source: trunk/src/series/civ_series.m @ 1096

Last change on this file since 1096 was 1096, checked in by sommeria, 4 years ago

bugs fixed

File size: 68.7 KB
Line 
1%'civ_series': PIV function activated by the general GUI series
2% --- call the sub-functions:
3%   civ: PIV function itself
4%   fix: removes false vectors after detection by various criteria
5%   filter_tps: make interpolation-smoothing
6%------------------------------------------------------------------------
7% function [Data,errormsg,result_conv]= civ_series(Param)
8%
9%OUTPUT
10% Data=structure containing the PIV results and information on the processing parameters
11% errormsg=error message char string, decd ..fault=''
12% resul_conv: image inter-correlation function for the last grid point (used for tests)
13%
14%INPUT:
15% Param: Matlab structure of input  parameters
16%     Param contains info of the GUI series using the fct read_GUI.
17%     Param.Action.RUN = 0 (to set the status of the GUI series) or =1 to RUN the computation
18%     Param.InputTable: sets the input file(s)
19%           if absent, the fct looks for input data in Param.ActionInput     (test mode)
20%     Param.OutputSubDir: sets the folder name of output file(s,
21%           if absent no file is produced, result in the output structure Data (test mode)
22%     Param.ActionInput: substructure with the parameters provided by the GUI civ_input
23%                      .Civ1: parameters for civ1
24%                      .Fix1: parameters for fix1
25%                      .Patch1:
26%                      .Civ2: for civ2
27%                      .Fix2:
28%                      .Patch2:
29
30%=======================================================================
31% Copyright 2008-2021, LEGI UMR 5519 / CNRS UGA G-INP, Grenoble, France
32%   http://www.legi.grenoble-inp.fr
33%   Joel.Sommeria - Joel.Sommeria (A) legi.cnrs.fr
34%
35%     This file is part of the toolbox UVMAT.
36%
37%     UVMAT is free software; you can redistribute it and/or modify
38%     it under the terms of the GNU General Public License as published
39%     by the Free Software Foundation; either version 2 of the license,
40%     or (at your option) any later version.
41%
42%     UVMAT is distributed in the hope that it will be useful,
43%     but WITHOUT ANY WARRANTY; without even the implied warranty of
44%     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
45%     GNU General Public License (see LICENSE.txt) for more details.
46%=======================================================================
47
48function [Data,errormsg,result_conv]= civ_series(Param)
49errormsg='';
50
51%% set the input elements needed on the GUI series when the action is selected in the menu ActionName or InputTable refreshed
52if isstruct(Param) && isequal(Param.Action.RUN,0)% function activated from the GUI series but not RUN
53    path_series=fileparts(which('series'));
54    addpath(fullfile(path_series,'series'))
55    Data=civ_input(Param);% introduce the civ parameters using the GUI civ_input
56    %Data=civ_input_App(Param);% introduce the civ parameters using the GUI civ_input
57    if isempty(Data)
58        Data=Param;% if  civ_input has been cancelled, keep previous parameters
59    end
60    Data.Program=mfilename;%gives the name of the current function
61    Data.AllowInputSort='off';% allow alphabetic sorting of the list of input file SubDir (options 'off'/'on', 'off' by default)
62    Data.WholeIndexRange='off';% prescribes the file index ranges from min to max (options 'off'/'on', 'off' by default)
63    Data.NbSlice='off'; %nbre of slices ('off' by default)
64    Data.VelType='off';% menu for selecting the velocity type (options 'off'/'one'/'two',  'off' by default)
65    Data.FieldName='on';% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default)
66    Data.FieldTransform = 'off';%can use a transform function
67    Data.ProjObject='off';%can use projection object(option 'off'/'on',
68    Data.Mask='off';%can use mask option   (option 'off'/'on', 'off' by default)
69    Data.OutputDirExt='.civ';%set the output dir extension
70    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)
71    Data.OutputFileMode='NbInput_i';% one output file expected per value of i index (used for waitbar)
72    Data.CheckOverwriteVisible='on'; % manage the overwrite of existing files (default=1)
73    if isfield(Data.ActionInput,'PairIndices') && strcmp(Data.ActionInput.PairIndices.ListPairMode,'pair j1-j2')
74        if isfield(Data.ActionInput.PairIndices,'ListPairCiv2')
75            str_civ=Data.ActionInput.PairIndices.ListPairCiv2;
76        else
77            str_civ=Data.ActionInput.PairIndices.ListPairCiv1;
78        end
79        r=regexp(str_civ,'^j= (?<num1>[a-z])-(?<num2>[a-z])','names');
80        if isempty(r)
81            r=regexp(str_civ,'^j= (?<num1>[A-Z])-(?<num2>[A-Z])','names');
82            if isempty(r)
83                r=regexp(str_civ,'^j= (?<num1>\d+)-(?<num2>\d+)','names');
84            end
85        end
86        if ~isempty(r)
87            Data.j_index_1=stra2num(r.num1);
88            Data.j_index_2=stra2num(r.num2);
89        end
90    end
91    % estimated CPUTime
92    CPUtime_unit=0.01;%estimated time for a multiplication (in microsecond)
93    if isfield(Param.SeriesData,'FileInfo')&&isfield(Param.SeriesData.FileInfo{1},'Height')&&isfield(Param.SeriesData.FileInfo{1},'Width')
94        pixnbre=Param.SeriesData.FileInfo{1}.Height*Param.SeriesData.FileInfo{1}.Width; % total number of pxels for input images 
95        CPUtime=0;
96        if isfield(Data.ActionInput,'Civ1')
97            %BoxSize=Data.ActionInput.Civ1.CorrBoxSize(1)*Data.ActionInput.Civ1.CorrBoxSize(2);
98            tic
99            testboxa=rand(Data.ActionInput.Civ1.CorrBoxSize(1),Data.ActionInput.Civ1.CorrBoxSize(2));
100            testboxb=rand(Data.ActionInput.Civ1.SearchBoxSize(1),Data.ActionInput.Civ1.SearchBoxSize(2));
101            anss=conv2(testboxa,testboxb);
102            CPUtime_unit=toc;
103            nb_box=pixnbre/(Data.ActionInput.Civ1.Dx*Data.ActionInput.Civ1.Dy);   
104            %nbpos=Data.ActionInput.Civ1.SearchBoxSize-Data.ActionInput.Civ1.CorrBoxSize;
105            CPUtime=2*CPUtime_unit*nb_box%*BoxSize*nbpos(1)*nbpos(2);% adjustement factor 2 used
106        end
107        if isfield(Data.ActionInput,'Patch1')
108            CPUtime=2*CPUtime;
109        end
110        if isfield(Data.ActionInput,'Civ2')
111            tic
112            testboxa=rand(Data.ActionInput.Civ2.CorrBoxSize(1),Data.ActionInput.Civ2.CorrBoxSize(2));
113            testboxb=rand(Data.ActionInput.Civ2.SearchBoxSize(1),Data.ActionInput.Civ2.SearchBoxSize(2));
114            anss=conv2(testboxa,testboxb);
115            CPUtime_unit=toc;
116            nb_box=pixnbre/(Data.ActionInput.Civ2.Dx*Data.ActionInput.Civ2.Dy);
117            %BoxSize=Data.ActionInput.Civ2.CorrBoxSize(1)*Data.ActionInput.Civ2.CorrBoxSize(2);
118            %nbpos=Data.ActionInput.Civ2.SearchBoxSize-Data.ActionInput.Civ2.CorrBoxSize;
119            CPUtime=CPUtime+2*CPUtime_unit*nb_box;%*BoxSize*nbpos(1)*nbpos(2);
120        end
121        if isfield(Data.ActionInput,'Patch2')
122            CPUtime=(4/3)*CPUtime;
123        end
124        Data.CPUTime=ceil(CPUtime/6); % estimated CPU time per field pair in minute
125        Data.CPUTime=Data.CPUTime/10; % displqy CPU time with 1 digit beyond dot
126    end
127    return
128end
129
130%% read input parameters from an xml file if input is a file name (batch mode)
131checkrun=1;
132if ischar(Param)
133    Param=xml2struct(Param);% read Param as input file (batch case)
134    checkrun=0;
135end
136
137%% test input
138if ~isfield(Param,'ActionInput')
139    disp_uvmat('ERROR','no parameter set for PIV',checkrun)
140    return
141end
142iview_A=0;%default values
143NbField=1;
144RUNHandle=[];
145CheckInputFile=isfield(Param,'InputTable');%= 1 in test use for TestCiv (no nc file involved)
146CheckOutputFile=isfield(Param,'OutputSubDir');%= 1 in test use for TestPatch (no nc file produced)
147
148%% input files and indexing (skipped in Test mode)
149if CheckInputFile
150    hseries=findobj(allchild(0),'Tag','series');
151    RUNHandle=findobj(hseries,'Tag','RUN');%handle of RUN button in GUI series
152    WaitbarHandle=findobj(hseries,'Tag','Waitbar');%handle of waitbar in GUI series
153    MaxIndex_i=Param.IndexRange.MaxIndex_i;
154    MinIndex_i=Param.IndexRange.MinIndex_i;
155    MaxIndex_j=ones(size(MaxIndex_i));MinIndex_j=ones(size(MinIndex_i));
156    if isfield(Param.IndexRange,'MaxIndex_j')&& isfield(Param.IndexRange,'MinIndex_j')
157        MaxIndex_j=Param.IndexRange.MaxIndex_j;
158        MinIndex_j=Param.IndexRange.MinIndex_j;
159    end
160    if isfield(Param,'InputTable')
161        [tild,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param);
162        iview_A=0;% series index (iview) for the first image series
163        iview_B=0;% series index (iview) for the second image series (only non zero for option 'shift' comparing two image series )
164        if Param.ActionInput.CheckCiv1
165            iview_A=1;% usual PIV, the image series is on the first line of the table
166        elseif Param.ActionInput.CheckCiv2 % civ2 is performed without Civ1, a netcdf file series is needed in the first table line
167            iview_A=2;% the second line is used for the input images of Civ2
168        end
169%         if strcmp(Param.ActionInput.ListCompareMode,'shift')
170%             iview_B=iview_A+1; % the second image series is on the next line of the input table
171%         end
172        if iview_A~=0
173            RootPath_A=Param.InputTable{iview_A,1};
174            RootFile_A=Param.InputTable{iview_A,3};
175            SubDir_A=Param.InputTable{iview_A,2};
176            NomType_A=Param.InputTable{iview_A,4};
177            FileExt_A=Param.InputTable{iview_A,5};
178            if iview_B==0
179                iview_B=iview_A;% the second image series is the same as the first
180            end
181            RootPath_B=Param.InputTable{iview_B,1};
182            RootFile_B=Param.InputTable{iview_B,3};
183            SubDir_B=Param.InputTable{iview_B,2};
184            NomType_B=Param.InputTable{iview_B,4};
185            FileExt_B=Param.InputTable{iview_B,5};
186        end
187       
188        PairCiv2='';
189        switch Param.ActionInput.ListCompareMode
190            case 'PIV'
191                PairCiv1=Param.ActionInput.PairIndices.ListPairCiv1;
192                if isfield(Param.ActionInput.PairIndices,'ListPairCiv2')
193                    PairCiv2=Param.ActionInput.PairIndices.ListPairCiv2;%string which determines the civ2 pair
194                end
195                if iview_A==1% if Civ1 is performed
196                    [i1_series_Civ1,i2_series_Civ1,j1_series_Civ1,j2_series_Civ1,check_bounds,NomTypeNc]=...
