source: trunk/src/series/civ_series.m @ 895

Last change on this file since 895 was 895, checked in by sommeria, 8 years ago
File size: 64.2 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, default=''
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%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
31%  Copyright 2011-2014, LEGI / CNRS UJF G-INP, Joel.Sommeria@legi.grenoble-inp.fr
32%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
33%     This is part of the toolbox UVMAT.
34%
35%     UVMAT is free software; you can redistribute it and/or modify
36%     it under the terms of the GNU General Public License as published by
37%     the Free Software Foundation; either version 2 of the License, or
38%     (at your option) any later version.
39%
40%     UVMAT is distributed in the hope that it will be useful,
41%     but WITHOUT ANY WARRANTY; without even the implied warranty of
42%     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
43%     GNU General Public License (open UVMAT/COPYING.txt) for more details.
44%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
45
46function [Data,errormsg,result_conv]= civ_series(Param)
47errormsg='';
48
49%% set the input elements needed on the GUI series when the action is selected in the menu ActionName or InputTable refreshed
50if isstruct(Param) && isequal(Param.Action.RUN,0)% function activated from the GUI series but not RUN
51    path_series=fileparts(which('series'));
52    addpath(fullfile(path_series,'series'))
53    Data=civ_input(Param);% introduce the civ parameters using the GUI civ_input
54    if isempty(Data)
55        Data=Param;% if  civ_input has been cancelled, keep previous parameters
56    end
57    Data.Program=mfilename;%gives the name of the current function
58    Data.AllowInputSort='off';% allow alphabetic sorting of the list of input file SubDir (options 'off'/'on', 'off' by default)
59    Data.WholeIndexRange='off';% prescribes the file index ranges from min to max (options 'off'/'on', 'off' by default)
60    if isfield(Data,'ActionInput') && isfield(Data.ActionInput,'PairIndices')&& strcmp(Data.ActionInput.PairIndices.ListPairMode,'pair j1-j2')
61        Data.Desable_j_index='on';% hide the j index in series (set by the pair choice in civ_input)
62    end
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    return
73end
74
75%% read input parameters from an xml file if input is a file name (batch mode)
76checkrun=1;
77if ischar(Param)
78    Param=xml2struct(Param);% read Param as input file (batch case)
79    checkrun=0;
80end
81
82%% test input
83if ~isfield(Param,'ActionInput')
84    disp_uvmat('ERROR','no parameter set for PIV',checkrun)
85    return
86end
87iview_A=0;%default values
88NbField=1;
89RUNHandle=[];
90CheckInputFile=isfield(Param,'InputTable');%= 1 in test use for TestCiv (no nc file involved)
91CheckOutputFile=isfield(Param,'OutputSubDir');%= 1 in test use for TestPatch (no nc file produced)
92
93%% input files and indexing (skipped in Test mode)
94if CheckInputFile
95    hseries=findobj(allchild(0),'Tag','series');
96    RUNHandle=findobj(hseries,'Tag','RUN');%handle of RUN button in GUI series
97    WaitbarHandle=findobj(hseries,'Tag','Waitbar');%handle of waitbar in GUI series
98    MaxIndex_i=Param.IndexRange.MaxIndex_i;
99    MinIndex_i=Param.IndexRange.MinIndex_i;
100    MaxIndex_j=ones(size(MaxIndex_i));MinIndex_j=ones(size(MinIndex_i));
101    if isfield(Param.IndexRange,'MaxIndex_j')&& isfield(Param.IndexRange,'MinIndex_j')
102        MaxIndex_j=Param.IndexRange.MaxIndex_j;
103        MinIndex_j=Param.IndexRange.MinIndex_j;
104    end
105    if isfield(Param,'InputTable')
106        [tild,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param);
107        iview_A=0;% series index (iview) for the first image series
108        iview_B=0;% series index (iview) for the second image series (only non zero for option 'shift' comparing two image series )
109        if Param.ActionInput.CheckCiv1
110            iview_A=1;% usual PIV, the image series is on the first line of the table
111        elseif Param.ActionInput.CheckCiv2 % civ2 is performed without Civ1, a netcdf file series is needed in the first table line
112            iview_A=2;% the second line is used for the input images of Civ2
113        end
114        if strcmp(Param.ActionInput.ListCompareMode,'shift')
115            iview_B=iview_A+1; % the second image series is on the next line of the input table
116        end
117        if iview_A~=0
118            RootPath_A=Param.InputTable{iview_A,1};
119            RootFile_A=Param.InputTable{iview_A,3};
120            SubDir_A=Param.InputTable{iview_A,2};
121            NomType_A=Param.InputTable{iview_A,4};
122            FileExt_A=Param.InputTable{iview_A,5};
123            if iview_B==0
124                iview_B=iview_A;% the second image series is the same as the first
125            end
126            RootPath_B=Param.InputTable{iview_B,1};
127            RootFile_B=Param.InputTable{iview_B,3};
128            SubDir_B=Param.InputTable{iview_B,2};
129            NomType_B=Param.InputTable{iview_B,4};
130            FileExt_B=Param.InputTable{iview_B,5};
131        end
132       
133        PairCiv2='';
134        switch Param.ActionInput.ListCompareMode
135            case 'PIV'
136                PairCiv1=Param.ActionInput.PairIndices.ListPairCiv1;
137                if isfield(Param.ActionInput.PairIndices,'ListPairCiv2')
138                    PairCiv2=Param.ActionInput.PairIndices.ListPairCiv2;%string which determines the civ2 pair
139                end
140                if iview_A==1% if Civ1 is performed
141                    [i1_series_Civ1,i2_series_Civ1,j1_series_Civ1,j2_series_Civ1,check_bounds,NomTypeNc]=...
142                        find_pair_indices(PairCiv1,i1_series{1},j1_series{1},MinIndex_i,MaxIndex_i,MinIndex_j,MaxIndex_j);
143                    if ~isempty(PairCiv2)
144                        [i1_series_Civ2,i2_series_Civ2,j1_series_Civ2,j2_series_Civ2,check_bounds_Civ2]=...
145                            find_pair_indices(PairCiv2,i1_series{1},j1_series{1},MinIndex_i(1),MaxIndex_i(1),MinIndex_j(1),MaxIndex_j(1));
146                        check_bounds=check_bounds | check_bounds_Civ2;
147                    end
148                else% we start from an existing Civ1 file
149                    i1_series_Civ1=i1_series{1};
150                    i2_series_Civ1=i2_series{1};
151                    j1_series_Civ1=j1_series{1};
152                    j2_series_Civ1=j2_series{1};
153                    NomTypeNc=Param.InputTable{1,4};
154                    if ~isempty(PairCiv2)
155                        [i1_series_Civ2,i2_series_Civ2,j1_series_Civ2,j2_series_Civ2,check_bounds,NomTypeNc]=...
