source: trunk/src/series/civ_3D.m @ 1157

Last change on this file since 1157 was 1157, checked in by sommeria, 3 months ago

filter_time added

File size: 55.5 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[~,i1_series,~,j1_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,~,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_3D';% states the conventions used for the description of field variables and attributes
171Data.Program='civ_3D';
172if isfield(Param,'UvmatRevision')
173    Data.Program=[Data.Program ', uvmat r' Param.UvmatRevision];
174end
175Data.CivStage=0;%default
176list_param=(fieldnames(Param.ActionInput.Civ1))';
177list_param(strcmp('TestCiv1',list_param))=[];% remove the parameter TestCiv1 from the list
178Civ1_param=regexprep(list_param,'^.+','Civ1_$0');% insert 'Civ1_' before  each string in list_param
179Civ1_param=[{'Civ1_ImageA','Civ1_ImageB','Civ1_Time','Civ1_Dt'} Civ1_param]; %insert the names of the two input images
180Data.ListGlobalAttribute=[ListGlobalAttribute Civ1_param];
181% set the list of variables
182Data.ListVarName={'Coord_z','Coord_y','Coord_x','Civ1_X','Civ1_Y','Civ1_U','Civ1_V','Civ1_W','Civ1_C','Civ1_FF'};%  cell array containing the names of the fields to record
183Data.VarDimName={'npz','npy','npx',{'npz','npy','npx'},{'npz','npy','npx'},{'npz','npy','npx'},{'npz','npy','npx'},...
184    {'npz','npy','npx'},{'npz','npy','npx'},{'npz','npy','npx'}};
185Data.VarAttribute{1}.Role='coord_x';
186Data.VarAttribute{2}.Role='coord_y';
187Data.VarAttribute{3}.Role='vector_x';
188Data.VarAttribute{4}.Role='vector_y';
189Data.VarAttribute{5}.Role='vector_z';
190Data.VarAttribute{6}.Role='ancillary';
191Data.VarAttribute{7}.Role='errorflag';
192Data.Coord_z=j1_series_Civ1;
193% path for output nc file
194OutputPath=fullfile(Param.OutputPath,num2str(Param.Experiment),num2str(Param.Device),[Param.OutputSubDir Param.OutputDirExt]);
195
196%% get timing from the ImaDoc file or input video
197if iview_A~=0
198    XmlFileName=find_imadoc(RootPath_A,SubDir_A);
199    Time=[];
200    if ~isempty(XmlFileName)
201        XmlData=imadoc2struct(XmlFileName);
202        if isfield(XmlData,'Time')
203            Time=XmlData.Time;
204        end
205        if isfield(XmlData,'Camera')
206            if isfield(XmlData.Camera,'NbSlice')&& ~isempty(XmlData.Camera.NbSlice)
207                NbSlice_calib{iview}=XmlData.Camera.NbSlice;% Nbre of slices for Zindex in phys transform
208                if ~isequal(NbSlice_calib{iview},NbSlice_calib{1})
209                    msgbox_uvmat('WARNING','inconsistent number of Z indices for the two field series');
210                end
211            end
212            if isfield(XmlData.Camera,'TimeUnit')&& ~isempty(XmlData.Camera.TimeUnit)
213                TimeUnit=XmlData.Camera.TimeUnit;
214            end
215        end
216    end
217end
218
219maskoldname='';% initiate the mask name
220FileType_A='';
221FileType_B='';
222CheckOverwrite=1;%default
223if isfield(Param,'CheckOverwrite')
224    CheckOverwrite=Param.CheckOverwrite;
225end
226   Data.Civ1_ImageA=fullfile_uvmat(RootPath_A,SubDir_A,RootFile_A,FileExt_A,NomType_A,i1_series_Civ1(1),[],j1_series_Civ1(1,1));
227   Data.Civ1_ImageB=fullfile_uvmat(RootPath_B,SubDir_B,RootFile_B,FileExt_B,NomType_B,i1_series_Civ1(1),[],j2_series_Civ1(1,1));
228    FileInfo=get_file_info(Data.Civ1_ImageA);
229        par_civ1=Param.ActionInput.Civ1;% parameters for civ1
230    par_civ1.ImageHeight=FileInfo.Height;npy=FileInfo.Height;
231    par_civ1.ImageWidth=FileInfo.Width;npx=FileInfo.Width;
232SearchRange_z=floor(Param.ActionInput.Civ1.SearchBoxSize(3)/2);
233    par_civ1.Dz=Param.ActionInput.Civ1.Dz;
234    par_civ1.ImageA=zeros(2*SearchRange_z+1,npy,npx);
235par_civ1.ImageB=zeros(2*SearchRange_z+1,npy,npx);
236
237
238
239%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
240%%%%% MAIN LOOP %%%%%%
241%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
242for ifield=1:NbField_i
243    tstart=tic;
244    time_civ1=0;
245    time_patch1=0;
246    time_civ2=0;
247    time_patch2=0;
248    if checkrun% update the waitbar in interactive mode with GUI series  (checkrun=1)
249        update_waitbar(WaitbarHandle,ifield/NbField_i)
250        if  checkrun && ~strcmp(get(RUNHandle,'BusyAction'),'queue')
251            disp('program stopped by user')
252            break
253        end
254    end
255   
256    %indicate the values of all the global attributes in the output data
257    i1=i1_series_Civ1(ifield);
258    i2=i1;
259    if ~isempty(i2_series_Civ1)
260        i2=i2_series_Civ1(ifield);
261    end
262    j1=1;
263    if ~isempty(j1_series_Civ1)
264        j1=j1_series_Civ1(ifield);
265    end
266    j2=j1;
267    if ~isempty(j2_series_Civ1)
268        j2=j2_series_Civ1(ifield);
269    end
270
271    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
272    Data.Civ1_Dt=Time(i2+1,j2+1)-Time(i1+1,j1+1);
273
274    for ilist=1:length(list_param)
275        Data.(Civ1_param{4+ilist})=Param.ActionInput.Civ1.(list_param{ilist});
276    end
277   
278    Data.CivStage=1;
279 
280    ncfile_out=fullfile_uvmat(OutputPath,'',Param.InputTable{1,3},'.nc',...
281                '_1-1',i1_series_Civ1(ifield),i2_series_Civ1(ifield)); %output file name
282
283    if ~CheckOverwrite && exist(ncfile_out,'file')
284        disp(['existing output file ' ncfile_out ' already exists, skip to next field'])
285        continue% skip iteration if the mode overwrite is desactivated and the result file already exists
286    end
287
288
289    %% Civ1
290    % if Civ1 computation is requested
291    if isfield (Param.ActionInput,'Civ1')
292
293        disp('civ1 started')
294
295        % read input images by vertical blocks with nbre of images equal to 2*SearchRange+1,
296        par_civ1.ImageA=zeros(2*SearchRange_z+1,npy,npx);%image block initiation
297        par_civ1.ImageB=zeros(2*SearchRange_z+1,npy,npx);
298       
299        z_index=1;%first vertical block centered at image index z_index=par_civ1.Dz
300        for iz=1:par_civ1.Dz+SearchRange_z
301            j_image_index=j1_series_Civ1(iz,1)% j index of the current image
302            ImageName_A=fullfile_uvmat(RootPath_A,SubDir_A,RootFile_A,FileExt_A,NomType_A,i1_series_Civ1(1,ifield),[],j_image_index);%
303            A= read_image(ImageName_A,FileType_A);
304            ImageName_B=fullfile_uvmat(RootPath_B,SubDir_B,RootFile_B,FileExt_B,NomType_B,i2_series_Civ1(1,ifield),[],j_image_index);
305            B= read_image(ImageName_B,FileType_B);
306            par_civ1.ImageA(iz+par_civ1.Dz-1,:,:) = A;
307            par_civ1.ImageB(iz+par_civ1.Dz-1,:,:) = B;
308        end
309        % calculate velocity data at the first position z, corresponding to j_index=par_civ1.Dz
310        [Data.Civ1_X(1,:,:),Data.Civ1_Y(1,:,:), Data.Civ1_U(1,:,:), Data.Civ1_V(1,:,:),Data.Civ1_W(1,:,:),...
