source: trunk/src/series/civ_3D.m @ 1156

Last change on this file since 1156 was 1156, checked in by sommeria, 3 months ago

bugs repaired

File size: 54.9 KB
Line 
1%'civ_3D': 3D PIV from image scan in a volume
2
3%------------------------------------------------------------------------
4% function [Data,errormsg,result_conv]= civ_3D(Param)
5%
6%OUTPUT
7% Data=structure containing the PIV results and information on the processing parameters
8% errormsg=error message char string, decd ..fault=''
9% resul_conv: image inter-correlation function for the last grid point (used for tests)
10%
11%INPUT:
12% Param: Matlab structure of input  parameters
13%     Param contains info of the GUI series using the fct read_GUI.
14%     Param.Action.RUN = 0 (to set the status of the GUI series) or =1 to RUN the computation
15%     Param.InputTable: sets the input file(s)
16%           if absent, the fct looks for input data in Param.ActionInput     (test mode)
17%     Param.OutputSubDir: sets the folder name of output file(s,
18%           if absent no file is produced, result in the output structure Data (test mode)
19%     Param.ActionInput: substructure with the parameters provided by the GUI civ_input
20%                      .Civ1: parameters for civ1cc
21%                      .Fix1: parameters for detect_false1
22%                      .Patch1:
23%                      .Civ2: for civ2
24%                      .Fix2:
25%                      .Patch2:
26
27%=======================================================================
28% Copyright 2008-2024, LEGI UMR 5519 / CNRS UGA G-INP, Grenoble, France
29%   http://www.legi.grenoble-inp.fr
30%   Joel.Sommeria - Joel.Sommeria (A) univ-grenoble-alpes.fr
31%
32%     This file is part of the toolbox UVMAT.
33%
34%     UVMAT is free software; you can redistribute it and/or modify
35%     it under the terms of the GNU General Public License as published
36%     by the Free Software Foundation; either version 2 of the license,
37%     or (at your option) any later version.
38%
39%     UVMAT is distributed in the hope that it will be useful,
40%     but WITHOUT ANY WARRANTY; without even the implied warranty of
41%     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
42%     GNU General Public License (see LICENSE.txt) for more details.
43%=======================================================================
44
45function [Data,errormsg,result_conv]= civ_3D(Param)
46errormsg='';
47
48%% set the input elements needed on the GUI series when the action is selected in the menu ActionName or InputTable refreshed
49if isstruct(Param) && isequal(Param.Action.RUN,0)% function activated from the GUI series but not RUN
50    path_series=fileparts(which('series'));
51    addpath(fullfile(path_series,'series'))
52
53   Data=civ_input(Param)
54
55    Data.Program=mfilename;%gives the name of the current function
56    Data.AllowInputSort='off';% allow alphabetic sorting of the list of input file SubDir (options 'off'/'on', 'off' by default)
57    Data.IndexRange_j='whole';% prescribes the file index ranges j from min to max (options 'off'/'on'/'whole', 'on' by default)
58    Data.NbSlice='off'; %nbre of slices ('off' by default)
59    Data.VelType='off';% menu for selecting the velocity type (options 'off'/'one'/'two',  'off' by default)
60    Data.FieldName='on';% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default)
61    Data.FieldTransform = 'off';%can use a transform function
62    Data.ProjObject='off';%can use projection object(option 'off'/'on',
63    Data.Mask='off';%can use mask option   (option 'off'/'on', 'off' by default)
64    Data.OutputDirExt='.civ_3D';%set the output dir extension
65    Data.OutputSubDirMode='last'; %select the last subDir in the input table as root of the output subdir name (option 'all'/'first'/'last', 'all' by default)
66    Data.OutputFileMode='NbInput_i';% one output file expected per value of i index (used for waitbar)
67    Data.CheckOverwriteVisible='on'; % manage the overwrite of existing files (default=1)
68    if isfield(Data,'ActionInput') && isfield(Data.ActionInput,'PairIndices') && strcmp(Data.ActionInput.PairIndices.ListPairMode,'pair j1-j2')
69        if isfield(Data.ActionInput.PairIndices,'ListPairCiv2')
70            str_civ=Data.ActionInput.PairIndices.ListPairCiv2;
71        else
72            str_civ=Data.ActionInput.PairIndices.ListPairCiv1;
73        end
74        r=regexp(str_civ,'^j= (?<num1>[a-z])-(?<num2>[a-z])','names');
75        if isempty(r)
76            r=regexp(str_civ,'^j= (?<num1>[A-Z])-(?<num2>[A-Z])','names');
77            if isempty(r)
78                r=regexp(str_civ,'^j= (?<num1>\d+)-(?<num2>\d+)','names');
79            end
80        end
81        if ~isempty(r)
82            Data.j_index_1=stra2num(r.num1);
83            Data.j_index_2=stra2num(r.num2);
84        end
85    end
86
87
88    return
89end
90%% END OF ENTERING INPUT PARAMETER MODE
91
92%% RUN MODE: read input parameters from an xml file if input is a file name (batch mode)
93if ischar(Param)
94    Param=xml2struct(Param);% read Param as input file (batch case)
95    checkrun=0;
96    RUNHandle=[];
97else
98    hseries=findobj(allchild(0),'Tag','series');
99    RUNHandle=findobj(hseries,'Tag','RUN');%handle of RUN button in GUI series
100    WaitbarHandle=findobj(hseries,'Tag','Waitbar');%handle of waitbar in GUI series
101    checkrun=1;
102end
103
104%% test input Param
105if ~isfield(Param,'InputTable')
106    disp('ERROR: no input file entered')
107    return
108end
109if ~isfield(Param,'ActionInput')
110    disp_uvmat('ERROR','no parameter set for PIV',checkrun)
111    return
112end
113iview_A=0;%default values
114
115if isfield(Param,'OutputSubDir')&& isfield(Param,'OutputDirExt')
116    OutputDir=[Param.OutputSubDir Param.OutputDirExt];
117     OutputPath=fullfile(Param.OutputPath,num2str(Param.Experiment),num2str(Param.Device));
118else
119    disp_uvmat('ERROR','no output folder defined',checkrun)
120    return
121end
122
123%% input files and indexing
124MaxIndex_i=Param.IndexRange.MaxIndex_i;
125MinIndex_i=Param.IndexRange.MinIndex_i;
126MaxIndex_j=ones(size(MaxIndex_i));MinIndex_j=ones(size(MinIndex_i));
127if isfield(Param.IndexRange,'MaxIndex_j')&& isfield(Param.IndexRange,'MinIndex_j')
128    MaxIndex_j=Param.IndexRange.MaxIndex_j;
129    MinIndex_j=Param.IndexRange.MinIndex_j;
130end
131
132[tild,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param);
133iview_A=0;% series index (iview) for the first image series
134iview_B=0;% series index (iview) for the second image series (only non zero for option 'shift' comparing two image series )
135if Param.ActionInput.CheckCiv1
136    iview_A=1;% usual PIV, the image series is on the first line of the table
137elseif Param.ActionInput.CheckCiv2 % civ2 is performed without Civ1, a netcdf file series is needed in the first table line
138    iview_A=2;% the second line is used for the input images of Civ2
139end
140if iview_A~=0
141    RootPath_A=Param.InputTable{iview_A,1};
142    RootFile_A=Param.InputTable{iview_A,3};
143    SubDir_A=Param.InputTable{iview_A,2};
144    NomType_A=Param.InputTable{iview_A,4};
145    FileExt_A=Param.InputTable{iview_A,5};
146    if iview_B==0
147        iview_B=iview_A;% the second image series is the same as the first
148    end
149    RootPath_B=Param.InputTable{iview_B,1};
150    RootFile_B=Param.InputTable{iview_B,3};
151    SubDir_B=Param.InputTable{iview_B,2};
152    NomType_B=Param.InputTable{iview_B,4};
153    FileExt_B=Param.InputTable{iview_B,5};
154end
155
156PairCiv1=Param.ActionInput.PairIndices.ListPairCiv1;
157
158[i1_series_Civ1,i2_series_Civ1,j1_series_Civ1,j2_series_Civ1,check_bounds,NomTypeNc]=...