156                            find_pair_indices(PairCiv2,i1_series{2},j1_series{2},MinIndex_i(2),MaxIndex_i(2),MinIndex_j(2),MaxIndex_j(2));
157                    end
158                end
159            case 'displacement'
160                i1_series_Civ1=Param.ActionInput.OriginIndex*ones(size(i1_series{1}));
161                i2_series_Civ1=i1_series{1};i2_series_Civ2=i1_series{1};
162                j1_series_Civ1=ones(size(i1_series{1}));% first j index is 1
163                if isempty(j1_series_Civ1)
164                    j2_series_Civ1=ones(size(i1_series{1}));
165                else
166                    j2_series_Civ1=j1_series_Civ1;
167                end
168                i1_series_Civ2=i1_series_Civ1;
169                j1_series_Civ2=j1_series_Civ1;
170                j2_series_Civ2=j2_series_Civ1;
171                NomTypeNc=Param.InputTable{1,4};
172            case 'PIV volume'
173                % TODO, TODO
174        end
175        if isempty(j1_series_Civ1)
176            FrameIndex_A_Civ1=i1_series_Civ1;
177            FrameIndex_B_Civ1=i2_series_Civ1;
178            j1_series_Civ1=ones(size(i1_series_Civ1));
179            j2_series_Civ1=ones(size(i1_series_Civ1));
180        else
181            FrameIndex_A_Civ1=j1_series_Civ1;
182            FrameIndex_B_Civ1=j2_series_Civ1;
183        end
184        if isempty(PairCiv2)
185            FrameIndex_A_Civ2=FrameIndex_A_Civ1;
186            FrameIndex_B_Civ2=FrameIndex_B_Civ1;
187        else
188            if isempty(j1_series_Civ2)
189                FrameIndex_A_Civ2=i1_series_Civ2;
190                FrameIndex_B_Civ2=i2_series_Civ2;
191                j1_series_Civ2=ones(size(i1_series_Civ2));
192                j2_series_Civ2=ones(size(i1_series_Civ2));
193            else
194                FrameIndex_A_Civ2=j1_series_Civ2;
195                FrameIndex_B_Civ2=j2_series_Civ2;
196            end
197        end
198        if isempty(i1_series_Civ1)||(~isempty(PairCiv2) && isempty(i1_series_Civ2))
199            disp_uvmat('ERROR','no image pair fo civ in the input file index range',checkrun)
200            return
201        end
202    end
203   
204    %% check the first image pair
205    try
206        if Param.ActionInput.CheckCiv1% Civ1 is performed
207            ImageName_A=fullfile_uvmat(RootPath_A,SubDir_A,RootFile_A,FileExt_A,NomType_A,i1_series_Civ1(1),[],j1_series_Civ1(1));
208            if ~exist(ImageName_A,'file')
209                disp_uvmat('ERROR',['first input image ' ImageName_A ' does not exist'],checkrun)
210                return
211            end
212            [FileInfo_A,VideoObject_A]=get_file_info(ImageName_A);
213            FileType_A=FileInfo_A.FileType;
214            if strcmp(FileInfo_A.FileType,'netcdf')
215                FieldName_A=Param.InputFields.FieldName;
216                [DataIn,tild,tild,errormsg]=nc2struct(ImageName_A,{FieldName_A});
217                par_civ1.ImageA=DataIn.(FieldName_A);
218            else
219                [par_civ1.ImageA,VideoObject_A] = read_image(ImageName_A,FileType_A,VideoObject_A,FrameIndex_A_Civ1(1));
220            end
221            ImageName_B=fullfile_uvmat(RootPath_B,SubDir_B,RootFile_B,FileExt_B,NomType_B,i2_series_Civ1(1),[],j2_series_Civ1(1));
222            if ~exist(ImageName_B,'file')
223                disp_uvmat('ERROR',['first input image ' ImageName_B ' does not exist'],checkrun)
224                return
225            end
226            [FileInfo_B,VideoObject_B]=get_file_info(ImageName_B);
227            FileType_B=FileInfo_B.FileType;
228            if strcmp(FileInfo_B.FileType,'netcdf')
229                FieldName_B=Param.InputFields.FieldName;
230                [DataIn,tild,tild,errormsg]=nc2struct(ImageName_B,{FieldName_B});
231                par_civ1.ImageB=DataIn.(FieldName_B);
232            else
233                [par_civ1.ImageB,VideoObject_B] = read_image(ImageName_B,FileType_B,VideoObject_B,FrameIndex_B_Civ1(1));
234            end
235            NbField=numel(i1_series_Civ1);
236        elseif Param.ActionInput.CheckCiv2 % Civ2 is performed without Civ1
237            ImageName_A=fullfile_uvmat(RootPath_A,SubDir_A,RootFile_A,FileExt_A,NomType_A,i1_series_Civ2(1),[],j1_series_Civ2(1));
238            if ~exist(ImageName_A,'file')
239                disp_uvmat('ERROR',['first input image ' ImageName_A ' does not exist'],checkrun)
240                return
241            end
242            [FileInfo_A,VideoObject_A]=get_file_info(ImageName_A);
243            FileType_A=FileInfo_A.FileType;
244            [par_civ1.ImageA,VideoObject_A] = read_image(ImageName_A,FileInfo_A.FileType,VideoObject_A,FrameIndex_A_Civ2(1));
245            ImageName_B=fullfile_uvmat(RootPath_B,SubDir_B,RootFile_B,FileExt_B,NomType_B,i2_series_Civ2(1),[],j2_series_Civ2(1));
246            if ~exist(ImageName_B,'file')
247                disp_uvmat('ERROR',['first input image ' ImageName_B ' does not exist'],checkrun)
248                return
249            end
250            [FileInfo_B,VideoObject_B]=get_file_info(ImageName_B);
251            FileType_B=FileInfo_B.FileType;
252            [par_civ1.ImageB,VideoObject_B] = read_image(ImageName_B,FileType_B,VideoObject_B,FrameIndex_B_Civ2(1));
253            NbField=numel(i1_series_Civ2);
254        else
255            NbField=numel(i1_series_Civ1);% no image used (only fix or patch) TO CHECK
256        end
257    catch ME
258        if ~isempty(ME.message)
259            disp_uvmat('ERROR', ['error reading input image: ' ME.message],checkrun)
260            return
261        end
262    end
263   
264   
265    %% Output directory
266    OutputDir='';
267    if CheckOutputFile
268        OutputDir=[Param.OutputSubDir Param.OutputDirExt];
269    end
270end
271
272%% prepare output Data
273ListGlobalAttribute={'Conventions','Program','CivStage'};
274Data.Conventions='uvmat/civdata';% states the conventions used for the description of field variables and attributes
275Data.Program='civ_series';
276Data.CivStage=0;%default
277check_civx=0;%default
278
279%% get timing from the ImaDoc file or input video
280if iview_A~=0
281    XmlFileName=find_imadoc(RootPath_A,SubDir_A,RootFile_A,FileExt_A);
282    time=[];
283    if ~isempty(XmlFileName)
284        XmlData=imadoc2struct(XmlFileName);
285        if isfield(XmlData,'Time')
286            time=XmlData.Time;
287            TimeSource='xml';
288        end
289        if isfield(XmlData,'Camera')
290            if isfield(XmlData.Camera,'NbSlice')&& ~isempty(XmlData.Camera.NbSlice)
291                NbSlice_calib{iview}=XmlData.Camera.NbSlice;% Nbre of slices for Zindex in phys transform
292                if ~isequal(NbSlice_calib{iview},NbSlice_calib{1})
293                    msgbox_uvmat('WARNING','inconsistent number of Z indices for the two field series');
294                end
295            end
296            if isfield(XmlData.Camera,'TimeUnit')&& ~isempty(XmlData.Camera.TimeUnit)
297                TimeUnit=XmlData.Camera.TimeUnit;
298            end
299        end
300    end
301    if isempty(time) && ~isempty(find(strcmp(FileType_A,{'mmreader','video'})))% case of video input
302        time=zeros(FileInfo_A.NumberOfFrames+1,2);
303        time(:,2)=(0:1/FileInfo_A.FrameRate:(FileInfo_A.NumberOfFrames)/FileInfo_A.FrameRate)';
304        TimeSource='video';
305        ColorType='truecolor';
306    end
307    if isempty(time)% time = index i +0.001 index j by default
308        %MinIndex_i=min(i1_series_Civ1);
309        MaxIndex_i=max(i2_series_Civ1);
310        %MinIndex_j=min(j1_series_Civ1);
311        MaxIndex_j=max(j2_series_Civ1);
312        time=(1:MaxIndex_i)'*ones(1,MaxIndex_j);
313        time=time+0.001*ones(MaxIndex_i,1)*(1:MaxIndex_j);
314        time=[zeros(1,MaxIndex_j);time];% insert a first line of zeros
315        time=[zeros(MaxIndex_i+1,1) time];% insert a first column of zeros
316    end
317   
318    if length(FileInfo_A) >1 %case of image with multiple frames
319        nbfield=length(FileInfo_A);
320        nbfield_j=1;
321    end
322end
323
324%%%%% MAIN LOOP %%%%%%
325maskname='';% initiate the mask name
326tic;
327for ifield=1:NbField
328    if ~isempty(RUNHandle)% update the waitbar in interactive mode with GUI series  (checkrun=1)
329        update_waitbar(WaitbarHandle,ifield/NbField)
330        if  get(RUNHandle,'Value')&& ~strcmp(get(RUNHandle,'BusyAction'),'queue')
331            disp('program stopped by user')
332            break
333        end
334    end
335    if CheckInputFile
336        if iview_A==0 % no nc file has been entered
337            ncfile=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},Param.InputTable{1,5},...
338                NomTypeNc,i1_series_Civ1(ifield),i2_series_Civ1(ifield),j1_series_Civ1(ifield),j2_series_Civ1(ifield));
339        else% an existing nc file has been entered
340            if iview_A==1% if Civ1 is performed
341                Civ1Dir=OutputDir;
342            else
343                Civ1Dir=Param.InputTable{1,2};
344            end
345            if strcmp(Param.ActionInput.ListCompareMode,'PIV')
346                ncfile=fullfile_uvmat(RootPath_A,Civ1Dir,RootFile_A,'.nc',NomTypeNc,i1_series_Civ1(ifield),i2_series_Civ1(ifield),...
347                    j1_series_Civ1(ifield),j2_series_Civ1(ifield));
348            else
349                ncfile=fullfile_uvmat(RootPath_A,Civ1Dir,RootFile_A,'.nc',NomTypeNc,i2_series_Civ1(ifield),[],...