197                        find_pair_indices(PairCiv1,i1_series{1},j1_series{1},MinIndex_i,MaxIndex_i,MinIndex_j,MaxIndex_j);
198                    if ~isempty(PairCiv2)
199                        [i1_series_Civ2,i2_series_Civ2,j1_series_Civ2,j2_series_Civ2,check_bounds_Civ2]=...
200                            find_pair_indices(PairCiv2,i1_series{1},j1_series{1},MinIndex_i(1),MaxIndex_i(1),MinIndex_j(1),MaxIndex_j(1));
201                        check_bounds=check_bounds | check_bounds_Civ2;
202                    end
203                else% we start from an existing Civ1 file
204                    i1_series_Civ1=i1_series{1};
205                    i2_series_Civ1=i2_series{1};
206                    j1_series_Civ1=j1_series{1};
207                    j2_series_Civ1=j2_series{1};
208                    NomTypeNc=Param.InputTable{1,4};
209                    if ~isempty(PairCiv2)
210                        [i1_series_Civ2,i2_series_Civ2,j1_series_Civ2,j2_series_Civ2,check_bounds,NomTypeNc]=...
211                            find_pair_indices(PairCiv2,i1_series{2},j1_series{2},MinIndex_i(2),MaxIndex_i(2),MinIndex_j(2),MaxIndex_j(2));
212                    end
213                end
214            case 'displacement'
215                if isfield(Param.ActionInput,'OriginIndex')
216                i1_series_Civ1=Param.ActionInput.OriginIndex*ones(size(i1_series{1}));
217                else
218                    i1_series_Civ1=ones(size(i1_series{1}));
219                end
220                i1_series_Civ2=i1_series_Civ1;
221                i2_series_Civ1=i1_series{1};
222                i2_series_Civ2=i1_series{1};
223                j1_series_Civ1=[];% no j index variation for the ref image
224                j1_series_Civ2=[];
225                if isempty(j1_series{1})
226                    j2_series_Civ1=ones(size(i1_series_Civ1));
227                else
228                    j2_series_Civ1=j1_series{1};% if j index exist 
229                end
230                j2_series_Civ2=j2_series_Civ1;
231                NomTypeNc='_1';
232            case 'PIV volume'
233                % TODO, TODO
234        end
235        %determine frame indices for input with movie or other multiframe input file
236        if isempty(j1_series_Civ1)% simple movie with index i
237            FrameIndex_A_Civ1=i1_series_Civ1;
238            FrameIndex_B_Civ1=i2_series_Civ1;
239            j1_series_Civ1=ones(size(i1_series_Civ1));
240            if strcmp(Param.ActionInput.ListCompareMode,'PIV')
241            j2_series_Civ1=ones(size(i1_series_Civ1));
242            end
243        else % movie for each burst or volume (index j)
244            FrameIndex_A_Civ1=j1_series_Civ1;
245            FrameIndex_B_Civ1=j2_series_Civ1;
246        end
247        if isempty(PairCiv2)
248            FrameIndex_A_Civ2=FrameIndex_A_Civ1;
249            FrameIndex_B_Civ2=FrameIndex_B_Civ1;
250        else
251            if isempty(j1_series_Civ2)
252                FrameIndex_A_Civ2=i1_series_Civ2;
253                FrameIndex_B_Civ2=i2_series_Civ2;
254                j1_series_Civ2=ones(size(i1_series_Civ2));
255                if strcmp(Param.ActionInput.ListCompareMode,'PIV')
256                j2_series_Civ2=ones(size(i1_series_Civ2));
257                end
258            else
259                FrameIndex_A_Civ2=j1_series_Civ2;
260                FrameIndex_B_Civ2=j2_series_Civ2;
261            end
262        end
263        if isempty(i1_series_Civ1)||(~isempty(PairCiv2) && isempty(i1_series_Civ2))
264            disp_uvmat('ERROR','no image pair for civ in the input file index range',checkrun)
265            return
266        end
267    end
268   
269    %% check the first image pair
270        if Param.ActionInput.CheckCiv1% Civ1 is performed
271            NbField=numel(i1_series_Civ1);
272        elseif Param.ActionInput.CheckCiv2 % Civ2 is performed without Civ1
273            NbField=numel(i1_series_Civ2);
274        else
275            NbField=numel(i1_series_Civ1);% no image used (only fix or patch) TO CHECK
276        end
277
278    %% Output directory
279    OutputDir='';
280    if CheckOutputFile
281        OutputDir=[Param.OutputSubDir Param.OutputDirExt];
282    end
283end
284
285%% prepare output Data
286ListGlobalAttribute={'Conventions','Program','CivStage'};
287Data.Conventions='uvmat/civdata';% states the conventions used for the description of field variables and attributes
288Data.Program='civ_series';
289Data.CivStage=0;%default
290check_civx=0;%default
291
292%% get timing from the ImaDoc file or input video
293if iview_A~=0
294    XmlFileName=find_imadoc(RootPath_A,SubDir_A,RootFile_A,FileExt_A);
295    Time=[];
296    if ~isempty(XmlFileName)
297        XmlData=imadoc2struct(XmlFileName);
298        if isfield(XmlData,'Time')
299            Time=XmlData.Time;
300        end
301        if isfield(XmlData,'Camera')
302            if isfield(XmlData.Camera,'NbSlice')&& ~isempty(XmlData.Camera.NbSlice)
303                NbSlice_calib{iview}=XmlData.Camera.NbSlice;% Nbre of slices for Zindex in phys transform
304                if ~isequal(NbSlice_calib{iview},NbSlice_calib{1})
305                    msgbox_uvmat('WARNING','inconsistent number of Z indices for the two field series');
306                end
307            end
308            if isfield(XmlData.Camera,'TimeUnit')&& ~isempty(XmlData.Camera.TimeUnit)
309                TimeUnit=XmlData.Camera.TimeUnit;
310            end
311        end
312    end
313end
314
315%%%%% MAIN LOOP %%%%%%
316maskoldname='';% initiate the mask name
317FileType_A='';
318FileType_B='';
319CheckOverwrite=1;%default
320if isfield(Param,'CheckOverwrite')
321    CheckOverwrite=Param.CheckOverwrite;
322end
323for ifield=1:NbField
324    tic
325    if ~isempty(RUNHandle)% update the waitbar in interactive mode with GUI series  (checkrun=1)
326        update_waitbar(WaitbarHandle,ifield/NbField)
327        if  checkrun && ~strcmp(get(RUNHandle,'BusyAction'),'queue')
328            disp('program stopped by user')
329            break
330        end
331    end
332    if CheckInputFile
333        OutputPath=fullfile(Param.OutputPath,num2str(Param.Experiment),num2str(Param.Device));
334        if iview_A==0 % no nc file has been entered
335            ncfile=fullfile_uvmat(OutputPath,Param.InputTable{1,2},Param.InputTable{1,3},Param.InputTable{1,5},...
336                NomTypeNc,i1_series_Civ1(ifield),i2_series_Civ1(ifield),j1_series_Civ1(ifield),j2_series_Civ1(ifield));
337        else% an existing nc file has been entered
338            if iview_A==1% if Civ1 is performed
339                Civ1Dir=OutputDir;
340            else
341                Civ1Dir=Param.InputTable{1,2};
342            end
343            if strcmp(Param.ActionInput.ListCompareMode,'PIV')
344                ncfile=fullfile_uvmat(OutputPath,Civ1Dir,RootFile_A,'.nc',NomTypeNc,i1_series_Civ1(ifield),i2_series_Civ1(ifield),...
345                    j1_series_Civ1(ifield),j2_series_Civ1(ifield));
346            else
347                ncfile=fullfile_uvmat(OutputPath,Civ1Dir,RootFile_A,'.nc',NomTypeNc,i2_series_Civ1(ifield),[],...
