirdat.type,'element') & isfield(dirdat,'name') + nbattrib_up= attributes(t,'length',uidparent); + for iattr_up=1:nbattrib_up + attr= attributes(t,'get',uidparent,iattr_up); +% if isequal(attr.key,'source')&isequal(attr.val,'directory')% look for 'source' attribute + if isequal(attr.key,'DirName') + cur_file=fullfile(attr.val,cur_file); + end + end + end + end + RootPath=fileparts(CurrentFile);%path to the current .xml file + cur_file=fullfile(RootPath,cur_file) + set(handles.CurrentAttributes,'UserData',cur_file)%will be searched by uvmat + [path,fil,ext]=fileparts(cur_file); + if ~exist(cur_file,'file') + warndlg_uvmat(['non-existent link file' cur_file],'ERROR') % A FAIRE: propose to updtate the .xml file + return + elseif isequal(ext,'.xml') + if ~isfield(Data,'UpFile') + Data.UpFile={CurrentFile}; + else + Data.UpFile=[{CurrentFile};Data.UpFile]; + end + set(heditxml,'UserData',Data) + set(handles.CurrentFile,'String',cur_file) + CurrentFile_Callback(handles.CurrentFile, [], handles) + else + if isequal(get(heditxml,'Tag'),'browser'); %if editxml has been called as a browser + set(heditxml,'Tag','idle')% signal for uvmat browser + else + uvmat({cur_file}); %open the link fiel with uvmat + end + return + end + end + %elseif isequal(attr.val,'dir') A FAIRE : check directory + %else A FAIRE: edit the element + end + end + attr_col=strvcat(attr_col,[attr.key ' = ' attr.val]); +end +set(handles.CurrentAttributes,'String',attr_col) + +%list subtree +if ~testsimple + list_element=[]; +% Data.CurrentUid=[Data.CurrentUid root_uid]%record new current uid + for iline=1:length(list_uid) + element=get(t,list_uid(iline)); + if isfield(element,'type')&isequal(element.type,'element') + list_element{iline,2}=element.name; + child_uid=children(t,list_uid(iline)); + subelem=get(t,child_uid); + if isfield(subelem,'type')& isfield(subelem,'value') & isequal(subelem.type,'chardata') + data_read=subelem.value; + list_element{iline,3}=['= ' data_read]; + end + if iscell(subelem)|(isfield(subelem,'type')&isequal(subelem.type,'element')) + list_element{iline,1}='+ ';%sign for subtree existence + else + list_element{iline,1}=' '; + end + nbattr=attributes(t,'length',list_uid(iline)); + if nbattr==1 + attr=attributes(t,'get',list_uid(iline)); + list_element{iline,4}=[attr.key '=']; + list_element{iline,5}=attr.val; + elseif nbattr>1 + for iattr=1:nbattr + attr=attributes(t,'get',list_uid(iline),iattr); + list_element{iline,2+2*iattr}=[attr.key '=']; + list_element{iline,3+2*iattr}=attr.val; + end + end + end + end + set(handles.list_element,'Value',1)%select the first line of list_element by default + set(handles.list_element,'String',cell2tab(list_element,' ') ) + list.uid=list_uid; + set(handles.list_element,'UserData',list) +end +%--------------------------------------------------------- +%------------------------------------- +%updates the interface +function update_ref_list(hh,xs_element,element,node,xs_subelem,subelem) +%----------------------------- +pref_col=''; +key_col=''; +equal_sign=''; +val_col=''; +for iline=1:length(subelem) + xsindex=subelem(iline).xsindex; + indexcur=subelem(iline).index; + subuid=subelem(iline).uid; + if isempty(subuid) + RefDataIn.uid(iline)=0; + else + RefDataIn.uid(iline)=subuid; + end + index(iline)=indexcur; + node(iline)=xs_subelem(xsindex).node; +% testmanual(iline)=subelem(iline).testmanual; + ikey=xs_subelem(xsindex).key; + if xs_subelem(xsindex).testsub + ival=[' + ' subelem(iline).val]; + else + ival=[' = ' subelem(iline).val]; + end + key_col=strvcat(key_col,ikey); + val_col=strvcat(val_col,ival); +end +RefDataIn.xs_uid=node; +list_element=[key_col val_col]; +siztext=size(list_element); +set(hh,'Value',[1:siztext(1)]) +set(hh,'String',list_element) +set(hh,'UserData',RefDataIn) + +% +% function RefFile_Callback(hObject, eventdata, handles) +% global t_ref xs +% t_ref=xmltree(get(hObject,'String'));%open the xml file fileinput +% heditxml=get(hObject,'parent'); +% DataIn=get(get(hObject,'parent'),'UserData'); +% % set(heditxml,'Units','pixel') +% figpos=get(heditxml,'Position') +% % title_element=get(handles.element_cur,'UserDataIn'); +% % xs_node=xsnode_index(1,ind); +% % index_chosen=xsnode_index(2,ind); +% if isfield(DataIn,'fig_ref')&ishandle(DataIn.fig_ref) +% figure(DataIn.fig_ref); +% else +% DataIn.fig_ref=figure; +% end +% set(DataIn.fig_ref,'Name',get(hObject,'String')) +% set(DataIn.fig_ref,'MenuBar','none') +% newfigpos=[figpos(1)+figpos(3) figpos(2)+0.4*figpos(4) 0.5*figpos(3) 0.3*figpos(4)]; +% set(DataIn.fig_ref,'Units','normalized') +% set(DataIn.fig_ref,'Position',newfigpos) +% DataIn.h_ref=uicontrol('Style','listbox', 'Max',2,'Units','pixel','Position', [0 0 newfigpos(3) newfigpos(4)], ... +% 'FontName','FixedWidth','Tag','listbox'); +% if isfield(DataIn,'xs_CurrentUid'); +% xs_CurrentUid=DataIn.xs_CurrentUid(end); +% else +% DataIn.xs_CurrentUid=find(xs,'/xs:schema/xs:element');%uid of the root element in the schema +% end +% [nodeup,path,xs_element,xs_subelem]=scan_schema(xs,xs_CurrentUid(end)); +% xs_element.key +% tag0=find(t_ref,['/' path '/' xs_element.key]); +% if length(tag0)>=1 +% CurrentRefNode=tag0(1);%chose the first occurence of the element +% else +% CurrentRefNode=0; +% end +% [ref_element,ref_subelem]=get_xml(t_ref,path,xs_element,CurrentRefNode,xs_subelem); +% update_ref_list(DataIn.h_ref,xs_element,ref_element,CurrentRefNode,xs_subelem,ref_subelem); +% siztext=size(get(DataIn.h_ref,'String')); +% set(DataIn.h_ref,'Value',[1:siztext(1)]); %select the whole list by default +% set(heditxml,'UserData',DataIn) +% set(handles.ref_data,'Value',siztext(1)); %select the whole list by default +% 'TESTimport' +% title_element=get(handles.element_cur,'UserDataIn') +% xs_node=title_element.xsnode;%uid of the element in the schema +% node=title_element.node; +% t=flush(t,node);%removes the corresponding subtree in t +% [nodeup,path,xs_element,xs_subelem]=scan_schema(xs,xs_node);%scan the schema +% tag0=find(t_import,['/' path '/' xs_element.key]) +% if isempty(tag) +% errordlg(['element /' path '/' xs_element.key ' not found in' fileinput]) +% return +% end +% % [element_import,node_import]=get_xml(t_import,path,xs_element,1,xs_subelem);% read the corresponding xml data +% node2_import=children(t_import,tag0); +% % t_import=branch(t_import,node_import);% extract branch of the new file +% % %removes the corresponding subtree in t +% for inode=1:length(node2_import) +% struct=get(t_import,node2_import(inode)) +% if isfield(struct,'type') & isfield(struct,'name')%if the node is an elmeent type +% node3_import=children(t_import,node2_import(inode)) +% [t,newuid]=add(t,node,struct.type,struct.name); +% for inode2=1:length(node3_import) +% struct2=get(t_import,node3_import(inode2)) +% if isequal(struct2.type,'chardata') +% t=add(t,newuid,'chardata',struct2.value); +% end +% end +% end +% end +% --- Executes on button press in replicate. +function replicate_Callback(hObject, eventdata, handles) +global xs t + +export_list=get(handles.export_list,'String'); +export_val=get(handles.export_list,'UserData'); +heditxml=get(handles.replicate,'parent'); +Data=get(heditxml,'UserData') + +hdataview=findobj(allchild(0),'Name','dataview') +if isempty(hdataview) + hdataview=dataview; + return +end +hhdataview=guidata(hdataview); +CurrentPath=get(hhdataview.CurrentFile,'String'); +ListExperiments=get(hhdataview.ListExperiments,'String'); +Value=get(hhdataview.ListExperiments,'Value'); +if ~isequal(Value,1) + ListExperiments=ListExperiments(Value); +end +ListDevices=get(hhdataview.ListDevices,'String'); +Value=get(hhdataview.ListDevices,'Value'); +if ~isequal(Value,1) + ListDevices=ListDevices(Value); +end +ListRecords=get(hhdataview.ListRecords,'String'); +Value=get(hhdataview.ListRecords,'Value'); +if ~isequal(Value,1) + ListRecords=ListRecords(Value); +end +% uvmat('runplus_Callback',hObject,eventdata,handleshaxes) +[ListDevices,ListRecords,ListXml,List]=ListDir(CurrentPath,ListExperiments,ListDevices,ListRecords); +ListXml=get(hhdataview.ListXml,'String'); +Value=get(hhdataview.ListXml,'Value'); +if isequal(Value,1) + warndlg_uvmat('you need to select the xml files to edit','ERROR') + return +end +ListXml=ListXml(Value);%list of +for iexp=1:length(List.Experiment) + ExpName=List.Experiment{iexp}.name; + if isfield(List.Experiment{iexp},'Device') + for idevice=1:length(List.Experiment{iexp}.Device) + DeviceName=List.Experiment{iexp}.Device{idevice}.name; + if isfield(List.Experiment{iexp}.Device{idevice},'xmlfile') + for ixml=1:length(List.Experiment{iexp}.Device{idevice}.xmlfile) + FileName=List.Experiment{iexp}.Device{idevice}.xmlfile{ixml}; + for ilistxml=1:length(ListXml) + if isequal(FileName,ListXml{ilistxml}) + xmlfullname=fullfile(CurrentPath,ExpName,DeviceName,FileName); + t_export=xmltree(xmlfullname); + rootelement=get(t_export,1,'name'); + uidlist=Data.CurrentUid; + if isequal(rootelement,get(t,1,'name')) + backupfile=xmlfullname; + testexist=2; + while testexist==2 + backupfile=[backupfile '~']; + testexist=exist(backupfile,'file'); + end + [success,message]=copyfile(xmlfullname,backupfile);%make backup + if ~isequal(success,1) + warndlg_uvmat(['Error in the backup of ' xmlfullname],'ERROR') + return + end + findstr=['/' rootelement]; + uid_export(1)=1; + % fill the root elements if absent + for index=2:length(uidlist) + name_t=get(t,uidlist(index),'name') + findstr=[findstr '/' name_t] + uid=find(t_export,findstr) + if isempty(uid) + [t_export,uid_export(index)]=add(t_export,uid_export(index-1),'element',name_t); + else + uid_export(index)=uid; + end + end + % chardata...... + end + break + end + end +% [Title,test]=check_heading(Currentpath,Campaign,ExpName,DeviceName,[],FileName,SubCampaignTest); +% if test +% [List.Experiment{iexp}.Device{idevice}.xmlfile{ixml} ' , Heading updated'] +% end + end + elseif isfield(List.Experiment{iexp}.Device{idevice},'Record') + for irecord=1:length(List.Experiment{iexp}.Device{idevice}.Record) + RecordName=List.Experiment{iexp}.Device{idevice}.Record{irecord}.name; + if isfield(List.Experiment{iexp}.Device{idevice}.Record{irecord},'xmlfile') + for ixml=1:length(List.Experiment{iexp}.Device{idevice}.Record{irecord}.xmlfile) + FileName=List.Experiment{iexp}.Device{idevice}.Record{irecord}.xmlfile{ixml}; + for ilistxml=1:length(ListXml) + if isequal(FileName,ListXml{ilistxml}) + xmlfullname=fullfile(CurrentPath,ExpName,DeviceName,RecordName,FileName) + break + end + end +% [Title,test]=check_heading(Currentpath,Campaign,ExpName,DeviceName,RecordName,FileName,SubCampaignTest); +% if test +% [FileName ' , Heading updated'] +% end + end + end + end + end + end + end +end +return +%%%%%%%%%%% A REVOIR +% Copier la liste des elements selectionnés dans dataview +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% +%ANCIEN: +heditxml=get(hObject,'parent'); +DataIn=get(heditxml,'UserData'); +if ~isfield(DataIn,'h_ref') + DataIn.h_ref=[]; +end +if ~ishandle(DataIn.h_ref) + errordlg('no source file opened for import') + return +end +%create the current root element if needed +LengthElement=length(DataIn.CurrentUid); +FilledUid=find(DataIn.CurrentUid~=0); +LengthFilled=FilledUid(end); +for irank=LengthFilled+1:LengthElement + attrib=attributes(xs,'get',DataIn.xs_CurrentUid(irank),1); + [t,DataIn.CurrentUid(irank)]=add(t,DataIn.CurrentUid(irank-1),'element',attrib.val); +end + +%copy list of subelements +RefDataIn=get(DataIn.h_ref,'UserData'); +list=get(handles.list_element,'UserData');%=,[node;index] +for ilist=get(DataIn.h_ref,'Value') + node_content=get(xs,RefDataIn.xs_uid(ilist)); + if ~isempty(node_content) & isfield(node_content,'attributes') + attrib=node_content.attributes; + for iattr=1:length(attrib) + struct=attrib{iattr}; + if isequal(struct.key,'name') + key=struct.val; % read element key name + end + end + end + value=''; + if ~isequal(RefDataIn.uid(ilist),0) + child_uid=children(t_ref,RefDataIn.uid(ilist)); + if isequal(length(child_uid),1) + content=get(t_ref,child_uid); + if isfield(content,'type') &isfield(content,'value')& isequal(content.type,'chardata') + value=content.value; + end + end + end + t=set_element(t,DataIn.CurrentUid(end),list.uid(ilist),key,value); +end +set(heditxml,'UserData',DataIn) +%update the current listing +[nodeup,path,xs_element,xs_subelem]=scan_schema(xs,DataIn.xs_CurrentUid(end)); +[element,subelem]=get_xml(t,path,xs_element,DataIn.CurrentUid(end),xs_subelem); +update_list(handles,path,xs_element,element,DataIn.CurrentUid(end),xs_subelem,subelem); +% t=set_xml(t,xs_DataIn,subelem) +%edit list of subelments: + +%A REVOIR +% xsnode_index=get(handles.list_element,'UserDataIn') +% xs_node=xsnode_index(1,ind); +% RefDataIn=get(handles.ref_data,'UserDataIn'); +% subelem=RefDataIn.subelem; +% xsnode_index=get(handles.list_element,'UserDataIn');%data on the xs_nodes of the subelements +% ref_list=get(handles.ref_data,'Value');%selected indices in the list of reference subelements +% xs_node=xsnode_index(1,ref_list);%xs_nodes of the selected subelements +% % index_chosen=xsnode_index(2,ref_list);% indices in the list of occurence for a subelement +% % for ilist=ref_list +% ilist=1; +% while icontinue +% 'TESTCOPY' +% [nodeup,path,xs_element,xs_subelem]=scan_schema(xs,xs_node(ilist)) +% xs_subelem.key +% tsub=subelem(ilist).tsub +% xsnode_index(2,ilist) +% [ref_elem,ref_node,ref_subelem]=get_xml(tsub,'',xs_element,1,xs_subelem) +% ref_subelem.val +% testedit= ~isfield(element.attrup,'source') | isequal(element.attrup.source,'manual') %| element vide +% +% +% icontinue=0 +% end +% function [element,node,subelem]=get_xml(t,path,xs_element,node,xs_subelem) +% element.attr_key='';%default +% element.attr_val='';%default +% element.val=''; +% % element.type=''; +% % element.testmanual=testmanual %inheritates the input manual editing flag by default +% subelem=[]; %default +% attrup=[]; +% % node=[]; +% +% % %find the element properties in the xml file +% if node >= 1 +% elem_struct=get(t,node); +% if ~xs_element.subtest +% elem_contents=get(t,elem_struct.contents); +% if isempty(elem_contents) +% element.val=[]; +% else +% element.val=elem_contents.value +% end +% end +% if isfield(elem_struct,'attributes') +% elem_attr=elem_struct.attributes; +% for iattr=1:length(elem_attr) +% element.attr_key{iattr}=elem_attr{iattr}.key ; +% element.attr_val{iattr}=elem_attr{iattr}.val; +% % attrup=setfield(attrup,elem_attr{iattr}.key,elem_attr{iattr}.val); +% breakdetect=find(elem_attr{iattr}.key=='/'| elem_attr{iattr}.key==':'| elem_attr{iattr}.key=='.');% find '/' +% if isempty(breakdetect) +% % comline=['attrup.' elem_attr{iattr}.key '=' elem_attr{iattr}.val ';'] +% eval(['attrup.' elem_attr{iattr}.key '=''' elem_attr{iattr}.val ''';']) +% end +% end +% end +% end +% %get the parent node attributes +% up=1 +% if node>0 +% nodeup=node; +% while up==1; +% nodeup=get(t,nodeup,'parent');%move up to the parent in the tree +% if isempty(nodeup) +% up=0; +% else +% nodeup_content=get(t,nodeup); +% attrib=nodeup_content.attributes; +% for iattr=1:length(attrib) +% key=attrib{iattr}.key; +% breakdetect=find(key=='/'| key==':'| key=='.');% find '/' +% if ~isfield(attrup,key) & isempty(breakdetect) +% eval(['attrup.' key '=''' attrib{iattr}.val ''';']) +% end +% end +% end +% end +% element.attrup=attrup; +% end +% %find the subelement properties in the xml file +% if xs_element.subtest +% iline=0; +% for k=1:length(xs_subelem)%node2: list of subelements in the sub-sequence +% % attr=attributes(xs,'get',node2(i),1);% +% % element=attr.val;%name of the element +% tag=find(t,['/' path '/' xs_element.key '/' xs_subelem(k).key]);%look for the corresponding element node in the .xml tree +% struct_element=get(t,tag);%get the content of the element +% if isempty(struct_element) +% iline=iline+1; +% subelem(iline).xsindex=k; +% subelem(iline).index=0; +% % subelem(iline).testmanual=element.testmanual;% inheritates the manual editing flag by default +% if isequal(xs_subelem(k).minOccurs,0) +% subelem(iline).val='[]';%element value not mandatory in the schema +% else +% subelem(iline).val='[MISSING]';%element value mandatory in the schema +% end +% % subelem(iline).attrup=attrup; %inheritated attributes +% elseif isequal(length(struct_element),1) +% contents=get(t,struct_element.contents); +% iline=iline+1; +% subelem(iline).xsindex=k; +% subelem(iline).index=1; +% % subelem(iline).testmanual=element.testmanual;% +% if isfield(contents,'value') & ~isempty(contents.value) +% subelem(iline).val=contents.value; +% elseif xs_subelem(k).testsub +% subelem(iline).val=''; +% elseif isequal(xs_subelem(k).minOccurs,0) +% subelem(iline).val='[]';%element value not mandatory in the schema +% else +% subelem(iline).val='[MISSING]';%element value mandatory in the schema +% end +% % subelem(iline).attrup=attrup; %inheritated attributes +% if isfield(struct_element,'attributes') +% element_attr=struct_element.attributes; +% attr_display=[]; +% for iattr=1:length(element_attr) +% % attr_display{iline}=[attr_display ' , ' element_attr{iattr}.key ' = ' element_attr{iattr}.val]; +% subelem(iline).val=[subelem(iline).val attr_display ' , ' element_attr{iattr}.key ' = ' element_attr{iattr}.val]; +% % subelem(iline).attrup=setfield(subelem(iline).attrup,element_attr{iattr}.key,element_attr{iattr}.val); +% end +% end +% else%case of a multiple element +% for subindex=1:length(struct_element) +% contents=get(t,struct_element{subindex}.contents); +% iline=iline+1; +% subelem(iline).index=subindex;%index of the element +% subelem(iline).xsindex=k; +% % subelem(iline).testmanual=element.testmanual;% +% if isfield(contents,'value')& ~isempty(contents.value) +% subelem(iline).val=contents.value; +% elseif xs_subelem(k).testsub +% subelem(iline).val=''; +% else +% subelem(iline).val='[]'; +% end +% % subelem(iline).attrup=attrup; %inheritated attributes +% if isfield(struct_element{subindex},'attributes') +% element_attr=struct_element{subindex}.attributes; +% attr_display=[]; +% for iattr=1:length(element_attr) +% % attr_display{iline}=[attr_display ' , ' element_attr{iattr}.key ' = ' element_attr{iattr}.val]; +% subelem(iline).val=[subelem(iline).val attr_display ' , ' element_attr{iattr}.key ' = ' element_attr{iattr}.val]; +% % subelem(iline).attrup=setfield(subelem(iline).attrup,element_attr{iattr}.key,element_attr{iattr}.val); +% end +% end +% end +% end +% end +% end + + +% --- Executes on button press in HELP. +function HELP_Callback(hObject, eventdata, handles) +path_to_uvmat=which ('uvmat')% check the path of uvmat +pathelp=fileparts(path_to_uvmat); +helpfile=fullfile(pathelp,'UVMAT_DOC','uvmat_doc.html'); +if isempty(dir(helpfile)), errordlg('Please put the help file uvmat_doc.html in the directory UVMAT/UVMAT_DOC') +else +web([helpfile '#editxml']) +end + + +% --- Executes on button press in Export. +function Export_Callback(hObject, eventdata, handles) +val=get(handles.Export,'Value'); +if val + set(handles.Export,'BackgroundColor',[0 1 0]) + set(handles.export_list,'Visible','on') + set(handles.replicate,'Visible','on') + h_dataview=findobj(allchild(0),'name',dataview'); + if isempty(h_dataview) + % CurrentFile=get(handles.CurrentFile,'String'); + dataview; + end +else + set(handles.Export,'BackgroundColor',[0.7 0.7 0.7]) + set(handles.export_list,'Visible','off') + set(handles.replicate,'Visible','off') +end + + +% --- Executes on button press in pushbutton9. +function pushbutton9_Callback(hObject, eventdata, handles) +% hObject handle to pushbutton9 (see GCBO) +% eventdata reserved - to be defined in a future version of MATLAB +% handles structure with handles and user data (see GUIDATA) + + Index: /trunk/src/find_field_indices.m =================================================================== --- /trunk/src/find_field_indices.m (revision 2) +++ /trunk/src/find_field_indices.m (revision 2) @@ -0,0 +1,181 @@ +%'find_file_indices': test field structure for input in proj_field and plot_field +%group the variables into 'fields' with common dimensions +%---------------------------------------------------------------------- +% function [DimVarIndex,CellVarIndex,NbDim,VarType]=find_field_indices(Data) +% +%OUTPUT: +% CellVaxIndex: cell whose elements are arrays of indices in the list data.ListVarName +% CellvarIndex{i} represents a set of variables with the same dimensions +% NbDim: array with the length of CellVarIndex, giving its space dimension +% VarType: cell array of structures with fields +% .coord_x, y, z: indices (in .ListVarname) of variables representing unstructured coordinates x, y, z +% .vector_x,_y,_z: indices of variables giving the vector components x, y, z +% .warnflag: index of warnflag +% .errorflag: index of error flag +% .ancillary: indices of ancillary variables +% .image : B/W image, (behaves like scalar) +% .color : color image, the last index, which is not a coordinate variable, represent the 3 color components rgb +% .discrete: like scalar, but set of data points without continuity, represented as dots in a usual plot, instead of continuous lines otherwise +% .scalar: scalar field (default) + +% +%INPUT: +% Data: structure representing fields, output of check_field_structure +% .ListDimName: cell listing the names of the array dimensions +% .ListVarName: cell listing the names of the variables +% .VarDimIndex: cell containing the set of dimension indices (in list .ListDimName) for each variable of .ListVarName +% +% HELP: +% to get the dimensions of arrays common to the field #icell +% VarIndex=CellVarIndex{icell}; % list of variable indices +% DimIndex=Data.VarDimIndex{VarIndex(1)} % list of dimensions for each variable in the cell #icell +% +%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +% Copyright Joel Sommeria, 2008, LEGI / CNRS-UJF-INPG, sommeria@coriolis-legi.org. +%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +% This file is part of the toolbox UVMAT. +% +% UVMAT is free software; you can redistribute it and/or modify +% it under the terms of the GNU General Public License as published by +% the Free Software Foundation; either version 2 of the License, or +% (at your option) any later version. +% +% UVMAT is distributed in the hope that it will be useful, +% but WITHOUT ANY WARRANTY; without even the implied warranty of +% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +% GNU General Public License (file UVMAT/COPYING.txt) for more details. +%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA + +function [CellVarIndex,NbDim,VarType,errormsg]=find_field_indices(Data) +CellVarIndex={}; +NbDim=[]; +VarType=[]; +errormsg=[]; +nbvar=numel(Data.ListVarName);%number of field variables +icell=0; +ivardim=0; +VarDimIndex=[]; +VarDimName={}; + +if ~isfield(Data,'VarDimName') + errormsg='missing .VarDimName'; + return +end + +%loop on the list of variables +for ivar=1:nbvar + DimCell=Data.VarDimName{ivar}; %dimensions associated with the variable #ivar + if ischar(DimCell) + DimCell={DimCell}; + Data.VarDimName{ivar}={Data.VarDimName{ivar}};%transform char chain into cell + end + testnewcell=1; + for icell_prev=1:numel(CellVarIndex)%detect whether the dimensions of ivar fit with an existing cell + PrevVarIndex=CellVarIndex{icell_prev}; + PrevDimName=Data.VarDimName{PrevVarIndex(1)}; + if isequal(PrevDimName,DimCell) + CellVarIndex{icell_prev}=[CellVarIndex{icell_prev} ivar];% add variable index #ivar to the cell #icell_prev + testnewcell=0; %existing cell detected + break + end + end + if testnewcell + icell=icell+1; + CellVarIndex{icell}=ivar;%put the current variabl index in the new cell + end + + %look for dimension variables + if numel(DimCell)==1% if the variable has a single dimension + Role=''; + if isfield(Data,'VarAttribute') && length(Data.VarAttribute)>=ivar && isfield(Data.VarAttribute{ivar},'Role') + Role=Data.VarAttribute{ivar}.Role; + end + if strcmp(DimCell{1},Data.ListVarName{ivar}) || strcmp(Role,'dimvar') + ivardim=ivardim+1; + VarDimIndex(ivardim)=ivar;%index of the variable + VarDimName{ivardim}=DimCell{1};%name of the dimension + end + end +end + +% find the spatial dimensions and vector components +ListRole={'coord_x','coord_y','coord_z','vector_x','vector_y','vector_z','warnflag','errorflag',... + 'ancillary','image','color','discrete','scalar'}; +for icell=1:length(CellVarIndex) + for ilist=1:numel(ListRole) + eval(['ivar_' ListRole{ilist} '=[];']) + end + VarIndex=CellVarIndex{icell};%set of variable indices with the same dim + DimCell=Data.VarDimName{VarIndex(1)};% list of dimensions for each variable in the cell #icell + if isfield(Data,'VarAttribute'); + VarAttribute=Data.VarAttribute; + else + VarAttribute={}; + end + test_2D=0; + for ivar=VarIndex + if length(VarAttribute)>=ivar + if isfield(VarAttribute{ivar},'Role') + role=VarAttribute{ivar}.Role; + switch role + case ListRole + eval(['ivar_' role '=[ivar_' role ' ivar];']) + otherwise + ivar_scalar=[ivar_scalar ivar];%variables are consiered as 'scalar' by default (in the absence of attribute 'Role') + end + else + ivar_scalar=[ivar_scalar ivar];% variable considered as scalar in the absence of Role attribute + end + if isfield(VarAttribute{ivar},'Coord_2') + test_2D=1; %obsolete convention + end + else + ivar_scalar=[ivar_scalar ivar];%variables are consiered as 'scalar' by default (in the absence of attribute 'Role') + end + end + for ilist=1:numel(ListRole) + eval(['VarType{icell}.' ListRole{ilist} '=ivar_' ListRole{ilist} ';']) + end + if numel(ivar_coord_x)>1 || numel(ivar_coord_y)>1 || numel(ivar_coord_z)>1 + errormsg='multiply defined coordinates in the same cell'; + return + end + if numel(ivar_vector_x)>1 || numel(ivar_vector_y)>1 || numel(ivar_vector_z)>1 + errormsg='multiply defined vector components in the same cell'; + return + end + if numel(ivar_errorflag)>1 + errormsg='multiply defined error flag in the same cell'; + return + end + if numel(ivar_warnflag)>1 + errormsg='multiply defined warning flag in the same cell'; + return + end + NbDim(icell)=0;% nbre of space dimensions + if ~isempty(ivar_coord_z) + NbDim(icell)=3; + elseif ~isempty(ivar_coord_y) + NbDim(icell)=2; + elseif ~isempty(ivar_coord_x) + NbDim(icell)=1; + end + + % look at coordinates variables + coord=zeros(1,numel(DimCell));%default + if NbDim(icell)==0 && ~isempty(VarDimName)% no unstructured coordinate found + for idim=1:numel(DimCell) %loop on the dimensions of the variables in cell #icell + for ivardim=1:numel(VarDimName) + if strcmp(VarDimName{ivardim},DimCell{idim}) + coord(idim)=VarDimIndex(ivardim); + break + end + end + end + NbDim(icell)=numel(find(coord)); + end + VarType{icell}.coord=coord; + if NbDim(icell)==0 && test_2D %look at attributes Coord_1, coord_2 (obsolete convention) + NbDim(icell)=2; + end +end Index: /trunk/src/geometry_calib.m =================================================================== --- /trunk/src/geometry_calib.m (revision 2) +++ /trunk/src/geometry_calib.m (revision 2) @@ -0,0 +1,1312 @@ +%'geometry_calib': performs geometric calibration from a set of reference points +% +% function varargout = geometry_calib(varargin) +% +%A%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +% Copyright Joel Sommeria, 2008, LEGI / CNRS-UJF-INPG, sommeria@coriolis-legi.org. +%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +% This file is part of the toolbox UVMAT. +% +% UVMAT is free software; you can redistribute it and/or modify +% it under the terms of the GNU General Public License as published by +% the Free Software Foundation; either version 2 of the License, or +% (at your option) any later version. +% +% UVMAT is distributed in the hope that it will be useful, +% but WITHOUT ANY WARRANTY; without even the implied warranty of +% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +% GNU General Public License (file UVMAT/COPYING.txt) for more details. +%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA + +function varargout = geometry_calib(varargin) +% GEOMETRY_CALIB M-file for geometry_calib.fig +% GEOMETRY_CALIB, by itself, creates a MenuCoord GEOMETRY_CALIB or raises the existing +% singleton*. +% +% H = GEOMETRY_CALIB returns the handle to a MenuCoord GEOMETRY_CALIB or the handle to +% the existing singleton*. +% +% GEOMETRY_CALIB('CALLBACK',hObject,eventData,handles,...) calls the local +% function named CALLBACK in GEOMETRY_CALIB.M with the given input arguments. +% +% GEOMETRY_CALIB('Property','Value',...) creates a MenuCoord GEOMETRY_CALIB or raises the +% existing singleton*. Starting from the left, property value pairs are +% applied to the GUI before geometry_calib_OpeningFunction gets called. An +% unrecognized property name or invalid value makes property application +% stop. All inputs are passed to geometry_calib_OpeningFcn via varargin. +% +% *See GUI Options on GUIDE's Tools menu. Choose "GUI allows only one +% instance to run (singleton)". +% +% See also: GUIDE, GUIDATA, GUIHANDLES + +% Edit the above text to modify the response to help geometry_calib + +% Last Modified by GUIDE v2.5 28-Dec-2009 23:41:18 + +% Begin initialization code - DO NOT edit +gui_Singleton = 1; +gui_State = struct('gui_Name', mfilename, ... + 'gui_Singleton', gui_Singleton, ... + 'gui_OpeningFcn', @geometry_calib_OpeningFcn, ... + 'gui_OutputFcn', @geometry_calib_OutputFcn, ... + 'gui_LayoutFcn', [] , ... + 'gui_Callback', []); +if nargin & isstr(varargin{1}) + gui_State.gui_Callback = str2func(varargin{1}); +end + +if nargout + [varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:}); +else + gui_mainfcn(gui_State, varargin{:}); +end +% End initialization code - DO NOT edit + + +% --- Executes just before geometry_calib is made visible. +%INPUT: +%handles: handles of the geometry_calib interface elements +% PlotHandles: set of handles of the elements contolling the plotting +% parameters on the uvmat interface (obtained by 'get_plot_handle.m') +function geometry_calib_OpeningFcn(hObject, eventdata, handles, handles_uvmat,pos,inputfile) +set(handles.Phi,'TooltipString','Phi: rotation angle of the physical point coordiantes (in degrees)')% TO PUT IN GUIDE +% Choose default command line output for geometry_calib +handles.output = hObject; + +% Update handles structure +guidata(hObject, handles); +movegui(hObject,'east');% position the GUI ton the right of the screen +if exist('handles_uvmat','var') %& isfield(data,'ParentButton') + set(hObject,'DeleteFcn',{@closefcn,handles_uvmat})% +end +%set the position of the interface +if exist('pos','var')& length(pos)>2 + pos_gui=get(hObject,'Position'); + pos_gui(1)=pos(1); + pos_gui(2)=pos(2); + set(hObject,'Position',pos_gui); +end +inputxml=''; +if exist('inputfile','var')& ~isempty(inputfile) + [Path,Name,ext]=fileparts(inputfile); + form=imformats(ext([2:end])); + if ~isempty(form)% if the input file is an image + struct.XmlInputfile=inputfile; + set(hObject,'UserData',struct) + [Pathsub,RootFile,field_count,str2,str_a,str_b,ext,nom_type,subdir]=name2display(inputfile); + inputxml=[fullfile(Pathsub,RootFile) '.xml']; + end +end +set(handles.ListCoord,'String',{''}) +if exist(inputxml,'file') + loadfile(handles,inputxml)% load the point coordiantes existing in the xml file +end + +set(handles.ListCoord,'KeyPressFcn',{@key_press_fcn,handles})%set keyboard action function +%set(hObject,'KeyPressFcn',{'keyboard_callback',handles})%set keyboard action function on uvmat interface when geometry_calib is on top +%htable=uitable(10,5) +%set(htable,'ColumnNames',{'x','y','z','X(pixels)','Y(pixels)'}) + +% --- Outputs from this function are returned to the command line. +function varargout = geometry_calib_OutputFcn(hObject, eventdata, handles) +% varargout cell array for returning output args (see VARARGOUT); +% hObject handle to figure +% eventdata reserved - to be defined in a future version of MATLAB +% handles structure with handles and user data (see GUIDATA) + +% Get default command line output from handles structure +varargout{1} = handles.output; +varargout{2}=handles; + +%------------ +function Phi_Callback(hObject, eventdata, handles) + + + + +%-------------------------------------------------- +%read input xml file and update the edit boxes +function loadfile(handles,fileinput) + +%read the input xml file +t=xmltree(fileinput); +s=convert(t);%convert to matlab structure +%read data currently displayed on the interface +PointCoord=[]; +Coord_cell=get(handles.ListCoord,'String'); +data=read_geometry_calib(Coord_cell); +%data=read_geometry_calib(handles); +Coord=[]; %default +if isfield(data,'Coord') + Coord=data.Coord; +end +TabChar_0=get(handles.ListCoord,'String'); +nbcoord_0=size(TabChar_0,1); +if isequal(get(handles.edit_append,'Value'),2) %edit mode A REVOIR + val=get(handles.ListCoord,'Value')-1; +else + val=length(TabChar_0); +end +nbcoord=0; + +%case of calibration (ImaDoc) input file +hcalib=get(handles.calib_type,'parent'); +CalibData=get(hcalib,'UserData'); +CalibData.XmlInput=fileinput; +if isfield(s,'Heading') + CalibData.Heading=s.Heading; +end + +set(hcalib,'UserData',CalibData);%store the heading in the interface 'UserData' +if isfield(s,'GeometryCalib') + Calib=s.GeometryCalib; + if isfield(Calib,'CalibrationType') + CalibrationType=Calib.CalibrationType; + switch CalibrationType + case 'linear' + set(handles.calib_type,'Value',2) + case 'tsai' + set(handles.calib_type,'Value',3) + end + end + if isfield(Calib,'SourceCalib') + if isfield(Calib.SourceCalib,'PointCoord') + PointCoord=Calib.SourceCalib.PointCoord; + end + end + nbcoord=length(PointCoord); + if ~isfield(Calib,'ErrorRms')&~isfield(Calib,'ErrorMax') %old convention of Gauthier (cord in mm) + for i=1:length(PointCoord) + line=str2num(PointCoord{i}); + Coord(i+val,4:5)=line(4:5);%px x + Coord(i+val,1:3)=line(1:3)/10;%phys x + end + else + for i=1:length(PointCoord) + line=str2num(PointCoord{i}); + Coord(i,4:5)=line(4:5);%px x + Coord(i,1:3)=line(1:3);%phys x + end + end +end +%case of xml files of points +if isfield(s,'Coord') + PointCoord=s.Coord; + nbcoord=length(PointCoord); + %case of image coordinates + if isfield(s,'CoordType')& isequal(s.CoordType,'px') + for i=1:nbcoord + line=str2num(PointCoord{i}); + Coord(i+val,4:5)=line(1:2); + end + %case of physical coordinates + else + for i=1:nbcoord + line=str2num(PointCoord{i}); + Coord(i+val,1:3)=line(1:3); + nbcolumn=size(Coord,2); + if nbcolumn<5 + Coord(i+val,nbcolumn+1:5)=zeros(1,5-nbcolumn); + end + end + end +end +CoordCell={}; +for iline=1:size(Coord,1) + for j=1:5 + CoordCell{iline,j}=num2str(Coord(iline,j),4); + end +end +Tabchar=cell2tab(CoordCell,' | ');%transform cells into table ready for display +set(handles.ListCoord,'Value',1) +set(handles.ListCoord,'String',Tabchar) + + +%---------------------------------------------------- +% executed when closing: set the parent interface button to value 0 +function closefcn(gcbo,eventdata,handles_uvmat) +huvmat=findobj(allchild(0),'Name','uvmat'); +if exist('handles_uvmat','var') + set(handles_uvmat.cal,'Value',0) + uvmat('cal_Callback',huvmat,[],handles_uvmat); +% set(parent_button,'Value',0)%put unactivated buttons to green +% set(parent_button,'BackgroundColor',[0 1 0]); +end + + +% % --- Executes on button press in MenuCoord. +% function MenuCoord_Callback(hObject, eventdata, handles) + +% +% % --- Executes on button press in delete. +% function delete_Callback(hObject, eventdata, handles) +% SetData=get(gcbf,'UserData');%get the interface data +% IndexObj=SetData.IndexObj; +% delete_object(IndexObj); + + +%------------------------------------------------------------------ +% --- Executes on button press in calibrate_lin. +function APPLY_Callback(hObject, eventdata, handles) +%------------------------------------------------------------------ +calib_cell=get(handles.calib_type,'String'); +val=get(handles.calib_type,'Value'); +calib_type=calib_cell{val}; +Coord_cell=get(handles.ListCoord,'String'); +Object=read_geometry_calib(Coord_cell); + +if isequal(calib_type,'rescale') + GeometryCalib=calib_rescale(Object.Coord); +elseif isequal(calib_type,'linear') + GeometryCalib=calib_linear(Object.Coord); +elseif isequal(calib_type,'tsai') + GeometryCalib=calib_tsai(Object.Coord); +end +unitlist=get(handles.CoordUnit,'String'); +unit=unitlist{get(handles.CoordUnit,'value')}; +GeometryCalib.CoordUnit=unit; + +huvmat=findobj(allchild(0),'Name','uvmat'); +hhuvmat=guidata(huvmat);%handles of elements in the GUI uvmat +RootPath=''; +RootFile=''; +if ~isempty(hhuvmat.RootPath)& ~isempty(hhuvmat.RootFile) + testhandle=1; + RootPath=get(hhuvmat.RootPath,'String'); + RootFile=get(hhuvmat.RootFile,'String'); + filebase=fullfile(RootPath,RootFile); + outputfile=[filebase '.xml']; +else + question={'save the calibration data and point coordinates in'}; + def={fullfile(RootPath,['ObjectCalib.xml'])}; + options.Resize='on'; + answer=inputdlg(question,'save average in a new file',1,def,options); + outputfile=answer{1}; +end +testappend=0; +if exist(outputfile,'file');%=1 if the output file already exists, 0 else + t=xmltree(outputfile); %read the file + backupfile=outputfile; + testexist=2; + while testexist==2 + backupfile=[backupfile '~'];% make a backup name by adding ~ to the xml file name + testexist=exist(backupfile,'file'); + end + [success,message]=copyfile(outputfile,backupfile);%make backup + t=xmltree(outputfile); %read the file + uid=find(t,'ImaDoc'); + if ~isequal(uid,1)%if the xml file is not ImaDoc, delete it (after backup) + if isequal(success,1) + delete(outputfile) + else + msgbox_uvmat('ERROR',['error in the backup of the existing xml file: ' message]) + return + end + else + uid_calib=find(t,'ImaDoc/GeometryCalib'); + testappend=1; + if isempty(uid_calib) + [t,uid_calib]=add(t,1,'element','GeometryCalib'); + else %if GeometryCalib already exists, delete its content + uid_child=children(t,uid_calib); + t=delete(t,uid_child); + testappend=1; + end + end +end +if ~testappend %create a new xml file for calibration data + t=xmltree; + t=set(t,1,'name','ImaDoc'); + [t,uid_calib]=add(t,1,'element','GeometryCalib'); +end +% hgrid=get(handles.REPLICATE,'parent');%read the calibration image source on the interface userdata +% imagename=get(hgrid,'UserData'); +% if exist(imagename,'file') +% GeometryCalib.SourceCalib.ImageCalib=imagename; +% end +GeometryCalib.SourceCalib.PointCoord=Object.Coord; +t=struct2xml(GeometryCalib,t,uid_calib); +save(t,outputfile); +msgbox_uvmat('CONFIRMATION',{[outputfile ' updated with calibration data'];... + ['Error rms (along x,y)=' num2str(GeometryCalib.ErrorRms) ' pixels'];... + ['Error max (along x,y)=' num2str(GeometryCalib.ErrorMax) ' pixels']}) + +%display image with new calibration in the currently opened uvmat interface +hhh=findobj(hhuvmat.axes3,'Tag','calib_marker');% delete calib points and markers +if ~isempty(hhh) + delete(hhh); +end +hhh=findobj(hhuvmat.axes3,'Tag','calib_points'); +if ~isempty(hhh) + delete(hhh); +end +set(hhuvmat.FixedLimits,'Value',0)% put FixedLimits option to 'off' +set(hhuvmat.FixedLimits,'BackgroundColor',[0.7 0.7 0.7]) +uvmat('RootPath_Callback',hObject,eventdata,hhuvmat); %file input with xml reading in uvmat + +%------------------------------------------------------------------ +% --- Executes on button press in calibrate_lin. +function REPLICATE_Callback(hObject, eventdata, handles) +%------------------------------------------------------------------ +calib_cell=get(handles.calib_type,'String'); +val=get(handles.calib_type,'Value'); +calib_type=calib_cell{val}; +Coord_cell=get(handles.ListCoord,'String'); +Object=read_geometry_calib(Coord_cell); + +if isequal(calib_type,'rescale') + GeometryCalib=calib_rescale(Object.Coord); +elseif isequal(calib_type,'linear') + GeometryCalib=calib_linear(Object.Coord); +elseif isequal(calib_type,'tsai') + GeometryCalib=calib_tsai(Object.Coord); +end +% %record image source +% hgrid=get(handles.REPLICATE,'parent');%read the calibration image source on the interface userdata +% imagename=get(hgrid,'UserData'); +% if exist(imagename,'file') +% GeometryCalib.SourceCalib.ImageCalib=imagename; +% end +GeometryCalib.SourceCalib.PointCoord=Object.Coord; + +%open and read the dataview GUI +h_dataview=findobj(allchild(0),'name','dataview'); +Device=[];%default +if isempty(h_dataview) + h_dataview=dataview; + hhdataview=guidata(h_dataview); + drawnow + hGUI=get(handles.REPLICATE,'parent');%read the calibration image source on the interface userdata + CalibData=get(hGUI,'UserData'); + if isfield(CalibData,'XmlInput') + XmlInput=fileparts(CalibData.XmlInput); + [XmlInput,filename,ext]=fileparts(XmlInput); + end + if isfield(CalibData,'Heading') + Heading=CalibData.Heading; + if isfield(Heading,'Record') && isequal([filename ext],Heading.Record) + [XmlInput,filename,ext]=fileparts(XmlInput); + end + if isfield(Heading,'Device') && isequal([filename ext],Heading.Device) + [XmlInput,filename,ext]=fileparts(XmlInput); + Device=Heading.Device; + end + if isfield(Heading,'Experiment') && isequal([filename ext],Heading.Experiment) + [PP,filename,ext]=fileparts(XmlInput); + end + testinput=0; + if isfield(Heading,'SubCampaign') && isequal([filename ext],Heading.SubCampaign) + set(hhdataview.RootDirectory,'String',XmlInput) + set(hhdataview.SubCampaignTest,'Value',1) + testinput=1; + elseif isfield(Heading,'Campaign') && isequal([filename ext],Heading.Campaign) + set(hhdataview.RootDirectory,'String',XmlInput) + set(hhdataview.SubCampaignTest,'Value',0) + testinput=1; + end + end + if testinput + dataview('RootDirectory_Callback',hObject,eventdata,hhdataview) + ListDevices=get(hhdataview.ListDevices,'String'); + for ilist=1:length(ListDevices) + if isequal(ListDevices{ilist},Device) + set(hhdataview.ListDevices,'Value',ilist) + dataview('ListDevices_Callback',hObject,eventdata,hhdataview) + break + end + end + end + return +end + +hhdataview=guidata(h_dataview); +CurrentPath=get(hhdataview.RootDirectory,'String'); +ListExperiments=get(hhdataview.ListExperiments,'String'); +Value=get(hhdataview.ListExperiments,'Value'); +if ~isequal(Value,1) + ListExperiments=ListExperiments(Value); +end +ListDevices=get(hhdataview.ListDevices,'String'); +Value=get(hhdataview.ListDevices,'Value'); +if isequal(Value,1) + warndlg_uvmat('manually select in the GUI dataview the device being calibrated','ERROR') + return +else + ListDevices=ListDevices(Value); +end +ListRecords=get(hhdataview.ListRecords,'String'); +Value=get(hhdataview.ListRecords,'Value'); +if ~isequal(Value,1) + ListRecords=ListRecords(Value); +end +[ListDevices,ListRecords,ListXml,List]=ListDir(CurrentPath,ListExperiments,ListDevices,ListRecords); +ListXml=get(hhdataview.ListXml,'String'); +Value=get(hhdataview.ListXml,'Value'); +if isequal(Value,1) + warndlg_uvmat('you need to select in the GUI dataview the xml files to edit','ERROR') + return +else + ListXml=ListXml(Value); +end + +%update all the selected xml files +answer=msgbox_uvmat('INPUT_Y-N',[num2str(length(Value)) ' xml files for device ' ListDevices{1} ' will be refreshed with ' calib_type ' calibration data']); +if ~isequal(answer{1},'OK') + return +end +% 'TEST' +% List +% return +for iexp=1:length(List.Experiment) + ExpName=List.Experiment{iexp}.name; + if isfield(List.Experiment{iexp},'Device') + for idevice=1:length(List.Experiment{iexp}.Device) + DeviceName=List.Experiment{iexp}.Device{idevice}.name; + if isfield(List.Experiment{iexp}.Device{idevice},'xmlfile') + for ixml=1:length(List.Experiment{iexp}.Device{idevice}.xmlfile) + FileName=List.Experiment{iexp}.Device{idevice}.xmlfile{ixml}; + for ilistxml=1:length(ListXml) + if isequal(FileName,ListXml{ilistxml}) + set(hhdataview.ListXml,'Value',Value(ilistxml)) + drawnow + xmlfullname=fullfile(CurrentPath,ExpName,DeviceName,FileName); + update_imadoc(GeometryCalib,xmlfullname) + break + end + end + end + elseif isfield(List.Experiment{iexp}.Device{idevice},'Record') + for irecord=1:length(List.Experiment{iexp}.Device{idevice}.Record) + RecordName=List.Experiment{iexp}.Device{idevice}.Record{irecord}.name; + if isfield(List.Experiment{iexp}.Device{idevice}.Record{irecord},'xmlfile') + for ixml=1:length(List.Experiment{iexp}.Device{idevice}.Record{irecord}.xmlfile) + FileName=List.Experiment{iexp}.Device{idevice}.Record{irecord}.xmlfile{ixml}; + for ilistxml=1:length(ListXml) + if isequal(FileName,ListXml{ilistxml}) + set(hhdataview.ListXml,'Value',Value(ilistxml)) + drawnow + xmlfullname=fullfile(CurrentPath,ExpName,DeviceName,RecordName,FileName); + update_imadoc(GeometryCalib,xmlfullname) + break + end + end + end + end + end + end + end + end +end +set(hhdataview.ListXml,'Value',Value) + + +%------------------------------------------------------------- +function update_imadoc(GeometryCalib,outputfile) +testappend=0; +if exist(outputfile,'file');%=1 if the output file already exists, 0 else + t=xmltree(outputfile); %read the file + uid=find(t,'ImaDoc'); + if isequal(uid,1)%if the xml file is ImaDoc + uid_calib=find(t,'ImaDoc/GeometryCalib'); + if ~isempty(uid) %if GeometryCalib already exists, delete its content + backupfile=outputfile; + testexist=2; + while testexist==2 + backupfile=[backupfile '~']; + testexist=exist(backupfile,'file'); + end + [success,message]=copyfile(outputfile,backupfile);%make backup + if isequal(success,1) + delete(outputfile) + else + return + end + uid_child=children(t,uid_calib); + t=delete(t,uid_child); + testappend=1; + end + end +end +if ~testappend + t=xmltree; + t=set(t,1,'name','ImaDoc'); + [t,uid_calib]=add(t,1,'element','GeometryCalib'); +% t=struct2xml(GeometryCalib,t,uid_calib); +end + +t=struct2xml(GeometryCalib,t,uid_calib); +save(t,outputfile); + + +%----------------------------------------------------------------- +% determine the parameters for a calibration by an affine function (rescaling and offset, no rotation) +function GeometryCalib=calib_rescale(Coord) +%------------------------------------------------------------------ + +X=Coord(:,1); +Y=Coord(:,2); +x_ima=Coord(:,4); +y_ima=Coord(:,5); +[px,sx]=polyfit(X,x_ima,1); +[py,sy]=polyfit(Y,y_ima,1); +T_x=px(2); +T_y=py(2); +GeometryCalib.CalibrationType='rescale'; +GeometryCalib.focal=1; +GeometryCalib.CoordUnit=[];% default value, to be updated by the calling function +GeometryCalib.Tx_Ty_Tz=[T_x T_y 1]; +GeometryCalib.R=[px(1),0,0;0,py(1),0;0,0,1]; + +%check error +Calib.dpx=1; +Calib.dpy=1; +Calib.sx=1; +Calib.Cx=0; +Calib.Cy=0; +Calib.Tz=1; +Calib.kappa1=0; +Calib.f=GeometryCalib.focal; +Calib.Tx=T_x; +Calib.Ty=T_y; +Calib.R=GeometryCalib.R; +[Xpoints,Ypoints]=px_XYZ(Calib,X,Y,0); +GeometryCalib.ErrorRms(1)=sqrt(mean((Xpoints-x_ima).*(Xpoints-x_ima))); +GeometryCalib.ErrorMax(1)=max(abs(Xpoints-x_ima)); +GeometryCalib.ErrorRms(2)=sqrt(mean((Ypoints-y_ima).*(Ypoints-y_ima))); +GeometryCalib.ErrorMax(2)=max(abs(Ypoints-y_ima)); + + +%------------------------------------------------------------------ +% determine the parameters for a calibration by a linear transform matrix (rescale and rotation) +function GeometryCalib=calib_linear(Coord) +%------------------------------------------------------------------ +X=Coord(:,1); +Y=Coord(:,2); +x_ima=Coord(:,4); +y_ima=Coord(:,5); +XY_mat=[ones(size(X)) X Y]; +a_X1=XY_mat\x_ima; %transformation matrix for X +x1=XY_mat*a_X1;%reconstruction +err_X1=max(abs(x1-x_ima));%error +a_Y1=XY_mat\y_ima;%transformation matrix for X +y1=XY_mat*a_Y1; +err_Y1=max(abs(y1-y_ima));%error +T_x=a_X1(1); +T_y=a_Y1(1); +GeometryCalib.CalibrationType='linear'; +GeometryCalib.focal=1; +GeometryCalib.CoordUnit=[];% default value, to be updated by the calling function +GeometryCalib.Tx_Ty_Tz=[T_x T_y 1]; +GeometryCalib.R=[a_X1(2),a_X1(3),0;a_Y1(2),a_Y1(3),0;0,0,1]; + +%check error +GeometryCalib.ErrorRms(1)=sqrt(mean((x1-x_ima).*(x1-x_ima))); +GeometryCalib.ErrorMax(1)=max(abs(x1-x_ima)); +GeometryCalib.ErrorRms(2)=sqrt(mean((y1-y_ima).*(y1-y_ima))); +GeometryCalib.ErrorMax(2)=max(abs(y1-y_ima)); + + + + +%------------------------------------------------------------------ +function GeometryCalib=calib_tsai(Coord) +%------------------------------------------------------------------ +%TSAI +% 'calibration_lin' provides a linear transform on coordinates, +path_uvmat=which('uvmat');% check the path detected for source file uvmat +path_UVMAT=fileparts(path_uvmat); %path to UVMAT +if isunix + %fid = fopen(fullfile(path_UVMAT,'PARAM_LINUX.txt'),'r');%open the file with civ binary names + xmlfile=fullfile(path_UVMAT,'PARAM_LINUX.xml'); + if exist(xmlfile,'file') + t=xmltree(xmlfile); + sparam=convert(t); + end +else + %fid = fopen(fullfile(path_UVMAT,'PARAM_WIN.txt'),'r');%open the file with civ binary names + xmlfile=fullfile(path_UVMAT,'PARAM_WIN.xml'); + if exist(xmlfile,'file') + t=xmltree(xmlfile); + sparam=convert(t); + end +end +if ~isfield(sparam,'GeometryCalib_exe') + warndlg_uvmat(['calibration program undefined in parameter file ' xmlfile],'ERROR') + return +end +Tsai_exe=sparam.GeometryCalib_exe; +if ~exist(Tsai_exe,'file') + warndlg_uvmat(['calibration program ' Tsai_exe ' does not exist'],'ERROR') + return +end + +textcoord=num2str(Coord,4); +dlmwrite('t.txt',textcoord,''); +% ['!' Tsai_exe ' -f1 0 -f2 t.txt'] + eval(['!' Tsai_exe ' -f t.txt > tsaicalib.log']); +if ~exist('calib.dat','file') + warndlg_uvmat('no output from calibration program Tsai_exe: possibly too few points','ERROR') +end +calibdat=dlmread('calib.dat'); +GeometryCalib.CalibrationType='tsai'; +GeometryCalib.focal=calibdat(10); +GeometryCalib.dpx_dpy=[calibdat(5) calibdat(6)]; +GeometryCalib.Cx_Cy=[calibdat(7) calibdat(8)]; +GeometryCalib.sx=calibdat(9); +GeometryCalib.kappa1=calibdat(11); +GeometryCalib.CoordUnit=[];% default value, to be updated by the calling function +GeometryCalib.Tx_Ty_Tz=[calibdat(12) calibdat(13) calibdat(14)]; +Rx_Ry_Rz=calibdat([15:17]); +sa = sin(Rx_Ry_Rz(1)) ; +ca=cos(Rx_Ry_Rz(1)); +sb=sin(Rx_Ry_Rz(2)); +cb =cos(Rx_Ry_Rz(2)); +sg =sin(Rx_Ry_Rz(3)); +cg =cos(Rx_Ry_Rz(3)); +r1 = cb * cg; +r2 = cg * sa * sb - ca * sg; +r3 = sa * sg + ca * cg * sb; +r4 = cb * sg; +r5 = sa * sb * sg + ca * cg; +r6 = ca * sb * sg - cg * sa; +r7 = -sb; +r8 = cb * sa; +r9 = ca * cb; +%EN DEDUIRE MATRICE R ?? +GeometryCalib.R=[r1,r2,r3;r4,r5,r6;r7,r8,r9]; +%erreur a caracteriser? +%check error +Calib.dpx=GeometryCalib.dpx_dpy(1); +Calib.dpy=GeometryCalib.dpx_dpy(2); +Calib.sx=GeometryCalib.sx; +Calib.Cx=GeometryCalib.Cx_Cy(1); +Calib.Cy=GeometryCalib.Cx_Cy(2); +Calib.kappa1=GeometryCalib.kappa1; +Calib.f=GeometryCalib.focal; +Calib.Tx=GeometryCalib.Tx_Ty_Tz(1); +Calib.Ty=GeometryCalib.Tx_Ty_Tz(2); +Calib.Tz=GeometryCalib.Tx_Ty_Tz(3); +Calib.R=GeometryCalib.R; +X=Coord(:,1); +Y=Coord(:,2); +Z=Coord(:,3); +x_ima=Coord(:,4); +y_ima=Coord(:,5); +[Xpoints,Ypoints]=px_XYZ(Calib,X,Y,Z); + +GeometryCalib.ErrorRms(1)=sqrt(mean((Xpoints-x_ima).*(Xpoints-x_ima))); +GeometryCalib.ErrorMax(1)=max(abs(Xpoints-x_ima)); +GeometryCalib.ErrorRms(2)=sqrt(mean((Ypoints-y_ima).*(Ypoints-y_ima))); +GeometryCalib.ErrorMax(2)=max(abs(Ypoints-y_ima)); +% Nfx +% dx +% dy +% 5 dpx +% 6 dpy +% cx +% cy +% sx +% f +% kappa1 +% tx +% ty +% tz +% rx +% ry +% rz +% p1 +% p2 + +%calibcoeff=str2num(calibdat) + + + +% --- Executes on button press in rotation. +function rotation_Callback(hObject, eventdata, handles) +angle_rot=(pi/180)*str2num(get(handles.Phi,'String')); +Coord_cell=get(handles.ListCoord,'String'); +data=read_geometry_calib(Coord_cell); +data.Coord(:,1)=cos(angle_rot)*data.Coord(:,1)+sin(angle_rot)*data.Coord(:,2); +data.Coord(:,1)=-sin(angle_rot)*data.Coord(:,1)+cos(angle_rot)*data.Coord(:,2); +set(handles.XObject,'String',num2str(data.Coord(:,1),4)); +set(handles.YObject,'String',num2str(data.Coord(:,2),4)); + + +function XImage_Callback(hObject, eventdata, handles) +update_list(hObject, eventdata,handles) + +function YImage_Callback(hObject, eventdata, handles) +update_list(hObject, eventdata,handles) + +function XObject_Callback(hObject, eventdata, handles) +update_list(hObject, eventdata,handles) + +function YObject_Callback(hObject, eventdata, handles) +update_list(hObject, eventdata,handles) + +function ZObject_Callback(hObject, eventdata, handles) +update_list(hObject, eventdata,handles) + +function update_list(hObject, eventdata, handles) +str4=get(handles.XImage,'String'); +str5=get(handles.YImage,'String'); +str1=get(handles.XObject,'String'); +tt=double(str1); +str2=get(handles.YObject,'String'); +str3=get(handles.ZObject,'String'); +if ~isempty(str1) & ~isequal(double(str1),32) & (isempty(str3)|isequal(double(str3),32)) + str3='0';%put z to 0 by default +end +strline=[str1 ' | ' str2 ' | ' str3 ' | ' str4 ' | ' str5]; +Coord=get(handles.ListCoord,'String'); +val=get(handles.ListCoord,'Value'); +Coord{val}=strline; +set(handles.ListCoord,'String',Coord) + +%-------------------------------------------------------------------- +% --- Executes on selection change in ListCoord. +%-------------------------------------------------------------------- +function ListCoord_Callback(hObject, eventdata, handles) +% hObject handle to ListCoord (see GCBO) +% eventdata reserved - to be defined in a future version of MATLAB +% handles structure with handles and user data (see GUIDATA) + +% Hints: contents = get(hObject,'String') returns ListCoord contents as cell array +% contents{get(hObject,'Value')} returns selected item from ListCoord +%set(handles.edit_append,'Value',2); %set to edit mode +Coord_cell=get(handles.ListCoord,'String'); +val=get(handles.ListCoord,'Value'); +if length(Coord_cell)>0 + coord_str=Coord_cell{val}; + k=findstr('|',coord_str); + if isempty(k) + return + end + set(handles.XObject,'String',coord_str(1:k(1)-5)) + set(handles.YObject,'String',coord_str(k(1)+5:k(2)-5)) + set(handles.ZObject,'String',coord_str(k(2)+5:k(3)-5)) + set(handles.XImage,'String',coord_str(k(3)+5:k(4)-5)) + set(handles.YImage,'String',coord_str(k(4)+5:end)) + huvmat=findobj(allchild(0),'Name','uvmat');%find the current uvmat interface handle + hplot=findobj(huvmat,'Tag','axes3');%main plotting axis of uvmat + h_menu_coord=findobj(huvmat,'Tag','menu_coord'); + menu=get(h_menu_coord,'String'); + choice=get(h_menu_coord,'Value'); + if iscell(menu) + option=menu{choice}; + else + option='px'; %default + end + if isequal(option,'phys') + XCoord=str2num(coord_str(1:k(1)-5)); + YCoord=str2num(coord_str(k(1)+5:k(2)-5)); + elseif isequal(option,'px')|| isequal(option,'') + XCoord=str2num(coord_str(k(3)+5:k(4)-5)); + YCoord=str2num(coord_str(k(4)+5:end)); + else + warndlg_uvmat('the choice in menu_coord of uvmat must be px or phys ','ERROR') + end + huvmat=findobj(allchild(0),'Name','uvmat');%find the current uvmat interface handle + hplot=findobj(huvmat,'Tag','axes3');%main plotting axis of uvmat + hhh=findobj(hplot,'Tag','calib_marker'); + if isempty(hhh) + axes(hplot) + line(XCoord,YCoord,'Color','m','Tag','calib_marker','LineStyle','.','Marker','o','MarkerSize',20); + else + set(hhh,'XData',XCoord) + set(hhh,'YData',YCoord) + end +end + + +%---------------------------------------------------- +% --- Executes on button press in rotation_plus. +function rotation_plus_Callback(hObject, eventdata, handles) +Phi=0; +Phi=get(handles.Phi,'String'); +if ~isempty(Phi) + Phi=str2num(Phi); +end +rotation(handles,Phi) + +%------------------------------------------------- +% --- Executes on button press in rotation_minus. +function rotation_minus_Callback(hObject, eventdata, handles) +Phi=0; +Phi=get(handles.Phi,'String'); +if ~isempty(Phi) + Phi=-str2num(Phi); +end +rotation(handles,Phi) + +%----------------------------------------------------- +%rotation +function rotation(handles,Phi) +O_x=str2num(get(handles.O_x,'String')); +O_y=str2num(get(handles.O_y,'String')); +if isempty(O_x) + O_x=0;%default +end +if isempty(O_y) + O_y=0;%default +end +Coord_cell=get(handles.ListCoord,'String'); +data=read_geometry_calib(Coord_cell); +%data=read_geometry_calib(handles); +r1=cos(pi*Phi/180); +r2=-sin(pi*Phi/180); +r3=sin(pi*Phi/180); +r4=cos(pi*Phi/180); +x=data.Coord(:,1); +y=data.Coord(:,2); +data.Coord(:,1)=r1*x+r2*y; +data.Coord(:,2)=r3*x+r4*y; +% data.Coord(:,[4 5])=data.Coord(:,[4 5]); +for i=1:size(data.Coord,1) + for j=1:5 + Coord{i,j}=num2str(data.Coord(i,j),4);%phys x,y,z + end +end +Tabchar=cell2tab(Coord,' | '); +set(handles.ListCoord,'Value',1) +set(handles.ListCoord,'String',Tabchar) + + +function O_x_Callback(hObject, eventdata, handles) + + +function O_y_Callback(hObject, eventdata, handles) + + +function O_z_Callback(hObject, eventdata, handles) + + +% --- Executes on selection change in edit_append. +function edit_append_Callback(hObject, eventdata, handles) +% val=get(handles.PLOT_append,'Value'); +% if isequal(val,2); %append mode +% %appeler mouse +% end +choice=get(handles.edit_append,'Value'); +if choice==1 + Coord=get(handles.ListCoord,'String'); + val=length(Coord); + if val>=1 & isequal(Coord{val},'') + val=val-1; %do not take into account blank + end + Coord{val+1}=''; + set(handles.ListCoord,'String',Coord) + set(handles.ListCoord,'Value',val+1) +end + + +%A REVOIR +% if choice==2 +% %display image with px coordinates +% hrootpath=findobj(huvmat,'Tag','RootPath'); +% hrootfile=findobj(huvmat,'Tag','RootFile'); +% RootPath=''; +% RootFile=''; +% % if ~isempty(hrootpath)& ~isempty(hrootfile) +% testhandle=1; +% RootPath=get(hrootpath,'String'); +% RootFile=get(hrootfile,'String'); +% % filebase=fullfile(RootPath,RootFile); +% % outputfile=[filebase '.xml']; +% Indices=get(findobj(huvmat,'Tag','FileIndex'),'String'); +% Ext=get(findobj(huvmat,'Tag','FileExt'),'String'); +% imagename=[fullfile(RootPath,RootFile) Indices Ext]; +% % input.menu_coord=1; +% h_menu_coord=findobj(huvmat,'Tag','menu_coord'); +% set(h_menu_coord,'Value',3) +% huvmat=uvmat(imagename);%open uvmat, set phys coord (Value 1) +% +% % end +% end + +function NEW_Callback(hObject, eventdata, handles) +%A METTRE SOUS UN BOUTON +huvmat=findobj(allchild(0),'Name','uvmat'); +hchild=get(huvmat,'children'); +hcoord=findobj(hchild,'Tag','menu_coord'); +coordtype=get(hcoord,'Value'); +haxes=findobj(hchild,'Tag','axes3'); +AxeData=get(haxes,'UserData'); +if ~isequal(hcoord,2) + set(hcoord,'Value',2) + huvmat=uvmat(AxeData); + 'relancer uvmat'; +end +if ~isfield(AxeData,'ZoomAxes') + warndlg_uvmat('first draw a window around a grid marker','ERRROR') + return +end +XLim=get(AxeData.ZoomAxes,'XLim'); +YLim=get(AxeData.ZoomAxes,'YLim'); +np=size(AxeData.A); +ind_sub_x=round(XLim); +ind_sub_y=np(1)-round(YLim); +Mfiltre=AxeData.A([ind_sub_y(2):ind_sub_y(1)] ,ind_sub_x,:); +Mfiltre_norm=double(Mfiltre); +Mfiltre_norm=Mfiltre_norm/sum(sum(Mfiltre_norm)); +Mfiltre_norm=100*(Mfiltre_norm-mean(mean(Mfiltre_norm))); +Atype=class(AxeData.A); +Data.NbDim=2; +Data.A=filter2(Mfiltre_norm,double(AxeData.A)); +Data.A=feval(Atype,Data.A); +Data.AName='image'; +Data.AX=AxeData.AX; +Data.AY=AxeData.AY; +Data.CoordType='px'; +plot_field(Data) + + + +%'key_press_fcn:' function activated when a key is pressed on the keyboard +%----------------------------------- +function key_press_fcn(hObject,eventdata,handles) +hh=get(hObject,'parent'); +xx=double(get(hh,'CurrentCharacter')); %get the keyboard character + +if ismember(xx,[8 127])%backspace or delete + Coord_cell=get(handles.ListCoord,'String'); + data=read_geometry_calib(Coord_cell); + Coord=[]; %default + if isfield(data,'Coord') + Coord=data.Coord; + end + val=get(handles.ListCoord,'Value'); + Coord(val,:)=[];%suppress the selected item in the list + CoordCell={}; + for iline=1:size(Coord,1) + for j=1:5 + CoordCell{iline,j}=num2str(Coord(iline,j),4); + end + end + Tabchar=cell2tab(CoordCell,' | ');%transform cells into table ready for display + val=min(size(Coord,1),val); + set(handles.ListCoord,'Value',max(val,1)) + set(handles.ListCoord,'String',Tabchar) + ListCoord_Callback(hObject, eventdata, handles) + PLOT_Callback(hObject,eventdata,handles) +end + + +% --- Executes on button press in append_point. +function append_point_Callback(hObject, eventdata, handles) + + Coord=get(handles.ListCoord,'String'); + val=length(Coord); + if val>=1 & isequal(Coord{val},'') + val=val-1; %do not take into account blank + end + Coord{val+1}=''; + set(handles.ListCoord,'String',Coord) + set(handles.ListCoord,'Value',val+1) + + +% -------------------------------------------------------------------- +function MenuOpen_Callback(hObject, eventdata, handles) +%get the object file +huvmat=findobj(allchild(0),'Name','uvmat'); +UvData=get(huvmat,'UserData'); +hchild=get(huvmat,'Children'); +hrootpath=findobj(hchild,'Tag','RootPath'); +oldfile=get(hrootpath,'String'); +if isempty(oldfile) + oldfile=''; +end +%[FileName,PathName] = uigetfile('*.civ','Select a .civ file',oldfile) +[FileName, PathName, filterindex] = uigetfile( ... + {'*.xml;*.mat', ' (*.xml,*.mat)'; + '*.xml', '.xml files '; ... + '*.mat', '.mat matlab files '}, ... + 'Pick a file',oldfile); +fileinput=[PathName FileName];%complete file name +testblank=findstr(fileinput,' ');%look for blanks +if ~isempty(testblank) + msgbox_uvmat('ERROR','forbidden input file name or path: no blank character allowed') + return +end +sizf=size(fileinput); +if (~ischar(fileinput)|~isequal(sizf(1),1)),return;end +loadfile(handles,fileinput) + + +% -------------------------------------------------------------------- +function Untitled_3_Callback(hObject, eventdata, handles) +% hObject handle to Untitled_3 (see GCBO) +% eventdata reserved - to be defined in a future version of MATLAB +% handles structure with handles and user data (see GUIDATA) + + +% -------------------------------------------------------------------- +function MenuPlot_Callback(hObject, eventdata, handles) + +huvmat=findobj(allchild(0),'Name','uvmat');%find the current uvmat interface handle +UvData=get(huvmat,'UserData');%Data associated to the current uvmat interface +hhuvmat=guidata(huvmat); %handles of GUI elements in uvmat +hplot=findobj(huvmat,'Tag','axes3');%main plotting axis of uvmat +h_menu_coord=findobj(huvmat,'Tag','menu_coord'); +menu=get(h_menu_coord,'String'); +choice=get(h_menu_coord,'Value'); +if iscell(menu) + option=menu{choice}; +else + option='px'; %default +end +Coord_cell=get(handles.ListCoord,'String'); +ObjectData=read_geometry_calib(Coord_cell); +%ObjectData=read_geometry_calib(handles);%read the interface input parameters defining the object +if isequal(option,'phys') + ObjectData.Coord=ObjectData.Coord(:,[1:3]); +elseif isequal(option,'px')||isequal(option,'') + ObjectData.Coord=ObjectData.Coord(:,[4:5]); +else + msgbox_uvmat('ERROR','the choice in menu_coord of uvmat must be px or phys ') +end +axes(hhuvmat.axes3) +hh=findobj('Tag','calib_points'); +if isempty(hh) + hh=line(ObjectData.Coord(:,1),ObjectData.Coord(:,2),'Color','m','Tag','calib_points','LineStyle','.','Marker','+'); +else + set(hh,'XData',ObjectData.Coord(:,1)) + set(hh,'YData',ObjectData.Coord(:,2)) +end + +% -------------------------------------------------------------------- +function MenuHelp_Callback(hObject, eventdata, handles) +path_to_uvmat=which ('uvmat');% check the path of uvmat +pathelp=fileparts(path_to_uvmat); + helpfile=fullfile(pathelp,'UVMAT_DOC','uvmat_doc.html'); +if isempty(dir(helpfile)), warndlg_uvmat('The help file uvmat_doc.html needs to be put in the directory UVMAT/UVMAT_DOC','ERROR') +else + web([helpfile '#geometry_calib']) +end + + + +% -------------------------------------------------------------------- +function MenuCreateGrid_Callback(hObject, eventdata, handles) +% hObject handle to MenuCreateGrid (see GCBO) +% eventdata reserved - to be defined in a future version of MATLAB +% handles structure with handles and user data (see GUIDATA) + + +% -------------------------------------------------------------------- +function MenuTranslatePoints_Callback(hObject, eventdata, handles) +hcalib=get(handles.calib_type,'parent');%handles of the GUI geometry_calib +CalibData=get(hcalib,'UserData') +Tinput=[];%default +if isfield(CalibData,'translate') + Tinput=CalibData.translate; +end +T=translate_points(Tinput);%display translate_points GUI and get shift parameters +CalibData.translate=T; +set(hcalib,'UserData',CalibData) +Coord_cell=get(handles.ListCoord,'String'); +data=read_geometry_calib(Coord_cell); +% data=read_geometry_calib(handles); +data.Coord(:,1)=T(1)+data.Coord(:,1); +data.Coord(:,2)=T(2)+data.Coord(:,2); +data.Coord(:,3)=T(3)+data.Coord(:,3); +data.Coord(:,[4 5])=data.Coord(:,[4 5]); +for i=1:size(data.Coord,1) + for j=1:5 + Coord{i,j}=num2str(data.Coord(i,j),4);%phys x,y,z + end +end +Tabchar=cell2tab(Coord,' | '); +set(handles.ListCoord,'Value',1) +set(handles.ListCoord,'String',Tabchar) + + +% -------------------------------------------------------------------- +function MenuRotatePoints_Callback(hObject, eventdata, handles) +% hObject handle to MenuRotatePoints (see GCBO) +% eventdata reserved - to be defined in a future version of MATLAB +% handles structure with handles and user data (see GUIDATA) + + +% -------------------------------------------------------------------- +function Untitled_8_Callback(hObject, eventdata, handles) +% hObject handle to Untitled_8 (see GCBO) +% eventdata reserved - to be defined in a future version of MATLAB +% handles structure with handles and user data (see GUIDATA) + + + +function edit27_Callback(hObject, eventdata, handles) + + +function edit28_Callback(hObject, eventdata, handles) +% hObject handle to O_y (see GCBO) +% eventdata reserved - to be defined in a future version of MATLAB +% handles structure with handles and user data (see GUIDATA) + +% Hints: get(hObject,'String') returns contents of O_y as text +% str2double(get(hObject,'String')) returns contents of O_y as a double + + +% --- Executes on button press in rotation_plus. +function pushbutton16_Callback(hObject, eventdata, handles) +% hObject handle to rotation_plus (see GCBO) +% eventdata reserved - to be defined in a future version of MATLAB +% handles structure with handles and user data (see GUIDATA) + + +% --- Executes on button press in rotation_minus. +function pushbutton17_Callback(hObject, eventdata, handles) +% hObject handle to rotation_minus (see GCBO) +% eventdata reserved - to be defined in a future version of MATLAB +% handles structure with handles and user data (see GUIDATA) + + + +function edit30_Callback(hObject, eventdata, handles) +% hObject handle to Phi (see GCBO) +% eventdata reserved - to be defined in a future version of MATLAB +% handles structure with handles and user data (see GUIDATA) + +% Hints: get(hObject,'String') returns contents of Phi as text +% str2double(get(hObject,'String')) returns contents of Phi as a double + + +% --- Executes during object creation, after setting all properties. +function O_y_CreateFcn(hObject, eventdata, handles) +% hObject handle to O_y (see GCBO) +% eventdata reserved - to be defined in a future version of MATLAB +% handles empty - handles not created until after all CreateFcns called + +% Hint: edit controls usually have a white background on Windows. +% See ISPC and COMPUTER. +if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor')) + set(hObject,'BackgroundColor','white'); +end + + +% --- Executes during object creation, after setting all properties. +function O_x_CreateFcn(hObject, eventdata, handles) +% hObject handle to O_x (see GCBO) +% eventdata reserved - to be defined in a future version of MATLAB +% handles empty - handles not created until after all CreateFcns called + +% Hint: edit controls usually have a white background on Windows. +% See ISPC and COMPUTER. +if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor')) + set(hObject,'BackgroundColor','white'); +end + + +% --- Executes during object creation, after setting all properties. +function T_x_CreateFcn(hObject, eventdata, handles) +% hObject handle to T_x (see GCBO) +% eventdata reserved - to be defined in a future version of MATLAB +% handles empty - handles not created until after all CreateFcns called + +% Hint: edit controls usually have a white background on Windows. +% See ISPC and COMPUTER. +if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor')) + set(hObject,'BackgroundColor','white'); +end + + +% --- Executes during object creation, after setting all properties. +function T_y_CreateFcn(hObject, eventdata, handles) +% hObject handle to T_y (see GCBO) +% eventdata reserved - to be defined in a future version of MATLAB +% handles empty - handles not created until after all CreateFcns called + +% Hint: edit controls usually have a white background on Windows. +% See ISPC and COMPUTER. +if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor')) + set(hObject,'BackgroundColor','white'); +end + + +% --- Executes during object creation, after setting all properties. +function T_z_CreateFcn(hObject, eventdata, handles) +% hObject handle to T_z (see GCBO) +% eventdata reserved - to be defined in a future version of MATLAB +% handles empty - handles not created until after all CreateFcns called + +% Hint: edit controls usually have a white background on Windows. +% See ISPC and COMPUTER. +if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor')) + set(hObject,'BackgroundColor','white'); +end + + + +function edit31_Callback(hObject, eventdata, handles) +% hObject handle to edit31 (see GCBO) +% eventdata reserved - to be defined in a future version of MATLAB +% handles structure with handles and user data (see GUIDATA) + +% Hints: get(hObject,'String') returns contents of edit31 as text +% str2double(get(hObject,'String')) returns contents of edit31 as a double + + +% --- Executes during object creation, after setting all properties. +function edit31_CreateFcn(hObject, eventdata, handles) +% hObject handle to edit31 (see GCBO) +% eventdata reserved - to be defined in a future version of MATLAB +% handles empty - handles not created until after all CreateFcns called + +% Hint: edit controls usually have a white background on Windows. +% See ISPC and COMPUTER. +if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor')) + set(hObject,'BackgroundColor','white'); +end + + + +function edit32_Callback(hObject, eventdata, handles) +% hObject handle to edit32 (see GCBO) +% eventdata reserved - to be defined in a future version of MATLAB +% handles structure with handles and user data (see GUIDATA) + +% Hints: get(hObject,'String') returns contents of edit32 as text +% str2double(get(hObject,'String')) returns contents of edit32 as a double + + +% --- Executes during object creation, after setting all properties. +function edit32_CreateFcn(hObject, eventdata, handles) +% hObject handle to edit32 (see GCBO) +% eventdata reserved - to be defined in a future version of MATLAB +% handles empty - handles not created until after all CreateFcns called + +% Hint: edit controls usually have a white background on Windows. +% See ISPC and COMPUTER. +if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor')) + set(hObject,'BackgroundColor','white'); +end + + + +function edit33_Callback(hObject, eventdata, handles) +% hObject handle to edit33 (see GCBO) +% eventdata reserved - to be defined in a future version of MATLAB +% handles structure with handles and user data (see GUIDATA) + +% Hints: get(hObject,'String') returns contents of edit33 as text +% str2double(get(hObject,'String')) returns contents of edit33 as a double + + +% --- Executes on button press in pushbutton18. +function pushbutton18_Callback(hObject, eventdata, handles) +% hObject handle to pushbutton18 (see GCBO) +% eventdata reserved - to be defined in a future version of MATLAB +% handles structure with handles and user data (see GUIDATA) + + +% --- Executes on button press in pushbutton19. +function pushbutton19_Callback(hObject, eventdata, handles) +% hObject handle to pushbutton19 (see GCBO) +% eventdata reserved - to be defined in a future version of MATLAB +% handles structure with handles and user data (see GUIDATA) + + + + Index: /trunk/src/get_field.m =================================================================== --- /trunk/src/get_field.m (revision 2) +++ /trunk/src/get_field.m (revision 2) @@ -0,0 +1,1958 @@ +%'get_field': display variables and attributes from a Netcdf file, and RUN selected fields +%------------------------------------------------------------------------ +%function varargout = get_field(varargin) +% associated with the GUI get_field.fig +% +%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +% Copyright Joel Sommeria, 2008, LEGI / CNRS-UJF-INPG, sommeria@coriolis-legi.org. +%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +% This file is part of the toolbox UVMAT. +% +% UVMAT is free software; you can redistribute it and/or modify +% it under the terms of the GNU General Public License as published by +% the Free Software Foundation; either version 2 of the License, or +% (at your option) any later version. +% +% UVMAT is distributed in the hope that it will be useful, +% but WITHOUT ANY WARRANTY; without even the implied warranty of +% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +% GNU General Public License (file UVMAT/COPYING.txt) for more details. +%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA + +function varargout = get_field(varargin) + +% Last Modified by GUIDE v2.5 13-Nov-2009 22:14:18 + +% Begin initialization code - DO NOT EDIT +gui_Singleton = 0; +gui_State = struct('gui_Name', mfilename, ... + 'gui_Singleton', gui_Singleton, ... + 'gui_OpeningFcn', @get_field_OpeningFcn, ... + 'gui_OutputFcn', @get_field_OutputFcn, ... + 'gui_LayoutFcn', [] , ... + 'gui_Callback', []); +if nargin & isstr(varargin{1}) + gui_State.gui_Callback = str2func(varargin{1}); +end + +if nargout + [varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:}); +else + gui_mainfcn(gui_State, varargin{:}); +end +% End initialization code - DO NOT EDIT + + +% --- Executes just before get_field is made visible. +function get_field_OpeningFcn(hObject, eventdata, handles,filename,Field,haxes) + +set(handles.dimensions,'enable','on')% should be put by guide +browse_fig(handles.list_fig) + +% Choose default command line output for get_field +handles.output = hObject; + +% Update handles structure +guidata(hObject, handles); +pathuvmat=fileparts(which('uvmat')); +addpath(fullfile(pathuvmat,'FIELD_FCT')) +set(handles.attributes,'enable','on')% TO BE SET BY GUIDE +set(hObject,'WindowButtonUpFcn',{@mouse_up_gui,handles})%set mouse click action function +if exist('filename','var')& ischar(filename) + set(handles.inputfile,'String',filename) + inputfile_Callback(hObject, eventdata, handles) +else + set(handles.inputfile,'String','') + %loads the information stored in prefdir to initiate the browser and the list of functions + menu_str={'PLOT'};%list of functions included in 'get_field.m' + %menu_str(end)=[];%remove from the list the last option 'more...' + path_get_field=which('get_field');%path of the function 'get_field' + for ilist=1:length(menu_str) + fct_path{ilist,1}=path_get_field;%paths of the fuctions buil-in in 'get_field.m' + end + dir_perso=prefdir; + profil_perso=fullfile(dir_perso,'uvmat_perso.mat'); + if exist(profil_perso,'file') + % menu={'RUN';'raw2phys';'histogram';'FFT';'peaklocking'}; + h=load (profil_perso); + if isfield(h,'get_field_fct') && iscell(h.get_field_fct) + for ilist=1:length(h.get_field_fct) + [path,file]=fileparts(h.get_field_fct{ilist}); + fct_path=[fct_path; {path}];%concatene the list of paths + menu_str=[menu_str; {file}]; + end + + end + end + menu_str=[menu_str;{'more...'}]; + set(handles.ACTION,'String',menu_str) + set(handles.ACTION,'UserData',fct_path)% store the list of path in UserData of ACTION + % display the GUI for the default action 'check_files' + ACTION_Callback(hObject, eventdata, handles) +end +% menu=[menu;h.fct_get_field]; +% menu=[menu;{'more...'}]; +% fct_path=h.fct_path_get_field; +% set(handles.ACTION,'String',menu) +% set(handles.ACTION,'UserData',fct_path) +% for ipath=1:length(fct_path) +% if exist(fct_path{ipath},'dir') +% addpath(fct_path{ipath}) +% end +% end +% end +% end +% end +if exist('Field','var') & isstruct(Field) + Field_input(eventdata,handles,Field) + if exist('haxes','var') + Field.PlotAxes=haxes; + end + set(hObject,'UserData',Field); +end + + + + + + +%----------------------------------------------------------- +% --- Outputs from this function are returned to the command line. +function varargout = get_field_OutputFcn(hObject, eventdata, handles) +varargout{1} = handles.output; + +%----------------------------------------------------------- +% --- Executes on button press in browse. +function browse_Callback(hObject, eventdata, handles) + + + + +%--------------------------------------------------------- +function inputfile_Callback(hObject, eventdata, handles) +inputfile=get(handles.inputfile,'String'); +Field=nc2struct(inputfile,[]);% reads only the lists of fields, dimensions and attributes +hfig=get(handles.inputfile,'parent'); +set(hfig,'UserData',Field); +Field_input(eventdata,handles,Field); + + +%--------------------------------------------------------- +function Field_input(eventdata,handles,Field) + +if isfield(Field,'ListDimName')&&~isempty(Field.ListDimName) + Tabcell(:,1)=Field.ListDimName; + for iline=1:length(Field.ListDimName) + Tabcell{iline,2}=num2str(Field.DimValue(iline)); + end + Tabchar=cell2tab(Tabcell,'='); + set(handles.dimensions,'String',Tabchar) +end +if ~isfield(Field,'ListVarName') + return +end +Txt=Field.ListVarName; +set(handles.variables,'Value',1) +set(handles.variables,'String',[{'*'} Txt]) +variables_Callback(handles.variables,[], handles) +set(handles.abscissa,'String',[{''} Txt ]) +set(handles.ordinate,'String',Txt) +set(handles.vector_x,'String',[Txt ]) +set(handles.vector_y,'String',[Txt ]) +set(handles.vector_z,'String',[{''} Txt ]) +set(handles.vec_color,'String',[{''} Txt ]) +set(handles.coord_x_scalar,'String',[{''} Txt ]) +set(handles.coord_y_scalar,'String',[{''} Txt ]) +set(handles.coord_x_vectors,'String',[{''} Txt ]) +set(handles.coord_y_vectors,'String',[{''} Txt ]) +set(handles.coord_z_scalar,'String',[{''} Txt ]) +set(handles.coord_z_vectors,'String',[{''} Txt ]) +set(handles.scalar,'Value',1) +set(handles.scalar,'String', Txt ) + +[CellVarIndex,NbDim,VarType,errormsg]=find_field_indices(Field); +if ~isempty(errormsg) + msgbox_uvmat('ERROR',['error in get_field/Field_input/find_field_indices: ' errormsg]) + return +end +[maxdim,imax]=max(NbDim); + +if maxdim>=3 + set(handles.vector_z,'Visible','on') + set(handles.vector_z,'String',[{''} Txt ]) + set(handles.coord_z_vectors,'Visible','on') + set(handles.coord_z_vectors,'String',[{''} Txt ]) + set(handles.coord_z_scalar,'Visible','on') + set(handles.coord_z_scalar,'String',[{''} Txt ]) +else + set(handles.vector_z,'Visible','off') + set(handles.coord_z_vectors,'Visible','off') + set(handles.coord_z_scalar,'Visible','off') +end +if maxdim>=2 + set(handles.check_1Dplot,'Value',0) + if ~isempty(VarType{imax}.vector_x) && ~isempty(VarType{imax}.vector_y) + set(handles.check_vector,'Value',1) + set(handles.vector_x,'Value',VarType{imax}.vector_x) + set(handles.vector_y,'Value',VarType{imax}.vector_y) + set(handles.check_scalar,'Value',0) + else + set(handles.check_scalar,'Value',1) + set(handles.check_vector,'Value',0) + if isfield(VarType{imax},'scalar') && length(VarType{imax}.scalar)>=1 + set(handles.scalar,'Value',VarType{imax}.scalar(1)) + end + end + check_1Dplot_Callback(handles.check_1Dplot, eventdata, handles) + check_scalar_Callback(handles.check_scalar, eventdata, handles) + check_vector_Callback(handles.check_vector, eventdata, handles) +end + + +%---------------------------------------------------------- +function ordinate_Callback(hObject, eventdata, handles) +%update_field(hObject, eventdata, handles) +% A REVOIR +hselect_field=get(handles.inputfile,'parent'); +Field=get(hselect_field,'UserData'); +% xindex=get(handles.abscissa,'Value'); +list=get(handles.ordinate,'String'); +yindex=get(handles.ordinate,'Value'); +yindex=name2index(list{yindex(1)},Field.ListVarName); +if ~isempty(yindex) + set(handles.variables,'Value',yindex+1) + variables_Callback(hObject, eventdata, handles) +end +[CellVarIndex,NbDim,VarType,errormsg]=find_field_indices(Field); +for icell=1:numel(CellVarIndex) + VarIndex=CellVarIndex{icell}; + if ~isempty(find(VarIndex==yindex)) && (isempty(VarType{icell}.coord_x)||~isequal(VarType{icell}.coord_x,VarIndex)) + cell_select=icell; + break + end +end + +val=get(handles.abscissa,'Value'); +set(handles.abscissa,'Value',min(val,2)); +coord_x_index=VarType{cell_select}.coord; +coord_x_index=coord_x_index(find(coord_x_index)); +set(handles.abscissa,'String',[{''}; (Field.ListVarName(coord_x_index))'; (Field.ListVarName(VarIndex))']) +% Field.VarIndex.y=yindex; +% set(hselect_field,'UserData',Field); +%update_UserData(handles) + +%---------------------------------------------------------------------- +% --- Executes on selection change in abscissa. +function abscissa_Callback(hObject, eventdata, handles) + hselect_field=get(handles.inputfile,'parent'); + Field=get(hselect_field,'UserData');%current input field + xdispindex=get(handles.abscissa,'Value');%index in the list of abscissa +% test_2D=get(handles.check_vector,'Value');% =1 for vector fields +% test_scalar=get(handles.check_scalar,'Value');% =1 for scalar fields +%if isequal(xdispindex,1)% blank selection, no selected variable for abscissa +% Txt=Field.ListVarName; +% set(handles.ordinate,'String',[{''} Txt ])% display all the varaibles in the list of ordinates +% xindex=[]; +% else + xlist=get(handles.abscissa,'String');%list of abscissa + VarName=xlist{xdispindex}; %selected variable name + update_field(hObject, eventdata, handles,VarName) +% xindex=name2index(xname,Field.ListVarName); %index of the selection in the total list of variables +% if ~isempty(xindex) +% set(handles.variables,'Value',xindex+1) +% variables_Callback(hObject, eventdata, handles) +% end +% set(handles.variables,'Value',xindex+1)%outline in the list of variables +% variables_Callback(hObject, eventdata, handles) %display properties of the variable (dim, attributes) +% if ~test_2D & ~test_scalar% look for possible varaibles to RUN in ordinate +% index=Field.VarDimIndex{xindex};%dimension indices of the variable selected for abscissa +% VarIndex=[]; +% for ilist=1:length(Field.VarDimIndex)%detect +% index_i=Field.VarDimIndex{ilist}; +% if ~isempty(index_i) +% if isequal(index_i(1),index(1))%if the first dimension of the variable coincide with the selected one, RUN is possible +% VarIndex=[VarIndex ilist]; +% end +% end +% end +% % set(handles.ordinate,'Value',1) +% set(handles.ordinate,'String',Field.ListVarName(VarIndex)) +% end +% end +% +% update_UserData(handles) + +%------------------------------------------------------- +% --- Executes on selection change in scalar menu. +function scalar_Callback(hObject, eventdata, handles) +%------------------------------------------------------- +Aindex=get(handles.scalar,'Value'); +Astring=get(handles.scalar,'String'); +VarName=Astring{Aindex}; +update_field(hObject, eventdata, handles,VarName) + +%------------------------------------------------------- +% --- Executes on selection change in coord_x_scalar. +function coord_x_scalar_Callback(hObject, eventdata, handles) +%------------------------------------------------------- +index=get(handles.coord_x_scalar,'Value'); +string=get(handles.coord_x_scalar,'String'); +VarName=string{index}; +update_field(hObject, eventdata, handles,VarName) + +%------------------------------------------------------- +% --- Executes on selection change in coord_y_scalar. +function coord_y_scalar_Callback(hObject, eventdata, handles) +%------------------------------------------------------- +index=get(handles.coord_y_scalar,'Value'); +string=get(handles.coord_y_scalar,'String'); +VarName=string{index}; +update_field(hObject, eventdata, handles,VarName) + +%------------------------------------------------------- +% --- Executes on selection change in coord_z_scalar. +function coord_z_scalar_Callback(hObject, eventdata, handles) +%------------------------------------------------------- +index=get(handles.coord_z_scalar,'Value'); +string=get(handles.coord_z_scalar,'String'); +VarName=string{index}; +update_field(hObject, eventdata, handles,VarName) + +%------------------------------------------------------- +% --- Executes on selection change in vector_x. +function vector_x_Callback(hObject, eventdata, handles) +%------------------------------------------------------- +index=get(handles.vector_x,'Value'); +string=get(handles.vector_x,'String'); +VarName=string{index}; +update_field(hObject, eventdata, handles,VarName) + +%------------------------------------------------------- +% --- Executes on selection change in vector_y. +function vector_y_Callback(hObject, eventdata, handles) +%------------------------------------------------------- +index=get(handles.vector_y,'Value'); +string=get(handles.vector_y,'String'); +VarName=string{index}; +update_field(hObject, eventdata, handles,VarName) + +%------------------------------------------------------- +% --- Executes on selection change in vector_z. +function vector_z_Callback(hObject, eventdata, handles) +%------------------------------------------------------- +index=get(handles.vector_z,'Value'); +string=get(handles.vector_z,'String'); +VarName=Astring{index}; +update_field(hObject, eventdata, handles,VarName) + +%------------------------------------------------------- +% --- Executes on selection change in coord_x_vectors. +function coord_x_vectors_Callback(hObject, eventdata, handles) +%------------------------------------------------------- +index=get(handles.coord_x_vectors,'Value'); +string=get(handles.coord_x_vectors,'String'); +VarName=string{index}; +update_field(hObject, eventdata, handles,VarName) + +%------------------------------------------------------- +% --- Executes on selection change in coord_y_vectors. +%------------------------------------------------------- +function coord_y_vectors_Callback(hObject, eventdata, handles) +index=get(handles.coord_y_vectors,'Value'); +string=get(handles.coord_y_vectors,'String'); +VarName=string{index}; +update_field(hObject, eventdata, handles,VarName) + +%------------------------------------------------------- +% --- Executes on selection change in coord_z_scalar. +function coord_z_vectors_Callback(hObject, eventdata, handles) +%------------------------------------------------------- +index=get(handles.coord_z_vectors,'Value'); +string=get(handles.coord_z_vectors,'String'); +VarName=string{index}; +update_field(hObject, eventdata, handles,VarName) + +%------------------------------------------------------- +% --- Executes on selection change in vec_color. +function vec_color_Callback(hObject, eventdata, handles) +%------------------------------------------------------- +index=get(handles.vec_color,'Value'); +string=get(handles.vec_color,'String'); +VarName=string{index}; +update_field(hObject, eventdata, handles,VarName) + +%--------------------------------- +function update_field(hObject, eventdata, handles,VarName) +% VarName= input variable name for scalar or vector plots +%if ischar(VarName) +hselect_field=get(handles.inputfile,'parent'); +Field=get(hselect_field,'UserData'); +index=name2index(VarName,Field.ListVarName); +if ~isempty(index) + set(handles.variables,'Value',index+1) + variables_Callback(hObject, eventdata, handles) +end +% +% +% hselect_field=get(handles.inputfile,'parent'); +% Field=get(hselect_field,'UserData'); +% ivar_sel=[];%default +% for ivar=1:length(Field.ListVarName)%detect +% if isequal(Field.ListVarName{ivar},VarName) +% ivar_sel=ivar; %ivar_sel = index of the input variable in the list ListVarName +% break +% end +% end +% if isempty(ivar_sel) +% return +% end +% set(handles.variables,'Value',ivar_sel+1)%select the corresponding item in the displayed list 'variables' +% variables_Callback(hObject, eventdata, handles)%show the dimensions and attributes of the input variable +% +% index=Field.VarDimIndex{ivar_sel};%dimension indices of the input variable +% DimValue=Field.DimValue(index);%dimension values of the input variable +% ind_1=find(DimValue==1); +% index(ind_1)=[];%Mremove singletons +% +% +% % detect possible variables for abscissa and ordinate +% VarIndex=[];%initiate list of selected variable indices +% ind_coordvar=[]; %initiate list of coordinate variables +% for ilist=1:length(Field.VarDimIndex) +% if ~isequal(ilist,ivar_sel) +% index_i=Field.VarDimIndex{ilist};%indices of dimensions associated with variable #ilist +% if length(index_i)>1 +% DimValue=Field.DimValue(index_i); +% ind_1=find(DimValue==1); +% index_i(ind_1)=[];%Mremove singletons +% if isequal(index,index_i) +% VarIndex=[VarIndex ilist]; %selected variable withb the same dimensions of the input variable +% end +% else +% idim=find(index==index_i(1)); +% if ~isempty(idim) +% VarIndex=[VarIndex ilist]; %possible dimension variable +% if isequal(Field.ListDimName{index_i(1)},Field.ListVarName{ilist}) +% ind_coordvar=[ind_coordvar length(VarIndex)]; +% end +% end +% end +% end +% end +% % val=get(handles.abscissa,'Value'); +% % if val>length(Field.ListVarName(VarIndex))+1 +% % set(handles.abscissa,'Value',length(Field.ListVarName(VarIndex))+1) +% % end +% % val=get(handles.ordinate,'Value'); +% % if val>length(Field.ListVarName(VarIndex))+1 +% % set(handles.abscissa,'Value',length(Field.ListVarName(VarIndex))+1) +% % end +% % val=get(handles.coord_z_vectors_scalar,'Value'); +% % if val>length(Field.ListVarName(VarIndex))+1 +% % set(handles.abscissa,'Value',length(Field.ListVarName(VarIndex))+1) +% % end +% set(handles.abscissa,'Value',1)%default +% set(handles.ordinate,'Value',1)%default +% set(handles.coord_z_scalar,'Value',1)%default +% set(handles.abscissa,'String',[{''} Field.ListVarName(VarIndex) ]) +% set(handles.ordinate,'String',[{''} Field.ListVarName(VarIndex) ]) +% set(handles.coord_z_scalar,'String',[{''} Field.ListVarName(VarIndex) ]) +% if length(ind_coordvar)>=1 +% set(handles.abscissa,'Value',ind_coordvar(1)+1) +% elseif length(index)==1 && length(VarIndex)>=1 +% set(handles.abscissa,'Value',2) +% end +% if length(ind_coordvar)>=2 +% set(handles.ordinate,'Value',ind_coordvar(2)+1) +% elseif length(index)==1 && length(VarIndex)>=2 +% set(handles.ordinate,'Value',3) +% end +% if length(ind_coordvar)>=3 +% set(handles.coord_z_scalar,'Value',ind_coordvar(3)+1) +% elseif length(index)==1 && length(VarIndex)>=3 +% set(handles.coord_z_scalar,'Value',4) +% end + +%--------------------------------------------------------- +% update the UserData Field for use of the selected variables outsde get_field (taken from RUN_Callback) +function update_UserData(handles) +%--------------------------------------------------------- +return +% global SubField +hselect_field=get(handles.inputfile,'parent');%handle of the get_field interface +Field=get(hselect_field,'UserData');% read the current field Structure in the get_field interface +if isfield(Field,'VarAttribute') + VarAttribute=Field.VarAttribute; +else + VarAttribute={}; +end + + +% select the indices of field variables for 2D plots +test_check_1Dplot=get(handles.check_1Dplot,'Value'); +test_scalar=get(handles.check_scalar,'Value'); +test_vector=get(handles.check_vector,'Value'); + +%transform if needed (calibration) +list=get(handles.menu_coord,'String'); +index=get(handles.menu_coord,'Value'); +transform=list{index}; +if ~isequal(transform,'') + Field=feval(transform,Field); +end +VarIndex.u=[]; +VarIndex.v=[]; +VarIndex.w=[]; +VarIndex.A=[]; +VarIndex_tot=[]; +iuA=[]; +if test_scalar + Astring=get(handles.scalar,'String'); + Aindex=get(handles.scalar,'Value');%selected indices in the ordinate listbox + list_var=Astring(Aindex); + VarIndex.A=name2index(list_var,Field.ListVarName);%index of the variable A in ListVarName + VarIndex_tot= [VarIndex_tot VarIndex.A]; + DimIndex=Field.VarDimIndex{VarIndex.A};%dimension indices of the variable + DimValue=Field.DimValue(DimIndex); + ind=find(DimValue==1); + DimIndex(ind)=[];%Mremove singleton +end +if test_vector + Ustring=get(handles.vector_x,'String'); + Uindex=get(handles.vector_x,'Value'); %selected indices in the ordinate listbox + list_var=Ustring{Uindex};%name of the selected scalar + VarIndex.u=name2index(list_var,Field.ListVarName); + Vstring=get(handles.vector_y,'String'); + Vindex=get(handles.vector_y,'Value'); %selected indices in the ordinate listbox + list_var=Ustring{Vindex};%name of the selected scalar + VarIndex.v=name2index(list_var,Field.ListVarName); + if isequal(VarIndex.u,VarIndex.A)|isequal(VarIndex.v,VarIndex.A) + iuA=VarIndex.A; %same variable used for vector and scalar + VarIndex_tot(iuA)=[]; + end + VarIndex_tot=[VarIndex_tot VarIndex.u VarIndex.v]; + %dimensions + DimIndex_u=Field.VarDimIndex{VarIndex.u};%dimension indices of the variable + DimValue=Field.DimValue(DimIndex_u); + ind=find(DimValue==1); + DimIndex_u(ind)=[];%Mremove singleton + DimIndex_v=Field.VarDimIndex{VarIndex.v};%dimension indices of the variable + DimValue=Field.DimValue(DimIndex_v); + ind=find(DimValue==1); + DimIndex_v(ind)=[];%Mremove singleton + if ~isequal(DimIndex_u,DimIndex_v) + warndlg_uvmat('inconsistent dimensions for u and v','ERROR') + set(handles.vector_y,'Value',1); + return + elseif test_scalar & ~isequal(DimIndex_u,DimIndex) + warndlg_uvmat('inconsistent dimensions for vector and scalar represented as vector color','ERROR') + set(handles.scalar,'Value',1); + return + end + DimIndex=DimIndex_u; + %TODO possibility of selecting 3 times the same variable for u, v, w components +end + + +% select the variable index (or indices) for z coordinates +test_grid=0; +if test_scalar | test_vector + nbdim=length(DimIndex); + if nbdim > 3 + warndlg_uvmat('array with more than three dimensions, not supported','ERROR') + return + else + perm_ind=[1:nbdim]; + end + if nbdim==3 + zstring=get(handles.coord_z_vectors_scalar,'String'); + zindex=get(handles.coord_z_vectors_scalar,'Value'); %selected indices in the ordinate listbox + list_var=zstring(zindex); + VarIndex_z=name2index(list_var,Field.ListVarName);%index of the selected variable + if isequal(VarIndex.A,VarIndex_z)|isequal(VarIndex.u,VarIndex_z)|isequal(VarIndex.v,VarIndex_z)|isequal(VarIndex.w,VarIndex_z) + if zindex ~= 1 + set(handles.coord_z_vectors_scalar,'Value',1)%ordinate cannot be the same as scalar or vector components + return + end + else + VarIndex_tot=[VarIndex_tot VarIndex_z]; + DimIndex_z=Field.VarDimIndex{VarIndex_z}; + DimValue=Field.DimValue(DimIndex_z); + ind=find(DimValue==1); + DimIndex_z(ind)=[];%Mremove singleton + if isequal(DimIndex_z,DimIndex) + VarAttribute{VarIndex_z}.Role='coord_z';%unstructured coordinates + elseif length(DimIndex_z)==1 + VarAttribute{VarIndex_z}.Role=Field.ListDimName{DimIndex_z}; %dimension variable + ind_z=find(DimIndex==DimIndex_z(1)); + perm_ind(ind_z)=1; + test_grid=1; + else + warndlg_uvmat('multiple dimensions for the z coordinate','ERROR') + return + end + end +% if ~isempty(VarIndex_z) +% DimIndex_z=Field.VarDimIndex{VarIndex_z};%dimension indices of the variable +% if length(DimIndex_z)==1 & nbdim==3 %dimension variable +% VarAttribute{VarIndex_z}.Role=Field.ListDimName{DimIndex_z}; +% ind_z=find(DimIndex==DimIndex_z(1)); +% perm_ind(ind_z)=1; +% test_grid=1; +% end +% end + end +end + +% select the variable index (or indices) for ordinate +ystring=get(handles.ordinate,'String'); +yindex=get(handles.ordinate,'Value'); %selected indices in the ordinate listbox +list_var=ystring(yindex); +VarIndex.y=name2index(list_var,Field.ListVarName); +if isequal(VarIndex.A,VarIndex.y) + set(handles.coord_y_scalar,'Value',1) +elseif isequal(VarIndex.u,VarIndex.y)||isequal(VarIndex.v,VarIndex.y)||isequal(VarIndex.w,VarIndex.y) + set(handles.coord_y_vectors,'Value',1)%ordinate cannot be the same as scalar or vector components +else + for ivar=1:length(VarIndex.y) + VarAttribute{VarIndex.y(ivar)}.Role='coord_y'; + end + VarIndex_tot=[VarIndex_tot VarIndex.y]; +end +if (test_scalar | test_vector) & ~isempty(VarIndex.y) + DimIndex_y=Field.VarDimIndex{VarIndex.y};%dimension indices of the variable + if length(DimIndex_y)==1 + ind_y=find(DimIndex==DimIndex_y(1)); + test_grid=1; + if nbdim==3 + VarAttribute{VarIndex.y}.Role=Field.ListDimName{DimIndex_y}; + perm_ind(ind_y)=2; + elseif nbdim==2 + VarAttribute{VarIndex.y}.Role=Field.ListDimName{DimIndex_y}; + perm_ind(ind_y)=1; + end + elseif test_grid + warndlg_uvmat('the dimension of the y coordinate variable should be 1','ERROR') + end +end + +%select the variable index for the abscissa +xstring=get(handles.abscissa,'String'); +xindex=get(handles.abscissa,'Value'); +list_var=xstring(xindex); +VarIndex.x=name2index(list_var,Field.ListVarName);%var index corresponding to var name list_var +if length(VarIndex.x)==1 + DimIndex_x=Field.VarDimIndex{VarIndex.x}; + DimValue=Field.DimValue(DimIndex_x); + ind=find(DimValue==1); + DimIndex_x(ind)=[];%Mremove singleton + VarAttribute{VarIndex.x}.Role=Field.ListDimName{DimIndex_x}; %dimension variable +% VarAttribute{VarIndex.x}.Role='coord_x';%default (may be modified) + index_detect=find(VarIndex_tot==VarIndex.x); +else + index_detect=[];%coord x variable not already used +end +if isempty(index_detect) + VarIndex_tot=[VarIndex_tot VarIndex.x]; +elseif ~test_check_1Dplot + VarIndex.x=[]; + set(handles.abscissa,'Value',1)%vchosen abscissa already chosen, suppres it as abscissa +end + +if (test_scalar | test_vector) & ~isempty(VarIndex.x) + DimIndex_x=Field.VarDimIndex{VarIndex.x};%dimension indices of the variable + if length(DimIndex_x)==1 + ind_x=find(DimIndex==DimIndex_x(1)); + if nbdim==3 + %VarAttribute{VarIndex.x}.Role=Field.ListDimName{DimIndex_x}; + perm_ind(ind_x)=3; + elseif nbdim==2 + %VarAttribute{VarIndex.x}.Role=Field.ListDimName{DimIndex_x}; + perm_ind(ind_x)=2; + end + if isequal(perm_ind,1:nbdim) + test_grid=0; + end + DimIndex=DimIndex(perm_ind); + elseif test_grid + warndlg_uvmat('the dimension of the x coordinate variable should be 1','ERROR') + end + if isequal(DimIndex_x,DimIndex) + VarAttribute{VarIndex.x}.Role='coord_x';%unstructured coordinates + end +end + +%defined the selected sub-field SubField +SubField.ListGlobalAttribute{1}='InputFile'; +SubField.InputFile=get(handles.inputfile,'String'); +SubField.ListDimName=Field.ListDimName; +SubField.DimValue=Field.DimValue; +SubField.ListVarName=Field.ListVarName(VarIndex_tot); +SubField.VarDimIndex=Field.VarDimIndex(VarIndex_tot); + +testperm=0; +testattr=0; +for ivar=VarIndex.u + VarAttribute{ivar}.Role='vector_x'; + testattr=1; + if test_grid + VarDimIndex{ivar}=DimIndex; %permute dimensions + testperm=1; + end +end +for ivar=VarIndex.v + VarAttribute{ivar}.Role='vector_y'; + testattr=1; + if test_grid + VarDimIndex{ivar}=DimIndex;%permute dimensions + testperm=1; + end +end +for ivar=VarIndex.A + if test_grid + VarDimIndex{ivar}=DimIndex;%permute dimensions + testperm=1; + end + if isempty(iuA) + VarAttribute{ivar}.Role='scalar';%Role =scalar + testattr=1; + else + VarAttribute=[VarAttribute VarAttribute(ivar)]; %duplicate the attribute for a new variable + nbattr=length(VarAttribute); + VarAttribute{nbattr}.Role='scalar'; + testattr=1; + end +end +if testperm + SubField.VarDimIndex=VarDimIndex(VarIndex_tot); +end +if testattr + SubField.VarAttribute=VarAttribute(VarIndex_tot); +end +set(hselect_field,'UserData',Field) + +%--------------------------------------------------------- +% --- Executes on button press in RUN. +function RUN_Callback(hObject, eventdata, handles) +%--------------------------------------------------------- +list=get(handles.ACTION,'String'); +index=get(handles.ACTION,'Value'); +ACTION=list{index}; +hselect_field=get(handles.inputfile,'parent');%handle of the get_field interface +feval(ACTION,hselect_field); +browse_fig(handles.list_fig); %update the list of new existing figures + +%--------------------------------------------------------- +% --- Executes on button press in RUN. +function PLOT(hget_field) +%--------------------------------------------------------- +[SubField,errormsg]=read_get_field(hget_field); +if ~isempty(errormsg) + msgbox_uvmat('ERROR',['error in get_field/PLOT input:' errormsg]) + return +end +handles=guidata(hget_field); +list_fig=get(handles.list_fig,'String'); +val=get(handles.list_fig,'Value'); +if strcmp(list_fig{val},'uvmat') + uvmat(SubField) +else +hfig=str2num(list_fig{val});% chosen figure number from tyhe GUI +if isempty(hfig) + hfig=figure; + list_fig=[list_fig;num2str(hfig)]; + set(handles.list_fig,'String',list_fig); + haxes=axes; +else + figure(hfig); +end +haxes=findobj(hfig,'Type','axes'); + +plot_field(SubField,haxes) +end + + +% +% return +% testuvmat=0; +% if test_scalar|test_vector +% [DimVarIndex,CellVarIndex,NbDim]=find_field_indices(SubField); +% NbDim=max(NbDim); +% if NbDim==3 +% testuvmat=1; %uvmat interface needed for 3D plots +% end +% end +% if iscell(list_fig) +% RUN_fig=list_fig{fig_index}; +% else +% RUN_fig='new fig...';%new plotting axes must be created +% end +% if isequal(RUN_fig,'new fig...') & (test_scalar|test_vector) +% RUN_fig='uvmat';%use uvmat for a new fig +% end +% if testuvmat +% RUN_fig='uvmat'; +% end +% if isequal(RUN_fig,'uvmat') +% +% huvmat=uvmat(SubField); +% menu=update_menu(handles.list_fig,'uvmat');%add the selected fct to the menu +% else +% test_new=1; +% if ~isequal(RUN_fig,'new fig...') +% sep=regexp(RUN_fig,'_')%look for subaxes in a fig +% if isempty(sep) +% axe_index=1; +% else +% axe_index=str2num(RUN_fig(sep+1:end)) +% RUN_fig=RUN_fig([1:sep-1]) +% end +% if ishandle(str2num(RUN_fig)) +% haxes=findobj(str2num(RUN_fig),'Type','axes') +% for iaxe=1:length(haxes) +% Tag=get(haxes(iaxe),'Tag'); +% if isequal(Tag,'Colorbar')|isequal(Tag,'legend') +% iselect(iaxe)=0; +% else +% iselect(iaxe)=1; +% end +% end +% haxes=haxes(find(iselect)); +% if length(haxes)>=axe_index +% test_new=0 +% haxes=haxes(axe_index); +% set(haxes,'NextPlot','add') +% end +% end +% end +% if test_new +% hfig=figure; +% haxes=axes; +% menu=update_menu(handles.list_fig,num2str(hfig));%add the selected fct to the menu +% end +% RUN_field(SubField,haxes) +% end +% end +% +% +% +% +% w components +% end +% +% +% % select the variable index (or indices) for z coordinates +% test_grid=0; +% if test_scalar | test_vector +% nbdim=length(DimIndex); +% if nbdim > 3 +% warndlg_uvmat('array with more than three dimensions, not supported','ERROR') +% return +% else +% perm_ind=[1:nbdim]; +% end +% if nbdim==3 +% zstring=get(handles.coord_z_vectors_scalar,'String'); +% zindex=get(handles.coord_z_vectors_scalar,'Value'); %selected indices in the ordinate listbox +% list_var=zstring(zindex); +% VarIndex_z=name2index(list_var,Field.ListVarName);%index of the selected variable +% if isequal(VarIndex.A,VarIndex_z)|isequal(VarIndex.u,VarIndex_z)|isequal(VarIndex.v,VarIndex_z)|isequal(VarIndex.w,VarIndex_z) +% if zindex ~= 1 +% set(handles.coord_z_vectors_scalar,'Value',1)%ordinate cannot be the same as scalar or vector components +% return +% end +% else +% VarIndex_tot=[VarIndex_tot VarIndex_z]; +% DimIndex_z=Field.VarDimIndex{VarIndex_z}; +% DimValue=Field.DimValue(DimIndex_z); +% ind=find(DimValue==1); +% DimIndex_z(ind)=[];%Mremove singleton +% if isequal(DimIndex_z,DimIndex) +% VarAttribute{VarIndex_z}.Role='coord_z';%unstructured coordinates +% elseif length(DimIndex_z)==1 +% VarAttribute{VarIndex_z}.Role=Field.ListDimName{DimIndex_z}; %dimension variable +% ind_z=find(DimIndex==DimIndex_z(1)); +% perm_ind(ind_z)=1; +% test_grid=1; +% else +% warndlg_uvmat('multiple dimensions for the z coordinate','ERROR') +% return +% end +% end +% % if ~isempty(VarIndex_z) +% % DimIndex_z=Field.VarDimIndex{VarIndex_z};%dimension indices of the variable +% % if length(DimIndex_z)==1 & nbdim==3 %dimension variable +% % VarAttribute{VarIndex_z}.Role=Field.ListDimName{DimIndex_z}; +% % ind_z=find(DimIndex==DimIndex_z(1)); +% % perm_ind(ind_z)=1; +% % test_grid=1; +% % end +% % end +% end +% end +% +% % select the variable index (or indices) for ordinate +% ystring=get(handles.ordinate,'String'); +% yindex=get(handles.ordinate,'Value'); %selected indices in the ordinate listbox +% list_var=ystring(yindex); +% VarIndex.y=name2index(list_var,Field.ListVarName); +% if isequal(VarIndex.A,VarIndex.y)|isequal(VarIndex.u,VarIndex.y)|isequal(VarIndex.v,VarIndex.y)|isequal(VarIndex.w,VarIndex.y) +% set(handles.ordinate,'Value',1)%ordinate cannot be the same as scalar or vector components +% else +% for ivar=1:length(VarIndex.y) +% VarAttribute{VarIndex.y(ivar)}.Role='coord_y'; +% end +% VarIndex_tot=[VarIndex_tot VarIndex.y]; +% end +% if (test_scalar | test_vector) & ~isempty(VarIndex.y) +% DimIndex_y=Field.VarDimIndex{VarIndex.y};%dimension indices of the variable +% if length(DimIndex_y)==1 +% ind_y=find(DimIndex==DimIndex_y(1)); +% test_grid=1; +% if nbdim==3 +% VarAttribute{VarIndex.y}.Role=Field.ListDimName{DimIndex_y}; +% perm_ind(ind_y)=2; +% elseif nbdim==2 +% VarAttribute{VarIndex.y}.Role=Field.ListDimName{DimIndex_y}; +% perm_ind(ind_y)=1; +% end +% elseif test_grid +% warndlg_uvmat('the dimension of the y coordinate variable should be 1','ERROR') +% end +% end +% +% %select the variable index for the abscissa +% xstring=get(handles.abscissa,'String'); +% xindex=get(handles.abscissa,'Value'); +% list_var=xstring(xindex); +% VarIndex.x=name2index(list_var,Field.ListVarName);%var index corresponding to var name list_var +% if length(VarIndex.x)==1 +% DimIndex_x=Field.VarDimIndex{VarIndex.x}; +% DimValue=Field.DimValue(DimIndex_x); +% ind=find(DimValue==1); +% DimIndex_x(ind)=[];%Mremove singleton +% VarAttribute{VarIndex.x}.Role=Field.ListDimName{DimIndex_x}; %dimension variable +% % VarAttribute{VarIndex.x}.Role='coord_x';%default (may be modified) +% index_detect=find(VarIndex_tot==VarIndex.x); +% else +% index_detect=[];%coord x variable not already used +% end +% if isempty(index_detect) +% VarIndex_tot=[VarIndex_tot VarIndex.x]; +% else +% VarIndex.x=[]; +% set(handles.abscissa,'Value',1)%vchosen abscissa already chosen, suppres it as abscissa +% end +% +% if (test_scalar | test_vector) & ~isempty(VarIndex.x) +% DimIndex_x=Field.VarDimIndex{VarIndex.x};%dimension indices of the variable +% if length(DimIndex_x)==1 +% ind_x=find(DimIndex==DimIndex_x(1)); +% if nbdim==3 +% %VarAttribute{VarIndex.x}.Role=Field.ListDimName{DimIndex_x}; +% perm_ind(ind_x)=3; +% elseif nbdim==2 +% %VarAttribute{VarIndex.x}.Role=Field.ListDimName{DimIndex_x}; +% perm_ind(ind_x)=2; +% end +% if isequal(perm_ind,[1:nbdim]) +% test_grid=0; +% end +% DimIndex=DimIndex(perm_ind); +% elseif test_grid +% warndlg_uvmat('the dimension of the x coordinate variable should be 1','ERROR') +% end +% if isequal(DimIndex_x,DimIndex) +% VarAttribute{VarIndex.x}.Role='coord_x';%unstructured coordinates +% end +% end +% +% %defined the selected sub-field SubField +% SubField.ListGlobalAttribute{1}='InputFile'; +% SubField.InputFile=get(handles.inputfile,'String'); +% SubField.ListVarName=Field.ListVarName(VarIndex_tot); +% VarDimIndex=Field.VarDimIndex; +% +% for ivar=VarIndex.u +% VarAttribute{ivar}.Role='vector_x'; +% if test_grid +% VarDimIndex{ivar}=DimIndex; %permute dimensions +% end +% end +% for ivar=VarIndex.v +% VarAttribute{ivar}.Role='vector_y'; +% if test_grid +% VarDimIndex{ivar}=DimIndex;%permute dimensions +% end +% end +% for ivar=VarIndex.A +% if test_grid +% VarDimIndex{ivar}=DimIndex;%permute dimensions +% end +% if isempty(iuA) +% VarAttribute{ivar}.Role='scalar';%Role =scalar +% else +% VarAttribute=[VarAttribute VarAttribute{ivar}]; %duplicate the attribute for a new variable +% nbattr=length(VarAttribute); +% VarAttribute{nbattr}.Role='scalar'; +% end +% end +% SubField.VarDimIndex=VarDimIndex(VarIndex_tot); +% SubField.VarAttribute=VarAttribute(VarIndex_tot); +% % Field.SubListVarName=SubField.ListVarName; +% % Field.SubVarDimIndex=SubField.VarDimIndex; +% % Field.SubVarAttribute=SubField.VarAttribute; +% set(hselect_field,'UserData',Field); +% % copy variables on SubField +% for ivar=1:length(VarIndex_tot) +% VarName=Field.ListVarName{VarIndex_tot(ivar)}; +% eval(['SubField.' VarName '=Field.' VarName ';']) +% end +% if test_grid +% for ivar=1:length(VarIndex.u) +% VarName=Field.ListVarName{VarIndex.u(ivar)}; +% eval(['SubField.' VarName '=permute(SubField.' VarName ',perm_ind);']) +% end +% +% for ivar=1:length(VarIndex.v) +% VarName=Field.ListVarName{VarIndex.v(ivar)}; +% eval(['SubField.' VarName '=permute(SubField.' VarName ',perm_ind);']) +% end +% for ivar=1:length(VarIndex.A) +% VarName=Field.ListVarName{VarIndex.A(ivar)}; +% eval(['SubField.' VarName '=permute(SubField.' VarName ',perm_ind);']) +% end +% end +% if ~isempty(iuA) +% VarName= ['A' Field.ListVarName{iuA}]; %create the new variable to distinguish the scaler form the velocity component +% SubField.ListVarName=[SubField.ListVarName VarName]; +% SubField.VarDimIndex=[SubField.VarDimIndex Field.VarDimIndex(iuA)]; +% eval(['SubField.' VarName '=Field.' Field.ListVarName{iuA} ';']) +% end +% % dimension of SubField +% if test_scalar|test_vector +% % SubField.NbDim=2; +% SubField.InputFile=get(handles.inputfile,'String'); +% SubField.get_field_handle=hselect_field; +% else +% SubField.NbDim=1; +% end +% +% list_fig=get(handles.list_fig,'String'); +% fig_index=get(handles.list_fig,'Value'); +% %ACTION on SubField +% index=get(handles.ACTION,'Value'); + +% +% % if (test_scalar|test_vector) +% % RUN_fig='uvmat'; +% % elseif iscell(list_fig) +% testuvmat=0; +% if test_scalar|test_vector +% [DimVarIndex,CellVarIndex,NbDim]=find_field_indices(SubField); +% NbDim=max(NbDim); +% if NbDim==3 +% testuvmat=1; %uvmat interface needed for 3D plots +% end +% end +% if iscell(list_fig) +% RUN_fig=list_fig{fig_index}; +% else +% RUN_fig='new fig...';%new plotting axes must be created +% end +% if isequal(RUN_fig,'new fig...') & (test_scalar|test_vector) +% RUN_fig='uvmat';%use uvmat for a new fig +% end +% if testuvmat +% RUN_fig='uvmat'; +% end +% if isequal(RUN_fig,'uvmat') +% +% huvmat=uvmat(SubField); +% menu=update_menu(handles.list_fig,'uvmat');%add the selected fct to the menu +% else +% test_new=1; +% if ~isequal(RUN_fig,'new fig...') +% sep=regexp(RUN_fig,'_')%look for subaxes in a fig +% if isempty(sep) +% axe_index=1; +% else +% axe_index=str2num(RUN_fig(sep+1:end)) +% RUN_fig=RUN_fig([1:sep-1]) +% end +% if ishandle(str2num(RUN_fig)) +% haxes=findobj(str2num(RUN_fig),'Type','axes') +% for iaxe=1:length(haxes) +% Tag=get(haxes(iaxe),'Tag'); +% if isequal(Tag,'Colorbar')|isequal(Tag,'legend') +% iselect(iaxe)=0; +% else +% iselect(iaxe)=1; +% end +% end +% haxes=haxes(find(iselect)); +% if length(haxes)>=axe_index +% test_new=0 +% haxes=haxes(axe_index); +% set(haxes,'NextPlot','add') +% end +% end +% end +% if test_new +% hfig=figure; +% haxes=axes; +% menu=update_menu(handles.list_fig,num2str(hfig));%add the selected fct to the menu +% end +% RUN_field(SubField,haxes) +% end +% end +% %Field.VarIndex=VarIndex; %save for use in uvmat +% % set(hselect_field,'UserData',Field) + + +%------------------------------------------------ +% --- Executes on button press in Plot_histo. +%RUN global histograms +%------------------------------------------------- +function RUN_histo_Callback(hObject, eventdata, handles) +% hObject handle to RUN (see GCBO) +% eventdata reserved - to be defined in a future version of MATLAB +% handles structure with handles and user data (see GUIDATA) + +%time plots +leg={}; +n=0; +if (get(handles.cm_switch,'Value')==1) + Uval_p=Uval_cm; + Vval_p=Vval_cm; + Uhist_p=Uhist_cm; + Vhist_p=Vhist_cm; + xlab='velocity (cm/s)'; +else + Uval_p=Uval; + Vval_p=Vval; + Uhist_p=Uhist; + Vhist_p=Vhist; + xlab='velocity (pixels)'; +end +if (get(handles.vector_y,'Value') == 1) + hhh=figure(2); + hold on + title([filebase ', ' strindex ', ' fieldtitle]) + plot(Uval_p,Uhist_p,'b-') + n=n+1; + leg{n}='Uhist'; + xlabel(xlab) +end +if (get(handles.Vhist_input,'Value') == 1) + hhh=figure(2); + hold on + title([filebase ', ' strindex ', ' fieldtitle]) + plot(Vval_p,Vhist_p,'r-') + n=n+1; + leg{n}='Vhist'; + xlabel(xlab); +end +if (get(handles.Chist_input,'Value') == 1) + hhhh=figure(3); + hold on + title([filebase ', ' strindex ', ' fieldtitle]) + plot(Cval,Chist,'k-') + leg{1}='Chist'; +end +% hold off +grid on +legend(leg); + +% %------------------------------------------------------------- +% % --- Executes on button press in Save_input. +% function Save_input_Callback(hObject, eventdata, handles) +% list_str=get(handles.abscissa,'String'); +% val=get(handles.abscissa,'Value'); +% var=list_str{val}; +% hselect_field=get(handles.Save_input,'parent') +% set(hselect_field,'UserData',var); +% set(hselect_field,'Tag','idle') + +% +% %------------------------------------------------------------- +% % --- Executes on button press in save_histo. +% function save_histo_Callback(hObject, eventdata, handles) +% global filebase +% +% pathstr = fileparts(filebase) +% if (get(handles.Chist_input,'Value') == 1) +% def = {[pathstr pathstr(1) 'PIV_corr_histo.fig']}; +% else + +% def = {[pathstr pathstr(1) 'vel_histo.fig']}; +% end +% prompt={'save figure(2) as'} +% dlg_title = 'save figure'; +% num_lines= 1; +% answer = inputdlg(prompt,dlg_title,num_lines,def) +% saveas(2,answer{1}) + +% +% % --- Executes on selection change in spectrum. +% function Field=FFT(Field) +% 'TESTFFT' +% Field +% nbfield=length(Field.ListVarName); +% if nbfield==0 +% warndlg_uvmat('no field selected for FFT','ERROR') +% elseif nbfield>2 +% warndlg_uvmat('select only one field for FFT','ERROR') +% end +% if nbfield==2 +% % list_fields=get(handles.spectrum,'String');% list menu fields +% % index_fields=get(handles.spectrum,'Value');% selected string index +% % fields= list_fields{index_fields(1)}; % selected action +% % func=eval(fields); +% dtmin=min(diff(time));%time step +% time1=time(1);timend=time(end); +% timeq=[time1:dtmin:timend];%equal time spacing +% funcinterp=interp1(time,func,timeq); %interpolated func +% else +% varname=Field.ListVarName{1}; +% eval(['funcinterp=Field.' varname ';']) +% end +% np=length(funcinterp); +% funcinterp=funcinterp-sum(funcinterp)/np; %substract mean +% fourier=fft(funcinterp);%take fft (complex) +% spec=abs(fourier).