Index: /trunk/src/calc_field_interp.m =================================================================== --- /trunk/src/calc_field_interp.m (revision 1001) +++ /trunk/src/calc_field_interp.m (revision 1002) @@ -82,5 +82,5 @@ Data.strain=Data.DjUi(:,1,2)+Data.DjUi(:,2,1); end - InputVarList=[InputVarList UName{ilist}]; %the variable is added to the list if it is not already in the list + InputVarList=[InputVarList UName{ilist}]; %the variable is added to the list if iTriScatteredInterpt is not already in the list else % case 'norm' for instance UName{ilist}=r.UName; Index: /trunk/src/proj_field.m =================================================================== --- /trunk/src/proj_field.m (revision 1001) +++ /trunk/src/proj_field.m (revision 1002) @@ -730,14 +730,14 @@ if strcmp(ProjData.VarAttribute{nbvar+ivar}.Role,'vector_x'); ivar_U=nbvar+ivar; - elseif strcmp(ProjData.VarAttribute{nbvar+ivar}.Role,'vector_y'); + elseif strcmp(ProjData.VarAttribute{nbvar+ivar}.Role,'vector_y');TriScatteredInterp ivar_V=nbvar+ivar; end end - ProjData.VarAttribute{ivar+nbvar}.Role='discrete';% will promote plots of the profiles with continuous lines + ProjData.VarAttribute{ivar+nbvar}.Role='discrete';% will promote plots of the profiles with continuoval(['us lines end elseif isequal(ProjMode,'interp_lin') %filtering %linear interpolation: if ~check_abscissa XName=FieldData.ListVarName{CellInfo{icell}.CoordIndex(end)}; - ProjData.ListVarName=[ProjData.ListVarName {XName}]; + ProjData.ListVarName=[ProjData.ListVarName {XName}];TriScatteredInterp ProjData.VarDimName=[ProjData.VarDimName {XName}]; nbvar=numel(ProjData.ListVarName); @@ -811,13 +811,54 @@ end% test_interp2=0;%default - AYName=FieldData.ListVarName{CellInfo{icell}.CoordIndex(end-1)}; - AXName=FieldData.ListVarName{CellInfo{icell}.CoordIndex(end)}; - AX=FieldData.(AXName);% set of x positions - AY=FieldData.(AYName);% set of y positions - AName=FieldData.ListVarName{VarIndex(1)}; - npxy=size(FieldData.(AName)); + if max(NbDim)==3 % 3D case + AZName=FieldData.ListVarName{CellInfo{icell}.CoordIndex(end)}; + AYName=FieldData.ListVarName{CellInfo{icell}.CoordIndex(end-1)}; + AXName=FieldData.ListVarName{CellInfo{icell}.CoordIndex(end-2)}; + AX=FieldData.(AXName);% set of x positions + AY=FieldData.(AYName);% set of y positions + AZ=FieldData.(AZName);% set of z positions + AName=FieldData.ListVarName{VarIndex(1)}; + npxy=size(FieldData.(AName)); + npz=npxy(1); + npy=npxy(2); + npx=npxy(1); + 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 + AZI=linspace(AZ(1),AZ(end), npy);%set of x positions for the interpolated input data + for ivar=VarIndex + VarName=FieldData.ListVarName{ivar}; + FieldData.(VarName)=interp3(FieldData.(AXName),FieldData.(AYName),FieldData.(AZName),FieldData.(VarName),AXI,AYI,AZI); + +% vec_A=reshape(squeeze(FieldData.(FieldData.ListVarName{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); +% ProjData.(FieldData.ListVarName{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); +% ProjData.(FieldData.ListVarName{ivar})=squeeze(sum(A_out,1)/npY); +% end + ProjData.ListVarName=[ProjData.ListVarName FieldData.ListVarName{ivar}]; + ProjData.VarDimName=[ProjData.VarDimName {AXName}];%to generalize with the initial name of the x coordinate + ProjData.VarAttribute{ivar}.Role='continuous';% for plot with continuous line + end + + + + else + AYName=FieldData.ListVarName{CellInfo{icell}.CoordIndex(end-1)}; + AXName=FieldData.ListVarName{CellInfo{icell}.CoordIndex(end)}; + AX=FieldData.