%'sub_background': substract a sliding background to an image series %------------------------------------------------------------------------ % Method: %calculate the background image by sorting the luminosity of each point % over a sliding sub-sequence of 'nbaver_ima' images. % The luminosity value of rank 'rank' is selected as the % 'background'. rank=nbimages/2 gives the median value. Smaller values are appropriate % for a dense set of particles. The extrem value rank=1 gives the true minimum % luminosity, but it can be polluted by noise. % Organization of image indices: % The program is working on a series of images, % In the mode 'volume', nbfield2=1 (1 image at each level)and NbSlice (=nbfield_j) % Else nbfield2=nbfield_j =nbre of images in a burst (j index) % function GUI_config=sub_background(Param) % %%%%%%%%%%% GENERAL TO ALL SERIES ACTION FCTS %%%%%%%%%%%%%%%%%%%%%%%%%%% % %OUTPUT % ParamOut: sets options in the GUI series.fig needed for the function % %INPUT: % In run mode, the input parameters are given as a Matlab structure Param copied from the GUI series. % In batch mode, Param is the name of the corresponding xml file containing the same information % when Param.Action.RUN=0 (as activated when the current Action is selected % in series), the function ouput paramOut set the activation of the needed GUI elements % % Param contains the elements:(use the menu bar command 'export/GUI config' in series to % see the current structure Param) % .InputTable: cell of input file names, (several lines for multiple input) % each line decomposed as {RootPath,SubDir,Rootfile,NomType,Extension} % .OutputSubDir: name of the subdirectory for data outputs % .OutputDirExt: directory extension for data outputs % .Action: .ActionName: name of the current activated function % .ActionPath: path of the current activated function % .ActionExt: fct extension ('.m', Matlab fct, '.sh', compiled Matlab fct % .RUN =0 for GUI input, =1 for function activation % .RunMode='local','background', 'cluster': type of function use % % .IndexRange: set the file or frame indices on which the action must be performed % .FieldTransform: .TransformName: name of the selected transform function % .TransformPath: path of the selected transform function % .InputFields: sub structure describing the input fields withfields % .FieldName: name(s) of the field % .VelType: velocity type % .FieldName_1: name of the second field in case of two input series % .VelType_1: velocity type of the second field in case of two input series % .Coord_y: name of y coordinate variable % .Coord_x: name of x coordinate variable % .ProjObject: %sub structure describing a projection object (read from ancillary GUI set_object) %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% function ParamOut=sub_background (Param) %% input preparation mode (no RUN) if isstruct(Param) && isequal(Param.Action.RUN,0) ParamOut.AllowInputSort='off';% allow alphabetic sorting of the list of input file SubDir (options 'off'/'on', 'off' by default) ParamOut.WholeIndexRange='on';% prescribes the file index ranges from min to max (options 'off'/'on', 'off' by default) ParamOut.NbSlice='on'; %nbre of slices ('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) ParamOut.FieldTransform = 'off';%can use a transform function ParamOut.ProjObject='off';%can use projection object(option 'off'/'on', ParamOut.Mask='off';%can use mask option (option 'off'/'on', 'off' by default) ParamOut.OutputDirExt='.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 [filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param); if ~exist(filecell{1,1},'file') msgbox_uvmat('WARNING','the first input file does not exist') 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 ImageTypeOptions={'image','multimage','mmreader','video'};%allowed input file types(images) FileType=get_file_type(filecell{1,1}); CheckImage=~isempty(find(strcmp(FileType,ImageTypeOptions), 1));% =1 for images if ~CheckImage msgbox_uvmat('ERROR',['invalid file type input: ' FileType{1} ' not an image']) return 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 if nbfield_i~=1 nbaver=floor(nbaver_init/nbfield_j); % number of bursts used for the sliding background, if isequal(floor(nbaver/2),nbaver) nbaver=nbaver+1;%put the number of burst to an odd number (so the middle burst is defined) end nbaver_init=nbaver*nbfield_j;%propose by default an integer number of bursts 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 ParamOut.ActionInput.CheckVolume=strcmp(answer{1},'Yes'); ParamOut.ActionInput.SlidingSequenceLength=nbaver_ima; ParamOut.ActionInput.BrightnessRankThreshold=str2num(answer{3}); % apply the image rescaling function 'level' (avoid the blinking effects of bright particles) answer=msgbox_uvmat('INPUT_Y-N','apply image rescaling function levels.m after