*abs(fourier);% take sqare of the modulus +% spec=spec([1:floor(np/2)]);%keep only the first half (the other is symmetric) +% eval(['Field.' varname '=spec;']) +% Field +% % dfreq=1/(time(end)-time(1));%frequency interval +% % freq=[0:dfreq:(floor(np/2)-1)*dfreq]; +% % figure(1) +% % hold on +% % RUN(freq,spec) +% % xlabel('frequency (Hz)') +% % ylabel('spectral intensity') +% % title(['spectrum of' fields]); +% % grid on + + + + + +%%------------------------------------------------------- +% --- Executes on button press in peaklocking. +%------------------------------------------------- +function peaklocking(handles) +%evaluation of peacklocking errors +%use splinhist: give spline coeff cc for a smooth histo (call spline4) +%use histsmooth(x,cc): calculate the smooth histo for any value x +%use histder(x,cc): calculate the derivative of the smooth histo +global hfig1 hfig2 hfig3 +global nbb Uval Vval Uhist Vhist % nbb resolution of the histogram nbb=10: 10 values in unity interval +global xval xerror yval yerror + +set(handles.vector_y,'Value',1)% trigger the option Uhist on the interface +set(handles.Vhist_input,'Value',1) +set(handles.cm_switch,'Value',0) % put the switch to 'pixel' + +%adjust the extremal values of the histogram in U with respect to integer +%values +minimU=round(min(Uval)-0.5)+0.5; %first value of the histogram with integer bins +maximU=round(max(Uval)-0.5)+0.5; +minim_fin=(minimU-0.5+1/(2*nbb)); % first bin valueat the beginning of an integer interval +maxim_fin=(maximU+0.5-1/(2*nbb)); % last integer value +nb_bin_min= round(-(minim_fin - min(Uval))*nbb); % nbre of bins added below +nb_bin_max=round((maxim_fin -max(Uval))*nbb); %nbre of bins added above +Uval=[minim_fin:(1/nbb):maxim_fin]; +histu_min=zeros(nb_bin_min,1); +histu_max=zeros(nb_bin_max,1); +Uhist=[histu_min; Uhist ;histu_max]; % column vector + +%adjust the extremal values of the histogram in V +minimV=round(min(Vval-0.5)+0.5); +maximV=round(max(Vval-0.5)+0.5); +minim_fin=minimV-0.5+1/(2*nbb); % first bin valueat the beginning of an integer interval +maxim_fin=maximV+0.5-1/(2*nbb); % last integer value +nb_bin_min=round((min(Vval) - minim_fin)*nbb); % nbre of bins added below +nb_bin_max=round((maxim_fin -max(Vval))*nbb); +Vval=[minim_fin:(1/nbb):maxim_fin]; +histu_min=zeros(nb_bin_min,1); +histu_max=zeros(nb_bin_max,1); +Vhist=[histu_min; Vhist ;histu_max]; % column vector + +% RUN_histo_Callback(hObject, eventdata, handles) +% %adjust the histogram to integer values: + +%histoU and V +[Uhistinter,xval,xerror]=peaklock(nbb,minimU,maximU,Uhist); +[Vhistinter,yval,yerror]=peaklock(nbb,minimV,maximV,Vhist); + +% selection of value ranges such that histo>=10 (enough statistics) +Uval_ind=find(Uhist>=10); +ind_min=min(Uval_ind); +ind_max=max(Uval_ind); +U_min=Uval(ind_min);% minimum allowed value +U_max=Uval(ind_max);%maximum allowed value + +% selection of value ranges such that histo>=10 (enough statistics) +Vval_ind=find(Vhist>=10); +ind_min=min(Vval_ind); +ind_max=max(Vval_ind); +V_min=Vval(ind_min);% minimum allowed value +V_max=Vval(ind_max);%maximum allowed value + +figure(4)% plot U histogram with smoothed one +plot(Uval,Uhist,'b') +grid on +hold on +plot(Uval,Uhistinter,'r'); +hold off + +figure(5)% plot V histogram with smoothed one +plot(Vval,Vhist,'b') +grid on +hold on +plot(Vval,Vhistinter,'r'); +hold off + +figure(6)% plot pixel error in two subplots +hfig4=subplot(2,1,1); +hfig5=subplot(2,1,2); +axes(hfig4) +plot(xval,xerror) +axis([U_min U_max -0.4 0.4]) +xlabel('velocity u (pix)') +ylabel('peaklocking error (pix)') +grid on +axes(hfig5) +plot(yval,yerror) +axis([V_min V_max -0.4 0.4]); +xlabel('velocity v (pix)') +ylabel('peaklocking error (pix)') +grid on + + +% ------------------------------------------------------------------ +function variables_Callback(hObject, eventdata, handles) +Tabchar={''};%default +Tabcell=[]; +hselect_field=get(handles.variables,'parent'); +Field=get(hselect_field,'UserData'); +index=get(handles.variables,'Value');%index in the list 'variables' +if isequal(index,1) + set(handles.attributes_txt,'String','global attributes') +% list global attribute names and values if index=1 (blank variable display) is selected + if isfield(Field,'ListGlobalAttribute') && ~isempty(Field.ListGlobalAttribute) + for iline=1:length(Field.ListGlobalAttribute) + Tabcell{iline,1}=Field.ListGlobalAttribute{iline}; + if isfield(Field, Field.ListGlobalAttribute{iline}) + eval(['val=Field.' Field.ListGlobalAttribute{iline} ';']) + if ischar(val); + Tabcell{iline,2}=val; + else + Tabcell{iline,2}=num2str(val); + end + end + end + Tabchar=cell2tab(Tabcell,'='); + end +else +%list attribute names and values associated to the variable # injdex-1 + list_var=get(handles.variables,'String'); + var_select=list_var{index}; + set(handles.attributes_txt,'String', ['attributes of ' var_select]) + if isfield(Field,'VarAttribute')& length(Field.VarAttribute)>=index-1 +% nbline=0; + VarAttr=Field.VarAttribute{index-1}; + if isstruct(VarAttr) + attr_list=fieldnames(VarAttr); + for iline=1:length(attr_list) + Tabcell{iline,1}=attr_list{iline}; + eval(['val=VarAttr.' attr_list{iline} ';']) + if ischar(val); + Tabcell{iline,2}=val; + else + Tabcell{iline,2}=num2str(val); + end + end + end + end + +end +if ~isempty(Tabcell) + Tabchar=cell2tab(Tabcell,'='); + Tabchar=[{''};Tabchar]; +end +set(handles.attributes,'String',Tabchar); + +% list_var=get(handles.dimensions,'String'); +% val=get(handles.dimensions,'Value'); + +% update dimensions; +if isfield(Field,'VarDimIndex') + Tabdim={};%default + if isequal(index,1) + dim_indices=1:length(Field.ListDimName); + set(handles.dimensions_txt,'String', 'dimensions') + else + dim_indices=Field.VarDimIndex{index-1}; + set(handles.dimensions_txt,'String', ['dimensions of ' var_select]) + end + for iline=1:length(dim_indices) + Tabdim{iline,1}=Field.ListDimName{dim_indices(iline)}; + Tabdim{iline,2}=num2str(Field.DimValue(dim_indices(iline))); + end + Tabchar=cell2tab(Tabdim,'='); + Tabchar=[{''} ;Tabchar]; + set(handles.dimensions,'String',Tabchar) +end + +% --- Executes on button press in check_1Dplot. +function check_1Dplot_Callback(hObject, eventdata, handles) +val=get(handles.check_1Dplot,'Value'); +if isequal(val,0) + set(handles.Panel1Dplot,'Visible','off') +% set(handles.scalar,'Visible','off') +% set(handles.ordinate,'Max',2.0)%allow multiple ordinate input option +% if isequal(get(handles.check_vector,'Value'),0); +% set(handles.coord_z_vectors_scalar,'Visible','off') +% end +else + set(handles.Panel1Dplot,'Visible','on') +% set(handles.scalar,'Visible','on') +% val=get(handles.ordinate,'Value'); +% val=val(1); +% set(handles.ordinate,'Value',val);%suppress multiple ordinates +% set(handles.ordinate,'Max',1.0);%suppress multiple ordinate input option +% set(handles.coord_z_vectors_scalar,'Visible','on') +end + +% --- Executes on button press in check_scalar. +function check_scalar_Callback(hObject, eventdata, handles) +val=get(handles.check_scalar,'Value'); +if isequal(val,0) + set(handles.PanelScalar,'Visible','off') +% set(handles.scalar,'Visible','off') +% set(handles.ordinate,'Max',2.0)%allow multiple ordinate input option +% if isequal(get(handles.check_vector,'Value'),0); +% set(handles.coord_z_vectors_scalar,'Visible','off') +% end +else + set(handles.PanelScalar,'Visible','on') +% set(handles.scalar,'Visible','on') +% val=get(handles.ordinate,'Value'); +% val=val(1); +% set(handles.ordinate,'Value',val);%suppress multiple ordinates +% set(handles.ordinate,'Max',1.0);%suppress multiple ordinate input option +% set(handles.coord_z_vectors_scalar,'Visible','on') +end + +%--------------------------- +% --- Executes on button press in check_vector. +function check_vector_Callback(hObject, eventdata, handles) +val=get(handles.check_vector,'Value'); +if isequal(val,0) + set(handles.PanelVectors,'Visible','off') +else + set(handles.PanelVectors,'Visible','on') +end + + + +%----------------------------- +function mouse_up_gui(ggg,eventdata,handles) +if isequal(get(ggg,'SelectionType'),'alt') + message=''; + global CurData + inputfield=get(handles.inputfile,'String'); + if exist(inputfield,'file') + CurData=nc2struct(inputfield); + else + CurData=get(ggg,'UserData');% get_field opened from a input field, not a file + end + %%%% TODO: put the matalb command window in front + evalin('base','global CurData')%make CurData global in the workspace + evalin('base','CurData') %display CurData in the workspace +end + +%--------------------------------------------- +% --- Executes on selection change in ACTION. +function ACTION_Callback(hObject, eventdata, handles) +list_ACTION=get(handles.ACTION,'String');% list menu fields +index_ACTION=get(handles.ACTION,'Value');% selected string index +ACTION= list_ACTION{index_ACTION}; % selected string +path_get_field=which('get_field');%path to series.m +list_path=get(handles.ACTION,'UserData'); +nb_builtin=0; +list_path +if iscell(list_path) +for ilist=1:length(list_path) + if isequal(list_path{ilist},path_get_field) + nb_builtin=nb_builtin+1; + else + break + end +end +end +if nb_builtin==0% the path to get_field has been changed, reinitialize + get_field_OpeningFcn(hObject, eventdata, handles) + return +end + +% add a new function to the menu +if isequal(ACTION,'more...') + pathfct=fileparts(path_get_field); + browse_name=fullfile(path_get_field,'FIELD_FCT'); + if length(list_path)>nb_builtin + browse_name=list_path{end};% initialize browser with the path of the last introduced function + end +% fct_name=''; +% dir_perso=prefdir; +% profil_perso=fullfile(dir_perso,'uvmat_perso.mat'); +% display(profil_perso) +% if exist(profil_perso,'file') +% h=load (profil_perso); +% if isfield(h,'get_field_fct') +% fct_name=h.get_field_fct; +% end +% else +% path_to_uvmat=which ('uvmat');% check the path of uvmat +% pathfct=fileparts(path_to_uvmat); +% fct_name=fullfile(pathfct,'USR_FCT');%go to UVMAT/USR_FCT by default +% end + [FileName, PathName] = uigetfile( ... + {'*.m', ' (*.m)'; + '*.m', '.m files '; ... + '*.*', 'All Files (*.*)'}, ... + 'Pick a file',browse_name); + if length(FileName)<2 + return + end + ext_fct=FileName(end-1:end); + if ~isequal(ext_fct,'.m') + msgbox_uvmat('ERROR','a Matlab function .m must be introduced'); + return + end + ACTION=FileName(1:end-2);% ACTION choice updated by the selected item + + % insert the choice in the action menu + menu_str=update_menu(handles.ACTION,ACTION);%new action menu in which the new item has been appended if needed + index_ACTION=get(handles.ACTION,'Value');% currently selected index in the list + list_path{index_ACTION}=PathName; + if length(menu_str)>nb_builtin+5; + nbremove=length(menu_str)-nb_builtin-5; + menu_str(nb_builtin+1:end-5)=[]; + list_path(nb_builtin+1:end-4)=[]; + index_ACTION=index_ACTION-nbremove; + set(handles.ACTION,'Value',index_ACTION) + set(handles.ACTION,'String',menu_str) + end + list_path{index_ACTION}=PathName; + set(handles.ACTION,'UserData',list_path); + set(handles.path_action,'enable','inactive')% indicate that the current path is accessible (not 'off') + + %record the current menu in personal file profil_perso + dir_perso=prefdir; + profil_perso=fullfile(dir_perso,'uvmat_perso.mat'); + for ilist=nb_builtin+1:length(menu_str)-1 + get_field_fct{ilist-nb_builtin}=fullfile(list_path{ilist},[menu_str{ilist} '.m']); + end + if exist(profil_perso,'file') + save(profil_perso,'get_field_fct','-append') + else + txt=ver; + Release=txt(1).Release; + relnumb=str2num(Release(3:4)); + if relnumb >= 14 + save(profil_perso,'get_field_fct','-V6') + else + save(profil_perso, 'get_field_fct') + end + end +end + + %check the current path to the selected function +PathName=list_path{index_ACTION};%current recorded path +if ~isequal(path_get_field,PathName) + CurrentPath=fileparts(which(ACTION)); + if ~isequal(PathName,CurrentPath) + addpath(PathName) + errormsg=check_functions; + msgbox_uvmat('CONFIRMATION',[['path ' PathName ' added to the current Matlab pathes'];errormsg]) + end +end +set(handles.path_action,'String',PathName); %show the path to the senlected function + + +% fct_name=fullfile(PathName, FileName); +% if ~exist(fct_name,'file') +% msgbox_uvmat('ERROR',['procesing fct ' fct_name ' not found']) +% else +% ACTION=FileName(1:end-2);% +% menu=update_menu(handles.ACTION,ACTION);%add the selected fct to the menu +% index_ACTION=get(handles.ACTION,'Value');% selected string index +% list_path{index_ACTION}=PathName; +% set(handles.ACTION,'UserData',list_path) +% if exist(profil_perso,'file') +% save (profil_perso,'coord_fct','-append'); %store the root name for future opening of uvmat +% end +% end +% +% +% fileinput=FileName;%complete file name +% eval(['spath=which(''' FileName ''');'])% current path to the function FileName +% if ~isequal(spath,PathName) +% addpath(PathName) +% end +% FileName([end-1:end])=[]; +% +% % insert the choice in the action menu +% nbACTION=length(list_ACTION); +% index=0; +% for ilist=1:nbACTION +% if isequal(FileName,list_ACTION{ilist})%look for the selected scalar in the fields_input menu +% index=ilist;% +% end +% end +% if index==0 +% list_ACTION{nbACTION}=FileName; %put the chosen fct at the penultimate place in the fields_input menu +% list_path{nbACTION}=PathName; +% index=nbACTION; +% list_ACTION{nbACTION+1}='more...'; +% set(handles.ACTION,'String',list_ACTION) +% end +% set(handles.ACTION,'Value',index);% store the selected scalar type +% set(handles.ACTION,'UserData',list_path); +% usr_defined_fct=fct_name; +% nbmenu=length(list_ACTION); +% nbadd=nbmenu-5; +% ilist=0; +% for imenu=nbmenu-min(4,nbadd):nbmenu-1 +% ilist=ilist+1; +% fct_get_field{ilist,1}=list_ACTION{imenu}; +% fct_path_get_field{ilist}=list_path{imenu}; +% end +% if exist(profil_perso,'file') +% save(profil_perso,'usr_defined_fct','fct_get_field','fct_path_get_field','-append') +% else +% save(profil_perso,'usr_defined_fct','fct_get_field','fct_path_get_field','-V6') +% end +% end + +% %check the current path to the selected function +% list_path +% PathName=list_path{index_ACTION} +% CurrentPath=fileparts(which(ACTION)) +% if ~isequal(PathName,CurrentPath) +% addpath(PathName) +% errormsg=check_functions; +% msgbox_uvmat('WARNING',[['path ' PathName ' added to the current Matlab pathes'];errormsg]) +% end +% set(handles.path_action,'String',fullfile(PathName,' ')); %show the path to the senlected function + +%default setting for the visibility of the GUI elements* +if ~isequal(ACTION,'PLOT') + varargout=feval(ACTION);% input list asked by the selected function + test_1Dplot=[]; + test_scalar=[]; + test_vector=[]; + for ilist=1:length(varargout)-1 + switch varargout{ilist} + %RootFile always visible + case 'check_1Dplot' + test_1Dplot=isequal(lower(varargout{ilist+1}),'y'); + case 'check_scalar' + test_scalar=isequal(lower(varargout{ilist+1}),'y'); + case 'check_vector' + test_vector=isequal(lower(varargout{ilist+1}),'y'); + end + end + if test_1Dplot==0 + set(handles.check_1Dplot,'Value',0); + end + if test_1Dplot==1 + set(handles.check_1Dplot,'Value',1); + end + if test_scalar==0 + set(handles.check_scalar,'Value',0); + end + if test_scalar==1 + set(handles.check_scalar,'Value',1); + end + if test_vector==0 + set(handles.check_vector,'Value',0); + end + if test_vector==1 + set(handles.check_vector,'Value',1); + end + check_1Dplot_Callback(hObject, eventdata, handles) + check_scalar_Callback(hObject, eventdata, handles) + check_vector_Callback(hObject, eventdata, handles) +end +% +% % --- Executes on selection change in menu_coord. +% function menu_coord_Callback(hObject, eventdata, handles) +% hget_field=get(handles.menu_coord,'parent'); +% menu=get(handles.menu_coord,'String'); +% ind_coord=get(handles.menu_coord,'Value'); +% coord_option=menu{ind_coord}; +% if isequal(coord_option,'more...'); +% fct_name=''; +% if exist('./TMP/current_usr_fct.mat','file')% if a file is found +% h=load('./TMP/current_usr_fct.mat'); +% if isfield(h,'fct_name'); +% fct_name=h.fct_name; +% end +% end +% prompt = {'Enter the name of the transform function'}; +% dlg_title = 'user defined transform'; +% num_lines= 1; +% [FileName, PathName, filterindex] = uigetfile( ... +% {'*.m', ' (*.m)'; +% '*.m', '.m files '; ... +% '*.*', 'All Files (*.*)'}, ... +% 'Pick a file', fct_name); +% fct_name=fullfile(PathName,FileName); +% addpath(PathName);%add the path to the selected fct +% [errormsg,date_str]=check_functions;%check whether new functions can oversed the uvmat package A UTILISER +% if ~exist(fct_name,'file') +% warndlg_uvmat(['image procesing fct ' fct_name ' not found'],'WARNING') +% else +% transform=FileName(1:end-2);% +% menu=update_menu(handles.menu_coord,transform);%add the selected fct to the menu +% % set(handles.mouse_coord,'String',menu([1:end-1])')%update the mouse coord menu +% save ('./TMP/current_usr_fct.mat','fct_name'); +% end +% end + +% --- Executes on selection change in menu_coord. +function HELP_Callback(hObject, eventdata, handles) +path_to_uvmat=which ('uvmat');% check the path of uvmat +pathelp=fileparts(path_to_uvmat); +helpfile=fullfile(pathelp,'UVMAT_DOC','uvmat_doc.html'); +if isempty(dir(helpfile)), errordlg('Please put the help file uvmat_doc.html in the directory UVMAT/UVMAT_DOC') +else +web([helpfile '#get_field']) +end + +%----------------------------------------------------- +% --- browse existing figures +%----------------------------------------------------- +function browse_fig(menu_handle) +hh=findobj(allchild(0),'Type','figure'); +ilist=0; +list={}; +for ifig=1:length(hh) %look for all existing figures + name=get(hh(ifig),'Name'); + if ~isequal(name,'uvmat')%case of uvmat GUI +% ilist=ilist+1; +% list{ilist,1}='uvmat'; +% else %other figures + hchild=get(hh(ifig),'children');% look for axes contained in each figure + nbaxe=0; + for ichild=1:length(hchild) + Type=get(hchild(ichild),'Type'); + Tag=get(hchild(ichild),'Tag'); + if isequal(Type,'axes') + if ~isequal(Tag,'Colorbar')& ~isequal(Tag,'legend')% don't select colorbars for plotting + nbaxe=nbaxe+1;%count the existing axis + end + end + end + if nbaxe==1 + ilist=ilist+1;%add a line in the list of axis + list{ilist,1}=num2str(hh(ifig)); + elseif nbaxe>1 + for iaxe=1:nbaxe + ilist=ilist+1;%add a line in the list of axis + list{ilist,1}=[num2str(hh(ifig)) '_' num2str(iaxe)]; + end + end + end +end +list=['new fig...';'uvmat';list]; +set(menu_handle,'Value',1) +set(menu_handle,'String',list) + + +%----------------------------------------------------- +function list_fig_Callback(hObject, eventdata, handles) +%----------------------------------------------------- +list_fig=get(handles.list_fig,'String'); +fig_val=get(handles.list_fig,'Value'); +plot_fig=list_fig{fig_val}; +if isequal(plot_fig,'uvmat') + huvmat=findobj(allchild(0),'name','uvmat'); + if ~isempty(huvmat) + uistack(huvmat,'top') + end +elseif ~isequal(plot_fig,'new fig...') & ~isequal(plot_fig,'uvmat') + sep=regexp(plot_fig,'_'); + if ~isempty(sep) + plot_fig=plot_fig([1:sep-1]); + end + if ishandle(str2num(plot_fig)) + figure(str2num(plot_fig))% display existing figure + else + browse_fig(handles.list_fig); %reset the current list of figures + end +end + + +%------------------------------------------------- +% give index numbers of the strings str in the list ListvarName +function VarIndex_y=name2index(cell_str,ListVarName) +VarIndex_y=[]; +if ischar(cell_str) + for ivar=1:length(ListVarName) + varlist=ListVarName{ivar}; + if isequal(varlist,cell_str) + VarIndex_y= ivar; + break + end + end +elseif iscell(cell_str) + for isel=1:length(cell_str) + varsel=cell_str{isel}; + for ivar=1:length(ListVarName) + varlist=ListVarName{ivar}; + if isequal(varlist,varsel) + VarIndex_y=[VarIndex_y ivar]; + end + end + end +end + +% -------------------------------------------------------------------- +function MenuOpen_Callback(hObject, eventdata, handles) +% hObject handle to MenuOpen (see GCBO) +% eventdata reserved - to be defined in a future version of MATLAB +% handles structure with handles and user data (see GUIDATA) + + +% -------------------------------------------------------------------- +function MenuExport_Callback(hObject, eventdata, handles) +% hObject handle to MenuExport (see GCBO) +% eventdata reserved - to be defined in a future version of MATLAB +% handles structure with handles and user data (see GUIDATA) + + +% -------------------------------------------------------------------- +function MenuBrowse_Callback(hObject, eventdata, handles) + +oldfile=get(handles.inputfile,'String'); +testrootfile=0; +testsubdir=0; +if isempty(oldfile)|isequal(oldfile,'') %loads the previously stored file name and set it as default in the file_input box + oldfile=''; + dir_perso=prefdir; + profil_perso=fullfile(dir_perso,'uvmat_perso.mat'); + if exist(profil_perso,'file') + h=load (profil_perso); + if isfield(h,'RootPath') + RootPath=h.RootPath; + end + if isfield(h,'SubDir') + SubDir=h.SubDir; + if ~isempty(SubDir) + testsubdir=1; + end + end + if isfield(h,'RootFile') + RootFile=h.RootFile; + if ~isempty(RootFile) + testrootfile=1; + end + end + end +end +if testrootfile + if ~testsubdir + oldfile=fullfile(RootPath,RootFile); + else + oldfile=fullfile(RootPath,SubDir,RootFile); + end +end +[FileName, PathName] = uigetfile( ... + {'*.nc', ' *.nc';... + '*.cdf', ' *.cdf';... + '*.*', 'All Files (*.*)'}, ... + 'Pick a file',oldfile); + +%global inputfile +fileinput=[PathName FileName];%complete file name +testblank=findstr(fileinput,' ');%look for blanks +if ~isempty(testblank) + warndlg_uvmat(['The input file name ' fileinput ' contains blank character : This is not allowed. Please change name'],'ERROR') + return +end +sizf=size(fileinput); +if (~ischar(fileinput)|~isequal(sizf(1),1)),return;end +set(handles.inputfile,'String',fileinput) +inputfile_Callback(hObject, eventdata, handles) + + +%update list of recent files in the menubar +MenuFile_1=fileinput; +MenuFile_2=get(handles.MenuFile_1,'Label'); +MenuFile_3=get(handles.MenuFile_2,'Label'); +MenuFile_4=get(handles.MenuFile_3,'Label'); +MenuFile_5=get(handles.MenuFile_4,'Label'); +set(handles.MenuFile_1,'Label',MenuFile_1) +set(handles.MenuFile_2,'Label',MenuFile_2) +set(handles.MenuFile_3,'Label',MenuFile_3) +set(handles.MenuFile_4,'Label',MenuFile_4) +set(handles.MenuFile_5,'Label',MenuFile_5) + + +% %store input file in personal file uvmat_perso.mat +% dir_perso=prefdir; +% profil_perso=fullfile(dir_perso,'uvmat_perso.mat'); +% if exist(profil_perso,'file') +% save (profil_perso,'RootPath','SubDir','RootFile','NomType', 'ext','-append'); %store the root name for future opening of uvmat +% else +% save (profil_perso,'RootPath','SubDir','RootFile','NomType', 'ext'); %store the root name for future opening of uvmat +% end + + +% -------------------------------------------------------------------- +function MenuFile_1_Callback(hObject, eventdata, handles) +% hObject handle to MenuFile_1 (see GCBO) +% eventdata reserved - to be defined in a future version of MATLAB +% handles structure with handles and user data (see GUIDATA) + + +% -------------------------------------------------------------------- +function MenuFile_2_Callback(hObject, eventdata, handles) +% hObject handle to MenuFile_2 (see GCBO) +% eventdata reserved - to be defined in a future version of MATLAB +% handles structure with handles and user data (see GUIDATA) + + +% -------------------------------------------------------------------- +function MenuFile_3_Callback(hObject, eventdata, handles) +% hObject handle to MenuFile_3 (see GCBO) +% eventdata reserved - to be defined in a future version of MATLAB +% handles structure with handles and user data (see GUIDATA) + + +% -------------------------------------------------------------------- +function MenuFile_4_Callback(hObject, eventdata, handles) +% hObject handle to MenuFile_4 (see GCBO) +% eventdata reserved - to be defined in a future version of MATLAB +% handles structure with handles and user data (see GUIDATA) + + +% -------------------------------------------------------------------- +function MenuFile_5_Callback(hObject, eventdata, handles) +% hObject handle to MenuFile_5 (see GCBO) +% eventdata reserved - to be defined in a future version of MATLAB +% handles structure with handles and user data (see GUIDATA) + + +% -------------------------------------------------------------------- +function ExportField_Callback(hObject, eventdata, handles) +% hObject handle to ExportField (see GCBO) +% eventdata reserved - to be defined in a future version of MATLAB +% handles structure with handles and user data (see GUIDATA) + + Index: /trunk/src/get_plot_handles.m =================================================================== --- /trunk/src/get_plot_handles.m (revision 2) +++ /trunk/src/get_plot_handles.m (revision 2) @@ -0,0 +1,73 @@ +%'get_plot_handles': list the handles of elements setting the plotting parameters in the uvmat interface +%-------------------------------------------------------- +%function [PlotHandles]=get_plot_handles(handles) +% +% OUTPUT: +% PlotHandles: structure containing the used to set plotting parameters +% INPUT: +% handles: structure of the handles of the graphic elements in the uvmat interface +% -- TODO: needs to be replaced by a cell listing the element tags -- + +function PlotHandles=get_plot_handles(handles) +PlotHandles.auto_xy=handles.auto_xy; +%For scalar field representation +PlotHandles.MaxA=handles.MaxA; +PlotHandles.MinA=handles.MinA; +PlotHandles.AutoScal=handles.AutoScal; +PlotHandles.BW=handles.BW; +PlotHandles.Contours=handles.Contours; +PlotHandles.IncrA=handles.IncrA; +PlotHandles.SCALAR_title=handles.SCALAR_title; +PlotHandles.min_title=handles.min_title; +PlotHandles.max_title=handles.max_title; +PlotHandles.frame_scal=handles.frame_scal; +PlotHandles.npx=handles.npx; +PlotHandles.npy=handles.npy; +PlotHandles.npx_title=handles.npx_title; +PlotHandles.npy_title=handles.npy_title; + +%For vector field representation +PlotHandles.frame_vect=handles.frame_vect; +PlotHandles.VECT_title=handles.VECT_title; +PlotHandles.VecScale=handles.VecScale; +PlotHandles.AutoVec=handles.AutoVec; +PlotHandles.HideFalse=handles.HideFalse; +PlotHandles.HideWarning=handles.HideWarning; +PlotHandles.record=handles.record; +PlotHandles.col_vec=handles.col_vec; +PlotHandles.Color_title=handles.Color_title; +PlotHandles.color_code=handles.color_code; +PlotHandles.colcode1=handles.colcode1; +PlotHandles.colcode2=handles.colcode2; +PlotHandles.vec_col_bar=handles.vec_col_bar; +PlotHandles.slider1=handles.slider1; +PlotHandles.slider2=handles.slider2; +PlotHandles.max_vec=handles.max_vec; +PlotHandles.min_vec=handles.min_vec; +PlotHandles.scale_title=handles.scale_title; +PlotHandles.AutoVecColor=handles.AutoVecColor; +PlotHandles.decimate4=handles.decimate4; +PlotHandles.min_C_title=handles.min_C_title; +PlotHandles.max_C_title=handles.max_C_title; +PlotHandles.MenuVectors=handles.MenuVectors; +PlotHandles.MenuEditVectors=handles.MenuEditVectors; +PlotHandles.edit_vect=handles.edit_vect; +%menu for the choice of the current plotting axes +%PlotHandles.MenuAxes=handles.MenuAxes; + +%handles for move_mouse +PlotHandles.mouse_coord=handles.mouse_coord; +% PlotHandles.POINTS=handles.POINTS; +% PlotHandles.LINE=handles.LINE; +% PlotHandles.PLANE=handles.PLANE; +% PlotHandles.PATCH=handles.PATCH; +PlotHandles.cal=handles.cal; +%PlotHandles.makemask=handles.makemask; +PlotHandles.edit=handles.edit; +PlotHandles.text_display_1=handles.text_display_1; +PlotHandles.text_display_2=handles.text_display_2; +PlotHandles.text_display_3=handles.text_display_3; +PlotHandles.text_display_4=handles.text_display_4; + +%handles for mouse_up +PlotHandles.zoom=handles.zoom; Index: /trunk/src/griddata_uvmat.m =================================================================== --- /trunk/src/griddata_uvmat.m (revision 2) +++ /trunk/src/griddata_uvmat.m (revision 2) @@ -0,0 +1,12 @@ +%'griddata_uvmat': function griddata_uvmat(vec2_X,vec2_Y,vec2_U,vec_X,vec_Y,'linear') +%adapt the input of the matlab function griddata to the appropriate version of Matlab +function ZI = griddata_uvmat(X,Y,Z,XI,YI) +txt=ver; +Release=txt(1).Release; +relnumb=str2num(Release(3:4)); +if relnumb >= 14 + ZI=griddata(X,Y,Z,XI,YI,'linear',{'QJ'}); +else + ZI=griddata(X,Y,Z,XI,YI,'linear'); +end + Index: /trunk/src/hist_update.m =================================================================== --- /trunk/src/hist_update.m (revision 2) +++ /trunk/src/hist_update.m (revision 2) @@ -0,0 +1,54 @@ +%'hist_update': update of a current global histogram by inclusion of a new field +%------------------------------------------------------------------------ +%[val,HIST]=hist_update(val,HIST,C,dC) +% +% OUTPUT: +% val: vector of field values at which the histogram is determined (middle of bins) +% HIST(:,icolor): nbre of occurence of the field value in the bins whose middle is given by val +% can be a column vector, same size as val, or a matrix with three columns, for color images +% +% INPUT: +% val: existing field values from the current histogram, =[] if there is no current histogram +% HIST(:,icolor): current histogram, =[] if there is none +% can be a column vector (icolor=1), same size as val, or a matrix with three columns, for color images +% C(:,icolor): vector representing the current field values +% can be a column vector (icolor=1), or a matrix with three columns, for color images +% dC: width of the new bins extending val to account for the new field. + +function [val,HIST]=hist_update(val,HIST,C,dC) + +valplus=[];valminus=[]; +HISTplus=[];HISTminus=[]; +if isempty(HIST) + HIST=0; +end +siz=size(C);nbfields=siz(2); +C=double(C); +valmin=min(val); +valmax=max(val); +Cmin=min(min(C)); Cmax=max(max(C)); +if isempty(val)%no current histogram + val=[Cmin-dC/2:dC:Cmax+dC/2]; +else %extending the current histogram beyond its maximum value + if Cmax>=valmax+dC/2; + valplus=[valmax+dC:dC:Cmax+dC/2];% we extend the values val + HISTplus=zeros(length(valplus),nbfields);% we put histogram to zero at these values + end + %extending the current histogram below its minimum value + if Cmin<=valmin-dC/2; + valminus=[valmin-dC:-dC:Cmin-dC/2];% we extend the values val + valminus=sort(valminus);% we reverse the order + HISTminus=zeros(length(valminus),nbfields);% we put histogram to zero at these values + end + val=[valminus val valplus]; +end +HIST=[HISTminus;HIST;HISTplus]; +if nbfields==1 + histC=(hist(C,val))';% initiate the global histogram +elseif nbfields==3 + HIST1=(hist(C(:,1),val))'; + HIST2=(hist(C(:,2),val))'; + HIST3=(hist(C(:,3),val))'; + histC=[HIST1 HIST2 HIST3]; +end +HIST=HIST+histC; Index: /trunk/src/imadoc2struct.m =================================================================== --- /trunk/src/imadoc2struct.m (revision 2) +++ /trunk/src/imadoc2struct.m (revision 2) @@ -0,0 +1,250 @@ +%'imadoc2struct': reads the xml file for image documentation +% +%function [s,errormsg]=imadoc2struct(ImaDoc) +%-------------------------------------------------------- +% OUTPUT: +% s: structure representing ImaDoc +% s.Heading: information about the data hierarchical structure +% s.Time: matrix of times +% s.TimeUnit +% s.GeometryCalib: substructure containing the parameters for geometric calibration +% errormsg: error message +% +% INPUT: +% ImaDoc: full name of the xml input file with head key ImaDoc +%function [s,error,Heading,nom_type_ima,ext_ima,abs_time,TimeUnit,mode,NbSlice]=imadoc2struct(ImaDoc) +function [s,errormsg]=imadoc2struct(ImaDoc) + +errormsg=[];%default +s.Heading=[];%default +s.Time=[]; %default +s.TimeUnit=[]; %default +s.GeometryCalib=[]; +nom_type_ima=[];%default +ext_ima=[];%default +% abs_time=[];%initiation +% GeometryCalib.CoordUnit='cm';%default +mode=[]; %default +NbSlice=1;%default +npx=[];%default +npy=[];%default +% GeometryCalib.Pxcmx=1; +% GeometryCalib.Pxcmy=1; +% GeometryCalib=[]; +NbDtj=1; +tsai=[];%default +% if ~exist('testime','var') +% testime=1;%default + +if exist(ImaDoc,'file')~=2, errormsg=[ ImaDoc ' does not exist']; return;end;%input file does not exist +try + t=xmltree(ImaDoc); +catch + errormsg={[ImaDoc ' is not a valid xml file']; lasterr}; + display(errormsg); + return +end + +uid_root=find(t,'/ImaDoc'); +if isempty(uid_root), errormsg=[ImaDoc ' is not an image documentation file ImaDoc']; return; end;%not an ImaDoc .xml file + +%Heading +uid_Heading=find(t,'/ImaDoc/Heading'); +if ~isempty(uid_Heading), + uid_Campaign=find(t,'/ImaDoc/Heading/Campaign'); + uid_Exp=find(t,'/ImaDoc/Heading/Experiment'); + uid_Device=find(t,'/ImaDoc/Heading/Device'); + uid_Record=find(t,'/ImaDoc/Heading/Record'); + uid_FirstImage=find(t,'/ImaDoc/Heading/ImageName'); + s.Heading.Campaign=get(t,children(t,uid_Campaign),'value'); + s.Heading.Experiment=get(t,children(t,uid_Exp),'value'); + s.Heading.Device=get(t,children(t,uid_Device),'value'); + if ~isempty(uid_Record) + s.Heading.Record=get(t,children(t,uid_Record),'value'); + end + s.Heading.ImageName=get(t,children(t,uid_FirstImage),'value'); + FirstImage=s.Heading.ImageName; + if ~isempty(FirstImage) + [Pathsub,RootFile,field_count,str2,str_a,str_b,ext,nom_type_ima]=name2display(FirstImage); + end +end + +%Camera +uid_Camera=find(t,'/ImaDoc/Camera'); +if ~isempty(uid_Camera) + uid_ImageSize=find(t,'/ImaDoc/Camera/ImageSize'); + if ~isempty(uid_ImageSize); + ImageSize=get(t,children(t,uid_ImageSize),'value'); + xindex=findstr(ImageSize,'x'); + if length(xindex)>=2 + npx=str2num(ImageSize(1:xindex(1)-1)); + npy=str2num(ImageSize(xindex(1)+1:xindex(2)-1)); + end + end + uid_NbSlice=find(t,'/ImaDoc/Camera/NbSlice'); + if ~isempty(uid_NbSlice) + NbSlice=str2num(get(t,children(t,uid_NbSlice),'value')); + if isempty(NbSlice),NbSlice=1;end; %default + end + uid_TimeUnit=find(t,'/ImaDoc/Camera/TimeUnit'); + if ~isempty(uid_TimeUnit) + s.TimeUnit=get(t,children(t,uid_TimeUnit),'value'); + end + uid_BurstTiming=find(t,'/ImaDoc/Camera/BurstTiming'); + if ~isempty(uid_BurstTiming) + for k=1:length(uid_BurstTiming) + Dtj=[];%default + NbDtj=1;%default + subt=branch(t,uid_BurstTiming(k));%subtree under BurstTiming + % reading Dtk + Frequency=get_value(subt,'/BurstTiming/FrameFrequency',1); + Dtj=get_value(subt,'/BurstTiming/Dtj',[]); + Dtj=Dtj/Frequency;%Dtj converted from frame unit to TimeUnit (e.g. 's') + NbDtj=get_value(subt,'/BurstTiming/NbDtj',1); + Dti=get_value(subt,'/BurstTiming/Dti',[]); + Dti=Dti/Frequency;%Dtj converted from frame unit to TimeUnit (e.g. 's') + NbDti=get_value(subt,'/BurstTiming/NbDti',1); + Time_val=get_value(subt,'/BurstTiming/Time',0);%time in TimeUnit + if ~isempty(Dti) + Dti=reshape(Dti'*ones(1,NbDti),NbDti*numel(Dti),1); %concatene Dti vector NbDti times + Time_val=[Time_val;Time_val(end)+cumsum(Dti)];%append the times defined by the intervals Dti + end + if ~isempty(Dtj) + Dtj=reshape(Dtj'*ones(1,NbDtj),1,NbDtj*numel(Dtj)); %concatene Dti vector NbDti times + Dtj=[0 Dtj]; +% Time_val' +% ones(1,numel(Dtj)) +% ones(numel(Time_val'),1) +% cumsum(Dtj) + Time_val=Time_val*ones(1,numel(Dtj))+ones(numel(Time_val),1)*cumsum(Dtj);% produce a time matrix with Dtj + end + % reading Dtk + Dtk=get_value(subt,'/BurstTiming/Dtk',[]); + NbDtk=get_value(subt,'/BurstTiming/NbDtk',1) + if isempty(Dtk) + s.Time=[s.Time;Time_val]; + else + for kblock=1:NbDtk+1 + Time_val=Time_val+(kblock-1)*Dtk; + s.Time=[s.Time;Time_val]; + end + end + end + end + if size(s.Time,1)==1 + s.Time=(s.Time)'; %change vector into column + end +end + +%read calibration +uid_GeometryCalib=find(t,'/ImaDoc/GeometryCalib'); +if ~isempty(uid_GeometryCalib) + if length(uid_GeometryCalib)>1 + error=['More than one GeometryCalib in ' filecivxml]; + return + end + subt=branch(t,uid_GeometryCalib);%subtree under GeometryCalib + cont=get(subt,1,'contents'); + if ~isempty(cont) + uid_pixcmx=find(subt,'/GeometryCalib/Pxcmx'); + uid_pixcmy=find(subt,'/GeometryCalib/Pxcmy'); + if ~isempty(uid_pixcmx) & ~isempty(uid_pixcmy)%NON UTILISE + pixcmx=str2num(get(subt,children(subt,uid_pixcmx),'value')); + if isempty(pixcmx),pixcmx=1;end; %default + pixcmy=str2num(get(subt,children(subt,uid_pixcmy),'value')); + if isempty(pixcmy),pixcmy=1;end; %default + tsai.Pxcmx=pixcmx; + tsai.Pxcmy=pixcmy; + end + %default values: + tsai.f=1; + tsai.dpx=1; + tsai.dpy=1; + tsai.sx=1; + tsai.Cx=0; + tsai.Cy=0; + tsai.Tz=1; + tsai.Tx=0; + tsai.Ty=0; + tsai.R=[1 0 0; 0 1 0; 0 0 0]; + tsai.kappa1=0; + uid_CoordUnit=find(subt,'/GeometryCalib/CoordUnit'); + if ~isempty(uid_CoordUnit) + tsai.CoordUnit=get(subt,children(subt,uid_CoordUnit),'value'); + end + uid_focal=find(subt,'/GeometryCalib/focal'); + uid_dpx_dpy=find(subt,'/GeometryCalib/dpx_dpy'); + uid_sx=find(subt,'/GeometryCalib/sx'); + uid_Cx_Cy=find(subt,'/GeometryCalib/Cx_Cy'); + uid_kappa1=find(subt,'/GeometryCalib/kappa1'); + uid_Tx_Ty_Tz=find(subt,'/GeometryCalib/Tx_Ty_Tz'); + uid_R=find(subt,'/GeometryCalib/R'); + if ~isempty(uid_focal) & ~isempty(uid_dpx_dpy) & ~isempty(uid_Cx_Cy) + tsai.f=str2num(get(subt,children(subt,uid_focal),'value')); + dpx_dpy=str2num(get(subt,children(subt,uid_dpx_dpy),'value')); + tsai.dpx=dpx_dpy(1); + tsai.dpy=dpx_dpy(2); + if ~isempty(uid_sx) + tsai.sx=str2num(get(subt,children(subt,uid_sx),'value')); + end + Cx_Cy=str2num(get(subt,children(subt,uid_Cx_Cy),'value')); + tsai.Cx=Cx_Cy(1); + tsai.Cy=Cx_Cy(2); + end + if ~isempty(uid_Tx_Ty_Tz) + Tx_Ty_T_char=get(subt,children(subt,uid_Tx_Ty_Tz),'value'); + Tx_Ty_Tz=str2num(Tx_Ty_T_char); + tsai.Tx=Tx_Ty_Tz(1); + tsai.Ty=Tx_Ty_Tz(2); + tsai.Tz=Tx_Ty_Tz(3); + end + if ~isempty(uid_R) + RR=get(subt,children(subt,uid_R),'value'); + if length(RR)==3 + tsai.R=[str2num(RR{1});str2num(RR{2});str2num(RR{3})]; + end + end + if ~isempty(uid_kappa1) + tsai.kappa1=str2num(get(subt,children(subt,uid_kappa1),'value')); + end + %look for laser plane definitions + uid_Angle=find(subt,'/GeometryCalib/PlaneAngle'); + uid_Pos=find(subt,'/GeometryCalib/PlanePos'); + if ~isempty(uid_Angle) + tsai.PlaneAngle=str2num(get(subt,children(subt,uid_Angle),'value')); + end + if ~isempty(uid_Pos) + for j=1:length(uid_Pos) + tsai.SliceCoord(j,:)=str2num(get(subt,children(subt,uid_Pos(j)),'value')); + end + end + s.GeometryCalib=tsai; + end +end + +%-------------------------------------------------- +% read an xml element +function val=get_value(t,label,default) +%-------------------------------------------------- +val=default; +uid=find(t,label);%find the element iud(s) +if ~isempty(uid) + uid_child=children(t,uid); + if ~isempty(uid_child) + data=get(t,uid_child,'type'); + if iscell(data) + for icell=1:numel(data) + val_read=str2num(get(t,uid_child(icell),'value')); + if ~isempty(val_read) + val(icell)=val_read; + end + end + val=val'; + else + val_read=str2num(get(t,uid_child,'value')); + if ~isempty(val_read) + val=val_read; + end + end + end +end Index: /trunk/src/interp2_uvmat.m =================================================================== --- /trunk/src/interp2_uvmat.m (revision 2) +++ /trunk/src/interp2_uvmat.m (revision 2) @@ -0,0 +1,25 @@ +% A matrix (npy,npx) to interpolate +%XIMA: matrix of non-integer x index values (npY,npX) +%YIMA: matrix of non-integer y index values (npY,npX), (with the same size as XIMA) +function A_out=interp2_uvmat(A,XIMA,YIMA) +npx=size(A,2); +npy=size(A,1); +npX=size(XIMA,2); +npY=size(XIMA,1) +XIMA=reshape(XIMA,1,npX*npY)+0.5;%indices corresponding to XIMA, reshaped in a matlab vector +YIMA=reshape(YIMA,1,npX*npY)+0.5;%indices corresponding to XIMA, reshaped in a matlab vector +X_delta=XIMA-floor(XIMA);%distance to the closest integer value +XIMA=floor(XIMA);%integer x index on the image +Y_delta=YIMA-floor(YIMA);%distance to the closest integer value +YIMA=floor(YIMA);%integer x index on the image +flagin=(XIMA>=1 & XIMA<=npx-1 & YIMA >=1 & YIMA<=npy-1);%flagin=1 inside the original image +ind_in=find(flagin);%list of indices of XIndex for valid values of image indices (inside the original image) +ind_out=find(~flagin); +vec_A=double(reshape(A(:,:,1),1,npx*npy));%reshape the original image as a Matlab image vector +ICOMB=((XIMA-1)*npy+(npy+1-YIMA));%determine the indices in the image Matlab vector corresponding to XIMA and YIMA +ICOMB=ICOMB(flagin);%selection of the valid indices +X_delta=X_delta(ind_in); +Y_delta=Y_delta(ind_in); +A_out(ind_in)=(1-Y_delta).*(1-X_delta).*vec_A(ICOMB)+Y_delta.*(1-X_delta).*vec_A(ICOMB-1)+X_delta.*(1-Y_delta).*vec_A(ICOMB+npy)+X_delta.*Y_delta.*vec_A(ICOMB+npy-1); +A_out(ind_out)=zeros(size(ind_out)); +A_out=reshape(A_out,npY,npX);%interpolated image Index: /trunk/src/keyboard_callback.m =================================================================== --- /trunk/src/keyboard_callback.m (revision 2) +++ /trunk/src/keyboard_callback.m (revision 2) @@ -0,0 +1,51 @@ +%'keyboard_callback:' function activated when a key is pressed on the keyboard +%----------------------------------- +function keyboard_callback(hObject,eventdata,handleshaxes) +xx=double(get(hObject,'CurrentCharacter')); %get the keyboard character +cur_axes=get(gcbf,'CurrentAxes'); +if ~isempty(cur_axes) + xlimit=get(cur_axes,'XLim'); + ylimit=get(cur_axes,'Ylim'); + dx=(xlimit(2)-xlimit(1))/10; + dy=(ylimit(2)-ylimit(1))/10; + + if isequal(xx,29)%move arrow right + xlimit=xlimit+dx; + elseif isequal(xx,28)%move arrow left + xlimit=xlimit-dx; + elseif isequal(xx,30)%move arrow up + ylimit=ylimit+dy; + elseif isequal(xx,31)%move arrow down + ylimit=ylimit-dy; + end + set(cur_axes,'XLim',xlimit) + set(cur_axes,'YLim',ylimit) +end +if ismember(xx,[8 127]) %if the delete or suppr key is pressed, delete the current object + currentobject=gco; + huvmat=findobj(allchild(0),'Name','uvmat'); +% UvData=get(huvmat,'UserData');%Data associated to the current uvmat interface + hlist_object=findobj(huvmat,'Tag','list_object'); + ObjIndex=get(hlist_object,'Value'); + if ObjIndex>1 + delete_object(ObjIndex) + end + if ishandle(currentobject) + tag=get(currentobject,'Tag');%tag of the current selected object + if isequal(tag,'proj_object') + delete_object(currentobject) + end + end +elseif isequal(xx,112)% key 'p' + uvmat('runplus_Callback',hObject,eventdata,handleshaxes) +elseif isequal(xx,109)% key 'm' + uvmat('runmin_Callback',hObject,eventdata,handleshaxes) +end + +AxeData=get(cur_axes,'UserData'); +if isfield(AxeData,'ParentRect')% update the position of the parent rectangle represneting the field + hparentrect=AxeData.ParentRect; + rect([1 2])=[xlimit(1) ylimit(1)]; + rect([3 4])=[xlimit(2)-xlimit(1) ylimit(2)-ylimit(1)]; + set(hparentrect,'Position',rect) +end Index: /trunk/src/mouse_down.m =================================================================== --- /trunk/src/mouse_down.m (revision 2) +++ /trunk/src/mouse_down.m (revision 2) @@ -0,0 +1,343 @@ +%'mouse_down': function activated when the mouse button is pressed on a figure (callback for 'WindowButtonDownFcn' +%-------------------------------------------------------------- +% xy=mouse_down(hObject,eventdata) +% activated by the command: +% set(hObject,'WindowButtonDownFcn',{'mouse_down'}), +% where hObject is the handle of the figure +% +%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +% Copyright Joel Sommeria, 2008, LEGI / CNRS-UJF-INPG, sommeria@coriolis-legi.org. +%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +% This file is part of the toolbox UVMAT. +% +% UVMAT is free software; you can redistribute it and/or modify +% it under the terms of the GNU General Public License as published by +% the Free Software Foundation; either version 2 of the License, or +% (at your option) any later version. +% +% UVMAT is distributed in the hope that it will be useful, +% but WITHOUT ANY WARRANTY; without even the implied warranty of +% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +% GNU General Public License (file UVMAT/COPYING.txt) for more details. +%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA + +function xy=mouse_down(hObject,eventdata) +testzoom=0;%default +MouseAction='none'; %default +huvmat=findobj(allchild(0),'Name','uvmat');%find the uvmat interface handle which controls theoption of mouse action +if ~isempty(huvmat) + hhuvmat=guidata(huvmat);%handles of elements in uvmat + UvData=get(huvmat,'UserData'); + testzoom=get(hhuvmat.zoom,'Value');% get the mouse action from the uvmat GUI: options: + if isfield(UvData,'MouseAction') + MouseAction=UvData.MouseAction;% get the mouse action from the uvmat GUI: options: + end +end +test_create=~testzoom && (isequal(MouseAction,'create_object') || isequal(MouseAction,'create_mask')); +%test_cal=get(handles.cal,'Value'); +test_cal=isequal(MouseAction,'calib'); +handles_coord=findobj(huvmat,'Tag','menu_coord'); +menu_coord=get(handles_coord,'String'); +coord_choice=get(handles_coord,'Value'); +coord_type=menu_coord{coord_choice}; +test_edit=isequal(MouseAction,'edit_object'); +test_edit_vect=isequal(MouseAction,'edit_vect'); +xdisplay=[];%default +ydisplay=[];%default +haxes=[]; +AxeData=[];%default + +%edit an existing point or line if found +hcurrentobject=gco;% current object handle (selected by the mouse) +hcurrentfig=gcbo;% current figure handle +tag_obj=get(gco,'Tag'); +xy=[];%default +xy_fig=get(hcurrentfig,'CurrentPoint');% current point of the current figure (gcbo) +hchild=get(hcurrentfig,'Children');%handles of all objects in the current figure +% loop on all the objects in the current figure (selected by the last mouse click) +for ichild=1:length(hchild) + obj_pos=get(hchild(ichild),'Position');%position of the object + if xy_fig(1) >=obj_pos(1) & xy_fig(2) >= obj_pos(2)& xy_fig(1) <=obj_pos(1)+obj_pos(3) & xy_fig(2) <= obj_pos(2)+obj_pos(4); + htype=get(hchild(ichild),'Type');%type of object child of the current figure + %if the mouse is over an axis, look at the data + if isequal(htype,'axes') + haxes=hchild(ichild); + xy=get(haxes,'CurrentPoint');%xy(1,1),xy(1,2): current x,y positions in axes coordinates + AxeData=get(haxes,'UserData');% data attached to the axis + AxeData.CurrentOrigin=[xy(1,1) xy(1,2)];% The current point set by the mouse becomes the current origin + if ~isequal(tag_obj,'proj_object') & ~test_create + x_mouse=xy(1,1);%default + y_mouse=xy(1,2);%default + u_mouse=[]; + v_mouse=[]; + w_mouse=[]; + A_mouse=[]; + c_text=[]; + f_text=[]; + ff_text=[]; + ivec=[]; + if isfield(AxeData,'X') & isfield(AxeData,'Y') & isfield(AxeData,'Mesh')% test on the existence of a vector field in the current axis + flag_vec=(AxeData.X<(xy(1,1)+AxeData.Mesh/4) & AxeData.X>(xy(1,1)-AxeData.Mesh/4)) & ...%flagx=1 for the vectors with x position selected by the mouse + (AxeData.Y<(xy(1,2)+AxeData.Mesh/4) & AxeData.Y>(xy(1,2)-AxeData.Mesh/4));%f + ivec=find(flag_vec);% search the selected vector index ivec + if length(ivec)>0 + ivec=ivec(1);%choice the first selected vector if several are selected + end + end + end + elseif isequal(get(hchild(ichild),'Visible'),'on')& ~isequal(get(hchild(ichild),'Style'),'frame') + %FAIRE UNE OPTION D'AIDE AVEC BOUTON SOURIS DROIT (ALT)?? + end + end +end +test2D=0; +if isfield(AxeData,'NbDim') + if isequal(AxeData.NbDim,2) + test2D=1; + end +end +if ~test2D %desable object creation and vector editing if NbDim different from 2 + test_create=0; + test_edit_vect=0; +end +%delete the current zoom rectangle +if isfield(AxeData,'CurrentRectZoom') & ishandle(AxeData.CurrentRectZoom) + delete(AxeData.CurrentRectZoom) + AxeData.CurrentRectZoom=[]; +end + +if testzoom %&& ~test_create && ~test_edit && ~test_edit_vect && exist('xy','var') + AxeData.Drawing='zoom'; %initiate drawing mode + AxeData.CurrentObject=[];%unselect objects +elseif ~isempty(huvmat) + %selection of an existing projection object + if test_edit && (isequal(tag_obj,'proj_object')||isequal(tag_obj,'DeformPoint')) + if ~(isfield(AxeData,'Drawing') && isequal(AxeData.Drawing,'create')) + userdata=get(hcurrentobject,'UserData'); + if ishandle(userdata)%the selected line depends on a parent line + AxeData.CurrentObject=userdata;% the parent object becomes the current one + else + AxeData.CurrentObject=hcurrentobject;% the selected object becomes the current one + end + ObjectData=get(AxeData.CurrentObject,'UserData'); + if test_edit & isfield(ObjectData,'IndexObj') + hother=findobj('Tag','proj_object','Type','line');%find all the proj objects + set(hother,'Color','b');%reset all the proj objects in 'blue' by default + set(hother,'Selected','off') + hother=findobj('Tag','proj_object','Type','rectangle'); + set(hother,'EdgeColor','b'); + set(hother,'Selected','off'); + hother=findobj('Tag','proj_object','Type','image'); + for iobj=1:length(hother) + Acolor=get(hother(iobj),'CData'); + Acolor(:,:,1)=zeros(size(Acolor,1),size(Acolor,2)); + set(hother(iobj),'CData',Acolor); + end + hother=findobj('Tag','DeformPoint'); + set(hother,'Color','b'); + set(hother,'Selected','off') + if isequal(get(AxeData.CurrentObject,'Type'),'line') + set(AxeData.CurrentObject,'Color','m'); %set the selected object to magenta color + elseif isequal(get(AxeData.CurrentObject,'Type'),'rectangle') + set(AxeData.CurrentObject,'EdgeColor','m'); %set the selected object to magenta color + end + if isfield(ObjectData,'SubObject')& ishandle(ObjectData.SubObject) + for iobj=1:length(ObjectData.SubObject) + hsub=ObjectData.SubObject(iobj); + if isequal(get(hsub,'Type'),'rectangle') + set(hsub,'EdgeColor','m'); %set the selected object to magenta color + elseif isequal(get(hsub,'Type'),'image') + Acolor=get(hsub,'CData'); + Acolor(:,:,1)=Acolor(:,:,3); + set(hsub,'CData',Acolor); + else + set(hsub,'Color','m') + end + end + end + if isequal(tag_obj,'DeformPoint') + set(hcurrentobject,'Color','m'); %set the selected DeformPoint to magenta color + end + IndexObj=ObjectData.IndexObj; + hlist_object=findobj(huvmat,'Tag','list_object'); + set(hlist_object,'Value',IndexObj); + testdeform=0; + set(gcbo,'Pointer','circle'); + AxeData.Drawing='deform'; + if isequal(tag_obj,'DeformPoint') + if isfield(ObjectData,'DeformPoint') + set(hcurrentobject,'Selected','on') + for ipt=1:length(ObjectData.DeformPoint) + if isequal(ObjectData.DeformPoint(ipt),hcurrentobject) + AxeData.CurrentIndex=ipt; + testdeform=1; + end + end + end + end + if testdeform==0 + AxeData.Drawing='translate'; + set(AxeData.CurrentObject,'Selected','on') + set(gcbo,'Pointer','fleur'); + end + end + end + end + % create new projection object + if test_create && ~isempty(xy) && ~(isfield(AxeData,'Drawing')&& isequal(AxeData.Drawing,'create')) + ObjectData=read_set_object(UvData.sethandles); + ObjectData.Coord=[]; %reset previous object coordinates + ObjectData.Coord(1,1)=xy(1,1); + ObjectData.Coord(1,2)=xy(1,2); + ObjectData.Coord(1,3)=0; + if isfield(AxeData,'ObjectCoord') & size(AxeData.ObjectCoord,2)==3 + ObjectData.Coord(1,3)=AxeData.ObjectCoord(1,3); %generaliser au cas avec angle + end + AxeData.CurrentObject=plot_object(ObjectData,[],haxes,'m');%draw the object and its handle becomes AxeData.CurrentObject + if isfield(UvData,'Object') + IndexObj=length(UvData.Object)+1;% add the object as index IndexObj on the list of the interface + else + IndexObj=2; + end + UvData.Object{IndexObj}=ObjectData; + UvData.Object{IndexObj}.HandlesDisplay(1)=AxeData.CurrentObject; + set(huvmat,'UserData',UvData) + list_str=get(hhuvmat.list_object,'String'); + list_str{IndexObj}=[num2str(IndexObj) '-' set_title(ObjectData.Style,ObjectData.ProjMode)]; + if ~isequal(list_str{end},'...') + list_str{end+1}='...'; + end + set(hhuvmat.list_object,'String',list_str) + set(hhuvmat.list_object,'Value',IndexObj) + PlotData=get(AxeData.CurrentObject,'UserData'); + PlotData.IndexObj=IndexObj; + set(AxeData.CurrentObject,'UserData',PlotData); %record the object index in the graph + AxeData.Drawing='create'; + end + + % create calibration points if the GUI geometry_calib is opened + if test_cal & ~isempty(xy) + h_geometry_calib=findobj(allchild(0),'Name','geometry_calib'); %find the geomterty_calib GUI + hh_geometry_calib=guidata(h_geometry_calib); + h_ListCoord=hh_geometry_calib.ListCoord; %findobj(h_geometry_calib,'Tag','ListCoord'); + h_edit_append=hh_geometry_calib.edit_append;%findobj(h_geometry_calib,'Tag','edit_append'); + if isequal(get(h_edit_append,'Value'),1) + if ~isequal(coord_type,'') + set(handles_coord,'Value',1) + coord_type=''; + set(hhuvmat.FixedLimits,'Value',0)% put FixedLimits option to 'off' + set(hhuvmat.FixedLimits,'BackgroundColor',[0.7 0.7 0.7]) + uvmat('run0_Callback',hObject,eventdata,hhuvmat); %file input with xml reading in uvmat + end +% if isequal(coord_type,'px')|isequal(coord_type,'');%px cordinates + strline=[ ' | ' ' | ' ' | ' num2str(xy(1,1),4) ' | ' num2str(xy(1,2),4)]; +% else %phys cordinates +% strline=[ num2str(xy(1,1),4) ' | ' num2str(xy(1,2),4) ' | 0 | ' ' | ' ]; +% end + Coord=get(h_ListCoord,'String'); + val=get(h_ListCoord,'Value'); + if isequal(Coord,{''}) + val=0; + end + if length(Coord)>val + Coord(val+2:length(Coord)+1)=Coord(val+1:length(Coord));% push the list forward beyond the current point + end + Coord{val+1}=strline; + set(h_ListCoord,'String',Coord) + set(h_ListCoord,'Value',val+1) + geometry_calib('ListCoord_Callback',hObject,eventdata,hh_geometry_calib) + data=read_geometry_calib(Coord); + if isequal(coord_type,'px')|isequal(coord_type,'');%px cordinates + XCoord=data.Coord(:,4); + YCoord=data.Coord(:,5); + else %phys cordinates + XCoord=data.Coord(:,1); + YCoord=data.Coord(:,2); + end + hh=findobj('Tag','calib_points') + if isempty(hh) + line(XCoord,YCoord,'Color','m','Tag','calib_points','LineStyle','.','Marker','+'); + else + set(hh,'XData',XCoord) + set(hh,'YData',YCoord) + end + hhh=findobj('Tag','calib_marker'); + if ~isempty(hhh) + set(hhh,'XData',xy(1,1)) + set(hhh,'YData',xy(1,2)) + else + line(xy(1,1),xy(1,2),'Color','m','Tag','calib_marker','LineStyle','.','Marker','o','MarkerSize',20); + end + %uistack(h_geometry_calib,'top') + end + end + + % edit vectors + if test_edit_vect & ~isempty(ivec) + % FF_100=FF-100*double(uint(abs(FF)/100); %value of FF without units and dizaines + if ~isfield(AxeData,'FF') + AxeData.FF=zeros(size(AxeData.X)); + end + if isequal(AxeData.FF(ivec),0) + + AxeData.FF(ivec)=100; %mark vector #ivec as false + + else + AxeData.FF(ivec)=0; + end + set(haxes,'UserData',AxeData) + update_plot + end +end +set(haxes,'UserData',AxeData); + +%------------------------------------------------------ +function update_plot +%-------------------------------------------- +huvmat=gcbf; +UvData=get(gcbf,'UserData'); +%determine the axes of action of the set_edit interface +% list_axes=get(handles.MenuAxes,'String');% list menu fields +% index_axes=get(handles.MenuAxes,'Value');% selected string index +% current_axes= list_axes{index_axes(1)} % selected string +% eval(['haxes=UvData.' current_axes '.Axes']); +% if isempty(haxes)|~ishandle(haxes)| ~isequal(get(haxes,'Type'),'axes') + haxes= findobj(huvmat,'Tag','axes3'); %main plotting axes as default +% set(handles.MenuAxes,'Value',1) +% end +AxeData=get(haxes,'UserData'); +%For vector field representation +%NEW +PlotHandles.VecScale=findobj(huvmat,'Tag','VecScale'); +PlotHandles.AutoVec=findobj(huvmat,'Tag','AutoVec'); +PlotHandles.checkyellow=findobj(huvmat,'Tag','checkyellow'); +PlotHandles.checkblack=findobj(huvmat,'Tag','checkblack'); +PlotHandles.col_vec=findobj(huvmat,'Tag','col_vec'); +PlotHandles.colcode1=findobj(huvmat,'Tag','colcode1'); +PlotHandles.colcode2=findobj(huvmat,'Tag','colcode2'); +PlotHandles.vec_col_bar=findobj(huvmat,'Tag','vec_col_bar'); +PlotHandles.slider1=findobj(huvmat,'Tag','slider1'); +PlotHandles.slider2=findobj(huvmat,'Tag','slider2'); +PlotHandles.max_vec=findobj(huvmat,'Tag','max_vec'); +PlotHandles.min_vec=findobj(huvmat,'Tag','min_vec'); +PlotHandles.AutoVecColor=findobj(huvmat,'Tag','AutoVecColor'); +PlotHandles.decimate4=findobj(huvmat,'Tag','decimate4'); + +%vectors +Vectors.VecScale=str2num(get(PlotHandles.VecScale,'String')); +Vectors.AutoVec=get(PlotHandles.AutoVec,'Value');%automatic vector length +Vectors.checkyellow=get(PlotHandles.checkyellow,'Value'); +Vectors.checkblack=get(PlotHandles.checkblack,'Value'); +Vectors.decimate4=get(PlotHandles.decimate4,'Value');% =1; for reducing the nbre of vectors +menu_col=get(PlotHandles.col_vec,'String'); +menu_val=get(PlotHandles.col_vec,'Value'); +Vectors.CName=menu_col{menu_val}; %'ima_cor','black','white',... +Vectors.colcode1=str2num(get(PlotHandles.colcode1,'String'));% first threshold for rgb, first value for'continuous' +Vectors.colcode2=str2num(get(PlotHandles.colcode2,'String'));% second threshold for rgb, last value (saturation) for 'continuous' +Vectors.option=get(PlotHandles.vec_col_bar,'Value'); % =1 (64 colors), =0 (3 colors) +Vectors.min=get(PlotHandles.slider1,'Min'); +Vectors.max=get(PlotHandles.slider1,'Max'); +Vectors.auto=get(PlotHandles.AutoVecColor,'Value');% =1; thresholds scaling relative to min and max, =0 fixed thresholds +PlotParam.Vectors=Vectors; + +[PlotType,ScalOut]= plot_field(AxeData,haxes,PlotParam,1); Index: /trunk/src/mouse_motion.m =================================================================== --- /trunk/src/mouse_motion.m (revision 2) +++ /trunk/src/mouse_motion.m (revision 2) @@ -0,0 +1,289 @@ +%'mouse_motion': permanently called by mouse motion over a figure (Callback for 'WindowButtonMotionFcn' of the figure) +%----------------------------------------------------------------------- +% +% function mouse_motion(hObject,eventdata,handles) +% activated by the command: +% set(hObject,'WindowButtonMotionFcn',{'mouse_motion',handles}) +% where hObject is the handle of the figure +% +%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +% Copyright Joel Sommeria, 2008, LEGI / CNRS-UJF-INPG, sommeria@coriolis-legi.org. +%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +% This file is part of the toolbox UVMAT. +% +% UVMAT is free software; you can redistribute it and/or modify +% it under the terms of the GNU General Public License as published by +% the Free Software Foundation; either version 2 of the License, or +% (at your option) any later version. +% +% UVMAT is distributed in the hope that it will be useful, +% but WITHOUT ANY WARRANTY; without even the implied warranty of +% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +% GNU General Public License (file UVMAT/COPYING.txt) for more details. +%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA + +function mouse_motion(hObject,eventdata,handles) +if ~exist('handles','var') + return +end +if ~isfield(handles, 'mouse_coord') + return +end +if ~ishandle(handles.mouse_coord) + return +end +proj_coord=get(handles.mouse_coord,'String'); +choice=get(handles.mouse_coord,'Value'); +if ~isempty(proj_coord); proj_coord=proj_coord{choice};else;proj_coord=[];end; +test_create=0;%default +test_edit=0;%default +if isfield(handles,'VOLUME') % mouse_motion not applied to the uvmat figure, no object creation + test_create=get(handles.create,'Value'); +end +test_edit=isfield(handles,'edit') & get(handles.edit,'Value');% edit test for mouse shap: an arrow +test_zoom=isfield(handles,'zoom')& get(handles.zoom,'Value');% edit test for mouse shap: an arrow + +%find the current axe 'haxes' and display the current mouse position or uicontrol tag +text_displ_1=''; +text_displ_2=''; +text_displ_3=''; +text_displ_4=''; + +haxes=[]; +AxeData=[];%default +mouse=[]; + +pointershape='arrow';% default pointer is an arrow + +xy_fig=get(gcbo,'CurrentPoint');% current point of the current figure (gcbo) +hchild=get(gcbo,'Children');%handles of all objects in the current figure +currentfig=gcbo;%store gcbo as variable currentfig +% loop on all the objects in the current figure (selected by the last mouse click) +for ichild=1:length(hchild) + obj_pos=get(hchild(ichild),'Position');%position of the object + if xy_fig(1) >=obj_pos(1) & xy_fig(2) >= obj_pos(2)& xy_fig(1) <=obj_pos(1)+obj_pos(3) & xy_fig(2) <= obj_pos(2)+obj_pos(4); + htype=get(hchild(ichild),'Type');%type of the crrent child + %if the mouse is over an axis, look at the data + if isequal(htype,'axes') + haxes=hchild(ichild); + xy=get(haxes,'CurrentPoint');%xy(1,1),xy(1,2): current x,y positions in axes coordinates + mouse.X=xy(1,1); + mouse.Y=xy(1,2); + u_mouse=[]; + v_mouse=[]; + w_mouse=[]; + A_mouse=[]; + c_text=[]; + f_text=[]; + ff_text=[]; + ivec=[]; + AxeData=get(haxes,'UserData');% data attached to the axis + if ~test_edit && ~test_zoom + pointershape='crosshair';%set pointer with cross shape (default when mouse is over an axis) +% % pointershape='crosshair';%set pointer with cross shape (default over axis) + end + if isfield(AxeData,'X') && isfield(AxeData,'Y') && isfield(AxeData,'Mesh')% test on the existence of a vector field in the current axis + if ~isempty(AxeData.Mesh) + flag_vec=(AxeData.X<(xy(1,1)+AxeData.Mesh/3) & AxeData.X>(xy(1,1)-AxeData.Mesh/3)) & ...%flagx=1 for the vectors with x position selected by the mouse + (AxeData.Y<(xy(1,2)+AxeData.Mesh/3) & AxeData.Y>(xy(1,2)-AxeData.Mesh/3));%f + ivec=find(flag_vec);% search the selected vector index ivec + if length(ivec)>0 + if ~test_create + pointershape='arrow'; %mouse indicates the detection of a vector + end + ivec=ivec(1);%choice the first selected vector if several are selected + mouse.X=AxeData.X(ivec); + mouse.Y=AxeData.Y(ivec); + u_mouse=AxeData.U(ivec);%displacement + v_mouse=AxeData.V(ivec); + w_mouse=0; %default + if isfield(AxeData,'W')&length(AxeData.W)>=ivec + w_text=[', w=' num2str(AxeData.W(ivec),3)]; + else + w_text=''; + end + if ~isfield(AxeData,'CName') + AxeData.CName='C';%REVOIR + end + c_text=[', ' AxeData.CName '=' num2str(AxeData.C(ivec),3)]; + if isfield(AxeData,'F')&length(AxeData.F)>=ivec + f_text=[', f=' num2str(AxeData.F(ivec),3)]; + else + f_text=''; + end + if isfield(AxeData,'FF')&length(AxeData.FF)>=ivec + ff_text=[', ff=' num2str(AxeData.FF(ivec),3)]; + else + ff_text=''; + end + end + end + end + if isfield(AxeData,'Z') + mouse.Z=AxeData.Z; %generaliser au cas avec angle + end + if isfield(AxeData,'ObjectCoord') & size(AxeData.ObjectCoord,2)==3 + mouse.Z=AxeData.ObjectCoord(1,3); %generaliser au cas avec angle + end + testscal= isfield(AxeData,'A')& isfield(AxeData,'AX')& isfield(AxeData,'AY');%test the existence of an image (or scalar represented by an image) + if testscal + testscal=~isempty(AxeData.A)&~isempty(AxeData.AX)& ~isempty(AxeData.AY); + end + if testscal%test the existence of an image (or scalar represented by an image) + nxy=size(AxeData.A); + MaxAY=max(AxeData.AY(1),AxeData.AY(end)); + MinAY=min(AxeData.AY(1),AxeData.AY(end)); + if (xy(1,1)>AxeData.AX(1))&(xy(1,1)MinAY) + indx0=1+round((nxy(2)-1)*(xy(1,1)-AxeData.AX(1))/(AxeData.AX(end)-AxeData.AX(1)));% index x of pixel + indy0=1+round((nxy(1)-1)*(xy(1,2)-AxeData.AY(1))/(AxeData.AY(end)-AxeData.AY(1)));% index y of pixel + if indx0>=1 & indx0<=nxy(2) & indy0>=1 & indy0<=nxy(1) + A_mouse=AxeData.A(indy0,indx0,:); + end + end + end + %coordinate transform if proj_coord differs from menu_coord + if isfield(AxeData,'CoordType') + mouse.CoordType=AxeData.CoordType; + end + if isfield(AxeData,'CoordUnit') + mouse.CoordUnit=AxeData.CoordUnit; + end + if isfield(mouse,'CoordType') &~isequal(mouse.CoordType,proj_coord) + huvmat=findobj(allchild(0),'Tag','uvmat');%find the uvmat interface handle + UvData=get(huvmat,'UserData'); %coord transformed stored in the uvmat interface, updated by file input + if isfield(AxeData,'CoordType') + mouse.CoordType=AxeData.CoordType; + end + if isfield(AxeData,'dt') + mouse.dt=AxeData.dt; + end +% if ~isempty(z_mouse) +% mouse.Z=z_mouse; +% end + if length(ivec)>0 %& isfield(AxeData,'dt') + mouse.U=u_mouse; + mouse.V=v_mouse; + end + mouse=feval(proj_coord,mouse,UvData);%apply transform proj_coord to the position + if length(ivec)>0%& isfield(AxeData,'dt') + u_mouse=mouse.U; + v_mouse=mouse.V; + end + end + if isfield(mouse,'CoordType') + if isequal(mouse.CoordType,'px') + mouse.CoordUnit='px'; + end + else + mouse.CoordUnit='';%default + end + text_displ_1=['x=' num2str(mouse.X,4) ',y=' num2str(mouse.Y,4)]; + if isfield(mouse,'Z')&~isempty(mouse.Z) + text_displ_1=[text_displ_1 ',z=' num2str(mouse.Z,3)]; + end + if isfield(mouse,'CoordUnit') + text_displ_1=[text_displ_1 ' ' mouse.CoordUnit]; + end + if ~isempty(ivec) + text_displ_4=['vec#=' num2str(ivec)]; + end + if ~isempty(u_mouse) + text_displ_3=['u=' num2str(u_mouse,3) ',v=' num2str(v_mouse,3) w_text ]; + if isfield(mouse,'CoordUnit') + if isequal(mouse.CoordUnit,'px') + text_displ_3=[text_displ_3 ' ' mouse.CoordUnit]; + elseif isfield(AxeData,'TimeUnit') + text_displ_3=[text_displ_3 ' ' mouse.CoordUnit '/' AxeData.TimeUnit]; + end + end + text_displ_4=[text_displ_4 c_text f_text ff_text]; + end + + if ~isempty(A_mouse) + text_displ_2=['A=' num2str(double(A_mouse)) ',i=' num2str(indx0) ',j=' num2str(indy0)]; + end + elseif isequal(get(hchild(ichild),'Visible'),'on')& ~isequal(get(hchild(ichild),'Style'),'frame') + text_displ_1=get(hchild(ichild),'Tag'); + end + end +end +set(handles.text_display_1,'String',text_displ_1); +set(handles.text_display_2,'String',text_displ_2); +set(handles.text_display_3,'String',text_displ_3); +set(handles.text_display_4,'String',text_displ_4); + +%%%%%%%%%%%%%%%%% +%create or modify an object +if isfield(AxeData,'CurrentObject') & ishandle(AxeData.CurrentObject) & isfield(AxeData,'Drawing') & ~isequal(AxeData.Drawing,'off') + PlotData=get(AxeData.CurrentObject,'UserData'); + huvmat=findobj(allchild(0),'Name','uvmat');%find the uvmat interface handle + if ~isempty(huvmat) + UvData=get(huvmat,'UserData'); + if ~isfield(PlotData,'IndexObj') + return + end + ObjectData=UvData.Object{PlotData.IndexObj}; + XYData=AxeData.CurrentOrigin; + if isequal(AxeData.Drawing,'create') && isfield(AxeData,'CurrentOrigin') && ~isempty(AxeData.CurrentOrigin) + if isequal(ObjectData.Style,'line')|isequal(ObjectData.Style,'polyline')|isequal(ObjectData.Style,'polygon')|isequal(ObjectData.Style,'points') + xy(1,3)=0; + ObjectData.Coord=[ObjectData.Coord ;xy(1,:)]; + % ObjectData.Coord(end,:)=xy(1,:); + elseif isequal(ObjectData.Style,'rectangle')|isequal(ObjectData.Style,'ellipse')|isequal(ObjectData.Style,'volume') + ObjectData.Coord(1,1)=(xy(1,1)+XYData(1))/2;%origin rectangle, x coordinate + ObjectData.Coord(1,2)=(xy(1,2)+XYData(2))/2; + ObjectData.RangeX=abs(xy(1,1)-XYData(1))/2;%rectangle width + ObjectData.RangeY=abs(xy(1,2)-XYData(2))/2;%rectangle height + elseif isequal(ObjectData.Style,'plane') %case of 'plane' + DX=(xy(1,1)-ObjectData.Coord(1,1)); + DY=(xy(1,2)-ObjectData.Coord(1,2)); + ObjectData.Phi=(angle(DX+i*DY))*180/pi;%rectangle widt + if isfield(ObjectData,'RangeX') + XMax=sqrt(DX*DX+DY*DY); + if XMax>max(ObjectData.RangeX) + ObjectData.RangeX=[min(ObjectData.RangeX) XMax]; + end + end + end + plot_object(ObjectData,[],AxeData.CurrentObject,'m'); + pointershape='crosshair'; + elseif isequal(AxeData.Drawing,'translate') + DX=xy(1,1)-XYData(1);%translation from initial position + DY=xy(1,2)-XYData(2); + ObjectData.Coord(:,1)=ObjectData.Coord(:,1)+DX; + ObjectData.Coord(:,2)=ObjectData.Coord(:,2)+DY; + plot_object(ObjectData,[],AxeData.CurrentObject,'m'); + pointershape='fleur'; + elseif isequal(AxeData.Drawing,'deform') + ind_move=AxeData.CurrentIndex; + ObjectData.Coord(ind_move,1)=xy(1,1); + ObjectData.Coord(ind_move,2)=xy(1,2); + plot_object(ObjectData,[],AxeData.CurrentObject,'m'); + pointershape='circle'; + end + end +end +%%%%%%%%%%%%% +%draw a rectangle if no object creation is selected +if ~isempty(haxes) & isfield(AxeData,'Drawing')& isequal(AxeData.Drawing,'zoom')& isfield(AxeData,'CurrentOrigin')... + & isequal(get(gcf,'SelectionType'),'normal')% + xy_rect=AxeData.CurrentOrigin; + if ~isempty(xy_rect) + rect(1)=min(xy(1,1),xy_rect(1));%origin rectangle, x coordinate + rect(2)=min(xy(1,2),xy_rect(2));%origin rectangle, y coordinate + rect(3)=abs(xy(1,1)-xy_rect(1));%rectangle width + rect(4)=abs(xy(1,2)-xy_rect(2));%rectangle height + if rect(3)>0 & rect(4)>0 + if isfield(AxeData,'CurrentRectZoom')& ishandle(AxeData.CurrentRectZoom) + set(AxeData.CurrentRectZoom,'Position',rect);%update the rectangle position + else + AxeData.CurrentRectZoom=rectangle('Position',rect,'LineStyle',':','Tag','rect_zoom'); + set(haxes,'UserData',AxeData) + end + end + end +end +if test_zoom + pointershape='arrow'; +end +set(currentfig,'Pointer',pointershape); Index: /trunk/src/mouse_up.m =================================================================== --- /trunk/src/mouse_up.m (revision 2) +++ /trunk/src/mouse_up.m (revision 2) @@ -0,0 +1,322 @@ +%'mouse_up': function activated when the mouse button is released +%---------------------------------------------------------------- +% function mouse_up(ggg,eventdata,handles) +% activated by the command: +% set(hObject,'WindowButtonUpFcn',{'mouse_up'}), +% where hObject is the handle of the figure +% +%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +% Copyright Joel Sommeria, 2008, LEGI / CNRS-UJF-INPG, sommeria@coriolis-legi.org. +%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +% This file is part of the toolbox UVMAT. +% +% UVMAT is free software; you can redistribute it and/or modify +% it under the terms of the GNU General Public License as published by +% the Free Software Foundation; either version 2 of the License, or +% (at your option) any later version. +% +% UVMAT is distributed in the hope that it will be useful, +% but WITHOUT ANY WARRANTY; without even the implied warranty of +% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +% GNU General Public License (file UVMAT/COPYING.txt) for more details. +%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA + +function mouse_up(ggg,eventdata,handles) +MouseAction='none'; %default +zoomstate=0;%default +if ~exist('handles','var') + handles=get(gcbo,'UserData'); +end +huvmat=findobj(allchild(0),'Name','uvmat');%find the uvmat interface handle +if ~isempty(huvmat) + hhuvmat=guidata(huvmat); + UvData=get(huvmat,'UserData'); + if isfield(UvData,'MouseAction') + MouseAction=UvData.MouseAction;% set the mouse action (edit, create objects...) + end + zoomstate=get(hhuvmat.zoom,'Value'); +end +if isequal(MouseAction,'calib') && ~zoomstate + return +end +currentfig=gcbo; +AxeData=get(gca,'UserData'); +currentaxes=gca; %store the current axes handle +test_drawing=0;%default + +%finalize the fabrication or the translation/deformation of an object and plot the corresponding projected field +if ~isempty(huvmat) & isfield(AxeData,'Drawing') & ~isequal(AxeData.Drawing,'off') & isfield(AxeData,'CurrentObject')... + & ishandle(AxeData.CurrentObject) + xy=get(currentaxes,'CurrentPoint');%xy(1,1),xy(1,2): current x,y positions in axes coordinates + PlotData=get(AxeData.CurrentObject,'UserData');%get data attached to the current projection object + IndexObj=PlotData.IndexObj; + ObjectData=UvData.Object{IndexObj}; + if isequal(AxeData.Drawing,'translate') + XYData=AxeData.CurrentOrigin; + DX=xy(1,1)-XYData(1);%translation from initial position + DY=xy(1,2)-XYData(2); + ObjectData.Coord(:,1)=ObjectData.Coord(:,1)+DX; + ObjectData.Coord(:,2)=ObjectData.Coord(:,2)+DY; + elseif isequal(AxeData.Drawing,'deform') + ind_move=AxeData.CurrentIndex; + ObjectData.Coord(ind_move,1)=xy(1,1); + ObjectData.Coord(ind_move,2)=xy(1,2); + else %creating object + if isequal(ObjectData.Style,'line')||isequal(ObjectData.Style,'polyline')||... + isequal(ObjectData.Style,'polygon')||isequal(ObjectData.Style,'points') + if isfield(AxeData,'ObjectCoord') && size(AxeData.ObjectCoord,2)==3 + xy(1,3)=AxeData.ObjectCoord(1,3); % z coordinate of the mouse: to generalise ... + else + xy(1,3)=0; % z coordinate set to 0 by default + end + if ~isequal(ObjectData.Coord,xy(1,:)) + ObjectData.Coord=[ObjectData.Coord ;xy(1,:)];% append the coordiantes marked by the mouse to the eobject + end + elseif isequal(ObjectData.Style,'rectangle')||isequal(ObjectData.Style,'ellipse')||isequal(ObjectData.Style,'volume') + XYData=AxeData.CurrentOrigin; + ObjectData.Coord(1,1)=(xy(1,1)+XYData(1))/2;%origin rectangle, x coordinate + ObjectData.Coord(1,2)=(xy(1,2)+XYData(2))/2; + ObjectData.RangeX=abs(xy(1,1)-XYData(1))/2;%rectangle width + ObjectData.RangeY=abs(xy(1,2)-XYData(2))/2;%rectangle height + elseif isequal(ObjectData.Style,'plane') %case of 'plane' + DX=(xy(1,1)-ObjectData.Coord(1,1)); + DY=(xy(1,2)-ObjectData.Coord(1,2)); + ObjectData.Phi=(angle(DX+i*DY))*180/pi;%rectangle widt + if isfield(ObjectData,'RangeX') + XMax=sqrt(DX*DX+DY*DY); + if XMax>max(ObjectData.RangeX) + ObjectData.RangeX=[min(ObjectData.RangeX) XMax]; + end + end + end + end + %set(AxeData.CurrentObject,'UserData',ObjectData); %update the object properties + if isequal(ObjectData.Style,'rectangle')||isequal(ObjectData.Style,'ellipse') + NbDefPoint=1; + elseif isequal(ObjectData.Style,'line')|| isequal(ObjectData.Style,'plane'); + NbDefPoint=2; + else + NbDefPoint=3; + end + + %show object coordinates in the GUI set_object + h_set_object=findobj(allchild(0),'Name','set_object'); + h_XObject=findobj(h_set_object,'Tag','XObject'); + h_YObject=findobj(h_set_object,'Tag','YObject'); + h_ZObject=findobj(h_set_object,'Tag','ZObject'); + set(h_XObject,'String',num2str(ObjectData.Coord(:,1),4)); + set(h_YObject,'String',num2str(ObjectData.Coord(:,2),4)); + set(h_ZObject,'String',num2str(ObjectData.Coord(:,3),4)); + if NbDefPoint<=2 || isequal(get(currentfig,'SelectionType'),'alt') ||... + isequal(AxeData.Drawing,'translate') || isequal(AxeData.Drawing,'deform');%stop drawing + AxeData.CurrentOrigin=[]; %suppress the current origin + if isequal(ObjectData.Style,'line') && size(ObjectData.Coord,1)<=1 + AxeData.Drawing='off'; + set(currentaxes,'UserData',AxeData); + return % line needs at leqst two points + end + if ~isempty(ObjectData) + testmask=0; + hmask=findobj(huvmat,'Tag','makemask'); + if ~isempty(hmask) + testmask=get(hmask,'Value'); + end + if testmask + PlotHandles=[];%do not project data on the object during mask creation + else + PlotHandles=get_plot_handles(handles);%get the handles of the graphic objects setting the plotting parameters + end + AxeData.hset_object=set_object(ObjectData,PlotHandles);% call the set_object interface ,* + UvData.Object{IndexObj}=update_obj(UvData,IndexObj,ObjectData,PlotHandles); + %ObjectData=update_obj(UvData,IndexObj,ObjectData,PlotHandles); + if isfield(UvData.Object{IndexObj},'PlotParam') + write_plot_param(PlotHandles,UvData.Object{IndexObj}.PlotParam); %update the display of plotting parameters for the current object + end + set(hhuvmat.create,'Value',0);% set to 'off' the button for object creation + set(hhuvmat.create,'BackgroundColor',[0 1 0]);% paint the creation button in green + set(hhuvmat.edit,'BackgroundColor',[1 1 0]);% paint the edit text in yellow + set(hhuvmat.edit,'Value',1);% + set(hhuvmat.edit,'Enable','on');% + set(hhuvmat.MenuEdit,'Enable','on');% + set(hhuvmat.MenuEdit,'Enable','on');% + set(hhuvmat.MenuObject,'Enable','on');% + UvData.MouseAction='edit_object'; % set the edit button to 'on' + end + else + AxeData.CurrentOrigin=[xy(1,1) xy(1,2)]; %the current point becomes the new current origin + test_drawing=1;%allow continuation of drawing object + UvData.Object{IndexObj}=ObjectData; + end + hother=findobj('Tag','deformpoint');%find all the deformpoints + set(hother,'Color','b');%reset all the deformpoints in 'blue' +else + test_drawing=0; +end + +%creation of a new zoom plot +test_replot=0; +if isequal(get(currentfig,'SelectionType'),'normal');%if left button has been pressed +% FigData=get(currentfig,'UserData'); + hparentfig=currentfig; + %open or update a new zoom figure if a rectangle has been drawn + if ishandle(currentaxes); + if isfield(AxeData,'CurrentRectZoom') & ishandle(AxeData.CurrentRectZoom) + PosRect=get(AxeData.CurrentRectZoom,'Position'); + if isfield(AxeData,'CurrentVec') & ishandle(AxeData.CurrentVec) + delete(AxeData.CurrentVec) + end + %update the axes UvData.Plane2 if it exists, else create it +% if isfield (UvData,'Plane2') & ishandle(UvData.Plane2.Fig)%if the second plan plotting axis already exists +% hfig2=UvData.Plane2.Fig; +% if isequal(gcf,hfig2)%if we are already on the secondary figure +% test_replot=1; +% else +% figure(hfig2)%set hfig2 as the current figure +% clf; %erase axes +% end +% else + hfig2=figure;%create new figure + set(hfig2,'name','zoom') + set(hfig2,'Units','normalized') + set(hfig2,'Position',[0.2 0.33 0.6 0.6]); +% UvData.Plane2.Fig=hfig2; + map=colormap(currentaxes); + colormap(map);%transmit the current colormap to the zoom fig + get(handles.RootFile,'String') +% end + set(hfig2,'Position',[0.2 0.33 0.6 0.6]); + if test_replot==0 + set(hfig2,'Unit','normalized') + set(hfig2,'KeyPressFcn',{@keyboard_callback,handles})%set keyboard action function + set(hfig2,'WindowButtonMotionFcn',{@mouse_motion,handles})%set mouse action function + set(hfig2,'WindowButtonDownFcn',{@mouse_down})%set mouse click action function + set(hfig2,'WindowButtonUpFcn',{@mouse_up,handles}) + set(hfig2,'DeleteFcn',{@close_fig,AxeData.CurrentRectZoom,'zoom'}) + set(hfig2,'UserData',AxeData.CurrentRectZoom)% record the parent object (zoom rectangle) in the new fig + %UvData.Plane2.Axes=copyobj(currentaxes,hfig2); %copy the current graph axes to the zoom figure + AxeData.ZoomAxes=copyobj(currentaxes,hfig2); %copy the current graph axes to the zoom figure + figure(hfig2) + set(AxeData.ZoomAxes,'Position',[0.1300 0.1100 0.7750 0.8150])% standard axes position on a figure + hcol=findobj(hparentfig,'Tag','Colorbar'); %look for colorbar axes + if ~isempty(hcol) + hcol_new=colorbar; + YTick=get(hcol,'YTick'); + YTicklabel=get(hcol,'Yticklabel'); + colbarlim=get(hcol,'YLim'); + newcolbarlim=get(hcol_new,'YLim'); + scale_bar=(newcolbarlim(2)-newcolbarlim(1))/(colbarlim(2)-colbarlim(1)); + YTick_rescaled=newcolbarlim(1)+scale_bar*(YTick-colbarlim(1)); + set(hcol_new,'YTick',YTick_rescaled); + set(hcol_new,'Yticklabel',YTicklabel); + end + end + if ishandle(AxeData.ZoomAxes) + hnew_rect=findobj(AxeData.ZoomAxes,'Tag','rect_zoom'); + if ~isempty(hnew_rect) + delete(hnew_rect); + ChildAxeData=get(AxeData.ZoomAxes,'UserData'); + ChildAxeData.CurrentRectZoom=[]; % no rect zoom in the new window + ChildAxeData.Drawing='off'; + ChildAxeData.ParentRect=AxeData.CurrentRectZoom;%set the rectangle as a 'parent' associated to the new axes + set(AxeData.ZoomAxes,'UserData',ChildAxeData);%update the AxeData of the new axes + % UvData.TopFig=hfig2;%put the new fig to the top of the stack for uvmat + % set(huvmat,'UserData',UvData) + set(AxeData.ZoomAxes,'Xlim',[PosRect(1) PosRect(1)+PosRect(3)]) + set(AxeData.ZoomAxes,'Ylim',[PosRect(2) PosRect(2)+PosRect(4)]) + end + end + end + end +end +%zoom in if no new figure is created +if zoomstate + if isequal(get(currentfig,'SelectionType'),'normal');%if left button has been pressed + %zoom(2)% zoom in by a factor of 2 + alpha=0.5; %zoom factor (zoom in by a factor 2) + xlim=get(currentaxes,'XLim'); + xlim_new(1)=(1+alpha)*xlim(1)/2+(1-alpha)*xlim(2)/2; + xlim_new(2)=(1-alpha)*xlim(1)/2+(1+alpha)*xlim(2)/2; + set(currentaxes,'XLim',xlim_new) + ylim=get(currentaxes,'YLim'); + ylim_new(1)=(1+alpha)*ylim(1)/2+(1-alpha)*ylim(2)/2; + ylim_new(2)=(1-alpha)*ylim(1)/2+(1+alpha)*ylim(2)/2; + set(currentaxes,'YLim',ylim_new) + if isfield(AxeData,'ParentRect')% update the position of the parent rectangle represneting the field + hparentrect=AxeData.ParentRect; + xlim=get(currentaxes,'XLim'); + ylim=get(currentaxes,'YLim'); + rect([1 2])=[xlim(1) ylim(1)]; + rect([3 4])=[xlim(2)-xlim(1) ylim(2)-ylim(1)]; + set(hparentrect,'Position',rect) + end + + elseif isequal(get(currentfig,'SelectionType'),'alt'); %if right button has been pressed + %zoom(0.5)% zoom out by a factor of 2 + alpha=2; %zoom factor (zoom out by a factor 2) + xlim=get(currentaxes,'XLim'); + xlim_new(1)=(1+alpha)*xlim(1)/2+(1-alpha)*xlim(2)/2; + xlim_new(2)=(1-alpha)*xlim(1)/2+(1+alpha)*xlim(2)/2; + ylim=get(currentaxes,'YLim'); + ylim_new(1)=(1+alpha)*ylim(1)/2+(1-alpha)*ylim(2)/2; + ylim_new(2)=(1-alpha)*ylim(1)/2+(1+alpha)*ylim(2)/2; + set(currentaxes,'XLim',xlim_new) + set(currentaxes,'YLim',ylim_new) + %test whther zoom out is operating (to inactivate AxedAta + if ~isfield(AxeData,'CurrentXLim')| ~isequal(xlim,AxeData.CurrentXLim) + AxeData.CurrentXLim=xlim;% + end + if isfield(AxeData,'ParentRect')% update the position of the parent rectangle represneting the field + hparentrect=AxeData.ParentRect; + xlim=get(currentaxes,'XLim'); + ylim=get(currentaxes,'YLim'); + rect([1 2])=[xlim(1) ylim(1)]; + rect([3 4])=[xlim(2)-xlim(1) ylim(2)-ylim(1)]; + set(hparentrect,'Position',rect) + end + end +end + +%display the data of the current object selected with the mouse right click +if isequal(get(currentfig,'SelectionType'),'alt') && ~zoomstate && (~isfield(AxeData,'Drawing')||~isequal(AxeData.Drawing,'create')) + hother=findobj('Tag','proj_object');%find all the proj objects + nbselect=0; + %test the existence of selected objects: + for iproj=1:length(hother); + iselect=isequal(get(hother(iproj),'Selected'),'on');%reset all the proj objects in 'blue' by default + nbselect=nbselect+iselect; + end + hother=findobj('Tag','proj_object','Type','line');%find all the proj objects + set(hother,'Color','b');%reset all the proj objects in 'blue' by default + set(hother,'Selected','off') + hother=findobj('Tag','proj_object','Type','rectangle'); + set(hother,'EdgeColor','b'); + set(hother,'Selected','off') + hother=findobj('Tag','proj_object','Type','patch'); + set(hother,'FaceColor','b'); + if isequal(get(gco,'Type'),'image') + currentobj=get(gco,'parent');%parent axes of the image + else + currentobj=gco;%default + end + if ((nbselect==0) && isequal(get(currentobj,'Type'),'axes')) || isequal(currentobj,huvmat) + global CurData + CurData=get(currentobj,'UserData'); + %plot_text(CurData) + %get_field([],CurData); + evalin('base','global CurData')%make CurData global in the workspace + objtype=get(currentobj,'Type'); + display(['UserData of ' objtype ':']) + evalin('base','CurData') %display CurData in the workspace + commandwindow + end +end +if test_drawing==0 + AxeData.Drawing='off';%stop current drawing action +end +set(currentaxes,'UserData',AxeData); +if ~isempty(huvmat) + set(huvmat,'UserData',UvData); +end + + + Index: /trunk/src/msgbox_uvmat.m =================================================================== --- /trunk/src/msgbox_uvmat.m (revision 2) +++ /trunk/src/msgbox_uvmat.m (revision 2) @@ -0,0 +1,203 @@ +%'msgbox_uvmat': associated with GUI msgbox_uvmat.fig to display message boxes, for error, warning or input calls +% msgbox_uvmat(title,display) +% +% OUTPUT: +% answer (text string)= 'yes', 'No', 'cancel', or the text string introduced as input +% +%INPUT: +% title: string indicating the type of message box: +% title= 'INPUT_TXT','CONFIMATION' ,'ERROR', 'WARNING', 'INPUT_Y-N', default = 'INPUT_TXT' (the title is displayed in the upper bar of the fig). +% if title='INPUT_TXT', input data is asked in an edit box +% if title='CONFIMATION'', 'ERROR', 'WARNING', the figure remains opened until a button 'OK' is pressed +% if title='INPUT_Y-N', an answer Yes/No is requested +% display, displayed text +% default_answer: default answer in the edit box (only used with title='INPUT_TXT') + +function varargout = msgbox_uvmat(varargin) + +% Last Modified by GUIDE v2.5 24-Oct-2009 21:55:17 + +% Begin initialization code - DO NOT EDIT +gui_Singleton = 1; +gui_State = struct('gui_Name', mfilename, ... + 'gui_Singleton', gui_Singleton, ... + 'gui_OpeningFcn', @msgbox_uvmat_OpeningFcn, ... + 'gui_OutputFcn', @msgbox_uvmat_OutputFcn, ... + 'gui_LayoutFcn', [] , ... + 'gui_Callback', []); +if nargin && ischar(varargin{1}) + gui_State.gui_Callback = str2func(varargin{1}); +end + +if nargout + [varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:}); +else + gui_mainfcn(gui_State, varargin{:}); +end +% End initialization code - DO NOT EDIT + +% --- Executes just before msgbox_uvmat is made visible. +function msgbox_uvmat_OpeningFcn(hObject, eventdata, handles,title,display,default_answer) +% This function has no output args, see OutputFcn. + +% Choose default command line output for msgbox_uvmat +handles.output = 'Cancel'; + +% Update handles structure +guidata(hObject, handles); +testNo=0; +testCancel=1; +testinputstring=0; +icontype='quest';%default question icon (text input asked) +if exist('title','var') + set(hObject, 'Name', title); + if isequal (title,'CONFIRMATION') + icontype=''; + testCancel=0; %no cancel button + elseif isequal (title,'ERROR') + icontype='error'; + testCancel=0; %no cancel button + elseif isequal (title,'WARNING') + icontype='warn'; + testCancel=0; %no cancel button + elseif isequal (title,'INPUT_Y-N') + icontype='quest'; + testNo=1; % button No activated + else + testinputstring=1; + end +end +if exist('display','var') + set(handles.text1, 'String', display); +end +if testinputstring + set(handles.edit_box, 'Visible', 'on'); +else + set(handles.text1, 'Position', [0.15 0.3 0.85 0.7]); +end +if exist('default_answer','var') && testinputstring + set(handles.edit_box, 'String', default_answer); +end +% Determine the position of the dialog - centered on the screen +FigPos=get(0,'DefaultFigurePosition'); +OldUnits = get(hObject, 'Units'); +set(hObject, 'Units', 'pixels'); +OldPos = get(hObject,'Position'); +FigWidth = OldPos(3); +FigHeight = OldPos(4); +ScreenUnits=get(0,'Units'); +set(0,'Units','pixels'); +ScreenSize=get(0,'ScreenSize'); +set(0,'Units',ScreenUnits); + +FigPos(1)=1/2*(ScreenSize(3)-FigWidth); +FigPos(2)=2/3*(ScreenSize(4)-FigHeight); +FigPos(3:4)=[FigWidth FigHeight]; +set(hObject, 'Position', FigPos); +set(hObject, 'Units', OldUnits); + +% Show a question icon from dialogicons.mat - variables questIconData and questIconMap +if isequal(icontype,'') + hima=findobj(handles.axes1,'Type','image'); + if ~isempty(hima) + delete(hima) + end +else + load dialogicons.mat + eval(['IconData=' icontype 'IconData;']) + eval(['IconCMap=' icontype 'IconMap;']) + questIconMap(256,:) = get(handles.figure1, 'Color'); + Img=image(IconData, 'Parent', handles.axes1); + set(handles.figure1, 'Colormap', IconCMap); + set(handles.axes1, ... + 'Visible', 'off', ... + 'YDir' , 'reverse' , ... + 'XLim' , get(Img,'XData'), ... + 'YLim' , get(Img,'YData') ... + ); +end +if testCancel + set(handles.Cancel,'Visible','on') +else + set(handles.Cancel,'Visible','off') +end +if testNo + set(handles.No,'Visible','on') +else + set(handles.No,'Visible','off') +end +set(handles.figure1,'WindowStyle','modal')% Make% Make the GUI modal +% UIWAIT makes msgbox_uvmat wait for user response (see UIRESUME) +uiwait(handles.figure1); + + +% --- Outputs from this function are returned to the command line. +function varargout = msgbox_uvmat_OutputFcn(hObject, eventdata, handles) + +% Get default command line output from handles structure +if isequal(handles.output,'Cancel') + varargout{1}='Cancel'; +elseif isequal(handles.output,'No') + varargout{1}='No'; +else + varargout{1}=get(handles.edit_box,'String'); + isequal(varargout{1},'') + if isempty(varargout{1}) || isequal(varargout{1},'') + varargout{1}='Yes'; + end +end +% The figure can be deleted now +delete(handles.figure1); + +% --- Executes on button press in OK. +function OK_Callback(hObject, eventdata, handles) +handles.output = get(hObject,'String'); +guidata(hObject, handles);% Update handles structure +uiresume(handles.figure1); + +% --- Executes on button press in No. +function No_Callback(hObject, eventdata, handles) +handles.output='No'; +guidata(hObject, handles); +uiresume(handles.figure1); + +% --- Executes on button press in Cancel. +function Cancel_Callback(hObject, eventdata, handles) +handles.output = get(hObject,'String'); +%handles.output = 'Cancel' +guidata(hObject, handles); % Update handles structure +% Use UIRESUME instead of delete because the OutputFcn needs +% to get the updated handles structure. +uiresume(handles.figure1); + + +% --- Executes when user attempts to close figure1. +function figure1_CloseRequestFcn(hObject, eventdata, handles) +if isequal(get(handles.figure1, 'waitstatus'), 'waiting') + % The GUI is still in UIWAIT, us UIRESUME + uiresume(handles.figure1); +else + % The GUI is no longer waiting, just close it + delete(handles.figure1); +end + +% --- Executes on key press over figure1 with no controls selected. +function figure1_KeyPressFcn(hObject, eventdata, handles) +% Check for "enter" or "escape" +if isequal(get(hObject,'CurrentKey'),'escape') + % User said no by hitting escape + handles.output = 'No'; + + % Update handles structure + guidata(hObject, handles); + + uiresume(handles.figure1); +end +if isequal(get(hObject,'CurrentKey'),'return') + uiresume(handles.figure1); +end + + + + + Index: /trunk/src/name2display.m =================================================================== --- /trunk/src/name2display.m (revision 2) +++ /trunk/src/name2display.m (revision 2) @@ -0,0 +1,205 @@ +%'name2display': extracts the root name and field numbers from an input filename +%-------------------------------------------------------------------- +%[RootPath,RootFile,field_count,str2,str_a,str_b,ext,nom_type,subdir]=name2display(fileinput) +% +%OUTPUT: +%filebasesub: filename without appendix +%field_count: string for the first number i +%str2: string for the second number i (only for .nc files) +%str_a: string for the first number j +%str_b:string for the second number j (only for .nc files) +%ext: file extension +%nom_type: char chain characterizing the file nomenclature: with values +% nom_type='': constant name [filebase ext] (default output if 'nom_type' is undefined) +% nom_type='*':constant name for a file representing a series (e.g. avi movie) +% nom_type='_i': series of files with a single index i preceded by '_'(e.g. 'aa_45.png'). +% nom_type='#', series of indexed images wich is not series_i [filebase index ext], e.g. 'aa045.jpg' or 'aa45.tif' +% nom_type='_i_j': matrix of files with two indices i and j separated by '_'(e.g. 'aa_45_2.png') +% nom_type='_i1-i2': from pairs from a single index (e.g. 'aa_45-47.nc') +% nom_type='_i_j1-j2': pairs of j indices (e.g. 'aa_45_2-3.nc') +% nom_type='_i1-i2_j': pairs of i indices (e.g. 'aa_45-46_2.nc') +% nom_type='#a','#A", with a numerical index and an index letter(e.g.'aa045b.png') (lower or upper case) +% nom_type='raw_SMD', same as '#' but with no extension ext='', OBSOLETE +% nom_type='#_ab', from pairs of '#' images (e.g. 'aa045bc.nc'), ext='.nc', OBSOLETE (replaced by '_i_j1-j2') +%subdir: name of the subdirectory for netcdf files +% +%INPUT: +%fileinput: complete name of the file, including path + +function [RootPath,RootFile,field_count,str2,str_a,str_b,ext,nom_type,subdir]=name2display(fileinput) +% siz=length(fileinput); +% indcur=siz; +% default values: +% test_=0; +field_count='';%character string +str2=''; +str_a=''; +str_b=''; +% ext=''; +nom_type=''; +subdir=''; + %select file extension +[RootPath,RootFile,ext]=fileparts(fileinput); +indcur=length(RootFile);% nbre of characters in fileraw + + %recognize the name form +filerawascii=double(RootFile);%ascci code +val=(48>filerawascii)|(filerawascii>57); % test for the non-numerical characters +indsel=find(val);% character indices of non numerical characters +filelit=RootFile(indsel);% fileraw name with numbers removed +nbchar=length(indsel); +if nbchar<4% put '*' before the name (remove at the end) + prefilelit(1:4-nbchar)='*';%insert 3_nbchar '*' in the file name + filelit=[prefilelit filelit]; + indsel=[1:4-nbchar indsel+4-nbchar]; + RootFile=[prefilelit RootFile]; + indcur=indcur+4-nbchar; +end +separ3=indsel(end);% index of last non numerical character in fileraw +separ2=indsel(end-1);% index of previous non numerical character +separ1=indsel(end-2); +separ0=indsel(end-3); +num1='';num2='';num3=''; +if separ1>=separ0+1,num0=RootFile(separ0+1:separ1-1);end +if separ2>=separ1+1,num1=RootFile(separ1+1:separ2-1);end +if separ3>=separ2+1,num2=RootFile(separ2+1:separ3-1);end +if indcur>=separ3+1,num3=RootFile(separ3+1:indcur);end +last_str=RootFile(indcur);%last character in fileraw +last=double(last_str);%corresponding ascii code +penult=double(RootFile(indcur-1));%ascii code of the penultimate character +testsub=0; %default +if strcmpi(ext,'.avi') + nom_type='*'; + %case of old image nomenclature +elseif (strcmp(ext,'.png') || strcmp(ext,'')) && penult >= 48 && penult <= 57 && (last < 48 || last > 57) + % if the penultimate character is a number and the last a letter + % search the appendix a,b,c, + str_a=last_str; %put appendix a,b,c.... + indcur=indcur-1; + if strcmp(ext,'.png'), nom_type='#a'; end + if strcmp(ext,''), nom_type='raw_SMD'; end + num=1;count=0; % extract the numerical appendix + while num==1; + filascii=double(RootFile(indcur)); + if (48>filascii)||(filascii>57); % select the non-numerical characters + num=0; + else + indcur=indcur-1; count=count+1; + end + end + if count~=0 + field_count=RootFile(indcur+1:indcur+count);% set the selected field number + end +elseif penult >= 48 && penult <= 57 && (last <= 66 && last >= 65)% PCO camera Toulouse, end with A or B (NEW) + % if the penultimate character is a number and the last a letter + % search the appendix a,b,c, + str_a=last_str; %put appendix a,b,c.... + indcur=indcur-1; + nom_type='#A'; + num=1;count=0; % extract the numerical appendix + while num==1; + filascii=double(RootFile(indcur)); + if (48>filascii)||(filascii>57); % select the non-numerical characters + num=0; + else + indcur=indcur-1; count=count+1; + end + end + if count~=0 + field_count=RootFile(indcur+1:indcur+count);% set the selected field number + end + indcur=indcur-1; +elseif strcmp(filelit(end-2:end),'-_-_')%new nomenclature appendix num1-num2_num_a-num_b + field_count=num0; + str2=num1; + str_a=num2; + str_b=num3; + nom_type='_i1-i2_j1-j2'; + testsub=1; + indcur=separ0-1; +elseif strcmp(filelit(end-2:end),'_-_')%new nomenclature appendix num1-num2_num_a + field_count=num1; + str2=num2; + str_a=num3; + nom_type='_i1-i2_j'; + testsub=1; + indcur=separ1-1; +elseif strcmp(filelit(end-2:end),'__-')%new nomenclature appendix num1_num2-num2 + indcur=separ1-1; + field_count=num1; + str_a=num2; + str_b=num3; + nom_type='_i_j1-j2'; + testsub=1; +elseif strcmp(filelit(end-1:end),'_-') + indcur=separ2-1; + field_count=num2; + str2=num3; + str_a=''; + nom_type='_i1-i2'; + testsub=1; +elseif strcmp(filelit(end-1:end),'__') + indcur=separ2-1; + field_count=num2; + str2=''; + str_a=num3; + nom_type='_i_j'; +elseif strcmp(filelit(end),'_') + indcur=separ3-1; +% field_count=num3; + str2=''; + str_a=''; + %detect zeros before the number +% count=0; % extract the numerical appendix + if strcmp('0',RootFile(separ3+1)); % select the non-numerical characters + nom_type=['_%0' num2str(length(RootFile(separ3+1:end))) 'd']; + else + nom_type='_i'; + end + field_count=RootFile(separ3+1:end);% set the selected field number'%03d' +elseif RootFile(indcur-2)=='_'% search appendix a,b,c,d + last=RootFile(indcur-1:indcur); + if isequal(length(last),2) && double(last(1)) >= 97 && double(last(1)) <= 122 ...% = 1 for letters + && double(last(2)) >= 97 && double(last(2)) <= 122 + str_a=last(1);%put appendix a,b,c, ou d + str_b=last(2);%put appendix a,b,c, ou d +% indcur=indcur-3; + separ0=indsel(end-3); + num0=RootFile(separ0+1:separ1-1); + field_count=num0; + indcur=separ0; + nom_type='#_ab'; + testsub=1; + end +%search for other names with counter +else + if length(ext)>1 + num=1;count=0; % extract the numerical appendix + while num==1; + filascii=double(RootFile(indcur)); + if (48>filascii)||(filascii>57); % select the non-numerical characters + num=0; + else + indcur=indcur-1; count=count+1; + end + end + if count~=0 + field_count=RootFile(indcur+1:indcur+count);% set the selected field number'%03d' + if isequal(field_count(1),'0') + nbfigures=length(field_count); + nom_type=['%0' num2str(nbfigures) 'd']; + else + nom_type='#'; + end + end + end +end + %select the root name in the file_input window +RootFile=RootFile(1:indcur); +if nbchar<4% put '*' before the name (remove at the end) + RootFile(1:4-nbchar)=[]; +end +if testsub + [RootPath,subdir,extdir]=fileparts(RootPath); + subdir=[subdir extdir]; +end Index: /trunk/src/name_generator.m =================================================================== --- /trunk/src/name_generator.m (revision 2) +++ /trunk/src/name_generator.m (revision 2) @@ -0,0 +1,284 @@ +%'name_generator': creates a file name from a root name and indices. +%--------------------------------------------------------------------- +% [filename,idetect,num_i1_out,num_j1_out,num_i2_out,num_j2_out,subdir_out]=... + % name_generator(filebase,num_i1,num_j1,ext,nom_type,comp_input,num_i2,num_j2,subdir); +%--------------------------------------------------------------------- +% This function detects the existence the constructed file name and it can +% find indices according to file existence if they are not specified +%%rmq: this function is related to the reverse functions display2name and name2diplay +%--------------------------------------------------------------------- +% OUTPUT: +%filename: string representing the file name (including path) +%idetect: =1 if the file is detected, 0 otherwise +%num_i1_out,num_j1_out,num_i2_out,num_j2_out,subdir_out: index numbers and subdirectory detected + %for free input (= to the corresponding input indices when comp_input=1) +%--------------------------------------------------------------------- +% INPUT: +% 'filebase': the root name, +% 'num_i1: first labelling index i +% 'num_j1', first labelling index j +% 'ext': file name extension (e.g. '.png' or '.nc') +% 'nom_type': string defining the kind of nomenclature used: + %nom_type='': constant name [filebase ext] (default output if 'nom_type' is undefined) + %nom_type='*': the same file [filebase ext] contains successive fields (ex avi movies) + %nom_type='_i': series of files with a single index i preceded by '_'(e.g. 'aa_45.png'). + %nom_type='#' series of indexed images wich is not series_i [filebase index ext], e.g. 'aa045.jpg' or 'aa45.tif' + %nom_type='_i_j' matrix of files with two indices i and j separated by '_'(e.g. 'aa_45_2.png') + %nom_type='_i1-i2' from pairs from a single index (e.g. 'aa_45-47.nc') + %nom_type='_i_j1-j2'pairs of j indices (e.g. 'aa_45_2-3.nc') + %nom_type='_i1-i2_j' pairs of i indices (e.g. 'aa_45-46_2.nc') + %nom_type='#a','#A' with a numerical index and an index letter(e.g.'aa045b.png'), OBSOLETE (replaced by 'series_i_j') + %nom_type='%03d' or '%04d', series of indexed images with numbers completed with zeros to 3 or 4 digits, e.g.'aa045.tif' + %nom_type='_%03d', '_%04d', or '_%05d', series of indexed images with _ and numbers completed with zeros to 3, 4 or 5 digits, e.g.'aa_045.tif' + %nom_type='raw_SMD', same as '#a' but with no extension ext='', OBSOLETE + %nom_type='#_ab' from pairs of '#a' images (e.g. 'aa045bc.nc'), ext='.nc', OBSOLETE (replaced by 'netc_2D') + %nom_type='%3dab' from pairs of '%3da' images (e.g. 'aa045bc.nc'), ext='.nc', OBSOLETE (replaced by 'netc_2D') +% A REVOIR: 'comp_input'=1 for writting =0 for reading , 'comp_input'(for nom_type involving index pairs (e.g. netc)) + %comp_input=1: the index pair is imposed, + %comp_input=0: the index pair is automatically searched, choosing the most recent file in case of multiple choice +% 'num_i2': second index i (for nom_type involving index pairs (e.g. netc)) +% 'num_j2': second index j (for nom_type involving index pairs (e.g. netc)) +% 'subdir': (used for nom_type=netc...) string representing the name of the subdirectory 'subdir' containing file. + %subdir='': no subdirectory, + %subdir='?', the file is first searched with no subdirectory, then in the most recently modified subdirectory if not detected. + +% A FAIRE: si comp_inpu=0, si _i_j n'existe pas, chercher _i, +function [filename,num_i1_out,num_j1_out,num_i2_out,num_j2_out,subdir_out]=... + name_generator(filebase,num_i1,num_j1,ext,nom_type,comp_input,num_i2,num_j2,subdir); +sizf=size(filebase); +if (~ischar(filebase)||~isequal(sizf(1),1)),filebase='';end +if ~ischar(ext),ext='';end +% filename=[filebase ext];%default +idetect=0; +if ~exist('num_i1','var') || isequal(num_i1,[]) + num_i1=1; %default +end +if ~exist('num_j1','var') || isequal(num_j1,[]) + num_j1=1; %default +end +if ~exist('num_i2','var') || isequal(num_i2,[]) + num_i2=num_i1; %default +end +if ~exist('subdir','var')|| isempty(subdir) + subdir='' ; %default +end +%detection of mask or mean: filebase of the form [root '_' xxx 'm$$$'] with xxx a number and $$$ three characters +% if length(filebase)>4 & filebase(end-3)=='m'; +% basedouble=double(filebase); +% val=(48>basedouble)|(basedouble>57);% select the non-numerical characters +% i=length(filebase)-4; +% while val(i)==0 & i>0 +% i=i-1; +% end +% nbslice=str2num(filebase(i+1:end-4)); +% if ~isequal(nbslice,[]) +% num_i1=mod(num_i1-1,nbslice)+1; %take the rest in the division +% if isequal(nom_type,'png_old')|isequal(nom_type,'#a') +% num_j1=1;% mask name must end by 'a' +% end +% end +% end +test_pairs=isequal(nom_type,'netc_old')| isequal(nom_type,'netc_2D') | isequal(nom_type,'netc_3D')| isequal(nom_type,'_i1-i2_j1-j2')| ... + isequal(nom_type,'netc_series')| isequal(nom_type,'#_ab')| isequal(nom_type,'_i_j1-j2')| isequal(nom_type,'_i1-i2_j')| isequal(nom_type,'_i1-i2'); +test_2D= isequal(nom_type,'netc_old') |isequal(nom_type,'netc_2D')|isequal(nom_type,'#_ab') |isequal(nom_type,'_i_j1-j2'); +test_3D=isequal(nom_type,'netc_3D') |isequal(nom_type,'netc_series')| isequal(nom_type,'_i1-i2_j')| isequal(nom_type,'_i1-i2'); +if isequal(nom_type,'series_i')| isequal(nom_type,'_i'); + filename=[filebase '_' num2str(num_i1) ext]; + % idetect=(exist(filename,'file')==2); +elseif length(nom_type)==5 && isequal(nom_type(1:3),'_%0')&& isequal(nom_type(5),'d'); + filename=[filebase '_' num2str(num_i1,nom_type(2:5)) ext]; + % idetect=(exist(filename,'file')==2); +elseif isequal(nom_type,'series_i_j')| isequal(nom_type,'_i_j') + filename=[filebase '_' num2str(num_i1) '_' num2str(num_j1) ext]; + % idetect=(exist(filename,'file')==2); +elseif isequal(nom_type,'png_old')| isequal(nom_type,'#a')| isequal(nom_type,'#A') + filename=[filebase num2str(num_i1,'%03d') num2stra(num_j1,nom_type) ext]; + % idetect=(exist(filename,'file')==2); +elseif length(nom_type)>=5 & isequal(nom_type(2:3),'%0') & isequal(nom_type(5),'d') %isequal(nom_type,'_%04dA') %camera PCO Toulouse + filename=[filebase nom_type(1) num2str(num_i1,nom_type(2:4)) num2stra(num_j1,nom_type) ext]; + % idetect=(exist(filename,'file')==2); +elseif isequal(nom_type,'raw_SMD') %suffix a, b, c without extension + filename=[filebase num2str(num_i1,'%03d') num2stra(num_j1,nom_type)]; +% idetect=(exist(filename,'file')==2); +elseif isequal(nom_type,'ima_num')| isequal(nom_type,'#') + filename=[filebase num2str(num_i1) ext]; +% idetect=(exist(filename,'file')==2); +elseif length(nom_type)>=4 & isequal(nom_type(1:2),'%0') & isequal(nom_type(end),'d') + filename=[filebase num2str(num_i1,nom_type) ext]; %test number with a 0 before +% idetect=(exist(filename,'file')==2); + +%case of derived file indexing (e.g. netcdf files) +elseif test_pairs + if (~exist('num_j2','var')| isequal(num_j2,[])) & test_2D + num_j2=num_j1+1; %default if num_j2 undefined + end + if (~exist('num_i2','var')| isequal(num_i2,[])) & test_3D + num_i2=num_i1+1; %default if num_i2 undefined + end + filebasesub=filebase; + % get the root name filebasesub for the netcdf files + if ~isequal(subdir,'') && ~isequal(subdir,'?') + [Path,Name]=fileparts(filebase); + filebasesub=fullfile(Path,subdir,Name); + end + %inexistant pair if num_i2=0 or num_j2=0 + if isequal(num_i2,0) + filename=[filebasesub '*-*_' num2str(num_i1) ext]; + return + end + if isequal(num_j2,0) + filename=[filebasesub '_' num2str(num_i1) '_*-*' ext]; + return + end + % case of an imposed image pair (comp_input=1) + if (exist('comp_input','var') & isequal(comp_input,1)) + if isequal(nom_type,'netc_old')|isequal(nom_type,'#_ab') + if isequal(num2str(num_j1),num2str(num_j2))% case of displacements at the same time + filename=[filebasesub num2str(num_i1,'%03d') '_' num2stra(num_j1,nom_type) ext]; + else + filename=[filebasesub num2str(num_i1,'%03d') '_' num2stra(num_j1,nom_type) num2stra(num_j2,nom_type) ext]; + end + elseif isequal(nom_type,'netc_2D')|isequal(nom_type,'_i_j1-j2') + if isequal(num2str(num_j1),num2str(num_j2))% case of displacements at the same time + filename=[filebasesub '_' num2str(num_i1) '_' num2str(num_j1) ext]; + else + filename=[filebasesub '_' num2str(num_i1) '_' num2str(num_j1) '-' num2str(num_j2) ext]; + end + elseif isequal(nom_type,'netc_3D') || isequal(nom_type,'_i1-i2_j') + if isequal(num2str(num_i1),num2str(num_i2))% case of displacements at the same time + filename=[filebasesub '_' num2str(num_i1) '_' num2str(num_j1) ext]; + else + filename=[filebasesub '_' num2str(num_i1) '-' num2str(num_i2) '_' num2str(num_j1) ext]; + end + elseif isequal(nom_type,'netc_series') || isequal(nom_type,'_i1-i2') + if isequal(num2str(num_i1),num2str(num_i2))% case of displacements at the same time + filename=[filebasesub '_' num2str(num_i1) ext]; + else + filename=[filebasesub '_' num2str(num_i1) '-' num2str(num_i2) ext]; + end + elseif isequal(nom_type,'_i1-i2_j1-j2') + if isequal(num2str(num_i1),num2str(num_i2))% case of displacements at the same time + app1= [num2str(num_i1)]; + else + app1= [num2str(num_i1) '-' num2str(num_i2)]; + end + if isequal(num2str(num_j1),num2str(num_j2))% case of displacements at the same time + app2= [num2str(num_j1)]; + else + app2= [num2str(num_j1) '-' num2str(num_j2)]; + end + filename=[filebasesub '_' app1 '_' app2 ext]; + end + idetect=1; + % idetect=(exist(filename,'file')==2); + % case of an image pair to determine (comp_input=0) + else + [filename,num_i1,num_j1,num_i2,num_j2,idetect]=search_pair(filebasesub,num_i1,num_j1,num_i2,nom_type); + end + + %look for sub-directories containing netcdf files + if idetect==0 && isequal(subdir,'?') + [pathfile,name]=fileparts(filebase); + direct=dir(pathfile);%directory containing filebase + datedir=[];%default + idir=0; + indir=find(cell2mat({direct.isdir}));% find indices of subdirectories + direct=direct(indir([3:end]));% keep only the subdirectories,eliminating the two first terms '.' and '..' + lengthdir=length(direct); + if lengthdir==0 + subdir='';% no subdirectory found + else + for idir=1:lengthdir + date_str=direct(idir).date;%string of the date of last modification + datedir(idir)=0;%default + char_code=double(date_str);% code of the date characters + special_char=(char_code>127); %non standard Ascii character (e.g. date in french) + if isempty(find(special_char))% standard Ascii character + datedir(idir)=datenum(date_str); + end +% datedir(idir)=datenum(direct(idir).date); %absolute date of last directory modification + end + [mostrec,indrec]=max(datedir);% most recently modified subdir chosen by default + subdir=direct(indrec).name; %chosen directory + end + filebasesub=fullfile(pathfile,subdir,name); + %if the image pair is imposed + if (exist('comp_input','var') & isequal(comp_input,1)) + if isequal(nom_type,'netc_old')|isequal(nom_type,'#_ab') + filename=[filebasesub num2str(num_i1,'%03d') '_' num2stra(num_j1,nom_type) num2stra(num_j2,nom_type) ext]; + elseif isequal(nom_type,'netc_2D')|isequal(nom_type,'_i1_j1-j2') + filename=[filebasesub '_' num2str(num_i1) '_' num2str(num_j1) '-' num2str(num_i2) ext]; + elseif isequal(nom_type,'netc_3D')|isequal(nom_type,'_i1-i2_j') + filename=[filebasesub '_' num2str(num_i1) '-' num2str(num_i2) '_' num2str(num_j1) ext]; + elseif isequal(nom_type,'netc_series')|isequal(nom_type,'_i1-i2') + filename=[filebasesub '_' num2str(num_i1) '-' num2str(num_i2) ext]; + end + idetect=(exist(filename,'file')==2); + else + [filename,num_i1,num_j1,num_i2,num_j2,idetect]=search_pair(filebasesub,num_i1,num_j1,num_i2,nom_type); + end + end +% elseif isequal(nom_type,'none')|isequal(nom_type,'')|isequal(nom_type,'*') +else + filebasesub=filebase; + if ~isequal(subdir,'') && ~isequal(subdir,'?') + [Path,Name]=fileparts(filebase); + filebasesub=fullfile(Path,subdir,Name); + end + filename=[filebasesub ext]; + idetect=(exist(filename,'file')==2); +end +num_i1_out=num_i1; +num_j1_out=num_j1; +if exist('num_i2','var'), num_i2_out=num_i2; else, num_i2_out=[]; end; +if exist('num_j2','var'), num_j2_out=num_j2; else, num_j2_out=[]; end; +if ~isequal(subdir,'?'), subdir_out=subdir; else, subdir_out='';end; + +%--------------------------------------------------------------- +% search the appropriate image pair (netcdf file) corresponding to a given +% image number +%------------------------------------------------------------------- +function [filename,num_i1,num_j1,num_i2,num_j2,idetect]=search_pair(filebasesub,num_i1,num_j1,num_i2,nom_type) +% for nom_type=netc_2D or netc_old, it searches all the pairs corresponding +% to num_i1, and chooses the most recent file. +%for nom_type=netc_3D or netc_series, it searches all the pairs (num_i1 +%num_i2), with num_i1 as the first index, and chooses the most recent file. + +filename=[];num_j2=[];idetect=0;%default values +if isequal(nom_type,'netc_old')|isequal(nom_type,'#_ab') + dirpair=dir([filebasesub num2str(num_i1,'%03d') '_*.nc']); +elseif isequal(nom_type,'netc_2D')|isequal(nom_type,'_i_j1-j2') + dirpair=dir([filebasesub '_' num2str(num_i1) '_*-*.nc']); +elseif isequal(nom_type,'netc_3D')|isequal(nom_type,'_i1-i2_j') + dirpair=dir([filebasesub '_' num2str(num_i1) '-*_' num2str(num_j1) '.nc']); +elseif isequal(nom_type,'netc_series')|isequal(nom_type,'_i1-i2') + dirpair=dir([filebasesub '_' num2str(num_i1) '-*.nc']); + if isempty(dirpair) + dirpair=dir([filebasesub '_*-' num2str(num_i2) '.nc']); + end +end +nbpair=length(dirpair); +if nbpair >= 1 %choose the most recent file if several are found + idetect=1; %detected pair + for ipair=1:nbpair + date_str=dirpair(ipair).date;%string of the date of last modification + datepair(ipair)=0;%default + char_code=double(date_str);% code of the date characters + special_char=(char_code>127); %non standard Ascii character (e.g. date in french) + if isempty(find(special_char))% standard Ascii character + datepair(ipair)=datenum(date_str); + end + % datepair(ipair)=datenum(dirpair(ipair).date); + end + [choice,indpair]=max(datepair); +% [filebase,field_count,str2,str_a,str_b,ext,nom_type]=name2display(dirpair(indpair).name); + [pathname,file,field_count,str2,str_a,str_b,ext,nom_type]=name2display(dirpair(indpair).name); + num_i1=str2num(field_count); + num_i2=str2num(str2); + num_j1=stra2num(str_a); + num_j2=stra2num(str_b); + pathname=fileparts(filebasesub);% CORRIGE LE 6 JUIN (ETAIT DESACTIVE) + filename=fullfile(pathname,dirpair(indpair).name); +end + + Index: /trunk/src/nc2struct.m =================================================================== --- /trunk/src/nc2struct.m (revision 2) +++ /trunk/src/nc2struct.m (revision 2) @@ -0,0 +1,269 @@ +%'nc2struct': transform a netcdf file in a corresponding matlab structure +% it reads all the global attributes and all variables, or a selected list. +% The corresponding dimensions and variable attributes are then extracted +%%%%%% TODO: add the possibility to read only attributes, see nc2struct_toolbox %%% +%---------------------------------------------------------------------- +% function [Data,var_detect,ichoice]=nc2struct(nc,ListVarName) +% +% OUTPUT: +% Data: structure containing all the information of the netcdf file (or netcdf object) +% with fields: +% .ListGlobalAttribute: cell listing the names of the global attributes +% .Att_1,Att_2... : values of the global attributes +% .ListDimName: cell listing the names of the array dimensions +% .DimValue: array dimension values (Matlab vector with the same length as .ListDimName +% .ListVarName: cell listing the names of the variables +% .VarDimIndex: cell containing the set of dimension indices (in list .ListDimName) for each variable of .ListVarName +% .VarDimName: cell containing a cell of dimension names (in list .ListDimName) for each variable of .ListVarName +% .VarAttribute: cell of structures s containing names and values of variable attributes (s.name=value) for each variable of .ListVarName +% .Var1, .Var2....: variables (Matlab arrays) with names listed in .ListVarName +% var_detect: vector with same length as ListVarName, with 1 for each detected variable and 0 else. +% ichoice: = line +% +%INPUT: +% nc: name of a netcdf file (char string) or netcdf object +% ListVarName: optional list of variable names to select (cell array of char strings {'VarName1', 'VarName2',...} ) +% if ListVarName=[] or {}, no variables is read (only global attributes and lists of dimensions, variables and attriburtes) +% if ListVarName is absent, or = '*', ALL the variables are read. +% if ListVarName is a cell array with n lines, the set of variables +% will be sought by order of priority in the list, while output names will be set by the first line +% +%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +% Copyright Joel Sommeria, 2008, LEGI / CNRS-UJF-INPG, sommeria@coriolis-legi.org. +%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +% This file is part of the toolbox UVMAT. +% +% UVMAT is free software; you can redistribute it and/or modify +% it under the terms of the GNU General Public License as published by +% the Free Software Foundation; either version 2 of the License, or +% (at your option) any later version. +% +% UVMAT is distributed in the hope that it will be useful, +% but WITHOUT ANY WARRANTY; without even the implied warranty of +% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +% GNU General Public License (file UVMAT/COPYING.txt) for more details. +%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA + +function [Data,var_detect,ichoice]=nc2struct(nc,varargin) +List=varargin; +if nargin==0 + List{1}='*'; +end +% if ~exist('ListVarName','var') +% ListVarName='*'; +% end +hhh=which('netcdf.open');% look for built-in matlab netcdf library + +if ~isequal(hhh,'') + %default output + Data=[]; + var_detect=[]; + ichoice=[];%default + %open the netcdf file for reading + if ischar(nc) + if exist(nc,'file') + nc=netcdf.open(nc,'NC_NOWRITE'); + testfile=1; + else + Data.Txt=['ERROR:file ' nc ' does not exist']; + return + end + else + testfile=0; + end + % short reading of global attributes + if isequal(List{1},'ListGlobalAttribute') + for ilist=2:numel(List) + valuestr = netcdf.getAtt(nc,netcdf.getConstant('NC_GLOBAL'),List{ilist}); + eval(['Data.' List{ilist} '=valuestr;']) + end + netcdf.close(nc) + return + end + + % reading of variables, including attributes + ListVarName=List{1}; + [ndims,nvars,ngatts]=netcdf.inq(nc);%nbre of dimensions, variables, attributes + + % -------- read global attributes (constants)----------- + att_key={};%default + iatt_g=0; + Data.ListGlobalAttribute={};%default + for iatt=1:ngatts + keystr= netcdf.inqAttName(nc,netcdf.getConstant('NC_GLOBAL'),iatt-1); + indstr1=regexp(keystr,'\\');%detect '\\' + indstr2=regexp(keystr,'\.');%detect '\.' + if isempty(indstr1) && isempty(indstr2) + valuestr = netcdf.getAtt(nc,netcdf.getConstant('NC_GLOBAL'),keystr); + if ischar(valuestr) && length(valuestr)<200 + iatt_g=iatt_g+1; + indstr1=regexp(keystr,'\\');%detect '\\' + indstr2=regexp(keystr,'\.');%detect '\.' + if isempty(indstr1) && isempty(indstr2) + eval(['Data.' keystr '=''' valuestr ''';']) + att_key{iatt_g}=keystr; + end + elseif isempty(valuestr) + iatt_g=iatt_g+1; + eval(['Data.' keystr '=[];']) + att_key{iatt_g}=keystr; + elseif isnumeric(valuestr) + iatt_g=iatt_g+1; + eval(['Data.' keystr '=valuestr;']) + att_key{iatt_g}=keystr; + end + end + end + Data.ListGlobalAttribute=att_key; + + % -------- read dimensions ----------- + dim_name={}; + dim_value=[]; + for idim=1:ndims%length(dim_read); + [dim_name{idim},dim_value(idim)] = netcdf.inqDim(nc,idim-1); + end + if ~isempty(dim_name) && ~isempty(dim_value) + Data.ListDimName=dim_name; + Data.DimValue=dim_value; +% DimIndices=[1:ndims]; %index of the dimension in the netcdf file + dim_used=zeros(1,ndims);%initialize test of used dimensions + end + + % -------- read variables ----------- + var_read={}; %default + dimids={}; + nbatt=[]; + for ivar=1:nvars + [var_read{ivar},xtype,dimids{ivar},nbatt(ivar)] = netcdf.inqVar(nc,ivar-1); + end + var_index=1:nvars; %default set of variable indices in the netcdf file + testmulti=0; + OutputList=[]; + %select input variables, if requested by the input ListVarName + if ~(isequal(ListVarName,'*')||isempty(ListVarName)) + sizvar=size(ListVarName); + testmulti=(sizvar(1)>1); + var_index=zeros(1,sizvar(2));%default + if testmulti + OutputList=ListVarName(1,:); + testend=0; + for iline=1:sizvar(1) + if testend + break + end + % var_index=zeros(size(ListVarName));%default + for ivar=1:sizvar(2) + if ~isempty(ListVarName{iline,ivar}) + for ilist=1:nvars + if isequal(var_read{ilist},ListVarName{iline,ivar}) + var_index(ivar)=ilist; + % var_detect(ivar)=1; + break + end + end + if ivar==1 + if var_index(ivar)==0 + break%go to next line if the first nc variable is not found + else + testend=1; %this line will be read + ichoice=iline-1; %selectedline number in the list of input names of variables + end + end + end + end + end + else %single list of input variables + for ivar=1:sizvar(2) + for ilist=1:nvars + if isequal(var_read{ilist},ListVarName{ivar}) + var_index(ivar)=ilist; + var_detect(ivar)=1; + break + end + end + end + end + list_index=find(var_index); + if ~isempty(list_index) + if testmulti + OutputList=OutputList(list_index); + end + var_index=var_index(list_index); + var_detect=(var_index~=0); + var_read=var_read(var_index); + end + end + + + %select variable attributes and associate dimensions +% var_dim_index=[]; %default + Data.ListVarName={};%default + VarDimIndex={};%default + for ivar=1:length(var_read) + if testmulti + Data.ListVarName{ivar}=OutputList{ivar};%new name given by ListVarName(1,:) + else + Data.ListVarName{ivar}=var_read{ivar};%name of the variable + end + var_dim=dimids{var_index(ivar)}+1; %dimension indices used by the variable + dim_used(var_dim)=ones(size(var_dim)); + VarDimIndex{ivar}=var_dim; + + %variable attributes + if ivar==1 + Data.VarAttribute={};%initialisation of the list of variable attributes + end + %variable attributes + for iatt=1:nbatt(var_index(ivar)) + attname = netcdf.inqAttName(nc,var_index(ivar)-1,iatt-1); + valuestr= netcdf.getAtt(nc,var_index(ivar)-1,attname); + if ischar(valuestr) + eval(['Data.VarAttribute{ivar}.' attname '=''' valuestr ''';']) + elseif isempty(valuestr) + eval(['Data.VarAttribute{ivar}.' attname '=[];']) + elseif isnumeric(valuestr) + eval(['Data.VarAttribute{ivar}.' attname '=valuestr;']) + end + end + end + + %select the used dimensions + if isempty(var_read) + if isfield(Data,'ListDimName') && isfield(Data,'DimValue') + Data=rmfield(Data,'ListDimName'); + Data=rmfield(Data,'DimValue'); + end + else +% list_dim=1:ndims; + dim_index=find(dim_used); +% list_dim=list_dim(dim_index); + old2new=cumsum(dim_used); + Data.ListDimName=Data.ListDimName(dim_index); + Data.DimValue=Data.DimValue(dim_index); + end + for ivar=1:length(var_read) + Data.VarDimIndex{ivar}=old2new(VarDimIndex{ivar});% ENLEVER Data.VarDimIndex ulterieurement + Data.VarDimName{ivar}=Data.ListDimName(Data.VarDimIndex{ivar}); + end + %variable values + if ~isempty(ListVarName) + for ivar=1:length(Data.ListVarName) + VarName=Data.ListVarName{ivar}; + indstr=regexp(VarName,'-');%detect '-' + if ~isempty(indstr) + VarName(indstr)=[]; + end + eval(['Data.' VarName '=netcdf.getVar(nc,var_index(ivar)-1);'])%read the variable data + eval(['siz=size(Data.' VarName ');']) + if numel(siz)<=2 + eval(['Data.' VarName '=Data.' VarName ''';'])%read the variable data + end + end + end + % -------- close fle----------- + if testfile==1 + netcdf.close(nc) + end +else + [Data,var_detect,ichoice]=nc2struct_toolbox(nc,varargin); +end Index: /trunk/src/nc2struct_toolbox.m =================================================================== --- /trunk/src/nc2struct_toolbox.m (revision 2) +++ /trunk/src/nc2struct_toolbox.m (revision 2) @@ -0,0 +1,260 @@ +%'nc2struct_toolbox': transform a netcdf file in a corresponding matlab structure, USE OLD NETCDF LIBRARY +%---------------------------------------------------------------------- +% function [Data,var_detect,ichoice]=nc2struct_toolbox(nc,ListField) +% +% OUTPUT: +% Data: structure containing all the information of the netcdf file (or netcdf object) +% with fields: +% .ListGlobalAttribute: cell listing the names of the global attributes +% .Att_1,Att_2... : values of the global attributes +% .ListDimName: cell listing the names of the array dimensions +% .DimValue: array dimension values (Matlab vector with the same length as .ListDimName +% .ListVarName: cell listing the names of the variables +% .VarDimIndex: cell containing the set of dimension indices (in list .ListDimName) for each variable of .ListVarName +% .VarDimName: cell containing a cell of dimension names (in list .ListDimName) for each variable of .ListVarName +% .VarAttribute: cell of structures s containing names and values of variable attributes (s.name=value) for each variable of .ListVarName +% .Var1, .Var2....: variables (Matlab arrays) with names listed in .ListVarName +% var_detect: vector with same length as ListVarName, with 1 for each detected variable and 0 else. +% ichoice: = line +% +%INPUT: +% nc: name of a netcdf file (char string) or netcdf object +% ListField: optional list of variable names to select (cell array of char strings {'VarName1', 'VarName2',...