(AXName);% set of x positions + AY=FieldData.(AYName);% set of y positions + AName=FieldData.ListVarName{VarIndex(1)}; + npxy=size(FieldData.(AName)); npx=npxy(2); npy=npxy(1); @@ -860,9 +901,9 @@ XMin=0; end - eval(['ProjData.' AXName '=linspace(XMin,XMin+linelength,linelength/DXY_line+1);'])%abscissa of the new pixels along the line + 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 ');']) + npX=length(ProjData.(AXName)); npY=length(y); %TODO: utiliser proj_grid - eval(['[X,Y]=meshgrid(ProjData.' AXName ',y);'])%grid in the line coordinates + [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); @@ -876,5 +917,4 @@ 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; @@ -886,5 +926,4 @@ return end - nbvar=length(ProjData.ListVarName);% number of var from previous cells ProjData.ListVarName=[ProjData.ListVarName {AXName}]; ProjData.VarDimName=[ProjData.VarDimName {AXName}]; @@ -916,6 +955,6 @@ end end - -end + + end if ~isempty(ivar_U) && ~isempty(ivar_V) vector_x =ProjData.(ProjData.ListVarName{ivar_U}); Index: /trunk/src/read_field.m =================================================================== --- /trunk/src/read_field.m (revision 1001) +++ /trunk/src/read_field.m (revision 1002) @@ -175,15 +175,17 @@ if CheckStructured for ilist=NbCoord+1:numel(Field.VarDimName) - rank(1)=find(strcmp(ParamIn.Coord_x,Field.VarDimName{ilist})); - rank(2)=find(strcmp(ParamIn.Coord_y,Field.VarDimName{ilist})); - if NbCoord==3 - rank(3)=find(strcmp(ParamIn.Coord_z,Field.VarDimName{ilist})); - end - rank=flip(rank); - VarName=Field.ListVarName{ilist}; - Field.(VarName)=permute(Field.(VarName),rank); - Field.VarDimName{ilist}=Field.VarDimName{ilist}(rank);% permute the order of dimensions - end - end + if numel(Field.VarDimName{ilist})==NbCoord + rank(1)=find(strcmp(ParamIn.Coord_x,Field.VarDimName{ilist})); + rank(2)=find(strcmp(ParamIn.Coord_y,Field.VarDimName{ilist})); + if NbCoord==3 + rank(3)=find(strcmp(ParamIn.Coord_z,Field.VarDimName{ilist})); + end + rank=rank(end:-1:1); + VarName=Field.ListVarName{ilist}; + Field.(VarName)=permute(Field.(VarName),rank); + Field.VarDimName{ilist}=Field.VarDimName{ilist}(rank);% permute the order of dimensions + end + end + end NormName=''; UName=''; Index: /trunk/src/series/extract_multitif.m =================================================================== --- /trunk/src/series/extract_multitif.m (revision 1001) +++ /trunk/src/series/extract_multitif.m (revision 1002) @@ -59,5 +59,5 @@ %======================================================================= -function ParamOut=extract_multitif(Param) +function ParamOut=extract_multitif_parallel(Param) %%%%%%%%%%%%%%%%% INPUT PREPARATION MODE (no RUN) %%%%%%%%%%%%%%%%% @@ -65,5 +65,5 @@ ParamOut.AllowInputSort='off';% allow alphabetic sorting of the list of input file SubDir (options 'off'/'on', 'off' by default) ParamOut.WholeIndexRange='on';% prescribes the file index ranges from min to max (options 'off'/'on', 'off' by default) - ParamOut.NbSlice=1; % impose calculation in a single process (no parallel processing to avoid 'holes')) + ParamOut.NbSlice='off'; % impose calculation in a single process (no parallel processing to avoid 'holes')) ParamOut.VelType='off';% 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) @@ -73,5 +73,5 @@ ParamOut.OutputDirExt='.png';%set the output dir extension ParamOut.OutputFileMode='NbSlice';% '=NbInput': 1 output file per input file index, '=NbInput_i': 