348                    j1_series_Civ1(ifield),j2_series_Civ1(ifield));
349            end
350        end
351        ncfile_out=ncfile;% by default
352       
353        if isfield (Param.ActionInput,'Civ2')
354            i1_civ2=i1_series_Civ2(ifield);
355            i2_civ2=i1_civ2;
356            if ~isempty(i2_series_Civ2)
357                i2_civ2=i2_series_Civ2(ifield);
358            end
359            j1_civ2=1;
360            if ~isempty(j1_series_Civ2)
361                j1_civ2=j1_series_Civ2(ifield);
362            end
363            j2_civ2=i1_civ2;
364            if ~isempty(j2_series_Civ2)
365                j2_civ2=j2_series_Civ2(ifield);
366            end
367            if strcmp(Param.ActionInput.ListCompareMode,'PIV')
368                ncfile_out=fullfile_uvmat(OutputPath,OutputDir,RootFile_A,'.nc',NomTypeNc,i1_civ2,i2_civ2,j1_civ2,j2_civ2);
369%                 ncfile_out=fullfile_uvmat(RootPath_A,OutputDir,RootFile_A,'.nc',NomTypeNc,i1_civ2,i2_civ2,j1_civ2,j2_civ2);
370            else % displacement
371                ncfile_out=fullfile_uvmat(OutputPath,OutputDir,RootFile_A,'.nc',NomTypeNc,i2_civ2,[],j2_civ2);
372            end
373        end
374        if ~CheckOverwrite && exist(ncfile_out,'file')
375            disp(['existing output file ' ncfile_out ' already exists, skip to next field'])
376            continue% skip iteration if the mode overwrite is desactivated and the result file already exists
377        end
378    end
379    %% Civ1
380    % if Civ1 computation is requested
381    if isfield (Param.ActionInput,'Civ1')
382        if CheckInputFile
383            disp('civ1 started')
384        end
385        par_civ1=Param.ActionInput.Civ1;% parameters for civ1
386        if CheckInputFile % read input images (except in mode Test where it is introduced directly in Param.ActionInput.Civ1.ImageNameA and B)
387            try
388                if strcmp(Param.ActionInput.ListCompareMode,'displacement')
389                    ImageName_A=Param.ActionInput.RefFile;
390                else
391                ImageName_A=fullfile_uvmat(RootPath_A,SubDir_A,RootFile_A,FileExt_A,NomType_A,i1_series_Civ1(ifield),[],j1_series_Civ1(ifield));
392                end
393                if strcmp(FileExt_A,'.nc')% case of input images in format netcdf
394                    FieldName_A=Param.InputFields.FieldName;
395                    [DataIn,tild,tild,errormsg]=nc2struct(ImageName_A,{FieldName_A});
396                    par_civ1.ImageA=DataIn.(FieldName_A);
397                else % usual image formats for image A
398                    if isempty(FileType_A)% open the image object if not already done in case of movie input
399                        [FileInfo_A,VideoObject_A]=get_file_info(ImageName_A);
400                        FileType_A=FileInfo_A.FileType;
401                        if isempty(Time) && ~isempty(find(strcmp(FileType_A,{'mmreader','video','cine_phantom'})))% case of video input
402                            Time=zeros(FileInfo_A.NumberOfFrames+1,2);
403                            Time(:,2)=(0:1/FileInfo_A.FrameRate:(FileInfo_A.NumberOfFrames)/FileInfo_A.FrameRate)';
404                        end
405                        if ~isempty(FileType_A) && isempty(Time)% Time = index i +0.001 index j by default
406                            MaxIndex_i=max(i2_series_Civ1);
407                            MaxIndex_j=max(j2_series_Civ1);
408                            Time=(1:MaxIndex_i)'*ones(1,MaxIndex_j);
409                            Time=Time+0.001*ones(MaxIndex_i,1)*(1:MaxIndex_j);
410                            Time=[zeros(1,MaxIndex_j);Time];% insert a first line of zeros
411                            Time=[zeros(MaxIndex_i+1,1) Time];% insert a first column of zeros
412                        end
413                    end
414                    if isempty(regexp(ImageName_A,'(^http://)|(^https://)')) && ~exist(ImageName_A,'file')
415                        disp([ImageName_A ' missing'])
416                        continue
417                    end
418                    [par_civ1.ImageA,VideoObject_A] = read_image(ImageName_A,FileType_A,VideoObject_A,FrameIndex_A_Civ1(ifield));
419                end
420                ImageName_B=fullfile_uvmat(RootPath_B,SubDir_B,RootFile_B,FileExt_B,NomType_B,i2_series_Civ1(ifield),[],j2_series_Civ1(ifield));
421                if strcmp(FileExt_B,'.nc') % case of input images in format netcdf
422                    FieldName_B=Param.InputFields.FieldName;
423                    [DataIn,tild,tild,errormsg]=nc2struct(ImageName_B,{FieldName_B});
424                    par_civ1.ImageB=DataIn.(FieldName_B);
425                else % usual image formats for image B
426                    if isempty(FileType_B)
427                        [FileInfo_B,VideoObject_B]=get_file_info(ImageName_B);
428                        FileType_B=FileInfo_B.FileType;
429                    end
430                    if isempty(regexp(ImageName_B,'(^http://)|(^https://)')) && ~exist(ImageName_B,'file')
431                        disp([ImageName_B ' missing'])
432                        continue
433                    end
434                    [par_civ1.ImageB,VideoObject_B] = read_image(ImageName_B,FileType_B,VideoObject_B,FrameIndex_B_Civ1(ifield));
435                end
436            catch ME % display errors in reading input images
437                if ~isempty(ME.message)
438                    disp_uvmat('ERROR', ['error reading input image: ' ME.message],checkrun)
439                    continue
440                end
441            end
442            par_civ1.ImageWidth=size(par_civ1.ImageA,2);
443            par_civ1.ImageHeight=size(par_civ1.ImageA,1);
444            list_param=(fieldnames(Param.ActionInput.Civ1))';
445            list_param(strcmp('TestCiv1',list_param))=[];% remove the parameter TestCiv1 from the list
446            Civ1_param=regexprep(list_param,'^.+','Civ1_$0');% insert 'Civ1_' before  each string in list_param
447            Civ1_param=[{'Civ1_ImageA','Civ1_ImageB','Civ1_Time','Civ1_Dt'} Civ1_param]; %insert the names of the two input images
448            %indicate the values of all the global attributes in the output data
449            Data.Civ1_ImageA=ImageName_A;
450            Data.Civ1_ImageB=ImageName_B;
451            i1=i1_series_Civ1(ifield);
452            i2=i1;
453            if ~isempty(i2_series_Civ1)
454                i2=i2_series_Civ1(ifield);
455            end
456            j1=1;
457            if ~isempty(j1_series_Civ1)
458                j1=j1_series_Civ1(ifield);
459            end
460            j2=j1;
461            if ~isempty(j2_series_Civ1)
462                j2=j2_series_Civ1(ifield);
463            end
464            if strcmp(Param.ActionInput.ListCompareMode,'displacement')
465                Data.Civ1_Time=Time(i2+1,j2+1);% the Time is the Time of the secodn image
466                Data.Civ1_Dt=1;% Time interval is 1, to yield displacement instead of velocity=displacement/Dt at reading
467            else
468                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
469                Data.Civ1_Dt=Time(i2+1,j2+1)-Time(i1+1,j1+1);
470            end
471            for ilist=1:length(list_param)
472                Data.(Civ1_param{4+ilist})=Param.ActionInput.Civ1.(list_param{ilist});
473            end
474            Data.ListGlobalAttribute=[ListGlobalAttribute Civ1_param];
475            Data.CivStage=1;
476        end
477        % set the list of variables
478        Data.ListVarName={'Civ1_X','Civ1_Y','Civ1_U','Civ1_V','Civ1_F','Civ1_C'};%  cell array containing the names of the fields to record
479        Data.VarDimName={'nb_vec_1','nb_vec_1','nb_vec_1','nb_vec_1','nb_vec_1','nb_vec_1'};
480        Data.VarAttribute{1}.Role='coord_x';
481        Data.VarAttribute{2}.Role='coord_y';
482        Data.VarAttribute{3}.Role='vector_x';
483        Data.VarAttribute{4}.Role='vector_y';
484        Data.VarAttribute{5}.Role='warnflag';
485        % case of mask
486        if par_civ1.CheckMask&&~isempty(par_civ1.Mask)
487            if isfield(par_civ1,'NbSlice')
488                [RootPath_mask,SubDir_mask,RootFile_mask,i1_mask,i2_mask,j1_mask,j2_mask,Ext_mask]=fileparts_uvmat(Param.ActionInput.Civ1.Mask);
489                i1_mask=mod(i1-1,par_civ1.NbSlice)+1;
490                maskname=fullfile_uvmat(RootPath_mask,SubDir_mask,RootFile_mask,Ext_mask,'_1',i1_mask);
491            else
492                maskname=Param.ActionInput.Civ1.Mask;
493            end
494            if strcmp(maskoldname,maskname)% mask exist, not already read in civ1
495                par_civ1.Mask=mask; %use mask already opened
496            else
497                if ~isempty(regexp(maskname,'(^http://)|(^https://)'))|| exist(maskname,'file')
498                    try
499                        par_civ1.Mask=imread(maskname);%update the mask, an store it for future use
500                    catch ME
501                        if ~isempty(ME.message)
502                            errormsg=['error reading input image: ' ME.message];
503                            disp_uvmat('ERROR',errormsg,checkrun)
504                            return
505                        end
506                    end
507                else
508                    par_civ1.Mask=[];
509                end
510                mask=par_civ1.Mask;
511                maskoldname=maskname;
512            end
513        end
514        if strcmp(Param.ActionInput.ListCompareMode, 'PIV volume')
515            Data.ListVarName=[Data.ListVarName 'Civ1_Z'];
516            Data.Civ1_X=[];Data.Civ1_Y=[];Data.Civ1_Z=[];
517            Data.Civ1_U=[];Data.Civ1_V=[];Data.Civ1_C=[];Data.Civ1_F=[];
518            for ivol=1:NbSlice
519                % caluclate velocity data (y and v in indices, reverse to y component)
520                [xtable, ytable, utable, vtable, ctable, F, result_conv, errormsg] = civ (par_civ1);
521                if ~isempty(errormsg)
522                    disp_uvmat('ERROR',errormsg,checkrun)
523                    return
524                end
525                Data.Civ1_X=[Data.Civ1_X reshape(xtable,[],1)];
526                Data.Civ1_Y=[Data.Civ1_Y reshape(Param.Civ1.ImageHeight-ytable+1,[],1)];
527                Data.Civ1_Z=[Data.Civ1_Z ivol*ones(numel(xtable),1)];% z=image index in image coordinates
528                Data.Civ1_U=[Data.Civ1_U reshape(utable,[],1)];
529                Data.Civ1_V=[Data.Civ1_V reshape(-vtable,[],1)];
530                Data.Civ1_C=[Data.Civ1_C reshape(ctable,[],1)];
531                Data.Civ1_F=[Data.Civ1_C reshape(F,[],1)];
532            end
533        else %usual PIV