311            Data.Civ1_C(1,:,:), Data.Civ1_FF(1,:,:), result_conv, errormsg] = civ3D (par_civ1);
312        if ~isempty(errormsg)
313            disp_uvmat('ERROR',errormsg,checkrun)
314            return
315        end
316        for z_index=2:floor((NbSlice-1)/par_civ1.Dz)% loop on slices
317            par_civ1.ImageA=circshift(par_civ1.ImageA,-par_civ1.Dz);%shift the indices in the image block upward by par_civ1.Dz
318            par_civ1.ImageB=circshift(par_civ1.ImageA,-par_civ1.Dz);
319            for iz=1:par_civ1.Dz %read the new images at the end of the image block
320                j_image_index=j1_series_Civ1(z_index*par_civ1.Dz+SearchRange_z-par_civ1.Dz+iz,1)
321                ImageName_A=fullfile_uvmat(RootPath_A,SubDir_A,RootFile_A,FileExt_A,NomType_A,i1_series_Civ1(1,ifield),[],j_image_index);%
322                A= read_image(ImageName_A,FileType_A);
323                ImageName_B=fullfile_uvmat(RootPath_B,SubDir_B,RootFile_B,FileExt_B,NomType_B,i2_series_Civ1(1,ifield),[],j_image_index);
324                B= read_image(ImageName_B,FileType_B);
325                par_civ1.ImageA(2*SearchRange_z+1-par_civ1.Dz+iz,:,:) = A;
326                par_civ1.ImageB(2*SearchRange_z+1-par_civ1.Dz+iz,:,:) = B;
327            end
328            % caluclate velocity data (y and v in indices, reverse to y component)
329            [Data.Civ1_X(z_index,:,:),Data.Civ1_Y(z_index,:,:), Data.Civ1_U(z_index,:,:), Data.Civ1_V(z_index,:,:),Data.Civ1_W(z_index,:,:),...
330                Data.Civ1_C(z_index,:,:), Data.Civ1_FF(z_index,:,:), result_conv, errormsg] = civ3D (par_civ1);
331
332            if ~isempty(errormsg)
333                disp_uvmat('ERROR',errormsg,checkrun)
334                return
335            end
336        end
337        Data.Civ1_C=double(Data.Civ1_C);
338        Data.Civ1_C(Data.Civ1_C==Inf)=0;
339        [npz,npy,npx]=size(Data.Civ1_X);
340        Data.Coord_z=1:npz;
341        Data.Coord_y=1:npy;
342        Data.Coord_x=1:npx;
343        % case of mask TO ADAPT
344        if par_civ1.CheckMask&&~isempty(par_civ1.Mask)
345            if isfield(par_civ1,'NbSlice')
346                [RootPath_mask,SubDir_mask,RootFile_mask,i1_mask,i2_mask,j1_mask,j2_mask,Ext_mask]=fileparts_uvmat(Param.ActionInput.Civ1.Mask);
347                i1_mask=mod(i1-1,par_civ1.NbSlice)+1;
348                maskname=fullfile_uvmat(RootPath_mask,SubDir_mask,RootFile_mask,Ext_mask,'_1',i1_mask);
349            else
350                maskname=Param.ActionInput.Civ1.Mask;
351            end
352            if strcmp(maskoldname,maskname)% mask exist, not already read in civ1
353                par_civ1.Mask=mask; %use mask already opened
354            else
355                if ~isempty(regexp(maskname,'(^http://)|(^https://)'))|| exist(maskname,'file')
356                    try
357                        par_civ1.Mask=imread(maskname);%update the mask, an store it for future use
358                    catch ME
359                        if ~isempty(ME.message)
360                            errormsg=['error reading input image: ' ME.message];
361                            disp_uvmat('ERROR',errormsg,checkrun)
362                            return
363                        end
364                    end
365                else
366                    par_civ1.Mask=[];
367                end
368                mask=par_civ1.Mask;
369                maskoldname=maskname;
370            end
371        end
372        % Data.ListVarName=[Data.ListVarName 'Civ1_Z'];
373        % Data.Civ1_X=[];Data.Civ1_Y=[];Data.Civ1_Z=[];
374        % Data.Civ1_U=[];Data.Civ1_V=[];Data.Civ1_C=[];
375        %
376        %
377        % Data.Civ1_X=[Data.Civ1_X reshape(xtable,[],1)];
378        % Data.Civ1_Y=[Data.Civ1_Y reshape(Param.Civ1.ImageHeight-ytable+1,[],1)];
379        % Data.Civ1_Z=[Data.Civ1_Z ivol*ones(numel(xtable),1)];% z=image index in image coordinates
380        % Data.Civ1_U=[Data.Civ1_U reshape(utable,[],1)];
381        % Data.Civ1_V=[Data.Civ1_V reshape(-vtable,[],1)];
382        % Data.Civ1_C=[Data.Civ1_C reshape(ctable,[],1)];
383        % Data.Civ1_FF=[Data.Civ1_FF reshape(F,[],1)];
384
385    end
386
387    %% Fix1
388    if isfield (Param.ActionInput,'Fix1')
389        disp('detect_false1 started')
390        if ~isfield (Param.ActionInput,'Civ1')% if we use existing Civ1, remove previous data beyond Civ1
391            Fix1_attr=find(strcmp('Fix1',Data.ListGlobalAttribute));
392            Data.ListGlobalAttribute(Fix1_attr)=[];
393            for ilist=1:numel(Fix1_attr)
394                Data=rmfield(Data,Data.ListGlobalAttribute{Fix1_attr(ilist)});
395            end
396        end
397        list_param=fieldnames(Param.ActionInput.Fix1)';
398        Fix1_param=regexprep(list_param,'^.+','Fix1_$0');% insert 'Fix1_' before  each string in ListFixParam
399        %indicate the values of all the global attributes in the output data
400        for ilist=1:length(list_param)
401            Data.(Fix1_param{ilist})=Param.ActionInput.Fix1.(list_param{ilist});
402        end
403        Data.ListGlobalAttribute=[Data.ListGlobalAttribute Fix1_param];
404        Data.Civ1_FF=uint8(detect_false(Param.ActionInput.Fix1,Data.Civ1_C,Data.Civ1_U,Data.Civ1_V,Data.Civ1_FF));
405        Data.CivStage=2;
406    end
407    %% Patch1
408    if isfield (Param.ActionInput,'Patch1')
409        disp('patch1 started')
410        tstart_patch1=tic;
411
412        % record the processing parameters of Patch1 as global attributes in the result nc file
413        list_param=fieldnames(Param.ActionInput.Patch1)';
414        list_param(strcmp('TestPatch1',list_param))=[];% remove 'TestPatch1' from the list of parameters
415        Patch1_param=regexprep(list_param,'^.+','Patch1_$0');% insert 'Patch1_' before  each parameter name
416        for ilist=1:length(list_param)
417            Data.(Patch1_param{ilist})=Param.ActionInput.Patch1.(list_param{ilist});
418        end
419        Data.CivStage=3;% record the new state of processing
420        Data.ListGlobalAttribute=[Data.ListGlobalAttribute Patch1_param];
421
422        % list the variables to record
423        nbvar=length(Data.ListVarName);
424        Data.ListVarName=[Data.ListVarName {'Civ1_U_smooth','Civ1_V_smooth','Civ1_SubRange','Civ1_NbCentres','Civ1_Coord_tps','Civ1_U_tps','Civ1_V_tps'}];
425        Data.VarDimName=[Data.VarDimName {'nb_vec_1','nb_vec_1',{'nb_coord','nb_bounds','nb_subdomain_1'},'nb_subdomain_1',...
