Index: /trunk/src/series/civ_input.m =================================================================== --- /trunk/src/series/civ_input.m (revision 757) +++ /trunk/src/series/civ_input.m (revision 758) @@ -82,10 +82,10 @@ %% input file info -RootPath=Param.InputTable{1,1}; -%set(handles.RootPath,'String',RootPath) -RootFile=Param.InputTable{1,3}; -SubDir=Param.InputTable{1,2}; +% RootPath=Param.InputTable{1,1}; +% %set(handles.RootPath,'String',RootPath) +% RootFile=Param.InputTable{1,3}; +% SubDir=Param.InputTable{1,2}; NomTypeInput=Param.InputTable{1,4}; -FileExt=Param.InputTable{1,5}; +% FileExt=Param.InputTable{1,5}; FileType='image';%fdefault FileInfo=[]; @@ -293,5 +293,5 @@ hparent=get(hcheckgrid(ilist),'parent');%handles of the parent panel hchildren=get(hparent,'children'); - handle_txtbox=findobj(hchildren,'tag','Grid');% look for the grid name box in the same panel + %handle_txtbox=findobj(hchildren,'tag','Grid');% look for the grid name box in the same panel handle_dx=findobj(hchildren,'tag','num_Dx'); handle_dy=findobj(hchildren,'tag','num_Dy'); @@ -901,37 +901,37 @@ function ListPairCiv2_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ -index_pair=get(handles.ListPairCiv2,'Value');%get the selected position index in the menu - -%update MinIndex_i and last_i according to the chosen image pairs -mode_list=get(handles.ListPairMode,'String'); -mode_value=get(handles.ListPairMode,'Value'); -mode=mode_list{mode_value}; -if isequal(mode,'series(Di)') - first_i=str2double(get(handles.MinIndex_i,'String')); - last_i=str2double(get(handles.last_i,'String')); - incr_i=str2double(get(handles.incr_i,'String')); - num_i=first_i:incr_i:last_i; - lastfield=str2double(get(handles.MaxIndex_i,'String')); - if ~isnan(lastfield) - test_find=(num_i-floor(index_pair/2)*ones(size(num_i))>0)& ... - (num_i+ceil(index_pair/2)*ones(size(num_i))<=lastfield); - num_i=num_i(test_find); - end - set(handles.MinIndex_i,'String',num2str(num_i(1))); - set(handles.last_i,'String',num2str(num_i(end))); -elseif isequal(mode,'series(Dj)') - first_j=str2double(get(handles.MinIndex_j,'String')); - last_j=str2double(get(handles.last_j,'String')); - incr_j=str2double(get(handles.incr_j,'String')); - num_j=first_j:incr_j:last_j; - lastfield2=str2double(get(handles.MaxIndex_j,'String')); - if ~isnan(lastfield2) - test_find=(num_j-floor(index_pair/2)*ones(size(num_j))>0)& ... - (num_j+ceil(index_pair/2)*ones(size(num_j))<=lastfield2); - num_j=num_j(test_find); - end - set(handles.MinIndex_j,'String',num2str(num_j(1))); - set(handles.last_j,'String',num2str(num_j(end))); -end +% index_pair=get(handles.ListPairCiv2,'Value');%get the selected position index in the menu +% +% %update MinIndex_i and last_i according to the chosen image pairs +% mode_list=get(handles.ListPairMode,'String'); +% mode_value=get(handles.ListPairMode,'Value'); +% mode=mode_list{mode_value}; +% if isequal(mode,'series(Di)') +% first_i=str2double(get(handles.MinIndex_i,'String')); +% last_i=str2double(get(handles.MaxIndex_i,'String')); +% incr_i=str2double(get(handles.incr_i,'String')); +% num_i=first_i:incr_i:last_i; +% % lastfield=str2double(get(handles.MaxIndex_i,'String')); +% if ~isnan(last_i) +% test_find=(num_i-floor(index_pair/2)*ones(size(num_i))>0)& ... +% (num_i+ceil(index_pair/2)*ones(size(num_i))<=last_i); +% num_i=num_i(test_find); +% end +% set(handles.MinIndex_i,'String',num2str(num_i(1))); +% set(handles.MaxIndex_i,'String',num2str(num_i(end))); +% elseif isequal(mode,'series(Dj)') +% first_j=str2double(get(handles.MinIndex_j,'String')); +% last_j=str2double(get(handles.last_j,'String')); +% incr_j=str2double(get(handles.incr_j,'String')); +% num_j=first_j:incr_j:last_j; +% lastfield2=str2double(get(handles.MaxIndex_j,'String')); +% if ~isnan(lastfield2) +% test_find=(num_j-floor(index_pair/2)*ones(size(num_j))>0)& ... +% (num_j+ceil(index_pair/2)*ones(size(num_j))<=lastfield2); +% num_j=num_j(test_find); +% end +% set(handles.MinIndex_j,'String',num2str(num_j(1))); +% set(handles.last_j,'String',num2str(num_j(end))); +% end %------------------------------------------------------------------------ @@ -1095,5 +1095,5 @@ end -%% determine the default selection in the pair menu +%% determine the default selection in the pair menu for Civ1 ichoice=find(select,1);% index of selected pair if (isempty(ichoice) || ichoice < 1); ichoice=1; end; @@ -1102,14 +1102,20 @@ set(handles.ListPairCiv1,'Value',ichoice);% first valid pair proposed by default in the menu end -initial=get(handles.ListPairCiv2,'Value'); -if initial>length(displ_pair')%|~isequal(select(initial),1) - if ichoice <= length(displ_pair') - set(handles.ListPairCiv2,'Value',ichoice);% same pair proposed by default for civ2 - else - set(handles.ListPairCiv2,'Value',1);% same pair proposed by default for civ2 - end + +%% determine the default selection in the pair menu for Civ2 +if strcmp(get(handles.ListPairCiv2,'Visible'),'on') + initial=get(handles.ListPairCiv2,'Value'); + if initial>length(displ_pair')%|~isequal(select(initial),1) + if ichoice <= length(displ_pair') + set(handles.ListPairCiv2,'Value',ichoice);% same pair proposed by default for civ2 + else + set(handles.ListPairCiv2,'Value',1);% same pair proposed by default for civ2 + end + end +else + set(handles.ListPairCiv2,'Value',get(handles.ListPairCiv1,'Value'))% initiate the choice of Civ2 as a reproduction of if civ1 end set(handles.ListPairCiv2,'String',displ_pair'); -set(gcf,'Pointer','arrow') +set(gcf,'Pointer','arrow')% Indicate that the process is finished Index: /trunk/src/series/civ_series.m =================================================================== --- /trunk/src/series/civ_series.m (revision 757) +++ /trunk/src/series/civ_series.m (revision 758) @@ -63,22 +63,11 @@ Data.OutputSubDirMode='last'; %select the last subDir in the input table as root of the output subdir name (option 'all'/'first'/'last', 'all' by default) Data.OutputFileMode='NbInput_i';% one output file expected per value of i index (used for waitbar) - % check the existence of the first file in the series - first_j=[]; - if isfield(Param.IndexRange,'first_j'); first_j=Param.IndexRange.first_j; end - last_j=[]; - if isfield(Param.IndexRange,'last_j'); last_j=Param.IndexRange.last_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']) - else - FileType=get_file_type(FirstFileName); - if isempty(find(strcmp(FileType,{'civdata','image','multimage','mmreader','video'})));% =1 for images - msgbox_uvmat('ERROR',['bad input file type for ' mfilename ': an image or civdata file is needed']) - end - end + % check the existence of the first file in the series: suppressed +% first_j=[]; +% if isfield(Param.IndexRange,'first_j'); first_j=Param.IndexRange.first_j; end +% last_j=[]; +% if