350                    j1_series_Civ1(ifield),j2_series_Civ1(ifield));
351            end
352        end
353    end
354    %% Civ1
355    % if Civ1 computation is requested
356    if isfield (Param.ActionInput,'Civ1')
357        par_civ1=Param.ActionInput.Civ1;
358        if CheckInputFile % read input images (except in mode Test where it is introduced directly in Param.ActionInput.Civ1.ImageNameA and B)
359            try
360                ImageName_A=fullfile_uvmat(RootPath_A,SubDir_A,RootFile_A,FileExt_A,NomType_A,i1_series_Civ1(ifield),[],j1_series_Civ1(ifield));
361                if strcmp(FileInfo_A.FileType,'netcdf')% case of input images in format netcdf
362                    FieldName_A=Param.InputFields.FieldName;
363                    [DataIn,tild,tild,errormsg]=nc2struct(ImageName_A,{FieldName_A});
364                    par_civ1.ImageA=DataIn.(FieldName_A);
365                else % usual image formats for image A
366                    [par_civ1.ImageA,VideoObject_A] = read_image(ImageName_A,FileType_A,VideoObject_A,FrameIndex_A_Civ1(ifield));
367                end
368                ImageName_B=fullfile_uvmat(RootPath_B,SubDir_B,RootFile_B,FileExt_B,NomType_B,i2_series_Civ1(ifield),[],j2_series_Civ1(ifield));
369                if strcmp(FileInfo_B.FileType,'netcdf') % case of input images in format netcdf
370                    FieldName_B=Param.InputFields.FieldName;
371                    [DataIn,tild,tild,errormsg]=nc2struct(ImageName_B,{FieldName_B});
372                    par_civ1.ImageB=DataIn.(FieldName_B);
373                else % usual image formats for image B
374                    [par_civ1.ImageB,VideoObject_B] = read_image(ImageName_B,FileType_B,VideoObject_B,FrameIndex_B_Civ1(ifield));
375                end
376            catch ME % display errors in reading input images
377                if ~isempty(ME.message)
378                    disp_uvmat('ERROR', ['error reading input image: ' ME.message],checkrun)
379                    return
380                end
381            end
382            par_civ1.ImageWidth=size(par_civ1.ImageA,2);%FileInfo_A.Width;
383            par_civ1.ImageHeight=size(par_civ1.ImageA,1);%FileInfo_A.Height;
384            list_param=(fieldnames(Param.ActionInput.Civ1))';
385            list_param(strcmp('TestCiv1',list_param))=[];% remove the parameter TestCiv1 from the list
386            Civ1_param=regexprep(list_param,'^.+','Civ1_$0');% insert 'Civ1_' before  each string in list_param
387            Civ1_param=[{'Civ1_ImageA','Civ1_ImageB','Civ1_Time','Civ1_Dt'} Civ1_param]; %insert the names of the two input images
388            %indicate the values of all the global attributes in the output data
389            Data.Civ1_ImageA=ImageName_A;
390            Data.Civ1_ImageB=ImageName_B;
391            i1=i1_series_Civ1(ifield);
392            i2=i1;
393            if ~isempty(i2_series_Civ1)
394                i2=i2_series_Civ1(ifield);
395            end
396            j1=1;
397            if ~isempty(j1_series_Civ1)
398                j1=j1_series_Civ1(ifield);
399            end
400            j2=j1;
401            if ~isempty(j2_series_Civ1)
402                j2=j2_series_Civ1(ifield);
403            end
404            if strcmp(Param.ActionInput.ListCompareMode,'displacement')
405                Data.Civ1_Time=time(i2+1,j2+1);% the time is the time of the secodn image
406                Data.Civ1_Dt=1;% time interval is 1, to yield displacement instead of velocity=displacement/Dt at reading
407            else
408            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
409            Data.Civ1_Dt=time(i2+1,j2+1)-time(i1+1,j1+1);
410            end
411            for ilist=1:length(list_param)
412                Data.(Civ1_param{4+ilist})=Param.ActionInput.Civ1.(list_param{ilist});
413            end
414            Data.ListGlobalAttribute=[ListGlobalAttribute Civ1_param];
415            Data.CivStage=1;
416        end
417        % set the list of variables
418        Data.ListVarName={'Civ1_X','Civ1_Y','Civ1_U','Civ1_V','Civ1_F','Civ1_C'};%  cell array containing the names of the fields to record
419        Data.VarDimName={'nb_vec_1','nb_vec_1','nb_vec_1','nb_vec_1','nb_vec_1','nb_vec_1'};
420        Data.VarAttribute{1}.Role='coord_x';
421        Data.VarAttribute{2}.Role='coord_y';
422        Data.VarAttribute{3}.Role='vector_x';
423        Data.VarAttribute{4}.Role='vector_y';
424        Data.VarAttribute{5}.Role='warnflag';
425        if par_civ1.CheckMask&&~isempty(par_civ1.Mask)
426            if strcmp(maskname,par_civ1.Mask)% mask exist, not already read in civ1
427                par_civ1.Mask=mask; %use mask already opened
428            else
429                try
430                    par_civ1.Mask=imread(par_civ1.Mask);%update the mask, an store it for future use
431                catch ME
432                    if ~isempty(ME.message)
433                        errormsg=['error reading input image: ' ME.message];
434                        disp_uvmat('ERROR',errormsg,checkrun)
435                        return
436                    end
437                end
438                mask=par_civ1.Mask;
439                maskname=par_civ1.Mask;
440            end
441        end
442        if strcmp(Param.ActionInput.ListCompareMode, 'PIV volume')
443            Data.ListVarName=[Data.ListVarName 'Civ1_Z'];
444            Data.Civ1_X=[];Data.Civ1_Y=[];Data.Civ1_Z=[];
445            Data.Civ1_U=[];Data.Civ1_V=[];Data.Civ1_C=[];Data.Civ1_F=[];
446            for ivol=1:NbSlice
447                % caluclate velocity data (y and v in indices, reverse to y component)
448                [xtable, ytable, utable, vtable, ctable, F, result_conv, errormsg] = civ (par_civ1);
449                if ~isempty(errormsg)
450                    disp_uvmat('ERROR',errormsg,checkrun)
451                    return
452                end
453                Data.Civ1_X=[Data.Civ1_X reshape(xtable,[],1)];
454                Data.Civ1_Y=[Data.Civ1_Y reshape(Param.Civ1.ImageHeight-ytable+1,[],1)];
455                Data.Civ1_Z=[Data.Civ1_Z ivol*ones(numel(xtable),1)];% z=image index in image coordinates
456                Data.Civ1_U=[Data.Civ1_U reshape(utable,[],1)];
457                Data.Civ1_V=[Data.Civ1_V reshape(-vtable,[],1)];
458                Data.Civ1_C=[Data.Civ1_C reshape(ctable,[],1)];
459                Data.Civ1_F=[Data.Civ1_C reshape(F,[],1)];
460            end
461        else %usual PIV
462            % caluclate velocity data (y and v in indices, reverse to y component)
463            [xtable, ytable, utable, vtable, ctable, F, result_conv, errormsg] = civ (par_civ1);
464            if ~isempty(errormsg)
465                disp_uvmat('ERROR',errormsg,checkrun)
466                return
467            end
468            Data.Civ1_X=reshape(xtable,[],1);
469            Data.Civ1_Y=reshape(par_civ1.ImageHeight-ytable+1,[],1);
470            Data.Civ1_U=reshape(utable,[],1);
471            Data.Civ1_V=reshape(-vtable,[],1);
472            Data.Civ1_C=reshape(ctable,[],1);
473            Data.Civ1_F=reshape(F,[],1);
474        end
475    else% we use existing Civ1 data
476        if exist('ncfile','var')
477            CivFile=ncfile;
478            [Data,tild,tild,errormsg]=nc2struct(CivFile,'ListGlobalAttribute','absolut_time_T0'); %look for the constant 'absolut_time_T0' to detect old civx data format
479            if ~isempty(errormsg)
480                disp_uvmat('ERROR',errormsg,checkrun)
481                return
482            end
483            [Data,tild,tild,errormsg]=nc2struct(CivFile);%read civ1 and fix1 data in the existing netcdf file
484        elseif isfield(Param,'Civ1_X')
485            Data.ListGlobalAttribute={};
486            Data.ListVarName={};
487            Data.VarDimName={};
488            Data.Civ1_X=Param.Civ1_X;
489            Data.Civ1_Y=Param.Civ1_Y;
490            Data.Civ1_U=Param.Civ1_U;
491            Data.Civ1_V=Param.Civ1_V;
492            Data.Civ1_FF=Param.Civ1_FF;
493        end
494    end
495   
496    %% Fix1
497    if isfield (Param.ActionInput,'Fix1')
498        if ~isfield (Param.ActionInput,'Civ1')% if we use existing Civ1, remove previous data beyond Civ1
499            Fix1_attr=find(strcmp('Fix1',Data.ListGlobalAttribute));
500            Data.ListGlobalAttribute(Fix1_attr)=[];
501            for ilist=1:numel(Fix1_attr)
502                Data=rmfield(Data,Data.ListGlobalAttribute{Fix1_attr(ilist)});
503            end
504        end
505        list_param=fieldnames(Param.ActionInput.Fix1)';
506        Fix1_param=regexprep(list_param,'^.+','Fix1_$0');% insert 'Fix1_' before  each string in ListFixParam
507        %indicate the values of all the global attributes in the output data
508        for ilist=1:length(list_param)
509            Data.(Fix1_param{ilist})=Param.ActionInput.Fix1.(list_param{ilist});
510        end
511        Data.ListGlobalAttribute=[Data.ListGlobalAttribute Fix1_param];
512        Data.ListVarName=[Data.ListVarName {'Civ1_FF'}];
513        Data.VarDimName=[Data.VarDimName {'nb_vec_1'}];
514        nbvar=length(Data.ListVarName);
515        Data.VarAttribute{nbvar}.Role='errorflag';
516        Data.Civ1_FF=fix(Param.ActionInput.Fix1,Data.Civ1_F,Data.Civ1_C,Data.Civ1_U,Data.Civ1_V);
517        Data.CivStage=2;
518    end
519    %% Patch1
520    if isfield (Param.ActionInput,'Patch1')
521        if check_civx
522            errormsg='Civ Matlab input needed for patch';
523            disp_uvmat('ERROR',errormsg,checkrun)
524            return
525        end
526       
527        % record the processing parameters of Patch1 as global attributes in the result nc file
528        list_param=fieldnames(Param.ActionInput.Patch1)';
529        list_param(strcmp('TestPatch1',list_param))=[];% remove 'TestPatch1' from the list of parameters
530        Patch1_param=regexprep(list_param,'^.+','Patch1_$0');% insert 'Patch1_' before  each parameter name
531        for ilist=1:length(list_param)
532            Data.(Patch1_param{ilist})=Param.ActionInput.Patch1.(list_param{ilist});
533        end
534        Data.CivStage=3;% record the new state of processing
535        Data.ListGlobalAttribute=[Data.ListGlobalAttribute Patch1_param];
536       
537        % list the variables to record
538        nbvar=length(Data.ListVarName);
539        Data.ListVarName=[Data.ListVarName {'Civ1_U_smooth','Civ1_V_smooth','Civ1_SubRange','Civ1_NbCentres','Civ1_Coord_tps','Civ1_U_tps','Civ1_V_tps'}];
540        Data.VarDimName=[Data.VarDimName {'nb_vec_1','nb_vec_1',{'nb_coord','nb_bounds','nb_subdomain_1'},'nb_subdomain_1',...