534            % caluclate velocity data (y and v in indices, reverse to y component)
535            [xtable, ytable, utable, vtable, ctable, F, result_conv, errormsg] = civ (par_civ1);
536            if ~isempty(errormsg)
537                disp_uvmat('ERROR',errormsg,checkrun)
538                return
539            end
540            Data.Civ1_X=reshape(xtable,[],1);
541            Data.Civ1_Y=reshape(par_civ1.ImageHeight-ytable+1,[],1);
542            Data.Civ1_U=reshape(utable,[],1);
543            Data.Civ1_V=reshape(-vtable,[],1);
544            Data.Civ1_C=reshape(ctable,[],1);
545            Data.Civ1_F=reshape(F,[],1);
546        end
547    else% we use existing Civ1 data
548        if exist('ncfile','var')
549            CivFile=ncfile;
550            [Data,tild,tild,errormsg]=nc2struct(CivFile,'ListGlobalAttribute','absolut_time_T0'); %look for the constant 'absolut_time_T0' to detect old civx data format
551            if ~isempty(errormsg)
552                disp_uvmat('ERROR',errormsg,checkrun)
553                return
554            end
555            [Data,tild,tild,errormsg]=nc2struct(CivFile);%read civ1 and fix1 data in the existing netcdf file
556        elseif isfield(Param,'Civ1_X')
557            Data.ListGlobalAttribute={};
558            Data.ListVarName={};
559            Data.VarDimName={};
560            Data.Civ1_X=Param.Civ1_X;
561            Data.Civ1_Y=Param.Civ1_Y;
562            Data.Civ1_U=Param.Civ1_U;
563            Data.Civ1_V=Param.Civ1_V;
564            Data.Civ1_FF=Param.Civ1_FF;
565        end
566    end
567   
568    %% Fix1
569    if isfield (Param.ActionInput,'Fix1')
570        disp('fix1 started')
571        if ~isfield (Param.ActionInput,'Civ1')% if we use existing Civ1, remove previous data beyond Civ1
572            Fix1_attr=find(strcmp('Fix1',Data.ListGlobalAttribute));
573            Data.ListGlobalAttribute(Fix1_attr)=[];
574            for ilist=1:numel(Fix1_attr)
575                Data=rmfield(Data,Data.ListGlobalAttribute{Fix1_attr(ilist)});
576            end
577        end
578        list_param=fieldnames(Param.ActionInput.Fix1)';
579        Fix1_param=regexprep(list_param,'^.+','Fix1_$0');% insert 'Fix1_' before  each string in ListFixParam
580        %indicate the values of all the global attributes in the output data
581        for ilist=1:length(list_param)
582            Data.(Fix1_param{ilist})=Param.ActionInput.Fix1.(list_param{ilist});
583        end
584        Data.ListGlobalAttribute=[Data.ListGlobalAttribute Fix1_param];
585        Data.ListVarName=[Data.ListVarName {'Civ1_FF'}];
586        Data.VarDimName=[Data.VarDimName {'nb_vec_1'}];
587        nbvar=length(Data.ListVarName);
588        Data.VarAttribute{nbvar}.Role='errorflag';
589        Data.Civ1_FF=int8(fix(Param.ActionInput.Fix1,Data.Civ1_F,Data.Civ1_C,Data.Civ1_U,Data.Civ1_V));
590        Data.CivStage=2;
591    end
592    %% Patch1
593    if isfield (Param.ActionInput,'Patch1')
594        disp('patch1 started')
595        if check_civx
596            errormsg='Civ Matlab input needed for patch';
597            disp_uvmat('ERROR',errormsg,checkrun)
598            return
599        end
600       
601        % record the processing parameters of Patch1 as global attributes in the result nc file
602        list_param=fieldnames(Param.ActionInput.Patch1)';
603        list_param(strcmp('TestPatch1',list_param))=[];% remove 'TestPatch1' from the list of parameters
604        Patch1_param=regexprep(list_param,'^.+','Patch1_$0');% insert 'Patch1_' before  each parameter name
605        for ilist=1:length(list_param)
606            Data.(Patch1_param{ilist})=Param.ActionInput.Patch1.(list_param{ilist});
607        end
608        Data.CivStage=3;% record the new state of processing
609        Data.ListGlobalAttribute=[Data.ListGlobalAttribute Patch1_param];
610       
611        % list the variables to record
612        nbvar=length(Data.ListVarName);
613        Data.ListVarName=[Data.ListVarName {'Civ1_U_smooth','Civ1_V_smooth','Civ1_SubRange','Civ1_NbCentres','Civ1_Coord_tps','Civ1_U_tps','Civ1_V_tps'}];
614        Data.VarDimName=[Data.VarDimName {'nb_vec_1','nb_vec_1',{'nb_coord','nb_bounds','nb_subdomain_1'},'nb_subdomain_1',...
615            {'nb_tps_1','nb_coord','nb_subdomain_1'},{'nb_tps_1','nb_subdomain_1'},{'nb_tps_1','nb_subdomain_1'}}];
616        Data.VarAttribute{nbvar+1}.Role='vector_x';
617        Data.VarAttribute{nbvar+2}.Role='vector_y';
618        Data.VarAttribute{nbvar+5}.Role='coord_tps';
619        Data.VarAttribute{nbvar+6}.Role='vector_x';
620        Data.VarAttribute{nbvar+7}.Role='vector_y';
621        Data.Civ1_U_smooth=Data.Civ1_U; % zeros(size(Data.Civ1_X));
622        Data.Civ1_V_smooth=Data.Civ1_V; %zeros(size(Data.Civ1_X));
623        if isfield(Data,'Civ1_FF')
624            ind_good=find(Data.Civ1_FF==0);
625        else
626            ind_good=1:numel(Data.Civ1_X);
627        end
628       
629        % perform Patch calculation using the UVMAT fct 'filter_tps'
630        [Data.Civ1_SubRange,Data.Civ1_NbCentres,Data.Civ1_Coord_tps,Data.Civ1_U_tps,Data.Civ1_V_tps,tild,Ures, Vres,tild,FFres]=...
631            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);
632        Data.Civ1_U_smooth(ind_good)=Ures;% take the interpolated (smoothed) velocity values for good vectors, keep civ1 data for the other
633        Data.Civ1_V_smooth(ind_good)=Vres;
634        Data.Civ1_FF(ind_good)=int8(FFres);
635        disp('patch1 performed')
636    end
637   
638    %% Civ2
639    if isfield (Param.ActionInput,'Civ2')
640        disp('civ2 started')
641        par_civ2=Param.ActionInput.Civ2;
642        if CheckInputFile % read input images (except in mode Test where it is introduced directly in Param.ActionInput.Civ1.ImageNameA and B)
643            par_civ2.ImageA=[];
644            par_civ2.ImageB=[];
645            if strcmp(Param.ActionInput.ListCompareMode,'displacement')
646                    ImageName_A_Civ2=Param.ActionInput.RefFile;
647                else
648            ImageName_A_Civ2=fullfile_uvmat(RootPath_A,SubDir_A,RootFile_A,FileExt_A,NomType_A,i1_civ2,[],j1_civ2);
649            end
650            if strcmp(ImageName_A_Civ2,ImageName_A) && isequal(FrameIndex_A_Civ1(ifield),FrameIndex_A_Civ2(ifield))
651                par_civ2.ImageA=par_civ1.ImageA;
652            else
653                [par_civ2.ImageA,VideoObject_A] = read_image(ImageName_A_Civ2,FileType_A,VideoObject_A,FrameIndex_A_Civ2(ifield));
654            end
655            ImageName_B_Civ2=fullfile_uvmat(RootPath_B,SubDir_B,RootFile_B,FileExt_B,NomType_B,i2_civ2,[],j2_civ2);
656            if strcmp(ImageName_B_Civ2,ImageName_B) && isequal(FrameIndex_B_Civ1(ifield),FrameIndex_B_Civ2)
657                par_civ2.ImageB=par_civ1.ImageB;
658            else
659                [par_civ2.ImageB,VideoObject_B] = read_image(ImageName_B_Civ2,FileType_B,VideoObject_B,FrameIndex_B_Civ2(ifield));
660            end
661            par_civ2.ImageWidth=FileInfo_A.Width;
662            par_civ2.ImageHeight=FileInfo_A.Height;
663            if isfield(par_civ2,'Grid')% grid points set as input file
664                if ischar(par_civ2.Grid)%read the grid file if the input is a file name
665                    par_civ2.Grid=dlmread(par_civ2.Grid);
666                    par_civ2.Grid(1,:)=[];%the first line must be removed (heading in the grid file)
667                end
668            else% automatic grid
669                minix=floor(par_civ2.Dx/2)-0.5;
670                maxix=minix+par_civ2.Dx*floor((par_civ2.ImageWidth-1)/par_civ2.Dx);
671                miniy=floor(par_civ2.Dy/2)-0.5;
672                maxiy=minix+par_civ2.Dy*floor((par_civ2.ImageHeight-1)/par_civ2.Dy);
673                [GridX,GridY]=meshgrid(minix:par_civ2.Dx:maxix,miniy:par_civ2.Dy:maxiy);
674                par_civ2.Grid(:,1)=reshape(GridX,[],1);
675                par_civ2.Grid(:,2)=reshape(GridY,[],1);
676            end
677        end
678       
679        % get the guess from patch1 or patch2 (case 'CheckCiv3')
680        if CheckInputFile % read input images (except in mode Test where it is introduced directly in Param.ActionInput.Civ1.ImageNameA and B)
681            if isfield (par_civ2,'CheckCiv3') && par_civ2.CheckCiv3 %get the guess from  patch2
682                SubRange= Data.Civ2_SubRange;
683                NbCentres=Data.Civ2_NbCentres;
684                Coord_tps=Data.Civ2_Coord_tps;
685                U_tps=Data.Civ2_U_tps;
686                V_tps=Data.Civ2_V_tps;
687                CivStage=Data.CivStage;%store the current CivStage
688                Civ1_Dt=Data.Civ2_Dt;
689                Data=[];%reinitialise the result structure Data
690                Data.ListGlobalAttribute={'Conventions','Program','CivStage'};
691                Data.Conventions='uvmat/civdata';% states the conventions used for the description of field variables and attributes
692                Data.Program='civ_series';
693                Data.CivStage=CivStage+1;%update the current civStage after reinitialisation of Data
694                Data.ListVarName={};
695                Data.VarDimName={};
696            else % get the guess from patch1
697                SubRange= Data.Civ1_SubRange;
698                NbCentres=Data.Civ1_NbCentres;
699                Coord_tps=Data.Civ1_Coord_tps;
700                U_tps=Data.Civ1_U_tps;
701                V_tps=Data.Civ1_V_tps;
702                Civ1_Dt=Data.Civ1_Dt;
703                Data.CivStage=4;
704            end
705        else
706            SubRange= par_civ2.Civ1_SubRange;
707            NbCentres=par_civ2.Civ1_NbCentres;
708            Coord_tps=par_civ2.Civ1_Coord_tps;
709            U_tps=par_civ2.Civ1_U_tps;
710            V_tps=par_civ2.Civ1_V_tps;
711            Civ1_Dt=par_civ2.Civ1_Dt;
712            Civ2_Dt=par_civ2.Civ1_Dt;
713            Data.ListVarName={};
714            Data.VarDimName={};
715        end
716        Shiftx=zeros(size(par_civ2.Grid,1),1);% shift expected from civ1 data
717        Shifty=zeros(size(par_civ2.Grid,1),1);
718        nbval=zeros(size(par_civ2.Grid,1),1);% nbre of interpolated values at each grid point (from the different patch subdomains)
719        if par_civ2.CheckDeformation
720            DUDX=zeros(size(par_civ2.Grid,1),1);
721            DUDY=zeros(size(par_civ2.Grid,1),1);
722            DVDX=zeros(size(par_civ2.Grid,1),1);
723            DVDY=zeros(size(par_civ2.Grid,1),1);
724        end
725        NbSubDomain=size(SubRange,3);
726        for isub=1:NbSubDomain% for each sub-domain of Patch1
727            nbvec_sub=NbCentres(isub);% nbre of Civ vectors in the subdomain
728            ind_sel=find(par_civ2.Grid(:,1)>=SubRange(1,1,isub) & par_civ2.Grid(:,1)<=SubRange(1,2,isub) &...