} ) +% if ListField is absent or ='*', ALL the attributes and variables are read. % +% if ListField='ListGlobalAttribute', followed by the arguments 'name1', name2'..., only thes global attributes will be read (short option) +% if ListField=[] or{}, no variables is read (only global attributes and lists of vdimensions, variables and attriburtes) +% if ListField is a cell array with n lines, the set of variables +% will be sought by order of priority in the list, while output names will be set by the first line +% +%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +% Copyright Joel Sommeria, 2008, LEGI / CNRS-UJF-INPG, sommeria@coriolis-legi.org. +%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +% This file is part of the toolbox UVMAT. +% +% UVMAT is free software; you can redistribute it and/or modify +% it under the terms of the GNU General Public License as published by +% the Free Software Foundation; either version 2 of the License, or +% (at your option) any later version. +% +% UVMAT is distributed in the hope that it will be useful, +% but WITHOUT ANY WARRANTY; without even the implied warranty of +% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +% GNU General Public License (file UVMAT/COPYING.txt) for more details. +%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA + +function [Data,var_detect,ichoice]=nc2struct_toolbox(nc,varargin) + +List=varargin{1}; +%default output +Data=[]; +var_detect=[]; +ichoice=[];%default + +%open the netcdf file for reading +if ischar(nc) + if exist(nc,'file') % rmq: time for exist search = 0.5 ms CPU + nc=netcdf(nc,'nowrite'); % rmq: time needed for opening = 2 ms CPU + testfile=1; + else + Data.Txt=['ERROR:file ' nc ' does not exist']; + return + end +else + testfile=0; +end + +% short reading of global attributes +if ~isempty(List) && isequal(List{1},'ListGlobalAttribute') + for ilist=2:numel(List) + att_str=List{ilist}; + eval(['Data.' att_str '=nc.' att_str '(:);']) + end + close(nc) + %total time from beginning : 15 ms for a single attribute + return +end + +% reading of variables, including attributes +if isempty(List) + ListVarName='*'; +else +if isempty(List{1}) + ListVarName='*'; +else + ListVarName=List{1}; +end +end +% -------- read global attributes ----------- +att_read=att(nc);%cell of 'global attributes' (nc objects), CPU time 30 ms +att_key={};%default +iatt_g=0; +for iatt=1:length(att_read) + aa=att_read{iatt}; + keystr=name(aa); + indstr1=regexp(keystr,'\\');%replace dots' + indstr2=regexp(keystr,'\.');%replace dots' + if ~isequal(keystr,'title') % PROBLEM WITH civx files do not read 'title' + if isempty(indstr1) && isempty(indstr2) % + eval(['valuestr=nc.' keystr '(:);']) + if ischar(valuestr) && length(valuestr)<200 + iatt_g=iatt_g+1; + indstr1=regexp(keystr,'\\');%replace dots' + indstr2=regexp(keystr,'\.');%replace dots' + if isempty(indstr1) && isempty(indstr2) + eval(['Data.' keystr '=''' valuestr ''';']) + att_key{iatt_g}=keystr; + end + elseif isempty(valuestr) + iatt_g=iatt_g+1; + eval(['Data.' keystr '=[];']) + att_key{iatt_g}=keystr; + elseif isnumeric(valuestr) + iatt_g=iatt_g+1; + eval(['Data.' keystr '=valuestr;']) + att_key{iatt_g}=keystr; + end + end + end +end +Data.ListGlobalAttribute=att_key; +nbattr=length(att_key); +neworder=[nbattr+1 (1:nbattr)]; +Data=orderfields(Data,neworder); + +% -------- read dimensions ----------- +dim_read=dim(nc);%cell of variable dimension names (nc objects): CPU time 0.0013 +dim_name={}; +dim_value=[]; +for idim=1:length(dim_read); + aa=dim_read{idim}; + if ~isempty(aa) + dim_name{idim}=name(aa); + dim_value(idim)=length(aa); + end +end +if ~isempty(dim_name) && ~isempty(dim_value) + Data.ListDimName=dim_name; + Data.DimValue=dim_value; + used=zeros(1,length(dim_value));%initialize test of used dimensions +end + +% -------- read variables ----------- +var_read={}; %default +testmulti=0; +OutputList=[]; +if isequal(ListVarName,'*')%|| isempty(ListVarName) + var_read=var(nc);%cell of all variables +elseif ~isempty(ListVarName) + sizvar=size(ListVarName); + testmulti=(sizvar(1)>1); + if testmulti + OutputList=ListVarName(1,:); + testend=0; + for iline=1:sizvar(1) + if testend + break + end + for ivar=1:sizvar(2) + var_read{ivar}=[];%default + var_detect(ivar)=0;%default + VarName=ListVarName{iline,ivar}; + if ~isempty(VarName) + var_read{ivar}=nc{VarName};%select the input variable names + if ivar==1 + if isempty (var_read{ivar}) + break%go to next line if the first nc variable is not found + else + testend=1; %this line will be read + ichoice=iline-1; %selectedline number in the list of input names of variables + var_detect(ivar)=1; + end + else + var_detect(ivar)=~isempty (var_read{ivar}); + end + end + end + end + if ~isempty(find(var_detect,1)) + OutputList=OutputList(find(var_detect)); + end + else %single list of input variables + var_detect=ones(size(ListVarName)); + for ivar=1:sizvar(2) + var_read{ivar}=nc{ListVarName{ivar}};%select the input variable names + var_detect(ivar)=~isempty(var_read{ivar}); + end + end + var_read=var_read(find(var_detect)); +end + +% var_dim_index=[]; %default +Data.ListVarName={};%default +for ivar=1:length(var_read) + vv=var_read{ivar}; + Data.ListVarName{ivar}=name(vv);%name of the variable + if testmulti + Data.ListVarName{ivar}=OutputList{ivar}; + else + Data.ListVarName{ivar}=name(vv);%name of the variable + end + var_dim=dim(vv);%dimension netcdf object of the variable + for ivardim=1:length(var_dim) + var_dim_name=name(var_dim{ivardim});%name of the dimension + for idim=1:length(dim_name)% find the index of the current dimension in the list of dimensions + if isequal(dim_name{idim},var_dim_name) + Data.VarDimIndex{ivar}(ivardim)=idim; + used(idim)=1; + break + end + end + end + Data.VarDimName{ivar}={}; + %variable attributes + Data.VarAttribute{ivar}=[];%initialisation of the list of variable attributes + %variable attributes + att_read=att(vv); + for iatt=1:length(att_read) + aa=att_read{iatt}; + eval(['valuestr=vv.' name(aa) '(:);']) + if ischar(valuestr) + eval(['Data.VarAttribute{ivar}.' name(aa) '=''' valuestr ''';']) + elseif isempty(valuestr) + eval(['Data.VarAttribute{ivar}.' name(aa) '=[];']) + elseif isnumeric(valuestr) + eval(['Data.VarAttribute{ivar}.' name(aa) '=valuestr;']) + end + end +end + +%select the used dimensions +if isempty(var_read) + if isfield(Data,'ListDimName') && isfield(Data,'DimValue') + Data=rmfield(Data,'ListDimName'); + Data=rmfield(Data,'DimValue'); + end +else + old_dim_index=find(used); %dimension indices which are used by the selected variables + old2new=cumsum(used); + Data.ListDimName=Data.ListDimName(old_dim_index); + Data.DimValue=Data.DimValue(old_dim_index); +end +for ivar=1:length(var_read) + Data.VarDimIndex{ivar}=(old2new(Data.VarDimIndex{ivar})); + Data.VarDimName{ivar}=(Data.ListDimName(Data.VarDimIndex{ivar})); +end +%variable values + +if ~isempty(ListVarName) + for ivar=1:length(Data.ListVarName) + vv=var_read{ivar}; + vdata=vv(:);%data array of the field variable + eval(['Data.' Data.ListVarName{ivar} '=vdata;'])%read the variable data + end +end +% -------- close fle----------- +if testfile==1 + close(nc) +end + +%total time from beginning : 150 ms for a full civ2 field, 65 ms for four fields + Index: /trunk/src/nomtype2pair.m =================================================================== --- /trunk/src/nomtype2pair.m (revision 2) +++ /trunk/src/nomtype2pair.m (revision 2) @@ -0,0 +1,70 @@ +%'nomtype2pair': creates nomencalture for index pairs. +%--------------------------------------------------------------------- +% [nom_type_nc]=nomtype2pair(nom_type); +%--------------------------------------------------------------------- +% This function detects the existence the constructed file name and it can +% find indices according to file existence if they are not specified +%%rmq: this function is related to the reverse functions display2name and name2diplay +%--------------------------------------------------------------------- +% OUTPUT: +%nom_type_nc + +%--------------------------------------------------------------------- +% INPUT: +% 'nom_type': string defining the kind of nomenclature used: + %nom_type='': constant name [filebase ext] (default output if 'nom_type' is undefined) + %nom_type='*': the same file [filebase ext] contains successive fields (ex avi movies) + %nom_type='_i': series of files with a single index i preceded by '_'(e.g. 'aa_45.png'). + %nom_type='#' series of indexed images wich is not series_i [filebase index ext], e.g. 'aa045.jpg' or 'aa45.tif' + %nom_type='_i_j' matrix of files with two indices i and j separated by '_'(e.g. 'aa_45_2.png') + %nom_type='_i1-i2' from pairs from a single index (e.g. 'aa_45-47.nc') + %nom_type='_i_j1-j2'pairs of j indices (e.g. 'aa_45_2-3.nc') + %nom_type='_i1-i2_j' pairs of i indices (e.g. 'aa_45-46_2.nc') + %nom_type='#a','#A', with a numerical index and an index letter(e.g.'aa045b.png'), OBSOLETE (replaced by 'series_i_j') + %nom_type='%03d' or '%04d', series of indexed images with numbers completed with zeros to 3 or 4 digits, e.g.'aa045.tif' + %nom_type='_%03d', '_%04d', or '_%05d', series of indexed images with _ and numbers completed with zeros to 3, 4 or 5 digits, e.g.'aa_045.tif' + %nom_type='raw_SMD', same as '#a' but with no extension ext='', OBSOLETE + %nom_type='#_ab' from pairs of '#a' images (e.g. 'aa045bc.nc'), ext='.nc', OBSOLETE (replaced by 'netc_2D') + %nom_type='%3dab' from pairs of '%3da' images (e.g. 'aa045bc.nc'), ext='.nc', OBSOLETE (replaced by 'netc_2D') +% Dti: ~=0 if i index pairs are used +% Dtj: ~=0 if i index pairs are used + +function [nom_type_pair]=nomtype2pair(nom_type,Dti,Dtj); + +%determine nom_type_nc: +nom_type_nc=[];%default +switch nom_type + case {'_i_j'} + if Dtj>0 || Dtj<0 + nom_type_pair='_i_j1-j2'; + if Dti>0 || Dti<0 + nom_type_pair='_i1-i2_j1-j2'; + end + elseif Dti>0 || Dti<0 + nom_type_pair='_i1-i21_j'; + else + nom_type_pair='_i_j'; + end + case {'_i1-i2_j'} + if Dtj>0 || Dtj<0 + nom_type_pair='_i1-i2_j1-j2'; + else + nom_type_pair='_i1-i2_j'; + end + case {'i_j1-j2'} + if Dti>0 || Dti<0 + nom_type_pair='_i1-i2_j1-j2'; + else + nom_type_pair='_i1-i2_j'; + end + case {'i1-i2_j1-j2'} + nom_type_pair='_i1-i2_j1-j2'; + case '#a' + if Dtj>0 || Dtj<0 + nom_type_pair='#_ab'; + end + otherwise + if Dti>0 || Dti<0 + nom_type_pair='_i1-i2'; + end +end Index: /trunk/src/num2stra.m =================================================================== --- /trunk/src/num2stra.m (revision 2) +++ /trunk/src/num2stra.m (revision 2) @@ -0,0 +1,41 @@ +%'num2stra': transform number to the corresponding character string depending on the nomenclature +%-------------------------------------------- +% function str=num2stra(num,nom_type) +% +% OUTPUT: +% str: character string +% +% INPUT: +% num: input number (file index) +% nom_type: nomencalture type (see fct name_generator) +% +% see also: stra2num, name_generator, name2display + +function str=num2stra(num,nom_type,index); +if ~exist('index','var') + index=2; %index 1 or 2 of the file indices +end +switch index + case 1 + if length(nom_type)>=4 && isequal(nom_type(1:2),'%0') && isequal(nom_type(4),'d') + str=num2str(num,nom_type(1:4)); + else + str=num2str(num); + end + case 2 + if isempty(nom_type) + nom_type='none'; + end + if isequal(nom_type,'png_old') || isequal(nom_type,'netc_old') || isequal(nom_type,'raw_SMD')||... + isequal(nom_type(end),'a')||isequal(nom_type(end),'b') + str=char(96+num); + elseif isequal(nom_type(end),'A')|isequal(nom_type(end),'B') + str=char(64+num); + elseif isequal(nom_type,'series_i')|isequal(nom_type,'netc_series')... + |isequal(nom_type,'ima_num')| isequal(nom_type,'avi')| isequal(nom_type,'none')... + isequal(nom_type,'_i')|isequal(nom_type,'_i1-i2') + str=''; + else + str=num2str(num); + end +end Index: /trunk/src/parseXML.m =================================================================== --- /trunk/src/parseXML.m (revision 2) +++ /trunk/src/parseXML.m (revision 2) @@ -0,0 +1,70 @@ +% PARSEXML Convert XML file to a MATLAB structure. (from matlab help) +function theStruct = parseXML(filename) + +try + tree = xmlread(filename); +catch + error('Failed to read XML file %s.',filename); +end + +% Recurse over child nodes. This could run into problems +% with very deeply nested trees. +try + theStruct = parseChildNodes(tree); +catch + error('Unable to parse XML file %s.'); +end + + +% ----- Subfunction PARSECHILDNODES ----- +function children = parseChildNodes(theNode) +% Recurse over node children. +children = []; +if theNode.hasChildNodes + childNodes = theNode.getChildNodes; + numChildNodes = childNodes.getLength; + allocCell = cell(1, numChildNodes); + + children = struct( ... + 'Name', allocCell, 'Attributes', allocCell, ... + 'Data', allocCell, 'Children', allocCell); + + for count = 1:numChildNodes + theChild = childNodes.item(count-1); + children(count) = makeStructFromNode(theChild); + end +end + +% ----- Subfunction MAKESTRUCTFROMNODE ----- +function nodeStruct = makeStructFromNode(theNode) +% Create structure of node info. + +nodeStruct = struct( ... + 'Name', char(theNode.getNodeName), ... + 'Attributes', parseAttributes(theNode), ... + 'Data', '', ... + 'Children', parseChildNodes(theNode)); + +if any(strcmp(methods(theNode), 'getData')) + nodeStruct.Data = char(theNode.getData); +else + nodeStruct.Data = ''; +end + +% ----- Subfunction PARSEATTRIBUTES ----- +function attributes = parseAttributes(theNode) +% Create attributes structure. + +attributes = []; +if theNode.hasAttributes + theAttributes = theNode.getAttributes; + numAttributes = theAttributes.getLength; + allocCell = cell(1, numAttributes); + attributes = struct('Name', allocCell, 'Value', allocCell); + + for count = 1:numAttributes + attrib = theAttributes.item(count-1); + attributes(count).Name = char(attrib.getName); + attributes(count).Value = char(attrib.getValue); + end +end Index: /trunk/src/peaklock.m =================================================================== --- /trunk/src/peaklock.m (revision 2) +++ /trunk/src/peaklock.m (revision 2) @@ -0,0 +1,197 @@ +%'peaklock': determines peacklocking errors from velocity histograms. +%------------------------------------------------------- +%first smooth the input histogram 'histu' in such a way that the integral over +%n-n+1 is preserved, then deduce the peaklocking 'error' function of the pixcel displacement 'x'. +% +% [histinter,x,error]=peaklock(nbb,minim,maxim,histu) +%OUTPUT: +%histinter: smoothed interpolated histogram +% x: vector of displacement values. +% error: vector of estimated errors corresponding to x +%INPUT: +%histu=vector representing the values of histogram of measured velocity ; +%minim, maxim: extremal values of the measured velocity (absica for histu) +%nbb: number of bins inside each integer interval for the histograms +%SUBROUTINES INCLUDED: +%spline4.m% spline interpolation at 4th order +%splinhist.m: give spline coeff cc for a smooth histo (call spline4) +%histsmooth.m(x,cc): calculate the smooth histo for any value x +%histder.m(x,cc): calculate the derivative of the smooth histo +function [histinter,x,error]=peaklock(nbb,minim,maxim,histu) + +nint=maxim-minim+1 +xfin=[minim-0.5+1/(2*nbb):(1/nbb):maxim+0.5-(1/(2*nbb))]; +histo=(reshape(histu,nbb,nint));%extract values with x between integer -1/2 integer +1/2 +Integ=sum(histo)/nbb; %integral of the pdf on each integer bin +[histinter,cc]=splinhist(Integ,minim,nbb); +histx=reshape(histinter,nbb,nint); +xint=[minim:1:maxim]; +x=zeros(nbb,nint); +%determination of the displacement x(j,:) +%j=1 +delx=histo(1,:)./histsmooth(-0.5*ones(1,nint),cc)/nbb; +%del(1,:)=delx; +x(1,:)=-0.5+delx-(delx.*delx/2).*histder(-0.5*ones(1,nint),cc); +%histx(1,:)=histsmooth(x(j-1,:),cc); +for j=2:nbb + delx=histo(j,:)./histsmooth(x(j-1,:),cc)/nbb; + %delx=delx.*(delx<3*ones(1,nint)/nbb)+3*ones(1,nint)/nbb.*~(delx <3*ones(1,nint)/nbb) + x(j,:)=x(j-1,:)+delx-(delx.*delx/2).*histder(x(j-1,:),cc); +end +%reshape +xint=ones(nbb,1)*xint; +x=x+xint; +x=reshape(x,1,nbb*nint); +error=xfin+1/(2*nbb)-x; + +%------------------------------------------------------- +% --- determine the spline coefficients cc for the interpolated histogram. +%------------------------------------------------- +function [histsmooth,cc]= splinhist(Integ,mini,nbb) +% provides a smooth histogramm histmooth, which remains always positive, +% and is such that its sum over each integer bin [i-1/2 i+1/2] is equal to +% Integ(i). The function determines histmooth as the exponential of a 4th +% order spline function and adjust the cefficients by a Newton method to +% fit the integral conditions Integ +% histmooth is determined at the abscissa +% xfin=[mini-0.5+1/(2*n):(1/n):maxi+0.5-(1/(2*n))] (maxi=mini+size(aa)-1) +%cc(1-5,i) provides the spline coefficients + +% order 0 +siz=size(Integ); +nint=siz(2); +izero=find(Integ==0); %indices of zero elements +inonzero=find(Integ); +Integ(izero)=min(Integ(inonzero)); +aa=log(Integ);%initial guess for a coeff +spli=spline4(aa,mini,nbb); %appel à la fonction spline4 +histsmooth=exp(spli); + +S=(sum(reshape(histsmooth,nbb,nint)))/nbb;% integral of the fit histsmooth on ]i-1/2 i+1/2[ +epsilon=max(abs(Integ-S)); +iter=0; +while epsilon > 0.000001 & iter<10 +ident=eye(nint); +dSda=ones(nint); +for j=1:nint% determination of the jacobian matrix dSda +dhistda=spline4(ident(j,:),mini,nbb); +expdhistda=dhistda.*histsmooth; +dSda(j,:)=(sum(reshape(expdhistda,nbb,nint)))/nbb; +end +aa=aa+(Integ-S)*inv(dSda);%new estimate of coefficients aa by linear interpolation +[spli,bb]=spline4(aa,mini,nbb);% new fit histsmooth +histsmooth=exp(spli); +S=(sum(reshape(histsmooth,nbb,nint)))/nbb;% integral of the fit histsmooth on ]i-1/2 i+1/2[ +epsilon=max(abs(Integ-S)); +iter=iter+1; +end +if iter==10, errordlg('splinhist did not converge after 10 iterations'),end +cc(1,:)=aa; +cc(2,:)=bb(1,:); +cc(3,:)=bb(2,:); +cc(4,:)=bb(3,:); +cc(5,:)=bb(4,:); + +%------------------------------------------------------- +% --- determine the 4th order spline coefficients from the function values aa. +%------------------------------------------------- +function [histsmooth,bb]= spline4(aa,mini,n) +% spline interpolation at 4th order +%aa=vector of values of a function at integer abscissa, starting at mini +%n=number of subdivisions for the interpolated function +% histmooth =interpolated values at absissa +% xfin=[mini-0.5+1/(2*n):(1/n):maxi+0.5-(1/(2*n))] (maxi=mini+size(aa)-1) +%bb=[b(i);c(i);d(i); e(i)] matrix of spline coeff +L1=[1/2 1/4 1/8 1/16;1 1 3/4 1/2;0 2 3 3;0 0 6 12]; +L2=[-1/2 1/4 -1/8 1/16;1 -1 3/4 -1/2;0 2 -3 3;0 0 6 -12]; +M=inv(L2)*L1; +[V,D]=eig(M); +F=-inv(V)*inv(L2)*[1 ;0 ;0;0]; +a1rev=[1 -1/D(1,1)]; +b1rev=[F(1)/D(1,1)]; +a2rev=[1 -1/D(2,2)]; +b2rev=[F(2)/D(2,2)]; +a3=[1 -D(3,3)]; +b3=[F(3)]; +a4=[1 -D(4,4)]; +b4=[F(4)]; + +%data +% n=10;% résolution de la pdf: nbre de points par unite de u +% mini=-10.0;%general mini=uint16(min(values)-1 CHOOSE maxi-mini+1 EVEN +% maxi=9.0; % general maxi=uint16(max(values))+1 +%nint=double(maxi-mini+1); % nombre d'intervals entiers EVEN! +siz=size(aa); +nint=siz(2); +maxi=mini+nint-1; +npdf=nint*n;% nbre total d'intervals à introduire dans la pdf: hist(u,npdf) +%simulation de pdf +xfin=[mini-0.5+1/(2*n):(1/n):maxi+0.5-(1/(2*n))];% valeurs d'interpolation: we take n values in each integer interval +%histolin=exp(-(xfin-1).*(xfin-1)).*(2+cos(10*(xfin-1)));% simulation d'une pdf +%histo=log(histolin); +%histo=sin(2*pi*xfin); +%histextract=(reshape(histo,n,nint)); +%aa=sum(histextract)/n %integral of the pdf on each integer bin +IP=[0 diff(aa)]; +Irev=zeros(size(aa)); +for i=1:nint + Irev(i)=aa(end-i+1); +end +IPrev=[0 diff(Irev)]; + +%get the spline coelfficients a_d, using filter on the eigen vectors A,B,C +Arev=filter(b1rev,a1rev,IPrev); +Brev=filter(b2rev,a2rev,IPrev); +C=filter(b3,a3,IP); +D=filter(b4,a4,IP); +A=zeros(size(Arev)); +B=zeros(size(Brev)); +for i=1:nint + A(i)=Arev(end-i+1); + B(i)=Brev(end-i+1); +end +%Matr=V*[A;B;C;D]; +bb=V*[A;B;C;D]; +%b=Matr(1,:); +%c=Matr(2,:); +%d=Matr(3,:); +%e=Matr(4,:); +%a=aa; + +%calculate the interpolation using the spline coefficients a-d +%xextract=(reshape(xfin,n,nint));% +chi=xfin+1/(2*n)-min(xfin)-double(int16(xfin+(1/(2*n))-min(xfin)))-0.5;% decimal part +chi2=chi.*chi; +chi3=chi2.*chi; +chi4=chi3.*chi; +avec=reshape(ones(n,1)*aa,1,n*nint); +bvec=reshape(ones(n,1)*bb(1,:),1,n*nint); +cvec=reshape(ones(n,1)*bb(2,:),1,n*nint); +dvec=reshape(ones(n,1)*bb(3,:),1,n*nint); +evec=reshape(ones(n,1)*bb(4,:),1,n*nint); +histsmooth=avec+bvec.*chi+cvec.*chi2+dvec.*chi3+evec.*chi4; + +%------------------------------------------------------- +% --- determine the interpolated histogram at points chi from the spline ceff cc. +%------------------------------------------------- +function histx= histsmooth(chi,cc) +% provides the value of the interpolated histogram at values chi=x-i +%(difference with the mnearest integer) +% cc(5,size(chi)) is the set of spline coefficients obtained by splinhist +chi2=chi.*chi; +chi3=chi2.*chi; +chi4=chi3.*chi; +histx=exp(cc(1,:)+cc(2,:).*chi+cc(3,:).*chi2+cc(4,:).*chi3+cc(5,:).*chi4); + +%------------------------------------------------------- +% --- determine the derivative p'/p of the interpolated histogram at points chi from the spline ceff cc. +%------------------------------------------------- +function histder= histder(chi,cc) +% provides the logarithmique derivative p'/p of the interpolated histogram +%at values chi=x-i +%(difference with the nearest integer) +% cc(5,size(chi)) is the set of spline coefficients obtained by splinhist +chi2=chi.*chi; +chi3=chi2.*chi; +chi4=chi3.*chi; +histder=cc(2,:)+2*cc(3,:).*chi+3*cc(4,:).*chi2+4*cc(5,:).*chi3; Index: /trunk/src/phys.m =================================================================== --- /trunk/src/phys.m (revision 2) +++ /trunk/src/phys.m (revision 2) @@ -0,0 +1,232 @@ +%'phys': transforms image (px) to real world (phys) coordinates using geometric calibration parameters +% OUTPUT: +% DataOut: structure representing the modified field +% DataOut_1: structure representing the second modified field + +%INPUT: +% Data: structure of input data +% with fields .A (image or scalar matrix), AX, AY +% .X,.Y,.U,.V, .DjUi +% .ZIndex: index of plane in multilevel case +% Data.CoordType='phys' or 'px', The function ACTS ONLY IF .CoordType='px' +% Calib: structure containing calibration parameters or a subtree Calib.GeometryCalib =calibration data (tsai parameters) + +function [DataOut,DataOut_1]=phys(varargin) +% A FAIRE: 1- verifier si DataIn est une 'field structure'(.ListVarName'): +% chercher ListVarAttribute, for each field (cell of variables): +% .CoordType: 'phys' or 'px' (default==phys, no transform) +% .scale_factor: =dt (to transform displacement into velocity) default=1 +% .covariance: 'scalar', 'coord', 'D_i': covariant (like velocity), 'D^i': contravariant (like gradient), 'D^jD_i' (like strain tensor) +% (default='coord' if .Role='coord_x,_y..., +% 'D_i' if '.Role='vector_x,...', +% 'scalar', else (thenno change except scale factor) +Calib{1}=[]; +if nargin==2||nargin==4 % nargin =nbre of input variables + Data=varargin{1}; + DataOut=Data;%default + DataOut_1=[];%default + CalibData=varargin{2}; + if isfield(CalibData,'GeometryCalib') + Calib{1}=CalibData.GeometryCalib; + end + Calib{2}=Calib{1}; +else + DataOut.Txt='wrong input: need two or four structures'; +end +test_1=0; +if nargin==4 + test_1=1; + Data_1=varargin{3}; + DataOut_1=Data_1;%default + CalibData_1=varargin{4}; + if isfield(CalibData_1,'GeometryCalib') + Calib{2}=CalibData_1.GeometryCalib; + end +end +iscalar=0; +if ~isempty(Calib{1}) + DataOut=phys_1(Data,Calib{1}); + %case of images or scalar: in case of two input fields, we need to project the transform of on the same regular grid + if isfield(Data,'A') && isfield(Data,'AX') && ~isempty(Data.AX) && isfield(Data,'AY')&&... + ~isempty(Data.AY) && length(Data.A)>1 + iscalar=1; + A{1}=Data.A; + end +end +%transform of X,Y coordinates for vector fields +if isfield(Data,'ZIndex')&&~isempty(Data.ZIndex) + ZIndex=Data.ZIndex; +else + ZIndex=0; +end +if test_1 + DataOut_1=phys_1(Data_1,Calib{2}); + if isfield(Data_1,'A')&&isfield(Data_1,'AX')&&~isempty(Data_1.AX) && isfield(Data_1,'AY')&&... + ~isempty(Data_1.AY)&&length(Data_1.A)>1 + iscalar=iscalar+1; + Calib{iscalar}=Calib{2}; + A{iscalar}=Data_1.A; + if isfield(Data_1,'ZIndex') && ~isequal(Data_1.ZIndex,ZIndex) + DataOut.Txt='inconsistent plane indexes in the two input fields'; + end + if iscalar==1% case for which only the second field is a scalar + [A,AX,AY]=phys_Ima(A,Calib,ZIndex); + DataOut_1.A=A{1}; + DataOut_1.AX=AX; + DataOut_1.AY=AY; + return + end + end +end +if iscalar~=0 + [A,AX,AY]=phys_Ima(A,Calib,ZIndex);%TODO : introduire interp2_uvmat ds phys_ima + DataOut.A=A{1}; + DataOut.AX=AX; + DataOut.AY=AY; + if iscalar==2 + DataOut_1.A=A{2}; + DataOut_1.AX=AX; + DataOut_1.AY=AY; + end +end + +%------------------------------------------------ +function DataOut=phys_1(Data,Calib) +% for icell=1:length(Data) + +DataOut=Data;%default +DataOut.CoordType='phys'; %put flag for physical coordinates +% The transform ACTS ONLY IF .CoordType='px'and Calib defined +if isfield(Data,'CoordType')&& isequal(Data.CoordType,'px')&& ~isempty(Calib) + if isfield(Calib,'CoordUnit') + DataOut.CoordUnit=Calib.CoordUnit; + else + DataOut.CoordUnit='cm'; %default +% elseif isfield(DataOut,'CoordUnit') +% DataOut=rmfield(DataOut,'CoordUnit'); + end + DataOut.TimeUnit='s'; + %transform of X,Y coordinates for vector fields + if isfield(Data,'ZIndex') && ~isempty(Data.ZIndex) + Z=Data.ZIndex; + else + Z=0; + end + if isfield(Data,'X') &&isfield(Data,'Y')&&~isempty(Data.X) && ~isempty(Data.Y) + [DataOut.X,DataOut.Y,DataOut.Z]=phys_XYZ(Calib,Data.X,Data.Y,Z); + if isfield(Data,'U')&&isfield(Data,'V')&&~isempty(Data.U) && ~isempty(Data.V)&& isfield(Data,'dt') + if ~isempty(Data.dt) + [XOut_1,YOut_1]=phys_XYZ(Calib,Data.X-Data.U/2,Data.Y-Data.V/2,Z); + [XOut_2,YOut_2]=phys_XYZ(Calib,Data.X+Data.U/2,Data.Y+Data.V/2,Z); + DataOut.U=(XOut_2-XOut_1)/Data.dt; + DataOut.V=(YOut_2-YOut_1)/Data.dt; + end + end + end + %transform of an image or scalar: done in phys_ima + + %transform of spatial derivatives + if isfield(Data,'X') && ~isempty(Data.X) && isfield(Data,'DjUi') && ~isempty(Data.DjUi)... + && isfield(Data,'dt') + if ~isempty(Data.dt) + % estimate the Jacobian matrix DXpx/DXphys + for ip=1:length(Data.X) + [Xp1,Yp1]=phys_XYZ(Calib,Data.X(ip)+0.5,Data.Y(ip),Z); + [Xm1,Ym1]=phys_XYZ(Calib,Data.X(ip)-0.5,Data.Y(ip),Z); + [Xp2,Yp2]=phys_XYZ(Calib,Data.X(ip),Data.Y(ip)+0.5,Z); + [Xm2,Ym2]=phys_XYZ(Calib,Data.X(ip),Data.Y(ip)-0.5,Z); + %Jacobian matrix DXpphys/DXpx + DjXi(1,1)=(Xp1-Xm1); + DjXi(2,1)=(Yp1-Ym1); + DjXi(1,2)=(Xp2-Xm2); + DjXi(2,2)=(Yp2-Ym2); + DjUi(:,:)=Data.DjUi(ip,:,:); + DjUi=(DjXi*DjUi')/DjXi;% =J-1*M*J , curvature effects (derivatives of J) neglected + DataOut.DjUi(ip,:,:)=DjUi'; + end + DataOut.DjUi = DataOut.DjUi/Data.dt; % min(Data.DjUi(:,1,1))=DUDX + end + end +end + + +%%%%%%%%%%%%%%%%%%%% +function [A_out,Rangx,Rangy]=phys_Ima(A,CalibIn,ZIndex) +xcorner=[]; +ycorner=[]; +npx=[]; +npy=[]; +for icell=1:length(A) + siz=size(A{icell}); + npx=[npx siz(2)]; + npy=[npy siz(1)]; + Calib=CalibIn{icell}; + xima=[0.5 siz(2)-0.5 0.5 siz(2)-0.5];%image coordiantes of corners + yima=[0.5 0.5 siz(1)-0.5 siz(1)-0.5]; + [xcorner_new,ycorner_new]=phys_XYZ(Calib,xima,yima,ZIndex);%corresponding physical coordinates + xcorner=[xcorner xcorner_new]; + ycorner=[ycorner ycorner_new]; +end +Rangx(1)=min(xcorner); +Rangx(2)=max(xcorner); +Rangy(2)=min(ycorner); +Rangy(1)=max(ycorner); +test_multi=(max(npx)~=min(npx)) | (max(npy)~=min(npy)); +npx=max(npx); +npy=max(npy); +x=linspace(Rangx(1),Rangx(2),npx); +y=linspace(Rangy(1),Rangy(2),npy); +[X,Y]=meshgrid(x,y);%grid in physical coordiantes +vec_B=[]; +A_out={}; +for icell=1:length(A) + Calib=CalibIn{icell}; + if (isfield(Calib,'R') && ~isequal(Calib.R(2,1),0) && ~isequal(Calib.R(1,2),0)) ||... + ((isfield(Calib,'kappa1')&& ~isequal(Calib.kappa1,0))) || test_multi || ~isequal(Calib,CalibIn{1}) + zphys=0; %default + if isfield(Calib,'SliceCoord') %.Z= index of plane + SliceCoord=Calib.SliceCoord(ZIndex,:); + zphys=SliceCoord(3); %to generalize for non-parallel planes + end + [XIMA,YIMA]=px_XYZ(CalibIn{icell},X,Y,zphys);%corresponding image indices for each point in the real space grid + XIMA=reshape(round(XIMA),1,npx*npy);%indices reorganized in 'line' + YIMA=reshape(round(YIMA),1,npx*npy); + flagin=XIMA>=1 & XIMA<=npx & YIMA >=1 & YIMA<=npy;%flagin=1 inside the original image + testuint8=isa(A{icell},'uint8'); + testuint16=isa(A{icell},'uint16'); + if numel(siz)==2 %(B/W images) + vec_A=reshape(A{icell},1,npx*npy);%put the original image in line + ind_in=find(flagin); + ind_out=find(~flagin); + ICOMB=((XIMA-1)*npy+(npy+1-YIMA)); + ICOMB=ICOMB(flagin);%index corresponding to XIMA and YIMA in the aligned original image vec_A + vec_B(ind_in)=vec_A(ICOMB); + vec_B(ind_out)=zeros(size(ind_out)); + A_out{icell}=reshape(vec_B,npy,npx);%new image in real coordinates + elseif numel(siz)==3 + for icolor=1:siz(3) + vec_A=reshape(A{icell}(:,:,icolor),1,npx*npy);%put the original image in line + ind_in=find(flagin); + ind_out=find(~flagin); + ICOMB=((XIMA-1)*npy+(npy+1-YIMA)); + ICOMB=ICOMB(flagin);%index corresponding to XIMA and YIMA in the aligned original image vec_A + vec_B(ind_in)=vec_A(ICOMB); + vec_B(ind_out)=zeros(size(ind_out)); + A_out{icell}(:,:,icolor)=reshape(vec_B,npy,npx);%new image in real coordinates + end + end + if testuint8 + A_out{icell}=uint8(A_out{icell}); + end + if testuint16 + A_out{icell}=uint16(A_out{icell}); + end + else% + + A_out{icell}=A{icell};%no transform + Rangx=[0.5 npx-0.5];%image coordiantes of corners + Rangy=[npy-0.5 0.5]; + [Rangx]=phys_XYZ(Calib,Rangx,[0.5 0.5],[ZIndex ZIndex]);%case of translations without rotation and quadratic deformation + [xx,Rangy]=phys_XYZ(Calib,[0.5 0.5],Rangy,[ZIndex ZIndex]); + end +end Index: /trunk/src/phys_XYZ.m =================================================================== --- /trunk/src/phys_XYZ.m (revision 2) +++ /trunk/src/phys_XYZ.m (revision 2) @@ -0,0 +1,54 @@ +%'phys_XYZ':transforms image (px) to real world (phys) coordinates using geometric calibration parameters +% function [Xphys,Yphys]=phys_XYZ(Calib,X,Y,Z) +% +%OUTPUT: +% +%INPUT: +%Z: index of plane +function [Xphys,Yphys,Zphys]=phys_XYZ(Calib,X,Y,Z) +if exist('Z','var')& isequal(Z,round(Z))& Z>0 & isfield(Calib,'SliceCoord')&length(Calib.SliceCoord)>=Z + Zindex=Z; + Zphys=Calib.SliceCoord(Zindex,3);%GENERALISER AUX CAS AVEC ANGLE +else +% if exist('Z','var') +% Zphys=Z; +% else + Zphys=0; +% end +end +if ~exist('X','var')||~exist('Y','var') + Xphys=[]; + Yphys=[];%default + return +end +Xphys=X;%default +Yphys=Y; +%image transform +if isfield(Calib,'R') + R=(Calib.R)'; + Dx=R(5)*R(7)-R(4)*R(8); + Dy=R(1)*R(8)-R(2)*R(7); + D0=Calib.f*(R(2)*R(4)-R(1)*R(5)); + Z11=R(6)*R(8)-R(5)*R(9); + Z12=R(2)*R(9)-R(3)*R(8); + Z21=R(4)*R(9)-R(6)*R(7); + Z22=R(3)*R(7)-R(1)*R(9); + Zx0=R(3)*R(5)-R(2)*R(6); + Zy0=R(1)*R(6)-R(3)*R(4); + A11=R(8)*Calib.Ty-R(5)*Calib.Tz+Z11*Zphys; + A12=R(2)*Calib.Tz-R(8)*Calib.Tx+Z12*Zphys; + A21=-R(7)*Calib.Ty+R(4)*Calib.Tz+Z21*Zphys; + A22=-R(1)*Calib.Tz+R(7)*Calib.Tx+Z11*Zphys; + X0=Calib.f*(R(5)*Calib.Tx-R(2)*Calib.Ty+Zx0*Zphys); + Y0=Calib.f*(-R(4)*Calib.Tx+R(1)*Calib.Ty+Zy0*Zphys); + %px to camera: + Xd=(Calib.dpx/Calib.sx)*(X-Calib.Cx); % sensor coordinates + Yd=Calib.dpy*(Y-Calib.Cy); + dist_fact=1+Calib.kappa1*(Xd.*Xd+Yd.*Yd); %distortion factor + Xu=dist_fact.*Xd;%undistorted sensor coordinates + Yu=dist_fact.*Yd; + denom=Dx*Xu+Dy*Yu+D0; + % denom2=denom.*denom; + Xphys=(A11.*Xu+A12.*Yu+X0)./denom;%world coordinates + Yphys=(A21.*Xu+A22.*Yu+Y0)./denom; +end Index: /trunk/src/phys_polar.m =================================================================== --- /trunk/src/phys_polar.m (revision 2) +++ /trunk/src/phys_polar.m (revision 2) @@ -0,0 +1,226 @@ +%transform image coordinates (px) to physical coordinates +% then transform to polar coordinates: +%[DataOut,DataOut_1]=phys_polar(varargin) +% +% OUTPUT: +% DataOut: structure of modified data field: .X=radius, .Y=azimuth angle, .U, .V are radial and azimuthal velocity components +% DataOut_1: second data field (if two fields are in input) +% +%INPUT: +% Data: structure of input data (like UvData) +% CalibData= structure containing the field .GeometryCalib with calibration parameters +% Data_1: second input field (not mandatory) +% CalibData_1= calibration parameters for the second field + +function [DataOut,DataOut_1]=phys_polar(varargin) +Calib{1}=[]; +if nargin==2||nargin==4 + Data=varargin{1}; + DataOut=Data;%default + DataOut_1=[];%default + CalibData=varargin{2}; + if isfield(CalibData,'GeometryCalib') + Calib{1}=CalibData.GeometryCalib; + end + Calib{2}=Calib{1}; +else + DataOut.Txt='wrong input: need two or four structures'; +end +test_1=0; +if nargin==4 + test_1=1; + Data_1=varargin{3}; + DataOut_1=Data_1;%default + CalibData_1=varargin{4}; + if isfield(CalibData_1,'GeometryCalib') + Calib{2}=CalibData_1.GeometryCalib; + end +end + +%parameters for polar coordinates (taken from the calibration data of the first field) +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% +origin_xy=[0 0];%center for the polar coordinates in the original x,y coordinates +if isfield(Calib{1},'PolarCentre') && isnumeric(Calib{1}.PolarCentre) + if isequal(length(Calib{1}.PolarCentre),2); + origin_xy= Calib{1}.PolarCentre; + end +end +radius_offset=0;%reference radius used to offset the radial coordinate r +angle_offset=0; %reference angle used as new origin of the polar angle (= axis Ox by default) +if isfield(Calib{1},'PolarReferenceRadius') && isnumeric(Calib{1}.PolarReferenceRadius) + radius_offset=Calib{1}.PolarReferenceRadius; +end +if radius_offset > 0 + angle_scale=radius_offset; %the azimuth is rescale in terms of the length along the reference radius +else + angle_scale=180/pi; %polar angle in degrees +end +if isfield(Calib{1},'PolarReferenceAngle') && isnumeric(Calib{1}.PolarReferenceAngle) + angle_offset=Calib{1}.PolarReferenceAngle; %offset angle (in unit of the final angle, degrees or arc length along the reference radius)) +end +% new x coordinate = radius-radius_offset; +% new y coordinate = theta*angle_scale-angle_offset + +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + +iscalar=0; +if ~isempty(Calib{1}) + DataOut=phys_1(Data,Calib{1},origin_xy,radius_offset,angle_offset,angle_scale); + %case of images or scalar + if isfield(Data,'A')&isfield(Data,'AX')&~isempty(Data.AX) & isfield(Data,'AY')&... + ~isempty(Data.AY)&length(Data.A)>1 + iscalar=1; + A{1}=Data.A; + end + %transform of X,Y coordinates for vector fields + if isfield(Data,'ZIndex')&~isempty(Data.ZIndex) + ZIndex=Data.ZIndex; + else + ZIndex=0; + end +end + +if test_1 + DataOut_1=phys_1(Data_1,Calib{2},origin_xy,radius_offset,angle_offset,angle_scale); + if isfield(Data_1,'A')&isfield(Data_1,'AX')&~isempty(Data_1.AX) & isfield(Data_1,'AY')&... + ~isempty(Data_1.AY)&length(Data_1.A)>1 + iscalar=iscalar+1; + Calib{iscalar}=Calib{2}; + A{iscalar}=Data_1.A; + if isfield(Data_1,'ZIndex')&~isequal(Data_1.ZIndex,ZIndex) + DataOut.Txt='inconsistent plane indexes in the two input fields'; + end + if iscalar==1% case for which only the second field is a scalar + [A,AX,AY]=phys_Ima(A,Calib,ZIndex,origin_xy,radius_offset,angle_offset,angle_scale); + DataOut_1.A=A{1}; + DataOut_1.AX=AX; + DataOut_1.AY=AY; + return + end + end +end +if iscalar~=0 + [A,AX,AY]=phys_Ima(A,Calib,ZIndex,origin_xy,radius_offset,angle_offset,angle_scale);% + DataOut.A=A{1}; + DataOut.AX=AX; + DataOut.AY=AY; + if iscalar==2 + DataOut_1.A=A{2}; + DataOut_1.AX=AX; + DataOut_1.AY=AY; + end +end + +%------------------------------------------------ +function DataOut=phys_1(Data,Calib,origin_xy,radius_offset,angle_offset,angle_scale) + +DataOut=Data; +DataOut.CoordType='phys'; %put flag for physical coordinates +if isfield(Calib,'CoordUnit') + DataOut.CoordUnit=Calib.CoordUnit; +else + DataOut.CoordUnit='cm'; %default +end +DataOut.TimeUnit='s'; +%perform a geometry transform if Calib contains a field .GeometryCalib +if isfield(Data,'CoordType') && isequal(Data.CoordType,'px') && ~isempty(Calib) + if isfield(Data,'CoordUnit') + DataOut=rmfield(DataOut,'CoordUnit'); + end + %transform of X,Y coordinates for vector fields + if isfield(Data,'ZIndex')&~isempty(Data.ZIndex) + Z=Data.ZIndex; + else + Z=0; + end + if isfield(Data,'X') &isfield(Data,'Y')&~isempty(Data.X) & ~isempty(Data.Y) + [DataOut.X,DataOut.Y,DataOut.Z]=phys_XYZ(Calib,Data.X,Data.Y,Z); %transform from pixels to physical + DataOut.X=DataOut.X-origin_xy(1);%origin of coordinates at the tank center + DataOut.Y=DataOut.Y-origin_xy(2);%origin of coordinates at the tank center + [theta,DataOut.X] = cart2pol(DataOut.X,DataOut.Y);%theta and X are the polar coordinates angle and radius + %shift and renormalize the polar coordinates + DataOut.X=DataOut.X-radius_offset;% + DataOut.Y=theta*angle_scale-angle_offset;% normalized angle: distance along reference radius + %transform velocity field if exists + if isfield(Data,'U')&isfield(Data,'V')&~isempty(Data.U) & ~isempty(Data.V)& isfield(Data,'dt') + if ~isempty(Data.dt) + [XOut_1,YOut_1]=phys_XYZ(Calib,Data.X-Data.U/2,Data.Y-Data.V/2,Z); + [XOut_2,YOut_2]=phys_XYZ(Calib,Data.X+Data.U/2,Data.Y+Data.V/2,Z); + UX=(XOut_2-XOut_1)/Data.dt; + VY=(YOut_2-YOut_1)/Data.dt; + %transform u,v into polar coordiantes + DataOut.U=UX.*cos(theta)+VY.*sin(theta);%radial velocity + DataOut.V=(-UX.*sin(theta)+VY.*cos(theta));%./(DataOut.X)%+radius_ref);%angular velocity calculated + %shift and renormalize the angular velocity + end + end + end +end + + +%%%%%%%%%%%%%%%%%%%% +function [A_out,Rangx,Rangy]=phys_Ima(A,CalibIn,ZIndex,origin_xy,radius_offset,angle_offset,angle_scale) +xcorner=[]; +ycorner=[]; +npx=[]; +npy=[]; + +for icell=1:length(A) + siz=size(A{icell}); + npx=[npx siz(2)]; + npy=[npy siz(1)]; + zphys=0; %default + if isfield(CalibIn{icell},'SliceCoord') %.Z= index of plane + SliceCoord=CalibIn{icell}.SliceCoord(ZIndex,:); + zphys=SliceCoord(3); %to generalize for non-parallel planes + end + xima=[0.5 siz(2)-0.5 0.5 siz(2)-0.5];%image coordiantes of corners + yima=[0.5 0.5 siz(1)-0.5 siz(1)-0.5]; + [xcorner_new,ycorner_new]=phys_XYZ(CalibIn{icell},xima,yima,ZIndex);%corresponding physical coordinates + %transform the corner coordinates into polar ones + xcorner_new=xcorner_new-origin_xy(1);%shift to the origin of the polar coordinates + ycorner_new=ycorner_new-origin_xy(2);%shift to the origin of the polar coordinates + [theta,xcorner_new] = cart2pol(xcorner_new,ycorner_new);%theta and X are the polar coordinates angle and radius + if (max(theta)-min(theta))>pi %if the polar origin is inside the image + xcorner_new=[0 max(xcorner_new)]; + theta=[-pi pi]; + end + %shift and renormalize the polar coordinates + xcorner_new=xcorner_new-radius_offset;% + ycorner_new=theta*angle_scale-angle_offset;% normalized angle: distance along reference radius + xcorner=[xcorner xcorner_new]; + ycorner=[ycorner ycorner_new]; +end +Rangx(1)=min(xcorner); +Rangx(2)=max(xcorner); +Rangy(2)=min(ycorner); +Rangy(1)=max(ycorner); +% test_multi=(max(npx)~=min(npx)) | (max(npy)~=min(npy)); +npx=max(npx); +npy=max(npy); +x=linspace(Rangx(1),Rangx(2),npx); +y=linspace(Rangy(1),Rangy(2),npy); +[X,Y]=meshgrid(x,y);%grid in physical coordinates +%transform X, Y in cartesian +X=X+radius_offset;% +Y=(Y+angle_offset)/angle_scale;% normalized angle: distance along reference radius +[X,Y] = pol2cart(Y,X); +X=X+origin_xy(1);%shift to the origin of the polar coordinates +Y=Y+origin_xy(2);%shift to the origin of the polar coordinates +for icell=1:length(A) + [XIMA,YIMA]=px_XYZ(CalibIn{icell},X,Y,zphys);%corresponding image indices for each point in the real space grid + XIMA=reshape(round(XIMA),1,npx*npy);%indices reorganized in 'line' + YIMA=reshape(round(YIMA),1,npx*npy); + flagin=XIMA>=1 & XIMA<=npx & YIMA >=1 & YIMA<=npy;%flagin=1 inside the original image + vec_A=reshape(A{icell}(:,:,1),1,npx*npy);%put the original image in line + ind_in=find(flagin); + ind_out=find(~flagin); + ICOMB=((XIMA-1)*npy+(npy+1-YIMA)); + ICOMB=ICOMB(flagin);%index corresponding to XIMA and YIMA in the aligned original image vec_A + vec_B(ind_in)=vec_A(ICOMB); + vec_B(ind_out)=zeros(size(ind_out)); + A_out{icell}=reshape(vec_B,npy,npx);%new image in real coordinates +end +%Rangx=Rangx-radius_offset; + + Index: /trunk/src/plot_field.m =================================================================== --- /trunk/src/plot_field.m (revision 2) +++ /trunk/src/plot_field.m (revision 2) @@ -0,0 +1,1160 @@ +%'plot_field': plot any field with the structure defined in the uvmat package +%------------------------------------------------------------------------ +% +% This function is used by uvmat to plot fields. It automatically chooses the representation +% appropriate to the input field structure: +% 2D vector fields are represented by arrows, 2D scalar fiedlds by grey scale images or contour plots, 1D fields are represented by usual plot with (abscissa, ordinate). +% The input field structure is first tested by check_field_structure.m, +% then split into blocks of related variables by find_field_indices.m. +% The dimensionality of each block is obtained by this fuction +% considering the presence of variables with the attribute .Role='coord_x' +% and/or coord_y and/or coord_z (case of unstructured coordinates), or +% dimension variables (case of matrices). +% +% function [PlotType,PlotParamOut,haxes]= plot_field(Data,haxes,PlotParam,KeepLim,PosColorbar) +% +% OUPUT: +% PlotType: type of plot: 'text','line'(curve plot),'plane':2D view,'volume' +% PlotParamOut: structure, representing the updated plotting parameters, in case of automatic scaling +% haxes: handle of the plotting axis, when a new figure is created. +% +%INPUT +% Data: structure describing the field to plot +% (optional) .ListGlobalAttribute: cell listing the names of the global attributes +% .Att_1,Att_2... : values of the global attributes +% (requested) .ListVarName: list of variable names to select (cell array of char strings {'VarName1', 'VarName2',...} ) +% (requested) .VarDimName: list of dimension names for each element of .ListVarName (cell array of string cells) +% .VarAttribute: cell of attributes for each element of .ListVarName (cell array of structures of the form VarAtt.key=value) +% (requested) .Var1, .Var2....: variables (Matlab arrays) with names listed in .ListVarName +% +% Variable attribute .Role : +% The only variable attribute used for plotting purpose is .Role which can take +% the values + % Role = 'scalar': (default) represents a scalar field + % = 'coord_x', 'coord_y', 'coord_z': represents a separate set of + % unstructured coordinate x, y or z + % = 'vector': represents a vector field whose number of components + % is given by the last dimension (called 'nb_dim') + % = 'vector_x', 'vector_y', 'vector_z' :represents the x, y or z component of a vector + % = 'warnflag' : provides a warning flag about the quality of data in a 'Field', default=0, no warning + % = 'errorflag': provides an error flag marking false data, + % default=0, no error. Different non zero values can represent different criteria of elimination. + + +% additional elements characterizing the projection object (should not be necessary)-- +% Data.Style : style of projection object +% Data.XObject,.YObject: set of coordinates defining the object position; +% Data.ProjMode=type of projection ; +% Data.ProjAngle=angle of projection; +% Data.DX,.DY,.DZ=increments; +% Data.MaxY,MinY: min and max Y + +% haxes: handle of the plotting axes to update with the new plot. If this input is absent or not a valid axes handle, a new figure is created. +% +% PlotParam: parameters for plotting, as read on the uvmat interface (by function 'read_plot_param.m') +% --scalars-- +% .Scalar.MaxA: upper bound (saturation color) for the scalar representation, max(field) by default +% .Scalar.MinA: lower bound (saturation) for the scalar representation, min(field) by default +% .Scalar.AutoScal: =1 (default) lower and upper bounds of the scalar representation set to the min and max of the field +% =0 lower and upper bound imposed by .AMax and .MinA +% .Scalar.BW= 1 black and white representation imposed, =0 by default. +% .Scalar.Contours= 1: represent scalars by contour plots (Matlab function 'contour'); =0 by default +% .IncrA : contour interval +% -- vectors-- +% .Vectors.VecScale: scale for the vector representation +% .Vectors.AutoVec: =0 (default) automatic length for vector representation, =1: length set by .VecScale +% .Vectors.HideFalse= 0 (default) false vectors represented in magenta, =1: false vectors not represented; +% .Vectors.HideWarning= 0 (default) vectors marked by warnflag~=0 marked in black, 1: no warning representation; +% .Vectors.decimate4 = 0 (default) all vectors reprtesented, =1: half of the vectors represented along each coordinate +% -- vector color-- +% .Vectors.ColorCode= 'black','white': imposed color (default ='blue') +% 'rgb', : three colors red, blue, green depending +% on thresholds .colcode1 and .colcode2 on the input scalar value (C) +% 'brg': like rgb but reversed color order (blue, green, red) +% '64 colors': continuous color from blue to red (multijet) +% .Vectors.colcode1 : first threshold for rgb, first value for'continuous' +% .Vectors.colcode2 : second threshold for rgb, last value (saturation) for 'continuous' +% .Vectors.FixedCbounds; =0 (default): the bounds on C representation are min and max, =1: they are fixed by .Minc and .MaxC +% .Vectors.MinC = imposed minimum of the scalar field used for vector color; +% .Vectors.MaxC = imposed maximum of the scalar field used for vector color; +% +% KeepLim:=0 (default) adjust axes limit to the X,Y data, =1: preserves the previous axes limits +% PosColorbar: if not empty, display a colorbar for B&W images +% imposed position of the colorbar (ex [0.821 0.471 0.019 0.445]) +% +%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +% Copyright Joel Sommeria, 2008, LEGI / CNRS-UJF-INPG, sommeria@coriolis-legi.org. +%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +% This file is part of the toolbox UVMAT. +% +% UVMAT is free software; you can redistribute it and/or modify +% it under the terms of the GNU General Public License as published by +% the Free Software Foundation; either version 2 of the License, or +% (at your option) any later version. +% +% UVMAT is distributed in the hope that it will be useful, +% but WITHOUT ANY WARRANTY; without even the implied warranty of +% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +% GNU General Public License (file UVMAT/COPYING.txt) for more details. +%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA + +function [PlotType,PlotParamOut,haxes]= plot_field(Data,haxes,PlotParam,KeepLim,PosColorbar) +%default output +if ~exist('PlotParam','var'),PlotParam=[];end; +if ~exist('KeepLim','var'),KeepLim=0;end; +if ~exist('PosColorbar','var'),PosColorbar=[];end; +PlotType='text'; %default +PlotParamOut=PlotParam;%default + +% check input structure +[Data,errormsg]=check_field_structure(Data); + +if ~isempty(errormsg) + msgbox_uvmat('ERROR',['input of plot_field/check_field_structure: ' errormsg]) + display(['input of plot_field/check_field_structure:: ' errormsg]) + return +end + +testnewfig=1;%test to create a new figure (default) +testzoomaxes=0;%test for the existence of a zoom secondary figure attached to the plotting axes +if exist('haxes','var') + if ishandle(haxes) + if isequal(get(haxes,'Type'),'axes') +% hfig=get(haxes,'Parent'); + axes(haxes) + testnewfig=0; + AxeData=get(haxes,'UserData'); + if isfield(AxeData,'ZoomAxes')&& ishandle(AxeData.ZoomAxes) + if isequal(get(AxeData.ZoomAxes,'Type'),'axes') + testzoomaxes=1; + zoomaxes=AxeData.ZoomAxes; + end + end + end + end +end +if testnewfig% create a new figure and axes if the plotting axes does not exist + hfig=figure; + if isfield(Data,'IndexObj')&isfield(Data,'Style')&isfield(Data,'ProjMode') + figname=[num2str(Data.IndexObj) '-' set_title(Data.Style,Data.ProjMode)]; + set(hfig,'Name',figname) + end + testhandle=0; + if isfield(PlotParam,'text_display_1')& ishandle(PlotParam.text_display_1) + set(hfig,'UserData',PlotParam) + testhandle=1; + end + set(hfig,'Units','normalized') + set(hfig,'WindowButtonDownFcn','mouse_down') + %set(hfig,'WindowButtonMotionFcn',{'mouse_motion',PlotParam})%set mouse action function + set(hfig,'WindowButtonMotionFcn','mouse_motion')%set mouse action function + set(hfig,'WindowButtonUpFcn','mouse_up')%set mouse action function + haxes=axes; + set(haxes,'position',[0.13,0.2,0.775,0.73]) +end +if isfield(PlotParam,'text_display_1')& ishandle(PlotParam.text_display_1) + PlotParam=read_plot_param(PlotParam); +end +if testnewfig + PlotParam.NextPlot='add'; %parameter for plot_profile and plot_hist +end +if isfield(PlotParam,'Auto_xy') && isequal(PlotParam.Auto_xy,1) + set(haxes,'DataAspectRatioMode','auto')%automatic aspect ratio +end + +% check the cells of fields : +testnbdim=1; +[CellVarIndex,NbDim,VarType,errormsg]=find_field_indices(Data); + +if ~isempty(errormsg) + msgbox_uvmat('ERROR',['input of plot_field/find_field_indices: ' errormsg]) + display(['input of plot_field: ' errormsg]) + return +end +if ~isfield(Data,'NbDim') %& ~isfield(Data,'Style')%determine the space dimensionb if not defined: choose the kind of plot + [Data.NbDim,imax]=max(NbDim); +end +if isequal(Data.NbDim,0) % TODO: chech whether this function is still used, replace by plot_profile ? +% if isfield(Data,'Style') & isequal(Data.Style,'points') + AxeData=plot_text(Data,haxes); + PlotType='text'; +% else +% [AxeData,haxes]=plot_hist(Data,haxes,PlotParam); +% end +elseif isequal(Data.NbDim,1) + [AxeData,haxes]=plot_profile(Data,CellVarIndex,VarType,haxes,PlotParam);% + if testzoomaxes + [AxeData,zoomaxes,PlotParamOut]=plot_profile(Data,CellVarIndex,VarType,zoomaxes,PlotParam); + AxeData.ZoomAxes=zoomaxes; + end + PlotType='line'; +elseif isequal(Data.NbDim,2) + ind_select=find(NbDim>=2); + if numel(ind_select)>2 + msgbox_uvmat('ERROR',['more than two fields to map']) + display(['more than two fields to map']) + return + end + [AxeData,haxes,PlotParamOut,PlotType]=plot_plane(Data,CellVarIndex(ind_select),VarType(ind_select),haxes,PlotParam,KeepLim,PosColorbar); + if testzoomaxes + [AxeData,zoomaxes,PlotParamOut]=plot_plane(Data,CellVarIndex(ind_select),VarType(ind_select),zoomaxes,PlotParam,1,PosColorbar); + AxeData.ZoomAxes=zoomaxes; + end +elseif isequal(Data.NbDim,3) + msgbox_uvmat('ERROR','volume plot not implemented yet') + return + %plot_volume(haxes,Data,PlotParam)% A FAIRE + %PlotType='volume'; +else + testnbdim=0; +end + +%display (or delete) error message +htext=findobj(haxes,'Tag','hTxt'); +if isfield(Data,'Txt') + if isempty(htext) + Xlim=get(haxes,'XLim'); + Ylim=get(haxes,'YLim'); + htext=text(Xlim(1),(Ylim(1)+Ylim(2))/2,Data.Txt,'Tag','hTxt','Color','r'); + set(htext,'Interpreter','none') + else + set(htext,'String',Data.Txt) + end +elseif ~isempty(htext) + delete(htext) +end + +% set graph aspect ratio + + +set(haxes,'UserData',AxeData) +%set(haxes,'Tag','uvmat'); + + +% %------------------------------------------- +% function [AxeData,haxes]=plot_hist(Data,haxes,PlotParam)% TODO: chech whether this function is still used, replace by plot_profile ? +% %------------------------------------------ +% AxeData=get(haxes,'UserData'); %defau +% hfig=get(haxes,'parent'); +% if ~isfield(Data,'ListVarName') +% return +% end +% ColorOrder=[1 0 0;0 0.5 0;0 0 1;0 0.75 0.75;0.75 0 0.75;0.75 0.75 0;0.25 0.25 0.25]; +% set(haxes,'ColorOrder',ColorOrder) +% if isfield(PlotParam,'NextPlot') +% set(haxes,'NextPlot',PlotParam.NextPlot) +% end +% charplot='''-'''; +% iplot=0; +% legend_str={}; +% label_str=''; +% textmean={}; +% plotstr='plot('; +% for ilist=1:length(Data.ListVarName) +% VarName=Data.ListVarName{ilist}; +% eval(['[' VarName 'hist,' VarName 'val]=hist(double(Data.' VarName '),100);']);%coordinate variable set as c +% plotstr=[plotstr VarName 'val,' VarName 'hist,' charplot ',']; +% eval(['nbcomponent2=size(Data.' VarName ',2);']); +% eval(['nbcomponent1=size(Data.' VarName ',1);']); +% eval(['varmean=mean(double(Data.' VarName '));']);%mean value +% textmean=[textmean; {[VarName 'mean= ' num2str(varmean,4)]}]; +% if nbcomponent1==1| nbcomponent2==1 +% legend_str=[legend_str {VarName}]; %variable with one component +% else +% for ic=1:min(nbcomponent1,nbcomponent2) +% legend_str=[legend_str [VarName '_' num2str(ic)]]; %variable with severals components +% % labeled by their index (e.g. color component) +% end +% end +% label_str=[label_str ' ' VarName]; +% end +% if ~isequal(plotstr,'plot(') +% plotstr(end)=')'; +% eval(plotstr) +% hlegend=findobj(hfig,'Tag','legend');%find existing legend on the plot +% if ~isempty(hlegend) +% legend_old=get(hlegend,'String'); +% if isequal(size(legend_old,1),size(legend_str,1)) +% legend_str=[legend_old legend_str]; +% end +% end +% legend(legend_str) +% xlabel(label_str) +% ylabel('nb values') +% grid on +% title_str=''; +% if isfield(Data,'filename') +% [Path, title_str, ext]=fileparts(Data.filename); +% title_str=[title_str ext]; +% end +% if isfield(Data,'Action') +% if ~isequal(title_str,'') +% title_str=[title_str ', ']; +% end +% title_str=[title_str Data.Action]; +% end +% htitle=title(title_str); +% set(htitle,'Interpreter','none')% desable tex interpreter +% hlist=findobj(gcf,'Style','listbox'); +% if isempty(hlist) +% uicontrol('Style','popupmenu','Position',[20 20 200 20],'String',textmean); +% else +% set(hlist(1),'String',textmean) +% end +% end +% AxeData=Data; + + +%---------------------------------------------------------- +function [AxeData,haxes]=plot_profile(data,CellVarIndex,VarType,haxes,PlotParam) +%----------------------------------------------------------- +axes(haxes) +hfig=get(haxes,'parent'); +AxeData=data; +ColorOrder=[1 0 0;0 0.5 0;0 0 1;0 0.75 0.75;0.75 0 0.75;0.75 0.75 0;0.25 0.25 0.25]; +set(haxes,'ColorOrder',ColorOrder) +if isfield(PlotParam,'NextPlot') + set(haxes,'NextPlot',PlotParam.NextPlot) +end +legend_str={}; + +%initiates string of the plot command +plotstr='plot('; +textmean={}; +abscissa_name=''; +coord_x_index=[]; +for icell=1:length(CellVarIndex) + testfalse=0; + VarIndex=CellVarIndex{icell};% indices of the selected variables in the list data.ListVarName + DimCell=data.VarDimName{VarIndex(1)}; + if ischar(DimCell) + DimCell={DimCell}; + end + XName=DimCell{1}; %first dimension considered as abscissa + if ~isempty(VarType{icell}.coord_x) + coord_x_index=VarType{icell}.coord_x; + else + coord_x_index_cell=VarType{icell}.coord(1); + if isequal(coord_x_index_cell,0) + continue % the cell has no abscissa, skip it + end + if ~isempty(coord_x_index)&&~isequal(coord_x_index_cell,coord_x_index) + continue %all the selected variables must have the same first dimension + else + coord_x_index=coord_x_index_cell; + end + end + testplot=ones(size(data.ListVarName));%default test for plotted variables + testcoordvar=0; + charplot_0='''-''';%default + if isfield(data,'ObjectProjMode')& isequal(data.ObjectProjMode,'projection') + charplot_0='''+'''; + end + xtitle=''; + + xtitle=data.ListVarName{coord_x_index}; + eval(['coord_x{icell}=data.' data.ListVarName{coord_x_index} ';']);%coordinate variable set as coord_x + if isfield(data,'VarAttribute')&& numel(data.VarAttribute)>=coord_x_index && isfield(data.VarAttribute{coord_x_index},'units') + xtitle=[xtitle '(' data.VarAttribute{coord_x_index}.units ')']; + end + eval(['coord_x{icell}=data.' data.ListVarName{coord_x_index} ';']);%coordinate variable set as coord_x + testcoordvar=1; + testplot(coord_x_index)=0; + if ~isempty(VarType{icell}.ancillary') + testplot(VarType{icell}.ancillary)=0; + end + if ~isempty(VarType{icell}.warnflag') + testplot(VarType{icell}.warnflag)=0; + end + if ~isempty(VarType{icell}.discrete') + charplot_0='''+'''; + else + charplot_0='''-'''; + end +% if testcoordvar==0 +% coord_x{icell}=[1:data.DimValue(DimIndices(1))];%abscissa by default if no coordinate variable +% % charplot_0='''-'''; +% end + if isfield(data,'VarAttribute') + VarAttribute=data.VarAttribute; + for ivar=1:length(VarIndex) + if length(VarAttribute)>=VarIndex(ivar) & isfield(VarAttribute{VarIndex(ivar)},'long_name') + plotname{VarIndex(ivar)}=VarAttribute{VarIndex(ivar)}.long_name; + else + plotname{VarIndex(ivar)}=data.ListVarName{VarIndex(ivar)};%name for display in plot A METTRE + end + end + end + for ivar=1:length(VarIndex) + if testplot(VarIndex(ivar)) + VarName=data.ListVarName{VarIndex(ivar)}; + eval(['data.' VarName '=squeeze(data.' VarName ');']) + if isequal(VarName,'A') + charplot='''-'''; + else + charplot=charplot_0; + end + plotstr=[plotstr 'coord_x{' num2str(icell) '},data.' VarName ',' charplot ',']; + eval(['nbcomponent2=size(data.' VarName ',2);']); + eval(['nbcomponent1=size(data.' VarName ',1);']); + if numel(coord_x{icell})==2 + coord_x{icell}=linspace(coord_x{icell}(1),coord_x{icell}(2),nbcomponent1); + end + eval(['varmean=mean(double(data.' VarName '));']);%mean value + textmean=[textmean; {[VarName 'mean= ' num2str(varmean,4)]}]; + if nbcomponent1==1| nbcomponent2==1 + legend_str=[legend_str {VarName}]; %variable with one component + else %variable with severals components + for ic=1:min(nbcomponent1,nbcomponent2) + legend_str=[legend_str [VarName '_' num2str(ic)]]; %variable with severals components + end % labeled by their index (e.g. color component) + end + end + end +end +if ~isequal(plotstr,'plot(') + plotstr(end)=')'; + %execute plot (instruction plotstr) + eval(plotstr) + %%%%% + grid on + hxlabel=xlabel(xtitle); + set(hxlabel,'Interpreter','none')% desable tex interpreter + if length(legend_str)>=1 + hylabel=ylabel(legend_str{end}); + set(hylabel,'Interpreter','none')% desable tex interpreter + end + if ~isempty(legend_str) + hlegend=findobj(hfig,'Tag','legend'); + if isempty(hlegend) + hlegend=legend(legend_str); + txt=ver; + Release=txt(1).Release; + relnumb=str2num(Release(3:4)); + if relnumb >= 14 + set(hlegend,'Interpreter','none')% desable tex interpreter + end + else + legend_old=get(hlegend,'String'); + if isequal(size(legend_old,1),size(legend_str,1))&~isequal(legend_old,legend_str) + set(hlegend,'String',[legend_old legend_str]); + end + end + end + title_str=''; + if isfield(data,'filename') + [Path, title_str, ext]=fileparts(data.filename); + title_str=[title_str ext]; + end + if isfield(data,'Action') + if ~isequal(title_str,'') + title_str=[title_str ', ']; + end + title_str=[title_str data.Action]; + end + htitle=title(title_str); + txt=ver; + Release=txt(1).Release; + relnumb=str2num(Release(3:4)); + if relnumb >= 14 + set(htitle,'Interpreter','none')% desable tex interpreter + end + % A REPRENDRE Mean +% hlist=findobj(gcf,'Style','listbox','Tag','liststat'); +% if isempty(hlist) +% 'text' +% textmean +% set(gca,'position',[0.13,0.2,0.775,0.73]) +% uicontrol('Style','popupmenu','Position',[20 20 200 20],'String',textmean,'Tag','liststat'); +% else +% set(hlist(1),'String',textmean) +% end +end + + +%--------------------------------------- +% plot_plane +%---------------------------------------- +function [AxeData,haxes,PlotParamOut,PlotType]=plot_plane(Data,CellVarIndex,VarTypeCell,haxes,PlotParam,KeepLim,PosColorbar) + +%default plotting parameters +PlotType='plane';%default +if ~exist('PlotParam','var') + PlotParam=[]; +end +if ~isfield(PlotParam,'Scalar') + PlotParam.Scalar=[]; +end +if ~isfield(PlotParam,'Vectors') + PlotParam.Vectors=[]; +end +PlotParamOut=PlotParam;%default + +%plotting axes +hfig=get(haxes,'parent'); +hcol=findobj(hfig,'Tag','Colorbar'); %look for colorbar axes +hima=findobj(haxes,'Tag','ima');% search existing image in the current axes +AxeData=get(haxes,'UserData'); %default +if ~isstruct(AxeData)% AxeData must be a structure + AxeData=[]; +end +AxeData.NbDim=2; +if isfield(Data,'ObjectCoord') + AxeData.ObjectCoord=Data.ObjectCoord; +end + +test_ima=0; %default: test for image or map plot +test_vec=0; %default: test for vector plots +test_black=0; +test_false=0; +test_C=0; +XName=''; +x_units=''; +YName=''; +y_units=''; +for icell=1:length(CellVarIndex) % length(CellVarIndex) =1 or 2 (from the calling function) +% VarIndex=CellVarIndex{icell}; + VarType=VarTypeCell{icell}; + ivar_X=VarType.coord_x; % defines (unique) index for the variable representing unstructured x coordinate (default =[]) + ivar_Y=VarType.coord_y; % defines (unique)index for the variable representing unstructured y coordinate (default =[]) + ivar_U=VarType.vector_x; % defines (unique) index for the variable representing x vector component (default =[]) + ivar_V=VarType.vector_y; % defines (unique) index for the variable representing y vector component (default =[]) + ivar_C=[VarType.scalar VarType.image VarType.color VarType.ancillary]; %defines index (indices) for the scalar or ancillary fields + if numel(ivar_C)>1 + msgbox_uvmat('ERROR','error in plot_field: too many scalar inputs') + return + end + ivar_F=VarType.warnflag; %defines index (unique) for warning flag variable + ivar_FF=VarType.errorflag; %defines index (unique) for error flag variable + ind_coord=find(VarType.coord); + if numel(ind_coord)==2 + VarType.coord=VarType.coord(ind_coord); + end + idim_Y=[]; + test_grid=0; + if ~isempty(ivar_U) && ~isempty(ivar_V)% vector components detected + if test_vec + msgbox_uvmat('ERROR','error in plot_field: attempt to plot two vector fields') + return + else + test_vec=1; + eval(['vec_U=Data.' Data.ListVarName{ivar_U} ';']) + eval(['vec_V=Data.' Data.ListVarName{ivar_V} ';']) + if ~isempty(ivar_X) && ~isempty(ivar_Y)% 2D field (with unstructured coordinates or structured ones (then ivar_X and ivar_Y empty) + eval(['vec_X=Data.' Data.ListVarName{ivar_X} ';']) + eval(['vec_Y=Data.' Data.ListVarName{ivar_Y} ';']) + elseif numel(VarType.coord)==2 & VarType.coord~=[0 0];%coordinates defines by dimension variables + eval(['y=Data.' Data.ListVarName{VarType.coord(1)} ';']) + eval(['x=Data.' Data.ListVarName{VarType.coord(2)} ';']) + if numel(y)==2 % y defined by first and last values on aregular mesh + y=linspace(y(1),y(2),size(vec_U,1)); + end + if numel(x)==2 % y defined by first and last values on aregular mesh + x=linspace(x(1),x(2),size(vec_U,2)); + end + [vec_X,vec_Y]=meshgrid(x,y); + else + msgbox_uvmat('ERROR','error in plot_field: invalid coordinate definition for vector field') + return + end + if ~isempty(ivar_C) + eval(['vec_C=Data.' Data.ListVarName{ivar_C} ';']) ; + vec_C=reshape(vec_C,1,numel(vec_C)); + test_C=1; + end + if ~isempty(ivar_F)%~(isfield(PlotParam.Vectors,'HideWarning')&& isequal(PlotParam.Vectors.HideWarning,1)) + if test_vec + eval(['vec_F=Data.' Data.ListVarName{ivar_F} ';']) % warning flags for dubious vectors + if ~(isfield(PlotParam.Vectors,'HideWarning') && isequal(PlotParam.Vectors.HideWarning,1)) + test_black=1; + end + end + end + if ~isempty(ivar_FF) %&& ~test_false + if test_vec% TODO: deal with FF for structured coordinates + eval(['vec_FF=Data.' Data.ListVarName{ivar_FF} ';']) % flags for false vectors + end + end + end + elseif ~isempty(ivar_C) %scalar or image + if test_ima + msgbox_uvmat('ERROR','attempt to plot two scalar fields or images') + return + end + eval(['A=squeeze(Data.' Data.ListVarName{ivar_C} ');']) ;% scalar represented as color image + test_ima=1; + if ~isempty(ivar_X) && ~isempty(ivar_Y)% 2D field (with unstructured coordinates or structured ones (then ivar_X and ivar_Y empty) + XName=Data.ListVarName{ivar_X}; + YName=Data.ListVarName{ivar_Y}; + eval(['AX=Data.' XName ';']) + eval(['AY=Data.' YName ';']) + [A,AX,AY]=proj_grid(AX',AY',A',[],[],'np>256'); % interpolate on a grid + if isfield(Data,'VarAttribute') + if numel(Data.VarAttribute)>=ivar_X & isfield(Data.VarAttribute{ivar_X},'units') + x_units=['(' Data.VarAttribute{ivar_X}.units ')']; + end + if numel(Data.VarAttribute)>=ivar_Y & isfield(Data.VarAttribute{ivar_Y},'units') + y_units=['(' Data.VarAttribute{ivar_Y}.units ')']; + end + end + elseif numel(VarType.coord)==2 %structured coordinates + XName=Data.ListVarName{VarType.coord(2)}; + YName=Data.ListVarName{VarType.coord(1)}; + eval(['AY=Data.' Data.ListVarName{VarType.coord(1)} ';']) + eval(['AX=Data.' Data.ListVarName{VarType.coord(2)} ';']) + test_interp_X=0; %default, regularly meshed X coordinate + test_interp_Y=0; %default, regularly meshed Y coordinate + if isfield(Data,'VarAttribute') + if numel(Data.VarAttribute)>=VarType.coord(2) & isfield(Data.VarAttribute{VarType.coord(2)},'units') + x_units=['(' Data.VarAttribute{VarType.coord(2)}.units ')']; + end + if numel(Data.VarAttribute)>=VarType.coord(1) & isfield(Data.VarAttribute{VarType.coord(1)},'units') + y_units=['(' Data.VarAttribute{VarType.coord(1)}.units ')']; + end + end + if numel(AY)>2 + DAY=diff(AY); + DAY_min=min(DAY); + DAY_max=max(DAY); + if sign(DAY_min)~=sign(DAY_max);% =1 for increasing values, 0 otherwise + errormsg=['errror in plot_field.m: non monotonic dimension variable # ' ListVarName{VarType.coord(1)} ]; + return + end + test_interp_Y=(DAY_max-DAY_min)> 0.0001*abs(DAY_max); + end + if numel(AX)>2 + DAX=diff(AX); + DAX_min=min(DAX); + DAX_max=max(DAX); + if sign(DAX_min)~=sign(DAX_max);% =1 for increasing values, 0 otherwise + errormsg=['errror in plot_field.m: non monotonic dimension variable # ' ListVarName{VarType.coord(2)} ]; + return + end + test_interp_X=(DAX_max-DAX_min)> 0.0001*abs(DAX_max); + end + if test_interp_Y + npxy(1)=max([256 floor((AY(end)-AY(1))/DAY_min) floor((AY(end)-AY(1))/DAY_max)]); + yI=linspace(AY(1),AY(end),npxy(1)); + if ~test_interp_X + xI=linspace(AX(1),AX(end),size(A,2));%default + AX=xI; + end + end + if test_interp_X + npxy(1)=max([256 floor((AX(end)-AX(1))/DAX_min) floor((AX(end)-AX(1))/DAX_max)]); + xI=linspace(AX(1),AX(end),npxy(2)); + if ~test_interp_Y + yI=linspace(AY(1),AY(end),size(A,1)); + AY=yI; + end + end + if test_interp_X || test_interp_Y + [AX2D,AY2D]=meshgrid(AX,AY); + A=interp2(AX2D,AY2D,double(A),xI,yI'); + end + AX=[AX(1) AX(end)];% keep only the lower and upper bounds for image represnetation + AY=[AY(1) AY(end)]; + else + msgbox_uvmat('ERROR','error in plot_field: invalid coordinate definition ') + return + end + x_label=[Data.ListVarName{ivar_X} '(' x_units ')']; + end +% if isfield(Data,'VarAttribute') +% VarAttribute=Data.VarAttribute; +% end +end + +%%%%%%%%%%%%%%%%%%%%% image or scalar plot %%%%%%%%%%%%%%%%%%%%%%%%%% + +if ~isfield(PlotParam.Scalar,'Contours') + PlotParam.Scalar.Contours=0; %default +end +PlotParamOut=PlotParam; %default +if test_ima + % distinguish B/W and color images + np=size(A);%size of image + siz=size(np); + %set the color map + if siz(2)==2 %for black and white images + if ~isfield(PlotParam.Scalar,'AutoScal') + PlotParam.Scalar.AutoScal=0;%default + end + if ~isfield(PlotParam.Scalar,'MinA') + PlotParam.Scalar.MinA=[];%default + end + if ~isfield(PlotParam.Scalar,'MaxA') + PlotParam.Scalar.MaxA=[];%default + end + if isequal(PlotParam.Scalar.AutoScal,0)|isempty(PlotParam.Scalar.MinA)|~isa(PlotParam.Scalar.MinA,'double') %correct if there is no numerical data in edit box + MinA=double(min(min(A))); + else + MinA=PlotParam.Scalar.MinA; + end; + if isequal(PlotParam.Scalar.AutoScal,0)|isempty(PlotParam.Scalar.MaxA)|~isa(PlotParam.Scalar.MaxA,'double') %correct if there is no numerical data in edit box + MaxA=double(max(max(A))); + else + MaxA=PlotParam.Scalar.MaxA; + end; + PlotParamOut.Scalar.MinA=MinA; + PlotParamOut.Scalar.MaxA=MaxA; + axes(haxes) + if isequal(PlotParam.Scalar.Contours,1) + if ~isempty(hima) & ishandle(hima) + delete(hima) + end + if ~isfield(PlotParam.Scalar,'IncrA') + PlotParam.Scalar.IncrA=[]; + end + if isempty(PlotParam.Scalar.IncrA)% | PlotParam.Scalar.AutoScal==0 + cont=colbartick(MinA,MaxA); + intercont=cont(2)-cont(1);%default + PlotParamOut.Scalar.IncrA=intercont; + else + intercont=PlotParam.Scalar.IncrA; + end + B=A; + abscontmin=intercont*floor(MinA/intercont); + abscontmax=intercont*ceil(MaxA/intercont); + contmin=intercont*floor(min(min(B))/intercont); + contmax=intercont*ceil(max(max(B))/intercont); + cont_pos_plus=[0:intercont:contmax]; + cont_pos_min=[double(contmin):intercont:-intercont]; + cont_pos=[cont_pos_min cont_pos_plus]; + sizpx=(AX(end)-AX(1))/(np(2)-1); + sizpy=(AY(1)-AY(end))/(np(1)-1); + x_cont=[AX(1):sizpx:AX(end)]; % pixel x coordinates for image display + y_cont=[AY(1):-sizpy:AY(end)]; % pixel x coordinates for image display + txt=ver;%version of Matlab + Release=txt(1).Release; + relnumb=str2num(Release(3:4)); + if relnumb >= 14 + vec=linspace(0,1,(abscontmax-abscontmin)/intercont);%define a greyscale colormap with steps intercont + map=[vec' vec' vec']; + colormap(map); + [var,hcontour]=contour(x_cont,y_cont,B,cont_pos); + set(hcontour,'Fill','on') + set(hcontour,'LineStyle','none') + hold on + end + [var_p,hcontour_p]=contour(x_cont,y_cont,B,cont_pos_plus,'k-'); + hold on + [var_m,hcontour_m]=contour(x_cont,y_cont,B,cont_pos_min,':'); + set(hcontour_m,'LineColor',[1 1 1]) + hold off + caxis([abscontmin abscontmax]) + colormap(map); + end + if ~isequal(PlotParam.Scalar.Contours,1) + % rescale the grey levels with min and max, put a grey scale colorbar + if (isfield(PlotParam.Scalar,'BW')& (isequal(PlotParam.Scalar.BW,1))|isa(A,'uint8')| isa(A,'uint16'))%images + B=A; + vec=linspace(0,1,255);%define a linear greyscale colormap + map=[vec' vec' vec']; + colormap(map); %grey scale color map + else + B=A; + colormap('default'); % standard faulse colors for div, vort , scalar fields + end + end + elseif siz(2)==3 %color images + axes(haxes) + B=uint8(A); + MinA=0; + MaxA=255; + end + if ~isequal(PlotParam.Scalar.Contours,1) + %interpolate to increase resolution + test_interp=1; + if max(np) <= 64 + npxy=8*np;% increase the resolution 8 times + elseif max(np) <= 128 + npxy=4*np;% increase the resolution 4 times + elseif max(np) <= 256 + npxy=2*np;% increase the resolution 2 times + else + npxy=np; + test_interp=0; % no interpolation done + end + if test_interp==1%if we interpolate + x=linspace(AX(1),AX(2),np(2)); + y=linspace(AY(1),AY(2),np(1)); + [X,Y]=meshgrid(x,y); + xi=linspace(AX(1),AX(2),npxy(2)); + yi=linspace(AY(1),AY(2),npxy(1)); + B = interp2(X,Y,double(B),xi,yi'); + end + if isempty(hima) + tag=get(haxes,'Tag'); + hima=imagesc(AX,AY,B,[MinA MaxA]); + set(hima,'Tag','ima','HitTest','off') + set(haxes,'Tag',tag);%preserve the axes tag (removed by image fct !!!) + else + set(hima,'CData',B); + if MinAMinA + if isequal(PlotParam.Scalar.Contours,1) + colbarlim=get(hcol,'YLim'); + scale_bar=(colbarlim(2)-colbarlim(1))/(abscontmax-abscontmin); + YTick=cont_pos(2:end-1); + YTick_scaled=colbarlim(1)+scale_bar*(YTick-abscontmin); + set(hcol,'YTick',YTick_scaled); + elseif (isfield(PlotParam.Scalar,'BW') & isequal(PlotParam.Scalar.BW,1))|isa(A,'uint8')| isa(A,'uint16')%images + hi=get(hcol,'children'); + if iscell(hi)%multiple images in colorbar + hi=hi{1}; + end + set(hi,'YData',[MinA MaxA]) + set(hi,'CData',[1:256]') + set(hcol,'YLim',[MinA MaxA]) + YTick=colbartick(MinA,MaxA); + set(hcol,'YTick',YTick) + else + hi=get(hcol,'children'); + if iscell(hi)%multiple images in colorbar + hi=hi{1}; + end + set(hi,'YData',[MinA MaxA]) + set(hi,'CData',[1:64]') + YTick=colbartick(MinA,MaxA); + set(hcol,'YLim',[MinA MaxA]) + set(hcol,'YTick',YTick) + end + set(hcol,'Yticklabel',num2str(YTick')); + end + elseif ishandle(hcol) + delete(hcol); %erase existing colorbar if not needed + end +else%no scalar plot + if ~isempty(hima) && ishandle(hima) + delete(hima) + end + if ~isempty(hcol)&& ishandle(hcol) + delete(hcol) + end + AxeData.A=[]; + AxeData.AX=[]; + AxeData.AY=[]; + PlotParamOut=rmfield(PlotParamOut,'Scalar'); +end + +%%%%%%%%%%%%%%%%%%%%% vector plot %%%%%%%%%%%%%%%%%%%%%%%%%% +if test_vec + %vector scale representation + if size(vec_U,1)==numel(vec_Y) && size(vec_U,2)==numel(vec_X); % x, y coordinate variables + [vec_X,vec_Y]=meshgrid(vec_X,vec_Y); + end + vec_X=reshape(vec_X,1,numel(vec_X));%reshape in matlab vectors + vec_Y=reshape(vec_Y,1,numel(vec_Y)); + vec_U=reshape(vec_U,1,numel(vec_U)); + vec_V=reshape(vec_V,1,numel(vec_V)); + MinMaxX=max(vec_X)-min(vec_X); + MinMaxY=max(vec_Y)-min(vec_Y); + AxeData.Mesh=sqrt((MinMaxX*MinMaxY)/length(vec_X)); + if ~isfield(PlotParam.Vectors,'AutoVec') || isequal(PlotParam.Vectors.AutoVec,0)|| ~isfield(PlotParam.Vectors,'VecScale')... + ||isempty(PlotParam.Vectors.VecScale)||~isa(PlotParam.Vectors.VecScale,'double') %automatic vector scale + scale=[]; + if test_false %remove false vectors + indsel=find(AxeData.FF==0);%indsel =indices of good vectors + else + indsel=[1:numel(vec_X)];% + end + if isempty(vec_U) + scale=1; + else + if isempty(indsel) + MaxU=max(abs(vec_U)); + MaxV=max(abs(vec_V)); + else + MaxU=max(abs(vec_U(indsel))); + MaxV=max(abs(vec_V(indsel))); + end + scale=MinMaxX/(max(MaxU,MaxV)*50); + PlotParam.Vectors.VecScale=scale;%update the 'scale' display + end + else + scale=PlotParam.Vectors.VecScale; %impose the length of vector representation + end; + + %record vectors on the plotting axes + if test_C==0 + vec_C=ones(1,numel(vec_X)); + end + AxeData.X=vec_X'; + AxeData.Y=vec_Y'; + AxeData.U=vec_U'; + AxeData.V=vec_V'; + AxeData.C=vec_C'; + if isempty(ivar_F) + AxeData.F=[]; + else + AxeData.F=vec_F'; + end + if isempty(ivar_FF) + AxeData.FF=[]; + else + AxeData.FF=vec_FF'; + end +% if isfield(Data,'W') +% AxeData.W=Data.W; +% end + + %decimate by a factor 2 in vector mesh(4 in nbre of vectors) + if isfield(PlotParam.Vectors,'decimate4')&isequal(PlotParam.Vectors.decimate4,1) + diffy=diff(vec_Y); %difference dy=vec_Y(i+1)-vec_Y(i) + dy_thresh=max(abs(diffy))/2; + ind_jump=find(abs(diffy) > dy_thresh); %indices with diff(vec_Y)> max/2, detect change of line + ind_sel=[1:ind_jump(1)];%select the first line + for i=2:2:length(ind_jump)-1 + ind_sel=[ind_sel [ind_jump(i)+1:ind_jump(i+1)]];% select the odd lines + end + nb_sel=length(ind_sel); + ind_sel=ind_sel([1:2:nb_sel]);% take half the points on a line + vec_X=vec_X(ind_sel); + vec_Y=vec_Y(ind_sel); + vec_U=vec_U(ind_sel); + vec_V=vec_V(ind_sel); + vec_C=vec_C(ind_sel); + if ~isempty(ivar_F) + vec_F=vec_F(ind_sel); + end + if ~isempty(ivar_FF) + vec_FF=vec_FF(ind_sel); + end + end + + %get main level color code + [colorlist,col_vec,PlotParamOut.Vectors]=set_col_vec(PlotParam.Vectors,vec_C); + % take flags into account: add flag colors to the list of colors + sizlist=size(colorlist); + nbcolor=sizlist(1); + if test_black + nbcolor=nbcolor+1; + colorlist(nbcolor,:)=[0 0 0]; %add black to the list of colors + if ~isempty(ivar_FF) + ind_flag=find(vec_F~=1 & vec_FF==0); %flag warning but not false + else + ind_flag=find(vec_F~=1); + end + col_vec(ind_flag)=nbcolor; + end + nbcolor=nbcolor+1; + if ~isempty(ivar_FF) + ind_flag=find(vec_FF~=0); + if isfield(PlotParam.Vectors,'HideFalse') && PlotParam.Vectors.HideFalse==1 + colorlist(nbcolor,:)=[NaN NaN NaN];% no plot of false vectors + else + colorlist(nbcolor,:)=[1 0 1];% magenta color + end + col_vec(ind_flag)=nbcolor; + end + %plot vectors: + quiresetn(haxes,vec_X,vec_Y,vec_U,vec_V,scale,colorlist,col_vec); +else + hvec=findobj(haxes,'Tag','vel'); + if ~isempty(hvec) + delete(hvec); + end + AxeData.X=[]; + AxeData.Y=[]; + AxeData.U=[]; + AxeData.V=[]; + AxeData.C=[]; + AxeData.W=[]; + AxeData.F=[]; + AxeData.FF=[]; + AxeData.Mesh=[]; + PlotParamOut=rmfield(PlotParamOut,'Vectors'); +end +if isfield(Data,'Z') + AxeData.Z=Data.Z;% A REVOIR +end +listfields={'AY','AX','A','X','Y','U','V','C','W','F','FF'}; +listdim={'AY','AX',{'AY','AX'},'nb_vectors','nb_vectors','nb_vectors','nb_vectors','nb_vectors','nb_vectors','nb_vectors','nb_vectors'}; +Role={'coord_y','coord_x','scalar','coord_x','coord_y','vector_x','vector_y','scalar','vector_z','warnflag','errorflag'}; +ind_select=[]; +nbvar=0; +AxeData.ListVarName={}; +AxeData.VarDimName={}; +AxeData.VarAttribute={}; +for ilist=1:numel(listfields) + eval(['testvar=isfield(AxeData,listfields{ilist}) && ~isempty(AxeData.' listfields{ilist} ');']) + if testvar + nbvar=nbvar+1; + AxeData.ListVarName{nbvar}=listfields{ilist}; + AxeData.VarDimName{nbvar}=listdim{ilist}; + AxeData.VarAttribute{nbvar}.Role=Role{ilist}; + end +end + +% adjust the size of the plot to include the whole field, except if KeepLim=1 +if ~(exist('KeepLim','var') && isequal(KeepLim,1)) %adjust the graph limits* + test_lim=0; + if test_vec + Xlim=[min(vec_X) max(vec_X)]; + Ylim=[min(vec_Y) max(vec_Y)]; + test_lim=1; + if test_ima%both background image and vectors coexist, take the wider bound + Xlim(1)=min(AX(1),Xlim(1)); + Xlim(2)=max(AX(end),Xlim(2)); + Ylim(1)=min(AY(end),Ylim(1)); + Ylim(2)=max(AY(1),Ylim(2)); + end + elseif test_ima %only image plot + Xlim(1)=min(AX(1),AX(end)); + Xlim(2)=max(AX(1),AX(end)); + Ylim(1)=min(AY(1),AY(end)); + Ylim(2)=max(AY(1),AY(end)); + test_lim=1; + end + if test_lim + set(haxes,'XLim',Xlim);% set x limits of frame in axes coordinates + set(haxes,'YLim',Ylim);% set y limits of frame in axes coordinate + end +end +if ~(isfield(PlotParam,'Auto_xy') && isequal(PlotParam.Auto_xy,1)) + set(haxes,'DataAspectRatio',[1 1 1]) +end +set(haxes,'YDir','normal') +set(get(haxes,'XLabel'),'String',[XName x_units]); +set(get(haxes,'YLabel'),'String',[YName y_units]); +%--------------------------------------------- +%function for plotting vectors +%------------------------------------------------ +%INPUT: +% haxes: handles of the plotting axes +%x,y,u,v: vectors coordinates and vector components to plot, arrays withb the same dimension +% scale: scaling factor for vector length representation +%colorlist(icolor,:): list of vector colors, dim (nbcolor,3), depending on color #i +%col_vec: matlab vector setting the color number #i for each velocity vector +function quiresetn(haxes,x,y,u,v,scale,colorlist,col_vec) + +%define arrows +theta=0.5 ;%angle arrow +alpha=0.3 ;%length arrow +rot=alpha*[cos(theta) -sin(theta); sin(theta) cos(theta)]'; +%find the existing lines +%h=findobj(gca,'Type','Line');% search existing lines in the current axes +h=findobj(haxes,'Tag','vel');% search existing lines in the current axes +sizh=size(h); +set(h,'EraseMode','xor'); +set(haxes,'NextPlot','replacechildren'); +%htext=findobj('Tag','scalevec'); + +%drawnow +%create lines (if no lines) or modify them +if ~isequal(size(col_vec),size(x)) + col_vec=ones(size(x));% case of error in col_vec input +end +sizlist=size(colorlist); +ncolor=sizlist(1); + +for icolor=1:ncolor + %determine the line positions for each color icolor + ind=find(col_vec==icolor); + xc=x(ind); + yc=y(ind); + uc=u(ind)*scale; + vc=v(ind)*scale; + n=size(xc); + xN=NaN*ones(size(xc)); + matx=[xc(:) xc(:)+uc(:) xN(:)]'; + matx=reshape(matx,1,3*n(2)); + maty=[yc(:) yc(:)+vc(:) xN(:)]'; + maty=reshape(maty,1,3*n(2)); + + %determine arrow heads + arrowplus=rot*[uc;vc]; + arrowmoins=rot'*[uc;vc]; + x1=xc+uc-arrowplus(1,:); + x2=xc+uc; + x3=xc+uc-arrowmoins(1,:); + y1=yc+vc-arrowplus(2,:); + y2=yc+vc; + y3=yc+vc-arrowmoins(2,:); + matxar=[x1(:) x2(:) x3(:) xN(:)]'; + matxar=reshape(matxar,1,4*n(2)); + matyar=[y1(:) y2(:) y3(:) xN(:)]'; + matyar=reshape(matyar,1,4*n(2)); + %draw the line or modify the existing ones + isn=isnan(colorlist(icolor,:));%test if color NaN + if 2*icolor > sizh(1) %if icolor exceeds the number of existing ones + axes(haxes) + if ~isn(1) %if the vectors are visible color not nan + if n(2)>0 + hold on + line(matx,maty,'Color',colorlist(icolor,:),'Tag','vel');% plot new lines + line(matxar,matyar,'Color',colorlist(icolor,:),'Tag','vel');% plot arrows + end + end + else + if isn(1) + delete(h(2*icolor-1)) + delete(h(2*icolor)) + else + set(h(2*icolor-1),'Xdata',matx,'Ydata',maty); + set(h(2*icolor-1),'Color',colorlist(icolor,:)); + set(h(2*icolor-1),'EraseMode','xor'); + set(h(2*icolor),'Xdata',matxar,'Ydata',matyar); + set(h(2*icolor),'Color',colorlist(icolor,:)); + set(h(2*icolor),'EraseMode','xor'); + end + end +end +if sizh(1) > 2*ncolor + for icolor=ncolor+1 : sizh(1)/2%delete additional objects + delete(h(2*icolor-1)) + delete(h(2*icolor)) + end +end + +%--------------------------------------- +%determine tick positions for colorbar +%------------------------------------ +function YTick=colbartick(MinA,MaxA) +%determine tick positions with "simple" values between MinA and MaxA +YTick=0;%default +maxabs=max([abs(MinA) abs(MaxA)]); +if maxabs>0 +ord=10^(floor(log10(maxabs)));%order of magnitude +div=1; +siz2=1; +while siz2<2 +% values=[-9:div:9]; + values=-10:div:10; + ind=find((ord*values-MaxA)<0 & (ord*values-MinA)>0);%indices of 'values' such that MinA0); + end + siz2=size(ind,2); +% siz2=siz(2) + div=div/10; +end +YTick=ord*values(ind); +end Index: /trunk/src/plot_object.m =================================================================== --- /trunk/src/plot_object.m (revision 2) +++ /trunk/src/plot_object.m (revision 2) @@ -0,0 +1,408 @@ +%'plot_object': draws a projection object (points, line, plane...) +%------------------------------------------------------------------- +% function [ObjectData_out,hh]=plot_object(ObjectData,hplot,col) +% +%OUTPUT +% hh: handles of the graphic object (core part) +% +%INPUT: +% +% ObjectDataIn: structure representing the object properties: +% .Style : style of projection object +% .Coord: set of coordinates defining the object position; +% .ProjMode=type of projection ; +% .ProjAngle=angle of projection; +% .DX,.DY,.DZ=increments; +% .YMax,YMin: min and max Y +% ProjObject: projection object corresponding to the current plot (e. g. plane) +% hplot: handle of the object plot to modify or if it is an axis, the axis +% where the object must be plotted, or if it is a figure the plotting figure +% col: color of the plot, e;g; 'm', 'b' ..; + +%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +% Copyright Joel Sommeria, 2008, LEGI / CNRS-UJF-INPG, sommeria@coriolis-legi.org. +%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +% This file is part of the toolbox UVMAT. +% +% UVMAT is free software; you can redistribute it and/or modify +% it under the terms of the GNU General Public License as published by +% the Free Software Foundation; either version 2 of the License, or +% (at your option) any later version. +% +% UVMAT is distributed in the hope that it will be useful, +% but WITHOUT ANY WARRANTY; without even the implied warranty of +% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +% GNU General Public License (file UVMAT/COPYING.txt) for more details. +%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA + +function [hh]=plot_object(ObjectDataIn,ProjObject,hplot,col) +hh=[];%default output +if isequal(ProjObject,ObjectDataIn)% object representation does not appear in its own projection plot + return +end +if ~isfield(ProjObject,'Style') + ObjectData=ObjectDataIn; +elseif isequal(ProjObject.Style,'plane') + ObjectData=ObjectDataIn;% TODO: modify take into account rotation of axis +else + return % no object representation yet available +end +if ~isfield(ObjectData,'Style')|isempty(ObjectData.Style)|~ischar(ObjectData.Style) + warndlg_uvmat('undefined ObjectData.Style in plot_object.m','ERROR') + return +end +if ~isfield(ObjectData,'Style')|isempty(ObjectData.Style)|~ischar(ObjectData.Style) + warndlg_uvmat('undefined ObjectData.Style in plot_object.m','ERROR') + return +end +XMin=0;%default +XMax=0; +YMin=0; +YMax=0; +ZMin=0; +ZMax=0; + +%determine the plotting axes (with handle 'haxes') +test_newobj=1; +if ishandle(hplot) + if isequal(get(hplot,'Tag'),'proj_object') + test_newobj=0; + haxes=get(hplot,'parent'); + elseif isequal(get(hplot,'Type'),'axes') + axes(hplot) + haxes=hplot; + elseif isequal(get(hplot,'Type'),'figure') + figure(hplot);%set the input figure as the current one + haxes=findobj(hplot,'Type','axes');%look for axes in the figure + haxes=haxes(1); + axes(haxes); %set the first found axis as the current one + else + figure; %create new figure + hplot=axes;%create new axes + haxes=hplot; + end +else + figure; %create new figure + hplot=axes;%create new axes + haxes=hplot; +end + +%default input parameters +if ~isfield(ObjectData,'ProjMode')|isempty(ObjectData.ProjMode) + ObjectData.ProjMode='projection';%default +end +if ~isfield(ObjectData,'Coord')|isempty(ObjectData.Coord) + ObjectData.Coord=[0 0 0];%default +end +if ~isfield(ObjectData,'Phi')|isempty(ObjectData.Phi) + ObjectData.Phi=0;%default +end +if ~isfield(ObjectData,'Range') + ObjectData.Range(1,1)=0; %edfault +end +if size(ObjectData.Range,2)>=2 + YMax=ObjectData.Range(1,2);%default +end +if size(ObjectData.Range,2)>=2 & size(ObjectData.Range,1)>=2 + YMin=ObjectData.Range(2,2); +else + YMin=0; +end +XMax=ObjectData.Range(1,1); +if size(ObjectData.Range,1)>=2 + XMin=ObjectData.Range(2,1); +end +if isfield(ObjectData,'RangeX') + XMax=max(ObjectData.RangeX); + XMin=min(ObjectData.RangeX); +end +if isfield(ObjectData,'RangeY') + YMax=max(ObjectData.RangeY); + YMin=min(ObjectData.RangeY); +end +if isfield(ObjectData,'RangeZ') + ZMax=max(ObjectData.RangeZ); + ZMin=min(ObjectData.RangeZ); +end +if isequal(ObjectData.Style,'points')&isequal(ObjectData.ProjMode,'projection') + YMax=max(XMax,YMax); + YMax=max(YMax,ZMax); +elseif isequal(ObjectData.Style,'rectangle')|isequal(ObjectData.Style,'ellipse')|isequal(ObjectData.Style,'volume') + if isequal(YMax,0) + ylim=get(haxes,'YLim'); + YMax=(ylim(2)-ylim(1))/100; + end + if isequal(XMax,0) + XMax=YMax;%default + end +elseif isequal(ObjectData.Style,'plane') + if isequal(XMax,0) + xlim=get(haxes,'XLim'); + XMax=xlim(2); + end + if isequal(YMax,0) + ylim=get(haxes,'YLim'); + YMax=ylim(2); + end +end +sizcoord=size(ObjectData.Coord); + +%determine the coordinates xline, yline,xsup,xinf, yinf,ysup determining the new object plot +test_line= isequal(ObjectData.Style,'points')|isequal(ObjectData.Style,'line')|isequal(ObjectData.Style,'polyline')|... + isequal(ObjectData.Style,'polygon')| isequal(ObjectData.Style,'plane')| isequal(ObjectData.Style,'volume'); +test_patch=isequal(ObjectData.ProjMode,'inside')||isequal(ObjectData.ProjMode,'outside')||isequal(ObjectData.Style,'volume')... + ||isequal(ObjectData.ProjMode,'mask_inside')||isequal(ObjectData.ProjMode,'mask_outside'); +if test_line + xline=ObjectData.Coord(:,1); + yline=ObjectData.Coord(:,2); + if isequal(ObjectData.Style,'polygon') + xline=[xline; ObjectData.Coord(1,1)];%closing the line + yline=[yline; ObjectData.Coord(1,2)]; + elseif isequal(ObjectData.Style,'plane')| isequal(ObjectData.Style,'volume') + phi=ObjectData.Phi*pi/180;%angle in radians + Xend_x=xline(1)+XMax*cos(phi); + Xend_y=yline(1)+XMax*sin(phi); + Xbeg_x=xline(1)+XMin*cos(phi); + Xbeg_y=yline(1)+XMin*sin(phi); + Yend_x=xline(1)-YMax*sin(phi); + Yend_y=yline(1)+YMax*cos(phi); + Ybeg_x=xline(1)-YMin*sin(phi); + Ybeg_y=yline(1)+YMin*cos(phi); + xline=[Xbeg_x Xend_x NaN Ybeg_x Yend_x]; + yline=[Xbeg_y Xend_y NaN Ybeg_y Yend_y]; + end + SubLineStyle='none';%default + if isfield(ObjectData,'ProjMode') + if isequal(ObjectData.ProjMode,'projection') + SubLineStyle='--'; %range of projection marked by dash + if isfield (ObjectData,'DX') + rmfield(ObjectData,'DX'); + end + if isfield (ObjectData,'DY') + rmfield(ObjectData,'DY'); + end + elseif isequal(ObjectData.ProjMode,'filter') + SubLineStyle=':';%range of projection not visible + end + end + if isequal(ObjectData.Style,'line')|isequal(ObjectData.Style,'polyline')|isequal(ObjectData.Style,'polygon') + if length(xline)<2 + theta=0; + else + theta=angle(diff(xline)+i*diff(yline)); + theta(length(xline))=theta(length(xline)-1); + end + xsup(1)=xline(1)+YMax*sin(theta(1)); + xinf(1)=xline(1)-YMax*sin(theta(1)); + ysup(1)=yline(1)-YMax*cos(theta(1)); + yinf(1)=yline(1)+YMax*cos(theta(1)); + for ip=2:length(xline) + xsup(ip)=xline(ip)+YMax*sin((theta(ip)+theta(ip-1))/2)/cos((theta(ip-1)-theta(ip))/2); + xinf(ip)=xline(ip)-YMax*sin((theta(ip)+theta(ip-1))/2)/cos((theta(ip-1)-theta(ip))/2); + ysup(ip)=yline(ip)-YMax*cos((theta(ip)+theta(ip-1))/2)/cos((theta(ip-1)-theta(ip))/2); + yinf(ip)=yline(ip)+YMax*cos((theta(ip)+theta(ip-1))/2)/cos((theta(ip-1)-theta(ip))/2); + end + end +end + +%shading image +if test_patch + npMx=512; + npMy=512; + flag=zeros(npMy,npMx); + if isequal(ObjectData.Style,'ellipse') + XimaMin=ObjectData.Coord(1,1)-XMax; + XimaMax=ObjectData.Coord(1,1)+XMax; + YimaMin=ObjectData.Coord(1,2)-YMax; + YimaMax=ObjectData.Coord(1,2)+YMax; + xlim=[1.2*XimaMin-0.2*XimaMax 1.2*XimaMax-0.2*XimaMin];%create an image around the ellipse + ylim=[1.2*YimaMin-0.2*YimaMax 1.2*YimaMax-0.2*YimaMin]; + scale_x=2*1.4*XMax/npMx; + scale_y=2*1.4*YMax/npMy; + xi=[0.5:npMx-0.5]*scale_x+xlim(1); + yi=[0.5:npMy-0.5]*scale_y+ylim(1); + [Xi,Yi]=meshgrid(xi,yi); + X2Max=XMax*XMax; + Y2Max=YMax*YMax; + distX=(Xi-ObjectData.Coord(1,1)); + distY=(Yi-ObjectData.Coord(1,2)); + flag=(distX.*distX/X2Max+distY.*distY/Y2Max)<1; + elseif isequal(ObjectData.Style,'rectangle')|isequal(ObjectData.Style,'volume') + XimaMin=ObjectData.Coord(1,1)-XMax; + XimaMax=ObjectData.Coord(1,1)+XMax; + YimaMin=ObjectData.Coord(1,2)-YMax; + YimaMax=ObjectData.Coord(1,2)+YMax; + xlim=[1.2*XimaMin-0.2*XimaMax 1.2*XimaMax-0.2*XimaMin];%create an image around the ellipse + ylim=[1.2*YimaMin-0.2*YimaMax 1.2*YimaMax-0.2*YimaMin]; + scale_x=2*1.4*XMax/npMx; + scale_y=2*1.4*YMax/npMy; + xi=[0.5:npMx-0.5]*scale_x+xlim(1); + yi=[0.5:npMy-0.5]*scale_y+ylim(1); + [Xi,Yi]=meshgrid(xi,yi); + distX=abs(Xi-ObjectData.Coord(1,1)); + distY=abs(Yi-ObjectData.Coord(1,2)); + flag=distXlength(PlotData.SubObject) + for ipt=length(PlotData.SubObject)+1:size(ObjectData.Coord,1) + PlotData.SubObject(ipt)=rectangle('Curvature',[1 1],... + 'Position',[ObjectData.Coord(ipt,1)-YMax ObjectData.Coord(ipt,2)-YMax 2*YMax 2*YMax],'EdgeColor',col,... + 'LineStyle',SubLineStyle,'Tag','proj_object'); + end + end + end + end + if isfield(PlotData,'DeformPoint') + for ipt=1:length(PlotData.DeformPoint) + if ishandle(PlotData.DeformPoint(ipt)) + if length(xline)>=ipt & length(yline)>=ipt + set(PlotData.DeformPoint(ipt),'XData',xline(ipt),'YData',yline(ipt)); + end + end + end + if length(xline)>length(PlotData.DeformPoint) + for ipt=length(PlotData.DeformPoint)+1:length(xline) + PlotData.DeformPoint(ipt)=line(xline(ipt),yline(ipt),'Color',col,'LineStyle','.','Tag','DeformPoint',... + 'SelectionHighlight','off','UserData',hplot); + end + set(hplot,'UserData',PlotData) + end + end + elseif isequal(ObjectData.Style,'rectangle')|isequal(ObjectData.Style,'ellipse') + set(hplot,'Position',[ObjectData.Coord(1,1)-XMax ObjectData.Coord(1,2)-YMax 2*XMax 2*YMax]) + end + if test_patch + for iobj=1:length(PlotData.SubObject) + objtype=get(PlotData.SubObject(iobj),'Type'); + if isequal(objtype,'image') + set(PlotData.SubObject(iobj),'CData',imflag,'AlphaData',(flag)*0.2) + set(PlotData.SubObject(iobj),'XData',[xlim(1)+dx/2 xlim(2)-dx/2]) + set(PlotData.SubObject(iobj),'YData',[ylim(1)+dy/2 ylim(2)-dy/2]) + end + end + end +end + +%create the object +if test_newobj + axes(haxes) + hother=findobj('Tag','proj_object');%find all the proj objects + for iobj=1:length(hother) + if isequal(get(hother(iobj),'Type'),'rectangle')|isequal(get(hother(iobj),'Type'),'patch') + set(hother(iobj),'EdgeColor','b') + if isequal(get(hother(iobj),'FaceColor'),'m') + set(hother(iobj),'FaceColor','b') + end + elseif isequal(get(hother(iobj),'Type'),'image') + Acolor=get(hother(iobj),'CData'); + Acolor(:,:,1)=zeros(size(Acolor,1),size(Acolor,2)); + set(hother(iobj),'CData',Acolor); + else + set(hother(iobj),'Color','b') + end + set(hother(iobj),'Selected','off') + end + hother=findobj('Tag','DeformPoint'); + set(hother,'Color','b'); + set(hother,'Selected','off') + if isequal(ObjectData.Style,'points') + hh=line(ObjectData.Coord(:,1),ObjectData.Coord(:,2),'Color',col,'LineStyle','.','Marker','+'); + for ipt=1:length(xline) + PlotData.DeformPoint(ipt)=line(ObjectData.Coord(ipt,1),ObjectData.Coord(ipt,2),'Color',... + col,'LineStyle','.','SelectionHighlight','off','UserData',hh,'Tag','DeformPoint'); + %create circle around each point + if ~isequal(YMax,0) + PlotData.SubObject(ipt)=rectangle('Curvature',[1 1],... + 'Position',[ObjectData.Coord(ipt,1)-YMax ObjectData.Coord(ipt,2)-YMax 2*YMax 2*YMax],'EdgeColor',col,... + 'LineStyle',SubLineStyle,'Tag','proj_object'); + end + end + elseif isequal(ObjectData.Style,'line')|isequal(ObjectData.Style,'polyline')|... + isequal(ObjectData.Style,'polygon') |isequal(ObjectData.Style,'plane')|isequal(ObjectData.Style,'volume')% (isequal(ObjectData.Style,'polygon') & ~test_patch) |isequal(ObjectData.Style,'plane') + hh=line(xline,yline,'Color',col); + if ~isequal(ObjectData.Style,'plane')& ~isequal(ObjectData.Style,'volume') + for ipt=1:sizcoord(1) + PlotData.DeformPoint(ipt)=line(ObjectData.Coord(ipt,1),ObjectData.Coord(ipt,2),'Color',... + col,'LineStyle','none','Marker','.','Tag','DeformPoint','SelectionHighlight','off','UserData',hh); + end + PlotData.SubObject(1)=line(xinf,yinf,'Color',col,'LineStyle',SubLineStyle,'Tag','proj_object');%draw sub-lines + PlotData.SubObject(2)=line(xsup,ysup,'Color',col,'LineStyle',SubLineStyle,'Tag','proj_object'); + end + + elseif isequal(ObjectData.Style,'rectangle') + hh=rectangle('Position',[ObjectData.Coord(1,1)-XMax ObjectData.Coord(1,2)-YMax 2*XMax 2*YMax],'EdgeColor',col); + elseif isequal(ObjectData.Style,'ellipse') + hh=rectangle('Curvature',[1 1],'Position',[ObjectData.Coord(1,1)-XMax ObjectData.Coord(1,2)-YMax 2*XMax 2*YMax],'EdgeColor',col); + else + warndlg_uvmat('unknown ObjectData.Style in plot_object.m','ERROR') + return + end + set(hh,'Tag','proj_object') + %set(hh,'UserData',ObjectData)% +% hh=hplot; +% set(hh,'DeleteFcn',@deletefcn) +% if isequal(ObjectData.ProjMode,'inside') +% if isequal(ObjectData.Style,'ellipse')|isequal(ObjectData.Style,'rectangle') +% set(hh,'FaceColor',col) +% set(hh,'EdgeColor',col) +% end +% end + if test_patch + hold on + hhh=image([xlim(1)+dx/2 xlim(2)-dx/2],[ylim(1)+dy/2 ylim(2)-dy/2],imflag,'Tag','proj_object','HitTest','off'); + set(hhh,'AlphaData',(flag)*0.2) + PlotData.SubObject=hhh; + end + if isfield(PlotData,'SubObject') + set(PlotData.SubObject,'UserData',hh)%record the parent handles in the SubObjects + end + if isfield(PlotData,'DeformPoint') + for ipt=1:sizcoord(1) + set(PlotData.DeformPoint(ipt),'UserData',hh);%record the parent handles in the SubObjects + end + set(PlotData.DeformPoint,'UserData',hh)%record the parent handles in the SubObjects + end +end +set(hh,'UserData',PlotData) Index: /trunk/src/plot_text.m =================================================================== --- /trunk/src/plot_text.m (revision 2) +++ /trunk/src/plot_text.m (revision 2) @@ -0,0 +1,86 @@ +%'plot_text': function for displaying the content of a Matlab structure in a figure +%------------------------------------------------------------------------ +% function hdisplay=plot_text(FieldData,hdisplay_in) +% +% OUTPUT: +% hdisplay: handle of the display edit box +% +% INPUT: +% FieldData: input Matlab structure +% hdisplay_in: handles of the display box, if it is not defined create a new figure +% +%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +% Copyright Joel Sommeria, 2008, LEGI / CNRS-UJF-INPG, sommeria@coriolis-legi.org. +%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +% This file is part of the toolbox UVMAT. +% +% UVMAT is free software; you can redistribute it and/or modify +% it under the terms of the GNU General Public License as published by +% the Free Software Foundation; either version 2 of the License, or +% (at your option) any later version. +% +% UVMAT is distributed in the hope that it will be useful, +% but WITHOUT ANY WARRANTY; without even the implied warranty of +% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +% GNU General Public License (file UVMAT/COPYING.txt) for more details. +%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA + +function hdisplay=plot_text(FieldData,hdisplay_in) + +if exist('hdisplay_in','var') & ishandle(hdisplay_in) & isequal(get(hdisplay_in,'Type'),'uicontrol') + hdisplay=hdisplay_in; +else + figure;%create new figure + hdisplay=uicontrol('Style','edit', 'Units','normalized','Position', [0 0 1 1],'Max',2,'FontName','monospaced'); +end + +ff=fields(FieldData);%list of field names +vv=struct2cell(FieldData);%list of field values + +for icell=1:length(vv) + Tabcell{icell,1}=ff{icell}; + ss=vv{icell}; + sizss=size(ss); + if isnumeric(ss) + if sizss(1)<=1 & length(ss)<5 + displ{icell}=num2str(ss); + else + displ{icell}=[class(ss) ', size ' num2str(size(ss))]; + end + elseif ischar(ss) + displ{icell}=ss; + elseif iscell(ss) + sizcell=size(ss); + if sizcell(1)==1 & length(sizcell)==2 %line cell + ssline='{'''; + for icolumn=1:sizcell(2) + if isnumeric(ss{icolumn}) + if size(ss{icolumn},1)<=1 & length(ss{icolumn})<5 + sscolumn=num2str(ss{icolumn});%line vector + else + sscolumn=[class(ss{icolumn}) ', size ' num2str(size(ss{icolumn}))]; + end + elseif ischar(ss{icolumn}) + sscolumn=ss{icolumn}; + else + sscolumn=class(ss{icolumn}); + end + if icolumn==1 + ssline=[ssline sscolumn]; + else + ssline=[ssline ''',''' sscolumn]; + end + end + displ{icell}=[ssline '''}']; + else + displ{icell}=[class(ss) ', size ' num2str(sizcell)]; + end + else + displ{icell}=class(ss); + end + Tabcell{icell,2}=displ{icell}; +end +Tabchar=cell2tab(Tabcell,': '); +set(hdisplay,'String', Tabchar) + + Index: /trunk/src/probe_calib.m =================================================================== --- /trunk/src/probe_calib.m (revision 2) +++ /trunk/src/probe_calib.m (revision 2) @@ -0,0 +1,877 @@ +%'probe_calib': performs geometric calibration from a set of reference points +function varargout = probe_calib(varargin) +% PROBE_CALIB M-file for probe_calib.fig +% PROBE_CALIB, by itself, creates a MenuCoord PROBE_CALIB or raises the existing +% singleton*. +% +% H = PROBE_CALIB returns the handle to a MenuCoord PROBE_CALIB or the handle to +% the existing singleton*. +% +% PROBE_CALIB('CALLBACK',hObject,eventData,handles,...) calls the local +% function named CALLBACK in PROBE_CALIB.M with the given input arguments. +% +% PROBE_CALIB('Property','Value',...) creates a MenuCoord PROBE_CALIB or raises the +% existing singleton*. Starting from the left, property value pairs are +% applied to the GUI before probe_calib_OpeningFunction gets called. An +% unrecognized property name or invalid value makes property application +% stop. All inputs are passed to probe_calib_OpeningFcn via varargin. +% +% *See GUI Options on GUIDE's Tools menu. Choose "GUI allows only one +% instance to run (singleton)". +% +% See also: GUIDE, GUIDATA, GUIHANDLES + +% Edit the above text to modify the response to help probe_calib + +% Last Modified by GUIDE v2.5 04-Feb-2008 15:46:42 + +% Begin initialization code - DO NOT EDIT +gui_Singleton = 1; +gui_State = struct('gui_Name', mfilename, ... + 'gui_Singleton', gui_Singleton, ... + 'gui_OpeningFcn', @probe_calib_OpeningFcn, ... + 'gui_OutputFcn', @probe_calib_OutputFcn, ... + 'gui_LayoutFcn', [] , ... + 'gui_Callback', []); +if nargin & isstr(varargin{1}) + gui_State.gui_Callback = str2func(varargin{1}); +end + +if nargout + [varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:}); +else + gui_mainfcn(gui_State, varargin{:}); +end +% End initialization code - DO NOT EDIT + + +% --- Executes just before probe_calib is made visible. +%INPUT: +%handles: handles of the probe_calib interface elements +% PlotHandles: set of handles of the elements contolling the plotting +% parameters on the uvmat interface (obtained by 'get_plot_handle.m') +function probe_calib_OpeningFcn(hObject, eventdata, handles, data,pos,inputfile) + +% Choose default command line output for probe_calib +handles.output = hObject; + +% Update handles structure +guidata(hObject, handles); + +%default +% set(hObject,'Unit','Normalized')% set the unit normalized to the screen size +% set(hObject,'Position',[0.7 0.1 0.25 0.5])%set the position of the probe_calib interface +set(hObject,'DeleteFcn',@closefcn) + +%set the position of the interface +if exist('pos','var')& length(pos)>2 + pos_gui=get(hObject,'Position'); + pos_gui(1)=pos(1); + pos_gui(2)=pos(2); + set(hObject,'Position',pos_gui); +end +% set(handles.XImage,'String','') +% set(handles.YImage,'String','') +% set(handles.XObject,'String','') +% set(handles.YObject,'String','') +% set(handles.ZObject,'String','') +inputxml=''; +if exist('inputfile','var')& ~isempty(inputfile) + [Path,Name,ext]=fileparts(inputfile); + if isequal(ext,'.png') + set(hObject,'UserData',inputfile) + [Pathsub,RootFile,field_count,str2,str_a,str_b,ext,nom_type,subdir]=name2display(inputfile); + inputxml=[fullfile(Pathsub,RootFile) '.xml']; + end +end +if exist(inputxml,'file') + loadfile(handles,inputxml) +end +set(handles.ListCoord,'KeyPressFcn',{@key_press_fcn,handles})%set keyboard action function + + +% --- Outputs from this function are returned to the command line. +function varargout = probe_calib_OutputFcn(hObject, eventdata, handles) +% varargout cell array for returning output args (see VARARGOUT); +% hObject handle to figure +% eventdata reserved - to be defined in a future version of MATLAB +% handles structure with handles and user data (see GUIDATA) + +% Get default command line output from handles structure +varargout{1} = handles.output; +varargout{2}=handles; + +%------------ +function Phi_Callback(hObject, eventdata, handles) + + +%----------------------------------------------------- +% --- Executes on button press in import. +function import_Callback(hObject, eventdata, handles) +%get the object file +huvmat=findobj('Tag','uvmat'); +UvData=get(huvmat,'UserData'); +hchild=get(huvmat,'Children'); +hrootpath=findobj(hchild,'Tag','RootPath'); +oldfile=get(hrootpath,'String'); +if isempty(oldfile) + oldfile=''; +end +%[FileName,PathName] = uigetfile('*.civ','Select a .civ file',oldfile) +[FileName, PathName, filterindex] = uigetfile( ... + {'*.xml;*.mat', ' (*.xml,*.mat)'; + '*.xml', '.xml files '; ... + '*.mat', '.mat matlab files '}, ... + 'Pick a file',oldfile); +fileinput=[PathName FileName];%complete file name +testblank=findstr(fileinput,' ');%look for blanks +if ~isempty(testblank) + warndlg_uvmat('forbidden input file name or path: no blank character allowed','ERROR') + return +end +sizf=size(fileinput); +if (~ischar(fileinput)|~isequal(sizf(1),1)),return;end +loadfile(handles,fileinput) + +%-------------------------------------------------- +%read input xml file and update the edit boxes +function loadfile(handles,fileinput) + +%read the input xml file +t=xmltree(fileinput); +s=convert(t);%convert to matlab structure + +%read data currently displayed on the interface +PointCoord=[]; +data=read_probe_calib(handles); +Coord=[]; %default +if isfield(data,'Coord') + Coord=data.Coord; +end +TabChar_0=get(handles.ListCoord,'String'); +nbcoord_0=size(TabChar_0,1); +if isequal(get(handles.edit_append,'Value'),1) %edit mode + val=get(handles.ListCoord,'Value')-1; +else + val=length(TabChar_0); +end +nbcoord=0; + +%case of calibration (ImaDoc) input file +if isfield(s,'GeometryCalib') + Calib=s.GeometryCalib; + if isfield(Calib,'SourceCalib') + if isfield(Calib.SourceCalib,'PointCoord') + PointCoord=Calib.SourceCalib.PointCoord; + end + if isfield(Calib.SourceCalib,'ImageCalib') + hcalib=get(handles.import,'parent'); + set(hcalib,'UserData',Calib.SourceCalib.ImageCalib);%store the source image name in the interface 'UserData' + end + end + nbcoord=length(PointCoord); + if ~isfield(Calib,'ErrorRms')&~isfield(Calib,'ErrorMax') %old convention of Gauthier (cord in mm) + for i=1:length(PointCoord) + line=str2num(PointCoord{i}); + Coord(i+val,4:5)=line(4:5);%px x + Coord(i+val,1:3)=line(1:3)/10;%phys x + end + else + for i=1:length(PointCoord) + line=str2num(PointCoord{i}); + Coord(i,4:5)=line(4:5);%px x + Coord(i,1:3)=line(1:3);%phys x + end + end +end + +%case of xml files of points +if isfield(s,'Coord') + PointCoord=s.Coord; + nbcoord=length(PointCoord); + %case of image coordinates + if isfield(s,'CoordType')& isequal(s.CoordType,'px') + for i=1:nbcoord + line=str2num(PointCoord{i}); + Coord(i+val,4:5)=line(1:2); + end + %case of physical coordinates + else + for i=1:nbcoord + line=str2num(PointCoord{i}) + Coord(i+val,1:3)=line(1:3); + nbcolumn=size(Coord,2); + if nbcolumn<5 + Coord(i+val,nbcolumn+1:5)=zeros(1,5-nbcolumn); + end + end + end +end +CoordCell={}; +for iline=1:size(Coord,1) + for j=1:5 + CoordCell{iline,j}=num2str(Coord(iline,j)); + end +end + +Tabchar=cell2tab(CoordCell,' | ');%transform cells into table ready for display +set(handles.ListCoord,'Value',1) +set(handles.ListCoord,'String',Tabchar) + + +%---------------------------------------------------- +% executed when closing: set the parent interface button to value 0 +function closefcn(gcbo,eventdata) +SetData=get(gcbf,'UserData'); +if isfield(SetData,'ParentButton') & ishandle(SetData.ParentButton) + set(SetData.ParentButton, 'Value',0) +end + +%----------------------------------------------------------------------- +% --- Executes on button press in edit: PLOT the defined object and its projected field +function edit_Callback(hObject, eventdata, handles) +%hsetobject=get(hObject,'parent'); +%SetData=get(hsetobject,'UserData');%get the hidden interface data +%IndexObj=SetData.IndexObj;%index of the current projection object in the list of projection objects (UvData.ProjObject) +huvmat=findobj(allchild(0),'name','uvmat');%find the current uvmat interface handle +UvData=get(huvmat,'UserData');%Data associated to the current uvmat interface +hplot=findobj(huvmat,'Tag','axes3'); +h_menu_coord=findobj(huvmat,'Tag','menu_coord'); +menu=get(h_menu_coord,'String'); +choice=get(h_menu_coord,'Value'); +if iscell(menu) + option=menu{choice}; +else + option='px'; %default +end +%get axis +%get CoordType +ObjectData=read_probe_calib(handles);%read the interface input parameters defining the object +if isequal(option,'phys') + ObjectData.Coord=ObjectData.Coord(:,[1:3]); +elseif isequal(option,'px') + ObjectData.Coord=ObjectData.Coord(:,[4:5]); +else + errordlg('the choice in coord_coord must be px or phys ') +end +% [UvData,IndexObj]=update_obj(UvData,IndexObj,ObjectData,SetData.PlotHandles); +% SetData.IndexObj=IndexObj; +% set(gcbf,'UserData',SetData)%update object index in the probe_calib interface +% set(huvmat,'UserData',UvData)%update the data in the uvmat interface +ObjectData.ProjMode='none'; +plot_object(ObjectData,[],hplot,'b'); + + +% --- Executes on button press in MenuCoord. +function MenuCoord_Callback(hObject, eventdata, handles) + + +% --- Executes on button press in delete. +function delete_Callback(hObject, eventdata, handles) +SetData=get(gcbf,'UserData');%get the interface data +IndexObj=SetData.IndexObj; +delete_object(IndexObj); + +% --- Executes on button press in calibrate_lin. +function calib_offset_Callback(hObject, eventdata, handles) +Object=read_probe_calib(handles); + +%make linear calibration +% 'calibration_lin' provides a linear transform on coordinates, +X=Object.Coord(:,1); +Y=Object.Coord(:,2); +x_ima=Object.Coord(:,4); +y_ima=Object.Coord(:,5); +[px,sx]=polyfit(X,x_ima,1); +[py,sy]=polyfit(Y,y_ima,1); +%err_X1=max(abs(x1-x_ima));%error +%err_Y1=max(abs(y1-y_ima));%error +T_x=px(2); +T_y=py(2); +GeometryCalib.focal=1; +GeometryCalib.Tx_Ty_Tz=[T_x T_y 1]; +GeometryCalib.R=[px(1),0,0;0,py(1),0;0,0,1]; +%check error +Calib.dpx=1; +Calib.dpy=1; +Calib.sx=1; +Calib.Cx=0; +Calib.Cy=0; +Calib.Tz=1; +Calib.kappa1=0; +Calib.f=GeometryCalib.focal; +Calib.Tx=T_x; +Calib.Ty=T_y; +Calib.R=GeometryCalib.R; +[Xpoints,Ypoints]=px_XYZ(Calib,X,Y,0); +GeometryCalib.ErrorRms(1)=sqrt(mean((Xpoints-x_ima).*(Xpoints-x_ima))); +GeometryCalib.ErrorMax(1)=max(abs(Xpoints-x_ima)); +GeometryCalib.ErrorRms(2)=sqrt(mean((Ypoints-y_ima).*(Ypoints-y_ima))); +GeometryCalib.ErrorMax(2)=max(abs(Ypoints-y_ima)) +%calibrate_lin calibration results and point coordinates +huvmat=findobj('Tag','uvmat'); +hchild=get(huvmat,'Children'); +hrootpath=findobj(hchild,'Tag','RootPath'); +hrootfile=findobj(hchild,'Tag','RootFile'); +RootPath=''; +RootFile=''; +if ~isempty(hrootpath)& ~isempty(hrootfile) + testhandle=1; + RootPath=get(hrootpath,'String'); + RootFile=get(hrootfile,'String'); + filebase=fullfile(RootPath,RootFile); + outputfile=[filebase '.xml'] +else + question={'save the calibration data and point coordinates in'}; + def={fullfile(RootPath,['ObjectCalib.xml'])}; + options.Resize='on'; + answer=inputdlg(question,'save average in a new file',1,def,options); + outputfile=answer{1}; +end +testappend=0; +if exist(outputfile,'file');%=1 if the output file already exists, 0 else + t=xmltree(outputfile); %read the file + uid=find(t,'ImaDoc'); + if ~isequal(uid,1)%if the xml file is not ImaDoc, delete it (after backup) + backupfile=outputfile; + testexist=2; + while testexist==2 + backupfile=[backupfile '~']; + testexist=exist(backupfile,'file'); + end + [success,message]=copyfile(outputfile,backupfile);%make backup + if isequal(success,1) + delete(outputfile) + else + return + end + else + uid_calib=find(t,'ImaDoc/GeometryCalib'); + if ~isempty(uid) %if GeometryCalib already exists, delete its content + backupfile=outputfile; + testexist=2; + while testexist==2 + backupfile=[backupfile '~']; + testexist=exist(backupfile,'file'); + end + [success,message]=copyfile(outputfile,backupfile)%make backup + if isequal(success,1) + delete(outputfile) + else + return + end + uid_child=children(t,uid_calib); + t=delete(t,uid_child); + testappend=1; + end + end +end +if ~testappend + t=xmltree; + t=set(t,1,'name','ImaDoc'); + [t,uid_calib]=add(t,1,'element','GeometryCalib'); +% t=struct2xml(GeometryCalib,t,uid_calib); +end +Object.Coord(:,[1:3])=Object.Coord(:,[1:3])*10; %transform in +GeometryCalib.SourceCalib.PointCoord=Object.Coord; +t=struct2xml(GeometryCalib,t,uid_calib); +save(t,outputfile) + +warndlg_uvmat([outputfile 'updated with linear calibration data'],'CONFIRMATION') + +%display image with new calibration in the currently opened uvmat interface +Indices=get(findobj(hchild,'Tag','FileIndex'),'String'); +Ext=get(findobj(hchild,'Tag','FileExt'),'String'); +imagename=[fullfile(RootPath,RootFile) Indices Ext]; +% input.menu_coord=1; +huvmat=uvmat(imagename,1);%open uvmat, set phys coord (Value 1) + + + +% --- Executes on button press in calibrate_lin. +function calib_lin_Callback(hObject, eventdata, handles) +Object=read_probe_calib(handles); + +%make linear calibration +% 'calibration_lin' provides a linear transform on coordinates, +X=Object.Coord(:,1); +Y=Object.Coord(:,2); +x_ima=Object.Coord(:,4); +y_ima=Object.Coord(:,5); +XY_mat=[ones(size(X)) X Y]; +a_X1=XY_mat\x_ima; %transformation matrix for X +x1=XY_mat*a_X1;%reconstruction +err_X1=max(abs(x1-x_ima));%error +a_Y1=XY_mat\y_ima;%transformation matrix for X +y1=XY_mat*a_Y1; +err_Y1=max(abs(y1-y_ima));%error +T_x=a_X1(1); +T_y=a_Y1(1); +GeometryCalib.focal=1; +GeometryCalib.Tx_Ty_Tz=[T_x T_y 1]; +GeometryCalib.R=[a_X1(2),a_X1(3),0;a_Y1(2),a_Y1(3),0;0,0,1]; + +%check error +GeometryCalib.ErrorRms(1)=sqrt(mean((x1-x_ima).*(x1-x_ima))); +GeometryCalib.ErrorMax(1)=max(abs(x1-x_ima)); +GeometryCalib.ErrorRms(2)=sqrt(mean((y1-y_ima).