source: trunk/src/series/civ_series.m

Last change on this file was 1097, checked in by sommeria, 12 days ago

various bug repairs

File size: 68.9 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') && 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        else
477            i1=Param.ActionInput.PairIndices.ref_i; %case of TESTmode
478        end
479        % set the list of variables
480        Data.ListVarName={'Civ1_X','Civ1_Y','Civ1_U','Civ1_V','Civ1_F','Civ1_C'};%  cell array containing the names of the fields to record
481        Data.VarDimName={'nb_vec_1','nb_vec_1','nb_vec_1','nb_vec_1','nb_vec_1','nb_vec_1'};
482        Data.VarAttribute{1}.Role='coord_x';
483        Data.VarAttribute{2}.Role='coord_y';
484        Data.VarAttribute{3}.Role='vector_x';
485        Data.VarAttribute{4}.Role='vector_y';
486        Data.VarAttribute{5}.Role='warnflag';
487        % case of mask
488        if par_civ1.CheckMask&&~isempty(par_civ1.Mask)
489            if isfield(par_civ1,'NbSlice')
490                [RootPath_mask,SubDir_mask,RootFile_mask,i1_mask,i2_mask,j1_mask,j2_mask,Ext_mask]=fileparts_uvmat(Param.ActionInput.Civ1.Mask);
491                i1_mask=mod(i1-1,par_civ1.NbSlice)+1;
492                maskname=fullfile_uvmat(RootPath_mask,SubDir_mask,RootFile_mask,Ext_mask,'_1',i1_mask);
493            else
494                maskname=Param.ActionInput.Civ1.Mask;
495            end
496            if strcmp(maskoldname,maskname)% mask exist, not already read in civ1
497                par_civ1.Mask=mask; %use mask already opened
498            else
499                if ~isempty(regexp(maskname,'(^http://)|(^https://)'))|| exist(maskname,'file')
500                    try
501                        par_civ1.Mask=imread(maskname);%update the mask, an store it for future use
502                    catch ME
503                        if ~isempty(ME.message)
504                            errormsg=['error reading input image: ' ME.message];
505                            disp_uvmat('ERROR',errormsg,checkrun)
506                            return
507                        end
508                    end
509                else
510                    par_civ1.Mask=[];
511                end
512                mask=par_civ1.Mask;
513                maskoldname=maskname;
514            end
515        end
516        if strcmp(Param.ActionInput.ListCompareMode, 'PIV volume')
517            Data.ListVarName=[Data.ListVarName 'Civ1_Z'];
518            Data.Civ1_X=[];Data.Civ1_Y=[];Data.Civ1_Z=[];
519            Data.Civ1_U=[];Data.Civ1_V=[];Data.Civ1_C=[];Data.Civ1_F=[];
520            for ivol=1:NbSlice
521                % caluclate velocity data (y and v in indices, reverse to y component)
522                [xtable, ytable, utable, vtable, ctable, F, result_conv, errormsg] = civ (par_civ1);
523                if ~isempty(errormsg)
524                    disp_uvmat('ERROR',errormsg,checkrun)
525                    return
526                end
527                Data.Civ1_X=[Data.Civ1_X reshape(xtable,[],1)];
528                Data.Civ1_Y=[Data.Civ1_Y reshape(Param.Civ1.ImageHeight-ytable+1,[],1)];
529                Data.Civ1_Z=[Data.Civ1_Z ivol*ones(numel(xtable),1)];% z=image index in image coordinates
530                Data.Civ1_U=[Data.Civ1_U reshape(utable,[],1)];
531                Data.Civ1_V=[Data.Civ1_V reshape(-vtable,[],1)];
532                Data.Civ1_C=[Data.Civ1_C reshape(ctable,[],1)];
533                Data.Civ1_F=[Data.Civ1_C reshape(F,[],1)];
534            end
535        else %usual PIV
536            % caluclate velocity data (y and v in indices, reverse to y component)
537            [xtable, ytable, utable, vtable, ctable, F, result_conv, errormsg] = civ (par_civ1);
538            if ~isempty(errormsg)
539                disp_uvmat('ERROR',errormsg,checkrun)
540                return
541            end
542            Data.Civ1_X=reshape(xtable,[],1);
543            Data.Civ1_Y=reshape(par_civ1.ImageHeight-ytable+1,[],1);
544            Data.Civ1_U=reshape(utable,[],1);
545            Data.Civ1_V=reshape(-vtable,[],1);
546            Data.Civ1_C=reshape(ctable,[],1);
547            Data.Civ1_F=reshape(F,[],1);
548        end
549    else% we use existing Civ1 data
550        if exist('ncfile','var')
551            CivFile=ncfile;
552            [Data,tild,tild,errormsg]=nc2struct(CivFile,'ListGlobalAttribute','absolut_time_T0'); %look for the constant 'absolut_time_T0' to detect old civx data format
553            if ~isempty(errormsg)
554                disp_uvmat('ERROR',errormsg,checkrun)
555                return
556            end
557            [Data,tild,tild,errormsg]=nc2struct(CivFile);%read civ1 and fix1 data in the existing netcdf file
558        elseif isfield(Param,'Civ1_X')
559            Data.ListGlobalAttribute={};
560            Data.ListVarName={};
561            Data.VarDimName={};
562            Data.Civ1_X=Param.Civ1_X;
563            Data.Civ1_Y=Param.Civ1_Y;
564            Data.Civ1_U=Param.Civ1_U;
565            Data.Civ1_V=Param.Civ1_V;
566            Data.Civ1_FF=Param.Civ1_FF;
567        end
568    end
569   
570    %% Fix1
571    if isfield (Param.ActionInput,'Fix1')
572        disp('fix1 started')
573        if ~isfield (Param.ActionInput,'Civ1')% if we use existing Civ1, remove previous data beyond Civ1
574            Fix1_attr=find(strcmp('Fix1',Data.ListGlobalAttribute));
575            Data.ListGlobalAttribute(Fix1_attr)=[];
576            for ilist=1:numel(Fix1_attr)
577                Data=rmfield(Data,Data.ListGlobalAttribute{Fix1_attr(ilist)});
578            end
579        end
580        list_param=fieldnames(Param.ActionInput.Fix1)';
581        Fix1_param=regexprep(list_param,'^.+','Fix1_$0');% insert 'Fix1_' before  each string in ListFixParam
582        %indicate the values of all the global attributes in the output data
583        for ilist=1:length(list_param)
584            Data.(Fix1_param{ilist})=Param.ActionInput.Fix1.(list_param{ilist});
585        end
586        Data.ListGlobalAttribute=[Data.ListGlobalAttribute Fix1_param];
587        Data.ListVarName=[Data.ListVarName {'Civ1_FF'}];
588        Data.VarDimName=[Data.VarDimName {'nb_vec_1'}];
589        nbvar=length(Data.ListVarName);
590        Data.VarAttribute{nbvar}.Role='errorflag';
591        Data.Civ1_FF=int8(fix(Param.ActionInput.Fix1,Data.Civ1_F,Data.Civ1_C,Data.Civ1_U,Data.Civ1_V));
592        Data.CivStage=2;
593    end
594    %% Patch1
595    if isfield (Param.ActionInput,'Patch1')
596        disp('patch1 started')
597        if check_civx
598            errormsg='Civ Matlab input needed for patch';
599            disp_uvmat('ERROR',errormsg,checkrun)
600            return
601        end
602       
603        % record the processing parameters of Patch1 as global attributes in the result nc file
604        list_param=fieldnames(Param.ActionInput.Patch1)';
605        list_param(strcmp('TestPatch1',list_param))=[];% remove 'TestPatch1' from the list of parameters
606        Patch1_param=regexprep(list_param,'^.+','Patch1_$0');% insert 'Patch1_' before  each parameter name
607        for ilist=1:length(list_param)
608            Data.(Patch1_param{ilist})=Param.ActionInput.Patch1.(list_param{ilist});
609        end
610        Data.CivStage=3;% record the new state of processing
611        Data.ListGlobalAttribute=[Data.ListGlobalAttribute Patch1_param];
612       
613        % list the variables to record
614        nbvar=length(Data.ListVarName);
615        Data.ListVarName=[Data.ListVarName {'Civ1_U_smooth','Civ1_V_smooth','Civ1_SubRange','Civ1_NbCentres','Civ1_Coord_tps','Civ1_U_tps','Civ1_V_tps'}];
616        Data.VarDimName=[Data.VarDimName {'nb_vec_1','nb_vec_1',{'nb_coord','nb_bounds','nb_subdomain_1'},'nb_subdomain_1',...