159                        find_pair_indices(PairCiv1,i1_series{1},j1_series{1},MinIndex_i,MaxIndex_i,MinIndex_j,MaxIndex_j);
160                   
161if isempty(i1_series_Civ1)
162    disp_uvmat('ERROR','no image pair for civ in the input file index range',checkrun)
163    return
164end
165NbField_i=size(i1_series_Civ1,2);
166NbSlice=size(i1_series_Civ1,1);
167
168%% prepare output Data
169ListGlobalAttribute={'Conventions','Program','CivStage'};
170Data.Conventions='uvmat/civdata';% states the conventions used for the description of field variables and attributes
171Data.Program='civ_series';
172Data.CivStage=0;%default
173list_param=(fieldnames(Param.ActionInput.Civ1))';
174    list_param(strcmp('TestCiv1',list_param))=[];% remove the parameter TestCiv1 from the list
175    Civ1_param=regexprep(list_param,'^.+','Civ1_$0');% insert 'Civ1_' before  each string in list_param
176    Civ1_param=[{'Civ1_ImageA','Civ1_ImageB','Civ1_Time','Civ1_Dt'} Civ1_param]; %insert the names of the two input images
177Data.ListGlobalAttribute=[ListGlobalAttribute Civ1_param];
178            % set the list of variables
179        Data.ListVarName={'Civ1_X','Civ1_Y','Civ1_U','Civ1_V','Civ1_W','Civ1_C','Civ1_FF'};%  cell array containing the names of the fields to record
180        Data.VarDimName={'nb_vec_1','nb_vec_1','nb_vec_1','nb_vec_1','nb_vec_1','nb_vec_1','nb_vec_1'};
181        Data.VarAttribute{1}.Role='coord_x';
182        Data.VarAttribute{2}.Role='coord_y';
183        Data.VarAttribute{3}.Role='vector_x';
184        Data.VarAttribute{4}.Role='vector_y';
185        Data.VarAttribute{5}.Role='vector_z';
186        Data.VarAttribute{6}.Role='ancillary';
187        Data.VarAttribute{7}.Role='errorflag';
188
189%% get timing from the ImaDoc file or input video
190if iview_A~=0
191    XmlFileName=find_imadoc(RootPath_A,SubDir_A);
192    Time=[];
193    if ~isempty(XmlFileName)
194        XmlData=imadoc2struct(XmlFileName);
195        if isfield(XmlData,'Time')
196            Time=XmlData.Time;
197        end
198        if isfield(XmlData,'Camera')
199            if isfield(XmlData.Camera,'NbSlice')&& ~isempty(XmlData.Camera.NbSlice)
200                NbSlice_calib{iview}=XmlData.Camera.NbSlice;% Nbre of slices for Zindex in phys transform
201                if ~isequal(NbSlice_calib{iview},NbSlice_calib{1})
202                    msgbox_uvmat('WARNING','inconsistent number of Z indices for the two field series');
203                end
204            end
205            if isfield(XmlData.Camera,'TimeUnit')&& ~isempty(XmlData.Camera.TimeUnit)
206                TimeUnit=XmlData.Camera.TimeUnit;
207            end
208        end
209    end
210end
211
212maskoldname='';% initiate the mask name
213FileType_A='';
214FileType_B='';
215CheckOverwrite=1;%default
216if isfield(Param,'CheckOverwrite')
217    CheckOverwrite=Param.CheckOverwrite;
218end
219   Data.Civ1_ImageA=fullfile_uvmat(RootPath_A,SubDir_A,RootFile_A,FileExt_A,NomType_A,i1_series_Civ1(1),[],j1_series_Civ1(1,1));
220   Data.Civ1_ImageB=fullfile_uvmat(RootPath_B,SubDir_B,RootFile_B,FileExt_B,NomType_B,i1_series_Civ1(1),[],j2_series_Civ1(1,1));
221    FileInfo=get_file_info(Data.Civ1_ImageA);
222        par_civ1=Param.ActionInput.Civ1;% parameters for civ1
223    par_civ1.ImageHeight=FileInfo.Height;npy=FileInfo.Height;
224    par_civ1.ImageWidth=FileInfo.Width;npx=FileInfo.Width;
225SearchRange_z=floor(Param.ActionInput.Civ1.SearchBoxSize(3)/2);
226    par_civ1.Dz=Param.ActionInput.Civ1.Dz;
227    par_civ1.ImageA=zeros(2*SearchRange_z+1,npy,npx);
228par_civ1.ImageB=zeros(2*SearchRange_z+1,npy,npx);
229
230%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
231%%%%% MAIN LOOP %%%%%%
232%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
233for ifield=1:NbField_i
234    tstart=tic;
235    time_civ1=0;
236    time_patch1=0;
237    time_civ2=0;
238    time_patch2=0;
239    if checkrun% update the waitbar in interactive mode with GUI series  (checkrun=1)
240        update_waitbar(WaitbarHandle,ifield/NbField_i)
241        if  checkrun && ~strcmp(get(RUNHandle,'BusyAction'),'queue')
242            disp('program stopped by user')
243            break
244        end
245    end
246   
247    %indicate the values of all the global attributes in the output data
248    i1=i1_series_Civ1(ifield);
249    i2=i1;
250    if ~isempty(i2_series_Civ1)
251        i2=i2_series_Civ1(ifield);
252    end
253    j1=1;
254    if ~isempty(j1_series_Civ1)
255        j1=j1_series_Civ1(ifield);
256    end
257    j2=j1;
258    if ~isempty(j2_series_Civ1)
259        j2=j2_series_Civ1(ifield);
260    end
261
262    Data.Civ1_Time=(Time(i2+1,j2+1)+Time(i1+1,j1+1))/2;% the Time is the Time at the middle of the image pair
263    Data.Civ1_Dt=Time(i2+1,j2+1)-Time(i1+1,j1+1);
264
265    for ilist=1:length(list_param)
266        Data.(Civ1_param{4+ilist})=Param.ActionInput.Civ1.(list_param{ilist});
267    end
268   
269    Data.CivStage=1;
270    % output nc file
271    ncfile_out=fullfile_uvmat(OutputPath,Param.InputTable{1,2},Param.InputTable{1,3},Param.InputTable{1,5},...
272        NomTypeNc,i1_series_Civ1(ifield),i2_series_Civ1(ifield),j1_series_Civ1(ifield),j2_series_Civ1(ifield));
273
274    if ~CheckOverwrite && exist(ncfile_out,'file')
275        disp(['existing output file ' ncfile_out ' already exists, skip to next field'])
276        continue% skip iteration if the mode overwrite is desactivated and the result file already exists
277    end
278
279
280    %% Civ1
281    % if Civ1 computation is requested
282    if isfield (Param.ActionInput,'Civ1')
283
284        disp('civ1 started')
285
286
287        % read input images (except in mode Test where it is introduced directly in Param.ActionInput.Civ1.ImageNameA and B)
288
289        par_civ1.ImageA=zeros(2*SearchRange_z+1,npy,npx);
290        par_civ1.ImageB=zeros(2*SearchRange_z+1,npy,npx);
291        %first vertical block centered at image index islice=par_civ1.Dz
292        islice=par_civ1.Dz;
293         for iz=1:par_civ1.Dz+SearchRange_z
294              ImageName_A=fullfile_uvmat(RootPath_A,SubDir_A,RootFile_A,FileExt_A,NomType_A,i1_series_Civ1(1,ifield),[],j1_series_Civ1(iz,1));%
295            A= read_image(ImageName_A,FileType_A);
296            ImageName_B=fullfile_uvmat(RootPath_B,SubDir_B,RootFile_B,FileExt_B,NomType_B,i2_series_Civ1(1,ifield),[],j1_series_Civ1(iz,1));
297            B= read_image(ImageName_B,FileType_B);
298            par_civ1.ImageA(iz+par_civ1.Dz-1,:,:) = A;
299            par_civ1.ImageB(iz+par_civ1.Dz-1,:,:) = B;
300         end
301         % caluclate velocity data (y and v in indices, reverse to y component)
302            [Data.Civ1_X(islice,:,:),Data.Civ1_Y(islice,:,:), utable, vtable,wtable, ctable, FF, result_conv, errormsg] = civ3D (par_civ1);
303            if ~isempty(errormsg)
304                disp_uvmat('ERROR',errormsg,checkrun)
305                return
306            end