*(y1-y_ima))); +GeometryCalib.ErrorMax(2)=max(abs(y1-y_ima)) + +%calibrate_lin calibration results and point coordinates +huvmat=findobj('Tag','uvmat'); +hchild=get(huvmat,'Children'); +hrootpath=findobj(hchild,'Tag','RootPath'); +hrootfile=findobj(hchild,'Tag','RootFile'); +RootPath=''; +RootFile=''; +if ~isempty(hrootpath)& ~isempty(hrootfile) + testhandle=1; + RootPath=get(hrootpath,'String'); + RootFile=get(hrootfile,'String'); + filebase=fullfile(RootPath,RootFile); + outputfile=[filebase '.xml']; +else + question={'save the calibration data and point coordinates in'}; + def={fullfile(RootPath,['ObjectCalib.xml'])}; + options.Resize='on'; + answer=inputdlg(question,'save average in a new file',1,def,options); + outputfile=answer{1}; +end +testappend=0; +if exist(outputfile,'file');%=1 if the output file already exists, 0 else + t=xmltree(outputfile); %read the file + uid=find(t,'ImaDoc'); + if ~isequal(uid,1)%if the xml file is not ImaDoc, delete it (after backup) + backupfile=outputfile; + testexist=2; + while testexist==2 + backupfile=[backupfile '~']; + testexist=exist(backupfile,'file'); + end + [success,message]=copyfile(outputfile,backupfile)%make backup + if isequal(success,1); + delete(outputfile) + else + return + end + else + uid_calib=find(t,'ImaDoc/GeometryCalib'); + if ~isempty(uid) %if GeometryCalib already exists, delete its content + backupfile=outputfile; + testexist=2; + while testexist==2 + backupfile=[backupfile '~']; + testexist=exist(backupfile,'file'); + end + [success,message]=copyfile(outputfile,backupfile)%make backup + if isequal(success,1) + delete(outputfile) + else + return + end + uid_child=children(t,uid_calib); + t=delete(t,uid_child); + testappend=1; + end + end +end +if ~testappend + t=xmltree; + t=set(t,1,'name','ImaDoc'); + [t,uid_calib]=add(t,1,'element','GeometryCalib'); +% t=struct2xml(GeometryCalib,t,uid_calib); +end +% Object.Coord(:,[1:3])=Object.Coord(:,[1:3]); %transform in +GeometryCalib.SourceCalib.PointCoord=Object.Coord; +t=struct2xml(GeometryCalib,t,uid_calib); +save(t,outputfile) + +warndlg_uvmat([outputfile 'updated with linear calibration data'],'CONFIRMATION') + +%display image with new calibration in the currently opened uvmat interface +Indices=get(findobj(hchild,'Tag','FileIndex'),'String'); +Ext=get(findobj(hchild,'Tag','FileExt'),'String'); +imagename=[fullfile(RootPath,RootFile) Indices Ext]; +% input.menu_coord=1; +if exist(imagename,'file') + huvmat=uvmat(imagename,1);%open uvmat, set phys coord (Value 1) +else + huvmat=uvmat; +end + + +% --- Executes on button press in translation. +function translation_Callback(hObject, eventdata, handles) + + +function T_x_Callback(hObject, eventdata, handles) +% hObject handle to T_x (see GCBO) +% eventdata reserved - to be defined in a future version of MATLAB +% handles structure with handles and user data (see GUIDATA) + +% Hints: get(hObject,'String') returns contents of T_x as text +% str2double(get(hObject,'String')) returns contents of T_x as a double + + + + + +function T_y_Callback(hObject, eventdata, handles) +% hObject handle to T_y (see GCBO) +% eventdata reserved - to be defined in a future version of MATLAB +% handles structure with handles and user data (see GUIDATA) + +% Hints: get(hObject,'String') returns contents of T_y as text +% str2double(get(hObject,'String')) returns contents of T_y as a double + + +function T_z_Callback(hObject, eventdata, handles) +% hObject handle to T_z (see GCBO) +% eventdata reserved - to be defined in a future version of MATLAB +% handles structure with handles and user data (see GUIDATA) + +% Hints: get(hObject,'String') returns contents of T_z as text +% str2double(get(hObject,'String')) returns contents of T_z as a double + + +% --- Executes on button press in rotation. +function rotation_Callback(hObject, eventdata, handles) +angle_rot=(pi/180)*str2num(get(handles.Phi,'String')) +data=read_probe_calib(handles) +data.Coord(:,1)=cos(angle_rot)*data.Coord(:,1)+sin(angle_rot)*data.Coord(:,2); +data.Coord(:,1)=-sin(angle_rot)*data.Coord(:,1)+cos(angle_rot)*data.Coord(:,2); +set(handles.XObject,'String',num2str(data.Coord(:,1))); +set(handles.YObject,'String',num2str(data.Coord(:,2))); + + +function XImage_Callback(hObject, eventdata, handles) +update_list(hObject, eventdata,handles) + +function YImage_Callback(hObject, eventdata, handles) +update_list(hObject, eventdata,handles) + +function XObject_Callback(hObject, eventdata, handles) +update_list(hObject, eventdata,handles) + +function YObject_Callback(hObject, eventdata, handles) +update_list(hObject, eventdata,handles) + +function ZObject_Callback(hObject, eventdata, handles) +update_list(hObject, eventdata,handles) + +function update_list(hObject, eventdata, handles) +str4=get(handles.XImage,'String'); +str5=get(handles.YImage,'String'); +str1=get(handles.XObject,'String'); +tt=double(str1); +str2=get(handles.YObject,'String'); +str3=get(handles.ZObject,'String'); +if ~isempty(str1) & ~isequal(double(str1),32) & (isempty(str3)|isequal(double(str3),32)) + str3='0';%put z to 0 by default +end +strline=[str1 ' | ' str2 ' | ' str3 ' | ' str4 ' | ' str5]; +Coord=get(handles.ListCoord,'String'); +testappend=get(handles.edit_append,'Value'); +if isequal(testappend,1); %edit mode + val=get(handles.ListCoord,'Value'); + Coord{val}=strline; +else + val=length(get(handles.ListCoord,'String')); + Coord{val+1}=strline; + set(handles.ListCoord,'Value',val+1) +% if val+1<=length(Coord) +% set(handles.ListCoord,'Value',val+1) +% ListCoord_Callback(hObject, eventdata, handles) +end +set(handles.ListCoord,'String',Coord) +%set(handles.ListCoord,'Value',val+1) + +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% +function data=read_probe_calib(handles) +data_XIma=[]; +data_YIma=[]; +data_XObject=[]; +data_YObject=[]; +data_ZObject=[]; +Coord=get(handles.ListCoord,'String'); +% XImage=get(handles.XImage,'String'); +% YImage=get(handles.YImage,'String'); +% XObject=get(handles.XObject,'String'); +% YObject=get(handles.YObject,'String'); +% ZObject=get(handles.ZObject,'String'); +% if ischar(Xcolumn) +% Xcolumn={Xcolumn}; +% end +nb_defining_points=length(Coord); +iline=0; +for i=1:nb_defining_points + coord_str=Coord{i};%character string of line number i + k=findstr('|',coord_str);%find separators '|' + data1=str2num(coord_str(1:k(1)-5)); + data2=str2num(coord_str(k(1)+5:k(2)-5)); + data3=str2num(coord_str(k(2)+5:k(3)-5)); + data4=str2num(coord_str(k(3)+5:k(4)-5)); + data5=str2num(coord_str(k(4)+5:end)); + if ~isempty(data1)|~isempty(data2)|~isempty(data3)|~isempty(data4)|~isempty(data5) + iline=iline+1; + if ~isempty(data1) + data.Coord(iline,1)=data1; + end + if ~isempty(data2) + data.Coord(iline,2)=data2; + end + if ~isempty(data3) + data.Coord(iline,3)=data3; + end + if ~isempty(data4) + data.Coord(iline,4)=data4; + end + if isempty(data5) + data.Coord(iline,5)=0; + else + data.Coord(iline,5)=data5; + end + end +end +data.Style='points'; + + +% --- Executes on selection change in ListCoord. +function ListCoord_Callback(hObject, eventdata, handles) +% hObject handle to ListCoord (see GCBO) +% eventdata reserved - to be defined in a future version of MATLAB +% handles structure with handles and user data (see GUIDATA) + +% Hints: contents = get(hObject,'String') returns ListCoord contents as cell array +% contents{get(hObject,'Value')} returns selected item from ListCoord +set(handles.edit_append,'Value',1); %set to edit mode +Coord=get(handles.ListCoord,'String'); +val=get(handles.ListCoord,'Value'); +if length(Coord)>0 +coord_str=Coord{val}; +k=findstr('|',coord_str); +set(handles.XObject,'String',coord_str(1:k(1)-5)) +set(handles.YObject,'String',coord_str(k(1)+5:k(2)-5)) +set(handles.ZObject,'String',coord_str(k(2)+5:k(3)-5)) +set(handles.XImage,'String',coord_str(k(3)+5:k(4)-5)) +set(handles.YImage,'String',coord_str(k(4)+5:end)) +end + +%------------------------------------------------------ +% --- Executes on button press in translation_plus. +function translation_plus_Callback(hObject, eventdata, handles) + +T=[0 0 0]; +T_x=get(handles.T_x,'String') +T_y=get(handles.T_y,'String') +T_z=get(handles.T_z,'String') +if ~isempty(T_x) + T(1)=str2num(T_x); +end +if ~isempty(T_y) + T(2)=str2num(T_y); +end +if ~isempty(T_z) + T(3)=str2num(T_z); +end +translation(handles,T) + + + +% --- Executes on button press in translation_minus. +function translation_minus_Callback(hObject, eventdata, handles) + +T=[0 0 0]; +T_x=get(handles.T_x,'String') +T_y=get(handles.T_y,'String') +T_z=get(handles.T_z,'String') +if ~isempty(T_x) + T(1)=-str2num(T_x); +end +if ~isempty(T_y) + T(2)=-str2num(T_y); +end +if ~isempty(T_z) + T(3)=-str2num(T_z); +end +translation(handles,T) + + +%%%-------------------------------------- +function translation(handles,T) +data=read_probe_calib(handles); +data.Coord(:,1)=T(1)+data.Coord(:,1); +data.Coord(:,2)=T(2)+data.Coord(:,2); +data.Coord(:,3)=T(3)+data.Coord(:,3); +data.Coord(:,[4 5])=data.Coord(:,[4 5]); +for i=1:size(data.Coord,1) + for j=1:5 + Coord{i,j}=num2str(data.Coord(i,j));%phys x,y,z + end +end +Tabchar=cell2tab(Coord,' | '); +set(handles.ListCoord,'String',Tabchar) + +%---------------------------------------------------- +% --- Executes on button press in rotation_plus. +function rotation_plus_Callback(hObject, eventdata, handles) +Phi=0; +Phi=get(handles.Phi,'String') +if ~isempty(Phi) + Phi=str2num(Phi); +end +rotation(handles,Phi) + +%------------------------------------------------- +% --- Executes on button press in rotation_minus. +function rotation_minus_Callback(hObject, eventdata, handles) +Phi=0; +Phi=get(handles.Phi,'String') +if ~isempty(Phi) + Phi=-str2num(Phi); +end +rotation(handles,Phi) + +%----------------------------------------------------- +%rotation +function rotation(handles,Phi) +O_x=str2num(get(handles.O_x,'String')); +O_y=str2num(get(handles.O_y,'String')); +if isempty(O_x) + O_x=0;%default +end +if isempty(O_y) + O_y=0;%default +end +data=read_probe_calib(handles); +r1=cos(pi*Phi/180); +r2=-sin(pi*Phi/180); +r3=sin(pi*Phi/180); +r4=cos(pi*Phi/180); +data.Coord(:,1)=r1*data.Coord(:,1)+r2*data.Coord(:,2); +data.Coord(:,2)=r3*data.Coord(:,1)+r4*data.Coord(:,2); +% data.Coord(:,[4 5])=data.Coord(:,[4 5]); +for i=1:size(data.Coord,1) + for j=1:5 + Coord{i,j}=num2str(data.Coord(i,j));%phys x,y,z + end +end +Tabchar=cell2tab(Coord,' | '); +set(handles.ListCoord,'String',Tabchar) + +function O_x_Callback(hObject, eventdata, handles) +% hObject handle to O_x (see GCBO) +% eventdata reserved - to be defined in a future version of MATLAB +% handles structure with handles and user data (see GUIDATA) + +% Hints: get(hObject,'String') returns contents of O_x as text +% str2double(get(hObject,'String')) returns contents of O_x as a double + + + +function O_y_Callback(hObject, eventdata, handles) +% hObject handle to O_y (see GCBO) +% eventdata reserved - to be defined in a future version of MATLAB +% handles structure with handles and user data (see GUIDATA) + +% Hints: get(hObject,'String') returns contents of O_y as text +% str2double(get(hObject,'String')) returns contents of O_y as a double + + +function O_z_Callback(hObject, eventdata, handles) +% hObject handle to O_z (see GCBO) +% eventdata reserved - to be defined in a future version of MATLAB +% handles structure with handles and user data (see GUIDATA) + +% Hints: get(hObject,'String') returns contents of O_z as text +% str2double(get(hObject,'String')) returns contents of O_z as a double + + + + + + + +% --- Executes on selection change in edit_append. +function edit_append_Callback(hObject, eventdata, handles) +val=get(handles.edit_append,'Value'); +if isequal(val,2); %append mode + %appeler mouse +end + + +function NEW_Callback(hObject, eventdata, handles) +%A METTRE SOUS UN BOUTON +huvmat=findobj('name','uvmat'); +hchild=get(huvmat,'children'); +hcoord=findobj(hchild,'Tag','menu_coord') +coordtype=get(hcoord,'Value') +haxes=findobj(hchild,'Tag','axes3'); +AxeData=get(haxes,'UserData'); +if ~isequal(hcoord,2) + set(hcoord,'Value',2) + huvmat=uvmat(AxeData) + 'relancer uvmat' +end +if ~isfield(AxeData,'ZoomAxes') + warndlg_uvmat('first draw a window around a grid marker','ERRROR') + return +end +XLim=get(AxeData.ZoomAxes,'XLim'); +YLim=get(AxeData.ZoomAxes,'YLim'); +np=size(AxeData.A); +ind_sub_x=round(XLim) +ind_sub_y=np(1)-round(YLim) +Mfiltre=AxeData.A([ind_sub_y(2):ind_sub_y(1)] ,ind_sub_x,:); +Mfiltre_norm=double(Mfiltre); +Mfiltre_norm=Mfiltre_norm/sum(sum(Mfiltre_norm)); +Mfiltre_norm=100*(Mfiltre_norm-mean(mean(Mfiltre_norm))); +Atype=class(AxeData.A) +Data.NbDim=2; +Data.A=filter2(Mfiltre_norm,double(AxeData.A)); +Data.A=feval(Atype,Data.A); +Data.AName='image'; +Data.AX=AxeData.AX; +Data.AY=AxeData.AY; +Data.CoordType='px'; +plot_field(Data) + + +% --- Executes on button press in HELP. +function HELP_Callback(hObject, eventdata, handles) +% hObject handle to HELP (see GCBO) +% eventdata reserved - to be defined in a future version of MATLAB +% handles structure with handles and user data (see GUIDATA) +path_to_uvmat=which ('uvmat');% check the path of uvmat +pathelp=fileparts(path_to_uvmat); +helpfile=fullfile(pathelp,'UVMAT_DOC','uvmat_doc.html'); +if isempty(dir(helpfile)), errordlg('Please put the help file uvmat_doc.html in the directory UVMAT/UVMAT_DOC') +else + web([helpfile '#probe_calib']) +end + +%'move_key:' function activated when a key is pressed on the keyboard +%----------------------------------- +function key_press_fcn(hObject,eventdata,handles) +hh=get(hObject,'parent') +xx=double(get(hh,'CurrentCharacter')) %get the keyboard character + +if isequal(xx,8)%move arrow right + data=read_probe_calib(handles); + Coord=[]; %default + if isfield(data,'Coord') + Coord=data.Coord + end + val=get(handles.ListCoord,'Value'); + Coord(val,:)=[]; + CoordCell={}; + for iline=1:size(Coord,1) + for j=1:5 + CoordCell{iline,j}=num2str(Coord(iline,j)); + end + end + Tabchar=cell2tab(CoordCell,' | ');%transform cells into table ready for display + val=min(size(Coord,1),val); + set(handles.ListCoord,'Value',max(val,1)) + set(handles.ListCoord,'String',Tabchar) +end Index: /trunk/src/proj_field.m =================================================================== --- /trunk/src/proj_field.m (revision 2) +++ /trunk/src/proj_field.m (revision 2) @@ -0,0 +1,1617 @@ +%'proj_field': projects the field on a projection object +%-------------------------------------------------------------------------- +% function [ProjData,errormsg]=proj_field(FieldData,ObjectData,IndexObj) +% +% OUTPUT: +% ProjData structure containing the fields of the input field FieldData, +% transmitted or projected on the object, plus the additional fields +% .UMax, .UMin, .VMax, .VMin: min and max of velocity components in a domain +% .UMean,VMean: mean of the velocity components in a domain +% .AMin, AMax: min and max of a scalar +% .AMean: mean of a scalar in a domain +% .NbPix; +% .DimName= names of the matrix dimensions (matlab cell) +% .DimValue= values of the matricx dimensions (matlab vector, same length as .DimName); +% .VarName= names of the variables [ProjData.VarName {'A','AMean','AMin','AMax'}]; +% .VarDimNameIndex= dimensions of the variables, indicated by indices in the list .DimName; +% +%INPUT +% ObjectData: structure characterizing the projection object +% .Style : style of projection object +% .ProjMode=type of projection ; +% .CoordType: 'px' or 'phys' type of coordinates defining the object position +% .Phi angle of rotation (=0 by default) +% .ProjAngle=angle of projection; +% .DX,.DY,.DZ=increments along each coordinate +% .Coord(nbpoints,3): set of coordinates defining the object position; + +%FieldData: data of the field to be projected on the projection object, with optional fields +% .Txt: error message, transmitted to the projection +% .CoordType: 'px' or 'phys' type of coordinates of the field, must be the same as for the projection object, transmitted +% .Mesh: typical distance between data points (used for mouse action or display), transmitted +% .CoordUnit, .TimeUnit, .dt: transmitted +% standardised description of fields, nc-formated Matlab structure with fields: +% .ListGlobalAttribute: cell listing the names of the global attributes +% .Att_1,Att_2... : values of the global attributes +% .ListDimName: cell listing the names of the array dimensions +% .DimValue: array dimension values (Matlab vector with the same length as .ListDimName +% .ListVarName: cell listing the names of the variables +% .VarDimIndex: cell containing the set of dimension indices (in list .ListDimName) for each variable of .ListVarName +% .VarAttribute: cell of structures s containing names and values of variable attributes (s.name=value) for each variable of .ListVarName +% .Var1, .Var2....: variables (Matlab arrays) with names listed in .ListVarName +% The variables are grouped in 'fields', made of a set of variables with common dimensions (using the function find_field_indices) +% The variable attribute 'Role' is used to define the role for plotting: +% Role = 'scalar': (default) represents a scalar field +% = 'coord': represents a set of unstructured coordinates, whose +% space dimension is given by the last array dimension (called 'nb_dim'). +% = 'coord_x', 'coord_y', 'coord_z': represents a separate set of +% unstructured coordinate x, y or z +% = 'vector': represents a vector field whose number of components +% is given by the last dimension (called 'nb_dim') +% = 'vector_x', 'vector_y', 'vector_z' :represents the x, y or z component of a vector +% = 'warnflag' : provides a warning flag about the quality of data in a 'Field', default=0, no warning +% = 'errorflag': provides an error flag marking false data, +% default=0, no error. Different non zero values can represent different criteria of elimination. +% +% Default role of variables (by name) +% vector field: +% .X,.Y: position of the velocity vectors, projected on the object +% .U, .V, .W: velocity components, projected on the object +% .C, .CName: scalar associated to the vector +% .F : equivalent to 'warnflag' +% .FF: equivalent to 'errorflag' +% scalar field or image: +% .AName: name of a scalar (to be calculated from velocity fields after projection), transmitted +% .A: scalar, projected on the object +% .AX, .AY: positions for the scalar +% case of a structured grid: A is a dim 2 matrix and .AX=[first last] (length 2 vector) represents the first and last abscissa of the grid +% case of an unstructured scalar: A is a vector, AX and AY the corresponding coordinates +% +%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +% Copyright Joel Sommeria, 2008, LEGI / CNRS-UJF-INPG, sommeria@coriolis-legi.org. +%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +% This file is part of the toolbox UVMAT. +% +% UVMAT is free software; you can redistribute it and/or modify +% it under the terms of the GNU General Public License as published by +% the Free Software Foundation; either version 2 of the License, or +% (at your option) any later version. +% +% UVMAT is distributed in the hope that it will be useful, +% but WITHOUT ANY WARRANTY; without even the implied warranty of +% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +% GNU General Public License (file UVMAT/COPYING.txt) for more details. +%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA + +function [ProjData,errormsg]=proj_field(FieldData,ObjectData,IndexObj) + +if isfield(ObjectData,'ProjMode') && (isequal(ObjectData.ProjMode,'none')||isequal(ObjectData.ProjMode,'mask_inside')||isequal(ObjectData.ProjMode,'mask_outside')) + ProjData=[]; + return +end +%introduce default field properties (reading old standards) +if ~isfield(ObjectData,'Style')||~isfield(ObjectData,'Coord')||~isfield(ObjectData,'ProjMode') + ProjData=FieldData; + return +end + +% OBSOLETE +if isfield(ObjectData,'XMax') && ~isempty(ObjectData.XMax) + ObjectData.RangeX(1)=ObjectData.XMax; +end +if isfield(ObjectData,'XMin') && ~isempty(ObjectData.XMin) + ObjectData.RangeX(2)=ObjectData.XMin; +end +if isfield(ObjectData,'YMax') && ~isempty(ObjectData.YMax) + ObjectData.RangeY(1)=ObjectData.YMax; +end +if isfield(ObjectData,'YMin') && ~isempty(ObjectData.YMin) + ObjectData.RangeY(2)=ObjectData.YMin; +end +if isfield(ObjectData,'ZMax') && ~isempty(ObjectData.ZMax) + ObjectData.RangeZ(1)=ObjectData.ZMax; +end +if isfield(ObjectData,'ZMin') && ~isempty(ObjectData.ZMin) + ObjectData.RangeZ(2)=ObjectData.ZMin; +end +%%%%%%%%%% + +% FieldData=document_field(FieldData);%transform FieldData to the standard format +% if ~isfield(FieldData,'VarAttribute') +% FieldData.VarAttribute={}; +% end + +if isequal(ObjectData.Style,'points') + [ProjData,errormsg]=proj_points(FieldData,ObjectData); +elseif isequal(ObjectData.Style,'line')|isequal(ObjectData.Style,'polyline') + [ProjData,errormsg] = proj_line(FieldData,ObjectData); +elseif isequal(ObjectData.Style,'polygon')|isequal(ObjectData.Style,'rectangle')|isequal(ObjectData.Style,'ellipse') + if isequal(ObjectData.ProjMode,'inside')|isequal(ObjectData.ProjMode,'outside') + [ProjData,errormsg] = proj_patch(FieldData,ObjectData); + else + [ProjData,errormsg] = proj_line(FieldData,ObjectData); + end + %A FAIRE : GERER MASK +elseif isequal(ObjectData.Style,'plane') +% if isfield(FieldData,'NbDim') & isequal(FieldData.NbDim,3) +% ProjData= proj_plane3D(FieldData,ObjectData);% +% else + [ProjData,errormsg] = proj_plane(FieldData,ObjectData); +% end +end +if exist('IndexObj','var') + ProjData.IndexObj=IndexObj;%transfer object index +end + +%----------------------------------------------------------------- +%project on a set of points +function [ProjData,errormsg]=proj_points(FieldData,ObjectData)%% +%------------------------------------------------------------------- + +siz=size(ObjectData.Coord); +width=0; +if isfield(ObjectData,'Range') + width=ObjectData.Range(1,2); +end +if isfield(ObjectData,'RangeX')&~isempty(ObjectData.RangeX) + width=max(ObjectData.RangeX); +end +if isfield(ObjectData,'RangeY')&~isempty(ObjectData.RangeY) + width=max(width,max(ObjectData.RangeY)); +end +if isfield(ObjectData,'RangeZ')&~isempty(ObjectData.RangeZ) + width=max(width,max(ObjectData.RangeZ)); +end +if isequal(ObjectData.ProjMode,'projection') + if width==0 + errormsg='projection range around points needed'; + return + end +elseif ~isequal(ObjectData.ProjMode,'interp') + errormsg=(['ProjMode option ' ObjectData.ProjMode ' not available in proj_field']); + return +end +ProjData=proj_heading(FieldData,ObjectData); +ProjData.NbDim=0; +%ProjData.ListDimName= {'nb_points'}; +%ProjData.DimValue=siz(1); %nbre of projection points + + +% idimvar=0; +[CellVarIndex,NbDim,VarTypeCell,errormsg]=find_field_indices(FieldData); +if ~isempty(errormsg) + errormsg=['error in proj_field/proj_points:' errormsg]; + return +end +%LOOP ON GROUPS OF VARIABLES SHARING THE SAME DIMENSIONS +% CellVarIndex=cells of variable index arrays +% ivar_new=0; % index of the current variable in the projected field +% icoord=0; +for icell=1:length(CellVarIndex) + if NbDim(icell)==1 + continue + end + VarIndex=CellVarIndex{icell};% indices of the selected variables in the list FieldData.ListVarName + VarType=VarTypeCell{icell}; + ivar_X=VarType.coord_x; + ivar_Y=VarType.coord_y; + ivar_Z=VarType.coord_z; +% ivar_U=VarType.vector_x; +% ivar_V=VarType.vector_y; +% ivar_W=VarType.vector_z; +% ivar_C=VarType.scalar ; + ivar_Anc=VarType.ancillary; +% test_anc=zeros(size(VarIndex)); + test_anc(ivar_Anc)=ones(size(ivar_Anc)); + ivar_F=VarType.warnflag; + ivar_FF=VarType.errorflag; + VarIndex([ivar_X ivar_Y ivar_Z ivar_Anc ivar_F ivar_FF])=[];% not projected variables removed frlom list + if isempty(ivar_X) + test_grid=1;%test for input data on regular grid (e.g. image)coordinates + + else + if length(ivar_X)>1 | length(ivar_Y)>1 | length(ivar_Z)>1 + errormsg='multiple coordinate input in proj_field.m'; + return + end + if length(ivar_Y)~=1 + errormsg='y coordinate not defined in proj_field.m'; + return + end + test_grid=0; + end + ProjData.ListVarName={'Y','X','NbVal'}; + ProjData.VarDimName={'nb_points','nb_points','nb_points'}; + %ProjData.VarDimIndex={[1],[1],[1]}; + ProjData.VarAttribute{1}.Role='ancillary'; + ProjData.VarAttribute{2}.Role='ancillary'; + ProjData.VarAttribute{3}.Role='ancillary'; + for ivar=VarIndex + VarName=FieldData.ListVarName{ivar}; + ProjData.ListVarName=[ProjData.ListVarName {VarName}]; + %ProjData.VarDimIndex=[ProjData.VarDimIndex {[1]}]; + ProjData.VarDimName=[ProjData.VarDimName {'nb_points'}]; + end + if ~test_grid + eval(['coord_x=FieldData.' FieldData.ListVarName{ivar_X} ';']) + eval(['coord_y=FieldData.' FieldData.ListVarName{ivar_Y} ';']) + test3D=0;% TEST 3D CASE : NOT COMPLETED , 3D CASE : NOT COMPLETED + if length(ivar_Z)==1 + eval(['coord_z=FieldData.' FieldData.ListVarName{ivar_Z} ';']) + test3D=1; + end +% if length(ivar_U)>1 | length(ivar_V)>1 | length(ivar_W)>1 +% warndlg_uvmat('multiple vector input in proj_field.m','ERROR') +% return +% end + if length(ivar_F)>1 | length(ivar_FF)>1 + warndlg_uvmat('multiple flag input in proj_field.m','ERROR') + return + end + + for ipoint=1:siz(1) + Xpoint=ObjectData.Coord(ipoint,:); + distX=coord_x-Xpoint(1); + distY=coord_y-Xpoint(2); + dist=distX.*distX+distY.*distY; + indsel=find(dist=2 & VarType.coord(1:2) > 0; + AYName=FieldData.ListVarName{VarType.coord(1)}; + AXName=FieldData.ListVarName{VarType.coord(2)}; + eval(['AX=FieldData.' AXName ';']);% set of x positions + eval(['AY=FieldData.' AYName ';']);% set of y positions + AName=FieldData.ListVarName{VarIndex(1)}; + eval(['A=FieldData.' AName ';']);% scalar + npxy=size(A); + +% % nbcolor=1; %default +% for idim=1:length(ListDimName) +% DimName=ListDimName{idim}; +% if isequal(DimName,'rgb')|isequal(DimName,'nb_coord')|isequal(DimName,'nb_coord_i') +% nbcolor=npxy(idim); +% DimIndices(idim)=[]; +% npxy(idim)=[]; +% end +% if isequal(DimName,'nb_coord_j')% NOTE: CASE OF TENSOR NOT TREATED +% DimIndices(idim)=[]; +% npxy(idim)=[]; +% end +% end + ind_1=find(npxy==1); + %DimIndices(ind_1)=[]; %suppress singleton dimensions +% indxy=find(DimVarIndex(DimIndices));%select dimension variables (DimIndices non zero) + %nb_dim=length(DimIndices)%number of space dimensions + nb_dim=numel(VarType.coord); + Coord_z=[]; + Coord_y=[]; + Coord_x=[]; + for idim=1:nb_dim %loop on space dimensions + test_interp(idim)=0;%test for coordiate interpolation (non regular grid), =0 by default + test_coord(idim)=0;%test for defined coordinates, =0 by default + %ivar=DimVarIndex(DimIndices(idim));% index of the variable corresponding to the current dimension + ivar=VarType.coord(idim); +% if ~isequal(ivar,0)% a variable corresponds to the current dimension + eval(['Coord{idim}=FieldData.' FieldData.ListVarName{ivar} ';']) ;% position for the first index + if numel(Coord{idim})==2 + DCoord_min(idim)= (Coord{idim}(2)-Coord{idim}(1))/(npxy(idim)-1); + else + DCoord=diff(Coord{idim}); + DCoord_min(idim)=min(DCoord); + DCoord_max=max(DCoord); + test_direct(idim)=DCoord_max>0;% =1 for increasing values, 0 otherwise + test_direct_min=DCoord_min(idim)>0;% =1 for increasing values, 0 otherwise + if ~isequal(test_direct(idim),test_direct_min) + errormsg=['non monotonic dimension variable # ' num2str(idim) ' in proj_field.m']; + return + end + test_interp(idim)=(DCoord_max-DCoord_min(idim))> 0.0001*abs(DCoord_max);% test grid regularity + test_coord(idim)=1; + end +% else % no variable associated with the first dimension, look fo variable attributes Coord_1, _2 or _3 +% Coord_i_str=['Coord_' num2str(idim)]; +% DCoord_min(idim)=1;%default +% Coord{idim}=[0.5 npxy(idim)]; +% test_direct(idim)=1; +% end + end + DX=DCoord_min(2); + DY=DCoord_min(1); + for ipoint=1:siz(1) + xwidth=width/(abs(DX)); + ywidth=width/(abs(DY)); + i_min=round((ObjectData.Coord(ipoint,1)-Coord{2}(1))/DX+0.5-xwidth); %minimum index of the selected region + i_min=max(1,i_min);%restrict to field limit + i_plus=round((ObjectData.Coord(ipoint,1)-Coord{2}(1))/DX+0.5+xwidth); + i_plus=min(npxy(2),i_plus); %restrict to field limit + j_min=round((ObjectData.Coord(ipoint,2)-Coord{1}(1))/DY-ywidth+0.5); + j_min=max(1,j_min); + j_plus=round((ObjectData.Coord(ipoint,2)-Coord{1}(1))/DY+ywidth+0.5); + j_plus=min(npxy(1),j_plus); + ProjData.X(ipoint,1)=ObjectData.Coord(ipoint,1); + ProjData.Y(ipoint,1)=ObjectData.Coord(ipoint,2); + i_int=[i_min:i_plus]; + j_int=[j_min:j_plus]; + ProjData.NbVal(ipoint,1)=length(j_int)*length(i_int); + if isempty(i_int) | isempty(j_int) + for ivar=VarIndex + eval(['ProjData.' FieldData.ListVarName{ivar} '(ipoint,:)=NaN;']); + end + errormsg=['no data points in the selected projection range ' num2str(width) ]; + else + %TODO: introduce circle in the selected subregion + %[I,J]=meshgrid([1:j_int],[1:i_int]); + for ivar=VarIndex + eval(['Avalue=FieldData.' FieldData.ListVarName{ivar} '(j_int,i_int,:);']); + eval(['ProjData.' FieldData.ListVarName{ivar} '(ipoint,:)=mean(mean(Avalue));']); + end + end + end + end + end +end + +%----------------------------------------------------------------- +%project in a patch +function [ProjData,errormsg]=proj_patch(FieldData,ObjectData)%% +%------------------------------------------------------------------- +ProjData=proj_heading(FieldData,ObjectData); + +objectfield=fieldnames(ObjectData); +widthx=0; +widthy=0; +if isfield(ObjectData,'RangeX')&~isempty(ObjectData.RangeX) + widthx=max(ObjectData.RangeX); +end +if isfield(ObjectData,'RangeY')&~isempty(ObjectData.RangeY) + widthy=max(ObjectData.RangeY); +end + +%A REVOIR, GENERALISER: UTILISER proj_line +ProjData.NbDim=1; +ProjData.ListDimName={};%name of dimension +ProjData.DimValue=[];%values of dimension (nbre of vectors) +ProjData.ListVarName={}; +%ProjData.VarDimIndex={}; +ProjData.VarDimName={}; +if isfield (FieldData,'ListVarAttribute') + ProjData.ListVarAttribute=FieldData.ListVarAttribute;%list of variable attribute names + for iattr=1:length(ProjData.ListVarAttribute)%initialization of variable attribute values + AttrName=ProjData.ListVarAttribute{iattr}; + eval(['ProjData.' AttrName '={};']) + end; +end + +%group the variables (fields of 'FieldData') in cells of variables with the same dimensions +testfalse=0; +ListIndex={}; +% DimVarIndex=0;%initilise list of indices for dimension variables +idimvar=0; +[CellVarIndex,NbDim,VarTypeCell,errormsg]=find_field_indices(FieldData); +if ~isempty(errormsg) + errormsg=['error in proj_field/proj_patch:' errormsg]; + return +end + +%LOOP ON GROUPS OF VARIABLES SHARING THE SAME DIMENSIONS +dimcounter=0; +for icell=1:length(CellVarIndex) + testX=0; + testY=0; + test_Amat=0; + testfalse=0; + VarIndex=CellVarIndex{icell};% indices of the selected variables in the list FieldData.ListVarName + VarType=VarTypeCell{icell}; + % DimIndices=FieldData.VarDimIndex{VarIndex(1)};%indices of the dimensions of the first variable (common to all variables in the cell) + if NbDim(icell)~=2% proj_patch acts only on fields of space dimension 2 + continue + end + testX=~isempty(VarType.coord_x) && ~isempty(VarType.coord_y); + testfalse=~isempty(VarType.errorflag); + testproj(VarIndex)=zeros(size(VarIndex));%default + testproj(VarType.scalar)=1; + testproj(VarType.vector_x)=1; + testproj(VarType.vector_y)=1; + testproj(VarType.vector_z)=1; + testproj(VarType.image)=1; + testproj(VarType.color)=1; + VarIndex=VarIndex(find(testproj(VarIndex)));%select only the projected variables + if testX %case of unstructured coordinates + eval(['nbpoint=numel(FieldData.' FieldData.ListVarName{VarIndex(1)} ');']) + for ivar=[VarIndex VarType.coord_x VarType.coord_y VarType.errorflag] + VarName=FieldData.ListVarName{ivar}; + eval(['FieldData.' VarName '=reshape(FieldData.' VarName ',nbpoint,1);']) + end + XName=FieldData.ListVarName{VarType.coord_x}; + YName=FieldData.ListVarName{VarType.coord_y}; + eval(['coord_x=FieldData.' XName ';']) + eval(['coord_y=FieldData.' YName ';']) + end + if testfalse + FFName=FieldData.ListVarName{VarType.errorflag}; + eval(['errorflag=FieldData.' FFName ';']) + end + % image or 2D matrix + if numel(VarType.coord)>=2 & VarType.coord(1:2) > 0; + test_Amat=1;%image or 2D matrix + AYName=FieldData.ListVarName{VarType.coord(1)}; + AXName=FieldData.ListVarName{VarType.coord(2)}; + eval(['AX=FieldData.' AXName ';'])% x coordinate + eval(['AY=FieldData.' AYName ';'])% y coordinate + VarName=FieldData.ListVarName{VarIndex(1)}; + eval(['DimValue=size(FieldData.' VarName ');']) + testcolor=find(numel(DimValue)==3); +% errormsg='multicomponent field not projected'; + + for idim=1:length(DimValue) + Coord_i_str=['Coord_' num2str(idim)]; + DCoord_min(idim)=1;%default + Coord{idim}=[0.5 DimValue(idim)]; + test_direct(idim)=1; +% if isfield(FieldData,'VarAttribute') +% for ivar=VarIndex +% if length(FieldData.VarAttribute)>=ivar & isfield(FieldData.VarAttribute{ivar},Coord_i_str)% if there is a variable attribute named Coord_1, _2 or _3 +% eval(['Coord_i=FieldData.VarAttribute{ivar}.' Coord_i_str ';']);%'range x +% if isnumeric(Coord_i) +% if length(Coord_i)>=2 +% Coord{idim}=[Coord_i(1) Coord_i(end)]; +% %test_direct(idim)=(Coord{idim}(2)>Coord{idim}(1)); +% else +% warndlg_uvmat(['two values needed for ' Coord_i_str 'in proj_field.m'],'ERROR') +% return +% end +% else +% warndlg_uvmat(['non numerical coordinate attributes' Coord_i_str 'in proj_field.m'],'ERROR') +% return +% end +% %test_coord(idim)=1; +% DCoord_min(idim)=(Coord{idim}(end)-Coord{idim}(1))/(DimValue(idim)-1); +% end +% end +% end + end + AX=linspace(Coord{2}(1),Coord{2}(2),DimValue(2)); + AY=linspace(Coord{1}(1),Coord{1}(2),DimValue(1)); %TODO : 3D case + if length(DimValue)==3 + testcolor=1; + npxy(3)=3; + else + testcolor=0; + npxy(3)=1; + end + [Xi,Yi]=meshgrid(AX,AY); + npxy(1)=length(AY); + npxy(2)=length(AX); + Xi=reshape(Xi,npxy(1)*npxy(2),1); + Yi=reshape(Yi,npxy(1)*npxy(2),1); + for ivar=1:length(VarIndex) + VarName=FieldData.ListVarName{VarIndex(ivar)}; + eval(['FieldData.' VarName '=reshape(FieldData.' VarName ',npxy(1)*npxy(2),npxy(3));']); % keep only non false vectors + end + end +%select the indices in the range of action + testin=[];%default + if isequal(ObjectData.Style,'rectangle') +% if ~isfield(ObjectData,'RangeX')|~isfield(ObjectData,'RangeY') +% errormsg='rectangle half sides RangeX and RangeY needed' +% return +% end + if testX + distX=abs(coord_x-ObjectData.Coord(1,1)); + distY=abs(coord_y-ObjectData.Coord(1,2)); + testin=distX=2 + width=abs(ObjectData.Range(1,2)); +end +if isfield(ObjectData,'RangeY') + width=max(ObjectData.RangeY); +end + +% default output +errormsg=[];%default +Xline=[]; +flux=0; +circul=0; +liny=ObjectData.Coord(:,2); +siz_line=size(ObjectData.Coord); +if siz_line(1)<2 + return% line needs at least 2 points to be defined +end +testfalse=0; +ListIndex={}; + +%angles of the polyline and boundaries of action +dlinx=diff(ObjectData.Coord(:,1)); +dliny=diff(ObjectData.Coord(:,2)); +theta=angle(dlinx+i*dliny);%angle of each segment +theta(siz_line(1))=theta(siz_line(1)-1); +% determine a rectangles at +-width from the line (only used for the ProjMode='projection or 'filter') +if isequal(ProjMode,'projection') || isequal(ProjMode,'filter') + xsup(1)=ObjectData.Coord(1,1)-width*sin(theta(1)); + xinf(1)=ObjectData.Coord(1,1)+width*sin(theta(1)); + ysup(1)=ObjectData.Coord(1,2)+width*cos(theta(1)); + yinf(1)=ObjectData.Coord(1,2)-width*cos(theta(1)); + for ip=2:siz_line(1) + xsup(ip)=ObjectData.Coord(ip,1)-width*sin((theta(ip)+theta(ip-1))/2)/cos((theta(ip-1)-theta(ip))/2); + xinf(ip)=ObjectData.Coord(ip,1)+width*sin((theta(ip)+theta(ip-1))/2)/cos((theta(ip-1)-theta(ip))/2); + ysup(ip)=ObjectData.Coord(ip,2)+width*cos((theta(ip)+theta(ip-1))/2)/cos((theta(ip-1)-theta(ip))/2); + yinf(ip)=ObjectData.Coord(ip,2)-width*cos((theta(ip)+theta(ip-1))/2)/cos((theta(ip-1)-theta(ip))/2); + end +end + +%group the variables (fields of 'FieldData') in cells of variables with the same dimensions +[CellVarIndex,NbDim,VarTypeCell,errormsg]=find_field_indices(FieldData); +if ~isempty(errormsg) + errormsg=['error in proj_field/proj_line:' errormsg]; + return +end + +% loop on variable cells with the same space dimension +ProjData.ListVarName={}; +ProjData.VarDimName={}; +for icell=1:length(CellVarIndex) + VarIndex=CellVarIndex{icell};% indices of the selected variables in the list FieldData.ListVarName + VarType=VarTypeCell{icell}; %types of variables + if NbDim(icell)~=2% proj_line acts only on fields of space dimension 2, TODO: check 3D case + continue + end + testX=~isempty(VarType.coord_x) && ~isempty(VarType.coord_y);% test for unstructured coordinates + testU=~isempty(VarType.vector_x) && ~isempty(VarType.vector_y);% test for vectors + testfalse=~isempty(VarType.errorflag);% test for error flag + testproj(VarIndex)=zeros(size(VarIndex));% test =1 for simply projected variables, default =0 + %=0 for vector components, treated separately + testproj(VarType.scalar)=1; + testproj(VarType.image)=1; + testproj(VarType.color)=1; + VarIndex=VarIndex(find(testproj(VarIndex)));%select only the projected variables + if testU + VarIndex=[VarIndex VarType.vector_x VarType.vector_y];%append u and v at the end of the list of variables + end + %identify vector components + if testU + UName=FieldData.ListVarName{VarType.vector_x}; + VName=FieldData.ListVarName{VarType.vector_y}; + eval(['vector_x=FieldData.' UName ';']) + eval(['vector_y=FieldData.' VName ';']) + end + %identify error flag + if testfalse + FFName=FieldData.ListVarName{VarType.errorflag}; + eval(['errorflag=FieldData.' FFName ';']) + end + % check needed object properties for unstructured positions (position given by the variables with role coord_x, coord_y + if testX + if ~isequal(ProjMode,'interp') + if width==0 + errormsg='range of the projection object is missing'; + return + else + lambda=2/(width*width); %smoothing factor used for filter: weight exp(-2) at distance width from the line + end + end + if ~isequal(ProjMode,'projection') + if isfield(ObjectData,'DX')&~isempty(ObjectData.DX) + DX=abs(ObjectData.DX);%mesh of interpolation points along the line + else + errormsg='DX missing'; + return + end + end + XName= FieldData.ListVarName{VarType.coord_x}; + YName= FieldData.ListVarName{VarType.coord_y}; + eval(['coord_x=FieldData.' XName ';']) + eval(['coord_y=FieldData.' YName ';']) + end + %initiate projection + for ivar=1:length(VarIndex) + ProjLine{ivar}=[]; + end + XLine=[]; + linelengthtot=0; + +% circul=0; +% flux=0; + %%%%%%% % A FAIRE CALCULER MEAN DES QUANTITES %%%%%% + %case of unstructured coordinates + if testX + for ip=1:siz_line(1)-1 %Loop on the segments of the polyline + linelength=sqrt(dlinx(ip)*dlinx(ip)+dliny(ip)*dliny(ip)); + %select the vector indices in the range of action + if testfalse + flagsel=(errorflag==0); % keep only non false vectors + else + flagsel=ones(size(coord_x)); + end + if isequal(ProjMode,'projection') | isequal(ProjMode,'filter') + flagsel=flagsel & ((coord_y -yinf(ip))*(xinf(ip+1)-xinf(ip))>(coord_x-xinf(ip))*(yinf(ip+1)-yinf(ip))) ... + & ((coord_y -ysup(ip))*(xsup(ip+1)-xsup(ip))<(coord_x-xsup(ip))*(ysup(ip+1)-ysup(ip))) ... + & ((coord_y -yinf(ip+1))*(xsup(ip+1)-xinf(ip+1))>(coord_x-xinf(ip+1))*(ysup(ip+1)-yinf(ip+1))) ... + & ((coord_y -yinf(ip))*(xsup(ip)-xinf(ip))<(coord_x-xinf(ip))*(ysup(ip)-yinf(ip))); + end + indsel=find(flagsel);%indsel =indices of good vectors + X_sel=coord_x(indsel); + Y_sel=coord_y(indsel); + nbvar=0; + for iselect=1:numel(VarIndex)-2*testU + VarName=FieldData.ListVarName{VarIndex(iselect)}; + eval(['ProjVar{iselect}=FieldData.' VarName '(indsel);']);%scalar value + end + if testU + ProjVar{numel(VarIndex)-1}=cos(theta(ip))*vector_x(indsel)+sin(theta(ip))*vector_y(indsel);% longitudinal component + ProjVar{numel(VarIndex)}=-sin(theta(ip))*vector_x(indsel)+cos(theta(ip))*vector_y(indsel);%transverse component + end + if isequal(ProjMode,'projection') + sintheta=sin(theta(ip)); + costheta=cos(theta(ip)); + Xproj=(X_sel-ObjectData.Coord(ip,1))*costheta + (Y_sel-ObjectData.Coord(ip,2))*sintheta; %projection on the line + [Xproj,indsort]=sort(Xproj); + for ivar=1:numel(ProjVar) + if ~isempty(ProjVar{ivar}) + ProjVar{ivar}=ProjVar{ivar}(indsort); + end + end + elseif isequal(ProjMode,'interp') %linear interpolation: + npoint=floor(linelength/DX)+1;% nbre of points in the profile (interval DX) + Xproj=[linelength/(2*npoint):linelength/npoint:linelength-linelength/(2*npoint)]; + xreg=cos(theta(ip))*Xproj+ObjectData.Coord(ip,1); + yreg=sin(theta(ip))*Xproj+ObjectData.Coord(ip,2); + for ivar=1:numel(ProjVar) + if ~isempty(ProjVar{ivar}) + ProjVar{ivar}=griddata_uvmat(X_sel,Y_sel,ProjVar{ivar},xreg,yreg); + end + end + elseif isequal(ProjMode,'filter') %filtering + npoint=floor(linelength/DX)+1;% nbre of points in the profile (interval DX) + Xproj=[linelength/(2*npoint):linelength/npoint:linelength-linelength/(2*npoint)]; + siz=size(X_sel); + xregij=cos(theta(ip))*Xproj'*ones(1,siz(2))+ObjectData.Coord(ip,1); + yregij=sin(theta(ip))*Xproj'*ones(1,siz(2))+ObjectData.Coord(ip,2); + xij=ones(npoint,1)*X_sel; + yij=ones(npoint,1)*Y_sel; + Aij=exp(-lambda*((xij-xregij).*(xij-xregij)+(yij-yregij).*(yij-yregij))); + norm=ones(1,siz(2))*Aij'; + for ivar=1:numel(ProjVar) + if ~isempty(ProjVar{ivar}) + ProjVar{ivar}=ProjVar{ivar}*Aij'./norm; + end + end + end + %prolongate the total record + for ivar=1:numel(ProjVar) + if ~isempty(ProjVar{ivar}) + ProjLine{ivar}=[ProjLine{ivar}; ProjVar{ivar}]; + end + end + XLine=[XLine ;(Xproj+linelengthtot)];%along line abscissa + linelengthtot=linelengthtot+linelength; + % circul=circul+(sum(U_sel))*linelength/npoint; + % flux=flux+(sum(V_sel))*linelength/npoint; + end + ProjData.X=XLine'; + cur_index=1; + ProjData.ListVarName=[ProjData.ListVarName {XName}]; + ProjData.VarDimName=[ProjData.VarDimName {XName}]; + ProjData.VarAttribute{1}.long_name='abscissa along line'; + for iselect=1:numel(VarIndex) + VarName=FieldData.ListVarName{VarIndex(iselect)}; + eval(['ProjData.' VarName '=ProjLine{iselect};']) + ProjData.ListVarName=[ProjData.ListVarName {VarName}]; + ProjData.VarDimName=[ProjData.VarDimName {XName}]; + ProjData.VarAttribute{iselect}=FieldData.VarAttribute{VarIndex(iselect)}; + end + + %case of structured coordinates + elseif numel(VarType.coord)>=2 & VarType.coord(1:2) > 0; + if ~isequal(ObjectData.Style,'line')% exclude polyline + errormsg=['no projection available on ' ObjectData.Style 'for structured coordinates']; % + else + test_Amat=1;%image or 2D matrix + test_interp2=0;%default +% if ~isempty(VarType.coord_y) + AYName=FieldData.ListVarName{VarType.coord(1)}; + AXName=FieldData.ListVarName{VarType.coord(2)}; + eval(['AX=FieldData.' AXName ';']);% set of x positions + eval(['AY=FieldData.' AYName ';']);% set of y positions + AName=FieldData.ListVarName{VarIndex(1)}; + eval(['A=FieldData.' AName ';']);% scalar + npxy=size(A); + npx=npxy(2); + npy=npxy(1); + if numel(AX)==2 + DX=(AX(2)-AX(1))/(npx-1); + else + DX_vec=diff(AX); + DX=max(DX_vec); + DX_min=min(DX_vec); + if (DX-DX_min)>0.0001*abs(DX) + test_interp2=1; + DX=DX_min; + end + end + if numel(AY)==2 + DY=(AY(2)-AY(1))/(npy-1); + else + DY_vec=diff(AY); + DY=max(DY_vec); + DY_min=min(DY_vec); + if (DY-DY_min)>0.0001*abs(DY) + test_interp2=1; + DY=DY_min; + end + end + AXI=linspace(AX(1),AX(end), npx);%set of x positions for the interpolated input data + AYI=linspace(AY(1),AY(end), npy);%set of x positions for the interpolated input data + if isfield(ObjectData,'DX') + DXY_line=ObjectData.DX;%mesh on the projection line + else + DXY_line=sqrt(abs(DX*DY));% mesh on the projection line + end + dlinx=ObjectData.Coord(2,1)-ObjectData.Coord(1,1); + dliny=ObjectData.Coord(2,2)-ObjectData.Coord(1,2); + linelength=sqrt(dlinx*dlinx+dliny*dliny); + theta=angle(dlinx+i*dliny);%angle of the line + if isfield(FieldData,'RangeX') + XMin=min(FieldData.RangeX);%shift of the origin on the line + else + XMin=0; + end + eval(['ProjData.' AXName '=linspace(XMin,XMin+linelength,linelength/DXY_line+1);'])%abscissa of the new pixels along the line + y=linspace(-width,width,2*width/DXY_line+1);%ordintes of the new pixels (coordinate across the line) + eval(['npX=length(ProjData.' AXName ');']) + npY=length(y); %TODO: utiliser proj_grid + eval(['[X,Y]=meshgrid(ProjData.' AXName ',y);'])%grid in the line coordinates + XIMA=ObjectData.Coord(1,1)+(X-XMin)*cos(theta)-Y*sin(theta); + YIMA=ObjectData.Coord(1,2)+(X-XMin)*sin(theta)+Y*cos(theta); + XIMA=(XIMA-AX(1))/DX+1;% index of the original image along x + YIMA=(YIMA-AY(1))/DY+1;% index of the original image along y + XIMA=reshape(round(XIMA),1,npX*npY);%indices reorganized in 'line' + YIMA=reshape(round(YIMA),1,npX*npY); + flagin=XIMA>=1 & XIMA<=npx & YIMA >=1 & YIMA<=npy;%flagin=1 inside the original image + ind_in=find(flagin); + ind_out=find(~flagin); + ICOMB=(XIMA-1)*npy+YIMA; + ICOMB=ICOMB(flagin);%index corresponding to XIMA and YIMA in the aligned original image vec_A + nbcolor=1; %color images + if numel(npxy)==2 + nbcolor=1; + elseif length(npxy)==3 + nbcolor=npxy(3); + else + errormsg='multicomponent field not projected'; + display(errormsg) + return + end + nbvar=length(ProjData.ListVarName);% number of var from previous cells + ProjData.ListVarName=[ProjData.ListVarName {AXName}]; + ProjData.VarDimName=[ProjData.VarDimName {AXName}]; + for ivar=VarIndex + VarName{ivar}=FieldData.ListVarName{ivar}; + if test_interp2% interpolate on new grid + eval(['FieldData.' VarName{ivar} '=interp2(FieldData.' AXName ',FieldData.' AYName ',FieldData.' VarName{ivar} ',AXI,AYI'');']) %TO TEST + end + eval(['vec_A=reshape(squeeze(FieldData.' VarName{ivar} '),npx*npy,nbcolor);']) %put the original image in colum + if nbcolor==1 + vec_B(ind_in)=vec_A(ICOMB); + vec_B(ind_out)=zeros(size(ind_out)); + A_out=reshape(vec_B,npY,npX); + eval(['ProjData.' VarName{ivar} '=((sum(A_out,1)/npY))'';']); + elseif nbcolor==3 + vec_B(ind_in,[1:3])=vec_A(ICOMB,:); + vec_B(ind_out,1)=zeros(size(ind_out)); + vec_B(ind_out,2)=zeros(size(ind_out)); + vec_B(ind_out,3)=zeros(size(ind_out)); + A_out=reshape(vec_B,npY,npX,nbcolor); + eval(['ProjData.' VarName{ivar} '=squeeze(sum(A_out,1)/npY);']); + end + ProjData.ListVarName=[ProjData.ListVarName VarName{ivar} ]; + ProjData.VarDimName=[ProjData.VarDimName {AXName}];%to generalize with the initial name of the x coordinate + end + if testU + eval(['vector_x =ProjData.' VarName{VarType.vector_x} ';']) + eval(['vector_y =ProjData.' VarName{VarType.vector_y} ';']) + eval(['ProjData.' VarName{VarType.vector_x} '=cos(theta)*vector_x+sin(theta)*vector_y;']) + eval(['ProjData.' VarName{VarType.vector_y} '=-sin(theta)*vector_x+cos(theta)*vector_y;']) + end + ProjData.VarAttribute{nbvar+1}.long_name='abscissa along line'; + if nbcolor==3 + ProjData.VarDimName{end}={XName,'rgb'}; + end + end + end +end + +% %shotarter case for horizontal or vertical line (A FAIRE +% % Rangx=[0.5 npx-0.5];%image coordiantes of corners +% % Rangy=[npy-0.5 0.5]; +% % if isfield(Calib,'Pxcmx')&isfield(Calib,'Pxcmy')%old calib +% % Rangx=Rangx/Calib.Pxcmx; +% % Rangy=Rangy/Calib.Pxcmy; +% % else +% % [Rangx]=phys_XYZ(Calib,Rangx,[0.5 0.5],[0 0]);%case of translations without rotation and quadratic deformation +% % [xx,Rangy]=phys_XYZ(Calib,[0.5 0.5],Rangy,[0 0]); +% % end +% +% % test_scal=0;%default% 3- 'UserData':(get(handles.Tag,'UserData') + + +%----------------------------------------------------------------- +%project on a plane +% AJOUTER flux,circul,error + function [ProjData,errormsg] = proj_plane(FieldData, ObjectData) +%----------------------------------------------------------------- + +%initialisation of the input parameters of the projection plane +%----------------------------------------------------------------- +ProjMode='projection';%direct projection by default +if isfield(ObjectData,'ProjMode'),ProjMode=ObjectData.ProjMode; end; + +%axis origin +if isempty(ObjectData.Coord) + ObjectData.Coord(1,1)=0;%origin of the plane set to [0 0] by default + ObjectData.Coord(1,2)=0; + ObjectData.Coord(1,3)=0; +end + +%rotation angles +Phi=0;%default +Theta=0; +Psi=0; +if isfield(ObjectData,'Phi')&& ~isempty(ObjectData.Phi) + Phi=(pi/180)*ObjectData.Phi;%first Euler angle in radian +end +if isfield(ObjectData,'Theta')&& ~isempty(ObjectData.Theta) + Theta=(pi/180)*ObjectData.Theta;%second Euler angle in radian +end +if isfield(ObjectData,'Psi')&& ~isempty(ObjectData.Psi) + Psi=(pi/180)*ObjectData.Psi;%third Euler angle in radian +end + +%components of the unity vector normal to the projection plane +NormVec_X=-sin(Phi)*sin(Theta); +NormVec_Y=cos(Phi)*sin(Theta); +NormVec_Z=cos(Theta); + +% test for 3D fields +test3D=0; +if isfield(FieldData,'NbDim') + test3D=isequal(FieldData.NbDim,3); +end +test3C=test3D; %default 3 vel components + +%mesh sizes DX and DY +DX=0; +DY=0; %default +if isfield(ObjectData,'DX')&~isempty(ObjectData.DX) + DX=abs(ObjectData.DX);%mesh of interpolation points +end +if isfield(ObjectData,'DY')&~isempty(ObjectData.DY) + DY=abs(ObjectData.DY);%mesh of interpolation points +end +if ~isequal(ProjMode,'projection') & (DX==0|DY==0) + errormsg='DX or DY missing'; + display(errormsg) + return +end + +%extrema along each axis +testXMin=0; +testXMax=0; +testYMin=0; +testYMax=0; +if isfield(ObjectData,'RangeX') + XMin=min(ObjectData.RangeX); + XMax=max(ObjectData.RangeX); + testXMin=XMax>XMin; + testXMax=1; +end +if isfield(ObjectData,'RangeY') + YMin=min(ObjectData.RangeY); + YMax=max(ObjectData.RangeY); + testYMin=YMax>YMin; + testYMax=1; +end +width=0;%default width of the projection band +if isfield(ObjectData,'RangeZ') + width=max(ObjectData.RangeZ); +end + +% initiate Matlab structure for physical field +ProjData=proj_heading(FieldData,ObjectData); +ProjData.NbDim=2; +ProjData.ListDimName={};%name of dimension +ProjData.DimValue=[];%values of dimension (nbre of vectors) +ProjData.ListVarName={}; +ProjData.VarDimName={}; + +error=0;%default +flux=0; +testfalse=0; +ListIndex={}; + +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% +%group the variables (fields of 'FieldData') in cells of variables with the same dimensions +%----------------------------------------------------------------- +idimvar=0; +[CellVarIndex,NbDim,VarTypeCell,errormsg]=find_field_indices(FieldData); +if ~isempty(errormsg) + errormsg=['error in proj_field/proj_plane:' errormsg]; + return +end +%LOOP ON GROUPS OF VARIABLES SHARING THE SAME DIMENSIONS +% CellVarIndex=cells of variable index arrays +ivar_new=0; % index of the current variable in the projected field +icoord=0; +nbcoord=0;%number of added coordinate variables brought by projection +for icell=1:length(CellVarIndex) + if NbDim(icell)<2 + continue + end + VarIndex=CellVarIndex{icell};% indices of the selected variables in the list FieldData.ListVarName + VarType=VarTypeCell{icell}; + ivar_X=VarType.coord_x; + ivar_Y=VarType.coord_y; + ivar_Z=VarType.coord_z; + ivar_U=VarType.vector_x; + ivar_V=VarType.vector_y; + ivar_W=VarType.vector_z; + ivar_C=VarType.scalar ; + ivar_Anc=VarType.ancillary; + test_anc=zeros(size(VarIndex)); + test_anc(ivar_Anc)=ones(size(ivar_Anc)); + ivar_F=VarType.warnflag; + ivar_FF=VarType.errorflag; + testX=~isempty(ivar_X) && ~isempty(ivar_Y); + %DimIndices=FieldData.VarDimIndex{VarIndex(1)};%indices of the dimensions of the first variable (common to all variables in the cell) + DimCell=FieldData.VarDimName{VarIndex(1)}; + if ischar(DimCell) + DimCell={DimCell};%name of dimensions + end + +%case of input fields with unstructured coordinates + if testX + XName=FieldData.ListVarName{ivar_X}; + YName=FieldData.ListVarName{ivar_Y}; + eval(['coord_x=FieldData.' XName ';']) + eval(['coord_y=FieldData.' YName ';']) + if length(ivar_Z)==1 + ZName=FieldData.ListVarName{ivar_X}; + eval(['coord_z=FieldData.' ZName ';']) + end + + % translate initial coordinates + coord_x=coord_x-ObjectData.Coord(1,1); + coord_y=coord_y-ObjectData.Coord(1,2); + if ~isempty(ivar_Z) + coord_z=coord_z-ObjectData.Coord(1,3); + end + + % selection of the vectors in the projection range (3D case) + if length(ivar_Z)==1 && width > 0 + %components of the unitiy vector normal to the projection plane + fieldZ=NormVec_X*coord_x + NormVec_Y*coord_y+ NormVec_Z*coord_z;% distance to the plane + indcut=find(abs(fieldZ) <= width); + for ivar=VarIndex + VarName=FieldData.ListVarName{ivar}; + eval(['FieldData.' VarName '=FieldData.' VarName '(indcut);']) +% end + % A VOIR : CAS DE VAR STRUCTUREE MAIS PAS GRILLE REGULIERE : INTERPOLER SUR GRILLE REGULIERE + end + coord_x=coord_x(indcut); + coord_y=coord_y(indcut); + coord_z=coord_z(indcut); + end + + %rotate coordinates if needed + if isequal(Phi,0) + coord_X=coord_x; + coord_Y=coord_y; + if ~isequal(Theta,0) + coord_Y=coord_Y *cos(Theta); + end + else + coord_X=(coord_x *cos(Phi) + coord_y* sin(Phi)); + coord_Y=(-coord_x *sin(Phi) + coord_y *cos(Phi))*cos(Theta); + end + if ~isempty(ivar_Z) + coord_Y=coord_Y+coord_z *sin(Theta); + end + if ~isequal(Psi,0) + coord_X=(coord_X *cos(Psi) - coord_Y* sin(Psi));%A VERIFIER + coord_Y=(coord_X *sin(Psi) + coord_Y* cos(Psi)); + end + + %restriction to the range of x and y if imposed + testin=ones(size(coord_X)); %default + testbound=0; + if testXMin + testin=testin & (coord_X >= XMin); + testbound=1; + end + if testXMax + testin=testin & (coord_X <= XMax); + testbound=1; + end + if testYMin + testin=testin & (coord_Y >= YMin); + testbound=1; + end + if testYMin + testin=testin & (coord_Y <= YMax); + testbound=1; + end + if testbound + indcut=find(testin); + for ivar=VarIndex + VarName=FieldData.ListVarName{ivar}; + eval(['FieldData.' VarName '=FieldData.' VarName '(indcut);']) + end + coord_X=coord_X(indcut); + coord_Y=coord_Y(indcut); + if length(ivar_Z)==1 + coord_Z=coord_Z(indcut); + end + end + % different cases of projection + if isequal(ObjectData.ProjMode,'projection') + ProjData.ListDimName=[ProjData.ListDimName FieldData.ListDimName(DimIndices(1))];%add the point index to the list of dimensions + ProjData.DimValue=[ProjData.DimValue length(coord_X)]; + nbvar=0; + for ivar=VarIndex %transfer variables to the projection plane + VarName=FieldData.ListVarName{ivar}; + if ivar==ivar_X %x coordinate + eval(['ProjData.' VarName '=coord_X;']) + elseif ivar==ivar_Y % y coordinate + eval(['ProjData.' VarName '=coord_Y;']) + elseif isempty(ivar_Z) || ivar~=ivar_Z % other variables (except Z coordinate wyhich is not reproduced) + eval(['ProjData.' VarName '=FieldData.' VarName ';']) + end + if isempty(ivar_Z) || ivar~=ivar_Z + ProjData.ListVarName=[ProjData.ListVarName VarName]; + ProjData.VarDimIndex=[ProjData.VarDimIndex DimIndices(1)]; + nbvar=nbvar+1; + if isfield(FieldData,'VarAttribute') & length(FieldData.VarAttribute) >=ivar + ProjData.VarAttribute{nbvar}=FieldData.VarAttribute{ivar}; + end + end + end + elseif isequal(ObjectData.ProjMode,'interp')||isequal(ObjectData.ProjMode,'filter')%interpolate data on a regular grid + coord_x_proj=[XMin:DX:XMax]; + coord_y_proj=[YMin:DY:YMax]; + DimCell={'coord_y','coord_x'}; + %ProjData.DimValue=[length(coord_y_proj) length(coord_x_proj)]; + ProjData.ListVarName={'coord_y','coord_x'}; + ProjData.VarDimName={'coord_y','coord_x'}; + nbcoord=2; + %ProjData.VarDimIndex={}; + ProjData.coord_y=[YMin YMax]; + ProjData.coord_x=[XMin XMax]; + if isempty(ivar_X), ivar_X=0; end; + if isempty(ivar_Y), ivar_Y=0; end; + if isempty(ivar_Z), ivar_Z=0; end; + if isempty(ivar_U), ivar_U=0; end; + if isempty(ivar_V), ivar_V=0; end; + if isempty(ivar_W), ivar_W=0; end; + if isempty(ivar_F), ivar_F=0; end; + if isempty(ivar_FF), ivar_FF=0; end; + if ~isequal(ivar_FF,0) + VarName_FF=FieldData.ListVarName{ivar_FF}; + eval(['indsel=find(FieldData.' VarName_FF '==0);']) + coord_X=coord_X(indsel); + coord_Y=coord_Y(indsel); + end + FF=zeros(1,length(coord_y_proj)*length(coord_x_proj)); + testFF=0; + for ivar=VarIndex + VarName=FieldData.ListVarName{ivar}; + if ~( ivar==ivar_X | ivar==ivar_Y | ivar==ivar_Z | ivar==ivar_F | ivar==ivar_FF | test_anc(ivar)==1) + ivar_new=ivar_new+1; + ProjData.ListVarName=[ProjData.ListVarName {VarName}]; + ProjData.VarDimName=[ProjData.VarDimName {DimCell}]; + %ProjData.VarDimIndex=[ProjData.VarDimIndex {[1 2]}]; + if isfield(FieldData,'VarAttribute') & length(FieldData.VarAttribute) >=ivar + ProjData.VarAttribute{ivar_new+nbcoord}=FieldData.VarAttribute{ivar}; + end +% ProjData.VarAttribute{ivar_new}.Coord_2=[XMin XMax]; +% ProjData.VarAttribute{ivar_new}.Coord_1=[YMin YMax]; + if ~isequal(ivar_FF,0) + eval(['FieldData.' VarName '=FieldData.' VarName '(indsel);']) + end + eval(['ProjData.' VarName '=griddata_uvmat(coord_X,coord_Y,FieldData.' VarName ',coord_x_proj,coord_y_proj'');']) + eval(['varline=reshape(ProjData.' VarName ',1,length(coord_y_proj)*length(coord_x_proj));']) + FFlag= isnan(varline); %detect undefined values NaN + indnan=find(FFlag); + if~isempty(indnan) + varline(indnan)=zeros(size(indnan)); + eval(['ProjData.' VarName '=reshape(varline,length(coord_y_proj),length(coord_x_proj));']) + FF(indnan)=ones(size(indnan)); +% eval(['ProjData.' VarName '(indnan)=zeros(size(indnan));'])%put NaN to 0 +% FF=FF|FFlag; + testFF=1; + end + if ivar==ivar_U + ivar_U=ivar_new; + end + if ivar==ivar_V + ivar_V=ivar_new; + end + if ivar==ivar_W + ivar_W=ivar_new; + end + end + end + if testFF + ProjData.FF=reshape(FF,length(coord_y_proj),length(coord_x_proj)); + ProjData.ListVarName=[ProjData.ListVarName {'FF'}]; + % ProjData.VarDimIndex=[ProjData.VarDimIndex {[1 2]}]; + ProjData.VarDimName=[ProjData.VarDimName {DimCell}]; + ProjData.VarAttribute{ivar_new+1+nbcoord}.Role='errorflag'; + end + end +%case of fields defined on a structured grid + else + AYName=FieldData.ListVarName{VarType.coord(1)}; + AXName=FieldData.ListVarName{VarType.coord(2)}; + eval(['AX=FieldData.' AXName ';']) + eval(['AY=FieldData.' AYName ';']) + VarName=FieldData.ListVarName{VarIndex(1)}; + eval(['DimValue=size(FieldData.' VarName ');']) + ListDimName=FieldData.ListDimName(DimIndices); + ProjData.ListVarName=[{AYName} {AXName} ProjData.ListVarName]; %TODO: check if it already exists in Projdata (several cells) + ProjData.VarDimName=[{AYName} {AXName} ProjData.VarDimName]; + nbcolor=1; %default + for idim=1:length(ListDimName) + DimName=ListDimName{idim}; + if isequal(DimName,'rgb')|isequal(DimName,'nb_coord')|isequal(DimName,'nb_coord_i') + nbcolor=DimValue(idim); + DimIndices(idim)=[]; + DimValue(idim)=[]; + end + if isequal(DimName,'nb_coord_j')% NOTE: CASE OF TENSOR NOT TREATED + DimIndices(idim)=[]; + DimValue(idim)=[]; + end + end + ind_1=find(DimValue==1); + DimIndices(ind_1)=[]; %suppress singleton dimensions +% indxy=find(DimVarIndex(DimIndices));%select dimension variables (DimIndices non zero) + nb_dim=length(DimIndices);%number of space dimensions + Coord_z=[]; + Coord_y=[]; + Coord_x=[]; + + for idim=1:nb_dim %loop on space dimensions + test_interp(idim)=0;%test for coordiate interpolation (non regular grid), =0 by default + test_coord(idim)=0;%test for defined coordinates, =0 by default + ivar=DimVarIndex(DimIndices(idim));% index of the variable corresponding to the current dimension + if ~isequal(ivar,0)% a variable corresponds to the current dimension + eval(['Coord{idim}=FieldData.' FieldData.ListVarName{ivar} ';']) ;% position for the first index + DCoord=diff(Coord{idim}); + DCoord_min(idim)=min(DCoord); + DCoord_max=max(DCoord); + test_direct(idim)=DCoord_max>0;% =1 for increasing values, 0 otherwise + test_direct_min=DCoord_min(idim)>0;% =1 for increasing values, 0 otherwise + if ~isequal(test_direct(idim),test_direct_min) + warndlg_uvmat(['non monotonic dimension variable # ' num2str(idim) ' in proj_field.m'],'ERROR') + return + end + test_interp(idim)=(DCoord_max-DCoord_min(idim))> 0.0001*abs(DCoord_max);% test grid regularity + test_coord(idim)=1; + + else % no variable associated with the first dimension, look for variable attributes Coord_1, _2 or _3 + Coord_i_str=['Coord_' num2str(idim)]; + DCoord_min(idim)=1;%default + Coord{idim}=[0.5 DimValue(idim)-0.5]; + test_direct(idim)=1; +% for ivar=VarIndex +% if isfield(FieldData.VarAttribute{ivar},Coord_i_str)% if there is a variable attribute named Coord_1, _2 or _3 +% eval(['Coord{idim}=FieldData.VarAttribute{ivar}.' Coord_i_str ';']);%'range x +% if isnumeric(Coord{idim}) +% if length(Coord{idim})>=2 +% test_direct(idim)=(Coord{idim}(2)>Coord{idim}(1)); +% else +% warndlg_uvmat(['two values needed for ' Coord_i_str 'in proj_field.m'],'ERROR') +% return +% end +% else +% warndlg_uvmat(['non numerical coordinate attributes' Coord_i_str 'in proj_field.m'],'ERROR') +% return +% end +% DCoord_min(idim)=(Coord{idim}(end)-Coord{idim}(1))/(DimValue(idim)-1); +% end +% end + end + end + if nb_dim==2 + if DY==0 + DY=abs(DCoord_min(1)); + end + npY=1+round(abs(Coord{1}(end)-Coord{1}(1))/DY);%nbre of points after interpolation + npy=1+round(abs(Coord{1}(end)-Coord{1}(1))/abs(DCoord_min(1)));%nbre of points after possible interpolation on a regular grid + if DX==0 + DX=abs(DCoord_min(2)); + end + npX=1+round(abs(Coord{2}(end)-Coord{2}(1))/DX);%nbre of points after interpol + npx=1+round(abs(Coord{2}(end)-Coord{2}(1))/abs(DCoord_min(2)));%nbre of points after possible interpolation on a regular grid + Coord_y=linspace(Coord{1}(1),Coord{1}(end),npY); + test_direct_y=test_direct(1); + Coord_x=linspace(Coord{2}(1),Coord{2}(end),npX); + test_direct_x=test_direct(2); + DAX=DCoord_min(2); + DAY=DCoord_min(1); + elseif nb_dim==3 + DZ=abs(DCoord_min(1)); + npz=1+round(abs(Coord{1}(end)-Coord{1}(1))/DZ);%nbre of points after interpolation + if DY==0 + DY=abs(DCoord_min(2)); + end + npY=1+round(abs(Coord{2}(end)-Coord{2}(1))/DY);%nbre of points after interpol + npy=1+round(abs(Coord{2}(end)-Coord{2}(1))/abs(DCoord_min(2)));%nbre of points before interpol + if DX==0 + DX=abs(DCoord_min(3)); + end + npX=1+round(abs(Coord{3}(end)-Coord{3}(1))/DX);%nbre of points after interpol + npx=1+round(abs(Coord{3}(end)-Coord{3}(1))/abs(DCoord_min(3)));%nbre of points before interpol + Coord_z=linspace(Coord{1}(1),Coord{1}(end),npz); + test_direct_z=test_direct(1); + Coord_y=linspace(Coord{2}(1),Coord{2}(end),npY); + test_direct_y=test_direct(2); + Coord_x=linspace(Coord{3}(1),Coord{3}(end),npX); + test_direct_x=test_direct(3); + end + minAX=min(Coord_x); + maxAX=max(Coord_x); + minAY=min(Coord_y); + maxAY=max(Coord_y); + xcorner=[minAX maxAX minAX maxAX]-ObjectData.Coord(1,1); + ycorner=[maxAY maxAY minAY minAY]-ObjectData.Coord(1,2); + xcor_new=xcorner*cos(Phi)+ycorner*sin(Phi);%coord new frame + ycor_new=-xcorner*sin(Phi)+ycorner*cos(Phi); + if ~testXMax + XMax=max(xcor_new); + end + if ~testXMin + XMin=min(xcor_new); + end + if ~testYMax + YMax=max(ycor_new); + end + if ~testYMin + YMin=min(ycor_new); + end + DXinit=(maxAX-minAX)/(npx-1); + DYinit=(maxAY-minAY)/(npy-1); + if DX==0 + DX=DXinit; + end + if DY==0 + DY=DYinit; + end + npX=floor((XMax-XMin)/DX+1); + npY=floor((YMax-YMin)/DY+1); + if test_direct_y + coord_y_proj=linspace(YMin,YMax,npY);%abscissa of the new pixels along the line + else + coord_y_proj=linspace(YMax,YMin,npY);%abscissa of the new pixels along the line + end + if test_direct_x + coord_x_proj=linspace(XMin,XMax,npX);%abscissa of the new pixels along the line + else + coord_x_proj=linspace(XMax,XMin,npX);%abscissa of the new pixels along the line + end + + % case with no rotation and interpolation + if isequal(ProjMode,'projection') && isequal(Phi,0) && isequal(Theta,0) && isequal(Psi,0) + if test_direct(1) + min_ind1=ceil((YMin-Coord{1}(1))/DYinit)+1; + max_ind1=floor((YMax-Coord{1}(1))/DYinit)+1; + Ybound(1)=Coord{1}(1)+DYinit*(min_ind1-1); + Ybound(2)=Coord{1}(1)+DYinit*(max_ind1-1); + else + min_ind1=ceil((Coord{1}(1)-YMax)/DYinit)+1; + max_ind1=floor((Coord{1}(1)-YMin)/DYinit)+1; + Ybound(2)=Coord{1}(1)-DYinit*(max_ind1-1); + Ybound(1)=Coord{1}(1)-DYinit*(min_ind1-1); + end + if test_direct(2)==1 + min_ind2=ceil((XMin-Coord{2}(1))/DXinit)+1; + max_ind2=floor((XMax-Coord{2}(1))/DXinit)+1; + Xbound(1)=Coord{2}(1)+DXinit*(min_ind2-1); + Xbound(2)=Coord{2}(1)+DXinit*(max_ind2-1); + else + min_ind2=ceil((Coord{2}(1)-XMax)/DXinit)+1; + max_ind2=floor((Coord{2}(1)-XMin)/DXinit)+1; + Xbound(2)=Coord{2}(1)+DXinit*(max_ind2-1); + Xbound(1)=Coord{2}(1)+DXinit*(min_ind2-1); + end + min_ind1=max(min_ind1,1);% deals with margin (bound lower than the first index) + min_ind2=max(min_ind2,1); + max_ind1=min(max_ind1,npy); + max_ind2=min(max_ind2,npx); + for ivar=VarIndex + VarName=FieldData.ListVarName{ivar}; +% if isequal(ObjectData.ProjMode,'interp')||isequal(ObjectData.ProjMode,'filter')% coordinates common to all fields +% ProjData.ListDimName={'coord_y','coord_x'}; +% ProjData.DimValue=[length(coord_y_proj) length(coord_x_proj)]; +% else +% icoord=icoord+1; +% ProjData.ListDimName=[ProjData.ListDimName {['coord_y_' num2str(icoord)],['coord_x_' num2str(icoord)]}]; +% ProjData.DimValue=[ProjData.DimValue length(coord_y_proj) length(coord_x_proj)]; +% end + ProjData.ListVarName=[ProjData.ListVarName VarName]; + ProjData.VarDimIndex=[ProjData.VarDimIndex [nb_dim-1 nb_dim]]; + if length(FieldData.VarAttribute)>=ivar + ProjData.VarAttribute{length(ProjData.ListVarName)}=FieldData.VarAttribute{ivar}; + end +% ProjData.VarAttribute{length(ProjData.ListVarName)}.Coord_2=Xbound; +% ProjData.VarAttribute{length(ProjData.ListVarName)}.Coord_1=Ybound; + eval(['ProjData.' VarName '=FieldData.' VarName '(min_ind1:max_ind1,min_ind2:max_ind2) ;']); + end + else + % case with rotation and/or interpolation + if isempty(Coord_z) %2D case + [X,Y]=meshgrid(coord_x_proj,coord_y_proj);%grid in the new coordinates + XIMA=ObjectData.Coord(1,1)+(X)*cos(Phi)-Y*sin(Phi);%corresponding coordinates in the original image + YIMA=ObjectData.Coord(1,2)+(X)*sin(Phi)+Y*cos(Phi); + XIMA=(XIMA-minAX)/DXinit+1;% image index along x + YIMA=(-YIMA+maxAY)/DYinit+1;% image index along y + XIMA=reshape(round(XIMA),1,npX*npY);%indices reorganized in 'line' + YIMA=reshape(round(YIMA),1,npX*npY); + flagin=XIMA>=1 & XIMA<=npx & YIMA >=1 & YIMA<=npy;%flagin=1 inside the original image + if isequal(ObjectData.ProjMode,'filter') + npx_filter=ceil(abs(DX/DAX)); + npy_filter=ceil(abs(DY/DAY)); + Mfilter=ones(npy_filter,npx_filter)/(npx_filter*npy_filter); + test_filter=1; + else + test_filter=0; + end + for ivar=VarIndex + VarName=FieldData.ListVarName{ivar} ; + if test_interp(1) | test_interp(2)%interpolate on a regular grid + eval(['FieldData.' VarName '=interp2(Coord{2},Coord{1},FieldData.' VarName ',Coord_x,Coord_y'');']) %TO TEST + end + %filter the field (image) if option 'filter' is used + if test_filter + Aclass=class(FieldData.A); + eval(['FieldData.' VarName '=filter2(Mfilter,FieldData.' VarName ',''valid'');']) + if ~isequal(Aclass,'double') + eval(['FieldData.' VarName '=' Aclass '(FieldData.' VarName ');'])%revert to integer values + end + end + eval(['vec_A=reshape(FieldData.' VarName ',npx*npy,nbcolor);'])%put the original image in line + ind_in=find(flagin); + ind_out=find(~flagin); + ICOMB=(XIMA-1)*npy+YIMA; + ICOMB=ICOMB(flagin);%index corresponding to XIMA and YIMA in the aligned original image vec_A + vec_B(ind_in,[1:nbcolor])=vec_A(ICOMB,:); + for icolor=1:nbcolor + vec_B(ind_out,icolor)=zeros(size(ind_out)); + end + % TODO: A REVOIR: +% if isequal(ObjectData.ProjMode,'interp') || isequal(ObjectData.ProjMode,'filter')% coordinates common to all fields +% ProjData.ListDimName={'coord_y','coord_x'}; +% ProjData.DimValue=[length(coord_y_proj) length(coord_x_proj)]; +% else +% icoord=icoord+1; +% ProjData.ListDimName=[ProjData.ListDimName {['coord_y_' num2str(icoord)],['coord_x_' num2str(icoord)]}]; +% ProjData.DimValue=[ProjData.DimValue length(coord_y_proj) length(coord_x_proj)]; +% end + ProjData.ListVarName=[ProjData.ListVarName VarName]; + % ProjData.VarDimIndex=[ProjData.VarDimIndex [nb_dim-1 nb_dim]]; + if length(FieldData.VarAttribute)>=ivar + ProjData.VarAttribute{length(ProjData.ListVarName)+nbcoord}=FieldData.VarAttribute{ivar}; + end + % A REVOIR: +% if test_direct(2)==1 +% ProjData.VarAttribute{length(ProjData.ListVarName)}.Coord_2=[XMin XMax]; +% else +% ProjData.VarAttribute{length(ProjData.ListVarName)}.Coord_2=[XMax XMin]; +% end +% if test_direct(1)==1 +% ProjData.VarAttribute{length(ProjData.ListVarName)}.Coord_1=[YMin YMax]; +% else +% ProjData.VarAttribute{length(ProjData.ListVarName)}.Coord_1=[YMax YMin]; +% end + eval(['ProjData.' VarName '=reshape(vec_B,npY,npX,nbcolor);']); + end + ProjData.FF=reshape(~flagin,npY,npX);%false flag A FAIRE: tenir compte d'un flga antérieur + ProjData.ListVarName=[ProjData.ListVarName 'FF']; + % ProjData.VarDimIndex=[ProjData.VarDimIndex [nb_dim-1 nb_dim]]; + ProjData.VarAttribute{length(ProjData.ListVarName)}.Role='errorflag'; + else %3D case + if isequal(Theta,0) & isequal(Phi,0) + test_sup=(Coord{1}>=ObjectData.Coord(1,3)); + iz_sup=find(test_sup); + iz=iz_sup(1); + if iz>=1 & iz<=npz + ProjData.ListDimName=[ProjData.ListDimName ListDimName(2:end)]; + ProjData.DimValue=[ProjData.DimValue npY npX]; + for ivar=VarIndex + VarName=FieldData.ListVarName{ivar}; + ProjData.ListVarName=[ProjData.ListVarName VarName]; + % ProjData.VarDimIndex=[ProjData.VarDimIndex [nb_dim-2 nb_dim-1]]; + ProjData.VarAttribute{length(ProjData.ListVarName)}=FieldData.VarAttribute{ivar}; %reproduce the variable attributes + % A REVOIR +% if test_direct_x==1 +% ProjData.VarAttribute{length(ProjData.ListVarName)}.Coord_2=[XMin XMax]; +% else +% ProjData.VarAttribute{length(ProjData.ListVarName)}.Coord_2=[XMax XMin]; +% end +% if test_direct_y==1 +% ProjData.VarAttribute{length(ProjData.ListVarName)}.Coord_1=[YMin YMax]; +% else +% ProjData.VarAttribute{length(ProjData.ListVarName)}.Coord_1=[YMax YMin]; +% end + eval(['ProjData.' VarName '=squeeze(FieldData.' VarName '(iz,:,:));'])% select the z index iz + %TODO : do a vertical average for a thick plane + if test_interp(2) | test_interp(3) + eval(['ProjData.' VarName '=interp2(Coord{3},Coord{2},ProjData.' VarName ',Coord_x,Coord_y'');']) + end + end + end + else + errormsg='projection of structured coordinates on oblique plane not yet implemented'; + %TODO: use interp3 + return + end + end + end + end + %projection of velocity components in the rotated coordinates + if ~isequal(Phi,0) & length(ivar_U)==1 + if isempty(ivar_V) + warndlg_uvmat('v velocity component missing in proj_field.m','ERROR') + return + end + UName=FieldData.ListVarName{ivar_U}; + VName=FieldData.ListVarName{ivar_V}; + eval(['ProjData.' UName '=cos(Phi)*ProjData.' UName '+ sin(Phi)*ProjData.' VName ';']) + eval(['ProjData.' VName '=cos(Theta)*(-sin(Phi)*ProjData.' UName '+ cos(Phi)*ProjData.' VName ');']) + if ~isempty(ivar_W) + WName=FieldData.ListVarName{ivar_W}; + eval(['ProjData.' VName '=ProjData.' VName '+ ProjData.' WName '*sin(Theta);'])% + eval(['ProjData.' WName '=NormVec_X*ProjData.' UName '+ NormVec_Y*ProjData.' VName '+ NormVec_Z* ProjData.' WName ';']); + end + if ~isequal(Psi,0) + eval(['ProjData.' UName '=cos(Psi)* ProjData.' UName '- sin(Psi)*ProjData.' VName ';']); + eval(['ProjData.' VName '=sin(Psi)* ProjData.' UName '+ cos(Psi)*ProjData.' VName ';']); + end + end +end + +%----------------------------------------------------------------- +%transmit the global attributes +function [ProjData,errormsg]=proj_heading(FieldData,ObjectData) +%----------------------------------------------------------------- +% ProjData=FieldData; +ProjData=[];%default +if ~isfield(FieldData,'ListGlobalAttribute') + ProjData.ListGlobalAttribute={}; +else + ProjData.ListGlobalAttribute=FieldData.ListGlobalAttribute; +end +if isfield(FieldData,'Txt') + errormsg=FieldData.Txt; %transmit erreur message + return; +end +for iattr=1:length(ProjData.ListGlobalAttribute) + AttrName=ProjData.ListGlobalAttribute{iattr}; + if isfield(FieldData,AttrName) + eval(['ProjData.' AttrName '=FieldData.' AttrName ';']); + end +end +if isfield(FieldData,'CoordType') + if isfield(ObjectData,'CoordType')&~isequal(FieldData.CoordType,ObjectData.CoordType) + errormsg=[ObjectData.Style ' in ' ObjectData.CoordType ' coordinates, while field in ' FieldData.CoordType ' coordinates']; + return + else + ProjData.CoordType=FieldData.CoordType; + end +end + +ListObject={'Style','ProjMode','RangeX','RangeY','RangeZ','Phi','Theta','Psi','Coord'}; +for ilist=1:length(ListObject) + if isfield(ObjectData,ListObject{ilist}) + eval(['val=ObjectData.' ListObject{ilist} ';']) + if ~isempty(val) + eval(['ProjData.Object' ListObject{ilist} '=val;']); + ProjData.ListGlobalAttribute=[ProjData.ListGlobalAttribute {['Object' ListObject{ilist}]}]; + end + end +end Index: /trunk/src/proj_grid.m =================================================================== --- /trunk/src/proj_grid.m (revision 2) +++ /trunk/src/proj_grid.m (revision 2) @@ -0,0 +1,83 @@ +%'proj_grid': project fields with unstructured coordinantes on a regular grid +% ------------------------------------------------------------------------- +% function [A,rangx,rangy]=proj_grid(vec_X,vec_Y,vec_A,rgx_in,rgy_in,npxy_in) + + +function [A,rangx,rangy]=proj_grid(vec_X,vec_Y,vec_A,rgx_in,rgy_in,npxy_in) + if length(vec_Y)<2 + warndlg_uvmat('less than 2 points in proj_grid.m','ERROR'); + return; + end + diffy=diff(vec_Y); %difference dy=vec_Y(i+1)-vec_Y(i) + index=find(diffy);% find the indices of vec_Y after wich a change of horizontal line occurs(diffy non zero) + if isempty(index); warndlg_uvmat('points aligned along abscissa in proj_grid.m','ERROR'); return; end;%points aligned% A FAIRE: switch to line plot. + diff2=diff(diffy(index));% diff2 = fluctuations of the detected vertical grid mesh dy + if max(abs(diff2))>0.001*abs(diffy(index(1))) % if max(diff2) is larger than 1/1000 of the first mesh dy + % the data are not regularly spaced and must be interpolated on a regular grid + if exist('rgx_in','var') & ~isempty (rgx_in) & isnumeric(rgx_in) & length(rgx_in)==2% positions imposed from input + rangx=rgx_in; % first and last positions + rangy=rgy_in; +% npxy=npxy_in; + dxy(1)=1/(npxy_in(1)-1);%grid mesh in y + dxy(2)=1/(npxy_in(2)-1);%grid mesh in x + dxy(1)=(rangy(2)-rangy(1))/(npxy_in(1)-1);%grid mesh in y + dxy(2)=(rangx(2)-rangx(1))/(npxy_in(2)-1);%grid mesh in x + else % interpolation grid automatically determined + rangx(1)=min(vec_X); + rangx(2)=max(vec_X); + rangy(2)=min(vec_Y); + rangy(1)=max(vec_Y); + dxymod=sqrt((rangx(2)-rangx(1))*(rangy(1)-rangy(2))/length(vec_X)); + dxy=[-dxymod/4 dxymod/4];% increase the resolution 4 times + end + xi=[rangx(1):dxy(2):rangx(2)]; + yi=[rangy(1):dxy(1):rangy(2)]; + [XI,YI]=meshgrid(xi,yi);% creates the matrix of regular coordinates + A=griddata_uvmat(vec_X,vec_Y,vec_A,xi,yi'); + A=reshape(A,length(yi),length(xi)); + else + x=vec_X(1:index(1));% the set of abscissa (obtained on the first line) + indexend=index(end);% last vector index of line change + ymax=vec_Y(indexend+1);% y coordinate AFTER line change + ymin=vec_Y(index(1)); + %y=[vec_Y(index) ymax]; % the set of y ordinates including the last one + y=vec_Y(index); + y(length(y)+1)=ymax; + nx=length(x); %number of grid points in x + ny=length(y); % number of grid points in y + B=(reshape(vec_A,nx,ny))'; %vec_A reshaped as a rectangular matrix + [X,Y]=meshgrid(x,y);% positions X and Y also reshaped as matrix + + %linear interpolation to improve the image resolution and/or adjust + %to prescribed positions + test_interp=1; + if exist('rgx_in','var') & ~isempty (rgx_in) & isnumeric(rgx_in) & length(rgx_in)==2% positions imposed from input + rangx=rgx_in; % first and last positions + rangy=rgy_in; + npxy=npxy_in; + else + rangx=[vec_X(1) vec_X(nx)];% first and last position found for x +% rangy=[ymin ymax]; + rangy=[max(ymax,ymin) min(ymax,ymin)]; + if max(nx,ny) <= 64 & isequal(npxy_in,'np>256') + npxy=[8*ny 8*nx];% increase the resolution 8 times + elseif max(nx,ny) <= 128 & isequal(npxy_in,'np>256') + npxy=[4*ny 4*nx];% increase the resolution 4 times + elseif max(nx,ny) <= 256 & isequal(npxy_in,'np>256') + npxy=[2*ny 2*nx];% increase the resolution 2 times + else + npxy=[ny nx]; + test_interp=0; % no interpolation done + end + end + if test_interp==1%if we interpolate + xi=[rangx(1):(rangx(2)-rangx(1))/(npxy(2)-1):rangx(2)]; + yi=[rangy(1):(rangy(2)-rangy(1))/(npxy(1)-1):rangy(2)]; + [XI,YI]=meshgrid(xi,yi); + A = interp2(X,Y,B,XI,YI); + else %no interpolation for a resolution higher than 256 + A=B; + XI=X; + YI=Y; + end + end Index: /trunk/src/px.m =================================================================== --- /trunk/src/px.m (revision 2) +++ /trunk/src/px.m (revision 2) @@ -0,0 +1,87 @@ +%'px': transform fields from physical coordinates (phys) to image (px) coordinates + +% OUTPUT: +% DataOut: structure of modified data (transforms DataIn) +% DataOut.CoordType='px': labels image coordinates +% DataOut.CoordUnit= 'px' : units of output coordinates +% DataOut.X and .Y arrays of image coordinates X, Y +% DataOut.U, .V velocity in pixel displacement on the image (unit=px), if velocity exists as input +% +%INPUT: +% DataIn: structure of possible input data (like UvData) or cell of structures (several fields): +% DataIn.CoordType='phys': allows transform to px, else no transform (DataOut=DataIn) +% DataIn.X and .Y arrays of physical coordinates X, Y +% DataIn.Z corresponding array of Z coordinates (=0 by default) +% DataIn.U, V corresponding array of velocity components +% DataIn.W corresponding array of the third velocity component in 3D case +% DataIn.dt: time interval of the image pair used for velocity measurement (NEEDED TO GET OUTPUT RESULT)) +% DataIn.A, AX, AY : image or scalar input -> EMPTY CORRESPONDING OUTPUT (A REVOIR) +% Other fields in DataIn: copied to DataOut without modification +% Calib: structure containing the calibration parameters (Tsai) or containing a subtree Calib.GeometryCalib with these parameters +% +% call the functions phys_XYZ or px_XYZ (case of images) for pointwise coordinate transforms + +function [DataOut,DataOut_1]=px(Data,CalibData,Data_1,CalibData_1)%DataIn,Calib) +% A FAIRE: 1- verifier si DataIn est une 'field structure'(.ListVarName'): +% chercher ListVarAttribute, for each field (cell of variables): +% .CoordType: 'phys' or 'px' (default==px, no transform) +% .scale_factor: =dt (to transform displacement into velocity) default=1 +% .covariance: 'scalar', 'coord', 'D_i': covariant (like velocity), 'D^i': contravariant (like gradient), 'D^jD_i' (like strain tensor) +% (default='coord' if .Role='coord_x,_y..., +% 'D_i' if '.Role='vector_x,...', +% 'scalar', else (thenno change except scale factor) +if ~(exist('CalibData','var') && isfield(CalibData,'GeometryCalib')) + DataOut=Data; +else + DataOut=px_1(Data,CalibData.GeometryCalib); +end +if exist('Data_1','var') + if ~(exist('CalibData_1','var') && isfield(CalibData_1,'GeometryCalib')) + DataOut_1=Data_1; + else + DataOut_1=px_1(Data_1,CalibData_1.GeometryCalib); + end +else + DataOut_1=[]; +end + + +%------------------------------------------------ +function DataOut=px_1(Data,Calib) +DataOut=Data;%default + +%Act only if .CoordType=phys, and Calib defined +if isfield(Data,'CoordType')& isequal(Data.CoordType,'phys')& ~isempty(Calib) + DataOut.CoordType='px'; %put flag for pixel coordinates + DataOut.CoordUnit='px'; + %transform of X,Y coordinates + if isfield(Data,'Z')&~isempty(Data.Z) + Z=Data.Z; + else + Z=0; + end + if isfield(Data,'X') & isfield(Data,'Y') + [DataOut.X,DataOut.Y]=px_XYZ(Calib,Data.X,Data.Y,Z); + if isfield(Data,'U')&isfield(Data,'V')& isfield(Data,'dt')& ~isequal(Data.dt,0) + Data.U=Data.U*Data.dt; + Data.V=Data.V*Data.dt; + if isfield(Data,'W') + W=Data.W*Data.dt; + else + W=0; + end + [XOut_1,YOut_1]=px_XYZ(Calib,Data.X-Data.U/2,Data.Y-Data.V/2,Z-W/2); + [XOut_2,YOut_2]=px_XYZ(Calib,Data.X+Data.U/2,Data.Y+Data.V/2,Z+W/2); + DataOut.U=XOut_2-XOut_1; + DataOut.V=YOut_2-YOut_1; + end + end + %transform of an image + if isfield(Data,'A')&isfield(Data,'AX')&~isempty(Data.AX) & isfield(Data,'AY')&... + isfield(Data,'AY')&~isempty(Data.AY)&length(Data.A)>1 +% if isfield(Data,'Field')&isequal(Data.Field,'images') + %NO TRANSFORM FROM phys to px for images + DataOut.A=[];% + end +end + Index: /trunk/src/px_XYZ.m =================================================================== --- /trunk/src/px_XYZ.m (revision 2) +++ /trunk/src/px_XYZ.m (revision 2) @@ -0,0 +1,50 @@ +%'px_XYZ': transform phys coordinates to image coordinates (px) +% +% OUPUT: +% X,Y: array of coordinates in the image cooresponding to the input physical positions +% (origin at lower leftcorner, unit=pixel) + +% INPUT: +% Calib: structure containing the calibration parameters (read from the ImaDoc .xml file) +% Xphys, Yphys: array of x,y physical coordinates +% [Zphys]: corresponding array of z physical coordinates (0 by default) + + +function [X,Y]=px_XYZ(Calib,Xphys,Yphys,Zphys) +X=[];%default +Y=[]; +% if exist('Z','var')& isequal(Z,round(Z))& Z>0 & isfield(Calib,'PlanePos')&length(Calib.PlanePos)>=Z +% Zindex=Z; +% planepos=Calib.PlanePos{Zindex}; +% zphys=planepos(3);%A GENERALISER CAS AVEC ANGLE +% else +% zphys=0; +% end +if ~exist('Zphys','var') + Zphys=0; +end + +%%%%%%%%%%%%% +if isfield(Calib,'R') + R=(Calib.R)'; + xc=R(1)*Xphys+R(2)*Yphys+R(3)*Zphys+Calib.Tx; + yc=R(4)*Xphys+R(5)*Yphys+R(6)*Zphys+Calib.Ty; + zc=R(7)*Xphys+R(8)*Yphys+R(9)*Zphys+Calib.Tz; +%undistorted image coordinates + Xu=Calib.f*xc./zc; + Yu=Calib.f*yc./zc; +%distorted image coordinates + distortion=(Calib.kappa1)*(Xu.*Xu+Yu.*Yu)+1; %A REVOIR +% distortion=1; + Xd=Xu./distortion; + Yd=Yu./distortion; +%pixel coordinates + X=Xd*Calib.sx/Calib.dpx+Calib.Cx; + Y=Yd/Calib.dpy+Calib.Cy; + +elseif isfield(Calib,'Pxcmx')&isfield(Calib,'Pxcmy')%old calib + X=Xphys*Calib.Pxcmx; + Y=Yphys*Calib.Pxcmy; +end + + Index: /trunk/src/pxcm_tsai.m =================================================================== --- /trunk/src/pxcm_tsai.m (revision 2) +++ /trunk/src/pxcm_tsai.m (revision 2) @@ -0,0 +1,79 @@ +%'pxcm_tsai': find differentials of the Tsai calibration +% +function [A11,A12,A13,A21,A22,A23]=pxcm_tsai(a,var_phys) +a_read=a; + +R=(a.R)'; + +x=var_phys(:,1); +y=var_phys(:,2); + +if isfield(a,'PlanePos') + prompt={'Plane 1 Index','Plane 2 Index'}; + Rep=inputdlg(prompt,'Target displacement test'); + Z1=str2double(Rep(1)); + Z2=str2double(Rep(2)); + z=(a.PlanePos(Z2,3)+a.PlanePos(Z1,3))/2 +else + z=0; +end + +%transform coeff for differentiels +a.C11=R(1)*R(8)-R(2)*R(7); +a.C12=R(2)*R(7)-R(1)*R(8); +a.C21=R(4)*R(8)-R(5)*R(7); +a.C22=R(5)*R(7)-R(4)*R(8); +a.C1x=R(3)*R(7)-R(9)*R(1); +a.C1y=R(3)*R(8)-R(9)*R(2); +a.C2x=R(6)*R(7)-R(9)*R(4); +a.C2y=R(6)*R(8)-R(9)*R(5); + + +%dependence in x,y +denom=(R(7)*x+R(8)*y+R(9)*z+a.Tz).*(R(7)*x+R(8)*y+R(9)*z+a.Tz); +A11=(a.f*a.sx*(a.C11*y-a.C1x*z+R(1)*a.Tz-R(7)*a.Tx)./denom)/a.dpx; +A12=(a.f*a.sx*(a.C12*x-a.C1y*z+R(2)*a.Tz-R(8)*a.Tx)./denom)/a.dpx; +A21=(a.f*a.sx*(a.C21*y-a.C2x*z+R(4)*a.Tz-R(7)*a.Ty)./denom)/a.dpy; +A22=(a.f*(a.C22*x-a.C2y*z+R(5)*a.Tz-R(8)*a.Ty)./denom)/a.dpy; +A13=(a.f*(a.C1x*x+a.C1y*y+R(3)*a.Tz-R(9)*a.Tx)./denom)/a.dpx; +A23=(a.f*(a.C2x*x+a.C2y*y+R(6)*a.Tz-R(9)*a.Ty)./denom)/a.dpy; + +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% +%Old Version for z=0 +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% +% %'camera' coordinates +% xc=R(1)*x+R(2)*y+a.Tx; +% yc=R(4)*x+R(5)*y+a.Ty; +% zc=R(7)*x+R(8)*y+a.Tz; +% %undistorted image coordinates +% Xu=a.f*xc./zc; +% Yu=a.f*yc./zc; +% %distorted image coordinates +% distortion=(a.kappa1)*(Xu.*Xu+Yu.*Yu)+1; %!! intégrer derivation kappa +% % distortion=1; +% Xd=Xu./distortion; +% Yd=Yu./distortion; +% %pixel coordinates +% X=Xd*a.sx/a.dpx+a.Cx; +% Y=Yd/a.dpy+a.Cy; +% +% %transform coeff for differentiels +% a.C11=R(1)*R(8)-R(2)*R(7); +% a.C12=R(2)*R(7)-R(1)*R(8); +% a.C21=R(4)*R(8)-R(5)*R(7); +% a.C22=R(5)*R(7)-R(4)*R(8); +% a.C1x=R(3)*R(7)-R(9)*R(1); +% a.C1y=R(3)*R(8)-R(9)*R(2); +% a.C2x=R(6)*R(7)-R(9)*R(4); +% a.C2y=R(6)*R(8)-R(9)*R(5); +% +% +% %dependence in x,y +% denom=(R(7)*x+R(8)*y+a.Tz).*(R(7)*x+R(8)*y+a.Tz); +% A11=(a.f*a.sx*(a.C11*y+R(1)*a.Tz-R(7)*a.Tx)./denom)/a.dpx; +% A12=(a.f*a.sx*(a.C12*x+R(2)*a.Tz-R(8)*a.Tx)./denom)/a.dpx; +% A21=(a.f*a.sx*(a.C21*y+R(4)*a.Tz-R(7)*a.Ty)./denom)/a.dpy; +% A22=(a.f*(a.C22*x+R(5)*a.Tz-R(8)*a.Ty)./denom)/a.dpy; +% A13=(a.f*(a.C1x*x+a.C1y*y+R(3)*a.Tz-R(9)*a.Tx)./denom)/a.dpx; +% A23=(a.f*(a.C2x*x+a.C2y*y+R(6)*a.Tz-R(9)*a.Ty)./denom)/a.dpy; +% Index: /trunk/src/raw2phys.m =================================================================== --- /trunk/src/raw2phys.m (revision 2) +++ /trunk/src/raw2phys.m (revision 2) @@ -0,0 +1,151 @@ +%'raw2phys': transform raw signal to physical values using different calibrations laws +% +function FieldPhys=raw2phys(Field) + +% do not transform if Field already in phys coordinates +FieldPhys=Field;%default +if isfield(Field,'CoordType') & isequal(Field.CoordType,'phys') + return %no transform if the data are already physical +else + FieldPhys.CoordType='phys'; +end + +%Filtering of the initial data +nbfilter=51; +nbhalf=floor(nbfilter/2); +for ivar=1:length(FieldPhys.ListVarName) + VarName=FieldPhys.ListVarName{ivar}; + if ~isequal(VarName,'time') + eval(['FirstVal=FieldPhys.' VarName '(1);']) + eval(['LastVal=FieldPhys.' VarName '(end);']) + FirstVal=ones(nbhalf,1)*FirstVal; + LastVal=ones(nbhalf,1)*LastVal; + eval(['FieldPhys.' VarName '=[FirstVal;FieldPhys.' VarName ';LastVal];']) + eval(['FieldPhys.' VarName '=conv(ones(1,nbfilter)/nbfilter,FieldPhys.' VarName ');']); + eval(['FieldPhys.' VarName '([1:nbfilter-1])=[];']); + eval(['FieldPhys.' VarName '([end-nbfilter+2:end])=[];']); + end +end + + + +ScanRate=240; %data points per second +VelTranslation=1; % 1 cm/s A VERIFIER +test_Offset=0; +test_Thermistance_B=0; +test_Thermistance_M=0; +if isfield(Field,'ListVarAttribute') + for ilist=1:length(Field.ListVarAttribute) + attr_name=Field.ListVarAttribute{ilist} + if isequal(attr_name,'PhysUnits') + FieldPhys.units =Field.PhysUnits; + end + if isequal(attr_name,'Offset') + test_Offset=1; + end + if isequal(attr_name,'ThermistanceCalib_B') + test_Thermistance_B=1; + end + if isequal(attr_name,'ThermistanceCalib_M') + test_Thermistance_M=1; + end + end +end + + + +% substract offset +if test_Offset + for ivar=1:length(Field.ListVarName) + Val_Offset=Field.Offset{ivar}; + if isnumeric(Val_Offset)&~isempty(Val_Offset) + VarName=Field.ListVarName{ivar}; + eval(['FieldPhys.' VarName '=FieldPhys.' VarName '-Val_Offset;']) + end + end +end + +%thermistance calibration +if test_Thermistance_M & test_Thermistance_B + for ivar=1:length(Field.ListVarName) + Val_B=Field.ThermistanceCalib_B{ivar}; + Val_M=Field.ThermistanceCalib_M{ivar}; + if isnumeric(Val_B) & ~isempty(Val_B) & isnumeric(Val_M) & ~isempty(Val_M) + VarName=Field.ListVarName{ivar}; + eval(['FieldPhys.' VarName '=(Val_M ./ (log( FieldPhys.' VarName ')-Val_B)) -273.15;']) + end + end +end +return + +%NON USED +%density profile +Density=(Conductivity-B)/A;%calibration +Density=Density(find(Motor>1));%restrict the record to the time motor on +Density=flipdim(Density,2)'; +%detect free surface +[dmax,imax]=max(diff(Density)); +nbpoints=length(Density); +Pos=linspace(0,nbpoints*VelTranslation/ScanRate,nbpoints); +Pos=Pos-imax*VelTranslation/ScanRate; + +%[dmax,jmax]=max(diff(Conductivity)) +napoints=length(Conductivity); +Pos1=linspace(0,napoints*VelTranslation/ScanRate,napoints); +%Pos1=Pos1-jmax*VelTranslation/ScanRate; + +figure(2); +clf +plot(Pos1,Conductivity) +grid on +figure(3); +size(Pos) +size(Density) +plot(Pos,Density) +hold on +grid on +%determination of N +PosCentr=Pos([floor(nbpoints/4):floor(3*nbpoints/4)]); +DensityCentr=Density([floor(nbpoints/4):floor(3*nbpoints/4)]); +p=polyfit(PosCentr,DensityCentr,1); +LinDens=polyval(p,PosCentr); +plot(PosCentr,LinDens,'r') +grad=p(1) +%find(Motor>1) + +% data.conductivity=flipdim(Conductivity(find(Motor>5)),1)'; +% data.deplacement=[100/size(data.conductivity,2):100/size(data.conductivity,2):100]; +% +% figure;plot(data.deplacement,data.conductivity);hold on; + +%data.density=flipdim(Conductivity(find(Motor>1)),1)'*3.4764+15.1367; +%data.density=flipdim(Conductivity(find(Motor>1)),2)'*5+14.6090; +%data.density=flipdim(Conductivity(find(Motor>1)),2)'*4.1525+19.50; +% data.density=flipdim(Conductivity(find(Motor>1)),2)' +% data.deplacement=[92/size(data.density,2):92/size(data.density,2):92]; +% figure(101) +% plot(data.deplacement,data.density);hold on; + +% t=data.deplacement(find(data.deplacement>20&data.deplacement<80)); +%t=data.deplacement(find(data.deplacement>0&data.deplacement<90)); +% X=[ones(size(t,2),1)';t]; +% Y=data.density(find(data.deplacement>20&data.deplacement<80)); +% %Y=data.density(find(data.deplacement>0&data.deplacement<90)); +% coeff=Y/X; + +% plot(data.deplacement,data.deplacement*coeff(2)+coeff(1),'r'); + +% grad=abs(coeff(2)*100) +Tbv=2*pi/sqrt(981*0.001*grad) +N=2*pi/Tbv +title(strcat('',name,'')) +xpos=get(gca,'XLim') +ypos=get(gca,'YLim') +%xtext=xpos(1)+(xpos(2)-xpos(1))*3/4 +xtext=xpos(1)+(xpos(2)-xpos(1))/2 +ytext=ypos(1)+(ypos(2)-ypos(1))/4 +TabText={strcat('Tbv : ',num2str(Tbv),'s'); strcat('Stratification : ',num2str(grad)); strcat('N : ',num2str(2*pi/Tbv),'rad.s-1')} +text(xtext,ytext,TabText) +% text(xtext,13,strcat('Tbv : ',num2str(Tbv),'s')); +% text(55,10,strcat('Stratification : ',num2str(grad))); +% text(55,16,strcat('N : ',num2str(2*pi/Tbv),'rad.s-1')); Index: /trunk/src/read_civxdata.m =================================================================== --- /trunk/src/read_civxdata.m (revision 2) +++ /trunk/src/read_civxdata.m (revision 2) @@ -0,0 +1,275 @@ +%'read_civxdata': reads civx data from netcdf files +%------------------------------------------------------------------ +% COMBINE ET REMPLACE read_ncfield, read_vel et read_scalar_new +%------------------------------------------------------------------ +% OUTPUT: +% nb_coord,nb_dim, +% Civ: =0 or 1, indicates whether the data is civ (A SUPPRIMER ?) +% CivStage: =0, ??? A UTILISER POUR REMPLACER civ +% =1, civ1 has been performed only +% =2, fix1 has been performed +% =3, pacth1 has been performed +% =4, civ2 has been performed +% =5, fix2 has been performed +% =6, pacth2 has been performed +% time: absolute time +% Field +% .Txt: (char string) error message if any +% .NbDim: number of dimensions (=0 by default) +% .NbCoord: number of vector components +% .CoordType: expresses the type of coordinate ('px' for image, 'sig' for instruments, or 'phys') +% .dt: time interval for the corresponding image pair +% .CivStage: =0, ??? A UTILISER POUR REMPLACER civ + % =1, civ1 has been performed only + % =2, fix1 has been performed + % =3, pacth1 has been performed + % =4, civ2 has been performed + % =5, fix2 has been performed + % =6, pacth2 has been performed +% .X, .Y, .Z: set of vector coordinates +% .U,.V,.W: corresponding set of vector components +% .F: warning flags +% .FF: error flag, =0 for good vectors +% .C: scalar associated with velocity (used for vector colors) +% .CoordType +% .DijU; matrix of spatial derivatives (DijU(1,1,:)=DUDX, +% DijU(1,2,:)=DUDY, Dij(2,1,:)=DVDX, DijU(2,2,:)=DVDY +% .A, .AX, .AY: additional scalar +% dt:time interval of the image pair red from a single file, or vector with + +% pixcmx,pixcmy: scaling factors (from the first file) +% vel_type_out: string representing the selected velocity type (civ1,civ2,filter1...) +% +% INPUT: +% filename: file name (string). +% FieldNames =cell of field names to get, which can contain the strings: +% 'ima_cor': image correlation, vec_c or vec2_C +% 'vort','div','strain': requires velocity derivatives DUDX... +% 'error': error estimate (vec_E or vec2_E) +% +% VelType : character string indicating the types of velocity fields to read ('civ1','civ2'...) +% if vel_type=[] or'*', a priority choice, given by vel_type_out{1,2}, is done depending +% if vel_type='filter'; a structured field is sought (filter2 in priority, then filter1) + + +% FUNCTIONS called: +% 'varcivx_generator':, sets the names of vaiables to read in the netcdf file +% 'nc2struct': reads a netcdf file + +function [Field,VelTypeOut]=read_civxdata(filename,FieldNames,VelType) + +if ~exist('VelType','var') + VelType=[]; +end +if isequal(VelType,'*') + VelType=[]; +end +if ~exist('FieldNames','var') + FieldNames=[]; %default +end + +VelTypeOut=VelType;%default +[var,role,units,vel_type_out_cell]=varcivx_generator(FieldNames,VelType);%determine the names of constants and variables to read +[Field,vardetect,ichoice]=nc2struct(filename,var); +if isfield(Field,'Txt') + return % error in file reading +end +if isequal(vardetect,0) + Field.Txt=[FieldNames ' not accessible in ' filename '/' VelType]; + return +end +var_ind=find(vardetect); +for ivar=1:length(var_ind) + Field.VarAttribute{ivar}.Role=role{var_ind(ivar)}; +% Field.VarAttribute{ivar}.units=units{var_ind(ivar)};% not necessary: set with calc_field +end +VelTypeOut=VelType; +if ~isempty(ichoice) + VelTypeOut=vel_type_out_cell{ichoice}; +end + +%adjust for Djui: +if isfield(Field,'DjUi') + Field.ListVarName(end-2:end)=[]; + Field.ListVarName{end}='DjUi'; + Field.VarDimIndex(end-2:end)=[]; + Field.VarAttribute(end-2:end)=[]; +end + +%determine the appropriate constant for time and dt for the PIV pair +test_civ1=isequal(VelTypeOut,'civ1')||isequal(VelTypeOut,'interp1')||isequal(VelTypeOut,'filter1'); +test_civ2=isequal(VelTypeOut,'civ2')||isequal(VelTypeOut,'interp2')||isequal(VelTypeOut,'filter2'); +if test_civ1 + Field.Time=Field.absolut_time_T0; +elseif test_civ2 + Field.Time=Field.absolut_time_T0_2; + Field.dt=Field.dt2; +else + Field.Txt='the input file is not civx'; + display(Field.Txt) +end + +% CivStage +if isfield(Field,'patch2')&& isequal(Field.patch2,1) + Field.CivStage=6; +elseif isfield(Field,'fix2')&& isequal(Field.fix2,1) + Field.CivStage=5; +elseif isfield(Field,'civ2')&& isequal(Field.civ2,1) + Field.CivStage=4; +elseif isfield(Field,'patch')&& isequal(Field.patch,1) + Field.CivStage=3; +elseif isfield(Field,'fix')&& isequal(Field.fix,1) + Field.CivStage=2; +else + Field.CivStage=1; +end + +%update list of global attributes +List=Field.ListGlobalAttribute; +ind_remove=[]; +for ilist=1:length(List) + switch(List{ilist}) + case {'patch2','fix2','civ2','patch','fix','dt2','absolut_time_T0','absolut_time_T0_2'} + ind_remove=[ind_remove ilist]; + Field=rmfield(Field,List{ilist}); + end +end +List(ind_remove)=[]; +Field.ListGlobalAttribute=[List {'Time','CivStage','CoordUnit'}]; + +% rescale to pixel coordiantes +if isfield(Field,'pixcmx') +Field.U=Field.U*Field.pixcmx; +Field.V=Field.V*Field.pixcmy; +Field.X=Field.X*Field.pixcmx; +Field.Y=Field.Y*Field.pixcmy; +end +if ~isequal(Field.dt,0) + Field.U=Field.U*Field.dt;%translate in px displacement + Field.V=Field.V*Field.dt; + if isfield(Field,'DjUi') + Field.DjUi(:,1,1)=Field.dt*Field.DjUi(:,1,1); + Field.DjUi(:,2,2)=Field.dt*Field.DjUi(:,2,2); + Field.DjUi(:,1,2)=(Field.pixcmy/Field.pixcmx)*Field.dt*Field.DjUi(:,1,2); + Field.DjUi(:,2,1)=(Field.pixcmx/Field.pixcmy)*Field.dt*Field.DjUi(:,2,1); + end +end +Field.CoordType='px';% TODO: abandon, use COORdUnit instead ? (to adapt 'px' and 'phys') +Field.CoordUnit='pixel'; + + +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% +% [var,role,units,vel_type_out]=varcivx_generator(FieldNames,vel_type) +%INPUT: +% FieldNames =cell of field names to get, which can contain the strings: +% 'ima_cor': image correlation, vec_c or vec2_C +% 'vort','div','strain': requires velocity derivatives DUDX... +% 'error': error estimate (vec_E or vec2_E) +% +% vel_type: character string indicating the types of velocity fields to read ('civ1','civ2'...) +% if vel_type=[] or'*', a priority choice, given by vel_type_out{1,2}, is done depending +% if vel_type='filter'; a structured field is sought (filter2 in priority, then filter1) + +function [var,role,units,vel_type_out]=varcivx_generator(FieldNames,vel_type) + +%default input values +if ~exist('vel_type','var'),vel_type=[];end; +if iscell(vel_type),vel_type=vel_type{1}; end;%transform cell to string if needed +% if ~exist('display','var'),display=[];end; +if ~exist('FieldNames','var'),FieldNames={'ima_cor'};end;%default scalar +if ischar(FieldNames), FieldNames={FieldNames}; end; + +%select the priority order for automatic vel_type selection +testder=0; +for ilist=1:length(FieldNames) + if ~isempty(FieldNames{ilist}) + switch FieldNames{ilist} + case {'vort','div','strain'} + testder=1; + end + end +end +if isempty(vel_type) || isequal(vel_type,'*') %undefined velocity type (civ1,civ2...) + if testder + vel_type_out{1}='filter2'; %priority to filter2 for scalar reading, filter1 as second + vel_type_out{2}='filter1'; + else + vel_type_out{1}='civ2'; %priority to civ2 for vector reading, civ1 as second priority + vel_type_out{2}='civ1'; + end +elseif isequal(vel_type,'filter') + vel_type_out{1}='filter2'; %priority to filter2 for scalar reading, filter1 as second + vel_type_out{2}='filter1'; + if ~testder + vel_type_out{3}='civ1';%civ1 as third priority if derivatives are not needed + end +elseif testder + test_civ1=isequal(vel_type,'civ1')||isequal(vel_type,'interp1')||isequal(vel_type,'filter1'); + if test_civ1 + vel_type_out{1}='filter1'; %switch to filter for reading spatial derivatives + else + vel_type_out{1}='filter2'; + end +else + vel_type_out{1}=vel_type;%imposed velocity field +end +vel_type_out=vel_type_out'; + +%determine names of netcdf variables to read +var={'X','Y','Z','U','V','W','C','F','FF'}; +role={'coord_x','coord_y','coord_z','vector_x','vector_y','vector_z','ancillary','warnflag','errorflag'}; +units={'pixel','pixel','pixel','pixel','pixel','pixel',[],[],[]}; +if testder + var=[var {'DjUi(:,1,1)','DjUi(:,1,2)','DjUi(:,2,1)','DjUi(:,2,2)'}]; + role=[role {'tensor','tensor','tensor','tensor'}]; + units=[units {'pixel','pixel','pixel','pixel'}]; +end +for ilist=1:length(vel_type_out) + var=[var;varname1(vel_type_out{ilist},FieldNames)]; +end + + +%------------------------- +%determine var names to read +%-------------------------------------- +function varin=varname1(vel_type,FieldNames) + +testder=0; +C1=''; +C2=''; +for ilist=1:length(FieldNames) + if ~isempty(FieldNames{ilist}) + switch FieldNames{ilist} + case 'ima_cor' %image correlation corresponding to a vel vector + C1='vec_C'; + C2='vec2_C'; + case 'error' + C1='vec_E'; + C2='vec2_E'; + case {'vort','div','strain'} + testder=1; + end + end +end +switch vel_type + case 'civ1' + varin={'vec_X','vec_Y','vec_Z','vec_U','vec_V','vec_W',C1,'vec_F','vec_FixFlag'}; + case 'interp1' + varin={'vec_patch_X','vec_patch_Y','','vec_patch0_U','vec_patch0_V','','','',''}; + case 'filter1' + varin={'vec_patch_X','vec_patch_Y','','vec_patch_U','vec_patch_V','','','',''}; + case 'civ2' + varin={'vec2_X','vec2_Y','vec2_Z','vec2_U','vec2_V','vec2_W',C2,'vec2_F','vec2_FixFlag'}; + case 'interp2' + varin={'vec2_patch_X','vec2_patch_Y','vec2_patch_Z','vec2_patch0_U','vec2_patch0_V','vec2_patch0_W','','',''}; + case 'filter2' + varin={'vec2_patch_X','vec2_patch_Y','vec2_patch_Z','vec2_patch_U','vec2_patch_V','vec2_patch0_W','','',''}; +end +if testder + switch vel_type + case 'filter1' + varin=[varin {'vec_patch_DUDX','vec_patch_DVDX','vec_patch_DUDY','vec_patch_DVDY'}]; + case 'filter2' + varin=[varin {'vec2_patch_DUDX','vec2_patch_DVDX','vec2_patch_DUDY','vec2_patch_DVDY'}]; + end +end Index: /trunk/src/read_geometry_calib.m =================================================================== --- /trunk/src/read_geometry_calib.m (revision 2) +++ /trunk/src/read_geometry_calib.m (revision 2) @@ -0,0 +1,51 @@ +%'read_geometry_calib': read data on the GUI geometry_calib +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% +function data=read_geometry_calib(Coord_cell) +data_XIma=[]; +data_YIma=[]; +data_XObject=[]; +data_YObject=[]; +data_ZObject=[]; +%Coord=get(handles.ListCoord,'String'); +% XImage=get(handles.XImage,'String'); +% YImage=get(handles.YImage,'String'); +% XObject=get(handles.XObject,'String'); +% YObject=get(handles.YObject,'String'); +% ZObject=get(handles.ZObject,'String'); +% if ischar(Xcolumn) +% Xcolumn={Xcolumn}; +% end +nb_defining_points=length(Coord_cell); +iline=0; +for i=1:nb_defining_points + coord_str=Coord_cell{i};%character string of line number i + k=findstr('|',coord_str);%find separators '|' + if length(k)>=4 % test for separators '|' + data1=str2num(coord_str(1:k(1)-5)); + data2=str2num(coord_str(k(1)+5:k(2)-5)); + data3=str2num(coord_str(k(2)+5:k(3)-5)); + data4=str2num(coord_str(k(3)+5:k(4)-5)); + data5=str2num(coord_str(k(4)+5:end)); + if ~isempty(data1)|~isempty(data2)|~isempty(data3)|~isempty(data4)|~isempty(data5) + iline=iline+1; + if ~isempty(data1) + data.Coord(iline,1)=data1; + end + if ~isempty(data2) + data.Coord(iline,2)=data2; + end + if ~isempty(data3) + data.Coord(iline,3)=data3; + end + if ~isempty(data4) + data.Coord(iline,4)=data4; + end + if isempty(data5) + data.Coord(iline,5)=0; + else + data.Coord(iline,5)=data5; + end + end + end +end +data.Style='points'; Index: /trunk/src/read_get_field.m =================================================================== --- /trunk/src/read_get_field.m (revision 2) +++ /trunk/src/read_get_field.m (revision 2) @@ -0,0 +1,743 @@ +%'read_get_field': read the list of selected variables from the GUI get_field (SAME AS THE FIRST +% INPUT: +% hget_field: handles of the GUI get_field + +function [SubField,errormsg]=read_get_field(hget_field) +%--------------------------------------------------------- +SubField=[];%default +errormsg=[]; %default +handles=guidata(hget_field);%handles of GUI elements in get_field +Field=get(hget_field,'UserData');% read the current field Structure in the get_field interface +if isfield(Field,'VarAttribute') + VarAttribute=Field.VarAttribute; +else + VarAttribute={}; +end + +% select the indices of field variables for 2D plots +test_1Dplot=get(handles.check_1Dplot,'Value'); +test_scalar=get(handles.check_scalar,'Value'); +test_vector=get(handles.check_vector,'Value'); + +nbvar=0; +empty_coord_x=0; +empty_coord_y=0; +dimname_y={}; +ListVarName={}; +VarDimName={}; +SubVarAttribute={}; +dim_x=0; +dim_y=0; +dim_z=0; +dim_vec_x=0; +dim_vec_y=0; +dim_vec_z=0; +c_index=[]; +if test_1Dplot + % select ordinate variable(s) + inputlist=get(handles.ordinate,'String'); + val=get(handles.ordinate,'Value');% selection(s) for ordinate + VarNameCell=inputlist(val); %names of the variable(s) in the list + for ilist=1:length(VarNameCell) + VarIndex_y(ilist)=name2index(VarNameCell{ilist},Field.ListVarName);%index of the variable in ListVarName + dim_ordinate{ilist}=Field.VarDimName{VarIndex_y(ilist)};% name of the corresponding dimension +% if iscell(dim_ordinate{ilist}) +% dim_ordinate{ilist}=dim_ordinate{ilist}{1};%take the first dimension name (char chain) in case of a matrix +% end + testpermute(ilist)=0;%default + nbvar=nbvar+1; + ListVarName{nbvar}=Field.ListVarName{VarIndex_y(ilist)}; + VarDimName{nbvar}=Field.VarDimName{VarIndex_y(ilist)}; + subvarindex(ilist)=nbvar; + if numel(VarAttribute)>=VarIndex_y(ilist) + SubVarAttribute{nbvar}=VarAttribute{VarIndex_y(ilist)}; + end + SubVarAttribute{nbvar}.Role='scalar'; + end + + % select abscissa variable + inputlist=get(handles.abscissa,'String'); + val=get(handles.abscissa,'Value');% a single selection is expected for abscissa + VarName=inputlist{val}; %name of the variable in the list + VarIndex=name2index(VarName,Field.ListVarName);%index of the variable in ListVarName + if isempty(VarIndex)% default abscissa = matrix index + coord_x_name=dim_ordinate{1};% name of the x coordinate = dimension of the plotted quantity + if iscell(coord_x_name) + coord_x_name=coord_x_name{1}; + end + empty_coord_x=1; + else + dimname_x=Field.VarDimName{VarIndex}; + if numel(dimname_x)~=1 + errormsg='abscissa must be a one-dimensional variable'; + return + end + nbvar=nbvar+1; + ListVarName{nbvar}=Field.ListVarName{VarIndex}; + VarDimName{nbvar}=Field.VarDimName{VarIndex}; + if numel(VarAttribute)>=VarIndex + SubVarAttribute{nbvar}=VarAttribute{VarIndex}; + end + SubVarAttribute{nbvar}.Role='coord_x'; + %check consistency of ordinate dimensions + for ilist=1:length(VarNameCell) + if iscell(dim_ordinate{ilist}) + if ~strcmp(dim_ordinate{ilist}{1},dimname_x) + if strcmp(dim_ordinate{ilist}{2},dimname_x) + testpermute(ilist)=1; + else + errormsg='inconsistent dimensions for ordinate and abscissa'; + return + end + end + end + end + end +end + +test3D=strcmp(get(handles.coord_z_scalar,'Visible'),'on')||strcmp(get(handles.coord_z_vectors,'Visible'),'on'); +VarSubIndexA=[]; + +%scalar variable +test_xdimvar=0;%default +test_ydimvar=0;%default +test_zdimvar=0;%defaul +dimname_x=[]; +dimname_y=[]; +dimname_z=[]; +if test_scalar + inputlist=get(handles.scalar,'String'); + if isempty(inputlist) + errormsg='empty input field'; + return + end + val=get(handles.scalar,'Value');%selected indices in the ordinate listbox + VarNameScalar=inputlist{val}; %name of the variable in the list + VarIndexA=name2index(VarNameScalar,Field.ListVarName);%index of the variable in ListVarName + dimname_A=Field.VarDimName{VarIndexA}; + nbvar=nbvar+1; + ListVarName{nbvar}=Field.ListVarName{VarIndexA}; + VarSubIndexA=nbvar; + VarDimName{nbvar}=dimname_A; + if numel(VarAttribute)>=VarIndexA + SubVarAttribute{nbvar}=VarAttribute{VarIndexA}; + end + SubVarAttribute{nbvar}.Role='scalar'; + field_var_index=VarIndexA; %store the last variable index to determine the absissa dimension if not defiend + + % select x variable + inputlist=get(handles.coord_x_scalar,'String'); + val=get(handles.coord_x_scalar,'Value');% a single selection is expected for abscissa + VarName=inputlist{val}; %name of the variable in the list + VarIndex=name2index(VarName,Field.ListVarName);%index of the variable in ListVarName + if isempty(VarIndex)% default abscissa = matrix index + empty_coord_x=1; + else + dimname_x=Field.VarDimName{VarIndex}; + nbvar=nbvar+1; + ListVarName{nbvar}=Field.ListVarName{VarIndex}; + VarDimName{nbvar}=dimname_x; + if numel(VarAttribute)>=VarIndex + SubVarAttribute{nbvar}=VarAttribute{VarIndex}; + end + %check consistency of dimensions + if ~isequal(dimname_x,dimname_A)% case of dimension variables + if iscell(dimname_x) + if numel(dimname_x)==1 + dimname_x=dimname_x{1};%transform to char chain + else + errormsg='invalid x coordinate selection in get_field'; + return + end + end + test_xdimvar=1; + SubVarAttribute{nbvar}.Role='dimvar';% dimension variable + else + SubVarAttribute{nbvar}.Role='coord_x';%abcissa with unstructured coordinates + end + end + + % select y variable + inputlist=get(handles.coord_y_scalar,'String'); + val=get(handles.coord_y_scalar,'Value');% a single selection is expected for abscissa + VarName=inputlist{val}; %name of the variable in the list + VarIndex=name2index(VarName,Field.ListVarName);%index of the variable in ListVarName + if isempty(VarIndex)% default abscissa = matrix index + empty_coord_y=1; + else + dimname_y=Field.VarDimName{VarIndex}; + %check consistency of dimensions + nbvar=nbvar+1; + ListVarName{nbvar}=Field.ListVarName{VarIndex}; + VarDimName{nbvar}=dimname_y; + if numel(VarAttribute)>=VarIndex + SubVarAttribute{nbvar}=VarAttribute{VarIndex}; + end + %check consistency of dimensions + if ~isequal(dimname_y,dimname_A)% case of dimension variables + if iscell(dimname_y) + if numel(dimname_y)==1 + dimname_y=dimname_y{1};%transform to char chain + else + errormsg='invalid y coordinate selection in get_field'; + return + end + end + test_ydimvar=1; + SubVarAttribute{nbvar}.Role='dimvar';% dimension variable + else + SubVarAttribute{nbvar}.Role='coord_y';%abcissa with unstructured coordinates + end + if isequal(dimname_y,dimname_x) + errormsg='identical x and y coordinates selected in get_field'; + return + end + end + + % select z variable + if test3D % TODO: Lire z comme x et y + inputlist=get(handles.coord_z_scalar,'String'); + val=get(handles.coord_z_scalar,'Value');% a single selection is expected for abscissa + VarName=inputlist{val}; %name of the variable in the list + VarIndex=name2index(VarName,Field.ListVarName);%index of the variable in ListVarName + if isempty(VarIndex)% default abscissa = matrix index +% coord_z_name=dimname_A{1};% name of the x coordinate = dimension of the plotted quantity + empty_coord_z=1; + else + dimname_z=Field.VarDimName{VarIndex}; + %check consistency of dimensions + if ~isequal(dimname_z,dimname_A) + for icoord=1:numel(dimname_A) + if strcmp(dimname_z,dimname_A{icoord})% a dimension variable + dim_z=icoord; + break + end + end + if ~dim_z + errormsg='inconsistent dimensions for coordinate z'; + return + end + end + nbvar=nbvar+1; + ListVarName{nbvar}=Field.ListVarName{VarIndex}; + VarDimName{nbvar}=dimname_z; + if numel(VarAttribute)>=VarIndex + SubVarAttribute{nbvar}=VarAttribute{VarIndex}; + end + if dim_z + SubVarAttribute{nbvar}.Role='dimvar';% dimension variable + else + SubVarAttribute{nbvar}.Role='coord_z';%z coordinate with unstructured coordinates + end + end + end +end +test_vec_x_dimvar=0;%default +test_vec_y_dimvar=0;%default +test_vec_z_dimvar=0;%defaul +dimname_vec_x=[]; +dimname_vec_y=[]; +dimname_vec_z=[]; +if test_vector + %select u variable + inputlist=get(handles.vector_x,'String'); + if isempty(inputlist) + errormsg='empty input field'; + return + end + val=get(handles.vector_x,'Value');%selected indices in the ordinate listbox + VarNameU=inputlist{val}; %name of the variable in the list + VarIndexU=name2index(VarNameU,Field.ListVarName);%index of the variable in ListVarName + nbvar=nbvar+1; + VarSubIndexU=nbvar; + ListVarName{nbvar}=Field.ListVarName{VarIndexU}; + dimname_u=Field.VarDimName{VarIndexU}; + VarDimName{nbvar}=dimname_u; + if numel(VarAttribute)>=VarIndexU + SubVarAttribute{nbvar}=VarAttribute{VarIndexU}; + end + SubVarAttribute{nbvar}.Role='vector_x'; + field_var_index=VarIndexU; %store the last variable index to determine the absissa dimension if not defiend + + %scalar v variable + inputlist=get(handles.vector_y,'String'); + val=get(handles.vector_y,'Value');%selected indices in the ordinate listbox + VarNameV=inputlist{val}; %name of the variable in the list + VarIndexV=name2index(VarNameV,Field.ListVarName);%index of the variable in ListVarName + %check consistency of dimensions with u + dimname_v=Field.VarDimName{VarIndexV}; + if ~isequal(dimname_v,dimname_u) + errormsg='inconsistent dimensions for u and v'; + return + end + nbvar=nbvar+1; + VarSubIndexV=nbvar; + ListVarName{nbvar}=Field.ListVarName{VarIndexV}; + VarDimName{nbvar}=dimname_u; + if numel(VarAttribute)>=VarIndexV + SubVarAttribute{nbvar}=VarAttribute{VarIndexV}; + end + SubVarAttribute{nbvar}.Role='vector_y'; + + + % select x variable for vector + inputlist=get(handles.coord_x_vectors,'String'); + val=get(handles.coord_x_vectors,'Value');% a single selection is expected for abscissa + VarName=inputlist{val}; %name of the variable in the list + VarIndex=name2index(VarName,Field.ListVarName);%index of the variable in ListVarName + if isempty(VarIndex)% default abscissa = matrix indexTODO like scalar +% coord_x_name=dimname_u{2};% name of the x coordinate = dimension of the plotted quantity + empty_coord_vec_x=1; + else + empty_coord_vec_x=0; + dimname_vec_x=Field.VarDimName{VarIndex}; + nbvar=nbvar+1; + ListVarName{nbvar}=Field.ListVarName{VarIndex}; + VarDimName{nbvar}=dimname_vec_x; + if numel(VarAttribute)>=VarIndex + SubVarAttribute{nbvar}=VarAttribute{VarIndex}; + end + %check consistency of dimensions + if ~isequal(dimname_vec_x,dimname_u)% case of dimension variables + if iscell(dimname_vec_x) + if numel(dimname_vec_x)==1 + dimname_vec_x=dimname_vec_x{1};%transform to char chain + else + errormsg='invalid x coordinate selection in get_field'; + return + end + end + test_vec_x_dimvar=1; + SubVarAttribute{nbvar}.Role='dimvar';% dimension variable + else + SubVarAttribute{nbvar}.Role='coord_x';%abcissa with unstructured coordinates + end + end + + % select y variable for vector + inputlist=get(handles.coord_y_vectors,'String'); + val=get(handles.coord_y_vectors,'Value');% a single selection is expected for abscissa + VarName=inputlist{val}; %name of the variable in the list + VarIndex=name2index(VarName,Field.ListVarName);%index of the variable in ListVarName + if isempty(VarIndex)% default abscissa = matrix indexTODO like scalar +% coord_x_name=dimname_u{2};% name of the x coordinate = dimension of the plotted quantity + empty_coord_vec_y=1; + else + empty_coord_vec_y=0; + dimname_vec_y=Field.VarDimName{VarIndex}; + nbvar=nbvar+1; + ListVarName{nbvar}=Field.ListVarName{VarIndex}; + VarDimName{nbvar}=dimname_vec_y; + if numel(VarAttribute)>=VarIndex + SubVarAttribute{nbvar}=VarAttribute{VarIndex}; + end + %check consistency of dimensions + if ~isequal(dimname_vec_y,dimname_u)% case of dimension variables + if iscell(dimname_vec_y) + if numel(dimname_vec_y)==1 + dimname_vec_y=dimname_vec_y{1};%transform to char chain + else + errormsg='invalid y coordinate selection in get_field'; + return + end + end + test_vec_y_dimvar=1; + SubVarAttribute{nbvar}.Role='dimvar';% dimension variable + else + SubVarAttribute{nbvar}.Role='coord_y';%abcissa with unstructured coordinates + end + end + + % select z variable for vector + if test3D + inputlist=get(handles.coord_z_vectors,'String'); + val=get(handles.coord_z_vectors,'Value');% a single selection is expected for abscissa + VarName=inputlist{val}; %name of the variable in the list + VarIndex=name2index(VarName,Field.ListVarName);%index of the variable in ListVarName + if isempty(VarIndex)% default abscissa = matrix indexTODO like scalar + % coord_x_name=dimname_u{2};% name of the x coordinate = dimension of the plotted quantity + empty_coord_vec_z=1; + else + dimname_vec_z=Field.VarDimName{VarIndex}; + nbvar=nbvar+1; + ListVarName{nbvar}=Field.ListVarName{VarIndex}; + VarDimName{nbvar}=dimname_vec_z; + if numel(VarAttribute)>=VarIndex + SubVarAttribute{nbvar}=VarAttribute{VarIndex}; + end + %check consistency of dimensions + if ~isequal(dimname_vec_z,dimname_u)% case of dimension variables + if iscell(dimname_vec_z) + if numel(dimname_vec_z)==1 + dimname_vec_z=dimname_vec_y{1};%transform to char chain + else + errormsg='invalid y coordinate selection in get_field'; + return + end + end + test_vec_z_dimvar=1; + SubVarAttribute{nbvar}.Role='dimvar';% dimension variable + else + SubVarAttribute{nbvar}.Role='coord_z';%abcissa with unstructured coordinates + end + end + end + + + if test3D % (a revoir) + %scalar w variable + inputlist=get(handles.vector_z,'String'); + val=get(handles.vector_z,'Value');%selected indices in the ordinate listbox + VarNameW=inputlist{val}; %name of the variable in the list + VarIndex=name2index(VarNameW,Field.ListVarName);%index of the variable in ListVarName + %check consistency of dimensions with u + dimname_w=Field.VarDimName{VarIndex}; + if ~isequal(dimname_w,dimname_u) + errormsg='inconsistent dimensions for u and v'; + return + end + nbvar=nbvar+1; + w_index=nbvar; + ListVarName{nbvar}=Field.ListVarName{VarIndex}; + VarDimName{nbvar}=dimname_u; + if numel(VarAttribute)>=VarIndex + SubVarAttribute{nbvar}=VarAttribute{VarIndex}; + end + SubVarAttribute{nbvar}.Role='vector_z'; + end + + % select color variable + inputlist=get(handles.vec_color,'String'); + val=get(handles.vec_color,'Value');% a single selection is expected for abscissa + VarNameC=inputlist{val}; %name of the variable in the list + VarIndex=name2index(VarNameC,Field.ListVarName);%index of the variable in ListVarName + %check consistency of dimensions with u + if ~isempty(VarIndex) + if ~isequal(Field.VarDimName{VarIndex},dimname_u) + errormsg='inconsistent dimensions for u and v'; + return + end + nbvar=nbvar+1; + c_index=nbvar; + ListVarName{nbvar}=Field.ListVarName{VarIndex}; + VarDimName{nbvar}=Field.VarDimName{VarIndex}; + if numel(VarAttribute)>=VarIndex + SubVarAttribute{nbvar}=VarAttribute{VarIndex}; + end + SubVarAttribute{nbvar}.Role='scalar'; + end +end + +% get the input field +inputfield=get(handles.inputfile,'String'); +if exist(inputfield,'file')% read the input data corresponding to the list of selected varaibles + SubField=nc2struct(inputfield,ListVarName); +else % subfield stored in memory + SubField.ListVarName=ListVarName; + SubField.VarDimName=VarDimName; +end +SubField.ListGlobalAttribute=['InputFile' SubField.ListGlobalAttribute]; +SubField.InputFile=get(handles.inputfile,'String'); +SubField.VarAttribute=SubVarAttribute; + +%permute indices if coord_y is not the first matrix index +if test_scalar + VarNameA=Field.ListVarName{VarIndexA}; + DimCellA=Field.VarDimName{VarIndexA}; + eval(['npxy=size(SubField.' VarNameA ')']) + SingleCellA={}; + if numel(npxy) < numel(DimCellA) + SingleCellA=DimCellA(1:end-numel(npxy)); + DimCellA=DimCellA(end-numel(npxy)+1:end); %suppress the first singletons) dimensions + end + ind_single=find(npxy==1); + SingleCellA=[SingleCellA DimCellA(ind_single)]; + ind_select=find(npxy~=1);%look for non singleton dimensions + DimCellA=DimCellA(ind_select); + npxy=npxy(ind_select); + dimA=[]; + if test_zdimvar%dim_x && dim_y && ~isempty(VarSubIndexA) + for icoord=1:numel(SingleCellA)% look for coincidence of dimension with one of the dimensions of the scalar + if strcmp(dimname_z,SingleCellA{icoord})% a singleton dimension + errormsg=['the singleton dimension ' dimname_z ' has been selected for z']; + return + end + end + for icoord=1:numel(DimCellA)% look for coincidence of dimension with one of the dimensions of the scalar + if strcmp(dimname_z,DimCellA{icoord})% a dimension variable + dimA=[dimA icoord]; + break + end + end + end + if test_ydimvar%dim_x && dim_y && ~isempty(VarSubIndexA) + for icoord=1:numel(SingleCellA)% look for coincidence of dimension with one of the dimensions of the scalar + if strcmp(dimname_y,SingleCellA{icoord})% a singleton dimension + errormsg=['the singleton dimension ' dimname_y ' has been selected for ordiante']; + return + end + end + for icoord=1:numel(DimCellA)% look for coincidence of dimension with one of the dimensions of the scalar + if strcmp(dimname_y,DimCellA{icoord})% a dimension variable + dimA=[dimA icoord]; + break + end + end + end + if test_xdimvar%dim_x && dim_y && ~isempty(VarSubIndexA) + for icoord=1:numel(SingleCellA)% look for coincidence of dimension with one of the dimensions of the scalar + if strcmp(dimname_x,SingleCellA{icoord})% a singleton dimension + errormsg=['the singleton dimension ' dimname_x ' has been selected for abscissa']; + return + end + end + for icoord=1:numel(DimCellA)% look for coincidence of dimension with one of the dimensions of the scalar + if strcmp(dimname_x,DimCellA{icoord})% a dimension variable + dimA=[dimA icoord]; + break + end + end + end + dimextra=(1:numel(DimCellA)); + dimextra(dimA)=[]; %list of unselected dimension indices + DimCellA=DimCellA([dimA dimextra]); + eval(['SubField.' VarNameA '=permute(squeeze(SubField.' VarNameA '),[dimA dimextra]);']) + SubField.VarDimName{VarSubIndexA}=DimCellA; + %add default coord_x and/or coord_y if empty + if empty_coord_x || empty_coord_y + VarName=Field.ListVarName{field_var_index}; + DimCell=Field.VarDimName{field_var_index}; + eval(['npxy=size(SubField.' VarName ')']) + if numel(npxy) < numel(DimCell) + DimCell=DimCell(end-numel(npxy)+1:end); %suppress the first singletons) dimensions + end + ind_select=find(npxy~=1) ;%look for non singleton dimensions + DimCell=DimCell(ind_select); + npxy=npxy(ind_select); + testold=0; + %old convention; use of coord_1 and Coord_2 + if isfield(Field,'VarAttribute') && numel(Field.VarAttribute)>=field_var_index + if isfield(Field.VarAttribute{field_var_index},'Coord_2')&& isfield(Field.VarAttribute{field_var_index},'Coord_1') + Coord_2=Field.VarAttribute{field_var_index}.Coord_2; + Coord_1=Field.VarAttribute{field_var_index}.Coord_1; + testold=1; + end + end + if empty_coord_x + coord_x_name=DimCell{2}; + SubField.ListVarName=[{coord_x_name} SubField.ListVarName]; + SubField.VarDimName=[{coord_x_name} SubField.VarDimName]; + if testold + eval(['SubField.' coord_x_name '=linspace(Coord_2(1),Coord_2(end),npxy(2));']) + else + eval(['SubField.' coord_x_name '=[0.5 npxy(2)-0.5];']) + end + + if ~testold + coord_x_attr.units='index'; + else + coord_x_attr.units='cm'; + end + SubField.VarAttribute=[{coord_x_attr} SubField.VarAttribute]; + end + if empty_coord_y + coord_y_name=DimCell{1}; + SubField.ListVarName=[{coord_y_name} SubField.ListVarName]; + SubField.VarDimName=[{coord_y_name} SubField.VarDimName]; + if testold + eval(['SubField.' coord_y_name '=linspace(Coord_1(1),Coord_1(end),npxy(1));']) + else + eval(['SubField.' coord_y_name '=[npxy(1)-0.5 0.5];']) + end + if ~testold + coord_y_attr.units='index'; + else + coord_y_attr.units='cm'; + end + SubField.VarAttribute=[{coord_y_attr} SubField.VarAttribute]; + end + end +end + +%permute indices if coord_y is not the first matrix index +if test_vector + VarNameU=Field.ListVarName{VarIndexU}; + DimCellU=Field.VarDimName{VarIndexU}; + eval(['npxy=size(SubField.' VarNameU ')']) + SingleCellU={}; + if numel(npxy) < numel(DimCellU) + SingleCellU=DimCellU(1:end-numel(npxy)); + DimCellU=DimCellU(end-numel(npxy)+1:end); %suppress the first singletons) dimensions + end + ind_single=find(npxy==1); + SingleCellU=[SingleCellU DimCellU(ind_single)]; + ind_select=find(npxy~=1);%look for non singleton dimensions + DimCellU=DimCellU(ind_select); + npxy=npxy(ind_select); + dimU=[]; + if test_zdimvar%dim_x && dim_y && ~isempty(VarSubIndexA) + for icoord=1:numel(SingleCellU)% look for coincidence of dimension with one of the dimensions of the scalar + if strcmp(dimname_vec_z,SingleCellU{icoord})% a singleton dimension + errormsg=['the singleton dimension ' dimname_vec_z ' has been selected for z']; + return + end + end + for icoord=1:numel(DimCellU)% look for coincidence of dimension with one of the dimensions of the scalar + if strcmp(dimname_vec_z,DimCellU{icoord})% a dimension variable + dimU=[dimU icoord]; + break + end + end + end + if test_ydimvar%dim_x && dim_y && ~isempty(VarSubIndexA) + for icoord=1:numel(SingleCellU)% look for coincidence of dimension with one of the dimensions of the scalar + if strcmp(dimname_vec_y,SingleCellU{icoord})% a singleton dimension + errormsg=['the singleton dimension ' dimname_vec_y ' has been selected for ordinate']; + return + end + end + for icoord=1:numel(DimCellU)% look for coincidence of dimension with one of the dimensions of the scalar + if strcmp(dimname_vec_y,DimCellU{icoord})% a dimension variable + dimU=[dimU icoord]; + break + end + end + end + if test_xdimvar + for icoord=1:numel(SingleCellU)% look for coincidence of dimension with one of the dimensions of the scalar + if strcmp(dimname_x,SingleCellU{icoord})% a singleton dimension + errormsg=['the singleton dimension ' dimname_vec_x ' has been selected for abscissa']; + return + end + end + for icoord=1:numel(DimCellA)% look for coincidence of dimension with one of the dimensions of the scalar + if strcmp(dimname_vec_x,DimCellU{icoord})% a dimension variable + dimU=[dimU icoord]; + break + end + end + end + dimextra=(1:numel(DimCellU)); + dimextra(dimU)=[]; %list of unselected dimension indices + DimCellU=DimCellU([dimU dimextra]); + eval(['SubField.' VarNameU '=permute(squeeze(SubField.' VarNameU '),[dimU dimextra]);']) + eval(['SubField.' VarNameV '=permute(squeeze(SubField.' VarNameV '),[dimU dimextra]);']) + SubField.VarDimName{VarSubIndexU}=DimCellU; + SubField.VarDimName{VarSubIndexV}=DimCellU; + + %add default coord_x and/or coord_y if empty + if empty_coord_vec_x || empty_coord_vec_y + VarName=Field.ListVarName{field_var_index}; + DimCell=Field.VarDimName{field_var_index}; + eval(['npxy=size(SubField.' VarName ')']) + if numel(npxy) < numel(DimCell) + DimCell=DimCell(end-numel(npxy)+1:end); %suppress the first singletons) dimensions + end + ind_select=find(npxy~=1) ;%look for non singleton dimensions + DimCell=DimCell(ind_select); + npxy=npxy(ind_select); + testold=0; + %old convention; use of coord_1 and Coord_2 + if isfield(Field,'VarAttribute') && numel(Field.VarAttribute)>=field_var_index + if isfield(Field.VarAttribute{field_var_index},'Coord_2')&& isfield(Field.VarAttribute{field_var_index},'Coord_1') + Coord_2=Field.VarAttribute{field_var_index}.Coord_2; + Coord_1=Field.VarAttribute{field_var_index}.Coord_1; + testold=1; + end + end + if empty_coord_vec_x + coord_x_name=DimCell{2}; + SubField.ListVarName=[{coord_x_name} SubField.ListVarName]; + SubField.VarDimName=[{coord_x_name} SubField.VarDimName]; + if