source: trunk/src/civ_matlab.m @ 411

Last change on this file since 411 was 411, checked in by sommeria, 12 years ago

bugs corrected in uvmat: fixed x/y and calc_field for the new PIV data

File size: 31.8 KB
Line 
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
40function [Data,errormsg,result_conv]= civ_matlab(Param,ncfile)
41errormsg='';
42Data.ListGlobalAttribute={'Conventions','Program','CivStage'};
43Data.Conventions='uvmat/civdata';% states the conventions used for the description of field variables and attributes
44Data.Program='civ_matlab';
45Data.CivStage=0;%default
46ListVarCiv1={'Civ1_X','Civ1_Y','Civ1_U','Civ1_V','Civ1_C','Civ1_F'}; %variables to read
47ListVarFix1={'Civ1_X','Civ1_Y','Civ1_U','Civ1_V','Civ1_C','Civ1_F','Civ1_FF'};
48mask='';
49maskname='';%default
50check_civx=0;%default
51check_civ1=0;%default
52check_patch1=0;%default
53
54if ischar(Param)
55    Param=xml2struct(Param); %if Param is the name of an xml file, read this file as a Matlab structure
56end
57
58%% Civ1
59if isfield (Param,'Civ1')
60%     check_civ1=1;% test for further use of civ1 results
61    % %% prepare images
62    par_civ1=Param.Civ1;
63    if isfield(par_civ1,'reverse_pair')
64        if par_civ1.reverse_pair
65            if ischar(par_civ1.ImageB)
66                temp=par_civ1.ImageA;
67                par_civ1.ImageA=imread(par_civ1.ImageB);
68            end
69            if ischar(temp)
70                par_civ1.ImageB=imread(temp);
71            end
72        end
73    else
74        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
75            [Field,ParamOut,errormsg] = read_field(par_civ1.ImageA,par_civ1.FileTypeA,[],par_civ1.i1);
76            par_civ1.ImageA=Field.A;%imread(par_civ1.ImageA);%[Field,ParamOut,errormsg] = read_field(ObjectName,FileType,ParamIn,num)
77        end
78        if isfield(par_civ1,'ImageB')&& (ischar(par_civ1.ImageB)||strcmp(class(par_civ1.ImageA),'VideoReader'))
79            [Field,ParamOut,errormsg] = read_field(par_civ1.ImageB,par_civ1.FileTypeB,[],par_civ1.i2);
80            par_civ1.ImageB=Field.A;%=imread(par_civ1.ImageB);
81        end
82    end
83   
84    % caluclate velocity data (y and v in indices, reverse to y component)
85    [xtable ytable utable vtable ctable F result_conv errormsg] = civ (par_civ1);
86   
87    % to try the reverse_pair method, uncomment below
88    %     [xtable1 ytable1 utable1 vtable1 ctable1 F1 result_conv1 errormsg1] = civ (Param.Civ1);
89    %     Param.Civ1.reverse_pair=1;
90    %     [xtable2 ytable2 utable2 vtable2 ctable2 F2 result_conv2 errormsg2] = civ (Param.Civ1);
91    %     xtable=[xtable1; xtable2];
92    %     ytable=[ytable1; ytable2];
93    %     utable=[utable1; -utable2];
94    %     vtable=[vtable1; -vtable2];
95    %     ctable=[ctable1; ctable2];
96    %     F=[F1; F2];
97    %     result_conv=[result_conv1; result_conv2];
98    %     errormsg=[errormsg1; errormsg2];
99    if ~isempty(errormsg)
100        return
101    end
102    list_param=(fieldnames(Param.Civ1))';
103    Civ1_param=list_param;%default
104    %set the values of all the global attributes in list_param
105    for ilist=1:length(list_param)
106        Civ1_param{ilist}=['Civ1_' list_param{ilist}];
107        Data.(['Civ1_' list_param{ilist}])=Param.Civ1.(list_param{ilist});
108    end
109    Data.ListGlobalAttribute=[Data.ListGlobalAttribute Civ1_param];% {'Civ1_Time','Civ1_Dt'}];
110    Data.ListVarName={'Civ1_X','Civ1_Y','Civ1_U','Civ1_V','Civ1_F','Civ1_C'};%  cell array containing the names of the fields to record
111    Data.VarDimName={'nb_vec_1','nb_vec_1','nb_vec_1','nb_vec_1','nb_vec_1','nb_vec_1'};
112    Data.VarAttribute{1}.Role='coord_x';
113    Data.VarAttribute{2}.Role='coord_y';
114    Data.VarAttribute{3}.Role='vector_x';
