Index: trunk/src/proj_field.m =================================================================== --- trunk/src/proj_field.m (revision 1120) +++ trunk/src/proj_field.m (revision 1121) @@ -1072,5 +1072,5 @@ end -%% initiate Matlab structure for physical fieldopen +%% initiate Matlab structure for physical field [ProjData,errormsg]=proj_heading(FieldData,ObjectData); if ~isempty(errormsg) @@ -1345,5 +1345,5 @@ % two cases of projection for scattered coordinates switch ProjMode{icell} - case 'projection' + case 'projection'% ptoject scattered data without interpolation nbvar=0; %nbvar=numel(ProjData.ListVarName); @@ -1366,5 +1366,5 @@ end end - case 'interp_lin'%interpolate data on a regular grid + case 'interp_lin'%interpolate scattered data on a regular grid if isfield(CellInfo{icell},'VarIndex_errorflag') VarName_FF=FieldData.ListVarName{CellInfo{icell}.VarIndex_errorflag}; @@ -1382,5 +1382,5 @@ end % interpolate and calculate field on the grid - + [VarVal,ListVarName,VarAttribute,errormsg]=calc_field_interp([coord_X coord_Y],FieldData,CellInfo{icell}.FieldName,XI,YI); @@ -1500,5 +1500,5 @@ end - if strcmp(ProjMode{icell},'projection')% && (~testangle || test90y || test90x) + if strcmp(ProjMode{icell},'projection')% project gridded data without interpolation if NbDim==2 && ~testXMin && ~testXMax && ~testYMin && ~testYMax% no range restriction ListVarName=[ListVarName FieldData.ListVarName(VarIndex)]; @@ -1606,5 +1606,5 @@ end end - else % case with interpolation on a grid + else % project gridded data with interpolation on a grid if NbDim==2 %2D case if isequal(ProjMode{icell},'interp_tps') @@ -1778,5 +1778,5 @@ %----------------------------------------------------------------- -ProjData=FieldData;%default output +ProjData=[];%default output %% axis origin @@ -1809,11 +1809,12 @@ DY=0; %default DZ=0; -if isfield(ObjectData,'DX')&~isempty(ObjectData.DX) +ProjMode=ObjectData.ProjMode; +if isfield(ObjectData,'DX')&&~isempty(ObjectData.DX) DX=abs(ObjectData.DX);%mesh of interpolation points end -if isfield(ObjectData,'DY')&~isempty(ObjectData.DY) +if isfield(ObjectData,'DY')&&~isempty(ObjectData.DY) DY=abs(ObjectData.DY);%mesh of interpolation points end -if isfield(ObjectData,'DZ')&~isempty(ObjectData.DZ) +if isfield(ObjectData,'DZ')&&~isempty(ObjectData.DZ) DZ=abs(ObjectData.DZ);%mesh of interpolation points end @@ -1872,4 +1873,6 @@ %----------------------------------------------------------------- idimvar=0; + +[CellInfo,NbDimArray,errormsg]=find_field_cells(FieldData); % LOOP ON GROUPS OF VARIABLES SHARING THE SAME DIMENSIONS % CellVarIndex=cells of variable index arrays @@ -1878,13 +1881,13 @@ nbcoord=0;%number of added coordinate variables brought by projection nbvar=0; -for icell=1:length(CellVarIndex) - NbDim=NbDimVec(icell); +for icell=1:length(CellInfo) + NbDim=NbDimArray(icell); if NbDim<3 continue end - VarIndex=CellVarIndex{icell};% indices of the selected variables in the list FieldData.ListVarName - VarType=VarTypeCell{icell}; + VarIndex=CellInfo{icell}.VarIndex;% indices of the selected variables in the list FieldData.ListVarName + VarType=CellInfo{icell}.VarType; ivar_X=VarType.coord_x; - ivar_Y=VarType.coord_y; + ivar_Y=VarType.coorCeld_y; ivar_Z=VarType.coord_z; ivar_U=VarType.vector_x; @@ -1897,5 +1900,5 @@ ivar_F=VarType.warnflag; ivar_FF=VarType.errorflag; - check_unstructured_coord=~isempty(ivar_X) && ~isempty(ivar_Y); + %check_unstructured_coord=~isempty(ivar_X) && ~isempty(ivar_Y); DimCell=FieldData.VarDimName{VarIndex(1)}; if ischar(DimCell) @@ -1904,14 +1907,13 @@ %% case of input fields with unstructured coordinates - if check_unstructured_coord + if strcmp(CellInfo{icell}.CoordType,'scattered') XName=FieldData.ListVarName{ivar_X}; YName=FieldData.ListVarName{ivar_Y}; - eval(['coord_x=FieldData.' XName ';']) - eval(['coord_y=FieldData.' YName ';']) + coord_x=FieldData.