Index: /trunk/src/series.m =================================================================== --- /trunk/src/series.m (revision 927) +++ /trunk/src/series.m (revision 928) @@ -1504,5 +1504,5 @@ end end - +ActionFullName=fullfile(get(handles.ActionPath,'String'),ActionName); %% If a compiled version has been selected (ext .sh) check weather it needs to be recompiled if strcmp(ActionExt,'.sh') Index: /trunk/src/series/extract_rdvision.m =================================================================== --- /trunk/src/series/extract_rdvision.m (revision 927) +++ /trunk/src/series/extract_rdvision.m (revision 928) @@ -64,5 +64,5 @@ 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='one'; ...%nbre of slices, 'one' prevents splitting in several processes, ('off' by default) + ParamOut.NbSlice=1; ...%nbre of slices, 1 prevents splitting in several processes, ('off' by default) 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) @@ -184,10 +184,10 @@ checkpreserve=0;% if =1, will npreserve the original images, else it erases them at the end for iview=1:size(Param.InputTable,1) - for iview_xml=1:size(Param.InputTable,1)% loojk for the xml files in the different data directories - filexml=[fullfile(RootPath,Param.InputTable{iview_xml,2},Param.InputTable{iview,3}) '.xml'];%new convention: xml at the level of the image folder - if exist(filexml,'file') - break - end - end + for iview_xml=1:size(Param.InputTable,1)% look for the xml files in the different data directories + filexml=[fullfile(RootPath,Param.InputTable{iview_xml,2},Param.InputTable{iview,3}) '.xml'];%new convention: xml at the level of the image folder + if exist(filexml,'file') + break + end + end if ~exist(filexml,'file') disp_uvmat('ERROR',[filexml ' missing'],checkrun) @@ -195,6 +195,7 @@ end [XmlData,errormsg]=imadoc2struct(filexml); - - newxml=[fullfile(RootPath,Param.InputTable{iview,3}) '.xml'] + newxml=fullfile(RootPath,Param.InputTable{iview,3}); + newxml=regexprep(newxml,'_Master_Dalsa_4M180$','');%suppress '_Master_Dalsa_4M180' + newxml=[newxml '.xml']; [success,errormsg] = copyfile(filexml,newxml); %copy the xml file in the upper folder @@ -306,15 +307,13 @@ end end - - % check images - -% delete(fullfile(RootPath,'Running.xml'))%delete the xml file to indicate that processing is finished -% if ~checkpreserve -% for ibin=1:numel(BinList) -% delete(BinList{ibin}) -% end -% rmdir(fullfile(RootPath,Param.InputTable{iview,2})) -% end -end +end + +%% remove binary files if transfer OK + if ~checkpreserve + for ibin=1:numel(BinList) + delete(BinList{ibin}) + end + rmdir(fullfile(RootPath,Param.InputTable{iview,2})) + end delete(fullfile(RootPath,'Running.xml'))%delete the xml file to indicate that processing is finished @@ -352,5 +351,7 @@ BitDepth=8*SeqData.bytesperpixel;%needed to write images (8 or 16 bits) binrepertoire=fullfile(PathDir,SeqData.binrepertoire); -OutputDir=fullfile(PathDir,SeqData.sequencename); +FileDir=SeqData.sequencename; +FileDir=regexprep(FileDir,'_Master_Dalsa_4M180$','');%suppress '_Master_Dalsa_4M180' +OutputDir=fullfile(PathDir,FileDir); if ~exist(OutputDir,'dir') % errormsg=[OutputDir ' already exist, delete it first']; @@ -371,5 +372,5 @@ end i1=floor((ii-1)/nbfield2)+1; - OutputFile=fullfile_uvmat(PathDir,SeqData.sequencename,'img','.png',NomTypeNew,i1,[],j1);% TODO: set NomTypeNew from SeqData.mode + OutputFile=fullfile_uvmat(PathDir,FileDir,'img','.png',NomTypeNew,i1,[],j1);% TODO: set NomTypeNew from SeqData.mode fname=fullfile(binrepertoire,sprintf('%s%.5d.bin',SeqData.binfile,SqbData(ii).file_idx)); if exist(OutputFile,'file') Index: /trunk/src/transform_field/ima_edge_detection.m =================================================================== --- /trunk/src/transform_field/ima_edge_detection.m (revision 927) +++ /trunk/src/transform_field/ima_edge_detection.m (revision 928) @@ -4,5 +4,5 @@ %%%% Use the general syntax for transform fields with a single input and parameters %%%% % OUTPUT: -% DataOut: output field structure +% Data: output field structure % %INPUT: @@ -29,8 +29,8 @@ %======================================================================= -function DataOut=ima_edge_detection(DataIn,Param) +function Data=ima_edge_detection(Data,Param,Data_1) %% request input parameters -if isfield(DataIn,'Action') && isfield(DataIn.Action,'RUN') && isequal(DataIn.Action.RUN,0) +if isfield(Data,'Action') && isfield(Data.Action,'RUN') && isequal(Data.Action.RUN,0) prompt = {'npx';'npy';'threshold'}; dlg_title = 'get the filter size in x and y'; @@ -42,12 +42,10 @@ end answer = inputdlg(prompt,dlg_title,num_lines,def); - DataOut.TransformInput.FilterBoxSize_x=str2num(answer{1}); %size of the filtering window - DataOut.TransformInput.FilterBoxSize_y=str2num(answer{2}); %size of the filtering window - DataOut.TransformInput.LumThreshold=str2num(answer{3}); %size of the filtering window + Data.TransformInput.FilterBoxSize_x=str2num(answer{1}); %size of the filtering window + Data.TransformInput.FilterBoxSize_y=str2num(answer{2}); %size of the filtering window + Data.TransformInput.LumThreshold=str2num(answer{3}); %size of the filtering window return end -DataOut=DataIn; %default -%DataOut.A=255*edge(DataIn.A); %definition of the cos shape matrix filter @@ -62,28 +60,38 @@ Mfiltre=Mfiltre/(sum(sum(Mfiltre)));%normalize filter +Afilt=filter2(Mfiltre,Data.A);% smooth the image, excluding the edges (spurious reflexions) + + %Afilt=filter2(Mfiltre,Data.A(100:end-100,100:end-100));% smooth the image, excluding the edges (spurious reflexions) + %Data.A= double(Data.A)-Afilt; - Afilt=filter2(Mfiltre,DataIn.A(100:end-100,100:end-100));% smooth the image, excluding the edges (spurious reflexions) + + +% Amax=max(max(Afilt)); Amin=min(min(Afilt)); +% Data.A( Data_1.A(100:end-100,100:end-100)==100)=(Amin+Amax)/2; + + + Athreshold=(Amin+Amax)*Param.TransformInput.LumThreshold; % -% DataOut.A=zeros(size(DataIn.A,1),size(DataIn.A,2),3); - DataOut.A=(DataIn.A>Athreshold);%transform to the initial image format -% DataOut.A(:,:,1)=DataIn.A;%transform to the initial image format, red -STATS = regionprops(DataOut.A, 'FilledArea','MinorAxisLength','MajorAxisLength','PixelIdxList'); +% Data.A=zeros(size(Data.A,1),size(Data.A,2),3); + Data.A=(Data.A>Athreshold);%transform to the initial image format +% Data.A(:,:,1)=Data.A;%transform to the initial image format, red +STATS = regionprops(Data.A, 'FilledArea','MinorAxisLength','MajorAxisLength','PixelIdxList'); Area=zeros(size(STATS)); for iobj=1:numel(STATS) Area(iobj)=STATS(iobj).FilledArea; end -[Area, main_obj]=max(Area); - MajorAxisLength=STATS(main_obj).MajorAxisLength - MinorAxisLength=STATS(main_obj).MinorAxisLength +[Area, main_obj]=max(Area) + MajorAxisLength=STATS(main_obj).MajorAxisLength; + MinorAxisLength=STATS(main_obj).MinorAxisLength; for iobj=1:numel(STATS) if iobj~=main_obj - DataOut.A(STATS(iobj).PixelIdxList)=0; + Data.A(STATS(iobj).PixelIdxList)=0; end end -DataOut.A=Amax*DataOut.A; +Data.A=Amax*Data.A; Index: /trunk/src/transform_field/ima_patch_detection.m =================================================================== --- /trunk/src/transform_field/ima_patch_detection.m (revision 927) +++ /trunk/src/transform_field/ima_patch_detection.m (revision 928) @@ -87,5 +87,8 @@ DataOut=DataIn; %default %Amask=imread('/fsnet/project/coriolis/2015/15MINI_MEDDY/0_REF_FILES/mask_patch.png'); -plot_mask(DataIn.A,Param.TransformInput.LumThreshold) +hfig=findobj(allchild(0),'Tag','set_threshold'); +hThreshold=findobj(hfig,'Tag','Threshold'); +Threshold=str2num(get(hThreshold,'String')); +plot_mask(DataIn.A,Threshold) % Athreshold=Param.TransformInput.LumThreshold; % %