115    Data.VarAttribute{4}.Role='vector_y';
116    Data.VarAttribute{5}.Role='warnflag';
117    Data.Civ1_X=reshape(xtable,[],1);
118    Data.Civ1_Y=reshape(Param.Civ1.ImageHeight-ytable+1,[],1);
119    Data.Civ1_U=reshape(utable,[],1);
120    Data.Civ1_V=reshape(-vtable,[],1);
121    Data.Civ1_C=reshape(ctable,[],1);
122    Data.Civ1_F=reshape(F,[],1);
123    Data.CivStage=1; 
124else
125    if exist('ncfile','var')
126        CivFile=ncfile;
127    elseif isfield(Param.Patch1,'CivFile')
128        CivFile=Param.Patch1.CivFile;
129    end
130    Data=nc2struct(CivFile,'ListGlobalAttribute','absolut_time_T0'); %look for the constant 'absolut_time_T0' to detect old civx data format
131    if isfield(Data,'Txt')
132        errormsg=Data.Txt;
133        return
134    end
135    if ~isempty(Data.absolut_time_T0')%read civx file
136        check_civx=1;% test for old civx data format
137        [Data,vardetect,ichoice]=nc2struct(CivFile);%read the variables in the netcdf file
138    else
139        Data=nc2struct(CivFile);%read civ1 and fix1 data in the existing netcdf file
140    end
141end
142
143%% Fix1
144if isfield (Param,'Fix1')
145    ListFixParam=fieldnames(Param.Fix1);
146    for ilist=1:length(ListFixParam)
147        ParamName=ListFixParam{ilist};
148        ListName=['Fix1_' ParamName];
149        eval(['Data.ListGlobalAttribute=[Data.ListGlobalAttribute ''' ParamName '''];'])
150        eval(['Data.' ListName '=Param.Fix1.' ParamName ';'])
151    end
152    if check_civx
153        if ~isfield(Data,'fix')
154            Data.ListGlobalAttribute=[Data.ListGlobalAttribute 'fix'];
155            Data.fix=1;
156            Data.ListVarName=[Data.ListVarName {'vec_FixFlag'}];
157            Data.VarDimName=[Data.VarDimName {'nb_vectors'}];
158        end
159        Data.vec_FixFlag=fix(Param.Fix1,Data.vec_F,Data.vec_C,Data.vec_U,Data.vec_V,Data.vec_X,Data.vec_Y);
160    else
161        Data.ListVarName=[Data.ListVarName {'Civ1_FF'}];
162        Data.VarDimName=[Data.VarDimName {'nb_vec_1'}];
163        nbvar=length(Data.ListVarName);
164        Data.VarAttribute{nbvar}.Role='errorflag';   
165        Data.Civ1_FF=fix(Param.Fix1,Data.Civ1_F,Data.Civ1_C,Data.Civ1_U,Data.Civ1_V);
166        Data.CivStage=2;   
167    end
168end   
169%% Patch1
170if isfield (Param,'Patch1')
171    if check_civx
172        errormsg='Civ Matlab input needed for patch';
173        return
174    end
175   
176    Data.ListGlobalAttribute=[Data.ListGlobalAttribute {'Patch1_Rho','Patch1_Threshold','Patch1_SubDomain'}];
177    Data.Patch1_Rho=Param.Patch1.SmoothingParam;
178    Data.Patch1_Threshold=Param.Patch1.MaxDiff;
179    Data.Patch1_SubDomain=Param.Patch1.SubdomainSize;
180    nbvar=length(Data.ListVarName);
181    Data.ListVarName=[Data.ListVarName {'Civ1_U_smooth','Civ1_V_smooth','Civ1_SubRange','Civ1_NbSites','Civ1_Coord_tps','Civ1_U_tps','Civ1_V_tps'}];
182        Data.VarDimName=[Data.VarDimName {'nb_vec_1','nb_vec_1',{'nb_coord','nb_bounds','nb_subdomain_1'},{'nb_subdomain_1'},...
183             {'nb_tps_1','nb_coord','nb_subdomain_1'},{'nb_tps_1','nb_subdomain_1'},{'nb_tps_1','nb_subdomain_1'}}];
184    Data.VarAttribute{nbvar+1}.Role='vector_x';
185    Data.VarAttribute{nbvar+2}.Role='vector_y';
186    Data.VarAttribute{nbvar+5}.Role='coord_tps';
187    Data.VarAttribute{nbvar+6}.Role='vector_x_tps';
188    Data.VarAttribute{nbvar+7}.Role='vector_y_tps';
189    Data.Civ1_U_smooth=zeros(size(Data.Civ1_X));
190    Data.Civ1_V_smooth=zeros(size(Data.Civ1_X));
191    if isfield(Data,'Civ1_FF')
192        ind_good=find(Data.Civ1_FF==0);
193    else
194        ind_good=1:numel(Data.Civ1_X);
195    end
196    [Data.Civ1_SubRange,Data.Civ1_NbSites,Data.Civ1_Coord_tps,Data.Civ1_U_tps,Data.Civ1_V_tps,tild,Ures, Vres,tild,FFres]=...