1 file per input file index i, '=NbSlice': 1 file per slice - ParamOut.CheckOverwriteVisible='on'; % manage the overwrite of existing files (default=1) + ParamOut.CheckOverwriteVisible='on'; % manage the overwrite of existing files (default=1) %% root input file(s) and type % check the existence of the first file in the series @@ -95,8 +95,5 @@ return end - xmlinput=uigetfile_uvmat('pick xml file for timing',fileparts(fileparts(FirstFileName)),'.xml'); - [tild,ParamOut.ActionInput.XmlFile]=fileparts(xmlinput); - ParamOut.ActionInput.XmlFile - + ParamOut.ActionInput.XmlFile=uigetfile_uvmat('pick xml file for timing',fileparts(fileparts(FirstFileName)),'.xml'); return end @@ -111,54 +108,79 @@ 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 + 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 %% list of input images -DirImages=fullfile(Param.InputTable{1,1},Param.InputTable{1,2}); -ListStruct=dir(DirImages); -ListCells=struct2cell(ListStruct);% transform dir struct to a cell arrray -check_bad=strcmp('.',ListCells(1,:))|strcmp('..',ListCells(1,:));%detect the dir '.' to exclude it -check_dir=cell2mat(ListCells(4,:));% =1 for directories, =0 for files -ListFile=ListCells(1,find(~check_dir & ~check_bad)); +% DirImages=fullfile(Param.InputTable{1,1},Param.InputTable{1,2}); +% ListStruct=dir(DirImages); +% ListCells=struct2cell(ListStruct);% transform dir struct to a cell arrray +% check_bad=strcmp('.',ListCells(1,:))|strcmp('..',ListCells(1,:));%detect the dir '.' to exclude it +% check_dir=cell2mat(ListCells(4,:));% =1 for directories, =0 for files +% ListFile=ListCells(1,find(~check_dir & ~check_bad)); %% check file names -RootName=regexprep(ListFile{1},'.tif$','') -for ilist=2:numel(ListFile) - rank=regexprep(ListFile{ilist},'.tif$',''); - rank=regexprep(rank,['^' RootName '@'],''); - if ~isequal(str2num(rank),ilist-1) - disp(['error in the list of input file # ' num2str(ilist-1)]) - return - end -end +% RootName=regexprep(ListFile{1},'.tif$','') +% rank(1)=1; +% for ilist=2:numel(ListFile) +% rank_str=regexprep(ListFile{ilist},'.tif$',''); +% rank(ilist)=regexprep(rank_str,['^' RootName '@'],''); +% % if ~isequal(str2num(rank),ilist-1) +% % disp(['error in the list of input file # ' num2str(ilist-1)]) +% % return +% % end +% end %% output directory - OutputDir=fullfile(Param.InputTable{1,1},[Param.OutputSubDir Param.OutputDirExt]); - -%% Timing -XmlInputFile=fullfile(Param.InputTable{1,1},[Param.ActionInput.XmlFile '.xml']) -XmlInput=imadoc2struct(XmlInputFile,'Camera'); +OutputDir=fullfile(Param.InputTable{1,1},[Param.OutputSubDir Param.OutputDirExt]); + +%% Timing +XmlInputFile=Param.ActionInput.XmlFile; +[XmlInput,errormsg]=imadoc2struct(XmlInputFile,'Camera'); +if ~isempty(errormsg) + disp(['bad xml input file: ' errormsg]) + return +end +ImagesPerLevel=size(XmlInput.Time,2)-1;%100;%use the xmlinformation to get the nbre of j indices + +%% create the xml file of PCO camera if it does not exist +Newxml=fullfile(Param.InputTable{1,1},[Param.InputTable{1,2} '.xml']); +if ~exist(Newxml,'file') +XmlInput.Camera.CameraName='PCO'; +XmlInput=rmfield(XmlInput,'Time'); +XmlInput=rmfield(XmlInput,'TimeUnit'); +t=struct2xml(XmlInput); +t=set(t,1,'name','ImaDoc'); +save(t,Newxml); +end %% Main loop -ImagesPerLevel=size(XmlInput.Time,2)-1;%100; -count=0; + +% count=0; %count=316;%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%CORRECTION EXP08: 4684 images -> start at 316 start 67->_11_1 %count=1934%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%CORRECTION EXP07: 3066 images -%% loop on the files -for ifile=1:numel(ListFile) - update_waitbar(WaitbarHandle,ifile/numel(ListFile)) - if ~isempty(RUNHandle)&& ~strcmp(get(RUNHandle,'BusyAction'),'queue') - disp('program stopped by user') - break - end - ImageName=fullfile(DirImages,ListFile{ifile}); +%% loop on the files +% include the first tiff file with no index in the first iteration +if Param.IndexRange.first_i==1% first slice of processing + firstindex=0; + count=0; +else + firstindex=Param.IndexRange.first_i; + ImageName=fullfile(Param.InputTable{1,1},Param.InputTable{1,2},'im.tif'); NbFrames=numel(imfinfo(ImageName)); - % loop on the frames within the tiff file - for iframe=1:NbFrames + count=Param.IndexRange.first_i*NbFrames; +end +for ifile=firstindex:Param.IndexRange.last_i + if firstindex==0 && ifile==0% first slice of processing + ImageName=fullfile(Param.InputTable{1,1},Param.InputTable{1,2},'im.tif') + else + ImageName=fullfile(Param.InputTable{1,1},Param.InputTable{1,2},['im@' num2str(ifile,'%04d') '.tif']) + end + NbFrames=numel(imfinfo(ImageName)); + for iframe=1:NbFrames + iframe if isequal(ImagesPerLevel,1)% mode series - i_index=count+1; OutputFile=fullfile(OutputDir,['img_' num2str(count+1) '.png']); else % indices i and j @@ -178,39 +200,4 @@ end -% for ifile=1:numel(ListFile) -% update_waitbar(WaitbarHandle,ifile/numel(ListFile)) -% if ~isempty(RUNHandle)&& ~strcmp(get(RUNHandle,'BusyAction'),'queue') -% disp('program stopped by user') -% break -% end -% ImageName=fullfile(DirImages,ListFile{ifile}); -% NbFrames=numel(imfinfo(ImageName)); -% % loop on the frames within the tiff file -% for iframe=1:NbFrames -% A=imread(ImageName,iframe); -% -% if isequal(ImagesPerLevel,1)% mode series -% i_index=count+1; -% OutputFile=fullfile(OutputDir,['img_' num2str(count+1) '.png']); -% else % indices i and j -% i_index=fix(count/ImagesPerLevel)+1; -% j_index=mod(count,ImagesPerLevel)+1; -% OutputFile=fullfile(OutputDir,['img_' num2str(i_index) '_' num2str(j_index) '.png']); -% end -% imwrite(A,OutputFile,'BitDepth',16) -% count=count+1; -% end -% end - -%% create the xml file of PCO camera -XmlInput.Camera.CameraName='PCO'; -t=struct2xml(XmlInput.Camera); -t=set(t,1,'name','ImaDoc'); -save(t,fullfile(Param.InputTable{1,1},'PCO.xml')) - -%% remove initial files if transfer OK -% if i_index== (size(XmlInput.Time,1)-1) -% -% [SUCCESS,MESSAGE]=rmdir(DirImages,'s') -% -% end + + Index: unk/src/series/extract_multitif_parallel.m =================================================================== --- /trunk/src/series/extract_multitif_parallel.m (revision 1001) +++ (revision ) @@ -1,203 +1,0 @@ -%'ima2netcdf': read image series and transform to netcdf -%------------------------------------------------------------------------ - - -% function ParamOut=ima2netcdf(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 2008-2017, 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=extract_multitif_parallel(Param) - -%%%%%%%%%%%%%%%%% INPUT PREPARATION MODE (no RUN) %%%%%%%%%%%%%%%%% -if isstruct(Param) && isequal(Param.Action.RUN,0) - ParamOut.AllowInputSort='off';% allow alphabetic sorting of the list of input file SubDir (options 'off'/'on', 'off' by default) - ParamOut.WholeIndexRange='on';% prescribes the file index ranges from min to max (options 'off'/'on', 'off' by default) - ParamOut.NbSlice='off'; % impose calculation in a single process (no parallel