729                par_civ2.Grid(:,2)>=SubRange(2,1,isub) & par_civ2.Grid(:,2)<=SubRange(2,2,isub));% grid points in the subdomain
730            if ~isempty(ind_sel)
731                epoints = par_civ2.Grid(ind_sel,:);% coordinates of interpolation sites (measurement grids)
732                ctrs=Coord_tps(1:nbvec_sub,:,isub) ;%(=initial points) ctrs
733                nbval(ind_sel)=nbval(ind_sel)+1;% records the number of values for each interpolation point (in case of subdomain overlap)
734                EM = tps_eval(epoints,ctrs);% thin plate spline (tps) coefficient
735                Shiftx(ind_sel)=Shiftx(ind_sel)+EM*U_tps(1:nbvec_sub+3,isub);%velocity shift estimated by tps from civ1
736                Shifty(ind_sel)=Shifty(ind_sel)+EM*V_tps(1:nbvec_sub+3,isub);
737                if par_civ2.CheckDeformation
738                    [EMDX,EMDY] = tps_eval_dxy(epoints,ctrs);%2D matrix of distances between extrapolation points epoints and spline centres (=site points) ctrs
739                    DUDX(ind_sel)=DUDX(ind_sel)+EMDX*U_tps(1:nbvec_sub+3,isub);
740                    DUDY(ind_sel)=DUDY(ind_sel)+EMDY*U_tps(1:nbvec_sub+3,isub);
741                    DVDX(ind_sel)=DVDX(ind_sel)+EMDX*V_tps(1:nbvec_sub+3,isub);
742                    DVDY(ind_sel)=DVDY(ind_sel)+EMDY*V_tps(1:nbvec_sub+3,isub);
743                end
744            end
745        end
746        if par_civ2.CheckMask&&~isempty(par_civ2.Mask)       
747            if isfield(par_civ2,'NbSlice')
748                [RootPath_mask,SubDir_mask,RootFile_mask,i1_mask,i2_mask,j1_mask,j2_mask,Ext_mask]=fileparts_uvmat(Param.ActionInput.Civ2.Mask);
749                i1_mask=mod(i1-1,par_civ2.NbSlice)+1;
750                maskname=fullfile_uvmat(RootPath_mask,SubDir_mask,RootFile_mask,Ext_mask,'_1',i1_mask);
751            else
752                maskname=Param.ActionInput.Civ2.Mask;
753            end
754            if strcmp(maskoldname,maskname)% mask exist, not already read in civ1
755                par_civ2.Mask=mask; %use mask already opened
756            else
757                if exist(maskname,'file')
758                try
759                    par_civ2.Mask=imread(maskname);%update the mask, an store it for future use
760                catch ME
761                    if ~isempty(ME.message)
762                        errormsg=['error reading input image: ' ME.message];
763                        disp_uvmat('ERROR',errormsg,checkrun)
764                        return
765                    end
766                end
767                else
768                    par_civ2.Mask=[];
769                end
770                mask=par_civ2.Mask;
771                maskoldname=maskname;
772            end
773        end
774
775        if CheckInputFile % else Dt given by par_civ2
776            if strcmp(Param.ActionInput.ListCompareMode,'displacement')
777                Civ1_Dt=1;
778                Civ2_Dt=1;
779            else
780                Civ2_Dt=Time(i2_civ2+1,j2_civ2+1)-Time(i1_civ2+1,j1_civ2+1);
781            end
782        end
783        par_civ2.SearchBoxShift=(Civ2_Dt/Civ1_Dt)*[Shiftx(nbval>=1)./nbval(nbval>=1) Shifty(nbval>=1)./nbval(nbval>=1)];
784        % shift the grid points by half the expected shift to provide the correlation box position in image A
785        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];
786        if par_civ2.CheckDeformation
787            par_civ2.DUDX=DUDX(nbval>=1)./nbval(nbval>=1);
788            par_civ2.DUDY=DUDY(nbval>=1)./nbval(nbval>=1);
789            par_civ2.DVDX=DVDX(nbval>=1)./nbval(nbval>=1);
790            par_civ2.DVDY=DVDY(nbval>=1)./nbval(nbval>=1);
791        end
792       
793        % calculate velocity data (y and v in image indices, reverse to y component)
794        [xtable, ytable, utable, vtable, ctable, F,result_conv,errormsg] = civ (par_civ2);
795       
796        list_param=(fieldnames(Param.ActionInput.Civ2))';
797        list_param(strcmp('TestCiv2',list_param))=[];% remove the parameter TestCiv2 from the list
798        Civ2_param=regexprep(list_param,'^.+','Civ2_$0');% insert 'Civ2_' before  each string in list_param
799        Civ2_param=[{'Civ2_ImageA','Civ2_ImageB','Civ2_Time','Civ2_Dt'} Civ2_param]; %insert the names of the two input images
800        %indicate the values of all the global attributes in the output data
801        if exist('ImageName_A','var')
802            Data.Civ2_ImageA=ImageName_A;
803            Data.Civ2_ImageB=ImageName_B;
804            if strcmp(Param.ActionInput.ListCompareMode,'displacement')
805                Data.Civ2_Time=Time(i2_civ2+1,j2_civ2+1);% the Time is the Time of the secodn image
806                Data.Civ2_Dt=1;% Time interval is 1, to yield displacement instead of velocity=displacement/Dt at reading
807            else
808                Data.Civ2_Time=(Time(i2_civ2+1,j2_civ2+1)+Time(i1_civ2+1,j1_civ2+1))/2;
809                Data.Civ2_Dt=Civ2_Dt;
810            end
811        end
812        for ilist=1:length(list_param)
813            Data.(Civ2_param{4+ilist})=Param.ActionInput.Civ2.(list_param{ilist});
814        end
815        Data.ListGlobalAttribute=[Data.ListGlobalAttribute Civ2_param];
816       
817        nbvar=numel(Data.ListVarName);
818        % define the Civ2 variable (if Civ2 data are not replaced from previous calculation)
819        if isempty(find(strcmp('Civ2_X',Data.ListVarName),1))
820            Data.ListVarName=[Data.ListVarName {'Civ2_X','Civ2_Y','Civ2_U','Civ2_V','Civ2_F','Civ2_C'}];%  cell array containing the names of the fields to record
821            Data.VarDimName=[Data.VarDimName {'nb_vec_2','nb_vec_2','nb_vec_2','nb_vec_2','nb_vec_2','nb_vec_2'}];
822            Data.VarAttribute{nbvar+1}.Role='coord_x';
823            Data.VarAttribute{nbvar+2}.Role='coord_y';
824            Data.VarAttribute{nbvar+3}.Role='vector_x';
825            Data.VarAttribute{nbvar+4}.Role='vector_y';
826            Data.VarAttribute{nbvar+5}.Role='warnflag';
827        end
828        Data.Civ2_X=reshape(xtable,[],1);
829        Data.Civ2_Y=reshape(size(par_civ2.ImageA,1)-ytable+1,[],1);
830        Data.Civ2_U=reshape(utable,[],1);
831        Data.Civ2_V=reshape(-vtable,[],1);
832        Data.Civ2_C=reshape(ctable,[],1);
833        Data.Civ2_F=reshape(F,[],1);
834        disp('civ2 performed')
835    elseif ~isfield(Data,'ListVarName') % we start there, using existing Civ2 data
836        if exist('ncfile','var')
837            CivFile=ncfile;
838            [Data,tild,tild,errormsg]=nc2struct(CivFile);%read civ1 and fix1 data in the existing netcdf file
839            if ~isempty(errormsg)
840                disp_uvmat('ERROR',errormsg,checkrun)
841                return
842            end
843        elseif isfield(Param,'Civ2_X')% use Civ2 data as input in Param (test mode)
844            Data.ListGlobalAttribute={};
845            Data.ListVarName={};
846            Data.VarDimName={};
847            Data.Civ2_X=Param.Civ2_X;
848            Data.Civ2_Y=Param.Civ2_Y;
849            Data.Civ2_U=Param.Civ2_U;
850            Data.Civ2_V=Param.Civ2_V;
851            Data.Civ2_FF=Param.Civ2_FF;
852        end
853    end
854   
855    %% Fix2
856    if isfield (Param.ActionInput,'Fix2')
857        disp('fix2 started')
858        list_param=fieldnames(Param.ActionInput.Fix2)';
859        Fix2_param=regexprep(list_param,'^.+','Fix2_$0');% insert 'Fix1_' before  each string in ListFixParam
860        %indicate the values of all the global attributes in the output data
861        for ilist=1:length(list_param)
862            Data.(Fix2_param{ilist})=Param.ActionInput.Fix2.(list_param{ilist});
863        end
864        Data.ListGlobalAttribute=[Data.ListGlobalAttribute Fix2_param];
865        %
866        %         ListFixParam=fieldnames(Param.ActionInput.Fix2);
867        %         for ilist=1:length(ListFixParam)
868        %             ParamName=ListFixParam{ilist};
869        %             ListName=['Fix2_' ParamName];
870        %             eval(['Data.ListGlobalAttribute=[Data.ListGlobalAttribute ''' ParamName '''];'])
871        %             eval(['Data.' ListName '=Param.ActionInput.Fix2.' ParamName ';'])
872        %         end
873        if check_civx
874            if ~isfield(Data,'fix2')
875                Data.ListGlobalAttribute=[Data.ListGlobalAttribute 'fix2'];
876                Data.fix2=1;
877                Data.ListVarName=[Data.ListVarName {'vec2_FixFlag'}];
878                Data.VarDimName=[Data.VarDimName {'nb_vectors2'}];
879            end
880            Data.vec_FixFlag=fix(Param.Fix2,Data.vec2_F,Data.vec2_C,Data.vec2_U,Data.vec2_V,Data.vec2_X,Data.vec2_Y);
881        else
882            Data.ListVarName=[Data.ListVarName {'Civ2_FF'}];
883            Data.VarDimName=[Data.VarDimName {'nb_vec_2'}];
884            nbvar=length(Data.ListVarName);
885            Data.VarAttribute{nbvar}.Role='errorflag';
886            Data.Civ2_FF=double(fix(Param.ActionInput.Fix2,Data.Civ2_F,Data.Civ2_C,Data.Civ2_U,Data.Civ2_V));
887            Data.CivStage=Data.CivStage+1;
888        end
889    end
890   
891    %% Patch2
892    if isfield (Param.ActionInput,'Patch2')
893        disp('patch2 started')
894        list_param=fieldnames(Param.ActionInput.Patch2)';
895        list_param(strcmp('TestPatch2',list_param))=[];% remove the parameter TestCiv1 from the list
896        Patch2_param=regexprep(list_param,'^.+','Patch2_$0');% insert 'Fix1_' before  each string in ListFixParam
897        %indicate the values of all the global attributes in the output data
898        for ilist=1:length(list_param)
899            Data.(Patch2_param{ilist})=Param.ActionInput.Patch2.(list_param{ilist});
900        end
901        Data.ListGlobalAttribute=[Data.ListGlobalAttribute Patch2_param];
902       
903        nbvar=length(Data.ListVarName);
904        Data.ListVarName=[Data.ListVarName {'Civ2_U_smooth','Civ2_V_smooth','Civ2_SubRange','Civ2_NbCentres','Civ2_Coord_tps','Civ2_U_tps','Civ2_V_tps'}];
905        Data.VarDimName=[Data.VarDimName {'nb_vec_2','nb_vec_2',{'nb_coord','nb_bounds','nb_subdomain_2'},{'nb_subdomain_2'},...
