1 | %'civ_matlab': Matlab version of the PIV programs CivX |
---|
2 | % --- call the sub-functions: |
---|
3 | % civ: PIV function itself |
---|
4 | % fix: removes false vectors after detection by various criteria |
---|
5 | % filter_tps: make interpolation-smoothing |
---|
6 | %------------------------------------------------------------------------ |
---|
7 | % function [Data,errormsg,result_conv]= civ_uvmat(Param,ncfile) |
---|
8 | % |
---|
9 | %OUTPUT |
---|
10 | % Data=structure containing the PIV results and information on the processing parameters |
---|
11 | % errormsg=error message char string, default='' |
---|
12 | % resul_conv: image inter-correlation function for the last grid point (used for tests) |
---|
13 | % |
---|
14 | %INPUT: |
---|
15 | % Param: input images and processing parameters |
---|
16 | % .Civ1: for civ1 |
---|
17 | % .Fix1: |
---|
18 | % .Patch1: |
---|
19 | % .Civ2: for civ2 |
---|
20 | % .Fix2: |
---|
21 | % .Patch2: |
---|
22 | % ncfile: name of a netcdf file to be created for the result (extension .nc) |
---|
23 | % |
---|
24 | %AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA |
---|
25 | % Copyright 2011, LEGI / CNRS-UJF-INPG, joel.sommeria@legi.grenoble-inp.fr. |
---|
26 | %AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA |
---|
27 | % This is part of the toolbox UVMAT. |
---|
28 | % |
---|
29 | % UVMAT is free software; you can redistribute it and/or modify |
---|
30 | % it under the terms of the GNU General Public License as published by |
---|
31 | % the Free Software Foundation; either version 2 of the License, or |
---|
32 | % (at your option) any later version. |
---|
33 | % |
---|
34 | % UVMAT is distributed in the hope that it will be useful, |
---|
35 | % but WITHOUT ANY WARRANTY; without even the implied warranty of |
---|
36 | % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
---|
37 | % GNU General Public License (open UVMAT/COPYING.txt) for more details. |
---|
38 | %AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA |
---|
39 | |
---|
40 | function [Data,errormsg,result_conv]= civ_matlab(Param,ncfile) |
---|
41 | errormsg=''; |
---|
42 | Data.ListGlobalAttribute={'Conventions','Program','CivStage'}; |
---|
43 | Data.Conventions='uvmat/civdata';% states the conventions used for the description of field variables and attributes |
---|
44 | Data.Program='civ_matlab'; |
---|
45 | Data.CivStage=0;%default |
---|
46 | ListVarCiv1={'Civ1_X','Civ1_Y','Civ1_U','Civ1_V','Civ1_C','Civ1_F'}; %variables to read |
---|
47 | ListVarFix1={'Civ1_X','Civ1_Y','Civ1_U','Civ1_V','Civ1_C','Civ1_F','Civ1_FF'}; |
---|
48 | mask=''; |
---|
49 | maskname='';%default |
---|
50 | check_civx=0;%default |
---|
51 | check_civ1=0;%default |
---|
52 | check_patch1=0;%default |
---|
53 | ImageFileA=Param.Civ1.ImageA; |
---|
54 | ImageFileB=Param.Civ1.ImageB; |
---|
55 | if isfield(Param,'Civ2') |
---|
56 | ImageFileA_civ2=Param.Civ2.ImageA; |
---|
57 | ImageFileB_civ2=Param.Civ2.ImageB; |
---|
58 | end |
---|
59 | % case of input Param set by an xml file (batch mode) |
---|
60 | if ischar(Param) |
---|
61 | Param=xml2struct(Param); %if Param is the name of an xml file, read this file as a Matlab structure |
---|
62 | if isfield(Param,'Civ1') |
---|
63 | if strcmp(Param.Civ1.FileTypeA,'video') |
---|
64 | Param.Civ1.ImageA=VideoReader(Param.Civ1.ImageA); |
---|
65 | elseif strcmp(Param.Civ1.FileTypeA,'mmreader') |
---|
66 | Param.Civ1.ImageA=mmreader(Param.Civ1.ImageA); |
---|
67 | end |
---|
68 | if strcmp(Param.Civ1.FileTypeB,'video') |
---|
69 | Param.Civ1.ImageB=VideoReader(Param.Civ1.ImageB); |
---|
70 | elseif strcmp(Param.Civ1.FileTypeB,'mmreader') |
---|
71 | Param.Civ1.ImageB=mmreader(Param.Civ1.ImageB); |
---|
72 | end |
---|
73 | end |
---|
74 | if isfield(Param,'Civ2') |
---|
75 | if strcmp(Param.Civ2.FileTypeA,'video') |
---|
76 | Param.Civ2.ImageA=VideoReader(Param.Civ2.ImageA); |
---|
77 | elseif strcmp(Param.Civ2.FileTypeA,'mmreader') |
---|
78 | Param.Civ2.ImageA=mmreader(Param.Civ2.ImageA); |
---|
79 | end |
---|
80 | if strcmp(Param.Civ2.FileTypeB,'video') |
---|
81 | Param.Civ2.ImageB=VideoReader(Param.Civ2.ImageB); |
---|
82 | elseif strcmp(Param.Civ2.FileTypeB,'mmreader') |
---|
83 | Param.Civ2.ImageB=mmreader(Param.Civ2.ImageB); |
---|
84 | end |
---|
85 | end |
---|
86 | end |
---|
87 | |
---|
88 | %% Civ1 |
---|
89 | if isfield (Param,'Civ1') |
---|
90 | % check_civ1=1;% test for further use of civ1 results |
---|
91 | % %% prepare images |
---|
92 | par_civ1=Param.Civ1; |
---|
93 | if isfield(par_civ1,'reverse_pair') |
---|
94 | if par_civ1.reverse_pair |
---|
95 | if ischar(par_civ1.ImageB) |
---|
96 | temp=par_civ1.ImageA; |
---|
97 | par_civ1.ImageA=imread(par_civ1.ImageB); |
---|
98 | end |
---|
99 | if ischar(temp) |
---|
100 | par_civ1.ImageB=imread(temp); |
---|
101 | end |
---|
102 | end |
---|
103 | else |
---|
104 | if isfield(par_civ1,'ImageA')&&(ischar(par_civ1.ImageA)||strcmp(class(par_civ1.ImageA),'VideoReader')) % case with no image: only the PIV grid is calculated |