(XName); + coord_y=FieldData.(YName); if length(ivar_Z)==1 ZName=FieldData.ListVarName{ivar_Z}; - eval(['coord_z=FieldData.' ZName ';']) - end - + coord_z=FieldData.(ZName); + end % translate initial coordinates coord_x=coord_x-ObjectData.Coord(1,1); @@ -1988,9 +1990,9 @@ VarName=FieldData.ListVarName{ivar}; if ivar==ivar_X %x coordinate - eval(['ProjData.' VarName '=coord_X;']) + ProjData.(VarName)=coord_X; elseif ivar==ivar_Y % y coordinate - eval(['ProjData.' VarName '=coord_Y;']) + 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 ';']) + ProjData.(VarName)=FieldData.(VarName); end if isempty(ivar_Z) || ivar~=ivar_Z @@ -2285,6 +2287,6 @@ test_interp_tps=0; end - eval(['ProjData.' AYName '=[coord_y_proj(1) coord_y_proj(end)];']) %record the new (projected ) y coordinates - eval(['ProjData.' AXName '=[coord_x_proj(1) coord_x_proj(end)];']) %record the new (projected ) x coordinates + ProjData.(AYName)=[coord_y_proj(1) coord_y_proj(end)]; %record the new (projected ) y coordinates + ProjData.(AXName)=[coord_x_proj(1) coord_x_proj(end)]; %record the new (projected ) x coordinates for ivar=VarIndex VarName=FieldData.ListVarName{ivar}; @@ -2354,5 +2356,5 @@ if testangle if isempty(ivar_V) - msgbox_uvmat('ERROR','v velocity component missing in proj_field.m') + errormsg='v velocity component missing in proj_field.m'; return end @@ -2372,4 +2374,8 @@ end end +if isempty(ProjData.ListVarName) + errormsg='input field is not 3D, no volume projection'; + ProjData=[]; +end %------------------------------------------------------------------------ Index: trunk/src/series/merge_proj_volume.m =================================================================== --- trunk/src/series/merge_proj_volume.m (revision 1121) +++ trunk/src/series/merge_proj_volume.m (revision 1121) @@ -0,0 +1,517 @@ +%'merge_proj_volume': concatene several fields from series, project on volumes +%------------------------------------------------------------------------ +% function ParamOut=merge_proj_volume(Param) +%------------------------------------------------------------------------ +%%%%%%%%%%% GENERAL TO ALL SERIES ACTION FCTS %%%%%%%%%%%%%%%%%%%%%%%%%%% +% +%OUTPUT +% ParamOut: sets options in the GUI series.fig needed for the function +% +%INPUT: +% In run mode, the input parameters are given as a Matlab structure Param copied from the GUI series. +% In batch mode, Param is the name of the corresponding xml file containing the same information +% when Param.Action.RUN=0 (as activated when the current Action is selected +% in series), the function ouput paramOut set the activation of the needed GUI elements +% +% Param contains the elements:(use the menu bar command 'export/GUI config' in series to +% see the current structure Param) +% .InputTable: cell of input file names, (several lines for multiple input) +% each line decomposed as {RootPath,SubDir,Rootfile,NomType,Extension} +% .OutputSubDir: name of the subdirectory for data outputs +% .OutputDirExt: directory extension for data outputs +% .Action: .ActionName: name of the current activated function +% .ActionPath: path of the current activated function +% .ActionExt: fct extension ('.m', Matlab fct, '.sh', compiled Matlab fct +% .RUN =0 for GUI input, =1 for function activation +% .RunMode='local','background', 'cluster': type of function use +% +% .IndexRange: set the file or frame indices on which the action must be performed +% .FieldTransform: .TransformName: name of the selected transform function +% .TransformPath: path of the selected transform function +% .InputFields: sub structure describing the input fields withfields +% .FieldName: name(s) of the field +% .VelType: velocity type +% .FieldName_1: name of the second field in case of two input series +% .VelType_1: velocity type of the second field in case of two input series +% .Coord_y: name of y coordinate