426            {'nb_tps_1','nb_coord','nb_subdomain_1'},{'nb_tps_1','nb_subdomain_1'},{'nb_tps_1','nb_subdomain_1'}}];
427        Data.VarAttribute{nbvar+1}.Role='vector_x';
428        Data.VarAttribute{nbvar+2}.Role='vector_y';
429        Data.VarAttribute{nbvar+5}.Role='coord_tps';
430        Data.VarAttribute{nbvar+6}.Role='vector_x';
431        Data.VarAttribute{nbvar+7}.Role='vector_y';
432        Data.Civ1_U_smooth=Data.Civ1_U; % zeros(size(Data.Civ1_X));
433        Data.Civ1_V_smooth=Data.Civ1_V; %zeros(size(Data.Civ1_X));
434        if isfield(Data,'Civ1_FF')
435            ind_good=find(Data.Civ1_FF==0);
436        else
437            ind_good=1:numel(Data.Civ1_X);
438        end
439        if isempty(ind_good)
440            disp_uvmat('ERROR','all vectors of civ1 are bad, check input parameters' ,checkrun)
441            return
442        end
443
444        % perform Patch calculation using the UVMAT fct 'filter_tps'
445
446        [Data.Civ1_SubRange,Data.Civ1_NbCentres,Data.Civ1_Coord_tps,Data.Civ1_U_tps,Data.Civ1_V_tps,tild,Ures, Vres,tild,FFres]=...
447            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);
448        Data.Civ1_U_smooth(ind_good)=Ures;% take the interpolated (smoothed) velocity values for good vectors, keep civ1 data for the other
449        Data.Civ1_V_smooth(ind_good)=Vres;
450        Data.Civ1_FF(ind_good)=uint8(FFres);
451        time_patch1=toc(tstart_patch1);
452        disp('patch1 performed')
453    end
454
455    %% Civ2
456    if isfield (Param.ActionInput,'Civ2')
457        disp('civ2 started')
458        tstart_civ2=tic;
459        par_civ2=Param.ActionInput.Civ2;
460        % read input images
461        par_civ2.ImageA=[];
462        par_civ2.ImageB=[];
463        if strcmp(Param.ActionInput.ListCompareMode,'displacement')
464            ImageName_A_Civ2=Param.ActionInput.RefFile;
465        else
466            ImageName_A_Civ2=fullfile_uvmat(RootPath_A,SubDir_A,RootFile_A,FileExt_A,NomType_A,i1_civ2,[],j1_civ2);
467        end
468        if strcmp(ImageName_A_Civ2,ImageName_A) && isequal(FrameIndex_A_Civ1(ifield),FrameIndex_A_Civ2(ifield))
469            par_civ2.ImageA=par_civ1.ImageA;
470        else
471            [par_civ2.ImageA,VideoObject_A] = read_image(ImageName_A_Civ2,FileType_A,VideoObject_A,FrameIndex_A_Civ2(ifield));
472        end
473        ImageName_B_Civ2=fullfile_uvmat(RootPath_B,SubDir_B,RootFile_B,FileExt_B,NomType_B,i2_civ2,[],j2_civ2);
474        if strcmp(ImageName_B_Civ2,ImageName_B) && isequal(FrameIndex_B_Civ1(ifield),FrameIndex_B_Civ2)
475            par_civ2.ImageB=par_civ1.ImageB;
476        else
477            [par_civ2.ImageB,VideoObject_B] = read_image(ImageName_B_Civ2,FileType_B,VideoObject_B,FrameIndex_B_Civ2(ifield));
478        end
479        [FileInfo_A,VideoObject_A]=get_file_info(ImageName_A_Civ2);
480        par_civ2.ImageWidth=FileInfo_A.Width;
481        par_civ2.ImageHeight=FileInfo_A.Height;
482        if isfield(par_civ2,'Grid')% grid points set as input file
483            if ischar(par_civ2.Grid)%read the grid file if the input is a file name
484                par_civ2.Grid=dlmread(par_civ2.Grid);
485                par_civ2.Grid(1,:)=[];%the first line must be removed (heading in the grid file)
486            end
487        else% automatic grid
488            minix=floor(par_civ2.Dx/2)-0.5;
489            maxix=minix+par_civ2.Dx*floor((par_civ2.ImageWidth-1)/par_civ2.Dx);
490            miniy=floor(par_civ2.Dy/2)-0.5;
491            maxiy=minix+par_civ2.Dy*floor((par_civ2.ImageHeight-1)/par_civ2.Dy);
492            [GridX,GridY]=meshgrid(minix:par_civ2.Dx:maxix,miniy:par_civ2.Dy:maxiy);
493            par_civ2.Grid(:,1)=reshape(GridX,[],1);
494            par_civ2.Grid(:,2)=reshape(GridY,[],1);
495        end
496        % end
497
498        % get the guess from patch1 or patch2 (case 'CheckCiv3')
499
500        if isfield (par_civ2,'CheckCiv3') && par_civ2.CheckCiv3 %get the guess from  patch2
501            SubRange= Data.Civ2_SubRange;
502            NbCentres=Data.Civ2_NbCentres;
503            Coord_tps=Data.Civ2_Coord_tps;
504            U_tps=Data.Civ2_U_tps;
505            V_tps=Data.Civ2_V_tps;
506            CivStage=Data.CivStage;%store the current CivStage
507            Civ1_Dt=Data.Civ2_Dt;
508            Data=[];%reinitialise the result structure Data
509            Data.ListGlobalAttribute={'Conventions','Program','CivStage'};
510            Data.Conventions='uvmat/civdata';% states the conventions used for the description of field variables and attributes
511            Data.Program='civ_series';
512            Data.CivStage=CivStage+1;%update the current civStage after reinitialisation of Data
513            Data.ListVarName={};
514            Data.VarDimName={};
515        else % get the guess from patch1
516            SubRange= Data.Civ1_SubRange;
517            NbCentres=Data.Civ1_NbCentres;
518            Coord_tps=Data.Civ1_Coord_tps;
519            U_tps=Data.Civ1_U_tps;
520            V_tps=Data.Civ1_V_tps;
521            Civ1_Dt=Data.Civ1_Dt;
522            Data.CivStage=4;
523        end
524        % else
525        %     SubRange= par_civ2.Civ1_SubRange;
526        %     NbCentres=par_civ2.Civ1_NbCentres;
527        %     Coord_tps=par_civ2.Civ1_Coord_tps;
528        %     U_tps=par_civ2.Civ1_U_tps;
529        %     V_tps=par_civ2.Civ1_V_tps;
530        %     Civ1_Dt=par_civ2.Civ1_Dt;
531        %     Civ2_Dt=par_civ2.Civ1_Dt;
532        %     Data.ListVarName={};
533        %     Data.VarDimName={};
534        % end
535        Shiftx=zeros(size(par_civ2.Grid,1),1);% shift expected from civ1 data
536        Shifty=zeros(size(par_civ2.Grid,1),1);
537        nbval=zeros(size(par_civ2.Grid,1),1);% nbre of interpolated values at each grid point (from the different patch subdomains)
538        if par_civ2.CheckDeformation
539            DUDX=zeros(size(par_civ2.Grid,1),1);
540            DUDY=zeros(size(par_civ2.Grid,1),1);
541            DVDX=zeros(size(par_civ2.Grid,1),1);
542            DVDY=zeros(size(par_civ2.Grid,1),1);
543        end
544        NbSubDomain=size(SubRange,3);
545        for isub=1:NbSubDomain% for each sub-domain of Patch1
546            nbvec_sub=NbCentres(isub);% nbre of Civ vectors in the subdomain
547            ind_sel=find(par_civ2.Grid(:,1)>=SubRange(1,1,isub) & par_civ2.Grid(:,1)<=SubRange(1,2,isub) &...
