source: trunk/src/civ_matlab.m @ 316

Last change on this file since 316 was 316, checked in by sommeria, 9 years ago

a few more bugs corrected, now the new civ_matlab works for civ1,fix1, patch1

File size: 35.6 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%   patch: 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% ncfile: name of a netcdf file to be created for the result (extension .nc)
17%
18%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
19%  Copyright  2011, LEGI / CNRS-UJF-INPG, joel.sommeria@legi.grenoble-inp.fr.
20%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
21%     This is part of the toolbox UVMAT.
22%
23%     UVMAT is free software; you can redistribute it and/or modify
24%     it under the terms of the GNU General Public License as published by
25%     the Free Software Foundation; either version 2 of the License, or
26%     (at your option) any later version.
27%
28%     UVMAT is distributed in the hope that it will be useful,
29%     but WITHOUT ANY WARRANTY; without even the implied warranty of
30%     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
31%     GNU General Public License (open UVMAT/COPYING.txt) for more details.
32%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
33
34function [Data,errormsg,result_conv]= civ_matlab(Param,ncfile)
35errormsg='';
36Data.ListGlobalAttribute={'Conventions','Program','CivStage'};
37Data.Conventions='uvmat/civdata';% states the conventions used for the description of field variables and attributes
38Data.Program='civ_matlab';
39Data.CivStage=0;%default
40ListVarCiv1={'Civ1_X','Civ1_Y','Civ1_U','Civ1_V','Civ1_C','Civ1_F'}; %variables to read
41ListVarFix1={'Civ1_X','Civ1_Y','Civ1_U','Civ1_V','Civ1_C','Civ1_F','Civ1_FF'};
42mask='';
43maskname='';%default
44check_civx=0;%default
45check_civ1=0;%default
46check_patch1=0;%default
47
48%% Civ1
49if isfield (Param,'Civ1')
50    check_civ1=1;% test for further use of civ1 results
51    % caluclate velocity data (y and v in indices, reverse to y component)
52    [xtable ytable utable vtable ctable F result_conv errormsg] = civ (Param.Civ1);
53    if ~isempty(errormsg)
54        return
55    end
56    list_param=(fieldnames(Param.Civ1))';
57    Civ1_param=list_param;%default
58    for ilist=1:length(list_param)
59        Civ1_param{ilist}=['Civ1_' list_param{ilist}];
60        %         eval(['Data.Civ1_' list_param{ilist} '=Param.Civ1.' list_param{ilist} ';'])
61        Data.(['Civ1_' list_param{ilist}])=Param.Civ1.(list_param{ilist});
62    end
63    Data.ListGlobalAttribute=[Data.ListGlobalAttribute Civ1_param];% {'Civ1_Time','Civ1_Dt'}];
64%     if exist('ncfile','var')% TEST for use interactively with mouse_motion (no file created)
65        Data.ListVarName={'Civ1_X','Civ1_Y','Civ1_U','Civ1_V','Civ1_C','Civ1_F'};%  cell array containing the names of the fields to record
66        Data.VarDimName={'nbvec1','nbvec1','nbvec1','nbvec1','nbvec1','nbvec1'};
67        Data.VarAttribute{1}.Role='coord_x';
68        Data.VarAttribute{2}.Role='coord_y';
69        Data.VarAttribute{3}.Role='vector_x';
70        Data.VarAttribute{4}.Role='vector_y';
71        Data.VarAttribute{5}.Role='warnflag';
72    Data.Civ1_X=reshape(xtable,[],1);
73    Data.Civ1_Y=reshape(Param.Civ1.ImageHeight-ytable+1,[],1);
74    Data.Civ1_U=reshape(utable,[],1);
75    Data.Civ1_V=reshape(-vtable,[],1);
76    Data.Civ1_C=reshape(ctable,[],1);
77    Data.Civ1_F=reshape(F,[],1);
78    Data.CivStage=1;
79
80else
81    Data=nc2struct(ncfile,'ListGlobalAttribute','absolut_time_T0'); %look for the constant 'absolut_time_T0' to detect old civx data format
82    if ~isempty(Data.absolut_time_T0')%read civx file
83        check_civx=1;% test for old civx data format
84        [Data,vardetect,ichoice]=nc2struct(ncfile);%read the variables in the netcdf file
85    else
86        if isfield(Param,'Fix1')
87            Data=nc2struct(ncfile,ListVarCiv1);%read civ1 data in the existing netcdf file
88        else
89            Data=nc2struct(ncfile,ListVarFix1);%read civ1 and fix1 data in the existing netcdf file
90        end
91    end
92    if isfield(Data,'Txt')
93        msgbox_uvmat('ERROR',Data.Txt)
94        return
95    end
96end
97
98%% Fix1
99if isfield (Param,'Fix1')
100    ListFixParam=fieldnames(Param.Fix1);
101    for ilist=1:length(ListFixParam)
102        ParamName=ListFixParam{ilist};
103        ListName=['Fix1_' ParamName];
104        eval(['Data.ListGlobalAttribute=[Data.ListGlobalAttribute ''' ParamName '''];'])
105        eval(['Data.' ListName '=Param.Fix1.' ParamName ';'])
106    end
107    if check_civx
108        if ~isfield(Data,'fix')
109            Data.ListGlobalAttribute=[Data.ListGlobalAttribute 'fix'];
110            Data.fix=1;
111            Data.ListVarName=[Data.ListVarName {'vec_FixFlag'}];
112            Data.VarDimName=[Data.VarDimName {'nb_vectors'}];
113        end
114        Data.vec_FixFlag=fix(Param.Fix1,Data.vec_F,Data.vec_C,Data.vec_U,Data.vec_V,Data.vec_X,Data.vec_Y);
115    else
116        Data.ListVarName=[Data.ListVarName {'Civ1_FF'}];
117        Data.VarDimName=[Data.VarDimName {'nbvec1'}];
118        nbvar=length(Data.ListVarName);
119        Data.VarAttribute{nbvar}.Role='errorflag';   
120        Data.Civ1_FF=fix(Param.Fix1,Data.Civ1_F,Data.Civ1_C,Data.Civ1_U,Data.Civ1_V);
121        Data.CivStage=2;   
122    end
123end   
124%% Patch1
125if isfield (Param,'Patch1')
126    check_patch1=1;
127    Param.Patch1
128    Data.ListGlobalAttribute=[Data.ListGlobalAttribute {'Patch1_Rho','Patch1_Threshold','Patch1_SubDomain'}];
129    Data.Patch1_Rho=Param.Patch1.SmoothingParam;
130    Data.Patch1_Threshold=Param.Patch1.MaxDiff;
131    Data.Patch1_SubDomain=Param.Patch1.SubdomainSize;
132    Data.ListVarName=[Data.ListVarName {'Civ1_U_Diff','Civ1_V_Diff','Civ1_X_SubRange','Civ1_Y_SubRange','Civ1_NbSites','Civ1_X_tps','Civ1_Y_tps','Civ1_U_tps','Civ1_V_tps'}];
133    Data.VarDimName=[Data.VarDimName {'NbVec1','NbVec1',{'NbSubDomain1','Two'},{'NbSubDomain1','Two'},'NbSubDomain1',...
