%---------------------------------------------------------------------- % --- substract background to the images: rank the images by luminosity at each point and substracts to the images %---------------------------------------------------------------------- % 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, labelled by two indices i and j, given % by the input matlab vectors num_i1 and num_j1 respectively. In the list, j is the fastest increasing index. % The processing can be done in slices (number nbslice), with bursts of % nbfield2 successive images for a given slice (mode 'multilevel') % In the mode 'volume', nbfield2=1 (1 image at each level), and % nbslice= %INPUT: % num_i1: matrix of image indices i % num_j1: matrix of image indices j, must be the same size as num_i1 % num_i2 and num_j2: not used for a function acting on images % Series: matlab structure containing parameters, as defined by the interface UVMAT/series % Series.RootPath: path to the image series % Series.RootFile: root file name % Series.FileExt: image file extension % Series.NomType: nomenclature type for file indexing % Series.NbSlice: %number of slices defined on the interface function GUI_input=sub_background (num_i1,num_i2,num_j1,num_j2,Series) %------------------------------------------------------------------------ %requests for the visibility of input windows in the GUI series (activated directly by the selection in the menu ACTION) if ~exist('num_i1','var') GUI_input={'RootPath';'on';... 'SubDir';'off';... % subdirectory of derived files (PIV fields), ('on' by default) 'RootFile';'on';... %root input file name ('on' by default) 'FileExt';'on';... %inputf file extension ('on' by default) 'NomType';'on';...%type of file indexing ('on' by default) 'NbSlice';'on'; ...%nbre of slices ('off' by default) %'VelTypeMenu';'on';...% menu for selecting the velocity type (civ1,..)('off' by default) %'FieldMenu';'on';...% menu for selecting the velocity field (s) in the input file ('off' by default) %'VelTypeMenu_1';'on';...% menu for selecting the velocity type (civ1,..)('off' by default) %'FieldMenu_1';'on';...% menu for selecting the velocity field (s) in the input file ('off' by default) %'CoordType';...%can use a transform function %'GetObject';...;%can use projection object %'GetMask';...;%can use mask option 'PARAMETER';'NbSliding';... 'PARAMETER';'VolumeScan';... 'PARAMETER';'RankBrightness';... ''}; return %exit the function end %---------------------------------------------------------------- % initiate the waitbar hseries=guidata(Series.hseries);%handles of the GUI series WaitbarPos=get(hseries.waitbar_frame,'Position'); %----------------------------------------------------------------- if iscell(Series.RootPath) wardlg_uvmat('This function use only one input file series','ERROR') end nbslice_i=Series.NbSlice; %number of slices siz=size(num_i1); nbaver_init=23;%approximate number of images used for the sliding background: to be adjusted later to include an integer number of bursts %adjust the proposed number of images in the sliding average to include an integer number of bursts if siz(2)~=1 nbaver=floor(nbaver_init/siz(1)); % 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*siz(1);%propose by default an integer number of bursts end filebase=fullfile(Series.RootPath,Series.RootFile); dir_images=Series.RootPath; nom_type=Series.NomType; %create dir of the new images [dir_images,namebase]=fileparts(filebase); [path,subdir_ima]=fileparts(dir_images); curdir=pwd; cd(path); mkdir([subdir_ima '_b']); cd(curdir); filebase_b=fullfile(path,[subdir_ima '_b'],namebase); prompt = {'Number of images for the sliding background';'The number of positions (laser slices)';'volume scan mode (Yes/No)';... '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, result in subdir ' subdir_ima '_b']; num_lines= 3; def = { num2str(nbaver_init);num2str(nbslice_i);'No';'0.1'}; answer = inputdlg(prompt,dlg_title,num_lines,def); set(hseries.ParamVal,'String',answer([1 [3:4]])) set(hseries.ParamVal,'Visible','on') nbaver_ima=str2num(answer{1});%number of images for the sliding background nbaver=ceil(nbaver_ima/siz(1))%number of bursts 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 % if isequal(nbaver,round(nbaver)) step=siz(1);%case of bursts: the sliding background is shifted by one burst % else % step=1; % end vol_test=answer{3}; if isequal(vol_test,'Yes') nbfield2=1;%case of volume: no consecutive series at a given level nbslice_i=siz(1);%number of slices else nbfield2=siz(1); %nb of consecutive images at each level(burst) if siz(2)>1 nbslice_i=str2num(answer{2})/(num_i1(1,2)-num_i1(1,1));% number of slices else nbslice_i=1; end if ~isequal(floor(nbslice_i),nbslice_i) msgbox_uvmat('ERROR','the number of slices must be a multiple of the i increment') return end end % nbaver=floor(nbaver_init/nbfield2); % 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 % end %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %nbaver_ima=nbaver*nbfield2;% adjust the number of sliding images A REMETRE % if ~isequal(nbaver_ima,nbaver_init) % hwarn=warndlg(['number of images