% 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='.track';%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 'particle_tracking' Par.Nblock=10;%size of image subblocks for background determination, =[]: no sublock Par.ThreshLum=70;% luminosity threshold for particle detection, < 0 for black particles, >0 for white particles ParamOut.ActionInput=Par; 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','cine_phantom'}; 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) Nblock=Param.ActionInput.Nblock; ThreshLum=Param.ActionInput.ThreshLum;% luminosity threshold for particle detection, < 0 for black particles, >0 for white particles %AbsThreshold=30; %threshold below which a pixel is considered belonging to a float % hh=ones(5,5); hh(1,1)=0; hh(1,5)=0;% sum luminosity on the 5x5 domain without corners hh(5,1)=0; hh(5,5)=0; hdx=[-2:1:2]; hdy=[-2:1:2]; [hdX,hdY]=meshgrid(hdx,hdy); hdX(1,1)=0; hdX(1,5)=0;% sum luminosity on the 5x5 domain -corners hdX(5,1)=0; hdX(5,5)=0; hdY(1,1)=0; hdY(1,5)=0;% sum luminosity on the 5x5 domain -corners hdY(5,1)=0; hdY(5,5)=0; %% mask to reduce the working area (optional) CheckMask=0; if isfield(Param,'CheckMask') && isequal(Param.CheckMask,1) [maskname,TestMask]=name_generator([filebase '_1mask'],1,1,'.png','_i'); MaskIma=imread(maskname); Mask=MaskIma>=200;%=1 for good points, 0 for bad CheckMask=1; end %%%%%% 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 j1=1; if ~isempty(j1_series)&&~isequal(j1_series,{[]}) j1=j1_series{1}(ifile); end filename=fullfile_uvmat(RootPath,SubDir,RootFile,FileExt,NomType,i1_series{1}(ifile),[],j1); A=read_image(filename,FileType,VideoObject,frame_index(ifile));% read the current frame if ndims(A)==3;%color images A=sum(double(A),3);% take the sum of color components end if ThreshLum<0 A=max(max(A))-A;%take the negative end if CheckMask A=A.*Mask; end if isempty(Nblock) A=A-min(min(A));%substract absolute mean else Aflagmin=sparse(imregionalmin(A));%Amin=1 for local image minima Amin=A.*Aflagmin;%values of A at local minima % local background: find all the local minima in image subblocks sumblock= inline('sum(sum(x(:)))'); Backgi=blkproc(Amin,[Nblock Nblock],sumblock);% take the sum in blocks Bmin=blkproc(Aflagmin,[Nblock Nblock],sumblock);% find the number of minima in blocks Backgi=Backgi./Bmin; % find the average of minima in blocks % Backg=Backg+Backgi; Backg=Backgi; A=A-imresize(Backg/nburst(1),size(A),'bilinear');% interpolate to the initial size image and substract end Aflagmax=sparse(imregionalmax(A));%find local maxima Plum=imfilter(A,hh);% sum A on 5x% domains Plum=Aflagmax.*Plum;% Plum gives the particle luminosity at each particle location, 0 elsewhere %make statistics on particles,restricted to a subdomain Sub [Js,Is,lum]=find(Plum);%particle luminosity Plum=(Plum>ThreshLum).*Plum;% introduce a threshold for particle luminosity Aflagmax=Aflagmax.*(Plum>ThreshLum); [Js,Is,lum]=find(Plum);%particle luminosity nbtotal=size(Is) nbtotal=nbtotal(1); %particle size Parea=Aflagmax.*(Plum./A); %particle luminosity/max luminosity=area Pdiam=sqrt(Parea); [Js,Is,diam]=find(Pdiam);%particle location %%%%%%%%%%%%%%%%%%%%% %nbre of particles per block % nbpart=blkproc(Aflagmax,[Nblock Nblock],sumblock);% % npb=size(nbpart); % rangxb=[0.5 (npb(2)-0.5)]*Nblock; % pixel x coordinates for image display % rangyb=[(npb(1)-0.5) 0.5]*Nblock; % pixel y coordinates for image display % image(rangxb,rangyb,nbpart); % get the particle centre of mass dx=imfilter(A,hdX); dy=imfilter(A,-hdY); dx=Aflagmax.