134             {'NbVec1Sub','NbSubDomain1'},{'NbVec1Sub','NbSubDomain1'},{'Nbtps1','NbSubDomain1'},{'Nbtps1','NbSubDomain1'}}];
135    nbvar=length(Data.ListVarName);
136    Data.VarAttribute{nbvar-1}.Role='vector_x';
137    Data.VarAttribute{nbvar}.Role='vector_y';
138    Data.Civ1_U_Diff=zeros(size(Data.Civ1_X));
139    Data.Civ1_V_Diff=zeros(size(Data.Civ1_X));
140    if isfield(Data,'Civ1_FF')
141        ind_good=find(Data.Civ1_FF==0);
142    else
143       
144        ind_good=1:numel(Data.Civ1_X);
145    end
146    [Data.Civ1_X_SubRange,Data.Civ1_Y_SubRange,Data.Civ1_NbSites,FFres,Ures, Vres,Data.Civ1_X_tps,Data.Civ1_Y_tps,Data.Civ1_U_tps,Data.Civ1_V_tps]=...
147                            patch(Data.Civ1_X(ind_good)',Data.Civ1_Y(ind_good)',Data.Civ1_U(ind_good)',Data.Civ1_V(ind_good)',Data.Patch1_Rho,Data.Patch1_Threshold,Data.Patch1_SubDomain);
148      Data.Civ1_U_Diff(ind_good)=Data.Civ1_U(ind_good)-Ures;
149      Data.Civ1_V_Diff(ind_good)=Data.Civ1_V(ind_good)-Vres;
150      Data.Civ1_FF(ind_good)=FFres;
151      Data.CivStage=3;                             
152end   
153
154%% Civ2
155if isfield (Param,'Civ2')
156    par_civ2=Param.Civ2;
157    if ~check_civ1 || ~strcmp(par_civ1.filename_ima_a,par_civ2.filename_ima_a)
158            par_civ2.ImageA=imread(par_civ2.filename_ima_a);%read first image if not already done for civ1
159    end
160    if ~check_civ1|| ~strcmp(par_civ1.filename_ima_b,par_civ2.filename_ima_b)
161            par_civ2.ImageB=imread(par_civ2.filename_ima_b);%read second image if not already done for civ1
162    end
163%     stepx=str2double(par_civ2.dx);
164%     stepy=str2double(par_civ2.dy);
165    ibx2=ceil(str2double(par_civ2.ibx)/2);
166    iby2=ceil(str2double(par_civ2.iby)/2);
167    isx2=ibx2+2;
168    isy2=iby2+2;
169
170    %get the previous guess for displacement
171   
172    if ~check_patch1
173        [Data,VelType]=read_civdata(ObjectName,InputField,ParamIn.VelType);%TO DEVELOP
174    end
175   
176    Guess =interp_tps(Data,X,Y)
177%         Data.Civ1_U_Diff=zeros(size(Data.Civ1_X));
178%         Data.Civ1_V_Diff=zeros(size(Data.Civ1_X));
179%         if isfield(Data,'Civ1_FF')
180%             ind_good=find(Data.Civ1_FF==0);
181%         else
182%             ind_good=1:numel(Data.Civ1_X);
183%         end
184%             [Data.Civ1_X_SubRange,Data.Civ1_Y_SubRange,Data.Civ1_NbSites,FFres,Ures, Vres,Data.Civ1_X_tps,Data.Civ1_Y_tps,Data.Civ1_U_tps,Data.Civ1_V_tps]=...
