Index: /trunk/src/series/sub_background.m =================================================================== --- /trunk/src/series/sub_background.m (revision 1123) +++ /trunk/src/series/sub_background.m (revision 1124) @@ -142,5 +142,6 @@ 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 - if nbfield_i~=1 + 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 @@ -150,6 +151,6 @@ end BrightnessRankThreshold=0.1; - CheckSubmedian='No'; - SaturationCoeff=0; + % CheckSubmedian='No'; +% SaturationCoeff=0; if isfield(Param,'ActionInput') if isfield(Param.ActionInput,'CheckVolume') && Param.ActionInput.CheckVolume @@ -162,9 +163,9 @@ BrightnessRankThreshold=Param.ActionInput.BrightnessRankThreshold; end - if isfield(Param.ActionInput,'CheckSubmedian') && Param.ActionInput.CheckSubmedian - CheckSubmedian='Yes'; - end - if isfield(Param.ActionInput,'SaturationCoeff') - SaturationCoeff=Param.ActionInput.SaturationCoeff; +% if isfield(Param.ActionInput,'CheckSubmedian') && Param.ActionInput.CheckSubmedian +% CheckSubmedian='Yes'; +% end + if isfield(Param.ActionInput,'SaturationValue') + SaturationValue=Param.ActionInput.SaturationValue; end end @@ -172,9 +173,8 @@ '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';... - 'set to 0 image levels below median(Yes/No)';... - 'image rescaling coefficient(=2 to reduce the influence of bright particles), =0 for no rescaling' }; + '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= 5; - def = { CheckVolume;num2str(nbaver_init);num2str(BrightnessRankThreshold);CheckSubmedian;num2str(SaturationCoeff)}; + num_lines= 4; + def = { CheckVolume;num2str(nbaver_init);num2str(BrightnessRankThreshold);num2str(SaturationValue)}; answer = inputdlg(prompt,dlg_title,num_lines,def); if isempty(answer) @@ -189,20 +189,14 @@ end if strcmp(answer{1},'Yes') - step=2;%the sliding background is shifted by the length of one burst, assumed =2 for volume ;ode + 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 - nbaver_ima=str2double(answer{2});%number of images for the sliding background - nbaver=ceil(nbaver_ima/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 - nbaver_ima=nbaver*step;% correct the nbre of images corresponding to nbaver + ParamOut.ActionInput.SlidingSequenceLength=adjust_slidinglength(str2num(answer{2}),step); ParamOut.ActionInput.CheckVolume=strcmp(answer{1},'Yes'); - ParamOut.ActionInput.SlidingSequenceLength=nbaver_ima; ParamOut.ActionInput.BrightnessRankThreshold=str2double(answer{3}); - ParamOut.ActionInput.CheckSubmedian=strcmp(answer{4},'Yes'); - ParamOut.ActionInput.SaturationCoeff=str2double(answer{5}); +% 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'); @@ -259,6 +253,4 @@ if strcmp(FileInfo{1}.FileType,'image') NomTypeOut=NomType{1}; -% if strcmp(lower(NomType{1}(end)),'a') -% NomTypeOut=NomType{1};%case of letter appendix elseif isempty(j1_series{1}) NomTypeOut='_1'; @@ -267,7 +259,8 @@ end OutputDir=[Param.OutputSubDir Param.OutputDirExt]; +OutputPath=fullfile(Param.OutputPath,Param.Experiment,Param.Device); %% file index parameters -% NbSlice_i: nbre of slices for i index: different of of 1 for multi-level, +% 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 @@ -280,13 +273,11 @@ nbfield_i=size(i1_series{1},2); %nb of fields for the i index -if Param.ActionInput.CheckVolume +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; - NbSlice=nbfield_j; nbfield_series=nbfield_i; else step=nbfield_j;%case of bursts: the sliding background is shifted by the length of one burst - NbSlice_j=1; - NbSlice=NbSlice_i; + NbSlice_j=1; %nbfield_i=floor(nbfield_i/NbSlice_i);%total number of indexes in a slice (adjusted to an integer number of slices) %nbfield=nbfield_i*NbSlice_i; %total number of fields after adjustement @@ -294,10 +285,5 @@ end nbfield=nbfield_j*nbfield_i; %total number of fields -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(mod(nbaver,2),0) - nbaver=nbaver+1;%set the number of bursts to an odd number (so the middle burst is defined) -end -nbaver_ima=nbaver*step; +[nbaver_ima,nbaver,step]=adjust_slidinglength(Param.ActionInput.SlidingSequenceLength,step); if nbaver_ima > nbfield display('number of images in a slice smaller than the proposed number of images for the sliding average') @@ -342,5 +328,5 @@ filename=filecell{1,ifile}; Aread=read_image(filename,FileType{1},MovieObject{1},frame_index{1}(ifile)); - if ndims(Aread)==3;%color images + if ndims(Aread)==3%color images Aread=sum(double(Aread),3);% take the sum of color components end @@ -352,5 +338,5 @@ %% substract the first background image to the first images display( 'first background image will be substracted') - for ifield=1:step*(halfnbaver+1);% nbre of images treated by the first background image + 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 @@ -360,9 +346,9 @@ j1=j1_series{1}(ifile); end - newname=fullfile_uvmat(RootPath{1},OutputDir,RootFile{1},FileExtOut,NomTypeOut,i1_series{1}(ifile),[],j1); + newname=fullfile_uvmat(OutputPath,OutputDir,RootFile{1},FileExtOut,NomTypeOut,i1_series{1}(ifile),[],j1); %write result file - if ~isequal(Param.ActionInput.SaturationCoeff,0) - C=levels(Acor,Param.ActionInput.CheckSubmedian,Param.ActionInput.SaturationCoeff); + if ~isequal(Param.ActionInput.SaturationValue,0) + C=levels(Acor,Param.ActionInput.SaturationValue); imwrite(C,newname,'BitDepth',16); % save the new image else @@ -400,7 +386,8 @@ j1=j1_series{1}(ifile); end + filename=fullfile_uvmat(RootPath{1},SubDir{1},RootFile{1},FileExt{1},NomType{1},i1_series{1}(ifile),[],j1); Aread=read_image(filename,FileType{1},MovieObject{1},frame_index{1}(ifile)); - if ndims(Aread)==3;%color images + if ndims(Aread)==3%case of color images Aread=sum(double(Aread),3);% take the sum of color components end @@ -417,8 +404,8 @@ j1=j1_series{1}(ifile); end - newname=fullfile_uvmat(RootPath{1},OutputDir,RootFile{1},FileExtOut,NomTypeOut,i1_series{1}(ifile),[],j1); + newname=fullfile_uvmat(OutputPath,OutputDir,RootFile{1},FileExtOut,NomTypeOut,i1_series{1}(ifile),[],j1); %write result file - if ~isequal(Param.ActionInput.SaturationCoeff,0) - C=levels(Acor,Param.ActionInput.CheckSubmedian,Param.ActionInput.SaturationCoeff); + if ~isequal(Param.ActionInput.SaturationValue,0) + C=levels(Acor,Param.ActionInput.SaturationValue); imwrite(C,newname,'BitDepth',16); % save the new image else @@ -445,8 +432,8 @@ j1=j1_series{1}(ifile); end - newname=fullfile_uvmat(RootPath{1},OutputDir,RootFile{1},FileExtOut,NomTypeOut,i1_series{1}(ifile),[],j1); + newname=fullfile_uvmat(OutputPath,OutputDir,RootFile{1},FileExtOut,NomTypeOut,i1_series{1}(ifile),[],j1); %write result file - if ~isequal(Param.ActionInput.SaturationCoeff,0) - C=levels(Acor,Param.ActionInput.CheckSubmedian,Param.ActionInput.SaturationCoeff); + if ~isequal(Param.ActionInput.SaturationValue,0) + C=levels(Acor,Param.ActionInput.SaturationValue); imwrite(C,newname,'BitDepth',16); % save the new image else @@ -463,26 +450,45 @@ end -function C=levels(A,CheckSubmedian,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))); +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 Index: /trunk/src/series/sub_background_special.m =================================================================== --- /trunk/src/series/sub_background_special.m (revision 1123) +++ /trunk/src/series/sub_background_special.m (revision 1124) @@ -106,5 +106,5 @@ Bfilter=ones(1,20)/20; %% root input file names and nomenclature type (cell arrays with one element) -OutputDir=[Param.OutputSubDir Param.OutputDirExt];4 +OutputDir=[Param.OutputSubDir Param.OutputDirExt]; nbj=numel(Param.IndexRange.first_i:Param.IndexRange.last_i); for i_ind=Param.IndexRange.first_i:Param.IndexRange.last_i