processing to avoid 'holes')) - ParamOut.VelType='off';% 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 = 'off';%can use a transform function - ParamOut.ProjObject='off';%can use projection object(option 'off'/'on', - ParamOut.Mask='off';%can use mask option (option 'off'/'on', 'off' by default) - ParamOut.OutputDirExt='.png';%set the output dir extension - ParamOut.OutputFileMode='NbSlice';% '=NbInput': 1 output file per input file index, '=NbInput_i': 1 file per input file index i, '=NbSlice': 1 file per slice - ParamOut.CheckOverwriteVisible='on'; % manage the overwrite of existing files (default=1) - %% root input file(s) and type - % check the existence of the first file in the series - first_j=[];% note that the function will propose to cover the whole range of indices - if isfield(Param.IndexRange,'MinIndex_j'); first_j=Param.IndexRange.MinIndex_j; end - last_j=[]; - if isfield(Param.IndexRange,'MaxIndex_j'); last_j=Param.IndexRange.MaxIndex_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 - - %% check the validity of input file types - FileInfo=get_file_info(FirstFileName); - if ~strcmp(FileInfo.FileType,'multimage') - msgbox_uvmat('ERROR',['invalid file type input: ' FileInfo.FileType ' not an image']) - return - end - ParamOut.ActionInput.XmlFile=uigetfile_uvmat('pick xml file for timing',fileparts(fileparts(FirstFileName)),'.xml'); - return -end -%%%%%%%%%%%%%%%%% STOP HERE FOR PAMETER INPUT MODE %%%%%%%%%%%%%%%%% - -%% read input parameters from an xml file if input is a file name (batch mode) -checkrun=1; -RUNHandle=[]; -WaitbarHandle=[]; -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 - -%% list of input images -% DirImages=fullfile(Param.InputTable{1,1},Param.InputTable{1,2}); -% ListStruct=dir(DirImages); -% ListCells=struct2cell(ListStruct);% transform dir struct to a cell arrray -% check_bad=strcmp('.',ListCells(1,:))|strcmp('..',ListCells(1,:));%detect the dir '.' to exclude it -% check_dir=cell2mat(ListCells(4,:));% =1 for directories, =0 for files -% ListFile=ListCells(1,find(~check_dir & ~check_bad)); - -%% check file names -% RootName=regexprep(ListFile{1},'.tif$','') -% rank(1)=1; -% for ilist=2:numel(ListFile) -% rank_str=regexprep(ListFile{ilist},'.tif$',''); -% rank(ilist)=regexprep(rank_str,['^' RootName '@'],''); -% % if ~isequal(str2num(rank),ilist-1) -% % disp(['error in the list of input file # ' num2str(ilist-1)]) -% % return -% % end -% end - -%% output directory -OutputDir=fullfile(Param.InputTable{1,1},[Param.OutputSubDir Param.OutputDirExt]); - -%% Timing -XmlInputFile=Param.ActionInput.XmlFile; -[XmlInput,errormsg]=imadoc2struct(XmlInputFile,'Camera'); -if ~isempty(errormsg) - disp(['bad xml input file: ' errormsg]) - return -end -ImagesPerLevel=size(XmlInput.Time,2)-1;%100;%use the xmlinformation to get the nbre of j indices - -%% create the xml file of PCO camera if it does not exist -Newxml=fullfile(Param.InputTable{1,1},[Param.InputTable{1,2} '.xml']); -if ~exist(Newxml,'file') -XmlInput.Camera.CameraName='PCO'; -XmlInput=rmfield(XmlInput,'Time'); -XmlInput=rmfield(XmlInput,'TimeUnit'); -t=struct2xml(XmlInput); -t=set(t,1,'name','ImaDoc'); -save(t,Newxml); -end - -%% Main loop - - -% count=0; -%count=316;%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%CORRECTION EXP08: 4684 images -> start at 316 start 67->_11_1 -%count=1934%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%CORRECTION EXP07: 3066 images -%% loop on the files -% include the first