197            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);
198      fill=zeros(3,2,size(Data.Civ1_SubRange,3)); %matrix of zeros to complement the matrix Data.Civ1_Coord_tps (conveninent for file storage)
199      Data.Civ1_Coord_tps=cat(1,Data.Civ1_Coord_tps,fill);
200      Data.Civ1_U_smooth(ind_good)=Ures;
201      Data.Civ1_V_smooth(ind_good)=Vres;
202      Data.Civ1_FF(ind_good)=FFres;
203      Data.CivStage=3;                             
204end   
205
206%% Civ2
207if isfield (Param,'Civ2')
208    par_civ2=Param.Civ2;
209    if ~isfield (Param,'Civ1') || ~strcmp(Param.Civ1.ImageA,par_civ2.ImageA)
210        %read first image if not already done for civ1
211        [Field,ParamOut,errormsg] = read_field(par_civ2.ImageA,par_civ2.FileTypeA,[],par_civ2.i1);
212        par_civ2.ImageA=Field.A;
213    else
214        par_civ2.ImageA=par_civ1.ImageA;
215    end
216    if ~isfield (Param,'Civ1') || ~strcmp(Param.Civ1.ImageB,par_civ2.ImageB)
217        %read first image if not already done for civ1
218        [Field,ParamOut,errormsg] = read_field(par_civ2.ImageB,par_civ2.FileTypeB,[],par_civ2.i2);
219        par_civ2.ImageB=Field.A;
220    else
221        par_civ2.ImageB=par_civ1.ImageB;
222    end
223    ibx2=ceil(par_civ2.Bx/2);
224    iby2=ceil(par_civ2.By/2);
225    isx2=ibx2+4;% search ara +-4 pixels around the guess
226    isy2=iby2+4;
227    % shift from par_civ2.filename_nc1
228    % shiftx=velocity interpolated at position
229    miniy=max(1+isy2,1+iby2);
230    minix=max(1+isx2,1+ibx2);
231    maxiy=min(size(par_civ2.ImageA,1)-isy2,size(par_civ2.ImageA,1)-iby2);
232    maxix=min(size(par_civ2.ImageA,2)-isx2,size(par_civ2.ImageA,2)-ibx2);
233    [GridX,GridY]=meshgrid(minix:par_civ2.Dx:maxix,miniy:par_civ2.Dy:maxiy);
234    GridX=reshape(GridX,[],1);
235    GridY=reshape(GridY,[],1);
236    Shiftx=zeros(size(GridX));% shift expected from civ1 data
237    Shifty=zeros(size(GridX));
238    nbval=zeros(size(GridX));
239    if par_civ2.CheckDeformation
240        DUDX=zeros(size(GridX));
241        DUDY=zeros(size(GridX));
242        DVDX=zeros(size(GridX));
243        DVDY=zeros(size(GridX));
244    end
245    NbSubDomain=size(Data.Civ1_SubRange,3);
246    % get the guess from patch1
247    for isub=1:NbSubDomain
248        nbvec_sub=Data.Civ1_NbSites(isub);
249        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));
250        epoints = [GridX(ind_sel) GridY(ind_sel)];% coordinates of interpolation sites
251        ctrs=Data.Civ1_Coord_tps(1:nbvec_sub,:,isub) ;%(=initial points) ctrs
252        nbval(ind_sel)=nbval(ind_sel)+1;% records the number of values for eacn interpolation point (in case of subdomain overlap)
253        EM = tps_eval(epoints,ctrs);
254        Shiftx(ind_sel)=Shiftx(ind_sel)+EM*Data.Civ1_U_tps(1:nbvec_sub+3,isub);
255        Shifty(ind_sel)=Shifty(ind_sel)+EM*Data.Civ1_V_tps(1:nbvec_sub+3,isub);
256        if par_civ2.CheckDeformation
257            [EMDX,EMDY] = tps_eval_dxy(epoints,ctrs);%2D matrix of distances between extrapolation points epoints and spline centres (=site points) ctrs
258            DUDX(ind_sel)=DUDX(ind_sel)+EMDX*Data.Civ1_U_tps(1:nbvec_sub+3,isub);
259            DUDY(ind_sel)=DUDY(ind_sel)+EMDY*Data.Civ1_U_tps(1:nbvec_sub+3,isub);
260            DVDX(ind_sel)=DVDX(ind_sel)+EMDX*Data.Civ1_V_tps(1:nbvec_sub+3,isub);
261            DVDY(ind_sel)=DVDY(ind_sel)+EMDY*Data.Civ1_V_tps(1:nbvec_sub+3,isub);
262        end
263    end
264    mask='';
265    if par_civ2.CheckMask&&~isempty(par_civ2.Mask)&& ~strcmp(maskname,par_civ2.Mask)% mask exist, not already read in civ1
266        mask=imread(par_civ2.Mask);
267    end
268    par_civ2.Searchx=2*isx2+1;
269    par_civ2.Searchy=2*isy2+1;
270    par_civ2.Shiftx=Shiftx(nbval>=1)./nbval(nbval>=1);
271    par_civ2.Shifty=Shifty(nbval>=1)./nbval(nbval>=1);
272    par_civ2.Grid=[GridX(nbval>=1)-par_civ2.Shiftx/2 GridY(nbval>=1)-par_civ2.Shifty/2];% grid taken at the extrapolated origin of the displacement vectors   
273    if par_civ2.CheckDeformation
274        par_civ2.DUDX=DUDX./nbval;
