% function ParamOut=particle_tracking(Param) % % Method: % Organization of image indices: %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{1}: path to the image series % Series.RootFile{1}: root file name % Series.FileExt{1}: image file extension % Series.NomType{1}: nomenclature type for file in % % Method: % Series.NbSlice: %number of slices defined on the interface % global A rangx0 rangy0 minA maxA; % make current image A accessible in workspace % global hfig1 hfig2 scalar % global Abackg nbpart lum diam %%%%%%%%%%%%%%� % %%%%%%%%%%% GENERAL TO ALL SERIES ACTION FCTS %%%%%%%%%%%%%%%%%%%%%%%%%%% % %OUTPUT % ParamOut: sets options in the GUI series.fig needed for the function % %INPUT: % In run mode, the input parameters are given as a Matlab structure Param copied from the GUI series. % In batch mode, Param is the name of the corresponding xml file containing the same information % when Param.Action.RUN=0 (as activated when the current Action is selected % in series), the function ouput paramOut set the activation of the needed GUI elements % % Param contains the elements:(use the menu bar command 'export/GUI config' in series to % see the current structure Param) % .InputTable: cell of input file names, (several lines for multiple input) % each line decomposed as {RootPath,SubDir,Rootfile,NomType,Extension} % .OutputSubDir: name of the subdirectory for data outputs % .OutputDirExt: directory extension for data outputs % .Action: .ActionName: name of the current activated function % .ActionPath: path of the current activated function % .ActionExt: fct extension ('.m', Matlab fct, '.sh', compiled Matlab fct % .RUN =0 for GUI input, =1 for function activation % .RunMode='local','background', 'cluster': type of function use % % .IndexRange: set the file or frame indices on which the action must be performed % .FieldTransform: .TransformName: name of the selected transform function % .TransformPath: path of the selected transform function % .InputFields: sub structure describing the input fields withfields % .FieldName: name(s) of the field % .VelType: velocity type % .FieldName_1: name of the second field in case of two input series % .VelType_1: velocity type of the second field in case of two input series % .Coord_y: name of y coordinate variable % .Coord_x: name of x coordinate variable % .ProjObject: %sub structure describing a projection object (read from ancillary GUI set_object) %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %======================================================================= % Copyright 2008-2017, 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 ParamOut=particle_tracking(Param) %% set the input elements needed on the GUI series when the action is selected in the menu ActionName if isstruct(Param) && isequal(Param.Action.RUN,0) % general settings of the GUI: ParamOut.AllowInputSort='off';% allow alphabetic sorting of the list of input file SubDir (options 'off'/'on', 'off' by default) ParamOut.WholeIndexRange='off';% prescribes the file index ranges from min to max (options 'off'/'on', 'off' by default) ParamOut.NbSlice='off'; %nbre of slices ('off' by default) ParamOut.VelType='off';% menu for selecting the velocity type (options 'off'/'one'/'two', 'off' by default) ParamOut.FieldName='off';% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default) ParamOut.FieldTransform = 'off';%can use a transform function ParamOut.ProjObject='off';%can use projection object(option 'off'/'on', ParamOut.Mask='off';%can use mask option (option 'off'/'on', 'off' by default) ParamOut.OutputDirExt='.patch';%set the output dir extension ParamOut.OutputFileMode='NbSlice';% '=NbInput': 1 output file per input file index, '=NbInput_i': 1 file per input file index i, '=NbSlice': 1 file per slice filecell=get_file_series(Param);%check existence of the first input file if ~exist(filecell{1,1},'file') msgbox_uvmat('WARNING','the first input file does not exist') end % parameters specific to the function prompt = {'threshold value'}; dlg_title = 'get threshold'; num_lines= 1; def = { '0'}; answer = inputdlg(prompt,dlg_title,num_lines,def); if isempty(answer) return end ParamOut.ActionInput.LumThreshold=str2double(answer{1}); return end %%%%%%%%%%%% STANDARD RUN PART %%%%%%%%%%%% ParamOut=[]; %% read