---|
105 | [Field,ParamOut,errormsg] = read_field(ImageFileA,par_civ1.FileTypeA,par_civ1.ImageA,par_civ1.FrameIndexA); |
---|
106 | if ~isempty(errormsg) |
---|
107 | errormsg=['error in civ_matlab/read_field:' errormsg]; |
---|
108 | return |
---|
109 | end |
---|
110 | par_civ1.ImageA=Field.A;%= image matrix A in the first input field |
---|
111 | end |
---|
112 | if isfield(par_civ1,'ImageB')&& (ischar(par_civ1.ImageB)||strcmp(class(par_civ1.ImageB),'VideoReader')) |
---|
113 | [Field,ParamOut,errormsg] = read_field(ImageFileB,par_civ1.FileTypeB,par_civ1.ImageB,par_civ1.FrameIndexB); |
---|
114 | if ~isempty(errormsg) |
---|
115 | errormsg=['error in civ_matlab/read_field:' errormsg]; |
---|
116 | return |
---|
117 | end |
---|
118 | par_civ1.ImageB=Field.A;%= image matrix A in the second input field |
---|
119 | end |
---|
120 | end |
---|
121 | |
---|
122 | % caluclate velocity data (y and v in indices, reverse to y component) |
---|
123 | [xtable ytable utable vtable ctable F result_conv errormsg] = civ (par_civ1); |
---|
124 | |
---|
125 | % to try the reverse_pair method, uncomment below |
---|
126 | % [xtable1 ytable1 utable1 vtable1 ctable1 F1 result_conv1 errormsg1] = civ (Param.Civ1); |
---|
127 | % Param.Civ1.reverse_pair=1; |
---|
128 | % [xtable2 ytable2 utable2 vtable2 ctable2 F2 result_conv2 errormsg2] = civ (Param.Civ1); |
---|
129 | % xtable=[xtable1; xtable2]; |
---|
130 | % ytable=[ytable1; ytable2]; |
---|
131 | % utable=[utable1; -utable2]; |
---|
132 | % vtable=[vtable1; -vtable2]; |
---|
133 | % ctable=[ctable1; ctable2]; |
---|
134 | % F=[F1; F2]; |
---|
135 | % result_conv=[result_conv1; result_conv2]; |
---|
136 | % errormsg=[errormsg1; errormsg2]; |
---|
137 | if ~isempty(errormsg) |
---|
138 | return |
---|
139 | end |
---|
140 | list_param=(fieldnames(Param.Civ1))'; |
---|
141 | Civ1_param=list_param;%default |
---|
142 | %set the values of all the global attributes in list_param |
---|
143 | for ilist=1:length(list_param) |
---|
144 | Civ1_param{ilist}=['Civ1_' list_param{ilist}]; |
---|
145 | Data.(['Civ1_' list_param{ilist}])=Param.Civ1.(list_param{ilist}); |
---|
146 | end |
---|
147 | Data.ListGlobalAttribute=[Data.ListGlobalAttribute Civ1_param];% {'Civ1_Time','Civ1_Dt'}]; |
---|
148 | Data.ListVarName={'Civ1_X','Civ1_Y','Civ1_U','Civ1_V','Civ1_F','Civ1_C'};% cell array containing the names of the fields to record |
---|
149 | Data.VarDimName={'nb_vec_1','nb_vec_1','nb_vec_1','nb_vec_1','nb_vec_1','nb_vec_1'}; |
---|
150 | Data.VarAttribute{1}.Role='coord_x'; |
---|
151 | Data.VarAttribute{2}.Role='coord_y'; |
---|
152 | Data.VarAttribute{3}.Role='vector_x'; |
---|
153 | Data.VarAttribute{4}.Role='vector_y'; |
---|
154 | Data.VarAttribute{5}.Role='warnflag'; |
---|
155 | Data.Civ1_X=reshape(xtable,[],1); |
---|
156 | Data.Civ1_Y=reshape(Param.Civ1.ImageHeight-ytable+1,[],1); |
---|
157 | Data.Civ1_U=reshape(utable,[],1); |
---|
158 | Data.Civ1_V=reshape(-vtable,[],1); |
---|
159 | Data.Civ1_C=reshape(ctable,[],1); |
---|
160 | Data.Civ1_F=reshape(F,[],1); |
---|
161 | Data.CivStage=1; |
---|
162 | else |
---|
163 | if exist('ncfile','var') |
---|
164 | CivFile=ncfile; |
---|
165 | elseif isfield(Param.Patch1,'CivFile') |
---|
166 | CivFile=Param.Patch1.CivFile; |
---|
167 | end |
---|
168 | Data=nc2struct(CivFile,'ListGlobalAttribute','absolut_time_T0'); %look for the constant 'absolut_time_T0' to detect old civx data format |
---|
169 | if isfield(Data,'Txt') |
---|
170 | errormsg=Data.Txt; |
---|
171 | return |
---|
172 | end |
---|
173 | if ~isempty(Data.absolut_time_T0')%read civx file |
---|
174 | check_civx=1;% test for old civx data format |
---|
175 | [Data,vardetect,ichoice]=nc2struct(CivFile);%read the variables in the netcdf file |
---|
176 | else |
---|
177 | Data=nc2struct(CivFile);%read civ1 and fix1 data in the existing netcdf file |
---|
178 | end |
---|
179 | end |
---|
180 | |
---|
181 | %% Fix1 |
---|
182 | if isfield (Param,'Fix1') |
---|
183 | ListFixParam=fieldnames(Param.Fix1); |
---|
184 | for ilist=1:length(ListFixParam) |
---|
185 | ParamName=ListFixParam{ilist}; |
---|
186 | ListName=['Fix1_' ParamName]; |
---|
187 | eval(['Data.ListGlobalAttribute=[Data.ListGlobalAttribute ''' ParamName '''];']) |
---|
188 | eval(['Data.' ListName '=Param.Fix1.' ParamName ';']) |
---|
189 | end |
---|
190 | if check_civx |
---|
191 | if ~isfield(Data,'fix') |
---|
192 | Data.ListGlobalAttribute=[Data.ListGlobalAttribute 'fix']; |
---|
193 | Data.fix=1; |
---|
194 | Data.ListVarName=[Data.ListVarName {'vec_FixFlag'}]; |
---|
195 | Data.VarDimName=[Data.VarDimName {'nb_vectors'}]; |
---|
196 | end |
---|
197 | Data.vec_FixFlag=fix(Param.Fix1,Data.vec_F,Data.vec_C,Data.vec_U,Data.vec_V,Data.vec_X,Data.vec_Y); |
---|
198 | else |
---|
199 | Data.ListVarName=[Data.ListVarName {'Civ1_FF'}]; |
---|
200 | Data.VarDimName=[Data.VarDimName {'nb_vec_1'}]; |
---|
201 | nbvar=length(Data.ListVarName); |
---|
202 | Data.VarAttribute{nbvar}.Role='errorflag'; |