185%                                 patch(Data.Civ1_X(ind_good)',Data.Civ1_Y(ind_good)',Data.Civ1_U(ind_good)',Data.Civ1_V(ind_good)',Data.Patch1_Rho,Data.Patch1_Threshold,Data.Patch1_SubDomain);
186%         end
187%     shiftx=str2num(par_civ1.shiftx);
188%     shifty=str2num(par_civ1.shifty);
189% TO GET shift from par_civ2.filename_nc1
190    % shiftx=velocity interpolated at position
191    miniy=max(1+isy2+shifty,1+iby2);
192    minix=max(1+isx2-shiftx,1+ibx2);
193    maxiy=min(size(par_civ2.ImageA,1)-isy2+shifty,size(par_civ2.ImageA,1)-iby2);
194    maxix=min(size(par_civ2.ImageA,2)-isx2-shiftx,size(par_civ2.ImageA,2)-ibx2);
195    [GridX,GridY]=meshgrid(minix:par_civ2.Dx:maxix,miniy:par_civ2.Dy:maxiy);
196    PointCoord(:,1)=reshape(GridX,[],1);
197    PointCoord(:,2)=reshape(GridY,[],1);
198    if ~isempty(par_civ2.maskname)&& ~strcmp(maskname,par_civ2.maskname)% mask exist, not already read in civ1
199        mask=imread(par_civ2.maskname);
200    end
201    % caluclate velocity data (y and v in indices, reverse to y component)
202    [xtable ytable utable vtable ctable F] = civ (par_civ2.ImageA,par_civ1.ImageB,ibx2,iby2,isx2,isy2,shiftx,-shifty,PointCoord,str2num(par_civ1.rho),mask);
203    list_param=(fieldnames(par_civ1))';
204    list_remove={'pxcmx','pxcmy','npx','npy','gridflag','maskflag','term_a','term_b','T0'};
205    index=zeros(size(list_param));
206    for ilist=1:length(list_remove)
207        index=strcmp(list_remove{ilist},list_param);
208        if ~isempty(find(index,1))
209            list_param(index)=[];
210        end
211    end
212    for ilist=1:length(list_param)
213        Civ1_param{ilist}=['Civ1_' list_param{ilist}];
214        eval(['Data.Civ1_' list_param{ilist} '=Param.Civ1.' list_param{ilist} ';'])
215    end
216    if isfield(Data,'Civ1_gridname') && strcmp(Data.Civ1_gridname(1:6),'noFile')
217        Data.Civ1_gridname='';
218    end
219    if isfield(Data,'Civ1_maskname') && strcmp(Data.Civ1_maskname(1:6),'noFile')
220        Data.Civ1_maskname='';
221    end
222    Data.ListGlobalAttribute=[Data.ListGlobalAttribute Civ1_param {'Civ1_Time','Civ1_Dt'}];
223    Data.Civ1_Time=str2double(par_civ1.T0);
224    Data.Civ1_Dt=str2double(par_civ1.Dt);
225    Data.ListVarName={'Civ1_X','Civ1_Y','Civ1_U','Civ1_V','Civ1_C','Civ1_F'};%  cell array containing the names of the fields to record
226    Data.VarDimName={'nbvec1','nbvec1','nbvec1','nbvec1','nbvec1','nbvec1'};
227    Data.VarAttribute{1}.Role='coord_x';
228    Data.VarAttribute{2}.Role='coord_y';
229    Data.VarAttribute{3}.Role='vector_x';
230    Data.VarAttribute{4}.Role='vector_y';
231    Data.VarAttribute{5}.Role='warnflag';
232    Data.Civ1_X=reshape(xtable,[],1);
233    Data.Civ1_Y=reshape(size(par_civ2.ImageA,1)-ytable+1,[],1);
234    Data.Civ1_U=reshape(utable,[],1);
235    Data.Civ1_V=reshape(-vtable,[],1);
236    Data.Civ1_C=reshape(ctable,[],1);
237    Data.Civ1_F=reshape(F,[],1);
238    Data.CivStage=Data.CivStage+1;
239end
240
241%% Fix2
242if isfield (Param,'Fix2')
243    ListFixParam=fieldnames(Param.Fix2);
244    for ilist=1:length(ListFixParam)
245        ParamName=ListFixParam{ilist};
246        ListName=['Fix1_' ParamName];
247        eval(['Data.ListGlobalAttribute=[Data.ListGlobalAttribute ''' ParamName '''];'])
248        eval(['Data.' ListName '=Param.Fix2.' ParamName ';'])
249    end
250    if check_civx
251        if ~isfield(Data,'fix2')
252            Data.ListGlobalAttribute=[Data.ListGlobalAttribute 'fix2'];
253            Data.fix2=1;
254            Data.ListVarName=[Data.ListVarName {'vec2_FixFlag'}];
255            Data.VarDimName=[Data.VarDimName {'nb_vectors2'}];
256        end
257        Data.vec_FixFlag=fix(Param.Fix2,Data.vec2_F,Data.vec2_C,Data.vec2_U,Data.vec2_V,Data.vec2_X,Data.vec2_Y);
258    else
259        Data.ListVarName=[Data.ListVarName {'Civ2_FF'}];
260        Data.VarDimName=[Data.VarDimName {'nbvec2'}];
261        nbvar=length(Data.ListVarName);
262        Data.VarAttribute{nbvar}.Role='errorflag';   
263        Data.Civ2_FF=fix(Param.Fix2,Data.Civ2_F,Data.Civ2_C,Data.Civ2_U,Data.Civ2_V);
264        Data.CivStage=5;   
265    end
266   
267end   
268
269%% Patch2
270if isfield (Param,'Patch2')
271    Data.ListGlobalAttribute=[Data.ListGlobalAttribute {'Patch2_Rho','Patch2_Threshold','Patch2_SubDomain'}];
272    Data.Patch2_Rho=str2double(Param.Patch2.Rho);
273    Data.Patch2_Threshold=str2double(Param.Patch2.Threshold);
274    Data.Patch2_SubDomain=str2double(Param.Patch2.SubDomain);
275    Data.ListVarName=[Data.ListVarName {'Civ2_U_Diff','Civ2_V_Diff','Civ2_X_SubRange','Civ2_Y_SubRange','Civ2_NbSites','Civ2_X_tps','Civ2_Y_tps','Civ2_U_tps','Civ2_V_tps'}];
276    Data.VarDimName=[Data.VarDimName {'NbVec2','NbVec2',{'NbSubDomain2','Two'},{'NbSubDomain2','Two'},'NbSubDomain2',...
277             {'NbVec2Sub','NbSubDomain2'},{'NbVec2Sub','NbSubDomain2'},{'Nbtps2','NbSubDomain2'},{'Nbtps2','NbSubDomain2'}}];
278    nbvar=length(Data.ListVarName);
279    Data.VarAttribute{nbvar-1}.Role='vector_x';
280    Data.VarAttribute{nbvar}.Role='vector_y';
281    Data.Civ2_U_Diff=zeros(size(Data.Civ2_X));
282    Data.Civ2_V_Diff=zeros(size(Data.Civ2_X));
283    if isfield(Data,'Civ2_FF')
284        ind_good=find(Data.Civ2_FF==0);
285    else
286        ind_good=1:numel(Data.Civ2_X);
287    end
288    [Data.Civ2_X_SubRange,Data.Civ2_Y_SubRange,Data.Civ2_NbSites,FFres,Ures, Vres,Data.Civ2_X_tps,Data.Civ2_Y_tps,Data.Civ2_U_tps,Data.Civ2_V_tps]=...
