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 | %%%%%%%%%%%%%%ï¿œ |
---|
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 | |
---|
60 | %======================================================================= |
---|
61 | % Copyright 2008-2019, LEGI UMR 5519 / CNRS UGA G-INP, Grenoble, France |
---|
62 | % http://www.legi.grenoble-inp.fr |
---|
63 | % Joel.Sommeria - Joel.Sommeria (A) legi.cnrs.fr |
---|
64 | % |
---|
65 | % This file is part of the toolbox UVMAT. |
---|
66 | % |
---|
67 | % UVMAT is free software; you can redistribute it and/or modify |
---|
68 | % it under the terms of the GNU General Public License as published |
---|
69 | % by the Free Software Foundation; either version 2 of the license, |
---|
70 | % or (at your option) any later version. |
---|
71 | % |
---|
72 | % UVMAT is distributed in the hope that it will be useful, |
---|
73 | % but WITHOUT ANY WARRANTY; without even the implied warranty of |
---|
74 | % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
---|
75 | % GNU General Public License (see LICENSE.txt) for more details. |
---|
76 | %======================================================================= |
---|
77 | |
---|
78 | function ParamOut=particle_tracking(Param) |
---|
79 | |
---|
80 | %% set the input elements needed on the GUI series when the action is selected in the menu ActionName |
---|
81 | if isstruct(Param) && isequal(Param.Action.RUN,0) |
---|
82 | % general settings of the GUI: |
---|
83 | ParamOut.AllowInputSort='off';% allow alphabetic sorting of the list of input file SubDir (options 'off'/'on', 'off' by default) |
---|
84 | ParamOut.WholeIndexRange='off';% prescribes the file index ranges from min to max (options 'off'/'on', 'off' by default) |
---|
85 | ParamOut.NbSlice='off'; %nbre of slices ('off' by default) |
---|
86 | ParamOut.VelType='off';% menu for selecting the velocity type (options 'off'/'one'/'two', 'off' by default) |
---|
87 | ParamOut.FieldName='off';% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default) |
---|
88 | ParamOut.FieldTransform = 'off';%can use a transform function |
---|
89 | ParamOut.ProjObject='off';%can use projection object(option 'off'/'on', |
---|
90 | ParamOut.Mask='off';%can use mask option (option 'off'/'on', 'off' by default) |
---|
91 | ParamOut.OutputDirExt='.track';%set the output dir extension |
---|
92 | 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 |
---|
93 | filecell=get_file_series(Param);%check existence of the first input file |
---|
94 | if ~exist(filecell{1,1},'file') |
---|
95 | msgbox_uvmat('WARNING','the first input file does not exist') |
---|
96 | end |
---|
97 | % parameters specific to the function 'particle_tracking' |
---|
98 | Par.Nblock=10;%size of image subblocks for background determination, =[]: no sublock |
---|
99 | Par.ThreshLum=210;% luminosity threshold for particle detection, < 0 for black particles, >0 for white particles |
---|
100 | ParamOut.ActionInput=Par; |
---|
101 | return |
---|
102 | end |
---|
103 | |
---|
104 | %%%%%%%%%%%% STANDARD RUN PART %%%%%%%%%%%% |
---|
105 | ParamOut=[]; |
---|
106 | %% read input parameters from an xml file if input is a file name (batch mode) |
---|
107 | checkrun=1; |
---|
108 | if ischar(Param) |
---|
109 | Param=xml2struct(Param);% read Param as input file (batch case) |
---|
110 | checkrun=0; |
---|
111 | end |
---|
112 | hseries=findobj(allchild(0),'Tag','series'); |
---|
113 | RUNHandle=findobj(hseries,'Tag','RUN');%handle of RUN button in GUI series |
---|
114 | WaitbarHandle=findobj(hseries,'Tag','Waitbar');%handle of waitbar in GUI series |
---|
115 | |
---|
116 | %% define the directory for result file |
---|
117 | OutputDir=[Param.OutputSubDir Param.OutputDirExt]; |
---|
118 | |
---|
119 | %% root input file(s) name, type and index series |
---|
120 | RootPath=Param.InputTable{1,1}; |