275        par_civ2.DUDY=DUDY./nbval;
276        par_civ2.DVDX=DVDX./nbval;
277        par_civ2.DVDY=DVDY./nbval;
278    end
279    % caluclate velocity data (y and v in indices, reverse to y component)
280    [xtable ytable utable vtable ctable F] = civ (par_civ2);
281%     diff_squared=(utable-par_civ2.Shiftx).*(utable-par_civ2.Shiftx)+(vtable+par_civ2.Shifty).*(vtable+par_civ2.Shifty);
282%     F(diff_squared>=4)=4; %flag vectors whose distance to the guess exceeds 2 pixels
283    list_param=(fieldnames(Param.Civ2))';
284    list_remove={'pxcmx','pxcmy','npx','npy','gridflag','maskflag','term_a','term_b','T0'};
285    for ilist=1:length(list_remove)
286        index=strcmp(list_remove{ilist},list_param);
287        if ~isempty(find(index,1))
288            list_param(index)=[];
289        end
290    end
291    for ilist=1:length(list_param)
292        Civ2_param{ilist}=['Civ2_' list_param{ilist}];
293        eval(['Data.Civ2_' list_param{ilist} '=Param.Civ2.' list_param{ilist} ';'])
294    end
295    if isfield(Data,'Civ2_gridname') && strcmp(Data.Civ1_gridname(1:6),'noFile')
296        Data.Civ1_gridname='';
297    end
298    if isfield(Data,'Civ2_maskname') && strcmp(Data.Civ1_maskname(1:6),'noFile')
299        Data.Civ2_maskname='';
300    end
301    Data.ListGlobalAttribute=[Data.ListGlobalAttribute Civ2_param {'Civ2_Time','Civ2_Dt'}];
302%     Data.Civ2_Time=par_civ2.Time;
303%     Data.Civ2_Dt=par_civ2.Dt;
304    nbvar=numel(Data.ListVarName);
305    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
306    Data.VarDimName=[Data.VarDimName {'nb_vec_2','nb_vec_2','nb_vec_2','nb_vec_2','nb_vec_2','nb_vec_2'}];
307    Data.VarAttribute{nbvar+1}.Role='coord_x';
308    Data.VarAttribute{nbvar+2}.Role='coord_y';
309    Data.VarAttribute{nbvar+3}.Role='vector_x';
310    Data.VarAttribute{nbvar+4}.Role='vector_y';
311    Data.VarAttribute{nbvar+5}.Role='warnflag';
312    Data.Civ2_X=reshape(xtable,[],1);
313    Data.Civ2_Y=reshape(size(par_civ2.ImageA,1)-ytable+1,[],1);
314    Data.Civ2_U=reshape(utable,[],1);
315    Data.Civ2_V=reshape(-vtable,[],1);
316    Data.Civ2_C=reshape(ctable,[],1);
317    Data.Civ2_F=reshape(F,[],1);
318    Data.CivStage=Data.CivStage+1;
319end
320
321%% Fix2
322if isfield (Param,'Fix2')
323    ListFixParam=fieldnames(Param.Fix2);
324    for ilist=1:length(ListFixParam)
325        ParamName=ListFixParam{ilist};
326        ListName=['Fix2_' ParamName];
327        eval(['Data.ListGlobalAttribute=[Data.ListGlobalAttribute ''' ParamName '''];'])
328        eval(['Data.' ListName '=Param.Fix2.' ParamName ';'])
329    end
330    if check_civx
331        if ~isfield(Data,'fix2')
332            Data.ListGlobalAttribute=[Data.ListGlobalAttribute 'fix2'];
333            Data.fix2=1;
334            Data.ListVarName=[Data.ListVarName {'vec2_FixFlag'}];
335            Data.VarDimName=[Data.VarDimName {'nb_vectors2'}];
336        end
337        Data.vec_FixFlag=fix(Param.Fix2,Data.vec2_F,Data.vec2_C,Data.vec2_U,Data.vec2_V,Data.vec2_X,Data.vec2_Y);
338    else
339        Data.ListVarName=[Data.ListVarName {'Civ2_FF'}];
340        Data.VarDimName=[Data.VarDimName {'nb_vec_2'}];
341        nbvar=length(Data.ListVarName);
342        Data.VarAttribute{nbvar}.Role='errorflag';   
343        Data.Civ2_FF=fix(Param.Fix2,Data.Civ2_F,Data.Civ2_C,Data.Civ2_U,Data.Civ2_V);
344        Data.CivStage=Data.CivStage+1;   
345    end
346   
347end   
348
349%% Patch2
350if isfield (Param,'Patch2')
351    Data.ListGlobalAttribute=[Data.ListGlobalAttribute {'Patch2_Rho','Patch2_Threshold','Patch2_SubDomain'}];
352    Data.Patch2_Rho=Param.Patch2.SmoothingParam;
353    Data.Patch2_Threshold=Param.Patch2.MaxDiff;
354    Data.Patch2_SubDomain=Param.Patch2.SubdomainSize;
355    nbvar=length(Data.ListVarName);
356    Data.ListVarName=[Data.ListVarName {'Civ2_U_smooth','Civ2_V_smooth','Civ2_SubRange','Civ2_NbSites','Civ2_Coord_tps','Civ2_U_tps','Civ2_V_tps'}];
357    Data.VarDimName=[Data.VarDimName {'nb_vec_2','nb_vec_2',{'nb_coord','nb_bounds','nb_subdomain_2'},{'nb_subdomain_2'},...