548                par_civ2.Grid(:,2)>=SubRange(2,1,isub) & par_civ2.Grid(:,2)<=SubRange(2,2,isub));% grid points in the subdomain
549            if ~isempty(ind_sel)
550                epoints = par_civ2.Grid(ind_sel,:);% coordinates of interpolation sites (measurement grids)
551                ctrs=Coord_tps(1:nbvec_sub,:,isub) ;%(=initial points) ctrs
552                nbval(ind_sel)=nbval(ind_sel)+1;% records the number of values for each interpolation point (in case of subdomain overlap)
553                EM = tps_eval(epoints,ctrs);% thin plate spline (tps) coefficient
554                Shiftx(ind_sel)=Shiftx(ind_sel)+EM*U_tps(1:nbvec_sub+3,isub);%velocity shift estimated by tps from civ1
555                Shifty(ind_sel)=Shifty(ind_sel)+EM*V_tps(1:nbvec_sub+3,isub);
556                if par_civ2.CheckDeformation
557                    [EMDX,EMDY] = tps_eval_dxy(epoints,ctrs);%2D matrix of distances between extrapolation points epoints and spline centres (=site points) ctrs
558                    DUDX(ind_sel)=DUDX(ind_sel)+EMDX*U_tps(1:nbvec_sub+3,isub);
559                    DUDY(ind_sel)=DUDY(ind_sel)+EMDY*U_tps(1:nbvec_sub+3,isub);
560                    DVDX(ind_sel)=DVDX(ind_sel)+EMDX*V_tps(1:nbvec_sub+3,isub);
561                    DVDY(ind_sel)=DVDY(ind_sel)+EMDY*V_tps(1:nbvec_sub+3,isub);
562                end
563            end
564        end
565        if par_civ2.CheckMask&&~isempty(par_civ2.Mask)
566            if isfield(par_civ2,'NbSlice')
567                [RootPath_mask,SubDir_mask,RootFile_mask,i1_mask,i2_mask,j1_mask,j2_mask,Ext_mask]=fileparts_uvmat(Param.ActionInput.Civ2.Mask);
568                i1_mask=mod(i1-1,par_civ2.NbSlice)+1;
569                maskname=fullfile_uvmat(RootPath_mask,SubDir_mask,RootFile_mask,Ext_mask,'_1',i1_mask);
570            else
571                maskname=Param.ActionInput.Civ2.Mask;
572            end
573            if strcmp(maskoldname,maskname)% mask exist, not already read in civ1
574                par_civ2.Mask=mask; %use mask already opened
575            else
576                if exist(maskname,'file')
577                    try
578                        par_civ2.Mask=imread(maskname);%update the mask, an store it for future use
579                    catch ME
580                        if ~isempty(ME.message)
581                            errormsg=['error reading input image: ' ME.message];
582                            disp_uvmat('ERROR',errormsg,checkrun)
583                            return
584                        end
585                    end
586                else
587                    par_civ2.Mask=[];
588                end
589                mask=par_civ2.Mask;
590                maskoldname=maskname;
591            end
592        end
593
594
595        if strcmp(Param.ActionInput.ListCompareMode,'displacement')
596            Civ1_Dt=1;
597            Civ2_Dt=1;
598        else
599            Civ2_Dt=Time(i2_civ2+1,j2_civ2+1)-Time(i1_civ2+1,j1_civ2+1);
600        end
601
602        par_civ2.SearchBoxShift=(Civ2_Dt/Civ1_Dt)*[Shiftx(nbval>=1)./nbval(nbval>=1) Shifty(nbval>=1)./nbval(nbval>=1)];
603        % shift the grid points by half the expected shift to provide the correlation box position in image A
604        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];
605        if par_civ2.CheckDeformation
606            par_civ2.DUDX=DUDX(nbval>=1)./nbval(nbval>=1);
607            par_civ2.DUDY=DUDY(nbval>=1)./nbval(nbval>=1);
608            par_civ2.DVDX=DVDX(nbval>=1)./nbval(nbval>=1);
609            par_civ2.DVDY=DVDY(nbval>=1)./nbval(nbval>=1);
610        end
611
612        % calculate velocity data (y and v in image indices, reverse to y component)
613
614        [xtable, ytable, utable, vtable, ctable, F,result_conv,errormsg] = civ (par_civ2);
615
616        list_param=(fieldnames(Param.ActionInput.Civ2))';
617        list_param(strcmp('TestCiv2',list_param))=[];% remove the parameter TestCiv2 from the list
618        Civ2_param=regexprep(list_param,'^.+','Civ2_$0');% insert 'Civ2_' before  each string in list_param
619        Civ2_param=[{'Civ2_ImageA','Civ2_ImageB','Civ2_Time','Civ2_Dt'} Civ2_param]; %insert the names of the two input images
620        %indicate the values of all the global attributes in the output data
621        if exist('ImageName_A','var')
622            Data.Civ2_ImageA=ImageName_A;
623            Data.Civ2_ImageB=ImageName_B;
624            if strcmp(Param.ActionInput.ListCompareMode,'displacement')
625                Data.Civ2_Time=Time(i2_civ2+1,j2_civ2+1);% the Time is the Time of the secodn image
626                Data.Civ2_Dt=1;% Time interval is 1, to yield displacement instead of velocity=displacement/Dt at reading
627            else
628                Data.Civ2_Time=(Time(i2_civ2+1,j2_civ2+1)+Time(i1_civ2+1,j1_civ2+1))/2;
629                Data.Civ2_Dt=Civ2_Dt;
630            end
631        end
632        for ilist=1:length(list_param)
633            Data.(Civ2_param{4+ilist})=Param.ActionInput.Civ2.(list_param{ilist});
634        end
635        Data.ListGlobalAttribute=[Data.ListGlobalAttribute Civ2_param];
636
637        nbvar=numel(Data.ListVarName);
638        % define the Civ2 variable (if Civ2 data are not replaced from previous calculation)
639        if isempty(find(strcmp('Civ2_X',Data.ListVarName),1))
640            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
641            Data.VarDimName=[Data.VarDimName {'nb_vec_2','nb_vec_2','nb_vec_2','nb_vec_2','nb_vec_2','nb_vec_2'}];
642            Data.VarAttribute{nbvar+1}.Role='coord_x';
643            Data.VarAttribute{nbvar+2}.Role='coord_y';
644            Data.VarAttribute{nbvar+3}.Role='vector_x';
645            Data.VarAttribute{nbvar+4}.Role='vector_y';
646            Data.VarAttribute{nbvar+5}.Role='ancillary';
647            Data.VarAttribute{nbvar+6}.Role='errorflag';
648        end
649        Data.Civ2_X=reshape(xtable,[],1);
650        Data.Civ2_Y=reshape(size(par_civ2.ImageA,1)-ytable+1,[],1);
651        Data.Civ2_U=reshape(utable,[],1);
652        Data.Civ2_V=reshape(-vtable,[],1);
653        Data.Civ2_C=reshape(ctable,[],1);
654        Data.Civ2_FF=reshape(F,[],1);
655        disp('civ2 performed')
656        time_civ2=toc(tstart_civ2);
657    elseif ~isfield(Data,'ListVarName') % we start there, using existing Civ2 data
658        if exist('ncfile','var')