617            {'nb_tps_1','nb_coord','nb_subdomain_1'},{'nb_tps_1','nb_subdomain_1'},{'nb_tps_1','nb_subdomain_1'}}];
618        Data.VarAttribute{nbvar+1}.Role='vector_x';
619        Data.VarAttribute{nbvar+2}.Role='vector_y';
620        Data.VarAttribute{nbvar+5}.Role='coord_tps';
621        Data.VarAttribute{nbvar+6}.Role='vector_x';
622        Data.VarAttribute{nbvar+7}.Role='vector_y';
623        Data.Civ1_U_smooth=Data.Civ1_U; % zeros(size(Data.Civ1_X));
624        Data.Civ1_V_smooth=Data.Civ1_V; %zeros(size(Data.Civ1_X));
625        if isfield(Data,'Civ1_FF')
626            ind_good=find(Data.Civ1_FF==0);
627        else
628            ind_good=1:numel(Data.Civ1_X);
629        end
630       
631        % perform Patch calculation using the UVMAT fct 'filter_tps'
632        [Data.Civ1_SubRange,Data.Civ1_NbCentres,Data.Civ1_Coord_tps,Data.Civ1_U_tps,Data.Civ1_V_tps,tild,Ures, Vres,tild,FFres]=...
633            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);
634        Data.Civ1_U_smooth(ind_good)=Ures;% take the interpolated (smoothed) velocity values for good vectors, keep civ1 data for the other
635        Data.Civ1_V_smooth(ind_good)=Vres;
636        Data.Civ1_FF(ind_good)=int8(FFres);
637        disp('patch1 performed')
638    end
639   
640    %% Civ2
641    if isfield (Param.ActionInput,'Civ2')
642        disp('civ2 started')
643        par_civ2=Param.ActionInput.Civ2;
644        if CheckInputFile % read input images (except in mode Test where it is introduced directly in Param.ActionInput.Civ1.ImageNameA and B)
645            par_civ2.ImageA=[];
646            par_civ2.ImageB=[];
647            if strcmp(Param.ActionInput.ListCompareMode,'displacement')
648                    ImageName_A_Civ2=Param.ActionInput.RefFile;
649                else
650            ImageName_A_Civ2=fullfile_uvmat(RootPath_A,SubDir_A,RootFile_A,FileExt_A,NomType_A,i1_civ2,[],j1_civ2);
651            end
652            if strcmp(ImageName_A_Civ2,ImageName_A) && isequal(FrameIndex_A_Civ1(ifield),FrameIndex_A_Civ2(ifield))
653                par_civ2.ImageA=par_civ1.ImageA;
654            else
655                [par_civ2.ImageA,VideoObject_A] = read_image(ImageName_A_Civ2,FileType_A,VideoObject_A,FrameIndex_A_Civ2(ifield));
656            end
657            ImageName_B_Civ2=fullfile_uvmat(RootPath_B,SubDir_B,RootFile_B,FileExt_B,NomType_B,i2_civ2,[],j2_civ2);
658            if strcmp(ImageName_B_Civ2,ImageName_B) && isequal(FrameIndex_B_Civ1(ifield),FrameIndex_B_Civ2)
659                par_civ2.ImageB=par_civ1.ImageB;
660            else
661                [par_civ2.ImageB,VideoObject_B] = read_image(ImageName_B_Civ2,FileType_B,VideoObject_B,FrameIndex_B_Civ2(ifield));
662            end
663            par_civ2.ImageWidth=FileInfo_A.Width;
664            par_civ2.ImageHeight=FileInfo_A.Height;
665            if isfield(par_civ2,'Grid')% grid points set as input file
666                if ischar(par_civ2.Grid)%read the grid file if the input is a file name
667                    par_civ2.Grid=dlmread(par_civ2.Grid);
668                    par_civ2.Grid(1,:)=[];%the first line must be removed (heading in the grid file)
669                end
670            else% automatic grid
671                minix=floor(par_civ2.Dx/2)-0.5;
672                maxix=minix+par_civ2.Dx*floor((par_civ2.ImageWidth-1)/par_civ2.Dx);
673                miniy=floor(par_civ2.Dy/2)-0.5;
674                maxiy=minix+par_civ2.Dy*floor((par_civ2.ImageHeight-1)/par_civ2.Dy);
675                [GridX,GridY]=meshgrid(minix:par_civ2.Dx:maxix,miniy:par_civ2.Dy:maxiy);
676                par_civ2.Grid(:,1)=reshape(GridX,[],1);
677                par_civ2.Grid(:,2)=reshape(GridY,[],1);
678            end
679        end
680       
681        % get the guess from patch1 or patch2 (case 'CheckCiv3')
682        if CheckInputFile % read input images (except in mode Test where it is introduced directly in Param.ActionInput.Civ1.ImageNameA and B)
683            if isfield (par_civ2,'CheckCiv3') && par_civ2.CheckCiv3 %get the guess from  patch2
684                SubRange= Data.Civ2_SubRange;
685                NbCentres=Data.Civ2_NbCentres;
686                Coord_tps=Data.Civ2_Coord_tps;
687                U_tps=Data.Civ2_U_tps;
688                V_tps=Data.Civ2_V_tps;
689                CivStage=Data.CivStage;%store the current CivStage
690                Civ1_Dt=Data.Civ2_Dt;
691                Data=[];%reinitialise the result structure Data
692                Data.ListGlobalAttribute={'Conventions','Program','CivStage'};
693                Data.Conventions='uvmat/civdata';% states the conventions used for the description of field variables and attributes
694                Data.Program='civ_series';
695                Data.CivStage=CivStage+1;%update the current civStage after reinitialisation of Data
696                Data.ListVarName={};
697                Data.VarDimName={};
698            else % get the guess from patch1
699                SubRange= Data.Civ1_SubRange;
700                NbCentres=Data.Civ1_NbCentres;
701                Coord_tps=Data.Civ1_Coord_tps;
702                U_tps=Data.Civ1_U_tps;
703                V_tps=Data.Civ1_V_tps;
704                Civ1_Dt=Data.Civ1_Dt;
705                Data.CivStage=4;
706            end
707        else
708            SubRange= par_civ2.Civ1_SubRange;
709            NbCentres=par_civ2.Civ1_NbCentres;
710            Coord_tps=par_civ2.Civ1_Coord_tps;
711            U_tps=par_civ2.Civ1_U_tps;
