Index: /trunk/src/series/aver_stat.m =================================================================== --- /trunk/src/series/aver_stat.m (revision 393) +++ /trunk/src/series/aver_stat.m (revision 394) @@ -55,7 +55,6 @@ if test_object%isfield(Series,'sethandles') hset_object=findobj(allchild(0),'tag','set_object'); - %ProjObject=read_set_object(guidata(hset_object)); ProjObject=read_GUI(hset_object); - answeryes=msgbox_uvmat('INPUT_Y-N',['field series projected on ' ProjObject.Style ' before averaging']); + answeryes=msgbox_uvmat('INPUT_Y-N',['field series projected on ' ProjObject.Type ' before averaging']); if ~isequal(answeryes,'Yes') return Index: /trunk/src/series/merge_proj.m =================================================================== --- /trunk/src/series/merge_proj.m (revision 393) +++ /trunk/src/series/merge_proj.m (revision 394) @@ -59,9 +59,9 @@ return end - if ~isequal(ProjObject.Style,'plane')|| isequal(ProjObject.ProjMode,'projection') + if ~isequal(ProjObject.Type,'plane')|| isequal(ProjObject.ProjMode,'projection') msgbox_uvmat('ERROR','The projection object must be a plane with projection mode interp or filter') return end - answeryes=msgbox_uvmat('INPUT_Y-N',['field series projected on ' ProjObject.Style]); + answeryes=msgbox_uvmat('INPUT_Y-N',['field series projected on ' ProjObject.Type]); if ~isequal(answeryes,'Yes') return Index: /trunk/src/series/sub_background.m =================================================================== --- /trunk/src/series/sub_background.m (revision 393) +++ /trunk/src/series/sub_background.m (revision 394) @@ -65,14 +65,19 @@ WaitbarPos=get(hseries.waitbar_frame,'Position'); end +filebase=fullfile(Param.InputTable{1,1},Param.InputTable{1,3}); +dir_images=Param.InputTable{1,1}; +NomType=Param.InputTable{1,4}; +FileExt=Param.InputTable{1,5}; [filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param); if size(filecell,1)>1 - msgbox_uvmat('ERROR','This function use only one input image series') - return -end + msgbox_uvmat('WARNING','This function uses only the first input image series') + return +end + %%% TODO: update with the new conventions%%%%%%%%%%%%%%%%% %% determine input image type FileType=[];%default MovieObject=[]; -FileExt=Series.FileExt; +%FileExt=Series.FileExt; if isequal(lower(FileExt),'.avi') @@ -86,13 +91,13 @@ elseif isequal(lower(FileExt),'.vol') FileType='vol'; -else - form=imformats(FileExt(2:end)); - if ~isempty(form)% if the extension corresponds to an image format recognized by Matlab - if isequal(Series.NomType,'*'); - FileType='multimage'; - else - FileType='image'; - end - end +else + form=imformats(FileExt(2:end)); + if ~isempty(form)% if the extension corresponds to an image format recognized by Matlab + if isequal(NomType,'*'); + FileType='multimage'; + else + FileType='image'; + end + end end if isempty(FileType) @@ -101,8 +106,8 @@ end -nbslice_i=Series.NbSlice; %number of slices -siz=size(num_i1); +nbslice_i=Param.NbSlice; %number of slices +siz=size(i1_series{1}); 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 %% apply the image rescaling function 'level' (avoid the blinking effects of bright particles) @@ -112,5 +117,5 @@ %% 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, + 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) @@ -118,8 +123,4 @@ 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 @@ -130,10 +131,10 @@ term='_b'; end -[pp,subdir_ima]=fileparts(Series.RootPath); +[pp,subdir_ima]=fileparts(Param.InputTable{1,1}); try mkdir([dir_images term]); catch ME - msgbox_uvmat('ERROR',ME.message); - return + msgbox_uvmat('ERROR',ME.message); + return end [xx,msg2] = fileattrib([dir_images term],'+w','g'); %yield writing access (+w) to user group (g) @@ -142,9 +143,9 @@ return end -filebase_b=fullfile([dir_images term],Series.RootFile); +filebase_b=fullfile([dir_images term],Param.InputTable{1,3}); %% set processing parameters prompt = {'Number of images for the sliding background (MUST FIT IN COMPUETER MEMORY)';'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'}; + '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 term]; num_lines= 3; @@ -157,15 +158,16 @@ 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 -step=siz(1);%case of bursts: the sliding background is shifted by one burst + nbaver=nbaver+1;%put the number of burst to an odd number (so the middle burst is defined) +end +step=siz(1);%case of bursts: the sliding background is shifted by one burst 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 + 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 + % nbslice_i=str2num(answer{2})/(num_i1(1,2)-num_i1(1,1));% number of slices + nbslice_i=str2num(answer{2})/(i1_series{1}(1,2)-i1_series{1}(1,1));% number of slices else nbslice_i=1; @@ -195,10 +197,11 @@ %% prealocate memory for the sliding background -first_image=name_generator(filebase,num_i1(1),num_j1(1),Series.FileExt,Series.NomType); -Afirst=read_image(first_image,FileType,num_i1(1),MovieObject); +% first_image=name_generator(filebase,num_i1(1),num_j1(1),FileExt,NomType); +% Afirst=read_image(first_image,FileType,num_i1(1),MovieObject); +Afirst=read_image(filecell{1,1},FileType,i1_series{1}(1),MovieObject); [npy,npx]=size(Afirst); -try -Ak=zeros(npy,npx,nbaver_ima,'uint16'); %prealocate memory -Asort=zeros(npy,npx,nbaver_ima,'uint16'); %prealocate memory +try + Ak=zeros(npy,npx,nbaver_ima,'uint16'); %prealocate memory + Asort=zeros(npy,npx,nbaver_ima,'uint16'); %prealocate memory catch ME msgbox_uvmat('ERROR',ME.message) @@ -215,11 +218,15 @@ if isempty(uid_Heading) [t,uid_Heading]=add(t,1,'element','Heading'); - end + end uid_ImageName=find(t,'ImaDoc/Heading/ImageName'); - ImageName=name_generator(filebase_b,num_i1(1),num_j1(1),'.png',Series.NomType); + if ~isempty(j1_series{1}) + j1=j1_series{1}(1); + end + ImageName=fullfile_uvmat([dir_images term],'',Param.InputTable{1,3},'.png',NomType,i1_series{1}(1),[],j1); + % ImageName=name_generator(filebase_b,num_i1(1),num_j1(1),'.png',NomType); [pth,ImageName]=fileparts(ImageName); ImageName=[ImageName '.png']; if isempty(uid_ImageName) - [t,uid_ImageName]=add(t,uid_Heading,'element','ImageName'); + [t,uid_ImageName]=add(t,uid_Heading,'element','ImageName'); end uid_value=children(t,uid_ImageName); @@ -228,13 +235,13 @@ else t=set(t,uid_value(1),'value',ImageName);%indicate name of the first image, with ;png extension - end - + 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]=add(t,NameFunction_uid,'chardata','sub_background'); if test_level - [t,NameFunction_uid]=add(t,new_uid,'element','NameFunction'); - [t]=add(t,NameFunction_uid,'chardata','levels'); + [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'); @@ -243,5 +250,5 @@ [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 + [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') @@ -250,5 +257,5 @@ %copy the mask if exist([filebase '_1mask_1'],'file') - copyfile([filebase '_1mask_1'],[filebase_b '_1mask_1']);% copy the mask file + copyfile([filebase '_1mask_1'],[filebase_b '_1mask_1']);% copy the mask file end @@ -261,28 +268,34 @@ indselect(iburst,ifield)=((ifield-1)*nbslice_i+(islice-1))*nbfield2+iburst; end - 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=name_generator(filebase,num_i1(ifile),num_j1(ifile),Series.FileExt,Series.NomType); - Aread=read_image(filename,FileType,num_i1(ifile),MovieObject); - Ak(:,:,ifield)=Aread; + filename=filecell{1,ifile}; + % filename=name_generator(filebase,num_i1(ifile),num_j1(ifile),FileExt,NomType); + Aread=read_image(filename,FileType,i1_series{1}(ifile),MovieObject); + 