541            {'nb_tps_1','nb_coord','nb_subdomain_1'},{'nb_tps_1','nb_subdomain_1'},{'nb_tps_1','nb_subdomain_1'}}];
542        Data.VarAttribute{nbvar+1}.Role='vector_x';
543        Data.VarAttribute{nbvar+2}.Role='vector_y';
544        Data.VarAttribute{nbvar+5}.Role='coord_tps';
545        Data.VarAttribute{nbvar+6}.Role='vector_x';
546        Data.VarAttribute{nbvar+7}.Role='vector_y';
547        Data.Civ1_U_smooth=Data.Civ1_U; % zeros(size(Data.Civ1_X));
548        Data.Civ1_V_smooth=Data.Civ1_V; %zeros(size(Data.Civ1_X));
549        if isfield(Data,'Civ1_FF')
550            ind_good=find(Data.Civ1_FF==0);
551        else
552            ind_good=1:numel(Data.Civ1_X);
553        end
554       
555        % perform Patch calculation using the UVMAT fct 'filter_tps'
556        [Data.Civ1_SubRange,Data.Civ1_NbCentres,Data.Civ1_Coord_tps,Data.Civ1_U_tps,Data.Civ1_V_tps,tild,Ures, Vres,tild,FFres]=...
557            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);
558        Data.Civ1_U_smooth(ind_good)=Ures;% take the interpolated (smoothed) velocity values for good vectors, keep 0 for the others
559        Data.Civ1_V_smooth(ind_good)=Vres;
560        Data.Civ1_FF(ind_good)=FFres;
561    end
562   
563    %% Civ2
564    if isfield (Param.ActionInput,'Civ2')
565        par_civ2=Param.ActionInput.Civ2;
566        if CheckInputFile % read input images (except in mode Test where it is introduced directly in Param.ActionInput.Civ1.ImageNameA and B)
567            par_civ2.ImageA=[];
568            par_civ2.ImageB=[];
569            i1=i1_series_Civ2(ifield);
570            i2=i1;
571            if ~isempty(i2_series_Civ2)
572                i2=i2_series_Civ2(ifield);
573            end
574            j1=1;
575            if ~isempty(j1_series_Civ2)
576                j1=j1_series_Civ2(ifield);
577            end
578            j2=j1;
579            if ~isempty(j2_series_Civ2)
580                j2=j2_series_Civ2(ifield);
581            end
582            ImageName_A_Civ2=fullfile_uvmat(RootPath_A,SubDir_A,RootFile_A,FileExt_A,NomType_A,i1,[],j1);
583           
584            if strcmp(ImageName_A_Civ2,ImageName_A) && isequal(FrameIndex_A_Civ1(ifield),FrameIndex_A_Civ2(ifield))
585                par_civ2.ImageA=par_civ1.ImageA;
586            else
587                [par_civ2.ImageA,VideoObject_A] = read_image(ImageName_A_Civ2,FileType_A,VideoObject_A,FrameIndex_A_Civ2(ifield));
588            end
589            ImageName_B_Civ2=fullfile_uvmat(RootPath_B,SubDir_B,RootFile_B,FileExt_B,NomType_B,i2,[],j2);
590            if strcmp(ImageName_B_Civ2,ImageName_B) && isequal(FrameIndex_B_Civ1(ifield),FrameIndex_B_Civ2)
591                par_civ2.ImageB=par_civ1.ImageB;
592            else
593                [par_civ2.ImageB,VideoObject_B] = read_image(ImageName_B_Civ2,FileType_B,VideoObject_B,FrameIndex_B_Civ2(ifield));
594            end
595            if strcmp(Param.ActionInput.ListCompareMode,'PIV')
596                ncfile=fullfile_uvmat(RootPath_A,OutputDir,RootFile_A,'.nc',NomTypeNc,i1,i2,j1,j2);
597            else % displacement
598                ncfile=fullfile_uvmat(RootPath_A,OutputDir,RootFile_A,'.nc',NomTypeNc,i2,[],j2);
599            end
600            par_civ2.ImageWidth=FileInfo_A.Width;
601            par_civ2.ImageHeight=FileInfo_A.Height;
602            if isfield(par_civ2,'Grid')% grid points set as input file
603                if ischar(par_civ2.Grid)%read the grid file if the input is a file name
604                    par_civ2.Grid=dlmread(par_civ2.Grid);
605                    par_civ2.Grid(1,:)=[];%the first line must be removed (heading in the grid file)
606                end
607            else% automatic grid
608                minix=floor(par_civ2.Dx/2)-0.5;
609                maxix=minix+par_civ2.Dx*floor((par_civ2.ImageWidth-1)/par_civ2.Dx);
610                miniy=floor(par_civ2.Dy/2)-0.5;
611                maxiy=minix+par_civ2.Dy*floor((par_civ2.ImageHeight-1)/par_civ2.Dy);
612                [GridX,GridY]=meshgrid(minix:par_civ2.Dx:maxix,miniy:par_civ2.Dy:maxiy);
613                par_civ2.Grid(:,1)=reshape(GridX,[],1);
614                par_civ2.Grid(:,2)=reshape(GridY,[],1);
615            end
616        end
617       
618        % get the guess from patch1 or patch2 (case 'CheckCiv3')
619        if CheckInputFile % read input images (except in mode Test where it is introduced directly in Param.ActionInput.Civ1.ImageNameA and B)
620            if isfield (par_civ2,'CheckCiv3') && par_civ2.CheckCiv3 %get the guess from  patch2
621                SubRange= Data.Civ2_SubRange;
622                NbCentres=Data.Civ2_NbCentres;
623                Coord_tps=Data.Civ2_Coord_tps;
624                U_tps=Data.Civ2_U_tps;
625                V_tps=Data.Civ2_V_tps;
626                CivStage=Data.CivStage;%store the current CivStage
627                Civ1_Dt=Data.Civ2_Dt;
628                Data=[];%reinitialise the result structure Data
629                Data.ListGlobalAttribute={'Conventions','Program','CivStage'};
630                Data.Conventions='uvmat/civdata';% states the conventions used for the description of field variables and attributes
631                Data.Program='civ_series';
632                Data.CivStage=CivStage+1;%update the current civStage after reinitialisation of Data
633                Data.ListVarName={};
634                Data.VarDimName={};
635            else % get the guess from patch1
636                SubRange= Data.Civ1_SubRange;
637                NbCentres=Data.Civ1_NbCentres;
638                Coord_tps=Data.Civ1_Coord_tps;
639                U_tps=Data.Civ1_U_tps;
640                V_tps=Data.Civ1_V_tps;
641                Civ1_Dt=Data.Civ1_Dt;
642                Data.CivStage=4;
643            end
644        else
645            SubRange= par_civ2.Civ1_SubRange;
646            NbCentres=par_civ2.Civ1_NbCentres;
647            Coord_tps=par_civ2.Civ1_Coord_tps;
648            U_tps=par_civ2.Civ1_U_tps;
649            V_tps=par_civ2.Civ1_V_tps;
650            Civ1_Dt=par_civ2.Civ1_Dt;
651            Civ2_Dt=par_civ2.Civ1_Dt;
652            Data.ListVarName={};
653            Data.VarDimName={};
654        end
655        Shiftx=zeros(size(par_civ2.Grid,1),1);% shift expected from civ1 data
656        Shifty=zeros(size(par_civ2.Grid,1),1);
657        nbval=zeros(size(par_civ2.Grid,1),1);% nbre of interpolated values at each grid point (from the different patch subdomains)
658        if par_civ2.CheckDeformation
659            DUDX=zeros(size(par_civ2.Grid,1),1);
660            DUDY=zeros(size(par_civ2.Grid,1),1);
661            DVDX=zeros(size(par_civ2.Grid,1),1);
662            DVDY=zeros(size(par_civ2.Grid,1),1);
663        end
664        NbSubDomain=size(SubRange,3);
665        for isub=1:NbSubDomain% for each sub-domain of Patch1
666            nbvec_sub=NbCentres(isub);% nbre of Civ vectors in the subdomain
667            ind_sel=find(par_civ2.Grid(:,1)>=SubRange(1,1,isub) & par_civ2.Grid(:,1)<=SubRange(1,2,isub) &...
