source: trunk/src/series/civ_series.m @ 1061

Last change on this file since 1061 was 1061, checked in by g7moreau, 2 years ago
  • Update copyright to year 2019
File size: 65.9 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 2008-2019, 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    if isempty(Data)
57        Data=Param;% if  civ_input has been cancelled, keep previous parameters
58    end
59    Data.Program=mfilename;%gives the name of the current function
60    Data.AllowInputSort='off';% allow alphabetic sorting of the list of input file SubDir (options 'off'/'on', 'off' by default)
61    Data.WholeIndexRange='off';% prescribes the file index ranges from min to max (options 'off'/'on', 'off' by default)
62    Data.NbSlice='off'; %nbre of slices ('off' by default)
63    Data.VelType='off';% menu for selecting the velocity type (options 'off'/'one'/'two',  'off' by default)
64    Data.FieldName='on';% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default)
65    Data.FieldTransform = 'off';%can use a transform function
66    Data.ProjObject='off';%can use projection object(option 'off'/'on',
67    Data.Mask='off';%can use mask option   (option 'off'/'on', 'off' by default)
68    Data.OutputDirExt='.civ';%set the output dir extension
69    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)
70    Data.OutputFileMode='NbInput_i';% one output file expected per value of i index (used for waitbar)
71    Data.CheckOverwriteVisible='on'; % manage the overwrite of existing files (default=1)
72    if isfield(Data.ActionInput,'PairIndices') && strcmp(Data.ActionInput.PairIndices.ListPairMode,'pair j1-j2')
73        if isfield(Data.ActionInput.PairIndices,'ListPairCiv2')
74            str_civ=Data.ActionInput.PairIndices.ListPairCiv2;
75        else
76            str_civ=Data.ActionInput.PairIndices.ListPairCiv1;
77        end
78        r=regexp(str_civ,'^j= (?<num1>[a-z])-(?<num2>[a-z])','names');
79        if isempty(r)
80            r=regexp(str_civ,'^j= (?<num1>[A-Z])-(?<num2>[A-Z])','names');
81            if isempty(r)
82                r=regexp(str_civ,'^j= (?<num1>\d+)-(?<num2>\d+)','names');
83            end
84        end
85        if ~isempty(r)
86            Data.j_index_1=stra2num(r.num1);
87            Data.j_index_2=stra2num(r.num2);
88        end
89    end
90    return
91end
92
93%% read input parameters from an xml file if input is a file name (batch mode)
94checkrun=1;
95if ischar(Param)
96    Param=xml2struct(Param);% read Param as input file (batch case)
97    checkrun=0;
98end
99
100%% test input
101if ~isfield(Param,'ActionInput')
102    disp_uvmat('ERROR','no parameter set for PIV',checkrun)
103    return
104end
105iview_A=0;%default values
106NbField=1;
107RUNHandle=[];
108CheckInputFile=isfield(Param,'InputTable');%= 1 in test use for TestCiv (no nc file involved)
109CheckOutputFile=isfield(Param,'OutputSubDir');%= 1 in test use for TestPatch (no nc file produced)
110
111%% input files and indexing (skipped in Test mode)
112if CheckInputFile
113    hseries=findobj(allchild(0),'Tag','series');
114    RUNHandle=findobj(hseries,'Tag','RUN');%handle of RUN button in GUI series
115    WaitbarHandle=findobj(hseries,'Tag','Waitbar');%handle of waitbar in GUI series
116    MaxIndex_i=Param.IndexRange.MaxIndex_i;
117    MinIndex_i=Param.IndexRange.MinIndex_i;
118    MaxIndex_j=ones(size(MaxIndex_i));MinIndex_j=ones(size(MinIndex_i));