307        for islice=2*par_civ1.Dz:NbSlice% loop on slices for the first image in the pair
308            par_civ1.ImageA=circshift(par_civ1.ImageA,-par_civ1.Dz);%shift the indces in the block upward by par_civ1.Dz
309            par_civ1.ImageB=circshift(par_civ1.ImageA,-par_civ1.Dz);
310              for iz=1:par_civ1.Dz
311            ImageName_A=fullfile_uvmat(RootPath_A,SubDir_A,RootFile_A,FileExt_A,NomType_A,i1_series_Civ1(1,ifield),[],j1_series_Civ1(islice+SearchRange_z-par_civ1.Dz+iz,1));%
312            A= read_image(ImageName_A,FileType_A);
313            ImageName_B=fullfile_uvmat(RootPath_B,SubDir_B,RootFile_B,FileExt_B,NomType_B,i2_series_Civ1(1,ifield),[],j1_series_Civ1(islice+SearchRange_z-par_civ1.Dz+iz,1));
314            B= read_image(ImageName_B,FileType_B);
315            par_civ1.ImageA(2*SearchRange_z+1-par_civ1.Dz+iz,:,:) = A;
316            par_civ1.ImageB(2*SearchRange_z+1-par_civ1.Dz+iz,:,:) = B;
317            end
318            % caluclate velocity data (y and v in indices, reverse to y component)
319            [Data.Civ1_X(islice,:,:),Data.Civ1_Y(islice,:,:), utable, vtable,wtable, ctable, FF, result_conv, errormsg] = civ3D (par_civ1);
320            if ~isempty(errormsg)
321                disp_uvmat('ERROR',errormsg,checkrun)
322                return
323            end
324
325        end
326        % case of mask TO ADAPT
327        if par_civ1.CheckMask&&~isempty(par_civ1.Mask)
328            if isfield(par_civ1,'NbSlice')
329                [RootPath_mask,SubDir_mask,RootFile_mask,i1_mask,i2_mask,j1_mask,j2_mask,Ext_mask]=fileparts_uvmat(Param.ActionInput.Civ1.Mask);
330                i1_mask=mod(i1-1,par_civ1.NbSlice)+1;
331                maskname=fullfile_uvmat(RootPath_mask,SubDir_mask,RootFile_mask,Ext_mask,'_1',i1_mask);
332            else
333                maskname=Param.ActionInput.Civ1.Mask;
334            end
335            if strcmp(maskoldname,maskname)% mask exist, not already read in civ1
336                par_civ1.Mask=mask; %use mask already opened
337            else
338                if ~isempty(regexp(maskname,'(^http://)|(^https://)'))|| exist(maskname,'file')
339                    try
340                        par_civ1.Mask=imread(maskname);%update the mask, an store it for future use
341                    catch ME
342                        if ~isempty(ME.message)
343                            errormsg=['error reading input image: ' ME.message];
344                            disp_uvmat('ERROR',errormsg,checkrun)
345                            return
346                        end
347                    end
348                else
349                    par_civ1.Mask=[];
350                end
351                mask=par_civ1.Mask;
352                maskoldname=maskname;
353            end
354        end
355        % Data.ListVarName=[Data.ListVarName 'Civ1_Z'];
356        % Data.Civ1_X=[];Data.Civ1_Y=[];Data.Civ1_Z=[];
357        % Data.Civ1_U=[];Data.Civ1_V=[];Data.Civ1_C=[];
358        %
359        %
360        % Data.Civ1_X=[Data.Civ1_X reshape(xtable,[],1)];
361        % Data.Civ1_Y=[Data.Civ1_Y reshape(Param.Civ1.ImageHeight-ytable+1,[],1)];
362        % Data.Civ1_Z=[Data.Civ1_Z ivol*ones(numel(xtable),1)];% z=image index in image coordinates
363        % Data.Civ1_U=[Data.Civ1_U reshape(utable,[],1)];
364        % Data.Civ1_V=[Data.Civ1_V reshape(-vtable,[],1)];
365        % Data.Civ1_C=[Data.Civ1_C reshape(ctable,[],1)];
366        % Data.Civ1_FF=[Data.Civ1_FF reshape(F,[],1)];
367
368    end
369
370    %% Fix1
371    if isfield (Param.ActionInput,'Fix1')
372        disp('detect_false1 started')
373        if ~isfield (Param.ActionInput,'Civ1')% if we use existing Civ1, remove previous data beyond Civ1
374            Fix1_attr=find(strcmp('Fix1',Data.ListGlobalAttribute));
375            Data.ListGlobalAttribute(Fix1_attr)=[];
376            for ilist=1:numel(Fix1_attr)
377                Data=rmfield(Data,Data.ListGlobalAttribute{Fix1_attr(ilist)});
378            end
379        end
380        list_param=fieldnames(Param.ActionInput.Fix1)';
381        Fix1_param=regexprep(list_param,'^.+','Fix1_$0');% insert 'Fix1_' before  each string in ListFixParam
382        %indicate the values of all the global attributes in the output data
383        for ilist=1:length(list_param)
384            Data.(Fix1_param{ilist})=Param.ActionInput.Fix1.(list_param{ilist});
385        end
386        Data.ListGlobalAttribute=[Data.ListGlobalAttribute Fix1_param];
387        Data.Civ1_FF=uint8(detect_false(Param.ActionInput.Fix1,Data.Civ1_C,Data.Civ1_U,Data.Civ1_V,Data.Civ1_FF));
388        Data.CivStage=2;
389    end
390    %% Patch1
391    if isfield (Param.ActionInput,'Patch1')
392        disp('patch1 started')
393        tstart_patch1=tic;
394
395        % record the processing parameters of Patch1 as global attributes in the result nc file
396        list_param=fieldnames(Param.ActionInput.Patch1)';
397        list_param(strcmp('TestPatch1',list_param))=[];% remove 'TestPatch1' from the list of parameters
398        Patch1_param=regexprep(list_param,'^.+','Patch1_$0');% insert 'Patch1_' before  each parameter name
399        for ilist=1:length(list_param)
400            Data.(Patch1_param{ilist})=Param.ActionInput.Patch1.(list_param{ilist});
401        end
402        Data.CivStage=3;% record the new state of processing
403        Data.ListGlobalAttribute=[Data.ListGlobalAttribute Patch1_param];
404
405        % list the variables to record
406        nbvar=length(Data.ListVarName);
407        Data.ListVarName=[Data.ListVarName {'Civ1_U_smooth','Civ1_V_smooth','Civ1_SubRange','Civ1_NbCentres','Civ1_Coord_tps','Civ1_U_tps','Civ1_V_tps'}];
408        Data.VarDimName=[Data.VarDimName {'nb_vec_1','nb_vec_1',{'nb_coord','nb_bounds','nb_subdomain_1'},'nb_subdomain_1',...
409            {'nb_tps_1','nb_coord','nb_subdomain_1'},{'nb_tps_1','nb_subdomain_1'},{'nb_tps_1','nb_subdomain_1'}}];
410        Data.VarAttribute{nbvar+1}.Role='vector_x';
411        Data.VarAttribute{nbvar+2}.Role='vector_y';
412        Data.VarAttribute{nbvar+5}.Role='coord_tps';
413        Data.VarAttribute{nbvar+6}.Role='vector_x';
414        Data.VarAttribute{nbvar+7}.Role='vector_y';
415        Data.Civ1_U_smooth=Data.Civ1_U; % zeros(size(Data.Civ1_X));
416        Data.Civ1_V_smooth=Data.Civ1_V; %zeros(size(Data.Civ1_X));
417        if isfield(Data,'Civ1_FF')
418            ind_good=find(Data.Civ1_FF==0);
419        else
420            ind_good=1:numel(Data.Civ1_X);
421        end
422        if isempty(ind_good)
423            disp_uvmat('ERROR','all vectors of civ1 are bad, check input parameters' ,checkrun)
424            return
425        end
426
427        % perform Patch calculation using the UVMAT fct 'filter_tps'
428
429        [Data.Civ1_SubRange,Data.Civ1_NbCentres,Data.Civ1_Coord_tps,Data.Civ1_U_tps,Data.Civ1_V_tps,tild,Ures, Vres,tild,FFres]=...