variable +% .Coord_x: name of x coordinate variable +% .ProjObject: %sub structure describing a projection object (read from ancillary GUI set_object) +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + +%======================================================================= +% Copyright 2008-2022, LEGI UMR 5519 / CNRS UGA G-INP, Grenoble, France +% http://www.legi.grenoble-inp.fr +% Joel.Sommeria - Joel.Sommeria (A) legi.cnrs.fr +% +% 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 (see LICENSE.txt) for more details. +%======================================================================= + +function ParamOut=merge_proj_volume(Param) + +%% set the input elements needed on the GUI series when the function is selected in the menu ActionName or InputTable refreshed +if isstruct(Param) && isequal(Param.Action.RUN,0) + ParamOut.AllowInputSort='on';% allow alphabetic sorting of the list of input file SubDir (options 'off'/'on', 'off' by default) + ParamOut.WholeIndexRange='off';% prescribes the file index ranges from min to max (options 'off'/'on', 'off' by default) + ParamOut.NbSlice='off'; %nbre of slices ('off' by default) + ParamOut.VelType='one';% menu for selecting the velocity type (options 'off'/'one'/'two', 'off' by default) + ParamOut.FieldName='off';% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default) + ParamOut.FieldTransform = 'on';%can use a transform function + ParamOut.TransformPath=fullfile(fileparts(which('uvmat')),'transform_field');% path to transform functions (needed for compilation only) + ParamOut.ProjObject='on';%can use projection object(option 'off'/'on', + ParamOut.Mask='off';%can use mask option (option 'off'/'on', 'off' by default) + ParamOut.OutputDirExt='.volume';%set the output dir extension + ParamOut.OutputFileMode='NbInput_i';% '=NbInput': 1 output file per input file index, '=NbInput_i': 1 file per input file index i, '=NbSlice': 1 file per slice + %check the input files + ParamOut.CheckOverwriteVisible='on'; % manage the overwrite of existing files (default=1) + first_j=[]; + if isfield(Param.IndexRange,'first_j'); first_j=Param.IndexRange.first_j; end + PairString=''; + if isfield(Param.IndexRange,'PairString'); PairString=Param.IndexRange.PairString; end + [i1,i2,j1,j2] = get_file_index(Param.IndexRange.first_i,first_j,PairString); + FirstFileName=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},... + Param.InputTable{1,5},Param.InputTable{1,4},i1,i2,j1,j2); + if ~exist(FirstFileName,'file') + msgbox_uvmat('WARNING',['the first input file ' FirstFileName ' does not exist']) + end + return +end + +%%%%%%%%%%%% STANDARD PART (DO NOT EDIT) %%%%%%%%%%%% +ParamOut=[]; %default output +RUNHandle=[]; +WaitbarHandle=[]; + +%% read input parameters from an xml file if input is a file name (batch mode) +checkrun=1; +if ischar(Param) + Param=xml2struct(Param);% read Param as input file (batch case) + checkrun=0; +else + hseries=findobj(allchild(0),'Tag','series'); + RUNHandle=findobj(hseries,'Tag','RUN');%handle of RUN button in GUI series + WaitbarHandle=findobj(hseries,'Tag','Waitbar');%handle of waitbar in GUI series +end +if ~(isfield(Param,'ProjObject') && strcmp(Param.ProjObject.Type,'volume')&& strcmp(Param.ProjObject.ProjMode,'interp_lin')) + msgbox_uvmat('ERROR','a projection object of type volume with ProjMode interp_lin must be introduced') + return +end + +%% root input file type +RootPath=Param.InputTable(:,1); +RootFile=Param.InputTable(:,3); +SubDir=Param.InputTable(:,2); +%NomType=Param.InputTable(:,4); +FileExt=Param.InputTable(:,5); +[filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param); +%%%%%%%%%%%% +% The cell array filecell is the list of input file names, while +% filecell{iview,fileindex}: +% iview: line in the table corresponding to a given file series +% fileindex: file index within the file