%'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) %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %======================================================================= % Copyright 2008-2024, LEGI UMR 5519 / CNRS UGA G-INP, Grenoble, France % http://www.legi.grenoble-inp.fr % Joel.Sommeria - Joel.Sommeria (A) univ-grenoble-alpes.fr % % This file is part of the toolbox UVMAT. % % UVMAT is free software; you can redistribute it and/or modify % it under the terms of the GNU General Public License as published % by the Free Software Foundation; either version 2 of the license, % or (at your option) any later version. % % UVMAT is distributed in the hope that it will be useful, % but WITHOUT ANY WARRANTY; without even the implied warranty of % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the % GNU General Public License (see LICENSE.txt) for more details. %======================================================================= 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'; % edit box nbre of slices made active 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 (option 'off'/'on','off' by default) ParamOut.ProjObject='off';%cannot use projection object(option 'off'/'on','off' by default) ParamOut.Mask='off';%cannot 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 %% check the validity of input file types if isfield(Param,'SeriesData')&& isfield(Param.SeriesData,'FileInfo') if ~strcmp(Param.SeriesData.FileInfo{1}.FieldType,'image') msgbox_uvmat('ERROR','invalid file type input: not an image series') return end end %% numbers of fields NbSlice_i=1;%default if isfield(Param.IndexRange,'NbSlice')&&~isempty(Param.IndexRange.NbSlice) NbSlice_i=Param.IndexRange.NbSlice; end incr_j=1;%default if isfield(Param.IndexRange,'incr_j')&&~isempty(Param.IndexRange.incr_j) incr_j=Param.IndexRange.incr_j; end if isfield(Param.IndexRange,'first_j')&&~isempty(Param.IndexRange.first_j) NbField_j=numel(Param.IndexRange.first_j:incr_j:Param.IndexRange.last_j);%nb of fields for the j index (bursts or volume slices) else NbField_j=1; end first_i=1;last_i=1;incr_i=1;%default if isfield(Param.IndexRange,'MinIndex_i'); first_i=Param.IndexRange.MinIndex_i; end if isfield(Param.IndexRange,'MaxIndex_i'); last_i=Param.IndexRange.MaxIndex_i; end if isfield(Param.IndexRange,'incr_i')&&~isempty(Param.IndexRange.incr_i) incr_i=Param.IndexRange.incr_i; end nbfield_i=numel(first_i:incr_i:last_i);%nb of fields for the i index (bursts or volume slices) nbfield=NbField_j*nbfield_i; %total number of fields nbfield_i=floor(nbfield/NbSlice_i);%total number of indexes in a slice (adjusted to an integer number of slices) %% setting of parameters specific to sub_background CheckVolume='No'; nbaver_init=23; %default number of images used for the sliding background: to be adjusted later to include an integer number of bursts SaturationValue=0; if nbfield_i~=1 && NbField_j<=nbaver_init nbaver=floor(nbaver_init/NbField_j); % number of bursts used for the sliding background, if isequal(mod(nbaver,2),0)% if nbaver is even 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 BrightnessRankThreshold=0.1; if isfield(Param,'ActionInput') if isfield(Param.ActionInput,'CheckVolume') && Param.ActionInput.CheckVolume CheckVolume='Yes'; end if isfield(Param.ActionInput,'SlidingSequenceLength') nbaver_init=Param.ActionInput.SlidingSequenceLength; end if isfield(Param.ActionInput,'BrightnessRankThreshold') BrightnessRankThreshold=Param.ActionInput.BrightnessRankThreshold; end if isfield(Param.ActionInput,'SaturationValue') SaturationValue=Param.ActionInput.SaturationValue; end 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';... 