712            V_tps=par_civ2.Civ1_V_tps;
713            Civ1_Dt=par_civ2.Civ1_Dt;
714            Civ2_Dt=par_civ2.Civ1_Dt;
715            Data.ListVarName={};
716            Data.VarDimName={};
717        end
718        Shiftx=zeros(size(par_civ2.Grid,1),1);% shift expected from civ1 data
719        Shifty=zeros(size(par_civ2.Grid,1),1);
720        nbval=zeros(size(par_civ2.Grid,1),1);% nbre of interpolated values at each grid point (from the different patch subdomains)
721        if par_civ2.CheckDeformation
722            DUDX=zeros(size(par_civ2.Grid,1),1);
723            DUDY=zeros(size(par_civ2.Grid,1),1);
724            DVDX=zeros(size(par_civ2.Grid,1),1);
725            DVDY=zeros(size(par_civ2.Grid,1),1);
726        end
727        NbSubDomain=size(SubRange,3);
728        for isub=1:NbSubDomain% for each sub-domain of Patch1
729            nbvec_sub=NbCentres(isub);% nbre of Civ vectors in the subdomain
730            ind_sel=find(par_civ2.Grid(:,1)>=SubRange(1,1,isub) & par_civ2.Grid(:,1)<=SubRange(1,2,isub) &...
731                par_civ2.Grid(:,2)>=SubRange(2,1,isub) & par_civ2.Grid(:,2)<=SubRange(2,2,isub));% grid points in the subdomain
732            if ~isempty(ind_sel)
733                epoints = par_civ2.Grid(ind_sel,:);% coordinates of interpolation sites (measurement grids)
734                ctrs=Coord_tps(1:nbvec_sub,:,isub) ;%(=initial points) ctrs
735                nbval(ind_sel)=nbval(ind_sel)+1;% records the number of values for each interpolation point (in case of subdomain overlap)
736                EM = tps_eval(epoints,ctrs);% thin plate spline (tps) coefficient
737                Shiftx(ind_sel)=Shiftx(ind_sel)+EM*U_tps(1:nbvec_sub+3,isub);%velocity shift estimated by tps from civ1
738                Shifty(ind_sel)=Shifty(ind_sel)+EM*V_tps(1:nbvec_sub+3,isub);
739                if par_civ2.CheckDeformation
740                    [EMDX,EMDY] = tps_eval_dxy(epoints,ctrs);%2D matrix of distances between extrapolation points epoints and spline centres (=site points) ctrs
741                    DUDX(ind_sel)=DUDX(ind_sel)+EMDX*U_tps(1:nbvec_sub+3,isub);
742                    DUDY(ind_sel)=DUDY(ind_sel)+EMDY*U_tps(1:nbvec_sub+3,isub);
743                    DVDX(ind_sel)=DVDX(ind_sel)+EMDX*V_tps(1:nbvec_sub+3,isub);
744                    DVDY(ind_sel)=DVDY(ind_sel)+EMDY*V_tps(1:nbvec_sub+3,isub);
745                end
746            end
747        end
748        if par_civ2.CheckMask&&~isempty(par_civ2.Mask)       
749            if isfield(par_civ2,'NbSlice')
750                [RootPath_mask,SubDir_mask,RootFile_mask,i1_mask,i2_mask,j1_mask,j2_mask,Ext_mask]=fileparts_uvmat(Param.ActionInput.Civ2.Mask);
751                i1_mask=mod(i1-1,par_civ2.NbSlice)+1;
752                maskname=fullfile_uvmat(RootPath_mask,SubDir_mask,RootFile_mask,Ext_mask,'_1',i1_mask);
753            else
754                maskname=Param.ActionInput.Civ2.Mask;
755            end
756            if strcmp(maskoldname,maskname)% mask exist, not already read in civ1
757                par_civ2.Mask=mask; %use mask already opened
758            else
759                if exist(maskname,'file')
760                try
761                    par_civ2.Mask=imread(maskname);%update the mask, an store it for future use
762                catch ME
763                    if ~isempty(ME.message)
764                        errormsg=['error reading input image: ' ME.message];
765                        disp_uvmat('ERROR',errormsg,checkrun)
766                        return
767                    end
768                end
769                else
770                    par_civ2.Mask=[];
771                end
772                mask=par_civ2.Mask;
773                maskoldname=maskname;
774            end
775        end
776
777        if CheckInputFile % else Dt given by par_civ2
778            if strcmp(Param.ActionInput.ListCompareMode,'displacement')
779                Civ1_Dt=1;
780                Civ2_Dt=1;
781            else
782                Civ2_Dt=Time(i2_civ2+1,j2_civ2+1)-Time(i1_civ2+1,j1_civ2+1);
783            end
784        end
785        par_civ2.SearchBoxShift=(Civ2_Dt/Civ1_Dt)*[Shiftx(nbval>=1)./nbval(nbval>=1) Shifty(nbval>=1)./nbval(nbval>=1)];
786        % shift the grid points by half the expected shift to provide the correlation box position in image A
787        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];
788        if par_civ2.CheckDeformation
789            par_civ2.DUDX=DUDX(nbval>=1)./nbval(nbval>=1);
790            par_civ2.DUDY=DUDY(nbval>=1)./nbval(nbval>=1);
791            par_civ2.DVDX=DVDX(nbval>=1)./nbval(nbval>=1);
792            par_civ2.DVDY=DVDY(nbval>=1)./nbval(nbval>=1);
793        end
794       
795        % calculate velocity data (y and v in image indices, reverse to y component)
796        [xtable, ytable, utable, vtable, ctable, F,result_conv,errormsg] = civ (par_civ2);
797       
798        list_param=(fieldnames(Param.ActionInput.Civ2))';
799        list_param(strcmp('TestCiv2',list_param))=[];% remove the parameter TestCiv2 from the list
800        Civ2_param=regexprep(list_param,'^.+','Civ2_$0');% insert 'Civ2_' before  each string in list_param
801        Civ2_param=[{'Civ2_ImageA','Civ2_ImageB','Civ2_Time','Civ2_Dt'} Civ2_param]; %insert the names of the two input images
802        %indicate the values of all the global attributes in the output data
803        if exist('ImageName_A','var')
804            Data.Civ2_ImageA=ImageName_A;
805            Data.Civ2_ImageB=ImageName_B;