430            filter_tps([Data.Civ1_X(ind_good) Data.Civ1_Y(ind_good)],Data.Civ1_U(ind_good),Data.Civ1_V(ind_good),[],Data.Patch1_SubDomainSize,Data.Patch1_FieldSmooth,Data.Patch1_MaxDiff);
431        Data.Civ1_U_smooth(ind_good)=Ures;% take the interpolated (smoothed) velocity values for good vectors, keep civ1 data for the other
432        Data.Civ1_V_smooth(ind_good)=Vres;
433        Data.Civ1_FF(ind_good)=uint8(FFres);
434        time_patch1=toc(tstart_patch1);
435        disp('patch1 performed')
436    end
437
438    %% Civ2
439    if isfield (Param.ActionInput,'Civ2')
440        disp('civ2 started')
441        tstart_civ2=tic;
442        par_civ2=Param.ActionInput.Civ2;
443        % read input images
444        par_civ2.ImageA=[];
445        par_civ2.ImageB=[];
446        if strcmp(Param.ActionInput.ListCompareMode,'displacement')
447            ImageName_A_Civ2=Param.ActionInput.RefFile;
448        else
449            ImageName_A_Civ2=fullfile_uvmat(RootPath_A,SubDir_A,RootFile_A,FileExt_A,NomType_A,i1_civ2,[],j1_civ2);
450        end
451        if strcmp(ImageName_A_Civ2,ImageName_A) && isequal(FrameIndex_A_Civ1(ifield),FrameIndex_A_Civ2(ifield))
452            par_civ2.ImageA=par_civ1.ImageA;
453        else
454            [par_civ2.ImageA,VideoObject_A] = read_image(ImageName_A_Civ2,FileType_A,VideoObject_A,FrameIndex_A_Civ2(ifield));
455        end
456        ImageName_B_Civ2=fullfile_uvmat(RootPath_B,SubDir_B,RootFile_B,FileExt_B,NomType_B,i2_civ2,[],j2_civ2);
457        if strcmp(ImageName_B_Civ2,ImageName_B) && isequal(FrameIndex_B_Civ1(ifield),FrameIndex_B_Civ2)
458            par_civ2.ImageB=par_civ1.ImageB;
459        else
460            [par_civ2.ImageB,VideoObject_B] = read_image(ImageName_B_Civ2,FileType_B,VideoObject_B,FrameIndex_B_Civ2(ifield));
461        end
462        [FileInfo_A,VideoObject_A]=get_file_info(ImageName_A_Civ2);
463        par_civ2.ImageWidth=FileInfo_A.Width;
464        par_civ2.ImageHeight=FileInfo_A.Height;
465        if isfield(par_civ2,'Grid')% grid points set as input file
466            if ischar(par_civ2.Grid)%read the grid file if the input is a file name
467                par_civ2.Grid=dlmread(par_civ2.Grid);
468                par_civ2.Grid(1,:)=[];%the first line must be removed (heading in the grid file)
469            end
470        else% automatic grid
471            minix=floor(par_civ2.Dx/2)-0.5;
472            maxix=minix+par_civ2.Dx*floor((par_civ2.ImageWidth-1)/par_civ2.Dx);
473            miniy=floor(par_civ2.Dy/2)-0.5;
474            maxiy=minix+par_civ2.Dy*floor((par_civ2.ImageHeight-1)/par_civ2.Dy);
475            [GridX,GridY]=meshgrid(minix:par_civ2.Dx:maxix,miniy:par_civ2.Dy:maxiy);
476            par_civ2.Grid(:,1)=reshape(GridX,[],1);
477            par_civ2.Grid(:,2)=reshape(GridY,[],1);
478        end
479        % end
480
481        % get the guess from patch1 or patch2 (case 'CheckCiv3')
482
483        if isfield (par_civ2,'CheckCiv3') && par_civ2.CheckCiv3 %get the guess from  patch2
484            SubRange= Data.Civ2_SubRange;
485            NbCentres=Data.Civ2_NbCentres;
486            Coord_tps=Data.Civ2_Coord_tps;
487            U_tps=Data.Civ2_U_tps;
488            V_tps=Data.Civ2_V_tps;
489            CivStage=Data.CivStage;%store the current CivStage
490            Civ1_Dt=Data.Civ2_Dt;
491            Data=[];%reinitialise the result structure Data
492            Data.ListGlobalAttribute={'Conventions','Program','CivStage'};
493            Data.Conventions='uvmat/civdata';% states the conventions used for the description of field variables and attributes
494            Data.Program='civ_series';
495            Data.CivStage=CivStage+1;%update the current civStage after reinitialisation of Data
496            Data.ListVarName={};
497            Data.VarDimName={};
498        else % get the guess from patch1
499            SubRange= Data.Civ1_SubRange;
500            NbCentres=Data.Civ1_NbCentres;
501            Coord_tps=Data.Civ1_Coord_tps;
502            U_tps=Data.Civ1_U_tps;
503            V_tps=Data.Civ1_V_tps;
504            Civ1_Dt=Data.Civ1_Dt;
505            Data.CivStage=4;
506        end
507        % else
508        %     SubRange= par_civ2.Civ1_SubRange;
509        %     NbCentres=par_civ2.Civ1_NbCentres;
510        %     Coord_tps=par_civ2.Civ1_Coord_tps;
511        %     U_tps=par_civ2.Civ1_U_tps;
512        %     V_tps=par_civ2.Civ1_V_tps;
513        %     Civ1_Dt=par_civ2.Civ1_Dt;
514        %     Civ2_Dt=par_civ2.Civ1_Dt;
515        %     Data.ListVarName={};
516        %     Data.VarDimName={};
517        % end
518        Shiftx=zeros(size(par_civ2.Grid,1),1);% shift expected from civ1 data
519        Shifty=zeros(size(par_civ2.Grid,1),1);
520        nbval=zeros(size(par_civ2.Grid,1),1);% nbre of interpolated values at each grid point (from the different patch subdomains)
521        if par_civ2.CheckDeformation
522            DUDX=zeros(size(par_civ2.Grid,1),1);
523            DUDY=zeros(size(par_civ2.Grid,1),1);
524            DVDX=zeros(size(par_civ2.Grid,1),1);
525            DVDY=zeros(size(par_civ2.Grid,1),1);
526        end
527        NbSubDomain=size(SubRange,3);
528        for isub=1:NbSubDomain% for each sub-domain of Patch1
529            nbvec_sub=NbCentres(isub);% nbre of Civ vectors in the subdomain
530            ind_sel=find(par_civ2.Grid(:,1)>=SubRange(1,1,isub) & par_civ2.Grid(:,1)<=SubRange(1,2,isub) &...
531                par_civ2.Grid(:,2)>=SubRange(2,1,isub) & par_civ2.Grid(:,2)<=SubRange(2,2,isub));% grid points in the subdomain
532            if ~isempty(ind_sel)
533                epoints = par_civ2.Grid(ind_sel,:);% coordinates of interpolation sites (measurement grids)
534                ctrs=Coord_tps(1:nbvec_sub,:,isub) ;%(=initial points) ctrs
535                nbval(ind_sel)=nbval(ind_sel)+1;% records the number of values for each interpolation point (in case of subdomain overlap)
536                EM = tps_eval(epoints,ctrs);% thin plate spline (tps) coefficient
537                Shiftx(ind_sel)=Shiftx(ind_sel)+EM*U_tps(1:nbvec_sub+3,isub);%velocity shift estimated by tps from civ1
538                Shifty(ind_sel)=Shifty(ind_sel)+EM*V_tps(1:nbvec_sub+3,isub);
539                if par_civ2.CheckDeformation
540                    [EMDX,EMDY] = tps_eval_dxy(epoints,ctrs);%2D matrix of distances between extrapolation points epoints and spline centres (=site points) ctrs
541                    DUDX(ind_sel)=DUDX(ind_sel)+EMDX*U_tps(1:nbvec_sub+3,isub);
542                    DUDY(ind_sel)=DUDY(ind_sel)+EMDY*U_tps(1:nbvec_sub+3,isub);
543                    DVDX(ind_sel)=DVDX(ind_sel)+EMDX*V_tps(1:nbvec_sub+3,isub);
544                    DVDY(ind_sel)=DVDY(ind_sel)+EMDY*V_tps(1:nbvec_sub+3,isub);
545                end
546            end
547        end
548        if par_civ2.CheckMask&&~isempty(par_civ2.Mask)
549            if isfield(par_civ2,'NbSlice')
550                [RootPath_mask,SubDir_mask,RootFile_mask,i1_mask,i2_mask,j1_mask,j2_mask,Ext_mask]=fileparts_uvmat(Param.ActionInput.Civ2.Mask);
551                i1_mask=mod(i1-1,par_civ2.NbSlice)+1;
552                maskname=fullfile_uvmat(RootPath_mask,SubDir_mask,RootFile_mask,Ext_mask,'_1',i1_mask);
553            else
554                maskname=Param.ActionInput.Civ2.Mask;
555            end
556            if strcmp(maskoldname,maskname)% mask exist, not already read in civ1
557                par_civ2.Mask=mask; %use mask already opened
558            else
559                if exist(maskname,'file')
560                    try
561                        par_civ2.Mask=imread(maskname);%update the mask, an store it for future use
562                    catch ME
563                        if ~isempty(ME.message)
564                            errormsg=['error reading input image: ' ME.message];