sub_background'); ParamOut.ActionInput.CheckLevelTransform=strcmp(answer,'Yes'); return end %%%%%%%%%%%%%%%%%%%%%% STOP HERE FOR PAMETER INPUT MODE %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %% read input parameters from an xml file if input is a file name (batch mode) checkrun=1; if ischar(Param) Param=xml2struct(Param);% read Param as input file (batch case) checkrun=0; end 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 %% Input preparation nbaver_ima=Param.ActionInput.SlidingSequenceLength; NbSlice=Param.IndexRange.NbSlice; if ~isequal(NbSlice,1) display(['multi-level splitting into ' num2str(NbSlice) ' slices']); end RootPath=Param.InputTable(:,1); RootFile=Param.InputTable(:,3); SubDir=Param.InputTable(:,2); NomType=Param.InputTable(:,4); FileExt=Param.InputTable(:,5); [filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param); [FileType{1},FileInfo{1},MovieObject{1}]=get_file_type(filecell{1,1}); if ~isempty(j1_series{1}) frame_index{1}=j1_series{1}; else frame_index{1}=i1_series{1}; end 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 %% Output FileExtOut='.png'; % write result as .png images for image inputs if strcmp(lower(NomType{1}(end)),'a') NomTypeOut=NomType{1};%case of letter appendix elseif isempty(j1_series) NomTypeOut='_1'; else NomTypeOut='_1_1';% caseof purely numerical indexing end OutputDir=[Param.OutputSubDir Param.OutputDirExt]; if isequal(Param.ActionInput.CheckVolume,1) step=1; else step=nbfield_j;%case of bursts: the sliding background is shifted by the length of one burst end nbaver_ima=Param.ActionInput.SlidingSequenceLength;%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; if nbaver_ima > nbfield display('number of images in a slice smaller than the proposed number of images for the sliding average') return end % calculate absolute brightness rank rank=floor(Param.ActionInput.BrightnessRankThreshold*nbaver_ima); if rank==0 rank=1;%rank selected in the sorted image series end %% prealocate memory for the sliding background try Afirst=read_image(filecell{1,1},FileType{1},MovieObject{1},frame_index{1}(1)); [npy,npx]=size(Afirst); if strcmp(class(Afirst),'uint8') % case of 8bit images Ak=zeros(npy,npx,nbaver_ima,'uint8'); %prealocate memory Asort=zeros(npy,npx,nbaver_ima,'uint8'); %prealocate memory else Ak=zeros(npy,npx,nbaver_ima,'uint16'); %prealocate memory Asort=zeros(npy,npx,nbaver_ima,'uint16'); %prealocate memory end catch ME msgbox_uvmat('ERROR',['sub_background/read_image/' ME.message]) return 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 indselect=1:step:nbfield;% select file indices of the slice for ifield=1:step-1 indselect=[indselect;indselect(end,:)+1]; end %% read the first series of nbaver_ima images and sort by luminosity at each pixel for ifield = 1:nbaver_ima ifile=indselect(ifield); filename=filecell{1,ifile}; Aread=read_image(filename,FileType{1},MovieObject{1},frame_index{1}(ifile)); if ndims(Aread)==3;%color images Aread=sum(double(Aread),3);% take the sum of color components end Ak(:,:,ifield)=Aread; end Asort=sort(Ak,3);%sort the luminosity of images at each point B=Asort(:,:,rank);%background image display( 'first background image will be substracted') nbfirst=(ceil(nbaver/2))*step; for ifield=1:nbfirst Acor=double(Ak(:,:,ifield))-double(B);%substract background to the current image Acor=(Acor>0).*Acor; % put to 0 the negative elements in Acor ifile=indselect(ifield); 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 %% repeat the operation on a sliding series of images 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 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 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 end end %% 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); Acor=(Acor>0).*Acor; % put to 0 the negative elements in Acor ifile=indselect(ifield); 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 function C=levels(A) %whos A; B=double(A(:,:,1)); windowsize=round(min(size(B,1),size(B,2))/20); windowsize=floor(windowsize/2)*2+1; ix=1/2-windowsize/2:-1/2+windowsize/2;% %del=np/3; %fct=exp(-(ix/del).^2); fct2=cos(ix/(windowsize-1)/2*pi/2); %Mfiltre=(ones(5,5)/5^2); %Mfiltre=fct2'; Mfiltre=fct2'*fct2; Mfiltre=Mfiltre/(sum(sum(Mfiltre))); C=filter2(Mfiltre,B); C(:,1:windowsize)=C(:,windowsize)*ones(1,windowsize); C(:,end-windowsize+1:end)=C(:,end-windowsize+1)*ones(1,windowsize); C(1:windowsize,:)=ones(windowsize,1)*C(windowsize,:); C(end-windowsize+1:end,:)=ones(windowsize,1)*C(end-windowsize,:); C=tanh(B./(2*C)); [n,c]=hist(reshape(C,1,[]),100); % figure;plot(c,n); [m,i]=max(n); c_max=c(i); [dummy,index]=sort(abs(c-c(i))); n=n(index); c=c(index); i_select = find(cumsum(n)<0.95*sum(n)); if isempty(i_select) i_select = 1:length(c); end c_select=c(i_select); n_select=n(i_select); cmin=min(c_select); cmax=max(c_select); C=(C-cmin)/(cmax-cmin)*256; C=uint8(C);