isfield(Param.IndexRange,'last_j'); last_j=Param.IndexRange.last_j; end +% PairString=''; +% if isfield(Param.IndexRange,'PairString'); PairString=Param.IndexRange.PairString; end return end @@ -99,5 +88,5 @@ %% input files and indexing -NbField=1; +% NbField=1; MaxIndex_i=Param.IndexRange.MaxIndex_i; MinIndex_i=Param.IndexRange.MinIndex_i; @@ -108,115 +97,76 @@ end if isfield(Param,'InputTable') - [filecell,i_series,tild,j_series]=get_file_series(Param); - if ~exist(filecell{1,1},'file') - disp_uvmat('ERROR',' the first input file does not exist',checkrun) - return - else - FileType=get_file_type(filecell{1,1}); - iview_nc=0;% series index (iview) for an input nc file (for civ2 or patch2) - 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' ) - switch FileType - case 'civdata';% =1 for images - iview_nc=1; - if size(filecell,1)>=2 - iview_A=2;iview_B=2; - if size(filecell,1)>=3 - iview_B=3; - end - end - case {'image','multimage','mmreader','video'} - iview_A=1; - if size(filecell,1)>=2 - iview_B=2; - end - end + [tild,i_series,tild,j_series]=get_file_series(Param); + % iview_nc=0;% series index (iview) for an input nc file (for civ2 or patch2) + 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 + elseif Param.ActionInput.CheckCiv2 % civ2 is performed without Civ1, a netcdf file series is needed in the first table line + iview_A=2;% the second line is used for the input images of Civ2 + end + if strcmp(Param.ActionInput.ListCompareMode,'shift') + iview_B=iview_A+1; % the second image series is on the next line of the tinput table end if iview_A~=0 - [FileType_A,FileInfo_A,VideoObject_A]=get_file_type(filecell{1,1}); - if isempty(strcmp(FileType_A,{'multimage','mmreader','video'})) - displ(['ERROR: the file line ' num2str(iview_A) ' must be an image']) - end - RootPath_A=Param.InputTable{1,1}; - RootFile_A=Param.InputTable{1,3}; - SubDir_A=Param.InputTable{1,2}; - NomType_A=Param.InputTable{1,4}; - FileExt_A=Param.InputTable{1,5}; - end - if iview_B==0 - FileType_B=FileType_A; - VideoObject_B=VideoObject_A; - RootPath_B=RootPath_A; - RootFile_B=RootFile_A; - SubDir_B=SubDir_A; - NomType_B=NomType_A; - FileExt_B=FileExt_A; - PairCiv2=''; - switch Param.ActionInput.ListCompareMode - case 'PIV' - PairCiv1=Param.ActionInput.PairIndices.ListPairCiv1; - if isfield(Param.ActionInput.PairIndices,'ListPairCiv2') - PairCiv2=Param.ActionInput.PairIndices.ListPairCiv2; - end - [i1_series_Civ1,i2_series_Civ1,j1_series_Civ1,j2_series_Civ1,check_bounds,NomTypeNc]=... - find_pair_indices(PairCiv1,i_series{1},j_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,i_series{1},j_series{1},MinIndex_i,MaxIndex_i,MinIndex_j,MaxIndex_j); - check_bounds=check_bounds | check_bounds_Civ2; - end - i1_series_Civ1=i1_series_Civ1(~check_bounds); - i2_series_Civ1=i2_series_Civ1(~check_bounds); - j1_series_Civ1=j1_series_Civ1(~check_bounds); - j2_series_Civ1=j2_series_Civ1(~check_bounds); - case 'displacement' - i1_series_Civ1=Param.ActionInput.OriginIndex*ones(size(i_series{1})); - i2_series_Civ1=i_series{1};i2_series_Civ2=i_series{1}; - j1_series_Civ1=ones(size(i_series{1}));% first j index is 1 - if isempty(j_series{1}) - j2_series_Civ1=ones(size(i_series{1})); - else - j2_series_Civ1=j_series{1}; - end - i1_series_Civ2=i1_series_Civ1; - j1_series_Civ2=j1_series_Civ1; - j2_series_Civ2=j2_series_Civ1; - NomTypeNc=NomType; - end - if ~isempty(PairCiv2) - i1_series_Civ2=i1_series_Civ2(~check_bounds); - i2_series_Civ2=i2_series_Civ2(~check_bounds); - j1_series_Civ2=j1_series_Civ2(~check_bounds); - j2_series_Civ2=j2_series_Civ2(~check_bounds); + 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; + end + [i1_series_Civ1,i2_series_Civ1,j1_series_Civ1,j2_series_Civ1,check_bounds,NomTypeNc]=... + find_pair_indices(PairCiv1,i_series{1},j_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,i_series{1},j_series{1},MinIndex_i,MaxIndex_i,MinIndex_j,MaxIndex_j); + check_bounds=check_bounds | check_bounds_Civ2; + end + i1_series_Civ1=i1_series_Civ1(~check_bounds); + i2_series_Civ1=i2_series_Civ1(~check_bounds); + j1_series_Civ1=j1_series_Civ1(~check_bounds); + j2_series_Civ1=j2_series_Civ1(~check_bounds); + case 'displacement' + i1_series_Civ1=Param.ActionInput.OriginIndex*ones(size(i_series{1})); + i2_series_Civ1=i_series{1};i2_series_Civ2=i_series{1}; + j1_series_Civ1=ones(size(i_series{1}));% first j index is 1 if isempty(j_series{1}) - FrameIndex_A_Civ2=i1_series_Civ2; - FrameIndex_B_Civ2=i2_series_Civ2; + j2_series_Civ1=ones(size(i_series{1})); else - FrameIndex_A_Civ2=j1_series_Civ2; - FrameIndex_B_Civ2=j2_series_Civ2; - end - end - else - [FileType_B,FileInfo,VideoObject_B]=get_file_type(filecell{2,1}); - if ~ismember(FileType_B,{'image','multimage','mmreader','video'}) - disp_uvmat('ERROR',['the file line ' num2str(iview_B) ' must be an image'],checkrun) - end - i1_series_Civ1=i_series{1};i1_series_Civ2=i_series{1}; - i2_series_Civ1=i_series{1};i2_series_Civ2=i_series{1}; - if isempty(j_series{1}) - j1_series_Civ1=ones(size(i_series{1})); - j2_series_Civ1=ones(size(i_series{1})); - else - j1_series_Civ1=j_series{1}; - j2_series_Civ1=j_series{1}; - end - j1_series_Civ2=j1_series_Civ1; - j2_series_Civ2=j2_series_Civ1; - NomTypeNc=NomType_A; - RootPath_B=Param.InputTable{2,1}; - RootFile_B=Param.InputTable{2,3}; - SubDir_B=Param.InputTable{2,2}; - NomType_B=Param.InputTable{2,4}; - FileExt_B=Param.InputTable{2,5}; + j2_series_Civ1=j_series{1}; + end + i1_series_Civ2=i1_series_Civ1; + j1_series_Civ2=j1_series_Civ1; + j2_series_Civ2=j2_series_Civ1; + NomTypeNc=NomType; + case 'shift' + i1_series_Civ1=i_series{1};i1_series_Civ2=i_series{1}; + i2_series_Civ1=i_series{1};i2_series_Civ2=i_series{1}; + if isempty(j_series{1}) + j1_series_Civ1=ones(size(i_series{1})); + j2_series_Civ1=ones(size(i_series{1})); + else + j1_series_Civ1=j_series{1}; + j2_series_Civ1=j_series{1}; + end + j1_series_Civ2=j1_series_Civ1; + j2_series_Civ2=j2_series_Civ1; + NomTypeNc=NomType_A; end if isempty(j_series{1}) @@ -227,6 +177,65 @@ FrameIndex_B_Civ1=j2_series_Civ1; end -end -NbField=numel(i1_series_Civ1); + if ~isempty(PairCiv2) + i1_series_Civ2=i1_series_Civ2(~check_bounds); + i2_series_Civ2=i2_series_Civ2(~check_bounds); + j1_series_Civ2=j1_series_Civ2(~check_bounds); + j2_series_Civ2=j2_series_Civ2(~check_bounds); + if isempty(j_series{1}) + FrameIndex_A_Civ2=i1_series_Civ2; + FrameIndex_B_Civ2=i2_series_Civ2; + 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 fo civ in the input file index range',checkrun) + return + end +end + +%% check the first image pair +try + if Param.ActionInput.CheckCiv1% Civ1 is performed + ImageName_A=fullfile_uvmat(RootPath_A,SubDir_A,RootFile_A,FileExt_A,NomType_A,i1_series_Civ1(1),[],j1_series_Civ1(1)); + if ~exist(ImageName_A,'file') + disp_uvmat('ERROR',['first input image ' ImageName_A ' does not