806            if strcmp(Param.ActionInput.ListCompareMode,'displacement')
807                Data.Civ2_Time=Time(i2_civ2+1,j2_civ2+1);% the Time is the Time of the secodn image
808                Data.Civ2_Dt=1;% Time interval is 1, to yield displacement instead of velocity=displacement/Dt at reading
809            else
810                Data.Civ2_Time=(Time(i2_civ2+1,j2_civ2+1)+Time(i1_civ2+1,j1_civ2+1))/2;
811                Data.Civ2_Dt=Civ2_Dt;
812            end
813        end
814        for ilist=1:length(list_param)
815            Data.(Civ2_param{4+ilist})=Param.ActionInput.Civ2.(list_param{ilist});
816        end
817        Data.ListGlobalAttribute=[Data.ListGlobalAttribute Civ2_param];
818       
819        nbvar=numel(Data.ListVarName);
820        % define the Civ2 variable (if Civ2 data are not replaced from previous calculation)
821        if isempty(find(strcmp('Civ2_X',Data.ListVarName),1))
822            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
823            Data.VarDimName=[Data.VarDimName {'nb_vec_2','nb_vec_2','nb_vec_2','nb_vec_2','nb_vec_2','nb_vec_2'}];
824            Data.VarAttribute{nbvar+1}.Role='coord_x';
825            Data.VarAttribute{nbvar+2}.Role='coord_y';
826            Data.VarAttribute{nbvar+3}.Role='vector_x';
827            Data.VarAttribute{nbvar+4}.Role='vector_y';
828            Data.VarAttribute{nbvar+5}.Role='warnflag';
829        end
830        Data.Civ2_X=reshape(xtable,[],1);
831        Data.Civ2_Y=reshape(size(par_civ2.ImageA,1)-ytable+1,[],1);
832        Data.Civ2_U=reshape(utable,[],1);
833        Data.Civ2_V=reshape(-vtable,[],1);
834        Data.Civ2_C=reshape(ctable,[],1);
835        Data.Civ2_F=reshape(F,[],1);
836        disp('civ2 performed')
837    elseif ~isfield(Data,'ListVarName') % we start there, using existing Civ2 data
838        if exist('ncfile','var')
839            CivFile=ncfile;
840            [Data,tild,tild,errormsg]=nc2struct(CivFile);%read civ1 and fix1 data in the existing netcdf file
841            if ~isempty(errormsg)
842                disp_uvmat('ERROR',errormsg,checkrun)
843                return
844            end
845        elseif isfield(Param,'Civ2_X')% use Civ2 data as input in Param (test mode)
846            Data.ListGlobalAttribute={};
847            Data.ListVarName={};
848            Data.VarDimName={};
849            Data.Civ2_X=Param.Civ2_X;
850            Data.Civ2_Y=Param.Civ2_Y;
851            Data.Civ2_U=Param.Civ2_U;
852            Data.Civ2_V=Param.Civ2_V;
853            Data.Civ2_FF=Param.Civ2_FF;
854        end
855    end
856   
857    %% Fix2
858    if isfield (Param.ActionInput,'Fix2')
859        disp('fix2 started')
860        list_param=fieldnames(Param.ActionInput.Fix2)';
861        Fix2_param=regexprep(list_param,'^.+','Fix2_$0');% insert 'Fix1_' before  each string in ListFixParam
862        %indicate the values of all the global attributes in the output data
863        for ilist=1:length(list_param)
864            Data.(Fix2_param{ilist})=Param.ActionInput.Fix2.(list_param{ilist});
865        end
866        Data.ListGlobalAttribute=[Data.ListGlobalAttribute Fix2_param];
867        %
868        %         ListFixParam=fieldnames(Param.ActionInput.Fix2);
869        %         for ilist=1:length(ListFixParam)
870        %             ParamName=ListFixParam{ilist};
871        %             ListName=['Fix2_' ParamName];
872        %             eval(['Data.ListGlobalAttribute=[Data.ListGlobalAttribute ''' ParamName '''];'])
873        %             eval(['Data.' ListName '=Param.ActionInput.Fix2.' ParamName ';'])
874        %         end
875        if check_civx
876            if ~isfield(Data,'fix2')
877                Data.ListGlobalAttribute=[Data.ListGlobalAttribute 'fix2'];
878                Data.fix2=1;
879                Data.ListVarName=[Data.ListVarName {'vec2_FixFlag'}];
880                Data.VarDimName=[Data.VarDimName {'nb_vectors2'}];
881            end
882            Data.vec_FixFlag=fix(Param.Fix2,Data.vec2_F,Data.vec2_C,Data.vec2_U,Data.vec2_V,Data.vec2_X,Data.vec2_Y);
883        else
884            Data.ListVarName=[Data.ListVarName {'Civ2_FF'}];
885            Data.VarDimName=[Data.VarDimName {'nb_vec_2'}];
886            nbvar=length(Data.ListVarName);
887            Data.VarAttribute{nbvar}.Role='errorflag';
888            Data.Civ2_FF=double(fix(Param.ActionInput.Fix2,Data.Civ2_F,Data.Civ2_C,Data.Civ2_U,Data.Civ2_V));
889            Data.CivStage=Data.CivStage+1;
890        end
891    end
892   
893    %% Patch2
894    if isfield (Param.ActionInput,'Patch2')
895        disp('patch2 started')
896        list_param=fieldnames(Param.ActionInput.Patch2)';
897        list_param(strcmp('TestPatch2',list_param))=[];% remove the parameter TestCiv1 from the list
898        Patch2_param=regexprep(list_param,'^.+','Patch2_$0');% insert 'Fix1_' before  each string in ListFixParam
899        %indicate the values of all the global attributes in the output data
900        for ilist=1:length(list_param)
901            Data.(Patch2_param{ilist})=Param.ActionInput.Patch2.(list_param{ilist});
902        end
903        Data.ListGlobalAttribute=[Data.ListGlobalAttribute Patch2_param];
904       
905        nbvar=length(Data.ListVarName);
906        Data.ListVarName=[Data.ListVarName {'Civ2_U_smooth','Civ2_V_smooth','Civ2_SubRange','Civ2_NbCentres','Civ2_Coord_tps','Civ2_U_tps','Civ2_V_tps'}];
907        Data.VarDimName=[Data.VarDimName {'nb_vec_2','nb_vec_2',{'nb_coord','nb_bounds','nb_subdomain_2'},{'nb_subdomain_2'},...
