source: trunk/src/series/float_tracking.m @ 804

Last change on this file since 804 was 804, checked in by sommeria, 9 years ago

float tracking updated

File size: 11.4 KB
Line 
1% function ParamOut=particle_tracking(Param)
2%
3% Method:
4   
5% Organization of image indices:
6   
7%INPUT:
8% num_i1: matrix of image indices i
9% num_j1: matrix of image indices j, must be the same size as num_i1
10% num_i2 and num_j2: not used for a function acting on images
11% Series: matlab structure containing parameters, as defined by the interface UVMAT/series
12%       Series.RootPath{1}: path to the image series
13%       Series.RootFile{1}: root file name
14%       Series.FileExt{1}: image file extension
15%       Series.NomType{1}: nomenclature type for file in
16%
17% Method:
18%       Series.NbSlice: %number of slices defined on the interface
19% global A rangx0 rangy0 minA maxA; % make current image A accessible in workspace
20% global hfig1 hfig2 scalar
21% global Abackg nbpart lum diam
22%%%%%%%%%%%%%%ù
23%
24%%%%%%%%%%% GENERAL TO ALL SERIES ACTION FCTS %%%%%%%%%%%%%%%%%%%%%%%%%%%
25%
26%OUTPUT
27% ParamOut: sets options in the GUI series.fig needed for the function
28%
29%INPUT:
30% In run mode, the input parameters are given as a Matlab structure Param copied from the GUI series.
31% In batch mode, Param is the name of the corresponding xml file containing the same information
32% when Param.Action.RUN=0 (as activated when the current Action is selected
33% in series), the function ouput paramOut set the activation of the needed GUI elements
34%
35% Param contains the elements:(use the menu bar command 'export/GUI config' in series to
36% see the current structure Param)
37%    .InputTable: cell of input file names, (several lines for multiple input)
38%                      each line decomposed as {RootPath,SubDir,Rootfile,NomType,Extension}
39%    .OutputSubDir: name of the subdirectory for data outputs
40%    .OutputDirExt: directory extension for data outputs
41%    .Action: .ActionName: name of the current activated function
42%             .ActionPath:   path of the current activated function
43%             .ActionExt: fct extension ('.m', Matlab fct, '.sh', compiled   Matlab fct
44%             .RUN =0 for GUI input, =1 for function activation
45%             .RunMode='local','background', 'cluster': type of function  use
46%             
47%    .IndexRange: set the file or frame indices on which the action must be performed
48%    .FieldTransform: .TransformName: name of the selected transform function
49%                     .TransformPath:   path  of the selected transform function
50%    .InputFields: sub structure describing the input fields withfields
51%              .FieldName: name(s) of the field
52%              .VelType: velocity type
53%              .FieldName_1: name of the second field in case of two input series
54%              .VelType_1: velocity type of the second field in case of two input series
55%              .Coord_y: name of y coordinate variable
56%              .Coord_x: name of x coordinate variable
57%    .ProjObject: %sub structure describing a projection object (read from ancillary GUI set_object)
58%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
59
60function ParamOut=particle_tracking(Param)
61
62%% set the input elements needed on the GUI series when the action is selected in the menu ActionName
63if isstruct(Param) && isequal(Param.Action.RUN,0)
64    % general settings of the GUI:
65    ParamOut.AllowInputSort='off';% allow alphabetic sorting of the list of input file SubDir (options 'off'/'on', 'off' by default)
66    ParamOut.WholeIndexRange='off';% prescribes the file index ranges from min to max (options 'off'/'on', 'off' by default)
67    ParamOut.NbSlice='off'; %nbre of slices ('off' by default)
68    ParamOut.VelType='off';% menu for selecting the velocity type (options 'off'/'one'/'two',  'off' by default)
69    ParamOut.FieldName='off';% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default)
70    ParamOut.FieldTransform = 'off';%can use a transform function