119    if isfield(Param.IndexRange,'MaxIndex_j')&& isfield(Param.IndexRange,'MinIndex_j')
120        MaxIndex_j=Param.IndexRange.MaxIndex_j;
121        MinIndex_j=Param.IndexRange.MinIndex_j;
122    end
123    if isfield(Param,'InputTable')
124        [tild,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param);
125        iview_A=0;% series index (iview) for the first image series
126        iview_B=0;% series index (iview) for the second image series (only non zero for option 'shift' comparing two image series )
127        if Param.ActionInput.CheckCiv1
128            iview_A=1;% usual PIV, the image series is on the first line of the table
129        elseif Param.ActionInput.CheckCiv2 % civ2 is performed without Civ1, a netcdf file series is needed in the first table line
130            iview_A=2;% the second line is used for the input images of Civ2
131        end
132%         if strcmp(Param.ActionInput.ListCompareMode,'shift')
133%             iview_B=iview_A+1; % the second image series is on the next line of the input table
134%         end
135        if iview_A~=0
136            RootPath_A=Param.InputTable{iview_A,1};
137            RootFile_A=Param.InputTable{iview_A,3};
138            SubDir_A=Param.InputTable{iview_A,2};
139            NomType_A=Param.InputTable{iview_A,4};
140            FileExt_A=Param.InputTable{iview_A,5};
141            if iview_B==0
142                iview_B=iview_A;% the second image series is the same as the first
143            end
144            RootPath_B=Param.InputTable{iview_B,1};
145            RootFile_B=Param.InputTable{iview_B,3};
146            SubDir_B=Param.InputTable{iview_B,2};
147            NomType_B=Param.InputTable{iview_B,4};
148            FileExt_B=Param.InputTable{iview_B,5};
149        end
150       
151        PairCiv2='';
152        switch Param.ActionInput.ListCompareMode
153            case 'PIV'
154                PairCiv1=Param.ActionInput.PairIndices.ListPairCiv1;
155                if isfield(Param.ActionInput.PairIndices,'ListPairCiv2')
156                    PairCiv2=Param.ActionInput.PairIndices.ListPairCiv2;%string which determines the civ2 pair
157                end
158                if iview_A==1% if Civ1 is performed
159                    [i1_series_Civ1,i2_series_Civ1,j1_series_Civ1,j2_series_Civ1,check_bounds,NomTypeNc]=...
160                        find_pair_indices(PairCiv1,i1_series{1},j1_series{1},MinIndex_i,MaxIndex_i,MinIndex_j,MaxIndex_j);
161                    if ~isempty(PairCiv2)
162                        [i1_series_Civ2,i2_series_Civ2,j1_series_Civ2,j2_series_Civ2,check_bounds_Civ2]=...
163                            find_pair_indices(PairCiv2,i1_series{1},j1_series{1},MinIndex_i(1),MaxIndex_i(1),MinIndex_j(1),MaxIndex_j(1));
164                        check_bounds=check_bounds | check_bounds_Civ2;
165                    end
166                else% we start from an existing Civ1 file
167                    i1_series_Civ1=i1_series{1};
168                    i2_series_Civ1=i2_series{1};
169                    j1_series_Civ1=j1_series{1};
170                    j2_series_Civ1=j2_series{1};
171                    NomTypeNc=Param.InputTable{1,4};
172                    if ~isempty(PairCiv2)
173                        [i1_series_Civ2,i2_series_Civ2,j1_series_Civ2,j2_series_Civ2,check_bounds,NomTypeNc]=...