---|
121 | RootFile=Param.InputTable{1,3}; |
---|
122 | SubDir=Param.InputTable{1,2}; |
---|
123 | NomType=Param.InputTable{1,4}; |
---|
124 | FileExt=Param.InputTable{1,5}; |
---|
125 | [filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param); |
---|
126 | %%%%%%%%%%%% |
---|
127 | % The cell array filecell is the list of input file names, while |
---|
128 | % filecell{iview,fileindex}: |
---|
129 | % iview: line in the table corresponding to a given file series |
---|
130 | % fileindex: file index within the file series, |
---|
131 | % 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 |
---|
132 | % i1_series(iview,fileindex) expresses the same indices as a 1D array in file indices |
---|
133 | %%%%%%%%%%%% |
---|
134 | nbview=numel(i1_series);%number of input file series (lines in InputTable) |
---|
135 | nbfield_j=size(i1_series{1},1); %nb of fields for the j index (bursts or volume slices) |
---|
136 | nbfield_i=size(i1_series{1},2); %nb of fields for the i index |
---|
137 | nbfield=nbfield_j*nbfield_i; %total number of fields |
---|
138 | |
---|
139 | %% frame index for movie or multimage file input |
---|
140 | if ~isempty(j1_series{1}) |
---|
141 | frame_index=j1_series{1}; |
---|
142 | else |
---|
143 | frame_index=i1_series{1}; |
---|
144 | end |
---|
145 | |
---|
146 | %% check the input file type |
---|
147 | [FileInfo,VideoObject]=get_file_info(filecell{1,1}); |
---|
148 | FileType=FileInfo.FileType; |
---|
149 | ImageTypeOptions={'image','multimage','mmreader','video','cine_phantom'}; |
---|
150 | if isempty(find(strcmp(FileType,ImageTypeOptions))) |
---|
151 | disp('input file not images') |
---|
152 | return |
---|
153 | end |
---|
154 | |
---|
155 | %% calibration data and timing: read the ImaDoc files |
---|
156 | [XmlData,NbSlice_calib,time,errormsg]=read_multimadoc(RootPath,SubDir,RootFile,FileExt,i1_series,i2_series,j1_series,j2_series); |
---|
157 | |
---|
158 | %%%%%%%%%%%% SPECIFIC PART (to edit) %%%%%%%%%%%% |
---|
159 | %filter for particle center of mass(luminosity) |
---|
160 | %Nblock=Param.ActionInput.Nblock; |
---|
161 | ThreshLum=Param.ActionInput.ThreshLum;% luminosity threshold for particle detection, < 0 for black particles, >0 for white particles |
---|
162 | %AbsThreshold=30; %threshold below which a pixel is considered belonging to a float |
---|
163 | SizePart=4; |
---|
164 | % |
---|
165 | hh=ones(5,5); |
---|
166 | hh(1,1)=0; |
---|
167 | hh(1,5)=0;% sum luminosity on the 5x5 domain without corners |
---|
168 | hh(5,1)=0; |
---|
169 | hh(5,5)=0; |
---|
170 | hdx=[-2:1:2]; |
---|
171 | hdy=[-2:1:2]; |
---|
172 | [hdX,hdY]=meshgrid(hdx,hdy); |
---|
173 | hdX(1,1)=0; |
---|
174 | hdX(1,5)=0;% sum luminosity on the 5x5 domain -corners |
---|
175 | hdX(5,1)=0; |
---|
176 | hdX(5,5)=0; |
---|
177 | hdY(1,1)=0; |
---|
178 | hdY(1,5)=0;% sum luminosity on the 5x5 domain -corners |
---|
179 | hdY(5,1)=0; |
---|
180 | hdY(5,5)=0; |
---|
181 | |
---|
182 | %% detection of particles on the first image |
---|
183 | |
---|
184 | %%%%%% MAIN LOOP ON FRAMES %%%%%% |
---|
185 | for ifile=1:nbfield |
---|
186 | if checkrun |
---|
187 | update_waitbar(WaitbarHandle,ifile/nbfield) |
---|
188 | if ~isempty(RUNHandle) &&ishandle(RUNHandle) && ~strcmp(get(RUNHandle,'BusyAction'),'queue') |
---|
189 | disp('program stopped by user') |
---|
190 | return |
---|
191 | end |
---|
192 | end |
---|
193 | j1=[]; |
---|
194 | if ~isempty(j1_series)&&~isequal(j1_series,{[]}) |
---|
195 | j1=j1_series{1}(ifile); |
---|
196 | end |
---|
197 | filename=fullfile_uvmat(RootPath,SubDir,RootFile,FileExt,NomType,i1_series{1}(ifile),[],j1); |
---|
198 | A=read_image(filename,FileType,VideoObject,frame_index(ifile));% read the current frame |
---|
199 | if ndims(A)==3;%color images |
---|
200 | A=sum(double(A),3);% take the sum of color components |
---|
201 | end |