71    ParamOut.ProjObject='off';%can use projection object(option 'off'/'on',
72    ParamOut.Mask='off';%can use mask option   (option 'off'/'on', 'off' by default)
73    ParamOut.OutputDirExt='.track';%set the output dir extension
74    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
75    filecell=get_file_series(Param);%check existence of the first input file
76    if ~exist(filecell{1,1},'file')
77        msgbox_uvmat('WARNING','the first input file does not exist')
78    end
79    % parameters specific to the function 'particle_tracking'
80        Par.Nblock=10;%size of image subblocks for background determination, =[]: no sublock
81    Par.ThreshLum=210;% luminosity threshold for particle detection, < 0 for black particles, >0 for white particles
82  ParamOut.ActionInput=Par;
83    return
84end
85
86%%%%%%%%%%%%  STANDARD RUN PART  %%%%%%%%%%%%
87ParamOut=[];
88%% read input parameters from an xml file if input is a file name (batch mode)
89checkrun=1;
90if ischar(Param)
91    Param=xml2struct(Param);% read Param as input file (batch case)
92    checkrun=0;
93end
94hseries=findobj(allchild(0),'Tag','series');
95RUNHandle=findobj(hseries,'Tag','RUN');%handle of RUN button in GUI series
96WaitbarHandle=findobj(hseries,'Tag','Waitbar');%handle of waitbar in GUI series
97
98%% define the directory for result file
99OutputDir=[Param.OutputSubDir Param.OutputDirExt];
100
101%% root input file(s) name, type and index series
102RootPath=Param.InputTable{1,1};
103RootFile=Param.InputTable{1,3};
104SubDir=Param.InputTable{1,2};
105NomType=Param.InputTable{1,4};
106FileExt=Param.InputTable{1,5};
107[filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param);
108%%%%%%%%%%%%
109% The cell array filecell is the list of input file names, while
110% filecell{iview,fileindex}:
111%        iview: line in the table corresponding to a given file series
112%        fileindex: file index within  the file series,
113% 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
114% i1_series(iview,fileindex) expresses the same indices as a 1D array in file indices
115%%%%%%%%%%%%
116nbview=numel(i1_series);%number of input file series (lines in InputTable)
117nbfield_j=size(i1_series{1},1); %nb of fields for the j index (bursts or volume slices)
118nbfield_i=size(i1_series{1},2); %nb of fields for the i index
119nbfield=nbfield_j*nbfield_i; %total number of fields
120
121%% frame index for movie or multimage file input 
122if ~isempty(j1_series{1})
123    frame_index=j1_series{1};
124else
125    frame_index=i1_series{1};
126end
127
128%% check the input file type 
129[FileInfo,VideoObject]=get_file_info(filecell{1,1});
130FileType=FileInfo.FileType;
131ImageTypeOptions={'image','multimage','mmreader','video'};
132if isempty(find(strcmp(FileType,ImageTypeOptions)))
133    disp('input file not images')
134    return
135end
136
137%% calibration data and timing: read the ImaDoc files
138[XmlData,NbSlice_calib,time,errormsg]=read_multimadoc(RootPath,SubDir,RootFile,FileExt,i1_series,i2_series,j1_series,j2_series);
139
140%%%%%%%%%%%%   SPECIFIC PART (to edit) %%%%%%%%%%%%
141%filter for particle center of mass(luminosity)
142%Nblock=Param.ActionInput.Nblock;
143ThreshLum=Param.ActionInput.ThreshLum;% luminosity threshold for particle detection, < 0 for black particles, >0 for white particles
144%AbsThreshold=30; %threshold below which a pixel is considered belonging to a float
145SizePart=4;
146%
147hh=ones(5,5);
148hh(1,1)=0;
149hh(1,5)=0;% sum luminosity on the 5x5 domain without corners
150hh(5,1)=0;
151hh(5,5)=0;
152hdx=[-2:1:2];
153hdy=[-2:1:2];
154[hdX,hdY]=meshgrid(hdx,hdy);
155hdX(1,1)=0;
156hdX(1,5)=0;% sum luminosity on the 5x5 domain -corners
157hdX(5,1)=0;
158hdX(5,5)=0;
159hdY(1,1)=0;
160hdY(1,5)=0;% sum luminosity on the 5x5 domain -corners
161hdY(5,1)=0;
162hdY(5,5)=0;
163
164%% detection of particles on the first image
165
166%%%%%% MAIN LOOP ON FRAMES %%%%%%
167for ifile=1:nbfield
168    if checkrun
169                update_waitbar(WaitbarHandle,ifile/nbfield)
170        if ~isempty(RUNHandle) &&ishandle(RUNHandle) && ~strcmp(get(RUNHandle,'BusyAction'),'queue')