174                            find_pair_indices(PairCiv2,i1_series{2},j1_series{2},MinIndex_i(2),MaxIndex_i(2),MinIndex_j(2),MaxIndex_j(2));
175                    end
176                end
177            case 'displacement'
178                if isfield(Param.ActionInput,'OriginIndex')
179                i1_series_Civ1=Param.ActionInput.OriginIndex*ones(size(i1_series{1}));
180                else
181                    i1_series_Civ1=ones(size(i1_series{1}));
182                end
183                i1_series_Civ2=i1_series_Civ1;
184                i2_series_Civ1=i1_series{1};
185                i2_series_Civ2=i1_series{1};
186                j1_series_Civ1=[];% no j index variation for the ref image
187                j1_series_Civ2=[];
188                if isempty(j1_series{1})
189                    j2_series_Civ1=ones(size(i1_series_Civ1));
190                else
191                    j2_series_Civ1=j1_series{1};% if j index exist 
192                end
193                j2_series_Civ2=j2_series_Civ1;
194                NomTypeNc='_1';
195            case 'PIV volume'
196                % TODO, TODO
197        end
198        %determine frame indices for input with movie or other multiframe input file
199        if isempty(j1_series_Civ1)% simple movie with index i
200            FrameIndex_A_Civ1=i1_series_Civ1;
201            FrameIndex_B_Civ1=i2_series_Civ1;
202            j1_series_Civ1=ones(size(i1_series_Civ1));
203            if strcmp(Param.ActionInput.ListCompareMode,'PIV')
204            j2_series_Civ1=ones(size(i1_series_Civ1));
205            end
206        else % movie for each burst or volume (index j)
207            FrameIndex_A_Civ1=j1_series_Civ1;
208            FrameIndex_B_Civ1=j2_series_Civ1;
209        end
210        if isempty(PairCiv2)
211            FrameIndex_A_Civ2=FrameIndex_A_Civ1;
212            FrameIndex_B_Civ2=FrameIndex_B_Civ1;
213        else
214            if isempty(j1_series_Civ2)
215                FrameIndex_A_Civ2=i1_series_Civ2;
216                FrameIndex_B_Civ2=i2_series_Civ2;
217                j1_series_Civ2=ones(size(i1_series_Civ2));
218                if strcmp(Param.ActionInput.ListCompareMode,'PIV')
219                j2_series_Civ2=ones(size(i1_series_Civ2));
220                end
221            else
222                FrameIndex_A_Civ2=j1_series_Civ2;
223                FrameIndex_B_Civ2=j2_series_Civ2;
224            end
225        end
226        if isempty(i1_series_Civ1)||(~isempty(PairCiv2) && isempty(i1_series_Civ2))
227            disp_uvmat('ERROR','no image pair for civ in the input file index range',checkrun)
228            return
229        end
230    end
231   
232    %% check the first image pair
233        if Param.ActionInput.CheckCiv1% Civ1 is performed
234            NbField=numel(i1_series_Civ1);
235        elseif Param.ActionInput.CheckCiv2 % Civ2 is performed without Civ1
236            NbField=numel(i1_series_Civ2);
237        else
238            NbField=numel(i1_series_Civ1);% no image used (only fix or patch) TO CHECK
239        end
240
241    %% Output directory
242    OutputDir='';
243    if CheckOutputFile
244        OutputDir=[Param.OutputSubDir Param.OutputDirExt];
245    end
246end
247
248%% prepare output Data
249ListGlobalAttribute={'Conventions','Program','CivStage'};
250Data.Conventions='uvmat/civdata';% states the conventions used for the description of field variables and attributes
251Data.Program='civ_series';
252Data.CivStage=0;%default
253check_civx=0;%default
254
255%% get timing from the ImaDoc file or input video
256if iview_A~=0
257    XmlFileName=find_imadoc(RootPath_A,SubDir_A,RootFile_A,FileExt_A);
258    Time=[];
259    if ~isempty(XmlFileName)
260        XmlData=imadoc2struct(XmlFileName);
261        if isfield(XmlData,'Time')
262            Time=XmlData.Time;
263        end
264        if isfield(XmlData,'Camera')
265            if isfield(XmlData.Camera,'NbSlice')&& ~isempty(XmlData.Camera.NbSlice)
266                NbSlice_calib{iview}=XmlData.Camera.NbSlice;% Nbre of slices for Zindex in phys transform
267                if ~isequal(NbSlice_calib{iview},NbSlice_calib{1})
268                    msgbox_uvmat('WARNING','inconsistent number of Z indices for the two field series');
269                end
270            end
271            if isfield(XmlData.Camera,'TimeUnit')&& ~isempty(XmlData.Camera.TimeUnit)
272                TimeUnit=XmlData.Camera.TimeUnit;
273            end
274        end
275    end
276end
277
278%%%%% MAIN LOOP %%%%%%
279maskoldname='';% initiate the mask name
280FileType_A='';
281FileType_B='';
282CheckOverwrite=1;%default
283if isfield(Param,'CheckOverwrite')
284    CheckOverwrite=Param.CheckOverwrite;
285end
286for ifield=1:NbField
287    tic
288    if ~isempty(RUNHandle)% update the waitbar in interactive mode with GUI series  (checkrun=1)
289        update_waitbar(WaitbarHandle,ifield/NbField)
290        if  checkrun && ~strcmp(get(RUNHandle,'BusyAction'),'queue')
291            disp('program stopped by user')
292            break
293        end
294    end
295    if CheckInputFile
296        if iview_A==0 % no nc file has been entered
297            ncfile=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},Param.InputTable{1,5},...