---|
203 | Data.Civ1_FF=fix(Param.Fix1,Data.Civ1_F,Data.Civ1_C,Data.Civ1_U,Data.Civ1_V); |
---|
204 | Data.CivStage=2; |
---|
205 | end |
---|
206 | end |
---|
207 | %% Patch1 |
---|
208 | if isfield (Param,'Patch1') |
---|
209 | if check_civx |
---|
210 | errormsg='Civ Matlab input needed for patch'; |
---|
211 | return |
---|
212 | end |
---|
213 | |
---|
214 | Data.ListGlobalAttribute=[Data.ListGlobalAttribute {'Patch1_Rho','Patch1_Threshold','Patch1_SubDomain'}]; |
---|
215 | Data.Patch1_Rho=Param.Patch1.FieldSmooth; |
---|
216 | Data.Patch1_Threshold=Param.Patch1.MaxDiff; |
---|
217 | Data.Patch1_SubDomain=Param.Patch1.SubdomainSize; |
---|
218 | nbvar=length(Data.ListVarName); |
---|
219 | Data.ListVarName=[Data.ListVarName {'Civ1_U_smooth','Civ1_V_smooth','Civ1_SubRange','Civ1_NbSites','Civ1_Coord_tps','Civ1_U_tps','Civ1_V_tps'}]; |
---|
220 | Data.VarDimName=[Data.VarDimName {'nb_vec_1','nb_vec_1',{'nb_coord','nb_bounds','nb_subdomain_1'},{'nb_subdomain_1'},... |
---|
221 | {'nb_tps_1','nb_coord','nb_subdomain_1'},{'nb_tps_1','nb_subdomain_1'},{'nb_tps_1','nb_subdomain_1'}}]; |
---|
222 | Data.VarAttribute{nbvar+1}.Role='vector_x'; |
---|
223 | Data.VarAttribute{nbvar+2}.Role='vector_y'; |
---|
224 | Data.VarAttribute{nbvar+5}.Role='coord_tps'; |
---|
225 | Data.VarAttribute{nbvar+6}.Role='vector_x_tps'; |
---|
226 | Data.VarAttribute{nbvar+7}.Role='vector_y_tps'; |
---|
227 | Data.Civ1_U_smooth=zeros(size(Data.Civ1_X)); |
---|
228 | Data.Civ1_V_smooth=zeros(size(Data.Civ1_X)); |
---|
229 | if isfield(Data,'Civ1_FF') |
---|
230 | ind_good=find(Data.Civ1_FF==0); |
---|
231 | else |
---|
232 | ind_good=1:numel(Data.Civ1_X); |
---|
233 | end |
---|
234 | [Data.Civ1_SubRange,Data.Civ1_NbSites,Data.Civ1_Coord_tps,Data.Civ1_U_tps,Data.Civ1_V_tps,tild,Ures, Vres,tild,FFres]=... |
---|
235 | filter_tps([Data.Civ1_X(ind_good) Data.Civ1_Y(ind_good)],Data.Civ1_U(ind_good),Data.Civ1_V(ind_good),[],Data.Patch1_SubDomain,Data.Patch1_Rho,Data.Patch1_Threshold); |
---|
236 | fill=zeros(3,2,size(Data.Civ1_SubRange,3)); %matrix of zeros to complement the matrix Data.Civ1_Coord_tps (conveninent for file storage) |
---|
237 | Data.Civ1_Coord_tps=cat(1,Data.Civ1_Coord_tps,fill); |
---|
238 | Data.Civ1_U_smooth(ind_good)=Ures; |
---|
239 | Data.Civ1_V_smooth(ind_good)=Vres; |
---|
240 | Data.Civ1_FF(ind_good)=FFres; |
---|
241 | Data.CivStage=3; |
---|
242 | end |
---|
243 | |
---|
244 | %% Civ2 |
---|
245 | if isfield (Param,'Civ2') |
---|
246 | par_civ2=Param.Civ2; |
---|
247 | if ~isfield (Param,'Civ1') || ~strcmp(Param.Civ1.ImageA,par_civ2.ImageA) |
---|
248 | %read first image if not already done for civ1 |
---|
249 | [Field,ParamOut,errormsg] = read_field(ImageFileA_civ2,par_civ2.FileTypeA,par_civ2.ImageA,par_civ2.FrameIndexA); |
---|
250 | if ~isempty(errormsg) |
---|
251 | errormsg=['error in civ_matlab/read_field:' errormsg]; |
---|
252 | return |
---|
253 | end |
---|
254 | par_civ2.ImageA=Field.A; |
---|
255 | else |
---|
256 | par_civ2.ImageA=par_civ1.ImageA; |
---|
257 | end |
---|
258 | if ~isfield (Param,'Civ1') || ~strcmp(Param.Civ1.ImageB,par_civ2.ImageB) |
---|
259 | %read first image if not already done for civ1 |
---|
260 | [Field,ParamOut,errormsg] = read_field(ImageFileB_civ2,par_civ2.FileTypeB,par_civ2.ImageB,par_civ2.FrameIndexB); |
---|
261 | if ~isempty(errormsg) |
---|
262 | errormsg=['error in civ_matlab/read_field:' errormsg]; |
---|
263 | return |
---|
264 | end |
---|
265 | par_civ2.ImageB=Field.A; |
---|
266 | else |
---|
267 | par_civ2.ImageB=par_civ1.ImageB; |
---|
268 | end |
---|
269 | ibx2=ceil(par_civ2.CorrBoxSize(1)/2); |
---|
270 | iby2=ceil(par_civ2.CorrBoxSize(2)/2); |
---|
271 | isx2=ibx2+4;% search ara +-4 pixels around the guess |
---|
272 | isy2=iby2+4; |
---|
273 | % shift from par_civ2.filename_nc1 |
---|
274 | % shiftx=velocity interpolated at position |
---|
275 | miniy=max(1+isy2,1+iby2); |
---|
276 | minix=max(1+isx2,1+ibx2); |
---|
277 | maxiy=min(size(par_civ2.ImageA,1)-isy2,size(par_civ2.ImageA,1)-iby2); |
---|
278 | maxix=min(size(par_civ2.ImageA,2)-isx2,size(par_civ2.ImageA,2)-ibx2); |
---|
279 | [GridX,GridY]=meshgrid(minix:par_civ2.Dx:maxix,miniy:par_civ2.Dy:maxiy); |
---|
280 | GridX=reshape(GridX,[],1); |
---|
281 | GridY=reshape(GridY,[],1); |
---|
282 | Shiftx=zeros(size(GridX));% shift expected from civ1 data |
---|
283 | Shifty=zeros(size(GridX)); |
---|
284 | nbval=zeros(size(GridX)); |
---|
285 | if par_civ2.CheckDeformation |
---|
286 | DUDX=zeros(size(GridX)); |
---|
287 | DUDY=zeros(size(GridX)); |
---|
288 | DVDX=zeros(size(GridX)); |
---|
289 | DVDY=zeros(size(GridX)); |
---|
290 | end |
---|
291 | NbSubDomain=size(Data.Civ1_SubRange,3); |
---|
292 | % get the guess from patch1 |
---|
293 | for isub=1:NbSubDomain |
---|
294 | nbvec_sub=Data.Civ1_NbSites(isub); |
---|
295 | ind_sel=find(GridX>=Data.Civ1_SubRange(1,1,isub) & GridX<=Data.Civ1_SubRange(1,2,isub) & GridY>=Data.Civ1_SubRange(2,1,isub) & GridY<=Data.Civ1_SubRange(2,2,isub)); |
---|
