Index: /trunk/src/series/calc_background.m =================================================================== --- /trunk/src/series/calc_background.m (revision 239) +++ /trunk/src/series/calc_background.m (revision 239) @@ -0,0 +1,219 @@ +%'sub_background': substract background to an image series, used with series.fig +%------------------------------------------------------------------------ +% function GUI_input=aver_stat(num_i1,num_i2,num_j1,num_j2,Series) +% +%OUTPUT +% GUI_input=list of options in the GUI series.fig needed for the function +% +%INPUT: +%num_i1: series of first indices i (given from the series interface as first_i:incr_i:last_i, mode and list_pair_civ) +%num_i2: series of second indices i (given from the series interface as first_i:incr_i:last_i, mode and list_pair_civ) +%num_j1: series of first indices j (given from the series interface as first_j:incr_j:last_j, mode and list_pair_civ ) +%num_j2: series of second indices j (given from the series interface as first_j:incr_j:last_j, mode and list_pair_civ) +%Series: Matlab structure containing information set by the series interface +% .RootPath: path to the image series +% .RootFile: root file name +% .FileExt: image file extension +% .NomType: nomenclature type for file indexing +% .NbSlice: %number of slices defined on the interface +%---------------------------------------------------------------------- +% 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) +% +function GUI_input=calc_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) + msgbox_uvmat('ERROR','This function use only one input image series') + return +end + +%% determine input image type +FileType=[];%default +MovieObject=[]; +FileExt=Series.FileExt; + +if isequal(lower(FileExt),'.avi') + hhh=which('mmreader'); + if ~isequal(hhh,'')&& mmreader.isPlatformSupported() + MovieObject=mmreader(fullfile(RootPath,[RootFile FileExt])); + FileType='movie'; + else + FileType='avi'; + end +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 +end +if isempty(FileType) + msgbox_uvmat('ERROR',['invalid file extension ' FileExt ': this function only accepts image or movie input']) + return +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 + +filebase=fullfile(Series.RootPath,Series.RootFile); +dir_images=Series.RootPath; +nom_type=Series.NomType; + +%% create dir of the new image +% [dir_images,namebase]=fileparts(filebase); +term='_background'; + +[pp,subdir_ima]=fileparts(Series.RootPath); +try + mkdir([dir_images term]); +catch ME + msgbox_uvmat('ERROR',ME.message); + return +end +[xx,msg2] = fileattrib([dir_images term],'+w','g'); %yield writing access (+w) to user group (g) +if ~strcmp(msg2,'') + msgbox_uvmat('ERROR',['pb of permission for ' subdir_ima term ': ' msg2])%error message for directory creation + return +end +filebase_b=fullfile([dir_images term],Series.RootFile); + +%% set processing parameters +prompt = {'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 background , result in subdir ' subdir_ima term]; +num_lines= 3; +def = {'1';'No';'0.1'}; +answer = inputdlg(prompt,dlg_title,num_lines,def); +vol_test=answer{2}; +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{1})/(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 +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 slic +rank=floor(str2num(answer{3})*nbfield_slice); +if rank==0 + rank=1;%rank selected in the sorted image series +end + +%% prealocate memory for the 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); +[npy,npx]=size(Afirst); +try + Ak=zeros(npy,npx,nbfield_slice,'uint16'); %prealocate memory +catch ME + msgbox_uvmat('ERROR',ME.message) + return +end + + +%MAIN LOOP ON SLICES +% +% nbfield_slice +% nbslice_i +% 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 ifile = 1:nbfield_slice +% 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(:,:,ifile)=Aread; + %finish the waitbar + update_waitbar(hseries.waitbar,WaitbarPos,1) + end + Ak=sort(Ak,3); + C=Ak(:,:,rank); + [newname]=... + name_generator(filebase_b,num_i1(1),num_j1(1),'.png','none') % makes the new file name + imwrite(C,newname,'BitDepth',16); % save the new image +% end + + + + +%------------------------------------------------------------------------ +%--read images and convert them to the uint16 format used for PIV +function A=read_image(filename,type_ima,num,MovieObject) +%------------------------------------------------------------------------ +%num is the view number needed for an avi movie +switch type_ima + case 'movie' + A=read(MovieObject,num); + case 'avi' + mov=aviread(filename,num); + A=frame2im(mov(1)); + case 'multimage' + A=imread(filename,num); + case 'image' + A=imread(filename); +end +siz=size(A); +if length(siz)==3;%color images + A=sum(double(A),3); +end + Index: /trunk/src/series/sub_background.m =================================================================== --- /trunk/src/series/sub_background.m (revision 238) +++ /trunk/src/series/sub_background.m (revision 239) @@ -129,7 +129,6 @@ try mkdir([dir_images term]); -catch - errormsg=lasterr - msgbox_uvmat('ERROR',errormsg); +catch ME + msgbox_uvmat('ERROR',ME.message); return end @@ -142,5 +141,5 @@ %% set processing parameters -prompt = {'Number of images for the sliding background';'The number of positions (laser slices)';'volume scan mode (Yes/No)';... +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'}; dlg_title = ['get (slice by slice) a sliding background and substract to each image, result in subdir ' subdir_ima term]; @@ -154,5 +153,5 @@ 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) + 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 @@ -181,5 +180,5 @@ nbfield_slice=nbfield*nbfield2;% number of fields per slice if nbaver_ima > nbfield*nbfield2 - errordlg('number of images in a slice smaller than the proposed number of images for the sliding average') + msgbox_uvmat('ERROR','number of images in a slice smaller than the proposed number of images for the sliding average') return end @@ -189,4 +188,16 @@ step=1; nbaver=nbaver_ima; +end + +%% 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); +[npy,npx]=size(Afirst); +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) + return end @@ -204,5 +215,5 @@ ImageName=name_generator(filebase_b,num_i1(1),num_j1(1),'.png',Series.NomType); [pth,ImageName]=fileparts(ImageName); - ImageName=[ImageName '.png'] + ImageName=[ImageName '.png']; if isempty(uid_ImageName) [t,uid_ImageName]=add(t,uid_Heading,'element','ImageName'); @@ -210,7 +221,7 @@ 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 + 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 + t=set(t,uid_value(1),'value',ImageName);%indicate name of the first image, with ;png extension end @@ -239,4 +250,5 @@ %MAIN LOOP ON SLICES + for islice=1:nbslice_i %% select the series of image indices at the level islice @@ -360,5 +372,5 @@ 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];% +ix=1/2-windowsize/2:-1/2+windowsize/2;% %del=np/3; %fct=exp(-(ix/del).^2);