565                            disp_uvmat('ERROR',errormsg,checkrun)
566                            return
567                        end
568                    end
569                else
570                    par_civ2.Mask=[];
571                end
572                mask=par_civ2.Mask;
573                maskoldname=maskname;
574            end
575        end
576
577
578        if strcmp(Param.ActionInput.ListCompareMode,'displacement')
579            Civ1_Dt=1;
580            Civ2_Dt=1;
581        else
582            Civ2_Dt=Time(i2_civ2+1,j2_civ2+1)-Time(i1_civ2+1,j1_civ2+1);
583        end
584
585        par_civ2.SearchBoxShift=(Civ2_Dt/Civ1_Dt)*[Shiftx(nbval>=1)./nbval(nbval>=1) Shifty(nbval>=1)./nbval(nbval>=1)];
586        % shift the grid points by half the expected shift to provide the correlation box position in image A
587        par_civ2.Grid=[par_civ2.Grid(nbval>=1,1)-par_civ2.SearchBoxShift(:,1)/2 par_civ2.Grid(nbval>=1,2)-par_civ2.SearchBoxShift(:,2)/2];
588        if par_civ2.CheckDeformation
589            par_civ2.DUDX=DUDX(nbval>=1)./nbval(nbval>=1);
590            par_civ2.DUDY=DUDY(nbval>=1)./nbval(nbval>=1);
591            par_civ2.DVDX=DVDX(nbval>=1)./nbval(nbval>=1);
592            par_civ2.DVDY=DVDY(nbval>=1)./nbval(nbval>=1);
593        end
594
595        % calculate velocity data (y and v in image indices, reverse to y component)
596
597        [xtable, ytable, utable, vtable, ctable, F,result_conv,errormsg] = civ (par_civ2);
598
599        list_param=(fieldnames(Param.ActionInput.Civ2))';
600        list_param(strcmp('TestCiv2',list_param))=[];% remove the parameter TestCiv2 from the list
601        Civ2_param=regexprep(list_param,'^.+','Civ2_$0');% insert 'Civ2_' before  each string in list_param
602        Civ2_param=[{'Civ2_ImageA','Civ2_ImageB','Civ2_Time','Civ2_Dt'} Civ2_param]; %insert the names of the two input images
603        %indicate the values of all the global attributes in the output data
604        if exist('ImageName_A','var')
605            Data.Civ2_ImageA=ImageName_A;
606            Data.Civ2_ImageB=ImageName_B;
607            if strcmp(Param.ActionInput.ListCompareMode,'displacement')
608                Data.Civ2_Time=Time(i2_civ2+1,j2_civ2+1);% the Time is the Time of the secodn image
609                Data.Civ2_Dt=1;% Time interval is 1, to yield displacement instead of velocity=displacement/Dt at reading
610            else
611                Data.Civ2_Time=(Time(i2_civ2+1,j2_civ2+1)+Time(i1_civ2+1,j1_civ2+1))/2;
612                Data.Civ2_Dt=Civ2_Dt;
613            end
614        end
615        for ilist=1:length(list_param)
616            Data.(Civ2_param{4+ilist})=Param.ActionInput.Civ2.(list_param{ilist});
617        end
618        Data.ListGlobalAttribute=[Data.ListGlobalAttribute Civ2_param];
619
620        nbvar=numel(Data.ListVarName);
621        % define the Civ2 variable (if Civ2 data are not replaced from previous calculation)
622        if isempty(find(strcmp('Civ2_X',Data.ListVarName),1))
623            Data.ListVarName=[Data.ListVarName {'Civ2_X','Civ2_Y','Civ2_U','Civ2_V','Civ2_C','Civ2_FF'}];%  cell array containing the names of the fields to record
624            Data.VarDimName=[Data.VarDimName {'nb_vec_2','nb_vec_2','nb_vec_2','nb_vec_2','nb_vec_2','nb_vec_2'}];
625            Data.VarAttribute{nbvar+1}.Role='coord_x';
626            Data.VarAttribute{nbvar+2}.Role='coord_y';
627            Data.VarAttribute{nbvar+3}.Role='vector_x';
628            Data.VarAttribute{nbvar+4}.Role='vector_y';
629            Data.VarAttribute{nbvar+5}.Role='ancillary';
630            Data.VarAttribute{nbvar+6}.Role='errorflag';
631        end
632        Data.Civ2_X=reshape(xtable,[],1);
633        Data.Civ2_Y=reshape(size(par_civ2.ImageA,1)-ytable+1,[],1);
634        Data.Civ2_U=reshape(utable,[],1);
635        Data.Civ2_V=reshape(-vtable,[],1);
636        Data.Civ2_C=reshape(ctable,[],1);
637        Data.Civ2_FF=reshape(F,[],1);
638        disp('civ2 performed')
639        time_civ2=toc(tstart_civ2);
640    elseif ~isfield(Data,'ListVarName') % we start there, using existing Civ2 data
641        if exist('ncfile','var')
642            CivFile=ncfile;
643            [Data,tild,tild,errormsg]=nc2struct(CivFile);%read civ1 and detect_false1 data in the existing netcdf file
644            if ~isempty(errormsg)
645                disp_uvmat('ERROR',errormsg,checkrun)
646                return
647            end
648            %         elseif isfield(Param,'Civ2_X')% use Civ2 data as input in Param (test mode)
649            %             Data.ListGlobalAttribute={};
650            %             Data.ListVarName={};
651            %             Data.VarDimName={};
652            %             Data.Civ2_X=Param.Civ2_X;
653            %             Data.Civ2_Y=Param.Civ2_Y;
654            %             Data.Civ2_U=Param.Civ2_U;
655            %             Data.Civ2_V=Param.Civ2_V;
656            %             Data.Civ2_FF=Param.Civ2_FF;
657        end
658    end
659
660    %% Fix2
661    if isfield (Param.ActionInput,'Fix2')
662        disp('detect_false2 started')
663        list_param=fieldnames(Param.ActionInput.Fix2)';
664        Fix2_param=regexprep(list_param,'^.+','Fix2_$0');% insert 'Fix1_' before  each string in ListFixParam
665        %indicate the values of all the global attributes in the output data
666        for ilist=1:length(list_param)
667            Data.(Fix2_param{ilist})=Param.ActionInput.Fix2.(list_param{ilist});
668        end
669        Data.ListGlobalAttribute=[Data.ListGlobalAttribute Fix2_param];
670        Data.Civ2_FF=double(detect_false(Param.ActionInput.Fix2,Data.Civ2_C,Data.Civ2_U,Data.Civ2_V,Data.Civ2_FF));
671        Data.CivStage=Data.CivStage+1;
672    end
673
674    %% Patch2
675    if isfield (Param.ActionInput,'Patch2')
676        disp('patch2 started')
677        tstart_patch2=tic;
678        list_param=fieldnames(Param.ActionInput.Patch2)';
679        list_param(strcmp('TestPatch2',list_param))=[];% remove the parameter TestCiv1 from the list
680        Patch2_param=regexprep(list_param,'^.+','Patch2_$0');% insert 'Fix1_' before  each string in ListFixParam
681        %indicate the values of all the global attributes in the output data
682        for ilist=1:length(list_param)
683            Data.(Patch2_param{ilist})=Param.ActionInput.Patch2.(list_param{ilist});
684        end
685        Data.ListGlobalAttribute=[Data.ListGlobalAttribute Patch2_param];
686
687        nbvar=length(Data.ListVarName);
688        Data.ListVarName=[Data.ListVarName {'Civ2_U_smooth','Civ2_V_smooth','Civ2_SubRange','Civ2_NbCentres','Civ2_Coord_tps','Civ2_U_tps','Civ2_V_tps'}];
689        Data.VarDimName=[Data.VarDimName {'nb_vec_2','nb_vec_2',{'nb_coord','nb_bounds','nb_subdomain_2'},{'nb_subdomain_2'},...
690            {'nb_tps_2','nb_coord','nb_subdomain_2'},{'nb_tps_2','nb_subdomain_2'},{'nb_tps_2','nb_subdomain_2'}}];
691
692        Data.VarAttribute{nbvar+1}.Role='vector_x';
693        Data.VarAttribute{nbvar+2}.Role='vector_y';
694        Data.VarAttribute{nbvar+5}.Role='coord_tps';
695        Data.VarAttribute{nbvar+6}.Role='vector_x';
696        Data.VarAttribute{nbvar+7}.Role='vector_y';
697        Data.Civ2_U_smooth=Data.Civ2_U;
698        Data.Civ2_V_smooth=Data.Civ2_V;
699        if isfield(Data,'Civ2_FF')
700            ind_good=find(Data.Civ2_FF==0);
701        else
702            ind_good=1:numel(Data.Civ2_X);
703        end
704        if isempty(ind_good)
705            disp_uvmat('ERROR','all vectors of civ2 are bad, check input parameters' ,checkrun)
706            return
707        end
708
709        [Data.Civ2_SubRange,Data.Civ2_NbCentres,Data.Civ2_Coord_tps,Data.Civ2_U_tps,Data.Civ2_V_tps,tild,Ures,Vres,tild,FFres]=...