289                            patch(Data.Civ2_X(ind_good)',Data.Civ2_Y(ind_good)',Data.Civ2_U(ind_good)',Data.Civ2_V(ind_good)',Data.Patch2_Rho,Data.Patch2_Threshold,Data.Patch2_SubDomain);
290      Data.Civ2_U_Diff(ind_good)=Data.Civ2_U(ind_good)-Ures;
291      Data.Civ2_V_Diff(ind_good)=Data.Civ2_V(ind_good)-Vres;
292      Data.Civ2_FF(ind_good)=FFres;
293      Data.CivStage=6;                             
294end   
295
296%% write result in a netcdf file if requested
297if exist('ncfile','var')
298    errormsg=struct2nc(ncfile,Data);
299end
300
301% 'civ': function piv.m adapted from PIVlab http://pivlab.blogspot.com/
302%--------------------------------------------------------------------------
303% function [xtable ytable utable vtable typevector] = civ (image1,image2,ibx,iby step, subpixfinder, mask, roi)
304%
305% OUTPUT:
306% xtable: set of x coordinates
307% ytable: set of y coordiantes
308% utable: set of u displacements (along x)
309% vtable: set of v displacements (along y)
310% ctable: max image correlation for each vector
311% typevector: set of flags, =1 for good, =0 for NaN vectors
312%
313%INPUT:
314% image1:first image (matrix)
315% image2: second image (matrix)
316% ibx2,iby2: half size of the correlation box along x and y, in px (size=(2*iby2+1,2*ibx2+1)
317% isx2,isy2: half size of the search box along x and y, in px (size=(2*isy2+1,2*isx2+1)
318% shiftx, shifty: shift of the search box (in pixel index, yshift reversed)
319% step: mesh of the measurement points (in px)
320% subpixfinder=1 or 2 controls the curve fitting of the image correlation
321% mask: =[] for no mask
322% roi: 4 element vector defining a region of interest: x position, y position, width, height, (in image indices), for the whole image, roi=[];
323function [xtable ytable utable vtable ctable F result_conv errormsg] = civ (par_civ)
324%this funtion performs the DCC PIV analysis. Recent window-deformation
325%methods perform better and will maybe be implemented in the future.
326
327%% prepare grid
328ibx2=ceil(par_civ.Bx/2);
329iby2=ceil(par_civ.By/2);
330isx2=ceil(par_civ.Searchx/2);
331isy2=ceil(par_civ.Searchy/2);
332shiftx=par_civ.Shiftx;
333shifty=-par_civ.Shifty;% sign minus because image j index increases when y decreases
334if isfield(par_civ,'Grid')
335    if ischar(par_civ.Grid)
336        par_civ.Grid;
337        par_civ.Grid=dlmread(par_civ.Grid);
338        par_civ.Grid(1,:)=[];%the first line must be removed (heading in the grid file)
339    end
340else% automatic measurement grid
341    ibx2=ceil(par_civ.Bx/2);
342    iby2=ceil(par_civ.By/2);
343    isx2=ceil(par_civ.Searchx/2);
344    isy2=ceil(par_civ.Searchy/2);
345    shiftx=par_civ.Shiftx;
346    shifty=-par_civ.Shifty;
347    miniy=max(1+isy2+shifty,1+iby2);
348    minix=max(1+isx2-shiftx,1+ibx2);
349    maxiy=min(par_civ.ImageHeight-isy2+shifty,par_civ.ImageHeight-iby2);
350    maxix=min(par_civ.ImageWidth-isx2-shiftx,par_civ.ImageWidth-ibx2);
351    [GridX,GridY]=meshgrid(minix:par_civ.Dx:maxix,miniy:par_civ.Dy:maxiy);
352    par_civ.Grid(:,1)=reshape(GridX,[],1);
353    par_civ.Grid(:,2)=reshape(GridY,[],1);
354end
355
356%% Default output
357nbvec=size(par_civ.Grid,1);
358xtable=par_civ.Grid(:,1);
359ytable=par_civ.Grid(:,2);
360utable=zeros(nbvec,1);
361vtable=zeros(nbvec,1);
362ctable=zeros(nbvec,1);
363F=zeros(nbvec,1);
364result_conv=[];
365errormsg='';
366
367%% prepare mask
368if isfield(par_civ,'Mask') && ~isempty(par_civ.Mask)
369    if strcmp(par_civ.Mask,'all')
370        return    % get the grid only, no civ calculation
371    elseif ischar(par_civ.Mask)
372        par_civ.Mask=imread(par_civ.Mask);
373    end
374end
375check_MinIma=isfield(par_civ,'MinIma');% test for image luminosity threshold
376check_MaxIma=isfield(par_civ,'MaxIma') && ~isempty(par_civ.MaxIma);
377
378%% prepare images
379if ischar(par_civ.ImageA)
380    par_civ.ImageA=imread(par_civ.ImageA);
381end
382if ischar(par_civ.ImageB)
383    par_civ.ImageB=imread(par_civ.ImageB);
384end
385[npy_ima npx_ima]=size(par_civ.ImageA);
386if ~isequal(size(par_civ.ImageB),[npy_ima npx_ima])
387    errormsg='image pair with unequal size';
388    return
389end
390par_civ.ImageA=double(par_civ.ImageA);
391par_civ.ImageB=double(par_civ.ImageB);
392
393
394%% Apply mask
395    % Convention for mask
396    % mask >200 : velocity calculated
397    %  200 >=mask>150;velocity not calculated, interpolation allowed (bad spots)
398    % 150>=mask >100: velocity not calculated, nor interpolated
399    %  100>=mask> 20: velocity not calculated, impermeable (no flux through mask boundaries) TO IMPLEMENT
400    %  20>=mask: velocity=0
401checkmask=0;
402if isfield(par_civ,'Mask') && ~isempty(par_civ.Mask)
403   checkmask=1;
404   if ~isequal(size(par_civ.Mask),[npy_ima npx_ima])
405        errormsg='mask must be an image with the same size as the images';