testold + eval(['SubField.' coord_x_name '=linspace(Coord_2(1),Coord_2(end),npxy(2));']) + else + eval(['SubField.' coord_x_name '=[0.5 npxy(2)-0.5];']) + end + + if ~testold + coord_x_attr.units='index'; + else + coord_x_attr.units='cm'; + end + SubField.VarAttribute=[{coord_x_attr} SubField.VarAttribute]; + end + if empty_coord_vec_y + coord_y_name=DimCell{1}; + SubField.ListVarName=[{coord_y_name} SubField.ListVarName]; + SubField.VarDimName=[{coord_y_name} SubField.VarDimName]; + if testold + eval(['SubField.' coord_y_name '=linspace(Coord_1(1),Coord_1(end),npxy(1));']) + else + eval(['SubField.' coord_y_name '=[npxy(1)-0.5 0.5];']) + end + if ~testold + coord_y_attr.units='index'; + else + coord_y_attr.units='cm'; + end + SubField.VarAttribute=[{coord_y_attr} SubField.VarAttribute]; + end + end +end +if test_1Dplot + for ilist=1:numel(VarIndex_y) + VarName=Field.ListVarName{VarIndex_y(ilist)}; + eval(['npxy=size(SubField.' VarName ');']) + ind_select=find(npxy~=1); + SubField.VarDimName{subvarindex(ilist)}=SubField.VarDimName{subvarindex(ilist)}(ind_select); + eval(['SubField.' VarName '=squeeze(SubField.' VarName ');'])%remove singleton dimensions + if testpermute(ilist) + eval(['SubField.' VarName '=permute(SubField.' VarName ',[2 1]);']) + subvarindex(ilist) + SubField.VarDimName{subvarindex(ilist)} + SubField.VarDimName{subvarindex(ilist)}=SubField.VarDimName{subvarindex(ilist)}([2 1]); + end + end + if empty_coord_x + SubField.ListVarName=[{[coord_x_name '_index']} SubField.ListVarName]; + SubField.VarDimName=[{coord_x_name } SubField.VarDimName]; + VarName=Field.ListVarName{VarIndex_y(1)}; + DimCell=Field.VarDimName{VarIndex_y(1)}; + eval(['npxy=size(SubField.' VarName ')']) + if numel(npxy) < numel(DimCell) + DimCell=DimCell(end-numel(npxy)+1:end); %suppress the first singletons) dimensions + end + ind_select=find(npxy~=1) ;%look for non singleton dimensions + DimCell=DimCell(ind_select); + npxy=npxy(ind_select); + if isfield(Field,'VarAttribute') && numel(Field.VarAttribute)>=VarIndex_y(1) ... + && isfield(Field.VarAttribute{VarIndex_y(1)},'Coord_1') + Coord_1=Field.VarAttribute{VarIndex_y(1)}.Coord_1;%old convention; use of coord_1 + eval(['SubField.' coord_x_name '_index=linspace(Coord_1(1),Coord_1(end),npxy(1));']) + else + eval(['SubField.' coord_x_name '_index=linspace(0.5,npxy(1)-0.5,npxy(1));']) + end + struct.Role='coord_x'; + SubField.VarAttribute=[{struct} SubField.VarAttribute]; + end +end + +%------------------------------------------------- +% give index numbers of the strings str in the list ListvarName +function VarIndex_y=name2index(cell_str,ListVarName) +VarIndex_y=[]; +if ischar(cell_str) + for ivar=1:length(ListVarName) + varlist=ListVarName{ivar}; + if isequal(varlist,cell_str) + VarIndex_y= ivar; + break + end + end +elseif iscell(cell_str) + for isel=1:length(cell_str) + varsel=cell_str{isel}; + for ivar=1:length(ListVarName) + varlist=ListVarName{ivar}; + if isequal(varlist,varsel) + VarIndex_y=[VarIndex_y ivar]; + end + end + end +end Index: /trunk/src/read_imadoc.m =================================================================== --- /trunk/src/read_imadoc.m (revision 2) +++ /trunk/src/read_imadoc.m (revision 2) @@ -0,0 +1,243 @@ +%'read_imadoc': reads the xml file for image documentation, OBSOLETE: replaced by imadoc2struct +% +%function [error,Heading,nom_type_ima,ext_ima,abs_time,TimeUnit,mode,NbSlice,npx,npy,GeometryCalib]=read_imadoc(filecivxml,testime) +%-------------------------------------------------------- +% OUTPUT: +%error= 0: all right +% 2: input file not found +% 1: input file is not an image documentation file 'ImaDoc' +% 1.1: 'ImaDoc/Heading' element absent +% 1.2: 'ImaDoc/Camera' element absent +% 1.21: 'ImaDoc/Camera/BurstTiming' absent +% 1.211: 'ImaDoc/Camera/BurstTiming/FrameFrequency' absent +% 1.212: 'ImaDoc/Camera/BurstTiming/Time' absent +% +% INPUT: +% filecivxml: full name of the xml input file +% testime=1 read the list of times), =0 (default) do not read it to save computing time +% +% -- TODO: should be replaced by xml2struct -- + +function [error,Heading,nom_type_ima,ext_ima,abs_time,TimeUnit,mode,NbSlice,npx,npy,GeometryCalib]=read_imadoc(filecivxml,testime) +% global t +error=0;%default +Heading=[];%default +nom_type_ima=[];%default +ext_ima=[];%default +abs_time=[];%initiation +TimeUnit='s'; %default +% GeometryCalib.CoordUnit='cm';%default +mode=[]; %default +NbSlice=1;%default +npx=[];%default +npy=[];%default +% GeometryCalib.Pxcmx=1; +% GeometryCalib.Pxcmy=1; +GeometryCalib=[]; +NbDtj=1; +tsai=[];%default +if ~exist('testime','var') + testime=1;%default +end +if exist(filecivxml,'file')~=2, error=2, return;end;%input file does not exist +filecivxml; +t=xmltree(filecivxml); +uid_root=find(t,'/ImaDoc'); +if isempty(uid_root), error=1; return; end;%not an ImaDoc .xml file +%Heading +uid_Heading=find(t,'/ImaDoc/Heading'); +if isempty(uid_Heading), + error=1.1; +else + uid_Campaign=find(t,'/ImaDoc/Heading/Campaign'); + uid_Exp=find(t,'/ImaDoc/Heading/Experiment'); + uid_Device=find(t,'/ImaDoc/Heading/Device'); + uid_Record=find(t,'/ImaDoc/Heading/Record'); + uid_FirstImage=find(t,'/ImaDoc/Heading/ImageName'); + Heading.Campaign=get(t,children(t,uid_Campaign),'value'); + Heading.Experiment=get(t,children(t,uid_Exp),'value'); + Heading.Device=get(t,children(t,uid_Device),'value'); + if ~isempty(uid_Record) + Heading.Record=get(t,children(t,uid_Record),'value'); + end + Heading.ImageName=get(t,children(t,uid_FirstImage),'value'); + FirstImage=Heading.ImageName; + if ~isempty(FirstImage) + [Pathsub,RootFile,field_count,str2,str_a,str_b,ext,nom_type_ima]=name2display(FirstImage); + end +end +%Camera +uid_Camera=find(t,'/ImaDoc/Camera'); +if isempty(uid_Camera) + error=1.2; +else + uid_ImageSize=find(t,'/ImaDoc/Camera/ImageSize'); + if ~isempty(uid_ImageSize); + ImageSize=get(t,children(t,uid_ImageSize),'value'); + xindex=findstr(ImageSize,'x'); + if length(xindex)>=2 + npx=str2num(ImageSize(1:xindex(1)-1)); + npy=str2num(ImageSize(xindex(1)+1:xindex(2)-1)); + end + end + uid_NbSlice=find(t,'/ImaDoc/Camera/NbSlice'); + if ~isempty(uid_NbSlice) + NbSlice=str2num(get(t,children(t,uid_NbSlice),'value')); + if isempty(NbSlice),NbSlice=1;end; %default + end + uid_TimeUnit=find(t,'/ImaDoc/Camera/TimeUnit'); + if ~isempty(uid_TimeUnit) + TimeUnit=get(t,children(t,uid_TimeUnit),'value'); + if isempty(TimeUnit),TimeUnit='s';end; %default + end + uid_BurstTiming=find(t,'/ImaDoc/Camera/BurstTiming'); + if isempty(uid_BurstTiming), error=1.12,return,end; + if testime + for k=1:length(uid_BurstTiming) + Dtj=[];%default + NbDtj=1;%default + subt=branch(t,uid_BurstTiming(k));%subtree under BurstTiming + uid_FrameFrequency=find(subt,'/BurstTiming/FrameFrequency'); + % if isempty(uid_FrameFrequency), error=1.211,return; + if isempty(uid_FrameFrequency), + Frequency=1; + else + Frequency=str2num(get(subt,children(subt,uid_FrameFrequency),'value')); + end + uid_Dtj=find(subt,'/BurstTiming/Dtj'); + uid_NbDtj=find(subt,'/BurstTiming/NbDtj'); + uid_Dti=find(subt,'/BurstTiming/Dti');%new + uid_NbDti=find(subt,'/BurstTiming/NbDti');%new + if ~isempty(uid_Dtj) + Dtj=str2num(get(subt,children(subt,uid_Dtj),'value'));%time intervals in frames + end + uid_child=children(subt,uid_NbDtj); + for ivalue=1:length(uid_child) + if isequal(get(subt,uid_child(ivalue),'type'),'chardata') + NbDtj=str2num(get(subt,uid_child(ivalue),'value'));%nbre of intervals Dtj + end + end + if isempty(uid_Dti)|isempty(uid_NbDti) + Dti=[]; %default + else + Dti=str2num(get(subt,children(subt,uid_Dti),'value'));%time intervals in frames + uid_child=children(subt,uid_NbDti); + for ivalue=1:length(uid_child) + if isequal(get(subt,uid_child(ivalue),'type'),'chardata') + NbDti=str2num(get(subt,uid_child(ivalue),'value'));%nbre of intervals Dti + end + end + end + if ~isempty(Dtj) + Dtj=reshape(Dtj'*ones(1,NbDtj),1,length(Dtj)*NbDtj); + end + Dtj=[0 Dtj]; + dtunit=Dtj/Frequency; + uid_Time=find(subt,'/BurstTiming/Time'); + if isempty(uid_Time) + error=1.212; + else + nbfield=length(uid_Time); + Time=get(subt,children(subt,uid_Time),'value'); + abstime_read=str2num(char(Time))*ones(1,length(Dtj))+ones(nbfield,1)*cumsum(dtunit); + abs_time=[abs_time;abstime_read]; + if ~isempty(Dti)&size(abs_time,1)==1 + abs_time=ones(NbDti+1,1)*abs_time+(Dti/Frequency)*[0:NbDti]'*ones(size(abs_time)); + end + end + end + end +end +% if isempty(abs_time) +% abs_time=0;%default +% end +%read calibration +uid_GeometryCalib=find(t,'/ImaDoc/GeometryCalib'); +if ~isempty(uid_GeometryCalib) + if length(uid_GeometryCalib)>1 + errordlg(['More than one GeometryCalib in ' filecivxml]) + return + end + subt=branch(t,uid_GeometryCalib);%subtree under GeometryCalib + cont=get(subt,1,'contents'); + if ~isempty(cont) + uid_pixcmx=find(subt,'/GeometryCalib/Pxcmx'); + uid_pixcmy=find(subt,'/GeometryCalib/Pxcmy'); + if ~isempty(uid_pixcmx) & ~isempty(uid_pixcmy)%NON UTILISE + pixcmx=str2num(get(subt,children(subt,uid_pixcmx),'value')); + if isempty(pixcmx),pixcmx=1;end; %default + pixcmy=str2num(get(subt,children(subt,uid_pixcmy),'value')); + if isempty(pixcmy),pixcmy=1;end; %default + tsai.Pxcmx=pixcmx; + tsai.Pxcmy=pixcmy; + end + %default values: + tsai.f=1; + tsai.dpx=1; + tsai.dpy=1; + tsai.sx=1; + tsai.Cx=0; + tsai.Cy=0; + tsai.Tz=1; + tsai.Tx=0; + tsai.Ty=0; + tsai.R=[1 0 0; 0 1 0; 0 0 0]; + tsai.kappa1=0; + uid_CoordUnit=find(subt,'/GeometryCalib/CoordUnit'); + if ~isempty(uid_CoordUnit) + tsai.CoordUnit=get(subt,children(subt,uid_CoordUnit),'value'); + end + uid_focal=find(subt,'/GeometryCalib/focal'); + uid_dpx_dpy=find(subt,'/GeometryCalib/dpx_dpy'); + uid_sx=find(subt,'/GeometryCalib/sx'); + uid_Cx_Cy=find(subt,'/GeometryCalib/Cx_Cy'); + uid_kappa1=find(subt,'/GeometryCalib/kappa1'); + uid_Tx_Ty_Tz=find(subt,'/GeometryCalib/Tx_Ty_Tz'); + uid_R=find(subt,'/GeometryCalib/R'); + if ~isempty(uid_focal) & ~isempty(uid_dpx_dpy) & ~isempty(uid_Cx_Cy) + tsai.f=str2num(get(subt,children(subt,uid_focal),'value')); + dpx_dpy=str2num(get(subt,children(subt,uid_dpx_dpy),'value')); + tsai.dpx=dpx_dpy(1); + tsai.dpy=dpx_dpy(2); + if ~isempty(uid_sx) + tsai.sx=str2num(get(subt,children(subt,uid_sx),'value')); + end + Cx_Cy=str2num(get(subt,children(subt,uid_Cx_Cy),'value')); + tsai.Cx=Cx_Cy(1); + tsai.Cy=Cx_Cy(2); + end + if ~isempty(uid_Tx_Ty_Tz) + Tx_Ty_T_char=get(subt,children(subt,uid_Tx_Ty_Tz),'value'); +% if ~ischar(Tx_Ty_T_char) +% error='multiple values for Tx_Ty_Tz'; +% else + Tx_Ty_Tz=str2num(Tx_Ty_T_char); +% end + tsai.Tx=Tx_Ty_Tz(1); + tsai.Ty=Tx_Ty_Tz(2); + tsai.Tz=Tx_Ty_Tz(3); + end + if ~isempty(uid_R) + RR=get(subt,children(subt,uid_R),'value'); + if length(RR)==3 + tsai.R=[str2num(RR{1});str2num(RR{2});str2num(RR{3})]; + end + end + if ~isempty(uid_kappa1) + tsai.kappa1=str2num(get(subt,children(subt,uid_kappa1),'value')); + end + %look for laser plane definitions + uid_Angle=find(subt,'/GeometryCalib/PlaneAngle'); + uid_Pos=find(subt,'/GeometryCalib/PlanePos'); + if ~isempty(uid_Angle) + tsai.PlaneAngle=str2num(get(subt,children(subt,uid_Angle),'value')); + end + if ~isempty(uid_Pos) + for j=1:length(uid_Pos) + tsai.PlanePos(j,:)=str2num(get(subt,children(subt,uid_Pos(j)),'value')); + end + end + GeometryCalib=tsai; + end +end + Index: /trunk/src/read_image.m =================================================================== --- /trunk/src/read_image.m (revision 2) +++ /trunk/src/read_image.m (revision 2) @@ -0,0 +1,36 @@ +%'read_image': reads an image from a single file or a movie file +function [A,error]=read_image(filename,NomType,num); + %read images in different formats. +A=[]; %default +error=0; %default +if ~exist(filename,'file') + error='input file not found in read_image' + return +end +testframe=0; +if ~exist('NomType','var') + NomType=[]; +end +if ~exist('num','var') + num=1; +end +[pth,fl,ext]=fileparts(filename); +if isequal(lower(ext),'.avi') + mov=aviread(filename,num); + A=frame2im(mov(1)); +elseif isequal(lower(ext),'.vol') + A=imread(filename); +else + form=imformats(ext([2:end])); + if ~isempty(form)% if the extension corresponds to an image format recognized by Matlab + if isequal(NomType,'*'); + A=imread(filename,num); + else + A=imread(filename); + end + else + error=['ERROR in read_image: file extension not recognized by matlab as image']; + return + end +end + Index: /trunk/src/read_imatext.m =================================================================== --- /trunk/src/read_imatext.m (revision 2) +++ /trunk/src/read_imatext.m (revision 2) @@ -0,0 +1,30 @@ +%'read_imatext': reads the .civ file for image documentation (obsolete) +% fileinput: name of the documentation file +% time: matrix of times for the set of images +%pxcmx: scale along x in pixels/cm +%pxcmy: scale along y in pixels/cm +function [error,time,TimeUnit,mode,npx,npy,pxcmx,pxcmy]=read_imatext(fileinput); +error=0;%default +time=[]; %default +TimeUnit='s'; +mode='pairs'; +npx=[]; %default +npy=[]; %default +pxcmx=1;%default +pxcmy=1;%default +if exist(fileinput,'file')~=2, error=2, return;end;%input file does not exist +dotciv=textread(fileinput); +sizdot=size(dotciv); +if ~isequal(sizdot(1)-8,dotciv(1,1)); + error=1; %inconsistent number of bursts +end +nbfield=sizdot(1)-8; +npx=(dotciv(2,1)); +npy=(dotciv(2,2)); +pxcmx=(dotciv(6,1));% pixels/cm in the .civ file +pxcmy=(dotciv(6,2)); +% nburst=dotciv(3,1); % nbre of bursts +abs_time1=dotciv([9:nbfield+8],2); +dtime=dotciv(5,1)*(dotciv([9:nbfield+8],[3:end-1])+1); +timeshift=[abs_time1 dtime]; +time=cumsum(timeshift,2); Index: /trunk/src/read_plot_param.m =================================================================== --- /trunk/src/read_plot_param.m (revision 2) +++ /trunk/src/read_plot_param.m (revision 2) @@ -0,0 +1,52 @@ +%'read_plot_param': read plotting parameters from the interface uvmat +%------------------------------------------ +% function PlotParam=read_plot_param(handles) +% +% OUTPUT: +% PlotParam: structure containing the values of all the relevant plotting parameters +% +% INPUT: +% handles: structure containing the handles of the relevant uicontrols in the uvmat interface +% +% -- TODO: get the handles using get_plot_handles and findobj as default input -- + +function PlotParam=read_plot_param(handles) + +PlotParam.Auto_xy=get(handles.auto_xy,'Value'); + +% scalars +Scalar.MaxA=str2double(get(handles.MaxA,'String')); +Scalar.MinA=str2double(get(handles.MinA,'String')); +Scalar.AutoScal=get(handles.AutoScal,'Value'); +Scalar.BW=get(handles.BW,'Value'); +Scalar.Contours=get(handles.Contours,'Value')==2; +Scalar.IncrA=str2double(get(handles.IncrA,'String')); +PlotParam.Scalar=Scalar; + +%vectors +Vectors.VecScale=str2double(get(handles.VecScale,'String')); +Vectors.AutoVec=get(handles.AutoVec,'Value');%automatic vector length +Vectors.HideFalse=get(handles.HideFalse,'Value'); +Vectors.HideWarning=get(handles.HideWarning,'Value'); +Vectors.decimate4=get(handles.decimate4,'Value');% =1; for reducing the nbre of vectors + +%vector color +code_list=get(handles.color_code,'String'); +val=get(handles.color_code,'Value'); +% menu_col=get(handles.col_vec,'String'); +% menu_val=get(handles.col_vec,'Value'); +colcode1=str2double(get(handles.colcode1,'String'));% first threshold for rgb, first value for'continuous' +colcode2=str2double(get(handles.colcode2,'String'));% second threshold for rgb, last value (saturation) for 'continuous' + +Vectors.ColorCode=code_list{val}; % option of color code for vectors +Vectors.FixedCbounds=get(handles.AutoVecColor,'Value');% =1; fixed scale for color vector, =0 otherwise (default) +Vectors.MinC=str2num(get(handles.min_vec,'String')); % imposed min of C, (needed if .FixedCbounds=1) +Vectors.MaxC=str2num(get(handles.max_vec,'String')); % imposed max of C, needed if .FixedCbounds=1 +if Vectors.MaxC <= Vectors.MinC + Vectors.ColorCode='black'; +else + Vectors.colcode1=Vectors.MinC+(colcode1-Vectors.MinC)/(Vectors.MaxC-Vectors.MinC);% relative thresholds + Vectors.colcode2=Vectors.MinC+(colcode2-Vectors.MinC)/(Vectors.MaxC-Vectors.MinC); +end +PlotParam.Vectors=Vectors; + Index: /trunk/src/read_set_object.m =================================================================== --- /trunk/src/read_set_object.m (revision 2) +++ /trunk/src/read_set_object.m (revision 2) @@ -0,0 +1,210 @@ +%'read_set_object': read the data on the 'set_object' interface +%-------------------------------------------------------- +% data=read_set_object(handles) +%-------------------------------------------------------- +%OUTPUT +%data: structure of data read on the set_object interface +% .Style : style of projection object +% .Coord(nbpos,3): set of coordinates defining the object position; +% .ProjMode=type of projection ; +% .Phi=angle of projection; +% .DX,.DY,.DZ=increments; +% .YMax,YMin: min and max Y +%INPUT: +% handles: structure describing the tags of the edit boxes and menus +function data=read_set_object(handles) +%menus +if isfield(handles,'ObjectStyle')%case of the set_object interface + menu=get(handles.ObjectStyle,'String'); + value=get(handles.ObjectStyle,'Value'); + data.Style=menu{value}; + menu=get(handles.ProjMode,'String'); + value=get(handles.ProjMode,'Value'); + data.ProjMode=menu{value}; + menu=get(handles.MenuCoord,'String'); + value=get(handles.MenuCoord,'Value'); + data.CoordType=menu{value}; + testcalib=0; +else %default + data.Style='points'; + testcalib=1; +end + +%Euler angles and projection ranges +if ~testcalib + if isequal(get(handles.Phi,'Visible'),'on') + data.Phi=str2num(get(handles.Phi,'String')); + end + if isequal(get(handles.Theta,'Visible'),'on') + data.Theta=str2num(get(handles.Theta,'String')); + end + if isequal(get(handles.Psi,'Visible'),'on') + data.Psi=str2num(get(handles.Psi,'String')); + end + if isequal(get(handles.DX,'Visible'),'on') + data.DX=str2num(get(handles.DX,'String')); + end + if isequal(get(handles.DY,'Visible'),'on') + data.DY=str2num(get(handles.DY,'String')); + end + if isequal(get(handles.DZ,'Visible'),'on') + data.DZ=str2num(get(handles.DZ,'String')); + end + dimrange=[1 1];%default + if isequal(get(handles.ZMin,'Visible'),'on') + ZMin=str2num(get(handles.ZMin,'String')); + if ~isempty(ZMin) + data.RangeZ(1)=ZMin; + dimrange=[2 3]; + end + end + if isequal(get(handles.ZMax,'Visible'),'on') + ZMax=str2num(get(handles.ZMax,'String')); + if isempty(ZMax) + if dimrange(1)>1 +% set(handles.ZMax,'String',get(handles.ZMin,'String')) + data.RangeZ(1)=ZMax; + end + else + data.RangeZ=ZMax; + dimrange=[dimrange(1) 3]; + end + end + if isequal(get(handles.YMin,'Visible'),'on') + YMin=str2num(get(handles.YMin,'String')); + if isempty(YMin) +% if dimrange(2)>2 +% % set(handles.YMin,'String','0') +% data.RangeY(2)=0; +% end + else + data.RangeY(2)=YMin; + dimrange=[2 max(dimrange(2),2)]; + end + end + if isequal(get(handles.YMax,'Visible'),'on') +% data.YMax=str2num(get(handles.YMax,'String')); + YMax=str2num(get(handles.YMax,'String')); + if isempty(YMax) +% if dimrange(1)>1 +% % set(handles.YMax,'String',get(handles.YMin,'String')) +% if ~isempty(YMin) +% data.RangeY(1)=YMin; +% end +% elseif dimrange(2)>2 +% % set(handles.YMax,'String',get(handles.ZMin,'String')) +% data.RangeY(2)=ZMin; +% end + else + data.RangeY(1)=YMax; + dimrange=[dimrange(1) max(dimrange(2),2)]; + end + end + if isequal(get(handles.XMin,'Visible'),'on') + XMin=str2num(get(handles.XMin,'String')); + if isempty(XMin) +% if ~isempty(YMin) +% if dimrange(2)>1 +% % set(handles.XMin,'String',get(handles.YMin,'String')) +% data.RangeX(2)=YMin; +% XMin=YMin; +% end +% end + else + data.RangeX(2)=XMin; + %dimrange=[2 max(dimrange(2),1)]; + end + end + if isequal(get(handles.XMax,'Visible'),'on') + XMax=str2num(get(handles.XMax,'String')); + if isempty(XMax) +% if dimrange(1)>1 +% % set(handles.XMax,'String',get(handles.XMin,'String')) +% if ~isempty(XMin) +% data.RangeX(2)=XMin; +% end +% elseif dimrange(2)>1 +% % set(handles.XMax,'String',get(handles.YMax,'String')) +% data.RangeX(1)=YMax; +% end + else + data.RangeX(1)=XMax; + end + end +end + + +%positions x,y,z +Xcolumn=get(handles.XObject,'String'); +Ycolumn=get(handles.YObject,'String'); +if ischar(Xcolumn) + sizchar=size(Xcolumn); + for icol=1:sizchar(1) + Xcolumn_cell{icol}=Xcolumn(icol,:); + end + Xcolumn=Xcolumn_cell; +end +if ischar(Ycolumn) + sizchar=size(Ycolumn); + for icol=1:sizchar(1) + Ycolumn_cell{icol}=Ycolumn(icol,:); + end + Ycolumn=Ycolumn_cell; +end +Zcolumn={};%default +if isequal(get(handles.ZObject,'Visible'),'on') + data.NbDim=3; %test 3D object + Zcolumn=get(handles.ZObject,'String'); + if ischar(Zcolumn) + Zcolumn={Zcolumn}; + end +end +nb_points=min(length(Xcolumn),length(Ycolumn));%number of point positions needed to define the object position +if isequal (data.Style,'line'); + nb_defining_points=2; +elseif isequal(data.Style,'plane')|isequal(data.Style,'rectangle')|isequal(data.Style,'ellipse') + nb_defining_points=1; +else + nb_defining_points=nb_points; +end +data_XObject=[]; +data_YObject=[]; +data_ZObject=[]; +for i=1:nb_points + Xnumber=str2num(Xcolumn{i}); + Ynumber=str2num(Ycolumn{i}); + if isempty(Xnumber)|isempty(Ynumber) + break + else + data_XObject=[data_XObject; Xnumber(1)]; + data_YObject=[data_YObject; Ynumber(1)]; + end + if length(Zcolumn) nb_points + for i=nb_points+1:nb_defining_points + data_XObject=[0;data_XObject]; + data_YObject=[0;data_YObject]; + data_ZObject=[0;data_ZObject]; + end +end +if isempty(data_XObject) + data_XObject=0; +end +if isempty(data_YObject) + data_YObject=0; +end +if isempty(data_ZObject) + data_ZObject=0; +end +data.Coord=[data_XObject data_YObject data_ZObject]; + +set(handles.XObject,'String',mat2cell(data_XObject,length(data_XObject)))%correct the interface display +set(handles.YObject,'String',mat2cell(data_YObject,length(data_XObject))) +set(handles.ZObject,'String',mat2cell(data_ZObject,length(data_XObject))) + + Index: /trunk/src/read_xls.m =================================================================== --- /trunk/src/read_xls.m (revision 2) +++ /trunk/src/read_xls.m (revision 2) @@ -0,0 +1,328 @@ +%'read_xls': function for reading and displaying Excel files +%------------------------------------------------------------------------ +% function [hfig_xls]=read_xls(fileinput,hfig) +% +% OUTPUT: +% hfig_xls: figure handle for display +% +% INPUT: +% fileinput: name of the input file (char string) +% hfig: handle of the display figure (a new display figure hfig_xls is created if hfig undefined) +% +%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +% Copyright Joel Sommeria, 2008, LEGI / CNRS-UJF-INPG, sommeria@coriolis-legi.org. +%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +% This file is part of the toolbox UVMAT. +% +% UVMAT is free software; you can redistribute it and/or modify +% it under the terms of the GNU General Public License as published by +% the Free Software Foundation; either version 2 of the License, or +% (at your option) any later version. +% +% UVMAT is distributed in the hope that it will be useful, +% but WITHOUT ANY WARRANTY; without even the implied warranty of +% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +% GNU General Public License (file UVMAT/COPYING.txt) for more details. +%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA + +function [hfig_xls]=read_xls(fileinput,hfig) +[Tabnum,Tabtext]=xlsread(fileinput); + [textnx,textny]=size(Tabtext); + [numnx,numny]=size(Tabnum); + ilastxt=textnx-numnx;%index of last text row + jlastxt=textny-numny;%index of last text column + for jtab=1:textny%read line + for itab=1:textnx% read column + textlu=cell2mat(Tabtext(itab,jtab)); + if isequal(textlu,[])& itab > ilastxt & jtab > jlastxt %replace txt by number + textlu=num2str(Tabnum(itab-ilastxt,jtab-jlastxt)); + end + Tabdisplay(itab,jtab)={textlu}; + lengthtext(itab)=length(textlu); + end + widthcolumn(jtab)=max(lengthtext); + end + Tabchar={};%default + for itab=1:textnx %justify table + charchain=[]; + for jtab=1:textny% read line + textlu=Tabdisplay{itab,jtab}; + if widthcolumn(jtab)>length(textlu) + blankstr=char(46*ones(1,widthcolumn(jtab)-length(textlu))); + textlu=[textlu blankstr ]; + end + charchain=[charchain textlu char(9) ' | ']; + end + Tabchar(itab)={charchain}; + end + if exist('hfig','var') & ishandle(hfig) + figure(hfig); + hfig_xls=hfig; + else + hfig_xls=figure; + end + set(hfig_xls,'Name',fileinput) + set(hfig_xls,'MenuBar','none') + hpos=get(hfig_xls,'Pos'); + ExpName.cell=Tabtext([2:textnx],1);%first column (dir name) + ExpName.Num=Tabnum; +% ExpName.Units=Tabtext(2,[2:textny]);%look for the units line (needs to be the second line) + iparam=0; + for icol=2:textny +% Tabtext(2,icol) + if ~isempty(Tabtext{2,icol})&~isequal(Tabtext{2,icol},'') + iparam=iparam+1; + ExpName.Param{iparam}=Tabtext{1,icol}; + ExpName.Units{iparam}=Tabtext{2,icol}; + ExpName.Column(iparam)=icol; + end + end + + ExpName.path=fileparts(fileinput); + h=uicontrol('Style','listbox', 'Position', [5 5 0.9*hpos(3) 0.9*hpos(4)], 'String', Tabchar, ... + 'FontName','Monospaced','Callback',@link2file,'UserData',ExpName,'Tag','listbox'); +% hh=uicontrol('Style','Pushbutton', 'Position', [0.93*hpos(1) 0.93*hpos(2) 0.05*hpos(3) 0.05*hpos(4)], 'String', 'Update','Callback',@project_update); +% set(h,'HorizontalAlignment','left') +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% +%called by xlsdisplay to navigate from a .xls file or create the +% the experiment directories +function link2file(obj,event,fileinput) +global t +bla=get(gcbo,'String'); +ind=get(gcbo,'Value') +if (ind==1|ind==2),return,end; %no action on the first line +ExpNameStruct=get(gcbo,'UserData') +ExpName=ExpNameStruct.cell{ind-1} +ProjectFullName=ExpNameStruct.path;%full name of the project (including path) +[Pth,ProjectName]=fileparts(ProjectFullName); +ExpPath=fullfile(ProjectFullName,ExpName);% full name of the experiment directory +ExpDocName=fullfile(ExpPath,[ExpName '.xml']);% full name of the .xml file ExpDoc +if exist(ExpDocName,'file') + hh=editxml({ExpDocName}) +% [FileName, PathName, filterindex] = uigetfile( ... +% {'*.xml','(*.xml)'; +% '*.xml', '.xml files '; +% '*.*', 'All Files (*.*)'}, ... +% 'Pick a file',ExpDocName); +% fileinput=[PathName FileName];%complete file name +% sizf=size(fileinput); +% if (~ischar(fileinput)|~isequal(sizf(1),1)),return;end +% [path,name,ext]=fileparts(fileinput); +% if isequal(ext,'.civ') | isequal(ext,'.log') | isequal(ext,'.cmx') isequal(ext,'.txt') +% edit(fileinput) +% elseif isequal(ext,'.xml') +% varargin{1}=fileinput; +% editxml(varargin) +% elseif isequal(ext,'.fig') +% open(fileinput) +% elseif isequal(ext,'.xls') +% xlsdisplay(fileinput) +% else +% uvmat({fileinput}) +% end +else + answer=questdlg({['ExpDoc file ' ExpDocName ' does not exist, create the experiment?'];''}) + if isequal(answer,'Yes') + if exist(ExpPath,'dir')~=7 %create a directory if it does not exist + dircur=pwd; %current working directory + cd(ProjectFullName); + [m1,m2,m3]=mkdir(ExpName); + cd(pwd);%come back to the initial working dir + end +% %copy exp parameters + ParamNames=ExpNameStruct.Param; + ParamValues=ExpNameStruct.Num(ind-1,ExpNameStruct.Column-1); + ParamUnits=ExpNameStruct.Units; + t=xmltree;%new xmltree + t=set(t,1,'name','ExpDoc'); + t=attributes(t,'add',1,'xmlns:xsi','none'); + [t,ExpElement]=add(t,1,'element','Exp'); + [t]=add(t,ExpElement,'chardata',ExpName); + for iparam=1:length(ParamNames) + [t,ParamElement]=add(t,1,'element',ParamNames{iparam}); + t=add(t,ParamElement,'chardata',num2str(ParamValues(iparam))); + t=attributes(t,'add',ParamElement,'unit',ParamUnits{iparam}); %ADD UNIT ATTRIBUTE + end + list_dir=dir(ExpPath);%list of the Exp directory, detect sub-directories,.xml and image files + nbdir_exp=0; + %scan the Exp directory + for idir_exp=3:length(list_dir) + %detect subdirectories + if list_dir(idir_exp).isdir% 'device' subdirectories + nbdir_exp=nbdir_exp+1; + ExpData.Device{nbdir_exp}=list_dir(idir_exp).name; + [t,DeviceElement]=add(t,1,'element',list_dir(idir_exp).name); + t=attributes(t,'add',DeviceElement,'type','DEVICE_DIR'); + t=attributes(t,'add',DeviceElement,'source','dir'); + list_subdir=dir(fullfile(ExpPath,list_dir(idir_exp).name)); + nbsubdir=0; + testrecord=1; + RootIma=''; + RootNc=''; + nbfile=0; +% nbfile={}; + %scan the Device subdirectory + for isubdir=3:length(list_subdir) + if list_subdir(isubdir).isdir + nbsubdir=nbsubdir+1; + Device.Record{nbsubdir}=list_subdir(isubdir).name; + else + nbfile=nbfile+1; + fname{nbfile}=list_subdir(isubdir).name; + end + end + if isunix%sort by root names and indices , change the separator '_' so that 1_1 come as the first name + fname_mod=regexprep(fname,'_','/'); + fname_mod=sort(fname_mod); %sort by name + fname=regexprep(fname_mod,'/','_'); + end + for ifile=1:nbfile; + [Path,Name,Ext]=fileparts(fname{ifile}); + if isequal(Ext,'.xml') + [t,ImaDocElement]=add(t,DeviceElement,'element','ImaDoc'); + t=add(t,ImaDocElement,'chardata',fname{ifile}); + t=attributes(t,'add',ImaDocElement,'source','file'); + testrecord=0;%we have an image series without 'record' subdir + elseif isequal(Ext,'.png') + [Path,Root,field_count,str2,str_a,str_b,ext,nom_type,subdir]=name2display(fname{ifile}); + if ~isequal(Root,RootIma)%only one image recorded for each root name + [t,ImaDocElement]=add(t,DeviceElement,'element','Image'); + t=add(t,ImaDocElement,'chardata',fname{ifile}); + t=attributes(t,'add',ImaDocElement,'source','file'); + RootIma=Root; + end + testrecord=0;%we have an image series without 'record' subdir + elseif isequal(Ext,'.nc') + [Path,Root,field_count,str2,str_a,str_b,ext,nom_type,subdir]=name2display(fname{ifile}); + if ~isequal(Root,RootNc)%only one image recorded for each root name + [t,ImaDocElement]=add(t,DeviceElement,'element','Ncdata'); + t=add(t,ImaDocElement,'chardata',fname{ifile}); + t=attributes(t,'add',ImaDocElement,'source','file'); + RootNc=Root; + end + testrecord=0;%we have an image series without 'record' subdir + end + end + if testrecord + %the subdevice directory is 'record' (no images detected at this level) + for idir_s=1:nbsubdir + [t,RecordElement]=add(t,DeviceElement,'element',Device.Record{idir_s}); + t=attributes(t,'add',RecordElement,'type','RECORD_DIR'); + t=attributes(t,'add',RecordElement,'source','dir'); + list_subdir=dir(fullfile(ExpPath,list_dir(idir_exp).name,Device.Record{idir_s})); + nbsubdir=0; + RootIma=''; + RootNc=''; + nbfile=0; + fname={}; + for isubdir=3:length(list_subdir) + if list_subdir(isubdir).isdir + nbsubdir=nbsubdir+1; + [t,RecordElement]=add(t,DeviceElement,'element',Device.Record{idir_exp}); + t=attributes(t,'add',RecordElement,'type','RECORD_DIR'); + t=attributes(t,'add',RecordElement,'source','dir'); + %VOIR les .netcdf a l'interieur + else + nbfile=nbfile+1; + fname{nbfile}=list_subdir(isubdir).name; + end + end + if isunix + fname_mod=regexprep(fname,'_','/'); + fname_mod=sort(fname_mod); %sort by name + fname=regexprep(fname_mod,'/','_'); + end + for ifile=1:nbfile; + [Path,Name,Ext]=fileparts(fname{ifile}); + if isequal(Ext,'.xml') + [t,ImaDocElement]=add(t,DeviceElement,'element','ImaDoc'); + t=add(t,ImaDocElement,'chardata',fname{ifile}); + t=attributes(t,'add',ImaDocElement,'source','file'); + elseif isequal(Ext,'.png') + [Path,Root,field_count,str2,str_a,str_b,ext,nom_type,subdir]=name2display(fname{ifile}); + if ~isequal(Root,RootIma) + [t,ImaDocElement]=add(t,DeviceElement,'element','Image'); + t=add(t,ImaDocElement,'chardata',fname{ifile}); + t=attributes(t,'add',ImaDocElement,'source','file'); + RootIma=Root; + end + elseif isequal(Ext,'.nc') + [Path,Root,field_count,str2,str_a,str_b,ext,nom_type,subdir]=name2display(fname{ifile}); + if ~isequal(Root,RootNc)%only one image recorded for each root name + [t,ImaDocElement]=add(t,DeviceElement,'element','Ncdata'); + t=add(t,ImaDocElement,'chardata',fname{ifile}); + t=attributes(t,'add',ImaDocElement,'source','file'); + RootNc=Root; + end + end + end + end + else%the subdevice directory is a civ directory (coexist with images) + for idir_s=1:nbsubdir + [t,RecordElement]=add(t,DeviceElement,'element',Device.Record{idir_s}); + t=attributes(t,'add',RecordElement,'type','CIV_DIR'); + t=attributes(t,'add',RecordElement,'source','dir'); + %list files under the civ directory + list_subdir=dir(fullfile(ExpPath,list_dir(idir_exp).name,Device.Record{idir_s})); + + nbsubdir=0; + nbfile=0; + RootXml=''; + RootNc=''; + fname={}; + for isubdir=3:length(list_subdir) + if list_subdir(isubdir).isdir + nbsubdir=nbsubdir+1; + [t,SubElement]=add(t,RecordElement,'element',list_subdir(isubdir).name); + t=attributes(t,'add',SubElement,'type','UNKNOWN_DIR'); + t=attributes(t,'add',SubElement,'source','dir'); + else + nbfile=nbfile+1; + fname{nbfile}=list_subdir(isubdir).name; + end + end + if isunix + fname_mod=regexprep(fname,'_','/'); + fname_mod=sort(fname_mod); %sort by name + fname=regexprep(fname_mod,'/','_'); + end + for ifile=1:nbfile; + [Path,Name,Ext]=fileparts(fname{ifile}); + if isequal(Ext,'.xml') + [Path,Root,field_count,str2,str_a,str_b,ext,nom_type,subdir]=name2display(fname{ifile}); + if ~isequal(Root,RootXml)%only one image recorded for each root name + [t,ImaDocElement]=add(t,RecordElement,'element','CivDoc'); + t=add(t,ImaDocElement,'chardata',fname{ifile}); + t=attributes(t,'add',ImaDocElement,'source','file'); + RootXml=Root; + end + elseif isequal(Ext,'.nc') + [Path,Root,field_count,str2,str_a,str_b,ext,nom_type,subdir]=name2display(fname{ifile}); + if ~isequal(Root,RootNc)%only one image recorded for each root name + [t,ImaDocElement]=add(t,RecordElement,'element','Ncdata'); + t=add(t,ImaDocElement,'chardata',fname{ifile}); + t=attributes(t,'add',ImaDocElement,'source','file'); + RootNc=Root; + end + end + end + end + end + end + end + save(t);%display xml file on the screen + save(t,ExpDocName); + end +end +% [erread,message]=fileattrib('./DATA'); +% if ~isempty(message) & ~isequal(message.UserWrite,1) +% errordlg(['Need writting access to ' message.Name]) +% return +% end + + + %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + function project_update(obj,event,fileinput) + hchild=get(gcbf,'children'); + h=findobj(gcbf,'Tag','listbox') + Index: /trunk/src/reinit.m =================================================================== --- /trunk/src/reinit.m (revision 2) +++ /trunk/src/reinit.m (revision 2) @@ -0,0 +1,9 @@ +%'reinit': delete the personal parameter file 'uvmat_perso.mat' +% +function reinit +dir_perso=prefdir; +profil_perso=fullfile(dir_perso,'uvmat_perso.mat') +if exist(profil_perso,'file') + delete(profil_perso) +end +display('deleted') Index: /trunk/src/series.m =================================================================== --- /trunk/src/series.m (revision 2) +++ /trunk/src/series.m (revision 2) @@ -0,0 +1,4549 @@ +%'series': master function associated to the GUI series.m for analysis field series +%------------------------------------------------------------------------ +% function varargout = series(varargin) +% associated with the GUI series.fig +% +%INPUT +% param: structure with input parameters (link with the GUI uvmat) +% .menu_coord_str: string for the CoordType (menu for coordinate transforms) +% .menu_coord_val: value for CoordType (menu for coordinate transforms) +% .FileName: input file name +% .FileName_1: second input file name +% .list_field: menu of input fields +% .index_fields: chosen index +% .civ1=0 or 1, .interp1, ... : input civ field type +% +%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +% Copyright Joel Sommeria, 2008, LEGI / CNRS-UJF-INPG, sommeria@coriolis-legi.org. +%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +% This file is part of the toolbox UVMAT. +% +% UVMAT is free software; you can redistribute it and/or modify +% it under the terms of the GNU General Public License as published by +% the Free Software Foundation; either version 2 of the License, or +% (at your option) any later version. +% +% UVMAT is distributed in the hope that it will be useful, +% but WITHOUT ANY WARRANTY; without even the implied warranty of +% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +% GNU General Public License (file UVMAT/COPYING.txt) for more details. +%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA + +function varargout = series(varargin) + +% Begin initialization code - DO NOT EDIT +gui_Singleton = 1; +gui_State = struct('gui_Name', mfilename, ... + 'gui_Singleton', gui_Singleton, ... + 'gui_OpeningFcn', @series_OpeningFcn, ... + 'gui_OutputFcn', @series_OutputFcn, ... + 'gui_LayoutFcn', [] , ... + 'gui_Callback', []); +if nargin && ischar(varargin{1}) + gui_State.gui_Callback = str2func(varargin{1}); +end + +if nargout + [varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:}); +else + gui_mainfcn(gui_State, varargin{:}); +end +% End initialization code - DO NOT EDIT + +%-------------------------------------------------------------------------- +% --- Executes just before series is made visible. +%-------------------------------------------------------------------------- +function series_OpeningFcn(hObject, eventdata, handles,param) + +% Choose default command line output for series +handles.output = hObject; +% Update handles structure +guidata(hObject, handles); +%default initial parameters + +%load the list of previously browsed files in menus Open and Open_1 +dir_perso=prefdir; +profil_perso=fullfile(dir_perso,'uvmat_perso.mat'); +if exist(profil_perso,'file') + h=load (profil_perso); + if isfield(h,'MenuFile_1') + set(handles.MenuFile_1,'Label',h.MenuFile_1); + set(handles.MenuFile_insert_1,'Label',h.MenuFile_1); + end + if isfield(h,'MenuFile_1') + set(handles.MenuFile_2,'Label',h.MenuFile_2); + set(handles.MenuFile_insert_2,'Label',h.MenuFile_2); + end + if isfield(h,'MenuFile_1') + set(handles.MenuFile_3,'Label',h.MenuFile_3); + set(handles.MenuFile_insert_3,'Label',h.MenuFile_3); + end + if isfield(h,'MenuFile_1') + set(handles.MenuFile_4,'Label',h.MenuFile_4); + set(handles.MenuFile_insert_4,'Label',h.MenuFile_4); + end + if isfield(h,'MenuFile_1') + set(handles.MenuFile_5,'Label',h.MenuFile_5); + set(handles.MenuFile_insert_5,'Label',h.MenuFile_5); + end +end + +%check default input data +if ~exist('param','var') + param=[]; %default +end + +%file name and browser initialisation +if isfield(param,'menu_coord_str') + set(handles.CoordType,'String',param.menu_coord_str) +end +if isfield(param,'menu_coord_val') + set(handles.CoordType,'Value',param.menu_coord_val); +else + set(handles.CoordType,'Value',1);%default +end + +if isfield(param,'FileName') + if isfield(param,'FileName_1') + update_file(hObject, eventdata, handles,param.FileName_1,0) + update_file(hObject, eventdata, handles,param.FileName,1) + else + update_file(hObject, eventdata, handles,param.FileName,0) + end +end + +%fields input initialisation +if isfield(param,'list_fields')&& isfield(param,'index_fields') &&~isempty(param.list_fields) &&~isempty(param.index_fields) + set(handles.FieldMenu,'String',param.list_fields);% list menu fields + set(handles.FieldMenu,'Value',param.index_fields);% selected string index + FieldCell{1}=param.list_fields{param.index_fields}; +end +if isfield(param,'civ1')&& islogical(param.civ1) && isfield(param,'civ2')&& islogical(param.civ2)&... + isfield(param,'interp1')&& islogical(param.interp1)&&isfield(param,'interp2')&& islogical(param.interp2)&... + isfield(param,'filter1')&& islogical(param.filter1)&&isfield(param,'filter2')&& islogical(param.filter2) + set(handles.civ1,'Value',param.civ1); + set(handles.civ2,'Value',param.civ1); + set(handles.interp1,'Value',param.interp1); + set(handles.interp2,'Value',param.interp2); + set(handles.filter1,'Value',param.filter1); + set(handles.filter2,'Value',param.filter2); +end +%set(hObject,'UserData', SeriesData) +set(hObject,'WindowButtonUpFcn',{@mouse_up_gui,handles}) +NomType_Callback(hObject, eventdata, handles) +%mode_Callback(hObject, eventdata, handles) + +%loads the information stored in prefdir to initiate the browser and the list of functions +menu_str=get(handles.ACTION,'String');%list of functions included in 'series.m' +menu_str(end)=[];%remove from the list the last option 'more...' +path_series=which('series');%path of the function 'series' +for ilist=1:length(menu_str) + fct_path{ilist,1}=path_series;%paths of the fuctions buil-in in 'series.m' +end +dir_perso=prefdir; +profil_perso=fullfile(dir_perso,'uvmat_perso.mat'); +if exist(profil_perso,'file') + h=load (profil_perso); + if isfield(h,'series_fct') && iscell(h.series_fct) + for ilist=1:length(h.series_fct) + [path,file]=fileparts(h.series_fct{ilist}); + fct_path=[fct_path; {path}];%concatene the list of paths + menu_str=[menu_str; {file}]; + end + menu_str=[menu_str;{'more...'}]; + set(handles.ACTION,'String',menu_str) + end +end +set(handles.ACTION,'UserData',fct_path)% store the list of path in UserData of ACTION + +% display the GUI for the default action 'check_files' +ACTION_Callback(hObject, eventdata, handles) + +%-------------------------------------------------------------- +% --- Outputs from this function are returned to the command line. +%----------------------------------------------------------------- +function varargout = series_OutputFcn(hObject, eventdata, handles) +% varargout cell array for returning output args (see VARARGOUT); +% hObject handle to figure +% eventdata reserved - to be defined in a future version of MATLAB +% handles structure with handles and user data (see GUIDATA) +% Get default command line output from handles structure +varargout{1} = handles.output; + + +% -------------------------------------------------------------------- +function MenuBrowse_Callback(hObject, eventdata, handles) + +RootPathCell=get(handles.RootPath,'String'); +SubDirCell=get(handles.SubDir,'String'); +RootFileCell=get(handles.RootFile,'String'); +oldfile=''; %default +if isempty(RootPathCell)|isequal(RootPathCell,{''})%loads the previously stored file name and set it as default in the file_input box + dir_perso=prefdir; + profil_perso=fullfile(dir_perso,'uvmat_perso.mat'); + if exist(profil_perso,'file') + h=load (profil_perso); + if isfield(h,'filebase')&ischar(h.filebase) + oldfile=h.filebase; + end + if isfield(h,'RootPath')&ischar(h.RootPath) + oldfile=h.RootPath; + end + end + else + oldfile=fullfile(RootPathCell{1},SubDirCell{1},RootFileCell{1}); + end +[FileName, PathName, filterindex] = uigetfile( ... + {'*.xml;*.xls;*.png;*.tif;*.avi;*.AVI;*.nc', ' (*.xml,*.xls, *.png,*.tif, *.avi,*.nc)'; + '*.xml', '.xml files '; ... + '*.xls', '.xls files '; ... + '*.png','.png image files'; ... + '*.tif','.tif image files'; ... + '*.avi;*.AVI','.avi movie files'; ... + '*.nc','.netcdf files'; ... + '*.*', 'All Files (*.*)'}, ... + 'Pick a file',oldfile); +fileinput=[PathName FileName];%complete file name +testblank=findstr(fileinput,' ');%look for blanks +if ~isempty(testblank) + errordlg('forbidden input file name: contain blanks') + return +end +sizf=size(fileinput); +if (~ischar(fileinput)|~isequal(sizf(1),1)),return;end +[path,name,ext]=fileparts(fileinput); +SeriesData=[];%dfault +if isequal(ext,'.xml') + errordlg('input file type not implemented')%A Faire: ouvrir le fichier pour naviguer +elseif isequal(ext,'.xls') + errordlg('input file type not implemented')%A Faire: ouvrir le fichier pour naviguer +else + update_file(hObject, eventdata, handles,fileinput,0) + %update list of recent files in the menubar + MenuFile_1=fileinput; + MenuFile_2=get(handles.MenuFile_1,'Label'); + MenuFile_3=get(handles.MenuFile_2,'Label'); + MenuFile_4=get(handles.MenuFile_3,'Label'); + MenuFile_5=get(handles.MenuFile_4,'Label'); + set(handles.MenuFile_1,'Label',MenuFile_1) + set(handles.MenuFile_2,'Label',MenuFile_2) + set(handles.MenuFile_3,'Label',MenuFile_3) + set(handles.MenuFile_4,'Label',MenuFile_4) + set(handles.MenuFile_5,'Label',MenuFile_5) + set(handles.MenuFile_insert_1,'Label',MenuFile_1) + set(handles.MenuFile_insert_2,'Label',MenuFile_2) + set(handles.MenuFile_insert_3,'Label',MenuFile_3) + set(handles.MenuFile_insert_4,'Label',MenuFile_4) + set(handles.MenuFile_insert_5,'Label',MenuFile_5) + dir_perso=prefdir; + profil_perso=fullfile(dir_perso,'uvmat_perso.mat'); + if exist(profil_perso,'file') + save (profil_perso,'MenuFile_1','MenuFile_2','MenuFile_3','MenuFile_4', 'MenuFile_5','-append'); %store the file names for future opening of uvmat + else + txt=ver; + Release=txt(1).Release; + relnumb=str2num(Release(3:4)); + if relnumb >= 14 + save (profil_perso,'MenuFile_1','MenuFile_2','MenuFile_3','MenuFile_4', 'MenuFile_5','-V6'); %store the file names for future opening of uvmat + else + save (profil_perso,'MenuFile_1','MenuFile_2','MenuFile_3','MenuFile_4', 'MenuFile_5'); %store the file names for future opening of uvmat + end + end +end +% set(hseries,'UserData',SeriesData); +% RootFile_Callback(hObject, eventdata, handles); +% FileExt_Callback(hObject, eventdata, handles); +% NomType_Callback(hObject, eventdata, handles) +% mode_Callback(hObject, eventdata, handles) + + +% -------------------------------------------------------------------- +function MenuFile_1_Callback(hObject, eventdata, handles) +fileinput=get(handles.MenuFile_1,'Label'); +update_file(hObject, eventdata, handles,fileinput,0) + +% -------------------------------------------------------------------- +function MenuFile_2_Callback(hObject, eventdata, handles) +fileinput=get(handles.MenuFile_2,'Label'); +update_file(hObject, eventdata, handles,fileinput,0) + +% -------------------------------------------------------------------- +function MenuFile_3_Callback(hObject, eventdata, handles) +fileinput=get(handles.MenuFile_3,'Label'); +update_file(hObject, eventdata, handles,fileinput,0) + +% -------------------------------------------------------------------- +function MenuFile_4_Callback(hObject, eventdata, handles) +fileinput=get(handles.MenuFile_4,'Label'); +update_file(hObject, eventdata, handles,fileinput,0) + +% -------------------------------------------------------------------- +function MenuFile_5_Callback(hObject, eventdata, handles) +fileinput=get(handles.MenuFile_5,'Label'); +update_file(hObject, eventdata, handles,fileinput,0) + +% -------------------------------------------------------------------- +function MenuBrowse_insert_Callback(hObject, eventdata, handles) + +%hseries=get(handles.browse_root,'parent'); +RootPathCell=get(handles.RootPath,'String'); +% SubDirCell=get(handles.SubDir,'String'); +RootFileCell=get(handles.RootFile,'String'); +oldfile=''; %default +if isempty(RootPathCell)|isequal(RootPathCell,{''})%loads the previously stored file name and set it as default in the file_input box + dir_perso=prefdir; + profil_perso=fullfile(dir_perso,'uvmat_perso.mat'); + if exist(profil_perso,'file') + h=load (profil_perso); + if isfield(h,'filebase')&ischar(h.filebase) + oldfile=h.filebase; + end + if isfield(h,'RootPath')&ischar(h.RootPath) + oldfile=h.RootPath; + end + end + else + oldfile=fullfile(RootPathCell{1},RootFileCell{1}); + end +[FileName, PathName, filterindex] = uigetfile( ... + {'*.xml;*.xls;*.png;*.avi;*.AVI;*.nc', ' (*.xml,*.xls, *.png, *.avi,*.nc)'; + '*.xml', '.xml files '; ... + '*.xls', '.xls files '; ... + '*.png','.png image files'; ... + '*.avi;*.AVI','.avi movie files'; ... + '*.nc','.netcdf files'; ... + '*.*', 'All Files (*.*)'}, ... + 'Pick a file',oldfile); +fileinput=[PathName FileName];%complete file name +testblank=findstr(fileinput,' ');%look for blanks +if ~isempty(testblank) + errordlg('forbidden input file name: contain blanks') + return +end +sizf=size(fileinput); +if (~ischar(fileinput)|~isequal(sizf(1),1)),return;end +[path,name,ext]=fileparts(fileinput); +SeriesData=[];%dfault +if isequal(ext,'.xml') + errordlg('input file type not implemented')%A Faire: ouvrir le fichier pour naviguer +elseif isequal(ext,'.xls') + errordlg('input file type not implemented')%A Faire: ouvrir le fichier pour naviguer +else + update_file(hObject, eventdata, handles,fileinput,1) + %update list of recent files in the menubar + MenuFile_1=fileinput; + MenuFile_2=get(handles.MenuFile_1,'Label'); + MenuFile_3=get(handles.MenuFile_2,'Label'); + MenuFile_4=get(handles.MenuFile_3,'Label'); + MenuFile_5=get(handles.MenuFile_4,'Label'); + set(handles.MenuFile_1,'Label',MenuFile_1) + set(handles.MenuFile_2,'Label',MenuFile_2) + set(handles.MenuFile_3,'Label',MenuFile_3) + set(handles.MenuFile_4,'Label',MenuFile_4) + set(handles.MenuFile_5,'Label',MenuFile_5) + set(handles.MenuFile_insert_1,'Label',MenuFile_1) + set(handles.MenuFile_insert_2,'Label',MenuFile_2) + set(handles.MenuFile_insert_3,'Label',MenuFile_3) + set(handles.MenuFile_insert_4,'Label',MenuFile_4) + set(handles.MenuFile_insert_5,'Label',MenuFile_5) + dir_perso=prefdir; + profil_perso=fullfile(dir_perso,'uvmat_perso.mat'); + if exist(profil_perso,'file') + save (profil_perso,'MenuFile_1','MenuFile_2','MenuFile_3','MenuFile_4', 'MenuFile_5','-append'); %store the file names for future opening of uvmat + else + txt=ver; + Release=txt(1).Release; + relnumb=str2num(Release(3:4)); + if relnumb >= 14 + save (profil_perso,'MenuFile_1','MenuFile_2','MenuFile_3','MenuFile_4', 'MenuFile_5','-V6'); %store the file names for future opening of uvmat + else + save (profil_perso,'MenuFile_1','MenuFile_2','MenuFile_3','MenuFile_4', 'MenuFile_5'); %store the file names for future opening of uvmat + end + end +end +%------------------------------------------------ + +% -------------------------------------------------------------------- +function MenuFile_insert_1_Callback(hObject, eventdata, handles) +fileinput=get(handles.MenuFile_insert_1,'Label'); +update_file(hObject, eventdata, handles,fileinput,1) + +% -------------------------------------------------------------------- +function MenuFile_insert_2_Callback(hObject, eventdata, handles) +fileinput=get(handles.MenuFile_insert_2,'Label'); +update_file(hObject, eventdata, handles,fileinput,1) + +% -------------------------------------------------------------------- +function MenuFile_insert_3_Callback(hObject, eventdata, handles) +fileinput=get(handles.MenuFile_insert_3,'Label'); +update_file(hObject, eventdata, handles,fileinput,1) + +% -------------------------------------------------------------------- +function MenuFile_insert_4_Callback(hObject, eventdata, handles) +fileinput=get(handles.MenuFile_insert_4,'Label'); +update_file(hObject, eventdata, handles,fileinput,1) + +% -------------------------------------------------------------------- +function MenuFile_insert_5_Callback(hObject, eventdata, handles) +fileinput=get(handles.MenuFile_insert_5,'Label'); +update_file(hObject, eventdata, handles,fileinput,1) + +% -------------------------------------------------------------------- +% refresh the GUI data after introduction of a new file series +function update_file(hObject, eventdata, handles,fileinput,addtest) +hseries=get(handles.RootPath,'parent'); +% refresh input root name, indices, file extension and nomenclature +[RootPath,RootFile,field_count,str2,str_a,str_b,FileExt,NomType,SubDir]=name2display(fileinput); +%check for movie image files +if ~isempty(imformats(FileExt(2:end))) + imainfo=imfinfo(fileinput); + if length(imainfo) >1 %case of image with multiple frames + NomType='*'; + [RootPath,RootFile]=fileparts(fileinput); + end +end +NcType='none';%default +if isequal(FileExt,'.nc') + Data=nc2struct(fileinput,[]); + if isfield(Data,'absolut_time_T0') + NcType='civx'; % test for civx velocity fields + end +end + +set(handles.RootPath,'Value',1) +set(handles.SubDir,'Value',1) +set(handles.RootFile,'Value',1) +set(handles.NomType,'Value',1) +set(handles.FileExt,'Value',1) +set(handles.nb_field,'Value',1) +set(handles.nb_field2,'Value',1) +if addtest + SeriesData=get(hseries,'UserData'); + SeriesData.displ_num=[0 0 0 0;SeriesData.displ_num]; + SeriesData.CurrentInputFile_1=SeriesData.CurrentInputFile; + RootPathCell=[{RootPath}; get(handles.RootPath,'String')] ; + SubDirCell=[{SubDir}; get(handles.SubDir,'String')]; + RootFileCell=[{RootFile}; get(handles.RootFile,'String')]; + NomTypeCell=[{NomType}; SeriesData.NomType]; + FileExtCell=[{FileExt}; get(handles.FileExt,'String')]; + NcTypeCell=[{NcType};SeriesData.NcType]; + set(handles.NomType,'String',[{};get(handles.NomType,'String')]) +else + SeriesData=[];%re-initialisation + SeriesData.displ_num=[0 0 0 0]; + RootPathCell={RootPath}; + SubDirCell={SubDir}; + RootFileCell={RootFile}; + NomTypeCell={NomType}; + FileExtCell={FileExt}; + NcTypeCell={NcType}; +end + +SeriesData.NomType=NomTypeCell; +SeriesData.NcType=NcTypeCell; +SeriesData.CurrentInputFile=fileinput; +set(handles.RootPath,'String',RootPathCell); +set(handles.SubDir,'String',SubDirCell); +set(handles.RootFile,'String',RootFileCell); +set(handles.NomType,'String',NomTypeCell); +set(handles.FileExt,'String',FileExtCell); + +%determine field indices +ref_i=1; %default ref_i is a reference frame index used to find existing pairs from PIV +if ~isempty(str2num(field_count)) + ref_i=str2num(field_count); + if ~isempty(str2num(str2)) + ref_i=floor((ref_i+str2num(str2))/2);% reference image number corresponding to the file + SeriesData.browse_Di=str2num(str2)-str2num(field_count); + end +end +set(handles.ref_i,'String',num2str(ref_i)); +set(handles.first_i,'String',num2str(ref_i)); +set(handles.last_i,'String',num2str(ref_i)); +ref_j=1; %default ref_j is a reference frame index used to find existing pairs from PIV +if ~isempty(str2num(str_a)) + ref_j=str2num(str_a); + if ~isempty(str2num(str_b)) + ref_j=floor((str2num(str_a)+str2num(str_b))/2); + SeriesData.browse_Dj=str2num(str_b)-str2num(str_a); + end +end +set(handles.ref_j,'String',num2str(ref_j)); +set(handles.first_j,'String',num2str(ref_j)) +set(handles.last_j,'String',num2str(ref_j)); +%set(hseries,'UserData',SeriesData); + +%enable other menus and uicontrols +set(handles.MenuOpen_insert,'Enable','on') +set(handles.MenuFile_insert_1,'Enable','on') +set(handles.MenuFile_insert_2,'Enable','on') +set(handles.MenuFile_insert_3,'Enable','on') +set(handles.MenuFile_insert_4,'Enable','on') +set(handles.MenuFile_insert_5,'Enable','on') +set(handles.RUN, 'Enable','On') +set(handles.RUN,'BackgroundColor',[1 0 0])% set RUN button to red +set(handles.RootPath,'BackgroundColor',[1 1 0]) % set RootPath edit box to yellow +drawnow + +% hseries=get(handles.RootFile,'parent'); +% SeriesData=get(hseries,'UserData');%read information set by the browser +% ext_ima_read=[]; +% field_count=1;%default +% pxcmx=1; +% pxcmy=1; +TimeUnit=''; %default +% CoordUnit='';%default +time=[];%default +GeometryCalib=[];%default +nb_field=[];%default +nb_field2=[];%default +% Heading=[]; +% [PD,Device]=fileparts(RootPathCell{1}); +SeriesData.PathCampaign=get(handles.PathCampaign,'String'); + +% read timing and total frame number from the current file (movie files) !! may be overrid by xml file +%icell=length(RootPathCell); +FileBase=fullfile(RootPath,RootFile); + +% nb_field{icell,1}='?';%default +% nb_field2{icell,1}='?';%default +testima=0; %test for image input +if isequal(lower(FileExt),'.avi') %.avi file + testima=1; + info=aviinfo([FileBase FileExt]); + time=[0:1/info.FramesPerSecond:(info.NumFrames-1)/info.FramesPerSecond]'; + nb_field=info.NumFrames; + nb_field2=1; +elseif ~isempty(imformats(FileExt(2:end))) + testima=1; + if isequal(NomType,'*')% multi-frame image + imainfo=imfinfo([FileBase FileExt]); + if length(imainfo) >1 %case of image with multiple frames + nb_field=length(imainfo); + nb_field2=1; + end + end +elseif isequal(FileExt,'.vol') + testima=1; +end + +% enable field and veltype menus +testfield=isequal(get(handles.FieldMenu,'enable'),'on'); +testfield_1=isequal(get(handles.FieldMenu_1,'enable'),'on'); +testveltype=isequal(get(handles.VelTypeMenu,'enable'),'on'); +testveltype_1=isequal(get(handles.VelTypeMenu_1,'enable'),'on'); +testtransform=isequal(get(handles.CoordType,'Enable'),'on'); +testnc=0; +testnc_1=0; +testcivx=0; +testcivx_1=0; +if length(FileExtCell)==1 || length(FileExtCell)>2 + for iview=1:length(FileExtCell) + if isequal(FileExtCell{iview},'.nc') + testnc=1; + end + if isequal(NcTypeCell{iview},'civx') + testcivx=1; + end + end +elseif length(FileExtCell)==2 + testnc=isequal(FileExtCell{1},'.nc'); + testnc_1=isequal(FileExtCell{2},'.nc'); + testcivx=isequal(NcTypeCell{1},'civx'); + testcivx_1=isequal(NcTypeCell{2},'civx'); +end +if testfield && testnc + view_FieldMenu(handles,'on') + if testcivx + menustr=get(handles.FieldMenu,'String'); + if isequal(menustr,{'get_field...'}) + set(handles.FieldMenu,'String',{'get_field...';'velocity';'vort';'div';'more...'}) + end + else + set(handles.FieldMenu,'Value',1) + set(handles.FieldMenu,'String',{'get_field...'}) + end +else + view_FieldMenu(handles,'off') +end +if testfield_1 && testnc_1 + view_FieldMenu_1(handles,'on') + if testcivx_1 + menustr=get(handles.FieldMenu_1,'String'); + if isequal(menustr,{'get_field...'}) + set(handles.FieldMenu_1,'String',{'get_field...';'velocity';'vort';'div';'more...'}) + end + else + set(handles.FieldMenu_1,'Value',1) + set(handles.FieldMenu_1,'String',{'get_field...'}) + end +else + view_FieldMenu_1(handles,'off') +end +if testveltype && testcivx + set(handles.VelTypeMenu,'Visible','on') + set(handles.VelType_text,'Visible','on'); +else + set(handles.VelTypeMenu,'Visible','off') + set(handles.VelType_text,'Visible','off'); +end +if testveltype_1 && testcivx_1 + set(handles.VelTypeMenu_1,'Visible','on') + set(handles.VelType_text_1,'Visible','on'); +else + set(handles.VelTypeMenu_1,'Visible','off') + set(handles.VelType_text_1,'Visible','off'); +end +if testtransform && (testcivx || testima) + view_TRANSFORM(handles,'on') +else + view_TRANSFORM(handles,'off') +end +if ~isequal(FileExt,'.nc') && ~isequal(FileExt,'.cdf') && ~testima + msgbox_uvmat('ERROR',['invalid input file extension ' FileExt]) + return +end + +%%%%%%%% read image documentation file if found%%%%%%%%%%%%%%%%%%%%%%%%%%% + %look for the file existence +ext_imadoc=''; +if isequal(FileExt,'.xml')||isequal(FileExt,'.civ') + ext_imadoc=FileExt; +elseif exist([FileBase '.xml'],'file') + ext_imadoc='.xml'; +elseif exist([FileBase '.civ'],'file') + ext_imadoc='.civ'; +end + %read the ImaDoc file +% mode=''; %default +% testheading=0; +XmlData=[]; +NbSlice_calib={}; +if isequal(ext_imadoc,'.xml') + [XmlData,warntext]=imadoc2struct([FileBase '.xml']); + if isfield(XmlData,'Heading') && isfield(XmlData.Heading,'ImageName') + [PP,FF,ext_ima_read]=fileparts(XmlData.Heading.ImageName); + end + if isfield(XmlData,'Time') + time=XmlData.Time; + end + if isfield(XmlData,'Camera') + if isfield(XmlData.Camera,'NbSlice')&& ~isempty(XmlData.Camera.NbSlice) + NbSlice_calib{iview}=XmlData.Camera.NbSlice;% Nbre of slices for Zindex in phys transform + if ~isequal(NbSlice_calib{iview},NbSlice_calib{1}) + msgbox_uvmat('WARNING','inconsistent number of Z indices for the two field series'); + end + end + if isfield(XmlData.Camera,'TimeUnit')&& ~isempty(XmlData.Camera.TimeUnit) + TimeUnit=XmlData.Camera.TimeUnit; + end + end + if ~isempty(warntext) + msgbox_uvmat('WARNING',warntext) + end +elseif isequal(ext_imadoc,'.civ') + [error,XmlData.Time,TimeUnit,mode,npx,npy,pxcmx,pxcmy]=read_imatext([FileBase '.civ']); + time=XmlData.Time; + size(time) + GeometryCalib.R=[pxcmx 0 0; 0 pxcmy 0;0 0 0]; + GeometryCalib.Tx=0; + GeometryCalib.Ty=0; + GeometryCalib.Tz=1; + GeometryCalib.dpx=1; + GeometryCalib.dpy=1; + GeometryCalib.sx=1; + GeometryCalib.Cx=0; + GeometryCalib.Cy=0; + GeometryCalib.f=1; + GeometryCalib.kappa1=0; + GeometryCalib.CoordUnit='cm'; + XmlData.GeometryCalib=GeometryCalib; + if error==2, warntext=['no file ' FileBase '.civ']; + elseif error==1, warntext='inconsistent number of fields in the .civ file'; + end +% set(handles.npx,'String',num2str(npx));%fills nbre of pixels x box +% set(handles.npy,'String',num2str(npy));%fills nbre of pixels y box +% set(handles.pxcm,'String',num2str(pxcmx));%fills scale x (pixel/cm) box +% set(handles.pycm,'String',num2str(pxcmy));%fills scale y (pixel/cm) box +% set(handles.pxcm,'Visible','on');%fills scale x (pixel/cm) box +% set(handles.pycm,'Visible','on');%fills scale y (pixel/cm) box +% set(handles.view_xml,'Visible','on') +% set(handles.view_xml,'String','view .civ') +end +if addtest + SeriesData.Time=[{time} SeriesData.Time]; +else + SeriesData.Time={time}; +end + +if ~isempty(time) + siztime=size(time); + nb_field=siztime(1); + nb_field2=siztime(2); +end +set(handles.TimeUnit,'String',TimeUnit) +if isempty(nb_field) + nb_field_str='?'; + nb_field_str2='?'; +else + nb_field_str=num2str(nb_field); + nb_field_str2=num2str(nb_field2); +end +if addtest + nb_field_cell=[{nb_field_str} ;get(handles.nb_field,'String')]; + nb_field2_cell=[{nb_field_str2} ;get(handles.nb_field2,'String')]; +else + nb_field_cell={nb_field_str}; + nb_field2_cell={nb_field_str2}; +end +set(handles.nb_field,'String',nb_field_cell); +set(handles.nb_field2,'String',nb_field2_cell); +set(hseries,'UserData',SeriesData); + +%number of slices +if isfield(XmlData,'GeometryCalib') && isfield(XmlData.GeometryCalib,'SliceCoord') + siz=size(XmlData.GeometryCalib.SliceCoord); + if siz(1)>1 + NbSlice=siz(1); + else + NbSlice=1; + end + set(handles.NbSlice,'String',num2str(NbSlice)) +end + +% set menus of index pairs +NomType_Callback(hObject, eventdata, handles) + +dir_perso=prefdir; +profil_perso=fullfile(dir_perso,'uvmat_perso.mat'); +% save(profil_perso, 'FileBase'); %store the root name for future opening of uvmat +if exist(profil_perso,'file') + save (profil_perso,'RootPath','SubDir','RootFile','NomType', '-append'); %store the root name for future opening of uvmat +else + txt=ver; + Release=txt(1).Release; + relnumb=str2num(Release(3:4)); + if relnumb >= 14 + save (profil_perso,'RootPath','SubDir','RootFile','NomType','-V6') %store the root name for future opening of uvmat + else + save(profil_perso,'RootPath','SubDir','RootFile','NomType') + end +end +set(handles.RootPath,'BackgroundColor',[1 1 1]) +set(handles.PathCampaign,'String',SeriesData.PathCampaign) +last_j_Callback(hObject, eventdata, handles) +last_i_Callback(hObject, eventdata, handles) + +%------------------------------------------------------------ +function RootPath_Callback(hObject, eventdata, handles) +Val=get(handles.RootPath,'Value'); +synchronise_view(handles,Val) +NomType_Callback(hObject, eventdata, handles) +%------------------------------------------------------------ + +function synchronise_view(handles,Val) +set(handles.RootPath,'Value',Val) +set(handles.SubDir,'Value',Val) +set(handles.RootFile,'Value',Val) +set(handles.NomType,'Value',Val) +set(handles.FileExt,'Value',Val) +set(handles.nb_field,'Value',Val) +set(handles.nb_field2,'Value',Val) +set(handles.time_first,'Value',Val) +set(handles.time_last,'Value',Val) + + +%--------------------------------------------------------- +% Executes on carriage return on the subdir civ1 edit window +%-------------------------------------------------------- +function SubDir_Callback(hObject, eventdata, handles) + +Val=get(handles.SubDir,'Value'); +synchronise_view(handles,Val) +NomType_Callback(hObject, eventdata, handles) + +%-------------------------------------------------------------- +%function activated when a new filebase (image series) is introduced +%------------------------------------------------------------ +function RootFile_Callback(hObject, eventdata, handles) +Val=get(handles.RootFile,'Value'); +synchronise_view(handles,Val) +NomType_Callback(hObject, eventdata, handles) + +%-------------------------------------------------------------- +%function activated when a new filebase (image series) is introduced +%------------------------------------------------------------ +function FileExt_Callback(hObject, eventdata, handles) +Val=get(handles.FileExt,'Value'); +synchronise_view(handles,Val) + +%-------------------------------------------------------------- +%function activated when a new filebase (image series) is introduced +%------------------------------------------------------------ +function nb_field_Callback(hObject, eventdata, handles) +Val=get(handles.nb_field,'Value'); +synchronise_view(handles,Val) + +%-------------------------------------------------------------- +%function activated when a new filebase (image series) is introduced +%------------------------------------------------------------ +function nb_field2_Callback(hObject, eventdata, handles) +Val=get(handles.nb_field2,'Value'); +synchronise_view(handles,Val) + +%-------------------------------------------------------------- +%function activated when a new filebase (image series) is introduced +%------------------------------------------------------------ +function time_first_Callback(hObject, eventdata, handles) +Val=get(handles.time_first,'Value'); +synchronise_view(handles,Val) + +%-------------------------------------------------------------- +%function activated when a new filebase (image series) is introduced +%------------------------------------------------------------ +function time_last_Callback(hObject, eventdata, handles) +Val=get(handles.time_last,'Value'); +synchronise_view(handles,Val) + +%-------------------------------------------------------------- +%function activated by NomType +%------------------------------------------------------------ +NomType_Callback(hObject, eventdata, handles) + +function NomType_Callback(hObject, eventdata, handles) +hseries=get(handles.ProjObject,'Parent'); +SeriesData=get(hseries,'UserData'); +if isfield(SeriesData,'NomType') + NomTypeCell=SeriesData.NomType; +else + NomTypeCell={}; +end +nbfield2_cell=get(handles.nb_field2,'String'); +val=get(handles.nb_field2,'Value'); +if iscell(nbfield2_cell) + nbfield2=str2num(nbfield2_cell{val}); +else + nbfield2=str2num(nbfield2_cell); +end +nbfield_cell=get(handles.nb_field,'String'); +if iscell(nbfield_cell) + nbfield=str2num(nbfield_cell{val}); +else + nbfield=str2num(nbfield_cell); +end + +set(handles.mode,'Visible','off') % do not show index pairs by default +set(handles.list_pair_civ,'Visible','off') +set(handles.ref_i,'Visible','off') +set(handles.ref_i_text,'Visible','off') +testpair=0; +state_j='off'; +%set the menus of image pairs and default selection for series +%list pairs if relevant +Val=get(handles.NomType,'Value'); +synchronise_view(handles,Val) +if ~isempty(NomTypeCell) + NomType=NomTypeCell{Val}; + switch NomType + case {'_i1-i2_j', '_i1-i2'} + set(handles.mode,'String',{'series(Di)'}) + set(handles.mode,'Value',1); + set(handles.mode,'Visible','on') + testpair=1; + case {'#_ab'} + set(handles.mode,'String',{'bursts'}) + set(handles.mode,'Value',1); + testpair=1; + case '_i_j1-j2' + set(handles.mode,'String',{'bursts';'series(Dj)'})%multiple choice + if ~isempty(nbfield) && ~isempty(nbfield2) && ((nbfield2>10) || (nbfield==1)) + set(handles.mode,'Value',2); + else + set(handles.mode,'Value',1);% advice 'bursts' for small bursts + end + set(handles.mode,'Visible','on') + testpair=1; + end + switch NomType + case {'_i_j','_i_j1-j2','_i1-i2_j','#_ab'},% two navigation indices + state_j='on'; + end +end +if testpair + mode_Callback(hObject, eventdata, handles) +else + set(handles.NomType,'String',NomTypeCell) +end +set(handles.first_j,'Visible',state_j) +set(handles.incr_j,'Visible',state_j) +set(handles.last_j,'Visible',state_j) +set(handles.nb_field2,'Visible',state_j) + +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%???????????? +% --- Executes on button press in mode. +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% +function mode_Callback(hObject, eventdata, handles) +hseries=get(handles.mode,'parent'); +SeriesData=get(hseries,'UserData'); +mode_list=get(handles.mode,'String'); +mode_value=get(handles.mode,'Value'); +mode=mode_list{mode_value}; +NomType=[]; +test_find_pair=0; +if isfield(SeriesData,'NomType') + NomTypeCell=SeriesData.NomType; + Val=get(handles.NomType,'Value'); + NomType=NomTypeCell{Val}; + test_find_pair=isequal(NomType,'_i_j1-j2')|| isequal(NomType,'_i1-i2_j')|| isequal(NomType,'_i1-i2')|| isequal(NomType,'#_ab'); +end +% displ_num=[];%default +% first_i=str2num(get(handles.first_i,'String')); +% last_i=str2num(get(handles.last_i,'String')); +time=[]; +if isfield(SeriesData,'Time') +time=SeriesData.Time{1}; %get the set of times +end +siztime=size(time); +nbfield=siztime(1); +nbfield2=siztime(2); +indchosen=1; %%first pair selected by default +if isequal(mode,'bursts') + enable_i(handles,'On') + enable_j(handles,'Off') +elseif isequal(NomType,'_i_j1-j2')|| isequal(NomType,'_i1-i2_j') + enable_i(handles,'On') + enable_j(handles,'On') +else + enable_i(handles,'On') + enable_j(handles,'Off') +end + + +% elseif isequal(mode,'series(Dj)') +% enable_j(handles,'On') +% if nbfield==1 +% enable_i(handles,'Off') +% else +% enable_i(handles,'On') +% end +% elseif isequal(mode,'series(Di)') +% if nbfield2 > 1 +% enable_j(handles,'On') +% else +% enable_j(handles,'Off') +% end +% end +set(handles.list_pair_civ,'Value',indchosen);%set the default choice of image pairs for civ1 +% SetSeries.displ_num=displ_num; +set(hseries,'UserData',SeriesData) + +%list pairs if relevant +if test_find_pair + find_netcpair_civ(hObject, eventdata, handles,Val) +end + +%------------------------------------- +function enable_i(handles,state) +set(handles.i_txt,'Visible',state) +set(handles.first_i,'Visible',state) +set(handles.last_i,'Visible',state) +set(handles.incr_i,'Visible',state) +set(handles.nb_field,'Visible',state) +set(handles.ref_i,'Visible',state) +set(handles.ref_i_text,'Visible',state) + +%----------------------------------- +function enable_j(handles,state) +set(handles.j_txt,'Visible',state) +set(handles.first_j,'Visible',state) +set(handles.last_j,'Visible',state) +set(handles.incr_j,'Visible',state) +set(handles.nb_field2,'Visible',state) +set(handles.ref_j,'Visible',state) +set(handles.ref_j_text,'Visible',state) + +%----------------------------------- +function view_FieldMenu(handles,state) +set(handles.FieldMenu,'Visible',state) +set(handles.Field_text,'Visible',state) +set(handles.Field_frame,'Visible',state) + +%----------------------------------- +function view_FieldMenu_1(handles,state) +set(handles.FieldMenu_1,'Visible',state) +set(handles.Field_text_1,'Visible',state) + +%----------------------------------- +function view_TRANSFORM(handles,state) +set(handles.TRANSFORM_frame,'Visible',state) +set(handles.CoordType,'Visible',state); +set(handles.TRANSFORM_title,'Visible',state) + +%-------------------------------------------------------------- +% determine the menu for civ1 pairs depending on existing netcdf file at the middle of +% the field series set by first_i, incr, last_i +%---------------------------------------------------------------- +function find_netcpair_civ(hObject, eventdata, handles,Val) +hseries=get(handles.list_pair_civ,'parent'); +SeriesData=get(hseries,'UserData'); +% NomTypeCell=get(handles.NomType,'String'); +NomTypeCell=SeriesData.NomType; +NomType=NomTypeCell{Val}; + set(handles.list_pair_civ,'Visible','on') +%nomenclature types +RootPathCell=get(handles.RootPath,'String'); +filepath=RootPathCell{Val}; +RootFileCell=get(handles.RootFile,'String'); +filename=RootFileCell{Val}; +filebase=fullfile(filepath,filename); +SubDirCell=get(handles.SubDir,'String'); +subdir=SubDirCell{Val}; +if ~exist(fullfile(filepath,subdir),'dir') + msgbox_uvmat('ERROR',['no civ file available: subdirectory ' subdir ' does not exist']) + set(handles.list_pair_civ,'String',{''}); + return +end +mode_list=get(handles.mode,'String'); +mode_value=get(handles.mode,'Value'); +mode=mode_list{mode_value}; + +%reads image numbers from the interface +ref_i=str2num(get(handles.ref_i,'String')); +ref_j=str2num(get(handles.ref_j,'String')); +% time=[]; +% ref_time=[]; + ref_time=0; +if isfield(SeriesData,'Time')&~isempty(SeriesData.Time{Val})&~isequal(SeriesData.Time{Val},0) + time=SeriesData.Time{Val}; %get the set of times + siztime=size(time); + nbfield=siztime(1); + nbfield2=siztime(2); +% test_imadoc=1; +else +% test_imadoc=0;%no image documentation file + nbfield=50; + nbfield2=50;%default max number of pairs +end +%look for existing processed pairs involving the field at the middle of the series if civ1 will not +% be performed, while the result is needed for next steps. +displ_pair={''}; +displ_num=[]; +ind_exist=0; +TimeUnit=get(handles.TimeUnit,'String'); +if length(TimeUnit)>=1 + dtunit=['m' TimeUnit]; +else + dtunit='e-03'; +end +if isequal(mode,'series(Di)') + for index=1:min(nbfield-1,50) + filename=name_generator(filebase,ref_i-floor(index/2),ref_j,'.nc',NomType,1,ref_i+ceil(index/2),ref_j,subdir); + select=(exist(filename,'file')==2); + if select==1 + ind_exist=ind_exist+1; + displ_num(1,ind_exist)=0; + displ_num(2,ind_exist)=0; + displ_num(3,ind_exist)=-floor(index/2); + displ_num(4,ind_exist)=ceil(index/2); + %[cte_detect,vdt,cte_read]=read_netcdf(filename,{'dt','dt2','absolut_time_T0','absolute_time_TO_2'}); + [Cte,var_detect,ichoice]=nc2struct(filename,{}); + if isfield(Cte,'dt2') + dt=Cte.dt2; + elseif isfield(Cte,'dt') + dt=Cte.dt; + end + if isfield(Cte,'absolut_time_TO_2') + ref_time(ind_exist)=Cte.absolut_time_TO_2;%civ2 data used in priority + elseif isfield(Cte,'absolut_time_TO') + ref_time(ind_exist)=Cte.absolut_time_TO;%civ2 data used in priorit + elseif isfield(Cte,'Time') + ref_time(ind_exist)=Cte.Time; + end + displ_pair{ind_exist}=['Di= ' num2str(-floor(index/2)) '|' num2str(ceil(index/2)) ' :dt= ' num2str(dt*1000) dtunit]; + end + end + set(handles.list_pair_civ,'String',[displ_pair';{'Di=*|*'}]); +elseif isequal(mode,'series(Dj)')% series on the j index + for index=1:min(nbfield2-1,50) + filename=name_generator(filebase,ref_i,ref_j-floor(index/2),'.nc',NomType,1,ref_i,ref_j+ceil(index/2),subdir); + select=(exist(filename,'file')==2); + if select==1 + ind_exist=ind_exist+1; + displ_num(1,ind_exist)=-floor(index/2); + displ_num(2,ind_exist)=ceil(index/2); + displ_num(3,ind_exist)=0; + displ_num(4,ind_exist)=0; + %[cte_detect,vdt,cte_read]=read_netcdf(filename,{'dt','dt2','absolut_time_T0','absolute_time_TO_2'}); + [Cte,var_detect,ichoice]=nc2struct(nc,{}); + if isfield(Cte,'dt2') + dt=Cte.dt2; + elseif isfield(Cte,'dt') + dt=Cte.dt; + end + if isfield(Cte,'absolut_time_TO_2') + ref_time(ind_exist)=Cte.absolut_time_TO_2;%civ2 data used in priority + elseif isfield(Cte,'absolut_time_TO') + ref_time(ind_exist)=Cte.absolut_time_TO;%civ2 data used in priorit + elseif isfield(Cte,'Time') + ref_time(ind_exist)=Cte.Time; + end +% if cte_detect(2)==1; +% dt=cte_read(2); +% ref_time(ind_exist)=cte_read(4);%civ2 data used in priority +% else +% dt=cte_read(1); +% ref_time(ind_exist)=cte_read(3); +% end + displ_pair{ind_exist}=['Dj= ' num2str(-floor(index/2)) '|' num2str(ceil(index/2)) ' :dt= ' num2str(dt*1000) dtunit]; + end + end + set(handles.list_pair_civ,'String',[displ_pair';{'Dj=*|*'}]); +elseif isequal(mode,'bursts') %case of bursts + for numod_a=1:nbfield2-1 %nbfield2 always >=2 for 'bursts' mode + for numod_b=(numod_a+1):nbfield2 + [filename]=name_generator(filebase,ref_i,numod_a,'.nc',NomType,1,ref_i,numod_b,subdir); + select=(exist(filename,'file')==2); + if select==1 + ind_exist=ind_exist+1; + numlist_a(ind_exist)=numod_a; + numlist_b(ind_exist)=numod_b; + Attr=nc2struct(filename,[]); + isfield(Attr,'absolut_time_T0_2') + if isfield(Attr,'dt2') + dt(ind_exist)=Attr.dt2; + ref_time(ind_exist)=Attr.absolut_time_T0_2; + elseif isfield(Attr,'dt')& isfield(Attr,'absolut_time_T0') + dt(ind_exist)=Attr.dt; + ref_time(ind_exist)=Attr.absolut_time_T0; + else + dt(ind_exist)=NaN;%no information on dt + end + %determine nom_type_ima for pair display (used in num2stra.m) + switch NomType + case {'#ab'} + nom_type_ima='#a'; + case {'#AB'} + nom_type_ima='#A'; + otherwise + nom_type_ima='_i_j'; + end + displ_pair{ind_exist}=['j= ' num2stra(numod_a,nom_type_ima,2) '-' num2stra(numod_b,nom_type_ima,2) ... + ' :dt= ' num2str(dt(ind_exist)*1000)]; + end + end + set(handles.list_pair_civ,'String',[displ_pair';{'j=*-*'}]); + end + if exist('dt','var') & ~isempty(dt) + [dtsort,indsort]=sort(dt); + displ_num(1,:)=numlist_a(indsort); + displ_num(2,:)=numlist_b(indsort); + displ_num(3,:)=0; + displ_num(4,:)=0; + displ_pair=displ_pair(indsort); + ref_time=ref_time(indsort); + end +end +if ind_exist==0 + if isequal(mode,'series(Dj)') | isequal(mode,'st_series(Dj)') + msgbox_uvmat('ERROR',['no .nc file available for the selected reference index j=' num2str(ref_j) ' and subdirectory ' subdir]) + else + msgbox_uvmat('ERROR',['no .nc file available for the selected reference index i=' num2str(ref_i) ' and subdirectory ' subdir]) + end + if isequal(mode,'bursts') %case of bursts + set(handles.list_pair_civ,'String',{'j=*-*'}); + elseif isequal(mode,'series(Di)') %case of bursts + set(handles.list_pair_civ,'String',{'Di=*|*'}); + elseif isequal(mode,'series(Dj)') %case of bursts + set(handles.list_pair_civ,'String',{'Dj=*|*'}); + end +end + +val=get(handles.list_pair_civ,'Value'); +if val > length(displ_pair) + set(handles.list_pair_civ,'Value',1);% first pair proposed by default in the menu + val=1; +end +iview=get(handles.NomType,'Value'); +SeriesData.displ_num(iview,:)=(displ_num(:,val))'; +SeriesData.ref_time=ref_time; +set(hseries,'UserData',SeriesData) +list_pair_civ_Callback(hObject, eventdata, handles) + +%------------------------------------------------------------- +% --- Executes on selection in list_pair_civ. +function list_pair_civ_Callback(hObject, eventdata, handles) +%------------------------------------------------------------ + +%update first_i and last_i according to the chosen image pairs +testupdate=0; +Val=get(handles.RootPath,'Value'); +IndexCell=get(handles.NomType,'String'); +hseries=get(handles.list_pair_civ,'parent'); +SeriesData=get(hseries,'UserData'); +NomType=SeriesData.NomType{Val}; +list_pair=get(handles.list_pair_civ,'String');%get the menu of image pairs +index_pair=get(handles.list_pair_civ,'Value'); +str_pair=list_pair{index_pair}; +ind_equ=strfind(str_pair,'=');%find '=' +ind_sep=strfind(str_pair,'|');%find pair separator '|' +ind_com=strfind(str_pair,':');%find ':' +test_bursts=0; +if isempty(ind_sep) + ind_sep=strfind(str_pair,'-');%find pair separator if it is not '|' + test_bursts=1;% we are in the case of bursts +end +displ_num=[0 0 0 0]; %default +if ~isempty(ind_sep)&& ~strcmp(str_pair(ind_sep-1),'*')% if there is a pair separator ('|' or '-') + num1_str=str_pair(ind_equ(1)+1:ind_sep-1); + num2_str=str_pair(ind_sep+1:ind_com-1); + num1=str2double(num1_str); + num2=str2double(num2_str); + if isequal(num1_str(1),' ') + num1_str(1)=[]; + end + if isequal(num2_str(end),' ') + num2_str(end)=[]; + end + switch NomType + case {'_i1-i2_j'} + if isequal(num1_str(1),'0') + IndexCell{Val}=['_(i-(i+' num2_str ')_j']; + else + IndexCell{Val}=['_(i' num1_str ')-(i+' num2_str ')_j']; + end + displ_num(3)=num1; + displ_num(4)=num2; + case {'_i1-i2'} + if isequal(num1_str(1),'0') + IndexCell{Val}=['_(i' num1_str ')-(i+' num2_str ')']; + else + IndexCell{Val}=['_(i' num1_str ')-(i+' num2_str ')']; + end + displ_num(3)=num1; + displ_num(4)=num2; + case '_i_j1-j2' + if test_bursts + IndexCell{Val}=['_i_' num1_str '-' num2_str ]; + else + if isequal(num1_str(1),'0') + IndexCell{Val}=['_i_j-(j+' num2_str ')']; + else + IndexCell{Val}=['_i_(j' num1_str ')-(j+' num2_str ')']; + end + end + displ_num(1)=num1; + displ_num(2)=num2; + case {'#_ab'} %TO COMPLETE + IndexCell{Val}=['_i_' num1_str '-' num2_str ]; + + end +end +set(handles.NomType,'String',IndexCell) +SeriesData.displ_num(Val,:)=displ_num; +set(hseries,'UserData',SeriesData) +% set(handles.NomType,'Value',Val) + +if ~isequal(str_pair,'Dj=*|*')&~isequal(str_pair,'Di=*|*') + mode_list=get(handles.mode,'String'); + mode_value=get(handles.mode,'Value'); + mode=mode_list{mode_value}; + if isequal(mode,'series(Di)') + first_i=str2num(get(handles.first_i,'String')); + last_i=str2num(get(handles.last_i,'String')); + incr_i=str2num(get(handles.incr_i,'String')); + num1=first_i:incr_i:last_i; + lastfieldCell=get(handles.nb_field,'String'); + lastfield=str2num(lastfieldCell{1}); + if ~isempty(lastfield) + ind=find((num1-floor(index_pair/2)*ones(size(num1))>0)& (num1+ceil(index_pair/2)*ones(size(num1))<=lastfield)); + num1=num1(ind); + end + set(handles.first_i,'String',num2str(num1(1))); + set(handles.last_i,'String',num2str(num1(end))); + testupdate=1; + elseif isequal(mode,'series(Dj)') + first_j=str2num(get(handles.first_j,'String')); + last_j=str2num(get(handles.last_j,'String')); + incr_j=str2num(get(handles.incr_j,'String')); + num_j=first_j:incr_j:last_j; + lastfieldCell=get(handles.nb_field2,'String'); + if ~isempty(lastfieldCell) + lastfield2=lastfieldCell{1}; + ind=find((num_j-floor(index_pair/2)*ones(size(num_j))>0)& ... + (num_j+ceil(index_pair/2)*ones(size(num_j))<=lastfield2)); + end + testupdate=1; + end + + %update the first and last times of the series + if testupdate & isfield(SeriesData,'Time') + if ~isempty(SeriesData.Time{1}) + displ_time(handles,SeriesData.Time{1}); + end + end +end +%--------------------------------------------------- +% --- Executes on button press in RUN. +%------------------------------------------------------ +function RUN_Callback(hObject, eventdata, handles) + +%read root name and field type +set(handles.RUN,'BusyAction','queue'); +hseries=get(handles.RUN,'parent'); +set(0,'CurrentFigure',hseries) +if isequal(get(handles.GetObject,'Value'),1) + Series.GetObject=1; + GetObject_Callback(hObject, eventdata, handles) +else + Series.GetObject=0; +end +SeriesData=get(hseries,'UserData'); +if isfield(SeriesData,'sethandles') + if iscell(SeriesData.sethandles) + Series.sethandles=SeriesData.sethandles{1}; + else + Series.sethandles=SeriesData.sethandles;%retrieve the handles of the set_object interface (to define projection objects) + end +end + +%reinitiate waitbar position +Series.WaitbarPos=get(handles.waitbar_frame,'Position');%TO SUPPRESS +waitbarpos=Series.WaitbarPos; +waitbarpos(4)=0.005;%reinitialize waitbar to zero height +waitbarpos(2)=Series.WaitbarPos(2)+Series.WaitbarPos(4)-0.005; +set(handles.waitbar,'Position',waitbarpos) + +% read input file parameters and set menus +Series.PathProject=get(handles.PathCampaign,'String'); +RootPath=get(handles.RootPath,'String');% path of the root name of the first field series +RootFile=get(handles.RootFile,'String');% root name of the first field series +SubDir=get(handles.SubDir,'String');% subdirectory for netcdf files +FileExt=get(handles.FileExt,'String');%file extension +if isempty(SeriesData) + msgbox_uvmat('ERROR','no input file series') + return +end +NomType=SeriesData.NomType; +if length(RootPath)==1 %string character input for user fct + Series.RootPath=RootPath{1}; + Series.RootFile=RootFile{1}; + Series.SubDir=SubDir{1}; + Series.FileExt=FileExt{1}; + Series.NomType=NomType{1}; +else %cell input for user fct + Series.RootPath=RootPath; + Series.RootFile=RootFile; + Series.SubDir=SubDir; + Series.FileExt=FileExt; + Series.NomType=NomType; +end +if isequal(get(handles.FieldMenu,'Visible'),'on') + FieldMenu=get(handles.FieldMenu,'String'); + FieldValue=get(handles.FieldMenu,'Value'); + Series.Field=FieldMenu(FieldValue); +end +menu_coord_state=get(handles.CoordType,'Visible'); +Series.CoordType='';%default +if isequal(menu_coord_state,'on') + menu_coord=get(handles.CoordType,'String'); + menu_index=get(handles.CoordType,'Value'); + Series.CoordType=menu_coord{menu_index}; +end +Series.hseries=get(hObject,'Parent'); +if isequal(get(handles.ParamVal,'Visible'),'on') + ParamKey=get(handles.ParamKey,'String'); + if ischar(ParamKey) + ParamKey{1}=ParamKey; + end + ParamString=get(handles.ParamVal,'String'); + if ischar(ParamString) + for ilist=1:size(ParamString,1) + ParamVal{ilist}=ParamString(ilist,:); + end + else + ParamVal=ParamString; + end +end + +%read the set of field numbers +first_i=str2num(get(handles.first_i,'String')); +last_i=str2num(get(handles.last_i,'String')); +incr_i=str2num(get(handles.incr_i,'String')); +first_j=str2num(get(handles.first_j,'String')); +last_j=str2num(get(handles.last_j,'String')); +incr_j=str2num(get(handles.incr_j,'String')); +if ~isequal(get(handles.first_i,'Visible'),'on') + first_i=1; + last_i=1; + incr_i=1; +end +if ~isequal(get(handles.first_j,'Visible'),'on') + first_j=1; + last_j=1; + incr_j=1; +end +Series.NbSlice=str2num(get(handles.NbSlice,'String')); +if isequal(first_i,[])|isequal(first_j,[]), msgbox_uvmat('ERROR','first field number not defined'),... + set(handles.RUN, 'Enable','On'), set(handles.RUN,'BackgroundColor',[1 0 0]),return,end; +if isequal(last_i,[])| isequal(last_j,[]),msgbox_uvmat('ERROR','last field number not defined'),... + set(handles.RUN, 'Enable','On'), set(handles.RUN,'BackgroundColor',[1 0 0]),return,end; +if isequal(incr_i,[])| isequal(incr_j,[]),msgbox_uvmat('ERROR','increment in field number not defined'),... + set(handles.RUN, 'Enable','On'), set(handles.RUN,'BackgroundColor',[1 0 0]),return,end; +if last_i < first_i | last_j < first_j , msgbox_uvmat('ERROR','last field number must be larger than the first one'),... + set(handles.RUN, 'Enable','On'), set(handles.RUN,'BackgroundColor',[1 0 0]),return,end; +num_i=[first_i:incr_i:last_i]; +num_j=[first_j:incr_j:last_j]; +nbfield_cell=get(handles.nb_field,'String'); +nbfield=[]; %default +for iview=1:length(nbfield_cell) + nb=str2num(nbfield_cell{iview}); + if ~isempty(nb) + nbfield=[nbfield nb]; + end +end +nbfield=min(nbfield); +nbfield2_cell=get(handles.nb_field2,'String'); +nbfield2=[]; %default +for iview=1:length(nbfield2_cell) + nb=str2num(nbfield2_cell{iview}); + if ~isempty(nb) + nbfield2=[nbfield2 nb]; + end +end +nbfield2=min(nbfield2); + +%get complementary information from the 'series' interface +list_action=get(handles.ACTION,'String');% list menu action +index_action=get(handles.ACTION,'Value');% selected string index +action= list_action{index_action}; % selected string +mode_list=get(handles.mode,'String'); +index_mode=get(handles.mode,'Value'); +mode=mode_list{index_mode}; +ind_shift=0;%default + +%determine the list of input file names +nbmissing=0; +for iview=1:length(RootPath) + %case of pairs (.nc files) + + if isequal(NomType{iview},'_i_j1-j2')| isequal(NomType{iview},'_i1-i2_j')| isequal(NomType{iview},'_i1-i2')| isequal(NomType{iview},'#_ab') + ind_shift=SeriesData.displ_num(iview,:); + if isequal(ind_shift,[0 0 0 0]) % undefined pairs + if isequal(NomType{iview},'#_ab') + mode='#_ab'; + end + [num_i1,num_i2,num_j1,num_j2,nbmissing]=netseries_generator(fullfile(RootPath{iview},RootFile{iview}),SubDir{iview},mode,first_i,incr_i,last_i,first_j,incr_j,last_j); + else + [num_i1,num_i2,num_j1,num_j2,num_i,num_j]=find_file_indices(num_i,num_j,ind_shift,NomType{iview},mode); + if isempty(num_i) + msgbox_uvmat('ERROR','ERROR: empty set of input files chosen') + return + end + if num_i(1)>first_i + set(handles.first_i,'String',num2str(num_i(1)))%update the display of first field + last_i_Callback(hObject, eventdata, handles) + end + if num_i(end)first_j + set(handles.first_j,'String',num2str(num_j(1)))%update the display of first field + last_j_Callback(hObject, eventdata, handles) + end + if num_j(end)1 + num_i1_cell{iview}=num_i1; + num_i2_cell{iview}=num_i2; + num_j1_cell{iview}=num_j1; + num_j2_cell{iview}=num_j2; + end +end + +% RUN RUN' +path_series=which('series'); +list_path=get(handles.ACTION,'UserData'); +index=get(handles.ACTION,'Value'); +fct_path=list_path{index}; %path stored for the function ACTION +if ~isequal(fct_path,path_series) + eval(['spath=which(''' action ''');']) %spath = current path of the selected function ACTION + if ~isequal(spath,fct_path)& exist(fct_path,'dir') + addpath(fct_path)% add the prescribed path if not the current one + end +end +Series.Action=action;%name of the processing programme +set(handles.RUN,'BackgroundColor',[0.831 0.816 0.784]) +drawnow +if length(RootPath)>1 + feval(action,num_i1_cell,num_i2_cell,num_j1_cell,num_j2_cell,Series); +else + feval(action,num_i1,num_i2,num_j1,num_j2,Series); +end +set(handles.RUN,'BackgroundColor',[1 0 0]) + +% %save the current interface setting as figure namefig, append .0 to the name if it already exists +% detect=1; +% while detect==1 +% namefigfull=[namedoc '.fig']; +% hh=dir(namefigfull); +% if ~isempty(hh) +% detect=1; +% namedoc=[namedoc '.0']; +% else +% detect=0; +% end +% end +% saveas(gcbf,namefigfull);%save the interface with name namefigfull (A CHANGER EN FICHIER .xml) + +%---------------------------------------------------- +function STOP_Callback(hObject, eventdata, handles) +set(handles.RUN, 'BusyAction','cancel') +set(handles.RUN,'BackgroundColor',[1 0 0]) + +%---------------------------------------------- + +%---------------------------------------------------- +function first_i_Callback(hObject, eventdata, handles) +last_i_Callback(hObject, eventdata, handles) + +%---------------------------------------------- +function last_i_Callback(hObject, eventdata, handles) + hseries=get(handles.last_i,'parent'); +first_i=str2num(get(handles.first_i,'String')); +last_i=str2num(get(handles.last_i,'String')); +ref_i=ceil((first_i+last_i)/2); +set(handles.ref_i,'String', num2str(ref_i)) +ref_i_Callback(hObject, eventdata, handles) +SeriesData=get(hseries,'UserData'); +if ~isfield(SeriesData,'Time') + SeriesData.Time{1}=[]; +end +displ_time(handles,SeriesData.Time{1}); + +%------------------------------------------------------- +function first_j_Callback(hObject, eventdata, handles) + last_j_Callback(hObject, eventdata, handles) + +%------------------------------------------------------- +function last_j_Callback(hObject, eventdata, handles) + hseries=get(handles.last_i,'parent'); +first_j=str2num(get(handles.first_j,'String')); +last_j=str2num(get(handles.last_j,'String')); +ref_j=ceil((first_j+last_j)/2); +set(handles.ref_j,'String', num2str(ref_j)) + +ref_j_Callback(hObject, eventdata, handles) +SeriesData=get(hseries,'UserData'); +if ~isfield(SeriesData,'Time') + SeriesData.Time{1}=[]; +end +displ_time(handles,SeriesData.Time{1}); + + + + +%------------------------------------------------------- +function ref_i_Callback(hObject, eventdata, handles) +mode_list=get(handles.mode,'String'); +mode_value=get(handles.mode,'Value'); +mode=mode_list{mode_value}; +hseries=get(handles.ref_i,'parent'); +SeriesData=get(hseries,'UserData'); +%NomTypeCell=get(handles.NomType,'String'); +NomTypeCell=SeriesData.NomType; +if ~isempty(NomTypeCell) +Val=get(handles.NomType,'Value'); +NomType=NomTypeCell{Val}; +% for ilist=1:length(NomType) + if isequal(NomType,'_i_j1-j2')|| isequal(NomType,'_i1-i2_j')|| isequal(NomType,'_i1-i2') + if isequal(mode,'series(Di)') + find_netcpair_civ(hObject, eventdata, handles,Val);% update the menu of pairs depending on the available netcdf files +% break + end + end +end + +%---------------------------------------------------- +function ref_j_Callback(hObject, eventdata, handles) +mode_list=get(handles.mode,'String'); +mode_value=get(handles.mode,'Value'); +mode=mode_list{mode_value}; +hseries=get(handles.ref_i,'parent'); +SeriesData=get(hseries,'UserData'); +%NomTypeCell=get(handles.NomType,'String'); +NomTypeCell=SeriesData.NomType; +if ~isempty(NomTypeCell) +Val=get(handles.NomType,'Value'); +NomType=NomTypeCell{Val}; +% NomType=get(handles.NomType,'String'); + if isequal(NomType,'_i_j1-j2')|| isequal(NomType,'_i1-i2_j')|| isequal(NomType,'_i1-i2') + if isequal(mode,'series(Dj)') + find_netcpair_civ(hObject, eventdata, handles,Val);% update the menu of pairs depending on the available netcdf files +% break + end + end +end + +%---------------------------------------------------- +% --- Executes on selection change in ACTION. +function ACTION_Callback(hObject, eventdata, handles) +list_ACTION=get(handles.ACTION,'String');% list menu fields +index_ACTION=get(handles.ACTION,'Value');% selected string index +ACTION= list_ACTION{index_ACTION}; % selected function name +path_series=which('series');%path to series.m +list_path=get(handles.ACTION,'UserData');%list of recorded paths to functions of the list ACTION +nb_builtin=0; +for ilist=1:length(list_path) + if isequal(list_path{ilist},path_series) + nb_builtin=nb_builtin+1; + else + break + end +end +if nb_builtin==0% the path of series has been changed, reinitialize + series_OpeningFcn(hObject, eventdata, handles) + return +end + +% add a new function to the menu +if isequal(ACTION,'more...') + pathfct=fileparts(path_series); + browse_name=fullfile(path_series,'SERIES_FCT');%go to UVMAT/SERIES_FCT by default + if length(list_path)>nb_builtin + browse_name=list_path{end};% initialize browser with the path of the last introduced function + end + [FileName, PathName, filterindex] = uigetfile( ... + {'*.m', ' (*.m)'; + '*.m', '.m files '; ... + '*.*', 'All Files (*.*)'}, ... + 'Pick a file',browse_name); + if length(FileName)<2 + return + end + ext_fct=FileName(end-1:end); + if ~isequal(ext_fct,'.m') + msgbox_uvmat('ERROR','a Matlab function .m must be introduced'); + return + end + ACTION=FileName(1:end-2);% ACTION choice updated by the selected item + + % insert the choice in the action menu + menu_str=update_menu(handles.ACTION,ACTION);%new action menu in which the new item has been appended if needed + index_ACTION=get(handles.ACTION,'Value');% currently selected index in the list + list_path{index_ACTION}=PathName; + if length(menu_str)>nb_builtin+5; + nbremove=length(menu_str)-nb_builtin-5; + menu_str(nb_builtin+1:end-5)=[]; + list_path(nb_builtin+1:end-4)=[]; + index_ACTION=index_ACTION-nbremove; + set(handles.ACTION,'Value',index_ACTION) + set(handles.ACTION,'String',menu_str) + end + list_path{index_ACTION}=PathName; + set(handles.ACTION,'UserData',list_path); + set(handles.path,'enable','inactive')% indicate that the current path is accessible (not 'off') + + %record the current menu in personal file profil_perso + dir_perso=prefdir; + profil_perso=fullfile(dir_perso,'uvmat_perso.mat'); + for ilist=nb_builtin+1:length(menu_str)-1 + series_fct{ilist-nb_builtin}=fullfile(list_path{ilist},[menu_str{ilist} '.m']); + end + if exist(profil_perso,'file') + save(profil_perso,'series_fct','-append') + else + txt=ver; + Release=txt(1).Release; + relnumb=str2num(Release(3:4)); + if relnumb >= 14 + save(profil_perso,'series_fct','-V6') + else + save(profil_perso, 'series_fct') + end + end +end + +%check the current path to the selected function +PathName=list_path{index_ACTION};%current recorded path +if ~isequal(path_series,PathName) + CurrentPath=fileparts(which(ACTION)); + if ~isequal(PathName,CurrentPath) + addpath(PathName) + errormsg=check_functions; + msgbox_uvmat('CONFIRMATION',[['path ' PathName ' added to the current Matlab pathes'];errormsg]) + end +end +set(handles.path,'String',PathName); %show the path to the senlected function + +%default setting for the visibility of the GUI elements +%set( handles.Field,'Visible','off')%default +set(handles.RootPath,'UserData','many') +set(handles.SubDir,'Visible','on') +set(handles.RootFile,'Visible','on') +set(handles.NomType,'Visible','on') +set(handles.FileExt,'Visible','on') +set(handles.NbSlice,'Visible','off') +set(handles.NbSlice_title,'Visible','off') +set(handles.VelTypeMenu,'Visible','off'); +set(handles.VelType_text,'Visible','off'); +set(handles.VelTypeMenu_1,'Visible','off'); +set(handles.VelType_text_1,'Visible','off'); +view_FieldMenu(handles,'off') +view_FieldMenu_1(handles,'off') +view_TRANSFORM(handles,'off') +set(handles.ProjObject_frame,'Visible','off'); +set(handles.GetMask,'Visible','off') +set(handles.Mask,'Visible','off') +set(handles.GetObject,'Visible','off'); +set(handles.ProjObject,'Visible','off'); +set(handles.OutputDir,'Visible','off'); +set(handles.PARAMETERS_frame,'Visible','off'); +set(handles.PARAMETERS_title,'Visible','off'); +set(handles.ParamKey,'Visible','off') +set(handles.ParamVal,'Visible','off') +ParamKey={}; +set(handles.FieldMenu,'Enable','off') +set(handles.VelTypeMenu,'Enable','off') +set(handles.FieldMenu_1,'Enable','off') +set(handles.VelTypeMenu_1,'Enable','off') +set(handles.CoordType,'Enable','off') +%set the displayed GUI item needed for input parameters +%list_input=feval(ACTION);% input list asked by the selected function +varargout=feval(ACTION);% input list asked by the selected function +Param_list={}; +% RootPath=get(handles.RootPath,'String'); +% RootFile=get(handles.RootFile,'String'); + +%nb_series=length(RootFile); +FileExt=get(handles.FileExt,'String'); +nb_series=length(FileExt); +testima_series=1; %test for a list of images only +testima=1; +testima_1=1; +testciv_series=1; +for iview=1:nb_series + ext=FileExt{iview}; + if length(ext)<2 + ext='.none'; + end + testimaview=~isempty(imformats(ext(2:end))) || isequal(lower(ext),'.avi'); + if ~testimaview + if iview==1 + testima=0; + end + if iview==2 + testima_1=0; + end + testima_series=0; + end +end +for ilist=1:length(varargout)-1 + switch varargout{ilist} + %RootFile always visible + case 'RootPath' %visible by default + value=lower(varargout{ilist+1}); + if isequal(value,'one')||isequal(value,'two')||isequal(value,'many') + set(handles.RootFile,'UserData',value)% for use in menu Open_insert + end + case 'SubDir' %visible by default + if isequal(lower(varargout{ilist+1}),'off') + set(handles.SubDir,'Visible','off') + end + case 'RootFile' %visible by default + value=lower(varargout{ilist+1}); + if isequal(value,'off') + set(handles.RootFile,'Visible','off') + elseif isequal(value,'one')||isequal(value,'two')||isequal(value,'many') + set(handles.RootFile,'Visible','on') + set(handles.RootFile,'UserData',value)% for use in menu Open_insert + end + case 'NomType' %visible by default + if isequal(lower(varargout{ilist+1}),'off') + set(handles.NomType,'Visible','off') + end + case 'FileExt' %visible by default + if isequal(lower(varargout{ilist+1}),'off') + set(handles.FileExt,'Visible','off') + end + case 'NbSlice' %hidden by default + if isequal(lower(varargout{ilist+1}),'on') + set(handles.NbSlice,'Visible','on') + set(handles.NbSlice_title,'Visible','on') + end + case 'VelTypeMenu' %hidden by default + if isequal(lower(varargout{ilist+1}),'one') || isequal(lower(varargout{ilist+1}),'two') + set(handles.VelTypeMenu,'Enable','on') + if nb_series >=1 && ~testima_series + set(handles.VelTypeMenu,'Visible','on') + set(handles.VelType_text,'Visible','on'); + set(handles.Field_frame,'Visible','on') + end + end + if isequal(lower(varargout{ilist+1}),'two') + set(handles.VelTypeMenu_1,'Enable','on') + if nb_series >=2 && ~testima_series + set(handles.VelTypeMenu_1,'Visible','on') + set(handles.VelType_text_1,'Visible','on'); + end + end + case 'FieldMenu' %hidden by default + if isequal(lower(varargout{ilist+1}),'one')||isequal(lower(varargout{ilist+1}),'two') + set(handles.FieldMenu,'Enable','on') % test for MenuBorser + if nb_series >=1 && ~testima_series + view_FieldMenu(handles,'on') + end + end + if isequal(lower(varargout{ilist+1}),'two') + set(handles.FieldMenu_1,'Enable','on') + if nb_series >=2 && ~testima_1 + view_FieldMenu_1(handles,'on') + end + end + case 'CoordType' %hidden by default + if isequal(lower(varargout{ilist+1}),'on') + set(handles.CoordType,'Enable','on') + view_TRANSFORM(handles,'on') + end + case 'GetObject' %hidden by default + if isequal(lower(varargout{ilist+1}),'on') + set(handles.ProjObject_frame,'Visible','on') + set(handles.GetObject,'Visible','on'); + end + case 'Mask' %hidden by default + if isequal(lower(varargout{ilist+1}),'on') + set(handles.ProjObject_frame,'Visible','on') + set(handles.GetMask,'Visible','on'); + end + case 'PARAMETER' + set(handles.PARAMETERS_frame,'Visible','on') + set(handles.PARAMETERS_title,'Visible','on') + set(handles.ParamKey,'Visible','on') + %set(handles.ParamVal,'Visible','on') + Param_str=varargout{ilist+1}; + Param_list=[Param_list; {Param_str}]; + end +end +if ~isempty(Param_list) + set(handles.ParamKey,'String',Param_list) + set(handles.ParamVal,'Visible','on') +end + +%------------------------------------------------------------------- +% --- Executes on selection change in FieldMenu. +%------------------------------------------------------------------- +function FieldMenu_Callback(hObject, eventdata, handles) + +field_str=get(handles.FieldMenu,'String'); +field_index=get(handles.FieldMenu,'Value'); +field=field_str{field_index(1)}; +if isequal(field,'get_field...') + hget_field=findobj(allchild(0),'name','get_field'); + if ~isempty(hget_field) + delete(hget_field)%delete opened versions of get_field + end + hseries=get(handles.FieldMenu,'parent'); + SeriesData=get(hseries,'UserData'); + filename=SeriesData.CurrentInputFile; + if exist(filename,'file') + get_field(filename) + end +elseif isequal(field,'more...') + str=calc_field; + [ind_answer,v] = listdlg('PromptString','Select a file:',... + 'SelectionMode','single',... + 'ListString',str); + % edit the choice in the fields and action menu + scalar=cell2mat(str(ind_answer)); + update_menu(handles.FieldMenu,scalar) +end + +%------------------------------------------------------ +% --- Executes on selection change in FieldMenu_1. +%----------------------------------------------------- +function FieldMenu_1_Callback(hObject, eventdata, handles) +field_str=get(handles.FieldMenu_1,'String'); +field_index=get(handles.FieldMenu_1,'Value'); +field=field_str{field_index}; +if isequal(field,'get_field...') + hget_field=findobj(allchild(0),'name','get_field_1'); + if ~isempty(hget_field) + delete(hget_field) + end + hseries=get(handles.FieldMenu,'parent'); + SeriesData=get(hseries,'UserData'); + filename=SeriesData.CurrentInputFile_1; + if exist(filename,'file') + hget_field=get_field(filename); + set(hget_field,'name','get_field_1') + end +elseif isequal(field,'more...') + str=calc_field; + [ind_answer,v] = listdlg('PromptString','Select a file:',... + 'SelectionMode','single',... + 'ListString',str); + % edit the choice in the fields and action menu + scalar=cell2mat(str(ind_answer)); + update_menu(handles.FieldMenu_1,scalar) +end + + +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + %detect the chosen series of files and check their date of modification: +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% +%INPUT: +%num_i1: series of first indices i (given from the series interface as first_i:incr_i:last_i, mode and list_pair_civ) +%num_i2: series of second indices i (given from the series interface as first_i:incr_i:last_i, mode and list_pair_civ) +%num_j1: series of first indices j (given from the series interface as first_j:incr_j:last_j, mode and list_pair_civ ) +%num_j2: series of second indices j (given from the series interface as first_j:incr_j:last_j, mode and list_pair_civ) +%OTHER INPUTS given by the structure Series +function GUI_input=check_files(num_i1_cell,num_i2_cell,num_j1_cell,num_j2_cell,Series) %(filecell,filecell_1,num_i,num_j,vel_type,field,param); + +%requests for the visibility of input windows in the GUI series (activated directly by the selection in the menu ACTION) +if ~exist('num_i1_cell','var') + GUI_input={'RootPath';'many';...%nbre of possible input series (options 'on'/'two'/'many', default:'one') + 'SubDir';'on';... % subdirectory of derived files (PIV fields), ('on' by default) + 'RootFile';'on';... %root input file name ('on' by default) + 'FileExt';'on';... %input file extension ('on' by default) + 'NomType';'on';...%type of file indexing ('on' by default) + 'NbSlice';'on'; ...%nbre of slices ('off' by default) + %'VelTypeMenu';'on';...% menu for selecting the velocity type (civ1,..) 'off' by default) + %'FieldMenu';'on';...% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default) + %'CoordType';'on'...%can use a transform function 'off' by default + %'GetObject';'on'...%can use projection object ,'off' by default + %'GetMask';'on'...%can use mask option ,'off' by default + %'PARAMETER'; options: name of the user defined parameter',repeat a line for each parameter + ''}; + return %exit the function +end + +%standard parameters for waitbar and STOP action (do not modify) +hseries=guidata(Series.hseries);%handles of the GUI series +WaitbarPos=get(hseries.waitbar_frame,'Position'); + +%%%%%%%%%%%%%%%%%%%%%%%% + +% number of slices +NbSlice=str2num(get(hseries.NbSlice,'String')); +if isempty(NbSlice) + NbSlice=1; +end +NbSlice_name=num2str(NbSlice); +if isequal(NbSlice,[]),NbSlice=1; end; %default + +% number of views +count=0; +testcell=iscell(Series.RootFile); +if ~testcell + Series.RootPath={Series.RootPath}; + Series.RootFile={Series.RootFile}; + Series.SubDir={Series.SubDir}; + Series.FileExt={Series.FileExt}; + Series.NomType={Series.NomType}; +end +nbview=length(Series.RootFile); +for iview=1:nbview + filebase=fullfile(Series.RootPath{iview},Series.RootFile{iview});%root file name + if testcell + num_i1=num_i1_cell{iview}; num_i2=num_i2_cell{iview}; num_j1=num_j1_cell{iview}; num_j2=num_j2_cell{iview}; + else + num_i1=num_i1_cell; num_i2=num_i2_cell; num_j1=num_j1_cell; num_j2=num_j2_cell; + end + siz=size(num_i1); + nbfield2=siz(1); %nb of consecutive fields at each level(burst + nbfield=siz(1)*siz(2); + nbfield=floor(nbfield/(nbfield2*NbSlice));%total number of i indexes (adjusted to an integer number of slices) + if isequal(lower(Series.FileExt{iview}),'.avi') + info=aviinfo([filebase Series.FileExt{iview}]); + message{1}=info.Filename; + message{2}=info.FileModDate; + message{3}=[num2str(info.FramesPerSecond) ' frames/s ']; + message{4}=info.ImageType; + message{5}=[' compression' info.VideoCompression]; + message{6}=[ 'quality ' num2str(info.Quality)]; + Tabchar=message; + else + datnum=[]; + Tabchar={}; + %LOOP ON SLICES + for i_slice=1:NbSlice + for ifield=1:nbfield + indselect(:,ifield)=((ifield-1)*NbSlice+(i_slice-1))*nbfield2+[1:nbfield2]';%selected indices on the list of files of a slice + end + for index=1:nbfield*nbfield2 + stopstate=get(hseries.RUN,'BusyAction'); + if isequal(stopstate,'queue')% enable STOP command + update_waitbar(hseries.waitbar,WaitbarPos,index/(nbfield*nbfield2)) + ifile=indselect(index); + file=... + name_generator(filebase,num_i1(ifile),num_j1(ifile),Series.FileExt{iview},Series.NomType{iview},1,num_i2(ifile),num_j2(ifile),Series.SubDir{iview}); + [Path,Name,ext]=fileparts(file); + detect=exist(file,'file'); % check the existence of the file + if detect==0 + count=count+1; + lastfield='not found'; + else + datfile=dir(file); + datnum(ifile)=datenum(datfile.date); + filefound(ifile)={datfile.name}; + lastfield=''; + if isequal(Series.FileExt{iview},'.nc') || isequal(Series.FileExt{iview},'.cdf') + % check the content netcdf file + Data=nc2struct(file,'ListGlobalAttribute','patch2','fix2','civ2','patch','fix','absolut_time_T0','hart'); + lastfield='civ1'; %default + if ~isempty(Data.patch2) && isequal(Data.patch2,1) + lastfield='patch2'; + elseif ~isempty(Data.fix2) && isequal(Data.fix2,1) + lastfield='fix2'; + elseif ~isempty(Data.civ2) && isequal(Data.civ2,1); + lastfield='civ2'; + elseif ~isempty(Data.patch) && isequal(Data.patch,1); + lastfield='patch1'; + elseif ~isempty(Data.fix) && isequal(Data.fix,1); + lastfield='fix1'; + elseif ~isempty(Data.absolut_time_T0) && ~isempty(Data.hart) + lastfield='civ1'; + end +% Data=nc2struct(file,[]); +% lastfield='civ1'; %default +% if isfield(Data,'patch2') & isequal(Data.patch2,1); +% lastfield='patch2'; +% elseif isfield(Data,'fix2') & isequal(Data.fix2,1); +% lastfield='fix2'; +% elseif isfield(Data,'civ2') & isequal(Data.civ2,1); +% lastfield='civ2'; +% elseif isfield(Data,'patch') & isequal(Data.patch,1); +% lastfield='patch1'; +% elseif isfield(Data,'fix') & isequal(Data.fix,1); +% lastfield='fix1'; +% elseif isfield(Data,'absolut_time_T0') & isfield(Data,'hart') +% lastfield='civ1'; +% end + + end + end + Tabchar(1,i_slice)={['slice #' num2str(i_slice)]}; + Tabchar(index+1,i_slice)={[file ' ' lastfield]}; + end + end + end + if isempty(datnum) + if NbSlice>1 + message=['no set of ' num2str(NbSlice) ' (NbSlices) files found']; + else + message='no file found'; + end + else + datnum=datnum(find(datnum));%keep the non zero values corresponding to existing files + [first,ind]=min(datnum); + [last,indlast]=max(datnum); + message={['oldest modification: ' cell2mat(filefound(ind)) ' : ' datestr(first)];... + ['latest modification: ' cell2mat(filefound(indlast)) ' : ' datestr(last)]}; + end + if ~isempty(Tabchar) + Tabchar=reshape(Tabchar,NbSlice*(nbfield*nbfield2+1),1); + end + end + hfig=figure(iview); + clf + if iview>1 + pos=get(iview-1,'Position'); + pos(1)=pos(1)+(iview-1)*pos(1)/nbview; + set(hfig,'Position',pos) + end + set(hfig,'name',['view= ' num2str(iview)]) + + h=uicontrol('Style','listbox', 'Position', [20 20 500 300], 'String', Tabchar, 'Callback', @ncbrowser_uvmat); + hh=uicontrol('Style','listbox', 'Position', [20 340 500 40], 'String', message); +end +%---------------------------------------------------- +% determine the list of index pairs of processing file +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% +function [num_i1,num_i2,num_j1,num_j2,num_i_out,num_j_out]=find_file_indices(num_i,num_j,ind_shift,NomType,mode) +num_i1=num_i;% set of first image numbers by default +num_i2=num_i; +num_j1=num_j; +num_j2=num_j; +num_i_out=num_i; +num_j_out=num_j; +if isequal (NomType,'_i1-i2_j') |isequal (NomType,'_i1-i2') + num_i1_line=num_i+ind_shift(3);% set of first image numbers + num_i2_line=num_i+ind_shift(4); + % adjust the first and last field number + indsel=find(num_i1_line >= 1); + num_i_out=num_i(indsel); + num_i1_line=num_i1_line(indsel); + num_i2_line=num_i2_line(indsel); + num_j1=meshgrid(num_j,ones(size(num_i1_line))); + num_j2=meshgrid(num_j,ones(size(num_i1_line))); + [xx,num_i1]=meshgrid(num_j,num_i1_line); + [xx,num_i2]=meshgrid(num_j,num_i2_line); +elseif isequal (NomType,'_i_j1-j2') || isequal (NomType,'#_ab') + if isequal(mode,'bursts') %case of bursts (png_old or png_2D) + num_j1=ind_shift(1)*ones(size(num_i)); + num_j2=ind_shift(2)*ones(size(num_i)); + else + num_j1_col=num_j+ind_shift(1);% set of first image numbers + num_j2_col=num_j+ind_shift(2); + % adjust the first field number + indsel=find((num_j1_col >= 1)); + num_j_out=num_j(indsel); + num_j1_col=num_j1_col(indsel); + num_j2_col=num_j2_col(indsel); + [num_i1,num_j1]=meshgrid(num_i,num_j1_col); + [num_i2,num_j2]=meshgrid(num_i,num_j2_col); + end +end + + +%---------------------------------------------------------------------- +% --- make average on a series of files +%---------------------------------------------------------------------- +%INPUT: +%num_i1: series of first indices i (given from the series interface as first_i:incr_i:last_i, mode and list_pair_civ) +%num_i2: series of second indices i (given from the series interface as first_i:incr_i:last_i, mode and list_pair_civ) +%num_j1: series of first indices j (given from the series interface as first_j:incr_j:last_j, mode and list_pair_civ ) +%num_j2: series of second indices j (given from the series interface as first_j:incr_j:last_j, mode and list_pair_civ) +%OTHER INPUTS given by the structure Series +% Series.Time: +% Series.GeometryCalib: +function GUI_input=aver_stat(num_i1,num_i2,num_j1,num_j2,Series) +%requests for the visibility of input windows in the GUI series (activated directly by the selection in the menu ACTION) +if ~exist('num_i1','var') + GUI_input={'RootPath';'two';...%nbre of possible input series (options 'on'/'two'/'many', default:'one') + 'SubDir';'on';... % subdirectory of derived files (PIV fields), ('on' by default) + 'RootFile';'on';... %root input file name ('on' by default) + 'FileExt';'on';... %input file extension ('on' by default) + 'NomType';'on';...%type of file indexing ('on' by default) + 'NbSlice';'on'; ...%nbre of slices ('off' by default) + 'VelTypeMenu';'two';...% menu for selecting the velocity type (options 'off'/'one'/'two', 'off' by default) + 'FieldMenu';'two';...% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default) + 'CoordType'; 'on';...%can use a transform function + 'GetObject';'on';...%can use projection object(option 'off'/'one'/'two', + %'GetMask';'on'...%can use mask option + %'PARAMETER'; %options: name of the user defined parameter',repeat a line for each parameter + ''}; + return +end + +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% +hseries=guidata(Series.hseries);%handles of the GUI series +WaitbarPos=get(hseries.waitbar_frame,'Position'); +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + +%root input file and type +if ~iscell(Series.RootPath)% case of a single input field series + num_i1={num_i1};num_j1={num_j1};num_i2={num_i2};num_j2={num_j2}; + RootPath={Series.RootPath}; + RootFile={Series.RootFile}; + SubDir={Series.SubDir}; + FileExt={Series.FileExt}; + NomType={Series.NomType}; +else + RootPath=Series.RootPath; + RootFile=Series.RootFile; + SubDir=Series.SubDir; + NomType=Series.NomType; + FileExt=Series.FileExt; +end +ext=FileExt{1}; +form=imformats(ext([2:end]));%test valid Matlab image formats +testima=0; +if ~isempty(form)||isequal(lower(ext),'.avi')||isequal(lower(ext),'.vol') + testima(1)=1; +end +if length(FileExt)>=2 + ext_1=FileExt{2}; + form=imformats(ext_1([2:end]));%test valid Matlab image formats + if ~isempty(form)||isequal(lower(ext_1),'.avi')||isequal(lower(ext_1),'.vol') + testima(2)=1; + end + if testima(2)~=testima(1) + msgbox_uvmat('ERROR','images and netcdf files cannot be compared') + return + end +end + +%Number of input series: this function accepts two input file series at most (then it operates on the difference of fields) +nbview=length(RootPath); +if nbview>2 + RootPath=RootPath(1:2); + set(hseries.RootPath,'String',RootPath) + SubDir=SubDir(1:2); + set(hseries.SubDir,'String',SubDir) + RootFile=RootFile(1:2); + set(hseries.RootFile,'String',RootFile) + NomType=NomType(1:2); + FileExt=FileExt(1:2); + set(hseries.FileExt,'String',FileExt) + nbview=2; +end +hhh=which('mmreader'); +for iview=1:nbview + test_movie(iview)=0; + if ~isequal(hhh,'')&& mmreader.isPlatformSupported() + if isequal(lower(FileExt{iview}),'.avi') + MovieObject{iview}=mmreader(fullfile(RootPath{iview},[RootFile{iview} FileExt{iview}])); + test_movie(iview)=1; + end + end +end + +% number of slices +NbSlice=str2num(get(hseries.NbSlice,'String')); +if isempty(NbSlice) + NbSlice=1; +end +NbSlice_name=num2str(NbSlice); + +% Field and velocity type (the same for the two views) +Field_str=get(hseries.FieldMenu,'String'); +FieldName=[]; %default +testfield=get(hseries.FieldMenu,'Visible'); +if isequal(testfield,'on') + val=get(hseries.FieldMenu,'Value'); + FieldName=Field_str(val);%the same set of fields for all views + if isequal(FieldName,{'get_field...'}) + hget_field=findobj(allchild(0),'name','get_field');%find the get_field... GUI + if length(hget_field)>1 + delete(hget_field(2:end)) + elseif isempty(hget_field) + filename=... + name_generator(fullfile(RootPath{1},RootFile{1}),num_i1{1}(1),num_j1{1}(1),FileExt{1},NomType{1},1,num_i2{1}(1),num_j2{1}(1),SubDir{1}); + get_field(filename); + return + end + hhget_field=guidata(hget_field);%handles of GUI elements in get_field + SubField=read_var_names(hhget_field); %read the names of the variables to plot in the get_field GUI + end +end +%detect whether the two files are 'images' or 'netcdf' +testima=0; +testvol=0; +testcivx=0; +testnc=0; +FileExt=get(hseries.FileExt,'String'); +% test_movie=0; +for iview=1:nbview + ext=FileExt{iview}; + form=imformats(ext([2:end])); + if isequal(lower(ext),'.vol') + testvol=testvol+1; + elseif ~isempty(form)||isequal(lower(ext),'.avi')% if the extension corresponds to an image format recognized by Matlab + testima=testima+1; + elseif isequal(ext,'.nc') + testnc=testnc+1; + end +end +if testvol + msgbox_uvmat('ERROR','volume images not implemented yet') + return +end +if testnc~=nbview && testima~=nbview && testvol~=nbview + msgbox_uvmat('ERROR','compare two image series or two netcdf files with the same fields as input') + return +end +if ~isequal(FieldName,{'get_field...'