710            filter_tps([Data.Civ2_X(ind_good) Data.Civ2_Y(ind_good)],Data.Civ2_U(ind_good),Data.Civ2_V(ind_good),[],Data.Patch2_SubDomainSize,Data.Patch2_FieldSmooth,Data.Patch2_MaxDiff);
711        Data.Civ2_U_smooth(ind_good)=Ures;
712        Data.Civ2_V_smooth(ind_good)=Vres;
713        Data.Civ2_FF(ind_good)=FFres;
714        Data.CivStage=Data.CivStage+1;
715        time_patch2=toc(tstart_patch2);
716        disp('patch2 performed')
717    end
718
719    %% write result in a netcdf file if requested
720    % if CheckOutputFile
721    errormsg=struct2nc(ncfile_out,Data);
722    if isempty(errormsg)
723        disp([ncfile_out ' written'])
724        %[success,msg] = fileattrib(ncfile_out ,'+w','g');% done in struct2nc
725    else
726        disp(errormsg)
727    end
728    time_total=toc(tstart);
729    disp(['ellapsed time ' num2str(time_total/60,2) ' minutes'])
730    disp(['time image reading ' num2str(time_input,2) ' s'])
731    disp(['time civ1 ' num2str(time_civ1,2) ' s'])
732    disp(['time patch1 ' num2str(time_patch1,2) ' s'])
733    disp(['time civ2 ' num2str(time_civ2,2) ' s'])
734    disp(['time patch2 ' num2str(time_patch2,2) ' s'])
735    disp(['time other ' num2str((time_total-time_input-time_civ1-time_patch1-time_civ2-time_patch2),2) ' s'])
736    % end
737end
738
739
740% 'civ': function piv.m adapted from PIVlab http://pivlab.blogspot.com/
741%--------------------------------------------------------------------------
742% function [xtable ytable utable vtable typevector] = civ (image1,image2,ibx,iby step, subpixfinder, mask, roi)
743%
744% OUTPUT:
745% xtable: set of x coordinates
746% ytable: set of y coordiantes
747% utable: set of u displacements (along x)
748% vtable: set of v displacements (along y)
749% ctable: max image correlation for each vector
750% typevector: set of flags, =1 for good, =0 for NaN vectors
751%
752%INPUT:
753% par_civ: structure of input parameters, with fields:
754%  .ImageA: first image for correlation (matrix)
755%  .ImageB: second image for correlation(matrix)
756%  .CorrBoxSize: 1,2 vector giving the size of the correlation box in x and y
757%  .SearchBoxSize:  1,2 vector giving the size of the search box in x and y
758%  .SearchBoxShift: 1,2 vector or 2 column matrix (for civ2) giving the shift of the search box in x and y
759%  .CorrSmooth: =1 or 2 determines the choice of the sub-pixel determination of the correlation max
760%  .ImageWidth: nb of pixels of the image in x
761%  .Dx, Dy: mesh for the PIV calculation
762%  .Grid: grid giving the PIV calculation points (alternative to .Dx .Dy): centres of the correlation boxes in Image A
763%  .Mask: name of a mask file or mask image matrix itself
764%  .MinIma: thresholds for image luminosity
765%  .MaxIma
766%  .CheckDeformation=1 for subpixel interpolation and image deformation (linear transform)
767%  .DUDX: matrix of deformation obtained from patch at each grid point
768%  .DUDY
769%  .DVDX:
770%  .DVDY
771
772function [xtable,ytable,utable,vtable,wtable,ctable,FF,result_conv,errormsg] = civ3D (par_civ)
773
774%% prepare measurement grid
775
776minix=floor(par_civ.Dx/2)-0.5;
777maxix=minix+par_civ.Dx*floor((par_civ.ImageWidth-1)/par_civ.Dx);
778miniy=floor(par_civ.Dy/2)-0.5;% first automatic grid point at half the mesh Dy
779maxiy=miniy+par_civ.Dy*floor((par_civ.ImageHeight-1)/par_civ.Dy);
780[GridX,GridY]=meshgrid(minix:par_civ.Dx:maxix,miniy:par_civ.Dy:maxiy);
781par_civ.Grid(:,:,1)=GridX;
782par_civ.Grid(:,:,2)=GridY;% increases with array index,
783[nbvec_y,nbvec_x,~]=size(par_civ.Grid);
784%
785%
786% minix=floor(par_civ.Dx/2)-0.5;
787%     maxix=minix+par_civ.Dx*floor((par_civ.ImageWidth-1)/par_civ.Dx);
788%     miniy=floor(par_civ.Dy/2)-0.5;% first automatic grid point at half the mesh Dy
789%     maxiy=miniy+par_civ.Dy*floor((par_civ.ImageHeight-1)/par_civ.Dy);
790%     [GridX,GridY]=meshgrid(minix:par_civ.Dx:maxix,miniy:par_civ.Dy:maxiy);
791%     par_civ.Grid(:,1)=reshape(GridX,[],1);
792%     par_civ.Grid(:,2)=reshape(GridY,[],1);% increases with array index
793
794%% prepare correlation and search boxes
795ibx2=floor(par_civ.CorrBoxSize(1)/2);
796iby2=floor(par_civ.CorrBoxSize(2)/2);
797isx2=floor(par_civ.SearchBoxSize(1)/2);
798isy2=floor(par_civ.SearchBoxSize(2)/2);
799isz2=floor(par_civ.SearchBoxSize(3)/2);
800kref=isz2+1;%middle index of the z slice
801shiftx=round(par_civ.SearchBoxShift(:,1));%use the input shift estimate, rounded to the next integer value
802shifty=-round(par_civ.SearchBoxShift(:,2));% sign minus because image j index increases when y decreases
803if numel(shiftx)==1% case of a unique shift for the whole field( civ1)
804    shiftx=shiftx*ones(nbvec_y,nbvec_x,1);
805    shifty=shifty*ones(nbvec_y,nbvec_x,1);
806end
807
808%% Array initialisation and default output  if par_civ.CorrSmooth=0 (just the grid calculated, no civ computation)
809xtable=round(par_civ.Grid(:,:,1)+0.5)-0.5;
810ytable=round(par_civ.ImageHeight-par_civ.Grid(:,:,2)+0.5)-0.5;% y index corresponding to the position in image coordiantes
811utable=shiftx;%zeros(nbvec,1);
812vtable=shifty;%zeros(nbvec,1);
813wtable=zeros(size(utable));
814ctable=zeros(nbvec_y,nbvec_x,1);
815FF=zeros(nbvec_y,nbvec_x,1);
816result_conv=[];
817errormsg='';
818
819%% prepare mask
820check_MinIma=isfield(par_civ,'MinIma');% test for image luminosity threshold
821check_MaxIma=isfield(par_civ,'MaxIma') && ~isempty(par_civ.MaxIma);
822
823[npz,npy_ima,npx_ima]=size(par_civ.ImageA);
824if ~isequal(size(par_civ.ImageB),[npz npy_ima npx_ima])
825    errormsg='image pair with unequal size';
826    return
827end
828
829%% Apply mask
830% Convention for mask, IDEAS NOT IMPLEMENTED
831% mask >200 : velocity calculated
832%  200 >=mask>150;velocity not calculated, interpolation allowed (bad spots)
833% 150>=mask >100: velocity not calculated, nor interpolated
834%  100>=mask> 20: velocity not calculated, impermeable (no flux through mask boundaries)
835%  20>=mask: velocity=0
836checkmask=0;
837MinA=min(min(min(par_civ.ImageA)));
838%MinB=min(min(par_civ.ImageB));
839%check_undefined=false(size(par_civ.ImageA));
840if isfield(par_civ,'Mask') && ~isempty(par_civ.Mask)
841    checkmask=1;
842    if ~isequal(size(par_civ.Mask),[npy_ima npx_ima])
843        errormsg='mask must be an image with the same size as the images';
844        return
845    end
846    check_undefined=(par_civ.Mask<200 & par_civ.Mask>=20 );
847end
848
849%% compute image correlations: MAINLOOP on velocity vectors
850corrmax=0;
851sum_square=1;% default
852mesh=1;% default
853CheckDeformation=isfield(par_civ,'CheckDeformation')&& par_civ.CheckDeformation==1;
854if CheckDeformation
855    mesh=0.25;%mesh in pixels for subpixel image interpolation (x 4 in each direction)
856    par_civ.CorrSmooth=2;% use SUBPIX2DGAUSS (take into account more points near the max)
857end
858
859if par_civ.CorrSmooth~=0 % par_civ.CorrSmooth=0 implies no civ computation (just input image and grid points given)
860    for ivec_x=1:nbvec_x
861        for ivec_y=1:nbvec_y
862            ivec_y
863            iref=round(par_civ.Grid(ivec_y,ivec_x,1)+0.5)% xindex on the image A for the middle of the correlation box
864            jref=round(par_civ.ImageHeight-par_civ.Grid(ivec_y,ivec_x,2)+0.5)%  j index  for the middle of the correlation box in the image A
865            subrange1_x=iref-ibx2:iref+ibx2;% x indices defining the first subimage
866            subrange1_y=jref-iby2:jref+iby2;% y indices defining the first subimage
867            subrange2_x=iref+shiftx(ivec_y,ivec_x)-isx2:iref+shiftx(ivec_y,ivec_x)+isx2;%x indices defining the second subimage