296 | epoints = [GridX(ind_sel) GridY(ind_sel)];% coordinates of interpolation sites |
---|
297 | ctrs=Data.Civ1_Coord_tps(1:nbvec_sub,:,isub) ;%(=initial points) ctrs |
---|
298 | nbval(ind_sel)=nbval(ind_sel)+1;% records the number of values for eacn interpolation point (in case of subdomain overlap) |
---|
299 | EM = tps_eval(epoints,ctrs); |
---|
300 | Shiftx(ind_sel)=Shiftx(ind_sel)+EM*Data.Civ1_U_tps(1:nbvec_sub+3,isub); |
---|
301 | Shifty(ind_sel)=Shifty(ind_sel)+EM*Data.Civ1_V_tps(1:nbvec_sub+3,isub); |
---|
302 | if par_civ2.CheckDeformation |
---|
303 | [EMDX,EMDY] = tps_eval_dxy(epoints,ctrs);%2D matrix of distances between extrapolation points epoints and spline centres (=site points) ctrs |
---|
304 | DUDX(ind_sel)=DUDX(ind_sel)+EMDX*Data.Civ1_U_tps(1:nbvec_sub+3,isub); |
---|
305 | DUDY(ind_sel)=DUDY(ind_sel)+EMDY*Data.Civ1_U_tps(1:nbvec_sub+3,isub); |
---|
306 | DVDX(ind_sel)=DVDX(ind_sel)+EMDX*Data.Civ1_V_tps(1:nbvec_sub+3,isub); |
---|
307 | DVDY(ind_sel)=DVDY(ind_sel)+EMDY*Data.Civ1_V_tps(1:nbvec_sub+3,isub); |
---|
308 | end |
---|
309 | end |
---|
310 | mask=''; |
---|
311 | if par_civ2.CheckMask&&~isempty(par_civ2.Mask)&& ~strcmp(maskname,par_civ2.Mask)% mask exist, not already read in civ1 |
---|
312 | mask=imread(par_civ2.Mask); |
---|
313 | end |
---|
314 | par_civ2.SearchBoxSize(1)=2*isx2+1; |
---|
315 | par_civ2.SearchBoxSize(2)=2*isy2+1; |
---|
316 | par_civ2.SearchBoxShift=[Shiftx(nbval>=1)./nbval(nbval>=1) Shifty(nbval>=1)./nbval(nbval>=1)]; |
---|
317 | % par_civ2.SearchBoxShift(2)=Shifty(nbval>=1)./nbval(nbval>=1); |
---|
318 | par_civ2.Grid=[GridX(nbval>=1)-par_civ2.SearchBoxShift(:,1)/2 GridY(nbval>=1)-par_civ2.SearchBoxShift(:,2)/2];% grid taken at the extrapolated origin of the displacement vectors |
---|
319 | if par_civ2.CheckDeformation |
---|
320 | par_civ2.DUDX=DUDX./nbval; |
---|
321 | par_civ2.DUDY=DUDY./nbval; |
---|
322 | par_civ2.DVDX=DVDX./nbval; |
---|
323 | par_civ2.DVDY=DVDY./nbval; |
---|
324 | end |
---|
325 | % caluclate velocity data (y and v in indices, reverse to y component) |
---|
326 | [xtable ytable utable vtable ctable F] = civ (par_civ2); |
---|
327 | % diff_squared=(utable-par_civ2.Shiftx).*(utable-par_civ2.Shiftx)+(vtable+par_civ2.Shifty).*(vtable+par_civ2.Shifty); |
---|
328 | % F(diff_squared>=4)=4; %flag vectors whose distance to the guess exceeds 2 pixels |
---|
329 | list_param=(fieldnames(Param.Civ2))'; |
---|
330 | list_remove={'pxcmx','pxcmy','npx','npy','gridflag','maskflag','term_a','term_b','T0'}; |
---|
331 | for ilist=1:length(list_remove) |
---|
332 | index=strcmp(list_remove{ilist},list_param); |
---|
333 | if ~isempty(find(index,1)) |
---|
334 | list_param(index)=[]; |
---|
335 | end |
---|
336 | end |
---|
337 | for ilist=1:length(list_param) |
---|
338 | Civ2_param{ilist}=['Civ2_' list_param{ilist}]; |
---|
339 | eval(['Data.Civ2_' list_param{ilist} '=Param.Civ2.' list_param{ilist} ';']) |
---|
340 | end |
---|
341 | if isfield(Data,'Civ2_gridname') && strcmp(Data.Civ1_gridname(1:6),'noFile') |
---|
342 | Data.Civ1_gridname=''; |
---|
343 | end |
---|
344 | if isfield(Data,'Civ2_maskname') && strcmp(Data.Civ1_maskname(1:6),'noFile') |
---|
345 | Data.Civ2_maskname=''; |
---|
346 | end |
---|
347 | Data.ListGlobalAttribute=[Data.ListGlobalAttribute Civ2_param {'Civ2_Time','Civ2_Dt'}]; |
---|
348 | % Data.Civ2_Time=par_civ2.Time; |
---|
349 | % Data.Civ2_Dt=par_civ2.Dt; |
---|
350 | nbvar=numel(Data.ListVarName); |
---|
351 | Data.ListVarName=[Data.ListVarName {'Civ2_X','Civ2_Y','Civ2_U','Civ2_V','Civ2_F','Civ2_C'}];% cell array containing the names of the fields to record |
---|
352 | Data.VarDimName=[Data.VarDimName {'nb_vec_2','nb_vec_2','nb_vec_2','nb_vec_2','nb_vec_2','nb_vec_2'}]; |
---|
353 | Data.VarAttribute{nbvar+1}.Role='coord_x'; |
---|
354 | Data.VarAttribute{nbvar+2}.Role='coord_y'; |
---|
355 | Data.VarAttribute{nbvar+3}.Role='vector_x'; |
---|
356 | Data.VarAttribute{nbvar+4}.Role='vector_y'; |
---|
357 | Data.VarAttribute{nbvar+5}.Role='warnflag'; |
---|
358 | Data.Civ2_X=reshape(xtable,[],1); |
---|
359 | Data.Civ2_Y=reshape(size(par_civ2.ImageA,1)-ytable+1,[],1); |
---|
360 | Data.Civ2_U=reshape(utable,[],1); |
---|
361 | Data.Civ2_V=reshape(-vtable,[],1); |
---|
362 | Data.Civ2_C=reshape(ctable,[],1); |
---|
363 | Data.Civ2_F=reshape(F,[],1); |
---|
364 | Data.CivStage=Data.CivStage+1; |
---|
365 | end |
---|
366 | |
---|
367 | %% Fix2 |
---|
368 | if isfield (Param,'Fix2') |
---|
369 | ListFixParam=fieldnames(Param.Fix2); |
---|
370 | for ilist=1:length(ListFixParam) |
---|
371 | ParamName=ListFixParam{ilist}; |
---|
372 | ListName=['Fix2_' ParamName]; |
---|
373 | eval(['Data.ListGlobalAttribute=[Data.ListGlobalAttribute ''' ParamName '''];']) |
---|
374 | eval(['Data.' ListName '=Param.Fix2.' ParamName ';']) |
---|
375 | end |
---|
376 | if check_civx |
---|
377 | if ~isfield(Data,'fix2') |
---|
378 | Data.ListGlobalAttribute=[Data.ListGlobalAttribute 'fix2']; |
---|
379 | Data.fix2=1; |
---|
380 | Data.ListVarName=[Data.ListVarName {'vec2_FixFlag'}]; |