668                par_civ2.Grid(:,2)>=SubRange(2,1,isub) & par_civ2.Grid(:,2)<=SubRange(2,2,isub));% grid points in the subdomain
669            if ~isempty(ind_sel)
670                epoints = par_civ2.Grid(ind_sel,:);% coordinates of interpolation sites (measurement grids)
671                ctrs=Coord_tps(1:nbvec_sub,:,isub) ;%(=initial points) ctrs
672                nbval(ind_sel)=nbval(ind_sel)+1;% records the number of values for each interpolation point (in case of subdomain overlap)
673                EM = tps_eval(epoints,ctrs);% thin plate spline (tps) coefficient
674                Shiftx(ind_sel)=Shiftx(ind_sel)+EM*U_tps(1:nbvec_sub+3,isub);%velocity shift estimated by tps from civ1
675                Shifty(ind_sel)=Shifty(ind_sel)+EM*V_tps(1:nbvec_sub+3,isub);
676                if par_civ2.CheckDeformation
677                    [EMDX,EMDY] = tps_eval_dxy(epoints,ctrs);%2D matrix of distances between extrapolation points epoints and spline centres (=site points) ctrs
678                    DUDX(ind_sel)=DUDX(ind_sel)+EMDX*U_tps(1:nbvec_sub+3,isub);
679                    DUDY(ind_sel)=DUDY(ind_sel)+EMDY*U_tps(1:nbvec_sub+3,isub);
680                    DVDX(ind_sel)=DVDX(ind_sel)+EMDX*V_tps(1:nbvec_sub+3,isub);
681                    DVDY(ind_sel)=DVDY(ind_sel)+EMDY*V_tps(1:nbvec_sub+3,isub);
682                end
683            end
684        end
685        if par_civ2.CheckMask&&~isempty(par_civ2.Mask)
686            if strcmp(maskname,par_civ2.Mask)% mask exist, not already read in civ1
687                par_civ2.Mask=mask; %use mask already opened
688            else
689                par_civ2.Mask=imread(par_civ2.Mask);%update the mask, and store it for future use
690                mask=par_civ2.Mask;
691                maskname=par_civ2.Mask;
692            end
693        end
694        if CheckInputFile % else Dt given by par_civ2
695            if strcmp(Param.ActionInput.ListCompareMode,'displacement')
696                Civ1_Dt=1;
697                Civ2_Dt=1;
698            else
699                Civ2_Dt=time(i2+1,j2+1)-time(i1+1,j1+1);
700            end
701        end
702        par_civ2.SearchBoxShift=(Civ2_Dt/Civ1_Dt)*[Shiftx(nbval>=1)./nbval(nbval>=1) Shifty(nbval>=1)./nbval(nbval>=1)];
703        % shift the grid points by half the expected shift to provide the correlation box position in image A
704        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];
705        if par_civ2.CheckDeformation
706            par_civ2.DUDX=DUDX(nbval>=1)./nbval(nbval>=1);
707            par_civ2.DUDY=DUDY(nbval>=1)./nbval(nbval>=1);
708            par_civ2.DVDX=DVDX(nbval>=1)./nbval(nbval>=1);
709            par_civ2.DVDY=DVDY(nbval>=1)./nbval(nbval>=1);
710        end
711       
712        % calculate velocity data (y and v in image indices, reverse to y component)
713        [xtable, ytable, utable, vtable, ctable, F,result_conv,errormsg] = civ (par_civ2);
714       
715        list_param=(fieldnames(Param.ActionInput.Civ2))';
716        list_param(strcmp('TestCiv2',list_param))=[];% remove the parameter TestCiv2 from the list
717        Civ2_param=regexprep(list_param,'^.+','Civ2_$0');% insert 'Civ2_' before  each string in list_param
718        Civ2_param=[{'Civ2_ImageA','Civ2_ImageB','Civ2_Time','Civ2_Dt'} Civ2_param]; %insert the names of the two input images
719        %indicate the values of all the global attributes in the output data
720        if exist('ImageName_A','var')
721            Data.Civ2_ImageA=ImageName_A;
722            Data.Civ2_ImageB=ImageName_B;
723             if strcmp(Param.ActionInput.ListCompareMode,'displacement')
724                Data.Civ2_Time=time(i2+1,j2+1);% the time is the time of the secodn image
725                Data.Civ2_Dt=1;% time interval is 1, to yield displacement instead of velocity=displacement/Dt at reading
726             else
727            Data.Civ2_Time=(time(i2+1,j2+1)+time(i1+1,j1+1))/2;
728            Data.Civ2_Dt=Civ2_Dt;
729             end
730        end
731        for ilist=1:length(list_param)
732            Data.(Civ2_param{4+ilist})=Param.ActionInput.Civ2.(list_param{ilist});
733        end
734        Data.ListGlobalAttribute=[Data.ListGlobalAttribute Civ2_param];
735       
736        nbvar=numel(Data.ListVarName);
737        % define the Civ2 variable (if Civ2 data are not replaced from previous calculation)
738        if isempty(find(strcmp('Civ2_X',Data.ListVarName),1))
739            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
740            Data.VarDimName=[Data.VarDimName {'nb_vec_2','nb_vec_2','nb_vec_2','nb_vec_2','nb_vec_2','nb_vec_2'}];
741            Data.VarAttribute{nbvar+1}.Role='coord_x';
742            Data.VarAttribute{nbvar+2}.Role='coord_y';
743            Data.VarAttribute{nbvar+3}.Role='vector_x';
744            Data.VarAttribute{nbvar+4}.Role='vector_y';
745            Data.VarAttribute{nbvar+5}.Role='warnflag';
746        end
747        Data.Civ2_X=reshape(xtable,[],1);
748        Data.Civ2_Y=reshape(size(par_civ2.ImageA,1)-ytable+1,[],1);
749        Data.Civ2_U=reshape(utable,[],1);
750        Data.Civ2_V=reshape(-vtable,[],1);
751        Data.Civ2_C=reshape(ctable,[],1);
752        Data.Civ2_F=reshape(F,[],1);
753    elseif ~isfield(Data,'ListVarName') % we start there, using existing Civ2 data
754        if exist('ncfile','var')
755            CivFile=ncfile;
756            [Data,tild,tild,errormsg]=nc2struct(CivFile);%read civ1 and fix1 data in the existing netcdf file
757            if ~isempty(errormsg)
758                disp_uvmat('ERROR',errormsg,checkrun)
759                return
760            end         
761        elseif isfield(Param,'Civ2_X')% use Civ2 data as input in Param (test mode)
762            Data.ListGlobalAttribute={};
763            Data.ListVarName={};
764            Data.VarDimName={};
765            Data.Civ2_X=Param.Civ2_X;
766            Data.Civ2_Y=Param.Civ2_Y;
767            Data.Civ2_U=Param.Civ2_U;
768            Data.Civ2_V=Param.Civ2_V;
769            Data.Civ2_FF=Param.Civ2_FF;
770        end
771    end
772   
773    %% Fix2
774    if isfield (Param.ActionInput,'Fix2')
775        list_param=fieldnames(Param.ActionInput.Fix2)';
776        Fix2_param=regexprep(list_param,'^.+','Fix2_$0');% insert 'Fix1_' before  each string in ListFixParam
777        %indicate the values of all the global attributes in the output data
778        for ilist=1:length(list_param)
779            Data.(Fix2_param{ilist})=Param.ActionInput.Fix2.(list_param{ilist});
780        end
781        Data.ListGlobalAttribute=[Data.ListGlobalAttribute Fix2_param];
782        %
783        %         ListFixParam=fieldnames(Param.ActionInput.Fix2);
784        %         for ilist=1:length(ListFixParam)
785        %             ParamName=ListFixParam{ilist};
786        %             ListName=['Fix2_' ParamName];
787        %             eval(['Data.ListGlobalAttribute=[Data.ListGlobalAttribute ''' ParamName '''];'])
788        %             eval(['Data.' ListName '=Param.ActionInput.Fix2.' ParamName ';'])
789        %         end
790        if check_civx
791            if ~isfield(Data,'fix2')
792                Data.ListGlobalAttribute=[Data.ListGlobalAttribute 'fix2'];
793                Data.fix2=1;
794                Data.ListVarName=[Data.ListVarName {'vec2_FixFlag'}];
795                Data.VarDimName=[Data.VarDimName {'nb_vectors2'}];
796            end
797            Data.vec_FixFlag=fix(Param.Fix2,Data.vec2_F,Data.vec2_C,Data.vec2_U,Data.vec2_V,Data.vec2_X,Data.vec2_Y);
798        else
799            Data.ListVarName=[Data.ListVarName {'Civ2_FF'}];
800            Data.VarDimName=[Data.VarDimName {'nb_vec_2'}];
801            nbvar=length(Data.ListVarName);
802            Data.VarAttribute{nbvar}.Role='errorflag';
803            Data.Civ2_FF=double(fix(Param.ActionInput.Fix2,Data.Civ2_F,Data.Civ2_C,Data.Civ2_U,Data.Civ2_V));
804            Data.CivStage=Data.CivStage+1;
805        end
806       
807    end
808   
809    %% Patch2
810    if isfield (Param.ActionInput,'Patch2')
811        list_param=fieldnames(Param.ActionInput.Patch2)';
812        list_param(strcmp('TestPatch2',list_param))=[];% remove the parameter TestCiv1 from the list
813        Patch2_param=regexprep(list_param,'^.+','Patch2_$0');% insert 'Fix1_' before  each string in ListFixParam
814        %indicate the values of all the global attributes in the output data
815        for ilist=1:length(list_param)
816            Data.(Patch2_param{ilist})=Param.ActionInput.Patch2.(list_param{ilist});
817        end
818        Data.ListGlobalAttribute=[Data.ListGlobalAttribute Patch2_param];
819       
820        nbvar=length(Data.ListVarName);
821        Data.ListVarName=[Data.ListVarName {'Civ2_U_smooth','Civ2_V_smooth','Civ2_SubRange','Civ2_NbCentres','Civ2_Coord_tps','Civ2_U_tps','Civ2_V_tps'}];
822        Data.VarDimName=[Data.VarDimName {'nb_vec_2','nb_vec_2',{'nb_coord','nb_bounds','nb_subdomain_2'},{'nb_subdomain_2'},...
