Index: /trunk/src/series/civ_series.m =================================================================== --- /trunk/src/series/civ_series.m (revision 675) +++ /trunk/src/series/civ_series.m (revision 676) @@ -546,6 +546,21 @@ Data.Civ2_ImageA=ImageName_A; Data.Civ2_ImageB=ImageName_B; - Data.Civ2_Time=1; - Data.Civ2_Dt=1; + i1=i1_series_Civ2(ifield); + i2=i1; + if ~isempty(i2_series_Civ2) + i2=i2_series_Civ2(ifield); + end + j1=1; + if ~isempty(j1_series_Civ2) + j1=j1_series_Civ2(ifield); + end + j2=j1; + if ~isempty(j2_series_Civ1) + j2=j2_series_Civ2(ifield); + end + Data.Civ2_Time=(time(i2+1,j2+1)+time(i1+1,j1+1))/2; + Data.Civ2_Dt=time(i2+1,j2+1)-time(i1+1,j1+1); +% Data.Civ2_Time=1; +% Data.Civ2_Dt=1; for ilist=1:length(list_param) Data.(Civ2_param{4+ilist})=Param.ActionInput.Civ2.(list_param{ilist}); Index: /trunk/src/series/merge_proj.m =================================================================== --- /trunk/src/series/merge_proj.m (revision 675) +++ /trunk/src/series/merge_proj.m (revision 676) @@ -129,7 +129,11 @@ diff_time=max(max(diff(time))); if diff_time>0 - disp_uvmat('WARNING',['times of series differ by (max) ' num2str(diff_time) ': time of first series chosen in result'],checkrun) + disp_uvmat('WARNING',['times of series differ by (max) ' num2str(diff_time) ': the mean time is chosen in result'],checkrun) end end +if ~isempty(errormsg) + disp_uvmat('WARNING',erromsg,checkrun) +end +time=mean(time,1); %averaged time taken for the merged field %% coordinate transform or other user defined transform @@ -174,4 +178,7 @@ MaskData=cell(NbView,1); if Param.CheckMask + if ischar(Param.MaskTable)% case of a single mask (char chain) + Param.MaskTable={Param.MaskTable}; + end for iview=1:numel(Param.MaskTable) if exist(Param.MaskTable{iview},'file') @@ -204,5 +211,5 @@ %%%%%%%%%%%%%%%% loop on views (input lines) %%%%%%%%%%%%%%%% Data=cell(1,NbView);%initiate the set Data - nbtime=0; + timeread=zeros(1,NbView); for iview=1:NbView %% reading input file(s) @@ -212,8 +219,7 @@ return end - timeread(iview)=0; - if isfield(Data{iview},'Time') + % get the time defined in the current file if not already defined from the xml file + if ~isempty(time) && isfield(Data{iview},'Time') timeread(iview)=Data{iview}.Time; - nbtime=nbtime+1; end if ~isempty(NbSlice_calib) @@ -258,8 +264,11 @@ %% time of the merged field: take the average of the different views - if ~isempty(time)% time defined from ImaDoc - timeread=time(:,index); - end - timeread=mean(timeread); + if ~isempty(time) + timeread=time(index); + elseif ~isempty(find(timeread))% time defined from ImaDoc + timeread=mean(timeread(timeread~=0));% take average over times form the files (when defined) + else + timeread=index;% take time=file index + end %% generating the name of the merged field @@ -320,5 +329,5 @@ else - MergeData.ListGlobalAttribute={'Conventions','Project','InputFile_1','InputFile_end','nb_coord','nb_dim','dt','Time','civ'}; + MergeData.ListGlobalAttribute={'Conventions','Project','InputFile_1','InputFile_end','nb_coord','nb_dim'}; MergeData.Conventions='uvmat'; MergeData.nb_coord=2; @@ -333,10 +342,12 @@ end end - if isempty(dt) - MergeData.ListGlobalAttribute(6)=[]; - else + if ~isempty(timeread) + MergeData.ListGlobalAttribute=[MergeData.ListGlobalAttribute {'Time'}]; + MergeData.Time=timeread; + end + if ~isempty(dt) + MergeData.ListGlobalAttribute=[MergeData.ListGlobalAttribute {'dt'}]; MergeData.dt=dt; end - MergeData.Time=timeread; error=struct2nc(OutputFile,MergeData);%save result file if isempty(error) @@ -381,5 +392,5 @@ case 'grid' %case of fields defined on a structured grid FFName=''; - if ~isempty(CellInfo{icell}.VarIndex_errorflag) + if isfield(CellInfo{icell},'VarIndex_errorflag') && ~isempty(CellInfo{icell}.VarIndex_errorflag) FFName=Data{1}.ListVarName{CellInfo{icell}.VarIndex_errorflag};% name of errorflag variable end Index: /trunk/src/series/sub_background.m =================================================================== --- /trunk/src/series/sub_background.m (revision 675) +++ /trunk/src/series/sub_background.m (revision 676) @@ -53,5 +53,5 @@ function ParamOut=sub_background (Param) -%% input preparation mode (no RUN) +%%%%%%%%%%%%%%%%% 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) @@ -65,6 +65,4 @@ ParamOut.OutputDirExt='.sback';%set the output dir extension ParamOut.OutputFileMode='NbInput';% '=NbInput': 1 output file per input file index, '=NbInput_i': 1 file per input file index i, '=NbSlice': 1 file per slice - filecell=get_file_series(Param);%check existence of the first input file - %%%%%%%%%%%% STANDARD PART (DO NOT EDIT) %%%%%%%%%%%% %% root input file(s) and type @@ -74,37 +72,4 @@ return end - %%%%%%%%%%%% - % The cell array filecell is the list of input file names, while - % filecell{iview,fileindex}: - % iview: line in the table corresponding to a given file series - % fileindex: file index within the file series, - % i1_series(iview,ref_j,ref_i)... are the corresponding arrays of indices i1,i2,j1,j2, depending on the input line iview and the two reference indices ref_i,ref_j - % i1_series(iview,fileindex) expresses the same indices as a 1D array in file indices - %%%%%%%%%%%% - NbSlice=1;%default - if isfield(Param.IndexRange,'NbSlice')&&~isempty(Param.IndexRange.NbSlice) - NbSlice=Param.IndexRange.NbSlice; - end - nbview=numel(i1_series);%number of input file series (lines in InputTable) - nbfield_j=size(i1_series{1},1); %nb of fields for the j index (bursts or volume slices) - nbfield_i=size(i1_series{1},2); %nb of fields for the i index - nbfield=nbfield_j*nbfield_i; %total number of fields - nbfield_i=floor(nbfield/NbSlice);%total number of indexes in a slice (adjusted to an integer number of slices) - nbfield=nbfield_i*NbSlice; %total number of fields after adjustement - - %determine the file type on each line from the first input file - - - %% calibration data and timing: read the ImaDoc files - %not relevant here - - %% check coincidence in time for several input file series - %not relevant here - - %% coordinate transform or other user defined transform - %not relevant here - - %%%%%%%%%%%% END STANDARD PART %%%%%%%%%%%% - % EDIT FROM HERE %% check the validity of input file types @@ -117,20 +82,17 @@ end - %% Set field names and velocity types - %not relevant here - - %% Initiate output fields - %not relevant here - - %%% SPECIFIC PART BEGINS HERE - NbSlice=1; - if isfield(Param.IndexRange,'NbSlice') - NbSlice=Param.IndexRange.NbSlice; %number of slices - end - %siz=size(i1_series); - nbaver_init=23;%approximate number of images used for the sliding background: to be adjusted later to include an integer number of bursts - j1=[];%default - - %% adjust the proposed number of images in the sliding average to include an integer number of bursts + %% numbers of fields + NbSlice=1;%default + if isfield(Param.IndexRange,'NbSlice')&&~isempty(Param.IndexRange.NbSlice) + NbSlice=Param.IndexRange.NbSlice; + end + %nbview=numel(i1_series);%number of input file series (lines in InputTable) + nbfield_j=size(i1_series{1},1); %nb of fields for the j index (bursts or volume slices) + nbfield_i=size(i1_series{1},2); %nb of fields for the i index + nbfield=nbfield_j*nbfield_i; %total number of fields + nbfield_i=floor(nbfield/NbSlice);%total number of indexes in a slice (adjusted to an integer number of slices) + + %% setting of parameters specific to sub_background + nbaver_init=23; %default number of images used for the sliding background: to be adjusted later to include an integer number of bursts if nbfield_i~=1 nbaver=floor(nbaver_init/nbfield_j); % number of bursts used for the sliding background, @@ -141,33 +103,29 @@ end - %% input of specific parameters - %if checkrun %get specific parameters interactively - if isequal(Param.Action.RUN,0) - prompt = {'volume scan mode (Yes/No)';'Number of images for the sliding background (MUST FIT IN COMPUTER MEMORY)';... - 'the luminosity rank chosen to define the background (0.1=for dense particle seeding, 0.5 (median) for sparse particles'}; - dlg_title = 'get (slice by slice) a sliding background and substract to each image'; - num_lines= 3; - def = { 'No';num2str(nbaver_init);'0.1'}; - answer = inputdlg(prompt,dlg_title,num_lines,def); - - %check input consistency - if strcmp(answer{1},'No') && ~isequal(NbSlice,1) - check=msgbox_uvmat('INPUT_Y-N',['confirm the multi-level splitting into ' num2str(NbSlice) ' slices']); - if ~strcmp(check,'Yes') - return - end - end - if strcmp(answer{1},'Yes') - step=1; - else - step=nbfield_j;%case of bursts: the sliding background is shifted by the length of one burst - end - nbaver_ima=str2num(answer{2});%number of images for the sliding background - nbaver=ceil(nbaver_ima/step);%number of bursts for the sliding background - if isequal(floor(nbaver/2),nbaver) - nbaver=nbaver+1;%set the number of bursts to an odd number (so the middle burst is defined) - end - nbaver_ima=nbaver*step; - end + prompt = {'volume scan mode (Yes/No)';'Number of images for the sliding background (MUST FIT IN COMPUTER MEMORY)';... + 'the luminosity rank chosen to define the background (0.1=for dense particle seeding, 0.5 (median) for sparse particles'}; + dlg_title = 'get (slice by slice) a sliding background and substract to each image'; + num_lines= 3; + def = { 'No';num2str(nbaver_init);'0.1'}; + answer = inputdlg(prompt,dlg_title,num_lines,def); + + %check input consistency + if strcmp(answer{1},'No') && ~isequal(NbSlice,1) + check=msgbox_uvmat('INPUT_Y-N',['confirm the multi-level splitting into ' num2str(NbSlice) ' slices']); + if ~strcmp(check,'Yes') + return + end + end + if strcmp(answer{1},'Yes') + step=1; + else + step=nbfield_j;%case of bursts: the sliding background is shifted by the length of one burst + end + nbaver_ima=str2num(answer{2});%number of images for the sliding background + nbaver=ceil(nbaver_ima/step);%number of bursts for the sliding background + if isequal(floor(nbaver/2),nbaver) + nbaver=nbaver+1;%set the number of bursts to an odd number (so the middle burst is defined) + end + nbaver_ima=nbaver*step;% correct the nbre of images corresponding to nbaver ParamOut.ActionInput.CheckVolume=strcmp(answer{1},'Yes'); ParamOut.ActionInput.SlidingSequenceLength=nbaver_ima; @@ -179,5 +137,5 @@ return end -%%%%%%%%%%%%%%%%%%%%%% STOP HERE FOR PAMETER INPUT MODE %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% +%%%%%%%%%%%%%%%%% STOP HERE FOR PAMETER INPUT MODE %%%%%%%%%%%%%%%%% %% read input parameters from an xml file if input is a file name (batch mode) @@ -190,5 +148,6 @@ RUNHandle=findobj(hseries,'Tag','RUN');%handle of RUN button in GUI series WaitbarHandle=findobj(hseries,'Tag','Waitbar');%handle of waitbar in GUI series -%% Input preparation + +%% input preparation nbaver_ima=Param.ActionInput.SlidingSequenceLength; NbSlice=Param.IndexRange.NbSlice; @@ -202,4 +161,12 @@ FileExt=Param.InputTable(:,5); [filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param); +%%%%%%%%%%%% + % The cell array filecell is the list of input file names, while + % filecell{iview,fileindex}: + % iview: line in the table corresponding to a given file series + % fileindex: file index within the file series, + % i1_series(iview,ref_j,ref_i)... are the corresponding arrays of indices i1,i2,j1,j2, depending on the input line iview and the two reference indices ref_i,ref_j + % i1_series(iview,fileindex) expresses the same indices as a 1D array in file indices +%%%%%%%%%%%% [FileType{1},FileInfo{1},MovieObject{1}]=get_file_type(filecell{1,1}); if ~isempty(j1_series{1}) @@ -214,5 +181,5 @@ nbfield=nbfield_i*NbSlice; %total number of fields after adjustement -%% Output +%% output FileExtOut='.png'; % write result as .png images for image inputs if strcmp(lower(NomType{1}(end)),'a') @@ -264,58 +231,13 @@ end -%% update the xml file -% SubDirBase=regexprep(Param.InputTable{1,2},'\..*','');%take the root part of SubDir, before the first dot '.' -% filexml=fullfile(RootPath{1},[SubDirBase '.xml']); -% if ~exist(filexml,'file') && exist([fullfile(RootPath{1},SubDir{1},RootFile{1}) '.xml'],'file')% xml inside the image directory -% copyfile([filebase '.xml'],filexml);% copy the .xml file -% end -% if exist(filexml,'file') -% t=xmltree(filexml); -% %update information on the first image name in the series -% uid_Heading=find(t,'ImaDoc/Heading'); -% if isempty(uid_Heading) -% [t,uid_Heading]=add(t,1,'element','Heading'); -% end -% uid_ImageName=find(t,'ImaDoc/Heading/ImageName'); -% if ~isempty(j1_series{1}) -% j1=j1_series{1}(1); -% end -% ImageName=fullfile_uvmat([dir_images term],'',RootFile{1},'.png',NomType,i1_series(1,1),[],j1); -% [pth,ImageName]=fileparts(ImageName); -% ImageName=[ImageName '.png']; -% if isempty(uid_ImageName) -% [t,uid_ImageName]=add(t,uid_Heading,'element','ImageName'); -% end -% uid_value=children(t,uid_ImageName); -% if isempty(uid_value) -% t=add(t,uid_ImageName,'chardata',ImageName);%indicate name of the first image, with ;png extension -% else -% t=set(t,uid_value(1),'value',ImageName);%indicate name of the first image, with ;png extension -% end -% -% %add information about image transform -% [t,new_uid]=add(t,1,'element','ImageTransform'); -% [t,NameFunction_uid]=add(t,new_uid,'element','NameFunction'); -% [t]=add(t,NameFunction_uid,'chardata','sub_background'); -% if GUI_config.CheckLevel -% [t,NameFunction_uid]=add(t,new_uid,'element','NameFunction'); -% [t]=add(t,NameFunction_uid,'chardata','levels'); -% end -% [t,NbSlice_uid]=add(t,new_uid,'element','NbSlice'); -% [t]=add(t,new_uid,'chardata',num2str(NbSlice)); -% [t,NbSlidingImages_uid]=add(t,new_uid,'element','NbSlidingImages'); -% [t]=add(t,NbSlidingImages_uid,'chardata',num2str(nbaver)); -% [t,LuminosityRank_uid]=add(t,new_uid,'element','RankBackground'); -% [t]=add(t,LuminosityRank_uid,'chardata',num2str(rank));% luminosity rank almong the nbaver sliding images -% save(t,filexml) -% end -%copy the mask -% if exist([filebase '_1mask_1'],'file') -% copyfile([filebase '_1mask_1'],[filebase_b '_1mask_1']);% copy the mask file -% end - -%MAIN LOOP ON SLICES -% for islice=1:NbSlice -%% select the series of image indices +%% summary of the parameters: +% nbfield : total number of images treated (in case of multislices the function sub_background is repeated for each slice) +% step: shift at each step of the sliding background (corresponding to the nbre of images in a burst) +% nbaver_ima: length of the sequence used for the sliding background + +% nbaver=nbaver_ima/step: nbaver_ima has been adjusted so that nbaver is an odd integer +halfnbaver=floor(nbaver/2); % half width (in unit of bursts) of the sliding background + +%% select the series of image indices to process indselect=1:step:nbfield;% select file indices of the slice for ifield=1:step-1 @@ -335,7 +257,8 @@ Asort=sort(Ak,3);%sort the luminosity of images at each point B=Asort(:,:,rank);%background image + +%% substract the first background image to the first images display( 'first background image will be substracted') -nbfirst=(ceil(nbaver/2))*step; -for ifield=1:nbfirst +for ifield=1:step*(halfnbaver+1);% nbre of images treated by the first background image Acor=double(Ak(:,:,ifield))-double(B);%substract background to the current image Acor=(Acor>0).*Acor; % put to 0 the negative elements in Acor @@ -365,52 +288,47 @@ display('sliding background image will be substracted') if nbfield_i > nbaver_ima - for ifield = step*ceil(nbaver/2)+1:step:nbfield_i-step*floor(nbaver/2) - update_waitbar(WaitbarHandle,ifield/nbfield_i) - if ~isempty(RUNHandle) &&ishandle(RUNHandle) && ~strcmp(get(RUNHandle,'BusyAction'),'queue') - disp('program stopped by user') - return - end -% if isequal(stopstate,'queue')% enable STOP command - Ak(:,:,1:nbaver_ima-step)=Ak(:,:,1+step:nbaver_ima);% shift the current image series by one burst (step) - %incorporate next burst in the current image series - for iburst=1:step - ifile=indselect(ifield+step*floor(nbaver/2)+iburst-1); - filename=fullfile_uvmat(RootPath{1},SubDir{1},RootFile{1},FileExt{1},NomType{1},i1_series{1}(ifile),[],j1_series{1}(ifile)); - Aread=read_image(filename,FileType{1},MovieObject{1},i1_series{1}(ifile)); - if ndims(Aread)==3;%color images - Aread=sum(double(Aread),3);% take the sum of color components + for ifield = step*(halfnbaver+1):step:nbfield_i-step*(halfnbaver+1)% ifield +iburst=index of the current processed image + update_waitbar(WaitbarHandle,ifield/nbfield_i) + if ~isempty(RUNHandle) &&ishandle(RUNHandle) && ~strcmp(get(RUNHandle,'BusyAction'),'queue') + disp('program stopped by user') + return + end + Ak(:,:,1:nbaver_ima-step)=Ak(:,:,1+step:nbaver_ima);% shift the current image series by one burst (step) + %incorporate next burst in the current image series + for iburst=1:step + ifile=indselect(ifield+iburst+step*halfnbaver); + filename=fullfile_uvmat(RootPath{1},SubDir{1},RootFile{1},FileExt{1},NomType{1},i1_series{1}(ifile),[],j1_series{1}(ifile)); + Aread=read_image(filename,FileType{1},MovieObject{1},i1_series{1}(ifile)); + if ndims(Aread)==3;%color images + Aread=sum(double(Aread),3);% take the sum of color components + end + Ak(:,:,nbaver_ima-step+iburst)=Aread;% fill the last burst of the current image series by the new image + end + Asort=sort(Ak,3);%sort the new current image series by luminosity + B=Asort(:,:,rank);%current background image + %substract the background for the current burst + for iburst=1:step + Acor=double(Ak(:,:,step*halfnbaver+iburst))-double(B); %the current image has been already read ans stored as index step*halfnbaver+iburst in the current series + Acor=(Acor>0).*Acor; % put to 0 the negative elements in Acor + ifile=indselect(ifield+iburst); + if ~isempty(j1_series{1}) + j1=j1_series{1}(ifile); + end + newname=fullfile_uvmat(RootPath{1},OutputDir,RootFile{1},FileExtOut,NomTypeOut,i1_series{1}(ifile),[],j1); + %write result file + if Param.ActionInput.CheckLevelTransform + C=levels(Acor); + imwrite(C,newname,'BitDepth',8); % save the new image + else + if isequal(FileInfo{1}.BitDepth,16) + C=uint16(Acor); + imwrite(C,newname,'BitDepth',16); % save the new image + else + C=uint8(Acor); + imwrite(C,newname,'BitDepth',8); % save the new image end - Ak(:,:,nbaver_ima-step+iburst)=Aread; end - Asort=sort(Ak,3);%sort the new current image series by luminosity - B=Asort(:,:,rank);%current background image - for iburst=1:step - index=step*floor(nbaver/2)+iburst; - Acor=double(Ak(:,:,index))-double(B); - Acor=(Acor>0).*Acor; % put to 0 the negative elements in Acor - ifile=indselect(ifield+iburst-1); - if ~isempty(j1_series{1}) - j1=j1_series{1}(ifile); - end - newname=fullfile_uvmat(RootPath{1},OutputDir,RootFile{1},FileExtOut,NomTypeOut,i1_series{1}(ifile),[],j1); - %write result file - if Param.ActionInput.CheckLevelTransform - C=levels(Acor); - imwrite(C,newname,'BitDepth',8); % save the new image - else - if isequal(FileInfo{1}.BitDepth,16) - C=uint16(Acor); - imwrite(C,newname,'BitDepth',16); % save the new image - else - C=uint8(Acor); - imwrite(C,newname,'BitDepth',8); % save the new image - end - end - display([newname ' written']) - - end -% else -% return -% end + display([newname ' written']) + end end end @@ -418,8 +336,6 @@ %% substract the background from the last images display('last background image will be substracted') -ifield=nbfield_i-(step*ceil(nbaver/2))+1:nbfield_i; -for ifield=nbfield_i-(step*floor(nbaver/2))+1:nbfield_i - index=ifield-nbfield_i+step*(2*floor(nbaver/2)+1); - Acor=double(Ak(:,:,index))-double(B); +for ifield=nbfield_i-step*halfnbaver+1:nbfield_i + Acor=double(Ak(:,:,ifield-nbfield_i+step*(2*halfnbaver+1)))-double(B); Acor=(Acor>0).*Acor; % put to 0 the negative elements in Acor ifile=indselect(ifield); @@ -427,6 +343,5 @@ j1=j1_series{1}(ifile); end - newname=fullfile_uvmat(RootPath{1},OutputDir,RootFile{1},FileExtOut,NomTypeOut,i1_series{1}(ifile),[],j1); - + newname=fullfile_uvmat(RootPath{1},OutputDir,RootFile{1},FileExtOut,NomTypeOut,i1_series{1}(ifile),[],j1); %write result file if Param.ActionInput.CheckLevelTransform Index: /trunk/src/series/time_series.m =================================================================== --- /trunk/src/series/time_series.m (revision 675) +++ /trunk/src/series/time_series.m (revision 676) @@ -214,4 +214,5 @@ %%%%%%%%%%%%%%%% loop on field indices %%%%%%%%%%%%%%%% for index=1:nbfield + index update_waitbar(WaitbarHandle,index/nbfield) if ~isempty(RUNHandle) && ~strcmp(get(RUNHandle,'BusyAction'),'queue')