659            CivFile=ncfile;
660            [Data,tild,tild,errormsg]=nc2struct(CivFile);%read civ1 and detect_false1 data in the existing netcdf file
661            if ~isempty(errormsg)
662                disp_uvmat('ERROR',errormsg,checkrun)
663                return
664            end
665            %         elseif isfield(Param,'Civ2_X')% use Civ2 data as input in Param (test mode)
666            %             Data.ListGlobalAttribute={};
667            %             Data.ListVarName={};
668            %             Data.VarDimName={};
669            %             Data.Civ2_X=Param.Civ2_X;
670            %             Data.Civ2_Y=Param.Civ2_Y;
671            %             Data.Civ2_U=Param.Civ2_U;
672            %             Data.Civ2_V=Param.Civ2_V;
673            %             Data.Civ2_FF=Param.Civ2_FF;
674        end
675    end
676
677    %% Fix2
678    if isfield (Param.ActionInput,'Fix2')
679        disp('detect_false2 started')
680        list_param=fieldnames(Param.ActionInput.Fix2)';
681        Fix2_param=regexprep(list_param,'^.+','Fix2_$0');% insert 'Fix1_' before  each string in ListFixParam
682        %indicate the values of all the global attributes in the output data
683        for ilist=1:length(list_param)
684            Data.(Fix2_param{ilist})=Param.ActionInput.Fix2.(list_param{ilist});
685        end
686        Data.ListGlobalAttribute=[Data.ListGlobalAttribute Fix2_param];
687        Data.Civ2_FF=detect_false(Param.ActionInput.Fix2,Data.Civ2_C,Data.Civ2_U,Data.Civ2_V,Data.Civ2_FF);
688        Data.CivStage=Data.CivStage+1;
689    end
690
691    %% Patch2
692    if isfield (Param.ActionInput,'Patch2')
693        disp('patch2 started')
694        tstart_patch2=tic;
695        list_param=fieldnames(Param.ActionInput.Patch2)';
696        list_param(strcmp('TestPatch2',list_param))=[];% remove the parameter TestCiv1 from the list
697        Patch2_param=regexprep(list_param,'^.+','Patch2_$0');% insert 'Fix1_' before  each string in ListFixParam
698        %indicate the values of all the global attributes in the output data
699        for ilist=1:length(list_param)
700            Data.(Patch2_param{ilist})=Param.ActionInput.Patch2.(list_param{ilist});
701        end
702        Data.ListGlobalAttribute=[Data.ListGlobalAttribute Patch2_param];
703
704        nbvar=length(Data.ListVarName);
705        Data.ListVarName=[Data.ListVarName {'Civ2_U_smooth','Civ2_V_smooth','Civ2_SubRange','Civ2_NbCentres','Civ2_Coord_tps','Civ2_U_tps','Civ2_V_tps'}];
706        Data.VarDimName=[Data.VarDimName {'nb_vec_2','nb_vec_2',{'nb_coord','nb_bounds','nb_subdomain_2'},{'nb_subdomain_2'},...
707            {'nb_tps_2','nb_coord','nb_subdomain_2'},{'nb_tps_2','nb_subdomain_2'},{'nb_tps_2','nb_subdomain_2'}}];
708
709        Data.VarAttribute{nbvar+1}.Role='vector_x';
710        Data.VarAttribute{nbvar+2}.Role='vector_y';
711        Data.VarAttribute{nbvar+5}.Role='coord_tps';
712        Data.VarAttribute{nbvar+6}.Role='vector_x';
713        Data.VarAttribute{nbvar+7}.Role='vector_y';
714        Data.Civ2_U_smooth=Data.Civ2_U;
715        Data.Civ2_V_smooth=Data.Civ2_V;
716        if isfield(Data,'Civ2_FF')
717            ind_good=find(Data.Civ2_FF==0);
718        else
719            ind_good=1:numel(Data.Civ2_X);
720        end
721        if isempty(ind_good)
722            disp_uvmat('ERROR','all vectors of civ2 are bad, check input parameters' ,checkrun)
723            return
724        end
725
726        [Data.Civ2_SubRange,Data.Civ2_NbCentres,Data.Civ2_Coord_tps,Data.Civ2_U_tps,Data.Civ2_V_tps,tild,Ures,Vres,tild,FFres]=...
727            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);
728        Data.Civ2_U_smooth(ind_good)=Ures;
729        Data.Civ2_V_smooth(ind_good)=Vres;
730        Data.Civ2_FF(ind_good)=FFres;
731        Data.CivStage=Data.CivStage+1;
732        time_patch2=toc(tstart_patch2);
733        disp('patch2 performed')
734    end
735
736    %% write result in a netcdf file if requested
737    % if CheckOutputFile
738    errormsg=struct2nc(ncfile_out,Data);
739    if isempty(errormsg)
740        disp([ncfile_out ' written'])
741        %[success,msg] = fileattrib(ncfile_out ,'+w','g');% done in struct2nc
742    else
743        disp(errormsg)
744    end
745    time_total=toc(tstart);
746    disp(['ellapsed time ' num2str(time_total/60,2) ' minutes'])
747    disp(['time civ1 ' num2str(time_civ1,2) ' s'])
748    disp(['time patch1 ' num2str(time_patch1,2) ' s'])
749    disp(['time civ2 ' num2str(time_civ2,2) ' s'])
750    disp(['time patch2 ' num2str(time_patch2,2) ' s'])
751
752end
753
754
755% 'civ': function piv.m adapted from PIVlab http://pivlab.blogspot.com/
756%--------------------------------------------------------------------------
757% function [xtable ytable utable vtable typevector] = civ (image1,image2,ibx,iby step, subpixfinder, mask, roi)
758%
759% OUTPUT:
760% xtable: set of x coordinates
761% ytable: set of y coordiantes
762% utable: set of u displacements (along x)
763% vtable: set of v displacements (along y)
764% ctable: max image correlation for each vector
765% typevector: set of flags, =1 for good, =0 for NaN vectors
766%
767%INPUT:
768% par_civ: structure of input parameters, with fields:
769%  .ImageA: first image for correlation (matrix)
770%  .ImageB: second image for correlation(matrix)
771%  .CorrBoxSize: 1,2 vector giving the size of the correlation box in x and y
772%  .SearchBoxSize:  1,2 vector giving the size of the search box in x and y
773%  .SearchBoxShift: 1,2 vector or 2 column matrix (for civ2) giving the shift of the search box in x and y
774%  .CorrSmooth: =1 or 2 determines the choice of the sub-pixel determination of the correlation max
775%  .ImageWidth: nb of pixels of the image in x
776%  .Dx, Dy: mesh for the PIV calculation
777%  .Grid: grid giving the PIV calculation points (alternative to .Dx .Dy): centres of the correlation boxes in Image A
778%  .Mask: name of a mask file or mask image matrix itself
779%  .MinIma: thresholds for image luminosity
780%  .MaxIma
781%  .CheckDeformation=1 for subpixel interpolation and image deformation (linear transform)
782%  .DUDX: matrix of deformation obtained from patch at each grid point
783%  .DUDY
784%  .DVDX:
785%  .DVDY
786
787function [xtable,ytable,utable,vtable,wtable,ctable,FF,result_conv,errormsg] = civ3D (par_civ)
788
789%% prepare measurement grid