823            {'nb_tps_2','nb_coord','nb_subdomain_2'},{'nb_tps_2','nb_subdomain_2'},{'nb_tps_2','nb_subdomain_2'}}];
824       
825        Data.VarAttribute{nbvar+1}.Role='vector_x';
826        Data.VarAttribute{nbvar+2}.Role='vector_y';
827        Data.VarAttribute{nbvar+5}.Role='coord_tps';
828        Data.VarAttribute{nbvar+6}.Role='vector_x';
829        Data.VarAttribute{nbvar+7}.Role='vector_y';
830        Data.Civ2_U_smooth=Data.Civ2_U; % zeros(size(Data.Civ2_X));
831        Data.Civ2_V_smooth=Data.Civ2_V; %zeros(size(Data.Civ2_X));
832        if isfield(Data,'Civ2_FF')
833            ind_good=find(Data.Civ2_FF==0);
834        else
835            ind_good=1:numel(Data.Civ2_X);
836        end
837        [Data.Civ2_SubRange,Data.Civ2_NbCentres,Data.Civ2_Coord_tps,Data.Civ2_U_tps,Data.Civ2_V_tps,tild,Ures, Vres,tild,FFres]=...
838            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);
839        Data.Civ2_U_smooth(ind_good)=Ures;
840        Data.Civ2_V_smooth(ind_good)=Vres;
841        Data.Civ2_FF(ind_good)=FFres;
842        Data.CivStage=Data.CivStage+1;
843    end
844   
845    %% write result in a netcdf file if requested
846    if CheckOutputFile
847        errormsg=struct2nc(ncfile,Data);
848        if isempty(errormsg)
849            disp([ncfile ' written'])
850        else
851            disp(errormsg)
852        end
853        disp(['ellapsed time ' num2str(toc) ' s'])
854    end
855end
856
857
858% 'civ': function piv.m adapted from PIVlab http://pivlab.blogspot.com/
859%--------------------------------------------------------------------------
860% function [xtable ytable utable vtable typevector] = civ (image1,image2,ibx,iby step, subpixfinder, mask, roi)
861%
862% OUTPUT:
863% xtable: set of x coordinates
864% ytable: set of y coordiantes
865% utable: set of u displacements (along x)
866% vtable: set of v displacements (along y)
867% ctable: max image correlation for each vector
868% typevector: set of flags, =1 for good, =0 for NaN vectors
869%
870%INPUT:
871% par_civ: structure of input parameters, with fields:
872%  .ImageA: first image for correlation (matrix)
873%  .ImageB: second image for correlation(matrix)
874%  .CorrBoxSize: 1,2 vector giving the size of the correlation box in x and y
875%  .SearchBoxSize:  1,2 vector giving the size of the search box in x and y
876%  .SearchBoxShift: 1,2 vector or 2 column matrix (for civ2) giving the shift of the search box in x and y
877%  .CorrSmooth: =1 or 2 determines the choice of the sub-pixel determination of the correlation max
878%  .ImageWidth: nb of pixels of the image in x
879%  .Dx, Dy: mesh for the PIV calculation
880%  .Grid: grid giving the PIV calculation points (alternative to .Dx .Dy): centres of the correlation boxes in Image A
881%  .Mask: name of a mask file or mask image matrix itself
882%  .MinIma: thresholds for image luminosity
883%  .MaxIma
884%  .CheckDeformation=1 for subpixel interpolation and image deformation (linear transform)
885%  .DUDX: matrix of deformation obtained from patch at each grid point
886%  .DUDY
887%  .DVDX:
888%  .DVDY
889
890function [xtable,ytable,utable,vtable,ctable,F,result_conv,errormsg] = civ (par_civ)
891
892%% prepare measurement grid
893if isfield(par_civ,'Grid')% grid points set as input, central positions of the sub-images in image A
894    if ischar(par_civ.Grid)%read the grid file if the input is a file name (grid in x, y image coordinates)
895        par_civ.Grid=dlmread(par_civ.Grid);
896        par_civ.Grid(1,:)=[];%the first line must be removed (heading in the grid file)
897    end
898    % else par_civ.Grid is already an array, no action here
899else% automatic grid in x, y image coordinates
900    minix=floor(par_civ.Dx/2)-0.5;
901    maxix=minix+par_civ.Dx*floor((par_civ.ImageWidth-1)/par_civ.Dx);
902    miniy=floor(par_civ.Dy/2)-0.5;% first automatic grid point at half the mesh Dy
903    maxiy=minix+par_civ.Dy*floor((par_civ.ImageHeight-1)/par_civ.Dy);
904    [GridX,GridY]=meshgrid(minix:par_civ.Dx:maxix,miniy:par_civ.Dy:maxiy);
905    par_civ.Grid(:,1)=reshape(GridX,[],1);
906    par_civ.Grid(:,2)=reshape(GridY,[],1);% increases with array index
907end
908nbvec=size(par_civ.Grid,1);
909
910%% prepare correlation and search boxes
911ibx2=floor(par_civ.CorrBoxSize(1)/2);
912iby2=floor(par_civ.CorrBoxSize(2)/2);
913isx2=floor(par_civ.SearchBoxSize(1)/2);
914isy2=floor(par_civ.SearchBoxSize(2)/2);
915shiftx=round(par_civ.SearchBoxShift(:,1));%use the input shift estimate, rounded to the next integer value
916shifty=-round(par_civ.SearchBoxShift(:,2));% sign minus because image j index increases when y decreases
917if numel(shiftx)==1% case of a unique shift for the whole field( civ1)
918    shiftx=shiftx*ones(nbvec,1);
919    shifty=shifty*ones(nbvec,1);
920end
921
922%% Array initialisation and default output  if par_civ.CorrSmooth=0 (just the grid calculated, no civ computation)
923xtable=round(par_civ.Grid(:,1)+0.5)-0.5;
924ytable=round(par_civ.ImageHeight-par_civ.Grid(:,2)+0.5)-0.5;% y index corresponding to the position in image coordiantes
925utable=shiftx;%zeros(nbvec,1);
926vtable=shifty;%zeros(nbvec,1);
927ctable=zeros(nbvec,1);
928F=zeros(nbvec,1);
929result_conv=[];
930errormsg='';
931
932%% prepare mask
933if isfield(par_civ,'Mask') && ~isempty(par_civ.Mask)
934    if strcmp(par_civ.Mask,'all')
935        return    % get the grid only, no civ calculation
936    elseif ischar(par_civ.Mask)
937        par_civ.Mask=imread(par_civ.Mask);% read the mask if not allready done
938    end
939end
940check_MinIma=isfield(par_civ,'MinIma');% test for image luminosity threshold
941check_MaxIma=isfield(par_civ,'MaxIma') && ~isempty(par_civ.MaxIma);
942
943par_civ.ImageA=sum(double(par_civ.ImageA),3);%sum over rgb component for color images
944par_civ.ImageB=sum(double(par_civ.ImageB),3);
945[npy_ima npx_ima]=size(par_civ.ImageA);
946if ~isequal(size(par_civ.ImageB),[npy_ima npx_ima])
947    errormsg='image pair with unequal size';
948    return
949end
950
951%% Apply mask
952% Convention for mask IDEAS TO IMPLEMENT ?
