Index: /trunk/src/civ.m =================================================================== --- /trunk/src/civ.m (revision 1168) +++ /trunk/src/civ.m (revision 1169) @@ -44,10 +44,4 @@ %% prepare measurement grid if not given as input if ~isfield(par_civ,'Grid')% grid points defining central positions of the sub-images in image A -% if ischar(par_civ.Grid)%read the grid file if the input is a file name (grid in x, y image coordinates) -% par_civ.Grid=dlmread(par_civ.Grid); -% par_civ.Grid(1,:)=[];%the first line must be removed (heading in the grid file) -% end -% % else par_civ.Grid is already an array, no action here -% else% automatic grid in x, y image coordinates nbinterv_x=floor((npx_ima-1)/par_civ.Dx); gridlength_x=nbinterv_x*par_civ.Dx; @@ -114,6 +108,4 @@ checkmask=0; MinA=min(min(par_civ.ImageA)); -%MinB=min(min(par_civ.ImageB)); -%check_undefined=false(size(par_civ.ImageA)); if isfield(par_civ,'Mask') && ~isempty(par_civ.Mask) checkmask=1; @@ -126,5 +118,4 @@ %% compute image correlations: MAINLOOP on velocity vectors -corrmax=0; sum_square=1;% default mesh=1;% default @@ -134,5 +125,5 @@ par_civ.CorrSmooth=2;% use SUBPIX2DGAUSS (take into account more points near the max) end - + if par_civ.CorrSmooth~=0 % par_civ.CorrSmooth=0 implies no civ computation (just input image and grid points given) for ivec=1:nbvec @@ -141,7 +132,7 @@ FF(ivec)=0; ibx2=floor(CorrBoxSizeX(ivec)/2); -iby2=floor(CorrBoxSizeY(ivec)/2); -isx2=ibx2+ceil(par_civ.SearchRange(1)); -isy2=iby2+ceil(par_civ.SearchRange(2)); + iby2=floor(CorrBoxSizeY(ivec)/2); + isx2=ibx2+ceil(par_civ.SearchRange(1)); + isy2=iby2+ceil(par_civ.SearchRange(2)); subrange1_x=iref-ibx2:iref+ibx2;% x indices defining the first subimage subrange1_y=jref-iby2:jref+iby2;% y indices defining the first subimage @@ -216,5 +207,5 @@ %%%%%%%%%%%%%%%%%%%%%%%%%%%%%% corrmax= max(max(result_conv)); - + %result_conv=(result_conv/corrmax); %normalize, peak=always 255 %Find the correlation max, at 255 @@ -280,9 +271,9 @@ peaky = y; peakx=x; if y < npy && y > 1 && x < npx-1 && x > 1 - FF=false; % no error by the limited search box + FF=false; % no error by the limited search box max_conv=result_conv(y,x);% max correlation %peak2noise= max(4,max_conv/std(reshape(result_conv,1,[])));% ratio of max conv to standard deviation of correlations (estiamtion of noise level), set to value 4 if it is too low peak2noise=100;% TODO: make this threshold more precise, depending on the image noise - result_conv=result_conv*peak2noise/max_conv;% renormalise the correlation with respect to the noise + result_conv=result_conv*peak2noise/max_conv;% renormalise the correlation with respect to the noise result_conv(result_conv<1)=1; %set to 1 correlation values smaller than 1 (=0 by discretisation, to avoid divergence in the log) Index: /trunk/src/mouse_motion.m =================================================================== --- /trunk/src/mouse_motion.m (revision 1168) +++ /trunk/src/mouse_motion.m (revision 1169) @@ -238,25 +238,8 @@ if test_piv [dd,ind_pt]=min(abs(Field.X-xy(1,1))+abs(Field.Y-xy(1,2))); - if isfield(hhciv,'TestCiv2') && strcmp(get(hhciv.Civ2,'Visible'),'on')&& ... - strcmp(get(hhciv.TestCiv2,'Visible'),'on')&& get(hhciv.TestCiv2,'Value')% if TestCiv2 is activated - CivOption='Civ2'; - Param.CheckCiv1=0; - par_civ=read_GUI(hhciv.Civ2);%read the Civ2 panel in civ_input - par_civ.Civ1_SubRange=Field.Civ1_SubRange;% get the subranges used for patch - par_civ.Civ1_NbCentres=Field.Civ1_NbCentres;% get the nbre of civ1 data points in each subrange - par_civ.Civ1_Coord_tps=Field.Civ1_Coord_tps;% get the positions of the centres (Civ1 data) - par_civ.Civ1_U_tps=Field.Civ1_U_tps;% get the tps coefficients for spline, U component - par_civ.Civ1_V_tps=Field.Civ1_V_tps;% get the tps coefficients for spline, V component - par_civ.Civ1_Dt=Field.Civ1_Dt; - par_civ.Civ2_Dt=Field.Civ2_Dt; - shiftx=Field.ShiftX(ind_pt);% get field info stored in the cuirrent figure - shifty=Field.ShiftY(ind_pt); - else - CivOption='Civ1'; Param.CheckCiv2=0; par_civ=read_GUI(hhciv.Civ1);%read the Civ1 panel in civ_input shiftx=par_civ.SearchBoxShift(1); shifty=par_civ.SearchBoxShift(2); - end xround=Field.X(ind_pt); yround=Field.Y(ind_pt); @@ -284,10 +267,4 @@ % perform the PIV calculation as the single point xround yround - Param.ActionInput.CheckCiv1=1; -% Param.CheckFix1=0; -% Param.CheckPatch1=0;%desactivate all calculations except Civ2 or Civ1 - Param.Action.RUN=1; - Param.ActionInput.ListCompareMode='PIV'; - Param.ActionInput.PairIndices=read_GUI(hhciv.PairIndices); par_civ.ImageA=Field.A; par_civ.ImageB=Field.B; @@ -295,13 +272,8 @@ par_civ.ImageWidth=size(par_civ.ImageA,2); par_civ.Grid=[xround yround];% PIV calculation with a single point - Param.ActionInput.(CivOption)=par_civ; - [Data,errormsg,result_conv]= civ_series(Param); + [~,~,utable,vtable,~,~,result_conv,errormsg]= civ(par_civ); if ~isempty(errormsg) text_displ_5=errormsg; else -% rangx(1)=-(isx2-ibx2)+shiftx; -% rangx(2)=isx2-ibx2+shiftx; -% rangy(1)=-(isy2-iby2)-shifty; -% rangy(2)=(isy2-iby2)-shifty; rangx(1)=-isx2+shiftx; rangx(2)=isx2+shiftx; @@ -320,5 +292,5 @@ set(0,'CurrentFigure',corrfig(1)) AxeData.CurrentCorrImage=imagesc(rangx,-rangy,result_conv,[0 1]);% plot the correlation map, with full colormap from 0 to 1 - AxeData.CurrentVector=line([0 Data.([CivOption '_U'])],[0 Data.([CivOption '_V'])],'Tag','vector'); + AxeData.CurrentVector=line([0 utable],[0 vtable],'Tag','vector'); AxeData.TitleHandle=title(['[x,y]= ' num2str(par_civ.Grid) ' px']); colorbar @@ -339,5 +311,5 @@ set(ParentAxe,'XLim',rangx) set(ParentAxe,'YLim',[-rangy(2) -rangy(1)]) - set(AxeData.CurrentVector,'XData',[0 Data.([CivOption '_U'])],'YData',[0 Data.([CivOption '_V'])]); + set(AxeData.CurrentVector,'XData',[0 utable],'YData',[0 vtable]); set(AxeData.TitleHandle,'String',['[x,y]= ' num2str(par_civ.Grid) ' px']) end Index: /trunk/src/read_civdata.m =================================================================== --- /trunk/src/read_civdata.m (revision 1168) +++ /trunk/src/read_civdata.m (revision 1169) @@ -93,5 +93,5 @@ %% reading data -[Data,tild,tild,errormsg]=nc2struct(FileName,'ListGlobalAttribute','Conventions','CivStage'); +[Data,tild,tild,errormsg]=nc2struct(FileName,'ListGlobalAttribute','Conventions','CivStage');% read the global attributes to get Data.CivStage if ~isempty(errormsg) errormsg=['read_civdata: ' errormsg]; Index: /trunk/src/series/civ_input.m =================================================================== --- /trunk/src/series/civ_input.m (revision 1168) +++ /trunk/src/series/civ_input.m (revision 1169) @@ -1532,5 +1532,5 @@ drawnow if get(handles.TestCiv1,'Value') - set(handles.TestCiv1,'BackgroundColor',[1 1 0])% paint TestCiv1 button to yellow to confirm civ launch + set(handles.TestCiv1,'BackgroundColor',[1 1 0])% paint TestCiv1 button to yellow to confirm civ launch set(handles.CheckFix1,'value',0)% desactivate next step set(handles.CheckPatch1,'value',0)% desactivate next step @@ -1539,64 +1539,89 @@ set(handles.CheckPatch2,'value',0)% desactivate next step update_CivOptions(handles,0) - hseries=findobj(allchild(0),'Tag','series'); - Param=read_GUI(hseries); - Param.Action.RUN=1; - Param.ActionInput=read_GUI(handles.civ_input); - if isfield(Param.ActionInput,'Fix1') - Param.ActionInput=rmfield(Param.ActionInput,'Fix1'); - end - if isfield(Param.ActionInput,'Patch1') - Param.ActionInput=rmfield(Param.ActionInput,'Patch1'); - end - if isfield(Param.ActionInput,'Civ2')%remove options that may be selected beyond Patch1 - Param.ActionInput=rmfield(Param.ActionInput,'Civ2'); - end - if isfield(Param.ActionInput,'Fix2') - Param.ActionInput=rmfield(Param.ActionInput,'Fix2'); - end - if isfield(Param.ActionInput,'Patch2') - Param.ActionInput=rmfield(Param.ActionInput,'Patch2'); - end - if isfield(Param,'OutputSubDir') - Param=rmfield(Param,'OutputSubDir'); %remove output file option from civ_series - end - Param.ActionInput.Civ1.CorrSmooth=0;% launch Civ1 with no data point (to get the image names for A and B) - Param.IndexRange.first_i=str2num(get(handles.ref_i,'String')); - Param.IndexRange.last_i=str2num(get(handles.ref_i,'String')); - if strcmp(get(handles.ref_j,'Visible'),'on') - Param.IndexRange.first_j=str2num(get(handles.ref_j,'String')); - Param.IndexRange.last_j=Param.IndexRange.first_j; - else - Param.IndexRange.first_j=1; - Param.IndexRange.last_j=1; - end - [Data,errormsg]=civ_series(Param);% get the civ1+fix1 results - if ~isempty(errormsg), return, end % rmq: error msg displayed in civ_series - - %% create image data ImageData for display - ImageData.ListVarName={'ny','nx','A'}; - ImageData.VarDimName= {'ny','nx',{'ny','nx'}}; - ImageData.VarAttribute{1}.Role='coord_y'; - ImageData.VarAttribute{2}.Role='coord_x'; - ImageData.VarAttribute{3}.Role='scalar'; - ImageData.A=imread(Data.Civ1_ImageA); % read the first image - if ndims(ImageData.A)==3 %case of color image - ImageData.VarDimName= {'ny','nx',{'ny','nx','rgb'}}; - end - ImageData.ny=[size(ImageData.A,1) 1]; - ImageData.nx=[1 size(ImageData.A,2)]; - ImageData.CoordUnit='pixel';% used to set equal scaling for x and y in image dispa=ly - - %% create the figure view_field for image visualization - hview_field=view_field(ImageData); %view the image in the GUI view_field - set(0,'CurrentFigure',hview_field) - hhview_field=guihandles(hview_field); - set(hview_field,'CurrentAxes',hhview_field.PlotAxes) - ViewData=get(hview_field,'UserData'); - ViewData.CivHandle=handles.civ_input;% indicate the handle of the civ GUI in view_field - ViewData.PlotAxes.X=Data.Civ1_X'; - ViewData.PlotAxes.Y=Data.Civ1_Y'; - ViewData.PlotAxes.B=imread(Data.Civ1_ImageB);%store the second image in the UserData of the GUI view_field - set(hview_field,'UserData',ViewData)% store the info in the UserData of image view_field + % get info from the GUI 'series' + hseries=findobj(allchild(0),'Tag','series'); + Param=read_GUI(hseries); + Param.Action.RUN=1; + Param.ActionInput=read_GUI(handles.civ_input); + i1=str2num(get(handles.ref_i,'String')); %references indices + i2=i1; + j1=1; + if strcmp(get(handles.ref_j,'Visible'),'on') + j1=str2num(get(handles.ref_j,'String')); + end + j2=j1; + str_civ=Param.ActionInput.PairIndices.ListPairCiv1; + r=regexp(str_civ,'^\D(?[i|j])=( -| )(?\d+)\|(?\d+)','names'); + if ~isempty(r) + if strmp(r.ind,'i') + i1=i1-str2num(r.num1); + i2=i2 +str2num(r.num2); + elseif strmp(r.ind,'j') + j1=j1-str2num(r.num1); + j2=j2 +str2num(r.num2); + end + else % mode='j1-j2'; + r=regexp(str_civ,'^j= (?[a-z])-(?[a-z])','names'); + if isempty(r) + r=regexp(str_civ,'^j= (?[A-Z])-(?[A-Z])','names'); + if isempty(r) + r=regexp(str_civ,'^j= (?\d+)-(?\d+)','names'); + end + end + if isempty(r) + disp('wrong pair mode input option') + else + j1=stra2num(r.num1); + j2=stra2num(r.num2); + end + end + + par_civ1=Param.ActionInput.Civ1; + + if strcmp(Param.ActionInput.ListCompareMode,'displacement') + ImageName_A=Param.ActionInput.RefFile; + else + RootPath_A=Param.InputTable{1,1}; + SubDir_A=Param.InputTable{1,2}; + RootFile_A=Param.InputTable{1,3}; + NomType_A=Param.InputTable{1,4}; + FileExt_A=Param.InputTable{1,5}; + ImageName_A=fullfile_uvmat(RootPath_A,SubDir_A,RootFile_A,FileExt_A,NomType_A,i1,[],j1); + ImageName_B=fullfile_uvmat(RootPath_A,SubDir_A,RootFile_A,FileExt_A,NomType_A,i2,[],j2); + end + par_civ1.ImageA = read_image(ImageName_A); + par_civ1.ImageB = read_image(ImageName_B); + par_civ1.CorrSmooth=0;% will give only the grid of data points expected for PIV, computations will be activated by the fct mouse_motion.m + [Data.Civ1_X,Data.Civ1_Y,Data.Civ1_U,Data.Civ1_V,Data.Civ1_C,Data.Civ1_FF, ~, errormsg]=civ(par_civ1); + if ~isempty(errormsg) + disp(errormsg) + return + end % rmq: error msg displayed in civ_series + + %% create image data ImageData for display + ImageData.ListVarName={'ny','nx','A'}; + ImageData.VarDimName= {'ny','nx',{'ny','nx'}}; + ImageData.VarAttribute{1}.Role='coord_y'; + ImageData.VarAttribute{2}.Role='coord_x'; + ImageData.VarAttribute{3}.Role='scalar'; + ImageData.A=par_civ1.ImageA; % get the first image + if ndims(ImageData.A)==3 %case of color image + ImageData.VarDimName= {'ny','nx',{'ny','nx','rgb'}}; + end + ImageData.ny=[size(ImageData.A,1) 1]; + ImageData.nx=[1 size(ImageData.A,2)]; + ImageData.CoordUnit='pixel';% used to set equal scaling for x and y in image dispa=ly + + %% create the figure view_field for image visualization + hview_field=view_field(ImageData); %view the image in the GUI view_field + set(0,'CurrentFigure',hview_field) + hhview_field=guihandles(hview_field); + set(hview_field,'CurrentAxes',hhview_field.PlotAxes) + ViewData=get(hview_field,'UserData'); + ViewData.CivHandle=handles.civ_input;% indicate the handle of the civ GUI in view_field + ViewData.PlotAxes.X=Data.Civ1_X'; + ViewData.PlotAxes.Y=Data.Civ1_Y'; + ViewData.PlotAxes.B=par_civ1.ImageB;%store the second image in the UserData of the GUI view_field + set(hview_field,'UserData',ViewData)% store the info in the UserData of image view_field, to be used by mouse_motion.m %% look for a current figure for image correlation display @@ -1623,5 +1648,5 @@ if ~isempty(hview_field) delete(hview_field) - end + end end @@ -1636,5 +1661,5 @@ %--------------------------------------------------------------------- function NomTypeNc=nomtype2pair(NomTypeIma,mode_selected) -%--------------------------------------------------------------------- +%--------------------------------------------------------------------- % OUTPUT: % NomTypeNc @@ -1645,21 +1670,21 @@ NomTypeNc=NomTypeIma;%default switch mode_selected - case 'pair j1-j2' - if ~isempty(regexp(NomTypeIma,'a$')) - NomTypeNc=[NomTypeIma 'b']; - elseif ~isempty(regexp(NomTypeIma,'A$')) - NomTypeNc=[NomTypeIma 'B']; - else - r=regexp(NomTypeIma,'(?\d+)_(?\d+)$','names'); - if ~isempty(r) - NomTypeNc='_1_1-2'; - end - end - case 'series(Dj)' -% r=regexp(NomTypeIma,'(?\d+)_(?