868            subrange2_y=jref+shifty(ivec_y,ivec_x)-isy2:jref+shifty(ivec_y,ivec_x)+isy2;%y indices defining the second subimage
869            image1_crop=MinA*ones(npz,numel(subrange1_y),numel(subrange1_x));% default value=min of image A
870            image2_crop=MinA*ones(npz,numel(subrange2_y),numel(subrange2_x));% default value=min of image A
871            check1_x=subrange1_x>=1 & subrange1_x<=par_civ.ImageWidth;% check which points in the subimage 1 are contained in the initial image 1
872            check1_y=subrange1_y>=1 & subrange1_y<=par_civ.ImageHeight;
873            check2_x=subrange2_x>=1 & subrange2_x<=par_civ.ImageWidth;% check which points in the subimage 2 are contained in the initial image 2
874            check2_y=subrange2_y>=1 & subrange2_y<=par_civ.ImageHeight;
875            image1_crop(:,check1_y,check1_x)=par_civ.ImageA(:,subrange1_y(check1_y),subrange1_x(check1_x));%extract a subimage (correlation box) from image A
876            image2_crop(:,check2_y,check2_x)=par_civ.ImageB(:,subrange2_y(check2_y),subrange2_x(check2_x));%extract a larger subimage (search box) from image B
877            if checkmask
878                mask1_crop=ones(numel(subrange1_y),numel(subrange1_x));% default value=1 for mask
879                mask2_crop=ones(numel(subrange2_y),numel(subrange2_x));% default value=1 for mask
880                mask1_crop(check1_y,check1_x)=check_undefined(subrange1_y(check1_y),subrange1_x(check1_x));%extract a mask subimage (correlation box) from image A
881                mask2_crop(check2_y,check2_x)=check_undefined(subrange2_y(check2_y),subrange2_x(check2_x));%extract a mask subimage (search box) from image B
882                sizemask=sum(sum(mask1_crop))/(numel(subrange1_y)*numel(subrange1_x));%size of the masked part relative to the correlation sub-image
883                if sizemask > 1/2% eliminate point if more than half of the correlation box is masked
884                    FF(ivec_y,ivec_x)=1; %
885                    utable(ivec_y,ivec_x)=NaN;
886                    vtable(ivec_y,ivec_x)=NaN;
887                else
888                    FF(ivec_y,ivec_x)=0;
889                    image1_crop=image1_crop.*~mask1_crop;% put to zero the masked pixels (mask1_crop='true'=1)
890                    image2_crop=image2_crop.*~mask2_crop;
891                    image1_mean=mean(mean(image1_crop))/(1-sizemask);
892                    image2_mean=mean(mean(image2_crop))/(1-sizemask);
893                end
894            else
895                image1_mean=mean(mean(image1_crop));
896                image2_mean=mean(mean(image2_crop));
897            end
898            %threshold on image minimum
899            if FF(ivec_y,ivec_x)==0
900                if check_MinIma && (image1_mean < par_civ.MinIma || image2_mean < par_civ.MinIma)
901                    FF(ivec_y,ivec_x)=1;
902                    %threshold on image maximum
903                elseif check_MaxIma && (image1_mean > par_civ.MaxIma || image2_mean > par_civ.MaxIma)
904                    FF(ivec_y,ivec_x)=1;
905                end
906                if FF(ivec_y,ivec_x)==1
907                    utable(ivec_y,ivec_x)=NaN;
908                    vtable(ivec_y,ivec_x)=NaN;
909                else
910                    %mask
911                    if checkmask
912                        image1_crop=(image1_crop-image1_mean).*~mask1_crop;%substract the mean, put to zero the masked parts
913                        image2_crop=(image2_crop-image2_mean).*~mask2_crop;
914                    else
915                        image1_crop=(image1_crop-image1_mean);
916                        image2_crop=(image2_crop-image2_mean);
917                    end
918
919               
920                    %reference: Oliver Pust, PIV: Direct Cross-Correlation
921                    for kz=1:par_civ.SearchBoxSize(3)
922                        subima2=squeeze(image2_crop(kz,:,:));
923                        subima1=squeeze(image1_crop(kref,:,:));
924                        correl_xy=conv2(subima2,flip(flip(subima1,2),1),'valid');
925                          result_conv(kz,:,:)= correl_xy;
926                        max_xy(kz)=max(max(correl_xy));
927                    [xk(kz),yk(kz)]=find(correl_xy==max_xy(kz),1);
928               
929                    end
930                    [corrmax,z]=max(max_xy);
931               
932                    x=xk(z);
933                    y=yk(z);
934                    result_conv=(result_conv/corrmax)*255; %normalize, peak=always 255
935                    subimage2_crop=squeeze(image2_crop(z,y:y+2*iby2/mesh,x:x+2*ibx2/mesh));%subimage of image 2 corresponding to the optimum displacement of first image
936                    sum_square=sum(sum(squeeze(image1_crop(z,:,:).*image1_crop(z,:,:))));
937                    sum_square=sum_square*sum(sum(subimage2_crop.*subimage2_crop));% product of variances of image 1 and 2
938                    sum_square=sqrt(sum_square);% srt of the variance product to normalise correlation
939                    if ~isempty(y) && ~isempty(x)
940       
941                            if par_civ.CorrSmooth==1
942                                [vector,FF(ivec_y,ivec_x)] = SUBPIXGAUSS (result_conv(z,:,:),x,y);%TODO: improve by max optimisation along z
943                            elseif par_civ.CorrSmooth==2
944                                [vector,FF(ivec_y,ivec_x)] = SUBPIX2DGAUSS (result_conv(z,:,:),x,y);
945                            else
946                                [vector,FF(ivec_y,ivec_x)] = quadr_fit(result_conv(z,:,:),x,y);
947                            end
948                            utable(ivec_y,ivec_x)=vector(1)*mesh+shiftx(ivec_y,ivec_x);
949                            vtable(ivec_y,ivec_x)=vector(2)*mesh+shifty(ivec_y,ivec_x);
950                            xtable(ivec_y,ivec_x)=iref+utable(ivec_y,ivec_x)/2-0.5;% convec flow (velocity taken at the point middle from imgae 1 and 2)
951                            ytable(ivec_y,ivec_x)=jref+vtable(ivec_y,ivec_x)/2-0.5;% and position of pixel 1=0.5 (convention for image coordinates=0 at the edge)
952                            iref=round(xtable(ivec_y,ivec_x)+0.5);% nearest image index for the middle of the vector
953                            jref=round(ytable(ivec_y,ivec_x)+0.5);
954                            wtable(ivec_y,ivec_x)=z-kref;
955                            % eliminate vectors located in the mask
956                            if  checkmask && (iref<1 || jref<1 ||iref>npx_ima || jref>npy_ima ||( par_civ.Mask(jref,iref)<200 && par_civ.Mask(jref,iref)>=100))
957                                utable(ivec_y,ivec_x)=0;
958                                vtable(ivec_y,ivec_x)=0;
959                                FF(ivec_y,ivec_x)=1;
960                            end
961                            ctable(ivec_y,ivec_x)=corrmax/sum_square;% correlation value
962
963                    else
964                        FF(ivec_y,ivec_x)=1;
965                    end
966                end
967            end
968        end
969    end
970end
971result_conv=result_conv*corrmax/(255*sum_square);% keep the last correlation matrix for output
972
973%------------------------------------------------------------------------
974% --- Find the maximum of the correlation function after interpolation
975% OUPUT:
976% vector = optimum displacement vector with subpixel correction
977% F =flag: =0 OK
978%           =-2 , warning: max too close to the edge of the search box (1 pixel margin)
979% INPUT:
