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source: trunk/src/series/float_tracking.m @ 635

Last change on this file since 635 was 635, checked in by sommeria, 11 years ago
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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=[];%size of image subblocks for background determination, =[]: no sublock
81%     Par.ThreshLum=-2000;% 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
94
95%% define the directory for result file
96OutputDir=[Param.OutputSubDir Param.OutputDirExt];
97
98%% root input file(s) name, type and index series
99RootPath=Param.InputTable{1,1};
100RootFile=Param.InputTable{1,3};
101SubDir=Param.InputTable{1,2};
102NomType=Param.InputTable{1,4};
103FileExt=Param.InputTable{1,5};
104[filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param);
105%%%%%%%%%%%%
106% The cell array filecell is the list of input file names, while
107% filecell{iview,fileindex}:
108%        iview: line in the table corresponding to a given file series
109%        fileindex: file index within  the file series,
110% 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
111% i1_series(iview,fileindex) expresses the same indices as a 1D array in file indices
112%%%%%%%%%%%%
113nbview=numel(i1_series);%number of input file series (lines in InputTable)
114nbfield_j=size(i1_series{1},1); %nb of fields for the j index (bursts or volume slices)
115nbfield_i=size(i1_series{1},2); %nb of fields for the i index
116nbfield=nbfield_j*nbfield_i; %total number of fields
117
118%% frame index for movie or multimage file input 
119if ~isempty(j1_series{1})
120    frame_index=j1_series{1};
121else
122    frame_index=i1_series{1};
123end
124
125%% check the input file type 
126[FileType,FileInfo,VideoObject]=get_file_type(filecell{1,1});
127ImageTypeOptions={'image','multimage','mmreader','video'};
128if isempty(find(strcmp(FileType,ImageTypeOptions)))
129    disp('input file not images')
130    return
131end
132
133%% calibration data and timing: read the ImaDoc files
134[XmlData,NbSlice_calib,time,errormsg]=read_multimadoc(RootPath,SubDir,RootFile,FileExt,i1_series,i2_series,j1_series,j2_series);
135
136%%%%%%%%%%%%   SPECIFIC PART (to edit) %%%%%%%%%%%%
137%filter for particle center of mass(luminosity)
138%Nblock=Param.ActionInput.Nblock;
139%ThreshLum=Param.ActionInput.ThreshLum;% luminosity threshold for particle detection, < 0 for black particles, >0 for white particles
140AbsThreshold=30; %threshold below which a pixel is considered belonging to a float
141SizePart=4;
142%
143hh=ones(5,5);
144hh(1,1)=0;
145hh(1,5)=0;% sum luminosity on the 5x5 domain without corners
146hh(5,1)=0;
147hh(5,5)=0;
148hdx=[-2:1:2];
149hdy=[-2:1:2];
150[hdX,hdY]=meshgrid(hdx,hdy);
151hdX(1,1)=0;
152hdX(1,5)=0;% sum luminosity on the 5x5 domain -corners
153hdX(5,1)=0;
154hdX(5,5)=0;
155hdY(1,1)=0;
156hdY(1,5)=0;% sum luminosity on the 5x5 domain -corners
157hdY(5,1)=0;
158hdY(5,5)=0;
159
160%% detection of particles on the first image
161
162%%%%%% MAIN LOOP ON FRAMES %%%%%%
163for ifile=1:nbfield
164    if checkrun
165        if strcmp(get(Param.RUNHandle,'BusyAction'),'queue')
166            update_waitbar(Param.WaitbarHandle,ifile/nbfield)
167        else
168            break% leave the loop if the STOP button is activated on the GUI series
169        end
170    end
171    j1=[];
172    if ~isempty(j1_series)&&~isequal(j1_series,{[]})
173        j1=j1_series{1}(ifile);
174    end
175    filename=fullfile_uvmat(RootPath,SubDir,RootFile,FileExt,NomType,i1_series{1}(ifile),[],j1);