906            {'nb_tps_2','nb_coord','nb_subdomain_2'},{'nb_tps_2','nb_subdomain_2'},{'nb_tps_2','nb_subdomain_2'}}];
907       
908        Data.VarAttribute{nbvar+1}.Role='vector_x';
909        Data.VarAttribute{nbvar+2}.Role='vector_y';
910        Data.VarAttribute{nbvar+5}.Role='coord_tps';
911        Data.VarAttribute{nbvar+6}.Role='vector_x';
912        Data.VarAttribute{nbvar+7}.Role='vector_y';
913        Data.Civ2_U_smooth=Data.Civ2_U;
914        Data.Civ2_V_smooth=Data.Civ2_V;
915        if isfield(Data,'Civ2_FF')
916            ind_good=find(Data.Civ2_FF==0);
917        else
918            ind_good=1:numel(Data.Civ2_X);
919        end
920        [Data.Civ2_SubRange,Data.Civ2_NbCentres,Data.Civ2_Coord_tps,Data.Civ2_U_tps,Data.Civ2_V_tps,tild,Ures,Vres,tild,FFres]=...
921            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);
922        Data.Civ2_U_smooth(ind_good)=Ures;
923        Data.Civ2_V_smooth(ind_good)=Vres;
924        Data.Civ2_FF(ind_good)=FFres;
925        Data.CivStage=Data.CivStage+1;
926        disp('patch2 performed')
927    end
928   
929    %% write result in a netcdf file if requested
930    if CheckOutputFile
931        errormsg=struct2nc(ncfile_out,Data);
932        if isempty(errormsg)
933            disp([ncfile_out ' written'])
934            %[success,msg] = fileattrib(ncfile_out ,'+w','g');% done in struct2nc
935        else
936            disp(errormsg)
937        end
938        disp(['ellapsed time ' num2str(toc/60,2) ' minutes'])
939    end
940end
941
942
943% 'civ': function piv.m adapted from PIVlab http://pivlab.blogspot.com/
944%--------------------------------------------------------------------------
945% function [xtable ytable utable vtable typevector] = civ (image1,image2,ibx,iby step, subpixfinder, mask, roi)
946%
947% OUTPUT:
948% xtable: set of x coordinates
949% ytable: set of y coordiantes
950% utable: set of u displacements (along x)
951% vtable: set of v displacements (along y)
952% ctable: max image correlation for each vector
953% typevector: set of flags, =1 for good, =0 for NaN vectors
954%
955%INPUT:
956% par_civ: structure of input parameters, with fields:
957%  .ImageA: first image for correlation (matrix)
958%  .ImageB: second image for correlation(matrix)
959%  .CorrBoxSize: 1,2 vector giving the size of the correlation box in x and y
960%  .SearchBoxSize:  1,2 vector giving the size of the search box in x and y
961%  .SearchBoxShift: 1,2 vector or 2 column matrix (for civ2) giving the shift of the search box in x and y
962%  .CorrSmooth: =1 or 2 determines the choice of the sub-pixel determination of the correlation max
963%  .ImageWidth: nb of pixels of the image in x
964%  .Dx, Dy: mesh for the PIV calculation
965%  .Grid: grid giving the PIV calculation points (alternative to .Dx .Dy): centres of the correlation boxes in Image A
966%  .Mask: name of a mask file or mask image matrix itself
967%  .MinIma: thresholds for image luminosity
968%  .MaxIma
969%  .CheckDeformation=1 for subpixel interpolation and image deformation (linear transform)
970%  .DUDX: matrix of deformation obtained from patch at each grid point
971%  .DUDY
972%  .DVDX:
973%  .DVDY
974
975function [xtable,ytable,utable,vtable,ctable,F,result_conv,errormsg] = civ (par_civ)
976
977%% prepare measurement grid
978if isfield(par_civ,'Grid')% grid points set as input, central positions of the sub-images in image A
979    if ischar(par_civ.Grid)%read the grid file if the input is a file name (grid in x, y image coordinates)
980        par_civ.Grid=dlmread(par_civ.Grid);
981        par_civ.Grid(1,:)=[];%the first line must be removed (heading in the grid file)
982    end
983    % else par_civ.Grid is already an array, no action here
984else% automatic grid in x, y image coordinates
985    minix=floor(par_civ.Dx/2)-0.5;
986    maxix=minix+par_civ.Dx*floor((par_civ.ImageWidth-1)/par_civ.Dx);
987    miniy=floor(par_civ.Dy/2)-0.5;% first automatic grid point at half the mesh Dy
988    maxiy=minix+par_civ.Dy*floor((par_civ.ImageHeight-1)/par_civ.Dy);
989    [GridX,GridY]=meshgrid(minix:par_civ.Dx:maxix,miniy:par_civ.Dy:maxiy);
990    par_civ.Grid(:,1)=reshape(GridX,[],1);
991    par_civ.Grid(:,2)=reshape(GridY,[],1);% increases with array index
992end
993nbvec=size(par_civ.Grid,1);
994
995%% prepare correlation and search boxes
996ibx2=floor(par_civ.CorrBoxSize(1)/2);
997iby2=floor(par_civ.CorrBoxSize(2)/2);
998isx2=floor(par_civ.SearchBoxSize(1)/2);
999isy2=floor(par_civ.SearchBoxSize(2)/2);
1000shiftx=round(par_civ.SearchBoxShift(:,1));%use the input shift estimate, rounded to the next integer value
1001shifty=-round(par_civ.SearchBoxShift(:,2));% sign minus because image j index increases when y decreases
1002if numel(shiftx)==1% case of a unique shift for the whole field( civ1)
1003    shiftx=shiftx*ones(nbvec,1);
1004    shifty=shifty*ones(nbvec,1);
1005end
1006
1007%% Array initialisation and default output  if par_civ.CorrSmooth=0 (just the grid calculated, no civ computation)
1008xtable=round(par_civ.Grid(:,1)+0.5)-0.5;
1009ytable=round(par_civ.ImageHeight-par_civ.Grid(:,2)+0.5)-0.5;% y index corresponding to the position in image coordiantes
1010utable=shiftx;%zeros(nbvec,1);
1011vtable=shifty;%zeros(nbvec,1);
1012ctable=zeros(nbvec,1);
1013F=zeros(nbvec,1);
1014result_conv=[];
1015errormsg='';
1016
1017%% prepare mask
1018if isfield(par_civ,'Mask') && ~isempty(par_civ.Mask)
1019    if strcmp(par_civ.Mask,'all')
1020        return    % get the grid only, no civ calculation
1021    elseif ischar(par_civ.Mask)
1022        par_civ.Mask=imread(par_civ.Mask);% read the mask if not allready done
1023    end
1024end
1025check_MinIma=isfield(par_civ,'MinIma');% test for image luminosity threshold
1026check_MaxIma=isfield(par_civ,'MaxIma') && ~isempty(par_civ.MaxIma);
1027
1028par_civ.ImageA=sum(double(par_civ.ImageA),3);%sum over rgb component for color images
1029par_civ.ImageB=sum(double(par_civ.ImageB),3);
1030[npy_ima npx_ima]=size(par_civ.ImageA);
1031if ~isequal(size(par_civ.ImageB),[npy_ima npx_ima])
1032    errormsg='image pair with unequal size';
1033    return
1034end
1035
1036%% Apply mask
1037% Convention for mask IDEAS TO IMPLEMENT ?