series, +% i1_series(iview,ref_j,ref_i)... are the corresponding arrays of indices i1,i2,j1,j2, depending on the input line iview and the two reference indices ref_i,ref_j +% i1_series(iview,fileindex) expresses the same indices as a 1D array in file indices +%%%%%%%%%%%% +NbView=numel(i1_series);%number of input file series (lines in InputTable) +NbField_j=size(i1_series{1},1); %nb of fields for the j index (bursts or volume slices) +NbField_i=size(i1_series{1},2); %nb of fields for the i index +NbField=NbField_j*NbField_i; %total number of fields + +%% define the name for result file (with path=RootPath{1}) +OutputDir=[Param.OutputSubDir Param.OutputDirExt];% subdirectory for output files + +if ~isfield(Param,'InputFields') + Param.InputFields.FieldName=''; +end + + +%% determine the file type on each line from the first input file +ImageTypeOptions={'image','multimage','mmreader','video','cine_phantom'}; +NcTypeOptions={'netcdf','civx','civdata'}; +for iview=1:NbView + if ~exist(filecell{iview,1}','file') + disp_uvmat('ERROR',['the first input file ' filecell{iview,1} ' does not exist'],checkrun) + return + end + [FileInfo{iview},MovieObject{iview}]=get_file_info(filecell{iview,1}); + FileType{iview}=FileInfo{iview}.FileType; + CheckImage{iview}=~isempty(find(strcmp(FileType{iview},ImageTypeOptions)));% =1 for images + if CheckImage{iview} + ParamIn{iview}=MovieObject{iview}; + else + ParamIn{iview}=Param.InputFields; + end + CheckNc{iview}=~isempty(find(strcmp(FileType{iview},NcTypeOptions)));% =1 for netcdf files + if ~isempty(j1_series{iview}) + frame_index{iview}=j1_series{iview}; + else + frame_index{iview}=i1_series{iview}; + end +end +if NbView >1 && max(cell2mat(CheckImage))>0 && ~isfield(Param,'ProjObject') + disp_uvmat('ERROR','projection on a common grid is needed to concatene images: use a Projection Object of type ''plane'' with ProjMode=''interp_lin''',checkrun) + return +end + +%% calibration data and timing: read the ImaDoc files +[XmlData,NbSlice_calib,time,errormsg]=read_multimadoc(RootPath,SubDir,RootFile,FileExt,i1_series,i2_series,j1_series,j2_series); +if size(time,1)>1 + diff_time=max(max(diff(time))); + if diff_time>0 + disp_uvmat('WARNING',['times of series differ by (max) ' num2str(diff_time) ': the mean time is chosen in result'],checkrun) + end +end +if ~isempty(errormsg) + disp_uvmat('WARNING',errormsg,checkrun) +end +time=mean(time,1); %averaged time taken for the merged field + +%% check calibration data +for iview=1:NbView + if isfield(XmlData{iview}.GeometryCalib,'CheckVolumeScan') %old convention (<2022) + CheckVolumeScan{iview}=XmlData{iview}.GeometryCalib.CheckVolumeScan; + XmlData{iview}.Slice.SliceCoord=XmlData{iview}.GeometryCalib.SliceCoord; + XmlData{iview}.Slice.SliceAngle=XmlData{iview}.GeometryCalib.SliceAngle; + elseif isfield(XmlData{1},'Slice')&& isfield(XmlData{iview}.Slice,'CheckVolumeScan') %new convention (>=2022) + CheckVolumeScan{iview}=XmlData{iview}.Slice.CheckVolumeScan; + else + disp('no volume info in calibration data (xml file)') + return + end + if CheckVolumeScan{iview}==0 + disp('input field sereis with volume scan (index j) is needed') + return + end +end + +%% initiate output field +DataVol.ListGlobalAttribute={'Conventions','CoordUnit','Time'}; +DataVol.Conventions='uvmat'; +DataVol.CoordUnit=XmlData{1}.GeometryCalib.CoordUnit; +DataVol.Time=0; %TO UPDATE +DataVol.ListVarName={'coord_x','coord_y','coord_z','A'}; +DataVol.VarDimName={'coord_x','coord_y','coord_z',{'coord_z','coord_y','coord_x'}}; +DataVol.VarAttribute{1}.Role='coord_x'; +DataVol.VarAttribute{2}.Role='coord_y'; +DataVol.VarAttribute{3}.Role='coord_z'; +DataVol.VarAttribute{4}.Role='scalar'; +DataVol.coord_x=Param.ProjObject.RangeX(1):Param.ProjObject.DX:Param.ProjObject.RangeX(2); +DataVol.coord_y=Param.ProjObject.RangeY(1):Param.ProjObject.DY:Param.ProjObject.RangeY(2); +DataVol.coord_z=Param.ProjObject.RangeZ(1):Param.ProjObject.DZ:Param.ProjObject.RangeZ(2); +DataVol.A=zeros(numel(DataVol.coord_z),numel(DataVol.coord_y),numel(DataVol.coord_x)); +%% coordinate