358             {'nb_tps_2','nb_coord','nb_subdomain_2'},{'nb_tps_2','nb_subdomain_2'},{'nb_tps_2','nb_subdomain_2'}}];
359
360        Data.VarAttribute{nbvar+1}.Role='vector_x';
361    Data.VarAttribute{nbvar+2}.Role='vector_y';
362    Data.VarAttribute{nbvar+5}.Role='coord_tps';
363    Data.VarAttribute{nbvar+6}.Role='vector_x_tps';
364    Data.VarAttribute{nbvar+7}.Role='vector_y_tps';
365    Data.Civ2_U_smooth=zeros(size(Data.Civ2_X));
366    Data.Civ2_V_smooth=zeros(size(Data.Civ2_X));
367    if isfield(Data,'Civ2_FF')
368        ind_good=find(Data.Civ2_FF==0);
369    else
370        ind_good=1:numel(Data.Civ2_X);
371    end
372    [Data.Civ2_SubRange,Data.Civ2_NbSites,Data.Civ2_Coord_tps,Data.Civ2_U_tps,Data.Civ2_V_tps,tild,Ures, Vres,tild,FFres]=...
373         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);
374           fill=zeros(3,2,size(Data.Civ2_SubRange,3)); %matrix of zeros to complement the matrix Data.Civ1_Coord_tps (conveninent for file storage)
375      Data.Civ2_Coord_tps=cat(1,Data.Civ2_Coord_tps,fill);
376    Data.Civ2_U_smooth(ind_good)=Ures;
377    Data.Civ2_V_smooth(ind_good)=Vres;
378    Data.Civ2_FF(ind_good)=FFres;
379    Data.CivStage=Data.CivStage+1;                             
380end 
381
382%% write result in a netcdf file if requested
383if exist('ncfile','var')
384    errormsg=struct2nc(ncfile,Data);
385end
386
387% 'civ': function piv.m adapted from PIVlab http://pivlab.blogspot.com/
388%--------------------------------------------------------------------------
389% function [xtable ytable utable vtable typevector] = civ (image1,image2,ibx,iby step, subpixfinder, mask, roi)
390%
391% OUTPUT:
392% xtable: set of x coordinates
393% ytable: set of y coordiantes
394% utable: set of u displacements (along x)
395% vtable: set of v displacements (along y)
396% ctable: max image correlation for each vector
397% typevector: set of flags, =1 for good, =0 for NaN vectors
398%
399%INPUT:
400% image1:first image (matrix)
401% image2: second image (matrix)
402% ibx2,iby2: half size of the correlation box along x and y, in px (size=(2*iby2+1,2*ibx2+1)
403% isx2,isy2: half size of the search box along x and y, in px (size=(2*isy2+1,2*isx2+1)
404% shiftx, shifty: shift of the search box (in pixel index, yshift reversed)
405% step: mesh of the measurement points (in px)
406% subpixfinder=1 or 2 controls the curve fitting of the image correlation
407% mask: =[] for no mask
408% roi: 4 element vector defining a region of interest: x position, y position, width, height, (in image indices), for the whole image, roi=[];
409function [xtable ytable utable vtable ctable F result_conv errormsg] = civ (par_civ)
410%this funtion performs the DCC PIV analysis. Recent window-deformation
411%methods perform better and will maybe be implemented in the future.