*(dx./Plum); dy=Aflagmax.*(dy./Plum); dx=dx/pxcm; dy=dy/pycm; I=([1:npxy(2)]-0.5)/pxcm; %x pos J=([npxy(1):-1:1]-0.5)/pycm; %y pos [Ipos,Jpos]=meshgrid(I,J); Ipos=reshape(Ipos,1,npxy(2)*npxy(1)); Jpos=reshape(Jpos,1,npxy(2)*npxy(1)); dx=reshape(dx,1,npxy(2)*npxy(1)); dy=reshape(dy,1,npxy(2)*npxy(1)); Aflag=reshape(Aflagmax,1,npxy(2)*npxy(1)); ind=find(Aflag);% select particle positions XPart{ifile}=Ipos(ind)+dx(ind); YPart{ifile}=Jpos(ind)+dy(ind); end hold off size(XPart{1}) %%%%%%%%%%%%%%%%%%%%%%%%%%%%% %Trajectoires %%%%%%%%%%%%%%%%%%%%%%%%%%%%% for ifile=1:nbfield [XPart{ifile},YPart{ifile}]=phys_XYZ(Calib,XPart{ifile},YPart{ifile}); end if nbfield>2 figpart=figure hold on plot(XPart{1}(:),YPart{1}(:),'r+') plot(XPart{2}(:),YPart{2}(:),'b+') plot(XPart{3}(:),YPart{3}(:),'y+') legend('particules image 1','particules image 2','particules image 3'); xlabel('x (cm)'); ylabel('y (cm)'); title('Position des particules') else figpart=figure hold on plot(XPart{1}(:),YPart{1}(:),'r+') plot(XPart{2}(:),YPart{2}(:),'b+') legend('particules image 1','particules image 2'); xlabel('x (cm)'); ylabel('y (cm)'); title('Position des particules') end % prompt={'Ymin (cm)','Ymax( cm)','Xmin (cm)','Xmax (cm)'}; % Rep=inputdlg(prompt,'Experiment'); % Ymin=str2double(Rep(1)); % Ymax=str2double(Rep(2)); % Xmin=str2double(Rep(3)); % Xmax=str2double(Rep(4)); Ymin=6; Ymax=14; Xmin=15; Xmax=35; plot(Xmin,Ymin,'g+') plot(Xmin,Ymax,'g+') plot(Xmax,Ymin,'g+') plot(Xmax,Ymax,'g+') for ima=2:nbfield t{1}=0*ones(size(XPart{1},2),1); burst(1)=0; burst(2)=0.018; burst(3)=0.036; % nburst=strcat('burst',num2str(ima-1),'-',num2str(ima),' (s)'); % prompt={'burst (s)'}; % Rep=inputdlg(prompt,nburst); % burst(ima)=str2double(Rep(1)); t{ima}=(burst(ima)+burst(ima-1))*ones(size(XPart{ima},2),1); end for ima=1:nbfield IndY{ima}=find(YPart{ima}>Ymin & YPart{ima}Xmin & XPart{ima}2 for ima=2:nbfield-1 for i=1:size(MatPos{ima},1) MatPos{ima+1}(i,1)=MatPos{ima}(i,1)+(burst(ima+1)*vitfu{ima-1}(i)); MatPos{ima+1}(i,2)=MatPos{ima}(i,2)+(burst(ima+1)*vitfv{ima-1}(i)); MatPos{ima+1}(i,3)=t{ima}(i); end for j=1:size(XPart{ima+1},2)-1 MatPos{ima+1}(j+size(MatPos{ima},1),1)=XPart{ima+1}(j); MatPos{ima+1}(j+size(MatPos{ima},1),2)=YPart{ima+1}(j); MatPos{ima+1}(j+size(MatPos{ima},1),3)=t{ima+1}(j); end result{ima}=track(MatPos{ima+1},0.15); izero=1; for itest=1:1:size(result{ima},1)-1 if result{ima}(itest+1,4)==result{ima}(itest,4) vitu{ima}(izero,1)=(result{ima}(itest+1,1)-result{ima}(itest,1))/burst(ima+1); vitu{ima}(izero,2)=result{ima}(itest,4); vitv{ima}(izero,1)=(result{ima}(itest+1,2)-result{ima}(itest,2))/burst(ima+1); vitv{ima}(izero,2)=result{ima}(itest,4); MatPos{ima+2}(izero,1)=result{ima}(itest,1); MatPos{ima+2}(izero,2)=result{ima}(itest,2); izero=izero+1; end end i=vitu{ima}(1,2):1:vitu{ima}(end,2) vitfu{ima}(:,1)=vitfu{ima-1}(i,1)+vitu{ima}(:,1); vitfv{ima}(:,1)=vitfv{ima-1}(i,1)+vitv{ima}(:,1); vitfu{ima}(:,2)=vitu{ima}(:,2); vitfv{ima}(:,2)=vitv{ima}(:,2); vitfu{ima-1}=vitfu{ima-1}(i,1); vitfu{ima-1}(:,2)=i; vitfv{ima-1}=vitfv{ima-1}(i,1); vitfv{ima-1}(:,2)=i; i=1:1:size(vitfu{ima-1},1) xpos=MatPos{2}(i,1) ypos=MatPos{2}(i,2) end end figure hold on plot(MatPos{1}(:,1),MatPos{1}(:,2),'r+') plot(MatPos{2}(:,1),MatPos{2}(:,2),'b+') plot(MatPos{4}(:,1),MatPos{4}(:,2),'y+') quiver(xpos(:),ypos(:),vitfu{1}(:,1),vitfv{1}(:,1),'g') quiver(MatPos{4}(:,1),MatPos{4}(:,2),vitfu{2}(:,1),vitfv{2}(:,1),'k') legend('particules