transform or other user defined transform +% transform_fct='';%default fct handle +% if isfield(Param,'FieldTransform')&&~isempty(Param.FieldTransform.TransformName) +% currentdir=pwd; +% cd(Param.FieldTransform.TransformPath) +% transform_fct=str2func(Param.FieldTransform.TransformName); +% cd (currentdir) +% if isfield(Param,'TransformInput') +% for iview=1:NbView +% XmlData{iview}.TransformInput=Param.TransformInput; +% end +% end +% end +%%%%%%%%%%%% END STANDARD PART %%%%%%%%%%%% +% EDIT FROM HERE + +% %% output file type +if isempty(j1_series{1}) + disp('error: no index j for z position label') + return +end +NomTypeOut='_1'; + +RootFileOut=RootFile{1}; +for iview=2:NbView + if ~strcmp(RootFile{iview},RootFile{1}) + RootFileOut='mproj'; + break + end +end + + +%% MAIN LOOP ON FIELDS +%%%%%%%%%%%%% STANDARD PART (DO NOT EDIT) %%%%%%%%%%%% +% for i_slice=1:NbSlice +% index_slice=i_slice:NbSlice:NbField;% select file indices of the slice +% NbFiles=0; +% nbmissing=0; + +%%%%%%%%%%%%%%%% loop on field indices %%%%%%%%%%%%%%%% +tstart=tic; %used to record the computing time +CheckOverwrite=1;%default +if isfield(Param,'CheckOverwrite') + CheckOverwrite=Param.CheckOverwrite; +end + + +for index_i=1:NbField_i + AMerge=zeros(NbField_j,numel(DataVol.coord_y),numel(DataVol.coord_x)); + for index_j=1:NbField_j + index_j + %% generating the name of the merged field + OutputFile=fullfile_uvmat(RootPath{1},OutputDir,RootFileOut,'.nc',NomTypeOut,index_i); + if ~CheckOverwrite && exist(OutputFile,'file') + disp(['existing output file ' OutputFile ' already exists, skip to next field']) + continue% skip iteration if the mode overwrite is desactivated and the result file already exists + end + + %%%%%%%%%%%%%%%% loop on views (input lines) %%%%%%%%%%%%%%%% + Data=cell(1,NbView);%initiate the set Data + timeread=zeros(1,NbView); + for iview=1:NbView + %% reading input file(s) + [Data{iview},tild,errormsg] = read_field(filecell{iview,index_j},FileType{iview},ParamIn{iview},frame_index{iview}(index_j)); + if ~isempty(errormsg) + disp_uvmat('ERROR',['ERROR in merge_proj/read_field/' errormsg],checkrun) + return + end + ListVar=Data{iview}.ListVarName; + for ilist=1:numel(ListVar) + Data{iview}.(ListVar{ilist})=double(Data{iview}.(ListVar{ilist}));% transform all fields in double before all operations + end + % get the time defined in the current file if not already defined from the xml file + if ~isempty(time) && isfield(Data{iview},'Time') + timeread(iview)=Data{iview}.Time; + end + Data{iview}.ZIndex=index_j; + [X,Y]=meshgrid(DataVol.coord_x,DataVol.coord_y);%grid in physical coordinates + Data{iview}=proj_plane(Data{iview},XmlData{iview},X,Y); %project on the common x,y plane + end + % merge the NbView fields only to merge views from several cameras) + + % [MergeData,errormsg]=merge_field(ProjData); + % if ~isempty(errormsg) + % disp_uvmat('ERROR',errormsg,checkrun); + % return + % end + AMerge(index_j,:,:)=Data{iview}.A; + + %%%%%%%%%%%%%%%% END LOOP FOR VOLUME SCAN %%%%%%%%%%%%%%%% + end + %interpolate on the vertical grid + Z=zeros(1,NbField_j); + for j_index=1:numel(DataVol.coord_y) + for i_index=1:numel(DataVol.coord_x) + for ZIndex=1:NbField_j + Z(ZIndex)=Zpos(XmlData{iview},ZIndex,X(j_index,i_index),Y(j_index,i_index)); + end + DataVol.A(:,j_index,i_index) = interp1(Z,AMerge(:,j_index,i_index),DataVol.coord_z); + end + end + error=struct2nc(OutputFile,DataVol)%save result file + + + % if index==1 + % TimeData.ListGlobalAttribute={'Conventions','Project','CoordUnit','TimeUnit','ZPos','Time'}; + % TimeData.Conventions='uvmat'; + % TimeData.Project='2016_Circumpolar'; + % TimeData.CoordUnit='cm'; + % TimeData.TimeUnit='s'; + % % TimeData.ZPos=ZPos; + % TimeData.ListVarName={'radius','azimuth','U','V','curl','div'}; + % TimeData.VarDimName={'radius','azimuth',{'radius','azimuth'},{'radius','azimuth'}... + % {'radius','azimuth'},{'radius','azimuth'}}; + % TimeData.VarAttribute{1}.Role=''; + % TimeData.VarAttribute{2}.Role=''; + % TimeData.VarAttribute{3}.Role='vector_x'; + % TimeData.VarAttribute{4}.Role='vector_y'; + % TimeData.VarAttribute{5}.Role='scalar'; + % TimeData.VarAttribute{6}.Role='scalar'; + % + % end + % + % %% append data to the netcdf file for next iterations + % + % + % error=struct2nc(OutputFile,TimeData);%save result file + % if isempty(error) + % disp(['output file ' OutputFile ' written']) + % else + % disp(error) + % end + % ellapsed_time=toc(tstart); + % disp(['ellapsed time since start ' num2str(ellapsed_time/60,2) ' minutes']) +end + +% disp([ num2str(ellapsed_time/(60*NbField),3) ' minutes per iteration']) + +% %'merge_field': concatene fields +% %------------------------------------------------------------------------ +% function [MergeData,errormsg]=merge_field(Data) +% %% default output +% if isempty(Data)||~iscell(Data) +% MergeData=[]; +% return +% end +% errormsg=''; +% MergeData=Data{1};% merged field= first field by default, reproduces the global attributes of the first field +% NbView=length(Data); +% if NbView==1% if there is only one field, just reproduce it in MergeData +% return +% end +% +% %% group the variables (fields of 'Data') in cells of variables with the same dimensions +% [CellInfo,NbDim,errormsg]=find_field_cells(Data{1}); +% if ~isempty(errormsg) +% return +% end +% +% %LOOP ON GROUPS OF VARIABLES SHARING THE SAME DIMENSIONS +% for icell=1:length(CellInfo) +% if NbDim(icell)~=1 % skip field cells which are of dim 1 +% switch CellInfo{icell}.CoordType +% case 'scattered' %case of input fields with unstructured coordinates: just concatene data +% for ivar=CellInfo{icell}.VarIndex % indices of the selected variables in the list FieldData.ListVarName +% VarName=Data{1}.ListVarName{ivar}; +% for iview=2:NbView +% MergeData.(VarName)=[MergeData.(VarName); Data{iview}.(VarName)]; +% end +% end +% case 'grid' %case of fields defined on a structured grid +% FFName=''; +% if isfield(CellInfo{icell},'VarIndex_errorflag') && ~isempty(CellInfo{icell}.VarIndex_errorflag) +% FFName=Data{1}.ListVarName{CellInfo{icell}.VarIndex_errorflag};% name of errorflag variable +% MergeData.ListVarName(CellInfo{icell}.VarIndex_errorflag)=[];%remove error flag variable in MergeData (will use NaN instead) +% MergeData.VarDimName(CellInfo{icell}.VarIndex_errorflag)=[]; +% MergeData.VarAttribute(CellInfo{icell}.VarIndex_errorflag)=[]; +% end +% % select good data on each view +% for ivar=CellInfo{icell}.VarIndex % indices of the selected variables in the list FieldData.ListVarName +% VarName=Data{1}.ListVarName{ivar}; +% for iview=1:NbView +% if isempty(FFName) +% check_bad=isnan(Data{iview}.(VarName));%=0 for NaN data values, 1 else +% else +% check_bad=isnan(Data{iview}.(VarName)) | Data{iview}.(FFName)~=0;%=0 for NaN or error flagged data values, 1 else +% end +% Data{iview}.(VarName)(check_bad)=0; %set to zero NaN or data marked by error flag +% if iview==1 +% %MergeData.(VarName)=Data{1}.(VarName);% initiate MergeData with the first field +% MergeData.(VarName)(check_bad)=0; %set to zero NaN or data marked by error flag +% NbAver=~check_bad;% initiate NbAver: the nbre of good data for each point +% elseif size(Data{iview}.(VarName))~=size(MergeData.(VarName)) +% errormsg='sizes of the input matrices do not agree, need to interpolate on a common grid using a projection object'; +% return +% else +% MergeData.(VarName)=MergeData.(VarName) +double(Data{iview}.(VarName));%add data +% NbAver=NbAver + ~check_bad;% add 1 for good data, 0 else +% end +% end +% MergeData.(VarName)(NbAver~=0)=MergeData.