908            {'nb_tps_2','nb_coord','nb_subdomain_2'},{'nb_tps_2','nb_subdomain_2'},{'nb_tps_2','nb_subdomain_2'}}];
909       
910        Data.VarAttribute{nbvar+1}.Role='vector_x';
911        Data.VarAttribute{nbvar+2}.Role='vector_y';
912        Data.VarAttribute{nbvar+5}.Role='coord_tps';
913        Data.VarAttribute{nbvar+6}.Role='vector_x';
914        Data.VarAttribute{nbvar+7}.Role='vector_y';
915        Data.Civ2_U_smooth=Data.Civ2_U;
916        Data.Civ2_V_smooth=Data.Civ2_V;
917        if isfield(Data,'Civ2_FF')
918            ind_good=find(Data.Civ2_FF==0);
919        else
920            ind_good=1:numel(Data.Civ2_X);
921        end
922        [Data.Civ2_SubRange,Data.Civ2_NbCentres,Data.Civ2_Coord_tps,Data.Civ2_U_tps,Data.Civ2_V_tps,tild,Ures,Vres,tild,FFres]=...
923            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);
924        Data.Civ2_U_smooth(ind_good)=Ures;
925        Data.Civ2_V_smooth(ind_good)=Vres;
926        Data.Civ2_FF(ind_good)=FFres;
927        Data.CivStage=Data.CivStage+1;
928        disp('patch2 performed')
929    end
930   
931    %% write result in a netcdf file if requested
932    if CheckOutputFile
933        errormsg=struct2nc(ncfile_out,Data);
934        if isempty(errormsg)
935            disp([ncfile_out ' written'])
936            %[success,msg] = fileattrib(ncfile_out ,'+w','g');% done in struct2nc
937        else
938            disp(errormsg)
939        end
940        disp(['ellapsed time ' num2str(toc/60,2) ' minutes'])
941    end
942end
943
944
945% 'civ': function piv.m adapted from PIVlab http://pivlab.blogspot.com/
946%--------------------------------------------------------------------------
947% function [xtable ytable utable vtable typevector] = civ (image1,image2,ibx,iby step, subpixfinder, mask, roi)
948%
949% OUTPUT:
950% xtable: set of x coordinates
951% ytable: set of y coordiantes
952% utable: set of u displacements (along x)
953% vtable: set of v displacements (along y)
954% ctable: max image correlation for each vector
955% typevector: set of flags, =1 for good, =0 for NaN vectors
956%
957%INPUT:
958% par_civ: structure of input parameters, with fields:
959%  .ImageA: first image for correlation (matrix)
960%  .ImageB: second image for correlation(matrix)
961%  .CorrBoxSize: 1,2 vector giving the size of the correlation box in x and y
962%  .SearchBoxSize:  1,2 vector giving the size of the search box in x and y
963%  .SearchBoxShift: 1,2 vector or 2 column matrix (for civ2) giving the shift of the search box in x and y
964%  .CorrSmooth: =1 or 2 determines the choice of the sub-pixel determination of the correlation max
965%  .ImageWidth: nb of pixels of the image in x
966%  .Dx, Dy: mesh for the PIV calculation
967%  .Grid: grid giving the PIV calculation points (alternative to .Dx .Dy): centres of the correlation boxes in Image A
968%  .Mask: name of a mask file or mask image matrix itself
969%  .MinIma: thresholds for image luminosity
970%  .MaxIma
971%  .CheckDeformation=1 for subpixel interpolation and image deformation (linear transform)
972%  .DUDX: matrix of deformation obtained from patch at each grid point
973%  .DUDY
974%  .DVDX:
975%  .DVDY
976
977function [xtable,ytable,utable,vtable,ctable,F,result_conv,errormsg] = civ (par_civ)
978
979%% prepare measurement grid
980if isfield(par_civ,'Grid')% grid points set as input, central positions of the sub-images in image A
981    if ischar(par_civ.Grid)%read the grid file if the input is a file name (grid in x, y image coordinates)
982        par_civ.Grid=dlmread(par_civ.Grid);
983        par_civ.Grid(1,:)=[];%the first line must be removed (heading in the grid file)
984    end
985    % else par_civ.Grid is already an array, no action here
986else% automatic grid in x, y image coordinates
987    minix=floor(par_civ.Dx/2)-0.5;
988    maxix=minix+par_civ.Dx*floor((par_civ.ImageWidth-1)/par_civ.Dx);
989    miniy=floor(par_civ.Dy/2)-0.5;% first automatic grid point at half the mesh Dy
990    maxiy=minix+par_civ.Dy*floor((par_civ.ImageHeight-1)/par_civ.Dy);
991    [GridX,GridY]=meshgrid(minix:par_civ.Dx:maxix,miniy:par_civ.Dy:maxiy);
992    par_civ.Grid(:,1)=reshape(GridX,[],1);
993    par_civ.Grid(:,2)=reshape(GridY,[],1);% increases with array index
994end
995nbvec=size(par_civ.Grid,1);
996
997%% prepare correlation and search boxes
998ibx2=floor(par_civ.CorrBoxSize(1)/2);
999iby2=floor(par_civ.CorrBoxSize(2)/2);
1000isx2=floor(par_civ.SearchBoxSize(1)/2);
1001isy2=floor(par_civ.SearchBoxSize(2)/2);
1002shiftx=round(par_civ.SearchBoxShift(:,1));%use the input shift estimate, rounded to the next integer value
1003shifty=-round(par_civ.SearchBoxShift(:,2));% sign minus because image j index increases when y decreases
1004if numel(shiftx)==1% case of a unique shift for the whole field( civ1)
1005    shiftx=shiftx*ones(nbvec,1);
1006    shifty=shifty*ones(nbvec,1);
1007end
1008
1009%% Array initialisation and default output  if par_civ.CorrSmooth=0 (just the grid calculated, no civ computation)
1010xtable=round(par_civ.Grid(:,1)+0.5)-0.5;
1011ytable=round(par_civ.ImageHeight-par_civ.Grid(:,2)+0.5)-0.5;% y index corresponding to the position in image coordiantes
1012utable=shiftx;%zeros(nbvec,1);
1013vtable=shifty;%zeros(nbvec,1);
1014ctable=zeros(nbvec,1);
1015F=zeros(nbvec,1);
1016result_conv=[];
1017errormsg='';
1018
1019%% prepare mask
1020if isfield(par_civ,'Mask') && ~isempty(par_civ.Mask)
1021    if strcmp(par_civ.Mask,'all')
1022        return    % get the grid only, no civ calculation
1023    elseif ischar(par_civ.Mask)
1024        par_civ.Mask=imread(par_civ.Mask);% read the mask if not allready done
1025    end
1026end
1027check_MinIma=isfield(par_civ,'MinIma');% test for image luminosity threshold
1028check_MaxIma=isfield(par_civ,'MaxIma') && ~isempty(par_civ.MaxIma);
1029
1030par_civ.ImageA=sum(double(par_civ.ImageA),3);%sum over rgb component for color images
1031par_civ.ImageB=sum(double(par_civ.ImageB),3);
1032[npy_ima npx_ima]=size(par_civ.ImageA);
1033if ~isequal(size(par_civ.ImageB),[npy_ima npx_ima])
1034    errormsg='image pair with unequal size';
1035    return
1036end
1037
1038%% Apply mask
1039% Convention for mask IDEAS TO IMPLEMENT ?