412
413%% prepare grid
414ibx2=ceil(par_civ.Bx/2);
415iby2=ceil(par_civ.By/2);
416isx2=ceil(par_civ.Searchx/2);
417isy2=ceil(par_civ.Searchy/2);
418shiftx=round(par_civ.Shiftx);
419shifty=-round(par_civ.Shifty);% sign minus because image j index increases when y decreases
420if isfield(par_civ,'Grid')
421    if ischar(par_civ.Grid)%read the drid file if the input is a file name
422        par_civ.Grid=dlmread(par_civ.Grid);
423        par_civ.Grid(1,:)=[];%the first line must be removed (heading in the grid file)
424    end
425else% automatic measurement grid
426    ibx2=ceil(par_civ.Bx/2);
427    iby2=ceil(par_civ.By/2);
428    isx2=ceil(par_civ.Searchx/2);
429    isy2=ceil(par_civ.Searchy/2);
430    miniy=max(1+isy2+shifty,1+iby2);
431    minix=max(1+isx2-shiftx,1+ibx2);
432    maxiy=min(par_civ.ImageHeight-isy2+shifty,par_civ.ImageHeight-iby2);
433    maxix=min(par_civ.ImageWidth-isx2-shiftx,par_civ.ImageWidth-ibx2);
434    [GridX,GridY]=meshgrid(minix:par_civ.Dx:maxix,miniy:par_civ.Dy:maxiy);
435    par_civ.Grid(:,1)=reshape(GridX,[],1);
436    par_civ.Grid(:,2)=reshape(GridY,[],1);
437end
438nbvec=size(par_civ.Grid,1);
439if numel(shiftx)==1
440    shiftx=shiftx*ones(nbvec,1);
441    shifty=shifty*ones(nbvec,1);
442end
443%% Default output
444xtable=par_civ.Grid(:,1);
445ytable=par_civ.Grid(:,2);
446utable=zeros(nbvec,1);
447vtable=zeros(nbvec,1);
448ctable=zeros(nbvec,1);
449F=zeros(nbvec,1);
450result_conv=[];
451errormsg='';
452
453%% prepare mask
454if isfield(par_civ,'Mask') && ~isempty(par_civ.Mask)
455    if strcmp(par_civ.Mask,'all')
456        return    % get the grid only, no civ calculation
457    elseif ischar(par_civ.Mask)
458        par_civ.Mask=imread(par_civ.Mask);
459    end
460end
461check_MinIma=isfield(par_civ,'MinIma');% test for image luminosity threshold
462check_MaxIma=isfield(par_civ,'MaxIma') && ~isempty(par_civ.MaxIma);
463
464% %% prepare images
465% if isfield(par_civ,'reverse_pair')
466%     if par_civ.reverse_pair
467%         if ischar(par_civ.ImageB)
468%             temp=par_civ.ImageA;
469%             par_civ.ImageA=imread(par_civ.ImageB);
470%         end
471%         if ischar(temp)
472%             par_civ.ImageB=imread(temp);
473%         end
474%     end
475% else
476%     if ischar(par_civ.ImageA)
477%         par_civ.ImageA=imread(par_civ.ImageA);
478%     end
479%     if ischar(par_civ.ImageB)
480%         par_civ.ImageB=imread(par_civ.ImageB);
481%     end
482% end
483par_civ.ImageA=sum(double(par_civ.ImageA),3);%sum over rgb component for color images
484par_civ.ImageB=sum(double(par_civ.ImageB),3);
485[npy_ima npx_ima]=size(par_civ.ImageA);
486if ~isequal(size(par_civ.ImageB),[npy_ima npx_ima])
487    errormsg='image pair with unequal size';
488    return
489end
490
491%% Apply mask
492    % Convention for mask IDEAS TO IMPLEMENT ?
493    % mask >200 : velocity calculated
494    %  200 >=mask>150;velocity not calculated, interpolation allowed (bad spots)
495    % 150>=mask >100: velocity not calculated, nor interpolated
496    %  100>=mask> 20: velocity not calculated, impermeable (no flux through mask boundaries)
497    %  20>=mask: velocity=0
498checkmask=0;
499if isfield(par_civ,'Mask') && ~isempty(par_civ.Mask)
500   checkmask=1;
501   if ~isequal(size(par_civ.Mask),[npy_ima npx_ima])
502        errormsg='mask must be an image with the same size as the images';
503        return
504   end
505  %  check_noflux=(par_civ.Mask<100) ;%TODO: to implement
506    check_undefined=(par_civ.Mask<200 & par_civ.Mask>=20 );
507    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
508    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
509end
510
511%% compute image correlations: MAINLOOP on velocity vectors
512corrmax=0;
513sum_square=1;% default
514mesh=1;% default
515CheckDecimal=isfield(par_civ,'CheckDecimal')&& par_civ.CheckDecimal==1;
516if CheckDecimal
517    mesh=0.2;%mesh in pixels for subpixel image interpolation
518    CheckDeformation=isfield(par_civ,'CheckDeformation')&& par_civ.CheckDeformation==1;
519end
520% vector=[0 0];%default
521for ivec=1:nbvec
522    iref=round(par_civ.Grid(ivec,1)+0.5);% xindex on the image A for the middle of the correlation box
523    jref=round(par_civ.ImageHeight-par_civ.Grid(ivec,2)+0.5);% yindex on the image B for the middle of the correlation box
524    if ~(checkmask && par_civ.Mask(jref,iref)<=20) %velocity not set to zero by the black mask
525        if jref-iby2<1 || jref+iby2>par_civ.ImageHeight|| iref-ibx2<1 || iref+ibx2>par_civ.ImageWidth||...