\d+)$','names'); -% if ~isempty(r) - NomTypeNc='_1_1-2'; -% end - case 'series(Di)' + case 'pair j1-j2' + if ~isempty(regexp(NomTypeIma,'a$')) + NomTypeNc=[NomTypeIma 'b']; + elseif ~isempty(regexp(NomTypeIma,'A$')) + NomTypeNc=[NomTypeIma 'B']; + else + r=regexp(NomTypeIma,'(?\d+)_(?\d+)$','names'); + if ~isempty(r) + NomTypeNc='_1_1-2'; + end + end + case 'series(Dj)' + % r=regexp(NomTypeIma,'(?\d+)_(?\d+)$','names'); + % if ~isempty(r) + NomTypeNc='_1_1-2'; + % end + case 'series(Di)' r=regexp(NomTypeIma,'(?\d+)_(?\d+)$','names'); if ~isempty(r) Index: /trunk/src/series/civ_series.m =================================================================== --- /trunk/src/series/civ_series.m (revision 1168) +++ /trunk/src/series/civ_series.m (revision 1169) @@ -3,5 +3,5 @@ % civ: PIV function itself % detect_false: put a flag to false vectors after detection by various criteria -% filter_tps: make interpolation-smoothing +% filter_tps: make interpolation-smoothing %------------------------------------------------------------------------ % function [Data,errormsg,result_conv]= civ_series(Param) @@ -15,5 +15,5 @@ % Param: Matlab structure of input parameters % Param contains info of the GUI series using the fct read_GUI. -% Param.Action.RUN = 0 (to set the status of the GUI series) or =1 to RUN the computation +% Param.Action.RUN = 0 (to set the status of the GUI series) or =1 to RUN the computation % Param.InputTable: sets the input file(s) % if absent, the fct looks for input data in Param.ActionInput (test mode) @@ -93,143 +93,135 @@ return end -iview_A=0;%default values +%iview_A=0;%default values NbField=1; RUNHandle=[]; -CheckInputFile=isfield(Param,'InputTable');%= 1 in test use for TestCiv (no nc file involved) -CheckOutputFile=isfield(Param,'OutputSubDir');%= 1 in test use for TestPatch (no nc file produced) +% CheckInputFile=isfield(Param,'InputTable');%= 1 in test use for TestCiv (no nc file involved) +% CheckOutputFile=isfield(Param,'OutputSubDir');%= 1 in test use for TestPatch (no nc file produced) %% input files and indexing (skipped in Test mode) -if CheckInputFile - 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 - MaxIndex_i=Param.IndexRange.MaxIndex_i; - MinIndex_i=Param.IndexRange.MinIndex_i; - MaxIndex_j=ones(size(MaxIndex_i));MinIndex_j=ones(size(MinIndex_i)); - if isfield(Param.IndexRange,'MaxIndex_j')&& isfield(Param.IndexRange,'MinIndex_j') - MaxIndex_j=Param.IndexRange.MaxIndex_j; - MinIndex_j=Param.IndexRange.MinIndex_j; - end - if isfield(Param,'InputTable') - [~,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param); - iview_A=0;% series index (iview) for the first image series - iview_B=0;% series index (iview) for the second image series (only non zero for option 'shift' comparing two image series ) - if Param.ActionInput.CheckCiv1 - iview_A=1;% usual PIV, the image series is on the first line of the table - else % Civ1 has been already stored in a netcdf file input - iview_A=2;% the second line is used for the input images - end - if iview_A~=0 - RootPath_A=Param.InputTable{iview_A,1}; - RootFile_A=Param.InputTable{iview_A,3}; - SubDir_A=Param.InputTable{iview_A,2}; - NomType_A=Param.InputTable{iview_A,4}; - FileExt_A=Param.InputTable{iview_A,5}; - if iview_B==0 - iview_B=iview_A;% the second image series is the same as the first - end - RootPath_B=Param.InputTable{iview_B,1}; - RootFile_B=Param.InputTable{iview_B,3}; - SubDir_B=Param.InputTable{iview_B,2}; - NomType_B=Param.InputTable{iview_B,4}; - FileExt_B=Param.InputTable{iview_B,5}; - end - - PairCiv2=''; - switch Param.ActionInput.ListCompareMode - case 'PIV' - PairCiv1=Param.ActionInput.PairIndices.ListPairCiv1; - if isfield(Param.ActionInput.PairIndices,'ListPairCiv2') - PairCiv2=Param.ActionInput.PairIndices.ListPairCiv2;%string which determines the civ2 pair +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 +MaxIndex_i=Param.IndexRange.MaxIndex_i; +MinIndex_i=Param.IndexRange.MinIndex_i; +MaxIndex_j=ones(size(MaxIndex_i));MinIndex_j=ones(size(MinIndex_i)); +if isfield(Param.IndexRange,'MaxIndex_j')&& isfield(Param.IndexRange,'MinIndex_j') + MaxIndex_j=Param.IndexRange.MaxIndex_j; + MinIndex_j=Param.IndexRange.MinIndex_j; +end +if isfield(Param,'InputTable') + [filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param); + % iview_A=0;% series index (iview) for the first image series + iview_B=0;% series index (iview) for the second image series (only non zero for option 'shift' comparing two image series ) + if Param.ActionInput.CheckCiv1 + iview_A=1;% usual PIV, the image series is on the first line of the table + else % Civ1 has been already stored in a netcdf file input + iview_A=2;% the second line is used for the input images + end + % if iview_A~=0 + RootPath_A=Param.InputTable{iview_A,1}; + RootFile_A=Param.InputTable{iview_A,3}; + SubDir_A=Param.InputTable{iview_A,2}; + NomType_A=Param.InputTable{iview_A,4}; + FileExt_A=Param.InputTable{iview_A,5}; + if iview_B==0 + iview_B=iview_A;% the second image series is the same as the first + end + RootPath_B=Param.InputTable{iview_B,1}; + RootFile_B=Param.InputTable{iview_B,3}; + SubDir_B=Param.InputTable{iview_B,2}; + NomType_B=Param.InputTable{iview_B,4}; + FileExt_B=Param.InputTable{iview_B,5}; + PairCiv2=''; + + switch Param.ActionInput.ListCompareMode + case 'PIV' + PairCiv1=Param.ActionInput.PairIndices.ListPairCiv1; + if isfield(Param.ActionInput.PairIndices,'ListPairCiv2') + PairCiv2=Param.ActionInput.PairIndices.ListPairCiv2;%string which determines the civ2 pair + end + if iview_A==1% if Civ1 is performed + [i1_series_Civ1,i2_series_Civ1,j1_series_Civ1,j2_series_Civ1,check_bounds,NomTypeNc]=... + find_pair_indices(PairCiv1,i1_series{1},j1_series{1},MinIndex_i,MaxIndex_i,MinIndex_j,MaxIndex_j); + if ~isempty(PairCiv2) + [i1_series_Civ2,i2_series_Civ2,j1_series_Civ2,j2_series_Civ2,check_bounds_Civ2]=... + find_pair_indices(PairCiv2,i1_series{1},j1_series{1},MinIndex_i(1),MaxIndex_i(1),MinIndex_j(1),MaxIndex_j(1)); + check_bounds=check_bounds | check_bounds_Civ2; end - if iview_A==1% if Civ1 is performed - [i1_series_Civ1,i2_series_Civ1,j1_series_Civ1,j2_series_Civ1,check_bounds,NomTypeNc]=... - find_pair_indices(PairCiv1,i1_series{1},j1_series{1},MinIndex_i,MaxIndex_i,MinIndex_j,MaxIndex_j); - if ~isempty(PairCiv2) - [i1_series_Civ2,i2_series_Civ2,j1_series_Civ2,j2_series_Civ2,check_bounds_Civ2]=... - find_pair_indices(PairCiv2,i1_series{1},j1_series{1},MinIndex_i(1),MaxIndex_i(1),MinIndex_j(1),MaxIndex_j(1)); - check_bounds=check_bounds | check_bounds_Civ2; - end - else% we start from an existing Civ1 file - i1_series_Civ1=i1_series{1}; - i2_series_Civ1=i2_series{1}; - j1_series_Civ1=j1_series{1}; - j2_series_Civ1=j2_series{1}; - NomTypeNc=Param.InputTable{1,4}; - if ~isempty(PairCiv2) - [i1_series_Civ2,i2_series_Civ2,j1_series_Civ2,j2_series_Civ2,check_bounds,NomTypeNc]=... - find_pair_indices(PairCiv2,i1_series{2},j1_series{2},MinIndex_i(2),MaxIndex_i(2),MinIndex_j(2),MaxIndex_j(2)); - end + else% we start from an existing Civ1 file + i1_series_Civ1=i1_series{1}; + i2_series_Civ1=i2_series{1}; + j1_series_Civ1=j1_series{1}; + j2_series_Civ1=j2_series{1}; + NomTypeNc=Param.InputTable{1,4}; + if ~isempty(PairCiv2) + [i1_series_Civ2,i2_series_Civ2,j1_series_Civ2,j2_series_Civ2,check_bounds,NomTypeNc]=... + find_pair_indices(PairCiv2,i1_series{2},j1_series{2},MinIndex_i(2),MaxIndex_i(2),MinIndex_j(2),MaxIndex_j(2)); end - case 'displacement' - if isfield(Param.ActionInput,'OriginIndex') + end + case 'displacement' + if isfield(Param.ActionInput,'OriginIndex') i1_series_Civ1=Param.ActionInput.OriginIndex*ones(size(i1_series{1})); - else - i1_series_Civ1=ones(size(i1_series{1})); - end - i1_series_Civ2=i1_series_Civ1; - i2_series_Civ1=i1_series{1}; - i2_series_Civ2=i1_series{1}; - j1_series_Civ1=[];% no j index variation for the ref image - j1_series_Civ2=[]; - if isempty(j1_series{1}) - j2_series_Civ1=ones(size(i1_series_Civ1)); - else - j2_series_Civ1=j1_series{1};% if j index exist - end - j2_series_Civ2=j2_series_Civ1; - NomTypeNc='_1'; - end - %determine frame indices for input with movie or other multiframe input file - if isempty(j1_series_Civ1)% simple movie with index i - FrameIndex_A_Civ1=i1_series_Civ1; - FrameIndex_B_Civ1=i2_series_Civ1; - j1_series_Civ1=ones(size(i1_series_Civ1)); + else + i1_series_Civ1=ones(size(i1_series{1})); + end + i1_series_Civ2=i1_series_Civ1; + i2_series_Civ1=i1_series{1}; + i2_series_Civ2=i1_series{1}; + j1_series_Civ1=[];% no j index variation for the ref image + j1_series_Civ2=[]; + if isempty(j1_series{1}) + j2_series_Civ1=ones(size(i1_series_Civ1)); + else + j2_series_Civ1=j1_series{1};% if j index exist + end + j2_series_Civ2=j2_series_Civ1; + NomTypeNc='_1'; + end + %determine frame indices for input with movie or other multiframe input file + if isempty(j1_series_Civ1)% simple movie with index i + FrameIndex_A_Civ1=i1_series_Civ1; + FrameIndex_B_Civ1=i2_series_Civ1; + j1_series_Civ1=ones(size(i1_series_Civ1)); + if strcmp(Param.ActionInput.ListCompareMode,'PIV') + j2_series_Civ1=ones(size(i1_series_Civ1)); + end + else % movie for each burst or volume (index j) + FrameIndex_A_Civ1=j1_series_Civ1; + FrameIndex_B_Civ1=j2_series_Civ1; + end + if isempty(PairCiv2) + FrameIndex_A_Civ2=FrameIndex_A_Civ1; + FrameIndex_B_Civ2=FrameIndex_B_Civ1; + else + if isempty(j1_series_Civ2) + FrameIndex_A_Civ2=i1_series_Civ2; + FrameIndex_B_Civ2=i2_series_Civ2; + j1_series_Civ2=ones(size(i1_series_Civ2)); if strcmp(Param.ActionInput.ListCompareMode,'PIV') - j2_series_Civ1=ones(size(i1_series_Civ1)); - end - else % movie for each burst or volume (index j) - FrameIndex_A_Civ1=j1_series_Civ1; - FrameIndex_B_Civ1=j2_series_Civ1; - end - if isempty(PairCiv2) - FrameIndex_A_Civ2=FrameIndex_A_Civ1; - FrameIndex_B_Civ2=FrameIndex_B_Civ1; + j2_series_Civ2=ones(size(i1_series_Civ2)); + end else - if isempty(j1_series_Civ2) - FrameIndex_A_Civ2=i1_series_Civ2; - FrameIndex_B_Civ2=i2_series_Civ2; - j1_series_Civ2=ones(size(i1_series_Civ2)); - if strcmp(Param.ActionInput.ListCompareMode,'PIV') - j2_series_Civ2=ones(size(i1_series_Civ2)); - end - else - FrameIndex_A_Civ2=j1_series_Civ2; - FrameIndex_B_Civ2=j2_series_Civ2; - end - end - if isempty(i1_series_Civ1)||(~isempty(PairCiv2) && isempty(i1_series_Civ2)) - disp_uvmat('ERROR','no image pair for civ in the input file index range',checkrun) - return - end - end - - %% check the first image pair - if Param.ActionInput.CheckCiv1% Civ1 is performed - NbField=numel(i1_series_Civ1); - elseif Param.ActionInput.CheckCiv2 % Civ2 is performed without Civ1 - NbField=numel(i1_series_Civ2); - else - NbField=numel(i1_series_Civ1);% no image used (only detect_false or patch) TO CHECK - end - - %% Output directory - OutputDir=''; - if CheckOutputFile - OutputDir=[Param.OutputSubDir Param.OutputDirExt]; - end + FrameIndex_A_Civ2=j1_series_Civ2; + FrameIndex_B_Civ2=j2_series_Civ2; + end + end + if isempty(i1_series_Civ1)||(~isempty(PairCiv2) && isempty(i1_series_Civ2)) + disp_uvmat('ERROR','no image pair for civ in the input file index range',checkrun) + return + end +end + +%% check the first image pair +if Param.ActionInput.CheckCiv1% Civ1 is performed + NbField=numel(i1_series_Civ1); +elseif Param.ActionInput.CheckCiv2 % Civ2 is performed without Civ1 + NbField=numel(i1_series_Civ2); +else + NbField=numel(i1_series_Civ1);% no image used (only detect_false or patch) TO CHECK end %% prepare output Data +OutputDir=[Param.OutputSubDir Param.OutputDirExt]; ListGlobalAttribute={'Conventions','Program','CivStage'}; Data.Conventions='uvmat/civdata';% states the conventions used for the description of field variables and attributes @@ -241,25 +233,25 @@ %% get timing from the ImaDoc file or input video -if iview_A~=0 - XmlFileName=find_imadoc(RootPath_A,SubDir_A); - Time=[]; - if ~isempty(XmlFileName) - XmlData=imadoc2struct(XmlFileName); - 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 - end -end +% if iview_A~=0 +XmlFileName=find_imadoc(RootPath_A,SubDir_A); +Time=[]; +if ~isempty(XmlFileName) + XmlData=imadoc2struct(XmlFileName);%read the time from XmlFileName + 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 +end +% end %%%%% MAIN LOOP %%%%%% @@ -284,51 +276,51 @@ end end -% if CheckInputFile - if CheckOutputFile - OutputPath=fullfile(Param.OutputPath,Param.Experiment,Param.Device); - if iview_A==0 % no nc file has been entered - ncfile=fullfile_uvmat(OutputPath,Param.InputTable{1,2},Param.InputTable{1,3},Param.InputTable{1,5},... - NomTypeNc,i1_series_Civ1(ifield),i2_series_Civ1(ifield),j1_series_Civ1(ifield),j2_series_Civ1(ifield)); - else% an existing nc file has been entered - if iview_A==1% if Civ1 is performed - Civ1Dir=OutputDir; - else - Civ1Dir=Param.InputTable{1,2}; - end - if strcmp(Param.ActionInput.ListCompareMode,'PIV') - ncfile=fullfile_uvmat(OutputPath,Civ1Dir,RootFile_A,'.nc',NomTypeNc,i1_series_Civ1(ifield),i2_series_Civ1(ifield),... - j1_series_Civ1(ifield),j2_series_Civ1(ifield)); - else - ncfile=fullfile_uvmat(OutputPath,Civ1Dir,RootFile_A,'.nc',NomTypeNc,i2_series_Civ1(ifield),[],... - j1_series_Civ1(ifield),j2_series_Civ1(ifield)); - end - end - ncfile_out=ncfile;% by default - - if isfield (Param.ActionInput,'Civ2') - i1_civ2=i1_series_Civ2(ifield); - i2_civ2=i1_civ2; - if ~isempty(i2_series_Civ2) - i2_civ2=i2_series_Civ2(ifield); - end - j1_civ2=1; - if ~isempty(j1_series_Civ2) - j1_civ2=j1_series_Civ2(ifield); - end - j2_civ2=i1_civ2; - if ~isempty(j2_series_Civ2) - j2_civ2=j2_series_Civ2(ifield); - end - if strcmp(Param.ActionInput.ListCompareMode,'PIV') - ncfile_out=fullfile_uvmat(OutputPath,OutputDir,RootFile_A,'.nc',NomTypeNc,i1_civ2,i2_civ2,j1_civ2,j2_civ2); - else % displacement - ncfile_out=fullfile_uvmat(OutputPath,OutputDir,RootFile_A,'.nc',NomTypeNc,i2_civ2,[],j2_civ2); - end - end - if ~CheckOverwrite && exist(ncfile_out,'file') - disp(['existing output file ' ncfile_out ' already exists, skip to next field']) - continue% skip iteration if the mode overwrite is desactivated and the result file already exists - end - end + % % if CheckInputFile + % if CheckOutputFile + OutputPath=fullfile(Param.OutputPath,Param.Experiment,Param.Device); + % if iview_A==0 % no nc file has been entered + % ncfile=fullfile_uvmat(OutputPath,Param.InputTable{1,2},Param.InputTable{1,3},Param.InputTable{1,5},... + % NomTypeNc,i1_series_Civ1(ifield),i2_series_Civ1(ifield),j1_series_Civ1(ifield),j2_series_Civ1(ifield)); + % else% an existing nc file has been entered + % if iview_A==1% if Civ1 is performed + % Civ1Dir=OutputDir; + % else + % Civ1Dir=Param.InputTable{1,2}; + % end + if strcmp(Param.ActionInput.ListCompareMode,'PIV') + ncfile=fullfile_uvmat(OutputPath,OutputDir,RootFile_A,'.nc',NomTypeNc,i1_series_Civ1(ifield),i2_series_Civ1(ifield),... + j1_series_Civ1(ifield),j2_series_Civ1(ifield)); + else + ncfile=fullfile_uvmat(OutputPath,OutputDir,RootFile_A,'.nc',NomTypeNc,i2_series_Civ1(ifield),[],... + j1_series_Civ1(ifield),j2_series_Civ1(ifield)); + end + % end + ncfile_out=ncfile;% by default + + if isfield (Param.ActionInput,'Civ2') + i1_civ2=i1_series_Civ2(ifield); + i2_civ2=i1_civ2; + if ~isempty(i2_series_Civ2) + i2_civ2=i2_series_Civ2(ifield); + end + j1_civ2=1; + if ~isempty(j1_series_Civ2) + j1_civ2=j1_series_Civ2(ifield); + end + j2_civ2=i1_civ2; + if ~isempty(j2_series_Civ2) + j2_civ2=j2_series_Civ2(ifield); + end + if strcmp(Param.ActionInput.ListCompareMode,'PIV') + ncfile_out=fullfile_uvmat(OutputPath,OutputDir,RootFile_A,'.nc',NomTypeNc,i1_civ2,i2_civ2,j1_civ2,j2_civ2); + else % displacement + ncfile_out=fullfile_uvmat(OutputPath,OutputDir,RootFile_A,'.nc',NomTypeNc,i2_civ2,[],j2_civ2); + end + end + if ~CheckOverwrite && exist(ncfile_out,'file') + disp(['existing output file ' ncfile_out ' already exists, skip to next field']) + continue% skip iteration if the mode overwrite is desactivated and the result file already exists + end + % end ImageName_A='';ImageName_B='';%default VideoObject_A=[];VideoObject_B=[]; @@ -337,99 +329,94 @@ % if Civ1 computation is requested if Param.ActionInput.CheckCiv1 - if CheckInputFile - disp('civ1 started') - end + disp('civ1 started') par_civ1=Param.ActionInput.Civ1;% parameters for civ1 - if CheckInputFile % read input images (except in mode Test where it is introduced directly in Param.ActionInput.Civ1.ImageNameA and B) - try - if strcmp(Param.ActionInput.ListCompareMode,'displacement') - ImageName_A=Param.ActionInput.RefFile; - else - ImageName_A=fullfile_uvmat(RootPath_A,SubDir_A,RootFile_A,FileExt_A,NomType_A,i1_series_Civ1(ifield),[],j1_series_Civ1(ifield)); + %if CheckInputFile % read input images (except in mode Test where it is introduced directly in Param.ActionInput.Civ1.ImageNameA and B) + try + if strcmp(Param.ActionInput.ListCompareMode,'displacement') + ImageName_A=Param.ActionInput.RefFile; + else + ImageName_A=fullfile_uvmat(RootPath_A,SubDir_A,RootFile_A,FileExt_A,NomType_A,i1_series_Civ1(ifield),[],j1_series_Civ1(ifield)); + end + if strcmp(FileExt_A,'.nc')% case of input images in format netcdf + FieldName_A=Param.InputFields.FieldName; + [DataIn,~,~,errormsg]=nc2struct(ImageName_A,{FieldName_A}); + par_civ1.ImageA=DataIn.(FieldName_A); + else % usual image formats for image A + if isempty(FileType_A)% open the image object if not already done in case of movie input + [FileInfo_A,VideoObject_A]=get_file_info(ImageName_A); + FileType_A=FileInfo_A.FileType; + if isempty(Time) && ~isempty(find(strcmp(FileType_A,{'mmreader','video','cine_phantom'}), 1))% case of video input + Time=zeros(FileInfo_A.NumberOfFrames+1,2); + Time(:,2)=(0:1/FileInfo_A.FrameRate:(FileInfo_A.NumberOfFrames)/FileInfo_A.FrameRate)'; + end + if ~isempty(FileType_A) && isempty(Time)% Time = index i +0.001 index j by default + MaxIndex_i=max(i2_series_Civ1); + MaxIndex_j=max(j2_series_Civ1); + Time=(1:MaxIndex_i)'*ones(1,MaxIndex_j); + Time=Time+0.001*ones(MaxIndex_i,1)*(1:MaxIndex_j); + Time=[zeros(1,MaxIndex_j);Time];% insert a first line of zeros + Time=[zeros(MaxIndex_i+1,1) Time];% insert a first column of zeros + end end - if strcmp(FileExt_A,'.nc')% case of input images in format netcdf - FieldName_A=Param.InputFields.FieldName; - [DataIn,~,~,errormsg]=nc2struct(ImageName_A,{FieldName_A}); - par_civ1.ImageA=DataIn.(FieldName_A); - else % usual image formats for image A - if isempty(FileType_A)% open the image object if not already done in case of movie input - [FileInfo_A,VideoObject_A]=get_file_info(ImageName_A); - FileType_A=FileInfo_A.FileType; - if isempty(Time) && ~isempty(find(strcmp(FileType_A,{'mmreader','video','cine_phantom'}), 1))% case of video input - Time=zeros(FileInfo_A.NumberOfFrames+1,2); - Time(:,2)=(0:1/FileInfo_A.FrameRate:(FileInfo_A.NumberOfFrames)/FileInfo_A.FrameRate)'; - end - if ~isempty(FileType_A) && isempty(Time)% Time = index i +0.001 index j by default - MaxIndex_i=max(i2_series_Civ1); - MaxIndex_j=max(j2_series_Civ1); - Time=(1:MaxIndex_i)'*ones(1,MaxIndex_j); - Time=Time+0.001*ones(MaxIndex_i,1)*(1:MaxIndex_j); - Time=[zeros(1,MaxIndex_j);Time];% insert a first line of zeros - Time=[zeros(MaxIndex_i+1,1) Time];% insert a first column of zeros - end - end - if isempty(regexp(ImageName_A,'(^http://)|(^https://)', 'once')) && ~exist(ImageName_A,'file') - disp([ImageName_A ' missing']) - continue - end - tsart_input=tic; - [par_civ1.ImageA,VideoObject_A] = read_image(ImageName_A,FileType_A,VideoObject_A,FrameIndex_A_Civ1(ifield)); - time_input=toc(tsart_input); - end - ImageName_B=fullfile_uvmat(RootPath_B,SubDir_B,RootFile_B,FileExt_B,NomType_B,i2_series_Civ1(ifield),[],j2_series_Civ1(ifield)); - if isempty(FileType_B)% determine the image type for the first field - [FileInfo_B,VideoObject_B]=get_file_info(ImageName_B); - FileType_B=FileInfo_B.FileType; - end - if isempty(regexp(ImageName_B,'(^http://)|(^https://)', 'once')) && ~exist(ImageName_B,'file') - disp([ImageName_B ' missing']) + if isempty(regexp(ImageName_A,'(^http://)|(^https://)', 'once')) && ~exist(ImageName_A,'file') + disp([ImageName_A ' missing']) continue end - [par_civ1.ImageB,VideoObject_B] = read_image(ImageName_B,FileType_B,VideoObject_B,FrameIndex_B_Civ1(ifield)); - catch ME % display errors in reading input images - if ~isempty(ME.message) - disp_uvmat('ERROR', ['error reading input image: ' ME.message],checkrun) - continue - end - end - - % par_civ1.ImageWidth=size(par_civ1.ImageA,2); - % par_civ1.ImageHeight=size(par_civ1.ImageA,1); - list_param=(fieldnames(Param.ActionInput.Civ1))'; - list_param(strcmp('TestCiv1',list_param))=[];% remove the parameter TestCiv1 from the list - Civ1_param=regexprep(list_param,'^.+','Civ1_$0');% insert 'Civ1_' before each string in list_param - Civ1_param=[{'Civ1_ImageA','Civ1_ImageB','Civ1_Time','Civ1_Dt'} Civ1_param]; %insert the names of the two input images - %indicate the values of all the global attributes in the output data - Data.Civ1_ImageA=ImageName_A; - Data.Civ1_ImageB=ImageName_B; - i1=i1_series_Civ1(ifield); - i2=i1; - if ~isempty(i2_series_Civ1) - i2=i2_series_Civ1(ifield); - end - j1=1; - if ~isempty(j1_series_Civ1) - j1=j1_series_Civ1(ifield); - end - j2=j1; - if ~isempty(j2_series_Civ1) - j2=j2_series_Civ1(ifield); - end - if strcmp(Param.ActionInput.ListCompareMode,'displacement') - Data.Civ1_Time=Time(i2+1,j2+1);% the Time is the Time of the secodn image - Data.Civ1_Dt=1;% Time interval is 1, to yield displacement instead of velocity=displacement/Dt at reading - else - Data.Civ1_Time=(Time(i2+1,j2+1)+Time(i1+1,j1+1))/2;% the Time is the Time at the middle of the image pair - Data.Civ1_Dt=Time(i2+1,j2+1)-Time(i1+1,j1+1); - end - for ilist=1:length(list_param) - Data.