1038% mask >200 : velocity calculated
1039%  200 >=mask>150;velocity not calculated, interpolation allowed (bad spots)
1040% 150>=mask >100: velocity not calculated, nor interpolated
1041%  100>=mask> 20: velocity not calculated, impermeable (no flux through mask boundaries)
1042%  20>=mask: velocity=0
1043checkmask=0;
1044MinA=min(min(par_civ.ImageA));
1045%MinB=min(min(par_civ.ImageB));
1046%check_undefined=false(size(par_civ.ImageA));
1047if isfield(par_civ,'Mask') && ~isempty(par_civ.Mask)
1048    checkmask=1;
1049    if ~isequal(size(par_civ.Mask),[npy_ima npx_ima])
1050        errormsg='mask must be an image with the same size as the images';
1051        return
1052    end
1053    check_undefined=(par_civ.Mask<200 & par_civ.Mask>=20 );
1054    %     par_civ.ImageA(check_undefined)=0;% put image A to zero (i.e. the min image value) in the undefined  area
1055    %     par_civ.ImageB(check_undefined)=0;% put image B to zero (i.e. the min image value) in the undefined  area
1056end
1057
1058%% compute image correlations: MAINLOOP on velocity vectors
1059corrmax=0;
1060sum_square=1;% default
1061mesh=1;% default
1062CheckDeformation=isfield(par_civ,'CheckDeformation')&& par_civ.CheckDeformation==1;
1063if CheckDeformation
1064    mesh=0.25;%mesh in pixels for subpixel image interpolation (x 4 in each direction)
1065    par_civ.CorrSmooth=2;% use SUBPIX2DGAUSS (take into account more points near the max)
1066end
1067
1068if par_civ.CorrSmooth~=0 % par_civ.CorrSmooth=0 implies no civ computation (just input image and grid points given)
1069    for ivec=1:nbvec
1070        iref=round(par_civ.Grid(ivec,1)+0.5);% xindex on the image A for the middle of the correlation box
1071        jref=round(par_civ.ImageHeight-par_civ.Grid(ivec,2)+0.5);%  j index  for the middle of the correlation box in the image A
1072        F(ivec)=0;
1073        subrange1_x=iref-ibx2:iref+ibx2;% x indices defining the first subimage
1074        subrange1_y=jref-iby2:jref+iby2;% y indices defining the first subimage
1075        subrange2_x=iref+shiftx(ivec)-isx2:iref+shiftx(ivec)+isx2;%x indices defining the second subimage
1076        subrange2_y=jref+shifty(ivec)-isy2:jref+shifty(ivec)+isy2;%y indices defining the second subimage
1077        image1_crop=MinA*ones(numel(subrange1_y),numel(subrange1_x));% default value=min of image A
1078        image2_crop=MinA*ones(numel(subrange2_y),numel(subrange2_x));% default value=min of image A
1079        check1_x=subrange1_x>=1 & subrange1_x<=par_civ.ImageWidth;% check which points in the subimage 1 are contained in the initial image 1
1080        check1_y=subrange1_y>=1 & subrange1_y<=par_civ.ImageHeight;
1081        check2_x=subrange2_x>=1 & subrange2_x<=par_civ.ImageWidth;% check which points in the subimage 2 are contained in the initial image 2
1082        check2_y=subrange2_y>=1 & subrange2_y<=par_civ.ImageHeight;
1083        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
1084        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
1085        if checkmask
1086            mask1_crop=ones(numel(subrange1_y),numel(subrange1_x));% default value=1 for mask
1087            mask2_crop=ones(numel(subrange2_y),numel(subrange2_x));% default value=1 for mask
1088            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
1089            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
1090            sizemask=sum(sum(mask1_crop))/(numel(subrange1_y)*numel(subrange1_x));%size of the masked part relative to the correlation sub-image
1091            if sizemask > 1/2% eliminate point if more than half of the correlation box is masked
1092                F(ivec)=3; %
1093                utable(ivec)=0;
1094                vtable(ivec)=0;
1095            else
1096                image1_crop=image1_crop.*~mask1_crop;% put to zero the masked pixels (mask1_crop='true'=1)
1097                image2_crop=image2_crop.*~mask2_crop;
1098                image1_mean=mean(mean(image1_crop))/(1-sizemask);
1099                image2_mean=mean(mean(image2_crop))/(1-sizemask);
1100            end
1101        else
1102            image1_mean=mean(mean(image1_crop));
1103            image2_mean=mean(mean(image2_crop));
1104        end
1105        %threshold on image minimum
1106        if F(ivec)~=3
1107            if check_MinIma && (image1_mean < par_civ.MinIma || image2_mean < par_civ.MinIma)
1108                F(ivec)=3;
1109                %threshold on image maximum
1110            elseif check_MaxIma && (image1_mean > par_civ.MaxIma || image2_mean > par_civ.MaxIma)
1111                F(ivec)=3;
1112            end
1113            if F(ivec)==3
1114                utable(ivec)=0;
1115                vtable(ivec)=0;
1116            else
1117                %mask
1118                if checkmask
1119                    image1_crop=(image1_crop-image1_mean).*~mask1_crop;%substract the mean, put to zero the masked parts
1120                    image2_crop=(image2_crop-image2_mean).*~mask2_crop;
1121                else
1122                    image1_crop=(image1_crop-image1_mean);
1123                    image2_crop=(image2_crop-image2_mean);
1124                end
1125                %deformation
1126                if CheckDeformation
1127                    xi=(1:mesh:size(image1_crop,2));
1128                    yi=(1:mesh:size(image1_crop,1))';
1129                    [XI,YI]=meshgrid(xi-ceil(size(image1_crop,2)/2),yi-ceil(size(image1_crop,1)/2));
1130                    XIant=XI-par_civ.DUDX(ivec)*XI+par_civ.DUDY(ivec)*YI+ceil(size(image1_crop,2)/2);
1131                    YIant=YI+par_civ.DVDX(ivec)*XI-par_civ.DVDY(ivec)*YI+ceil(size(image1_crop,1)/2);
1132                    image1_crop=interp2(image1_crop,XIant,YIant);
1133                    image1_crop(isnan(image1_crop))=0;
1134                    xi=(1:mesh:size(image2_crop,2));
1135                    yi=(1:mesh:size(image2_crop,1))';
1136                    image2_crop=interp2(image2_crop,xi,yi,'*spline');
1137                    image2_crop(isnan(image2_crop))=0;
1138                end
1139                sum_square=sum(sum(image1_crop.*image1_crop));
1140                %reference: Oliver Pust, PIV: Direct Cross-Correlation
1141                result_conv= conv2(image2_crop,flipdim(flipdim(image1_crop,2),1),'valid');
1142                corrmax= max(max(result_conv));
1143                result_conv=(result_conv/corrmax)*255; %normalize, peak=always 255
1144                %Find the correlation max, at 255
1145                [y,x] = find(result_conv==255,1);
1146                subimage2_crop=image2_crop(y:y+2*iby2/mesh,x:x+2*ibx2/mesh);%subimage of image 2 corresponding to the optimum displacement of first image
1147                sum_square=sum_square*sum(sum(subimage2_crop.*subimage2_crop));% product of variances of image 1 and 2
1148                sum_square=sqrt(sum_square);% srt of the variance product to normalise correlation
1149                if ~isempty(y) && ~isempty(x)
1150                    try
1151                        if par_civ.CorrSmooth==1
1152                            [vector,F(ivec)] = SUBPIXGAUSS (result_conv,x,y);
1153                        elseif par_civ.CorrSmooth==2
1154                            [vector,F(ivec)] = SUBPIX2DGAUSS (result_conv,x,y);
1155                        else
1156                            [vector,F(ivec)] = quadr_fit(result_conv,x,y);
1157                        end
1158                        utable(ivec)=vector(1)*mesh+shiftx(ivec);
1159                        vtable(ivec)=vector(2)*mesh+shifty(ivec);
1160                        xtable(ivec)=iref+utable(ivec)/2-0.5;% convec flow (velocity taken at the point middle from imgae 1 and 2)
1161                        ytable(ivec)=jref+vtable(ivec)/2-0.5;% and position of pixel 1=0.5 (convention for image coordinates=0 at the edge)
1162                        iref=round(xtable(ivec)+0.5);% nearest image index for the middle of the vector
1163                        jref=round(ytable(ivec)+0.5);
1164                        % eliminate vectors located in the mask
1165                        if  checkmask && (iref<1 || jref<1 ||iref>npx_ima || jref>npy_ima ||( par_civ.Mask(jref,iref)<200 && par_civ.Mask(jref,iref)>=100))
1166                            utable(ivec)=0;
1167                            vtable(ivec)=0;
1168                            F(ivec)=3;
1169                        end
1170                        ctable(ivec)=corrmax/sum_square;% correlation value
1171                    catch ME
1172                        F(ivec)=3;
1173                        disp(ME.message)
1174                    end
1175                else
1176                    F(ivec)=3;
1177                end
1178            end
1179        end
1180    end
1181end
1182result_conv=result_conv*corrmax/(255*sum_square);% keep the last correlation matrix for output
1183
1184%------------------------------------------------------------------------
1185% --- Find the maximum of the correlation function after interpolation
1186% OUPUT:
1187% vector = optimum displacement vector with subpixel correction
1188% F =flag: =0 OK