790
791minix=floor(par_civ.Dx/2)-0.5;
792maxix=minix+par_civ.Dx*floor((par_civ.ImageWidth-1)/par_civ.Dx);
793miniy=floor(par_civ.Dy/2)-0.5;% first automatic grid point at half the mesh Dy
794maxiy=miniy+par_civ.Dy*floor((par_civ.ImageHeight-1)/par_civ.Dy);
795[GridX,GridY]=meshgrid(minix:par_civ.Dx:maxix,miniy:par_civ.Dy:maxiy);
796par_civ.Grid(:,:,1)=GridX;
797par_civ.Grid(:,:,2)=GridY;% increases with array index,
798[nbvec_y,nbvec_x,~]=size(par_civ.Grid);
799%
800%
801% minix=floor(par_civ.Dx/2)-0.5;
802%     maxix=minix+par_civ.Dx*floor((par_civ.ImageWidth-1)/par_civ.Dx);
803%     miniy=floor(par_civ.Dy/2)-0.5;% first automatic grid point at half the mesh Dy
804%     maxiy=miniy+par_civ.Dy*floor((par_civ.ImageHeight-1)/par_civ.Dy);
805%     [GridX,GridY]=meshgrid(minix:par_civ.Dx:maxix,miniy:par_civ.Dy:maxiy);
806%     par_civ.Grid(:,1)=reshape(GridX,[],1);
807%     par_civ.Grid(:,2)=reshape(GridY,[],1);% increases with array index
808
809%% prepare correlation and search boxes
810ibx2=floor(par_civ.CorrBoxSize(1)/2);
811iby2=floor(par_civ.CorrBoxSize(2)/2);
812isx2=floor(par_civ.SearchBoxSize(1)/2);
813isy2=floor(par_civ.SearchBoxSize(2)/2);
814isz2=floor(par_civ.SearchBoxSize(3)/2);
815kref=isz2+1;%middle index of the z slice
816shiftx=round(par_civ.SearchBoxShift(:,1));%use the input shift estimate, rounded to the next integer value
817shifty=-round(par_civ.SearchBoxShift(:,2));% sign minus because image j index increases when y decreases
818if numel(shiftx)==1% case of a unique shift for the whole field( civ1)
819    shiftx=shiftx*ones(nbvec_y,nbvec_x,1);
820    shifty=shifty*ones(nbvec_y,nbvec_x,1);
821end
822
823%% Array initialisation and default output  if par_civ.CorrSmooth=0 (just the grid calculated, no civ computation)
824xtable=round(par_civ.Grid(:,:,1)+0.5)-0.5;
825ytable=round(par_civ.ImageHeight-par_civ.Grid(:,:,2)+0.5)-0.5;% y index corresponding to the position in image coordiantes
826utable=shiftx;%zeros(nbvec,1);
827vtable=shifty;%zeros(nbvec,1);
828wtable=zeros(size(utable));
829ctable=zeros(nbvec_y,nbvec_x,1);
830FF=zeros(nbvec_y,nbvec_x,1);
831result_conv=[];
832errormsg='';
833
834%% prepare mask
835check_MinIma=isfield(par_civ,'MinIma');% test for image luminosity threshold
836check_MaxIma=isfield(par_civ,'MaxIma') && ~isempty(par_civ.MaxIma);
837
838[npz,npy_ima,npx_ima]=size(par_civ.ImageA);
839if ~isequal(size(par_civ.ImageB),[npz npy_ima npx_ima])
840    errormsg='image pair with unequal size';
841    return
842end
843
844%% Apply mask
845% Convention for mask, IDEAS NOT IMPLEMENTED
846% mask >200 : velocity calculated
847%  200 >=mask>150;velocity not calculated, interpolation allowed (bad spots)
848% 150>=mask >100: velocity not calculated, nor interpolated
849%  100>=mask> 20: velocity not calculated, impermeable (no flux through mask boundaries)
850%  20>=mask: velocity=0
851checkmask=0;
852MinA=min(min(min(par_civ.ImageA)));
853%MinB=min(min(par_civ.ImageB));
854%check_undefined=false(size(par_civ.ImageA));
855if isfield(par_civ,'Mask') && ~isempty(par_civ.Mask)
856    checkmask=1;
857    if ~isequal(size(par_civ.Mask),[npy_ima npx_ima])
858        errormsg='mask must be an image with the same size as the images';
859        return
860    end
861    check_undefined=(par_civ.Mask<200 & par_civ.Mask>=20 );
862end
863
864%% compute image correlations: MAINLOOP on velocity vectors
865corrmax=0;
866sum_square=1;% default
867mesh=1;% default
868CheckDeformation=isfield(par_civ,'CheckDeformation')&& par_civ.CheckDeformation==1;
869if CheckDeformation
870    mesh=0.25;%mesh in pixels for subpixel image interpolation (x 4 in each direction)
871    par_civ.CorrSmooth=2;% use SUBPIX2DGAUSS (take into account more points near the max)
872end
873
874if par_civ.CorrSmooth~=0 % par_civ.CorrSmooth=0 implies no civ computation (just input image and grid points given)
875    for ivec_x=1:nbvec_x
876        for ivec_y=1:nbvec_y
877            iref=round(par_civ.Grid(ivec_y,ivec_x,1)+0.5);% xindex on the image A for the middle of the correlation box
878            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
879            subrange1_x=iref-ibx2:iref+ibx2;% x indices defining the first subimage
880            subrange1_y=jref-iby2:jref+iby2;% y indices defining the first subimage
881            subrange2_x=iref+shiftx(ivec_y,ivec_x)-isx2:iref+shiftx(ivec_y,ivec_x)+isx2;%x indices defining the second subimage
882            subrange2_y=jref+shifty(ivec_y,ivec_x)-isy2:jref+shifty(ivec_y,ivec_x)+isy2;%y indices defining the second subimage
883            image1_crop=MinA*ones(npz,numel(subrange1_y),numel(subrange1_x));% default value=min of image A
884            image2_crop=MinA*ones(npz,numel(subrange2_y),numel(subrange2_x));% default value=min of image A
885            check1_x=subrange1_x>=1 & subrange1_x<=par_civ.ImageWidth;% check which points in the subimage 1 are contained in the initial image 1
886            check1_y=subrange1_y>=1 & subrange1_y<=par_civ.ImageHeight;
887            check2_x=subrange2_x>=1 & subrange2_x<=par_civ.ImageWidth;% check which points in the subimage 2 are contained in the initial image 2
888            check2_y=subrange2_y>=1 & subrange2_y<=par_civ.ImageHeight;
889            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
890            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
891            if checkmask
892                mask1_crop=ones(numel(subrange1_y),numel(subrange1_x));% default value=1 for mask
893                mask2_crop=ones(numel(subrange2_y),numel(subrange2_x));% default value=1 for mask
894                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
895                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
896                sizemask=sum(sum(mask1_crop))/(numel(subrange1_y)*numel(subrange1_x));%size of the masked part relative to the correlation sub-image
897                if sizemask > 1/2% eliminate point if more than half of the correlation box is masked
898                    FF(ivec_y,ivec_x)=1; %
899                    utable(ivec_y,ivec_x)=NaN;
900                    vtable(ivec_y,ivec_x)=NaN;
901                else
902                    FF(ivec_y,ivec_x)=0;
903                    image1_crop=image1_crop.*~mask1_crop;% put to zero the masked pixels (mask1_crop='true'=1)
904                    image2_crop=image2_crop.*~mask2_crop;