}) + testcivx=testnc; +end + +if testcivx + VelType_str=get(hseries.VelTypeMenu,'String'); + VelType_val=get(hseries.VelTypeMenu,'Value'); + VelType{1}=VelType_str{VelType_val}; + if nbview==2 + VelType_str=get(hseries.VelTypeMenu_1,'String'); + VelType_val=get(hseries.VelTypeMenu_1,'Value'); + VelType{2}=VelType_str{VelType_val}; + end +end + +%Calibration data and timing: read the ImaDoc files +mode=''; %default +timecell={}; +itime=0; +NbSlice_calib={}; +for iview=1:nbview%Loop on views + XmlData{iview}=[];%default + filebase{iview}=fullfile(RootPath{iview},RootFile{iview}); + if exist([filebase{iview} '.xml'],'file') + [XmlData{iview},error]=imadoc2struct([filebase{iview} '.xml']); + if isfield(XmlData{iview},'Time') + itime=itime+1; + timecell{itime}=XmlData{iview}.Time; + end + if isfield(XmlData{iview},'GeometryCalib') && isfield(XmlData{iview}.GeometryCalib,'SliceCoord') + NbSlice_calib{iview}=size(XmlData{iview}.GeometryCalib.SliceCoord,1);%nbre of slices for Zindex in phys transform + if ~isequal(NbSlice_calib{iview},NbSlice_calib{1}) + msgbox_uvmat('WARNING','inconsistent number of Z indices for the two field series'); + end + end + elseif exist([filebase{iview} '.civ'],'file') + [error,time,TimeUnit,mode,npx,npy,pxcmx,pxcmy]=read_imatext([filebase{iview} '.civ']); + itime=itime+1; + timecell{itime}=time; + XmlData{iview}.Time=time; + GeometryCalib.R=[pxcmx 0 0; 0 pxcmy 0;0 0 0]; + GeometryCalib.Tx=0; + GeometryCalib.Ty=0; + GeometryCalib.Tz=1; + GeometryCalib.dpx=1; + GeometryCalib.dpy=1; + GeometryCalib.sx=1; + GeometryCalib.Cx=0; + GeometryCalib.Cy=0; + GeometryCalib.f=1; + GeometryCalib.kappa1=0; + GeometryCalib.CoordUnit='cm'; + XmlData{iview}.GeometryCalib=GeometryCalib; + if error==1 + msgbox_uvmat('WARNING','inconsistent number of fields in the .civ file'); + end + end +end + +%check coincidence in time +multitime=0; +if length(timecell)==0 + time=[]; +elseif length(timecell)==1 + time=timecell{1}; +elseif length(timecell)>1 + multitime=1; + for icell=1:length(timecell) + if ~isequal(size(timecell{icell}),size(timecell{1})) + msgbox_uvmat('WARNING','inconsistent time array dimensions in ImaDoc fields, the time for the first series is used') + time=timecell{1}; + multitime=0; + break + end + end +end +if multitime + for icell=1:length(timecell) + time(icell,:,:)=timecell{icell}; + end + diff_time=max(max(diff(time))); + if diff_time>0 + msgbox_uvmat('WARNING',['times of series differ by more than ' num2str(diff_time)]) + end +end +if size(time,2) < num_i2{1}(end) || size(time,3) < num_j2{1}(end)% ime array absent or too short in ImaDoc xml file' + time=[]; +end + +% Root name of output files (TO GENERALISE FOR TWO INPUT SERIES) +filebasesub=fullfile(RootPath{1},SubDir{1},RootFile{1}); +if isempty(SubDir{1}) % create a subdirectory '/mean' + subdir_result='mean'; +% filebasemean=fullfile(RootPath{1},subdir_result); + if ~exist(fullfile(RootPath{1},subdir_result),'dir') + dircur=pwd; %record current working directory + cd(RootPath{1})% goes to the iamge directory + [m1,m2,m3]=mkdir(subdir_result); + if ~isequal(m2,'') + msgbox_uvmat('CONFIRMATION',m2);%error message for directory creation + end + cd(dircur) %back to the initial working directory + end + filebase_out=filebase{1}; +else + subdir_result=SubDir{1}; + filebase_out=[filebase{1} '_mean'];% output root name obtained by adding the suffix _mean to the input +end +%output nomtype (to generalise) +NomTypeOut=nomtype2pair(NomType{1},num_i2{end}(end)-num_i1{1}(1),num_j2{end}(end)-num_j1{1}(1)); + +if NbSlice==1 + filebase_out=[filebasesub '_mean']; +else + filebase_out=[filebasesub '_' NbSlice_name 'mean']; + answeryes=questdlg({['will make average in ' num2str(NbSlice) ' slices'];['results stored as files ' filebase_out ' ...']}); + if ~isequal(answeryes,'Yes') + return + end +end + +% coordinate transform or other user defined transform +Coord_menu=get(hseries.CoordType,'String'); +menu_val=get(hseries.CoordType,'Value'); +usrfct=Coord_menu{menu_val}; +testfct=~isequal(usrfct,''); + +%slice loop +siz=size(num_i1{1}); +lengthtot=siz(1)*siz(2); +nbfield=floor(lengthtot/(siz(1)*NbSlice));%total number of i indexes (adjusted to an integer number of slices) +nbfield_slice=nbfield*siz(1);% number of fields per slice + +for i_slice=1:NbSlice + S=0; %initiate the image sum S + nbfiles=0; + nbmissing=0; + %averaging loop + for ifile=i_slice:NbSlice:lengthtot + stopstate=get(hseries.RUN,'BusyAction'); + if isequal(stopstate,'queue') % enable STOP command + update_waitbar(hseries.waitbar,WaitbarPos,ifile/lengthtot) + for iview=1:nbview + [filename]=... + name_generator(filebase{iview},num_i1{iview}(ifile),num_j1{iview}(ifile),FileExt{iview},NomType{iview},1,num_i2{iview}(ifile),num_j2{iview}(ifile),SubDir{iview}); + if testima + Data{iview}.ListVarName={'A'}; + Data{iview}.AName='image'; + if test_movie(iview) + Data{iview}.A=read(MovieObject{iview},num_i1{iview}(ifile)); + else + Data{iview}.A=read_image(filename,NomType{iview},num_i1{iview}(ifile));% read the image, num2 is the counter for avi files + end + Atype{iview}=class(Data{iview}.A); + Data{iview}.A=double(Data{iview}.A); + elseif testcivx + [Data{iview},VelTypeOut]=read_civxdata(filename,FieldName,VelType); + else + [Data{iview},var_detect]=nc2struct(filename,SubField.ListVarName); %read the corresponding input data + Data{iview}.VarAttribute=SubField.VarAttribute; + end + if isfield(Data{iview},'Txt') + msgbox_uvmat('ERROR',['error of input reading: ' Data{iview}.Txt]) + return + end + end + % coordinate transform (or other user defined transform) + if ~isequal(Series.CoordType,'') + % z index + if ~isempty(NbSlice_calib) + Data{iview}.ZIndex=mod(num_i1{iview}(ifile)-1,NbSlice_calib{1})+1;%Zindex for phys transform + end + if nbview==2 + [Data{1},Data{2}]=feval(Series.CoordType,Data{1},XmlData{1},Data{2},XmlData{2}); + if isempty(Data{2}) + Data(2)=[]; + end + else + Data{1}=feval(Series.CoordType,Data{1},XmlData); + end + end + if testcivx + Data{iview}=calc_field(FieldName,Data{iview});%calculate field (vort..) + end + if length(Data)==2 + [Field,errormsg]=sub_field(Data{1},Data{2}); %substract the two fields + if ~isempty(errormsg) + msgbox_uvmat('ERROR',['error in aver_stat/sub_field:' errormsg]) + return + end + else + Field=Data{1}; + end + if isfield(Series,'ProjObject') + [Field,errormsg]=proj_field(Field,Series.ProjObject); + if ~isempty(errormsg) + msgbox_uvmat('ERROR',['error in aver_stat/proj_field:' errormsg]) + return + end + end + nbfiles=nbfiles+1; + if nbfiles==1 %first field + time_1=[]; + if isfield(Field,'Time') + time_1=Field.Time(1); + end + DataMean=Field;%default + else + for ivar=1:length(Field.ListVarName) + VarName=Field.ListVarName{ivar}; + eval(['sizmean=size(DataMean.' VarName ');']); + eval(['siz=size(Field.' VarName ');']); + if ~isequal(siz,sizmean) + warndlg_uvmat(['unequal size of input field ' VarName ', need to interpolate on a grid'],'WARNING') + nbmissing=nbmissing+1; + break + else + eval(['DataMean.' VarName '=DataMean.' VarName '+ Field.' VarName ';']); % update the sum + end + end + end +% else +% nbmissing=nbmissing+1; +% end + end + end %end averaging loop + for ivar=1:length(Field.ListVarName) + VarName=Field.ListVarName{ivar}; + eval(['DataMean.' VarName '=DataMean.' VarName '/nbfiles;']); % normalize the mean + end + if nbmissing~=0 + msgbox_uvmat('WARNING',[num2str(nbmissing) ' input files are missing or skipted']) + end + if isempty(time) % time read from files prevails + time_end=[]; + if isfield(Field,'Time') + time_end=Field.Time(1);%last time read + if ~isempty(time_1) + DataMean.Time=time_1; + DataMean.Time_end=time_end; + end + end + else % time from ImaDoc prevails + DataMean.Time=time(1,num_i1{1}(1),num_j1{1}(1)); + DataMean.Time_end=time(end,num_i1{end}(end),num_j1{end}(end)); + end + + %writing the result file + if testima + if NbSlice==1 + [filemean]=name_generator(filebase_out,num_i1{1}(1),num_j1{1}(1),'.png',NomTypeOut,1,num_i2{end}(end),num_j2{end}(end)); + else % label the file number by the slice # for simplicity + [filemean]=name_generator(filebase_out,i_slice,1,'.png','_i'); + end + if exist(filemean,'file') + backupfile=filemean; + testexist=2; + while testexist==2 + backupfile=[backupfile(1:end-4) '~.png']; + testexist=exist(backupfile,'file'); + end + [success,message]=copyfile(filemean,backupfile);%make backup + if ~isequal(success,1) + msgbox_uvmat('ERROR',['previous file result ' filemean ' already exists, problem in backup']) + return + end + end + if isequal(Atype{1},'uint16') + imwrite(uint16(DataMean.A),filemean,'BitDepth',16); + else + imwrite(uint8(DataMean.A),filemean,'BitDepth',8); + end + display([filemean ' written']); + else %determine global attributes + DataMean.ListGlobalAttribute=[DataMean.ListGlobalAttribute {Series.Action}]; + ActionKey='Action'; + while isfield(DataMean,ActionKey) + ActionKey=[ActionKey '_1']; + end + eval(['DataMean.' ActionKey '=Series.Action;']) + DataMean.ListGlobalAttribute=[DataMean.ListGlobalAttribute {ActionKey}]; + if isfield(DataMean,'Time') + DataMean.ListGlobalAttribute=[DataMean.ListGlobalAttribute {'Time','Time_end'}]; + end + if NbSlice==1 + filemean=name_generator(filebase_out,num_i1{1}(1),num_j1{1}(1),'.nc',NomTypeOut,1,num_i2{end}(end),num_j2{end}(end)); + else % label the file number by the slice # for simplicity + [filemean]=name_generator(filebase_out,i_slice,1,'.nc','_i'); + end + if exist(filemean,'file') + backupfile=filemean; + testexist=2; + while testexist==2 + backupfile=[backupfile(1:end-3) '~.nc']; + testexist=exist(backupfile,'file'); + end + [success,message]=copyfile(filemean,backupfile);%make backup + if ~isequal(success,1) + msgbox_uvmat('ERROR',['previous file result ' filemean ' already exists, problem in backup']) + display(['previous file result ' filemean ' already exists, problem in backup']) + return + end + end + errormsg=struct2nc(filemean,DataMean); %save result file + if isempty(errormsg) + display([filemean ' written']); + else + msgbox_uvmat('ERROR',['error in writting result file: ' errormsg]) + display(errormsg) + end + end +end +hget_field=findobj(allchild(0),'name','get_field');%find the get_field... GUI +delete(hget_field) +uvmat(filemean) + + +% %---------------------------------------------------------------------- +% % --makes a time averaged velocity field +% %---------------------------------------------------------------------- +% function aver_vel(num_i1,num_i2,num_j1,num_j2,Series) +% %handles of the GUI series +% +% hseries=guidata(Series.hseries);%handles of the GUI series +% WaitbarPos=get(hseries.waitbar_frame,'Position'); +% Field_list=get(hseries.FieldMenu,'String'); +% val=get(hseries.FieldMenu,'Value'); +% FieldName=Field_list{val(1)}; +% set(hseries.FieldMenu,'Value',val(1))% select only one input field +% if isequal(FieldName,'get_field...') +% hget_field=findobj(allchild(0),'Name','get_field');%find the get_field... GUI +% end +% %root input file and type +% RootPath=get(hseries.RootPath,'String'); +% SubDir=get(hseries.SubDir,'String'); +% RootFile=get(hseries.RootFile,'String'); +% %NomType=get(hseries.NomType,'String'); +% NomType=Series.NomType; +% FileExt=get(hseries.FileExt,'String'); +% ext=FileExt{1}; +% VelType_str=get(hseries.VelTypeMenu,'String'); +% VelType_val=get(hseries.VelTypeMenu,'Value'); +% VelType{1}=VelType_str{VelType_val}; +% +% time=0; %default +% % number of slices +% NbSlice=str2num(get(hseries.NbSlice,'String')); +% if isempty(NbSlice) +% NbSlice=1; +% end +% NbSlice_name=num2str(NbSlice); +% filebase=fullfile(RootPath{1},RootFile{1}); +% Calib=[]; +% if exist([filebase '.xml'],'file') +% %[error,Heading,nom_type_read,ext_ima_read,time_imadoc,TimeUnit,mode,NbSlice,npx,npy,Calib]=read_imadoc([filebase '.xml']); +% [XmlData,warntext]=imadoc2struct([filebase '.xml']); +% end +% if NbSlice==1 +% filebase_mean=[filebase '_mean']; %root name for the result +% else +% filebase_mean=[filebase '_' NbSlice_name 'mean']; %root name for the results +% answeryes=questdlg({['will make average in ' num2str(NbSlice) ' slices'];['results stored as files ' filebase_mean ' ...']}); +% if ~isequal(answeryes,'Yes') +% return +% end +% end +% siz=size(num_i1); +% nbfield2=siz(1); %nb of consecutive fields at each level(burst) +% lengthtot=siz(1)*siz(2); +% nbfield=floor(lengthtot/(nbfield2*NbSlice));%total number of i indexes (adjusted to an integer number of slices) +% nbfield_slice=nbfield*nbfield2;% number of fields per slice +% %projection object +% GridX=[]; +% GridY=[]; +% if isfield(Series,'sethandles') +% Series.ProjObject=read_set_object(Series.sethandles); +% if isfield(Series.ProjObject,'Style') +% answeryes=questdlg({['statistics on field series projected on ' Series.ProjObject.Style]}); +% if ~isequal(answeryes,'Yes') +% return +% end +% end +% end +% +% %LOOP ON SLICES +% for i_slice=1:NbSlice +% %select the series of image indices at the level islice +% for ifield=1:nbfield +% indselect(:,ifield)=((ifield-1)*NbSlice+(i_slice-1))*nbfield2+[1:nbfield2]';%selected indices on the list of files of a slice +% end +% %name of result file +% [filemean,idetect]=... +% name_generator(filebase_mean,num_i1(i_slice),num_j1(1),Series.FileExt{1},'_i1-i2_j1-j2',1,num_i2(i_slice+nbfield_slice*NbSlice-1),num_j2(end),Series.SubDir{1}); +% +% % field=get(handles.civ1,'UserData');%read current selected field type (civ1,civ2...) +% itime=0; +% dt=[]; +% %LOOP ON FIELDS IN A SLICE +% test_interpolate=0;%default +% for index=1:nbfield*nbfield2 +% ifile=indselect(index); +% stopstate=get(hseries.RUN,'BusyAction'); +% if isequal(stopstate,'queue')% enable STOP command +% update_waitbar(hseries.waitbar,WaitbarPos,ifile/(nbfield*nbfield2)) +% %name of the current file +% [filename,idetect]=name_generator(filebase,num_i1(ifile),num_j1(ifile),Series.FileExt{1},Series.NomType{1},1,num_i2(ifile),num_j2(ifile),Series.SubDir{1}); +% %read input file +% itime=itime+1; +% if isequal(FieldName,'get_field...') +% hhget_field=guidata(hget_field);%handles of GUI elements in get_field +% hObject=0; +% eventdata=0; +% SubField=get_field('read_var_names',hObject,eventdata,hhget_field); %read the names of the variables to plot in the get_field GUI +% [Data,var_detect]=nc2struct(filename,SubField.ListVarName); %read input data +% time(itime)=itime; +% dt=1; +% Calib_read=[]; +% else +% [nb_coord,nb_dim,Civ,CivStage,timeread,Data,VelTypeOut,Calib_read]=read_ncfield(filename,VelType{1});%reading the first file +% time(itime)=timeread; +% if isequal(Civ,1) +% Data.CoordType='px';%test for pixel coordinates +% if isequal(itime,1) +% dt=Data.dt; +% elseif ~isequal(Data.dt,dt) +% warndlg_uvmat('series with non constant dt, need phys coordinates','ERROR') +% return +% end +% end +% end +% %increment the detected fields, skip the others +% if idetect==0 +% warndlg_uvmat(['input file ' filename ' not found'],'ERROR') +% %A FAIRE STOCKER LE RESULT ACTUEL S'IL EXISTE +% end +% % itime=itime+1; +% % time(itime)=timeread; +% +% %coordinate transform +% if isempty(Calib) +% Calib=Calib_read;%use Calib from xml file in priority, then Calib from the current file +% end +% if ~isequal(Series.CoordType,'') +% Data=feval(Series.CoordType,Data,Calib); +% end +% %projection on object if defined +% if isfield(Series,'ProjObject'); +% Data=proj_field(Data,Series.ProjObject); +% if isequal(itime,1)%use the positions on the first field for the whole series, ou utiliser grille +% if isfield(Data,'Txt')%display error message +% warndlg(Data.Txt,'ERROR') +% return +% end +% end +% else%remove false vectors and interpolate on the positions of the first field +% Data=document_field(Data); +% Data.Style='plane'; +% end +% %%%%%%%%% initiate the average at the first iteration: check list and structure of variables +% if ifile==i_slice%first field in the slice +% testfalse=0; +% ListIndex={}; +% testnewcell=1; +% %group the variables (fields of 'Data') in cells of variables with the same dimensions +% [DimVarIndex,CellVarIndex]=find_field_indices(Data); +% VarIndex=CellVarIndex{1}; % ONLY THE FIRST VAR GROUP IS AVERAGED +% DimIndex=Data.VarDimIndex{VarIndex(1)};%indices of the dimensions of the first variable (common to all variables in the cell) +% MeanData=Data;%transfer heading +% MeanData.Time=[time(1) time(end)]; +% MeanData.Action=Series.Action;%name of the processing programme +% MeanData.ListDimName=Data.ListDimName(DimIndex);%name of dimension +% MeanData.DimValue=Data.DimValue(DimIndex);%values of dimension (nbre of vectors) +% MeanData.ListVarName=Data.ListVarName; +% MeanData.VarDimIndex=Data.VarDimIndex; +% MeanData.ListVarAttribute={'Role'};%list of variable attribute names A FAIRE: transferer les autres attributs +% testsum=ones(size(VarIndex)); +% indexfalse=0; +% CoordName={}; +% indexremove=[]; +% if isfield(Data,'Role') % look for coordinate and flag variables +% for ivar=1:length(VarIndex) +% VarName=Data.ListVarName{VarIndex(ivar)}; +% var_role=Data.Role{VarIndex(ivar)};%'role' of the variable +% MeanData.Role{ivar}=var_role; +% if isequal(var_role,'falseflag') +% indexfalse=ivar; %test for false flag +% indexremove=ivar; +% FFName=VarName; +% testsum(ivar)=0; +% eval(['MeanData=rmfield(MeanData,''' VarName ''');']);%remove variable +% end +% if isequal(var_role,'warnflag') +% testsum(ivar)=0; %do not sum warn flag +% eval(['MeanData=rmfield(MeanData,''' VarName ''');']);%remove variable +% indexremove=[indexremove ivar]; +% end +% if isequal(var_role,'coord_x')| isequal(var_role,'coord_y')|isequal(var_role,'coord_z') +% eval(['MeanData.' VarName '=Data.' VarName ';']); +% testsum(ivar)=0; +% eval(['CoordName=[CoordName ''' VarName '''];']); +% end +% if testsum(ivar)~=0 +% eval(['MeanData.' VarName '=zeros(size(Data.' VarName '));']);%initialise sum +% end +% end +% end +% findsum=find(testsum); +% VarIndexSum=VarIndex(findsum);%indices of variables to sum (not coordinates nor flags) +% if length(CoordName)==0 +% if isempty(DimVarIndex)|isequal(DimVarIndex,0)% no coordinate variable for structured coordinates, prepare histograms +% for ilist=1:length(VarIndexSum) +% VarName=Data.ListVarName{VarIndexSum(ilist)}; +% eval(['MeanData=rmfield(MeanData,''' VarName ''');']);%remove variable +% indexremove=[indexremove ilist]; +% eval(['[MeanData.' VarName 'hist,MeanData.' VarName 'val]=hist(Data.' VarName ',100);']);%make histo +% eval(['sizhist=size(MeanData.' VarName 'hist);']) +% if sizhist(1)==1 +% eval(['MeanData.' VarName 'hist=MeanData.' VarName 'hist'';']) +% end +% eval(['maxval=max(MeanData.' VarName 'val);']); +% eval(['minval=min(MeanData.' VarName 'val);']); +% dC(ilist)=(maxval-minval)/100;%size of the histogram bin +% end +% else +% % icoord=0; +% % for ilist=1:length(DimVarIndex) +% % VarDim=Data.ListVarName{DimVarIndex(ilist)}; +% % icoord=icoord+1; +% % % eval(['Coord{' num2str(icord) '}=[' CoordName ''' VarName ''']']); +% % %eval(['Data.' CoordName{icoord} '=Data.' CoordName{icoord} '(indsel);']); +% % end +% end +% end +% if ~isempty(indexremove) +% MeanData.ListVarName(VarIndex(indexremove))=[]; +% MeanData.VarDimIndex(VarIndex(indexremove))=[]; +% if isfield(MeanData,'Role')%generaliser aus autres attributs +% MeanData.Role(VarIndex(indexremove))=[]; +% end +% end +% % END OF INITIALISATION +% +% end +% +% % A FAIRE: regular grid if coord_x undefined +% if indexfalse~=0 %suppress false data +% eval(['testexist=isfield(Data,''' FFName ''');']) +% if testexist +% eval(['indsel=find(Data.' FFName '==0);']); +% for icoord=1:length(CoordName) +% eval(['Data.' CoordName{icoord} '=Data.' CoordName{icoord} '(indsel);']); +% end +% end +% end +% for ilist=1:length(VarIndexSum) +% VarName=Data.ListVarName{VarIndexSum(ilist)}; +% if indexfalse~=0 & testexist +% eval(['Data.' VarName '=Data.' VarName '(indsel);']); +% end +% if length(CoordName)==0%no variable use dfor unstructured coordinates +% if isempty(DimVarIndex)|isequal(DimVarIndex,0)% no coordinate variable for structured coordinates +% % %update histogram with the current field #ifile +% str_left=['[MeanData.' VarName 'val,MeanData.' VarName 'hist]=']; +% str_right=['hist_update(MeanData.' VarName 'val,MeanData.' VarName 'hist,Data.' VarName ',dC(ilist));']; +% eval([str_left str_right]);%update global histo +% else +% %INTERPOLER +% +% eval(['MeanData.' VarName '=MeanData.' VarName '+Data.' VarName ';']);%increment sum%CAS x,y change +% end +% else +% if length(CoordName)==2 +% eval(['test_interp= ~isequal(Data.' CoordName{1} ',MeanData.' CoordName{1} ... +% ')|~isequal(Data.' CoordName{2} ',MeanData.' CoordName{2} ');']) +% if test_interp +% eval(['Data.' VarName '=griddata_uvmat(Data.' CoordName{1} ',Data.' CoordName{2}... +% ',Data.' VarName ',MeanData.' CoordName{1} ',MeanData.' CoordName{2} ');']); +% test_interpolate=1; +% end +% end +% eval(['MeanData.' VarName '=MeanData.' VarName '+Data.' VarName ';']);%increment sum +% end +% end +% end +% end +% if length(CoordName)~=0 | ~isequal(DimVarIndex,0)% no coordinate variable for structured coordinates +% for ilist=1:length(VarIndexSum) +% VarName=Data.ListVarName{VarIndexSum(ilist)}; +% eval(['MeanData.' VarName '=MeanData.' VarName '/itime;']);%normalize sum by the number of fields +% end +% else +% MeanData.NbDim=1; +% MeanData.ListDimName={}; +% MeanData.DimValue=[]; +% for ilist=1:length(VarIndexSum) +% VarName=Data.ListVarName{VarIndexSum(ilist)}; +% MeanData.ListVarName=[MeanData.ListVarName {[VarName 'val']} {[VarName 'hist']}]; +% MeanData.VarDimIndex=[MeanData.VarDimIndex {[ilist]} {[ilist]}]; +% MeanData.ListDimName=[MeanData.ListDimName {[VarName 'val']}]; +% eval(['MeanData.DimValue=[MeanData.DimValue length(MeanData.' VarName 'val)];']); +% end +% end +% figure +% haxes=axes; +% plot_field(MeanData,haxes)%plot the resulting average +% % change variable names for consitency with civ1 data (need to generalize these programs) +% if length(MeanData.ListVarName) >= 4 & isequal(MeanData.ListVarName(1:4), {'X' 'Y' 'U' 'V'}) +% MeanData.ListGlobalAttribute={'nb_coord','nb_dim','dt','absolut_time_T0','pixcmx','pixcmy','hart','civ','fix'}; +% MeanData.nb_coord=2; +% MeanData.nb_dim=2; +% MeanData.dt=1; +% MeanData.absolut_time_T0=0; +% MeanData.pixcmx=1; %pix per cm (1 by default) +% MeanData.pixcmy=1; %pix per cm (1 by default) +% MeanData.hart=0; +% if isequal(Data.CoordType,'px') +% MeanData.civ=1; +% else +% MeanData.civ=0; +% end +% MeanData.fix=0; +% MeanData.ListVarName(1:4)={'vec_X' 'vec_Y' 'vec_U' 'vec_V'}; +% MeanData.vec_X=MeanData.X; +% MeanData.vec_Y=MeanData.Y; +% MeanData.vec_U=MeanData.U; +% MeanData.vec_V=MeanData.V; +% end +% error=struct2nc(filemean,MeanData); %save result file +% if isequal(error,0) +% if test_interpolate +% 'fields interpolated to the positions of the first one' +% end +% [filemean ' written'] +% else +% warndlg_uvmat(error,'ERROR') +% end +% end + +%---------------------------------------------------------------------- +% --project fields on a projection object (e. g. a regular grid), possibly +% merge several fields +%---------------------------------------------------------------------- +%INPUT: +%num_i1: series of first indices i (given from the series interface as first_i:incr_i:last_i, mode and list_pair_civ) +%num_i2: series of second indices i (given from the series interface as first_i:incr_i:last_i, mode and list_pair_civ) +%num_j1: series of first indices j (given from the series interface as first_j:incr_j:last_j, mode and list_pair_civ ) +%num_j2: series of second indices j (given from the series interface as first_j:incr_j:last_j, mode and list_pair_civ) +%OTHER INPUTS given by the structure Series +function GUI_input=merge_proj(num_i1,num_i2,num_j1,num_j2,Series); + +%requests for the visibility of input windows in the GUI series (activated directly by the selection in the menu ACTION) +if ~exist('num_i1','var') + GUI_input={'RootPath';'two';...%nbre of possible input series (options 'on'/'two'/'many', default:'one') + 'SubDir';'on';... % subdirectory of derived files (PIV fields), ('on' by default) + 'RootFile';'on';... %root input file name ('on' by default) + 'FileExt';'on';... %input file extension ('on' by default) + 'NomType';'on';...%type of file indexing ('on' by default) + 'NbSlice';'on'; ...%nbre of slices ('off' by default) + 'VelTypeMenu';'one';...% menu for selecting the velocity type (civ1,..) options 'off'/'one'/'two', 'off' by default) + 'FieldMenu';'one';...% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default) + 'CoordType';'on';...%can use a transform function 'off' by default + 'GetObject';'on';...%can use projection object ,'off' by default + %'GetMask';'on'...%can use mask option ,'off' by default + %'PARAMETER'; options: name of the user defined parameter',repeat a line for each parameter + ''}; + return %exit the function +end + +%------------------------------------------------- +hseries=guidata(Series.hseries);%handles of the GUI series +WaitbarPos=get(hseries.waitbar_frame,'Position'); %positiopn of waitbar frame +%------------------------------------------------- + +%numbers of view fields (nbre of inputs in RootPath) +testcell=iscell(Series.RootFile); +if ~testcell + Series.RootPath={Series.RootPath}; + Series.RootFile={Series.RootFile}; + Series.SubDir={Series.SubDir}; + Series.FileExt={Series.FileExt}; + Series.NomType={Series.NomType}; + num_i1={num_i1}; + num_i2={num_i2}; + num_j1={num_j1}; + num_j2={num_j2}; +end +nbview=length(Series.RootFile);%number of views (file series to merge) +nbfield=size(num_i1{1},1)*size(num_i1{1},2);%number of fields in the time series +transform=Series.CoordType; % field transform function +hhh=which('mmreader'); +for iview=1:nbview + test_movie(iview)=0; + if ~isequal(hhh,'')&& mmreader.isPlatformSupported() + if isequal(lower(FileExt{iview}),'.avi') + MovieObject{iview}=mmreader(fullfile(RootPath{iview},[RootFile{iview} FileExt{iview}])); + test_movie(iview)=1; + end + end +end + +%Calibration data and timing: read the ImaDoc files +mode=''; %default +timecell={}; +itime=0; +NbSlice_calib={}; %test for z index +for iview=1:nbview%Loop on views + XmlData{iview}=[];%default + filebase{iview}=fullfile(Series.RootPath{iview},Series.RootFile{iview}); + if exist([filebase{iview} '.xml'],'file') + [XmlData{iview},error]=imadoc2struct([filebase{iview} '.xml']); + if isfield(XmlData{iview},'Time') + itime=itime+1; + timecell{itime}=XmlData{iview}.Time; + end + if isfield(XmlData{iview},'GeometryCalib') && isfield(XmlData{iview}.GeometryCalib,'SliceCoord') + NbSlice_calib{iview}=size(XmlData{iview}.GeometryCalib.SliceCoord,1); + if ~isequal(NbSlice_calib{iview},NbSlice_calib{1}) + msgbox_uvmat('WARNING','inconsistent number of Z indices for the two field series'); + end + end + elseif exist([filebase{iview} '.civ'],'file') + [error,time,TimeUnit,mode,npx,npy,pxcmx,pxcmy]=read_imatext([filebase{iview} '.civ']); + itime=itime+1; + timecell{itime}=time; + XmlData{iview}.Time=time; + GeometryCalib.R=[pxcmx 0 0; 0 pxcmy 0;0 0 0]; + GeometryCalib.Tx=0; + GeometryCalib.Ty=0; + GeometryCalib.Tz=1; + GeometryCalib.dpx=1; + GeometryCalib.dpy=1; + GeometryCalib.sx=1; + GeometryCalib.Cx=0; + GeometryCalib.Cy=0; + GeometryCalib.f=1; + GeometryCalib.kappa1=0; + GeometryCalib.CoordUnit='cm'; + XmlData{iview}.GeometryCalib=GeometryCalib; + if error==1 + msgbox_uvmat('WARNING','inconsistent number of fields in the .civ file'); + end + end +end + +%check coincidence in time +multitime=0; +if length(timecell)==0 + time=[]; +elseif length(timecell)==1 + time=timecell{1}; +elseif length(timecell)>1 + multitime=1; + for icell=1:length(timecell) + if ~isequal(size(timecell{icell}),size(timecell{1})) + msgbox_uvmat('WARNING','inconsistent time array dimensions in ImaDoc fields, the time for the first series is used') + time=timecell{1}; + multitime=0; + break + end + end +end +if multitime + for icell=1:length(timecell) + time(icell,:,:)=timecell{icell}; + end + diff_time=max(max(diff(time))); + if diff_time>0 + msgbox_uvmat('WARNING',['times of series differ by more than ' num2str(diff_time)]) + end +end +if size(time,2) < num_i2{1}(end) || size(time,3) < num_j2{1}(end)% ime array absent or too short in ImaDoc xml file' + time=[]; +end + +% Field and velocity type (the same for all views) +Field_str=get(hseries.FieldMenu,'String'); +val=get(hseries.FieldMenu,'Value'); +FieldName=Field_str(val);%the same set of fields for all views +VelType_str=get(hseries.VelTypeMenu,'String'); +VelType_val=get(hseries.VelTypeMenu,'Value'); +VelType=VelType_str{VelType_val}; %the same for all views +if isequal(FieldName,'get_field...') + hget_field=findobj(allchild(0),'Name','get_field');%find the get_field... GUI + hhget_field=guidata(hget_field);%handles of GUI elements in get_field + SubField=get_field('read_var_names',hObject,eventdata,hhget_field); %read the names of the variables to plot in the get_field GUI + if isequal(get(hhget_field.menu_coord,'Visible'),'on') + list_transform=get(hhget_field.menu_coord,'String'); + val_list=get(hhget_field.menu_coord,'Value'); + transform=list_transform{val_list}; + end +end +%detect whether all the files are 'images' or 'netcdf' +testima=0; +testvol=0; +testcivx=0; +testnc=0; +FileExt=get(hseries.FileExt,'String'); +for iview=1:nbview + ext=FileExt{iview}; + form=imformats(ext([2:end])); + if isequal(lower(ext),'.vol') + testvol=testvol+1; + elseif ~isempty(form)||isequal(lower(ext),'.avi')% if the extension corresponds to an image format recognized by Matlab + testima=testima+1; + elseif isequal(ext,'.nc') + testnc=testnc+1; + end +end +if testvol + msgbox_uvmat('ERROR','volume images not implemented yet') + return +end +if testnc~=nbview && testima~=nbview && testvol~=nbview + msgbox_uvmat('ERROR','need a set of images or a set of netcdf files with the same fields as input') + return +end +if ~isequal(FieldName,'get_field...') + testcivx=testnc; +end +%name of output files and directory: +% res_subdir=fullfile(Series.RootPath{1},[Series.SubDir{1} '_STAT']); +ProjectDir=fileparts(fileparts(Series.RootPath{1}));% preoject directory (GERK) +prompt={['result directory (in' ProjectDir ')']}; +RootPath=get(hseries.RootPath,'String'); +SubDir=get(hseries.SubDir,'String'); +if isequal(length(RootPath),1) + fulldir=RootPath{1}; + subdir='GRID'; + res_subdir=fullfile(fulldir,subdir); +else + def={fullfile(ProjectDir,'0_RESULTS')}; + dlgTitle='result directory'; + lineNo=1; + answer=msgbox_uvmat('INPUT_TXT',dlgTitle,def); + fulldir=answer{1}; + subdir=[]; + dirlist=sort(Series.RootFile); + for iview=1:nbview + if ~isempty(subdir) + subdir=[subdir '-']; + end + subdir=[subdir dirlist{iview}]; + end + res_subdir=fullfile(fulldir,subdir); +end +ext=FileExt{1}; +if ~exist(fulldir,'dir') + msgbox_uvmat('ERROR',['directory ' fulldir ' needs to be created']) + return +end +if ~exist(res_subdir,'dir') + dircur=pwd; + cd(fulldir) + error=mkdir(subdir); + cd(dircur) +end +filebasesub=fullfile(res_subdir,Series.RootFile{1}); +filebase_merge=fullfile(res_subdir,'merged');%root name for the merged files + +%projection object +if isfield(Series,'sethandles') + if ishandle(Series.sethandles.set_object) + Series.ProjObject=read_set_object(Series.sethandles); + if ~isfield(Series.ProjObject,'Style') + msgbox_uvmat('ERROR','Undefined projection object style') + return + end + if ~isequal(Series.ProjObject.Style,'plane') + msgbox_uvmat('ERROR','The projection object must be a plane') + return + end + end +end + + %MAIN LOOP +for ifile=1:nbfield + stopstate=get(hseries.RUN,'BusyAction'); + if isequal(stopstate,'queue')% enable STOP command from the 'series' interface + update_waitbar(hseries.waitbar,WaitbarPos,ifile/nbfield) + Amerge=0; + + %----------LOOP ON VIEWS---------------------- + nbtime=0; + for iview=1:nbview + %name of the current file + filename=name_generator(filebase{iview},num_i1{iview}(ifile),num_j1{iview}(ifile),Series.FileExt{iview},Series.NomType{iview},1,num_i2{iview}(ifile),num_j2{iview}(ifile),SubDir{iview}); + if ~exist(filename,'file') + msgbox_uvmat('ERROR',['missing input file' filename]) + break + end + + %reading the current file + if testima + if test_movie(iview) + Field{iview}.A=read(MovieObject{iview},num_i1{iview}(ifile)); + else + Field{iview}.A=read_image(filename,Series.NomType{iview},num_i1{iview}(ifile)); + end % TODO: introduce ListVarName + npxy=size(Field{iview}.A); + Field{iview}.AX=[0.5 npxy(2)-0.5]; % coordinates of the first and last pixel centers + Field{iview}.AY=[npxy(1)-0.5 0.5]; + Field{iview}.CoordType='px'; + Field{iview}.AName='image'; + else + if testcivx + [Field{iview},VelTypeOut]=read_civxdata(filename,FieldName,VelType); + else + [Field{iview},var_detect]=nc2struct(filename,SubField.ListVarName); %read the corresponding input data + Field{iview}.VarAttribute=SubField.VarAttribute; + end + if isfield(Field{iview},'Time') + timeread(iview)=Field{iview}.Time; + nbtime=nbtime+1; + end + end + % coord transform + % z index + if ~isempty(NbSlice_calib) + Field{iview}.ZIndex=mod(num_i1{iview}(ifile)-1,NbSlice_calib{1})+1; + end + if ~isequal(transform,'') + Field{iview}=feval(Series.CoordType,Field{iview},XmlData{iview});%transform to phys if requested + end + if testcivx + Field{iview}=calc_field(FieldName,Field{iview}); + end + + %projection on object (gridded plane) + if isfield(Series,'ProjObject') + Field{iview}=proj_field(Field{iview},Series.ProjObject); + end + end + + %----------END LOOP ON VIEWS---------------------- + + %merge the nbview fields + MergeData=merge_field(Field); + if isfield(MergeData,'Txt') + msgbox_uvmat('ERROR',MergeData.Txt) + return + end + + % generating the name of the merged field + mergename=name_generator(filebase_merge,num_i1{iview}(ifile),num_j1{iview}(ifile),Series.FileExt{iview},Series.NomType{iview},1,num_i2{iview}(ifile),num_j2{iview}(ifile)); + + % time: + time_i=0;%default + if isempty(time)% time from ImaDoc prevails + time_i=sum(timeread)/nbtime; + else + time_i=(time(iview,num_i1{iview}(ifile),num_j1{iview}(ifile))+time(iview,num_i2{iview}(ifile),num_j2{iview}(ifile)))/2; + end + + % recording the merged field + if testima %in case of input images an image is produced + if isa(MergeData.A,'uint8') + bitdepth=8; + elseif isa(MergeData.A,'uint16') + bitdepth=16; + end + imwrite(MergeData.A,mergename,'BitDepth',bitdepth); + %write xml calibration file + siz=size(MergeData.A); + npy=siz(1); + npx=siz(2); + if isfield(MergeData,'VarAttribute')&&isfield(MergeData.VarAttribute{1},'Coord_2')&&isfield(MergeData.VarAttribute{1},'Coord_1') + Rangx=MergeData.VarAttribute{1}.Coord_2; + Rangy=MergeData.VarAttribute{1}.Coord_1; + elseif isfield(MergeData,'AX')&& isfield(MergeData,'AY') + Rangx=[MergeData.AX(1) MergeData.AX(end)]; + Rangy=[MergeData.AY(1) MergeData.AY(end)]; + else + Rangx=[0.5 npx-0.5]; + Rangy=[npy-0.5 0.5];%default + end + pxcmx=(npx-1)/(Rangx(2)-Rangx(1)); + pxcmy=(npy-1)/(Rangy(1)-Rangy(2)); + T_x=-pxcmx*Rangx(1)+0.5; + T_y=-pxcmy*Rangy(2)+0.5; + GeometryCal.focal=1; + GeometryCal.R=[pxcmx,0,0;0,pxcmy,0;0,0,1]; + GeometryCal.Tx_Ty_Tz=[T_x T_y 1]; + ImaDoc.GeometryCalib=GeometryCal; + t=struct2xml(ImaDoc); + t=set(t,1,'name','ImaDoc'); + save(t,[filebase_merge '.xml']) + display([filebase_merge '.xml saved']) + else + MergeData.ListGlobalAttribute={'Project','InputFile_1','InputFile_end','nb_coord','nb_dim','dt','Time','civ'}; + MergeData.nb_coord=2; + MergeData.nb_dim=2; + MergeData.dt=1; + MergeData.Time=time_i; + error=struct2nc(mergename,MergeData); %save result file + if isempty(error) + display(['output file ' mergename ' written']) + else + display(error) + end + end + end +end + +%-------------------------------------------------------------------------- +function MergeData=merge_field(Data) +% initiate Matlab structure for physical field +if isempty(Data)||~iscell(Data) + MergeData=[]; + return +end +MergeData=Data{1};%default +error=0; +nbview=length(Data); +if nbview==1 + return +end +for iview=1:nbview + if ~isequal(MergeData.ListDimName,Data{iview}.ListDimName) + error=1; + end + if ~isequal(MergeData.ListVarName,Data{iview}.ListVarName) + error=1; + end +% if ~isequal(MergeData.VarDimIndex,Data{iview}.VarDimIndex) +% error=1; +% end +end +if error + MergeData.Txt='ERROR: attempt at merging fields of incompatible type'; + return +end +%group the variables (fields of 'FieldData') in cells of variables with the same dimensions +%----------------------------------------------------------------- +[CellVarIndex,NbDim,VarTypeCell]=find_field_indices(Data{1}); +%LOOP ON GROUPS OF VARIABLES SHARING THE SAME DIMENSIONS +% CellVarIndex=cells of variable index arrays +ivar_new=0; % index of the current variable in the projected field +icoord=0; +for icell=1:length(CellVarIndex) + if NbDim(icell)==1 + continue + end + VarIndex=CellVarIndex{icell};% indices of the selected variables in the list FieldData.ListVarName + VarType=VarTypeCell{icell}; + ivar_X=VarType.coord_x; + ivar_Y=VarType.coord_y; + ivar_FF=VarType.errorflag; + if isempty(ivar_X) + test_grid=1;%test for input data on regular grid (e.g. image)coordinates + else + if length(ivar_Y)~=1 + msgbox_uvmat('ERROR','y coordinate missing in proj_field.m') + return + end + test_grid=0; + end + % DimIndices=Data{1}.VarDimIndex{VarIndex(1)};%indices of the dimensions of the first variable (common to all variables in the cell) + %case of input fields with unstructured coordinates + if ~test_grid + for ivar=VarIndex + VarName=MergeData.ListVarName{ivar}; + for iview=1:nbview + eval(['MergeData.' VarName '=[MergeData.' VarName '; Data{iview}.' VarName ';']) + end + end + %case of fields defined on a structured grid + else +% DimValue=MergeData.DimValue(DimIndices);%set of dimension values + testFF=0; + for iview=2:nbview +% if ~isequal(DimValue,Data{iview}.DimValue(DimIndices)) +% MergeData.Txt='ERROR: attempt at merging structured fields with different sizes'; +% return +% end + for ivar=VarIndex + VarName=MergeData.ListVarName{ivar}; + if isfield(MergeData,'VarAttribute') + if length(MergeData.VarAttribute)>=ivar && isfield(MergeData.VarAttribute{ivar},'Role') && isequal(MergeData.VarAttribute{ivar}.Role,'errorflag') + testFF=1; + end + end + eval(['MergeData.' VarName '=MergeData.' VarName '+ Data{iview}.' VarName ';']) + end + end + if testFF + nbaver=nbview-MergeData.FF; + indgood=find(nbaver>0); + for ivar=VarIndex + VarName=MergeData.ListVarName{ivar}; + eval(['MergeData.' VarName '(indgood)=double(MergeData.' VarName '(indgood))./nbaver(indgood);']) + end + else + for ivar=VarIndex + VarName=MergeData.ListVarName{ivar}; + eval(['MergeData.' VarName '=double(MergeData.' VarName ')./nbview;']) + end + end + end +end + + +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + %detect the chosen series of files and check their date of modification: +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% +%INPUT: +%num_i1: series of first indices i (given from the series interface as first_i:incr_i:last_i, mode and list_pair_civ) +%num_i2: series of second indices i (given from the series interface as first_i:incr_i:last_i, mode and list_pair_civ) +%num_j1: series of first indices j (given from the series interface as first_j:incr_j:last_j, mode and list_pair_civ ) +%num_j2: series of second indices j (given from the series interface as first_j:incr_j:last_j, mode and list_pair_civ) +%OTHER INPUTS given by the structure Series +function GUI_input=clean_civ_cmx(num_i1,num_i2,num_j1,num_j2,Series) %(filecell,filecell_1,num_i,num_j,vel_type,field,param); + +%requests for the visibility of input windows in the GUI series (activated directly by the selection in the menu ACTION) +if ~exist('num_i1','var') + GUI_input={'RootPath';'many';...%nbre of possible input series (options 'on'/'two'/'many', default:'one') + 'SubDir';'on';... % subdirectory of derived files (PIV fields), ('on' by default) + %'RootFile';'on';... %root input file name ('on' by default) + %'FileExt';'on';... %input file extension ('on' by default) + %'NomType';'on';...%type of file indexing ('on' by default) + %'NbSlice';'on'; ...%nbre of slices ('off' by default) + %'VelTypeMenu';'one';...% menu for selecting the velocity type (civ1,..) options 'off'/'one'/'two', 'off' by default) + %'FieldMenu';'one';...% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default) + %'CoordType';'on'...%can use a transform function 'off' by default + %'GetObject';'on'...%can use projection object ,'off' by default + %'GetMask';'on'...%can use mask option ,'off' by default + %'PARAMETER'; options: name of the user defined parameter',repeat a line for each parameter + ''}; + return %exit the function +end +%--------------------------------------------------------- +hseries=guidata(Series.hseries);%handles of the GUI series +WaitbarPos=get(hseries.waitbar_frame,'Position'); + +%%%%%%%%%%%%%%%%%%%%%%%% +message='this function will delete all files with extensions .log, .bat, .cmx,.cmx2,.errors in the input directory(ies)'; +answer=msgbox_uvmat('INPUT_Y-N',message); +if ~isequal(answer,'Yes') + return +end +nbdelete=0; +testcell=iscell(Series.RootFile); +if ~testcell + Series.RootPath={Series.RootPath}; + Series.RootFile={Series.RootFile}; + Series.SubDir={Series.SubDir}; + Series.FileExt={Series.FileExt}; + Series.NomType={Series.NomType}; +end +for iview=1:length(Series.RootFile) + hdir=dir(fullfile(Series.RootPath{iview},Series.SubDir{iview}));%list files + for ilist=1:length(hdir) + update_waitbar(hseries.waitbar,WaitbarPos,ilist/length(hdir)) + FileName=hdir(ilist).name; + [dd,ff,Ext]=fileparts(FileName); + if isequal(Ext,'.log')||isequal(Ext,'.bat')||isequal(Ext,'.cmx')||isequal(Ext,'.cmx2')|| isequal(Ext,'.errors') + delete(fullfile(Series.RootPath{iview},Series.SubDir{iview},FileName)) + nbdelete=nbdelete+1; + end + end +end +msgbox_uvmat('CONFIRMATION',['END: ' num2str(nbdelete) ' files deleted by clean_civ_cmx']) + + + + + +%----------------------------- +function mouse_up_gui(ggg,eventdata,handles) +if isequal(get(ggg,'SelectionType'),'alt') + display('global CurData, UserData of GUI series') + global CurData + CurData=get(ggg,'UserData'); + evalin('base','global CurData');%make CurData global in the workspace + evalin('base','CurData'); %display CurData in the workspace + commandwindow + % plot_text(CurData) +end + + + +% %---------------------------------------------------------------------- +% % --- display image movie and display time average +% %OBSOLETE: A SUPPRIMER +% %---------------------------------------------------------------------- +% function movie_ima(handles,filecell,filecell_1,num1,num_a,field) +% +% global hfig1 hfig2 hfig3 poscolbar +% global A val HIST +% +% A=[];aviobj=[]; +% % set(hfig1,'UserData','ima')% set the current field state to 'image' +% set(handles.zoom,'Value',1); %put zoom on +% nom_type=get(handles.file_input,'UserData'); +% % field=get(handles.civ1,'UserData'); +% % fields=field(1).fields; +% set(handles.speed,'Visible','On')%show slider to set movie speed +% set(handles.mo_speed_txt,'Visible','On') +% +% if ~isempty(filecell_1) +% file1=get(handles.file1_input,'UserData'); +% field1=file1.field; +% scal_type1=field1.fields; +% vel_type1=field1.vel_type; +% filename_1=filecell_1(1);% first file name in the series +% else +% filename_1=[]; +% end +% scal_type{1}=field(1).fields; +% vel_type{1}=field(1).vel_type; +% % display the first field +% [A,time,dt,rangx0,rangy0]=view_ima(handles,cell2mat(filecell(1)),filename_1,num1(1),num_a(1)); +% +% % calculate the histogram of the first image +% nxy=size(A); +% ndim=length(nxy); +% if ndim==2 % case of B/W images +% nxy(3)=1; +% end +% C=reshape(A,nxy(1)*nxy(2),nxy(3)); +% Amaxmax=double(max(max(max(A)))); +% Aminmin=double(min(min(min(A)))); +% if isa(C,'uint8')|isa(C,'uint16') +% C=double(C); +% dC=1; +% else +% dC=(Amaxmax-Aminmin)/100; +% end +% val=[Aminmin:dC:Amaxmax];% define bins for histogram +% HIST=hist(C,val);% initiate the global histogram +% if ndim==2, HIST=HIST'; end; +% +% auto_scale=get(handles.auto_scale,'Value'); +% min_input=str2num(get(handles.min_input,'String'));% select the minimum +% max_input=str2num(get(handles.scale_input,'String'));% select the max +% zoomstate=get(handles.zoom,'Value'); +% +% if isequal(get(handles.window_input,'String'),'avi'), +% basename=get(handles.file_input,'String'); +% prompt = {'file name';'frames per second';'frame resolution ([nbpixels x y])';'axis position relative to the frame'}; +% dlg_title = 'select properties of the output avi movie'; +% num_lines= 1; +% def = {[basename '_out.avi'];'5';'[1024 768]';'[0.05 0.07 0.87 0.88]'}; +% answer = inputdlg(prompt,dlg_title,num_lines,def); +% aviname=answer{1}; +% fps=str2num(answer{2}); +% if exist(aviname,'file')==2 +% delete(aviname); +% end; +% aviobj=avifile(aviname,'Compression','None','fps',fps); +% +% %display first view for tests +% figure(2); +% hh=get(gcf,'CurrentAxes'); +% if isempty(hh), +% hfig1=axes; +% else +% hfig1=hh; +% end; +% if isequal(filecell_1,{}) +% filename_1=[]; +% else +% filename_1=cell2mat(filecell_1(1)); +% end +% poscolbar=[0.93 0.15 0.02 0.7]; +% view_ima(handles,cell2mat(filecell(1)),filename_1,num1(1),num_a(1));% show the first field +% nbpix=eval(answer{3}); +% set(gcf,'Position',[1 1 nbpix])% resolution XVGA +% set(hfig1,'Position',eval(answer{4})); +% +% msgbox({'adjust figure 2 with its matlab edit menu ' ;... +% 'then type any keyboard key to get the avi movie as a copy of figure 2 display'}) +% pause; +% hh=colorbar; +% poscolbar=get(hh,'Position'); +% end +% +% %%%%%%%%%%%%%%%% +% %mask and usrdfct +% maskname=[]; %default +% if isequal(get(handles.mask_test,'Value'),1) +% maskbase=get(handles.mask_test,'UserData'); +% end +% % image or scalar processing programme set by user +% % if (get(handles.usr_fct,'Value')==1) +% % usrfct=get(handles.usr_fct,'UserData'); +% % else +% % usrfct=''; +% % end +% nburst=1; % nburst(1) =nbre of names in filename= nbre of bursts +% set(handles.text_display_1,'String',['image movie']) +% nbfield=length(filecell); +% if nbfield >1 +% for ifile=2:nbfield +% stopstate=get(handles.run0,'BusyAction'); +% if isequal(stopstate,'queue')% enable STOP command +% pausetime=1.02-get(handles.speed,'Value'); +% pause(pausetime) +% if isequal(get(handles.mask_test,'Value'),1) +% maskname=name_generator(maskbase,num1(ifile),1,'.png','png_series'); +% end +% if isequal(AName{1},'image') +% A=read_image(cell2mat(filecell(ifile)),num1(ifile),maskname);% read the first image, num2 is the counter for avi files +% else % read the first field from the netcdf file, imposing the pixel positions in the selected domain +% [A,time(ifile),dtr,rgx,rgy,vt_out,erread]=read_scalar(filecell{ifile},vel_type,scal_type,rangx0,rangy0,nxy,maskname); +% if erread==1; +% errordlg({['no spatial derivative in ' filecell{ifile}]; 'run patch first'}); return +% elseif erread==2; +% errordlg(['no field ' vel_type{1} ' in ' filecell{ifile}]); return +% elseif erread==3; +% errordlg(['scalar ' scal_type{1} ' not found in' filecell{ifile}]); return +% elseif erread==4; +% errordlg(['all points aligned in' filecell{ifile}]); return +% end +% end +% +% % read the second image +% if ~isempty(filecell_1) +% if isequal(scal_type{1},'image') +% A1=read_image(cell2mat(filecell_1(ifile)),num1(ifile),maskname);% read the second image, num2 is the counter for avi files +% Avalue_1=double(A1(indy,indx,:)); +% else % read the second field from the netcdf file, imposing the pixel positions in the selected domain +% [Avalue_1,time1(ifile),dtr,rgx,rgy,vt_out,erread]=read_scalar(filecell_1{ifile},{vel_type1},{scal_type1},rangx0,rangy0,npxy,maskname,usrfct); +% if erread==1; +% errordlg({['no spatial derivative in ' filecell_1{ifile}]; 'run patch first'}); return +% elseif erread==2; +% errordlg(['no field ' vel_type1 ' in ' filecell_1{ifile}]); return +% elseif erread==3; +% errordlg(['scalar ' scal_type1 ' not found in' filecell_1{ifile}]); return +% elseif erread==4; +% errordlg(['all points aligned in' filecell_1{ifile}]); return +% end +% end +% time(ifile)=(time(ifile)+time1(ifile))/2; +% Avalue=Avalue-Avalue_1; +% end +% set(handles.abs_time,'String',time); +% set(handles.field_counter,'String',num2str(num1(ifile))); +% set(handles.a_input,'String',num2stra(num_a(ifile),nom_type)); +% C=reshape(A,nxy(1)*nxy(2),nxy(3));% reshape in a vector +% [val,HIST]=hist_update(val,HIST,C,dC); +% [h,Amin,Amax]=plot_image(hfig1,rangx0,rangy0,1,scal_type{1},auto_scale,min_input,max_input,poscolbar,A); +% set(handles.min_input,'String',num2str(Amin));% select the minimum +% set(handles.scale_input,'String',num2str(Amax));% select the minimum +% if ~isequal(aviobj,[]), +% % mov=getframe(hfig1); +% mov=getframe(gcf); +% aviobj=addframe(aviobj,mov);end +% if (get(handles.zoom,'Value') == get(handles.zoom,'Max')),zoom on,end +% set(handles.field_counter,'String',num2str(num1(ifile))) +% % end +% end +% end +% end +% aviobj=close(aviobj); +% +% %plot global image histogram +% HIST=HIST/(nbfield*nxy(1)*nxy(2));% normalized by the number of points +% axes(hfig2) %in main window +% if ndim==2 +% plot(val,HIST) +% else +% plot(val,HIST(:,1),'r',val,HIST(:,2),'g',val,HIST(:,3),'b') +% end +% residu=1-sum(HIST,1); +% title(['histo, residu ' num2str(residu)]) +% grid on +% axes(hfig3) +% cla %clear the second histogram window +% + + +%---------------------------------------------------------------------- +% --- make a time series analysis +%---------------------------------------------------------------------- +%INPUT: +%num_i1: series of first indices i (given from the series interface as first_i:incr_i:last_i, mode and list_pair_civ) +%num_i2: series of second indices i (given from the series interface as first_i:incr_i:last_i, mode and list_pair_civ) +%num_j1: series of first indices j (given from the series interface as first_j:incr_j:last_j, mode and list_pair_civ ) +%num_j2: series of second indices j (given from the series interface as first_j:incr_j:last_j, mode and list_pair_civ) +%OTHER INPUTS given by the structure Series +function GUI_input=time_series(num_i1,num_i2,num_j1,num_j2,Series) + +%requests for the visibility of input windows in the GUI series (activated directly by the selection in the menu ACTION) +if ~exist('num_i1','var') + GUI_input={'RootPath';'two';...%nbre of possible input series (options 'on'/'two'/'many', default:'one') + 'SubDir';'on';... % subdirectory of derived files (PIV fields), ('on' by default) + 'RootFile';'on';... %root input file name ('on' by default) + 'FileExt';'on';... %input file extension ('on' by default) + 'NomType';'on';...%type of file indexing ('on' by default) + 'NbSlice';'on'; ...%nbre of slices ('off' by default) + 'VelTypeMenu';'two';...% menu for selecting the velocity type (civ1,..) options 'off'/'one'/'two', 'off' by default) + 'FieldMenu';'two';...% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default) + 'CoordType';'on';...%can use a transform function 'off' by default + 'GetObject';'on';...%can use projection object ,'off' by default + %'GetMask';'on'...%can use mask option ,'off' by default + %'PARAMETER'; options: name of the user defined parameter',repeat a line for each parameter + ''}; + return %exit the function +end + +%------------------------------------------------------ +hseries=guidata(Series.hseries);%handles in the GUI series +WaitbarPos=get(hseries.waitbar_frame,'Position'); %position of the waitbar frame + +%projection object +test_object=get(hseries.GetObject,'Value'); +if test_object%isfield(Series,'sethandles') + Series.ProjObject=read_set_object(Series.sethandles); + answeryes=questdlg({['field series projected on ' Series.ProjObject.Style]}); + if ~isequal(answeryes,'Yes') + return + end +else + msgbox_uvmat('ERROR','a projection object is needed'); + return +end + +% root names +if iscell(Series.RootPath) + RootPath=Series.RootPath; + RootFile=Series.RootFile; + SubDir=Series.SubDir; + FileExt=Series.FileExt; + NomType=Series.NomType; +else + RootPath={Series.RootPath}; + RootFile={Series.RootFile}; + SubDir={Series.SubDir}; + FileExt={Series.FileExt}; + NomType={Series.NomType}; + num_i1={num_i1}; + num_i2={num_i2}; + num_j1={num_j1}; + num_j2={num_j2}; +end +ext=FileExt{1}; +form=imformats(ext([2:end]));%test valid Matlab image formats +testima=0; +if ~isempty(form)||isequal(lower(ext),'.avi') + testima=1; +end +nbview=length(RootPath);%number of series (1 or 2) +nbfield=size(num_i1{1},1)*size(num_i1{1},2); %number of fields in the time series + +%Number of input series: this function accepts only a single input file series +nbview=length(RootPath); +if nbview>2 + RootPath=RootPath(1:2); + set(hseries.RootPath,'String',RootPath) + SubDir=SubDir(1:2); + set(hseries.SubDir,'String',SubDir) + RootFile=RootFile(1:2); + set(hseries.RootFile,'String',RootFile) + NomType=NomType(1:2); + %set(hseries.NomType,'String',NomType) + FileExt=FileExt(1:2); + set(hseries.FileExt,'String',FileExt) + nbview=2; +end +hhh=which('mmreader'); +for iview=1:nbview + test_movie(iview)=0; + if ~isequal(hhh,'')&& mmreader.isPlatformSupported() + if isequal(lower(FileExt{iview}),'.avi') + MovieObject{iview}=mmreader(fullfile(RootPath{iview},[RootFile{iview} FileExt{iview}])); + test_movie(iview)=1; + end + end +end +filebase{1}=fullfile(RootPath{1},RootFile{1}); +% FileDisplay=fullfile(RootPath{1},SubDir{1},RootFile{1}); + +% number of slices +NbSlice=str2num(get(hseries.NbSlice,'String')); +if isempty(NbSlice) + NbSlice=1; +end +NbSlice_name=num2str(NbSlice); + +% Field and velocity type (the same for the two views) +if isfield(Series,'Field') + FieldName=Series.Field;%the same set of fields for all views +else + FieldName={''}; +end +if isequal(FieldName,{'get_field...'}) + hget_field=findobj(allchild(0),'name','get_field');%find the get_field... GUI + if length(hget_field)>1 + delete(hget_field(2:end)) + elseif isempty(hget_field) + filename=... + name_generator(filebase{1},num_i1{1}(1),num_j1{1}(1),FileExt{1},NomType{1},1,num_i2{1}(1),num_j2{1}(1),SubDir{1}); + idetect(iview)=exist(filename,'file'); + hget_field=get_field(filename); + return + end + hhget_field=guidata(hget_field);%handles of GUI elements in get_field + SubField=read_var_names(hhget_field); %read the names of the variables to plot in the get_field GUI + if isequal(get(hhget_field.menu_coord,'Visible'),'on') + list_transform=get(hhget_field.menu_coord,'String'); + val_list=get(hhget_field.menu_coord,'Value'); + transform=list_transform{val_list}; + end +end + +%detect whether the two files are 'images' or 'netcdf' +testima=0; +testvol=0; +testcivx=0; +testnc=0; +FileExt=get(hseries.FileExt,'String'); +for iview=1:nbview + ext=FileExt{iview}; + form=imformats(ext([2:end])); + if isequal(lower(ext),'.vol') + testvol=testvol+1; + elseif ~isempty(form)||isequal(lower(ext),'.avi')% if the extension corresponds to an image format recognized by Matlab + testima=testima+1; + elseif isequal(ext,'.nc') + testnc=testnc+1; + end +end +if testvol + msgbox_uvmat('ERROR','volume images not implemented yet') + return +end +if testnc~=nbview && testima~=nbview && testvol~=nbview + msgbox_uvmat('need a set of images or a set of netcdf files with the same fields as input','ERROR') + return +end +if ~isequal(FieldName,{'get_field...'}) + testcivx=testnc; +end + +% Root name of output files (TO GENERALISE FOR TWO INPUT SERIES) +filebasesub=fullfile(RootPath{1},RootFile{1}); +if NbSlice==1 + filebase_out=[filebasesub '_time']; +else + filebase_out=[filebasesub '_' NbSlice_name 'mtim']; + increment=num_i1{1}(2)-num_i1{1}(1); + if ~isequal(increment,1) % if an increment is set + answeryes=msgbox_uvmat('INPUT_Y-N',['will take time series in ' num2str(NbSlice) 'slices with increment = ' num2str(increment) '!']) + else + answeryes=msgbox_uvmat('INPUT_Y-N',{['will take time series in ' num2str(NbSlice) ' slices'];['results stored as files ' filebase_out ' ...']}); + end + if ~isequal(answeryes,'Yes') + return + end +end +VelType_str=get(hseries.VelTypeMenu,'String'); +VelType_val=get(hseries.VelTypeMenu,'Value'); +VelType{1}=VelType_str{VelType_val}; +if nbview==2 + VelType_str=get(hseries.VelTypeMenu_1,'String'); + VelType_val=get(hseries.VelTypeMenu_1,'Value'); + VelType{2}=VelType_str{VelType_val}; +end + +%Calibration data and timing: read the ImaDoc files +mode=''; %default +timecell={}; +XmlData={}; +itime=0; +NbSlice_calib={}; +for iview=1:nbview%Loop on views + XmlData{iview}=[];%default + filebase{iview}=fullfile(RootPath{iview},RootFile{iview}); + if exist([filebase{iview} '.xml'],'file') + [XmlData{iview},error]=imadoc2struct([filebase{iview} '.xml']); + if isfield(XmlData{iview},'Time') + itime=itime+1; + timecell{itime}=XmlData{iview}.Time; + end + if isfield(XmlData{iview},'GeometryCalib') && isfield(XmlData{iview}.GeometryCalib,'SliceCoord') + NbSlice_calib{iview}=size(XmlData{iview}.GeometryCalib.SliceCoord,1);%nbre of slices for Zindex in phys transform + if ~isequal(NbSlice_calib{iview},NbSlice_calib{1}) + msgbox_uvmat('WARNING','inconsistent number of Z indices for the field series'); + end + end + elseif exist([filebase{iview} '.civ'],'file') + [error,time,TimeUnit,mode,npx,npy,pxcmx,pxcmy]=read_imatext([filebase{iview} '.civ']); + itime=itime+1; + timecell{itime}=time; + XmlData{iview}.Time=time; + GeometryCalib.R=[pxcmx 0 0; 0 pxcmy 0;0 0 0]; + GeometryCalib.Tx=0; + GeometryCalib.Ty=0; + GeometryCalib.Tz=1; + GeometryCalib.dpx=1; + GeometryCalib.dpy=1; + GeometryCalib.sx=1; + GeometryCalib.Cx=0; + GeometryCalib.Cy=0; + GeometryCalib.f=1; + GeometryCalib.kappa1=0; + GeometryCalib.CoordUnit='cm'; + XmlData{iview}.GeometryCalib=GeometryCalib; + if error==1 + msgbox_uvmat('WARNING','inconsistent number of fields in the .civ file'); + end + end +end + +%check coincidence in time +multitime=0; +if length(timecell)==0 + time=[]; +elseif length(timecell)==1 + time=timecell{1}; +elseif length(timecell)>1 + multitime=1; + for icell=1:length(timecell) + if ~isequal(size(timecell{icell}),size(timecell{1})) + warndlg_uvmat('inconsistent time array dimensions in ImaDoc fields, the time for the first series is used','WARNING') + time=timecell{1}; + multitime=0; + break + end + end +end +if multitime + for icell=1:length(timecell) + time(icell,:,:)=timecell{icell}; + end + diff_time=max(max(diff(time))); + if diff_time>0 + warndlg_uvmat(['times of series differ by more than ' num2str(diff_time)],'WARNING') + end +end +if size(time,2) < num_i2{1}(end) || size(time,3) < num_j2{1}(end)% ime array absent or too short in ImaDoc xml file' + time=[]; +end + +% image or scalar processing programme set by user +Coord_menu=get(hseries.CoordType,'String'); +menu_val=get(hseries.CoordType,'Value'); +usrfct=Coord_menu{menu_val}; +testfct=~isequal(usrfct,''); + +% to update: +VelType_str=get(hseries.VelTypeMenu,'String'); +VelType_val=get(hseries.VelTypeMenu,'Value'); +VelType{1}=VelType_str{VelType_val}; +if nbview==2 + VelType_str=get(hseries.VelTypeMenu_1,'String'); + VelType_val=get(hseries.VelTypeMenu_1,'Value'); + VelType{2}=VelType_str{VelType_val}; +end + +%LOOP ON SLICES +for i_slice=1:NbSlice + dt=[]; + nbmissing=0; %number of undetected files + nbfiles=0; + %%%%%%%%%%%%%%%%%%%%%%%%%%%%LOOP ON FIELDS IN A SLICE + for ifile=i_slice:NbSlice:nbfield + stopstate=get(hseries.RUN,'BusyAction'); + if isequal(stopstate,'queue')% enable STOP command + update_waitbar(hseries.waitbar,WaitbarPos,ifile/nbfield) + for iview=1:nbview + filename=... + name_generator(filebase{iview},num_i1{iview}(ifile),num_j1{iview}(ifile),FileExt{iview},NomType{iview},1,num_i2{iview}(ifile),num_j2{iview}(ifile),SubDir{iview}); + idetect(iview)=exist(filename,'file'); + Data{iview}=[]; %default + if testima + Data{iview}.ListVarName={'A'}; + Data{iview}.AName='image'; + if test_movie(iview) + A=read(MovieObject{iview},num_i1{iview}(ifile)); + else + A=double(read_image(filename,NomType{iview},num_i1{iview}(ifile)));% read the image, num2 is the counter for avi files + end + Data{iview}.ListVarName={'coord_y','coord_x','A'}; % + npy=size(A,1); + npx=size(A,2); + nbcolor=size(A,3); + if nbcolor==3 +% Data{iview}.ListDimName={'coord_y','coord_x','rgb'}; +% Data{iview}.DimValue=[npy npx 3]; +% Data{iview}.VarDimIndex={[1 2 3]}; + Data{iview}.VarDimName={'coord_y','coord_x',{'coord_y','coord_x','rgb'}}; + else +% Data{iview}.ListDimName={'coord_y','coord_x'}; +% Data{iview}.DimValue=[npy npx]; +% Data{iview}.VarDimIndex={[1 2]}; +% Data{iview}.VarAttribute{1}.Coord_1=[npy-0.5 0.5]; +% Data{iview}.VarAttribute{1}.Coord_2=[0.5 npx-0.5]; + Data{iview}.VarDimName={'coord_y','coord_x',{'coord_y','coord_x'}}; + end + Data{iview}.coord_y=[npy-0.5 0.5]; + Data{iview}.coord_x=[0.5 npx-0.5]; + Data{iview}.A=A; + Data{iview}.CoordType='px'; + elseif testcivx + [Data{iview},VelTypeOut]=read_civxdata(filename,FieldName,VelType); + else + [Data{iview},var_detect]=nc2struct(filename,SubField.ListVarName); %read the corresponding input data + Data{iview}.VarAttribute=SubField.VarAttribute; + end + if ~isempty(NbSlice_calib) % z index + Data{iview}.ZIndex=mod(num_i1{iview}(ifile)-1,NbSlice_calib{1})+1; + end + end + % geometry transform or other user defined transform + if ~isequal(Series.CoordType,'') + if nbview==2 + [Data{1},Data{2}]=feval(Series.CoordType,Data{1},XmlData{1},Data{2},XmlData{2}); + if isempty(Data{2}) + Data(2)=[]; + end + else + Data{1}=feval(Series.CoordType,Data{1},XmlData{1}); + end + end + if testcivx + Data{iview}=calc_field(FieldName,Data{iview});%calculate field (vort..) + end + if length(Data)==2 + [Field,errormsg]=sub_field(Data{1},Data{2}); %substract the two fields + if ~isempty(errormsg) + msgbox_uvmat('ERROR',['error in time_series/sub_field:' errormsg]) + return + end + else + Field=Data{1}; + end + if isfield(Series,'ProjObject') + [Field,errormsg]=proj_field(Field,Series.ProjObject); + if ~isempty(errormsg) + msgbox_uvmat('ERROR',['error in time_series/proj_field:' errormsg]) + return + end + end + if min(idetect)>=1% the input file(s) have been detected + nbfiles=nbfiles+1; + if nbfiles==1 %first field: initiate the time series + RecordData=Field;%default + RecordData.NbDim=Field.NbDim+1; %add the time dimension for plots + nbvar=length(Field.ListVarName); + if nbvar==0 + msgbox_uvmat('ERROR','no input variable selected in get_field') + return + end + testsum=2*ones(1,nbvar);%initiate flag for action on each variable + indexfalse=0; + CoordName={}; + indexremove=[]; + if isfield(Field,'VarAttribute') % look for coordinate and flag variables + for ivar=1:nbvar + if length(Field.VarAttribute)>=ivar && isfield(Field.VarAttribute{ivar},'Role') + var_role=Field.VarAttribute{ivar}.Role;%'role' of the variable + if isequal(var_role,'errorflag') + msgbox_uvmat('ERROR','do not handle error flags in time series') + return + end + if isequal(var_role,'warnflag') + testsum(ivar)=0; % not recorded variable + eval(['RecordData=rmfield(RecordData,''' Field.ListVarName{ivar} ''');']);%remove variable + end + if isequal(var_role,'coord_x')| isequal(var_role,'coord_y')|... + isequal(var_role,'coord_z')|isequal(var_role,'coord') + testsum(ivar)=1; %constant coordinates, record without time evolution + end + % check whether the variable ivar is a dimension variable + %index=Field.VarDimIndex{ivar};%dimension indices of the variable #ivar + DimCell=Field.VarDimName{ivar}; + if ischar(DimCell) + DimCell={DimCell}; + end + if numel(DimCell)==1 && isequal(Field.ListVarName{ivar},DimCell)%TODO generalise with attribute + % if length(Field.ListDimName)>=index & isequal(Field.ListVarName{ivar},Field.ListDimName{index})%detect dimension variables + testsum(ivar)=1; + end + end + end + end + for ivar=1:nbvar + if testsum(ivar)==2 + eval(['RecordData.' Field.ListVarName{ivar} '=[];']) + end + end + % RecordData.ListDimName=[{'Time'} RecordData.ListDimName];%name of dimension + RecordData.ListVarName=[{'Time'} RecordData.ListVarName]; + end + for ivar=1:length(Field.ListVarName) + VarName=Field.ListVarName{ivar}; + eval(['VarVal=Field.' VarName ';']); + if testsum(ivar)==2% test for recorded variable + eval(['VarVal=Field.' VarName ';']); + if isequal(Series.ProjObject.ProjMode,'inside')% take the average in the domain for 'inside' mode + if isempty(VarVal) + msgbox_uvmat('ERROR',['empty result at frame index ' num2str(num_i1{iview}(ifile))]) + return + end + VarVal=mean(VarVal,1); + end + VarVal=shiftdim(VarVal,-1); %shift dimension + eval(['RecordData.' VarName '=cat(1,RecordData.' VarName ',VarVal);']);%concanete the current field to the time series + elseif testsum(ivar)==1% variable representing fixed coordinates + eval(['VarInit=RecordData.' VarName ';']); + if ~isequal(VarVal,VarInit) + msgbox_uvmat('ERROR',['time series requires constant coordinates ' VarName]) + return + end + end + end + % time: + if isempty(time)% time read in ncfiles + if isfield(Field,'Time') + RecordData.Time(nbfiles,1)=Field.Time; + else + RecordData.Time(nbfiles,1)=nbfiles;%default + end + else % time from ImaDoc prevails + RecordData.Time(nbfiles,1)=(time(1,num_i1{1}(ifile),num_j1{1}(ifile))+time(end,num_i2{end}(ifile),num_j2{end}(ifile)))/2; + end + else + nbmissing=nbmissing+1; + end + end + end + %remove time for global attributes if exists + for iattr=1:numel(RecordData.ListGlobalAttribute) + if strcmp(RecordData.ListGlobalAttribute{iattr},'Time') + RecordData.ListGlobalAttribute(iattr)=[]; + break + end + end + for ivar=1:numel(RecordData.ListVarName) + VarName=RecordData.ListVarName{ivar}; + eval(['RecordData.' VarName '=squeeze(RecordData.' VarName ');']) %remove singletons + end + % add time dimension and update VarDimIndex: + %if ~isequal(Series.ProjObject.ProjMode,'inside')% take the average in the domain for 'inside' mode + for ivar=1:length(Field.ListVarName) +% vardimindex=Field.VarDimIndex{ivar};% array of dimension indices for variable VarIndex(ivar) + DimCell=Field.VarDimName(ivar); + if testsum(ivar)==2%variable used as time series +% RecordData.VarDimIndex{ivar}=[1 vardimindex+1]; + RecordData.VarDimName{ivar}=[{'Time'} DimCell]; + elseif testsum(ivar)==1 +% RecordData.VarDimIndex{ivar}=[vardimindex+1]; + RecordData.VarDimName{ivar}=DimCell; + end + end + % end + indexremove=find(~testsum); + if ~isempty(indexremove) + RecordData.ListVarName(1+indexremove)=[]; + RecordData.VarDimName(indexremove)=[]; + if isfield(RecordData,'Role')&~isempty(RecordData.Role{1})%generaliser aus autres attributs + RecordData.Role(1+indexremove)=[]; + end + end + %RecordData.VarDimIndex=[{[1]} RecordData.VarDimIndex]; %time dimension + %shift variable attributes + if isfield(RecordData,'VarAttribute') + RecordData.VarAttribute=[{[]} RecordData.VarAttribute]; + end + RecordData.VarDimName=[{'Time'} RecordData.VarDimName]; + RecordData.Action=Series.Action;%name of the processing programme + %name of result file + [filemean]=... + name_generator(filebase_out,num_i1{1}(i_slice),num_j1{1}(i_slice),'.nc','_i1-i2_j1-j2',1,num_i2{end}(ifile),num_j2{end}(ifile),SubDir{1}); + RecordData + RecordData.VarDimName{1} + RecordData.VarDimName{2} + RecordData.VarDimName{3} + errormsg=struct2nc(filemean,RecordData); %save result file + if isempty(errormsg) + display([filemean ' written']) + else + msgbox_uvmat('ERROR',['error in Series/struct2nc' errormsg]) + end +end +figure +haxes=axes; + +plot_field(RecordData,haxes) +hget_field=findobj(allchild(0),'name','get_field'); +if ~isempty(hget_field) + delete(hget_field) +end +get_field(filemean,RecordData) + +%----------------------------------------------------------------------- +% --- Executes on selection change in CoordType. +function CoordType_Callback(hObject, eventdata, handles) +menu_str=get(handles.CoordType,'String'); +ind_coord=get(handles.CoordType,'Value'); +coord_option=menu_str{ind_coord}; +if isequal(coord_option,'more...'); + fct_name=''; + if exist('./TMP/current_usr_fct.mat','file')% if a file is found + h=load('./TMP/current_usr_fct.mat'); + if isfield(h,'fct_name'); + fct_name=h.fct_name; + end + end + prompt = {'Enter the name of the transform function'}; + dlg_title = 'user defined transform'; + num_lines= 1; + [FileName, PathName, filterindex] = uigetfile( ... + {'*.m', ' (*.m)'; + '*.m', '.m files '; ... + '*.*', 'All Files (*.*)'}, ... + 'Pick a file', fct_name); + fct_name=fullfile(PathName,FileName); + addpath(PathName);%add the path to the selected fct + [errormsg,date_str]=check_functions;%check whether new functions can oversed the uvmat package A UTILISER + if ~exist(fct_name,'file') + warndlg(['image procesing fct ' fct_name ' not found']) + else + transform=FileName(1:end-2);% + update_menu(handles.CoordType,transform)%add the selected fct to the menu + % set(handles.mouse_coord,'String',menu([1:end-1])')%update the mouse coord menu + %save ('./TMP/current_usr_fct.mat','fct_name'); + end +end +ind_coord=get(handles.CoordType,'Value'); + +%--------------------------------------------------------------------- +% --- Executes on selection change in ProjObject. +function ProjObject_Callback(hObject, eventdata, handles) + +list_object=get(handles.ProjObject,'String'); +index=get(handles.ProjObject,'Value'); +hseries=get(handles.ProjObject,'Parent'); +SeriesData=get(hseries,'UserData'); +Obj=SeriesData.ProjObject{index}; +[SeriesData.hset_object,SeriesData.sethandles]=set_object(SeriesData.ProjObject{index}); +set(hseries,'UserData',SeriesData); + +%------------------------------------------------------------- +%generates a series of file names with reference numbers between range1 and +%range2 with increment incr. The reference number num_ref is the image number at the middle of the +%image pair. The set of first numbers num1 of the image pairs is also +%given as output +%------------------------------------------------------ +function [num_i1,num_i2,num_j1,num_j2,nbmissing]=netseries_generator(filebase,subdir,mode,first_i,incr_i,last_i,first_j,incr_j,last_j) +[Path,Name]=fileparts(filebase); +filebasesub=fullfile(Path,subdir,Name); +filecell={};%default +num_i1=[]; +num_i2=[]; +num_j1=[]; +num_j2=[]; +ind0_i=first_i:incr_i:last_i; +nbcolumn=length(ind0_i); +ind0_j=first_j:incr_j:last_j; +nbline=length(ind0_j); +if isequal(mode,'#_ab') + dirpair=dir([filebasesub '*_*.nc']); +elseif isequal(mode,'bursts')|isequal(mode,'series(Dj)') + dirpair=dir([filebasesub '_*_*-*.nc']); +elseif isequal(mode,'series(Di)') + dirpair=dir([filebasesub '_*-*_*.nc']); +else + errordlg('option *|* not yet implemented') + return +end +if isempty(dirpair) + errordlg('no pair detected in the selected range') + return +end + %ind0_i=first_i:incr_i:last_i; + %nbcolumn=length(ind0_i); + %dirpair=dir([filebasesub '_*_*-*.nc']); +if isequal(mode,'bursts')|isequal(mode,'#_ab') + icount=0; + for ifile=1:length(dirpair) + [RootPath,RootFile,str_1,str_2,str_a,str_b,ext,nom_type]=name2display(dirpair(ifile).name); + +% if isempty(str2num(str_1)) +% dirpair(ifile).name +% end + num1_r=str2num(str_1); + if isequal(RootFile,Name) & ~isempty(num1_r) + num_i1(ifile)=num1_r; + num_a(ifile)=stra2num(str_a); + num_b(ifile)=stra2num(str_b); +% icount=icount+1; + end + end + length(dirpair) +% num_j=floor((num_a+num_b)/2); %list of reference indices of the detected files + test_range= (num_i1 >=first_i)&(num_i1<= last_i);% =1 when both numbers are in the range + ind_i=((num_i1-first_i)/incr_i)+1;%indices i in the list of prescribed file indices + select=find(test_range &(floor(ind_i)==ind_i));%selected indices of num_i1 in the file directory + ind_i=ind_i(select);%set of selected indices ind_i + [ind_i,indsort]=sort(ind_i);%sorted list of ind_i + select=select(indsort); + num_i1=num_i1(select); + num_a=num_a(select); + num_b=num_b(select); + dirpair=dirpair(select); + [ind_remove]=find_pairs(dirpair,ind_i,nbcolumn); + ind_i(ind_remove)=[]; + num_a(ind_remove)=[]; + num_b(ind_remove)=[]; + num_j1=zeros(1,nbcolumn);%default + num_j2=num_j1; + num_j1(ind_i)=num_a; + num_j2(ind_i)=num_b; + num_i1=first_i:incr_i:last_i; + num_i2=num_i1; + nbmissing=nbcolumn-length(ind_i); + +elseif isequal(mode,'series(Di)') + %ind0_i=first_i:incr_i:last_i; + %nbcolumn=length(ind0_i); + %ind0_j=first_j:incr_j:last_j; + %nbline=length(ind0_j); + %dirpair=dir([filebasesub '_*-*_*.nc']); + for ifile=1:length(dirpair) + [RootPath,RootFile,str_1,str_2,str_a,str_b,ext,nom_type]=name2display(dirpair(ifile).name); + num_i1_r(ifile)=str2num(str_1); + num_i2_r(ifile)=str2num(str_2); + num_j(ifile)=str2num(str_a); + end + num_i=floor((num_i1_r+num_i2_r)/2); %list of reference indices of the detected files + test_range= (num_i >=first_i)&(num_i<= last_i)&(num_j >=first_j)&(num_j<= last_j);% =1 when both numbers are in the range + ind_i=((num_i-first_i)/incr_i)+1;%indices i and j in the list of prescribed file indices + ind_j=((num_j-first_j)/incr_j)+1; + ind_ij=ind_j+nbline*(ind_i-1);%indices in the reshhaped series of prescribed file indices + select=find(test_range &(floor(ind_i)==ind_i)&(floor(ind_j)==ind_j));%selected indices in the file directory + ind_ij=ind_ij(select);%set of selected indices ind_ij + [ind_ij,indsort]=sort(ind_ij);%sorted list of ind_ij + select=select(indsort); + num_i1_r=num_i1_r(select); + num_i2_r=num_i2_r(select); +% num_j=num_j(select); + dirpair=dirpair(select); + [ind_remove]=find_pairs(dirpair,ind_ij,nbcolumn*nbline) ; + ind_ij(ind_remove)=[]; + num_i1_r(ind_remove)=[]; + num_i2_r(ind_remove)=[]; + num_i1=zeros(1,nbline*nbcolumn);%default + num_i2=num_i1; + num_i1(ind_ij)=num_i1_r; + num_j2(ind_ij)=num_i2_r; + num_i1=reshape(num_i1,nbline,nbcolumn); + num_i2=reshape(num_i2,nbline,nbcolumn); + num_j1=meshgrid(ind0_i,ind0_j); + num_j2=num_j1; + nbmissing=nbline*nbcolumn-length(ind_ij); +elseif isequal(mode,'series(Dj)') + % ind0_i=first_i:incr_i:last_i; + % nbcolumn=length(ind0_i); + % ind0_j=first_j:incr_j:last_j; + % nbline=length(ind0_j); + % dirpair=dir([filebasesub '_*_*-*.nc']); + for ifile=1:length(dirpair) + [RootPath,RootFile,str_1,str_2,str_a,str_b,ext,nom_type]=name2display(dirpair(ifile).name); + num_i(ifile)=str2num(str_1); + num_a(ifile)=str2num(str_a); + num_b(ifile)=str2num(str_b); + end + num_j=floor((num_a+num_b)/2); %list of reference indices of the detected files + test_range= (num_i >=first_i)&(num_i<= last_i)&(num_j >=first_j)&(num_j<= last_j);% =1 when both numbers are in the range + ind_i=((num_i-first_i)/incr_i)+1;%indices i and j in the list of prescribed file indices + ind_j=((num_j-first_j)/incr_j)+1; + ind_ij=ind_j+nbline*(ind_i-1);%indices in the reshhaped series of prescribed file indices + select=find(test_range &(floor(ind_i)==ind_i)&(floor(ind_j)==ind_j));%selected indices in the file directory + ind_ij=ind_ij(select);%set of selected indices ind_ij + [ind_ij,indsort]=sort(ind_ij);%sorted list of ind_ij + select=select(indsort); + num_i=num_i(select); + num_a=num_a(select); + num_b=num_b(select); + dirpair=dirpair(select); + [ind_remove]=find_pairs(dirpair,ind_ij,nbcolumn*nbline) ; + ind_ij(ind_remove)=[]; + num_a(ind_remove)=[]; + num_b(ind_remove)=[]; + num_j1=zeros(1,nbline*nbcolumn);%default + num_j2=num_j1; + num_j1(ind_ij)=num_a; + num_j2(ind_ij)=num_b; + num_j1=reshape(num_j1,nbline,nbcolumn); + num_j2=reshape(num_j2,nbline,nbcolumn); + num_i1=meshgrid(ind0_i,ind0_j); + num_i2=num_i1; + nbmissing=nbline*nbcolumn-length(ind_ij); +% for i=1:length(indsel);%A SUPPRIMER ULTERIEUREMENT +% if indsel(i)==0 +% filecell{i}=''; +% else +% Name=dirpair(indsel(i)).name; +% filecell{i}=fullfile(Path,subdir,Name); +% end +% end +%else +% errordlg('option *|* not yet implemented') +% return +end + +%%%%%%%%%%%%% +function [ind_remove]=find_pairs(dirpair,ind_i,last_i) + + indsel=ind_i; + indiff=diff(ind_i); %test index increment to detect multiplets (several pairs with the same index ind_i) and holes in the series + indiff=[1 indiff last_i-ind_i(end)+1];%for testing gaps with the imposed bounds + if ~isempty(indiff) + indiff2=diff(indiff); + indiffp=[indiff2 1]; + indiffm=[1 indiff2]; + ind_multi_m=find((indiff==0)&(indiffm<0))-1;%indices of first members of multiplets + ind_multi_p=find((indiff==0)&(indiffp>0));%indices of last members of multiplets + %for each multiplet, select the most recent file + ind_remove=[]; + for i=1:length(ind_multi_m) + ind_pairs=ind_multi_m(i):ind_multi_p(i); + for imulti=1:length(ind_pairs) + datepair(imulti)=datenum(dirpair(ind_pairs(imulti)).date);%dates of creation + end + [datenew,indsort2]=sort(datepair); %sort the multiplet by creation date + ind_s=indsort2(1:end-1);% + ind_remove=[ind_remove ind_pairs(ind_s)];%remove these indices, leave the last one + end + end + +%-------------------------------------------------------- + + +%----------------------------------------------------------- +% find the times corresponding to the first and last indices of a series +% +function displ_time(handles,times) +hseries=get(handles.last_i,'parent'); +SeriesData=get(hseries,'UserData');% +first_i=str2num(get(handles.first_i,'String')); +first_j=str2num(get(handles.first_j,'String')); +last_i=str2num(get(handles.last_i,'String')); +last_j=str2num(get(handles.last_j,'String')); +% index_civ=get(handles.list_pair_civ,'Value'); +% NomType=get(handles.NomType,'String'); +NomType=SeriesData.NomType; +mode_list=get(handles.mode,'String'); +index_mode=get(handles.mode,'Value'); +mode=mode_list{index_mode}; +% ind_shift=0;%default + +time_first=[]; +time_last=[]; +if ~isfield(SeriesData,'Time') + SeriesData.Time{1}=[]; +end +for iview=1:length(NomType) + time_first_cell{iview}='?'; + time_last_cell{iview}='?';%default + time=SeriesData.Time{iview}; + if isequal(NomType{iview},'_i1-i2_j')|isequal(NomType{iview},'_i_j1-j2')|isequal(NomType{iview},'#_ab')|isequal(NomType{iview},'_i1-i2') + if isfield(SeriesData,'displ_num')& ~isempty(SeriesData.displ_num) + ind_shift=SeriesData.displ_num(iview,:); + if isequal(mode,'bursts') + first_j=0; + last_j=0; + end + first_i1=first_i +ind_shift(3); + first_i2 =first_i +ind_shift(4); + first_j1 =first_j +ind_shift(1); + first_j2 =first_j +ind_shift(2); + last_i1=last_i +ind_shift(3); + last_i2 =last_i +ind_shift(4); + last_j1 =last_j +ind_shift(1); + last_j2 =last_j +ind_shift(2); + siz=size(SeriesData.Time{1}); + if siz(1)>=last_i2 & siz(2)>=last_j2 + time_first=(time(first_i1,first_j1)+time(first_i2,first_j2))/2; + time_last=(time(last_i1,last_j1)+time(last_i2,last_j2))/2; + else%read the time in the nc files + RootPath=get(handles.RootPath,'String'); + RootFile=get(handles.RootFile,'String'); + SubDir=get(handles.SubDir,'String'); + %VelType=get(handles.VelType,'String'); + VelType_str=get(handles.VelTypeMenu,'String'); + VelType_val=get(handles.VelTypeMenu,'Value'); + VelType=VelType_str{VelType_val}; + filebase=fullfile(RootPath{1},RootFile{1}); + [filefirst]=name_generator(filebase,first_i1,first_j1,'.nc',NomType{iview},1,first_i2,first_j2,SubDir{iview}); + if exist(filefirst,'file') + Attrib=nc2struct(filefirst,[]); + if isfield(Attrib,'Time') + time_first=Attrib.Time; + else + if isfield(Attrib,'absolut_time_T0') + time_first=Attrib.absolut_time_T0; + end + if isfield(Attrib,'absolut_time_T0_2')&~(isequal(VelType,'civ1')|isequal(VelType,'interp1')|isequal(VelType,'filter1')) + time_first=Attrib.absolut_time_T0_2; + end + end + end + [filelast]=name_generator(filebase,last_i1,last_j1,'.nc',NomType{iview},1,last_i2,last_j2,SubDir{iview}); + if exist(filelast,'file') + Attrib=nc2struct(filelast,[]); + if isfield(Attrib,'Time') + time_last=Attrib.Time; + else + if isfield(Attrib,'absolut_time_T0') + time_last=Attrib.absolut_time_T0; + end + if isfield(Attrib,'absolut_time_T0_2')&~(isequal(VelType,'civ1')|isequal(VelType,'interp1')|isequal(VelType,'filter1')) + time_last=Attrib.absolut_time_T0_2; + end + end + end + end + end + else + siz=size(times); + if siz(1)>=last_i & siz(2)>=last_j + time_first=times(first_i,first_j); + time_last=times(last_i,last_j); + end + end + time_first_cell{iview}=num2str(time_first,4); + time_last_cell{iview}=num2str(time_last,4); +end +set(handles.time_first,'Value',1) +set(handles.time_last,'Value',1) +set(handles.time_first,'String',time_first_cell); +set(handles.time_last,'String',time_last_cell); + +%-------------------------------------------------------------------- +% --- Executes on selection change in VelTypeMenu. +function VelTypeMenu_Callback(hObject, eventdata, handles) +% VelTypeList=get(handles.VelTypeMenu,'String'); +% VelTypeIndex=get(handles.VelTypeMenu,'Value'); +% VelTypeCell=get(handles.VelType,'String'); +% VelTypeCell{1}=VelTypeList{VelTypeIndex}; +% set(handles.VelType,'String',VelTypeCell) + + +%-------------------------------------------------------------------- +% --- Executes on button press in GetObject. +function GetObject_Callback(hObject, eventdata, handles) +hseries=get(handles.GetObject,'parent'); +SeriesData=get(hseries,'UserData'); +value=get(handles.GetObject,'Value'); +if value + set(handles.GetObject,'BackgroundColor',[1 1 0])%put unactivated buttons to yellow + DataInit.ParentButton=handles.GetObject; + hset_object=findobj(allchild(0),'Name','set_object');%find the set_object interface handle + if ishandle(hset_object) + [SeriesData.hset_object,SeriesData.sethandles]=set_object(DataInit); %open the set_object interface + else + DataInit.TITLE='POINTS';%default option + [SeriesData.hset_object,SeriesData.sethandles]=set_object(DataInit); %open the set_object interface + end +else + set(handles.GetObject,'BackgroundColor',[0 1 0])%put activated buttons to green + if isfield(SeriesData,'hset_object')&& ishandle(SeriesData.hset_object) + close(SeriesData.hset_object) + end +end +set(hseries,'UserData',SeriesData) + +%-------------------------------------------------------------- +function GetMask_Callback(hObject, eventdata, handles) +value=get(handles.GetMask,'Value'); +if value + errordlg('not implemented yet') +end +%-------------------------------------------------------------- + +%-------------------------------------------------------------------------- +%'uv_ncbrowser': interactively calls the netcdf file browser 'get_field.m' +function ncbrowser_uvmat(hObject, eventdata) + bla=get(gcbo,'String'); + ind=get(gcbo,'Value'); + filename=cell2mat(bla(ind)); + blank=find(filename==' '); + filename=filename(1:blank-1); + get_field(filename) + + + +% -------------------------------------------------------------------- +function MenuHelp_Callback(hObject, eventdata, handles) + +path_to_uvmat=which ('uvmat');% check the path of uvmat +pathelp=fileparts(path_to_uvmat); +helpfile=fullfile(pathelp,'UVMAT_DOC','uvmat_doc.html'); +if isempty(dir(helpfile)), errordlg('Please put the help file uvmat_doc.html in the directory UVMAT/UVMAT_DOC') +else +web([helpfile '#series']) +end + + + + + + Index: /trunk/src/set_col_vec.m =================================================================== --- /trunk/src/set_col_vec.m (revision 2) +++ /trunk/src/set_col_vec.m (revision 2) @@ -0,0 +1,89 @@ +%'set_col_vec': sets the color code for vectors depending on a scalar vec_C and parameters given by the struct colcode +%function [colorlist,col_vec,minC,colcode1,colcode2,maxC]=colvec(colcode,vec_C) +%OUTPUT +%colorlist(nb,3); %list of nb colors +%col_vec, size=[length(vec_C),3)];%list of color indices corresponding to vec_C +%minC, maxC: min and max of vec_C +%colcode1, colcode2: absolute threshold in vec_C corresponding to colcode.colcode1 and colcode.colcode2 +%INPUT +% colcode: struture setting the colorcode for vectors + % colcode.CName: 'ima_cor','black','white',... + % colcode.ColorCode ='black', 'white', 'rgb','brg', '64 colors' + % colcode.FixedCbounds =0; thresholds scaling relative to min and max, =1 fixed thresholds + % colcode.MinC; min + % colcode.MaxC; max + % colcode.colcode1: first threshold for rgb, relative to min (0) and max (1) + % colcode.colcode2: second threshold for rgb, relative to min (0) and max (1), + % rmq: we need min <= colcode1 <= colcode2 <= max, otherwise + % colcode1 and colcode2 are adjusted to the bounds +% vec_C: matlab vector representing the scalar setting the color +function [colorlist,col_vec,colcode_out]=set_col_vec(colcode,vec_C) + +col_vec=[]; +colcode_out=colcode;%default +if isempty(vec_C) || ~isnumeric(vec_C) + colorlist=[0 0 1]; %blue + return +end +if (isfield(colcode,'FixedCbounds') && isequal(colcode.FixedCbounds,1)) + minC=colcode.MinC; + maxC=colcode.MaxC; +else + minC=min(vec_C); + maxC=max(vec_C); +end + +%default input parameters +if ~isstruct(colcode),colcode=[];end; +if ~isfield(colcode,'ColorCode') || isempty(colcode.ColorCode) + colorlist=[0 0 1]; %blue + return +end +if isfield(colcode,'colcode1') + colcode1=minC+colcode.colcode1*(maxC-minC); +else + colcode1=minC+(maxC-minC)/3;%default +end +if isfield(colcode,'colcode2') + colcode2=minC+colcode.colcode2*(maxC-minC); +else + colcode2=minC+2*(maxC-minC)/3;%default +end +colcode_out.MinC=minC; +colcode_out.MaxC=maxC; + +if strcmp(colcode.ColorCode,'black') + colorlist(1,:)=[0 0 0];%black + col_vec=ones(size(vec_C));%all vectors at color#1 +elseif strcmp(colcode.ColorCode,'white') + colorlist(1,:)=[1 1 1];%white + col_vec=ones(size(vec_C));%all vectors at color#1 +elseif strcmp(colcode.ColorCode,'rgb')|| strcmp(colcode.ColorCode,'bgr')% 3 color representation + ind1=find(vec_C < colcode1); % =1 for red vectors + ind_green=find((vec_C >= colcode1) & (vec_C < colcode2));% =1 for green vectors + ind3=find(vec_C >= colcode2);% =1 for blue vectors + colorlist(2,:)=[0 1 0];%green + col_vec(ind1)=1; + col_vec(ind_green)=2; + col_vec(ind3)=3; + if strcmp(colcode.ColorCode,'rgb') + colorlist(1,:)=[1 0 0];%red + colorlist(3,:)=[0 0 1];%blue + else + colorlist(1,:)=[0 0 1];%blue + colorlist(3,:)=[1 0 0];%red + end +else + colorjet=jet;% ususal colormap from blue to red + sizlist=size(colorjet); + indsel=ceil((sizlist(1)/64)*(1:64)); + colorlist(:,1)=colorjet(indsel,1); + colorlist(:,2)=colorjet(indsel,2); + colorlist(:,3)=colorjet(indsel,3); + sizlist=size(colorlist); + nblevel=sizlist(1); + col2_1=maxC-minC; + col_vec=1+floor(nblevel*(vec_C-minC)/col2_1); + col_vec=col_vec.*(col_vec<= nblevel)+nblevel*(col_vec >nblevel);% take color #nblevel at saturation + col_vec=col_vec.*(col_vec>= 1)+ (col_vec <1);% take color #1 for values below 1 +end Index: /trunk/src/set_grid.m =================================================================== --- /trunk/src/set_grid.m (revision 2) +++ /trunk/src/set_grid.m (revision 2) @@ -0,0 +1,684 @@ +%'set_grid':produce grid for PIV with one or two images (stereo case) +%------------------------------------------------------------------------ +% function varargout = set_grid(varargin) +% associated with the GUI set_grid.fig +% +%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +% Copyright Joel Sommeria, 2008, LEGI / CNRS-UJF-INPG, sommeria@coriolis-legi.org. +%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +% This file is part of the toolbox UVMAT. +% +% UVMAT is free software; you can redistribute it and/or modify +% it under the terms of the GNU General Public License as published by +% the Free Software Foundation; either version 2 of the License, or +% (at your option) any later version. +% +% UVMAT is distributed in the hope that it will be useful, +% but WITHOUT ANY WARRANTY; without even the implied warranty of +% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +% GNU General Public License (file UVMAT/COPYING.txt) for more details. +%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA + +function varargout = set_grid(varargin) + +% Last Modified by GUIDE v2.5 04-Feb-2008 16:05:02 + +% Begin initialization code - DO NOT EDIT +gui_Singleton = 1; +gui_State = struct('gui_Name', mfilename, ... + 'gui_Singleton', gui_Singleton, ... + 'gui_OpeningFcn', @set_grid_OpeningFcn, ... + 'gui_OutputFcn', @set_grid_OutputFcn, ... + 'gui_LayoutFcn', [] , ... + 'gui_Callback', []); +if nargin & isstr(varargin{1}) + gui_State.gui_Callback = str2func(varargin{1}); +end + +if nargout + [varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:}); +else + gui_mainfcn(gui_State, varargin{:}); +end +% End initialization code - DO NOT EDIT + +%------------------------------------------------------------------- +% --- Executes just before set_grid is made visible. +%INPUT: +% handles: handles of the set_grid interface elements +%'IndexObj': index of the object (on the UvData list) that set_grid will modify +% if =[] or absent: index still undefined (create mode in uvmat) +% if=0; no associated object (used for series), the button 'PLOT' is then unvisible +%'data': read from an existing object selected in the interface +% .TITLE : class of object ('POINTS','LINE',....) +% .DX,DY,DZ; meshes for regular grids +% .Coord: object position coordinates +% .ParentButton: handle of the uicontrol object calling the interface +% PlotHandles: set of handles of the elements contolling the plotting of the projected field: +% if =[] or absent, no plot (mask mode in uvmat) +% parameters on the uvmat interface (obtained by 'get_plot_handle.m') +function set_grid_OpeningFcn(hObject, eventdata, handles,inputfile) + +% Choose default command line output for set_grid +handles.output = hObject; + +% Update handles structure +guidata(hObject, handles); + +%default +% set(hObject,'Unit','Normalized')% set the unit normalized to the screen size +% set(hObject,'Position',[0.7 0.1 0.25 0.5])%set the position of the set_grid interface +set(hObject,'DeleteFcn',@closefcn) +set(handles.TITLE,'Value',1) +set(handles.ObjectStyle,'Value',1) +set(handles.ProjMode,'Value',1) +set(handles.MenuCoord,'ListboxTop',1) +set(handles.MenuCoord,'Value',1); +set(handles.MenuCoord,'String',{'phys';'px'}); +if exist('inputfile','var')& ~isempty(inputfile) + set(handles.image_1,'String',inputfile) + set(handles.image_2,'String',inputfile) +end + + +% --- Outputs from this function are returned to the command line. +function varargout = set_grid_OutputFcn(hObject, eventdata, handles) +% varargout cell array for returning output args (see VARARGOUT); +% hObject handle to figure +% eventdata reserved - to be defined in a future version of MATLAB +% handles structure with handles and user data (see GUIDATA) + +% Get default command line output from handles structure +varargout{1} = handles.output; +varargout{2}=handles; + +% --- Executes on selection change in ObjectStyle. +function ObjectStyle_Callback(hObject, eventdata, handles) + +ProjMode_Callback(hObject, eventdata, handles) + +%---------------------------------------------- +function xObject_Callback(hObject, eventdata, handles) + + +function yObject_Callback(hObject, eventdata, handles) + + +% --- Executes on selection change in zObject. +function zObject_Callback(hObject, eventdata, handles) + + +%--------------------------------------------------- +% --- Executes on selection change in ProjMode. +function ProjMode_Callback(hObject, eventdata, handles) +menu=get(handles.ProjMode,'String'); +value=get(handles.ProjMode,'Value'); +ProjMode=menu{value}; +menu=get(handles.ObjectStyle,'String'); +value=get(handles.ObjectStyle,'Value'); +ObjectStyle=menu{value}; +test3D=isequal(get(handles.ZObject,'Visible'),'on');%3D case +if isequal(ObjectStyle,'plane')||isequal(ObjectStyle,'volume') + set(handles.Phi,'Visible','on') + if test3D%3D case + set(handles.Theta,'Visible','on') + set(handles.Psi,'Visible','on') + end + set(handles.XMin,'Visible','on') + set(handles.XMax,'Visible','on') + set(handles.YMin,'Visible','on') + set(handles.YMax,'Visible','on') + if test3D + set(handles.Theta,'Visible','on') + set(handles.Psi,'Visible','on') + set(handles.ZMin,'Visible','on') + set(handles.ZMax,'Visible','on') + end +else + set(handles.Phi,'Visible','off') + set(handles.Theta,'Visible','off') + set(handles.Psi,'Visible','off') + set(handles.XMin,'Visible','off') + set(handles.XMax,'Visible','off') + set(handles.YMin,'Visible','off') + if isequal(ProjMode,'interp') + set(handles.YMax,'Visible','off') + else + set(handles.YMax,'Visible','on') + end + if isequal(ObjectStyle,'rectangle')|isequal(ObjectStyle,'ellipse') + set(handles.XMax,'Visible','on') + else + set(handles.XMax,'Visible','off') + end + set(handles.ZMin,'Visible','off') + set(handles.ZMax,'Visible','off') +end +if isequal(ProjMode,'projection')|isequal(ProjMode,'inside')|isequal(ProjMode,'outside')|isequal(ObjectStyle,'points') + set(handles.DX,'Visible','off') + set(handles.DY,'Visible','off') + set(handles.DZ,'Visible','off') +else + set(handles.DX,'Visible','on') + set(handles.DY,'Visible','on') + if test3D%3D case + set(handles.DZ,'Visible','on') + end +end + +%--------------------------------------------- +% --- Executes on selection change in TITLE. +function TITLE_Callback(hObject, eventdata, handles) +hsetobject=get(handles.TITLE,'parent'); +SetData=get(hsetobject,'UserData');%get the hidden interface data +% function named CALLBACK in UNTITLED.M with the given input arguments. +menu=get(handles.TITLE,'String'); +value=get(handles.TITLE,'Value'); +titl=menu{value}; +if isequal(titl,'POINTS') + menu_style={'points'}; + menu_proj={'projection';'interp';'filter';'none'}; +elseif isequal(titl,'LINE') + menu_style={'line';'polyline';'rectangle';'polygon';'ellipse'};%'line' =default + menu_proj={'projection';'interp';'filter';'none'}; +elseif isequal(titl,'PATCH') + menu_style={'rectangle';'polygon';'ellipse'};%'line' =default + menu_proj={'inside';'outside';'none'}; + elseif isequal(titl,'PLANE') + menu_style={'plane'}; + menu_proj={'projection';'interp'}; +elseif isequal(titl,'VOLUME') + menu_style={'volume'}; + menu_proj={'none'}; + +end +set(handles.ObjectStyle,'String',menu_style) +set(handles.ObjectStyle,'Value',1) +set(handles.ProjMode,'String',menu_proj) +set(handles.ProjMode,'Value',1) +if isfield(SetData,'ParentButton') + update_parentbutton(SetData.ParentButton,titl) +end +ObjectStyle_Callback(hObject, eventdata, handles) + +%----------- +function update_parentbutton(ParentButton,titl) + +if isstruct(ParentButton) + parentfields=fields(ParentButton); + for ibutton=1:length(parentfields) + buttonhandle=eval(['ParentButton.' parentfields{ibutton}]); + if ishandle(buttonhandle) + set(buttonhandle,'Value',0) + set(buttonhandle,'BackgroundColor',[0 1 0])%put unactivated buttons to green + end + end + if isfield(ParentButton,titl) + buttonhandle=eval(['ParentButton.' titl]); + if ishandle(buttonhandle) + set(buttonhandle,'Value',1) + set(buttonhandle,'BackgroundColor',[1 1 0])%put activated button to yellow + end + end +end +%------------ +function Phi_Callback(hObject, eventdata, handles) +update_slider(hObject, eventdata,handles) + +function Theta_Callback(hObject, eventdata, handles) +update_slider(hObject, eventdata,handles) + +function update_slider(hObject, eventdata,handles) +%rotation angles +Phi=(pi/180)*str2num(get(handles.Phi,'String'));%first Euler angle in radian +Theta=(pi/180)*str2num(get(handles.Theta,'String'));%second Euler angle in radian + +%components of the unitiy vector normal to the projection plane +NormVec_X=-sin(Phi)*sin(Theta); +NormVec_Y=cos(Phi)*sin(Theta); +NormVec_Z=cos(Theta); +huvmat=findobj('Tag','uvmat');%find the current uvmat interface handle +UvData=get(huvmat,'UserData');%Data associated to the current uvmat interface +Z=NormVec_X *(UvData.X)+NormVec_Y *(UvData.Y)+NormVec_Z *(UvData.Z); +set(handles.z_slider,'Min',min(Z)) +set(handles.z_slider,'Max',max(Z)) +ZMax_Callback(hObject, eventdata, handles) + +function DX_Callback(hObject, eventdata, handles) + + +function DY_Callback(hObject, eventdata, handles) + + +function DZ_Callback(hObject, eventdata, handles) + + + +%----------------------------------------------------- +% --- Executes on button press in import. +function import_Callback(hObject, eventdata, handles) +%get the object file +oldfile=''; +huvmat=findobj('Tag','uvmat'); +if isempty(huvmat) + huvmat=findobj(allchild(0),'Name','series'); +end +hchild=get(huvmat,'Children'); +hrootpath=findobj(hchild,'Tag','RootPath'); +oldfile=get(hrootpath,'String'); +if iscell(oldfile) + oldfile=oldfile{1}; +end +%[FileName,PathName] = uigetfile('*.civ','Select a .civ file',oldfile) +[FileName, PathName, filterindex] = uigetfile( ... + {'*.xml;*.mat', ' (*.xml,*.mat)'; + '*.xml', '.xml files '; ... + '*.mat', '.mat matlab files '}, ... + 'Pick a file',oldfile); +fileinput=[PathName FileName];%complete file name +testblank=findstr(fileinput,' ');%look for blanks +if ~isempty(testblank) + errordlg('forbidden input file name: contain blanks') + return +end +sizf=size(fileinput); +if (~ischar(fileinput)|~isequal(sizf(1),1)),return;end + +%read the file + t=xmltree(fileinput); + s=convert(t); +%Display title +title=set_title(s.Style,s.ProjMode);%update the title +% menu=get(handles.TITLE,'String') +% for iline=1:length(menu) +% if isequal(menu{iline},title) +% set(handles.TITLE,'Value',iline) +% break +% end +% end +% TITLE_Callback(hObject, eventdata, handles) +% teststyle=0; +% if isfield(s,'Style') +% menu=get(handles.ObjectStyle,'String'); +% for iline=1:length(menu) +% if isequal(menu{iline},s.Style) +% set(handles.ObjectStyle,'Value',iline) +% teststyle=1; +% break +% end +% end +% end +% if teststyle==0; +% s.Style='points'; +% set(handles.ObjectStyle,'Value',1); %default (points) +% end +testmode=0; +if isfield(s,'ProjMode') + menu=get(handles.ProjMode,'String'); + for iline=1:length(menu) + if isequal(menu{iline},s.ProjMode) + set(handles.ProjMode,'Value',iline) + testmode=1; + break + end + end +end + +ProjMode_Callback(hObject, eventdata, handles);%visualize the appropriate edit boxes +if isfield(s,'CoordType') + if isequal(s.CoordType,'phys') + set(handles.MenuCoord,'Value',1) + elseif isequal(s.CoordType,'px') + set(handles.MenuCoord,'Value',2) + else + warndlg('unknown CoordType (px or phys) in set_grid.m') + end +end +if isfield(s,'XMax') + set(handles.XMax,'String',s.XMax) +end +if isfield(s,'XMin') + set(handles.XMin,'String',s.XMin) +end +if isfield(s,'YMax') + set(handles.YMax,'String',s.YMax) +end +if isfield(s,'YMin') + set(handles.YMin,'String',s.YMin) +end +if isfield(s,'DX') + set(handles.DX,'String',s.DX) +end +if isfield(s,'DY') + set(handles.DY,'String',s.DY) +end +if ~isfield(s,'Coord') + XObject='0';%default + YObject='0'; +elseif ischar(s.Coord) + line=str2num(s.Coord); + XObject=num2str(line(1)); + YObject=num2str(line(2)); +else + for i=1:length(s.Coord) + line=str2num(s.Coord{i}); + XObject{i}=num2str(line(1)); + YObject{i}=num2str(line(2)); + end +end +set(handles.XObject,'String',XObject) +set(handles.YObject,'String',YObject) +%METTRA A JOUR ASPECT DE L'INTERFACE (COMME set_grid_Opening + +%---------------------------------------------------- +% executed when closing: set the parent interface button to value 0 +function closefcn(gcbo,eventdata) +huvmat=findobj(allchild(0),'Name','uvmat');%find the current uvmat interface handle +parent_button=findobj(huvmat,'Tag','grid'); +if ~isempty(parent_button) + set(parent_button,'Value',0)%put unactivated buttons to green + tag=get(parent_button,'Tag'); + if isequal(tag,'edit') + set(parent_button,'BackgroundColor',[0.7 0.7 0.7]); + else + set(parent_button,'BackgroundColor',[0 1 0]); + end +end + +%----------------------------------------------------------------------- +% --- Executes on button press in edit: PLOT the defined object and its projected field +function edit_Callback(hObject, eventdata, handles) +hsetobject=get(hObject,'parent'); +SetData=get(hsetobject,'UserData');%get the hidden interface data +%IndexObj=SetData.IndexObj%index of the current projection object in the list of projection objects (UvData.ProjObject) +huvmat=findobj('Tag','uvmat');%find the current uvmat interface handle +UvData=get(huvmat,'UserData');%Data associated to the current uvmat interface +if isfield(UvData,'CuurentObjectIndex') + IndexObj=UvData.CurrentObjectIndex; +else + IndexObj=[]; +end +ObjectData=read_set_grid(handles);%read the interface input parameters defining the object +[UvData,IndexObj]=update_obj(UvData,IndexObj,ObjectData,SetData.PlotHandles); +uvmat('write_plot_param',PlotHandles,UvData.Object{IndexObj}.PlotParam); %update the display of plotting parameters for the current object +SetData.IndexObj=IndexObj; +set(gcbf,'UserData',SetData)%update object index in the set_grid interface +set(huvmat,'UserData',UvData)%update the data in the uvmat interface + + +% --- Executes on button press in MenuCoord. +function MenuCoord_Callback(hObject, eventdata, handles) + + +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% +% --- Executes on button press in delete. +function delete_Callback(hObject, eventdata, handles) + +%SetData=get(gcbf,'UserData');%get the interface data +%IndexObj=SetData.IndexObj; +huvmat=findobj('Name','uvmat');%find the current uvmat interface handle +UvData=get(huvmat,'UserData');%Data associated to the current uvmat interface +if isfield(UvData,'CurrentObjectIndex') + IndexObj=UvData.CurrentObjectIndex; +else + IndexObj=[]; +end +delete_object(IndexObj); + +%---------------------------------------------------- +function YMin_Callback(hObject, eventdata, handles) +% hObject handle to YMin (see GCBO) +% eventdata reserved - to be defined in a future version of MATLAB +% handles structure with handles and user data (see GUIDATA) + +% Hints: get(hObject,'String') returns contents of YMin as text +% str2double(get(hObject,'String')) returns contents of YMin as a double + + +function ZMin_Callback(hObject, eventdata, handles) + + +function ZMax_Callback(hObject, eventdata, handles) +DZ=str2num(get(handles.ZMax,'String')); +ZMin=get(handles.z_slider,'Min'); +ZMax=get(handles.z_slider,'Max'); +rel_step(1)=DZ/(ZMax-ZMin); +rel_step(2)=0.2; +set(handles.z_slider,'SliderStep',rel_step) + +function YMax_Callback(hObject, eventdata, handles) + + +function XMin_Callback(hObject, eventdata, handles) + + +function XMax_Callback(hObject, eventdata, handles) + + +% ------------------------------------------------------ +function save_Callback(hObject, eventdata, handles) +% ------------------------------------------------------ +Object=read_set_object(handles);%read the set_grid interface; +DX=Object.DX; +DY=Object.DY; +RangeX=Object.RangeX; +RangeY=Object.RangeY; + array_realx=[RangeX(2):DX:RangeX(1)]; + array_realy=[RangeY(2):DY:RangeY(1)]; + nx_patch=length(array_realx); + ny_patch=length(array_realy); + [grid_realx,grid_realy]=meshgrid(array_realx,array_realy); + grid_real(:,1)=reshape(grid_realx,nx_patch*ny_patch,1); + grid_real(:,2)=reshape(grid_realy,nx_patch*ny_patch,1); + grid_real(:,3)=zeros(nx_patch*ny_patch,1); + +imageA=get(handles.image_1,'String'); +imageB=get(handles.image_2,'String'); +testB=1; +if isempty(imageA) | isequal(imageA,'') + if isempty(imageB) | isequal(imageB,'') + warndlg_uvmat('at least one image file name must be introduced','ERROR') + else + imageA=imageB; + testB=0; + end +end +if isempty(imageB) || isequal(imageB,'') || isequal(imageA,imageB) + testB=0; +end + +testexist=exist(imageA,'file'); +if isequal(testexist,0) + msgbox_uvmat('ERROR',['input image file' imageA 'does not exist']) + return +end +[Pathsub,RootFile,field_count,str2,str_a,str_b,ext,nom_type,subdir]=name2display(imageA); +form=imformats(ext([2:end])); +if isempty(form)% if the extension corresponds to an image format recognized by Matlab + msgbox_uvmat('ERROR',['error in read_image.m: ' imageA ' is not an image name recognized by Matlab ']) + return +end +fileAxml=[fullfile(Pathsub,RootFile) '.xml']; +[XmlDataA,error]=imadoc2struct(fileAxml); +if isfield(XmlDataA,'GeometryCalib') + tsaiA=XmlDataA.GeometryCalib; + else + msgbox_uvmat('WARNING','no geometric calibration available for image A') + tsaiA=[]; +end +[grid_imaA(:,1),grid_imaA(:,2)]=px_XYZ(tsaiA,grid_real(:,1),grid_real(:,2),0); + A=imread(imageA); + siz=size(A); + npxA=siz(2); + npyA=siz(1); + +flagA=grid_imaA(:,1)>0 & grid_imaA(:,1)0 & grid_imaA(:,2)0 & grid_imaB(:,1)0 & grid_imaB(:,2)=2 + sizcoord=size(data.Coord); + for i=1:sizcoord(1) + XObject{i}=num2str(data.Coord(i,1),4); + YObject{i}=num2str(data.Coord(i,2),4); + end + set(handles.XObject,'String',XObject) + set(handles.YObject,'String',YObject) + %set(handles.XObject,'String',mat2cell(data.Coord(:,1),sizcoord(1))) + %set(handles.YObject,'String',mat2cell(data.Coord(:,2),sizcoord(1))) + if sizcoord(2)>3 + for i=1:sizcoord(1) + ZObject{i}=num2str(data.Coord(i,3),4); + end + set(handles.ZObject,'String',ZObject) + end + end + if isfield(data,'DX') + set(handles.DX,'String',num2str(data.DX,3)) + end + if isfield(data,'DY') + set(handles.DY,'String',num2str(data.DY,3)) + end + %OBSOLETE (replaced by Range) +% if isfield(data,'XMin') +% set(handles.XMin,'String',num2str(data.XMin,3)) +% end +% if isfield(data,'XMax') +% set(handles.XMax,'String',num2str(data.XMax,3)) +% end +% if isfield(data,'YMin') +% set(handles.YMin,'String',num2str(data.YMin,3)) +% end +% if isfield(data,'YMax') +% set(handles.YMax,'String',num2str(data.YMax,3)) +% end + if isfield(data,'RangeZ') && length(ZBounds) >= 2 + set(handles.ZMax,'String',num2str(max(data.RangeZ),3)) + DZ=max(data.RangeZ);%slider step + if ZBounds(2)~=ZBounds(1) + rel_step(1)=min(DZ/(ZBounds(2)-ZBounds(1)),0.2);%must be smaller than 1 + rel_step(2)=0.1; + set(handles.z_slider,'Visible','on') + set(handles.z_slider,'Min',ZBounds(1)) + set(handles.z_slider,'Max',ZBounds(2)) + set(handles.z_slider,'SliderStep',rel_step) + set(handles.z_slider,'Value',(ZBounds(1)+ZBounds(2))/2) + end + end + if isfield(data,'RangeX') + set(handles.XMax,'String',num2str(max(data.RangeX),3)) + set(handles.XMin,'String',num2str(min(data.RangeX),3)) + end + if isfield(data,'RangeY') + set(handles.YMax,'String',num2str(max(data.RangeY),3)) + set(handles.YMin,'String',num2str(min(data.RangeY),3)) + end + if isfield(data,'RangeZ') + set(handles.ZMax,'String',num2str(max(data.RangeZ),3)) + set(handles.ZMin,'String',num2str(min(data.RangeZ),3)) + end + if isfield(data,'Phi') + set(handles.Phi,'String',num2str(data.Phi,3)) + end + if isfield(data,'Theta') + set(handles.Theta,'String',num2str(data.Theta,3)) + end + if isfield(data,'Psi') + set(handles.Psi,'String',num2str(data.Psi,3)) + end + if isfield(data,'DZ') + set(handles.DZ,'String',num2str(data.DZ,3)) + end + if isfield(data,'CoordType') + if isequal(data.CoordType,'phys') + set(handles.MenuCoord,'Value',1) + elseif isequal(data.CoordType,'px') + set(handles.MenuCoord,'Value',2) + end + end +end +if desable_open + set(handles.OPEN,'Visible','off') +else + set(handles.OPEN,'Visible','on') +end +if desable_plot + set(handles.PLOT,'Visible','off') +else + set(handles.PLOT,'Visible','on') +end + + +% --- Outputs from this function are returned to the command line. +function varargout = set_object_OutputFcn(hObject, eventdata, handles) +% varargout cell array for returning output args (see VARARGOUT); +% hObject handle to figure +% eventdata reserved - to be defined in a future version of MATLAB +% handles structure with handles and user data (see GUIDATA) + +% Get default command line output from handles structure +varargout{1} = handles.output; +varargout{2}=handles; + +%----------------------------------------------- +% --- Executes on selection change in ObjectStyle. +function ObjectStyle_Callback(hObject, eventdata, handles) +style_prev=get(handles.ObjectStyle,'UserData'); +str=get(handles.ObjectStyle,'String'); +val=get(handles.ObjectStyle,'Value'); +% make correspondance between different object styles +% if ~isequal(str{val},style_prev) +Xcolumn=get(handles.XObject,'String'); +Ycolumn=get(handles.YObject,'String'); +if ischar(Xcolumn) + sizchar=size(Xcolumn); + for icol=1:sizchar(1) + Xcolumn_cell{icol}=Xcolumn(icol,:); + end + Xcolumn=Xcolumn_cell; +end +if ischar(Ycolumn) + sizchar=size(Ycolumn); + for icol=1:sizchar(1) + Ycolumn_cell{icol}=Ycolumn(icol,:); + end + Ycolumn=Ycolumn_cell; +end +Zcolumn={};%default +z_new={}; +if isequal(get(handles.ZObject,'Visible'),'on') + data.NbDim=3; %test 3D object + Zcolumn=get(handles.ZObject,'String'); + if ischar(Zcolumn) + Zcolumn={Zcolumn}; + end +end +x_new{1}=Xcolumn{1}; +y_new{1}=Ycolumn{1}; +if ~isempty(Zcolumn) + z_new{1}=Zcolumn{1}; +end +if isequal(str{val},'line') + if isequal(style_prev,'rectangle')|isequal(style_prev,'ellipse') + XMax=get(handles.XMax,'String'); + YMax=get(handles.YMax,'String'); + x_new{2}=num2str(XMax,4); + y_new{2}=num2str(YMax,4); + set(handles.XObject,'String',x_new) + set(handles.YObject,'String',y_new) + set(handles.ZObject,'String',z_new) + end +elseif isequal(str{val},'polyline') +elseif isequal(str{val},'rectangle')| isequal(str{val},'ellipse') + set(handles.XObject,'String',x_new) + set(handles.YObject,'String',y_new) + set(handles.ZObject,'String',z_new) +end +% end + + + +ProjMode_Callback(hObject, eventdata, handles) +%store the current option +str=get(handles.ObjectStyle,'String'); +val=get(handles.ObjectStyle,'Value'); +set(handles.ObjectStyle,'UserData',str{val}) + +%---------------------------------------------- +function xObject_Callback(hObject, eventdata, handles) + + +function yObject_Callback(hObject, eventdata, handles) + + +% --- Executes on selection change in zObject. +function zObject_Callback(hObject, eventdata, handles) + + + +% --- Executes on selection change in ProjMode. +function ProjMode_Callback(hObject, eventdata, handles) +menu=get(handles.ProjMode,'String'); +value=get(handles.ProjMode,'Value'); +ProjMode=menu{value}; +menu=get(handles.ObjectStyle,'String'); +value=get(handles.ObjectStyle,'Value'); +ObjectStyle=menu{value}; +test3D=isequal(get(handles.ZObject,'Visible'),'on');%3D case +if isequal(ObjectStyle,'plane')|isequal(ObjectStyle,'volume') + set(handles.Phi,'Visible','on') + if test3D%3D case + set(handles.Theta,'Visible','on') + set(handles.Psi,'Visible','on') + end + set(handles.XMin,'Visible','on') + set(handles.XMax,'Visible','on') + set(handles.YMin,'Visible','on') + set(handles.YMax,'Visible','on') + if test3D + set(handles.Theta,'Visible','on') + set(handles.Psi,'Visible','on') + set(handles.ZMin,'Visible','on') + set(handles.ZMax,'Visible','on') + end +else + set(handles.Phi,'Visible','off') + set(handles.Theta,'Visible','off') + set(handles.Psi,'Visible','off') + set(handles.XMin,'Visible','off') + set(handles.XMax,'Visible','off') + set(handles.YMin,'Visible','off') + if isequal(ProjMode,'interp') + set(handles.YMax,'Visible','off') + else + set(handles.YMax,'Visible','on') + end + if isequal(ObjectStyle,'rectangle')|isequal(ObjectStyle,'ellipse') + set(handles.XMax,'Visible','on') + else + set(handles.XMax,'Visible','off') + end + set(handles.ZMin,'Visible','off') + set(handles.ZMax,'Visible','off') +end +TITLE_list=get(handles.TITLE,'String'); +val=get(handles.TITLE,'Value'); +TITLE=TITLE_list{val}; +switch TITLE + case {'POINTS','PATCH','MASK'} + set(handles.DX,'Visible','off') + set(handles.DY,'Visible','off') + set(handles.DZ,'Visible','off') + case {'LINE'} + if isequal(ProjMode,'interp')|| isequal(ProjMode,'filter') + set(handles.DX,'Visible','on') + else + set(handles.DX,'Visible','off') + end + case {'PLANE'} + if isequal(ProjMode,'interp')|| isequal(ProjMode,'filter') + set(handles.DX,'Visible','on') + set(handles.DY,'Visible','on') + else + set(handles.DX,'Visible','off') + set(handles.DY,'Visible','off') + end + case {'VOLUME'} + if isequal(ProjMode,'interp') + set(handles.DX,'Visible','on') + set(handles.DY,'Visible','on') + set(handles.DZ,'Visible','on') + else + set(handles.DX,'Visible','off') + set(handles.DY,'Visible','off') + set(handles.DZ,'Visible','off') + end +end + +%--------------------------------------------- +% --- Executes on selection change in TITLE. +function TITLE_Callback(hObject, eventdata, handles) +%--------------------------------------------- +hsetobject=get(handles.TITLE,'parent'); +SetData=get(hsetobject,'UserData');%get the hidden interface data +% function named CALLBACK in UNTITLED.M with the given input arguments. +menu=get(handles.TITLE,'String'); +value=get(handles.TITLE,'Value'); +titl=menu{value}; +if isequal(titl,'POINTS'); + menu_style={'points'}; + menu_proj={'projection';'interp';'filter';'none'}; +elseif isequal(titl,'LINE') + menu_style={'line';'polyline';'rectangle';'polygon';'ellipse'};%'line' =default + menu_proj={'projection';'interp';'filter';'none'}; +elseif isequal(titl,'PATCH') + menu_style={'rectangle';'polygon';'ellipse'};%'line' =default + menu_proj={'inside';'outside'}; +elseif isequal(titl,'MASK') + menu_style={'polygon'};%'line' =default + menu_proj={'mask_inside';'mask_outside'}; +elseif isequal(titl,'PLANE') + menu_style={'plane'}; + menu_proj={'projection';'interp';'filter';'none'}; +elseif isequal(titl,'VOLUME') + menu_style={'volume'}; + menu_proj={'none'}; + +end +old_menu=get(handles.ObjectStyle,'String'); +value=get(handles.ObjectStyle,'Value'); +old_style=old_menu{value}; +teststyle=0; +for iline=1:length(menu_style) + if isequal(menu_style{iline},old_style) + styleval=iline; + teststyle=1; + break + end +end +if ~teststyle + new_style=[];%default + switch old_style + case 'polyline' + new_style='polygon'; + case 'polygon' + new_style='polyline'; + end + if ~isempty(new_style) + for iline=1:length(menu_style) + if isequal(menu_style{iline},new_style) + styleval=iline; + teststyle=1; + break + end + end + end +end +if ~teststyle + styleval=1; +end +set(handles.ObjectStyle,'String',menu_style) +set(handles.ObjectStyle,'Value',styleval) +set(handles.ProjMode,'String',menu_proj) +set(handles.ProjMode,'Value',1) +ObjectStyle_Callback(hObject, eventdata, handles) + +%--------------------------------------------- +function Phi_Callback(hObject, eventdata, handles) +update_slider(hObject, eventdata,handles) +%--------------------------------------------- + +function Theta_Callback(hObject, eventdata, handles) +update_slider(hObject, eventdata,handles) + +function update_slider(hObject, eventdata,handles) +%rotation angles +Phi=(pi/180)*str2num(get(handles.Phi,'String'));%first Euler angle in radian +Theta=(pi/180)*str2num(get(handles.Theta,'String'));%second Euler angle in radian + +%components of the unitiy vector normal to the projection plane +NormVec_X=-sin(Phi)*sin(Theta); +NormVec_Y=cos(Phi)*sin(Theta); +NormVec_Z=cos(Theta); +huvmat=findobj('Tag','uvmat');%find the current uvmat interface handle +UvData=get(huvmat,'UserData');%Data associated to the current uvmat interface +if isfield(UvData,'X') & isfield(UvData,'Y') & isfield(UvData,'Z') + Z=NormVec_X *(UvData.X)+NormVec_Y *(UvData.Y)+NormVec_Z *(UvData.Z); + set(handles.z_slider,'Min',min(Z)) + set(handles.z_slider,'Max',max(Z)) + ZMax_Callback(hObject, eventdata, handles) +end + +function DX_Callback(hObject, eventdata, handles) + + +function DY_Callback(hObject, eventdata, handles) + + +function DZ_Callback(hObject, eventdata, handles) + + + +%----------------------------------------------------- +% --- Executes on button press in OPEN. +function OPEN_Callback(hObject, eventdata, handles) +%get the object file +oldfile=' '; +huvmat=findobj('Tag','uvmat'); +% if isempty(huvmat) +% huvmat=findobj(allchild(0),'Name','series'); +% end +hchild=get(huvmat,'Children'); +hrootpath=findobj(hchild,'Tag','RootPath'); +if ~isempty(hrootpath) + oldfile=get(hrootpath,'String'); + if iscell(oldfile) + oldfile=oldfile{1}; + end +end +%[FileName,PathName] = uigetfile('*.civ','Select a .civ file',oldfile) +[FileName, PathName, filterindex] = uigetfile( ... + {'*.xml;*.mat', ' (*.xml,*.mat)'; + '*.xml', '.xml files '; ... + '*.mat', '.mat matlab files '}, ... + 'Pick a file',oldfile); +fileinput=[PathName FileName];%complete file name +testblank=findstr(fileinput,' ');%look for blanks +if ~isempty(testblank) + errordlg('forbidden input file name: contain blanks') + return +end +sizf=size(fileinput); +if (~ischar(fileinput)|~isequal(sizf(1),1)),return;end + +%read the file + t=xmltree(fileinput); + s=convert(t); + if ~isfield(s,'Style') + s.Style='points'; + end + if ~isfield(s,'ProjMode') + s.ProjMode='none'; + end +%Display title +title=set_title(s.Style,s.ProjMode);%update the title +if ~isempty(huvmat) + hhuvmat=guidata(huvmat); +% set(hhuvmat.POINTS,'Value',0) +% set(hhuvmat.POINTS,'BackgroundColor',[0 1 0])%put unactivated buttons to green +% set(hhuvmat.LINE,'Value',0) +% set(hhuvmat.LINE,'BackgroundColor',[0 1 0])%put unactivated buttons to green +% set(hhuvmat.PATCH,'Value',0) +% set(hhuvmat.PATCH,'BackgroundColor',[0 1 0])%put unactivated buttons to green +% set(hhuvmat.PLANE,'Value',0) +% set(hhuvmat.PLANE,'BackgroundColor',[0 1 0])%put unactivated buttons to green +% set(hhuvmat.VOLUME,'Value',0) +% set(hhuvmat.VOLUME,'BackgroundColor',[0 1 0])%put unactivated buttons to green +% if ~isequal(title,'MASK') +% eval(['set(hhuvmat.' title ',''Value'',1)']) +% eval(['set(hhuvmat.' title ',''BackgroundColor'',[1 1 0])']) +% end +end +menu=get(handles.TITLE,'String'); +for iline=1:length(menu) + if isequal(menu{iline},title) + set(handles.TITLE,'Value',iline) + break + end +end +TITLE_Callback(hObject, eventdata, handles) +teststyle=0; +% if isfield(s,'Style') +menu=get(handles.ObjectStyle,'String'); +for iline=1:length(menu) + if isequal(menu{iline},s.Style) + set(handles.ObjectStyle,'Value',iline) + teststyle=1; + break + end +end +testmode=0; +menu=get(handles.ProjMode,'String'); +for iline=1:length(menu) + if isequal(menu{iline},s.ProjMode) + set(handles.ProjMode,'Value',iline) + testmode=1; + break + end +end + +ProjMode_Callback(hObject, eventdata, handles);%visualize the appropriate edit boxes +if isfield(s,'CoordType') + if isequal(s.CoordType,'phys') + set(handles.MenuCoord,'Value',1) + elseif isequal(s.CoordType,'px') + set(handles.MenuCoord,'Value',2) + else + warndlg('unknown CoordType (px or phys) in set_object.m') + end +end +if isfield(s,'XMax') + set(handles.XMax,'String',s.XMax) +end +if isfield(s,'XMin') + set(handles.XMin,'String',s.XMin) +end +if isfield(s,'YMax') + set(handles.YMax,'String',s.YMax) +end +if isfield(s,'YMin') + set(handles.YMin,'String',s.YMin) +end +Range=0; +if isfield(s,'Range') + if ischar(s.Range) + Range=str2num(s.Range); + else + Range(1,:)=str2num(s.Range{1}); + Range(2,:)=str2num(s.Range{2}); + end +end +if size(Range,2)>=3 + if size(Range,1)>=2 + set(handles.ZMin,'String',num2str(Range(2,3),3)) + end + if size(Range,1)>=2 + set(handles.ZMax,'String',num2str(Range(1,3),3)) + end +end +if size(Range,2)>=2 + if size(Range,1)>=2 + set(handles.YMin,'String',num2str(Range(2,2),3)) + end + if size(Range,1)>=2 + set(handles.YMax,'String',num2str(Range(1,2),3)) + end +end +if size(Range,2)>=1 + if size(Range,1)>=2 + set(handles.XMin,'String',num2str(Range(2,1),3)) + end + if size(Range,1)>=2 + set(handles.XMax,'String',num2str(Range(1,1),3)) + end +end +if isfield(s,'RangeX') & ischar(s.RangeX) + RangeX=str2num(s.RangeX); + set(handles.XMax,'String',num2str(max(RangeX),3)) + set(handles.XMin,'String',num2str(min(RangeX),3)) +end + +if isfield(s,'RangeY') + if ischar(s.RangeY) + RangeY=str2num(s.RangeY); + set(handles.YMax,'String',num2str(max(RangeY),3)) + set(handles.YMin,'String',num2str(min(RangeY),3)) + end +end +if isfield(s,'RangeZ') + if ischar(s.RangeZ) + RangeZ=str2num(s.RangeZ); + set(handles.ZMax,'String',num2str(max(RangeZ),3)) + set(handles.ZMin,'String',num2str(min(RangeZ),3)) + end +end +if isfield(s,'Phi') + set(handles.Phi,'String',s.Phi) +end +if isfield(s,'Theta') + set(handles.Theta,'String',s.Theta) +end +if isfield(s,'Psi') + set(handles.Psi,'String',s.Psi) +end + +if isfield(s,'DX') + set(handles.DX,'String',s.DX) +end +if isfield(s,'DY') + set(handles.DY,'String',s.DY) +end +if ~isfield(s,'Coord') + XObject='0';%default + YObject='0'; +elseif ischar(s.Coord) + line=str2num(s.Coord); + XObject=num2str(line(1),4); + YObject=num2str(line(2),4); +else + for i=1:length(s.Coord) + line=str2num(s.Coord{i}); + XObject{i}=num2str(line(1),4); + YObject{i}=num2str(line(2),4); + end +end +set(handles.XObject,'String',XObject) +set(handles.YObject,'String',YObject) +%METTRA A JOUR ASPECT DE L'INTERFACE (COMME set_object_Opening + +%---------------------------------------------------- +% executed when closing: set the parent interface button to value 0 +function closefcn(gcbo,eventdata,parent_button) + +huvmat=findobj(allchild(0),'Name','uvmat');%find the current uvmat interface handle +if ~isempty(huvmat) + hhuvmat=guidata(huvmat); + set(hhuvmat.create,'Value',0) + set(hhuvmat.create,'BackgroundColor',[0 1 0])%put unactivated buttons to green +% set(hhuvmat.LINE,'Value',0) +% set(hhuvmat.LINE,'BackgroundColor',[0 1 0])%put unactivated buttons to green +% set(hhuvmat.PATCH,'Value',0) +% set(hhuvmat.PATCH,'BackgroundColor',[0 1 0])%put unactivated buttons to green +% set(hhuvmat.PLANE,'Value',0) +% set(hhuvmat.PLANE,'BackgroundColor',[0 1 0])%put unactivated buttons to green +% set(hhuvmat.VOLUME,'Value',0) +% set(hhuvmat.VOLUME,'BackgroundColor',[0 1 0])%put unactivated buttons to green + set(hhuvmat.edit,'Value',0) + set(hhuvmat.edit,'BackgroundColor',[0.7 0.7 0.7])%put unactivated buttons to gree +end +hseries=findobj(allchild(0),'Name','series');%find the current series interface handle +if ~isempty(hseries) + hhseries=guidata(hseries); + set(hhseries.GetObject,'Value',0) + set(hhseries.GetObject,'BackgroundColor',[0 1 0])%put unactivated buttons to green +end + +%----------------------------------------------------------------------- +% --- Executes on button press in PLOT: PLOT the defined object and its projected field +function PLOT_Callback(hObject, eventdata, handles) + +hsetobject=get(handles.PLOT,'parent'); +SetData=get(hsetobject,'UserData');%get the hidden interface data +huvmat=findobj('Name','uvmat');%find the current uvmat interface handle +hlist_object=findobj(huvmat,'Tag','list_object');%handles of the object list in the GUI uvmat +IndexObj=get(hlist_object,'Value');%position in the objet list +UvData=get(huvmat,'UserData');%Data associated to the GUI uvmat +ObjectData=read_set_object(handles);%read the input parameters defining the object in the GUI set_object +ObjectData.HandlesDisplay=[]; % new object plot by default +if length(UvData.Object) >= IndexObj && isfield(UvData.Object{IndexObj},'HandlesDisplay') + hdisplay=UvData.Object{IndexObj}.HandlesDisplay; + if isequal(UvData.Object{IndexObj}.Style, ObjectData.Style) && isequal(UvData.Object{IndexObj}.ProjMode, ObjectData.ProjMode) + ObjectData.HandlesDisplay=UvData.Object{IndexObj}.HandlesDisplay; + else % for a new object styl, delete the existing object plots + for ih=1:length(hdisplay) + PlotData=get(hdisplay(ih),'UserData'); + if isfield(PlotData,'SubObject') & ishandle(PlotData.SubObject) + delete(PlotData.SubObject); + end + if isfield(PlotData,'DeformPoint') & ishandle(PlotData.DeformPoint) + delete(PlotData.DeformPoint); + end + if ~isequal(hdisplay(ih),0) + delete(hdisplay(ih)); + end + end + if isfield(ObjectData,'plotaxes') && ishandle(ObjectData.plotaxes) + delete(ObjectData.plotaxes)%delete the axes for plotting the current projection result + end + end +end + +% update the object plot and projection field +UvData.Object{IndexObj}=update_obj(UvData,IndexObj,ObjectData,SetData.PlotHandles); + +set(huvmat,'UserData',UvData)%update the data in the uvmat interface +list_str=get(hlist_object,'String'); +TITLE=set_title(ObjectData.Style,ObjectData.ProjMode); +list_str{IndexObj}=[num2str(IndexObj) '-' TITLE]; +if isequal(length(list_str),IndexObj) + list_str{IndexObj+1}='more...'; +end +set(hlist_object,'String',list_str) +set(hlist_object,'Value',IndexObj) + +%update create buttons on the GUI uvmat: set to object edit mode after object plotting +hhuvmat=guidata(huvmat);%handles of elements in the uvmat GUI +%desactivate all create buttons in mode edit +% if isequal(get(hhuvmat.edit,'Value'),0) + set(hhuvmat.create,'Value',0) + set(hhuvmat.create,'BackgroundColor',[0 1 0])%put unactivated buttons to green +% set(hhuvmat.LINE,'Value',0) +% set(hhuvmat.LINE,'BackgroundColor',[0 1 0])%put unactivated buttons to green +% set(hhuvmat.PATCH,'Value',0) +% set(hhuvmat.PATCH,'BackgroundColor',[0 1 0])%put unactivated buttons to green +% set(hhuvmat.PLANE,'Value',0) +% set(hhuvmat.PLANE,'BackgroundColor',[0 1 0])%put unactivated buttons to green +% set(hhuvmat.VOLUME,'Value',0) +% set(hhuvmat.VOLUME,'BackgroundColor',[0 1 0])%put unactivated buttons to green +% end +set(hhuvmat.edit,'Value',1) +set(hhuvmat.edit,'BackgroundColor',[1 1 0]);% paint the edit text in yellow +set(hhuvmat.edit,'Value',1);% +UvData.MouseAction='edit_object'; % set the edit button to 'on' +set(huvmat,'UserData',UvData) + +% --- Executes on button press in MenuCoord. +function MenuCoord_Callback(hObject, eventdata, handles) + +%---------------------------------------------------- +function YMin_Callback(hObject, eventdata, handles) + + +function ZMin_Callback(hObject, eventdata, handles) + + +function ZMax_Callback(hObject, eventdata, handles) +DZ=str2num(get(handles.ZMax,'String')); +ZMin=get(handles.z_slider,'Min'); +ZMax=get(handles.z_slider,'Max'); +if ~isequal(ZMax-ZMin,0) + rel_step(1)=DZ/(ZMax-ZMin); + rel_step(2)=0.2; + set(handles.z_slider,'SliderStep',rel_step) +end + +function YMax_Callback(hObject, eventdata, handles) + + +function XMin_Callback(hObject, eventdata, handles) + + +function XMax_Callback(hObject, eventdata, handles) + + +% ------------------------------------------------------ +function SAVE_Callback(hObject, eventdata, handles) +% ------------------------------------------------------ +Object=read_set_object(handles); +huvmat=findobj('Tag','uvmat'); +% UvData=get(huvmat,'UserData'); +if isempty(huvmat) + huvmat=findobj(allchild(0),'Name','series'); +end +hchild=get(huvmat,'Children'); +hrootpath=findobj(hchild,'Tag','RootPath'); +if isempty(hrootpath) + RootPath=''; +else + RootPath=get(hrootpath,'String'); + if iscell(RootPath) + RootPath=RootPath{1}; + end +end +title={'object name'}; +dir_save=uigetdir(RootPath); +def={fullfile(dir_save,['Object' Object.CoordType '.xml'])}; +options.Resize='on'; +displ_txt='save object as an .xml file';%default display +menu=get(handles.ProjMode,'String'); +value=get(handles.ProjMode,'Value'); +ProjMode=menu{value}; +if strcmp(ProjMode,'mask_inside')||strcmp(ProjMode,'mask_outside') + displ_txt='save mask contour as an .xml file: to create a mask image, use save_mask on the GUI uvmat (lower right)'; +end +answer=msgbox_uvmat('INPUT_TXT','save object as an .xml file',def); +%answer=inputdlg('','save object in a new .xml file',1,def,'on'); +if ~isempty(answer) + t=struct2xml(Object); + save(t,answer{1}) +end +msgbox_uvmat('CONFIRMATION',[answer{1} ' saved']) +%--------------------------------------------------------- +% --- Executes on slider movement. +function z_slider_Callback(hObject, eventdata, handles) +%--------------------------------------------------------- +%A ADAPTER +Z_value=get(handles.z_slider,'Value'); + +%rotation angles +Phi=(pi/180)*str2num(get(handles.Phi,'String'));%first Euler angle in radian +Theta=(pi/180)*str2num(get(handles.Theta,'String'));%second Euler angle in radian + +%components of the unity vector normal to the projection plane +NormVec_X=-sin(Phi)*sin(Theta); +NormVec_Y=cos(Phi)*sin(Theta); +NormVec_Z=cos(Theta); + +%set new plane position and update graph +set(handles.XObject,'String',num2str(NormVec_X*Z_value,4)) +set(handles.YObject,'String',num2str(NormVec_Y*Z_value,4)) +set(handles.ZObject,'String',num2str(NormVec_Z*Z_value,4)) +PLOT_Callback(hObject, eventdata, handles) + + + +function XObject_Callback(hObject, eventdata, handles) + + +function YObject_Callback(hObject, eventdata, handles) + + + + +function ZObject_Callback(hObject, eventdata, handles) + + +% --- Executes on button press in HELP. +function HELP_Callback(hObject, eventdata, handles) +path_to_uvmat=which ('uvmat');% check the path of uvmat +pathelp=fileparts(path_to_uvmat); +helpfile=fullfile(pathelp,'UVMAT_DOC','uvmat_doc.html'); +if isempty(dir(helpfile)), errordlg('Please put the help file uvmat_doc.html in the directory UVMAT/UVMAT_DOC') +else + web([helpfile '#set_object']) +end + + + + Index: /trunk/src/set_title.m =================================================================== --- /trunk/src/set_title.m (revision 2) +++ /trunk/src/set_title.m (revision 2) @@ -0,0 +1,30 @@ +%'set_title': defines the 'TITLE' of a projection object +%----------------------------------------------------------- +% function TITLE=set_title(Style,ProjMode) +% OUTPUT: +% TITLE: char string defining the title +% +% INPUT: +% Style: char string defining the style of the projection opbject +% ProjMode: char string defining the projection mode +%------------------------------------------------ +function TITLE=set_title(Style,ProjMode) +%------------------------------------------------ +TITLE=[]; %default +if isequal(Style,'points') + TITLE='POINTS'; +elseif isequal(Style,'line')|isequal(Style,'polyline') + TITLE='LINE'; +elseif isequal(Style,'plane') + TITLE='PLANE'; +elseif isequal(Style,'volume') + TITLE='VOLUME'; +elseif isequal(Style,'polygon')|isequal(Style,'rectangle')|isequal(Style,'ellipse') + if isequal(ProjMode,'inside')|isequal(ProjMode,'outside') + TITLE='PATCH'; + elseif isequal(ProjMode,'mask_inside')|isequal(ProjMode,'mask_outside') + TITLE='MASK'; + else + TITLE='LINE'; + end +end Index: /trunk/src/stra2num.m =================================================================== --- /trunk/src/stra2num.m (revision 2) +++ /trunk/src/stra2num.m (revision 2) @@ -0,0 +1,21 @@ +%'stra2num': transform letters (a, b, c) or numerical strings ('1','2'..) to the corresponding numbers +%-------------------------------------------- +% function numres=stra2num(str) +% +% OUTPUT: +% numres: number (double) +% +% INPUT: +% str: string corresponding to a number or a letter 'a' 'b',.., otherwise the output is empty +% +% see also num2stra, name_generator, name2display + +function numres=stra2num(str) +numres=[]; %default +if double(str) >= 48 & double(str) <= 57 % = test for number strings + numres=str2num(str); +elseif double(str) >= 65 & double(str) <= 90 % test on ascii code for capital letters + numres=double(str)-64; %change capital letters to corresponding number in the alphabet +elseif double(str) >= 97 & double(str) <= 122 % test on ascii code for small letters + numres=double(str)-96; %change small letters to corresponding number in the alphabet +end Index: /trunk/src/struct2nc.m =================================================================== --- /trunk/src/struct2nc.m (revision 2) +++ /trunk/src/struct2nc.m (revision 2) @@ -0,0 +1,144 @@ +%'struct2nc': create a netcdf file from a Matlab structure +%--------------------------------------------------------------------- +% errormsg=struct2nc(flname,Data) +% +%OUPUT: +%errormsg=error message, =[]: default, no error +% +%INPUT: +%flname: name of the netcdf file to create (must end with the extension '.nc') +% Data: structure containing all the information of the netcdf file (or netcdf object) +% with fields: +% .ListGlobalAttribute: cell listing the names of the global attributes (note that a global atribute with the same name as a variable is excluded) +% .Att_1,Att_2... : values of the global attributes +% .ListDimName: cell listing the names of the array dimensions +% .DimValue: array dimension values (Matlab vector with the same length as .ListDimName +% .ListVarName: cell listing the names of the variables +% .VarDimIndex: cell containing the set of dimension indices (in list .ListDimName) for each variable of .ListVarName +% .VarAttribute: cell of structures s containing names and values of variable attributes (s.name=value) for each variable of .ListVarName +% .Var1, .Var2....: variables (Matlab arrays) with names listed in .ListVarName +% +%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +% Copyright Joel Sommeria, 2008, LEGI / CNRS-UJF-INPG, sommeria@coriolis-legi.org. +%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +% This file is part of the toolbox UVMAT. +% +% UVMAT is free software; you can redistribute it and/or modify +% it under the terms of the GNU General Public License as published by +% the Free Software Foundation; either version 2 of the License, or +% (at your option) any later version. +% +% UVMAT is distributed in the hope that it will be useful, +% but WITHOUT ANY WARRANTY; without even the implied warranty of +% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +% GNU General Public License (file UVMAT/COPYING.txt) for more details. +%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA + +function errormsg=struct2nc(flname,Data) +if ~ischar(flname) + errormsg='no name input for the netcf file'; + return +end +if ~exist('Data','var') + errormsg='no data input for the netcdf file'; + return +end +hhh=which('netcdf.create');% look for built-in matlab library + +%USE OF built-in netcdf library +if ~isequal(hhh,'') + FilePath=fileparts(flname); + if ~strcmp(FilePath,'') && ~exist(FilePath,'dir') + errormsg=['directory ' FilePath ' needs to be created']; + return + end + [Data,errormsg]=check_field_structure(Data);%check the validity of the input field structure + ListVarName=Data.ListVarName; + nc=netcdf.create(flname,'NC_CLOBBER');%,'clobber'); %create the netcdf file with name flname + %write global constants + if isfield(Data,'ListGlobalAttribute') + keys=Data.ListGlobalAttribute; + for iattr=1:length(keys) + if isfield(Data,keys{iattr}) + testvar=0; + for ivar=1:length(ListVarName)% eliminate possible global attributes with the same name as a variable + if isequal(ListVarName{ivar}, keys{iattr}) + testvar=1; + break + end + end + if ~testvar + eval(['cte=Data.' keys{iattr} ';']) + if (ischar(cte) ||isnumeric(cte)) && ~isempty(cte)&& ~isequal(cte,'') + netcdf.putAtt(nc,netcdf.getConstant('NC_GLOBAL'),keys{iattr},cte) + else + errormsg='global attributes must be characters or numbers'; + return + end + end + end + end + end + %create dimensions + dimid=[]; + for idim=1:length(Data.ListDimName) + dimid(idim) = netcdf.defDim(nc,Data.ListDimName{idim},Data.DimValue(idim)); + end + VarAttribute={}; %default + testattr=0; + if isfield(Data,'VarAttribute') + VarAttribute=Data.VarAttribute; + testattr=1; + end + varid=[]; + for ivar=1:length(ListVarName) + varid(ivar)=netcdf.defVar(nc,ListVarName{ivar},'double',dimid(Data.VarDimIndex{ivar}));%define variable + end + %write variable attributes + if testattr + for ivar=1:length(VarAttribute) + if isstruct(VarAttribute{ivar}) + attr_names=fields(VarAttribute{ivar}); + for iattr=1:length(attr_names) + eval(['attr_val=VarAttribute{ivar}.' attr_names{iattr} ';']); + netcdf.putAtt(nc,varid(ivar),attr_names{iattr},attr_val); + end + end + end + end + netcdf.endDef(nc); %put in data mode + for ivar=1:length(ListVarName) + if isfield(Data,ListVarName{ivar}) + eval(['VarVal=Data.' ListVarName{ivar} ';'])%varval=values of the current variable + VarDimIndex=Data.VarDimIndex{ivar}; %indices of the variable dimensions in the list of dimensions + siz=size(VarVal); + VarDimName=Data.VarDimName{ivar};%NEW + if ischar(VarDimName)%NEW + VarDimName={VarDimName};%NEW + end%NEW + testrange=(numel(VarDimName)==1 && strcmp(VarDimName{1},ListVarName{ivar}) && numel(VarVal)==2); %NEW + testline=isequal(length(siz),2) && isequal(siz(1),1)&& isequal(siz(2), Data.DimValue(VarDimIndex)); + testcolumn=isequal(length(siz),2) && isequal(siz(1), Data.DimValue(VarDimIndex))&& isequal(siz(2),1); + if ~testline && ~testcolumn && ~isequal(siz,Data.DimValue(VarDimIndex)) + errormsg=['wrong dimensions declared for ' ListVarName{ivar} ' in struct2nc.m']; + break + end + if testline || testrange%NEW + if testrange + VarVal=linspace(VarVal(1),VarVal(2),Data.DimValue(VarDimIndex));%NEW + end + %nc{ListVarName{ivar}}=ncfloat(Data.ListDimName(VarDimIndex));%vector of x coordinates + netcdf.putVar(nc,varid(ivar), VarVal'); + else + netcdf.putVar(nc,varid(ivar), VarVal); + %nc{ListVarName{ivar}}(:) = VarVal; + end + + end + end +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% +%OLD netcdf toolbox +else + errormsg=struct2nc_toolbox(flname,Data); +end + Index: /trunk/src/struct2nc_toolbox.m =================================================================== --- /trunk/src/struct2nc_toolbox.m (revision 2) +++ /trunk/src/struct2nc_toolbox.m (revision 2) @@ -0,0 +1,132 @@ +%'struct2nc_toolbox': create a netcdf file from a Matlab structure: use of netcdf toolbox +%--------------------------------------------------------------------- +% errormsg=struct2nc_toolbox(flname,Data) +% +%OUPUT: +%errormsg=error message, =[]: default, no error +% +%INPUT: +%flname: name of the netcdf file to create (must end with the extension '.nc') +% Data: structure containing all the information of the netcdf file (or netcdf object) +% with fields: +% .ListGlobalAttribute: cell listing the names of the global attributes (note that a global atribute with the same name as a variable is excluded) +% .Att_1,Att_2... : values of the global attributes +% .ListDimName: cell listing the names of the array dimensions +% .DimValue: array dimension values (Matlab vector with the same length as .ListDimName +% .ListVarName: cell listing the names of the variables +% .VarDimIndex: cell containing the set of dimension indices (in list .ListDimName) for each variable of .ListVarName +% .VarAttribute: cell of structures s containing names and values of variable attributes (s.name=value) for each variable of .ListVarName +% .Var1, .Var2....: variables (Matlab arrays) with names listed in .ListVarName +% +%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +% Copyright Joel Sommeria, 2008, LEGI / CNRS-UJF-INPG, sommeria@coriolis-legi.org. +%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +% This file is part of the toolbox UVMAT. +% +% UVMAT is free software; you can redistribute it and/or modify +% it under the terms of the GNU General Public License as published by +% the Free Software Foundation; either version 2 of the License, or +% (at your option) any later version. +% +% UVMAT is distributed in the hope that it will be useful, +% but WITHOUT ANY WARRANTY; without even the implied warranty of +% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +% GNU General Public License (file UVMAT/COPYING.txt) for more details. +%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA + +function errormsg=struct2nc_toolbox(flname,Data) + +FilePath=fileparts(flname); +if ~strcmp(FilePath,'') &&~exist(FilePath,'dir') + errormsg=['directory ' FilePath ' needs to be created']; + return +end +[Data,errormsg]=check_field_structure(Data); +if ~isempty(errormsg) + return +end +ListVarName=Data.ListVarName; +nc=netcdf(flname,'clobber'); %create the netcdf file with name flname +%write global constants +if isfield(Data,'ListGlobalAttribute') + keys=Data.ListGlobalAttribute; + for iattr=1:length(keys) + if isfield(Data,keys{iattr}) + testvar=0; + for ivar=1:length(ListVarName)% eliminate possible global attributes with the same name as a variable + if isequal(ListVarName{ivar}, keys{iattr}) + testvar=1; + break + end + end + if ~testvar + eval(['cte=Data.' keys{iattr} ';']) + if ischar(cte) && ~isequal(cte,'') + eval(['nc.' keys{iattr} '=''' cte ''';']); + elseif isnumeric(cte)&& ~isempty(cte) + eval(['nc.' keys{iattr} '= cte; ']); + else + errormsg='global attributes must be characters or numbers'; + return + end + end + end + end +end +for idim=1:length(Data.ListDimName) + nc(Data.ListDimName{idim})=Data.DimValue(idim);%create dimensions +end + +VarAttribute={}; %default +testattr=0; +if isfield(Data,'VarAttribute') + VarAttribute=Data.VarAttribute; + testattr=1; +end +for ivar=1:length(ListVarName) + if isfield(Data,ListVarName{ivar}) + eval(['VarVal=Data.' ListVarName{ivar} ';'])%varval=values of the current variable + siz=size(VarVal); + VarDimIndex=Data.VarDimIndex{ivar}; %indices of the variable dimensions in the list of dimensions + VarDimName=Data.VarDimName{ivar};%NEW + if ischar(VarDimName)%NEW + VarDimName={VarDimName};%NEW + end%NEW + testrange=(numel(VarDimName)==1 && strcmp(VarDimName{1},ListVarName{ivar}) && numel(VarVal)==2); %NEW + testline=isequal(length(siz),2) & isequal(siz(1),1)& isequal(siz(2), Data.DimValue(VarDimIndex)); + testcolumn=isequal(length(siz),2) & isequal(siz(1), Data.DimValue(VarDimIndex))& isequal(siz(2),1); + if ~testrange && ~testline && ~testcolumn && ~isequal(siz,Data.DimValue(VarDimIndex)) + errormsg=['wrong dimensions declared for ' ListVarName{ivar} ' in struct2nc.m']; + break + end + if testline || testrange%NEW + dimname=Data.ListDimName{VarDimIndex}; + if testrange%NEW + VarVal=linspace(VarVal(1),VarVal(2),Data.DimValue(VarDimIndex));%NEW + end%NEW + nc{ListVarName{ivar}}=ncfloat(dimname);%vector of x coordinates + nc{ListVarName{ivar}}(:) = VarVal'; + else + nc{ListVarName{ivar}}=ncfloat(Data.ListDimName(VarDimIndex));%vector of x coordinates + nc{ListVarName{ivar}}(:) = VarVal; + end + %write variable attributes + if testattr + for ivar=1:length(VarAttribute) + if isstruct(VarAttribute{ivar}) + attr_names=fields(VarAttribute{ivar}); + for iattr=1:length(attr_names) + eval(['attr_val=VarAttribute{ivar}.' attr_names{iattr} ';']); + if ischar(attr_val) && ~isequal(attr_val,'') + eval(['nc{''' ListVarName{ivar} '''}.' attr_names{iattr} '=''' attr_val ''';']) + elseif isnumeric(attr_val)&& ~isempty(attr_val) + eval(['nc{''' ListVarName{ivar} '''}.' attr_names{iattr} '=attr_val ;']) + end + end + end + end + end + end +end + +close(nc); Index: /trunk/src/struct2xml.m =================================================================== --- /trunk/src/struct2xml.m (revision 2) +++ /trunk/src/struct2xml.m (revision 2) @@ -0,0 +1,62 @@ +%'struct2xml': transform a matlab structure to a xml tree. +%-------------------------------------------------------------- +% each field with char string or num vector is transformed into a corresponding xml element +% each field with a matrix containing n lines is transformed into a xml element repeated n times +% WARNING: PROBLEM WITH HIERARCHICAL structures +%%%%%%%%%%%%%%%%%%%%%%% +% OUTPUT: +% t: xmltree reproducing the structure of Object +% type 'save(t)' to visualize the xml text and save(filename,t) to save it in a file +% +% INPUT: +% Object: matlab structure, possibly hierarchical +% t: optional input xml tree in which a new branch needs to be appended +% root_uid: optional uid of the xml element under which the new subtree must be appended + +function t=struct2xml(Object,t,root_uid) +get(t,root_uid) +if ~exist('t','var') + t=xmltree; +end +if ~exist('root_uid','var') + root_uid=1; +end +fieldnames=fields(Object); +for ilist=1:length(fieldnames) + eval(['val=Object.' fieldnames{ilist} ';']) + if isstruct(val) + [t,uid]=add(t,root_uid,'element',fieldnames{ilist}); + fieldnames_sub=fields(val); + for ilist_sub=1:length(fieldnames_sub) + if isstruct(fieldnames_sub{ilist_sub}) + t=struct2xml(fieldnames_sub{ilist_sub},t,uid); + save(t) + else + eval(['val_sub=val.' fieldnames_sub{ilist_sub} ';']) + t=add_element(t,uid,fieldnames_sub{ilist_sub},val_sub); + end + end + else + t=add_element(t,root_uid,fieldnames{ilist},val); + end +end + + +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% +function t=add_element(t,uid,key,val) + if ischar(val) + [t,new_uid]=add(t,uid,'element',key); + [t]=add(t,new_uid,'chardata',val); + elseif isnumeric(val) + siz=size(val); + if length(siz)<=2 %do not translate matrices with more than 2 indices + for iline=1:siz(1) + val_str=num2str(val(iline,:),'%g\t'); + [t,new_uid]=add(t,uid,'element',key); + if siz(1)>1 + t = attributes(t,'add',new_uid,'i',num2str(iline)); + end + [t]=add(t,new_uid,'chardata',val_str); + end + end + end Index: /trunk/src/sub_field.m =================================================================== --- /trunk/src/sub_field.m (revision 2) +++ /trunk/src/sub_field.m (revision 2) @@ -0,0 +1,354 @@ +%'sub_field': combines two input fields +%----------------------------------------------------------------------- +% function SubData=sub_field(Field,Field_1) +% +% OUPUT: +% SubData: structure representing the resulting field +% +% INPUT: +% UvData: main structure UvData associated to the uvmat GUI as 'UserData' +% Field: cell of Matlab structures representing the input fields +% +% -- TODO: need to be rationalized -- + +function [SubData,errormsg]=sub_field(Field,Field_1) +test_attr=0; +if isfield(Field,'ListGlobalAttribute') + SubData.ListGlobalAttribute=Field.ListGlobalAttribute; + for ilist=1:numel(Field.ListGlobalAttribute) + AttrName=Field.ListGlobalAttribute{ilist}; + eval(['SubData.' AttrName '=Field.' AttrName ';']) + end + test_attr=1; +end +if isfield(Field_1,'ListGlobalAttribute') + for ilist=1:numel(Field_1.ListGlobalAttribute) + test_1=1; + AttrName=Field_1.ListGlobalAttribute{ilist}; + if test_attr + for i_prev=1:numel(Field.ListGlobalAttribute) + if isequal(Field.ListGlobalAttribute{i_prev},AttrName) + test_1=0; %attribute already written + eval(['Val=Field.' AttrName ';']) + eval(['Val_1=Field_1.' AttrName ';']) + if isequal(Val,Val_1) + break% data already written + else + eval(['SubData.' AttrName '_1=Field_1.' AttrName ';']) + end + end + end + end + if test_1 + eval(['SubData.' AttrName '=Field_1.' AttrName ';']) + end + end +end +SubData.ListVarName=Field.ListVarName; +SubData.VarDimName=Field.VarDimName; +if isfield(Field,'VarAttribute') + SubData.VarAttribute=Field.VarAttribute; +end +%reproduce Field by default +for ivar=1:numel(Field.ListVarName) + VarName=Field.ListVarName{ivar}; + eval(['SubData.' VarName '=Field.' VarName ';']) +end + +%fields +[CellVarIndex,NbDim,VarTypeCell,errormsg]=find_field_indices(Field); +if ~isempty(errormsg) + errormsg=['invalid first input to sub_field:' errormsg]; + return +end +[CellVarIndex_1,NbDim_1,VarTypeCell_1,errormsg]=find_field_indices(Field_1); +if ~isempty(errormsg) + errormsg=['invalid second input to sub_field:' errormsg]; + return +end +iselect=find(NbDim==2); +if ~isequal(numel(iselect),1) + errormsg='invalid first input to sub_field: it must contain a single 2D field cell'; + return +end +iselect_1=find(NbDim_1==2); +if ~isequal(numel(iselect_1),1) + errormsg='invalid second input to sub_field: it must contain a single 2D field cell'; + return +end +% VarIndex=CellVarIndex{iselect}; +% VarIndex_1=CellVarIndex_1{iselect_1}; +VarType=VarTypeCell{iselect}; +VarType_1=VarTypeCell_1{iselect_1}; +testX=~isempty(VarType.coord_x)&& ~isempty(VarType.coord_y);%unstructured coordiantes +testX_1=~isempty(VarType_1.coord_x)&& ~isempty(VarType_1.coord_y);%unstructured coordiantes +testU=~isempty(VarType.vector_x)&& ~isempty(VarType.vector_y);%vector field +testU_1=~isempty(VarType_1.vector_x)&& ~isempty(VarType_1.vector_y);%vector field +% testfalse=~isempty(VarType.errorflag); +testfalse_1=~isempty(VarType_1.errorflag); +ivar_C=[VarType.scalar VarType.image VarType.color VarType.ancillary]; %defines index (indices) for the scalar or ancillary fields +if numel(ivar_C)>1 + errormsg='too many scalar fields in the first input of sub_field.m'; + return +end +ivar_C_1=[VarType_1.scalar VarType_1.image VarType_1.color VarType_1.ancillary]; %defines index (indices) for the scalar or ancillary fields +if numel(ivar_C_1)>1 + errormsg='too many scalar fields in the second input of sub_field.m'; + return +end + +%substract two vector fields or two scalars +if (testU && testU_1) || (~testU && ~testU_1) + %check coincidence in positions + %unstructured coordinates + if testX + XName=Field.ListVarName{VarType.coord_x}; + YName=Field.ListVarName{VarType.coord_y}; + eval(['vec_X=Field.' XName ';']) + eval(['vec_Y=Field.' YName ';']) + nbpoints=numel(vec_X); + vec_X=reshape(vec_X,1,nbpoints); + vec_Y=reshape(vec_Y,1,nbpoints); + if testX_1 %unstructured coordinates for the second field + X_1_Name=Field_1.ListVarName{VarType_1.coord_x}; + Y_1_Name=Field_1.ListVarName{VarType_1.coord_y}; + eval(['vec_X_1=Field_1.' X_1_Name ';']) + eval(['vec_Y_1=Field_1.' Y_1_Name ';']) + nbpoints_1=numel(vec_X_1); + else %structured coordinates for the second field + y_1_Name=Field_1.ListVarName{VarType_1.coord(1)}; + x_1_Name=Field_1.ListVarName{VarType_1.coord(2)}; + eval(['y_1=Field_1.' y_1_Name ';']) + eval(['x_1=Field_1.' x_1_Name ';']) + npxy(1)=numel(y_1); + npxy(2)=numel(x_1); + nbpoints_1=npxy(1)*npxy(2); + [vec_X_1,vec_Y_1]=meshgrid(x_1,y_1); + end + vec_X_1=reshape(vec_X_1,1,nbpoints_1); + vec_Y_1=reshape(vec_Y_1,1,nbpoints_1); + if testfalse_1 + FFName_1=Field_1.ListVarName{VarType_1.errorflag}; + eval(['vec_FF_1=Field_1.' FFName_1 ';']) + vec_FF_1=reshape(vec_FF_1,1,nbpoints_1); + indsel=find(~vec_FF_1); + vec_X_1=vec_X_1(indsel); + vec_Y_1=vec_Y_1(indsel); + end + if testU % vector fields + U_1_Name=Field_1.ListVarName{VarType_1.vector_x}; + V_1_Name=Field_1.ListVarName{VarType_1.vector_y}; + eval(['vec_U_1=Field_1.' U_1_Name ';']) + eval(['vec_V_1=Field_1.' V_1_Name ';']) + vec_U_1=reshape(vec_U_1,1,nbpoints_1); + vec_V_1=reshape(vec_V_1,1,nbpoints_1); + if testfalse_1 + vec_U_1=vec_U_1(indsel); + vec_V_1=vec_V_1(indsel); + end + else + A_1_Name=Field_1.ListVarName{ivar_C_1}; + eval(['vec_A_1=Field_1.' A_1_Name ';']) + vec_A_1=reshape(vec_A_1,1,nbpoints_1); + if testfalse_1 + vec_A_1=vec_A_1(indsel); + end + end + if ~isequal(vec_X_1,vec_X) && ~isequal(vec_Y_1,vec_Y) % if the unstructured positions are not the same + if testU + vec_U_1=griddata_uvmat(vec_X_1,vec_Y_1,vec_U_1,vec_X,vec_Y); %interpolate vectors in the second field + vec_V_1=griddata_uvmat(vec_X_1,vec_Y_1,vec_V_1,vec_X,vec_Y); %interpolate vectors in the second field + else + vec_A_1=griddata_uvmat(vec_X_1,vec_Y_1,vec_A_1,vec_X,vec_Y); %interpolate vectors in the second field + end + end + if testU + UName=Field.ListVarName{VarType.vector_x}; + VName=Field.ListVarName{VarType.vector_y}; + eval(['vec_U=Field.' UName ';']) + eval(['vec_V=Field.' VName ';']) + vec_U=reshape(vec_U,1,numel(vec_U)); + vec_V=reshape(vec_V,1,numel(vec_V)); + eval(['SubData.' UName '=vec_U-vec_U_1;']) + eval(['SubData.' VName '=vec_V-vec_V_1;']) + else + AName=Field.ListVarName{ivar_C}; + eval(['SubData.' AName '=Field.' AName '-vec_A_1;']) + end + else %structured coordiantes + XName=Field.ListVarName{VarType.coord(2)}; + YName=Field.ListVarName{VarType.coord(1)}; + eval(['x=Field.' XName ';']) + eval(['y=Field.' YName ';']) + if testX_1 %unstructured coordinates for the second field + errormsg='the second input scalar is not on a regular grid: comparison option not implemented'; + return + else + XName_1=Field.ListVarName{VarType_1.coord(2)}; + YName_1=Field.ListVarName{VarType_1.coord(1)}; + eval(['x_1=Field_1.' XName_1 ';']) + eval(['y_1=Field_1.' YName_1 ';']) + end + if testU % vector fields + UName=Field.ListVarName{VarType.vector_x}; + VName=Field.ListVarName{VarType.vector_y}; + U_1_Name=Field_1.ListVarName{VarType_1.vector_x}; + V_1_Name=Field_1.ListVarName{VarType_1.vector_y}; + eval(['U_1=Field_1.' U_1_Name ';']) + eval(['V_1=Field_1.' V_1_Name ';']) + if ~isequal(x_1,x)||~isequal(y_1,y) + [X_1,Y_1]=meshgrid(x_1,y_1); + U_1 =interp2(X_1,Y_1,U_1,x,y'); + V_1 =interp2(X_1,Y_1,V_1,x,y'); + end + val(['SubData.' UName '=Field.' UName '-U_1;']) + val(['SubData.' VName '=Field.' VName '-V_1;']) + else + AName=Field.ListVarName{ivar_C}; + A_1_Name=Field_1.ListVarName{ivar_C_1}; + eval(['A_1=double(Field_1.' A_1_Name ');']) + if ~isequal(x_1,x)||~isequal(y_1,y) + [X_1,Y_1]=meshgrid(x_1,y_1); + A_1 =interp2(X_1,Y_1,A_1,x,y'); + end + eval(['SubData.' AName '=double(Field.' AName ')-A_1;']) + end + end +end + +% merge a vector field and a scalar as second input +if testU && ~testU_1 + AName_1=Field_1.ListVarName{ivar_C_1}; + if isfield(Field_1,'VarAttribute') && numel(Field_1.VarAttribute)>=ivar_C_1 + AAttr=Field_1.VarAttribute{ivar_C_1} ; + else + AAttr=[]; + end + if testX_1 %unstructured coordinate + XName_1=Field_1.ListVarName{VarType_1.coord_x}; + YName_1=Field_1.ListVarName{VarType_1.coord_y}; + SubData.ListVarName=[SubData.ListVarName {XName_1} {YName_1}]; + DimCell=Field_1.VarDimName([VarType_1.coord_x VarType_1.coord_y ]); + if isfield(Field_1,'VarAttribute') + if numel(Field_1.VarAttribute)>=VarType_1.coord_x + XAttr=Field_1.VarAttribute{VarType_1.coord_x} ; + else + XAttr=[]; + end + if numel(Field_1.VarAttribute)>=VarType_1.coord_y + YAttr=Field_1.VarAttribute{VarType_1.coord_y} ; + else + YAttr=[]; + end + SubData.VarAttribute=[SubData.VarAttribute {XAttr} {YAttr}]; + end + else + XName_1=Field_1.ListVarName{VarType_1.coord(2)}; + YName_1=Field_1.ListVarName{VarType_1.coord(1)}; +% DimCell=[{YName_1} {XName_1}]; + if isfield(Field_1,'VarAttribute') + if numel(Field_1.VarAttribute)>=VarType_1.coord(2) + XAttr=Field_1.VarAttribute{VarType_1.coord(2)} ; + else + XAttr=[]; + end + if numel(Field_1.VarAttribute)>=VarType_1.coord(1) + YAttr=Field_1.VarAttribute{VarType_1.coord(1)} ; + else + YAttr=[]; + end + SubData.VarAttribute=[SubData.VarAttribute {YAttr} {XAttr}]; + end + end + %look for previously used variable names + XName_1_1=XName_1;%default + YName_1_1=YName_1;%default + AName_1_1=AName_1;%default + for iprev=1:numel(SubData.ListVarName) + switch SubData.ListVarName{iprev} + case XName_1 + XName_1_1=[XName_1 '_1']; + case YName_1 + YName_1_1=[YName_1 '_1']; + case AName_1 + AName_1_1=[AName_1 '_1']; + end + end + if ~testX_1 + DimCell=[{XName_1_1} {YName_1_1}]; + end + SubData.ListVarName=[SubData.ListVarName {XName_1_1} {YName_1_1} {AName_1_1}]; + DimCell=[DimCell Field_1.VarDimName(ivar_C_1)]; %(TODO: check for dimension names) + SubData.VarDimName=[SubData.VarDimName DimCell]; + if isfield(Field_1,'VarAttribute') + SubData.VarAttribute=[SubData.VarAttribute {AAttr}]; + end + eval(['SubData.' XName_1_1 '=Field_1.' XName_1 ';']) + eval(['SubData.' YName_1_1 '=Field_1.' YName_1 ';']) + eval(['SubData.' AName_1_1 '=Field_1.' AName_1 ';']) +end + +%merge a scalar as the first input and a vector field as second input +if ~testU && testU_1 + UName_1=Field_1.ListVarName{VarType_1.vector_x}; + VName_1=Field_1.ListVarName{VarType_1.vector_y}; + UAttr=Field_1.VarAttribute{VarType_1.vector_x}; + VAttr=Field_1.VarAttribute{VarType_1.vector_y}; + if testX_1 %unstructured coordinate for the second field + XName_1=Field_1.ListVarName{VarType_1.coord_x}; + YName_1=Field_1.ListVarName{VarType_1.coord_y}; + + XAttr=Field_1.VarAttribute{VarType_1.coord_x}; + YAttr=Field_1.VarAttribute{VarType_1.coord_y}; +% SubData.ListVarName=[SubData.ListVarName {XName_1} {YName_1}]; + DimCell=Field_1.VarDimName([VarType_1.coord_x VarType_1.coord_y ]); + else + XName_1=Field_1.ListVarName{VarType_1.coord(2)}; + YName_1=Field_1.ListVarName{VarType_1.coord(1)}; + if numel(Field_1.VarAttribute)>=VarType_1.coord(2) + XAttr=Field_1.VarAttribute{VarType_1.coord(2)}; + else + XAttr=[]; + end + if numel(Field_1.VarAttribute)>=VarType_1.coord(1) + YAttr=Field_1.VarAttribute{VarType_1.coord(1)}; + else + YAttr=[]; + end + end + %check for the existence of the same variable name + XName_1_1=XName_1; %default + YName_1_1=YName_1; %default + UName_1_1=UName_1; %default + VName_1_1=VName_1; %default + for iprev=1:numel(SubData.ListVarName) + switch SubData.ListVarName{iprev} + case XName_1 + XName_1_1=[XName_1 '_1']; + case YName_1 + YName_1_1=[YName_1 '_1']; + case UName_1 + UName_1_1=[UName_1 '_1']; + case VName_1 + VName_1_1=[VName_1 '_1']; + end + end + if ~testX_1 + DimCell=[{XName_1_1} {YName_1_1}]; + end + SubData.ListVarName=[SubData.ListVarName {XName_1_1} {YName_1_1} {UName_1_1} {VName_1_1}]; + DimCell=[DimCell Field_1.VarDimName([VarType_1.vector_x VarType_1.vector_y ])]; + SubData.VarDimName=[SubData.VarDimName DimCell]; + if ~(isfield(SubData,'VarAttribute') && numel(SubData.VarAttribute)==numel(SubData.ListVarName)) + for ivar=numel(SubData.VarAttribute)+1:numel(SubData.ListVarName)-4 + SubData.VarAttribute{ivar}=[]; + end + end + SubData.VarAttribute=[SubData.VarAttribute {XAttr} {YAttr} {UAttr} {VAttr}]; + eval(['SubData.' XName_1_1 '=Field_1.' XName_1 ';']) + eval(['SubData.' YName_1_1 '=Field_1.' YName_1 ';']) + eval(['SubData.' UName_1_1 '=Field_1.' UName_1 ';']) + eval(['SubData.' VName_1_1 '=Field_1.' VName_1 ';']) +end + + Index: /trunk/src/translate_points.m =================================================================== --- /trunk/src/translate_points.m (revision 2) +++ /trunk/src/translate_points.m (revision 2) @@ -0,0 +1,166 @@ +%'translate_points': associated with GUI translate_points.fig to display message boxes, for error, warning or input calls +% translate_points(title,display) +% +% OUTPUT: +% answer (text string)= 'yes', 'No', 'cancel', or the text string introduced as input +% +%INPUT: +% title: string indicating the type of message box: +% title= 'INPUT_TXT','CONFIMATION' ,'ERROR', 'WARNING', 'INPUT_Y-N', default = 'INPUT_TXT' (the title is displayed in the upper bar of the fig). +% if title='INPUT_TXT', input data is asked in an edit box +% if title='CONFIMATION'', 'ERROR', 'WARNING', the figure remains opened until a button 'OK' is pressed +% if title='INPUT_Y-N', an answer Yes/No is requested +% display, displayed text +% default_answer: default answer in the edit box (only used with title='INPUT_TXT') + +function varargout = translate_points(varargin) + +% Last Modified by GUIDE v2.5 05-Jan-2010 09:49:31 + +% Begin initialization code - DO NOT EDIT +gui_Singleton = 1; +gui_State = struct('gui_Name', mfilename, ... + 'gui_Singleton', gui_Singleton, ... + 'gui_OpeningFcn', @translate_points_OpeningFcn, ... + 'gui_OutputFcn', @translate_points_OutputFcn, ... + 'gui_LayoutFcn', [] , ... + 'gui_Callback', []); +if nargin && ischar(varargin{1}) + gui_State.gui_Callback = str2func(varargin{1}); +end + +if nargout + [varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:}); +else + gui_mainfcn(gui_State, varargin{:}); +end +% End initialization code - DO NOT EDIT + +% --- Executes just before translate_points is made visible. +function translate_points_OpeningFcn(hObject, eventdata, handles,input_shift) +% This function has no output args, see OutputFcn. + +% Choose default command line output for translate_points +handles.output = 'Cancel'; + +% Update handles structure +guidata(hObject, handles); +testNo=0; +testCancel=1; +testinputstring=0; +icontype='quest';%default question icon (text input asked) + +% Determine the position of the dialog - centered on the screen +FigPos=get(0,'DefaultFigurePosition'); +OldUnits = get(hObject, 'Units'); +set(hObject, 'Units', 'pixels'); +OldPos = get(hObject,'Position'); +FigWidth = OldPos(3); +FigHeight = OldPos(4); +ScreenUnits=get(0,'Units'); +set(0,'Units','pixels'); +ScreenSize=get(0,'ScreenSize'); +set(0,'Units',ScreenUnits); + +FigPos(1)=1/2*(ScreenSize(3)-FigWidth); +FigPos(2)=2/3*(ScreenSize(4)-FigHeight); +FigPos(3:4)=[FigWidth FigHeight]; +set(hObject, 'Position', FigPos); +set(hObject, 'Units', OldUnits); + +% Show a question icon from dialogicons.mat - variables questIconData and questIconMap +load dialogicons.mat +eval(['IconData=' icontype 'IconData;']) +eval(['IconCMap=' icontype 'IconMap;']) +questIconMap(256,:) = get(handles.figure1, 'Color'); +Img=image(IconData, 'Parent', handles.axes1); +set(handles.figure1, 'Colormap', IconCMap); +set(handles.axes1, ... + 'Visible', 'off', ... + 'YDir' , 'reverse' , ... + 'XLim' , get(Img,'XData'), ... + 'YLim' , get(Img,'YData') ... + ); + +if exist('input_shift','var') && ~isempty(input_shift) + set(handles.x_shift,'String',num2str(input_shift(1))); + if numel(input_shift)>=2 + set(handles.y_shift,'String',num2str(input_shift(2))); + end + if numel(input_shift)>=3 + set(handles.z_shift,'String',num2str(input_shift(3))); + end +end + +set(handles.figure1,'WindowStyle','modal')% Make% Make the GUI modal +% UIWAIT makes translate_points wait for user response (see UIRESUME) +uiwait(handles.figure1); + + +% --- Outputs from this function are returned to the command line. +function varargout = translate_points_OutputFcn(hObject, eventdata, handles) + +% Get default command line output from handles structure +varargout{1}=[0 0 0];%default +if ~isequal(handles.output,'Cancel') + x_shift=str2num(get(handles.x_shift,'String')); + y_shift=str2num(get(handles.y_shift,'String')); + z_shift=str2num(get(handles.z_shift,'String')); + if ~isempty(x_shift) + varargout{1}(1)=x_shift; + end + if ~isempty(y_shift) + varargout{1}(2)=y_shift; + end + if ~isempty(z_shift) + varargout{1}(3)=z_shift; + end +end +% The figure can be deleted now +delete(handles.figure1); + +% --- Executes on button press in OK. +function OK_Callback(hObject, eventdata, handles) +handles.output = get(hObject,'String'); +guidata(hObject, handles);% Update handles structure +uiresume(handles.figure1); + +% --- Executes on button press in Cancel. +function Cancel_Callback(hObject, eventdata, handles) +handles.output = get(hObject,'String'); +%handles.output = 'Cancel' +guidata(hObject, handles); % Update handles structure +% Use UIRESUME instead of delete because the OutputFcn needs +% to get the updated handles structure. +uiresume(handles.figure1); + +% --- Executes when user attempts to close figure1. +function figure1_CloseRequestFcn(hObject, eventdata, handles) +if isequal(get(handles.figure1, 'waitstatus'), 'waiting') + % The GUI is still in UIWAIT, us UIRESUME + uiresume(handles.figure1); +else + % The GUI is no longer waiting, just close it + delete(handles.figure1); +end + +% --- Executes on key press over figure1 with no controls selected. +function figure1_KeyPressFcn(hObject, eventdata, handles) +% Check for "enter" or "escape" +if isequal(get(hObject,'CurrentKey'),'escape') + % User said no by hitting escape + handles.output = 'Cancel'; + + % Update handles structure + guidata(hObject, handles); + + uiresume(handles.figure1); +end +if isequal(get(hObject,'CurrentKey'),'return') + uiresume(handles.figure1); +end + + + + + Index: /trunk/src/update_menu.m =================================================================== --- /trunk/src/update_menu.m (revision 2) +++ /trunk/src/update_menu.m (revision 2) @@ -0,0 +1,27 @@ +%'update_menu': find an input string in a menu, add it to the menu at the penultimate position if it does not exist +%----------------------------------------------- +% function menu_str=update_menu(handle,strinput) +% +% OUTPUT: +% menu_str: new menu; cell of strings +% +% INPUT: +% handle: handle of the menu to modify (listbox uicontrol) +% strinput: char string to detect or add in the menu + +function menu_str=update_menu(handle,strinput) +menu_str=get(handle,'String'); +nbmenu=length(menu_str); +ichoice=0;%default +for imenu=1:nbmenu + if isequal(menu_str{imenu},strinput) + ichoice=imenu; + end +end +if ichoice==0%the input string does not exist in the menu + menu_str{nbmenu+1}=menu_str{nbmenu};%shift the last item ('more...') + menu_str{nbmenu}=strinput; + set(handle,'String',menu_str) + ichoice=nbmenu; +end +set(handle,'Value',ichoice) Index: /trunk/src/update_obj.m =================================================================== --- /trunk/src/update_obj.m (revision 2) +++ /trunk/src/update_obj.m (revision 2) @@ -0,0 +1,75 @@ +%'update_obj': update the object graph representation and its projection field, record it in the uvmat interface +%------------------------------------------------------------------- +%Object=update_obj(UvData,IndexObj,ObjectData,PlotHandles); +% +%OUTPUT: +%UvData: data to be stored as 'Userdata' on the uvmat interface +%IndexObj: object index for a new object added to the list in UvData +% the function updates UvData.Object{IndexObj}, and possibly adds a new plot (UvData.Plane or Line) in the list atached to the interface +% +%INPUT: +%UvIn: structure stored as 'Userdata' on the uvmat interface +%IndexObjIn: object index for an existing objects stored in UvData +%ObjectData: structure containing the input object properties +%PlotHandles: structure containing the handles of the plotting parameter buttons on the uvmat interface (obtained by get_plot_handles.m) +%------------------------------------- + +function Object_out=update_obj(UvData,IndexObj,ObjectData,PlotHandles) + +%default input and output +Object_out=ObjectData;%default +if isfield(UvData,'Object') + Object_set=UvData.Object; +else + Object_set={};%create the object +end + +% object representation in the different projected field plots +for iview=1:length(Object_set) %loop on projection planes iview + if isfield(Object_set{iview},'plotaxes') + haxes=Object_set{iview}.plotaxes;% axes for the field plot + if ishandle(haxes) & isequal(get(haxes,'Type'),'axes')% update the representation of the object IndexObj on this axes if it exists + testupdate=0; + HandlesDisplay=[];%default + if length(Object_set)>= IndexObj && isfield(Object_set{IndexObj},'HandlesDisplay') + HandlesDisplay=Object_set{IndexObj}.HandlesDisplay;%list of handles of object representations + end + hplot_list=findobj(haxes,'Tag','proj_object'); + for ih=1:length(HandlesDisplay) + plot_detect=find(hplot_list==HandlesDisplay(ih)); + if ~isempty(plot_detect) + Object_out.HandlesDisplay(ih)=plot_object(ObjectData,Object_set{iview},HandlesDisplay(ih),'m');%update the the object representation + testupdate=1; + break + end + end + if ~testupdate% draw new object plot + hh=plot_object(ObjectData,Object_set{iview},haxes,'m');%draw the object with the new object data + Object_out.HandlesDisplay=[Object_out.HandlesDisplay hh]; + PlotData=get(hh,'UserData'); + PlotData.IndexObj=IndexObj; + set(hh,'UserData',PlotData); %record the object index in the graph + end + end + end +end + +% plot the field projected on the object +if ~isempty(PlotHandles) %&& ~testmask + ProjData= proj_field(UvData.Field,ObjectData,IndexObj);%project the current interface field on ObjectData + if ~isempty(ProjData) + plotaxes=[];%default + if length(Object_set)>= IndexObj && isfield(Object_set{IndexObj},'plotaxes') + plotaxes=Object_set{IndexObj}.plotaxes; + end + [PlotType,Object_out.PlotParam,plotaxes]=plot_field(ProjData,plotaxes,PlotHandles); + Object_out.plotaxes=plotaxes; + plotfig=get(plotaxes,'parent'); + name_str=get(plotfig,'Name'); + if ~isequal(name_str,'uvmat') + set(plotfig,'Name',['Projection on' num2str(IndexObj) '-' set_title(ObjectData.Style,ObjectData.ProjMode)]); + end + end +end + + Index: /trunk/src/update_waitbar.m =================================================================== --- /trunk/src/update_waitbar.m (revision 2) +++ /trunk/src/update_waitbar.m (revision 2) @@ -0,0 +1,14 @@ +%'update_waitbar': update the waitbar display, used for ACTION functions in the GUI 'series' +%------------------------------------------------------------------ +%INPUT: +% hwaitbar: handles of the waitbar to update +% bar_size: vector with 4 elements, representing the abscissa, ordinate, width, height of the waitbar relative to the GUI +% advance_ratio: number between 0 and 1 representing the advancement of the calculation (loop index relative to the total length) + +function update_waitbar(hwaitbar,bar_size,advance_ratio) +waitbarpos(1)=bar_size(1); +waitbarpos(3)=bar_size(3); +waitbarpos(4)=advance_ratio*bar_size(4); +waitbarpos(2)=bar_size(4)+bar_size(2)-waitbarpos(4); +set(hwaitbar,'Position',waitbarpos) +drawnow Index: /trunk/src/uvmat.m =================================================================== --- /trunk/src/uvmat.m (revision 2) +++ /trunk/src/uvmat.m (revision 2) @@ -0,0 +1,4821 @@ +%'uvmat': function associated with the GUI 'uvmat.fig' for images and data field visualization +%------------------------------------------------------------------------ +% function huvmat=uvmat(input) +% +%OUTPUT +% huvmat=current handles of the GUI uvmat.fig +% +%INPUT: +% input: input file name (if character chain), or input image matrix to +% visualize, or Matlab structure representing netcdf fields (with fields +% ListVarName....) +% +%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +% Copyright Joel Sommeria, 2008, LEGI / CNRS-UJF-INPG, sommeria@coriolis-legi.org. +%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +% This open is part of the toolbox UVMAT. +% +% UVMAT is free software; you can redistribute it and/or modify +% it under the terms of the GNU General Public License as published by +% the Free Software Foundation; either version 2 of the License, or +% (at your option) any later version. +% +% UVMAT is distributed in the hope that it will be useful, +% but WITHOUT ANY WARRANTY; without even the implied warranty of +% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +% GNU General Public License (open UVMAT/COPYING.txt) for more details. +%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +% +% Information stored on the interface: +% 'Strings' of all edit boxes and menus: get(handles.Tag,'String') +% 'Values' of all menus and toggle buttons: get(handles.Tag,'Value') +% Matlab structure stored as 'UserData' of the figure uvmat.fig,(can be obtained by right mouse click on the interface). +% It contains the following fields: +% - Fixed specifiacation of plotting figures and axes (defined bu uvmat_OpeningFcn) +% .PosColorbar: [0.8210 0.4710 0.0190 0.4450]; specified position of the colorbar on figures +% - Information read in the documentation open of a series (activated by RootPath_Callback) : +% .XmlData, with fields: +% .Time: matrix of times of the images with index i and j +% .GeometryCalib: [1x1 struct] +% - Information defined from the interface: +% .NewSeries: =1 when the first view of a new field series is displayed, else 0 +% .filename:(char string) +% .VelType:(char string) type of velocity field selected +% .VelType_1:(char string) REMPLACER LE CELL ACTUEL +% .FieldName: (char string) main field selected('image', 'velocity'...) +% .FieldName_1:(char string) second field selected('image', 'velocity'...) +% .CName: (char string)name of the scalar used for vector colors +% .CoordType: (char string) coordinate transform: e.g. 'phys' or 'px' +% .MouseAction: store the current effect of mouse button (create or edit objects) +% - Information on projection objects +% .Object: {[1x1 struct]} +% .CurrentObjectIndex: index of the projection object .Object currently selected for editing +% -Information on the current field (Field{i}) +% .Txt : text information to display (e.g. error message) +% .NbDim: number of dimensions (=0 by default) +% .NbCoord: number of vector components +% .CoordType: expresses the type of coordinate ('px' for image, 'sig' for instruments, or 'phys') +% .dt: time interval for the corresponding image pair +% .Mesh: estimated typical distance between vectors +% .ZMax: +% .ZMin: +% .X, .Y, .Z: set of vector coordinates +% .U,.V,.W: corresponding set of vector components +% .F: corresponding set of warning flags +% .FF: corresponding set of false flags, =0 for good vectors +% .C: corresponding values of the scalar used for vector color +% (.X, .Y, .Z,.U,.V,.W,.F,.FF,.C are matlab vectors of the same length, +% equal to the number of vectors stored in the input open) +% .CName: name of the scalar .C +% .CType: type of the scalar .C, setting how the scalar is obtained (see 'Scalars' below) +% .A image or scalar +% .AX: vector of dimension 2 representing the first and last values +% of the X coordinates for the image or scalar known on a regular grid, +% or vector of dimension .A for a scaler defined on irregular grid. +% .AY: same as .AX along the Y direction +% .AName: name of the scalar, ='image' for an image + +% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%% DATA FLOW (for run0_Callback) %%%%%%%%%%%%%%%%%%%%: +% +% Main input open second input open(_1) second image (pair animation) +% read_ncfield.m | | +% read_image.m | | +% Field{1} Field{2} +% | +% coord transform (phys.m) or other user defined fct acting on Field{i} | +% Field{i} +% | +% calc_field.m: calculate scalar or other derived fields (vort, div..). +% +% sub_field.m: combine the input Field{i} in a single set of fields (vector + scalar): +% Field{i=1->3}.X --> UvData.X | +% | +% UvData +% | +% plot histograms of the whole field +% proj_field.m: project the set of fields on the current projection objects defined by UvData.Object +% | | +% ObjectData +% | +% plot_field.m: plot the projected fields and store them as user | +% data of the plotting axes | +% | +% AxeData +% +%%%%%%%%%%%%%% SCALARS: %%%%%%%%%%%%ùù%%% +% scalars are displayed either as an image or countour plot, either as a color of +% velocity vectors. The scalar values in the first case is represented by +% UvData.Field.A, and by UvData.Field.C in the second case. The corresponding set of X +% and Y coordinates are represented by UvData.Field.AX and UvData.Field.AY, and .X and +% .Y for C (the same as velocity vectors). If A is a nxxny matrix (scalar +% on a regtular grid), then .AX andf.AY contains only two elements, represneting the +% coordinates of the four image corners. The scalar name is represented by +% the strings .AName and/or .CName. +% If the scalar exists in an input open (image or scalar stored under its +% name in a netcdf open), it is directly read at the level of Field{1}or Field{2}. +% Else only its name AName is recorded in Field{i}, and its field is then calculated +%by the fuction calc_scal after the coordinate transform or after projection on an edit + +% Properties attached to plotting figures (standard Matlab properties): +% 'CurrentAxes'= gca or get(gcf,'CurrentAxes'); +% 'CurrentPoint'=get(gcf,'CurrentPoint'): figure coordinates of the point over which the mouse is positioned +% 'CurrentCharacter'=get(gcf,'CurrentCharacter'): last character typed over the figure where the mouse is positioned +% 'WindowButtonMotionFcn': function permanently called by mouse motion over the figure +% 'KeyPressFcn': function called by pressing a key on the key board +% 'WindowButtonDownFcn': function called by pressing the mouse over the figure +% 'WindowButtonUpFcn': function called by releasing the mouse pressure over the figure + +% Properties attached to plotting axes: +% 'CurrentPoint'=get(gca,'CurrentPoint'); (standard Matlab) same as for the figure, but position in plot coordinates. +% AxeData:=get(gca,'UserData'); +% AxeData.Drawing = create: create a new edit +% = deform: modify an existing edit by moving its defining create +% = off: no current drawing action +% = translate: translate an existing edit +% = zoom: isolate a subregion for zoom in=1 if an edit is being currently drawn, 0 else (set to 0 by releasing mouse button) +% .hset_edit=handle of the set_edit interface (if a projection edit is edited); +% .CurrentOrigin: Origin of a curently drawn edit +% .CurrentLine: currently drawn menuline (A REVOIR) +% .CurrentObject: handle of the currently drawn edit +% .CurrentRectZoom: current rectangle used for zoom +% .zoomon : zoom state (a revoir) +% .X, .Y, .Z: array of coordinates defining the position of the vector: ASSOCIER AU PLAN (OBJET) PLUTOT QU'A L'AXE ? +% .U, .V, .W: array of components of the vector +% .C: +% .F: +% .FF: +% .A + +% Properties attached to projection objects (create, menuline, menuplane...): +% 'Tag'='proj_edit': for all projection objects +% ObjectData.Style=...: style of projection edit: +% .ProjMode +% .Coord: defines the position of the edit +% .XMin,YMin.... +% .XMax,YMax.... +% .DX,DY,DZ +% .Phi, .Theta, .Psi : Euler angles +% .X,.Y,.U,.V.... : field data projected on the edit +% .IndexObj: index in the list of UvData.Object + %during plotting +% .plotaxes: handles of the current axes used to plot the result of field projection on the object +% .plothandle: vector of handle(s) of the object graphic represnetation in all the opened plotting axes +% To each projection object #iobj, corresponds an axis +% Object{iobj}.plotaxes and nbobj representation graphs Object{iobj}.plothandles(:) (where nbobj is the +% nbre of current objects opened in uvmat. Note that Object{iobj}.plothandles(iobj)=[] : an object is not represented in its own projection field; +%------------------------------------------------------------------- +%------------------------------------------------------------------- +% I - MAIN FUNCTION UVMAT (DO NOT MODIFY) +%------------------------------------------------------------------- +%------------------------------------------------------------------- +function varargout = uvmat(varargin) + +% Begin initialization code - DO NOT EDIT +gui_Singleton = 1; +gui_State = struct('gui_Name', mfilename, ... + 'gui_Singleton', gui_Singleton, ... + 'gui_OpeningFcn', @uvmat_OpeningFcn, ... + 'gui_OutputFcn', @uvmat_OutputFcn, ... + 'gui_LayoutFcn', [], ... + 'gui_Callback', []); +if nargin && ischar(varargin{1}) + gui_State.gui_Callback = str2func(varargin{1}); +end + +if nargout + varargout{1:nargout} = gui_mainfcn(gui_State, varargin{:}); +else + gui_mainfcn(gui_State, varargin{:}); +end +% End initialization code - DO NOT EDIT + +%------------------------------------------------------------------- +% --- Executes just before uvmat is made visible. +function uvmat_OpeningFcn(hObject, eventdata, handles, input ) +%------------------------------------------------------------------- +%WARNING: avoid the second input parameter, leads to erros +global dircur dir_opening +% Choose default command menuline output for uvmat +handles.output = hObject; + +% %group handles for input file in a structure handles.InputFile +% handlesInputFile={handles.RootPath,handles.SubDir,handles.RootFile,handles.FileIndex,handles.FileExt}; +% TagsInputFile={'RootPath','SubDir','RootFile','FileIndex','FileExt'}; +% handles.InputFile=cell2struct(handlesInputFile,TagsInputFile,2); +% +% %group handles for the second input file in a structure handles.InputFile_1 +% handlesInputFile={handles.RootPath_1,handles.SubDir_1,handles.RootFile_1,handles.FileIndex_1,handles.FileExt_1}; +% TagsInputFile={'RootPath','SubDir','RootFile','FileIndex','FileExt'}; +% handles.InputFile_1=cell2struct(handlesInputFile,TagsInputFile,2); + +% Update handles structure +guidata(hObject, handles); + +dircur=pwd; %current working directory +dir_opening=dircur; + +% set the position of colorbar and ancillary GUIs: +set(hObject,'Units','Normalized') +movegui(hObject,'center') +UvData.PosColorbar=[0.805 0.022 0.019 0.445]; +UvData.SetObjectOrigin=[-0.05 -0.03]; %position for set_object +UvData.SetObjectSize=[0.3 0.7]; +UvData.CalOrigin=[0.95 -0.03];%position for geometry_calib (TO IMPROVE) +UvData.CalSize=[0.28 1]; + +%functions for the mouse and keyboard +set(handles.histo_u,'NextPlot','replacechildren'); +set(handles.histo_v,'NextPlot','replacechildren'); +set(hObject,'KeyPressFcn',{'keyboard_callback',handles})%set keyboard action function +set(hObject,'WindowButtonMotionFcn',{'mouse_motion',handles})%set mouse action functio +set(hObject,'WindowButtonDownFcn',{'mouse_down'})%set mouse click action function +set(hObject,'WindowButtonUpFcn',{'mouse_up',handles}) +%set(hObject,'ResizeFcn',{@resize_uvmat}) + +%load the list of previously browsed files in menus Open and Open_1 + dir_perso=prefdir; + profil_perso=fullfile(dir_perso,'uvmat_perso.mat'); + if exist(profil_perso,'file') + h=load (profil_perso); + if isfield(h,'MenuFile_1') + set(handles.MenuFile_1,'Label',h.MenuFile_1); + set(handles.MenuFile_1_1,'Label',h.MenuFile_1); + end + if isfield(h,'MenuFile_1') + set(handles.MenuFile_2,'Label',h.MenuFile_2); + set(handles.MenuFile_2_1,'Label',h.MenuFile_2); + end + if isfield(h,'MenuFile_1') + set(handles.MenuFile_3,'Label',h.MenuFile_3); + set(handles.MenuFile_3_1,'Label',h.MenuFile_3); + end + if isfield(h,'MenuFile_1') + set(handles.MenuFile_4,'Label',h.MenuFile_4); + set(handles.MenuFile_4_1,'Label',h.MenuFile_4); + end + if isfield(h,'MenuFile_1') + set(handles.MenuFile_5,'Label',h.MenuFile_5); + set(handles.MenuFile_5_1,'Label',h.MenuFile_5); + end + end + +%initiates menu of vector colors +list_menu=calc_field; +%list_menu=[{'ima_cor'};{'black'};{'white'};list_menu(3:end)]; +set(handles.col_vec,'String',list_menu) + +%check the path and date of modification of all functions in uvmat +path_to_uvmat=which ('uvmat');% check the path detected for source file uvmat +[errormsg,date_str]=check_functions;%check the path of the functions called by uvmat.m + +%check the path of menu_coord transform +%set(handles.menu_coord,'String',{'';'phys';'px';'more...'}) +path_fct{1}=''; +path_fct{2}=fileparts(path_to_uvmat); +path_fct{3}=fileparts(path_to_uvmat); +path_fct{4}=fileparts(path_to_uvmat); +set(handles.menu_coord,'UserData',path_fct) + +%case of an input argument for uvmat +testinputfield=0; +inputfile=[]; +Field=[]; +if exist('input','var') + if ~isempty(errormsg) + warndlg_uvmat(errormsg,'WARNING') + end + if ishandle(handles.UVMAT_title) + delete(handles.UVMAT_title) + end + if isstruct(input) + if isfield(input,'InputFile') + inputfile=input.InputFile; + end + Field=input; + elseif ischar(input)% file name introduced as input + inputfile=input; + elseif isnumeric(input) + sizinput=size(input); + if sizinput(1)<=1 || sizinput(2)<=1 + warndlg_uvmat('bad input for uvmat: file name, structure or numerical matrix accepted','ERROR') + return + end + Field.A=input; + Field.AX=[0.5 size(input,2)-0.5]; + Field.AY=[size(input,1)-0.5 0.5]; + end + if ~isempty(inputfile) + display_file_name(hObject, eventdata, handles,inputfile) + testinputfield=1; + else + UvData.TestInputFile=0; + end + if ~isempty(Field) + set(handles.Fields,'Value',1) + set(handles.Fields,'String',{'get_field...'}) +% set(handles.Fields,'Value',2)% option 'get_field...' + set(handles.Fields,'UserData',Field) + testinputfield=1; + + % set the colorbar position on the interface: + UvData.PosColorbar=[0.805 0.022 0.019 0.445]; + elseif ischar(input) + scan_i_Callback(handles.scan_i, eventdata, handles); + end +else + if ishandle(handles.UVMAT_title) + set(handles.UVMAT_title,'String',[{'Copyright Joel Sommeria, 2008, Coriolis/ LEGI / CNRS-UJF-INPG';'GNU General Public License'; path_to_uvmat; 'version 2.2.beta';date_str};errormsg]); + end +end +UvData.NewSeries=1; +set(hObject,'UserData',UvData) +if testinputfield + %delete drawn objects + hother=findobj(handles.axes3,'Tag','proj_object');%find all the proj objects + for iobj=1:length(hother) + delete_object(hother(iobj)) + end + if isempty(inputfile) + run0_Callback(hObject, eventdata, handles) + set(handles.MenuTools,'Enable','on') + set(handles.OBJECT_txt,'Visible','on') + set(handles.edit,'Visible','on') + set(handles.list_object,'Visible','on') + set(handles.frame_object,'Visible','on') + else + update_rootinfo(hObject,eventdata,handles); + end +end +set_vec_col_bar(handles) + +%------------------------------------------------------------------- +% --- Outputs from this function are returned to the command menuline. +function varargout = uvmat_OutputFcn(hObject, eventdata, handles) +varargout{1} = handles.output;% the only output argument is the handle to the GUI figure + +%------------------------------------------------------------------- +%------------------------------------------------------------------- +% II - FUNCTIONS FOR INTRODUCING THE INPUT FILES +% automatically sets the global properties when the rootfile name is introduced +% then activate the view-field action if selected +% it is activated either by clicking on the RootPath window or by the +% browser +%------------------------------------------------------------------ +%------------------------------------------------------------------ + +% --- Executes on the menu Open/Browse... +% search the files, recognize their type according to their name and fill the rootfile input windows +function MenuBrowse_Callback(hObject, eventdata, handles) +oldfile=read_file_boxes(handles); + +if isempty(oldfile)||isequal(oldfile,'') %loads the previously stored file name and set it as default in the file_input box + dir_perso=prefdir; + profil_perso=fullfile(dir_perso,'uvmat_perso.mat'); + if exist(profil_perso,'file') + h=load (profil_perso); + if isfield(h,'MenuFile_1') + oldfile=h.MenuFile_1; + end + end +end +[FileName, PathName] = uigetfile( ... + {'*.xml;*.xls;*.civ;*.png;*.jpg;*.tif;*.avi;*.AVI;*.nc;*.cmx;*.fig;*.log;*.dat', ' (*.xml,*.xls,*.civ,*.jpg ,*.png, .tif, *.avi,*.nc,*.cmx ,*.fig,*.log,*.dat)'; + '*.xml', '.xml files '; ... + '*.xls', '.xls files '; ... + '*.civ', '.civ files '; ... + '*.jpg',' jpeg image files'; ... + '*.png','.png image files'; ... + '*.tif','.tif image files'; ... + '*.avi;*.AVI','.avi movie files'; ... + '*.nc','.netcdf files'; ... + '*.cdf','.netcdf files'; ... + '*.cmx','.cmx text files';... + '*.cmx2','.cmx2 text files';... + '*.fig','.fig files (matlab fig)';... + '*.log','.log text files ';... + '*.dat','.dat text files ';... + '*.*', 'All Files (*.*)'}, ... + 'Pick a file',oldfile); +%global filebase +fileinput=[PathName FileName];%complete file name +testblank=findstr(fileinput,' ');%look for blanks +if ~isempty(testblank) + warndlg_uvmat(['The input file name ' fileinput ' contains blank character : This is not allowed. Please change name'],'ERROR') + return +end +sizf=size(fileinput); +if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end + +% display the selected field and related information +display_file_name(hObject, eventdata, handles,fileinput) + +%update list of recent files in the menubar +MenuFile_1=fileinput; +MenuFile_2=get(handles.MenuFile_1,'Label'); +MenuFile_3=get(handles.MenuFile_2,'Label'); +MenuFile_4=get(handles.MenuFile_3,'Label'); +MenuFile_5=get(handles.MenuFile_4,'Label'); +set(handles.MenuFile_1,'Label',MenuFile_1) +set(handles.MenuFile_2,'Label',MenuFile_2) +set(handles.MenuFile_3,'Label',MenuFile_3) +set(handles.MenuFile_4,'Label',MenuFile_4) +set(handles.MenuFile_5,'Label',MenuFile_5) +set(handles.MenuFile_1_1,'Label',MenuFile_1) +set(handles.MenuFile_2_1,'Label',MenuFile_2) +set(handles.MenuFile_3_1,'Label',MenuFile_3) +set(handles.MenuFile_4_1,'Label',MenuFile_4) +set(handles.MenuFile_5_1,'Label',MenuFile_5) +dir_perso=prefdir; +profil_perso=fullfile(dir_perso,'uvmat_perso.mat'); +if exist(profil_perso,'file') + save (profil_perso,'MenuFile_1','MenuFile_2','MenuFile_3','MenuFile_4', 'MenuFile_5','-append'); %store the file names for future opening of uvmat +else + txt=ver; + Release=txt(1).Release; + relnumb=str2double(Release(3:4)); + if relnumb >= 14 + save (profil_perso,'MenuFile_1','MenuFile_2','MenuFile_3','MenuFile_4', 'MenuFile_5','-V6'); %store the file names for future opening of uvmat + else + save (profil_perso,'MenuFile_1','MenuFile_2','MenuFile_3','MenuFile_4', 'MenuFile_5'); %store the file names for future opening of uvmat + end +end + +% -------------------------------------------------------------------- +function MenuFile_1_Callback(hObject, eventdata, handles) +fileinput=get(handles.MenuFile_1,'Label'); +display_file_name(hObject, eventdata, handles,fileinput) + +% -------------------------------------------------------------------- +function MenuFile_2_Callback(hObject, eventdata, handles) +fileinput=get(handles.MenuFile_2,'Label'); +display_file_name(hObject, eventdata, handles,fileinput) + +% -------------------------------------------------------------------- +function MenuFile_3_Callback(hObject, eventdata, handles) +fileinput=get(handles.MenuFile_3,'Label'); +display_file_name(hObject, eventdata, handles,fileinput) + +% -------------------------------------------------------------------- +function MenuFile_4_Callback(hObject, eventdata, handles) +fileinput=get(handles.MenuFile_4,'Label'); +display_file_name(hObject, eventdata, handles,fileinput) + +% -------------------------------------------------------------------- +function MenuFile_5_Callback(hObject, eventdata, handles) +fileinput=get(handles.MenuFile_5,'Label'); +display_file_name(hObject, eventdata, handles,fileinput) + +%----------------------------------------------------------------- +% fills the edit boxes RootPath, RootFile,NomType...from an input file name 'fileinput' +%---------------------------------------------------------------- +function display_file_name(hObject, eventdata, handles,fileinput) +[RootPath,RootFile,i1,i2,str_a,str_b,ext,NomType,SubDir]=name2display(fileinput); +form=imformats(ext(2:end));%test valid Matlab image formats +if ~isempty(form) + ext_test='.image'; + imainfo=imfinfo(fileinput); + if length(imainfo) >1 %case of image with multiple frames + i1='1'; % set the frame counter to 1 by default + i2=''; + str_a=''; + str_b=''; + NomType='*'; %indicate a set of indexed frames within a single file + [RootPath,RootFile]=fileparts(fileinput); %include the indices in the root file + end +elseif isequal(lower(ext),'.avi') + ext_test='.image'; + i1='1'; % set the frame counter to 1 by default + i2=''; + str_a=''; + str_b=''; + NomType='*'; %indicate a set of indexed frames within a single file + [RootPath,RootFile]=fileparts(fileinput); %include the indices in the root file +else + ext_test=lower(ext); +end +switch ext_test + case {'.civ','.log','.cmx','.cmx2','.txt'} %display text file + edit(fileinput) + case '.fig' %display matlab figure + hfig=open(fileinput); + set(hfig,'WindowButtonMotionFcn','mouse_motion')%set mouse action functio + set(hfig,'WindowButtonUpFcn','mouse_up')%set mouse click action function + set(hfig,'WindowButtonUpFcn','mouse_down')%set mouse click action function + case {'.xml','.xls'} % edit xml or Excel files + editxml(fileinput); + case {'.avi','.image','.vol','.nc','.cdf'} + set(handles.RootPath,'String',RootPath); + if isequal(SubDir,'') + rootname=fullfile(RootPath,RootFile); + else + rootname=fullfile(RootPath,SubDir,RootFile); + SubDir=['/' SubDir]; %display the separator + end + set(handles.SubDir,'String',SubDir); + set(handles.RootFile,'String',['/' RootFile]); %display the separator + indices=fileinput(length(rootname)+1:end); + indices(end-length(ext)+1:end)=[]; %remove extension + set(handles.FileIndex,'String',indices); + set(handles.FileIndex,'UserData',NomType); + set(handles.FileExt,'String',ext); + % fill file index counters + set(handles.i1,'String',i1); + + set(handles.i2,'String',i2); + set(handles.j1,'String',str_a); + set(handles.j2,'String',str_b); + + % synchronise indices of the second input file if it exists + if get(handles.SubField,'Value')==1% if the subfield button is activated, update the field numbers + [FileName_1,RootPath_1,FileBase_1,FileIndices_1,FileExt_1,SubDir_1]=read_file_boxes_1(handles); + NomType_1=get(handles.FileIndex_1,'UserData'); + [FileName_1,idetect]=name_generator(FileBase_1,stra2num(i1),stra2num(i2),FileExt_1,NomType_1,1,stra2num(str_a),stra2num(str_b),SubDir_1); + if idetect + FileIndex_1=name_generator('',stra2num(i1),stra2num(i2),'',NomType_1,1,stra2num(str_a),stra2num(str_b),''); + set(handles.FileIndex_1,'String',FileIndex_1) + else + set(handles.SubField,'Value',0) + SubField_Callback(hObject, eventdata, handles) + end + end + + %enable other menus + set(handles.MenuOpen_1,'Enable','on') + set(handles.MenuFile_1_1,'Enable','on') + set(handles.MenuFile_2_1,'Enable','on') + set(handles.MenuFile_3_1,'Enable','on') + set(handles.MenuFile_4_1,'Enable','on') + set(handles.MenuFile_5_1,'Enable','on') + set(handles.MenuExport,'Enable','on') + set(handles.MenuExportFigure,'Enable','on') + set(handles.MenuExportMovie,'Enable','on') + set(handles.MenuTools,'Enable','on') + set(handles.OBJECT_txt,'Visible','on') + set(handles.edit,'Visible','on') + set(handles.list_object,'Visible','on') + set(handles.frame_object,'Visible','on') + % initiate input file: + update_rootinfo(hObject,eventdata,handles); + otherwise + msgbox_uvmat('ERROR',['invalid input file extension' ext]) +end + +%------------------------------------------------------------------- +function RootPath_Callback(hObject,eventdata,handles) +update_rootinfo(hObject,eventdata,handles); + +%------------------------------------------------------------------- +%-- called by action in RootFile edit box +%------------------------------------------------------------------- +function SubDir_Callback(hObject, eventdata, handles) +%refresh the menu of input fields +Fields_Callback(hObject, eventdata, handles); +% refresh the current field +run0_Callback(hObject, eventdata, handles); + + +%------------------------------------------------------------------- +%-- called by action in RootFile edit box +%------------------------------------------------------------------- +function RootFile_Callback(hObject, eventdata, handles) +update_rootinfo(hObject,eventdata,handles) + +%------------------------------------------------------------------- +%-- called by action in FileIndex edit box +%------------------------------------------------------------------- +function FileIndex_Callback(hObject, eventdata, handles) +NomType_str=get(handles.FileIndex,'String') ; +[P,F,str1,str2,str_a,str_b]=name2display(['xx' NomType_str get(handles.FileExt,'String')]); +% display the new index values on the counters +set(handles.i1,'String',str1); +set(handles.i2,'String',str2); +set(handles.j1,'String',str_a); +set(handles.j2,'String',str_b); + +%------------------------------------------------------------------- +% -- update information about a new field series (indices to scan, timing, calibration from an xml file, then refresh current plots +%------------------------------------------------------------------- +function update_rootinfo(hObject,eventdata,handles) +global dircur dir_opening + +set(handles.RootPath,'BackgroundColor',[1 1 0]) +drawnow +set(handles.Fields,'UserData',[])% reinialize data from uvmat opening +huvmat=get(handles.RootPath,'parent'); +UvData=get(huvmat,'UserData');%huvmat=handles of the uvmat interface +UvData.NewSeries=1; %flag for run0: begin a new series +UvData.TestInputFile=1; +set(handles.fix_pair,'Value',0) % desactivate by default the comp_input '-'input window +%FileIndex_Callback(hObject, eventdata, handles)% update field counters + +[FileName,RootPath,FileBase,FileIndices,FileExt,SubDir]=read_file_boxes(handles); +if ~exist(FileName,'file') + msgbox_uvmat('ERROR',['input file ' FileName ' not found']); + return +end +nbfield=[];%default +nburst=[];%default + +% read timing and total frame number from the current file (movie files) !! may be overrid by xml file +XmlData.Time=[];%default +XmlData.GeometryCalib=[];%default +TimeUnit=[];%default +testima=0; %test for image input +if isequal(lower(FileExt),'.avi') %.avi file + testima=1; + info=aviinfo([FileBase FileIndices FileExt]); + nbfield=info.NumFrames; + nburst=1; + set(handles.Dt_txt,'String',['Dt=' num2str(1000/info.FramesPerSecond) 'ms']);%display the elementary time interval in millisec + XmlData.Time=[0:1/info.FramesPerSecond:(info.NumFrames-1)/info.FramesPerSecond]'; + TimeUnit='s'; + set(handles.npx,'String',num2str(info.Width));%fills nbre of pixels x box + set(handles.npy,'String',num2str(info.Height));%fills nbre of pixels y box + hhh=which('mmreader'); + if ~isequal(hhh,'')&& mmreader.isPlatformSupported()% if the function is found (recent version of matlab) + UvData.MovieObject=mmreader([FileBase FileIndices FileExt]); + end +elseif ~isempty(imformats(FileExt(2:end))) || isequal(FileExt,'.vol')%&& isequal(NomType,'*')% multi-frame image + testima=1; + if ~isequal(SubDir,'') + RootFile=get(handles.RootFile,'String'); + imainfo=imfinfo([fullfile(RootPath,SubDir,RootFile) FileIndices FileExt]); + else + imainfo=imfinfo([FileBase FileIndices FileExt]); + end + if length(imainfo) >1 %case of image with multiple frames + nbfield=length(imainfo); + nburst=1; + end + if isfield(UvData,'MovieObject') + UvData=rmfield(UvData,'MovieObject'); + end +else + %set(handles.last_i,'String','');%fills last_field box + set(handles.npx,'String','');%fills nbre of pixels x box + set(handles.npy,'String','');%fills nbre of pixels y box + if isfield(UvData,'MovieObject') + UvData=rmfield(UvData,'MovieObject'); + end +end + +% read parameters (time, geometric calibration..) from a documentation file (.xml advised) +filexml=[FileBase '.xml']; +fileciv=[FileBase '.civ']; +warntext='';%default warning message +NbSlice=1;%default + +if exist(filexml,'file') + set(handles.view_xml,'Visible','on') + set(handles.view_xml,'BackgroundColor',[1 1 0]) + set(handles.RootPath,'BackgroundColor',[1 1 1]) + set(handles.view_xml,'String','view .xml') + drawnow + [XmlData,warntext]=imadoc2struct(filexml); + if ~isempty(warntext) + msgbox_uvmat('WARNING',warntext) + end + if isfield(XmlData,'TimeUnit') + if isfield(XmlData,'TimeUnit')&& ~isempty(XmlData.TimeUnit) + TimeUnit=XmlData.TimeUnit; + end + end + set(handles.view_xml,'BackgroundColor',[1 1 1]) + drawnow +elseif exist(fileciv,'file')% if .civ file found + [error,XmlData.Time,TimeUnit,mode,npx,npy,pxcmx,pxcmy]=read_imatext([FileBase '.civ']); + GeometryCalib.R=[pxcmx 0 0; 0 pxcmy 0;0 0 0]; + GeometryCalib.Tx=0; + GeometryCalib.Ty=0; + GeometryCalib.Tz=1; + GeometryCalib.dpx=1; + GeometryCalib.dpy=1; + GeometryCalib.sx=1; + GeometryCalib.Cx=0; + GeometryCalib.Cy=0; + GeometryCalib.f=1; + GeometryCalib.kappa1=0; + GeometryCalib.CoordUnit='cm'; + XmlData.GeometryCalib=GeometryCalib; + if error==2, warntext=['no file ' FileBase '.civ']; + elseif error==1, warntext='inconsistent number of fields in the .civ file'; + end + set(handles.npx,'String',num2str(npx));%fills nbre of pixels x box + set(handles.npy,'String',num2str(npy));%fills nbre of pixels y box + set(handles.pxcm,'String',num2str(pxcmx));%fills scale x (pixel/cm) box + set(handles.pycm,'String',num2str(pxcmy));%fills scale y (pixel/cm) box + set(handles.pxcm,'Visible','on');%fills scale x (pixel/cm) box + set(handles.pycm,'Visible','on');%fills scale y (pixel/cm) box + set(handles.view_xml,'Visible','on') + set(handles.view_xml,'String','view .civ') +else + set(handles.view_xml,'Visible','off') +end + +% store last index in handles.lat_i and .last_j +if ~isempty(XmlData.Time) + nbfield=size(XmlData.Time,1); + nburst=size(XmlData.Time,2); +end +last_i_cell=get(handles.last_i,'String'); +if isempty(nbfield) + last_i_cell{1}=''; +else + last_i_cell{1}=num2str(nbfield); +end +set(handles.last_i,'String',last_i_cell) +last_j_cell=get(handles.last_j,'String'); +if isempty(nburst) + last_j_cell{1}=''; +else + last_j_cell{1}=num2str(nburst); +end +set(handles.last_j,'String',last_j_cell); + +% store geometric calibration in UvData +if isfield(XmlData,'GeometryCalib') + GeometryCalib=XmlData.GeometryCalib; + if isempty(GeometryCalib) + set(handles.pxcm,'String','') + set(handles.pycm,'String','') + set(handles.menu_coord,'Value',1); % no transform by default + else + if (isfield(GeometryCalib,'R')& ~isequal(GeometryCalib.R(2,1),0) & ~isequal(GeometryCalib.R(1,2),0)) |... + (isfield(GeometryCalib,'kappa1')& ~isequal(GeometryCalib.kappa1,0)) + set(handles.pxcm,'String','var') + set(handles.pycm,'String','var') + else + pixcmx=GeometryCalib.f*GeometryCalib.R(1,1)*GeometryCalib.sx/(GeometryCalib.Tz*GeometryCalib.dpx); + pixcmy=GeometryCalib.f*GeometryCalib.R(2,2)/(GeometryCalib.Tz*GeometryCalib.dpy); + set(handles.pxcm,'String',num2str(pixcmx)) + set(handles.pycm,'String',num2str(pixcmy)) + end + set(handles.menu_coord,'Value',2); % phys transform by default + if isfield(GeometryCalib,'SliceCoord') + siz=size(GeometryCalib.SliceCoord); + if siz(1)>1 + NbSlice=siz(1); + set(handles.slices,'Visible','on') + set(handles.slices,'Value',1) + end + set(handles.nb_slice,'String',num2str(NbSlice)) + slices_Callback(hObject, eventdata, handles) + % Coord=UvData.XmlData.GeometryCalib.SliceCoord; + % ZIndex=num_i1-NbSlice*(floor((num_i1-1)/NbSlice)); + end + end +end + +%update the data attached to the uvmat interface +set(handles.nb_slice,'String',num2str(NbSlice)) +if ~isempty(TimeUnit) + set(handles.time_txt,'String',['time (' TimeUnit ')']) +end +%set(handles.DtUnit,'String',['10^(-3)' TimeUnit]) +UvData.TimeUnit=TimeUnit; +UvData.XmlData=XmlData; +UvData.NewSeries=1; +set(huvmat,'UserData',UvData) + +%display warning message +if ~isequal(warntext,'') + msgbox_uvmat('WARNING',warntext); +end + +% set default options in menu 'Fields' +if testima + set(handles.Fields,'Value',1) % set menu to 'image' + set(handles.Fields,'String',{'image';'get_field...';'velocity';'vort';'div';'more...'}) +elseif isequal(FileExt,'.nc')|isequal(FileExt,'.cdf') + Data=nc2struct(FileName,[]); + col_vec=get(handles.col_vec,'String'); + if isfield(Data,'absolut_time_T0')&& (isfield(Data,'civ1')||isfield(Data,'civ')) + set(handles.Fields,'String',{'image';'get_field...';'velocity';'vort';'div';'more...'}) + set(handles.Fields,'Value',3) % set menu to 'velocity' + col_vec{1}='ima_cor'; + else + set(handles.Fields,'Value',1) % set menu to 'get_field... + set(handles.Fields,'String',{'get_field...'}) + col_vec{1}='get_field...'; + end + set(handles.col_vec,'String',col_vec) +else + msgbox_uvmat('ERROR',['invalid input file extension ' FileExt]) + return +end + +% set index navigation options and refresh plots +set(handles.RootPath,'BackgroundColor',[1 1 1]) +drawnow +set_scan_options(hObject, eventdata, handles) + + +%------------------------------------------------------------------- +%-- set index navigation options for new series input and refresh plot +%------------------------------------------------------------------- +function set_scan_options(hObject, eventdata, handles) + +% set the corresponding index navigation options (TO CHECK WITH THE SECOND FIELD) +NomType=get(handles.FileIndex,'UserData'); +NomType_1=get(handles.FileIndex_1,'UserData'); +state_j='off'; %default +scan_option='i'; +switch NomType + case {'_i_j','_i_j1-j2','_i1-i2_j','#_ab'},% two navigation indices + state_j='on'; + if exist('nbfield','var') && isequal(nbfield,1) + scan_option='j'; + else + scan_option='i'; + end +end +if ~isempty(NomType_1) + switch NomType_1 + case {'_i_j','_i_j1-j2','_i1-i2_j','#_ab'},% two navigation indices + state_j='on'; + if exist('nbfield','var') && isequal(nbfield,1) + scan_option='j'; + else + scan_option='i'; + end + end +end +if isequal(scan_option,'i') + set(handles.scan_i,'Value',1) + scan_i_Callback(hObject, eventdata, handles); +else + set(handles.scan_j,'Value',1) + scan_j_Callback(hObject, eventdata, handles); +end +set(handles.scan_j,'Visible',state_j) +set(handles.j1,'Visible',state_j) +set(handles.j2,'Visible',state_j) +set(handles.last_j,'Visible',state_j); +set(handles.frame_j,'Visible',state_j); +set(handles.j_text,'Visible',state_j); + +% view the field +run0_Callback(hObject, eventdata, handles); %view field +mask_test=get(handles.mask_test,'value'); +if mask_test + MaskData=get(handles.mask_test,'UserData'); + if isfield(MaskData,'maskhandle') && ishandle(MaskData.maskhandle) + delete(MaskData.maskhandle) %delete old mask + end + mask_test_Callback(hObject, eventdata, handles) +end +%------------------------------------------------------------------- +function MenuBrowse_1_Callback(hObject, eventdata, handles) +%------------------------------------------------------------------- +huvmat=get(handles.run0,'parent'); +UvData=get(huvmat,'UserData'); + +RootPath=get(handles.RootPath,'String'); +[FileName, PathName, filterindex] = uigetfile( ... + {'*.xml;*.xls;*.civ;*.jpg;*.png;*.avi;*.AVI;*.nc;*.cmx;*.fig;*.log;*.dat', ' (*.xml,*.xls,*.civ, *.jpg,*.png, *.avi,*.nc,*.cmx ,*.fig,*.log,*.dat)'; + '*.xml', '.xml files '; ... + '*.xls', '.xls files '; ... + '*.civ', '.civ files '; ... + '*.jpg','.jpg image files'; ... + '*.png','.png image files'; ... + '*.avi;*.AVI','.avi movie files'; ... + '*.nc','.netcdf files'; ... + '*.cdf','.netcdf files'; ... + '*.cmx','.cmx text files';... + '*.cmx2','.cmx2 text files';... + '*.fig','.fig files (matlab fig)';... + '*.log','.log text files ';... + '*.dat','.dat text files ';... + '*.*', 'All Files (*.*)'}, ... + 'Pick a file',RootPath); +fileinput_1=[PathName FileName];%complete file name +testblank=findstr(fileinput_1,' ');%look for blanks +if ~isempty(testblank) + warndlg_uvmat(['The input file name ' fileinput_1 ' contains blank character : This is not allowed. Please change name'],'ERROR') + return +end +sizf=size(fileinput_1); +if (~ischar(fileinput_1)|~isequal(sizf(1),1)),return;end + +% refresh the current displayed field +display_file_name_1(hObject,eventdata,handles,fileinput_1) + +%update list of recent files in the menubar +MenuFile_1=fileinput_1; +MenuFile_2=get(handles.MenuFile_1,'Label'); +MenuFile_3=get(handles.MenuFile_2,'Label'); +MenuFile_4=get(handles.MenuFile_3,'Label'); +MenuFile_5=get(handles.MenuFile_4,'Label'); +set(handles.MenuFile_1,'Label',MenuFile_1) +set(handles.MenuFile_2,'Label',MenuFile_2) +set(handles.MenuFile_3,'Label',MenuFile_3) +set(handles.MenuFile_4,'Label',MenuFile_4) +set(handles.MenuFile_5,'Label',MenuFile_5) +set(handles.MenuFile_1_1,'Label',MenuFile_1) +set(handles.MenuFile_2_1,'Label',MenuFile_2) +set(handles.MenuFile_3_1,'Label',MenuFile_3) +set(handles.MenuFile_4_1,'Label',MenuFile_4) +set(handles.MenuFile_5_1,'Label',MenuFile_5) +dir_perso=prefdir; +profil_perso=fullfile(dir_perso,'uvmat_perso.mat'); +if exist(profil_perso,'file') + save (profil_perso,'MenuFile_1','MenuFile_2','MenuFile_3','MenuFile_4', 'MenuFile_5','-append'); %store the file names for future opening of uvmat +else + txt=ver; + Release=txt(1).Release; + relnumb=str2num(Release(3:4)); + if relnumb >= 14 + save (profil_perso,'MenuFile_1','MenuFile_2','MenuFile_3','MenuFile_4', 'MenuFile_5','-V6'); %store the file names for future opening of uvmat + else + save (profil_perso,'MenuFile_1','MenuFile_2','MenuFile_3','MenuFile_4', 'MenuFile_5'); %store the file names for future opening of uvmat + end +end + +% -------------------------------------------------------------------- +function MenuFile_1_1_Callback(hObject, eventdata, handles) +fileinput_1=get(handles.MenuFile_1_1,'Label'); +display_file_name_1(hObject,eventdata,handles,fileinput_1) + +% -------------------------------------------------------------------- +function MenuFile_2_1_Callback(hObject, eventdata, handles) +fileinput_1=get(handles.MenuFile_2_1,'Label'); +display_file_name_1(hObject,eventdata,handles,fileinput_1) + +% -------------------------------------------------------------------- +function MenuFile_3_1_Callback(hObject, eventdata, handles) +fileinput_1=get(handles.MenuFile_3_1,'Label'); +display_file_name_1(hObject,eventdata,handles,fileinput_1) + +% -------------------------------------------------------------------- +function MenuFile_4_1_Callback(hObject, eventdata, handles) +fileinput_1=get(handles.MenuFile_4_1,'Label'); +display_file_name_1(hObject,eventdata,handles,fileinput_1) + +% -------------------------------------------------------------------- +function MenuFile_5_1_Callback(hObject, eventdata, handles) +fileinput_1=get(handles.MenuFile_5_1,'Label'); +display_file_name_1(hObject,eventdata,handles,fileinput_1) + +%----------------------------------------------------------------- +% fills the edit boxes RootPath, RootFile,NomType...from an input file name 'fileinput' +%---------------------------------------------------------------- +function display_file_name_1(hObject,eventdata,handles,fileinput_1) + +%[path,name,ext]=fileparts(fileinput_1); +[RootPath_1,RootFile_1,field_count,str2,str_a,str_b,FileExt_1,NomType_1,SubDir_1]=name2display(fileinput_1); +nbfield_1=1; %default +ext_test=FileExt_1;%default +form=imformats(FileExt_1(2:end)); +if ~isempty(form) % if the extension corresponds to an image format recognized by Matlab + imainfo=imfinfo(fileinput_1); + nbfield_1=length(imainfo); + ext_test='.image'; +elseif isequal(lower(FileExt_1),'.avi') + info=aviinfo(fileinput_1); + nbfield_1=info.NumFrames; + ext_test='.image'; +end + +%open directly fig or text files +switch ext_test + case {'.civ','.log','.cmx','.cmx2','.txt'} %display text file + edit(fileinput) + return + case '.fig' %display matlab figure + hfig=open(fileinput); + set(hfig,'WindowButtonMotionFcn','mouse_motion')%set mouse action functio + set(hfig,'WindowButtonUpFcn','mouse_up')%set mouse click action function + set(hfig,'WindowButtonUpFcn','mouse_down')%set mouse click action function + return + case {'.xml','.xls'} % edit xml or Excel files + heditxml=editxml(fileinput); + return + case {'.image','.nc','.cdf'} +% set(handles.FileIndex,'UserData',NomType_1); + otherwise + warndlg_uvmat(['invalid input file extension ' FileExt_1 ' for uvmat'],'ERROR') + return +end + +% test for image series in a single file and synchronise file indices of the two series +if nbfield_1 >1 %case of image with multiple frames + if nbfield_1 < num_i1 + warndlg_uvmat('current frame index beyond the input movie length','ERROR') + return + else + NomType_1='*'; %indicate a set of indexed frames within a single file + filename_new=fileinput_1; + end +else % cases of data files + RootPath=get(handles.RootPath,'String'); + RootFile=get(handles.RootFile,'String'); + FileBase=fullfile(RootPath,RootFile); + FileBase_1=fullfile(RootPath_1,RootFile_1); + if isequal(FileBase,FileBase_1) + filename_new=fileinput_1; + else + num_i1=stra2num(get(handles.i1,'String'));%get the current file indices from counters + num_j1=stra2num(get(handles.j1,'String')); + num_i2=stra2num(get(handles.i2,'String')); + num_j2=stra2num(get(handles.j2,'String')); + [filename_new,idetect]=... + name_generator(FileBase_1,num_i1,num_j1,FileExt_1,NomType_1,1,num_i2,num_j2,SubDir_1);%create name with indices synchronised with the first file + indices=''; %default + if ~idetect + warndlg_uvmat('second input file with indices corresponding to the first one does not exist','ERROR') + return + end + end +end +set(handles.FileIndex,'UserData',NomType_1); + +% make visible and fill the second raw of edit boxes +set(handles.RootPath_1,'Visible','on') +set(handles.RootFile_1,'Visible','on') +set(handles.SubDir_1,'Visible','on'); +set(handles.FileIndex_1,'Visible','on'); +set(handles.FileExt_1,'Visible','on'); +[FileName,RootPath,FileBase,FileIndices,FileExt,SubDir]=read_file_boxes(handles); +if isequal(FileBase,FileBase_1) + set(handles.RootPath_1,'String','"') + set(handles.RootFile_1,'String','"'); +else + set(handles.RootPath_1,'String',RootPath_1) + set(handles.RootFile_1,'String',['/' RootFile_1]); +end +if isequal(SubDir_1,'') + set(handles.SubDir_1,'String',''); + FileBaseSub_1=FileBase_1; +else + set(handles.SubDir_1,'String',['/' SubDir_1]); + FileBaseSub_1=fullfile(FileBase_1,SubDir_1); +end +indices=filename_new(length(FileBaseSub_1)+1:end); +indices(end-length(FileExt_1)+1:end)=[]; %remove extension +set(handles.FileIndex_1,'String',indices) +set(handles.FileIndex_1,'UserData',NomType_1) +set(handles.FileExt_1,'String',FileExt_1); + +% default choice of fields +if isequal(ext_test,'.image') + set(handles.Fields_1,'String',{'';'image';'get_field...';'velocity';'vort';'div';'more...'}) + set(handles.Fields_1,'Value',2) % set menu to 'image' +elseif isequal(FileExt_1,'.nc')|isequal(FileExt_1,'.cdf') + Data=nc2struct(fileinput_1,[]); + if isfield(Data,'absolut_time_T0') + set(handles.Fields_1,'String',{'';'image';'get_field...';'velocity';'vort';'div';'more...'}) + set(handles.Fields_1,'Value',4) % set menu to 'velocity' + else + set(handles.Fields_1,'Value',2) % set menu to 'get_field...' + set(handles.Fields_1,'String',{'';'get_field...'}); + end +end +set(handles.SubField,'Visible','on') +set(handles.SubField,'Value',1) +RootPath_1_Callback(hObject,eventdata,handles); + + +%----------------------------------------------------- +function RootPath_1_Callback(hObject,eventdata,handles) +update_rootinfo_1(hObject,eventdata,handles) + +%------------------------------------------------------------------- +function RootFile_1_Callback(hObject, eventdata, handles) +update_rootinfo_1(hObject,eventdata,handles) +%------------------------------------------------------------------- + +%------------------------------------------------------------------- +function update_rootinfo_1(hObject,eventdata,handles) %A REVOIR + +set(handles.RootPath_1,'BackgroundColor',[1 1 0])% indicate active program by yellow color +drawnow +huvmat=get(handles.RootPath,'parent'); +UvData=get(huvmat,'UserData');%huvmat=handles of the uvmat interface +UvData.NewSeries=1; %flag for run0: begin a new series + +[FileName,RootPath,FileBase,FileIndices,FileExt]=read_file_boxes_1(handles); +if ~exist(FileName,'file') + msgbox_uvmat('ERROR',['input file ' FileName ' not found']); +end +nbfield_1=[];%default +nburst_1=[];%default +XmlData.Time=[]; +XmlData.GeometryCalib=[];%default +TimeUnit=[]; +if isfield(UvData,'TimeUnit') + TimeUnit=UvData.TimeUnit; +end +TimeUnit_1=[]; +testima=0; %test for image input +if isequal(lower(FileExt),'.avi') %.avi file + testima=1; + info=aviinfo([FileBase FileIndices FileExt]); + nbfield_1=info.NumFrames; + nburst_1=1; + %set(handles.last_i,'String',num2str(info.NumFrames));%fills last_field box + set(handles.Dt_txt,'String',['Dt=' num2str(1000/info.FramesPerSecond) 'ms']);%display the elementary time interval in millisec +% set(handles.dt,'UserData',info.FramesPerSecond); + time=[0:1/info.FramesPerSecond:(info.NumFrames-1)/info.FramesPerSecond]'; + npx=get(handles.npx,'String'); + npy=get(handles.npy,'String'); + if isequal(npx,'') || isequal(npy,'') + set(handles.npx,'String',num2str(info.Width));%fills nbre of pixels x box + set(handles.npy,'String',num2str(info.Height));%fills nbre of pixels y box + end +elseif ~isempty(imformats(FileExt(2:end))) %&& isequal(NomType,'*')% multi-frame image + testima=1; + imainfo=imfinfo([FileBase FileIndices FileExt]); + if length(imainfo) >1 %case of image with multiple frames + nbfield_1=length(imainfo); + nburst_1=1; + %set(handles.last_i,'String',num2str(length(imainfo)));%fills last_field box + end +else + %set(handles.last_i,'String','');%fills last_field box + set(handles.npx,'String','');%fills nbre of pixels x box + set(handles.npy,'String','');%fills nbre of pixels y box +end + +% find scaling parameters +filexml=[FileBase '.xml']; +fileciv=[FileBase '.civ']; +warntext='';%default warning text +if exist(filexml,'file') + [XmlData,warntext]=imadoc2struct(filexml); + if ~isempty(warntext) + msgbox_uvmat('WARNING',warntext) + end + if isfield(XmlData,'Camera') +% if isfield(XmlData.Camera,'NbSlice')&& ~isempty(XmlData.Camera.NbSlice) +% NbSlice=XmlData.Camera.NbSlice; +% end + if isfield(XmlData.Camera,'TimeUnit')&& ~isempty(XmlData.Camera.TimeUnit) + TimeUnit=XmlData.Camera.TimeUnit; + end + end +elseif exist(fileciv,'file')% if .civ file found + [error,XmlData.Time,TimeUnit,mode,npx,npy,pxcmx,pxcmy]=read_imatext([FileBase '.civ']); + GeometryCalib.R=[pxcmx 0 0; 0 pxcmy 0;0 0 0]; + GeometryCalib.Tx=0; + GeometryCalib.Ty=0; + GeometryCalib.Tz=1; + GeometryCalib.dpx=1; + GeometryCalib.dpy=1; + GeometryCalib.sx=1; + GeometryCalib.Cx=0; + GeometryCalib.Cy=0; + GeometryCalib.f=1; + GeometryCalib.kappa1=0; + GeometryCalib.CoordUnit='cm'; + XmlData.GeometryCalib=GeometryCalib; + if error==2, warntext=['no file ' FileBase '.civ']; + elseif error==1, warntext='inconsistent number of fields in the .civ file'; + end + + set(handles.npx,'String',num2str(npx));%fills nbre of pixels x box + set(handles.npy,'String',num2str(npy));%fills nbre of pixels y box + set(handles.pxcm,'String',num2str(pxcmx));%fills scale x (pixel/cm) box + set(handles.pycm,'String',num2str(pxcmy));%fills scale y (pixel/cm) box + set(handles.pxcm,'Visible','on');%fills scale x (pixel/cm) box + set(handles.pycm,'Visible','on');%fills scale y (pixel/cm) box +end +if ~isempty(TimeUnit_1) && ~isequal(TimeUnit_1,TimeUnit) + warndlg_uvmat('the time units for the second series differs from the first one','WARNING') +end + +% store last index in handles.lat_i and .last_j +if ~isempty(XmlData.Time) + nbfield_1=size(XmlData.Time,1); + nburst_1=size(XmlData.Time,2); +end +last_i_cell=get(handles.last_i,'String'); +if isempty(nbfield_1) + last_i_cell{2}=''; +else + last_i_cell{2}=num2str(nbfield_1); +end +set(handles.last_i,'String',last_i_cell) +last_j_cell=get(handles.last_j,'String'); +if isempty(nburst_1) + last_j_cell{2}=''; +else + last_j_cell{2}=num2str(nburst_1); +end +set(handles.last_j,'String',last_j_cell); +if ~isequal(last_i_cell{1},last_i_cell{2}) || ~isequal(last_j_cell{1},last_j_cell{2}) + warndlg_uvmat('the numbers of input file of the second series differs from the first one','WARNING') +end + +% store calibration data +GeometryCalib=XmlData.GeometryCalib; +if isempty(GeometryCalib) + if isfield(UvData, 'GeometryCalib_1') + UvData=rmfield(UvData,'GeometryCalib_1'); + end +else + UvData.GeometryCalib_1=GeometryCalib; + if (isfield(GeometryCalib,'R')& ~isequal(GeometryCalib.R(2,1),0) & ~isequal(GeometryCalib.R(1,2),0)) |... + (isfield(GeometryCalib,'kappa1')& ~isequal(GeometryCalib.kappa1,0)) + set(handles.pxcm,'String','var') + set(handles.pycm,'String','var') + else + pixcmx=GeometryCalib.f*GeometryCalib.R(1,1)*GeometryCalib.sx/(GeometryCalib.Tz*GeometryCalib.dpx); + pixcmy=GeometryCalib.f*GeometryCalib.R(2,2)/(GeometryCalib.Tz*GeometryCalib.dpy); + set(handles.pxcm,'String',num2str(pixcmx)) + set(handles.pycm,'String',num2str(pixcmy)) + end +end +UvData.XmlData_1=XmlData; +set(huvmat,'UserData',UvData)%update the data attached to the uvmat interface + +if ~isequal(warntext,'') + warndlg_uvmat(warntext,'WARNING') +end + +set(handles.RootPath_1,'BackgroundColor',[1 1 1])% signa the end the input operation +drawnow + +set_scan_options(hObject, eventdata, handles) + + +%--------------------------------------------------- +% switch file index scanning options scan_i and scan_j in an exclusive way +function scan_i_Callback(hObject, eventdata, handles) +%--------------------------------------------------- +if get(handles.scan_i,'Value')==1 + set(handles.scan_i,'BackgroundColor',[1 1 0]) + set(handles.scan_j,'Value',0) + set(handles.scan_j,'BackgroundColor',[0.831 0.816 0.784]) +else + set(handles.scan_i,'BackgroundColor',[0.831 0.816 0.784]) + set(handles.scan_j,'Value',1) + set(handles.scan_j,'BackgroundColor',[1 1 0]) +end +%------------------------------------------------------------------- +%--------------------------------------------------- +% switch file index scanning options scan_i and scan_j in an exclusive way +function scan_j_Callback(hObject, eventdata, handles) +%--------------------------------------------------- +%------------------------------------------------------------------- +if get(handles.scan_j,'Value')==1 + set(handles.scan_j,'BackgroundColor',[1 1 0]) + set(handles.scan_i,'Value',0) + set(handles.scan_i,'BackgroundColor',[0.831 0.816 0.784]) +else + set(handles.scan_j,'BackgroundColor',[0.831 0.816 0.784]) + set(handles.scan_i,'Value',1) + set(handles.scan_i,'BackgroundColor',[1 1 0]) +end + +%------------------------------------------------------------------- +function i1_Callback(hObject, eventdata, handles) +%------------------------------------------------------------------- +% [filebase,num1,num_a,num2,num_b,ext,NomType,subdir]=read_input_file(handles); +[FileName,RootPath,filebase,xx,FileExt]=read_file_boxes(handles); +NomType=get(handles.FileIndex,'UserData'); +num1=stra2num(get(handles.i1,'String')); +num2=stra2num(get(handles.i2,'String')); +num_a=stra2num(get(handles.j1,'String')); +num_b=stra2num(get(handles.j2,'String')); +indices=name_generator('',num1,num_a,'',NomType,1,num2,num_b,''); +set(handles.FileIndex,'String',indices) +if get(handles.SubField,'Value')==1 + NomType_1=get(handles.FileIndex_1,'String'); + FileExt_1=get(handles.FileExt_1,'String'); + [P,F,str1,str2,str_a,str_b,Ext,NomType_1]=name2display(['xx' NomType_1 FileExt_1]); + indices=name_generator('',num1,num_a,'',NomType_1,1,num2,num_b,''); + set(handles.FileIndex_1,'String',indices) +end +run0_Callback(hObject, eventdata, handles) + +%------------------------------------------------------------------- +function i2_Callback(hObject, eventdata, handles) +i1_Callback(hObject, eventdata, handles) +%------------------------------------------------------------------- + +%------------------------------------------------------------------- +function j1_Callback(hObject, eventdata, handles) +i1_Callback(hObject, eventdata, handles) +%------------------------------------------------------------------- + +%------------------------------------------------------------------- +function j2_Callback(hObject, eventdata, handles) +i1_Callback(hObject, eventdata, handles) +%------------------------------------------------------------------- + +%------------------------------------------------------------------- +function slices_Callback(hObject, eventdata, handles) +%------------------------------------------------------------------- +if get(handles.slices,'Value')==1 + set(handles.slices,'BackgroundColor',[1 1 0]) + set(handles.nb_slice,'Visible','on') + set(handles.z_text,'Visible','on') + set(handles.z_index,'Visible','on') + nb_slice_Callback(hObject, eventdata, handles) +% z=mod(num_i1-1,nbslice)+1; +% set(handles.z_index,'String',num2str(z)) +else + set(handles.nb_slice,'Visible','off') + set(handles.slices,'BackgroundColor',[0.7 0.7 0.7]) + set(handles.z_text,'Visible','off') + set(handles.z_index,'Visible','off') + set(handles.masklevel,'Value',1) + set(handles.masklevel,'String',{'1'}) +end + +%------------------------------------------------------------------- +function nb_slice_Callback(hObject, eventdata, handles) +%------------------------------------------------------------------- +num_i1=str2num(get(handles.i1,'String')); +nbslice=str2num(get(handles.nb_slice,'String')); +z=mod(num_i1-1,nbslice)+1; +set(handles.z_index,'String',num2str(z)) +for ilist=1:nbslice + list_index{ilist,1}=num2str(ilist); +end +set(handles.masklevel,'String',list_index) +set(handles.masklevel,'Value',z) + + +%------------------------------------------------------------------- +% --- Executes on button press in view_xml. +function view_xml_Callback(hObject, eventdata, handles) +[FileName,RootPath,FileBase,FileIndices,FileExt]=read_file_boxes(handles); +option=get(handles.view_xml,'String'); +if isequal(option,'view .xml') + FileXml=[FileBase '.xml']; + heditxml=editxml(FileXml); +end + +%------------------------------------------------------------------- +% --- Executes on button press in mask_test. +function mask_test_Callback(hObject, eventdata, handles) +%------------------------------------------------------------------- +if isequal(get(handles.mask_test,'Value'),1) + [FF,RootPath,FileBase]=read_file_boxes(handles); + num_i1=stra2num(get(handles.i1,'String')); + num_j1=stra2num(get(handles.j1,'String')); + currentdir=pwd; + cd(RootPath); + maskfiles=dir('*_*mask_*.png');%look for a mask file + cd(currentdir);%come back to the working directory + mdetect=0; + if isempty(maskfiles) + msgbox_uvmat('ERROR','no mask file detected (format ..._xxmask_ii.png needed), use the menu bar Tools/Make mask') + return + end + for ilist=1:length(maskfiles) + maskname=maskfiles(ilist).name;% take the first mask file in the list + [rr,ff,x1,x2,xa,xb,xext,Mask_NomType{ilist}]=name2display(maskname); + if ~strcmp(Mask_NomType{ilist},Mask_NomType{1}) + msgbox_uvmat('ERROR',['inconsistent mask types ' Mask_NomType{1} Mask_NomType{ilist } ' coexist in the current image directory']) + return + end + [Path2,Name,ext]=fileparts(maskname); + Namedouble=double(Name); + val=(48>Namedouble)|(Namedouble>57);% select the non-numerical characters + ind_mask=findstr('mask',Name); + i=ind_mask-1; + while val(i)==0 & i>0 + i=i-1; + end + nbmask_str=str2num(Name(i+1:ind_mask-1)); + if ~isempty(nbmask_str) + nbslice(ilist)=nbmask_str; % number of different masks (slices) + end + end + if isequal(min(nbslice),max(nbslice)) + nbslice=nbslice(1); + else + msgbox_uvmat('ERROR','several inconsistent mask sets coexist in the current image directory') + return + end + if ~isempty(nbslice) && Name(i)=='_' + Mask.Base=[FileBase Name(i:ind_mask+3)]; + Mask.NbSlice=nbslice; + num_i1=mod(num_i1-1,nbslice)+1 + Mask.NomType=Mask_NomType{1}; + [maskname,mdetect]=name_generator(Mask.Base,num_i1,num_j1,'.png',Mask.NomType)% + mdetect=exist(maskname,'file') + if mdetect + set(handles.nb_slice,'String',Name(i+1:ind_mask-1)); + set(handles.nb_slice,'BackgroundColor',[1 1 0]) + set(handles.mask_test,'UserData',Mask); + set(handles.mask_test,'BackgroundColor',[1 1 0]) + if nbslice > 1 + set(handles.slices,'value',1) + slices_Callback(hObject, eventdata, handles) + end + end + end + if mdetect==0 + msgbox_uvmat('ERROR','no mask file detected (format ..._xxmask_ii.png needed), use the menu bar Tools/Make mask') + set(handles.mask_test,'Value',0) + return + end + update_mask(handles,num_i1,num_j1); +else + MaskData=get(handles.mask_test,'UserData'); + if isfield(MaskData,'maskhandle') && ishandle(MaskData.maskhandle) + delete(MaskData.maskhandle) + end + set(handles.mask_test,'UserData',[]) + huvmat=get(handles.mask_test,'parent'); + UvData=get(huvmat,'UserData'); + if isfield(UvData,'MaskName') + UvData=rmfield(UvData,'MaskName'); + set(huvmat,'UserData',UvData) + end + set(handles.mask_test,'BackgroundColor',[0.7 0.7 0.7]) +end + +%------------------------------------------------------------------- +function update_mask(handles,num_i1,num_j1) +%------------------------------------------------------------------- + +MaskData=get(handles.mask_test,'UserData'); +if isfield(MaskData,'maskhandle')&& ishandle(MaskData.maskhandle) + uistack(MaskData.maskhandle,'top'); +end +num_i1_mask=mod(num_i1-1,MaskData.NbSlice)+1; +[MaskName,mdetect]=name_generator(MaskData.Base,num_i1_mask,num_j1,'.png',MaskData.NomType); +huvmat=get(handles.mask_test,'parent'); +UvData=get(huvmat,'UserData'); + +%update mask image if the mask is new +if ~ (isfield(UvData,'MaskName') && isequal(UvData.MaskName,MaskName)) + UvData.MaskName=MaskName; %update the recorded name on UvData + set(huvmat,'UserData',UvData); + if mdetect==0 + if isfield(MaskData,'maskhandle')&& ishandle(MaskData.maskhandle) + delete(MaskData.maskhandle) + end + else + %read mask image + Mask.AName='image'; + Mask.A=imread(MaskName); + npxy=size(Mask.A); + Mask.AX=[0.5 npxy(2)-0.5]; + Mask.AY=[npxy(1)-0.5 0.5 ]; + Mask.CoordType='px'; + if isequal(get(handles.slices,'Value'),1) + NbSlice=str2num(get(handles.nb_slice,'String')); + num_i1=str2num(get(handles.i1,'String')); + Mask.ZIndex=mod(num_i1-1,NbSlice)+1; + end + %px to phys or other transform on field + menu_transform=get(handles.menu_coord,'String'); + choice_value=get(handles.menu_coord,'Value'); + transform=menu_transform{choice_value};%name of the transform fct given by the menu 'menu_coord' + if ~isequal(transform,'') && ~isequal(transform,'px') + if isfield(UvData,'XmlData') && isfield(UvData.XmlData,'GeometryCalib')%use geometry calib recorded from the ImaDoc xml file as first priority + Calib=UvData.XmlData.GeometryCalib; + Mask=feval(transform,Mask,UvData.XmlData); + end + end + flagmask=Mask.A < 200; + + %make brown color image + imflag(:,:,1)=0.9*flagmask; + imflag(:,:,2)=0.7*flagmask; + imflag(:,:,3)=zeros(size(flagmask)); + + %update mask image + hmask=[]; %default + if isfield(MaskData,'maskhandle')&& ishandle(MaskData.maskhandle) + hmask=MaskData.maskhandle; + end + if ~isempty(hmask) + set(hmask,'CData',imflag) + set(hmask,'AlphaData',flagmask*0.6) + set(hmask,'XData',Mask.AX); + set(hmask,'YData',Mask.AY); +% uistack(hmask,'top') + else + axes(handles.axes3) + hold on + MaskData.maskhandle=image(Mask.AX,Mask.AY,imflag,'Tag','mask','HitTest','off','AlphaData',0.6*flagmask); +% set(MaskData.maskhandle,'AlphaData',0.6*flagmask) + set(handles.mask_test,'UserData',MaskData) + end + end +end + + +%------------------------------------------------------------------- +function MenuExportFigure_Callback(hObject, eventdata, handles) +%------------------------------------------------------------------- +huvmat=get(handles.MenuExport,'parent'); +UvData=get(huvmat,'UserData'); +hfig=figure; +newaxes=copyobj(handles.axes3,hfig); +map=colormap(handles.axes3); +colormap(map);%transmit the current colormap to the zoom fig +colorbar + +%------------------------------------------------------------------- +%------------------------------------------------------------------- +% III - MAIN REFRESH FUNCTIONS : 'FRAME PLOT' +%------------------------------------------------------------------- +%------------------------------------------------------------------- + +%Executes on button press in runplus: make one step forward and call +%run0. The step forward is along the fields series 1 or 2 depending on +%the scan_i and scan_j check box (exclusive each other) +%------------------------------------------------------------------- +function runplus_Callback(hObject, eventdata, handles) +increment=str2num(get(handles.increment_scan,'String')); %get the field increment d +runpm(hObject,eventdata,handles,increment) + +%------------------------------------------------------------------- +%Executes on button press in runmin: make one step backward and call +%run0. The step backward is along the fields series 1 or 2 depending on +%the scan_i and scan_j check box (exclusive each other) +%------------------------------------------------------------------- +function runmin_Callback(hObject, eventdata, handles) +increment=-str2num(get(handles.increment_scan,'String')); %get the field increment d +runpm(hObject,eventdata,handles,increment) + +%------------------------------------------------------------------- +%Executes on button press in runmin: make one step backward and call +%run0. The step backward is along the fields series 1 or 2 depending on +%the scan_i and scan_j check box (exclusive each other) +%------------------------------------------------------------------- +function RunMovie_Callback(hObject, eventdata, handles) +%------------------------------------------------------------------ +set(handles.RunMovie,'BackgroundColor',[1 1 0])%paint the command button in yellow +drawnow +increment=str2num(get(handles.increment_scan,'String')); %get the field increment d +set(handles.STOP,'Visible','on') +set(handles.speed,'Visible','on') +set(handles.speed_txt,'Visible','on') +set(handles.RunMovie,'BusyAction','queue') +testavi=0; +huvmat=get(handles.RunMovie,'parent'); +UvData=get(huvmat,'UserData'); + +while get(handles.speed,'Value')~=0 & isequal(get(handles.RunMovie,'BusyAction'),'queue') % enable STOP command + runpm(hObject,eventdata,handles,increment) + pause(1.02-get(handles.speed,'Value'))% wait for next image +end +if isfield(UvData,'aviobj') && ~isempty( UvData.aviobj), + UvData.aviobj=close(UvData.aviobj); + set(huvmat,'UserData',UvData); +end +set(handles.RunMovie,'BackgroundColor',[1 0 0])%paint the command buttonback to red + +%------------------------------------------------------------------- +function STOP_Callback(hObject, eventdata, handles) +%------------------------------------------------------------------- +set(handles.run0,'BusyAction','Cancel') +set(handles.RunMovie,'BusyAction','Cancel') +set(handles.MenuExportMovie,'BusyAction','Cancel') + + +%------------------------------------------------------------------ +function runpm(hObject,eventdata,handles,increment) +%------------------------------------------------------------------ +%read the data on the current input rootfile(s) + +[FileName,RootPath,filebase,FileIndices,FileExt,subdir]=read_file_boxes(handles); +NomType=get(handles.FileIndex,'UserData'); + +num1=stra2num(get(handles.i1,'String')); +num2=stra2num(get(handles.i2,'String')); +num_a=stra2num(get(handles.j1,'String')); +num_b=stra2num(get(handles.j2,'String')); + +sub_value= get(handles.SubField,'Value'); +if sub_value ==1 + [FileName_1,RootPath_1,filebase_1,FileIndices_1,FileExt_1,SubDir_1]=read_file_boxes_1(handles); +end + +comp_input=get(handles.fix_pair,'Value'); +if isequal(NomType,'_i1-i2')|isequal(NomType,'_i1-i2_j') + comp_input=1; %impose a fixed pair interval + set(handles.fix_pair,'Value',1) +end + +%case of scanning along the first direction (rootfile numbers) +if get(handles.scan_i,'Value')==1% case of scanning along field numbers + num1=num1+increment; + num2=num2+increment; + if comp_input==0% find a free pair + [filename,num_i1_out,num_j1_out,num_i2_out,num_j2_out]=... + name_generator(filebase,num1,num_a,FileExt,NomType,0,num2,num_b,subdir); + if exist(filename,'file') + num_a=num_j1_out; + num_b=num_j2_out; + end + end + if sub_value>=2 + num_i1=num_i1+increment; + num_i2=num_i2+increment; + end +else % case of scanning along the second direction (burst numbers) + lastfield_cell=get(handles.last_j,'String'); % get the last field number + lastfield=str2num(lastfield_cell{1}); + num_a=num_a+increment; + num_b=num_b+increment; + if sub_value >=2 + num_j1=num_j1+increment; + num_j2=num_j2+increment; + elseif ~isempty(lastfield) && num_a>lastfield + num_a=1; + num1=num1+1; + num2=num2+1; + end +end + +% display the new open numbers +set(handles.i1,'String',num2stra(num1,NomType,1)); +set(handles.i2,'String',num2stra(num2,NomType,1)); +set(handles.j1,'String',num2stra(num_a,NomType,2)); +set(handles.j2,'String',num2stra(num_b,NomType,2)); +[indices]=name_generator('',num1,num_a,'',NomType,1,num2,num_b,''); +set(handles.FileIndex,'String',indices); +if sub_value ==1 + NomType_1=get(handles.FileIndex_1,'UserData'); + [indices]=... + name_generator('',num1,num_a,'',NomType_1,1,num2,num_b,''); + set(handles.FileIndex_1,'String',indices); +end + +% refresh plots +run0_Callback(hObject, eventdata, handles); %run + + +%------------------------------------------------------- +% --- Executes on button press in movie_pair. +%------------------------------------------------------- +function movie_pair_Callback(hObject, eventdata, handles) +%initialisation +set(handles.movie_pair,'BackgroundColor',[1 1 0])%paint the command button in yellow +drawnow +list_fields=get(handles.Fields,'String');% list menu fields +index_fields=get(handles.Fields,'Value');% selected string index +FieldName=list_fields{index_fields}; % selected field +huvmat=get(handles.movie_pair,'parent'); +if isequal(FieldName,'image') + run0_Callback(hObject, eventdata, handles)%display the first image + UvData=get(huvmat,'UserData'); +else + warndlg_uvmat('an image or movie must be first introduced as input','ERROR') + return +end +[ff,rr,filebase,xx,Ext,SubDir]=read_file_boxes(handles); +NomType=get(handles.FileIndex,'UserData'); +num_i2=str2num(get(handles.i2,'String')); +num_j2=str2num(get(handles.j2,'String')); +if ~isempty(num_j2) + num_i1=str2num(get(handles.i1,'String')); + [imaname_1,idetect]=name_generator(filebase,num_i1,num_j2,Ext,NomType); + if idetect==0 + warndlg_uvmat(['second input open (-) ' imaname_1 ' not found'],'ERROR'); + return + end + set(handles.i2,'String',''); % indicates that the second index i2 is not used +elseif ~isempty(num_i2) + num_j1=str2num(get(handles.j1,'String')); + [imaname_1,idetect]=name_generator(filebase,num_i2,num_j1,Ext,NomType); + if idetect==0 + warndlg_uvmat(['second input open (-) ' imaname_1 ' not found'],'ERROR'); + return + end +else + warndlg_uvmat('a second image index i2 or j2 is needed to show the pair as a movie','ERROR') + return +end + +%read the second image +Field.AName='image'; +% Field.ListDimName={'AY','AX'}; %A FAIRE +% Field.DimValue=[]; +% Field.ListVarName={'A'}; +Field.AX=UvData.Field.AX; +Field.AY=UvData.Field.AY; +Field.CoordType='px'; +[Field.A,error]=read_image(imaname_1,NomType,num_i2); + + +%px to phys or other transform on field +menu_transform=get(handles.menu_coord,'String'); +choice_value=get(handles.menu_coord,'Value'); +transform=menu_transform{choice_value};%name of the transform fct given by the menu 'menu_coord' +if ~isequal(transform,'') && ~isequal(transform,'px') + if isfield(UvData,'XmlData') && isfield(UvData.XmlData,'GeometryCalib')%use geometry calib recorded from the ImaDoc xml file as first priority + Field=feval(transform,Field,UvData.XmlData); + end +end + + % make movie until movie speed is set to 0 or STOP is activated +hima=findobj(handles.axes3,'Tag','ima');% %handles.axes3 =main plotting window (A GENERALISER) +set(handles.STOP,'Visible','on') +set(handles.speed,'Visible','on') +set(handles.speed_txt,'Visible','on') +while get(handles.speed,'Value')~=0 & isequal(get(handles.run0,'BusyAction'),'queue'); % enable STOP command + % read and plot the series of images in non erase mode + set(hima,'CData',Field.A); + pause(1.02-get(handles.speed,'Value'));% wait for next image + set(hima,'CData',UvData.Field.A); + pause(1.02-get(handles.speed,'Value'));% wait for next image +end +set(handles.movie_pair,'BackgroundColor',[1 0 0])%paint the command button in red + +%run0_Callback(hObject, eventdata, handles) + +%------------------------------------------------------- +% --- Executes on button press in run0. +%------------------------------------------------- +function run0_Callback(hObject, eventdata, handles) + +%initialisation +set(handles.run0,'BackgroundColor',[1 1 0])%paint the command button in yellow +drawnow +abstime=[]; +abstime_1=[]; +dt=[]; +CalibCell={};%default +Field={}; +huvmat=get(handles.run0,'parent'); +UvData=get(huvmat,'UserData'); +if isfield(UvData,'Txt') + UvData=rmfield(UvData,'Txt');%erase previous error message +end +set(handles.run0,'BusyAction','queue'); +if ishandle(handles.UVMAT_title) %remove title panel on uvmat + delete(handles.UVMAT_title) +end + +% determine the main input file information for action +TestInputFile=1;%default +if isfield(UvData,'TestInputFile')&& isequal(UvData.TestInputFile,0), + TestInputFile=0; +end +num_i1=[];%default +if TestInputFile + [filename,RootPath,filebase,xx,Ext,SubDir]=read_file_boxes(handles); + if ~exist(filename,'file') + msgbox_uvmat('ERROR',['input file ' filename ' does not exist']) + return + end + num_i1=stra2num(get(handles.i1,'String')); + num_i2=stra2num(get(handles.i2,'String')); + num_j1=stra2num(get(handles.j1,'String')); + num_j2=stra2num(get(handles.j2,'String')); + NomType=get(handles.FileIndex,'UserData'); + %update the z position index +% if isequal(get(handles.nb_slice,'String'),'vol.')