---|
381 | Data.VarDimName=[Data.VarDimName {'nb_vectors2'}]; |
---|
382 | end |
---|
383 | Data.vec_FixFlag=fix(Param.Fix2,Data.vec2_F,Data.vec2_C,Data.vec2_U,Data.vec2_V,Data.vec2_X,Data.vec2_Y); |
---|
384 | else |
---|
385 | Data.ListVarName=[Data.ListVarName {'Civ2_FF'}]; |
---|
386 | Data.VarDimName=[Data.VarDimName {'nb_vec_2'}]; |
---|
387 | nbvar=length(Data.ListVarName); |
---|
388 | Data.VarAttribute{nbvar}.Role='errorflag'; |
---|
389 | Data.Civ2_FF=fix(Param.Fix2,Data.Civ2_F,Data.Civ2_C,Data.Civ2_U,Data.Civ2_V); |
---|
390 | Data.CivStage=Data.CivStage+1; |
---|
391 | end |
---|
392 | |
---|
393 | end |
---|
394 | |
---|
395 | %% Patch2 |
---|
396 | if isfield (Param,'Patch2') |
---|
397 | Data.ListGlobalAttribute=[Data.ListGlobalAttribute {'Patch2_Rho','Patch2_Threshold','Patch2_SubDomain'}]; |
---|
398 | Data.Patch2_Rho=Param.Patch2.FieldSmooth; |
---|
399 | Data.Patch2_Threshold=Param.Patch2.MaxDiff; |
---|
400 | Data.Patch2_SubDomain=Param.Patch2.SubdomainSize; |
---|
401 | nbvar=length(Data.ListVarName); |
---|
402 | Data.ListVarName=[Data.ListVarName {'Civ2_U_smooth','Civ2_V_smooth','Civ2_SubRange','Civ2_NbSites','Civ2_Coord_tps','Civ2_U_tps','Civ2_V_tps'}]; |
---|
403 | Data.VarDimName=[Data.VarDimName {'nb_vec_2','nb_vec_2',{'nb_coord','nb_bounds','nb_subdomain_2'},{'nb_subdomain_2'},... |
---|
404 | {'nb_tps_2','nb_coord','nb_subdomain_2'},{'nb_tps_2','nb_subdomain_2'},{'nb_tps_2','nb_subdomain_2'}}]; |
---|
405 | |
---|
406 | Data.VarAttribute{nbvar+1}.Role='vector_x'; |
---|
407 | Data.VarAttribute{nbvar+2}.Role='vector_y'; |
---|
408 | Data.VarAttribute{nbvar+5}.Role='coord_tps'; |
---|
409 | Data.VarAttribute{nbvar+6}.Role='vector_x_tps'; |
---|
410 | Data.VarAttribute{nbvar+7}.Role='vector_y_tps'; |
---|
411 | Data.Civ2_U_smooth=zeros(size(Data.Civ2_X)); |
---|
412 | Data.Civ2_V_smooth=zeros(size(Data.Civ2_X)); |
---|
413 | if isfield(Data,'Civ2_FF') |
---|
414 | ind_good=find(Data.Civ2_FF==0); |
---|
415 | else |
---|
416 | ind_good=1:numel(Data.Civ2_X); |
---|
417 | end |
---|
418 | [Data.Civ2_SubRange,Data.Civ2_NbSites,Data.Civ2_Coord_tps,Data.Civ2_U_tps,Data.Civ2_V_tps,tild,Ures, Vres,tild,FFres]=... |
---|
419 | filter_tps([Data.Civ2_X(ind_good) Data.Civ2_Y(ind_good)],Data.Civ2_U(ind_good),Data.Civ2_V(ind_good),[],Data.Patch2_SubDomain,Data.Patch2_Rho,Data.Patch2_Threshold); |
---|
420 | fill=zeros(3,2,size(Data.Civ2_SubRange,3)); %matrix of zeros to complement the matrix Data.Civ1_Coord_tps (conveninent for file storage) |
---|
421 | Data.Civ2_Coord_tps=cat(1,Data.Civ2_Coord_tps,fill); |
---|
422 | Data.Civ2_U_smooth(ind_good)=Ures; |
---|
423 | Data.Civ2_V_smooth(ind_good)=Vres; |
---|
424 | Data.Civ2_FF(ind_good)=FFres; |
---|
425 | Data.CivStage=Data.CivStage+1; |
---|
426 | end |
---|
427 | |
---|
428 | %% write result in a netcdf file if requested |
---|
429 | if exist('ncfile','var') |
---|
430 | errormsg=struct2nc(ncfile,Data); |
---|
431 | end |
---|
432 | |
---|
433 | % 'civ': function piv.m adapted from PIVlab http://pivlab.blogspot.com/ |
---|
434 | %-------------------------------------------------------------------------- |
---|
435 | % function [xtable ytable utable vtable typevector] = civ (image1,image2,ibx,iby step, subpixfinder, mask, roi) |
---|
436 | % |
---|
437 | % OUTPUT: |
---|
438 | % xtable: set of x coordinates |
---|
439 | % ytable: set of y coordiantes |
---|
440 | % utable: set of u displacements (along x) |
---|
441 | % vtable: set of v displacements (along y) |
---|
442 | % ctable: max image correlation for each vector |
---|
443 | % typevector: set of flags, =1 for good, =0 for NaN vectors |
---|
444 | % |
---|
445 | %INPUT: |
---|
446 | % image1:first image (matrix) |
---|
447 | % image2: second image (matrix) |
---|
448 | % ibx2,iby2: half size of the correlation box along x and y, in px (size=(2*iby2+1,2*ibx2+1) |
---|
449 | % isx2,isy2: half size of the search box along x and y, in px (size=(2*isy2+1,2*isx2+1) |
---|
450 | % shiftx, shifty: shift of the search box (in pixel index, yshift reversed) |
---|
451 | % step: mesh of the measurement points (in px) |
---|
452 | % subpixfinder=1 or 2 controls the curve fitting of the image correlation |
---|
453 | % mask: =[] for no mask |
---|
454 | % roi: 4 element vector defining a region of interest: x position, y position, width, height, (in image indices), for the whole image, roi=[]; |
---|
455 | function [xtable ytable utable vtable ctable F result_conv errormsg] = civ (par_civ) |
---|
456 | %this funtion performs the DCC PIV analysis. Recent window-deformation |
---|
457 | %methods perform better and will maybe be implemented in the future. |
---|
458 | |
---|
459 | %% prepare grid |
---|
460 | ibx2=ceil(par_civ.CorrBoxSize(1)/2); |
---|
461 | iby2=ceil(par_civ.CorrBoxSize(2)/2); |
---|
462 | isx2=ceil(par_civ.SearchBoxSize(1)/2); |
---|
463 | isy2=ceil(par_civ.SearchBoxSize(2)/2); |
---|
464 | shiftx=round(par_civ.SearchBoxShift(:,1)); |
---|