905                    image1_mean=mean(mean(image1_crop))/(1-sizemask);
906                    image2_mean=mean(mean(image2_crop))/(1-sizemask);
907                end
908            else
909                image1_mean=mean(mean(image1_crop));
910                image2_mean=mean(mean(image2_crop));
911            end
912            %threshold on image minimum
913            if FF(ivec_y,ivec_x)==0
914                if check_MinIma && (image1_mean < par_civ.MinIma || image2_mean < par_civ.MinIma)
915                    FF(ivec_y,ivec_x)=1;
916                    %threshold on image maximum
917                elseif check_MaxIma && (image1_mean > par_civ.MaxIma || image2_mean > par_civ.MaxIma)
918                    FF(ivec_y,ivec_x)=1;
919                end
920                if FF(ivec_y,ivec_x)==1
921                    utable(ivec_y,ivec_x)=NaN;
922                    vtable(ivec_y,ivec_x)=NaN;
923                else
924                    %mask
925                    if checkmask
926                        image1_crop=(image1_crop-image1_mean).*~mask1_crop;%substract the mean, put to zero the masked parts
927                        image2_crop=(image2_crop-image2_mean).*~mask2_crop;
928                    else
929                        image1_crop=(image1_crop-image1_mean);
930                        image2_crop=(image2_crop-image2_mean);
931                    end
932
933               
934                   
935                    for kz=1:par_civ.SearchBoxSize(3)
936                        subima2=squeeze(image2_crop(kz,:,:));
937                        subima1=squeeze(image1_crop(kref,:,:));
938                        correl_xy=conv2(subima2,flip(flip(subima1,2),1),'valid');
939                          result_conv(kz,:,:)= correl_xy;
940                        max_xy(kz)=max(max(correl_xy));
941                    [xk(kz),yk(kz)]=find(correl_xy==max_xy(kz),1);
942               
943                    end
944                    [corrmax,zmax]=max(max_xy);
945               
946                    x=xk(zmax);
947                    y=yk(zmax);
948                    result_conv=(result_conv/corrmax)*255; %normalize, peak=always 255
949                    subimage2_crop=squeeze(image2_crop(zmax,y:y+2*iby2/mesh,x:x+2*ibx2/mesh));%subimage of image 2 corresponding to the optimum displacement of first image
950                    sum_square=sum(sum(squeeze(image1_crop(zmax,:,:).*image1_crop(zmax,:,:))));
951                    sum_square=sum_square*sum(sum(subimage2_crop.*subimage2_crop));% product of variances of image 1 and 2
952                    sum_square=sqrt(sum_square);% srt of the variance product to normalise correlation
953                    if ~isempty(y) && ~isempty(x)
954       
955                            if par_civ.CorrSmooth==1
956                                [vector,FF(ivec_y,ivec_x)] = SUBPIXGAUSS (squeeze(result_conv(zmax,:,:)),x,y);%TODO: improve by max optimisation along z
957                            elseif par_civ.CorrSmooth==2
958                                [vector,FF(ivec_y,ivec_x)] = SUBPIX2DGAUSS (squeeze(result_conv(zmax,:,:)),x,y);
959                            else
960                                [vector,FF(ivec_y,ivec_x)] = quadr_fit(squeeze(result_conv(zmax,:,:)),x,y);
961                            end
962                            utable(ivec_y,ivec_x)=vector(1)*mesh+shiftx(ivec_y,ivec_x);
963                            vtable(ivec_y,ivec_x)=vector(2)*mesh+shifty(ivec_y,ivec_x);
964                            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)
965                            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)
966                            iref=round(xtable(ivec_y,ivec_x)+0.5);% nearest image index for the middle of the vector
967                            jref=round(ytable(ivec_y,ivec_x)+0.5);
968                            wtable(ivec_y,ivec_x)=zmax-kref;
969                            % eliminate vectors located in the mask
970                            if  checkmask && (iref<1 || jref<1 ||iref>npx_ima || jref>npy_ima ||( par_civ.Mask(jref,iref)<200 && par_civ.Mask(jref,iref)>=100))
971                                utable(ivec_y,ivec_x)=0;
972                                vtable(ivec_y,ivec_x)=0;
973                                FF(ivec_y,ivec_x)=1;
974                            end
975                            ctable(ivec_y,ivec_x)=corrmax/sum_square;% correlation value
976
977                    else
978                        FF(ivec_y,ivec_x)=true;
979                    end
980                end
981            end
982        end
983    end
984end
985result_conv=result_conv*corrmax/(255*sum_square);% keep the last correlation matrix for output
986
987%------------------------------------------------------------------------
988% --- Find the maximum of the correlation function after interpolation
989% OUPUT:
990% vector = optimum displacement vector with subpixel correction
991% FF =flag: ='true' max too close to the edge of the search box (1 pixel margin)
992% INPUT:
993% x,y: position of the maximum correlation at integer values
994
995function [vector,FF] = SUBPIXGAUSS (result_conv,x,y)
996%------------------------------------------------------------------------
997vector=[0 0]; %default
998[npy,npx]=size(result_conv);
999result_conv(result_conv<1)=1; %set to 1 correlation values smaller than 1  (=0 by discretisation, to avoid divergence in the log)
1000%the following 8 lines are copyright (c) 1998, Uri Shavit, Roi Gurka, Alex Liberzon, Technion ??? Israel Institute of Technology
1001%http://urapiv.wordpress.com
1002FF=false;
1003    peaky = y;
1004    if y < npy && y > 1
1005        f0 = log(result_conv(y,x));
1006        f1 = log(result_conv(y-1,x));
1007        f2 = log(result_conv(y+1,x));
1008        peaky = peaky+ (f1-f2)/(2*f1-4*f0+2*f2);
1009    else
1010        FF=true; % error flag for vector truncated by the limited search box in y
1011    end
1012    peakx=x;
1013    if x < npx-1 && x > 1
1014        f0 = log(result_conv(y,x));
1015        f1 = log(result_conv(y,x-1));
1016        f2 = log(result_conv(y,x+1));
1017        peakx = peakx+ (f1-f2)/(2*f1-4*f0+2*f2);
1018    else
1019        FF=true; % warning flag for vector truncated by the limited search box in x
1020    end
1021    vector=[peakx-floor(npx/2)-1 peaky-floor(npy/2)-1];
1022