exist'],checkrun) + return + end + [FileType_A,FileInfo_A,VideoObject_A]=get_file_type(ImageName_A); + [par_civ1.ImageA,VideoObject_A] = read_image(ImageName_A,FileType_A,VideoObject_A,FrameIndex_A_Civ1(1)); + ImageName_B=fullfile_uvmat(RootPath_B,SubDir_B,RootFile_B,FileExt_B,NomType_B,i2_series_Civ1(1),[],j2_series_Civ1(1)); + if ~exist(ImageName_B,'file') + disp_uvmat('ERROR',['first input image ' ImageName_B ' does not exist'],checkrun) + return + end + [FileType_B,FileInfo_B,VideoObject_B]=get_file_type(ImageName_B); + [par_civ1.ImageB,VideoObject_B] = read_image(ImageName_B,FileType_B,VideoObject_B,FrameIndex_B_Civ1(1)); + NbField=numel(i1_series_Civ1); + elseif Param.ActionInput.CheckCiv2 % Civ2 is performed without Civ1 + ImageName_A=fullfile_uvmat(RootPath_A,SubDir_A,RootFile_A,FileExt_A,NomType_A,i1_series_Civ2(1),[],j1_series_Civ2(1)); + if ~exist(ImageName_A,'file') + disp_uvmat('ERROR',['first input image ' ImageName_A ' does not exist'],checkrun) + return + end + [FileType_A,FileInfo_A,VideoObject_A]=get_file_type(ImageName_A); + [par_civ1.ImageA,VideoObject_A] = read_image(ImageName_A,FileType_A,VideoObject_A,FrameIndex_A_Civ2(1)); + ImageName_B=fullfile_uvmat(RootPath_B,SubDir_B,RootFile_B,FileExt_B,NomType_B,i2_series_Civ2(1),[],j2_series_Civ2(1)); + if ~exist(ImageName_B,'file') + disp_uvmat('ERROR',['first input image ' ImageName_B ' does not exist'],checkrun) + return + end + [FileType_B,FileInfo_B,VideoObject_B]=get_file_type(ImageName_B); + [par_civ1.ImageB,VideoObject_B] = read_image(ImageName_B,FileType_B,VideoObject_B,FrameIndex_B_Civ2(1)); + NbField=numel(i1_series_Civ2); + end +catch ME + if ~isempty(ME.message) + disp_uvmat('ERROR', ['error reading input image: ' ME.message],checkrun) + return + end +end + %% Output directory @@ -237,11 +246,11 @@ Data.Program='civ_series'; Data.CivStage=0;%default -ListVarCiv1={'Civ1_X','Civ1_Y','Civ1_U','Civ1_V','Civ1_C','Civ1_F'}; %variables to read -ListVarFix1={'Civ1_X','Civ1_Y','Civ1_U','Civ1_V','Civ1_C','Civ1_F','Civ1_FF'}; -mask=''; +% ListVarCiv1={'Civ1_X','Civ1_Y','Civ1_U','Civ1_V','Civ1_C','Civ1_F'}; %variables to read +% ListVarFix1={'Civ1_X','Civ1_Y','Civ1_U','Civ1_V','Civ1_C','Civ1_F','Civ1_FF'}; +% mask=''; maskname='';%default check_civx=0;%default -check_civ1=0;%default -check_patch1=0;%default +% check_civ1=0;%default +% check_patch1=0;%default %% get timing from the ImaDoc file or input video @@ -303,19 +312,14 @@ if isfield (Param.ActionInput,'Civ1') par_civ1=Param.ActionInput.Civ1; - if isfield(par_civ1,'reverse_pair')% A REVOIR - if par_civ1.reverse_pair - if ischar(par_civ1.ImageB) - temp=par_civ1.ImageA; - par_civ1.ImageA=imread(par_civ1.ImageB); - end - if ischar(temp) - par_civ1.ImageB=imread(temp); - end - end - else + try ImageName_A=fullfile_uvmat(RootPath_A,SubDir_A,RootFile_A,FileExt_A,NomType_A,i1_series_Civ1(ifield),[],j1_series_Civ1(ifield)); [par_civ1.ImageA,VideoObject_A] = read_image(ImageName_A,FileType_A,VideoObject_A,FrameIndex_A_Civ1(ifield)); ImageName_B=fullfile_uvmat(RootPath_B,SubDir_B,RootFile_B,FileExt_B,NomType_B,i2_series_Civ1(ifield),[],j2_series_Civ1(ifield)); [par_civ1.ImageB,VideoObject_B] = read_image(ImageName_B,FileType_B,VideoObject_B,FrameIndex_B_Civ1(ifield)); + catch ME + if ~isempty(ME.message) + disp_uvmat('ERROR', ['error reading input image: ' ME.message],checkrun) + return + end end par_civ1.ImageWidth=FileInfo_A.Width;