526              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
527            F(ivec)=3;
528        else
529            image1_crop=par_civ.ImageA(jref-iby2:jref+iby2,iref-ibx2:iref+ibx2);%extract a subimage (correlation box) from image A
530            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
531            image1_mean=mean(mean(image1_crop));
532            image2_mean=mean(mean(image2_crop));
533            %threshold on image minimum
534            if check_MinIma && (image1_mean < par_civ.MinIma || image2_mean < par_civ.MinIma)
535                F(ivec)=3;
536            end
537            %threshold on image maximum
538            if check_MaxIma && (image1_mean > par_civ.MaxIma || image2_mean > par_civ.MaxIma)
539                F(ivec)=3;
540            end
541        end     
542        if F(ivec)~=3
543            image1_crop=image1_crop-image1_mean;%substract the mean
544            image2_crop=image2_crop-image2_mean;
545            if CheckDecimal
546                xi=(1:mesh:size(image1_crop,2));
547                yi=(1:mesh:size(image1_crop,1))';
548                if CheckDeformation
549                    [XI,YI]=meshgrid(xi-ceil(size(image1_crop,2)/2),yi-ceil(size(image1_crop,1)/2));
550                    XIant=XI-par_civ.DUDX(ivec)*XI-par_civ.DUDY(ivec)*YI+ceil(size(image1_crop,2)/2);
551                    YIant=YI-par_civ.DVDX(ivec)*XI-par_civ.DVDY(ivec)*YI+ceil(size(image1_crop,1)/2);
552                    image1_crop=interp2(image1_crop,XIant,YIant);
553                else
554                    image1_crop=interp2(image1_crop,xi,yi);
555                end
556                xi=(1:mesh:size(image2_crop,2));
557                yi=(1:mesh:size(image2_crop,1))';
558                image2_crop=interp2(image2_crop,xi,yi);
559            end
560            sum_square=sum(sum(image1_crop.*image1_crop));
561            %reference: Oliver Pust, PIV: Direct Cross-Correlation
562            result_conv= conv2(image2_crop,flipdim(flipdim(image1_crop,2),1),'valid');
563            corrmax= max(max(result_conv));
564            result_conv=(result_conv/corrmax)*255; %normalize, peak=always 255
565            %Find the correlation max, at 255
566            [y,x] = find(result_conv==255,1);
567            if ~isempty(y) && ~isempty(x)
568                try
569                    if par_civ.Rho==1
570                        [vector,F(ivec)] = SUBPIXGAUSS (result_conv,x,y);
571                    elseif par_civ.Rho==2
572                        [vector,F(ivec)] = SUBPIX2DGAUSS (result_conv,x,y);
573                    end
574                    utable(ivec)=vector(1)*mesh+shiftx(ivec);
575                    vtable(ivec)=vector(2)*mesh+shifty(ivec);                 
576                    xtable(ivec)=iref+utable(ivec)/2-0.5;% convec flow (velocity taken at the point middle from imgae 1 and 2)
577                    ytable(ivec)=jref+vtable(ivec)/2-0.5;% and position of pixel 1=0.5 (convention for image coordinates=0 at the edge)
578                    iref=round(xtable(ivec));% image index for the middle of the vector
579                    jref=round(ytable(ivec));
580                    if checkmask && par_civ.Mask(jref,iref)<200 && par_civ.Mask(jref,iref)>=100
581                        utable(ivec)=0;
582                        vtable(ivec)=0;
583                        F(ivec)=3;
584                    end
585                    ctable(ivec)=corrmax/sum_square;% correlation value
586                catch ME
587                    F(ivec)=3;
588                end
589            else
590                F(ivec)=3;
591            end
592        end
593    end
594   
595    %Create the vector matrix x, y, u, v
596end
597result_conv=result_conv*corrmax/(255*sum_square);% keep the last correlation matrix for output
598
599%------------------------------------------------------------------------
600% --- Find the maximum of the correlation function after interpolation
601function [vector,F] = SUBPIXGAUSS (result_conv,x,y)
602%------------------------------------------------------------------------
603vector=[0 0]; %default
604F=0;
605[npy,npx]=size(result_conv);
606
607% if (x <= (size(result_conv,1)-1)) && (y <= (size(result_conv,1)-1)) && (x >= 1) && (y >= 1)
608    %the following 8 lines are copyright (c) 1998, Uri Shavit, Roi Gurka, Alex Liberzon, Technion ï¿œ Israel Institute of Technology
609    %http://urapiv.wordpress.com
610    peaky = y;
611    if y <= npy-1 && y >= 1
612        f0 = log(result_conv(y,x));
613        f1 = real(log(result_conv(y-1,x)));