%case of volume +% set(handles.z_index,'String',get(handles.j1,'String')); +% else + nbslice=str2num(get(handles.nb_slice,'String')); + z_index=mod(num_i1-1,nbslice)+1; + if ~isempty(nbslice) + z_index=mod(num_i1-1,nbslice)+1; + set(handles.z_index,'String',num2str(z_index)) + % refresh menu for save_mask if relevant + masknumber=get(handles.masklevel,'String'); + if length(masknumber)>=z_index + set(handles.masklevel,'Value',z_index) + end + end +% end + % choose the main field + testima=0; + if isequal(lower(Ext),'.avi')||isequal(lower(Ext),'.vol') + testima=1; + FieldName='image'; + else + form=imformats(Ext([2:end])); + if ~isempty(form)% if the extension corresponds to an image format recognized by Matlab + testima=1; + FieldName='image'; + end + end +else + filename=[]; + FieldName='get_field...'; + testima=0; +end +VelType=[];%default + +if ~testima + list_fields=get(handles.Fields,'String');% list menu fields + index_fields=get(handles.Fields,'Value');% selected string index + FieldName= list_fields{index_fields}; % selected field + if isequal(FieldName,'get_field...')% read the field names on the interface get_field... + VelType=get(handles.Fields,'UserData'); + Field{1}=get(handles.Fields,'UserData'); + else + VelType=setfield(handles); + %enable_transform(handles,'on')% no field transform (possible transform in the GUI get_field) + end +end + +% choose a second field if Subfield option is 'on' +filename_1=[]; +VelType_1=[];%default +FieldName_1=[]; +scal_color=[]; +testvel=0; +testX=0;%default +VelType_1=setfield_1(handles); +sub_value=get(handles.SubField,'Value'); +if sub_value==1 + filename_1=read_file_boxes_1(handles); + if ~exist(filename_1,'file') + msgbox_uvmat('ERROR',['second file ' filename_1 ' does not exist']) + return + end + NomType_1=get(handles.FileIndex_1,'UserData'); + list_fields=get(handles.Fields_1,'String');% list menu fields + index_fields=get(handles.Fields_1,'Value');% selected string index + FieldName_1= list_fields{index_fields}; % selected field + if isequal(VelType_1,'*')% free veltype choice + VelType_1=[]; + elseif isequal(VelType_1,'"')% veltype the same as for the first field + if isempty(VelType) + VelType_1=[]; + else + VelType_1=VelType; + end + end +end + +% test for keeping the previous stored data if the input files are unchanged +test_keepdata_1=0;%defautl +test_keepdata=0; +if sub_value>=2 + if ~isequal(NomType_1,'*')%in cas of a series of files (not avi movie) + if isfield(UvData,'filename_1')& isfield(UvData,'VelType_1') & isfield(UvData,'FieldName_1') + test_keepdata_1= isequal(filename_1,UvData.filename_1)&... + isequal(VelType_1,UvData.filename_1) & isequal(FieldName_1,UvData.FieldName_1); + + end + end +end + +%read the input field(s) +testima_1=isequal(FieldName_1,'image'); +%read images +if ~isempty(filename) && testima + if isfield(UvData,'MovieObject') + A=read(UvData.MovieObject,num_i1); + else + [A,error]=read_image(filename,NomType,num_i1); + if ~isequal(error,0) + msgbox_uvmat('ERROR',error) + return + end + end + npxy=size(A); + set(handles.npx,'String',num2str(npxy(2)));% display image size on the interface + set(handles.npy,'String',num2str(npxy(1))); + Rangx=[0.5 npxy(2)-0.5]; % coordinates of the first and last pixel centers + Rangy=[npxy(1)-0.5 0.5]; % + npx=str2num(get(handles.npx,'String')); + npy=str2num(get(handles.npy,'String')); + if isfield(UvData.XmlData,'Time') + abs_time=UvData.XmlData.Time; + end + Field{1}.AName='image'; + Field{1}.ListVarName={'AY','AX','A'}; % + if size(A,3)==3;%color + Field{1}.VarDimName={'AY','AX',{'AY','AX','rgb'}}; % + else + Field{1}.VarDimName={'AY','AX',{'AY','AX'}}; % + end + Field{1}.AY=Rangy; + Field{1}.AX=Rangx; + Field{1}.A=A; + Field{1}.CoordType='px'; %used for mouse_motion + Field{1}.CoordUnit='pixel'; %used for mouse_motion +end +if ~isfield(UvData,'Txt')& ~isempty(filename_1) & testima_1 + [A,error]=read_image(filename_1,NomType_1,num_i1); + if ~isequal(error,0) + msgbox_uvmat('ERROR',error) + return + end + npxy=size(A); + set(handles.npx,'String',num2str(npxy(2)));% display image size on the interface + set(handles.npy,'String',num2str(npxy(1))); + Rangx=[0.5 npxy(2)-0.5]; % coordinates of the first and last pixel centers + Rangy=[npxy(1)-0.5 0.5]; % + npx=str2num(get(handles.npx,'String')); + npy=str2num(get(handles.npy,'String')); + if isfield(UvData,'XmlData_1') && isfield(UvData.XmlData_1,'Time') + abs_time=UvData.XmlData_1.Time; + end + Field{2}.AName='image'; + Field{2}.ListVarName={'AY','AX','A'}; % + if size(A,3)==3;%color + Field{2}.VarDimName={'AY','AX',{'AY','AX','rgb'}}; % + else + Field{2}.VarDimName={'AY','AX',{'AY','AX'}}; % + end + Field{2}.AY=Rangy; + Field{2}.AX=Rangx; + Field{2}.A=A; + Field{2}.CoordType='px'; %used for mouse_motion + Field{2}.CoordUnit='px'; %used for move_mou +end + +%read ncfile(s) +CivStage_1=0;%default +VelType_out_1=[]; +InputField={FieldName}; +InputField_1={FieldName_1}; +if ~isfield(UvData,'Txt') && ((~isempty(filename)&~testima) || (~isempty(filename_1)&~testima_1)) ; + %read the velocity field(s) from netcdf rootfile(s) + list_code=get(handles.col_vec,'String');% list menu fields + index_code=get(handles.col_vec,'Value');% selected string index + scal_color= list_code{index_code(1)}; % selected field + if isequal(FieldName,'velocity')&& ~isequal(scal_color,'black') && ~isequal(scal_color,'white') + InputField=[InputField scal_color]; + end + if isequal(FieldName_1,'velocity') && ~isequal(scal_color,'black') && ~isequal(scal_color,'white') + InputField_1=[InputField_1 scal_color]; + end + if ~testima %read the first nc field + if isequal(FieldName,'get_field...')% read the field names on the interface get_field. + test_detect=0;%default + VelType=get(handles.Fields,'UserData'); + hget_field=findobj(allchild(0),'Name','get_field');%find the get_field... GUI + if isempty(hget_field) + hget_field= get_field(filename);%open the get_field GUI + end + test_detect=1; + hhget_field=guidata(hget_field); + set(hhget_field.inputfile,'String',filename)% update the list of input fields in get_field + set(hhget_field.ACTION,'Value',1)% PLOT option selected + set(hhget_field.list_fig,'Value',2)% plotting axes =uvmat selected + [Field{1},errormsg]=read_get_field(hget_field); %read the names of the variables to plot in the get_field GUI + if ~isempty(errormsg) + msgbox_uvmat('ERROR',['error in uvmat/run0_Callback/read_get_field: ' errormsg]) + return + end + CivStage=0; + VelType_out=[]; + else + [Field{1},VelType_out]=read_civxdata(filename,InputField,VelType); + if isfield(Field{1},'Txt') + msgbox_uvmat('ERROR',Field{1}.Txt) + return + end + CivStage=Field{1}.CivStage; + UvData.NbDim=Field{1}.nb_dim; + end + end + if ~isempty(filename_1) && ~testima_1 %read the second file + if isequal(FieldName_1,'get_field...')% read the field names on the interface get_field. + test_detect=0;%default + hget_field=findobj(allchild(0),'Name','get_field_1');%find the get_field... GUI + if isempty(hget_field) + hget_field= get_field(filename_1);%open the get_field GUI + set(hget_field,'name','get_field_1') +% enable_transform(handles,'off')% no field transform (possible transform in the GUI get_field) + end + test_detect=1; + hhget_field=guidata(hget_field);%handles of GUI elements in get_field + SubField=get_field('read_var_names',hObject,eventdata,hhget_field); %read the names of the variables to plot in the get_field GUI + [Field{2},var_detect]=nc2struct(filename_1,SubField.ListVarName); %read the corresponding input data + Field{2}.VarAttribute=SubField.VarAttribute; + if isequal(get(hhget_field.menu_coord,'Visible'),'on') + list_transform=get(hhget_field.menu_coord,'String'); + val_list=get(hhget_field.menu_coord,'Value'); + transf=list_transform{val_list}; + if ~isempty(transf) + Field{2}=feval(transf,Field{2}); + end + end + + %update the display on get_field + set(hhget_field.inputfile,'String',filename_1) + set(hhget_field.variables,'Value',1) + Tabchar={''};%default + Tabcell=[]; + if isfield(Field{2},'ListGlobalAttribute')& ~isempty(Field{2}.ListGlobalAttribute) + for iline=1:length(Field{2}.ListGlobalAttribute) + Tabcell{iline,1}=Field{2}.ListGlobalAttribute{iline}; + if isfield(Field{2}, Field{2}.ListGlobalAttribute{iline}) + eval(['val=Field{2}.' Field{2}.ListGlobalAttribute{iline} ';']) + if ischar(val); + Tabcell{iline,2}=val; + else + Tabcell{iline,2}=num2str(val); + end + end + end + if ~isempty(Tabcell) + Tabchar=cell2tab(Tabcell,'='); + Tabchar=[{''};Tabchar]; + end + end + set(hhget_field.attributes,'String',Tabchar);%update list of global attributes in get_field + else + [Field{2},VelType_out_1]=read_civxdata(filename_1,[],VelType_1); + CivStage_1=Field{2}.CivStage; + end + if testima + VelType_out=VelType_out_1; + end + end +end + +%update the display buttons for the first velocity type (first menuline) +veltype_handles=[handles.civ1 handles.interp1 handles.filter1 handles.civ2 handles.interp2 handles.filter2]; +if testima + reset_vel_type(veltype_handles) +elseif isempty(VelType) + set_veltype_display(veltype_handles,CivStage)%update the display of available velocity types for the first field + if isempty(VelType_out) + reset_vel_type(veltype_handles) + else + handle1=eval(['handles.' VelType_out]); + reset_vel_type(veltype_handles,handle1) + end +end + +%update the display buttons for the second velocity type (second menuline) +veltype_handles_1=[handles.civ1_1 handles.interp1_1 handles.filter1_1 handles.civ2_1 handles.interp2_1 handles.filter2_1]; +if testima_1 + reset_vel_type(veltype_handles_1) +elseif isempty(VelType_1) + set_veltype_display(veltype_handles_1,CivStage_1)%update the display of available velocity types for the first field + if isempty(VelType_out_1) + reset_vel_type(veltype_handles_1) + else + handle1=eval(['handles.' VelType_out_1 '_1']); + reset_vel_type(veltype_handles_1,handle1) + end +end + +%introduce w as background image by default for a new series (only for nbdim=2) +if ~isfield(UvData,'NewSeries') + UvData.NewSeries=1; +end +%put W as background image by default if NbDim=2: +if ~isfield(UvData,'NbDim')|isempty(UvData.NbDim)|~isequal(UvData.NbDim,3) + if UvData.NewSeries && isequal(get(handles.SubField,'Value'),0) && isfield(Field{1},'W') && ~isempty(Field{1}.W); + set(handles.SubField,'Value',1); + menu=update_menu(handles.Fields_1,'w');%update the menu for the background scalar nd set the choice to 'w' + set(handles.RootPath_1,'String','"') + set(handles.RootFile_1,'String','"') + set(handles.SubDir_1,'String','"'); + [indices]=name_generator('',num_i1,num_j1,'',NomType,1,num_i2,num_j2,''); + set(handles.FileIndex_1,'String',indices) + set(handles.FileExt_1,'String','"'); + set(handles.Fields_1,'Visible','on'); + set(handles.Fields_1,'Visible','on'); + set(handles.RootPath_1,'Visible','on') + set(handles.RootFile_1,'Visible','on') + set(handles.SubDir_1,'Visible','on'); + set(handles.FileIndex_1,'Visible','on'); + set(handles.FileExt_1,'Visible','on'); + set(handles.Fields_1,'Visible','on'); + Field{1}.AName='w'; + testscal=1; + end +end + +%multislice case +if TestInputFile &&(~isfield(UvData,'NbDim') || isequal(UvData.NbDim,2))&&...%2D case + isfield(UvData,'XmlData') && isfield(UvData.XmlData,'GeometryCalib')&& isfield(UvData.XmlData.GeometryCalib,'SliceCoord') +% nbfield2=str2num(get(handles.last_j,'String')); + siz=size(UvData.XmlData.GeometryCalib.SliceCoord); + if siz(1)>1 + NbSlice=siz(1); + set(handles.slices,'Visible','on') + set(handles.slices,'Value',1) + else + NbSlice=1; + end + set(handles.nb_slice,'String',num2str(NbSlice)) + slices_Callback(hObject, eventdata, handles) +% Coord=UvData.XmlData.GeometryCalib.SliceCoord; +% ZIndex=num_i1-NbSlice*(floor((num_i1-1)/NbSlice)); +% Field{1}.Z=ZIndex; +end + +%store the current open names, fields and vel types in uvmat interface +UvData.filename=filename; +UvData.filename_1=filename_1; +UvData.VelType=VelType; +UvData.VelType_1=VelType_1; +UvData.FieldName=FieldName; +UvData.FieldName_1=FieldName_1; +if ~isempty(scal_color) + UvData.CName=scal_color; +end + +%coordinate transform or user fct +XmlData=[];%default +if isfield(UvData,'XmlData')%use geometry calib recorded from the ImaDoc xml file as first priority + XmlData=UvData.XmlData; +end +XmlData_1=[];%default +if isfield(UvData,'XmlData_1') + XmlData_1=UvData.XmlData_1; +end +menu_transform=get(handles.menu_coord,'String'); +choice_value=get(handles.menu_coord,'Value'); +transform=menu_transform{choice_value};%name of the transform fct given by the menu 'menu_coord' + +% z index +if TestInputFile + Field{1}.ZIndex=mod(num_i1-1,nbslice)+1; +end +%px to phys or other transform on field +if ~isequal(transform,'') + if length(Field)>=2 + Field{2}.ZIndex=mod(num_i1-1,nbslice)+1; + [Field{1},Field{2}]=feval(transform,Field{1},XmlData,Field{2},XmlData_1); + if isempty(Field{2}) + Field(2)=[]; + end + else + Field{1}=feval(transform,Field{1},XmlData); + end +end + +%calculate scalar +if ~testima && ~isequal(FieldName,'get_field...')% + Field{1}=calc_field(InputField,Field{1}); +end +if length(Field)==2 && ~testima_1 && ~isequal(FieldName,'get_field...') + Field{2}=calc_field(InputField_1,Field{2}); +end + +% combine the two input fields (e.g. substract velocity fields) +if numel(Field)==2 + if ~(isequal(get(handles.movie_pair,'Value'),1) & isequal(FieldName,'image') & isequal(FieldName_1,'image')) %combine fields if not viewing image pairs + UvData.Field=sub_field(Field{1},Field{2}); %TO UPDATE FOR MORE GENERAL INPUT + end +else + UvData.Field=Field{1}; +end +UvData.NewSeries=0;% put to 0 the test for a new field series (set by RootPath_callback) +% test 3D , default projection menuplane and typical mesh (needed to menuopen set_object) +test_x=0; +test_z=0;% test for unstructured z coordinate +UvData.ZMax=0; +UvData.ZMin=0;%default +UvData.Mesh=1; %default +[UvData.Field,errormsg]=check_field_structure(UvData.Field); +if ~isempty(errormsg) + msgbox_uvmat('ERROR',['error in uvmat/run0_Callback/check_field_structure: ' errormsg]) + return +end +[CellVarIndex,NbDim,VarType]=find_field_indices(UvData.Field); +[NbDim,imax]=max(NbDim); +if isempty(imax) + DimVarIndex=0; + coord_x=[]; +else + VarIndex=CellVarIndex{imax}; + coord_x=VarType{imax}.coord_x; +end +if isfield(UvData,'NbDim') & ~isempty(UvData.NbDim) + NbDim=UvData.NbDim; +else + UvData.NbDim=NbDim; +end +if ~isempty(CellVarIndex) & ~isempty(VarType{imax}.coord_x) & ~isempty(VarType{imax}.coord_y) %unstructured coordinate z + XName=UvData.Field.ListVarName{VarType{imax}.coord_x}; + YName=UvData.Field.ListVarName{VarType{imax}.coord_y}; + test_x=1; +elseif isfield(UvData.Field,'X')&isfield(UvData.Field,'Y') + XName='X'; + YName='Y'; + test_x=1; +end +if test_x + eval(['UvData.XMax=max(UvData.Field.' XName ');']) + eval(['UvData.XMin=min(UvData.Field.' XName ');']) + eval(['UvData.YMax=max(UvData.Field.' YName ');']) + eval(['UvData.YMin=min(UvData.Field.' YName ');']) + eval(['nbvec=length(UvData.Field.' XName ');']) + if NbDim==3% + if ~isempty(CellVarIndex) & ~isempty(VarType{imax}.coord_z)%unstructured coordinate z + ZName=UvData.ListVarName{VarType{imax}.coord_z}; + eval(['UvData.ZMax=max(UvData.Field.' ZName ');']) + eval(['UvData.ZMin=min(UvData.Field.' ZName ');']) + test_z=1; + elseif isfield(UvData,'Z')% usual civ data + UvData.ZMax=max(UvData.Z); + UvData.ZMin=min(UvData.Z); + test_z=1; + end + end + if isequal(UvData.ZMin,UvData.ZMax)%no z dependency + NbDim=2; + test_z=0; + end + if test_z + UvData.Mesh=((UvData.XMax-UvData.XMin)*(UvData.YMax-UvData.YMin)*(UvData.ZMax-UvData.ZMin))/nbvec;% volume per vector + UvData.Mesh=(UvData.Mesh)^(1/3); + else + UvData.Mesh=sqrt((UvData.XMax-UvData.XMin)*(UvData.YMax-UvData.YMin)/nbvec);%2D + end +end +%case of structured coordinates +if isfield(UvData.Field,'AX') & isfield(UvData.Field,'AY')& isfield(UvData.Field,'A') + UvData.XMax=max(UvData.Field.AX); + UvData.XMin=min(UvData.Field.AX); + UvData.YMax=max(UvData.Field.AY); + UvData.YMin=min(UvData.Field.AY); + np_A=size(UvData.Field.A); + UvData.Mesh=sqrt((UvData.XMax-UvData.XMin)*(UvData.YMax-UvData.YMin)/((np_A(1)-1) * (np_A(2)-1))) ; +end +if isempty(coord_x)&~isempty(CellVarIndex) + VarIndex=CellVarIndex{imax}; % list of variable indices + DimIndex=UvData.Field.VarDimIndex{VarIndex(1)}; %list of dim indices for the variable + if NbDim==3 + nbpoints=UvData.Field.DimValue(DimIndex(1)); + %Zvar=DimVarIndex(DimIndex(1)); + %Zvar=DimVarIndex(1); + Zvar=VarType{imax}.coord_3; + if Zvar~=0 % z is a dimension variable + ZName=UvData.Field.ListVarName{Zvar}; + eval(['UvData.ZMax=max(UvData.Field.' ZName ');']) + eval(['UvData.ZMin=min(UvData.Field.' ZName ');']) + else + testcoord_z=0; + if length(UvData.Field.VarAttribute)>=VarIndex(1) + if isfield(UvData.Field.VarAttribute{VarIndex(1)},'Coord_1')%regular grid + Coord_z=UvData.Field.VarAttribute{VarIndex(1)}.Coord_1; + UvData.ZMax=max(Coord_z); + UvData.ZMin=min(Coord_z); + testcoord_z=1; + end + end + if ~testcoord_z + UvData.ZMin=1; + UvData.ZMax=UvData.Field.DimValue(DimIndex(1)); + end + end + UvData.Mesh=(UvData.ZMax-UvData.ZMin)/(nbpoints-1); + elseif NbDim==2 + nbpoints_y=UvData.Field.DimValue(DimIndex(1)); + Yvar=VarType{imax}.coord_y; + if Yvar~=0 % x is a dimension variable + YName=UvData.Field.ListVarName{Yvar}; + eval(['UvData.YMax=max(UvData.Field.' YName ');']) + eval(['UvData.YMin=min(UvData.Field.' YName ');']) + else + testcoord_y=0; + if ~testcoord_y + UvData.YMin=1; + UvData.YMax=UvData.Field.DimValue(DimIndex(1)); + end + end + DY=(UvData.YMax-UvData.YMin)/(nbpoints_y-1); + nbpoints_x=UvData.Field.DimValue(DimIndex(2)); + Xvar=VarType{imax}.coord_x; + if Xvar~=0 % x is a dimension variable + XName=UvData.Field.ListVarName{Xvar}; + eval(['UvData.XMax=max(UvData.Field.' XName ');']) + eval(['UvData.XMin=min(UvData.Field.' XName ');']) + else + testcoord_x=0; + if ~testcoord_x + UvData.XMin=1; + UvData.XMax=UvData.Field.DimValue(DimIndex(2)); + end + end + DX=(UvData.XMax-UvData.XMin)/(nbpoints_x-1); + UvData.Mesh= sqrt(DX*DY); + end +end + +%create a default projection menuplane +UvData.Object{1}.Style='plane';%main plotting plane +UvData.Object{1}.ProjMode='projection';%main plotting plane +if ~isfield(UvData.Object{1},'plotaxes') + UvData.Object{1}.plotaxes=handles.axes3;%default plotting axis + set(handles.list_object,'String',{'1-PLANE';'...'}); + set(handles.list_object,'Value',1); +end + +%3D case (menuvolume) +if NbDim==3 + UvData.Object{1}.NbDim=UvData.NbDim;%test for 3D objects + UvData.Object{1}.RangeZ=UvData.Mesh;%main plotting plane + UvData.Object{1}.Coord(1,3)=(UvData.ZMin+UvData.ZMax)/2;%section at a middle plane chosen + UvData.Object{1}.Phi=0; + UvData.Object{1}.Theta=0; + UvData.Object{1}.Psi=0; + UvData.Object{1}.HandlesDisplay=plot(0,0,'Tag','proj_object');% A REVOIR + PlotHandles=get_plot_handles(handles); + ZBounds(1)=UvData.ZMin; %minimum for the Z slider + ZBounds(2)=UvData.ZMax;%maximum for the Z slider + set_object(UvData.Object{1},PlotHandles,ZBounds); + set(handles.list_object,'Value',1); +%multilevel case (single menuplane in a 3D space) +elseif isfield(UvData,'Z') + if isfield(UvData,'CoordType')& isequal(UvData.CoordType,'phys') & isfield(UvData,'XmlData') + XmlData=UvData.XmlData; + if isfield(XmlData,'PlanePos') + UvData.Object{1}.Coord=XmlData.PlanePos(UvData.ZIndex,:); + end + if isfield(XmlData,'PlaneAngle') + siz=size(XmlData.PlaneAngle); + indangle=min(siz(1),UvData.ZIndex);%take first angle if a single angle is defined (translating scanning) + UvData.Object{1}.Phi=XmlData.PlaneAngle(indangle,1); + UvData.Object{1}.Theta=XmlData.PlaneAngle(indangle,2); + UvData.Object{1}.Psi=XmlData.PlaneAngle(indangle,3); + end + elseif isfield(UvData,'ZIndex') + UvData.Object{1}.ZObject=UvData.ZIndex; + end +end + +%Plot the projections on all existing projection objects +keeplim=get(handles.FixedLimits,'Value'); +%reset the min and max of scalar if only the mask is displayed +if isfield(UvData,'Mask')&~isfield(UvData,'A') + set(handles.MinA,'String','0') + set(handles.MaxA,'String','255') +end + +Object=UvData.Object; +for iobj=1:length(Object) + if ~isempty(Object{iobj})%& isfield(Object{iobj},'plotaxes')& ishandle(Object{iobj}.plotaxes) + %Projeter les champs sur l'objet:* + ObjectData=proj_field(UvData.Field,Object{iobj},iobj); + + %use of mask + if isfield(ObjectData,'NbDim')&isequal(ObjectData.NbDim,2) + if isfield(ObjectData,'Mask') & isfield(ObjectData,'A') + flag_mask=double(ObjectData.Mask>200);%=0 for masked regions + AX=ObjectData.AX; + AY=ObjectData.AY; + MaskX=ObjectData.MaskX; + MaskY=ObjectData.MaskY; + if ~isequal(MaskX,AX)|~isequal(MaskY,AY) + nxy=size(flag_mask); + sizpx=(ObjectData.MaskX(end)-ObjectData.MaskX(1))/(nxy(2)-1);%size of a mask pixel + sizpy=(ObjectData.MaskY(1)-ObjectData.MaskY(end))/(nxy(1)-1); + x_mask=[ObjectData.MaskX(1):sizpx:ObjectData.MaskX(end)]; % pixel x coordinates for image display + y_mask=[ObjectData.MaskY(1):-sizpy:ObjectData.MaskY(end)];% pixel x coordinates for image display + %project on the positions of the scalar + npxy=size(ObjectData.A); + dxy(1)=(ObjectData.AY(end)-ObjectData.AY(1))/(npxy(1)-1);%grid mesh in y + dxy(2)=(ObjectData.AX(end)-ObjectData.AX(1))/(npxy(2)-1);%grid mesh in x + xi=[ObjectData.AX(1):dxy(2):ObjectData.AX(end)]; + yi=[ObjectData.AY(1):dxy(1):ObjectData.AY(end)]; + [XI,YI]=meshgrid(xi,yi);% creates the matrix of regular coordinates + flag_mask = interp2(x_mask,y_mask,flag_mask,XI,YI); + end + AClass=class(ObjectData.A); + ObjectData.A=flag_mask.*double(ObjectData.A); + ObjectData.A=feval(AClass,ObjectData.A); + ind_off=[]; + if isfield(ObjectData,'ListVarName') + for ilist=1:length(ObjectData.ListVarName) + if isequal(ObjectData.ListVarName{ilist},'Mask')|isequal(ObjectData.ListVarName{ilist},'MaskX')|isequal(ObjectData.ListVarName{ilist},'MaskY') + ind_off=[ind_off ilist]; + end + end + ObjectData.ListVarName(ind_off)=[]; + ObjectData.VarDimIndex(ind_off)=[]; + ind_off=[]; + for ilist=1:length(ObjectData.ListDimName) + if isequal(ObjectData.ListDimName{ilist},'MaskX')|isequal(ObjectData.ListDimName{ilist},'MaskY') + ind_off=[ind_off ilist]; + end + end + ObjectData.ListDimName(ind_off)=[]; + ObjectData.DimValue(ind_off)=[]; + end + end + end + if ~isempty(ObjectData) + haxes=[];%default + if isfield(Object{iobj},'plotaxes') + haxes=Object{iobj}.plotaxes;%axes used for representing the projection on the object + end + PosColorbar=[];%default: no colorbar + if ishandle(haxes) & isequal(get(haxes,'Tag'),'axes3')& isfield(UvData,'PosColorbar') + PosColorbar=UvData.PosColorbar;%prescribe the colorbar position on the uvmat interface + else + PosColorbar='*';%default position + end + PlotParam=read_plot_param(handles);%read plotting parameters on the uvmat interface + [PlotType,ScalOut,UvData.Object{iobj}.plotaxes]=plot_field(ObjectData,haxes,PlotParam,keeplim,PosColorbar); + if isequal(PlotType,'none') + hget_field=findobj(allchild(0),'name','get_field'); + if isempty(hget_field) + get_field([],ObjectData)% the projected field cannot be automatically plotted: use get_field to specify the variablesdelete(hget_field) + else + msgbox_uvmat('ERROR','The field defined by get_field cannot be plotted') + end + end + UvData.Object{iobj}.PlotParam=ScalOut; %record the plotting parameters + end + + end +end + +%display the updated plotting parameters for the base menuplane +write_plot_param(handles,UvData.Object{1}.PlotParam);% update the display of the plotting parameters +set(huvmat,'UserData',UvData) + +%update the mask +if isequal(get(handles.mask_test,'Value'),1)%if the mask option is on + update_mask(handles,num_i1,num_i2); +end + +%prepare the menus of histograms (for the whole menuvolume in 3D case) +menu_histo=(UvData.Field.ListVarName)'; +ind_bad=[]; +nb_histo=1; +for ivar=1:numel(menu_histo) + if isfield(UvData.Field,'VarAttribute') && numel(UvData.Field.VarAttribute)>=ivar && isfield(UvData.Field.VarAttribute{ivar},'Role') + Role=UvData.Field.VarAttribute{ivar}.Role; + switch Role + case {'coord_x','coord_y','coord_z','dimvar'} + ind_bad=[ind_bad ivar]; + case {'vector_y'} + nb_histo=nb_histo+1; + end + end + DimCell=UvData.Field.VarDimName{ivar}; + DimName=''; + if ischar(DimCell) + DimName=DimCell; + elseif iscell(DimCell)&& numel(DimCell)==1 + DimName=DimCell{1}; + end + if strcmp(DimName,menu_histo{ivar}) + ind_bad=[ind_bad ivar]; + end +end +menu_histo(ind_bad)=[]; +test_v=0; +if ~isempty(menu_histo) + set(handles.histo1_menu,'Value',1) + set(handles.histo1_menu,'String',menu_histo) + histo1_menu_Callback(hObject, eventdata, handles) + if nb_histo > 1 + test_v=1; + set(handles.histo2_menu,'Visible','on') + set(handles.histo_v,'Visible','on') + set(handles.histo2_menu,'String',menu_histo) + set(handles.histo2_menu,'Value',2) + histo2_menu_Callback(hObject, eventdata, handles) + end +end +if ~test_v + set(handles.histo2_menu,'Visible','off') + set(handles.histo_v,'Visible','off') + cla(handles.histo_v) + set(handles.histo2_menu,'Value',1) +end + +%display time +testimedoc=0; +if isfield(UvData,'XmlData') && isfield(UvData.XmlData,'Time') + if isempty(num_i2) + num_i2=num_i1; + end + if isempty(num_j1) + num_j1=1; + end + if isempty(num_j2) + num_j2=num_j1; + end + siz=size(UvData.XmlData.Time); + if siz(1)>=max(num_i1,num_i2) & siz(2)>=max(num_j1,num_j2) + abstime=(UvData.XmlData.Time(num_i1,num_j1)+UvData.XmlData.Time(num_i2,num_j2))/2;%overset the time read from files + dt=(UvData.XmlData.Time(num_i2,num_j2)-UvData.XmlData.Time(num_i1,num_j1)); + testimedoc=1; + end +end +if isfield(UvData,'XmlData_1') && isfield(UvData.XmlData_1,'Time') + [P,F,str1,str2,str_a,str_b,E,NomType]=name2display(['xx' get(handles.FileIndex_1,'String') get(handles.FileExt_1,'String')]); + num_i2=str2num(str2); + if isempty(num_i2) + num_i2=num_i1; + end + num_j1=str2num(str_a); + if isempty(num_j1) + num_j1=1; + end + num_j2=str2num(str_b); + if isempty(num_j2) + num_j2=num_j1; + end + num_i1=str2num(str1); + siz=size(UvData.XmlData_1.Time); + if siz(1)>=max(num_i1,num_i2) & siz(2)>=max(num_j1,num_j2) + abstime_1=(UvData.XmlData_1.Time(num_i1,num_j1)+UvData.XmlData_1.Time(num_i2,num_j2))/2;%overset the time read from files + end +end +set(handles.abs_time,'String',num2str(abstime,4)) +set(handles.abs_time_1,'String',num2str(abstime_1,4)) +if testimedoc && isfield(UvData,'dt') + dt=UvData.dt; +end +if isequal(dt,0) + set(handles.Dt_txt,'String','') +else + if ~(isfield(UvData,'TimeUnit') && ~isempty(UvData.TimeUnit)) + set(handles.Dt_txt,'String',['Dt=' num2str(1000*dt,3) ' 10^(-3)'] ) + else + set(handles.Dt_txt,'String',['Dt=' num2str(1000*dt,3) ' m' UvData.TimeUnit] ) + end +end +set(handles.run0,'BackgroundColor',[1 0 0]) + + + +%------------------------------------------------------------------- +% --- translate coordinate to matrix index +%------------------------------------------------------------------- +function [indx,indy]=pos2ind(x0,rangx0,nxy) +indx=1+round((nxy(2)-1)*(x0-rangx0(1))/(rangx0(2)-rangx0(1)));% index x of pixel +indy=1+round((nxy(1)-1)*(y12-rangy0(1))/(rangy0(2)-rangy0(1)));% index y of pixel + +%------------------------------------------------------------------- +% --- Executes on button press in 'FixedLimits'. +%------------------------------------------------------------------- +function FixedLimits_Callback(hObject, eventdata, handles) +test=get(handles.FixedLimits,'Value'); +if test + set(handles.FixedLimits,'BackgroundColor',[1 1 0]) +else + set(handles.FixedLimits,'BackgroundColor',[0.7 0.7 0.7]) +end + +%------------------------------------------------------------------- +% --- Executes on button press in auto_xy. +function auto_xy_Callback(hObject, eventdata, handles) +test=get(handles.auto_xy,'Value'); +if test + set(handles.auto_xy,'BackgroundColor',[1 1 0]) + cla(handles.axes3) + update_plot(handles) +else + set(handles.auto_xy,'BackgroundColor',[0.7 0.7 0.7]) + update_plot(handles) +% axis(handles.axes3,'image') +end + + +%------------------------------------------------------------------- + +%------------------------------------------------------------------- +% --- Executes on button press in 'zoom'. +%------------------------------------------------------------------- +function zoom_Callback(hObject, eventdata, handles) +huvmat=get(handles.zoom,'parent');%general input +UvData=get(huvmat,'UserData'); +if (get(handles.zoom,'Value') == 1); + set(handles.zoom,'BackgroundColor',[1 1 0]) + set(handles.FixedLimits,'Value',1)% propose by default fixed limits for the plotting axes + set(handles.FixedLimits,'BackgroundColor',[1 1 0]) + %UvData.ZoomOn=1; %test for mouse action +else + set(handles.zoom,'BackgroundColor',[0.7 0.7 0.7]) + %UvData.ZoomOn=0; %test for mouse action +end +set(huvmat,'UserData',UvData); + +%------------------------------------------------------------------- +%----Executes on button press in 'record': records the current flags of manual correction. +%------------------------------------------------------------------- +function record_Callback(hObject, eventdata, handles) +% [filebase,num_i1,num_j1,num_i2,num_j2,Ext,NomType,SubDir]=read_input_file(handles); +filename=read_file_boxes(handles); +AxeData=get(gca,'UserData'); +[erread,message]=fileattrib(filename); +if ~isempty(message) & ~isequal(message.UserWrite,1) + msgbox_uvmat('ERROR',['no writting access to ' filename]) + return +end +nc=netcdf(filename,'write'); %open netcdf file +result=redef(nc); +if isempty(result), warndlg_uvmat('##Bad redef operation.','ERROR'),end +test_civ2=isequal(get(handles.civ2,'BackgroundColor'),[1 1 0]); +if ~test_civ2 + test_civ1=isequal(get(handles.civ1,'BackgroundColor'),[1 1 0]); +end +if test_civ2 % for civ2 + + theDim=nc('nb_vectors2') ;% get the number of velocity vectors + nb_vectors2=size(theDim); + var_FixFlag=ncvar('vec2_FixFlag',nc);% var_FixFlag will be written as the netcdf variable vec_FixFlag + var_FixFlag(1:nb_vectors2)=AxeData.FF;% +elseif test_civ1 % for civ1 + + theDim=nc('nb_vectors') ;% get the number of velocity vectors + nb_vectors=size(theDim); + var_FixFlag=ncvar('vec_FixFlag',nc);% var_FixFlag will be written as the netcdf variable vec_FixFlag + var_FixFlag(1:nb_vectors)=AxeData.FF;% +else + msgbox_uvmat('ERROR','manual correction only possible for CIV1 or CIV2 velocity fields') +end +fin=close(nc); + + + +%------------------------------------------------------------------- +%determines the fields to read from the interface +%------------------------------------------------------------------ +function [VelType,civ]=setfield(handles) + +VelType=[]; %default +if (get(handles.civ1,'Value') == 1); + VelType='civ1'; +% interp1 +elseif (get(handles.interp1,'Value') == 1); + VelType='interp1'; +% filter1 +elseif (get(handles.filter1,'Value') == 1); + VelType='filter1'; +% CIV2 +elseif (get(handles.civ2,'Value') == 1); + VelType='civ2'; +% interp2 +elseif (get(handles.interp2,'Value') == 1); + VelType='interp2'; +% filter2 +elseif (get(handles.filter2,'Value') == 1); + VelType='filter2'; +end + +if isequal(get(handles.filter2,'Visible'),'on'); + civ=6; +% interp1 +elseif isequal(get(handles.interp2,'Visible'),'on'); + civ=5; +% filter1 +elseif isequal(get(handles.civ2,'Visible'),'on'); + civ=4; +% CIV2 +elseif isequal(get(handles.filter1,'Visible'),'on'); + civ=3; +% interp2 +elseif isequal(get(handles.interp1,'Visible'),'on'); + civ=2; +% filter2 +elseif isequal(get(handles.civ1,'Visible'),'on'); + civ=1; +else + civ=0; +end + +%------------------------------------------------------------------- +%determines the veltype of the second field to read from the iinterface +%------------------------------------------------------------------ +function VelType=setfield_1(handles) + +VelType=[]; %default +if (get(handles.civ1_1,'Value') == 1); + VelType='civ1'; +% interp1 +elseif (get(handles.interp1_1,'Value') == 1); + VelType='interp1'; +% filter1 +elseif (get(handles.filter1_1,'Value') == 1); + VelType='filter1'; +% CIV2 +elseif (get(handles.civ2_1,'Value') == 1); + VelType='civ2'; +% interp2 +elseif (get(handles.interp2_1,'Value') == 1); + VelType='interp2'; +% filter2 +elseif (get(handles.filter2_1,'Value') == 1); + VelType='filter2'; +end + + +%--------------------------------------------------- +% --- Executes on button press in SubField +function SubField_Callback(hObject, eventdata, handles) +huvmat=get(handles.run0,'parent'); +UvData=get(huvmat,'UserData'); +if get(handles.SubField,'Value')==0% if the subfield button is desactivated + set(handles.RootPath_1,'String','') + set(handles.RootFile_1,'String','') + set(handles.SubDir_1,'String',''); + set(handles.FileIndex_1,'String',''); + set(handles.FileExt_1,'String',''); + set(handles.RootPath_1,'Visible','off') + set(handles.RootFile_1,'Visible','off') + set(handles.SubDir_1,'Visible','off'); + set(handles.FileIndex_1,'Visible','off'); + set(handles.FileExt_1,'Visible','off'); + set(handles.Fields_1,'Value',1);%set to blank state + set_veltype_display([handles.civ1_1 handles.interp1_1 handles.filter1_1 ... + handles.civ2_1 handles.interp2_1 handles.filter2_1],0) + if isfield(UvData,'XmlData_1') + UvData=rmfield(UvData,'XmlData_1'); + end + set(huvmat,'UserData',UvData); + run0_Callback(hObject, eventdata, handles); %run +else + MenuBrowse_1_Callback(hObject, eventdata, handles) +end + +% %---------------------------------------------- +% %read the data displayed for the input rootfile windows (new) +% %------------------------------------------------- +function [FileName,RootPath,FileBase,FileIndices,FileExt,SubDir]=read_file_boxes(handles) +RootPath=get(handles.RootPath,'String'); +FileName=RootPath; %default +SubDir=get(handles.SubDir,'String'); +if ~isempty(SubDir) && ~isequal(SubDir,'') + if (isequal(SubDir(1),'/')|| isequal(SubDir(1),'\')) + SubDir(1)=[]; %suppress possible / or \ separator + end + FileName=fullfile(RootPath,SubDir); +end +RootFile=get(handles.RootFile,'String'); +if ~isempty(RootFile) && ~isequal(RootFile,'') + if (isequal(RootFile(1),'/')|| isequal(RootFile(1),'\')) + RootFile(1)=[]; %suppress possible / or \ separator + end + FileName=fullfile(FileName,RootFile); +end +FileBase=fullfile(RootPath,RootFile); +FileIndices=get(handles.FileIndex,'String'); +FileExt=get(handles.FileExt,'String'); +FileName=[FileName FileIndices FileExt]; + +%---------------------------------------------- +%read the data displayed for the second input rootfile windows +%------------------------------------------------- +function [FileName_1,RootPath_1,FileBase_1,FileIndices_1,FileExt_1,SubDir_1]=read_file_boxes_1(handles) +RootPath_1=get(handles.RootPath_1,'String'); % read the data from the file1_input window +if isequal(RootPath_1,'"'),RootPath_1=get(handles.RootPath,'String'); end; +FileName_1=RootPath_1; %default +SubDir_1=get(handles.SubDir_1,'String'); +if isequal(SubDir_1,'"') + SubDir_1=get(handles.SubDir,'String'); +end +if ~isempty(SubDir_1) && ~isequal(SubDir_1,'') + if (isequal(SubDir_1(1),'/')|| isequal(SubDir_1(1),'\')) + SubDir_1(1)=[]; %suppress possible / or \ separator + end + FileName_1=fullfile(RootPath_1,SubDir_1); +end +RootFile_1=get(handles.RootFile_1,'String'); +if isequal(RootFile_1,'"'),RootFile_1=get(handles.RootFile,'String'); end; +if ~isempty(RootFile_1) && ~isequal(RootFile_1,'') + if ~(isequal(RootFile_1(1),'/')|isequal(RootFile_1(1),'\')) + RootFile_1(1)=[];%suppress possible / or \ separator + end + FileName_1=fullfile(FileName_1,RootFile_1); +end +FileBase_1=fullfile(RootPath_1,RootFile_1); +FileIndices_1=get(handles.FileIndex_1,'String'); +FileExt_1=get(handles.FileExt_1,'String'); +if isequal(FileExt_1,'"'),FileExt_1=get(handles.FileExt,'String'); end; +FileName_1=[FileName_1 FileIndices_1 FileExt_1]; + +%--------------------------------------------------- +% --- Executes on menu selection Fields +function Fields_Callback(hObject, eventdata, handles) +%------------------------------------------------- +huvmat=get(handles.Fields,'parent'); +list_fields=get(handles.Fields,'String');% list menu fields +index_fields=get(handles.Fields,'Value');% selected string index +field= list_fields{index_fields(1)}; % selected string +if isequal(field,'get_field...') + veltype_handles=[handles.civ1 handles.interp1 handles.filter1 handles.civ2 handles.interp2 handles.filter2]; + set_veltype_display(veltype_handles,0) % unvisible civ buttons + filename=read_file_boxes(handles); + hget_field=findobj(allchild(0),'name','get_field'); + if ~isempty(hget_field) + delete(hget_field) + end + get_field(filename) + return %no action +end +list_fields=get(handles.Fields_1,'String');% list menu fields +index_fields=get(handles.Fields_1,'Value');% selected string index +field_1= list_fields{index_fields(1)}; % selected string +UvData=get(huvmat,'UserData'); + +%read the rootfile input display +FileExt=get(handles.FileExt,'String'); +[P,F,str1,str2,str_a,str_b,E,NomType]=name2display(['xxx' get(handles.FileIndex,'String') FileExt]); +NomTypeNew=NomType;%default +if isequal(field,'image') + % transform netc type to the corresponding image type + if isequal(NomType,'_i1-i2_j')||isequal(NomType,'_i_j1-j2')|| isequal(NomType,'#_ab')|| isequal(NomType,'_i1-i2') + UvData.SubDir=get(handles.SubDir,'String'); %preserve the subdir in memory + if ~isempty(UvData.SubDir) && (isequal(UvData.SubDir(1),'/')|isequal(UvData.SubDir(1),'/')) + UvData.SubDir(1)=[]; + end + set(handles.SubDir,'String','') + set(handles.FileExt,'String','.png'); + if isequal(NomType,'_i1-i2_j')|isequal(NomType,'_i_j1-j2') + NomTypeNew='_i_j'; + elseif isequal(NomType,'#_ab') + NomTypeNew='#a'; + elseif isequal(NomType,'_i1-i2') + NomTypeNew='_i'; + end + end + veltype_handles=[handles.civ1 handles.interp1 handles.filter1 handles.civ2 handles.interp2 handles.filter2]; + set_veltype_display(veltype_handles,0) % unvisible civ buttons +else + ext=get(handles.FileExt,'String'); + if ~isequal(ext,'.nc') %find the new NomType if the previous display was not already a netcdf file + MenuBrowse_Callback(hObject, eventdata, handles) + end + if isequal(field,'vort') || isequal(field,'div') || isequal(field,'strain') + set(handles.civ1,'BackgroundColor',[0.702 0.702 0.702]) % put their color to grey + set(handles.civ2,'BackgroundColor',[0.702 0.702 0.702]) + set(handles.interp1,'BackgroundColor',[0.702 0.702 0.702]) + set(handles.interp2,'BackgroundColor',[0.702 0.702 0.702]) + elseif isequal(field,'more...'); + set(handles.civ1,'BackgroundColor',[0.702 0.702 0.702]) % put their color to grey + set(handles.civ2,'BackgroundColor',[0.702 0.702 0.702]) + str=calc_field;%get the list of available scalars by the function calc_scal + [ind_answer,v] = listdlg('PromptString','Select a file:',... + 'SelectionMode','single',... + 'ListString',str); + % edit the choice in the field and action menu + scalar=cell2mat(str(ind_answer)); + menu=update_menu(handles.Fields,scalar); + menu=[{''};menu]; + set(handles.Fields_1,'String',menu);% store the selected scalar type + end +end +indices=name_generator('',str2num(str1),str2num(str_a),'',NomTypeNew,1,str2num(str2),str2num(str_b),''); +set(handles.FileIndex,'String',indices) +set(handles.FileIndex,'UserData',NomTypeNew) +%common to Fields_1_Callback +if isequal(field,'image')|isequal(field_1,'image') + set(handles.npx_title,'Visible','on')% visible npx,pxcm... buttons + set(handles.npy_title,'Visible','on') + set(handles.npx,'Visible','on') + set(handles.npy,'Visible','on') + set(handles.fix_pair,'Value',0) +else + set(handles.npx_title,'Visible','off')% visible npx,pxcm... buttons + set(handles.npy_title,'Visible','off') + set(handles.npx,'Visible','off') + set(handles.npy,'Visible','off') + set(handles.fix_pair,'Value',1) +end +if isequal(field,'velocity')|isequal(field_1,'velocity'); + state_vect='on'; +else + state_vect='off'; +end +if ~isequal(field,'velocity')|(~isequal(field_1,'velocity')); + state_scal='on'; +else + state_scal='off'; +end +setfield(handles);% update the field structure ('civ1'....) + +if ~isfield(UvData,'NewSeries')|isequal(UvData.NewSeries,0) + run0_Callback(hObject, eventdata, handles) +end + +%--------------------------------------------------- +% --- Executes on menu selection Fields +function Fields_1_Callback(hObject, eventdata, handles) +%------------------------------------------------- +huvmat=get(handles.Fields_1,'parent'); +list_fields=get(handles.Fields,'String');% list menu fields +index_fields=get(handles.Fields,'Value');% selected string index +field= list_fields{index_fields(1)}; % selected string +list_fields=get(handles.Fields_1,'String');% list menu fields +index_fields=get(handles.Fields_1,'Value');% selected string index +field_1= list_fields{index_fields(1)}; % selected string for the second field +if isequal(field_1,'') %remove second field if 'blank' field is selected + set(handles.SubField,'Value',0) + SubField_Callback(hObject, eventdata, handles) + return +end +UvData=get(huvmat,'UserData'); + +%read the rootfile input display +FileExt_prev=get(handles.FileExt_1,'String'); +if isempty(FileExt_prev)|isequal(FileExt_prev,'') + FileExt_1=get(handles.FileExt,'String'); +else + FileExt_1=FileExt_prev; +end +NomType_1=get(handles.FileIndex_1,'UserData'); +if isempty(NomType_1)|isequal(NomType_1,'') + NomType_1=get(handles.FileIndex,'UserData'); +end +NomTypeNew=NomType_1;%default + +set(handles.SubField,'Value',1)%introduce second field +if isfield(UvData,'XmlData') + UvData.XmlData_1=UvData.XmlData; +end +set(handles.FileIndex_1,'Visible','on') +set(handles.FileExt_1,'Visible','on') +RootPath_1=get(handles.RootPath_1,'String'); +RootFile_1=get(handles.RootFile_1,'String'); +if isempty(RootPath_1)|isequal(RootPath_1,'') + set(handles.RootPath_1,'String','"') +end +if isempty(RootFile_1) | isequal(RootFile_1,'') + set(handles.RootFile_1,'String','"') +end +if ~isempty(RootFile_1)&(isequal(RootFile_1(1),'/')|isequal(RootFile_1(1),'\')) + RootFile_1(1)=[]; +end + +if isequal(field_1,'get_field...') + veltype_handles=[handles.civ1 handles.interp1 handles.filter1 handles.civ2 handles.interp2 handles.filter2]; + set_veltype_display(veltype_handles,0) % unvisible civ buttons + filename=read_file_boxes_1(handles); + hget_field=findobj(allchild(0),'name','get_field_1'); + if ~isempty(hget_field) + delete(hget_field) + end + hget_field=get_field(filename); + set(hget_field,'name','get_field_1') + return %no action +end +if isequal(field_1,'image') + % transform netc type to the corresponding image type + set(handles.FileExt_1,'String','.png'); + if isequal(NomType_1,'_i1-i2_j')|isequal(NomType_1,'_i_j1-j2')| isequal(NomType_1,'#_ab')| isequal(NomType_1,'_i1-i2') + UvData.SubDir_1=get(handles.SubDir_1,'String'); %preserve the subdir in memory + set(handles.SubDir_1,'String','') +% set(handles.FileExt_1,'String','.png'); + if isequal(NomType_1,'_i1-i2_j')|isequal(NomType_1,'_i_j1-j2') + NomTypeNew='_i_j'; + elseif isequal(NomType_1,'#_ab') + NomTypeNew='#a'; + elseif isequal(NomType_1,'_i1-i2') + NomTypeNew='_i'; + end + end + veltype_handles=[handles.civ1_1 handles.interp1_1 handles.filter1_1 handles.civ2_1 handles.interp2_1 handles.filter2_1]; + set_veltype_display(veltype_handles,0) % unvisible civ buttons +else + set(handles.SubDir_1,'Visible','on') + if ~isequal(FileExt_prev,'.nc') %find the new NomType if the previous display was not already a netcdf file + veltype_handles=[handles.civ1_1 handles.interp1_1 handles.filter1_1 handles.civ2_1 handles.interp2_1 handles.filter2_1]; + set_veltype_display(veltype_handles,6); % make all civ buttons visible + RootPath_1=get(handles.RootPath_1,'String'); + RootFile_1=get(handles.RootFile_1,'String'); + if isempty(RootPath_1)|isequal(RootPath_1,'') + set(handles.RootPath_1,'String','"') + end + if isempty(RootFile_1) | isequal(RootFile_1,'') + set(handles.RootFile_1,'String','"') + end + if ~isempty(RootFile_1)&(isequal(RootFile_1(1),'/')|isequal(RootFile_1(1),'\')) + RootFile_1(1)=[]; + end + filebase_1=fullfile(RootPath_1,RootFile_1); + SubDir_1=get(handles.SubDir,'String'); + if isempty(SubDir_1)|isequal(SubDir_1,'') + if isfield(UvData,'SubDir_1') + SubDir_1=UvData.SubDir_1;%retrieve previous subdir + else + SubDir_1='?'; + end + end + if isequal(NomType_1,'#_ab')|isequal(NomType_1,'_i1-i2_j')|isequal(NomType_1,'_i_j1-j2')|isequal(NomType_1,'_i1-i2') + NomTypeNew=NomType_1; + elseif isequal(NomType_1,'#a') + [filename,idetect,n1,na,n2,nb,SubDir_1]=name_generator(filebase_1, str2num(str1),str2num(str_a),'.nc','#_ab',0,[],[],SubDir_1); + NomTypeNew='#_ab'; + elseif isequal(NomType_1,'_i_j') + [filename,idetect,n1,na,n2,nb,SubDir_1]=name_generator(filebase_1,str2num(str1),str2num(str_a),'.nc','_i1-i2_j',0,str2num(str1),[],SubDir_1); + if idetect==1 + NomTypeNew='_i1-i2_j'; + else + NomTypeNew='_i_j1-j2'; + end + else %for instance avi files or any ima_num series + [filename,idetect,n1,na,n2,nb,SubDir_1]=name_generator(filebase_1,str2num(str1),str2num(str_a),'.nc','_i1-i2',0,str2num(str1),[],SubDir_1); + NomTypeNew='_i1-i2'; + end + [Path,Name]=fileparts(filebase_1); + set(handles.FileExt_1,'String','.nc'); + if ~isempty(SubDir_1) & ~isequal(SubDir_1,'''')& ~isequal(SubDir_1,'"') + SubDir_1=['/' SubDir_1]; + end + set(handles.SubDir_1,'String',SubDir_1); + end + if isequal(field,'vort') | isequal(field,'div') | isequal(field,'strain') + set(handles.civ1_1,'BackgroundColor',[0.702 0.702 0.702]) % put their color to grey + set(handles.civ2_1,'BackgroundColor',[0.702 0.702 0.702]) + set(handles.interp1_1,'BackgroundColor',[0.702 0.702 0.702]) + set(handles.interp2_1,'BackgroundColor',[0.702 0.702 0.702]) + elseif isequal(field_1,'more...'); %add new item to the menu + set(handles.civ1_1,'BackgroundColor',[0.702 0.702 0.702]) % put their color to grey + set(handles.civ2_1,'BackgroundColor',[0.702 0.702 0.702]) + str=calc_field;%get the list of available scalars by the function calc_scal + [ind_answer,v] = listdlg('PromptString','Select a file:',... + 'SelectionMode','single',... + 'ListString',str); + % edit the choice in the field and action menu + scalar=cell2mat(str(ind_answer)); + menu=update_menu(handles.Fields_1,scalar); + set(handles.Fields_1,'String',menu);% store the selected scalar type + end +end +str1=get(handles.i1,'String'); +str2=get(handles.i2,'String'); +str_a=get(handles.j1,'String'); +str_b=get(handles.j2,'String'); +indices=name_generator('',str2num(str1),stra2num(str_a),'',NomTypeNew,1,str2num(str2),stra2num(str_b),''); +set(handles.FileIndex_1,'String',indices) +set(handles.FileIndex_1,'UserData',NomTypeNew) + +%common to Fields_Callback +if isequal(field,'image')|isequal(field_1,'image') + set(handles.npx_title,'Visible','on')% visible npx,pxcm... buttons + set(handles.npy_title,'Visible','on') + set(handles.npx,'Visible','on') + set(handles.npy,'Visible','on') + set(handles.fix_pair,'Value',0) +else + set(handles.npx_title,'Visible','off')% visible npx,pxcm... buttons + set(handles.npy_title,'Visible','off') + set(handles.npx,'Visible','off') + set(handles.npy,'Visible','off') + set(handles.fix_pair,'Value',1) +end +if isequal(field,'velocity')|isequal(field_1,'velocity'); + state_vect='on'; +else + state_vect='off'; +end +if ~isequal(field,'velocity')|(~isequal(field_1,'velocity')&~isequal(field_1,'')); + state_scal='on'; +else + state_scal='off'; +end +set(huvmat,'UserData',UvData) +setfield(handles);% update the field structure ('civ1'....) +if ~isfield(UvData,'NewSeries')|isequal(UvData.NewSeries,0) + run0_Callback(hObject, eventdata, handles) +end + + +%----------------------------------- +%set the visibility of relevant velocity type menus: +%----------------------------------- +%Civ=0; all states 'off' +%Civ=6; all states 'on' +function set_veltype_display(handles,Civ) +if isequal(Civ,0) + imax=0; +% set(handles(1),'Visible','on') % unvisible civ buttons +% else +% set(handles(1),'String','civ1') +% end +elseif isequal(Civ,1) + imax=1; +elseif isequal(Civ,2) | isequal(Civ,3) + imax=3; +elseif isequal(Civ,4) | isequal(Civ,5) + imax=4; +elseif isequal(Civ,6) + imax=6; +end +for ibutton=1:imax; + set(handles(ibutton),'Visible','on') % unvisible civ buttons +end +% for ibutton=max(imax+1,2):6; +for ibutton=imax+1:6; + set(handles(ibutton),'Visible','off') % unvisible civ buttons + set(handles(ibutton),'Value',0)%unactivate unvisible buttons +end + +%------------------------------------------------------------------- +% --- Executes on button press in civ1. +function civ1_Callback(hObject, eventdata, handles) +%------------------------------------------------------------------- +if get(handles.civ1,'Value')==1 + reset_vel_type([handles.interp1 handles.civ2 handles.filter1 handles.interp1 handles.interp2 handles.filter2],handles.civ1) +else + reset_vel_type([handles.civ1 handles.filter1 handles.interp1 handles.civ2 handles.interp2 handles.filter2]) +end +run0_Callback(hObject, eventdata, handles) + +%------------------------------------------------------------------- +% --- Executes on button press in interp1. +function interp1_Callback(hObject, eventdata, handles) +%------------------------------------------------------------------- +if get(handles.interp1,'Value')==1 + reset_vel_type([handles.civ1 handles.civ2 handles.filter1 handles.interp2 handles.filter2],handles.interp1) +else + reset_vel_type([handles.civ1 handles.filter1 handles.interp1 handles.civ2 handles.interp2 handles.filter2]) +end +run0_Callback(hObject, eventdata, handles) + +%------------------------------------------------------------------- +% --- Executes on button press in filter1. +function filter1_Callback(hObject, eventdata, handles) +%------------------------------------------------------------------- +if get(handles.filter1,'Value')==1 + reset_vel_type([handles.civ1 handles.civ2 handles.interp1 handles.interp2 handles.filter2],handles.filter1) +else + reset_vel_type([handles.civ1 handles.filter1 handles.interp1 handles.civ2 handles.interp2 handles.filter2]) +end +run0_Callback(hObject, eventdata, handles) + +%------------------------------------------------------------------- +% --- Executes on button press in civ2. +function civ2_Callback(hObject, eventdata, handles) +%------------------------------------------------------------------- +if get(handles.civ2,'Value')==1 + reset_vel_type([handles.civ1 handles.filter1 handles.interp1 handles.interp2 handles.filter2],handles.civ2) +else + reset_vel_type([handles.civ1 handles.filter1 handles.interp1 handles.civ2 handles.interp2 handles.filter2]) +end +run0_Callback(hObject, eventdata, handles) + +%----------------------------------------- +% --- Executes on button press in interp2. +%------------------------------------------- +function interp2_Callback(hObject, eventdata, handles) +if get(handles.interp2,'Value')==1 + reset_vel_type([handles.civ1 handles.filter1 handles.interp1 handles.civ2 handles.filter2],handles.interp2) +else + reset_vel_type([handles.civ1 handles.filter1 handles.interp1 handles.civ2 handles.interp2 handles.filter2]) +end +run0_Callback(hObject, eventdata, handles) +%--------------------------------------------- +% --- Executes on button press in filter2. +%------------------------------------------- +function filter2_Callback(hObject, eventdata, handles) +if get(handles.filter2,'Value')==1 + reset_vel_type([handles.civ1 handles.filter1 handles.interp1 handles.civ2 handles.interp2],handles.filter2) +else + reset_vel_type([handles.civ1 handles.filter1 handles.interp1 handles.civ2 handles.interp2 handles.filter2]) +end +run0_Callback(hObject, eventdata, handles) + +%--------------------------------------------- +function civ1_1_Callback(hObject, eventdata, handles) +%--------------------------------------------- +if get(handles.civ1_1,'Value')==1 + reset_vel_type([handles.interp1_1 handles.civ2_1 handles.filter1_1 handles.interp1_1 handles.interp2_1 handles.filter2_1],handles.civ1_1) +else + reset_vel_type([handles.civ1_1 handles.filter1_1 handles.interp1_1 handles.civ2_1 handles.interp2_1 handles.filter2_1]) +end +run0_Callback(hObject, eventdata, handles) + +%-------------------------------------------- +function interp1_1_Callback(hObject, eventdata, handles) +%-------------------------------------------- +if get(handles.interp1_1,'Value')==1 + reset_vel_type([handles.civ1_1 handles.civ2_1 handles.filter1_1 handles.interp2_1 handles.filter2_1],handles.interp1_1) +else + reset_vel_type([handles.civ1_1 handles.filter1_1 handles.interp1_1 handles.civ2_1 handles.interp2_1 handles.filter2_1]) +end +run0_Callback(hObject, eventdata, handles) + +%-------------------------------------------- +function filter1_1_Callback(hObject, eventdata, handles) +%-------------------------------------------- +if get(handles.filter1_1,'Value')==1 + reset_vel_type([handles.interp1_1 handles.civ2_1 handles.interp1_1 handles.interp2_1 handles.filter2_1],handles.filter1_1) +else + reset_vel_type([handles.civ1_1 handles.filter1_1 handles.interp1_1 handles.civ2_1 handles.interp2_1 handles.filter2_1]) +end +run0_Callback(hObject, eventdata, handles) + +%-------------------------------------------- +function civ2_1_Callback(hObject, eventdata, handles) +%-------------------------------------------- +if get(handles.civ2_1,'Value')==1 + reset_vel_type([handles.civ1_1 handles.interp1_1 handles.filter1_1 handles.interp2_1 handles.filter2_1],handles.civ2_1) +else + reset_vel_type([handles.civ1_1 handles.filter1_1 handles.interp1_1 handles.civ2_1 handles.interp2_1 handles.filter2_1]) +end +run0_Callback(hObject, eventdata, handles) + +%-------------------------------------------- +function interp2_1_Callback(hObject, eventdata, handles) +%-------------------------------------------- +if get(handles.interp2_1,'Value')==1 + reset_vel_type([handles.civ1_1 handles.civ2_1 handles.filter1_1 handles.interp1_1 handles.filter2_1],handles.interp2_1) +else + reset_vel_type([handles.civ1_1 handles.filter1_1 handles.interp1_1 handles.civ2_1 handles.interp2_1 handles.filter2_1]) +end +run0_Callback(hObject, eventdata, handles) + +%-------------------------------------------- +function filter2_1_Callback(hObject, eventdata, handles) +%-------------------------------------------- +if get(handles.filter2_1,'Value')==1 + reset_vel_type([handles.civ1_1 handles.interp1_1 handles.civ2_1 handles.filter1_1 handles.interp1_1 handles.interp2_1],handles.filter2_1) +else + reset_vel_type([handles.civ1_1 handles.filter1_1 handles.interp1_1 handles.civ2_1 handles.interp2_1 handles.filter2_1]) +end +run0_Callback(hObject, eventdata, handles) + +%----------------------------------------------- +% --- reset civ buttons +function reset_vel_type(handles_civ0,handle1) +for ibutton=1:length(handles_civ0) + set(handles_civ0(ibutton),'BackgroundColor',[0.831 0.816 0.784]) + set(handles_civ0(ibutton),'Value',0) +end +if exist('handle1','var')%handles of selected button + set(handle1,'BackgroundColor',[1 1 0]) +end + +%------------------------------------------------ +function create_Callback(hObject,eventdata,handles) +%------------------------------------------------ +if ishandle(handles.UVMAT_title) + delete(handles.UVMAT_title) +end +huvmat=get(handles.create,'parent'); +UvData=get(huvmat,'UserData');%read UvData properties stored on the uvmat interface (handles huvmat) +if isequal(get(handles.create,'Value'),1) + set(handles.zoom,'Value',0) + zoom_Callback(hObject, eventdata, handles) + set(handles.create,'BackgroundColor',[1 1 0]) %visualise in yellow + set(handles.edit_vect,'Value',0) + edit_vect_Callback(hObject, eventdata, handles) + set(handles.edit,'Value',0) + set(handles.edit,'BackgroundColor',[0.7 0.7 0.7]) + list_object=get(handles.list_object,'String'); + if ~isempty(list_object) + set(handles.list_object,'Value',length(list_object)) + end + MouseAction='create_object'; + hset_object=findobj(allchild(0),'Name','set_object'); + uistack(hset_object,'top') +else + set(handles.create,'BackgroundColor',[0 1 0]) + set(handles.edit,'Value',1) + set(handles.edit,'BackgroundColor',[1 1 0]) + MouseAction='none'; +end + +UvData.MouseAction=MouseAction; +set(huvmat,'UserData',UvData); + +%------------------------------------------------ +function POINTS_Callback(hObject,eventdata,handles) +%------------------------------------------------ +if ishandle(handles.UVMAT_title) + delete(handles.UVMAT_title) +end +huvmat=get(handles.create,'parent'); +UvData=get(huvmat,'UserData');%read UvData properties stored on the uvmat interface (handles huvmat) +if isequal(get(handles.create,'Value'),1) + set(handles.zoom,'Value',0) + zoom_Callback(hObject, eventdata, handles) + set(handles.edit_vect,'Value',0) + edit_vect_Callback(hObject, eventdata, handles) + set(handles.edit,'Value',0) + set(handles.edit,'BackgroundColor',[0.7 0.7 0.7]) + %set(handles.grid,'Value',0) + %set(handles.grid,'BackgroundColor',[0 1 0]) + % initiate set_object GUI + data.TITLE='POINTS'; + if isfield(UvData,'CoordType') + data.CoordType=UvData.CoordType; + end + if isfield(UvData,'Mesh')&~isempty(UvData.Mesh) + data.RangeY=UvData.Mesh; + elseif isfield(UvData,'AX')&isfield(UvData,'AY')& isfield(UvData,'A')%only image + np=size(UvData.Field.A); + meshx=(UvData.Field.AX(end)-UvData.Field.AX(1))/np(2); + meshy=abs(UvData.Field.AY(end)-UvData.Field.AY(1))/np(1); + data.RangeY=max(meshx,meshy); + data.DX=max(meshx,meshy); + end + data.Coord=[0 0 0]; %default + data.ParentButton=handles.create; + PlotHandles=get_plot_handles(handles);%get the handles of the graphic objects setting the plotting parameters + [hset_object,UvData.sethandles]=set_object(data,PlotHandles);% call the set_object interface + if isfield(UvData,'SetObjectOrigin') + pos_uvmat=get(huvmat,'Position'); + pos_set_object(1:2)=UvData.SetObjectOrigin + pos_uvmat(1:2); + pos_set_object(3:4)=UvData.SetObjectSize .* pos_uvmat(3:4); + set(hset_object,'Position',pos_set_object) + end + %set(hset_object,'Position',[pos_uvmat(1) pos_uvmat(2)-0.05*pos_uvmat(4) 0.2*pos_uvmat(3) 0.5*pos_uvmat(4)]); + list_object=get(handles.list_object,'String'); + if ~isempty(list_object) + set(handles.list_object,'Value',length(list_object)) + end + MouseAction='create_object'; + %UvData.ZoomOn=0; +else + set(handles.create,'BackgroundColor',[0 1 0]) + set(handles.edit,'Value',1) + set(handles.edit,'BackgroundColor',[1 1 0]) + MouseAction='none'; +end + +UvData.MouseAction=MouseAction; +set(huvmat,'UserData',UvData); + +%----------------------------------------------------------- +function LINE_Callback(hObject, eventdata, handles) +%------------------------------------------------- +if ishandle(handles.UVMAT_title) + delete(handles.UVMAT_title) +end +huvmat=get(handles.create,'parent'); +UvData=get(huvmat,'UserData');%read UvData properties stored on the uvmat interface +% if (get(handles.LINE,'Value')==1) + %suppress the other options if MENULINE is chosen + set(handles.zoom,'Value',0) + zoom_Callback(hObject, eventdata, handles) +% set(handles.create,'Value',0) +% set(handles.create,'BackgroundColor',[0 1 0]) +% set(handles.LINE,'Value',1) +% set(handles.LINE,'BackgroundColor',[1 1 0]) +% set(handles.PATCH,'Value',0) +% set(handles.PATCH,'BackgroundColor',[0 1 0]) +% set(handles.PLANE,'Value',0) +% set(handles.PLANE,'BackgroundColor',[0 1 0])%put activated buttons to yellow +% set(handles.VOLUME,'Value',0) +% set(handles.VOLUME,'BackgroundColor',[0 1 0]) + %et(handles.makemask,'Value',0) + %makemask_Callback(hObject, eventdata, handles) + set(handles.edit_vect,'BackgroundColor',[0.7 0.7 0.7]) + set(handles.edit_vect,'Value',0) + edit_vect_Callback(hObject, eventdata, handles) + set(handles.edit,'BackgroundColor',[0.7 0.7 0.7]) + set(handles.edit,'Value',0) + set(handles.list_object,'Value',1); + edit_vect_Callback(hObject, eventdata, handles) + set(handles.edit,'BackgroundColor',[0.7 0.7 0.7]) + set(handles.cal,'Value',0) + set(handles.cal,'BackgroundColor',[0 1 0]) + % set(handles.grid,'Value',0) + % set(handles.grid,'BackgroundColor',[0 1 0]) +% initiate the set_object GUI + data.TITLE='LINE'; + if isfield(UvData,'CoordType') + data.CoordType=UvData.CoordType; + end + if isfield(UvData,'Mesh')&~isempty(UvData.Mesh) + data.RangeX=UvData.Mesh; + data.RangeY=UvData.Mesh; +% data.YMax=UvData.Mesh; +% data.XMax=UvData.Mesh; + data.DX=UvData.Mesh; + data.DY=UvData.Mesh; + elseif isfield(UvData.Field,'AX')&isfield(UvData.Field,'AY')& isfield(UvData.Field,'A')%only image + np=size(UvData.Field.A); + meshx=(UvData.Field.AX(end)-UvData.Field.AX(1))/np(2); + meshy=abs(UvData.Field.AY(end)-UvData.Field.AY(1))/np(1); + data.RangeY=max(meshx,meshy); + data.RangeX=max(meshx,meshy); +% data.YMax=max(meshx,meshy); +% data.XMax=max(meshx,meshy); + data.DX=max(meshx,meshy); + end + if isfield(data,'DX') + data.Coord=[[0 0 0];[data.DX 0 0]]; %default + else + data.Coord=[[0 0 0];[1 0 0]]; %default + end + data.ParentButton=handles.create; + PlotHandles=get_plot_handles(handles);%get the handles of the interface elements setting the plotting parameters + [hset_object,UvData.sethandles]=set_object(data,PlotHandles);% call the set_object interface with action on haxes, + % associate the set_edit interface handle to the plotting axes + pos_uvmat=get(huvmat,'Position'); + if isfield(UvData,'SetObjectOrigin') + pos_set_object(1:2)=UvData.SetObjectOrigin + pos_uvmat(1:2); + pos_set_object(3:4)=UvData.SetObjectSize .* pos_uvmat(3:4); + set(hset_object,'Position',pos_set_object) + end + list_object=get(handles.list_object,'String'); + if ~isempty(list_object) + set(handles.list_object,'Value',length(list_object)) + end + MouseAction='create_object'; +% else +% set(handles.LINE,'BackgroundColor',[0 1 0]) +% MouseAction='none'; +% end + +UvData.MouseAction=MouseAction; +set(huvmat,'UserData',UvData) + +%----------------------------------------------------------- +function PATCH_Callback(hObject, eventdata, handles) +%----------------------------------------------------------- +if ishandle(handles.UVMAT_title) + delete(handles.UVMAT_title) +end +huvmat=get(handles.create,'parent'); +UvData=get(huvmat,'UserData');%read UvData properties stored on the uvmat interface +% if isequal(get(handles.PATCH,'Value'),1) + set(handles.zoom,'Value',0) + set(handles.zoom,'BackgroundColor',[0.7 0.7 0.7]) +% set(handles.create,'Value',0)%suppress the other options if LINE is chosen +% set(handles.create,'BackgroundColor',[0 1 0]) +% set(handles.LINE,'Value',0) +% set(handles.LINE,'BackgroundColor',[0 1 0]) +% set(handles.PATCH,'Value',1) +% set(handles.PATCH,'BackgroundColor',[1 1 0]) +% set(handles.PLANE,'Value',0) +% set(handles.PLANE,'BackgroundColor',[0 1 0])%put activated buttons to yellow +% set(handles.VOLUME,'Value',0) +% set(handles.VOLUME,'BackgroundColor',[0 1 0]) + %set(handles.makemask,'Value',0) + %makemask_Callback(hObject, eventdata, handles) + set(handles.edit_vect,'Value',0) + edit_vect_Callback(hObject, eventdata, handles) + set(handles.edit,'Value',0) + set(handles.edit,'BackgroundColor',[0.7 0.7 0.7]) + set(handles.edit_vect,'Value',0) + edit_vect_Callback(hObject, eventdata, handles) + set(handles.cal,'Value',0) + set(handles.cal,'BackgroundColor',[0 1 0]) + %set(handles.grid,'Value',0) + %set(handles.grid,'BackgroundColor',[0 1 0]) + %initiate set_object GUI + data.TITLE='PATCH'; + if isfield(UvData,'CoordType') + data.CoordType=UvData.CoordType; + end + if isfield(UvData,'Mesh')&~isempty(UvData.Mesh) + data.YMax=UvData.Mesh; + elseif isfield(UvData.Field,'AX')&isfield(UvData.Field,'AY')& isfield(UvData.Field,'A')%only image + np=size(UvData.Field.A); + meshx=(UvData.Field.AX(end)-UvData.Field.AX(1))/(np(2)-1); + meshy=abs(UvData.Field.AY(end)-UvData.Field.AY(1))/(np(1)-1); + data.YMax=max(meshx,meshy); + data.DX=max(meshx,meshy); + end + data.Coord=[0 0 0]; %default + data.ParentButton=handles.create; + PlotHandles=get_plot_handles(handles);%get the handles of the graphic objects setting the plotting parameters + [hset_object,UvData.sethandles]=set_object(data,PlotHandles);% call the set_object interface + pos_uvmat=get(huvmat,'Position'); + if isfield(UvData,'SetObjectOrigin') + pos_set_object(1:2)=UvData.SetObjectOrigin + pos_uvmat(1:2); + pos_set_object(3:4)=UvData.SetObjectSize .* pos_uvmat(3:4); + set(hset_object,'Position',pos_set_object) + end + list_object=get(handles.list_object,'String'); + if ~isempty(list_object) + set(handles.list_object,'Value',length(list_object)) + end + UvData.MouseAction='create_object'; + set(huvmat,'UserData',UvData); +%------------------------------------------------------- +function PLANE_Callback(hObject, eventdata, handles) +%------------------------------------------------------- +if ishandle(handles.UVMAT_title) + delete(handles.UVMAT_title) +end +huvmat=get(handles.create,'parent'); +UvData=get(huvmat,'UserData');%read UvData properties stored on the uvmat interface +set(handles.zoom,'Value',0) +set(handles.zoom,'BackgroundColor',[0.7 0.7 0.7]) +set(handles.edit_vect,'Value',0) +edit_vect_Callback(hObject, eventdata, handles) +set(handles.edit,'Value',0) +set(handles.edit,'BackgroundColor',[0.7 0.7 0.7]) +set(handles.cal,'Value',0) +set(handles.cal,'BackgroundColor',[0 1 0]) +%set(handles.grid,'Value',0) +%set(handles.grid,'BackgroundColor',[0 1 0]) +%initiate set_object GUI +data.TITLE='PLANE'; +if isfield(UvData,'CoordType') + data.CoordType=UvData.CoordType; +end +%Si 3D data.nbdim=3; +%Si 2D +if isfield(UvData,'Mesh')&~isempty(UvData.Mesh) + data.ZMax=UvData.Mesh; + data.DX=UvData.Mesh; + data.DY=UvData.Mesh; +elseif isfield(UvData.Field,'AX')&isfield(UvData.Field,'AY')& isfield(UvData.Field,'A')%only image + np=size(UvData.Field.A); + meshx=(UvData.Field.AX(end)-UvData.Field.AX(1))/(np(2)-1); + meshy=abs(UvData.Field.AY(end)-UvData.Field.AY(1))/(np(1)-1); + data.DX=max(meshx,meshy); +end +if isfield(UvData,'DX') + data.DX=UvData.DX; +end +if isfield(UvData,'DY') + data.DY=UvData.DY; +elseif isfield(UvData,'Mesh') + data.DY=UvData.Mesh; +end +if isfield(UvData.Field,'X')& isfield(UvData.Field,'Y') + data.Coord=[0 0 0]; + data.Style='plane'; + data.Phi=0; + data.IndexObj=1; %act on the first reference plane by default + haxes= handles.axes3;%GENERALISER + plot_object(data,[],haxes,'m'); %plot the axes of the default plane +end +data.ParentButton=handles.create; +PlotHandles=get_plot_handles(handles);%get the handles of the graphic objects setting the plotting parameters +ZBounds=0; % default +if isfield(UvData,'ZMin') && isfield(UvData,'ZMax') + ZBounds(1)=UvData.ZMin; %minimum for the Z slider + ZBounds(2)=UvData.ZMax;%maximum for the Z slider +end +[hset_object,UvData.sethandles]=set_object(data,PlotHandles,ZBounds);% call the set_object interface with action on haxes, +if isfield(UvData,'SetObjectOrigin') +pos_uvmat=get(huvmat,'Position'); +pos_set_object(1:2)=UvData.SetObjectOrigin + pos_uvmat(1:2); +pos_set_object(3:4)=UvData.SetObjectSize .* pos_uvmat(3:4); +set(hset_object,'Position',pos_set_object) +end +list_object=get(handles.list_object,'String'); +nbobject=length(list_object); +set(handles.list_object,'Value',nbobject) +UvData.MouseAction='create_object'; +set(huvmat,'UserData',UvData) + +%------------------------------------------------------- +% --- Executes on button press in MENUVOLUME. +%------------------------------------------------------- +function VOLUME_Callback(hObject, eventdata, handles) +%errordlg('command VOL not implemented yet') +if ishandle(handles.UVMAT_title) + delete(handles.UVMAT_title) +end +huvmat=get(handles.create,'parent'); +UvData=get(huvmat,'UserData');%read UvData properties stored on the uvmat interface +if isequal(get(handles.VOLUME,'Value'),1) + set(handles.zoom,'Value',0) + set(handles.zoom,'BackgroundColor',[0.7 0.7 0.7]) + set(handles.edit_vect,'Value',0) + edit_vect_Callback(hObject, eventdata, handles) + set(handles.edit,'Value',0) + set(handles.edit,'BackgroundColor',[0.7 0.7 0.7]) + set(handles.cal,'Value',0) + set(handles.cal,'BackgroundColor',[0 1 0]) + set(handles.edit_vect,'Value',0) + edit_vect_Callback(hObject, eventdata, handles) + %initiate set_object GUI + data.TITLE='VOLUME'; + if isfield(UvData,'CoordType') + data.CoordType=UvData.CoordType; + end + if isfield(UvData,'Mesh')&~isempty(UvData.Mesh) + data.RangeY=UvData.Mesh; + data.RangeX=UvData.Mesh; + data.DX=UvData.Mesh; + data.DY=UvData.Mesh; + elseif isfield(UvData.Field,'AX')&isfield(UvData.Field,'AY')& isfield(UvData.Field,'A')%only image + np=size(UvData.Field.A); + meshx=(UvData.Field.AX(end)-UvData.Field.AX(1))/np(2); + meshy=abs(UvData.Field.AY(end)-UvData.Field.AY(1))/np(1); + data.RangeY=max(meshx,meshy); + data.RangeX=max(meshx,meshy); + data.DX=max(meshx,meshy); + end + data.ParentButton=handles.VOLUME; + PlotHandles=get_plot_handles(handles);%get the handles of the interface elements setting the plotting parameters + [hset_object,UvData.sethandles]=set_object(data,PlotHandles);% call the set_object interface with action on haxes, + % associate the set_edit interface handle to the plotting axes + if isfield(UvData,'SetObjectOrigin') + pos_uvmat=get(huvmat,'Position'); + pos_set_object(1:2)=UvData.SetObjectOrigin + pos_uvmat(1:2); + pos_set_object(3:4)=UvData.SetObjectSize .* pos_uvmat(3:4); + set(hset_object,'Position',pos_set_object) + end + UvData.MouseAction='create_object'; +else + set(handles.VOLUME,'BackgroundColor',[0 1 0]) + UvData.MouseAction='none'; +end +set(huvmat,'UserData',UvData) + +%------------------------------------------------------- +function edit_vect_Callback(hObject, eventdata, handles) +%------------------------------------------------------- +huvmat=get(handles.edit_vect,'parent'); +UvData=get(huvmat,'UserData');%read UvData properties stored on the uvmat interface +if isequal(get(handles.edit_vect,'Value'),1) + set(handles.record,'Visible','on') + set(handles.edit_vect,'BackgroundColor',[1 1 0]) + set(handles.edit,'Value',0) + set(handles.create,'Value',0) + set(handles.create,'BackgroundColor',[0 1 0]) + set(handles.edit,'BackgroundColor',[0.7 0.7 0.7]) + set(gcf,'Pointer','arrow') + UvData.MouseAction='edit_vect'; +else + set(handles.record,'Visible','off') + set(handles.edit_vect,'BackgroundColor',[0.7 0.7 0.7]) + UvData.MouseAction='none'; +end +set(huvmat,'UserData',UvData) + +%---------------------------------------------- +function save_mask_Callback(hObject, eventdata, handles) +%----------------------------------------------------------------------- +huvmat=get(handles.save_mask,'parent'); +UvData=get(huvmat,'UserData'); + +hpatch=findobj(huvmat,'Type','patch'); +flag=1; +npx=size(UvData.Field.A,2); +npy=size(UvData.Field.A,1); +xi=[0.5:npx-0.5]; +yi=[0.5:npy-0.5]; +[Xi,Yi]=meshgrid(xi,yi); +if isfield(UvData,'Object') + for iobj=1:length(UvData.Object) + ObjectData=UvData.Object{iobj}; + if isfield(ObjectData,'ProjMode') &&(isequal(ObjectData.ProjMode,'mask_inside')||isequal(ObjectData.ProjMode,'mask_outside')); + flagobj=1; + testphys=0; %coordinates in pixels by default + if isfield(ObjectData,'CoordType') && isequal(ObjectData.CoordType,'phys') + if isfield(UvData,'XmlData')&& isfield(UvData.XmlData,'GeometryCalib') + Calib=UvData.XmlData.GeometryCalib; + testphys=1; + end + end + if isfield(ObjectData,'Coord')& isfield(ObjectData,'Style') + if isequal(ObjectData.Style,'polygon') + X=ObjectData.Coord(:,1); + Y=ObjectData.Coord(:,2); + if testphys + [X,Y]=px_XYZ(Calib,X,Y,0);% to generalise with 3D cases + end + flagobj=~inpolygon(Xi,Yi,X,Y);%=0 inside the polygon, 1 outside + elseif isequal(ObjectData.Style,'ellipse') + if testphys + %[X,Y]=px_XYZ(Calib,X,Y,0);% TODO:create a polygon boundary and transform to phys + end + RangeX=max(ObjectData.RangeX); + RangeY=max(ObjectData.RangeY); + X2Max=RangeX*RangeX; + Y2Max=RangeY*RangeY; + distX=(Xi-ObjectData.Coord(1,1)); + distY=(Yi-ObjectData.Coord(1,2)); + flagobj=(distX.*distX/X2Max+distY.*distY/Y2Max)>1; + elseif isequal(ObjectData.Style,'rectangle') + if testphys + %[X,Y]=px_XYZ(Calib,X,Y,0);% TODO:create a polygon boundary and transform to phys + end + distX=abs(Xi-ObjectData.Coord(1,1)); + distY=abs(Yi-ObjectData.Coord(1,2)); + flagobj=distX>max(ObjectData.RangeX) | distY>max(ObjectData.RangeY); + end + if isequal(ObjectData.ProjMode,'mask_outside') + flagobj=~flagobj; + end + flag=flag & flagobj; + end + end + end +end +% flag=~flag; +%mask name +RootPath=get(handles.RootPath,'String'); +RootFile=get(handles.RootFile,'String'); +if ~isempty(RootFile)&(isequal(RootFile(1),'/')| isequal(RootFile(1),'\')) + RootFile(1)=[]; +end +filebase=fullfile(RootPath,RootFile); +list=get(handles.masklevel,'String'); +masknumber=num2str(length(list)); +maskindex=get(handles.masklevel,'Value'); +mask_name=name_generator([filebase '_' masknumber 'mask'],maskindex,1,'.png','_i'); +imflag=uint8(255*(0.392+0.608*flag));% =100 for flag=0 (vectors not computed when 20 col)%move also the first slider at the same value if needed + set(handles.slider1,'Value',col) + set(handles.colcode1,'String',num2str(col)) +end +colcode2_Callback(hObject, eventdata, handles) + +%---------------------------------------------------------------- +%execute on return carriage on the edit box corresponding to slider 1 +%---------------------------------------------------------------- +function colcode1_Callback(hObject, eventdata, handles) +% col=str2num(get(handles.colcode1,'String')); +% set(handles.slider1,'Value',col) +set_vec_col_bar(handles) +update_plot(handles) + +%---------------------------------------------------------------- +%execute on return carriage on the edit box corresponding to slider 2 +%---------------------------------------------------------------- +function colcode2_Callback(hObject, eventdata, handles) +% col=str2num(get(handles.colcode2,'String')); +% set(handles.slider2,'Value',col) +% slider2_Callback(hObject, eventdata, handles) +set_vec_col_bar(handles) +update_plot(handles) +%------------------------------------------------------------ +%update the slider values after displaying vectors +%-------------------------------------------------------- +% function slider_update(handles,auto,minC,colcode1,colcode2,maxC) +% set(handles.slider1,'Min',minC) +% set(handles.slider1,'Max',maxC) +% set(handles.slider2,'Min',minC) +% set(handles.slider2,'Max',maxC) +% set(handles.min_title_vec,'String',num2str(minC)) +% set(handles.max_vec,'String',num2str(maxC)) +% if auto +% set(handles.colcode1,'String',num2str(colcode1,3))%update display +% set(handles.colcode2,'String',num2str(colcode2,3)) +% end +% set(handles.slider1,'Value',colcode1)%update slider with constant display +% set(handles.slider2,'Value',colcode2) +% set_vec_col_bar(handles) + + +%------------------------------------------------------- +% --- Executes on button press in AutoVecColor. +%------------------------------------------------------- +function vec_col_bar_Callback(hObject, eventdata, handles) +set_vec_col_bar(handles) + +% %-------------------------------------------- +% %update the display of color code for vectors +% %-------------------------------------------- +% function set_vec_col_bar(handles) +% %get the image of the color display button 'vec_col_bar' in pixels +% uni=get(handles.vec_col_bar,'Unit'); +% set(handles.vec_col_bar,'Unit','pixel') +% pos_vert=get(handles.vec_col_bar,'Position'); +% set(handles.vec_col_bar,'Unit','Normalized') +% width=ceil(pos_vert(3)); +% height=ceil(pos_vert(4)); +% %get slider indications +% colcode.min=get(handles.slider1,'Min'); +% colcode.max=get(handles.slider1,'Max'); +% colcode.colcode1=get(handles.slider1,'Value'); +% colcode.colcode2=get(handles.slider2,'Value'); +% colcode.option=get(handles.vec_col_bar,'Value'); +% colcode.auto=1; +% list_code=get(handles.col_vec,'String');% list menu fields +% index_code=get(handles.col_vec,'Value');% selected string index +% colcode.CName= list_code{index_code(1)}; % selected field used for vector color +% vec_C=colcode.min+(colcode.max-colcode.min)*[0.5:width-0.5]/width;%sample of vec_C values from min to max +% [colorlist,col_vec]=set_col_vec(colcode,vec_C); +% oneheight=ones(1,height); +% A1=colorlist(col_vec,1)*oneheight; +% A2=colorlist(col_vec,2)*oneheight; +% A3=colorlist(col_vec,3)*oneheight; +% A(:,:,1)=A1'; +% A(:,:,2)=A2'; +% A(:,:,3)=A3'; +% set(handles.vec_col_bar,'Cdata',A) + +%-------------------------------------------------------- +% --- Executes on button press in cal. +function cal_Callback(hObject, eventdata, handles) + +huvmat=get(handles.cal,'parent');%handles of the uvmat interface +UvData=get(huvmat,'UserData');%read UvData properties stored on the uvmat interface +%reinitialize the edit interface associated with uvmat +value=get(handles.cal,'Value'); +if value + set(handles.cal,'BackgroundColor',[1 1 0]) + %suppress the other options if MENULINE is chosen + set(handles.zoom,'Value',0) + set(handles.zoom,'BackgroundColor',[0.7 0.7 0.7]) + set(handles.create,'Value',0) + set(handles.create,'BackgroundColor',[0 1 0]) + set(handles.create,'enable','off') + set(handles.edit_vect,'Value',0) + set(handles.edit_vect,'enable','off') + edit_vect_Callback(hObject, eventdata, handles) + set(handles.edit,'Value',0) + set(handles.edit,'BackgroundColor',[0.7 0.7 0.7]) + set(handles.edit,'enable','off') + set(handles.list_object,'Value',1) + % initiate display of GUI geometry_calib + data=[]; %default + if isfield(UvData,'CoordType') + data.CoordType=UvData.CoordType; + end + %data.ParentButton=handles.cal; % transmit the handles of the calling button to the GUI geometry_calib + pos=get(huvmat,'Position'); + pos(1)=pos(1)+pos(3)-0.311+0.04; %0.311= width of the geometry_calib interface (units relative to the srcreen) + pos(2)=pos(2)-0.02; + [FileName,RootPath,FileBase,FileIndices,FileExt,SubDir]=read_file_boxes(handles); +% [filebase,num_i1,num_j1,num_i2,num_j2,Ext,NomType,SubDir]=read_input_file(handles); +% [inputfile,idetect]=name_generator(filebase,num_i1,num_j1,Ext,NomType,1,num_i2,num_j2,SubDir); + [UvData.hset_object,UvData.sethandles]=geometry_calib(handles,pos,FileName);% call the set_object interface + pos_uvmat=get(huvmat,'Position'); + %pos_cal(1:2)=UvData.CalOrigin + pos_uvmat(1:2); + if isfield(UvData,'CalOrigin') + pos_cal(1)=pos_uvmat(1)+UvData.CalOrigin(1)*pos_uvmat(3); + pos_cal(2)=pos_uvmat(2)+UvData.CalOrigin(2)*pos_uvmat(4); + pos_cal(3:4)=UvData.CalSize .* pos_uvmat(3:4); + set(UvData.hset_object,'Position',pos_cal) + end + UvData.MouseAction='calib'; +else + UvData.MouseAction='none'; + hgeometry_calib=findobj(allchild(0),'Name','geometry_calib'); +% if ~isempty(hgeometry_calib) +% answer=questdlg('close the GUI geometry-calib?'); +% if isequal(answer,'Yes') +% delete(hgeometry_calib) +% set(handles.cal,'BackgroundColor',[0 1 0]) +% else +% set(handles.cal,'Value',1)% keep the calibration function active +% end +% end + set(handles.edit_vect,'enable','on') + set(handles.edit,'enable','on') + set(handles.create,'enable','on') +% set(handles.LINE,'enable','on') +% set(handles.PATCH,'enable','on') +% set(handles.PLANE,'enable','on') +% set(handles.VOLUME,'enable','on') + %set(handles.makemask,'enable','on') + hh=findobj(handles.axes3,'Tag','calib_points'); + if ~isempty(hh) + delete(hh) + end + hhh=findobj(handles.axes3,'Tag','calib_marker'); + if ~isempty(hhh) + delete(hhh) + end +end +set(huvmat,'UserData',UvData); + +%------------------------------------------------------------- +% --- Executes on selection change in menu_coord. +function menu_coord_Callback(hObject, eventdata, handles) +%------------------------------------------------------------- +huvmat=get(handles.menu_coord,'parent'); +menu=get(handles.menu_coord,'String'); +ind_coord=get(handles.menu_coord,'Value'); +coord_option=menu{ind_coord}; +list_path=get(handles.menu_coord,'UserData'); + +if isequal(coord_option,'more...'); + coord_fct=''; + dir_perso=prefdir; + profil_perso=fullfile(dir_perso,'uvmat_perso.mat'); + if exist(profil_perso,'file') + h=load (profil_perso); + if isfield(h,'coord_fct') + coord_fct=h.coord_fct; + end + end + prompt = {'Enter the name of the transform function'}; + dlg_title = 'user defined transform'; + num_lines= 1; + [FileName, PathName, filterindex] = uigetfile( ... + {'*.m', ' (*.m)'; + '*.m', '.m files '; ... + '*.*', 'All Files (*.*)'}, ... + 'Pick a file', coord_fct); + if isequal(PathName(end),'/')||isequal(PathName(end),'\') + PathName(end)=[]; + end + coord_fct=fullfile(PathName,FileName); + if ~exist(coord_fct,'file') + msgbox_uvmat('ERROR',['image procesing fct ' coord_fct ' not found']) + else + transform=FileName(1:end-2);% + menu=update_menu(handles.menu_coord,transform);%add the selected fct to the menu + ind_coord=get(handles.menu_coord,'Value'); + list_path{ind_coord}=PathName; + set(handles.menu_coord,'UserData',list_path) + if exist(profil_perso,'file') + save (profil_perso,'coord_fct','-append'); %store the root name for future opening of uvmat + end + end +end + +%check the current path to the selected function +PathName=list_path{ind_coord}; +CurrentPath=fileparts(which(coord_option)); +if ~isequal(PathName,CurrentPath) + addpath(PathName) + errormsg=check_functions; + msgbox_uvmat('WARNING',[['path ' PathName ' added to the current Matlab pathes'];errormsg]) +end +set(handles.path_transform,'String',fullfile(PathName,' ')); %show the path to the senlected function +set(handles.FixedLimits,'Value',0) +set(handles.FixedLimits,'BackgroundColor',[0.7 0.7 0.7]) + +UvData=get(huvmat,'UserData'); + +%delete drawn objects +hother=findobj('Tag','proj_object');%find all the proj objects +for iobj=1:length(hother) + delete_object(hother(iobj)) +end +hother=findobj('Tag','DeformPoint');%find all the proj objects +for iobj=1:length(hother) + delete_object(hother(iobj)) +end +hh=findobj('Tag','calib_points'); +if ~isempty(hh) + delete(hh) +end +hhh=findobj('Tag','calib_marker'); +if ~isempty(hhh) + delete(hhh) +end +if isfield(UvData,'Object') + nbobject=length(UvData.Object); + UvData.Object([2:nbobject])=[]; +end + +%delete mask if it is displayed +if isequal(get(handles.mask_test,'Value'),1)%if the mask option is on + UvData=rmfield(UvData,'MaskName'); %will impose mask refresh +end +set(huvmat,'UserData',UvData) +run0_Callback(hObject, eventdata, handles) + +%-------------------------------------------- +function histo1_menu_Callback(hObject, eventdata, handles) +%-------------------------------------------- +%plot first histo +huvmat=get(handles.histo1_menu,'parent'); +histo_menu=get(handles.histo1_menu,'String'); +histo_value=get(handles.histo1_menu,'Value'); +FieldName=histo_menu{histo_value}; +UvData=get(huvmat,'UserData'); +update_histo(handles.histo_u,huvmat,FieldName) + +%---------------------------------------------- +function histo2_menu_Callback(hObject, eventdata, handles) +%---------------------------------------------- +%plot second histo +huvmat=get(handles.histo2_menu,'parent'); +histo_menu=get(handles.histo2_menu,'String'); +histo_value=get(handles.histo2_menu,'Value'); +FieldName=histo_menu{histo_value}; +UvData=get(huvmat,'UserData'); +update_histo(handles.histo_v,huvmat,FieldName) + + +%-------------------------------------------- +%read the field .Fieldname stored in UvData and plot its histogram +function update_histo(haxes,huvmat,FieldName) +UvData=get(huvmat,'UserData'); + +if ~isfield(UvData.Field,FieldName) + msgbox_uvmat('ERROR',['no field ' FieldName ' for histogram']) + return +end +Field=UvData.Field; +FieldHisto=eval(['Field.' FieldName]); +if isfield(Field,'FF') & ~isempty(Field.FF) & isequal(size(Field.FF),size(FieldHisto)) + indsel=find(Field.FF==0);%find values marked as false + if ~isempty(indsel) + FieldHisto=FieldHisto(indsel); + end +end +if isempty(Field) + msgbox_uvmat('ERROR',['empty field ' FieldName]) +else + nxy=size(FieldHisto); + Amin=double(min(min(min(FieldHisto))));%min of image + Amax=double(max(max(max(FieldHisto))));%max of image + if isequal(Amin,Amax) + Histo.Txt=['uniform field =' num2str(Amin)]; + else + Histo.ListVarName={FieldName,'histo'}; + if numel(nxy)==2 + Histo.VarDimName={FieldName,FieldName}; %dimensions for the histogram + else %color images + Histo.VarDimName={FieldName,{FieldName,'rgb'}}; %dimensions for the histogram + end + %unit + units=[]; %default + for ivar=1:numel(Field.ListVarName) + if strcmp(Field.ListVarName{ivar},FieldName) + if isfield(Field,'VarAttribute') && numel(Field.VarAttribute)>=ivar && isfield(Field.VarAttribute{ivar},'units') + units=Field.VarAttribute{ivar}.units; + break + end + end + end + if ~isempty(units) + Histo.VarAttribute{1}.units=units; + end + eval(['Histo.' FieldName '=linspace(Amin,Amax,50);'])%absissa values for histo + for col=1:size(FieldHisto,3) + B=FieldHisto(:,:,col); + C=reshape(double(B),1,nxy(1)*nxy(2));% reshape in a vector + eval(['Histo.histo(:,col)=hist(C, Histo.' FieldName ');']); %calculate histogram + end + set(haxes,'XLimMode','auto')%reset auto mode (after zoom effect) + set(haxes,'YLimMode','auto') + plot_field(Histo,haxes); + end +end + + + +%------------------------------------------------ +%CALLBACKS FOR PLOTTING PARAMETERS +%------------------------------------------------- + +%----------------------------------------------------------------- +function MinA_Callback(hObject, eventdata, handles) +%------------------------------------------ +set(handles.AutoScal,'Value',1) %suppress auto mode +set(handles.AutoScal,'BackgroundColor',[1 1 0]) +update_plot(handles) + +%----------------------------------------------------------------- +function MaxA_Callback(hObject, eventdata, handles) +%-------------------------------------------- +set(handles.AutoScal,'Value',1) %suppress auto mode +set(handles.AutoScal,'BackgroundColor',[1 1 0]) +update_plot(handles) + +%----------------------------------------------- +function AutoScal_Callback(hObject, eventdata, handles) +%-------------------------------------------- +test=get(handles.AutoScal,'Value'); +if test + set(handles.AutoScal,'BackgroundColor',[1 1 0]) +else + set(handles.AutoScal,'BackgroundColor',[0.7 0.7 0.7]) + update_plot(handles); +% set(handles.MinA,'String',num2str(ScalOut.MinA,3)) +% set(handles.MaxA,'String',num2str(ScalOut.MaxA,3)) +end + +%------------------------------------------------------------------- +function BW_Callback(hObject, eventdata, handles) +%------------------------------------------------------------------- +update_plot(handles) + +%------------------------------------------------------------------- +function Contours_Callback(hObject, eventdata, handles) +%------------------------------------------------------------------- +val=get(handles.Contours,'Value'); +if val==2 + set(handles.interval_txt,'Visible','on') + set(handles.IncrA,'Visible','on') +else + set(handles.interval_txt,'Visible','off') + set(handles.IncrA,'Visible','off') +end +update_plot(handles) + +%------------------------------------------------------------------- +function IncrA_Callback(hObject, eventdata, handles) +%------------------------------------------------------------------- +update_plot(handles) + +%------------------------------------------------------------------- +function HideWarning_Callback(hObject, eventdata, handles) +%------------------------------------------------------------------- +update_plot(handles) + +%------------------------------------------------------------------- +function HideFalse_Callback(hObject, eventdata, handles) +%------------------------------------------------------------------- +update_plot(handles) + +%------------------------------------------------------------------- +function VecScale_Callback(hObject, eventdata, handles) +%------------------------------------------------------------------- +set(handles.AutoVec,'Value',1); +set(handles.AutoVec,'BackgroundColor',[1 1 0]) +update_plot(handles) + +%------------------------------------------------------------------- +function AutoVec_Callback(hObject, eventdata, handles) +%------------------------------------------------------------------- +test=get(handles.AutoVec,'Value'); +if test + set(handles.AutoVec,'BackgroundColor',[1 1 0]) +else + update_plot(handles); + %set(handles.VecScale,'String',num2str(ScalOut.VecScale,3)) + set(handles.AutoVec,'BackgroundColor',[0.7 0.7 0.7]) +end + +%------------------------------------------------------- +% --- Executes on selection change in decimate4 (nb_vec/4). +%------------------------------------------------------- +function decimate4_Callback(hObject, eventdata, handles) +update_plot(handles) + + +%------------------------------------------------------- +% --- Executes on selection change in color_code menu +%------------------------------------------------------- +function color_code_Callback(hObject, eventdata, handles) +set_vec_col_bar(handles) +update_plot(handles); + +%------------------------------------------------------- +% --- Executes on button press in AutoVecColor. +%------------------------------------------------------- +function AutoVecColor_Callback(hObject, eventdata, handles) +test=get(handles.AutoVecColor,'Value'); +if test + set(handles.AutoVecColor,'BackgroundColor',[1 1 0]) +else + update_plot(handles); + %set(handles.VecScale,'String',num2str(ScalOut.VecScale,3)) + set(handles.AutoVecColor,'BackgroundColor',[0.7 0.7 0.7]) +end +%set_vec_col_bar(handles) + +%------------------------------------------------------- +% --- Executes on selection change in max_vec. +%------------------------------------------------------- +function min_vec_Callback(hObject, eventdata, handles) +max_vec_Callback(hObject, eventdata, handles) + +% --- Executes on selection change in max_vec. +function max_vec_Callback(hObject, eventdata, handles) +set(handles.AutoVecColor,'Value',1) +AutoVecColor_Callback(hObject, eventdata, handles) +min_val=str2num(get(handles.min_vec,'String')); +max_val=str2num(get(handles.max_vec,'String')); +slider1=get(handles.slider1,'Value'); +slider2=get(handles.slider2,'Value'); +colcode1=min_val+(max_val-min_val)*slider1; +colcode2=min_val+(max_val-min_val)*slider2; +set(handles.colcode1,'String',num2str(colcode1)) +set(handles.colcode2,'String',num2str(colcode2)) +update_plot(handles); + +%------------------------------------------------------------------- +%update the display of color code for vectors +function set_vec_col_bar(handles) +%------------------------------------------------------------------- +%get the image of the color display button 'vec_col_bar' in pixels +set(handles.vec_col_bar,'Unit','pixel'); +pos_vert=get(handles.vec_col_bar,'Position'); +set(handles.vec_col_bar,'Unit','Normalized'); +width=ceil(pos_vert(3)); +height=ceil(pos_vert(4)); + +%get slider indications +list=get(handles.color_code,'String'); +ichoice=get(handles.color_code,'Value'); +colcode.ColorCode=list{ichoice}; +colcode.MinC=str2num(get(handles.min_vec,'String')); +colcode.MaxC=str2num(get(handles.max_vec,'String')); +test3color=strcmp(colcode.ColorCode,'rgb') || strcmp(colcode.ColorCode,'bgr'); +if test3color +% set(handles.colcode1,'Visible','on') +% set(handles.colcode2,'Visible','on') +% set(handles.slider1,'Visible','on') +% set(handles.slider2,'Visible','on') + colcode.colcode1=str2num(get(handles.colcode1,'String')); + colcode.colcode2=str2num(get(handles.colcode2,'String')); +else +% set(handles.colcode1,'Visible','off') +% set(handles.colcode2,'Visible','off') +% set(handles.slider1,'Visible','off') +% set(handles.slider2,'Visible','off') +% colcode.colcode1=colcode.min; +% colcode.colcode2=colcode.max; +end +% colcode.option=get(handles.vec_col_bar,'Value'); +colcode.FixedCbounds=0; +% list_code=get(handles.col_vec,'String');% list menu fields +% index_code=get(handles.col_vec,'Value');% selected string index +% colcode.CName= list_code{index_code(1)}; % selected field used for vector color +colcode.FixedCbounds=1; +vec_C=colcode.MinC+(colcode.MaxC-colcode.MinC)*[0.5:width-0.5]/width;%sample of vec_C values from min to max +[colorlist,col_vec]=set_col_vec(colcode,vec_C); +oneheight=ones(1,height); +A1=colorlist(col_vec,1)*oneheight; +A2=colorlist(col_vec,2)*oneheight; +A3=colorlist(col_vec,3)*oneheight; +A(:,:,1)=A1'; +A(:,:,2)=A2'; +A(:,:,3)=A3'; +set(handles.vec_col_bar,'Cdata',A) + + +%------------------------------------------------------------------- +function [PlotType,ScalOut]=update_plot(handles) +%------------------------------------------------------------------- +haxes= handles.axes3; +AxeData=get(haxes,'UserData'); +PlotParam=read_plot_param(handles); +[PlotType,PlotParamOut]= plot_field(AxeData,haxes,PlotParam,1); +write_plot_param(handles,PlotParamOut); %update the auto plot parameters + +%------------------------------------------------------------------- +% --- Executes on button press in grid. +function grid_Callback(hObject, eventdata, handles) +%------------------------------------------------------------------- +huvmat=get(handles.create,'parent'); +UvData=get(huvmat,'UserData');%read UvData properties stored on the uvmat interface + +%suppress the other options if grid is chosen +set(handles.create,'Value',0) +set(handles.create,'BackgroundColor',[0 1 0]) +set(handles.edit_vect,'Value',0) +edit_vect_Callback(hObject, eventdata, handles) +set(handles.edit,'BackgroundColor',[0.7 0.7 0.7]) +set(handles.edit_vect,'Value',0) +edit_vect_Callback(hObject, eventdata, handles) +set(handles.edit,'BackgroundColor',[0.7 0.7 0.7]) +set(handles.list_object,'Value',1) +set(handles.cal,'Value',0) +set(handles.cal,'BackgroundColor',[0 1 0]) + +%prepare display of the set_grid GUI +data.fixedtitle=1; +FileName=read_file_boxes(handles); +[hset_object,UvData.sethandles]=set_grid(FileName);% call the set_object interface +set(huvmat,'UserData',UvData); + + +%------------------------------------------------------------------- +% --- Executes on selection change in edit. +function edit_Callback(hObject, eventdata, handles) +%------------------------------------------------------------------- +huvmat=get(handles.list_object,'parent'); +UvData=get(huvmat,'UserData');%read UvData properties stored on the uvmat interface +test=get(handles.edit,'Value'); +if test + UvData.MouseAction='edit_object'; + set(handles.edit,'BackgroundColor',[1,1,0]) + %suppress the other options + set(handles.zoom,'Value',0) + zoom_Callback(hObject, eventdata, handles) + set(handles.create,'Value',0) + set(handles.create,'BackgroundColor',[0 1 0]) +% set(handles.LINE,'Value',0) +% set(handles.LINE,'BackgroundColor',[0 1 0]) +% set(handles.PATCH,'Value',0) +% set(handles.PATCH,'BackgroundColor',[0 1 0]) +% set(handles.PLANE,'Value',0) +% set(handles.PLANE,'BackgroundColor',[0 1 0])%put activated buttons to yellow +% set(handles.VOLUME,'Value',0) +% set(handles.VOLUME,'BackgroundColor',[0 1 0]) + set(handles.edit_vect,'Value',0) + edit_vect_Callback(hObject, eventdata, handles) + set(handles.cal,'Value',0) + set(handles.cal,'BackgroundColor',[0 1 0]) + %set(handles.grid,'Value',0) + %set(handles.grid,'BackgroundColor',[0 1 0]) + list_object_Callback(hObject, eventdata, handles) +else + UvData.MouseAction='none'; + set(handles.edit,'BackgroundColor',[0.7,0.7,0.7]) +end +set(huvmat,'UserData',UvData); + +%-------------------------------------------------------- +% --- Executes on selection change in list_object. +%-------------------------------------------------------- +function list_object_Callback(hObject, eventdata, handles) +huvmat=get(handles.list_object,'parent'); +UvData=get(huvmat,'UserData');%read UvData properties stored on the uvmat interface +list_str=get(handles.list_object,'String'); +IndexObj=get(handles.list_object,'Value'); + +if ~(length(UvData.Object)>=IndexObj); + return +end +ObjectData=UvData.Object{IndexObj}; +ObjectData.desable_open=1; % desable the OPEN option in the set_object GUI (editing mode) +if isequal(get(handles.edit,'Value'),0) + ObjectData.desable_plot=1; % desable the PLOT option in the set_object GUI (editing mode +end +PlotHandles=get_plot_handles(handles);%get the handles of the interface elements setting the plotting parameters +ZBounds=0; % default + if isfield(UvData,'ZMin') && isfield(UvData,'ZMax') + ZBounds(1)=UvData.ZMin; %minimum for the Z slider + ZBounds(2)=UvData.ZMax;%maximum for the Z slider + end +AxeData.hset_object=set_object(ObjectData,PlotHandles,ZBounds);% call the set_object interface, +pos_uvmat=get(huvmat,'Position'); +if isfield(UvData,'SetObjectOrigin') +pos_set_object(1:2)=UvData.SetObjectOrigin + pos_uvmat(1:2); +pos_set_object(3:4)=UvData.SetObjectSize .* pos_uvmat(3:4); +set(AxeData.hset_object,'Position',pos_set_object) +end +hother=findobj('Tag','proj_object');%find all the proj objects +for iobj=1:length(hother) + if isequal(get(hother(iobj),'Type'),'rectangle')|isequal(get(hother(iobj),'Type'),'patch') + set(hother(iobj),'EdgeColor','b') + if isequal(get(hother(iobj),'FaceColor'),'m') + set(hother(iobj),'FaceColor','b') + end + elseif isequal(get(hother(iobj),'Type'),'image') + Acolor=get(hother(iobj),'CData'); + Acolor(:,:,1)=zeros(size(Acolor,1),size(Acolor,2)); + set(hother(iobj),'CData',Acolor); + else + set(hother(iobj),'Color','b') + end + set(hother(iobj),'Selected','off') +end +hother=findobj('Tag','DeformPoint'); +set(hother,'Color','b'); +set(hother,'Selected','off') +if isfield(ObjectData,'HandlesDisplay') + for iview=1:length(ObjectData.HandlesDisplay) + if ishandle(ObjectData.HandlesDisplay(iview)) + uistack(ObjectData.HandlesDisplay(iview),'top') + linetype=get(ObjectData.HandlesDisplay(iview),'Type'); + if isequal(linetype,'line') + set(ObjectData.HandlesDisplay(iview),'Color','m'); %set the selected object to magenta color + elseif isequal(linetype,'rectangle') + set(ObjectData.HandlesDisplay(iview),'EdgeColor','m'); %set the selected object to magenta color + elseif isequal(linetype,'patch') + set(ObjectData.HandlesDisplay(iview),'FaceColor','m'); %set the selected object to magenta color + end + SubObjectData=get(ObjectData.HandlesDisplay(iview),'UserData'); + if isfield(SubObjectData,'SubObject')& ishandle(SubObjectData.SubObject) + uistack(SubObjectData.SubObject,'top') + for iobj=1:length(SubObjectData.SubObject) + hsub=SubObjectData.SubObject(iobj); + if isequal(get(hsub,'Type'),'rectangle') + set(hsub,'EdgeColor','m'); %set the selected object to magenta color + elseif isequal(get(hsub,'Type'),'image') + Acolor=get(hsub,'CData'); + Acolor(:,:,1)=Acolor(:,:,3); + set(hsub,'CData',Acolor); + else + set(hsub,'Color','m') + end + end + end + if isfield(SubObjectData,'DeformPoint')& ishandle(SubObjectData.DeformPoint) + set(SubObjectData.DeformPoint,'Color','m') + end + end + end +end + +%------------------------------------------------------ +% --- Executes on button press in Menu/Export/field in workspace. +%------------------------------------------------------ +function MenuExportField_Callback(hObject, eventdata, handles) + +global CurData +huvmat=get(handles.RootPath,'parent'); +CurData=get(huvmat,'UserData'); +evalin('base','global CurData')%make CurData global in the workspace +display(['UserData of uvmat :']) +evalin('base','CurData') %display CurData in the workspace +commandwindow; + +%------------------------------------------------------ +% --- Executes on button press in Menu/Export/extract figure. +%------------------------------------------------------ +function MenuExport_plot_Callback(hObject, eventdata, handles) +huvmat=get(handles.MenuExport_plot,'parent'); +UvData=get(huvmat,'UserData'); +hfig=figure; +newaxes=copyobj(handles.axes3,hfig); +map=colormap(handles.axes3); +colormap(map);%transmit the current colormap to the zoom fig +colorbar + + +% -------------------------------------------------------------------- +function Insert_Callback(hObject, eventdata, handles) + + +% -------------------------------------------------------------------- +function MenuRun_Callback(hObject, eventdata, handles) +% -------------------------------------------------------------------- + +% -------------------------------------------------------------------- +function MenuHelp_Callback(hObject, eventdata, handles) +% -------------------------------------------------------------------- +path_to_uvmat=which ('uvmat');% check the path of uvmat +pathelp=fileparts(path_to_uvmat); +helpfile=fullfile(pathelp,'UVMAT_DOC','uvmat_doc.html'); +if isempty(dir(helpfile)), errordlg('Please put the help file uvmat_doc.html in the directory UVMAT/UVMAT_DOC') +else + web(helpfile); +end + +% -------------------------------------------------------------------- +function MenuOpen_Callback(hObject, eventdata, handles) +% -------------------------------------------------------------------- +% -------------------------------------------------------------------- +function MenuOpen_1_Callback(hObject, eventdata, handles) +% -------------------------------------------------------------------- +% -------------------------------------------------------------------- +function MenuExport_Callback(hObject, eventdata, handles) +% -------------------------------------------------------------------- + +% -------------------------------------------------------------------- +function MenuExportMovie_Callback(hObject, eventdata, handles) +% -------------------------------------------------------------------- +set(handles.MenuExportMovie,'BusyAction','queue')% activate the button +huvmat=get(handles.run0,'parent'); +UvData=get(huvmat,'UserData'); +[xx,xx,FileBase]=read_file_boxes(handles); + %read the current input file name +prompt = {'movie file name';'frames per second';'frame resolution (*[512x384] pixels)';'axis position relative to the frame';'total frame number (starting from the current uvmat display)'}; +dlg_title = 'select properties of the output avi movie'; +num_lines= 1; +nbfield_cell=get(handles.last_i,'String'); +def = {[FileBase '_out.avi'];'10';'1';'[0.03 0.05 0.95 0.92]';'10'}; +answer = inputdlg(prompt,dlg_title,num_lines,def,'on'); +aviname=answer{1}; +fps=str2num(answer{2}); +% check for existing file with output name aviname +if exist(aviname,'file') + backup=aviname; + testexist=2; + while testexist==2 + backup=[backup '~']; + testexist=exist(backup,'file'); + end + [success,message]=copyfile(aviname,backup);%make backup of the existing file + if isequal(success,1) + delete(aviname)%delete existing file + else + msgbox_uvmat('ERROR',message) + return + end +end +%create avi open +aviobj=avifile(aviname,'Compression','None','fps',fps); + +%display first view for tests +newfig=figure; +newaxes=copyobj(handles.axes3,newfig);%new plotting axes in the new figure +set(newaxes,'Tag','movieaxes') +nbpix=[512 384]*str2num(answer{3}); +set(gcf,'Position',[1 1 nbpix])% resolution XVGA +set(newaxes,'Position',eval(answer{4})); +map=colormap(handles.axes3); +colormap(map);%transmit the current colormap to the zoom fig +msgbox_uvmat('INPUT_Y-N',{['adjust figure ' num2str(newfig) ' with its matlab edit menu '] ;... + ['then press OK to get the avi movie as a copy of figure ' num2str(newfig) ' display']}); +UvData.Object{1}.plotaxes=newaxes;% the axis in the new figure becomes the current main plotting axes +set(huvmat,'UserData',UvData); +increment=str2num(get(handles.increment_scan,'String')); %get the field increment d +set(handles.STOP,'Visible','on') +set(handles.speed,'Visible','on') +set(handles.speed_txt,'Visible','on') +set(handles.RunMovie,'BusyAction','queue') + +imin=str2num(get(handles.i1,'String')); +imax=str2num(answer{5}); +% if isfield(UvData,'Time') +htitle=get(newaxes,'Title'); +xlim=get(newaxes,'XLim'); +ylim=get(newaxes,'YLim'); +set(htitle,'Position',[xlim(2)+0.07*(xlim(2)-xlim(1)) ylim(2)-0.05*(ylim(2)-ylim(1)) 0]) +time_str=get(handles.abs_time,'String'); +set(htitle,'String',['t=' time_str]) +set(handles.speed,'Value',1) +for i=1:imax + if get(handles.speed,'Value')~=0 & isequal(get(handles.MenuExportMovie,'BusyAction'),'queue') % enable STOP command + runpm(hObject,eventdata,handles,increment) + drawnow + time_str=get(handles.abs_time,'String'); + if ishandle(htitle) + set(htitle,'String',['t=' time_str]) + end + mov=getframe(newfig); + aviobj=addframe(aviobj,mov); + end +end +aviobj=close(aviobj); +UvData.Object{1}.plotaxes=handles.axes3; +set(huvmat,'UserData',UvData); +msgbox_uvmat('CONFIRMATION',{['movie ' aviname ' created '];['with ' num2str(imax) ' frames']}) + +% -------------------------------------------------------------------- +function MenuPoints_Callback(hObject, eventdata, handles) +set(handles.create,'Visible','on') +set(handles.create,'Value',1) +POINTS_Callback(hObject,eventdata,handles) + +% -------------------------------------------------------------------- +function MenuLine_Callback(hObject, eventdata, handles) +set(handles.create,'Visible','on') +set(handles.create,'Value',1) +LINE_Callback(hObject,eventdata,handles) + +% ------------------------------------------------------------------ +function MenuPatch_Callback(hObject, eventdata, handles) +set(handles.create,'Visible','on') +set(handles.create,'Value',1) +PATCH_Callback(hObject,eventdata,handles) + +% ------------------------------------------------------------------ +function MenuPlane_Callback(hObject, eventdata, handles) +set(handles.create,'Visible','on') +set(handles.create,'Value',1) +PLANE_Callback(hObject,eventdata,handles) + +% ------------------------------------------------------------------ +function MenuVolume_Callback(hObject, eventdata, handles) +set(handles.create,'Visible','on') +set(handles.create,'Value',1) +VOLUME_Callback(hObject,eventdata,handles) + +% ------------------------------------------------------------------ +function MenuCalib_Callback(hObject, eventdata, handles) +set(handles.TOOLS_txt,'Visible','on') +set(handles.frame_tools,'Visible','on') +set(handles.cal,'Visible','on') +set(handles.cal,'Value',1) +cal_Callback(hObject,eventdata,handles) + +% ------------------------------------------------------------------ +function MenuMask_Callback(hObject, eventdata, handles) +set(handles.TOOLS_txt,'Visible','on') +set(handles.frame_tools,'Visible','on') +set(handles.create,'Visible','on') +set(handles.create,'Value',1) +set(handles.create,'BackgroundColor',[1 1 0]) %visualise in yellow +set(handles.save_mask,'Visible','on') +set(handles.masklevel,'Visible','on') +if isequal(get(handles.z_index,'Visible'),'on') + nb_slice=str2num(get(handles.nb_slice,'String')); + for ilist=1:nb_slice + list_index{ilist,1}=num2str(ilist); + end + set(handles.masklevel,'String',list_index) + val=str2num(get(handles.z_index,'String')); + if val<=nb_slice + set(handles.masklevel,'Value',val) + end +else + set(handles.masklevel,'String',{'1'}) + set(handles.masklevel,'Value',1) +end +if ishandle(handles.UVMAT_title) + delete(handles.UVMAT_title) +end +huvmat=get(handles.create,'parent'); +UvData=get(huvmat,'UserData');%read UvData properties stored on the uvmat interface +set(handles.zoom,'Value',0) +set(handles.zoom,'BackgroundColor',[0.7 0.7 0.7]) +set(handles.edit_vect,'Value',0) +edit_vect_Callback(hObject, eventdata, handles) +set(handles.edit,'Value',0) +set(handles.edit,'BackgroundColor',[0.7 0.7 0.7]) +set(handles.edit_vect,'Value',0) +edit_vect_Callback(hObject, eventdata, handles) +set(handles.cal,'Value',0) +set(handles.cal,'BackgroundColor',[0 1 0]) + +%initiate the GUI set_object +data.TITLE='MASK'; +if isfield(UvData,'CoordType') + data.CoordType=UvData.CoordType; +end +if isfield(UvData,'Mesh')&&~isempty(UvData.Mesh) + data.YMax=UvData.Mesh; +elseif isfield(UvData.Field,'AX')&&isfield(UvData.Field,'AY')&& isfield(UvData.Field,'A')%only image + np=size(UvData.Field.A); + meshx=(UvData.Field.AX(end)-UvData.Field.AX(1))/(np(2)-1); + meshy=abs(UvData.Field.AY(end)-UvData.Field.AY(1))/(np(1)-1); + data.YMax=max(meshx,meshy); + data.DX=max(meshx,meshy); +end +data.Coord=[0 0 0]; %default +PlotHandles=get_plot_handles(handles);%get the handles of the graphic objects setting the plotting parameters +[hset_object,UvData.sethandles]=set_object(data,PlotHandles);% call the set_object interface +pos_uvmat=get(huvmat,'Position'); +if isfield(UvData,'SetObjectOrigin') + pos_set_object(1:2)=UvData.SetObjectOrigin + pos_uvmat(1:2); + pos_set_object(3:4)=UvData.SetObjectSize .* pos_uvmat(3:4); + set(hset_object,'Position',pos_set_object) +end +list_object=get(handles.list_object,'String'); +if ~isempty(list_object) + set(handles.list_object,'Value',length(list_object)) +end +UvData.MouseAction='create_object'; +set(huvmat,'UserData',UvData); + +% ------------------------------------------------------------------ +%-- open the GUI set_grid.fig to create grid +function MenuGrid_Callback(hObject, eventdata, handles) +set(handles.TOOLS_txt,'Visible','on') +set(handles.frame_tools,'Visible','on') +grid_Callback(hObject,eventdata,handles) + +%---------------------------------------------------------------- +% open the GUI 'series' +%---------------------------------------------------------------- +function MenuSeries_Callback(hObject, eventdata, handles) + +[param.FileName]=read_file_boxes(handles); +if isequal(get(handles.SubField,'Value'),1) + FileName_1=read_file_boxes_1(handles);% + if ~isequal(FileName_1,param.FileName) + param.FileName_1=FileName_1; + end +end +param.NomType=get(handles.FileIndex,'UserData'); +param.NomType_1=get(handles.FileIndex_1,'UserData'); +param.comp_input=get(handles.fix_pair,'Value'); +huvmat=get(handles.MenuSeries,'parent'); +UvData=get(huvmat,'UserData'); +if isfield(UvData,'Time') + param.Time=UvData.XmlData.Time; +end +if isequal(get(handles.scan_i,'Value'),1) + param.incr_i=str2num(get(handles.increment_scan,'String')); +elseif isequal(get(handles.scan_j,'Value'),1) + param.incr_j=str2num(get(handles.increment_scan,'String')); +end +param.list_fields=get(handles.Fields,'String');% list menu fields +param.list_fields(1)=[]; %suppress 'image' option +param.index_fields=get(handles.Fields,'Value');% selected string index +if param.index_fields>1 + param.index_fields=param.index_fields-1; +end +param.list_fields_1=get(handles.Fields_1,'String');% list menu fields +param.list_fields_1(1)=[]; %suppress 'image' option +param.index_fields_1=get(handles.Fields_1,'Value')-1;% selected string index +if param.index_fields_1>1 + param.index_fields_1=param.index_fields_1-1; +end +param.civ1=get(handles.civ1,'Value'); +param.civ2=get(handles.civ2,'Value'); +param.interp1=get(handles.interp1,'Value'); +param.interp2=get(handles.interp2,'Value'); +param.filter1=get(handles.filter1,'Value'); +param.filter2=get(handles.filter2,'Value'); +param.menu_coord_str=get(handles.menu_coord,'String'); +param.menu_coord_val=get(handles.menu_coord,'Value'); + +series(param); %run the series interface + +% ------------------------------------------------------------------ +% -- open the GUI civ.fig for civx (PIV) +% ------------------------------------------------------------------ +function MenuPIV_Callback(hObject, eventdata, handles) + +[FileName,RootPath,filebase,FileIndices,ext,SubDir]=read_file_boxes(handles); +[P,F,str1,str2,str_a,str_b]=name2display(FileName); +num1=stra2num(str1); +num2=stra2num(str2); +num_a=stra2num(str_a); +num_b=stra2num(str_b); +NomType=get(handles.FileIndex,'UserData'); +ind_opening=1; % default (images): will advice civ1 option by default in the civ interface +if isequal(ext,'.nc') || isequal(ext,'.cdf')% netcdf files + ind_opening=2;% propose 'fix' as the default option +% +read the current netcdf rootfile + Data=nc2struct(FileName,[]); + if isfield(Data,'fix') & isequal(Data.fix,1) + ind_opening=3; + end + if isfield(Data,'patch') & isequal(Data.patch,1) + ind_opening=4; + end + if isfield(Data,'civ2') & isequal(Data.civ2,1) + ind_opening=5; + end + if isfield(Data,'fix2') & isequal(Data.fix2,1) + ind_opening=6; + end +end +varargin{1}=filebase; +varargin{2}=NomType; +varargin{3}=num1; +varargin{4}=num2; +varargin{5}=num_a; +varargin{6}=num_b; +varargin{7}=SubDir; +varargin{8}=ind_opening;% A REVOIR +TRANSMETTRE IMADOC INFO +varargin{11}=ext; +civ(varargin);% interface de civ(not in the uvmat file) + +% ------------------------------------------------------------------ +function MenuTools_Callback(hObject, eventdata, handles) + +% ------------------------------------------------------------------ +function MenuEdit_Callback(hObject, eventdata, handles) + +%-------------------------------------------------------------------------- +function enable_transform(handles,state) +set(handles.menu_coord,'Visible',state) +set(handles.TRANSFORM_txt,'Visible',state) +set(handles.menu_coord,'Visible',state) +set(handles.path_transform,'Visible',state) +set(handles.pxcmx_txt,'Visible',state) +set(handles.pxcmy_txt,'Visible',state) +set(handles.pxcm,'Visible',state) +set(handles.pycm,'Visible',state) + +% -------------------------------------------------------------------- +function MenuEditVectors_Callback(hObject, eventdata, handles) +set(handles.edit_vect,'Visible','on') +set(handles.edit_vect,'Value',1) +edit_vect_Callback(hObject, eventdata, handles) + + + + Index: /trunk/src/warndlg_uvmat.m =================================================================== --- /trunk/src/warndlg_uvmat.m (revision 2) +++ /trunk/src/warndlg_uvmat.m (revision 2) @@ -0,0 +1,18 @@ +%'warndlg_uvmat': display warning message (error, warning, confirmation) in a given figure +%--------------------------------------------------------------------- +% hwarn=warndlg_uvmat(warntext,title) +%--------------------------------------------------------------------- +% OUTPUT: +% hwarn: string representing the file name (including path) +% +% INPUT: +% warntext: text to display +% title: string indicating the type of message box: +% title= 'ERROR', 'WARNING', 'CONFIRMATION' . + +function hwarn=warndlg_uvmat(warntext,title) +hwarn=msgbox_uvmat(title,warntext); +%if isequal(title,'ERROR')||isequal(title,'WARNING') + %delete(hwarn) +%end + Index: /trunk/src/write_plot_param.m =================================================================== --- /trunk/src/write_plot_param.m (revision 2) +++ /trunk/src/write_plot_param.m (revision 2) @@ -0,0 +1,109 @@ +%'write_plot_param': update the plotting parameters on the uvmat interface after a plotting operation +function write_plot_param(handles,PlotParam) + +%scalar or image parameters +if isfield(PlotParam,'Scalar') + set_scal_display(handles,'on') + if isfield(PlotParam.Scalar,'MaxA') + set(handles.MaxA,'String',num2str(PlotParam.Scalar.MaxA,3)); + end + if isfield(PlotParam.Scalar,'MinA') + set(handles.MinA,'String',num2str(PlotParam.Scalar.MinA,3)); + end + + if isfield(PlotParam.Scalar,'IncrA') + set(handles.IncrA,'String',num2str(PlotParam.Scalar.IncrA,3)) + end +else + set_scal_display(handles,'off') +end + +% parameter for vector field +if isfield(PlotParam,'Vectors') + set_vect_display(handles,'on') + if isfield(PlotParam.Vectors,'VecScale') + set(handles.VecScale,'String',num2str(PlotParam.Vectors.VecScale,3)) + end + if isfield(PlotParam.Vectors,'MinC')&& isfield(PlotParam.Vectors,'MaxC') + MinC=PlotParam.Vectors.MinC; + MaxC=PlotParam.Vectors.MaxC; + set(handles.min_vec,'String', num2str(MinC,3)); + set(handles.max_vec,'String',num2str(MaxC,3)); + list=get(handles.color_code,'String'); + ichoice=get(handles.color_code,'Value'); + color_option=list{ichoice}; + test3color=strcmp(color_option,'rgb')||strcmp(color_option,'bgr'); + if test3color% need to update color thresholds + set(handles.colcode1,'Visible','on') + set(handles.colcode2,'Visible','on') + set(handles.slider1,'Visible','on') + set(handles.slider2,'Visible','on') +% slider1=get(handles.slider1,'Value'); +% slider2=get(handles.slider2,'Value'); + colcode1=MinC+(MaxC-MinC)*PlotParam.Vectors.colcode1; + colcode2=MinC+(MaxC-MinC)*PlotParam.Vectors.colcode2; + set(handles.colcode1,'String',num2str(colcode1,3)) + set(handles.colcode2,'String',num2str(colcode2,3)) + set(handles.slider1,'Value',PlotParam.Vectors.colcode1) + set(handles.slider2,'Value',PlotParam.Vectors.colcode2) + else + set(handles.colcode1,'Visible','off') + set(handles.colcode2,'Visible','off') + set(handles.slider1,'Visible','off') + set(handles.slider2,'Visible','off') + end + end +else + set_vect_display(handles,'off') + set(handles.edit_vect,'Visible','off') +end + +%------------------------------------------------------------------ +%prepare interface for scalar display: state ='on' or 'off' +function set_scal_display(handles,state) +%------------------------------------------------------------------ +set(handles.SCALAR_title,'Visible',state) +set(handles.MaxA,'Visible',state) +set(handles.MinA,'Visible',state) +%set(handles.IncrA,'Visible',state) +set(handles.AutoScal,'Visible',state) +set(handles.BW,'Visible',state) +set(handles.Contours,'Visible',state) +set(handles.SCALAR_title,'Visible',state) +set(handles.min_title,'Visible',state) +set(handles.max_title,'Visible',state) +set(handles.frame_scal,'Visible',state) +set(handles.npx,'Visible',state) +set(handles.npy,'Visible',state) +set(handles.npx_title,'Visible',state) +set(handles.npy_title,'Visible',state) +%set(handles.makemask,'Visible',state) + +%--------------------------------------------- +%prepare interface for vector display: state ='on' or 'off' +function set_vect_display(handles,state) +%------------------------------------------------------------------ +set(handles.frame_vect,'Visible',state) +set(handles.VECT_title,'Visible',state) +set(handles.VecScale,'Visible',state) +set(handles.AutoVec,'Visible',state) +set(handles.HideFalse,'Visible',state) +set(handles.HideWarning,'Visible',state) +set(handles.record,'Visible',state) +set(handles.colcode1,'Visible',state) +set(handles.colcode2,'Visible',state) +set(handles.min_vec,'Visible',state) +set(handles.max_vec,'Visible',state) +set(handles.scale_title,'Visible',state) +set(handles.slider1,'Visible',state) +set(handles.slider2,'Visible',state) +set(handles.col_vec,'Visible',state) +set(handles.Color_title,'Visible',state) +set(handles.color_code,'Visible',state) +set(handles.vec_col_bar,'Visible',state) +set(handles.record,'Visible',state) +set(handles.AutoVecColor,'Visible',state) +set(handles.decimate4,'Visible',state) +set(handles.min_C_title,'Visible',state) +set(handles.max_C_title,'Visible',state) +set(handles.MenuEditVectors,'Enable',state)