1040% mask >200 : velocity calculated
1041%  200 >=mask>150;velocity not calculated, interpolation allowed (bad spots)
1042% 150>=mask >100: velocity not calculated, nor interpolated
1043%  100>=mask> 20: velocity not calculated, impermeable (no flux through mask boundaries)
1044%  20>=mask: velocity=0
1045checkmask=0;
1046MinA=min(min(par_civ.ImageA));
1047%MinB=min(min(par_civ.ImageB));
1048%check_undefined=false(size(par_civ.ImageA));
1049if isfield(par_civ,'Mask') && ~isempty(par_civ.Mask)
1050    checkmask=1;
1051    if ~isequal(size(par_civ.Mask),[npy_ima npx_ima])
1052        errormsg='mask must be an image with the same size as the images';
1053        return
1054    end
1055    check_undefined=(par_civ.Mask<200 & par_civ.Mask>=20 );
1056    %     par_civ.ImageA(check_undefined)=0;% put image A to zero (i.e. the min image value) in the undefined  area
1057    %     par_civ.ImageB(check_undefined)=0;% put image B to zero (i.e. the min image value) in the undefined  area
1058end
1059
1060%% compute image correlations: MAINLOOP on velocity vectors
1061corrmax=0;
1062sum_square=1;% default
1063mesh=1;% default
1064CheckDeformation=isfield(par_civ,'CheckDeformation')&& par_civ.CheckDeformation==1;
1065if CheckDeformation
1066    mesh=0.25;%mesh in pixels for subpixel image interpolation (x 4 in each direction)
1067    par_civ.CorrSmooth=2;% use SUBPIX2DGAUSS (take into account more points near the max)
1068end
1069
1070if par_civ.CorrSmooth~=0 % par_civ.CorrSmooth=0 implies no civ computation (just input image and grid points given)
1071    for ivec=1:nbvec
1072        iref=round(par_civ.Grid(ivec,1)+0.5);% xindex on the image A for the middle of the correlation box
1073        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
1074        F(ivec)=0;
1075        subrange1_x=iref-ibx2:iref+ibx2;% x indices defining the first subimage
1076        subrange1_y=jref-iby2:jref+iby2;% y indices defining the first subimage
1077        subrange2_x=iref+shiftx(ivec)-isx2:iref+shiftx(ivec)+isx2;%x indices defining the second subimage
1078        subrange2_y=jref+shifty(ivec)-isy2:jref+shifty(ivec)+isy2;%y indices defining the second subimage
1079        image1_crop=MinA*ones(numel(subrange1_y),numel(subrange1_x));% default value=min of image A
1080        image2_crop=MinA*ones(numel(subrange2_y),numel(subrange2_x));% default value=min of image A
1081        check1_x=subrange1_x>=1 & subrange1_x<=par_civ.ImageWidth;% check which points in the subimage 1 are contained in the initial image 1
1082        check1_y=subrange1_y>=1 & subrange1_y<=par_civ.ImageHeight;
1083        check2_x=subrange2_x>=1 & subrange2_x<=par_civ.ImageWidth;% check which points in the subimage 2 are contained in the initial image 2
1084        check2_y=subrange2_y>=1 & subrange2_y<=par_civ.ImageHeight;
1085        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
1086        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
1087        if checkmask
1088            mask1_crop=ones(numel(subrange1_y),numel(subrange1_x));% default value=1 for mask
1089            mask2_crop=ones(numel(subrange2_y),numel(subrange2_x));% default value=1 for mask
1090            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
1091            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
1092            sizemask=sum(sum(mask1_crop))/(numel(subrange1_y)*numel(subrange1_x));%size of the masked part relative to the correlation sub-image
1093            if sizemask > 1/2% eliminate point if more than half of the correlation box is masked
1094                F(ivec)=3; %
1095                utable(ivec)=0;
1096                vtable(ivec)=0;
1097            else
1098                image1_crop=image1_crop.*~mask1_crop;% put to zero the masked pixels (mask1_crop='true'=1)
1099                image2_crop=image2_crop.*~mask2_crop;
1100                image1_mean=mean(mean(image1_crop))/(1-sizemask);
1101                image2_mean=mean(mean(image2_crop))/(1-sizemask);
1102            end
1103        else
1104            image1_mean=mean(mean(image1_crop));
1105            image2_mean=mean(mean(image2_crop));
1106        end
1107        %threshold on image minimum
1108        if F(ivec)~=3
1109            if check_MinIma && (image1_mean < par_civ.MinIma || image2_mean < par_civ.MinIma)
1110                F(ivec)=3;
1111                %threshold on image maximum
1112            elseif check_MaxIma && (image1_mean > par_civ.MaxIma || image2_mean > par_civ.MaxIma)
1113                F(ivec)=3;
1114            end
1115            if F(ivec)==3
1116                utable(ivec)=0;
1117                vtable(ivec)=0;
1118            else
1119                %mask
1120                if checkmask
1121                    image1_crop=(image1_crop-image1_mean).*~mask1_crop;%substract the mean, put to zero the masked parts
1122                    image2_crop=(image2_crop-image2_mean).*~mask2_crop;
1123                else
1124                    image1_crop=(image1_crop-image1_mean);
1125                    image2_crop=(image2_crop-image2_mean);
1126                end
1127                %deformation
1128                if CheckDeformation
1129                    xi=(1:mesh:size(image1_crop,2));
1130                    yi=(1:mesh:size(image1_crop,1))';
1131                    [XI,YI]=meshgrid(xi-ceil(size(image1_crop,2)/2),yi-ceil(size(image1_crop,1)/2));
1132                    XIant=XI-par_civ.DUDX(ivec)*XI+par_civ.DUDY(ivec)*YI+ceil(size(image1_crop,2)/2);
1133                    YIant=YI+par_civ.DVDX(ivec)*XI-par_civ.DVDY(ivec)*YI+ceil(size(image1_crop,1)/2);
1134                    image1_crop=interp2(image1_crop,XIant,YIant);
1135                    image1_crop(isnan(image1_crop))=0;
1136                    xi=(1:mesh:size(image2_crop,2));
1137                    yi=(1:mesh:size(image2_crop,1))';
1138                    image2_crop=interp2(image2_crop,xi,yi,'*spline');
1139                    image2_crop(isnan(image2_crop))=0;
1140                end