406        return
407   end
408  %  check_noflux=(par_civ.Mask<100) ;%TODO: to implement
409    check_undefined=(par_civ.Mask<200 & par_civ.Mask>=100 );
410    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
411    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
412end
413
414%% compute image correlations: MAINLOOP on velocity vectors
415% corrmax=0;
416% sum_square=1;% default
417% vector=[0 0];%default
418for ivec=1:nbvec
419    iref=par_civ.Grid(ivec,1);% xindex on the image A for the middle of the correlation box
420    jref=par_civ.Grid(ivec,2);% yindex on the image B for the middle of the correlation box
421%     xtable(ivec)=iref;
422%     ytable(ivec)=jref;%default
423    if ~(checkmask && par_civ.Mask(jref,iref)<=20) %velocity not set to zero by the black mask
424        if jref-iby2<1 || jref+iby2>par_civ.ImageHeight|| iref-ibx2<1 || iref+ibx2>par_civ.ImageWidth
425            F(ivec)=3;
426        else
427            image1_crop=par_civ.ImageA(jref-iby2:jref+iby2,iref-ibx2:iref+ibx2);%extract a subimage (correlation box) from image A
428            image2_crop=par_civ.ImageB(jref+shifty-isy2:jref+shifty+isy2,iref+shiftx-isx2:iref+shiftx+isx2);%extract a larger subimage (search box) from image B
429            image1_mean=mean(mean(image1_crop));
430            image2_mean=mean(mean(image2_crop));
431            %threshold on image minimum
432            if check_MinIma && (image1_mean < par_civ.MinIma || image2_mean < par_civ.MinIma)
433                F(ivec)=3;
434            end
435        end
436        %threshold on image maximum
437        if check_MaxIma && (image1_mean > par_civ.MaxIma || image2_mean > par_civ.MaxIma)
438            F(ivec)=3;
439        end
440        if F(ivec)~=3
441            image1_crop=image1_crop-image1_mean;%substract the mean
442            image2_crop=image2_crop-image2_mean;
443            sum_square=sum(sum(image1_crop.*image1_crop));
444            %reference: Oliver Pust, PIV: Direct Cross-Correlation
445            result_conv= conv2(image2_crop,flipdim(flipdim(image1_crop,2),1),'valid');
446            corrmax= max(max(result_conv));
447            result_conv=(result_conv/corrmax)*255; %normalize, peak=always 255
448            %Find the correlation max, at 255
449            [y,x] = find(result_conv==255,1);
450            if ~isempty(y) && ~isempty(x)
451                try
452                    if par_civ.Rho==1
453                        [vector,F(ivec)] = SUBPIXGAUSS (result_conv,x,y);
454                    elseif par_civ.Rho==2
455                        [vector,F(ivec)] = SUBPIX2DGAUSS (result_conv,x,y);
456                    end
457                    utable(ivec)=vector(1)+shiftx;
458                    vtable(ivec)=vector(2)+shifty;
459                    xtable(ivec)=iref+utable(ivec)/2;% convec flow (velocity taken at the point middle from imgae1 and 2)
460                    ytable(ivec)=jref+vtable(ivec)/2;
461                    iref=round(xtable(ivec));% image index for the middle of the vector
462                    jref=round(ytable(ivec));
463                    if checkmask && par_civ.Mask(jref,iref)<200 && par_civ.Mask(jref,iref)>=100
464                        utable(ivec)=0;
465                        vtable(ivec)=0;
466                        F(ivec)=3;
467                    end
468                    ctable(ivec)=corrmax/sum_square;% correlation value
469                catch ME
470                    %                     vector=[0 0]; %if something goes wrong with cross correlation.....
471                    F(ivec)=3;
472                end
473            else
474                F(ivec)=3;
475            end
476        end
477    end
478   
479    %Create the vector matrix x, y, u, v
480end
481result_conv=result_conv*corrmax/(255*sum_square);% keep the last correlation matrix for output
482
483%------------------------------------------------------------------------
484% --- Find the maximum of the correlation function after interpolation
485function [vector,F] = SUBPIXGAUSS (result_conv,x,y)
486%------------------------------------------------------------------------
487vector=[0 0]; %default
488F=0;
489[npy,npx]=size(result_conv);
490
491% if (x <= (size(result_conv,1)-1)) && (y <= (size(result_conv,1)-1)) && (x >= 1) && (y >= 1)
492    %the following 8 lines are copyright (c) 1998, Uri Shavit, Roi Gurka, Alex Liberzon, Technion – Israel Institute of Technology
493    %http://urapiv.wordpress.com
494    peaky = y;
495    if y <= npy-1 && y >= 1
496        f0 = log(result_conv(y,x));
497        f1 = real(log(result_conv(y-1,x)));
498        f2 = real(log(result_conv(y+1,x)));
499        peaky = peaky+ (f1-f2)/(2*f1-4*f0+2*f2);
500    else
501        F=-2; % warning flag for vector truncated by the limited search box
502    end
503    peakx=x;
504    if x <= npx-1 && x >= 1