(VarName)(NbAver~=0)./NbAver(NbAver~=0);% take average of defined data at each point +% MergeData.(VarName)(NbAver==0)=NaN;% set to NaN the points with no good data +% end +% end +% +% end +% end + +% get the X position corresponding to X,Y for a given plane (labelled by ZIndex) + +function Z=Zpos(XmlData,ZIndex,X,Y)% Z positions correspoonding to X,Y positions +Z=XmlData.Slice.SliceCoord(ZIndex,3)*ones(size(X)); +if isfield(XmlData.Slice,'SliceAngle')&&~isequal(XmlData.Slice.SliceAngle,[0 0 0]) + [norm_plane(1), norm_plane(2), norm_plane(3)] =rotate_vector(XmlData.SliceAngle(ZIndex,:)*pi/180,0,0,1); + Z=Z-(norm_plane(1)*(X-XmlData.Slice.SliceCoord(ZIndex,1))+norm_plane(2)*(Y-XmlData.Slice.SliceCoord(ZIndex,2)))/norm_plane(3); +end + +% proj_plane: poject each image on a common grid given by coord_x and coord_y +function DataOut=proj_plane(DataIn,XmlData,X,Y) + +DataOut=DataIn; %default output + +%% initial image coordinates +[npy,npx]=size(DataIn.A); +xima=0.5:npx-0.5;%image coordinates of corners +yima=npy-0.5:-1:0.5; +[XIMA_init,YIMA_init]=meshgrid(xima,yima);%grid of initial image in px coordinates + +%% projected coordinates +Z=Zpos(XmlData,DataIn.ZIndex,X,Y);% Z positions correspoonding to X,Y positions + +%% interpolation on the new grid +[XIMA,YIMA]=px_XYZ(XmlData.GeometryCalib,XmlData.Slice,X,Y,Z);% image coordinates for each point in the real +DataOut.A=interp2(XIMA_init,YIMA_init,DataIn.A,XIMA,YIMA); + + + + + +%'merge_field': concatene fields +%------------------------------------------------------------------------ +function [MergeData,errormsg]=merge_field(Data) +%% default output +if isempty(Data)||~iscell(Data) + MergeData=[]; + return +end +errormsg=''; +MergeData=Data{1};% merged field= first field by default, reproduces the global attributes of the first field +NbView=length(Data); +if NbView==1% if there is only one field, just reproduce it in MergeData + return +end + +%% group the variables (fields of 'Data') in cells of variables with the same dimensions +[CellInfo,NbDim,errormsg]=find_field_cells(Data{1}); +if ~isempty(errormsg) + return +end + +%LOOP ON GROUPS OF VARIABLES SHARING THE SAME DIMENSIONS +for icell=1:length(CellInfo) + if NbDim(icell)~=1 % skip field cells which are of dim 1 + switch CellInfo{icell}.CoordType + case 'scattered' %case of input fields with unstructured coordinates: just concatene data + for ivar=CellInfo{icell}.VarIndex % indices of the selected variables in the list FieldData.ListVarName + VarName=Data{1}.ListVarName{ivar}; + for iview=2:NbView + MergeData.(VarName)=[MergeData.(VarName); Data{iview}.(VarName)]; + end + end + case 'grid' %case of fields defined on a structured grid + FFName=''; + if isfield(CellInfo{icell},'VarIndex_errorflag') && ~isempty(CellInfo{icell}.VarIndex_errorflag) + FFName=Data{1}.ListVarName{CellInfo{icell}.VarIndex_errorflag};% name of errorflag variable + MergeData.ListVarName(CellInfo{icell}.VarIndex_errorflag)=[];%remove error flag variable in MergeData (will use NaN instead) + MergeData.VarDimName(CellInfo{icell}.VarIndex_errorflag)=[]; + MergeData.VarAttribute(CellInfo{icell}.VarIndex_errorflag)=[]; + end + % select good data on each view + for ivar=CellInfo{icell}.VarIndex % indices of the selected variables in the list FieldData.ListVarName + VarName=Data{1}.ListVarName{ivar}; + for iview=1:NbView + if isempty(FFName) + check_bad=isnan(Data{iview}.(VarName));%=0 for NaN data values, 1 else + else + check_bad=isnan(Data{iview}.(VarName)) | Data{iview}.(FFName)~=0;%=0 for NaN or error flagged data values, 1 else + end + Data{iview}.(VarName)(check_bad)=0; %set to zero NaN or data marked by error flag + if iview==1 + %MergeData.(VarName)=Data{1}.(VarName);% initiate MergeData with the first field + MergeData.(VarName)(check_bad)=0; %set to zero NaN or data marked by error flag + NbAver=~check_bad;% initiate NbAver: the nbre of good data for each point + elseif size(Data{iview}.