953% mask >200 : velocity calculated
954%  200 >=mask>150;velocity not calculated, interpolation allowed (bad spots)
955% 150>=mask >100: velocity not calculated, nor interpolated
956%  100>=mask> 20: velocity not calculated, impermeable (no flux through mask boundaries)
957%  20>=mask: velocity=0
958checkmask=0;
959MinA=min(min(par_civ.ImageA));
960%MinB=min(min(par_civ.ImageB));
961%check_undefined=false(size(par_civ.ImageA));
962if isfield(par_civ,'Mask') && ~isempty(par_civ.Mask)
963    checkmask=1;
964    if ~isequal(size(par_civ.Mask),[npy_ima npx_ima])
965        errormsg='mask must be an image with the same size as the images';
966        return
967    end
968    check_undefined=(par_civ.Mask<200 & par_civ.Mask>=20 );
969%     par_civ.ImageA(check_undefined)=0;% put image A to zero (i.e. the min image value) in the undefined  area
970%     par_civ.ImageB(check_undefined)=0;% put image B to zero (i.e. the min image value) in the undefined  area
971end
972
973%% compute image correlations: MAINLOOP on velocity vectors
974corrmax=0;
975sum_square=1;% default
976mesh=1;% default
977CheckDeformation=isfield(par_civ,'CheckDeformation')&& par_civ.CheckDeformation==1;
978if CheckDeformation
979    mesh=0.25;%mesh in pixels for subpixel image interpolation (x 4 in each direction)
980    par_civ.CorrSmooth=2;% use SUBPIX2DGAUSS (take into account more points near the max)
981end
982
983if par_civ.CorrSmooth~=0 % par_civ.CorrSmooth=0 implies no civ computation (just input image and grid points given)
984    for ivec=1:nbvec
985        iref=round(par_civ.Grid(ivec,1)+0.5);% xindex on the image A for the middle of the correlation box
986        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
987        F(ivec)=0;
988        subrange1_x=iref-ibx2:iref+ibx2;% x indices defining the first subimage
989        subrange1_y=jref-iby2:jref+iby2;% y indices defining the first subimage
990        subrange2_x=iref+shiftx(ivec)-isx2:iref+shiftx(ivec)+isx2;%x indices defining the second subimage
991        subrange2_y=jref+shifty(ivec)-isy2:jref+shifty(ivec)+isy2;%y indices defining the second subimage
992        image1_crop=MinA*ones(numel(subrange1_y),numel(subrange1_x));% default value=min of image A
993        image2_crop=MinA*ones(numel(subrange2_y),numel(subrange2_x));% default value=min of image A
994        check1_x=subrange1_x>=1 & subrange1_x<=par_civ.ImageWidth;% check which points in the subimage 1 are contained in the initial image 1
995        check1_y=subrange1_y>=1 & subrange1_y<=par_civ.ImageHeight;
996        check2_x=subrange2_x>=1 & subrange2_x<=par_civ.ImageWidth;% check which points in the subimage 2 are contained in the initial image 2
997        check2_y=subrange2_y>=1 & subrange2_y<=par_civ.ImageHeight;
998        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
999        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
1000        if checkmask
1001            mask1_crop=ones(numel(subrange1_y),numel(subrange1_x));% default value=1 for mask
1002            mask2_crop=ones(numel(subrange2_y),numel(subrange2_x));% default value=1 for mask
1003            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
1004            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
1005            sizemask=sum(sum(mask1_crop))/(numel(subrange1_y)*numel(subrange1_x));%size of the masked part relative to the correlation sub-image
1006            if sizemask > 1/2% eliminate point if more than half of the correlation box is masked
1007                F(ivec)=3; %
1008            else
1009                image1_crop=image1_crop.*~mask1_crop;% put to zero the masked pixels (mask1_crop='true'=1)
1010                image2_crop=image2_crop.*~mask2_crop;
1011                image1_mean=mean(mean(image1_crop))/(1-sizemask);
1012                image2_mean=mean(mean(image2_crop))/(1-sizemask);
1013            end
1014        else
1015            image1_mean=mean(mean(image1_crop));
1016            image2_mean=mean(mean(image2_crop));
1017        end
1018        %threshold on image minimum
1019        if F(ivec)~=3
1020            if check_MinIma && (image1_mean < par_civ.MinIma || image2_mean < par_civ.MinIma)
1021                F(ivec)=3;
1022                %threshold on image maximum
1023            elseif check_MaxIma && (image1_mean > par_civ.MaxIma || image2_mean > par_civ.MaxIma)
1024                F(ivec)=3;
1025            end
1026            if F(ivec)~=3
1027                %mask
1028                if checkmask
1029                    image1_crop=(image1_crop-image1_mean).*~mask1_crop;%substract the mean, put to zero the masked parts
1030                    image2_crop=(image2_crop-image2_mean).*~mask2_crop;
1031                else
1032                    image1_crop=(image1_crop-image1_mean);
1033                    image2_crop=(image2_crop-image2_mean);
1034                end
1035                %deformation
1036                if CheckDeformation
1037                    xi=(1:mesh:size(image1_crop,2));
1038                    yi=(1:mesh:size(image1_crop,1))';
1039                    [XI,YI]=meshgrid(xi-ceil(size(image1_crop,2)/2),yi-ceil(size(image1_crop,1)/2));
1040                    XIant=XI-par_civ.DUDX(ivec)*XI+par_civ.DUDY(ivec)*YI+ceil(size(image1_crop,2)/2);
1041                    YIant=YI+par_civ.DVDX(ivec)*XI-par_civ.DVDY(ivec)*YI+ceil(size(image1_crop,1)/2);
1042                    image1_crop=interp2(image1_crop,XIant,YIant);
1043                    image1_crop(isnan(image1_crop))=0;
1044                    xi=(1:mesh:size(image2_crop,2));
1045                    yi=(1:mesh:size(image2_crop,1))';
1046                    image2_crop=interp2(image2_crop,xi,yi,'*spline');
1047                    image2_crop(isnan(image2_crop))=0;
1048                end
1049                sum_square=sum(sum(image1_crop.*image1_crop));
1050                %reference: Oliver Pust, PIV: Direct Cross-Correlation
1051                result_conv= conv2(image2_crop,flipdim(flipdim(image1_crop,2),1),'valid');
1052                corrmax= max(max(result_conv));
1053                result_conv=(result_conv/corrmax)*255; %normalize, peak=always 255
1054                %Find the correlation max, at 255
1055                [y,x] = find(result_conv==255,1);
1056                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
1057                sum_square=sum_square*sum(sum(subimage2_crop.*subimage2_crop));% product of variances of image 1 and 2
1058                sum_square=sqrt(sum_square);% srt of the variance product to normalise correlation
1059                if ~isempty(y) && ~isempty(x)
1060                    try
1061                        if par_civ.CorrSmooth==1
1062                            [vector,F(ivec)] = SUBPIXGAUSS (result_conv,x,y);
1063                        elseif par_civ.CorrSmooth==2
1064                            [vector,F(ivec)] = SUBPIX2DGAUSS (result_conv,x,y);
1065                        else
1066                            [vector,F(ivec)] = quadr_fit(result_conv,x,y);
1067                        end
1068                        utable(ivec)=vector(1)*mesh+shiftx(ivec);
1069                        vtable(ivec)=vector(2)*mesh+shifty(ivec);
1070                        xtable(ivec)=iref+utable(ivec)/2-0.5;% convec flow (velocity taken at the point middle from imgae 1 and 2)
1071                        ytable(ivec)=jref+vtable(ivec)/2-0.5;% and position of pixel 1=0.5 (convention for image coordinates=0 at the edge)
1072                        iref=round(xtable(ivec));% nearest image index for the middle of the vector
1073                        jref=round(ytable(ivec));
1074                        % eliminate vectors located in the mask
1075                        if checkmask && par_civ.Mask(jref,iref)<200 && par_civ.Mask(jref,iref)>=100
1076                            utable(ivec)=0;
1077                            vtable(ivec)=0;
1078                            F(ivec)=3;
1079                        end
1080                        ctable(ivec)=corrmax/sum_square;% correlation value
1081                    catch ME
1082                        F(ivec)=3;
1083                    end
1084                else
1085                    F(ivec)=3;
1086                end
1087            end
1088        end
1089    end
1090end
1091result_conv=result_conv*corrmax/(255*sum_square);% keep the last correlation matrix for output
1092
1093%------------------------------------------------------------------------
1094% --- Find the maximum of the correlation function after interpolation
1095% OUPUT:
1096% vector = optimum displacement vector with subpixel correction
1097% F =flag: =0 OK
1098%           =-2 , warning: max too close to the edge of the search box (1 pixel margin)
1099% INPUT:
1100% x,y: position of the maximum correlation at integer values
1101
1102function [vector,F] = SUBPIXGAUSS (result_conv,x,y)