614        f2 = real(log(result_conv(y+1,x)));
615        peaky = peaky+ (f1-f2)/(2*f1-4*f0+2*f2);
616    else
617        F=-2; % warning flag for vector truncated by the limited search box
618    end
619    peakx=x;
620    if x <= npx-1 && x >= 1
621        f0 = log(result_conv(y,x));
622        f1 = real(log(result_conv(y,x-1)));
623        f2 = real(log(result_conv(y,x+1)));
624        peakx = peakx+ (f1-f2)/(2*f1-4*f0+2*f2);
625    else
626        F=-2; % warning flag for vector truncated by the limited search box
627    end
628    vector=[peakx-floor(npx/2)-1 peaky-floor(npy/2)-1];
629
630%------------------------------------------------------------------------
631% --- Find the maximum of the correlation function after interpolation
632function [vector,F] = SUBPIX2DGAUSS (result_conv,x,y)
633%------------------------------------------------------------------------
634vector=[0 0]; %default
635F=-2;
636peaky=y;
637peakx=x;
638[npy,npx]=size(result_conv);
639if (x <= npx-1) && (y <= npy-1) && (x >= 1) && (y >= 1)
640    F=0;
641    for i=-1:1
642        for j=-1:1
643            %following 15 lines based on
644            %H. Nobach ï¿œ M. Honkanen (2005)
645            %Two-dimensional Gaussian regression for sub-pixel displacement
646            %estimation in particle image velocimetry or particle position
647            %estimation in particle tracking velocimetry
648            %Experiments in Fluids (2005) 38: 511ï¿œ515
649            c10(j+2,i+2)=i*log(result_conv(y+j, x+i));
650            c01(j+2,i+2)=j*log(result_conv(y+j, x+i));
651            c11(j+2,i+2)=i*j*log(result_conv(y+j, x+i));
652            c20(j+2,i+2)=(3*i^2-2)*log(result_conv(y+j, x+i));
653            c02(j+2,i+2)=(3*j^2-2)*log(result_conv(y+j, x+i));
654        end
655    end
656    c10=(1/6)*sum(sum(c10));
657    c01=(1/6)*sum(sum(c01));
658    c11=(1/4)*sum(sum(c11));
659    c20=(1/6)*sum(sum(c20));
660    c02=(1/6)*sum(sum(c02));
661    deltax=(c11*c01-2*c10*c02)/(4*c20*c02-c11^2);
662    deltay=(c11*c10-2*c01*c20)/(4*c20*c02-c11^2);
663    if abs(deltax)<1
664        peakx=x+deltax;
665    end
666    if abs(deltay)<1
667        peaky=y+deltay;
668    end
669end
670vector=[peakx-floor(npx/2)-1 peaky-floor(npy/2)-1];
671
672%'RUN_FIX': function for fixing velocity fields:
673%-----------------------------------------------
674% RUN_FIX(filename,field,flagindex,thresh_vecC,thresh_vel,iter,flag_mask,maskname,fileref,fieldref)
675%
676%filename: name of the netcdf file (used as input and output)
677%field: structure specifying the names of the fields to fix (depending on civ1 or civ2)
678    %.vel_type='civ1' or 'civ2';
679    %.nb=name of the dimension common to the field to fix ('nb_vectors' for civ1);
680    %.fixflag=name of fix flag variable ('vec_FixFlag' for civ1)
681%flagindex: flag specifying which values of vec_f are removed:
682        % if flagindex(1)=1: vec_f=-2 vectors are removed
683        % if flagindex(2)=1: vec_f=3 vectors are removed
684        % if flagindex(3)=1: vec_f=2 vectors are removed (if iter=1) or vec_f=4 vectors are removed (if iter=2)
685%iter=1 for civ1 fields and iter=2 for civ2 fields
686%thresh_vecC: threshold in the image correlation vec_C
687%flag_mask: =1 mask used to remove vectors (0 else)
688%maskname: name of the mask image file for fix
689%thresh_vel: threshold on velocity, or on the difference with the reference file fileref if exists
690%inf_sup=1: remove values smaller than threshold thresh_vel, =2, larger than threshold
691%fileref: .nc file name for a reference velocity (='': refrence 0 used)
692%fieldref: 'civ1','filter1'...feld used in fileref
693
694function FF=fix(Param,F,C,U,V,X,Y)
695FF=zeros(size(F));%default
696
697%criterium on warn flags
698FlagName={'CheckFmin2','CheckF2','CheckF3','CheckF4'};
699FlagVal=[-2 2 3 4];
700for iflag=1:numel(FlagName)
701    if isfield(Param,FlagName{iflag}) && Param.(FlagName{iflag})
702        FF=(FF==1| F==FlagVal(iflag));
703    end
704end
705%criterium on correlation values
706if isfield (Param,'MinCorr')
707    FF=FF==1 | C<Param.MinCorr;
708end
709if (isfield(Param,'MinVel')&&~isempty(Param.MinVel))||(isfield (Param,'MaxVel')&&~isempty(Param.MaxVel))
710    Umod= U.*U+V.*V;
711    if isfield (Param,'MinVel')&&~isempty(Param.MinVel)
712        FF=FF==1 | Umod<(Param.MinVel*Param.MinVel);
713    end
714    if isfield (Param,'MaxVel')&&~isempty(Param.MaxVel)
715        FF=FF==1 | Umod>(Param.MaxVel*Param.MaxVel);
716    end
717end
718
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