(Civ1_param{4+ilist})=Param.ActionInput.Civ1.(list_param{ilist}); - end - Data.ListGlobalAttribute=[ListGlobalAttribute Civ1_param]; - - Data.CivStage=1; + tsart_input=tic; + [par_civ1.ImageA,VideoObject_A] = read_image(ImageName_A,FileType_A,VideoObject_A,FrameIndex_A_Civ1(ifield)); + time_input=toc(tsart_input); + end + ImageName_B=fullfile_uvmat(RootPath_B,SubDir_B,RootFile_B,FileExt_B,NomType_B,i2_series_Civ1(ifield),[],j2_series_Civ1(ifield)); + if isempty(FileType_B)% determine the image type for the first field + [FileInfo_B,VideoObject_B]=get_file_info(ImageName_B); + FileType_B=FileInfo_B.FileType; + end + if isempty(regexp(ImageName_B,'(^http://)|(^https://)', 'once')) && ~exist(ImageName_B,'file') + disp([ImageName_B ' missing']) + continue + end + [par_civ1.ImageB,VideoObject_B] = read_image(ImageName_B,FileType_B,VideoObject_B,FrameIndex_B_Civ1(ifield)); + catch ME % display errors in reading input images + if ~isempty(ME.message) + disp_uvmat('ERROR', ['error reading input image: ' ME.message],checkrun) + continue + end + end + + % par_civ1.ImageWidth=size(par_civ1.ImageA,2); + % par_civ1.ImageHeight=size(par_civ1.ImageA,1); + list_param=(fieldnames(Param.ActionInput.Civ1))'; + list_param(strcmp('TestCiv1',list_param))=[];% remove the parameter TestCiv1 from the list + Civ1_param=regexprep(list_param,'^.+','Civ1_$0');% insert 'Civ1_' before each string in list_param + Civ1_param=[{'Civ1_ImageA','Civ1_ImageB','Civ1_Time','Civ1_Dt'} Civ1_param]; %insert the names of the two input images + %indicate the values of all the global attributes in the output data + Data.Civ1_ImageA=ImageName_A; + Data.Civ1_ImageB=ImageName_B; + i1=i1_series_Civ1(ifield); + i2=i1; + if ~isempty(i2_series_Civ1) + i2=i2_series_Civ1(ifield); + end + j1=1; + if ~isempty(j1_series_Civ1) + j1=j1_series_Civ1(ifield); + end + j2=j1; + if ~isempty(j2_series_Civ1) + j2=j2_series_Civ1(ifield); + end + if strcmp(Param.ActionInput.ListCompareMode,'displacement') + Data.Civ1_Time=Time(i2+1,j2+1);% the Time is the Time of the second image + Data.Civ1_Dt=1;% Time interval is 1, to yield displacement instead of velocity=displacement/Dt at reading else - i1=Param.ActionInput.PairIndices.ref_i; %case of TESTmode - end + Data.Civ1_Time=(Time(i2+1,j2+1)+Time(i1+1,j1+1))/2;% the Time is the Time at the middle of the image pair + Data.Civ1_Dt=Time(i2+1,j2+1)-Time(i1+1,j1+1); + end + for ilist=1:length(list_param) + Data.(Civ1_param{4+ilist})=Param.ActionInput.Civ1.(list_param{ilist}); + end + Data.ListGlobalAttribute=[ListGlobalAttribute Civ1_param]; + Data.CivStage=1; + % set the list of variables Data.ListVarName={'Civ1_X','Civ1_Y','Civ1_U','Civ1_V','Civ1_C','Civ1_FF'};% cell array containing the names of the fields to record @@ -489,5 +476,4 @@ % caluclate velocity data - % tstart_civ1=tic; [Data.Civ1_X,Data.Civ1_Y,Data.Civ1_U,Data.Civ1_V,Data.Civ1_C,Data.Civ1_FF, result_conv, errormsg] = civ (par_civ1); if ~isempty(errormsg) @@ -495,29 +481,6 @@ return end -% -% if exist('ncfile','var') -% CivFile=ncfile; -% % [Data,tild,tild,errormsg]=nc2struct(CivFile,'ListGlobalAttribute','absolut_time_T0'); %look for the constant 'absolut_time_T0' to detect old civx data format -% % if ~isempty(errormsg) -% % disp_uvmat('ERROR',errormsg,checkrun) -% % return -% % end -% [Data,tild,tild,errormsg]=nc2struct(CivFile);%read civ1 and fix1 data in the existing netcdf file -% if ~isempty(errormsg) -% disp(errormsg) -% return -% end -% elseif isfield(Param,'Civ1_X') -% Data.ListGlobalAttribute={}; -% Data.ListVarName={}; -% Data.VarDimName={}; -% Data.Civ1_X=Param.Civ1_X; -% Data.Civ1_Y=Param.Civ1_Y; -% Data.Civ1_U=Param.Civ1_U; -% Data.Civ1_V=Param.Civ1_V; -% Data.Civ1_FF=Param.Civ1_FF; -% end - end - + end + %% Fix1 @@ -542,8 +505,8 @@ end %% Patch1 - if isfield (Param.ActionInput,'Patch1') + if Param.ActionInput.CheckPatch1 && isfield (Param.ActionInput,'Patch1') disp('patch1 started') - tstart_patch1=tic; - + tstart_patch1=tic; + % record the processing parameters of Patch1 as global attributes in the result nc file list_param=fieldnames(Param.ActionInput.Patch1)'; @@ -574,8 +537,8 @@ end if isempty(ind_good) - disp_uvmat('ERROR','all vectors of civ1 are bad, check input parameters' ,checkrun) - return - end - + disp_uvmat('ERROR','all vectors of civ1 are bad, check input parameters' ,checkrun) + return + end + % perform Patch calculation using the UVMAT fct 'filter_tps' [Data.Civ1_SubRange,Data.Civ1_NbCentres,Data.Civ1_Coord_tps,Data.Civ1_U_tps,Data.Civ1_V_tps,~,Ures, Vres,~,FFres]=... @@ -593,63 +556,62 @@ tstart_civ2=tic; par_civ2=Param.ActionInput.Civ2; - if CheckInputFile % read input images (except in mode Test where it is introduced directly in Param.ActionInput.Civ1.ImageNameA and B) - par_civ2.ImageA=[]; - par_civ2.ImageB=[]; - if strcmp(Param.ActionInput.ListCompareMode,'displacement') - ImageName_A_Civ2=Param.ActionInput.RefFile; - else - ImageName_A_Civ2=fullfile_uvmat(RootPath_A,SubDir_A,RootFile_A,FileExt_A,NomType_A,i1_civ2,[],j1_civ2); - end - if strcmp(ImageName_A_Civ2,ImageName_A) && isequal(FrameIndex_A_Civ1(ifield),FrameIndex_A_Civ2(ifield)) - par_civ2.ImageA=par_civ1.ImageA; - else - [par_civ2.ImageA,VideoObject_A] = read_image(ImageName_A_Civ2,FileType_A,VideoObject_A,FrameIndex_A_Civ2(ifield)); - end - ImageName_B_Civ2=fullfile_uvmat(RootPath_B,SubDir_B,RootFile_B,FileExt_B,NomType_B,i2_civ2,[],j2_civ2); - if strcmp(ImageName_B_Civ2,ImageName_B) && isequal(FrameIndex_B_Civ1(ifield),FrameIndex_B_Civ2) - par_civ2.ImageB=par_civ1.ImageB; - else - [par_civ2.ImageB,VideoObject_B] = read_image(ImageName_B_Civ2,FileType_B,VideoObject_B,FrameIndex_B_Civ2(ifield)); - end - [FileInfo_A,VideoObject_A]=get_file_info(ImageName_A_Civ2); - [npy_ima,npx_ima]=size(par_civ2.ImageA(:,:)); - % par_civ2.ImageWidth=FileInfo_A.Width; - % par_civ2.ImageHeight=FileInfo_A.Height; - - if par_civ2.CheckGrid &&~isempty(par_civ2.Grid) % case of input grid - GridData=nc2struct(Param.ActionInput.Civ2.Grid); - par_civ2.Grid=GridData.Grid; - par_civ2.CorrBoxSize=GridData.CorrBox; - - else% automatic grid - nbinterv_x=floor((npx_ima-1)/par_civ2.Dx); - gridlength_x=nbinterv_x*par_civ2.Dx; - minix=ceil((npx_ima-gridlength_x)/2); - nbinterv_y=floor((npy_ima-1)/par_civ2.Dy); - gridlength_y=nbinterv_y*par_civ2.Dy; - miniy=ceil((npy_ima-gridlength_y)/2); - [GridX,GridY]=meshgrid(minix:par_civ2.Dx:npx_ima-1,miniy:par_civ2.Dy:npy_ima-1); - par_civ2.Grid=zeros(numel(GridX),2); - par_civ2.Grid(:,1)=reshape(GridX,[],1); - par_civ2.Grid(:,2)=reshape(GridY,[],1);% increases