'image saturation level for rescaling( reduce the influence of particles brighter than this value), =0 for no rescaling' }; dlg_title = 'get (slice by slice) a sliding background and substract to each image'; num_lines= 4; def = { CheckVolume;num2str(nbaver_init);num2str(BrightnessRankThreshold);num2str(SaturationValue)}; answer = inputdlg(prompt,dlg_title,num_lines,def); if isempty(answer) return end %check input consistency if strcmp(answer{1},'No') && ~isequal(NbSlice_i,1) check=msgbox_uvmat('INPUT_Y-N',['confirm the multi-level splitting into ' num2str(NbSlice_i) ' slices']); if ~strcmp(check,'Yes') return end end if strcmp(answer{1},'Yes') step=2;%the sliding background is shifted by the length of one burst, assumed =2 for volume ParamOut.NbSlice=1; %nbre of slices displayed else step=NbField_j;%case of bursts: the sliding background is shifted by the length of one burst end ParamOut.ActionInput.SlidingSequenceLength=adjust_slidinglength(str2double(answer{2}),step); ParamOut.ActionInput.CheckVolume=strcmp(answer{1},'Yes'); ParamOut.ActionInput.BrightnessRankThreshold=str2double(answer{3}); % ParamOut.ActionInput.CheckSubmedian=strcmp(answer{4},'Yes'); ParamOut.ActionInput.SaturationValue=str2double(answer{4}); % 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; RUNHandle=[]; % WaitbarHandle=[]; if ischar(Param) Param=xml2struct(Param);% read Param as input file (batch case) else 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 end %% input preparation NbSlice_i=Param.IndexRange.NbSlice; if ~isequal(NbSlice_i,1) disp(['multi-level splitting into ' num2str(NbSlice_i) ' slices']); end RootPath=Param.InputTable{1,1}; RootFile=Param.InputTable{1,3}; SubDir=Param.InputTable{1,2}; NomType=Param.InputTable{1,4}; FileExt=Param.InputTable{1,5}; %[filecell,i1_series,i2_series,j1_series]=get_file_series(Param);%series of file names organised as a single array %% file index parameters % NbSlice_i: nbre of slices for i index in multi-level mode: equal to 1 for a single level % the function sub_background is then relaunched by the GUI series for each % slice, incrementing the first index i by 1 % NbSlice_j: nbre of slices in volume mode % nbfield : total number of images treated per slice % step: shift of image index at each step of the sliding background (corresponding to the nbre of images in a burst) % nbaver_ima: nbre of the images in the sliding sequence used for the background % nbaver=nbaver_ima/step: nbre of bursts corresponding to nbaver_ima images. It has been adjusted so that nbaver is an odd integer i_indices=Param.IndexRange.first_i:Param.IndexRange.incr_i:Param.IndexRange.last_i; if isfield(Param.IndexRange,'first_j') j_indices=Param.IndexRange.first_j:Param.IndexRange.incr_j:Param.IndexRange.last_j; else j_indices=1; end nbfield_i=numel(i_indices); %nb of fields for the i index (bursts or volume slices) NbField_j=numel(j_indices); %nb of fields for the j index j_indices=j_indices'*ones(1,nbfield_i); i_indices=ones(NbField_j,1)*i_indices; if Param.ActionInput.CheckVolume% case of volume scan: the background images must be determined for each index j step=2;% we assume the burst contains only one image pair NbSlice_j=NbField_j; nbfield_series=nbfield_i; else if Param.ActionInput.SlidingSequenceLength nbfield disp('number of images in a slice smaller than the proposed number of images for the sliding average') return end halfnbaver=floor(nbaver/2); % half width (in unit of bursts) of the sliding background %% File relabeling documented by the xml file CheckRelabel=isfield(Param,'FileSeries' ); %% Input file info if CheckRelabel [RootFileOut,frame_index]=index2filename(Param.FileSeries,Param.IndexRange.first_i,j_indices(1),NbField_j); FirstFileName=fullfile(RootPath,SubDir,RootFileOut); else FirstFileName=fullfile_uvmat(RootPath,SubDir,RootFile,FileExt,NomType,Param.IndexRange.first_i,[],j_indices(1));%get first file name RootFileOut=RootFile; end [FileInfo,MovieObject]=get_file_info(FirstFileName); FileType=FileInfo.FileType; if ~CheckRelabel if isfield(FileInfo,'NumberOfFrames') && FileInfo.NumberOfFrames >1 if isempty(regexp(NomType,'1$', 'once'))% no file indexing frame_index=i_indices;% the index i denotes the frame number in a movie, no index j else frame_index=j_indices;% the index j denotes the frame number in a movie MovieObject=[]; %not a single video object end else frame_index=ones(1,nbfield); end end %% output file naming FileExtOut='.png'; % write result as .png images for image inputsFileInfo.FileType='image' if strcmp(FileInfo.FileType,'image') NomTypeOut=NomType; elseif NbField_j==1 NomTypeOut='_1'; else NomTypeOut='_1_1';% case of purely numerical indexing end OutputDir=[Param.OutputSubDir Param.OutputDirExt]; OutputPath=fullfile(Param.OutputPath,Param.Experiment,Param.Device); %% 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 Ak=zeros(FileInfo.Height,FileInfo.Width,nbaver_ima,['uint' num2str(FileInfo.BitDepth)]); %prealocate memory %% selection of frame indices if Param.ActionInput.CheckVolume nbfield=floor(nbfield/NbSlice_j)*NbSlice_j;% truncate the total number of frames in case of incomplete series indselect=1:nbfield; indselect=reshape(indselect,NbSlice_j,[]); NbSlice=NbSlice_j; else NbSlice=NbSlice_i; nbfield=floor(nbfield/NbSlice)*NbSlice;% truncate the total number of frames in case of incomplete series indselect=reshape(1:nbfield,NbSlice,[]); for j_slice=1:NbSlice indselect(j_slice,:)=j_slice:NbSlice:nbfield;% select file indices of the slice end end %%%%%%% LOOP ON SLICES %%%%%%% for j_slice=1:NbSlice %% read the first series of nbaver_ima images and sort by luminosity at each pixel for ifield = 1:nbaver_ima ifile=indselect(j_slice,ifield); %filename=filecell{1,ifile}; if CheckRelabel [filename,FrameIndex]=index2filename(Param.FileSeries,i_indices(ifile),j_indices(ifile),NbField_j); filename=fullfile(RootPath,SubDir,filename); else filename=fullfile_uvmat(RootPath,SubDir,RootFile,FileExt,NomType,i_indices(ifile),[],j_indices(ifile)); FrameIndex=frame_index(ifile); end Aread=read_image(filename,FileType,MovieObject,FrameIndex); 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 %% substract the first background image to the first images disp( 'first background image will be substracted') 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 ifile=indselect(j_slice,ifield); newname=fullfile_uvmat(OutputPath,OutputDir,RootFileOut,FileExtOut,NomTypeOut,i_indices(ifile),[],j_indices(ifile)); %write result file if ~isequal(Param.ActionInput.SaturationValue,0) C=levels(Acor,Param.ActionInput.SaturationValue); imwrite(C,newname,'BitDepth',16); % save the new image else if isequal(FileInfo.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 disp([newname ' written']) end %% repeat the operation on a sliding series of images disp('sliding background image will be substracted') if nbfield_series > nbaver_ima for ifield = step*(halfnbaver+1):step:nbfield_series-step*(halfnbaver+1)% ifield +iburst=index of the current processed image % update_waitbar(WaitbarHandle,ifield/nbfield_series) if ~isempty(RUNHandle)&&~strcmp(get(RUNHandle,'BusyAction'),'queue') disp('program stopped by user') return end if nbaver_ima>step Ak(:,:,1:nbaver_ima-step)=Ak(:,:,1+step:nbaver_ima);% shift the current image series by one burst (step) end %incorporate next burst in the current image series for iburst=1:step ifile=indselect(j_slice,ifield+iburst+step*halfnbaver); if CheckRelabel [filename,FrameIndex]=index2filename(Param.FileSeries,i_indices(ifile),j_indices(ifile),NbField_j); filename=fullfile(RootPath,SubDir,filename); else filename=fullfile_uvmat(RootPath,SubDir,RootFile,FileExt,NomType,i_indices(ifile),[],j_indices(ifile)); FrameIndex=frame_index(ifile); end Aread=read_image(filename,FileType,MovieObject,FrameIndex); if ndims(Aread)==3%case of 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(j_slice,ifield+iburst); newname=fullfile_uvmat(OutputPath,OutputDir,RootFileOut,FileExtOut,NomTypeOut,i_indices(ifile),[],j_indices(ifile)); %write result file if ~isequal(Param.ActionInput.SaturationValue,0) C=levels(Acor,Param.ActionInput.SaturationValue); imwrite(C,newname,'BitDepth',16); % save the new image else if isequal(FileInfo.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 disp([newname ' written']) end end end %% substract the background from the last images disp('last background image will be substracted') for ifield=nbfield_series-step*halfnbaver+1:nbfield_series Acor=double(Ak(:,:,ifield-nbfield_series+step*(2*halfnbaver+1)))-double(B); Acor=(Acor>0).*Acor; % put to 0 the negative elements in Acor ifile=indselect(j_slice,ifield); newname=fullfile_uvmat(OutputPath,OutputDir,RootFileOut,FileExtOut,NomTypeOut,i_indices(ifile),[],j_indices(ifile)); %write result file if ~isequal(Param.ActionInput.SaturationValue,0) C=levels(Acor,Param.ActionInput.SaturationValue); imwrite(C,newname,'BitDepth',16); % save the new image else if isequal(FileInfo.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 disp([newname ' written']) end end function C=levels(A,Coeff) % nblock_y=100;%2*Param.TransformInput.BlockSize; % nblock_x=100;%2*Param.TransformInput.BlockSize; % [npy,npx]=size(A); % [X,Y]=meshgrid(1:npx,1:npy); % % %Backg=zeros(size(A)); % %Aflagmin=sparse(imregionalmin(A));%Amin=1 for local image minima % %Amin=A.*Aflagmin;%values of A at local minima % % local background: find all the local minima in image subblocks % if CheckSubmedian % fctblock= inline('median(x(:))'); % Backg=blkproc(A,[nblock_y nblock_x],fctblock);% take the median in blocks % %B=imresize(Backg,size(A),'bilinear');% interpolate to the initial size image % A=A-imresize(Backg,size(A),'bilinear');% substract background interpolated to the initial size image % end % fctblock= inline('mean(x(:))'); % AMean=blkproc(A,[nblock_y nblock_x],fctblock);% take the mean in blocks % fctblock= inline('var(x(:))'); % AVar=blkproc(A,[nblock_y nblock_x],fctblock);% take the mean in blocks % Avalue=AVar./AMean;% typical value of particle luminosity % Avalue=imresize(Avalue,size(A),'bilinear');% interpolate to the initial size image %C=uint16(1000*tanh(A./(Coeff*Avalue))); C=uint16(Coeff*tanh(A./Coeff)); %------------------------------------------ % adjust the number of images used for the sliding average function [nbaver_ima,nbaver,step_out]=adjust_slidinglength(nb_aver_in,step) %nbaver_ima=str2double(nb_aver_in);%number of images for the sliding background nbaver=ceil(nb_aver_in/step);%number of bursts for the sliding background if isequal(mod(nbaver,2),0)% if nbaver is even nbaver=nbaver+1;%set the number of bursts to an odd number (so the middle burst is defined) end step_out=step; if nbaver>1 nbaver_ima=nbaver*step;% correct the nbre of images corresponding to nbaver else nbaver_ima=nb_aver_in; if isequal(mod(nbaver_ima,2),0)% if nbaver_ima is even nbaver_ima=nbaver_ima+1;%set the number of bursts to an odd number (so the middle burst is defined) end step_out=1; end