in the sliding average adjusted to ' num2str(nbaver_ima)]); % set(hwarn,'Units','normalized') % set(hwarn,'Position',[0.3 0.3 0.4 0.1]) % end %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% rank=floor(str2num(answer{4})*nbaver_ima); if rank==0 rank=1;%rank selected in the sorted image series end lengthtot=siz(1)*siz(2); nbfield=floor(lengthtot/(nbfield2*nbslice_i));%total number of i indexes (adjusted to an integer number of slices) nbfield_slice=nbfield*nbfield2;% number of fields per slice % test_plot=isequal(answer{5},'Yes'); %=1 to display background images if nbaver_ima > nbfield*nbfield2 errordlg('number of images in a slice smaller than the proposed number of images for the sliding average') return end nbfirst=(ceil(nbaver/2))*step; if nbfirst>nbaver_ima nbfirst=ceil(nbaver_ima/2) step=1; nbaver=nbaver_ima; end %copy the xml file if exist([filebase '.xml'],'file') copyfile([filebase '.xml'],[filebase_b '.xml']);% copy the .civ file t=xmltree([filebase_b '.xml']); %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'); ImageName=name_generator(filebase_b,num_i1(1),num_j1(1),'.png',Series.NomType); [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'); [t,NbSlice_uid]=add(t,new_uid,'element','NbSlice'); [t]=add(t,new_uid,'chardata',num2str(nbslice_i)); [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,[filebase_b '.xml']) elseif exist([filebase '.civ'],'file') copyfile([filebase '.civ'],[filebase_b '.civ']);% copy the .civ file 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_i %select the series of image indices at the level islice for ifield=1:nbfield for iburst=1:nbfield2 indselect(iburst,ifield)=((ifield-1)*nbslice_i+(islice-1))*nbfield2+iburst; end 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,idetect]=... name_generator(filebase,num_i1(ifile),num_j1(ifile),Series.FileExt,Series.NomType); Aread=imread(filename); size(Aread) if size(Aread,3)>1 %(color images) Aread=sum(Aread,3); %sum over color components end Ak(:,:,ifield)=Aread; end Asort=sort(Ak,3);%sort the luminosity of images at each point B=Asort(:,:,rank);%background image % % namemean=name_generator([filebase '_back'],islice,[],'.png','_i');% makes the file name % imwrite(B,namemean,'BitDepth',16); % save the first background image % ['background image for slice ' num2str(islice) ' saved in ' namemean] %substract the background from each of the first images and save the new images % for ifield=1:floor(nbaver_ima/2)+1 'first background image will be substracted' 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 C=uint16(Acor);% set to integer 16 bits ifile=indselect(ifield); newname=name_generator(filebase_b,num_i1(ifile),num_j1(ifile),'.png',nom_type)% makes the new file name imwrite(C,newname,'BitDepth',16); % save the new image end %repeat the operation on a sliding series of nbaver*nbfield2 images 'sliding background image will be substracted' if nbfield_slice > nbaver_ima % for ifield = floor(nbaver_ima/2)+2:step:nbfield_slice-floor(nbaver_ima/2) for ifield = step*ceil(nbaver/2)+1:step:nbfield_slice-step*floor(nbaver/2) stopstate=get(hseries.RUN,'BusyAction'); if isequal(stopstate,'queue')% enable STOP command % waitbarpos(4)=((ifield+(islice-1)*nbfield_slice)/(nbfield_slice*nbslice_i))*Series.WaitbarPos(4); % waitbarpos(2)=Series.WaitbarPos(4)+Series.WaitbarPos(2)-waitbarpos(4); % set(hwaitbar,'Position',waitbarpos) % drawnow update_waitbar(hseries.waitbar,WaitbarPos,(ifield+(islice-1)*nbfield_slice)/(nbfield_slice*nbslice_i)) (ifield+(islice-1)*nbfield_slice)/(nbfield_slice*nbslice_i) 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,idetect]=... name_generator(filebase,num_i1(ifile),num_j1(ifile),Series.FileExt,Series.NomType); Aread=imread(filename); if size(Aread,3)>1 %(color images) Aread=sum(Aread,3); %sum over 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 % Acor=double(Ak(:,:,floor(nbaver_ima/2)+iburst-1))-double(B); index=step*floor(nbaver/2)+iburst; Acor=double(Ak(:,:,index))-double(B); Acor=(Acor>0).*Acor; % put to 0 the negative elements in Acor C=uint16(Acor); ifile=indselect(ifield+iburst-1); [newname]=... name_generator(filebase_b,num_i1(ifile),num_j1(ifile),'.png',Series.NomType) % newname=name_generator(filebase_b,num_i1(indselect(ifield+iburst-1)),num_j1(indselect(ifield+iburst-1)),'.png',nom_type)% makes the new file name imwrite(C,newname,'BitDepth',16); % save the new image end else return end end end %substract the background from the last images % for ifield=nbfield_slice-floor(nbaver_ima/2)+1:nbfield_slice 'last background image will be substracted' ifield=nbfield_slice-(step*ceil(nbaver/2))+1:nbfield_slice; for ifield=nbfield_slice-(step*floor(nbaver/2))+1:nbfield_slice index=ifield-nbfield_slice+step*(2*floor(nbaver/2)+1); Acor=double(Ak(:,:,index))-double(B); Acor=(Acor>0).*Acor; % put to 0 the negative elements in Acor C=uint16(Acor); ifile=indselect(ifield); newname=name_generator(filebase_b,num_i1(ifile),num_j1(ifile),'.png',nom_type)% makes the new file name imwrite(C,newname,'BitDepth',16); % save the new image end end %finish the waitbar update_waitbar(hseries.waitbar,WaitbarPos,1)