298                NomTypeNc,i1_series_Civ1(ifield),i2_series_Civ1(ifield),j1_series_Civ1(ifield),j2_series_Civ1(ifield));
299        else% an existing nc file has been entered
300            if iview_A==1% if Civ1 is performed
301                Civ1Dir=OutputDir;
302            else
303                Civ1Dir=Param.InputTable{1,2};
304            end
305            if strcmp(Param.ActionInput.ListCompareMode,'PIV')
306                ncfile=fullfile_uvmat(RootPath_A,Civ1Dir,RootFile_A,'.nc',NomTypeNc,i1_series_Civ1(ifield),i2_series_Civ1(ifield),...
307                    j1_series_Civ1(ifield),j2_series_Civ1(ifield));
308            else
309                ncfile=fullfile_uvmat(RootPath_A,Civ1Dir,RootFile_A,'.nc',NomTypeNc,i2_series_Civ1(ifield),[],...
310                    j1_series_Civ1(ifield),j2_series_Civ1(ifield));
311            end
312        end
313        ncfile_out=ncfile;% by default
314        if isfield (Param.ActionInput,'Civ2')
315            i1_civ2=i1_series_Civ2(ifield);
316            i2_civ2=i1_civ2;
317            if ~isempty(i2_series_Civ2)
318                i2_civ2=i2_series_Civ2(ifield);
319            end
320            j1_civ2=1;
321            if ~isempty(j1_series_Civ2)
322                j1_civ2=j1_series_Civ2(ifield);
323            end
324            j2_civ2=i1_civ2;
325            if ~isempty(j2_series_Civ2)
326                j2_civ2=j2_series_Civ2(ifield);
327            end
328            if strcmp(Param.ActionInput.ListCompareMode,'PIV')
329                ncfile_out=fullfile_uvmat(RootPath_A,OutputDir,RootFile_A,'.nc',NomTypeNc,i1_civ2,i2_civ2,j1_civ2,j2_civ2);
330            else % displacement
331                ncfile_out=fullfile_uvmat(RootPath_A,OutputDir,RootFile_A,'.nc',NomTypeNc,i2_civ2,[],j2_civ2);
332            end
333        end
334        if ~CheckOverwrite && exist(ncfile_out,'file')
335            disp(['existing output file ' ncfile_out ' already exists, skip to next field'])
336            continue% skip iteration if the mode overwrite is desactivated and the result file already exists
337        end
338    end
339    %% Civ1
340    % if Civ1 computation is requested
341    if isfield (Param.ActionInput,'Civ1')
342        if CheckInputFile
343            disp('civ1 started')
344        end
345        par_civ1=Param.ActionInput.Civ1;% parameters for civ1
346        if CheckInputFile % read input images (except in mode Test where it is introduced directly in Param.ActionInput.Civ1.ImageNameA and B)
347            try
348                if strcmp(Param.ActionInput.ListCompareMode,'displacement')
349                    ImageName_A=Param.ActionInput.RefFile;
350                else
351                ImageName_A=fullfile_uvmat(RootPath_A,SubDir_A,RootFile_A,FileExt_A,NomType_A,i1_series_Civ1(ifield),[],j1_series_Civ1(ifield));
352                end
353                if strcmp(FileExt_A,'.nc')% case of input images in format netcdf
354                    FieldName_A=Param.InputFields.FieldName;
355                    [DataIn,tild,tild,errormsg]=nc2struct(ImageName_A,{FieldName_A});
356                    par_civ1.ImageA=DataIn.(FieldName_A);
357                else % usual image formats for image A
358                    if isempty(FileType_A)% open the image object if not already done in case of movie input
359                        [FileInfo_A,VideoObject_A]=get_file_info(ImageName_A);
360                        FileType_A=FileInfo_A.FileType;
361                        if isempty(Time) && ~isempty(find(strcmp(FileType_A,{'mmreader','video','cine_phantom'})))% case of video input
362                            Time=zeros(FileInfo_A.NumberOfFrames+1,2);
363                            Time(:,2)=(0:1/FileInfo_A.FrameRate:(FileInfo_A.NumberOfFrames)/FileInfo_A.FrameRate)';
364                        end
365                        if ~isempty(FileType_A) && isempty(Time)% Time = index i +0.001 index j by default