505        f0 = log(result_conv(y,x));
506        f1 = real(log(result_conv(y,x-1)));
507        f2 = real(log(result_conv(y,x+1)));
508        peakx = peakx+ (f1-f2)/(2*f1-4*f0+2*f2);
509    else
510        F=-2; % warning flag for vector truncated by the limited search box
511    end
512    vector=[peakx-floor(npx/2)-1 peaky-floor(npy/2)-1];
513
514%------------------------------------------------------------------------
515% --- Find the maximum of the correlation function after interpolation
516function [vector,F] = SUBPIX2DGAUSS (result_conv,x,y)
517%------------------------------------------------------------------------
518vector=[0 0]; %default
519F=-2;
520peaky=y;
521peakx=x;
522[npy,npx]=size(result_conv);
523if (x <= npx-1) && (y <= npy-1) && (x >= 1) && (y >= 1)
524    F=0;
525    for i=-1:1
526        for j=-1:1
527            %following 15 lines based on
528            %H. Nobach Æ M. Honkanen (2005)
529            %Two-dimensional Gaussian regression for sub-pixel displacement
530            %estimation in particle image velocimetry or particle position
531            %estimation in particle tracking velocimetry
532            %Experiments in Fluids (2005) 38: 511–515
533            c10(j+2,i+2)=i*log(result_conv(y+j, x+i));
534            c01(j+2,i+2)=j*log(result_conv(y+j, x+i));
535            c11(j+2,i+2)=i*j*log(result_conv(y+j, x+i));
536            c20(j+2,i+2)=(3*i^2-2)*log(result_conv(y+j, x+i));
537            c02(j+2,i+2)=(3*j^2-2)*log(result_conv(y+j, x+i));
538        end
539    end
540    c10=(1/6)*sum(sum(c10));
541    c01=(1/6)*sum(sum(c01));
542    c11=(1/4)*sum(sum(c11));
543    c20=(1/6)*sum(sum(c20));
544    c02=(1/6)*sum(sum(c02));
545    deltax=(c11*c01-2*c10*c02)/(4*c20*c02-c11^2);
546    deltay=(c11*c10-2*c01*c20)/(4*c20*c02-c11^2);
547    if abs(deltax)<1
548        peakx=x+deltax;
549    end
550    if abs(deltay)<1
551        peaky=y+deltay;
552    end
553end
554vector=[peakx-floor(npx/2)-1 peaky-floor(npy/2)-1];
555
556%'RUN_FIX': function for fixing velocity fields:
557%-----------------------------------------------
558% RUN_FIX(filename,field,flagindex,thresh_vecC,thresh_vel,iter,flag_mask,maskname,fileref,fieldref)
559%
560%filename: name of the netcdf file (used as input and output)
561%field: structure specifying the names of the fields to fix (depending on civ1 or civ2)
562    %.vel_type='civ1' or 'civ2';
563    %.nb=name of the dimension common to the field to fix ('nb_vectors' for civ1);
564    %.fixflag=name of fix flag variable ('vec_FixFlag' for civ1)
565%flagindex: flag specifying which values of vec_f are removed:
566        % if flagindex(1)=1: vec_f=-2 vectors are removed
567        % if flagindex(2)=1: vec_f=3 vectors are removed
568        % if flagindex(3)=1: vec_f=2 vectors are removed (if iter=1) or vec_f=4 vectors are removed (if iter=2)
569%iter=1 for civ1 fields and iter=2 for civ2 fields
570%thresh_vecC: threshold in the image correlation vec_C
571%flag_mask: =1 mask used to remove vectors (0 else)
572%maskname: name of the mask image file for fix
573%thresh_vel: threshold on velocity, or on the difference with the reference file fileref if exists
574%inf_sup=1: remove values smaller than threshold thresh_vel, =2, larger than threshold
575%fileref: .nc file name for a reference velocity (='': refrence 0 used)
576%fieldref: 'civ1','filter1'...feld used in fileref
577
578function FF=fix(Param,F,C,U,V,X,Y)
579FF=zeros(size(F));%default
580Param
581
582%criterium on warn flags
583FlagName={'CheckFmin2','CheckF2','CheckF3','CheckF4'};
584FlagVal=[-2 2 3 4];
585for iflag=1:numel(FlagName)
586    if isfield(Param,FlagName{iflag}) && Param.(FlagName{iflag})
587        FF=(FF==1| F==FlagVal(iflag));
588% if isfield (Param,'WarnFlags')
589%     for iflag=1:numel(Param.WarnFlags)
590%         FF=(FF==1| F==Param.WarnFlags(iflag));
591%     end
592% end
593    end
594end
595%criterium on correlation values
596if isfield (Param,'MinCorr')
597    FF=FF==1 | C<Param.MinCorr;
598end
599if (isfield(Param,'MinVel')&&~isempty(Param.MinVel))||(isfield (Param,'MaxVel')&&~isempty(Param.MaxVel))
600    Umod= U.*U+V.*V;
601    if isfield (Param,'MinVel')&&~isempty(Param.MinVel)
602        FF=FF==1 | Umod<(Param.MinVel*Param.MinVel);
603    end
604    if isfield (Param,'MaxVel')&&~isempty(Param.MaxVel)
605        FF=FF==1 | Umod>(Param.MaxVel*Param.MaxVel);
606    end
607end
608return
609
610%
611% if isfield (Param,'LowerBoundVel')&& ~isequal(Param.LowerBoundVel,0)
612%     thresh=Param.LowerBoundVel*Param.LowerBoundVel;
613%     FF=FF==1 | (U.*U+V.*V)<thresh;
614% end
615% if isfield (Param,'UpperBoundVel')&& ~isequal(Param.UpperBoundVel,0)
616%     thresh=Param.UpperBoundVel*Param.UpperBoundVel;
617%     FF=FF==1 | (U.*U+V.*V)>thresh;
618% end
619% if isfield(Param,'MaskName')
620%    M=imread(Param.MaskName);
621%    nxy=size(M);