176    A=read_image(filename,FileType,VideoObject,frame_index(ifile));% read the current frame
177    if ndims(A)==3;%color images
178        A=sum(double(A),3);% take the sum of color components
179    end
180        %%  mask to reduce the  working area (optional)
181    Mask=ones(size(A));
182    Mask(1:SizePart,:)=0;
183    Mask(end-SizePart:end,:)=0;
184    Mask(:,1:SizePart)=0;
185    Mask(:,end-SizePart:end)=0; 
186    if ifile ==1
187        [Js,Is]=find(A<AbsThreshold & Mask==1);%indices (I,J) of dark pixels
188    else
189        Is=round(Xtime(ifile-1,:));
190        Js=round(Ytime(ifile-1,:));
191    end
192    X=zeros(size(Is));
193    Y=zeros(size(Js));
194    F=zeros(size(Js));
195    for ipart=1:numel(Is)
196        if Mask(Js(ipart),Is(ipart))==1
197            subimage=A(Js(ipart)-SizePart:Js(ipart)+SizePart,Is(ipart)-SizePart:Is(ipart)+SizePart);
198            subimage=max(max(subimage))-subimage;%take negative of the image
199            [vector,F(ipart)] = SUBPIX2DGAUSS (subimage,SizePart+1,SizePart+1);
200            %             X0(ipart)=Is(ipart);%TEST
201            %             Y0(ipart)=Js(ipart);%TEST
202            X(ipart)=Is(ipart)+vector(1);%corrected position
203            Y(ipart)=Js(ipart)+vector(2);
204            Xround=round(X(ipart));
205            Yround=round(Y(ipart));
206            if ifile==1
207                Mask(Yround-SizePart:Yround+SizePart,Xround-SizePart:Xround+SizePart)=0;% mask the subregion already treated to
208                % avoid double counting
209            end
210        end
211    end
212    %             X0=X0(X>0);
213    %     Y0=Y0(Y>0);
214    if ifile ==1
215        Ftime(1,:)=F(X>0);
216        Xtime(1,:)=X(X>0);
217        Ytime(1,:)=Y(Y>0);
218    else
219        Ftime(ifile,:)=F;
220        Xtime(ifile,:)=X;
221        Ytime(ifile,:)=Y;
222    end
223end
224figure(1)
225plot(Xtime)
226figure(2)
227plot(Ytime)
228
229%------------------------------------------------------------------------
230% --- Find the maximum of the correlation function after interpolation
231function [vector,F] = SUBPIX2DGAUSS (result_conv,x,y)
232%------------------------------------------------------------------------
233vector=[0 0]; %default
234F=-2;
235peaky=y;
236peakx=x;
237[npy,npx]=size(result_conv);
238if (x <= npx-1) && (y <= npy-1) && (x >= 1) && (y >= 1)
239    F=0;
240    for i=-1:1
241        for j=-1:1
242            %following 15 lines based on
243            %H. Nobach ï¿œ M. Honkanen (2005)
244            %Two-dimensional Gaussian regression for sub-pixel displacement
245            %estimation in particle image velocimetry or particle position
246            %estimation in particle tracking velocimetry
247            %Experiments in Fluids (2005) 38: 511ï¿œ515
248            c10(j+2,i+2)=i*log(result_conv(y+j, x+i));
249            c01(j+2,i+2)=j*log(result_conv(y+j, x+i));
250            c11(j+2,i+2)=i*j*log(result_conv(y+j, x+i));
251            c20(j+2,i+2)=(3*i^2-2)*log(result_conv(y+j, x+i));
252            c02(j+2,i+2)=(3*j^2-2)*log(result_conv(y+j, x+i));
253        end
254    end
255    c10=(1/6)*sum(sum(c10));
256    c01=(1/6)*sum(sum(c01));
257    c11=(1/4)*sum(sum(c11));
258    c20=(1/6)*sum(sum(c20));
259    c02=(1/6)*sum(sum(c02));
260    deltax=(c11*c01-2*c10*c02)/(4*c20*c02-c11^2);
261    deltay=(c11*c10-2*c01*c20)/(4*c20*c02-c11^2);
262    if abs(deltax)<1
263        peakx=x+deltax;
264    end
265    if abs(deltay)<1
266        peaky=y+deltay;
267    end
268end
269vector=[peakx-floor(npx/2)-1 peaky-floor(npy/2)-1];
270
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