980% x,y: position of the maximum correlation at integer values
981
982function [vector,F] = SUBPIXGAUSS (result_conv,x,y)
983%------------------------------------------------------------------------
984% vector=[0 0]; %default
985F=0;
986[npy,npx]=size(result_conv);
987result_conv(result_conv<1)=1; %set to 1 correlation values smaller than 1  (=0 by discretisation, to avoid divergence in the log)
988%the following 8 lines are copyright (c) 1998, Uri Shavit, Roi Gurka, Alex Liberzon, Technion ??? Israel Institute of Technology
989%http://urapiv.wordpress.com
990peaky = y;
991if y < npy && y > 1
992    f0 = log(result_conv(y,x));
993    f1 = log(result_conv(y-1,x));
994    f2 = log(result_conv(y+1,x));
995    peaky = peaky+ (f1-f2)/(2*f1-4*f0+2*f2);
996else
997    F=1; % warning flag for vector truncated by the limited search box
998end
999peakx=x;
1000if x < npx-1 && x > 1
1001    f0 = log(result_conv(y,x));
1002    f1 = log(result_conv(y,x-1));
1003    f2 = log(result_conv(y,x+1));
1004    peakx = peakx+ (f1-f2)/(2*f1-4*f0+2*f2);
1005else
1006    F=1; % warning flag for vector truncated by the limited search box
1007end
1008vector=[peakx-floor(npx/2)-1 peaky-floor(npy/2)-1];
1009
1010%------------------------------------------------------------------------
1011% --- Find the maximum of the correlation function after interpolation
1012function [vector,F] = SUBPIX2DGAUSS (result_conv,x,y)
1013%------------------------------------------------------------------------
1014% vector=[0 0]; %default
1015F=1;
1016peaky=y;
1017peakx=x;
1018result_conv(result_conv<1)=1; %set to 1 correlation values smaller than 1 (to avoid divergence in the log)
1019[npy,npx]=size(result_conv);
1020if (x < npx) && (y < npy) && (x > 1) && (y > 1)
1021    F=0;
1022    for i=-1:1
1023        for j=-1:1
1024            %following 15 lines based on
1025            %H. Nobach ??? M. Honkanen (2005)
1026            %Two-dimensional Gaussian regression for sub-pixel displacement
1027            %estimation in particle image velocimetry or particle position
1028            %estimation in particle tracking velocimetry
1029            %Experiments in Fluids (2005) 38: 511???515
1030            c10(j+2,i+2)=i*log(result_conv(y+j, x+i));
1031            c01(j+2,i+2)=j*log(result_conv(y+j, x+i));
1032            c11(j+2,i+2)=i*j*log(result_conv(y+j, x+i));
1033            c20(j+2,i+2)=(3*i^2-2)*log(result_conv(y+j, x+i));
1034            c02(j+2,i+2)=(3*j^2-2)*log(result_conv(y+j, x+i));
1035        end
1036    end
1037    c10=(1/6)*sum(sum(c10));
1038    c01=(1/6)*sum(sum(c01));
1039    c11=(1/4)*sum(sum(c11));
1040    c20=(1/6)*sum(sum(c20));
1041    c02=(1/6)*sum(sum(c02));
1042    deltax=(c11*c01-2*c10*c02)/(4*c20*c02-c11^2);
1043    deltay=(c11*c10-2*c01*c20)/(4*c20*c02-c11^2);
1044    if abs(deltax)<1
1045        peakx=x+deltax;
1046    end
1047    if abs(deltay)<1
1048        peaky=y+deltay;
1049    end
1050end
1051vector=[peakx-floor(npx/2)-1 peaky-floor(npy/2)-1];
1052
1053%------------------------------------------------------------------------
1054% --- Find the maximum of the correlation function after quadratic interpolation
1055function [vector,F] = quadr_fit(result_conv,x,y)
1056[npy,npx]=size(result_conv);
1057if x<4 || y<4 || npx-x<4 ||npy-y <4
1058    F=1;
1059    vector=[x y];
1060else
1061    F=0;
1062    x_ind=x-4:x+4;
1063    y_ind=y-4:y+4;
1064    x_vec=0.25*(x_ind-x);
1065    y_vec=0.25*(y_ind-y);
1066    [X,Y]=meshgrid(x_vec,y_vec);
1067    coord=[reshape(X,[],1) reshape(Y,[],1)];
1068    result_conv=reshape(result_conv(y_ind,x_ind),[],1);
1069   
1070   
1071    % n=numel(X);
1072    % x=[X Y];
1073    % X=X-0.5;
1074    % Y=Y+0.5;
1075    % y = (X.*X+2*Y.*Y+X.*Y+6) + 0.1*rand(n,1);
1076    p = polyfitn(coord,result_conv,2);
1077    A(1,1)=2*p.Coefficients(1);
1078    A(1,2)=p.Coefficients(2);
1079    A(2,1)=p.Coefficients(2);
1080    A(2,2)=2*p.Coefficients(4);
1081    vector=[x y]'-A\[p.Coefficients(3) p.Coefficients(5)]';
1082    vector=vector'-[floor(npx/2) floor(npy/2)]-1 ;
1083    % zg = polyvaln(p,coord);
1084    % figure
1085    % surf(x_vec,y_vec,reshape(zg,9,9))
1086    % hold on
1087    % plot3(X,Y,reshape(result_conv,9,9),'o')
1088    % hold off
1089end
1090
1091
1092function FF=detect_false(Param,C,U,V,FFIn)
1093FF=FFIn;%default, good vectors
1094% FF=1, for correlation max at edge, not set in this function
1095% FF=2, for too small correlation
1096% FF=3, for velocity outside bounds
1097% FF=4 for exclusion by difference with the smoothed field, not set in this function
1098
1099if isfield (Param,'MinCorr')
1100     FF(C<Param.MinCorr & FFIn==0)=2;
1101end
1102if (isfield(Param,'MinVel')&&~isempty(Param.MinVel))||(isfield (Param,'MaxVel')&&~isempty(Param.MaxVel))
1103    Umod= U.*U+V.*V;
1104    if isfield (Param,'MinVel')&&~isempty(Param.MinVel)
1105        U2Min=Param.MinVel*Param.MinVel;
1106        FF(Umod<U2Min & FFIn==0)=3;
1107    end
1108    if isfield (Param,'MaxVel')&&~isempty(Param.MaxVel)
1109         U2Max=Param.MaxVel*Param.MaxVel;
1110        FF(Umod>U2Max & FFIn==0)=3;
1111    end
1112end
1113
1114%------------------------------------------------------------------------
1115% --- determine the list of index pairs of processing file
1116function [i1_series,i2_series,j1_series,j2_series,check_bounds,NomTypeNc]=...
1117    find_pair_indices(str_civ,i_series,j_series,MinIndex_i,MaxIndex_i,MinIndex_j,MaxIndex_j)
1118%------------------------------------------------------------------------
1119i1_series=i_series;% set of first image indexes
1120i2_series=i_series;
1121j1_series=j_series;%ones(size(i_series));% set of first image numbers
1122j2_series=j_series;%ones(size(i_series));
1123r=regexp(str_civ,'^\D(?<ind>[i|j])=( -| )(?<num1>\d+)\|(?<num2>\d+)','names');
1124if ~isempty(r)
1125    mode=['D' r.ind];
1126    ind1=str2num(r.num1);
1127    ind2=str2num(r.num2);
1128else
1129    mode='j1-j2';
1130    r=regexp(str_civ,'^j= (?<num1>[a-z])-(?<num2>[a-z])','names');
1131    if ~isempty(r)
1132        NomTypeNc='_1ab';
1133    else
1134        r=regexp(str_civ,'^j= (?<num1>[A-Z])-(?<num2>[A-Z])','names');
1135        if ~isempty(r)
1136            NomTypeNc='_1AB';
1137        else
1138            r=regexp(str_civ,'^j= (?<num1>\d+)-(?<num2>\d+)','names');
1139            if ~isempty(r)
1140                NomTypeNc='_1_1-2';
1141            end
1142        end
1143    end
1144    if isempty(r)
1145        display('wrong pair mode input option')
1146    else
1147        ind1=stra2num(r.num1);
1148        ind2=stra2num(r.num2);
1149    end
1150end
1151switch mode
1152    case 'Di'
1153        i1_series=i_series-ind1;% set of first image numbers
1154        i2_series=i_series+ind2;
1155        check_bounds=i1_series<MinIndex_i | i2_series>MaxIndex_i;
1156        if isempty(j_series)
1157            NomTypeNc='_1-2';
1158        else
1159            j1_series=j_series;
1160            j2_series=j_series;
1161            NomTypeNc='_1-2_1';
1162        end
1163    case 'Dj'
1164        j1_series=j_series-ind1;
1165        j2_series=j_series+ind2;
1166        check_bounds=j1_series<MinIndex_j | j2_series>MaxIndex_j;
1167        NomTypeNc='_1_1-2';
1168    otherwise %bursts
1169        i1_series=i_series(1,:);% do not sweep the j index
1170        i2_series=i_series(1,:);
1171        j1_series=ind1*ones(1,size(i_series,2));% j index is fixed by pair choice
1172        j2_series=ind2*ones(1,size(i_series,2));
1173        check_bounds=zeros(size(i1_series));% no limitations due to min-max indices
1174end
1175
1176
1177
1178
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