465 | shifty=-round(par_civ.SearchBoxShift(:,2));% sign minus because image j index increases when y decreases |
---|
466 | if isfield(par_civ,'Grid') |
---|
467 | if ischar(par_civ.Grid)%read the drid file if the input is a file name |
---|
468 | par_civ.Grid=dlmread(par_civ.Grid); |
---|
469 | par_civ.Grid(1,:)=[];%the first line must be removed (heading in the grid file) |
---|
470 | end |
---|
471 | else% automatic measurement grid |
---|
472 | % ibx2=ceil(par_civ.Bx/2); |
---|
473 | % iby2=ceil(par_civ.By/2); |
---|
474 | % isx2=ceil(par_civ.Searchx/2); |
---|
475 | % isy2=ceil(par_civ.Searchy/2); |
---|
476 | miniy=max(1+isy2+shifty,1+iby2); |
---|
477 | minix=max(1+isx2-shiftx,1+ibx2); |
---|
478 | maxiy=min(par_civ.ImageHeight-isy2+shifty,par_civ.ImageHeight-iby2); |
---|
479 | maxix=min(par_civ.ImageWidth-isx2-shiftx,par_civ.ImageWidth-ibx2); |
---|
480 | [GridX,GridY]=meshgrid(minix:par_civ.Dx:maxix,miniy:par_civ.Dy:maxiy); |
---|
481 | par_civ.Grid(:,1)=reshape(GridX,[],1); |
---|
482 | par_civ.Grid(:,2)=reshape(GridY,[],1); |
---|
483 | end |
---|
484 | nbvec=size(par_civ.Grid,1); |
---|
485 | if numel(shiftx)==1 |
---|
486 | shiftx=shiftx*ones(nbvec,1); |
---|
487 | shifty=shifty*ones(nbvec,1); |
---|
488 | end |
---|
489 | %% Default output |
---|
490 | xtable=par_civ.Grid(:,1); |
---|
491 | ytable=par_civ.Grid(:,2); |
---|
492 | utable=zeros(nbvec,1); |
---|
493 | vtable=zeros(nbvec,1); |
---|
494 | ctable=zeros(nbvec,1); |
---|
495 | F=zeros(nbvec,1); |
---|
496 | result_conv=[]; |
---|
497 | errormsg=''; |
---|
498 | |
---|
499 | %% prepare mask |
---|
500 | if isfield(par_civ,'Mask') && ~isempty(par_civ.Mask) |
---|
501 | if strcmp(par_civ.Mask,'all') |
---|
502 | return % get the grid only, no civ calculation |
---|
503 | elseif ischar(par_civ.Mask) |
---|
504 | par_civ.Mask=imread(par_civ.Mask); |
---|
505 | end |
---|
506 | end |
---|
507 | check_MinIma=isfield(par_civ,'MinIma');% test for image luminosity threshold |
---|
508 | check_MaxIma=isfield(par_civ,'MaxIma') && ~isempty(par_civ.MaxIma); |
---|
509 | |
---|
510 | % %% prepare images |
---|
511 | % if isfield(par_civ,'reverse_pair') |
---|
512 | % if par_civ.reverse_pair |
---|
513 | % if ischar(par_civ.ImageB) |
---|
514 | % temp=par_civ.ImageA; |
---|
515 | % par_civ.ImageA=imread(par_civ.ImageB); |
---|
516 | % end |
---|
517 | % if ischar(temp) |
---|
518 | % par_civ.ImageB=imread(temp); |
---|
519 | % end |
---|
520 | % end |
---|
521 | % else |
---|
522 | % if ischar(par_civ.ImageA) |
---|
523 | % par_civ.ImageA=imread(par_civ.ImageA); |
---|
524 | % end |
---|
525 | % if ischar(par_civ.ImageB) |
---|
526 | % par_civ.ImageB=imread(par_civ.ImageB); |
---|
527 | % end |
---|
528 | % end |
---|
529 | par_civ.ImageA=sum(double(par_civ.ImageA),3);%sum over rgb component for color images |
---|
530 | par_civ.ImageB=sum(double(par_civ.ImageB),3); |
---|
531 | [npy_ima npx_ima]=size(par_civ.ImageA); |
---|
532 | if ~isequal(size(par_civ.ImageB),[npy_ima npx_ima]) |
---|
533 | errormsg='image pair with unequal size'; |
---|
534 | return |
---|
535 | end |
---|
536 | |
---|
537 | %% Apply mask |
---|
538 | % Convention for mask IDEAS TO IMPLEMENT ? |
---|
539 | % mask >200 : velocity calculated |
---|
540 | % 200 >=mask>150;velocity not calculated, interpolation allowed (bad spots) |
---|
541 | % 150>=mask >100: velocity not calculated, nor interpolated |
---|
542 | % 100>=mask> 20: velocity not calculated, impermeable (no flux through mask boundaries) |
---|
543 | % 20>=mask: velocity=0 |
---|
544 | checkmask=0; |
---|
545 | if isfield(par_civ,'Mask') && ~isempty(par_civ.Mask) |
---|
546 | checkmask=1; |
---|
547 | if ~isequal(size(par_civ.Mask),[npy_ima npx_ima]) |
---|
548 | errormsg='mask must be an image with the same size as the images'; |
---|
549 | return |
---|
550 | end |
---|
551 | % check_noflux=(par_civ.Mask<100) ;%TODO: to implement |
---|
552 | check_undefined=(par_civ.Mask<200 & par_civ.Mask>=20 ); |
---|
553 | par_civ.ImageA(check_undefined)=min(min(par_civ.ImageA));% put image A to zero (i.e. the min image value) in the undefined area |
---|
554 | par_civ.ImageB(check_undefined)=min(min(par_civ.ImageB));% put image B to zero (i.e. the min image value) in the undefined area |
---|
555 | end |
---|
556 | |
---|
557 | %% compute image correlations: MAINLOOP on velocity vectors |
---|
558 | corrmax=0; |
---|
559 | sum_square=1;% default |
---|
560 | mesh=1;% default |
---|
561 | CheckDecimal=isfield(par_civ,'CheckDecimal')&& par_civ.CheckDecimal==1; |
---|
562 | if CheckDecimal |
---|
563 | mesh=0.2;%mesh in pixels for subpixel image interpolation |
---|
564 | CheckDeformation=isfield(par_civ,'CheckDeformation')&& par_civ.CheckDeformation==1; |
---|
565 | end |
---|
566 | % vector=[0 0];%default |
---|
567 | for ivec=1:nbvec |
---|
568 | iref=round(par_civ.Grid(ivec,1)+0.5);% xindex on the image A for the middle of the correlation box |
---|
569 | jref=round(par_civ.ImageHeight-par_civ.Grid(ivec,2)+0.5);% yindex on the image B for the middle of the correlation box |
