%'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) %======================================================================= % Copyright 2008-2018, LEGI UMR 5519 / CNRS UGA G-INP, Grenoble, France % http://www.legi.grenoble-inp.fr % Joel.Sommeria - Joel.Sommeria (A) legi.cnrs.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 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) try Aread=read_image(filename,FileType,num_i1(ifile),MovieObject); catch ME msgbox_uvmat('ERROR',ME.message) return end 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