1141                sum_square=sum(sum(image1_crop.*image1_crop));
1142                %reference: Oliver Pust, PIV: Direct Cross-Correlation
1143                result_conv= conv2(image2_crop,flipdim(flipdim(image1_crop,2),1),'valid');
1144                corrmax= max(max(result_conv));
1145                result_conv=(result_conv/corrmax)*255; %normalize, peak=always 255
1146                %Find the correlation max, at 255
1147                [y,x] = find(result_conv==255,1);
1148                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
1149                sum_square=sum_square*sum(sum(subimage2_crop.*subimage2_crop));% product of variances of image 1 and 2
1150                sum_square=sqrt(sum_square);% srt of the variance product to normalise correlation
1151                if ~isempty(y) && ~isempty(x)
1152                    try
1153                        if par_civ.CorrSmooth==1
1154                            [vector,F(ivec)] = SUBPIXGAUSS (result_conv,x,y);
1155                        elseif par_civ.CorrSmooth==2
1156                            [vector,F(ivec)] = SUBPIX2DGAUSS (result_conv,x,y);
1157                        else
1158                            [vector,F(ivec)] = quadr_fit(result_conv,x,y);
1159                        end
1160                        utable(ivec)=vector(1)*mesh+shiftx(ivec);
1161                        vtable(ivec)=vector(2)*mesh+shifty(ivec);
1162                        xtable(ivec)=iref+utable(ivec)/2-0.5;% convec flow (velocity taken at the point middle from imgae 1 and 2)
1163                        ytable(ivec)=jref+vtable(ivec)/2-0.5;% and position of pixel 1=0.5 (convention for image coordinates=0 at the edge)
1164                        iref=round(xtable(ivec)+0.5);% nearest image index for the middle of the vector
1165                        jref=round(ytable(ivec)+0.5);
1166                        % eliminate vectors located in the mask
1167                        if  checkmask && (iref<1 || jref<1 ||iref>npx_ima || jref>npy_ima ||( par_civ.Mask(jref,iref)<200 && par_civ.Mask(jref,iref)>=100))
1168                            utable(ivec)=0;
1169                            vtable(ivec)=0;
1170                            F(ivec)=3;
1171                        end
1172                        ctable(ivec)=corrmax/sum_square;% correlation value
1173                    catch ME
1174                        F(ivec)=3;
1175                        disp(ME.message)
1176                    end
1177                else
1178                    F(ivec)=3;
1179                end
1180            end
1181        end
1182    end
1183end
1184result_conv=result_conv*corrmax/(255*sum_square);% keep the last correlation matrix for output
1185
1186%------------------------------------------------------------------------
1187% --- Find the maximum of the correlation function after interpolation
1188% OUPUT:
1189% vector = optimum displacement vector with subpixel correction
1190% F =flag: =0 OK
1191%           =-2 , warning: max too close to the edge of the search box (1 pixel margin)
1192% INPUT:
1193% x,y: position of the maximum correlation at integer values
1194
1195function [vector,F] = SUBPIXGAUSS (result_conv,x,y)
1196%------------------------------------------------------------------------
1197% vector=[0 0]; %default
1198F=0;
1199[npy,npx]=size(result_conv);
1200result_conv(result_conv<1)=1; %set to 1 correlation values smaller than 1  (=0 by discretisation, to avoid divergence in the log)
1201%the following 8 lines are copyright (c) 1998, Uri Shavit, Roi Gurka, Alex Liberzon, Technion ??? Israel Institute of Technology
1202%http://urapiv.wordpress.com
1203peaky = y;
1204if y < npy && y > 1
1205    f0 = log(result_conv(y,x));
1206    f1 = log(result_conv(y-1,x));
1207    f2 = log(result_conv(y+1,x));
1208    peaky = peaky+ (f1-f2)/(2*f1-4*f0+2*f2);
1209else
1210    F=-2; % warning flag for vector truncated by the limited search box
1211end
1212peakx=x;
1213if x < npx-1 && x > 1
1214    f0 = log(result_conv(y,x));
1215    f1 = log(result_conv(y,x-1));
1216    f2 = log(result_conv(y,x+1));
1217    peakx = peakx+ (f1-f2)/(2*f1-4*f0+2*f2);
1218else
1219    F=-2; % warning flag for vector truncated by the limited search box
1220end
1221vector=[peakx-floor(npx/2)-1 peaky-floor(npy/2)-1];
1222
1223%------------------------------------------------------------------------
1224% --- Find the maximum of the correlation function after interpolation
1225function [vector,F] = SUBPIX2DGAUSS (result_conv,x,y)
1226%------------------------------------------------------------------------
1227% vector=[0 0]; %default
1228F=-2;
1229peaky=y;
1230peakx=x;
1231result_conv(result_conv<1)=1; %set to 1 correlation values smaller than 1 (to avoid divergence in the log)
1232[npy,npx]=size(result_conv);
1233if (x < npx) && (y < npy) && (x > 1) && (y > 1)
1234    F=0;
1235    for i=-1:1
1236        for j=-1:1
1237            %following 15 lines based on
1238            %H. Nobach ??? M. Honkanen (2005)
1239            %Two-dimensional Gaussian regression for sub-pixel displacement
1240            %estimation in particle image velocimetry or particle position
1241            %estimation in particle tracking velocimetry
1242            %Experiments in Fluids (2005) 38: 511???515
1243            c10(j+2,i+2)=i*log(result_conv(y+j, x+i));
1244            c01(j+2,i+2)=j*log(result_conv(y+j, x+i));
1245            c11(j+2,i+2)=i*j*log(result_conv(y+j, x+i));
1246            c20(j+2,i+2)=(3*i^2-2)*log(result_conv(y+j, x+i));
1247            c02(j+2,i+2)=(3*j^2-2)*log(result_conv(y+j, x+i));
1248        end
1249    end
1250    c10=(1/6)*sum(sum(c10));
1251    c01=(1/6)*sum(sum(c01));
1252    c11=(1/4)*sum(sum(c11));
1253    c20=(1/6)*sum(sum(c20));
1254    c02=(1/6)*sum(sum(c02));
1255    deltax=(c11*c01-2*c10*c02)/(4*c20*c02-c11^2);
1256    deltay=(c11*c10-2*c01*c20)/(4*c20*c02-c11^2);
1257    if abs(deltax)<1
1258        peakx=x+deltax;
1259    end
1260    if abs(deltay)<1
1261        peaky=y+deltay;
1262    end
1263end
1264vector=[peakx-floor(npx/2)-1 peaky-floor(npy/2)-1];