622%    M=reshape(M,1,[]);
623%    rangx0=[0.5 nxy(2)-0.5];
624%    rangy0=[0.5 nxy(1)-0.5];
625%    vec_x1=X-U/2;%beginning points
626%    vec_x2=X+U/2;%end points of vectors
627%    vec_y1=Y-V/2;%beginning points
628%    vec_y2=Y+V/2;%end points of vectors
629%    indx=1+round((nxy(2)-1)*(vec_x1-rangx0(1))/(rangx0(2)-rangx0(1)));% image index x at abcissa vec_x1
630%    indy=1+round((nxy(1)-1)*(vec_y1-rangy0(1))/(rangy0(2)-rangy0(1)));% image index y at ordinate vec_y1   
631%    check_in=~(indx < 1 |indy < 1 | indx > nxy(2) |indy > nxy(1)); %=0 out of the mask image, 1 inside
632%    indx=indx.*check_in+(1-check_in); %replace indx by 1 out of the mask range
633%    indy=indy.*check_in+(1-check_in); %replace indy by 1 out of the mask range
634%    ICOMB=((indx-1)*nxy(1)+(nxy(1)+1-indy));%determine the indices in the image reshaped in a Matlab vector
635%    Mvalues=M(ICOMB);
636%    flag7b=((20 < Mvalues) & (Mvalues < 200))| ~check_in';
637%    indx=1+round((nxy(2)-1)*(vec_x2-rangx0(1))/(rangx0(2)-rangx0(1)));% image index x at abcissa vec_x2
638%    indy=1+round((nxy(1)-1)*(vec_y2-rangy0(1))/(rangy0(2)-rangy0(1)));% image index y at ordinate vec_y2
639%    check_in=~(indx < 1 |indy < 1 | indx > nxy(2) |indy > nxy(1)); %=0 out of the mask image, 1 inside
640%    indx=indx.*check_in+(1-check_in); %replace indx by 1 out of the mask range
641%    indy=indy.*check_in+(1-check_in); %replace indy by 1 out of the mask range
642%    ICOMB=((indx-1)*nxy(1)+(nxy(1)+1-indy));%determine the indices in the image reshaped in a Matlab vector
643%    Mvalues=M(ICOMB);
644%    flag7e=((Mvalues > 20) & (Mvalues < 200))| ~check_in';
645%    FF=FF==1 |(flag7b|flag7e)';
646% end
647% %    flag7=0;
648% % end   
649%
650
651FF=double(FF);
652%
653% % criterium on velocity values
654% delta_u=Field.U;%default without ref file
655% delta_v=Field.V;
656% if exist('fileref','var') && ~isempty(fileref)
657%     if ~exist(fileref,'file')
658%         error='reference file not found in RUN_FIX.m';
659%         display(error);
660%         return
661%     end
662%     FieldRef=read_civxdata(fileref,[],fieldref);   
663%     if isfield(FieldRef,'FF')
664%         index_true=find(FieldRef.FF==0);
665%         FieldRef.X=FieldRef.X(index_true);
666%         FieldRef.Y=FieldRef.Y(index_true);
667%         FieldRef.U=FieldRef.U(index_true);
668%         FieldRef.V=FieldRef.V(index_true);
669%     end
670%     if ~isfield(FieldRef,'X') || ~isfield(FieldRef,'Y') || ~isfield(FieldRef,'U') || ~isfield(FieldRef,'V')
671%         error='reference file is not a velocity field in RUN_FIX.m '; %bad input file
672%         return
673%     end
674%     if length(FieldRef.X)<=1
675%         errordlg('reference field with one vector or less in RUN_FIX.m')
676%         return
677%     end
678%     vec_U_ref=griddata_uvmat(FieldRef.X,FieldRef.Y,FieldRef.U,Field.X,Field.Y);  %interpolate vectors in the ref field
679%     vec_V_ref=griddata_uvmat(FieldRef.X,FieldRef.Y,FieldRef.V,Field.X,Field.Y);  %interpolate vectors in the ref field to the positions  of the main field     
680%     delta_u=Field.U-vec_U_ref;%take the difference with the interpolated ref field
681%     delta_v=Field.V-vec_V_ref;
682% end
683% thresh_vel_x=thresh_vel;
684% thresh_vel_y=thresh_vel;
685% if isequal(inf_sup,1)
686%     flag5=abs(delta_u)<thresh_vel_x & abs(delta_v)<thresh_vel_y &(flag1~=1)&(flag2~=1)&(flag3~=1)&(flag4~=1);
687% elseif isequal(inf_sup,2)
688%     flag5=(abs(delta_u)>thresh_vel_x | abs(delta_v)>thresh_vel_y) &(flag1~=1)&(flag2~=1)&(flag3~=1)&(flag4~=1);
689% end
690%
691%             % flag7 introduce a grey mask, matrix M
692
693% flagmagenta=flag1|flag2|flag3|flag4|flag5|flag7;
694% fixflag_unit=Field.FF-10*floor(Field.FF/10); %unity term of fix_flag
695
696
697
698%------------------------------------------------------------------------
699% patch function
700function [SubRangx,SubRangy,nbpoints,FF,U_smooth,V_smooth,X_tps,Y_tps,U_tps,V_tps] =patch(X,Y,U,V,Rho,Threshold,SubDomain)
701%subdomain decomposition
702warning off
703U=reshape(U,[],1);
704V=reshape(V,[],1);
705X=reshape(X,[],1);
706Y=reshape(Y,[],1);
707nbvec=numel(X);
708NbSubDomain=ceil(nbvec/SubDomain);
709MinX=min(X);
710MinY=min(Y);
711MaxX=max(X);
712MaxY=max(Y);
713RangX=MaxX-MinX;
714RangY=MaxY-MinY;
715AspectRatio=RangY/RangX;
716NbSubDomainX=max(floor(sqrt(NbSubDomain/AspectRatio)),1);
717NbSubDomainY=max(floor(sqrt(NbSubDomain*AspectRatio)),1);
718NbSubDomain=NbSubDomainX*NbSubDomainY;
719SizX=RangX/NbSubDomainX;%width of subdomains
720SizY=RangY/NbSubDomainY;%height of subdomains
721CentreX=linspace(MinX+SizX/2,MaxX-SizX/2,NbSubDomainX);
722CentreY=linspace(MinY+SizY/2,MaxY-SizY/2,NbSubDomainY);
723[CentreX,CentreY]=meshgrid(CentreX,CentreY);
724CentreY=reshape(CentreY,1,[]);% Y positions of subdomain centres
725CentreX=reshape(CentreX,1,[]);% X positions of subdomain centres