171            disp('program stopped by user')
172            return
173        end
174    end
175    j1=[];
176    if ~isempty(j1_series)&&~isequal(j1_series,{[]})
177        j1=j1_series{1}(ifile);
178    end
179    filename=fullfile_uvmat(RootPath,SubDir,RootFile,FileExt,NomType,i1_series{1}(ifile),[],j1);
180    A=read_image(filename,FileType,VideoObject,frame_index(ifile));% read the current frame
181    if ndims(A)==3;%color images
182        A=sum(double(A),3);% take the sum of color components
183    end
184        %%  mask to reduce the  working area (optional)
185    Mask=ones(size(A));
186    Mask(1:SizePart,:)=0;
187    Mask(end-SizePart:end,:)=0;
188    Mask(:,1:SizePart)=0;
189    Mask(:,end-SizePart:end)=0; 
190    if ifile ==1
191        if ThreshLum>0 %brigth particles
192        [Js,Is]=find(A>ThreshLum & Mask==1);%indices (I,J) of dark pixels
193        else %black particle
194               [Js,Is]=find(A<ThreshLum & Mask==1);%indices (I,J) of dark pixels
195        end
196    else
197        Is=round(Xtime(ifile-1,:));
198        Js=round(Ytime(ifile-1,:));
199    end
200    X=zeros(size(Is));
201    Y=zeros(size(Js));
202    F=zeros(size(Js));
203    for ipart=1:numel(Is)
204        if Mask(Js(ipart),Is(ipart))==1
205            subimage=A(Js(ipart)-SizePart:Js(ipart)+SizePart,Is(ipart)-SizePart:Is(ipart)+SizePart);
206            subimage=max(max(subimage))-subimage;%take negative of the image
207            [vector,F(ipart)] = SUBPIX2DGAUSS (subimage,SizePart+1,SizePart+1);
208            %             X0(ipart)=Is(ipart);%TEST
209            %             Y0(ipart)=Js(ipart);%TEST
210            X(ipart)=Is(ipart)+vector(1);%corrected position
211            Y(ipart)=Js(ipart)+vector(2);
212            Xround=round(X(ipart));
213            Yround=round(Y(ipart));
214            if ifile==1
215                Mask(Yround-SizePart:Yround+SizePart,Xround-SizePart:Xround+SizePart)=0;% mask the subregion already treated to
216                % avoid double counting
217            end
218        end
219    end
220    %             X0=X0(X>0);
221    %     Y0=Y0(Y>0);
222    if ifile ==1
223        Ftime(1,:)=F(X>0);
224        Xtime(1,:)=X(X>0);
225        Ytime(1,:)=Y(Y>0);
226    else
227        Ftime(ifile,:)=F;
228        Xtime(ifile,:)=X;
229        Ytime(ifile,:)=Y;
230    end
231end
232figure(1)
233plot(Xtime)
234figure(2)
235plot(Ytime)
236
237%------------------------------------------------------------------------
238% --- Find the maximum of the correlation function after interpolation
239function [vector,F] = SUBPIX2DGAUSS (result_conv,x,y)
240%------------------------------------------------------------------------
241vector=[0 0]; %default
242F=-2;
243peaky=y;
244peakx=x;
245[npy,npx]=size(result_conv);
246if (x <= npx-1) && (y <= npy-1) && (x >= 1) && (y >= 1)
247    F=0;
248    for i=-1:1
249        for j=-1:1
250            %following 15 lines based on
251            %H. Nobach ï¿œ M. Honkanen (2005)
252            %Two-dimensional Gaussian regression for sub-pixel displacement
253            %estimation in particle image velocimetry or particle position
254            %estimation in particle tracking velocimetry
255            %Experiments in Fluids (2005) 38: 511ï¿œ515
256            c10(j+2,i+2)=i*log(result_conv(y+j, x+i));
257            c01(j+2,i+2)=j*log(result_conv(y+j, x+i));
258            c11(j+2,i+2)=i*j*log(result_conv(y+j, x+i));
259            c20(j+2,i+2)=(3*i^2-2)*log(result_conv(y+j, x+i));
260            c02(j+2,i+2)=(3*j^2-2)*log(result_conv(y+j, x+i));
261        end
262    end
263    c10=(1/6)*sum(sum(c10));
264    c01=(1/6)*sum(sum(c01));
265    c11=(1/4)*sum(sum(c11));
266    c20=(1/6)*sum(sum(c20));
267    c02=(1/6)*sum(sum(c02));
268    deltax=(c11*c01-2*c10*c02)/(4*c20*c02-c11^2);
269    deltay=(c11*c10-2*c01*c20)/(4*c20*c02-c11^2);
270    if abs(deltax)<1
271        peakx=x+deltax;
272    end
273    if abs(deltay)<1
274        peaky=y+deltay;
275    end
276end
277vector=[peakx-floor(npx/2)-1 peaky-floor(npy/2)-1];
278
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