tiff file with no index in the first iteration -if Param.IndexRange.first_i==1% first slice of processing - firstindex=0; - count=0; -else - firstindex=Param.IndexRange.first_i; - ImageName=fullfile(Param.InputTable{1,1},Param.InputTable{1,2},'im.tif'); - NbFrames=numel(imfinfo(ImageName)); - count=Param.IndexRange.first_i*NbFrames; -end -for ifile=firstindex:Param.IndexRange.last_i - if firstindex==0 && ifile==0% first slice of processing - ImageName=fullfile(Param.InputTable{1,1},Param.InputTable{1,2},'im.tif') - else - ImageName=fullfile(Param.InputTable{1,1},Param.InputTable{1,2},['im@' num2str(ifile,'%04d') '.tif']) - end - NbFrames=numel(imfinfo(ImageName)); - for iframe=1:NbFrames - iframe - if isequal(ImagesPerLevel,1)% mode series - OutputFile=fullfile(OutputDir,['img_' num2str(count+1) '.png']); - else % indices i and j - i_index=fix(count/ImagesPerLevel)+1; - j_index=mod(count,ImagesPerLevel)+1; - OutputFile=fullfile(OutputDir,['img_' num2str(i_index) '_' num2str(j_index) '.png']); - end - if Param.CheckOverwrite ||~exist(OutputFile,'file') - A=imread(ImageName,iframe); - imwrite(A,OutputFile,'BitDepth',16); - disp([OutputFile ' written']) - else - disp([OutputFile ' already exists']) - end - count=count+1; - end -end - - - Index: /trunk/src/series/turb_correlation_time.m =================================================================== --- /trunk/src/series/turb_correlation_time.m (revision 1001) +++ /trunk/src/series/turb_correlation_time.m (revision 1002) @@ -57,5 +57,5 @@ %======================================================================= -function ParamOut=turb_stat(Param) +function ParamOut=turb_correlation_time(Param) %% set the input elements needed on the GUI series when the action is selected in the menu ActionName @@ -63,5 +63,5 @@ ParamOut.AllowInputSort='off';% 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.NbSlice=1; %nbre of slices ('off' by default) ParamOut.VelType='off';% menu for selecting the velocity type (options 'off'/'one'/'two', 'off' by default) ParamOut.FieldName='one';% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default) @@ -277,26 +277,26 @@ FFCorr=false(NpTime+1,npy,npx); end + Field.U=Field.U-UMean; + Field.V=Field.V-VMean; FF=isnan(Field.U);%|Field.U<-60|Field.U>30;% threshold on U Field.U(FF)=0;% set to 0 the nan values,'delta_x' Field.V(FF)=0; - Field.U=Field.U-UMean; - Field.V=Field.V-VMean; if index<=NpTime+1 - U_shift(index,:,:)=Field.U; - V_shift(index,:,:)=Field.V; - FF_shift(index,:,:)=FF; + U_shift(NpTime+2-index,:,:)=Field.U; + V_shift(NpTime+2-index,:,:)=Field.V; + FF_shift(NpTime+2-index,:,:)=FF; else - U_shift=circshift(U_shift,[-1 0 0]); %shift U by ishift along the first index - V_shift=circshift(V_shift,[-1 0 0]); %shift U by ishift along the first index - FF_shift=circshift(FF_shift,[-1 0 0]); %shift U by ishift along the first index - U_shift(NpTime+1,:,:)=Field.U; - V_shift(NpTime+1,:,:)=Field.V; - FF_shift(NpTime+1,:,:)=FF; - end - for ishift=1:NpTime% calculate the field U shifted - UUCorr(ishift,:,:)=Field.U.*U_shift(ishift,:,:); - VVCorr(ishift,:,:)=Field.V.*V_shift(ishift,:,:); - UVCorr(ishift,:,:)=Field.U.*V_shift(ishift,:,:); - FFCorr(ishift,:,:)=FF | FF_shift; + U_shift=circshift(U_shift,[1 0 0]); %shift U by ishift along the first index + V_shift=circshift(V_shift,[1 0 0]); %shift U by ishift along the first index + FF_shift=circshift(FF_shift,[1 0 0]); %shift U by ishift along the first index + U_shift(1,:,:)=Field.U; + V_shift(1,:,:)=Field.V; + FF_shift(1,:,:)=FF; + end + for ishift=1:NpTime+1% calculate the field U shifted + UUCorr(ishift,:,:)=Field.U.