1189%           =-2 , warning: max too close to the edge of the search box (1 pixel margin)
1190% INPUT:
1191% x,y: position of the maximum correlation at integer values
1192
1193function [vector,F] = SUBPIXGAUSS (result_conv,x,y)
1194%------------------------------------------------------------------------
1195% vector=[0 0]; %default
1196F=0;
1197[npy,npx]=size(result_conv);
1198result_conv(result_conv<1)=1; %set to 1 correlation values smaller than 1  (=0 by discretisation, to avoid divergence in the log)
1199%the following 8 lines are copyright (c) 1998, Uri Shavit, Roi Gurka, Alex Liberzon, Technion ??? Israel Institute of Technology
1200%http://urapiv.wordpress.com
1201peaky = y;
1202if y < npy && y > 1
1203    f0 = log(result_conv(y,x));
1204    f1 = log(result_conv(y-1,x));
1205    f2 = log(result_conv(y+1,x));
1206    peaky = peaky+ (f1-f2)/(2*f1-4*f0+2*f2);
1207else
1208    F=-2; % warning flag for vector truncated by the limited search box
1209end
1210peakx=x;
1211if x < npx-1 && x > 1
1212    f0 = log(result_conv(y,x));
1213    f1 = log(result_conv(y,x-1));
1214    f2 = log(result_conv(y,x+1));
1215    peakx = peakx+ (f1-f2)/(2*f1-4*f0+2*f2);
1216else
1217    F=-2; % warning flag for vector truncated by the limited search box
1218end
1219vector=[peakx-floor(npx/2)-1 peaky-floor(npy/2)-1];
1220
1221%------------------------------------------------------------------------
1222% --- Find the maximum of the correlation function after interpolation
1223function [vector,F] = SUBPIX2DGAUSS (result_conv,x,y)
1224%------------------------------------------------------------------------
1225% vector=[0 0]; %default
1226F=-2;
1227peaky=y;
1228peakx=x;
1229result_conv(result_conv<1)=1; %set to 1 correlation values smaller than 1 (to avoid divergence in the log)
1230[npy,npx]=size(result_conv);
1231if (x < npx) && (y < npy) && (x > 1) && (y > 1)
1232    F=0;
1233    for i=-1:1
1234        for j=-1:1
1235            %following 15 lines based on
1236            %H. Nobach ??? M. Honkanen (2005)
1237            %Two-dimensional Gaussian regression for sub-pixel displacement
1238            %estimation in particle image velocimetry or particle position
1239            %estimation in particle tracking velocimetry
1240            %Experiments in Fluids (2005) 38: 511???515
1241            c10(j+2,i+2)=i*log(result_conv(y+j, x+i));
1242            c01(j+2,i+2)=j*log(result_conv(y+j, x+i));
1243            c11(j+2,i+2)=i*j*log(result_conv(y+j, x+i));
1244            c20(j+2,i+2)=(3*i^2-2)*log(result_conv(y+j, x+i));
1245            c02(j+2,i+2)=(3*j^2-2)*log(result_conv(y+j, x+i));
1246        end
1247    end
1248    c10=(1/6)*sum(sum(c10));
1249    c01=(1/6)*sum(sum(c01));
1250    c11=(1/4)*sum(sum(c11));
1251    c20=(1/6)*sum(sum(c20));
1252    c02=(1/6)*sum(sum(c02));
1253    deltax=(c11*c01-2*c10*c02)/(4*c20*c02-c11^2);
1254    deltay=(c11*c10-2*c01*c20)/(4*c20*c02-c11^2);
1255    if abs(deltax)<1
1256        peakx=x+deltax;
1257    end
1258    if abs(deltay)<1
1259        peaky=y+deltay;
1260    end
1261end
1262vector=[peakx-floor(npx/2)-1 peaky-floor(npy/2)-1];
1263
1264%------------------------------------------------------------------------
1265% --- Find the maximum of the correlation function after quadratic interpolation
1266function [vector,F] = quadr_fit(result_conv,x,y)
1267[npy,npx]=size(result_conv);
1268if x<4 || y<4 || npx-x<4 ||npy-y <4
1269    F=-2;
1270    vector=[x y];
1271else
1272    F=0;
1273    x_ind=x-4:x+4;
1274    y_ind=y-4:y+4;
1275    x_vec=0.25*(x_ind-x);
1276    y_vec=0.25*(y_ind-y);
1277    [X,Y]=meshgrid(x_vec,y_vec);
1278    coord=[reshape(X,[],1) reshape(Y,[],1)];
1279    result_conv=reshape(result_conv(y_ind,x_ind),[],1);
1280   
1281   
1282    % n=numel(X);
1283    % x=[X Y];
1284    % X=X-0.5;
1285    % Y=Y+0.5;
1286    % y = (X.*X+2*Y.*Y+X.*Y+6) + 0.1*rand(n,1);
1287    p = polyfitn(coord,result_conv,2);
1288    A(1,1)=2*p.Coefficients(1);
1289    A(1,2)=p.Coefficients(2);
1290    A(2,1)=p.Coefficients(2);
1291    A(2,2)=2*p.Coefficients(4);
1292    vector=[x y]'-A\[p.Coefficients(3) p.Coefficients(5)]';
1293    vector=vector'-[floor(npx/2) floor(npy/2)]-1 ;
1294    % zg = polyvaln(p,coord);
1295    % figure
1296    % surf(x_vec,y_vec,reshape(zg,9,9))
1297    % hold on
1298    % plot3(X,Y,reshape(result_conv,9,9),'o')
1299    % hold off
1300end
1301
1302%'RUN_FIX': function for fixing velocity fields:
1303%-----------------------------------------------
1304% RUN_FIX(filename,field,flagindex,thresh_vecC,thresh_vel,iter,flag_mask,maskname,fileref,fieldref)
1305%
1306%filename: name of the netcdf file (used as input and output)
1307%field: structure specifying the names of the fields to fix (depending on civ1 or civ2)
1308%.vel_type='civ1' or 'civ2';
1309%.nb=name of the dimension common to the field to fix ('nb_vectors' for civ1);
1310%.fixflag=name of fix flag variable ('vec_FixFlag' for civ1)
1311%flagindex: flag specifying which values of vec_f are removed:
1312% if flagindex(1)=1: vec_f=-2 vectors are removed
1313% if flagindex(2)=1: vec_f=3 vectors are removed
1314% if flagindex(3)=1: vec_f=2 vectors are removed (if iter=1) or vec_f=4 vectors are removed (if iter=2)
1315%iter=1 for civ1 fields and iter=2 for civ2 fields
1316%thresh_vecC: threshold in the image correlation vec_C
1317%flag_mask: =1 mask used to remove vectors (0 else)
1318%maskname: name of the mask image file for fix
1319%thresh_vel: threshold on velocity, or on the difference with the reference file fileref if exists
1320%inf_sup=1: remove values smaller than threshold thresh_vel, =2, larger than threshold
1321%fileref: .nc file name for a reference velocity (='': refrence 0 used)
1322%fieldref: 'civ1','filter1'...feld used in fileref
1323
1324function FF=fix(Param,F,C,U,V,X,Y)
1325FF=zeros(size(F));%default
1326
1327%criterium on warn flags
1328FlagName={'CheckFmin2','CheckF2','CheckF3','CheckF4'};
1329FlagVal=[-2 2 3 4];
1330for iflag=1:numel(FlagName)
1331    if isfield(Param,FlagName{iflag}) && Param.(FlagName{iflag})
1332        FF=(FF==1| F==FlagVal(iflag));
1333    end
1334end
1335%criterium on correlation values
1336if isfield (Param,'MinCorr')
1337    FF=FF==1 | C<Param.MinCorr;
1338end
1339if (isfield(Param,'MinVel')&&~isempty(Param.MinVel))||(isfield (Param,'MaxVel')&&~isempty(Param.MaxVel))
1340    Umod= U.*U+V.*V;
1341    if isfield (Param,'MinVel')&&~isempty(Param.MinVel)
1342        FF=FF==1 | Umod<(Param.MinVel*Param.MinVel);
1343    end
1344    if isfield (Param,'MaxVel')&&~isempty(Param.MaxVel)
1345        FF=FF==1 | Umod>(Param.MaxVel*Param.MaxVel);
1346    end
1347end
1348
1349
1350%------------------------------------------------------------------------
1351% --- determine the list of index pairs of processing file
1352function [i1_series,i2_series,j1_series,j2_series,check_bounds,NomTypeNc]=...
1353    find_pair_indices(str_civ,i_series,j_series,MinIndex_i,MaxIndex_i,MinIndex_j,MaxIndex_j)
1354%------------------------------------------------------------------------
1355i1_series=i_series;% set of first image indexes
1356i2_series=i_series;
1357j1_series=j_series;%ones(size(i_series));% set of first image numbers
1358j2_series=j_series;%ones(size(i_series));
1359r=regexp(str_civ,'^\D(?<ind>[i|j])=( -| )(?<num1>\d+)\|(?<num2>\d+)','names');
1360if ~isempty(r)
1361    mode=['D' r.ind];
1362    ind1=str2num(r.num1);
1363    ind2=str2num(r.num2);
1364else
1365    mode='j1-j2';
1366    r=regexp(str_civ,'^j= (?<num1>[a-z])-(?<num2>[a-z])','names');
1367    if ~isempty(r)
1368        NomTypeNc='_1ab';
1369    else
1370        r=regexp(str_civ,'^j= (?<num1>[A-Z])-(?<num2>[A-Z])','names');
1371        if ~isempty(r)
1372            NomTypeNc='_1AB';
1373        else
1374            r=regexp(str_civ,'^j= (?<num1>\d+)-(?<num2>\d+)','names');
1375            if ~isempty(r)
1376                NomTypeNc='_1_1-2';
1377            end
1378        end
1379    end
1380    if isempty(r)
1381        display('wrong pair mode input option')
1382    else
1383        ind1=stra2num(r.num1);
1384        ind2=stra2num(r.num2);
1385    end
1386end
1387switch mode
1388    case 'Di'
1389        i1_series=i_series-ind1;% set of first image numbers
1390        i2_series=i_series+ind2;
1391        check_bounds=i1_series<MinIndex_i | i2_series>MaxIndex_i;
1392        if isempty(j_series)
1393            NomTypeNc='_1-2';
1394        else
1395            j1_series=j_series;
1396            j2_series=j_series;
1397            NomTypeNc='_1-2_1';
1398        end
1399    case 'Dj'
1400        j1_series=j_series-ind1;
1401        j2_series=j_series+ind2;
1402        check_bounds=j1_series<MinIndex_j | j2_series>MaxIndex_j;
1403        NomTypeNc='_1_1-2';
1404    otherwise %bursts
1405        i1_series=i_series(1,:);% do not sweep the j index
1406        i2_series=i_series(1,:);
1407        j1_series=ind1*ones(1,size(i_series,2));% j index is fixed by pair choice
1408        j2_series=ind2*ones(1,size(i_series,2));
1409        check_bounds=zeros(size(i1_series));% no limitations due to min-max indices
1410end
1411
1412
1413
1414
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