with array index - - end - end - + % if CheckInputFile % read input images (except in mode Test where it is introduced directly in Param.ActionInput.Civ1.ImageNameA and B) + par_civ2.ImageA=[]; + par_civ2.ImageB=[]; + if strcmp(Param.ActionInput.ListCompareMode,'displacement') + ImageName_A_Civ2=Param.ActionInput.RefFile; + else + ImageName_A_Civ2=fullfile_uvmat(RootPath_A,SubDir_A,RootFile_A,FileExt_A,NomType_A,i1_civ2,[],j1_civ2); + end + if strcmp(ImageName_A_Civ2,ImageName_A) && isequal(FrameIndex_A_Civ1(ifield),FrameIndex_A_Civ2(ifield)) + par_civ2.ImageA=par_civ1.ImageA; + else + [par_civ2.ImageA,VideoObject_A] = read_image(ImageName_A_Civ2,FileType_A,VideoObject_A,FrameIndex_A_Civ2(ifield)); + end + ImageName_B_Civ2=fullfile_uvmat(RootPath_B,SubDir_B,RootFile_B,FileExt_B,NomType_B,i2_civ2,[],j2_civ2); + if strcmp(ImageName_B_Civ2,ImageName_B) && isequal(FrameIndex_B_Civ1(ifield),FrameIndex_B_Civ2) + par_civ2.ImageB=par_civ1.ImageB; + else + [par_civ2.ImageB,VideoObject_B] = read_image(ImageName_B_Civ2,FileType_B,VideoObject_B,FrameIndex_B_Civ2(ifield)); + end + % [FileInfo_A,VideoObject_A]=get_file_info(ImageName_A_Civ2); + npy_ima=size(par_civ2.ImageA,1); + npx_ima=size(par_civ2.ImageA,2); + if par_civ2.CheckGrid &&~isempty(par_civ2.Grid) % case of input grid + GridData=nc2struct(Param.ActionInput.Civ2.Grid); + par_civ2.Grid=GridData.Grid; + par_civ2.CorrBoxSize=GridData.CorrBox; + else% automatic grid + nbinterv_x=floor((npx_ima-1)/par_civ2.Dx); + gridlength_x=nbinterv_x*par_civ2.Dx; + minix=ceil((npx_ima-gridlength_x)/2); + nbinterv_y=floor((npy_ima-1)/par_civ2.Dy); + gridlength_y=nbinterv_y*par_civ2.Dy; + miniy=ceil((npy_ima-gridlength_y)/2); + [GridX,GridY]=meshgrid(minix:par_civ2.Dx:npx_ima-1,miniy:par_civ2.Dy:npy_ima-1); + par_civ2.Grid=zeros(numel(GridX),2); + par_civ2.Grid(:,1)=reshape(GridX,[],1); + par_civ2.Grid(:,2)=reshape(GridY,[],1);% increases with array index + end + % get the guess from patch1 or patch2 (case 'CheckCiv3') - % if CheckInputFile % read input images (except in mode Test where it is introduced directly in Param.ActionInput.Civ1.ImageNameA and B) - if isfield (par_civ2,'CheckCiv3') && par_civ2.CheckCiv3 %get the guess from patch2 - SubRange= Data.Civ2_SubRange; - NbCentres=Data.Civ2_NbCentres; - Coord_tps=Data.Civ2_Coord_tps; - U_tps=Data.Civ2_U_tps; - V_tps=Data.Civ2_V_tps; - CivStage=Data.CivStage;%store the current CivStage - Civ1_Dt=Data.Civ2_Dt; + if iview_A==2 && isfield (par_civ2,'CheckCiv3') && strcmp(par_civ2.CheckCiv3,'iterate(civ3)') %get the guess from patch2% Civ1 data read in a netcdf file + [DataIn,~,~,errormsg]=nc2struct(filecell{1,ifield}); + if ~isempty(errormsg) + disp(errormsg) + return + end + SubRange= DataIn.Civ2_SubRange; + NbCentres=DataIn.Civ2_NbCentres; + Coord_tps=DataIn.Civ2_Coord_tps; + U_tps=DataIn.Civ2_U_tps; + V_tps=DataIn.Civ2_V_tps; + %CivStage=DataIn.CivStage;%store the current CivStage + Civ1_Dt=DataIn.Civ2_Dt; Data=[];%reinitialise the result structure Data Data.ListGlobalAttribute={'Conventions','Program','CivStage'}; Data.Conventions='uvmat/civdata';% states the conventions used for the description of field variables and attributes Data.Program='civ_series'; - Data.CivStage=CivStage+1;%update the current civStage after reinitialisation of Data + % Data.CivStage=CivStage+1;%update the current civStage after reinitialisation of Data Data.ListVarName={}; Data.VarDimName={}; @@ -661,18 +623,18 @@ V_tps=Data.Civ1_V_tps; Civ1_Dt=Data.Civ1_Dt; - Data.CivStage=4; - end - % else - % SubRange= par_civ2.Civ1_SubRange; - % NbCentres=par_civ2.Civ1_NbCentres; - % Coord_tps=par_civ2.Civ1_Coord_tps; - % U_tps=par_civ2.Civ1_U_tps; - % V_tps=par_civ2.Civ1_V_tps; - % Civ1_Dt=par_civ2.Civ1_Dt; - % Civ2_Dt=par_civ2.Civ1_Dt; - % Data.ListVarName={}; - % Data.VarDimName={}; - % end - Shiftx=zeros(size(par_civ2.Grid,1),1);% shift expected from civ1 data +% Data.CivStage=4; + end + Data.CivStage=4; + % SubRange= par_civ2.Civ1_SubRange; + % NbCentres=par_civ2.Civ1_NbCentres; + % Coord_tps=par_civ2.Civ1_Coord_tps; + % U_tps=par_civ2.Civ1_U_tps; + % V_tps=par_civ2.Civ1_V_tps; + % Civ1_Dt=par_civ2.Civ1_Dt; + % Civ2_Dt=par_civ2.Civ1_Dt; + % Data.ListVarName={}; + % Data.VarDimName={}; + % end + Shiftx=zeros(size(par_civ2.Grid,1),1);% initialise the shift expected from civ1 data Shifty=zeros(size(par_civ2.Grid,1),1); nbval=zeros(size(par_civ2.Grid,1),1);% nbre of interpolated values at each grid point (from the different patch subdomains) @@ -713,5 +675,5 @@ Shiftx(nbval>0)=Shiftx(nbval>0)./nbval(nbval>0); Shifty(nbval>0)=Shifty(nbval>0)./nbval(nbval>0); - + % introduce mask if par_civ2.CheckMask && ~isempty(par_civ2.Mask) @@ -753,19 +715,16 @@ end end - - if CheckInputFile % else Dt given by par_civ2 - if strcmp(Param.ActionInput.ListCompareMode,'displacement') - Civ1_Dt=1; - Civ2_Dt=1; - else - Civ2_Dt=Time(i2_civ2+1,j2_civ2+1)-Time(i1_civ2+1,j1_civ2+1); - end + + + if strcmp(Param.ActionInput.ListCompareMode,'displacement') + Civ1_Dt=1; + Civ2_Dt=1; + else + Civ2_Dt=Time(i2_civ2+1,j2_civ2+1)-Time(i1_civ2+1,j1_civ2+1); end par_civ2.SearchBoxShift=zeros(size(par_civ2.Grid)); - par_civ2.SearchBoxShift(:,1)=(Civ2_Dt/Civ1_Dt)*Shiftx; + par_civ2.SearchBoxShift(:,1)=(Civ2_Dt/Civ1_Dt)*Shiftx;%rescale the shift in case of Dt different for Civ1 and Civ2 par_civ2.SearchBoxShift(:,2)=(Civ2_Dt/Civ1_Dt)*Shifty; - % shift the grid points by half the expected shift to provide the correlation box position in image A - %par_civ2.Grid=[par_civ2.Grid(nbval>=1,1)-par_civ2.SearchBoxShift(:,1)/2 par_civ2.Grid(nbval>=1,2)-par_civ2.SearchBoxShift(:,2)/2]; - + if par_civ2.CheckDeformation par_civ2.DUDX(nbval>0)=DUDX(nbval>0)./nbval(nbval>0); @@ -774,9 +733,9 @@ par_civ2.DVDY(nbval>0)=DVDY(nbval>0)./nbval(nbval>0); end - + % calculate velocity data (y and v in image indices, reverse to y component) - + [Data.Civ2_X,Data.Civ2_Y,Data.Civ2_U,Data.Civ2_V,Data.Civ2_C,Data.Civ2_FF,~, errormsg] = civ (par_civ2); - + list_param=(fieldnames(Param.ActionInput.Civ2))'; list_param(strcmp('TestCiv2',list_param))=[];% remove the parameter TestCiv2 from the list @@ -799,5 +758,5 @@ end Data.ListGlobalAttribute=[Data.ListGlobalAttribute Civ2_param]; - + nbvar=numel(Data.ListVarName); % define the Civ2 variable (if Civ2 data are not replaced from previous calculation) @@ -817,5 +776,5 @@ if exist('ncfile','var') CivFile=ncfile; - [Data,tild,tild,errormsg]=nc2struct(CivFile);%read civ1 and detect_false1 data in the existing netcdf file + [Data,~,~,errormsg]=nc2struct(CivFile);%read civ1 and detect_false1 data in the existing netcdf file if ~isempty(errormsg) disp_uvmat('ERROR',errormsg,checkrun) @@ -824,7 +783,7 @@ end end - + %% Fix2 - if isfield (Param.ActionInput,'Fix2') + if Param.ActionInput.CheckFix2 && isfield (Param.ActionInput,'Fix2')% if Fix2 computation is requested disp('detect_false2 started') list_param=fieldnames(Param.ActionInput.Fix2)'; @@ -840,5 +799,6 @@ %% Patch2 - if isfield (Param.ActionInput,'Patch2') + if Param.ActionInput.CheckPatch2 && isfield (Param.ActionInput,'Patch2')% if Patch2 computation is requested + disp('patch2 started') tstart_patch2=tic; @@ -869,9 +829,9 @@ ind_good=1:numel(Data.Civ2_X); end - if isempty(ind_good) - disp_uvmat('ERROR','all vectors of civ2 are bad, check input parameters' ,checkrun) - return - end - + if isempty(ind_good) + disp_uvmat('ERROR','all vectors of civ2 are bad, check input parameters' ,checkrun) + return + end + [Data.Civ2_SubRange,Data.Civ2_NbCentres,Data.Civ2_Coord_tps,Data.Civ2_U_tps,Data.Civ2_V_tps,tild,Ures,Vres,tild,FFres]=... filter_tps([Data.Civ2_X(ind_good) Data.Civ2_Y(ind_good)],Data.Civ2_U(ind_good),Data.Civ2_V(ind_good),[],Data.Patch2_SubDomainSize,Data.Patch2_FieldSmooth,Data.Patch2_MaxDiff); @@ -884,24 +844,24 @@ end - %% write result in a netcdf file if requested - if CheckOutputFile - errormsg=struct2nc(ncfile_out,Data); - if isempty(errormsg) - disp([ncfile_out ' written']) - else - disp(errormsg) - end - time_total=toc(tstart); - disp(['ellapsed time ' num2str(time_total/60,2) ' minutes']) - disp(['time civ1 ' num2str(time_civ1,2) ' s']) - disp(['time patch1 ' num2str(time_patch1,2) ' s']) - disp(['time civ2 ' num2str(time_civ2,2) ' s']) - disp(['time patch2 ' num2str(time_patch2,2) ' s']) - if exist('time_input','var') - disp(['time image reading ' num2str(time_input,2) ' s']) - disp(['time other ' num2str((time_total-time_input-time_civ1-time_patch1-time_civ2-time_patch2),2) ' s']) - end - end -end + %% write result in a netcdf file + errormsg=struct2nc(ncfile_out,Data); + if isempty(errormsg) + disp([ncfile_out ' written']) + else + disp(errormsg) + end + time_total=toc(tstart); + disp(['ellapsed time ' num2str(time_total/60,2) ' minutes']) + disp(['time civ1 ' num2str(time_civ1,2) ' s']) + disp(['time patch1 ' num2str(time_patch1,2) ' s']) + disp(['time civ2 ' num2str(time_civ2,2) ' s']) + disp(['time patch2 ' num2str(time_patch2,2) ' s']) + if exist('time_input','var') + disp(['time image reading ' num2str(time_input,2) ' s']) + disp(['time other ' num2str((time_total-time_input-time_civ1-time_patch1-time_civ2-time_patch2),2) ' s']) + end +end + + %------------------------------------------------------------------------ @@ -967,4 +927,6 @@ end +%------------------------------------------------------------------------ +% --- set the flag for false vectors function FF=detect_false(Param,C,U,V,FFIn) FF=FFIn;%default, good vectors Index: /trunk/src/uvmat.m =================================================================== --- /trunk/src/uvmat.m (revision 1168) +++ /trunk/src/uvmat.m (revision 1169) @@ -2898,38 +2898,41 @@ %case of view mask selection if isequal(get(handles.CheckMask,'Value'),1) - [RootPath,SubDir,RootFile,FileIndex,FileExt]=read_file_boxes(handles); -% if isempty(regexp(RootPath,'^http://')) -% fileinput=[fullfile(RootPath,SubDir,RootFile) FileIndex FileExt];% build the input file name (first line) -% else -% fileinput=[RootPath '/' SubDir '/' RootFile FileIndex FileExt];% -% end -% FileInfo=get_file_info(fileinput); - -% MaskSubDir=regexprep(SubDir,'\..*','');%take the root part of SubDir, before the first dot '.' -% MaskPath=fullfile(RootPath,[MaskSubDir '.mask']); - mdetect=0; -% if exist(MaskPath,'dir') -% ListStruct=dir(MaskPath);%look for a mask file -% ListCells=struct2cell(ListStruct);% transform dir struct to a cell arrray -% check_dir=cell2mat(ListCells(4,:));% =1 for directories, =0 for files -% ListFiles=ListCells(1,:);%list of file and dri names -% ListFiles=ListFiles(~check_dir);%list of file names (excluding dir) -% if ~isempty(ListFiles) -% for ifile=1:numel(ListFiles) -% [tild,tild,MaskExt]=fileparts(ListFiles{1}); -% [tild,tild,MaskFile{ifile},i1_series,i2_series,j1_series,j2_series,MaskNomType,MaskFileInfo]=find_file_series(MaskPath,ListFiles{ifile},0); -% MaskFileType=MaskFileInfo.FileType; -% if strcmp(MaskFileType,'image') && isempty(i2_series) && isempty(j2_series) -% mdetect=1; -% end -% if ~strcmp(MaskFile{ifile},MaskFile{1}) -% mdetect=0;% cancel detection test in case of multiple masks, use the brower for selection -% break -% end -% end -% end -% RootPath=MaskPath; -% end - filemask= uigetfile_uvmat('pick a mask image file:',RootPath,'image'); + [RootPath,SubDir,RootFile,FileIndex,FileExt]=read_file_boxes(handles); + if isempty(regexp(RootPath,'^http://')) + fileinput=[fullfile(RootPath,SubDir,RootFile) FileIndex FileExt];% build the input file name (first line) + else + fileinput=[RootPath '/' SubDir '/' RootFile FileIndex FileExt];% + end + FileInfo=get_file_info(fileinput); + if isfield(FileInfo,'MaskFile')&& exist(FileInfo.MaskFile,'file') + filemask=FileInfo.MaskFile; + else + % MaskSubDir=regexprep(SubDir,'\..*','');%take the root part of SubDir, before the first dot '.' + % MaskPath=fullfile(RootPath,[MaskSubDir '.mask']); + % mdetect=0; + % if exist(MaskPath,'dir') + % ListStruct=dir(MaskPath);%look for a mask file + % ListCells=struct2cell(ListStruct);% transform dir struct to a cell arrray + % check_dir=cell2mat(ListCells(4,:));% =1 for directories, =0 for files + % ListFiles=ListCells(1,:);%list of file and dri names + % ListFiles=ListFiles(~check_dir);%list of file names (excluding dir) + % if ~isempty(ListFiles) + % for ifile=1:numel(ListFiles) + % [tild,tild,MaskExt]=fileparts(ListFiles{1}); + % [tild,tild,MaskFile{ifile},i1_series,i2_series,j1_series,j2_series,MaskNomType,MaskFileInfo]=find_file_series(MaskPath,ListFiles{ifile},0); + % MaskFileType=MaskFileInfo.FileType; + % if strcmp(MaskFileType,'image') && isempty(i2_series) && isempty(j2_series) + % mdetect=1; + % end + % if ~strcmp(MaskFile{ifile},MaskFile{1}) + % mdetect=0;% cancel detection test in case of multiple masks, use the brower for selection + % break + % end + % end + % end + % RootPath=MaskPath; + % end + filemask= uigetfile_uvmat('pick a mask image file:',RootPath,'image'); + end if ~isempty(filemask) [MaskPath,FileName,FileExt]=fileparts(filemask); @@ -2949,5 +2952,5 @@ errormsg=update_mask(handles); if ~isempty(errormsg) - msgbox_uvmat(['ERROR','error in displaying mask, ' errormsg]); + msgbox_uvmat(['ERROR','error in displaying mask, ' errormsg]); end testmask=1; @@ -2956,5 +2959,6 @@ MaskData=get(handles.CheckMask,'UserData'); if isfield(MaskData,'maskhandle') && ishandle(MaskData.maskhandle) - delete(MaskData.maskhandle) + % delete(MaskData.maskhandle) + set(MaskData.maskhandle,'Visible','off') end set(handles.CheckMask,'UserData',[]) @@ -3037,5 +3041,5 @@ if ~isempty(hmask) set(hmask,'CData',imflag) - set(hmask,'AlphaData',flagmask*0.6) + set(hmask,'AlphaData',flagmask*0.3) set(hmask,'XData',MaskField.Coord_x); set(hmask,'YData',MaskField.Coord_y); @@ -3044,5 +3048,5 @@ axes(handles.PlotAxes) hold on - MaskInfo.maskhandle=image(MaskField.Coord_x,MaskField.Coord_y,imflag,'Tag','mask','HitTest','off','AlphaData',0.6*ones(size(flagmask))); + MaskInfo.maskhandle=image(MaskField.Coord_x,MaskField.Coord_y,imflag,'Tag','mask','HitTest','off','AlphaData',0.3*ones(size(flagmask))); set(handles.CheckMask,'UserData',MaskInfo) end