*squeeze(U_shift(ishift,:,:)); + VVCorr(ishift,:,:)=Field.V.*squeeze(V_shift(ishift,:,:)); + UVCorr(ishift,:,:)=Field.U.*squeeze(V_shift(ishift,:,:)); + FFCorr(ishift,:,:)=FF | squeeze(FF_shift(ishift,:,:)); end DataOut.UUCorr=DataOut.UUCorr+UUCorr; @@ -306,8 +306,9 @@ end %%%%%%%%%%%%%%%% end loop on field indices %%%%%%%%%%%%%%%% -% DataOut.UUCorr=DataOut.UUCorr./DataOut.Counter; -% DataOut.VVCorr=DataOut.VVCorr./DataOut.Counter; -% DataOut.VUVCorr=DataOut.UVCorr./DataOut.Counter; -%DataOut.Counter(DataOut.Counter==0)=1;% put counter to 1 when it is zero +DataOut.Counter(DataOut.Counter==0)=1;% put counter to 1 when it is zero (to avoid NaN) +DataOut.UUCorr=DataOut.UUCorr./DataOut.Counter; +DataOut.VVCorr=DataOut.VVCorr./DataOut.Counter; +DataOut.UVCorr=DataOut.UVCorr./DataOut.Counter; + % DataOut.UMean=DataOut.UMean./DataOut.Counter; % normalize the mean % DataOut.VMean=DataOut.VMean./DataOut.Counter; % normalize the mean Index: /trunk/src/series/turb_correlation_x.m =================================================================== --- /trunk/src/series/turb_correlation_x.m (revision 1001) +++ /trunk/src/series/turb_correlation_x.m (revision 1002) @@ -57,5 +57,5 @@ %======================================================================= -function ParamOut=turb_stat(Param) +function ParamOut=turb_correlation_x(Param) %% set the input elements needed on the GUI series when the action is selected in the menu ActionName @@ -290,5 +290,5 @@ DataOut.UUCorr=DataOut.UUCorr./DataOut.Counter; DataOut.VVCorr=DataOut.VVCorr./DataOut.Counter; -DataOut.VUVCorr=DataOut.UVCorr./DataOut.Counter; +DataOut.UVCorr=DataOut.UVCorr./DataOut.Counter; %DataOut.Counter(DataOut.Counter==0)=1;% put counter to 1 when it is zero % DataOut.UMean=DataOut.UMean./DataOut.Counter; % normalize the mean Index: /trunk/src/uvmat.m =================================================================== --- /trunk/src/uvmat.m (revision 1001) +++ /trunk/src/uvmat.m (revision 1002) @@ -977,6 +977,11 @@ data.RangeX=UvData.Field.XMin ; data.RangeY=UvData.Field.CoordMesh; - data.Coord=[UvData.Field.XMin (UvData.Field.YMin +UvData.Field.YMax)/2;... - UvData.Field.XMax (UvData.Field.YMin +UvData.Field.YMax)/2];% put line at the middle of the y axis + if isfield(UvData.Field,'ZMin') && isfield(UvData.Field,'ZMax') + Coord_z=(UvData.Field.ZMin +UvData.Field.ZMax)/2; + else + Coord_z=0; + end + data.Coord=[UvData.Field.XMin (UvData.Field.YMin +UvData.Field.YMax)/2 Coord_z;... + UvData.Field.XMax (UvData.Field.YMin +UvData.Field.YMax)/2 Coord_z];% put line at the middle of the y axis case 'line_y' check_plot=1; %plot the line directly when set_object is opened @@ -984,6 +989,11 @@ data.RangeX=UvData.Field.YMin ; data.RangeY=UvData.Field.CoordMesh; - data.Coord=[(UvData.Field.XMin+UvData.Field.XMax)/2 UvData.Field.YMin;... - (UvData.Field.XMin +UvData.Field.XMax)/2 UvData.Field.YMax];% put line at the middle of the y axis + if isfield(UvData.Field,'ZMin') && isfield(UvData.Field,'ZMax') + Coord_z=(UvData.Field.ZMin +UvData.Field.ZMax)/2; + else + Coord_z=0; + end + data.Coord=[(UvData.Field.XMin+UvData.Field.XMax)/2 UvData.Field.YMin Coord_z;... + (UvData.Field.XMin +UvData.Field.XMax)/2 UvData.Field.YMax Coord_z];% put line at the middle of the y axis case {'rectangle','ellipse'} data.RangeY=[UvData.Field.YMin UvData.Field.YMax];