---|
202 | %% mask to reduce the working area (optional) |
---|
203 | Mask=ones(size(A)); |
---|
204 | Mask(1:SizePart,:)=0; |
---|
205 | Mask(end-SizePart:end,:)=0; |
---|
206 | Mask(:,1:SizePart)=0; |
---|
207 | Mask(:,end-SizePart:end)=0; |
---|
208 | if ifile ==1 |
---|
209 | if ThreshLum>0 %brigth particles |
---|
210 | [Js,Is]=find(A>ThreshLum & Mask==1);%indices (I,J) of dark pixels |
---|
211 | else %black particle |
---|
212 | [Js,Is]=find(A<ThreshLum & Mask==1);%indices (I,J) of dark pixels |
---|
213 | end |
---|
214 | else |
---|
215 | Is=round(Xtime(ifile-1,:)); |
---|
216 | Js=round(Ytime(ifile-1,:)); |
---|
217 | end |
---|
218 | X=zeros(size(Is)); |
---|
219 | Y=zeros(size(Js)); |
---|
220 | F=zeros(size(Js)); |
---|
221 | for ipart=1:numel(Is) |
---|
222 | if Mask(Js(ipart),Is(ipart))==1 |
---|
223 | subimage=A(Js(ipart)-SizePart:Js(ipart)+SizePart,Is(ipart)-SizePart:Is(ipart)+SizePart); |
---|
224 | subimage=max(max(subimage))-subimage;%take negative of the image |
---|
225 | [vector,F(ipart)] = SUBPIX2DGAUSS (subimage,SizePart+1,SizePart+1); |
---|
226 | % X0(ipart)=Is(ipart);%TEST |
---|
227 | % Y0(ipart)=Js(ipart);%TEST |
---|
228 | X(ipart)=Is(ipart)+vector(1);%corrected position |
---|
229 | Y(ipart)=Js(ipart)+vector(2); |
---|
230 | Xround=round(X(ipart)); |
---|
231 | Yround=round(Y(ipart)); |
---|
232 | if ifile==1 |
---|
233 | Mask(Yround-SizePart:Yround+SizePart,Xround-SizePart:Xround+SizePart)=0;% mask the subregion already treated to |
---|
234 | % avoid double counting |
---|
235 | end |
---|
236 | end |
---|
237 | end |
---|
238 | % X0=X0(X>0); |
---|
239 | % Y0=Y0(Y>0); |
---|
240 | if ifile ==1 |
---|
241 | Ftime(1,:)=F(X>0); |
---|
242 | Xtime(1,:)=X(X>0); |
---|
243 | Ytime(1,:)=Y(Y>0); |
---|
244 | else |
---|
245 | Ftime(ifile,:)=F; |
---|
246 | Xtime(ifile,:)=X; |
---|
247 | Ytime(ifile,:)=Y; |
---|
248 | end |
---|
249 | end |
---|
250 | figure(1) |
---|
251 | plot(Xtime) |
---|
252 | figure(2) |
---|
253 | plot(Ytime) |
---|
254 | |
---|
255 | %------------------------------------------------------------------------ |
---|
256 | % --- Find the maximum of the correlation function after interpolation |
---|
257 | function [vector,F] = SUBPIX2DGAUSS (result_conv,x,y) |
---|
258 | %------------------------------------------------------------------------ |
---|
259 | vector=[0 0]; %default |
---|
260 | F=-2; |
---|
261 | peaky=y; |
---|
262 | peakx=x; |
---|
263 | [npy,npx]=size(result_conv); |
---|
264 | if (x <= npx-1) && (y <= npy-1) && (x >= 1) && (y >= 1) |
---|
265 | F=0; |
---|
266 | for i=-1:1 |
---|
267 | for j=-1:1 |
---|
268 | %following 15 lines based on |
---|
269 | %H. Nobach ï¿œ M. Honkanen (2005) |
---|
270 | %Two-dimensional Gaussian regression for sub-pixel displacement |
---|
271 | %estimation in particle image velocimetry or particle position |
---|
272 | %estimation in particle tracking velocimetry |
---|
273 | %Experiments in Fluids (2005) 38: 511ï¿œ515 |
---|
274 | c10(j+2,i+2)=i*log(result_conv(y+j, x+i)); |
---|
275 | c01(j+2,i+2)=j*log(result_conv(y+j, x+i)); |
---|
276 | c11(j+2,i+2)=i*j*log(result_conv(y+j, x+i)); |
---|
277 | c20(j+2,i+2)=(3*i^2-2)*log(result_conv(y+j, x+i)); |
---|
278 | c02(j+2,i+2)=(3*j^2-2)*log(result_conv(y+j, x+i)); |
---|
279 | end |
---|
280 | end |
---|
281 | c10=(1/6)*sum(sum(c10)); |
---|
282 | c01=(1/6)*sum(sum(c01)); |
---|
283 | c11=(1/4)*sum(sum(c11)); |
---|
284 | c20=(1/6)*sum(sum(c20)); |
---|
285 | c02=(1/6)*sum(sum(c02)); |
---|
286 | deltax=(c11*c01-2*c10*c02)/(4*c20*c02-c11^2); |
---|
287 | deltay=(c11*c10-2*c01*c20)/(4*c20*c02-c11^2); |
---|
288 | if abs(deltax)<1 |
---|
289 | peakx=x+deltax; |
---|
290 | end |
---|
291 | if abs(deltay)<1 |
---|
292 | peaky=y+deltay; |
---|
293 | end |
---|
294 | end |
---|
295 | vector=[peakx-floor(npx/2)-1 peaky-floor(npy/2)-1]; |
---|
296 | |
---|