1023%------------------------------------------------------------------------
1024% --- Find the maximum of the correlation function after interpolation
1025function [vector,F] = SUBPIX2DGAUSS (result_conv,x,y)
1026%------------------------------------------------------------------------
1027% vector=[0 0]; %default
1028F=1;
1029peaky=y;
1030peakx=x;
1031result_conv(result_conv<1)=1; %set to 1 correlation values smaller than 1 (to avoid divergence in the log)
1032[npy,npx]=size(result_conv);
1033if (x < npx) && (y < npy) && (x > 1) && (y > 1)
1034    F=0;
1035    for i=-1:1
1036        for j=-1:1
1037            %following 15 lines based on
1038            %H. Nobach ??? M. Honkanen (2005)
1039            %Two-dimensional Gaussian regression for sub-pixel displacement
1040            %estimation in particle image velocimetry or particle position
1041            %estimation in particle tracking velocimetry
1042            %Experiments in Fluids (2005) 38: 511???515
1043            c10(j+2,i+2)=i*log(result_conv(y+j, x+i));
1044            c01(j+2,i+2)=j*log(result_conv(y+j, x+i));
1045            c11(j+2,i+2)=i*j*log(result_conv(y+j, x+i));
1046            c20(j+2,i+2)=(3*i^2-2)*log(result_conv(y+j, x+i));
1047            c02(j+2,i+2)=(3*j^2-2)*log(result_conv(y+j, x+i));
1048        end
1049    end
1050    c10=(1/6)*sum(sum(c10));
1051    c01=(1/6)*sum(sum(c01));
1052    c11=(1/4)*sum(sum(c11));
1053    c20=(1/6)*sum(sum(c20));
1054    c02=(1/6)*sum(sum(c02));
1055    deltax=(c11*c01-2*c10*c02)/(4*c20*c02-c11^2);
1056    deltay=(c11*c10-2*c01*c20)/(4*c20*c02-c11^2);
1057    if abs(deltax)<1
1058        peakx=x+deltax;
1059    end
1060    if abs(deltay)<1
1061        peaky=y+deltay;
1062    end
1063end
1064vector=[peakx-floor(npx/2)-1 peaky-floor(npy/2)-1];
1065
1066%------------------------------------------------------------------------
1067% --- Find the maximum of the correlation function after quadratic interpolation
1068function [vector,F] = quadr_fit(result_conv,x,y)
1069[npy,npx]=size(result_conv);
1070if x<4 || y<4 || npx-x<4 ||npy-y <4
1071    F=1;
1072    vector=[x y];
1073else
1074    F=0;
1075    x_ind=x-4:x+4;
1076    y_ind=y-4:y+4;
1077    x_vec=0.25*(x_ind-x);
1078    y_vec=0.25*(y_ind-y);
1079    [X,Y]=meshgrid(x_vec,y_vec);
1080    coord=[reshape(X,[],1) reshape(Y,[],1)];
1081    result_conv=reshape(result_conv(y_ind,x_ind),[],1);
1082   
1083   
1084    % n=numel(X);
1085    % x=[X Y];
1086    % X=X-0.5;
1087    % Y=Y+0.5;
1088    % y = (X.*X+2*Y.*Y+X.*Y+6) + 0.1*rand(n,1);
1089    p = polyfitn(coord,result_conv,2);
1090    A(1,1)=2*p.Coefficients(1);
1091    A(1,2)=p.Coefficients(2);
1092    A(2,1)=p.Coefficients(2);
1093    A(2,2)=2*p.Coefficients(4);
1094    vector=[x y]'-A\[p.Coefficients(3) p.Coefficients(5)]';
1095    vector=vector'-[floor(npx/2) floor(npy/2)]-1 ;
1096    % zg = polyvaln(p,coord);
1097    % figure
1098    % surf(x_vec,y_vec,reshape(zg,9,9))
1099    % hold on
1100    % plot3(X,Y,reshape(result_conv,9,9),'o')
1101    % hold off
1102end
1103
1104
1105function FF=detect_false(Param,C,U,V,FFIn)
1106FF=FFIn;%default, good vectors
1107% FF=1, for correlation max at edge, not set in this function
1108% FF=2, for too small correlation
1109% FF=3, for velocity outside bounds
1110% FF=4 for exclusion by difference with the smoothed field, not set in this function
1111
1112if isfield (Param,'MinCorr')
1113     FF(C<Param.MinCorr & FFIn==0)=2;
1114end
1115if (isfield(Param,'MinVel')&&~isempty(Param.MinVel))||(isfield (Param,'MaxVel')&&~isempty(Param.MaxVel))
1116    Umod= U.*U+V.*V;
1117    if isfield (Param,'MinVel')&&~isempty(Param.MinVel)
1118        U2Min=Param.MinVel*Param.MinVel;
1119        FF(Umod<U2Min & FFIn==0)=3;
1120    end
1121    if isfield (Param,'MaxVel')&&~isempty(Param.MaxVel)
1122         U2Max=Param.MaxVel*Param.MaxVel;
1123        FF(Umod>U2Max & FFIn==0)=3;
1124    end
1125end
1126
1127%------------------------------------------------------------------------
1128% --- determine the list of index pairs of processing file
1129function [i1_series,i2_series,j1_series,j2_series,check_bounds,NomTypeNc]=...
1130    find_pair_indices(str_civ,i_series,j_series,MinIndex_i,MaxIndex_i,MinIndex_j,MaxIndex_j)
1131%------------------------------------------------------------------------
1132i1_series=i_series;% set of first image indexes
1133i2_series=i_series;
1134j1_series=j_series;%ones(size(i_series));% set of first image numbers
1135j2_series=j_series;%ones(size(i_series));
1136r=regexp(str_civ,'^\D(?<ind>[i|j])=( -| )(?<num1>\d+)\|(?<num2>\d+)','names');
1137if ~isempty(r)
1138    mode=['D' r.ind];
1139    ind1=str2num(r.num1);
1140    ind2=str2num(r.num2);
1141else
1142    mode='j1-j2';
1143    r=regexp(str_civ,'^j= (?<num1>[a-z])-(?<num2>[a-z])','names');
1144    if ~isempty(r)
1145        NomTypeNc='_1ab';
1146    else
1147        r=regexp(str_civ,'^j= (?<num1>[A-Z])-(?<num2>[A-Z])','names');
1148        if ~isempty(r)
1149            NomTypeNc='_1AB';
1150        else
1151            r=regexp(str_civ,'^j= (?<num1>\d+)-(?<num2>\d+)','names');
1152            if ~isempty(r)
1153                NomTypeNc='_1_1-2';
1154            end
1155        end
1156    end
1157    if isempty(r)
1158        display('wrong pair mode input option')
1159    else
1160        ind1=stra2num(r.num1);
1161        ind2=stra2num(r.num2);
1162    end
1163end
1164switch mode
1165    case 'Di'
1166        i1_series=i_series-ind1;% set of first image numbers
1167        i2_series=i_series+ind2;
1168        check_bounds=i1_series<MinIndex_i | i2_series>MaxIndex_i;
1169        if isempty(j_series)
1170            NomTypeNc='_1-2';
1171        else
1172            j1_series=j_series;
1173            j2_series=j_series;
1174            NomTypeNc='_1-2_1';
1175        end
1176    case 'Dj'
1177        j1_series=j_series-ind1;
1178        j2_series=j_series+ind2;
1179        check_bounds=j1_series<MinIndex_j | j2_series>MaxIndex_j;
1180        NomTypeNc='_1_1-2';
1181    otherwise %bursts
1182        i1_series=i_series(1,:);% do not sweep the j index
1183        i2_series=i_series(1,:);
1184        j1_series=ind1*ones(1,size(i_series,2));% j index is fixed by pair choice
1185        j2_series=ind2*ones(1,size(i_series,2));
1186        check_bounds=zeros(size(i1_series));% no limitations due to min-max indices
1187end
1188
1189
1190
1191
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