726rho=SizX*SizY*Rho/1000000;%optimum rho increase as the area of the subdomain (division by 10^6 to reach good values with the default GUI input)
727U_tps_sub=zeros(length(X),NbSubDomain);%default spline
728V_tps_sub=zeros(length(X),NbSubDomain);%default spline
729U_smooth=zeros(length(X),1);
730V_smooth=zeros(length(X),1);
731
732nb_select=zeros(length(X),1);
733FF=zeros(length(X),1);
734check_empty=zeros(1,NbSubDomain);
735for isub=1:NbSubDomain
736    SubRangx(isub,:)=[CentreX(isub)-SizX/2 CentreX(isub)+SizX/2];
737    SubRangy(isub,:)=[CentreY(isub)-SizY/2 CentreY(isub)+SizY/2];
738    ind_sel_previous=[];
739    ind_sel=0;
740    while numel(ind_sel)>numel(ind_sel_previous) %increase the subdomain during four iterations at most
741        ind_sel_previous=ind_sel;
742        ind_sel=find(X>SubRangx(isub,1) & X<SubRangx(isub,2) & Y>SubRangy(isub,1) & Y<SubRangy(isub,2));
743        % if no vector in the subdomain, skip the subdomain
744        if isempty(ind_sel)
745            check_empty(isub)=1;   
746            U_tps(1,isub)=0;%define U_tps and V_tps by default
747            V_tps(1,isub)=0;
748            break
749            % if too few selected vectors, increase the subrange for next iteration
750        elseif numel(ind_sel)<SubDomain/4 && ~isequal( ind_sel,ind_sel_previous);
751            SubRangx(isub,1)=SubRangx(isub,1)-SizX/4;
752            SubRangx(isub,2)=SubRangx(isub,2)+SizX/4;
753            SubRangy(isub,1)=SubRangy(isub,1)-SizY/4;
754            SubRangy(isub,2)=SubRangy(isub,2)+SizY/4;
755        else
756            [U_smooth_sub,U_tps_sub]=tps_coeff(X(ind_sel),Y(ind_sel),U(ind_sel),rho);
757            [V_smooth_sub,V_tps_sub]=tps_coeff(X(ind_sel),Y(ind_sel),V(ind_sel),rho);
758            UDiff=U_smooth_sub-U(ind_sel);
759            VDiff=V_smooth_sub-V(ind_sel);
760            NormDiff=UDiff.*UDiff+VDiff.*VDiff;
761            FF(ind_sel)=20*(NormDiff>Threshold);%put FF value to 20 to identify the criterium of elimmination
762            ind_ind_sel=find(FF(ind_sel)==0); % select the indices of ind_sel corresponding to the remaining vectors
763            % no value exceeds threshold, the result is recorded
764            if isequal(numel(ind_ind_sel),numel(ind_sel))
765                U_smooth(ind_sel)=U_smooth(ind_sel)+U_smooth_sub;
766                V_smooth(ind_sel)=V_smooth(ind_sel)+V_smooth_sub;
767                nbpoints(isub)=numel(ind_sel);
768                X_tps(1:nbpoints(isub),isub)=X(ind_sel);
769                Y_tps(1:nbpoints(isub),isub)=Y(ind_sel);
770                U_tps(1:nbpoints(isub)+3,isub)=U_tps_sub;
771                V_tps(1:nbpoints(isub)+3,isub)=V_tps_sub;         
772                nb_select(ind_sel)=nb_select(ind_sel)+1;
773                 display('good')
774                break
775                % too few selected vectors, increase the subrange for next iteration
776            elseif numel(ind_ind_sel)<SubDomain/4 && ~isequal( ind_sel,ind_sel_previous);
777                SubRangx(isub,1)=SubRangx(isub,1)-SizX/4;
778                SubRangx(isub,2)=SubRangx(isub,2)+SizX/4;
779                SubRangy(isub,1)=SubRangy(isub,1)-SizY/4;
780                SubRangy(isub,2)=SubRangy(isub,2)+SizY/4;
781%                 display('fewsmooth')
782                % interpolation-smoothing is done again with the selected vectors
783            else
784                [U_smooth_sub,U_tps_sub]=tps_coeff(X(ind_sel(ind_ind_sel)),Y(ind_sel(ind_ind_sel)),U(ind_sel(ind_ind_sel)),rho);
785                [V_smooth_sub,V_tps_sub]=tps_coeff(X(ind_sel(ind_ind_sel)),Y(ind_sel(ind_ind_sel)),V(ind_sel(ind_ind_sel)),rho);
786                U_smooth(ind_sel(ind_ind_sel))=U_smooth(ind_sel(ind_ind_sel))+U_smooth_sub;
787                V_smooth(ind_sel(ind_ind_sel))=V_smooth(ind_sel(ind_ind_sel))+V_smooth_sub;
788                nbpoints(isub)=numel(ind_ind_sel);
789                X_tps(1:nbpoints(isub),isub)=X(ind_sel(ind_ind_sel));
790                Y_tps(1:nbpoints(isub),isub)=Y(ind_sel(ind_ind_sel));
791                U_tps(1:nbpoints(isub)+3,isub)=U_tps_sub;
792                V_tps(1:nbpoints(isub)+3,isub)=V_tps_sub;
793                nb_select(ind_sel(ind_ind_sel))=nb_select(ind_sel(ind_ind_sel))+1;
794                display('good2')
795                break
796            end
797        end
798    end
799end
800ind_empty=find(check_empty);
801%remove empty subdomains
802if ~isempty(ind_empty)
803    SubRangx(ind_empty,:)=[];
804    SubRangy(ind_empty,:)=[];
805    X_tps(:,ind_empty)=[];
806    Y_tps(:,ind_empty)=[];
807    U_tps(:,ind_empty)=[];
808    V_tps(:,ind_empty)=[];
809end
810nb_select(nb_select==0)=1;%ones(size(find(nb_select==0)));
811U_smooth=U_smooth./nb_select;
812V_smooth=V_smooth./nb_select;
813
814
815
816
817
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