1265
1266%------------------------------------------------------------------------
1267% --- Find the maximum of the correlation function after quadratic interpolation
1268function [vector,F] = quadr_fit(result_conv,x,y)
1269[npy,npx]=size(result_conv);
1270if x<4 || y<4 || npx-x<4 ||npy-y <4
1271    F=-2;
1272    vector=[x y];
1273else
1274    F=0;
1275    x_ind=x-4:x+4;
1276    y_ind=y-4:y+4;
1277    x_vec=0.25*(x_ind-x);
1278    y_vec=0.25*(y_ind-y);
1279    [X,Y]=meshgrid(x_vec,y_vec);
1280    coord=[reshape(X,[],1) reshape(Y,[],1)];
1281    result_conv=reshape(result_conv(y_ind,x_ind),[],1);
1282   
1283   
1284    % n=numel(X);
1285    % x=[X Y];
1286    % X=X-0.5;
1287    % Y=Y+0.5;
1288    % y = (X.*X+2*Y.*Y+X.*Y+6) + 0.1*rand(n,1);
1289    p = polyfitn(coord,result_conv,2);
1290    A(1,1)=2*p.Coefficients(1);
1291    A(1,2)=p.Coefficients(2);
1292    A(2,1)=p.Coefficients(2);
1293    A(2,2)=2*p.Coefficients(4);
1294    vector=[x y]'-A\[p.Coefficients(3) p.Coefficients(5)]';
1295    vector=vector'-[floor(npx/2) floor(npy/2)]-1 ;
1296    % zg = polyvaln(p,coord);
1297    % figure
1298    % surf(x_vec,y_vec,reshape(zg,9,9))
1299    % hold on
1300    % plot3(X,Y,reshape(result_conv,9,9),'o')
1301    % hold off
1302end
1303
1304%'RUN_FIX': function for fixing velocity fields:
1305%-----------------------------------------------
1306% RUN_FIX(filename,field,flagindex,thresh_vecC,thresh_vel,iter,flag_mask,maskname,fileref,fieldref)
1307%
1308%filename: name of the netcdf file (used as input and output)
1309%field: structure specifying the names of the fields to fix (depending on civ1 or civ2)
1310%.vel_type='civ1' or 'civ2';
1311%.nb=name of the dimension common to the field to fix ('nb_vectors' for civ1);
1312%.fixflag=name of fix flag variable ('vec_FixFlag' for civ1)
1313%flagindex: flag specifying which values of vec_f are removed:
1314% if flagindex(1)=1: vec_f=-2 vectors are removed
1315% if flagindex(2)=1: vec_f=3 vectors are removed
1316% if flagindex(3)=1: vec_f=2 vectors are removed (if iter=1) or vec_f=4 vectors are removed (if iter=2)
1317%iter=1 for civ1 fields and iter=2 for civ2 fields
1318%thresh_vecC: threshold in the image correlation vec_C
1319%flag_mask: =1 mask used to remove vectors (0 else)
1320%maskname: name of the mask image file for fix
1321%thresh_vel: threshold on velocity, or on the difference with the reference file fileref if exists
1322%inf_sup=1: remove values smaller than threshold thresh_vel, =2, larger than threshold
1323%fileref: .nc file name for a reference velocity (='': refrence 0 used)
1324%fieldref: 'civ1','filter1'...feld used in fileref
1325
1326function FF=fix(Param,F,C,U,V,X,Y)
1327FF=zeros(size(F));%default
1328
1329%criterium on warn flags
1330FlagName={'CheckFmin2','CheckF2','CheckF3','CheckF4'};
1331FlagVal=[-2 2 3 4];
1332for iflag=1:numel(FlagName)
1333    if isfield(Param,FlagName{iflag}) && Param.(FlagName{iflag})
1334        FF=(FF==1| F==FlagVal(iflag));
1335    end
1336end
1337%criterium on correlation values
1338if isfield (Param,'MinCorr')
1339    FF=FF==1 | C<Param.MinCorr;
1340end
1341if (isfield(Param,'MinVel')&&~isempty(Param.MinVel))||(isfield (Param,'MaxVel')&&~isempty(Param.MaxVel))
1342    Umod= U.*U+V.*V;
1343    if isfield (Param,'MinVel')&&~isempty(Param.MinVel)
1344        FF=FF==1 | Umod<(Param.MinVel*Param.MinVel);
1345    end
1346    if isfield (Param,'MaxVel')&&~isempty(Param.MaxVel)
1347        FF=FF==1 | Umod>(Param.MaxVel*Param.MaxVel);
1348    end
1349end
1350
1351
1352%------------------------------------------------------------------------
1353% --- determine the list of index pairs of processing file
1354function [i1_series,i2_series,j1_series,j2_series,check_bounds,NomTypeNc]=...
1355    find_pair_indices(str_civ,i_series,j_series,MinIndex_i,MaxIndex_i,MinIndex_j,MaxIndex_j)
1356%------------------------------------------------------------------------
1357i1_series=i_series;% set of first image indexes
1358i2_series=i_series;
1359j1_series=j_series;%ones(size(i_series));% set of first image numbers
1360j2_series=j_series;%ones(size(i_series));
1361r=regexp(str_civ,'^\D(?<ind>[i|j])=( -| )(?<num1>\d+)\|(?<num2>\d+)','names');
1362if ~isempty(r)
1363    mode=['D' r.ind];
1364    ind1=str2num(r.num1);
1365    ind2=str2num(r.num2);
1366else
1367    mode='j1-j2';
1368    r=regexp(str_civ,'^j= (?<num1>[a-z])-(?<num2>[a-z])','names');
1369    if ~isempty(r)
1370        NomTypeNc='_1ab';
1371    else
1372        r=regexp(str_civ,'^j= (?<num1>[A-Z])-(?<num2>[A-Z])','names');
1373        if ~isempty(r)
1374            NomTypeNc='_1AB';
1375        else
1376            r=regexp(str_civ,'^j= (?<num1>\d+)-(?<num2>\d+)','names');
1377            if ~isempty(r)
1378                NomTypeNc='_1_1-2';
1379            end
1380        end
1381    end
1382    if isempty(r)
1383        display('wrong pair mode input option')
1384    else
1385        ind1=stra2num(r.num1);
1386        ind2=stra2num(r.num2);
1387    end
1388end
1389switch mode
1390    case 'Di'
1391        i1_series=i_series-ind1;% set of first image numbers
1392        i2_series=i_series+ind2;
1393        check_bounds=i1_series<MinIndex_i | i2_series>MaxIndex_i;
1394        if isempty(j_series)
1395            NomTypeNc='_1-2';
1396        else
1397            j1_series=j_series;
1398            j2_series=j_series;
1399            NomTypeNc='_1-2_1';
1400        end
1401    case 'Dj'
1402        j1_series=j_series-ind1;
1403        j2_series=j_series+ind2;
1404        check_bounds=j1_series<MinIndex_j | j2_series>MaxIndex_j;
1405        NomTypeNc='_1_1-2';
1406    otherwise %bursts
1407        i1_series=i_series(1,:);% do not sweep the j index
1408        i2_series=i_series(1,:);
1409        j1_series=ind1*ones(1,size(i_series,2));% j index is fixed by pair choice
1410        j2_series=ind2*ones(1,size(i_series,2));
1411        check_bounds=zeros(size(i1_series));% no limitations due to min-max indices
1412end
1413
1414
1415
1416
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