input parameters from an xml file if input is a file name (batch mode) checkrun=1; if ischar(Param) Param=xml2struct(Param);% read Param as input file (batch case) checkrun=0; end hseries=findobj(allchild(0),'Tag','series'); RUNHandle=findobj(hseries,'Tag','RUN');%handle of RUN button in GUI series WaitbarHandle=findobj(hseries,'Tag','Waitbar');%handle of waitbar in GUI series %% define the directory for result file OutputDir=[Param.OutputSubDir Param.OutputDirExt]; %% root input file(s) name, type and index series RootPath=Param.InputTable{1,1}; RootFile=Param.InputTable{1,3}; SubDir=Param.InputTable{1,2}; NomType=Param.InputTable{1,4}; FileExt=Param.InputTable{1,5}; [filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param); %%%%%%%%%%%% % The cell array filecell is the list of input file names, while % filecell{iview,fileindex}: % iview: line in the table corresponding to a given file series % fileindex: file index within the file series, % i1_series(iview,ref_j,ref_i)... are the corresponding arrays of indices i1,i2,j1,j2, depending on the input line iview and the two reference indices ref_i,ref_j % i1_series(iview,fileindex) expresses the same indices as a 1D array in file indices %%%%%%%%%%%% nbview=numel(i1_series);%number of input file series (lines in InputTable) nbfield_j=size(i1_series{1},1); %nb of fields for the j index (bursts or volume slices) nbfield_i=size(i1_series{1},2); %nb of fields for the i index nbfield=nbfield_j*nbfield_i; %total number of fields %% frame index for movie or multimage file input if ~isempty(j1_series{1}) frame_index=j1_series{1}; else frame_index=i1_series{1}; end %% check the input file type [FileInfo,VideoObject]=get_file_info(filecell{1,1}); FileType=FileInfo.FileType; ImageTypeOptions={'image','multimage','mmreader','video'}; if isempty(find(strcmp(FileType,ImageTypeOptions))) disp('input file not images') return end %% calibration data and timing: read the ImaDoc files [XmlData,NbSlice_calib,time,errormsg]=read_multimadoc(RootPath,SubDir,RootFile,FileExt,i1_series,i2_series,j1_series,j2_series); %%%%%%%%%%%% SPECIFIC PART (to edit) %%%%%%%%%%%% %filter for particle center of mass(luminosity) Threshold=Param.ActionInput.LumThreshold;% luminosity threshold for particle detection, < 0 for black particles, >0 for white particles %% fixed mask to avoid tube image Amask=imread('/fsnet/project/coriolis/2015/15MINI_MEDDY/0_REF_FILES/mask_patch.png'); %% initiate output statistics data Data.ListVarName={'Time','z','Area', 'MajorAxisLength' , 'MinorAxisLength'}; Data.VarDimName={'Time','z',{'Time','z'},{'Time','z'},{'Time','z'}}; Data.Time = 1:nbfield_i; %default Data.z=1:nbfield_j; Data.Area=zeros(nbfield_i,nbfield_j); Data.MajorAxisLength=zeros(nbfield_i,nbfield_j); Data.MinorAxisLength=zeros(nbfield_i,nbfield_j); %%%%%% MAIN LOOP ON FRAMES %%%%%% for ifile=1:nbfield if checkrun update_waitbar(WaitbarHandle,ifile/nbfield) if ~isempty(RUNHandle) &&ishandle(RUNHandle) && ~strcmp(get(RUNHandle,'BusyAction'),'queue') disp('program stopped by user') return end end i1=i1_series{1}(ifile); j1=1; if ~isempty(j1_series)&&~isequal(j1_series,{[]}) j1=j1_series{1}(ifile); end filename=fullfile_uvmat(RootPath,SubDir,RootFile,FileExt,NomType,i1,[],j1); A=read_image(filename,FileType,VideoObject,frame_index(ifile));% read the current frame A=(A>Threshold) & Amask>100;%transform to binary image format try STATS = regionprops(A, 'FilledArea','MinorAxisLength','MajorAxisLength','PixelIdxList'); Area=zeros(size(STATS)); for iobj=1:numel(STATS) Area(iobj)=STATS(iobj).FilledArea; end [Data.Area(i1,j1), main_obj]=max(Area); Data.MajorAxisLength(i1,j1)=STATS(main_obj).MajorAxisLength; Data.MinorAxisLength(i1,j1)=STATS(main_obj).MinorAxisLength; for iobj=1:numel(STATS) if iobj~=main_obj A(STATS(iobj).PixelIdxList)=0; end end catch ME disp('image toolbox not available, program stopped') % return end filename_out=fullfile_uvmat(RootPath,OutputDir,RootFile,'.png',NomType,i1,[],j1); imwrite(255*A,filename_out,'BitDepth',8) disp([filename_out ' written']) end %% record time series of stat [filename_nc,idetect]=name_generator(RootPath,OutputDir,RootFile,'.nc','_i1-i2',1,nbfield_i) errormsg=struct2nc(filename_nc,Data); if isempty(errormsg) [filename_nc ' written'] else disp(errormsg) end