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') + display( '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 - if test_level - C=levels(C); - imwrite(C,newname,'BitDepth',8); % save the new image - else - imwrite(C,newname,'BitDepth',16); % save the new image - end + 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',NomType)% makes the new file name + if ~isempty(j1_series{1}) + j1=j1_series{1}(ifile); + end + newname=fullfile_uvmat([dir_images term],'',Param.InputTable{1,3},'.png',NomType,i1_series{1}(ifile),[],j1); + %newname=name_generator(filebase_b,i1_series{1}(ifile),j1_series{1}(ifile),'.png',NomType);% makes the new file name + if test_level + C=levels(C); + imwrite(C,newname,'BitDepth',8); % save the new image + else + imwrite(C,newname,'BitDepth',16); % save the new image + end end @@ -299,5 +312,5 @@ for iburst=1:step ifile=indselect(ifield+step*floor(nbaver/2)+iburst-1); - filename=name_generator(filebase,num_i1(ifile),num_j1(ifile),Series.FileExt,Series.NomType); + filename=name_generator(filebase,num_i1(ifile),num_j1(ifile),FileExt,NomType); Aread=read_image(filename,FileType,num_i1(ifile),MovieObject); Ak(:,:,nbaver_ima-step+iburst)=Aread; @@ -311,6 +324,9 @@ C=uint16(Acor); ifile=indselect(ifield+iburst-1); - [newname]=... - name_generator(filebase_b,num_i1(ifile),num_j1(ifile),'.png',Series.NomType) % makes the new file name + if ~isempty(j1_series{1}) + j1=j1_series{1}(ifile); + end + newname=fullfile_uvmat([dir_images term],'',Param.InputTable{1,3},'.png',NomType,i1_series{1}(ifile),[],j1); + %[newname]=name_generator(filebase_b,num_i1(ifile),num_j1(ifile),'.png',NomType) % makes the new file name if test_level C=levels(C); @@ -325,22 +341,26 @@ end end - -%% substract the background from the last images + + %% substract the background from the last images display('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 - if test_level - C=levels(C); - imwrite(C,newname,'BitDepth',8); % save the new image - else - imwrite(C,newname,'BitDepth',16); % save the new image - end - end + 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); + if ~isempty(j1_series{1}) + j1=j1_series{1}(ifile); + end + newname=fullfile_uvmat([dir_images term],'',Param.InputTable{1,3},'.png',NomType,i1_series{1}(ifile),[],j1); + %newname=name_generator(filebase_b,num_i1(ifile),num_j1(ifile),'.png',NomType);% makes the new file name + if test_level + C=levels(C); + imwrite(C,newname,'BitDepth',8); % save the new image + else + imwrite(C,newname,'BitDepth',16); % save the new image + end + end end Index: /trunk/src/series/time_series.m =================================================================== --- /trunk/src/series/time_series.m (revision 393) +++ /trunk/src/series/time_series.m (revision 394) @@ -53,7 +53,6 @@ if test_object hset_object=findobj(allchild(0),'tag','set_object'); -% ProjObject=read_set_object(guidata(hset_object)); ProjObject=read_GUI(hset_object); - answeryes=msgbox_uvmat('INPUT_Y-N',['field series projected on ' ProjObject.Style]); + answeryes=msgbox_uvmat('INPUT_Y-N',['field series projected on ' ProjObject.Type]); if ~isequal(answeryes,'Yes') return @@ -65,11 +64,11 @@ %% features of the input fields - RootPath=Param.InputTable(:,1); - RootFile=Param.InputTable(:,3); - SubDir=Param.InputTable(:,2); - NomType=Param.InputTable(:,4); - FileExt=Param.InputTable(:,5); -ext=FileExt{1}; -form=imformats(ext(2:end));%test valid Matlab image formats +RootPath=Param.InputTable(:,1); +RootFile=Param.InputTable(:,3); +% SubDir=Param.InputTable(:,2); +NomType=Param.InputTable(:,4); +FileExt=Param.InputTable(:,5); +% ext=FileExt{1}; +% form=imformats(ext(2:end));%test valid Matlab image formats nbfield=size(i1_series{1},1)*size(i1_series{1},2); %number of fields in the time series