1103%------------------------------------------------------------------------
1104% vector=[0 0]; %default
1105F=0;
1106[npy,npx]=size(result_conv);
1107result_conv(result_conv<1)=1; %set to 1 correlation values smaller than 1 (to avoid divergence in the log)
1108%the following 8 lines are copyright (c) 1998, Uri Shavit, Roi Gurka, Alex Liberzon, Technion ᅵ Israel Institute of Technology
1109%http://urapiv.wordpress.com
1110peaky = y;
1111if y <= npy-1 && y >= 1
1112    f0 = log(result_conv(y,x));
1113    f1 = log(result_conv(y-1,x));
1114    f2 = log(result_conv(y+1,x));
1115    peaky = peaky+ (f1-f2)/(2*f1-4*f0+2*f2);
1116else
1117    F=-2; % warning flag for vector truncated by the limited search box
1118end
1119peakx=x;
1120if x <= npx-1 && x >= 1
1121    f0 = log(result_conv(y,x));
1122    f1 = log(result_conv(y,x-1));
1123    f2 = log(result_conv(y,x+1));
1124    peakx = peakx+ (f1-f2)/(2*f1-4*f0+2*f2);
1125else
1126    F=-2; % warning flag for vector truncated by the limited search box
1127end
1128vector=[peakx-floor(npx/2)-1 peaky-floor(npy/2)-1];
1129
1130%------------------------------------------------------------------------
1131% --- Find the maximum of the correlation function after interpolation
1132function [vector,F] = SUBPIX2DGAUSS (result_conv,x,y)
1133%------------------------------------------------------------------------
1134% vector=[0 0]; %default
1135F=-2;
1136peaky=y;
1137peakx=x;
1138result_conv(result_conv<1)=1; %set to 1 correlation values smaller than 1 (to avoid divergence in the log)
1139[npy,npx]=size(result_conv);
1140if (x <= npx-1) && (y <= npy-1) && (x >= 1) && (y >= 1)
1141    F=0;
1142    for i=-1:1
1143        for j=-1:1
1144            %following 15 lines based on
1145            %H. Nobach ï¿œ M. Honkanen (2005)
1146            %Two-dimensional Gaussian regression for sub-pixel displacement
1147            %estimation in particle image velocimetry or particle position
1148            %estimation in particle tracking velocimetry
1149            %Experiments in Fluids (2005) 38: 511ï¿œ515
1150            c10(j+2,i+2)=i*log(result_conv(y+j, x+i));
1151            c01(j+2,i+2)=j*log(result_conv(y+j, x+i));
1152            c11(j+2,i+2)=i*j*log(result_conv(y+j, x+i));
1153            c20(j+2,i+2)=(3*i^2-2)*log(result_conv(y+j, x+i));
1154            c02(j+2,i+2)=(3*j^2-2)*log(result_conv(y+j, x+i));
1155        end
1156    end
1157    c10=(1/6)*sum(sum(c10));
1158    c01=(1/6)*sum(sum(c01));
1159    c11=(1/4)*sum(sum(c11));
1160    c20=(1/6)*sum(sum(c20));
1161    c02=(1/6)*sum(sum(c02));
1162    deltax=(c11*c01-2*c10*c02)/(4*c20*c02-c11^2);
1163    deltay=(c11*c10-2*c01*c20)/(4*c20*c02-c11^2);
1164    if abs(deltax)<1
1165        peakx=x+deltax;
1166    end
1167    if abs(deltay)<1
1168        peaky=y+deltay;
1169    end
1170end
1171vector=[peakx-floor(npx/2)-1 peaky-floor(npy/2)-1];
1172
1173%------------------------------------------------------------------------
1174% --- Find the maximum of the correlation function after quadratic interpolation
1175function [vector,F] = quadr_fit(result_conv,x,y)
1176[npy,npx]=size(result_conv);
1177if x<4 || y<4 || npx-x<4 ||npy-y <4
1178    F=-2;
1179    vector=[x y];
1180else
1181    F=0;
1182    x_ind=x-4:x+4;
1183    y_ind=y-4:y+4;
1184    x_vec=0.25*(x_ind-x);
1185    y_vec=0.25*(y_ind-y);
1186    [X,Y]=meshgrid(x_vec,y_vec);
1187    coord=[reshape(X,[],1) reshape(Y,[],1)];
1188    result_conv=reshape(result_conv(y_ind,x_ind),[],1);
1189   
1190   
1191    % n=numel(X);
1192    % x=[X Y];
1193    % X=X-0.5;
1194    % Y=Y+0.5;
1195    % y = (X.*X+2*Y.*Y+X.*Y+6) + 0.1*rand(n,1);
1196    p = polyfitn(coord,result_conv,2);
1197    A(1,1)=2*p.Coefficients(1);
1198    A(1,2)=p.Coefficients(2);
1199    A(2,1)=p.Coefficients(2);
1200    A(2,2)=2*p.Coefficients(4);
1201    vector=[x y]'-A\[p.Coefficients(3) p.Coefficients(5)]';
1202    vector=vector'-[floor(npx/2) floor(npy/2)]-1 ;
1203    % zg = polyvaln(p,coord);
1204    % figure
1205    % surf(x_vec,y_vec,reshape(zg,9,9))
1206    % hold on
1207    % plot3(X,Y,reshape(result_conv,9,9),'o')
1208    % hold off
1209end
1210
1211%'RUN_FIX': function for fixing velocity fields:
1212%-----------------------------------------------
1213% RUN_FIX(filename,field,flagindex,thresh_vecC,thresh_vel,iter,flag_mask,maskname,fileref,fieldref)
1214%
1215%filename: name of the netcdf file (used as input and output)
1216%field: structure specifying the names of the fields to fix (depending on civ1 or civ2)
1217%.vel_type='civ1' or 'civ2';
1218%.nb=name of the dimension common to the field to fix ('nb_vectors' for civ1);
1219%.fixflag=name of fix flag variable ('vec_FixFlag' for civ1)
1220%flagindex: flag specifying which values of vec_f are removed:
1221% if flagindex(1)=1: vec_f=-2 vectors are removed
1222% if flagindex(2)=1: vec_f=3 vectors are removed
1223% if flagindex(3)=1: vec_f=2 vectors are removed (if iter=1) or vec_f=4 vectors are removed (if iter=2)
1224%iter=1 for civ1 fields and iter=2 for civ2 fields
1225%thresh_vecC: threshold in the image correlation vec_C
1226%flag_mask: =1 mask used to remove vectors (0 else)
1227%maskname: name of the mask image file for fix
1228%thresh_vel: threshold on velocity, or on the difference with the reference file fileref if exists
1229%inf_sup=1: remove values smaller than threshold thresh_vel, =2, larger than threshold
1230%fileref: .nc file name for a reference velocity (='': refrence 0 used)
1231%fieldref: 'civ1','filter1'...feld used in fileref
1232
1233function FF=fix(Param,F,C,U,V,X,Y)
1234FF=zeros(size(F));%default
1235
1236%criterium on warn flags
1237FlagName={'CheckFmin2','CheckF2','CheckF3','CheckF4'};
1238FlagVal=[-2 2 3 4];
1239for iflag=1:numel(FlagName)
1240    if isfield(Param,FlagName{iflag}) && Param.(FlagName{iflag})
1241        FF=(FF==1| F==FlagVal(iflag));
1242    end
1243end
1244%criterium on correlation values
1245if isfield (Param,'MinCorr')
1246    FF=FF==1 | C<Param.MinCorr;
1247end
1248if (isfield(Param,'MinVel')&&~isempty(Param.MinVel))||(isfield (Param,'MaxVel')&&~isempty(Param.MaxVel))
1249    Umod= U.*U+V.*V;
1250    if isfield (Param,'MinVel')&&~isempty(Param.MinVel)
1251        FF=FF==1 | Umod<(Param.MinVel*Param.MinVel);
1252    end
1253    if isfield (Param,'MaxVel')&&~isempty(Param.MaxVel)
1254        FF=FF==1 | Umod>(Param.MaxVel*Param.MaxVel);
1255    end
1256end
1257
1258
1259%------------------------------------------------------------------------
1260% --- determine the list of index pairs of processing file
1261function [i1_series,i2_series,j1_series,j2_series,check_bounds,NomTypeNc]=...
1262    find_pair_indices(str_civ,i_series,j_series,MinIndex_i,MaxIndex_i,MinIndex_j,MaxIndex_j)
1263%------------------------------------------------------------------------
1264i1_series=i_series;% set of first image indexes
1265i2_series=i_series;
1266j1_series=j_series;%ones(size(i_series));% set of first image numbers
1267j2_series=j_series;%ones(size(i_series));
1268r=regexp(str_civ,'^\D(?<ind>[i|j])=( -| )(?<num1>\d+)\|(?<num2>\d+)','names');
1269if ~isempty(r)
1270    mode=['D' r.ind];
1271    ind1=str2num(r.num1);
1272    ind2=str2num(r.num2);
1273else
1274    mode='j1-j2';
1275    r=regexp(str_civ,'^j= (?<num1>[a-z])-(?<num2>[a-z])','names');
1276    if ~isempty(r)
1277        NomTypeNc='_1ab';
1278    else
1279        r=regexp(str_civ,'^j= (?<num1>[A-Z])-(?<num2>[A-Z])','names');
1280        if ~isempty(r)
1281            NomTypeNc='_1AB';
1282        else
1283            r=regexp(str_civ,'^j= (?<num1>\d+)-(?<num2>\d+)','names');
1284            if ~isempty(r)
1285                NomTypeNc='_1_1-2';
1286            end
1287        end
1288    end
1289    if isempty(r)
1290        display('wrong pair mode input option')
1291    else
1292        ind1=stra2num(r.num1);
1293        ind2=stra2num(r.num2);
1294    end
1295end
1296switch mode
1297    case 'Di'
1298        i1_series=i_series-ind1;% set of first image numbers
1299        i2_series=i_series+ind2;
1300        check_bounds=i1_series<MinIndex_i | i2_series>MaxIndex_i;
1301        if isempty(j_series)
1302            NomTypeNc='_1-2';
1303        else
1304            j1_series=j_series;
1305            j2_series=j_series;
1306            NomTypeNc='_1-2_1';
1307        end
1308    case 'Dj'
1309        j1_series=j_series-ind1;
1310        j2_series=j_series+ind2;
1311        check_bounds=j1_series<MinIndex_j | j2_series>MaxIndex_j;
1312        NomTypeNc='_1_1-2';
1313    otherwise %bursts
1314        i1_series=i_series(1,:);% do not sweep the j index
1315        i2_series=i_series(1,:);
1316        j1_series=ind1*ones(1,size(i_series,2));% j index is fixed by pair choice
1317        j2_series=ind2*ones(1,size(i_series,2));
1318        check_bounds=zeros(size(i1_series));% no limitations due to min-max indices
1319end
1320
1321
1322
1323
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