image 1','particules image 2', 'particules image 3','vitesse 1-2 (cm/s)','vitesse 2-3 (cm/s)'); xlabel('x (cm)'); ylabel('y (cm)'); title('Position et vitesse (cm/s) des particules') for i=1:size(vitfu{end},1) vitfuadd(i)=0; vitfvadd(i)=0; end for i=1:1:size(vitfu{end}(:,1)) for j=1:nbfield-1 vitfuadd(i)= vitfuadd(i)+vitfu{j}(i,1); vitfvadd(i)= vitfvadd(i)+vitfv{j}(i,1); xpos1(i)=MatPos{1}(i,1); ypos1(i)=MatPos{1}(i,2); xpos2(i)=MatPos{2}(i,1); ypos2(i)=MatPos{2}(i,2); end end sizexpos1=size(xpos1) vitfumoy=vitfuadd./(nbfield-1) vitfvmoy=vitfvadd./(nbfield-1) testresult1=result{1} testresult2=result{2} if nbfield>2 figure hold on plot(MatPos{1}(:,1),MatPos{1}(:,2),'r+') plot(MatPos{2}(:,1),MatPos{2}(:,2),'b+') quiver(xpos2(:),ypos2(:),vitfumoy(:),vitfvmoy(:),'g') legend('particules image 1','particules image 2', 'vitesse moyenne (cm/s)'); xlabel('x (cm)'); ylabel('y (cm)'); title('Position et vitesse (cm/s) des particules') else figure hold on plot(MatPos{1}(:,1),MatPos{1}(:,2),'r+') plot(MatPos{2}(:,1),MatPos{2}(:,2),'b+') quiver(MatPos{2}(:,1),MatPos{2}(:,2),vitfu{1}(:),vitfv{1}(:),'g') legend('particules image 1','particules image 2','vitesse 1-2 (cm/s)'); xlabel('x (cm)'); ylabel('y (cm)'); title('Position et vitesse (cm/s) des particules') vitfumoy=vitfu{1}; vitfvmoy=vitfv{1}; end VitData.NbDim=2; VitData.NbCoord=2; VitData.CoordType='phys'; VitData.dt=0.0185; VitData.CoordUnit='cm'; VitData.Z=0; VitData.ListDimName={'nb_vectors'}; VitData.DimValue=size(vitfumoy,2); VitData.ListVarName={'X' 'Y' 'U' 'V' 'F'}; VitData.VarDimIndex={[1] [1] [1] [1] [1]}; VitData.ListVarAttribute={'Role'}; VitData.Role={'coord_x' 'coord_y' 'vector_x' 'vector_y' 'warnflag'}; if nbfield>2 VitData.X=size(MatPos{4},1); VitData.Y=size(MatPos{4},2); else VitData.X=size(MatPos{2},1); VitData.Y=size(MatPos{2},2); end VitData.U=size(vitfumoy,2); VitData.V=size(vitfvmoy,2); VitData.Style='plane'; VitData.Time=[198.5203 198.5203]; VitData.Action=Series.Action; if nbfield>2 VitData.X=MatPos{4}(:,1)'; VitData.Y=MatPos{4}(:,2)'; else VitData.X=MatPos{2}(:,1)'; VitData.Y=MatPos{2}(:,2)'; end VitData.U=vitfumoy(:)'; VitData.V=vitfvmoy(:)'; if length(VitData.ListVarName) >= 4 & isequal(VitData.ListVarName(1:4), {'X' 'Y' 'U' 'V'}) VitData.ListAttribute={'nb_coord','nb_dim','dt','pixcmx','pixcmy','hart','civ','fix'}; VitData.nb_coord=2; VitData.nb_dim=2; VitData.dt=0.018; VitData.absolut_time_T0=0; VitData.pixcmx=1; %pix per cm (1 by default) VitData.pixcmy=1; %pix per cm (1 by default) VitData.hart=0; if isequal(VitData.CoordType,'px') VitData.civ=1; else VitData.civ=0; end VitData.fix=0; VitData.ListVarName(1:4)={'vec_X' 'vec_Y' 'vec_U' 'vec_V'}; VitData.vec_X=VitData.X; VitData.vec_Y=VitData.Y; VitData.vec_U=VitData.U; VitData.vec_V=VitData.V; end currentdir=pwd;%store the current working directory [Path_ima,Name]=fileparts(filebase);%Path of the image files (.civ) cd(Path_ima);%move to the directory of the images: needed to create the result dir by 'mkdir' dircur=pwd; %current working directory [m1,m2,m3]=mkdir('TRACK_test') cd(currentdir) [filename_nc,idetect]=name_generator(filebase,num_i1(1),num_j1(1),'.nc','_i_j1-j2',1,num_i1(1),num_j1(2),'TRACK_test') error=struct2nc(filename_nc,VitData); %save result file if isequal(error,0) [filename_nc ' written'] else warndlg_uvmat(error,'ERROR') end