(VarName))~=size(MergeData.(VarName)) + errormsg='sizes of the input matrices do not agree, need to interpolate on a common grid using a projection object'; + return + else + MergeData.(VarName)=MergeData.(VarName) +double(Data{iview}.(VarName));%add data + NbAver=NbAver + ~check_bad;% add 1 for good data, 0 else + end + end + MergeData.(VarName)(NbAver~=0)=MergeData.(VarName)(NbAver~=0)./NbAver(NbAver~=0);% take average of defined data at each point + MergeData.(VarName)(NbAver==0)=NaN;% set to NaN the points with no good data + end + end + end +end Index: trunk/src/set_object.m =================================================================== --- trunk/src/set_object.m (revision 1120) +++ trunk/src/set_object.m (revision 1121) @@ -363,6 +363,6 @@ set(handles.num_RangeY_1,'Visible','on') set(handles.num_RangeY_2,'Visible','on') - set(handles.XObject,'TooltipString',['XObject: x coordinate of the axis origin for the ' ObjectStyle]) - set(handles.YObject,'TooltipString',['YObject: y coordinate of the axis origin for the ' ObjectStyle]) +% set(handles.XObject,'TooltipString',['XObject: x coordinate of the axis origin for the ' ObjectStyle]) +% set(handles.YObject,'TooltipString',['YObject: y coordinate of the axis origin for the ' ObjectStyle]) set(handles.num_Angle_1,'Visible','on') set(handles.num_Angle_2,'Visible','on') Index: trunk/src/uvmat.m =================================================================== --- trunk/src/uvmat.m (revision 1120) +++ trunk/src/uvmat.m (revision 1121) @@ -1313,11 +1313,11 @@ % raw 6 of the GUI uicontrol('Style','edit','Units','normalized', 'Position', [3*ii+2*ww 0.95-5*ii-4.2*hh ww hh],'tag','num_SliceAngle_1_1','BackgroundColor',[1 1 1],... - 'String',num2str(SliceAngle(1,1)),'FontUnits','points','FontSize',12,'FontWeight','bold','TooltipString','''num_SliceAngle_1_1'':first slice angle of inclination around the x axis');%edit box + 'String',num2str(SliceAngle(1,1)),'FontUnits','points','FontSize',12,'FontWeight','bold','TooltipString','''num_SliceAngle_1_1'':first slice angle of inclination (in degrees) around the x axis');%edit box uicontrol('Style','edit','Units','normalized', 'Position', [4*ii+3*ww 0.95-5*ii-4.2*hh ww hh],'tag','num_SliceAngle_1_2','BackgroundColor',[1 1 1],... - 'String',num2str(SliceAngle(end,1)),'FontUnits','points','FontSize',12,'FontWeight','bold','TooltipString','''num_SliceAngle_1_2'':last slice angle of inclination around the x axis');%edit box + 'String',num2str(SliceAngle(end,1)),'FontUnits','points','FontSize',12,'FontWeight','bold','TooltipString','''num_SliceAngle_1_2'':last slice angle of inclination (in degrees) around the x axis');%edit box uicontrol('Style','edit','Units','normalized', 'Position', [3*ii+2*ww 0.95-6*ii-5.2*hh ww hh],'tag','num_SliceAngle_2_1','BackgroundColor',[1 1 1],... - 'String',num2str(SliceAngle(1,2)),'FontUnits','points','FontSize',12,'FontWeight','bold','TooltipString','''num_SliceAngle_2_1'':first slice angle of inclination around the y axis');%edit box + 'String',num2str(SliceAngle(1,2)),'FontUnits','points','FontSize',12,'FontWeight','bold','TooltipString','''num_SliceAngle_2_1'':first slice angle of inclination (in degrees) around the y axis');%edit box uicontrol('Style','edit','Units','normalized', 'Position', [4*ii+3*ww 0.95-6*ii-5.2*hh ww hh],'tag','num_SliceAngle_2_2','BackgroundColor',[1 1 1],... - 'String',num2str(SliceAngle(end,2)),'FontUnits','points','FontSize',12,'FontWeight','bold','TooltipString','''num_SliceAngle_2_2'':last slice angle of inclination around the y axis');%edit box + 'String',num2str(SliceAngle(end,2)),'FontUnits','points','FontSize',12,'FontWeight','bold','TooltipString','''num_SliceAngle_2_2'':last slice angle of inclination (in degrees) around the y axis');%edit box % raw 7 of the GUI: pushbuttons