---|
570 | if ~(checkmask && par_civ.Mask(jref,iref)<=20) %velocity not set to zero by the black mask |
---|
571 | if jref-iby2<1 || jref+iby2>par_civ.ImageHeight|| iref-ibx2<1 || iref+ibx2>par_civ.ImageWidth||... |
---|
572 | jref+shifty(ivec)-isy2<1||jref+shifty(ivec)+isy2>par_civ.ImageHeight|| iref+shiftx(ivec)-isx2<1 || iref+shiftx(ivec)+isx2>par_civ.ImageWidth % we are outside the image |
---|
573 | F(ivec)=3; |
---|
574 | else |
---|
575 | image1_crop=par_civ.ImageA(jref-iby2:jref+iby2,iref-ibx2:iref+ibx2);%extract a subimage (correlation box) from image A |
---|
576 | image2_crop=par_civ.ImageB(jref+shifty(ivec)-isy2:jref+shifty(ivec)+isy2,iref+shiftx(ivec)-isx2:iref+shiftx(ivec)+isx2);%extract a larger subimage (search box) from image B |
---|
577 | image1_mean=mean(mean(image1_crop)); |
---|
578 | image2_mean=mean(mean(image2_crop)); |
---|
579 | %threshold on image minimum |
---|
580 | if check_MinIma && (image1_mean < par_civ.MinIma || image2_mean < par_civ.MinIma) |
---|
581 | F(ivec)=3; |
---|
582 | end |
---|
583 | %threshold on image maximum |
---|
584 | if check_MaxIma && (image1_mean > par_civ.MaxIma || image2_mean > par_civ.MaxIma) |
---|
585 | F(ivec)=3; |
---|
586 | end |
---|
587 | end |
---|
588 | if F(ivec)~=3 |
---|
589 | image1_crop=image1_crop-image1_mean;%substract the mean |
---|
590 | image2_crop=image2_crop-image2_mean; |
---|
591 | if CheckDecimal |
---|
592 | xi=(1:mesh:size(image1_crop,2)); |
---|
593 | yi=(1:mesh:size(image1_crop,1))'; |
---|
594 | if CheckDeformation |
---|
595 | [XI,YI]=meshgrid(xi-ceil(size(image1_crop,2)/2),yi-ceil(size(image1_crop,1)/2)); |
---|
596 | XIant=XI-par_civ.DUDX(ivec)*XI-par_civ.DUDY(ivec)*YI+ceil(size(image1_crop,2)/2); |
---|
597 | YIant=YI-par_civ.DVDX(ivec)*XI-par_civ.DVDY(ivec)*YI+ceil(size(image1_crop,1)/2); |
---|
598 | image1_crop=interp2(image1_crop,XIant,YIant); |
---|
599 | else |
---|
600 | image1_crop=interp2(image1_crop,xi,yi); |
---|
601 | end |
---|
602 | xi=(1:mesh:size(image2_crop,2)); |
---|
603 | yi=(1:mesh:size(image2_crop,1))'; |
---|
604 | image2_crop=interp2(image2_crop,xi,yi); |
---|
605 | end |
---|
606 | sum_square=sum(sum(image1_crop.*image1_crop)); |
---|
607 | %reference: Oliver Pust, PIV: Direct Cross-Correlation |
---|
608 | result_conv= conv2(image2_crop,flipdim(flipdim(image1_crop,2),1),'valid'); |
---|
609 | corrmax= max(max(result_conv)); |
---|
610 | result_conv=(result_conv/corrmax)*255; %normalize, peak=always 255 |
---|
611 | %Find the correlation max, at 255 |
---|
612 | [y,x] = find(result_conv==255,1); |
---|
613 | if ~isempty(y) && ~isempty(x) |
---|
614 | try |
---|
615 | if par_civ.CorrSmooth==1 |
---|
616 | [vector,F(ivec)] = SUBPIXGAUSS (result_conv,x,y); |
---|
617 | elseif par_civ.CorrSmooth==2 |
---|
618 | [vector,F(ivec)] = SUBPIX2DGAUSS (result_conv,x,y); |
---|
619 | end |
---|
620 | utable(ivec)=vector(1)*mesh+shiftx(ivec); |
---|
621 | vtable(ivec)=vector(2)*mesh+shifty(ivec); |
---|
622 | xtable(ivec)=iref+utable(ivec)/2-0.5;% convec flow (velocity taken at the point middle from imgae 1 and 2) |
---|
623 | ytable(ivec)=jref+vtable(ivec)/2-0.5;% and position of pixel 1=0.5 (convention for image coordinates=0 at the edge) |
---|
624 | iref=round(xtable(ivec));% image index for the middle of the vector |
---|
625 | jref=round(ytable(ivec)); |
---|
626 | if checkmask && par_civ.Mask(jref,iref)<200 && par_civ.Mask(jref,iref)>=100 |
---|
627 | utable(ivec)=0; |
---|
628 | vtable(ivec)=0; |
---|
629 | F(ivec)=3; |
---|
630 | end |
---|
631 | ctable(ivec)=corrmax/sum_square;% correlation value |
---|
632 | catch ME |
---|
633 | F(ivec)=3; |
---|
634 | end |
---|
635 | else |
---|
636 | F(ivec)=3; |
---|
637 | end |
---|
638 | end |
---|
639 | end |
---|
640 | |
---|
641 | %Create the vector matrix x, y, u, v |
---|
642 | end |
---|
643 | result_conv=result_conv*corrmax/(255*sum_square);% keep the last correlation matrix for output |
---|
644 | |
---|
645 | %------------------------------------------------------------------------ |
---|
646 | % --- Find the maximum of the correlation function after interpolation |
---|
647 | function [vector,F] = SUBPIXGAUSS (result_conv,x,y) |
---|
648 | %------------------------------------------------------------------------ |
---|
649 | vector=[0 0]; %default |
---|
650 | F=0; |
---|
651 | [npy,npx]=size(result_conv); |
---|
652 | |
---|
653 | % if (x <= (size(result_conv,1)-1)) && (y <= (size(result_conv,1)-1)) && (x >= 1) && (y >= 1) |
---|
654 | %the following 8 lines are copyright (c) 1998, Uri Shavit, Roi Gurka, Alex Liberzon, Technion ᅵ Israel Institute of Technology |
---|
655 | %http://urapiv.wordpress.com |
---|
656 | peaky = y; |
---|
657 | if y <= npy-1 && y >= 1 |
---|
658 | f0 = log(result_conv(y,x)); |
---|
659 | f1 = real(log(result_conv(y-1,x))); |
---|
660 | f2 = real(log(result_conv(y+1,x))); |
---|
661 | peaky = peaky+ (f1-f2)/(2*f1-4*f0+2*f2); |
---|
662 | else |
---|
663 | F=-2; % warning flag for vector truncated by the limited search box |
---|
664 | end |
---|
665 | peakx=x; |
---|
666 | if x <= npx-1 && x >= 1 |
---|
667 | f0 = log(result_conv(y,x)); |
---|
668 | f1 = real(log(result_conv(y,x-1))); |
---|
669 | f2 = real(log(result_conv(y,x+1))); |
---|
670 | peakx = peakx+ (f1-f2)/(2*f1-4*f0+2*f2); |
---|
671 | else |
---|
672 | F=-2; % warning flag for vector truncated by the limited search box |
---|
673 | end |
---|
674 | vector=[peakx-floor(npx/2)-1 peaky-floor(npy/2)-1]; |
---|
675 | |
---|
676 | %------------------------------------------------------------------------ |
---|
677 | % --- Find the maximum of the correlation function after interpolation |
---|
678 | function [vector,F] = SUBPIX2DGAUSS (result_conv,x,y) |
---|
679 | %------------------------------------------------------------------------ |
---|
680 | vector=[0 0]; %default |
---|
681 | F=-2; |
---|
682 | peaky=y; |
---|
683 | peakx=x; |
---|
684 | [npy,npx]=size(result_conv); |
---|
685 | if (x <= npx-1) && (y <= npy-1) && (x >= 1) && (y >= 1) |
---|
686 | F=0; |
---|
687 | for i=-1:1 |
---|
688 | for j=-1:1 |
---|
689 | %following 15 lines based on |
---|
690 | %H. Nobach ᅵ M. Honkanen (2005) |
---|
691 | %Two-dimensional Gaussian regression for sub-pixel displacement |
---|
692 | %estimation in particle image velocimetry or particle position |
---|
693 | %estimation in particle tracking velocimetry |
---|
694 | %Experiments in Fluids (2005) 38: 511ᅵ515 |
---|
695 | c10(j+2,i+2)=i*log(result_conv(y+j, x+i)); |
---|
696 | c01(j+2,i+2)=j*log(result_conv(y+j, x+i)); |
---|
697 | c11(j+2,i+2)=i*j*log(result_conv(y+j, x+i)); |
---|
698 | c20(j+2,i+2)=(3*i^2-2)*log(result_conv(y+j, x+i)); |
---|
699 | c02(j+2,i+2)=(3*j^2-2)*log(result_conv(y+j, x+i)); |
---|
700 | end |
---|
701 | end |
---|
702 | c10=(1/6)*sum(sum(c10)); |
---|
703 | c01=(1/6)*sum(sum(c01)); |
---|
704 | c11=(1/4)*sum(sum(c11)); |
---|
705 | c20=(1/6)*sum(sum(c20)); |
---|
706 | c02=(1/6)*sum(sum(c02)); |
---|
707 | deltax=(c11*c01-2*c10*c02)/(4*c20*c02-c11^2); |
---|
708 | deltay=(c11*c10-2*c01*c20)/(4*c20*c02-c11^2); |
---|
709 | if abs(deltax)<1 |
---|
710 | peakx=x+deltax; |
---|
711 | end |
---|
712 | if abs(deltay)<1 |
---|
713 | peaky=y+deltay; |
---|
714 | end |
---|
715 | end |
---|
716 | vector=[peakx-floor(npx/2)-1 peaky-floor(npy/2)-1]; |
---|
717 | |
---|
718 | %'RUN_FIX': function for fixing velocity fields: |
---|
719 | %----------------------------------------------- |
---|
720 | % RUN_FIX(filename,field,flagindex,thresh_vecC,thresh_vel,iter,flag_mask,maskname,fileref,fieldref) |
---|
721 | % |
---|
722 | %filename: name of the netcdf file (used as input and output) |
---|
723 | %field: structure specifying the names of the fields to fix (depending on civ1 or civ2) |
---|
724 | %.vel_type='civ1' or 'civ2'; |
---|
725 | %.nb=name of the dimension common to the field to fix ('nb_vectors' for civ1); |
---|
726 | %.fixflag=name of fix flag variable ('vec_FixFlag' for civ1) |
---|
727 | %flagindex: flag specifying which values of vec_f are removed: |
---|
728 | % if flagindex(1)=1: vec_f=-2 vectors are removed |
---|
729 | % if flagindex(2)=1: vec_f=3 vectors are removed |
---|
730 | % if flagindex(3)=1: vec_f=2 vectors are removed (if iter=1) or vec_f=4 vectors are removed (if iter=2) |
---|
731 | %iter=1 for civ1 fields and iter=2 for civ2 fields |
---|
732 | %thresh_vecC: threshold in the image correlation vec_C |
---|
733 | %flag_mask: =1 mask used to remove vectors (0 else) |
---|
734 | %maskname: name of the mask image file for fix |
---|
735 | %thresh_vel: threshold on velocity, or on the difference with the reference file fileref if exists |
---|
736 | %inf_sup=1: remove values smaller than threshold thresh_vel, =2, larger than threshold |
---|
737 | %fileref: .nc file name for a reference velocity (='': refrence 0 used) |
---|
738 | %fieldref: 'civ1','filter1'...feld used in fileref |
---|
739 | |
---|
740 | function FF=fix(Param,F,C,U,V,X,Y) |
---|
741 | FF=zeros(size(F));%default |
---|
742 | |
---|
743 | %criterium on warn flags |
---|
744 | FlagName={'CheckFmin2','CheckF2','CheckF3','CheckF4'}; |
---|
745 | FlagVal=[-2 2 3 4]; |
---|
746 | for iflag=1:numel(FlagName) |
---|
747 | if isfield(Param,FlagName{iflag}) && Param.(FlagName{iflag}) |
---|
748 | FF=(FF==1| F==FlagVal(iflag)); |
---|
749 | end |
---|
750 | end |
---|
751 | %criterium on correlation values |
---|
752 | if isfield (Param,'MinCorr') |
---|
753 | FF=FF==1 | C<Param.MinCorr; |
---|
754 | end |
---|
755 | if (isfield(Param,'MinVel')&&~isempty(Param.MinVel))||(isfield (Param,'MaxVel')&&~isempty(Param.MaxVel)) |
---|
756 | Umod= U.*U+V.*V; |
---|
757 | if isfield (Param,'MinVel')&&~isempty(Param.MinVel) |
---|
758 | FF=FF==1 | Umod<(Param.MinVel*Param.MinVel); |
---|
759 | end |
---|
760 | if isfield (Param,'MaxVel')&&~isempty(Param.MaxVel) |
---|
761 | FF=FF==1 | Umod>(Param.MaxVel*Param.MaxVel); |
---|
762 | end |
---|
763 | end |
---|
764 | |
---|
765 | |
---|
766 | |
---|
767 | |
---|
768 | |
---|
769 | |
---|
770 | |
---|