366                            MaxIndex_i=max(i2_series_Civ1);
367                            MaxIndex_j=max(j2_series_Civ1);
368                            Time=(1:MaxIndex_i)'*ones(1,MaxIndex_j);
369                            Time=Time+0.001*ones(MaxIndex_i,1)*(1:MaxIndex_j);
370                            Time=[zeros(1,MaxIndex_j);Time];% insert a first line of zeros
371                            Time=[zeros(MaxIndex_i+1,1) Time];% insert a first column of zeros
372                        end
373                    end
374                    if ~exist(ImageName_A,'file')
375                        disp([ImageName_A ' missing'])
376                        continue
377                    end
378                    [par_civ1.ImageA,VideoObject_A] = read_image(ImageName_A,FileType_A,VideoObject_A,FrameIndex_A_Civ1(ifield));
379                end
380                ImageName_B=fullfile_uvmat(RootPath_B,SubDir_B,RootFile_B,FileExt_B,NomType_B,i2_series_Civ1(ifield),[],j2_series_Civ1(ifield));
381                if strcmp(FileExt_B,'.nc') % case of input images in format netcdf
382                    FieldName_B=Param.InputFields.FieldName;
383                    [DataIn,tild,tild,errormsg]=nc2struct(ImageName_B,{FieldName_B});
384                    par_civ1.ImageB=DataIn.(FieldName_B);
385                else % usual image formats for image B
386                    if isempty(FileType_B)
387                        [FileInfo_B,VideoObject_B]=get_file_info(ImageName_B);
388                        FileType_B=FileInfo_B.FileType;
389                    end
390                    if ~exist(ImageName_B,'file')
391                        disp([ImageName_B ' missing'])
392                        continue
393                    end
394                    [par_civ1.ImageB,VideoObject_B] = read_image(ImageName_B,FileType_B,VideoObject_B,FrameIndex_B_Civ1(ifield));
395                end
396            catch ME % display errors in reading input images
397                if ~isempty(ME.message)
398                    disp_uvmat('ERROR', ['error reading input image: ' ME.message],checkrun)
399                    continue
400                end
401            end
402            par_civ1.ImageWidth=size(par_civ1.ImageA,2);
403            par_civ1.ImageHeight=size(par_civ1.ImageA,1);
404            list_param=(fieldnames(Param.ActionInput.Civ1))';
405            list_param(strcmp('TestCiv1',list_param))=[];% remove the parameter TestCiv1 from the list
406            Civ1_param=regexprep(list_param,'^.+','Civ1_$0');% insert 'Civ1_' before  each string in list_param
407            Civ1_param=[{'Civ1_ImageA','Civ1_ImageB','Civ1_Time','Civ1_Dt'} Civ1_param]; %insert the names of the two input images
408            %indicate the values of all the global attributes in the output data
409            Data.Civ1_ImageA=ImageName_A;
410            Data.Civ1_ImageB=ImageName_B;
411            i1=i1_series_Civ1(ifield);
412            i2=i1;
413            if ~isempty(i2_series_Civ1)
414                i2=i2_series_Civ1(ifield);
415            end
416            j1=1;
417            if ~isempty(j1_series_Civ1)
418                j1=j1_series_Civ1(ifield);
419            end
420            j2=j1;
421            if ~isempty(j2_series_Civ1)
422                j2=j2_series_Civ1(ifield);
423            end
424            if strcmp(Param.ActionInput.ListCompareMode,'displacement')
425                Data.Civ1_Time=Time(i2+1,j2+1);% the Time is the Time of the secodn image
426                Data.Civ1_Dt=1;% Time interval is 1, to yield displacement instead of velocity=displacement/Dt at reading
427            else
428                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
429                Data.Civ1_Dt=Time(i2+1,j2+1)-Time(i1+1,j1+1);
430            end
431            for ilist=1:length(list_param)
432                Data.(Civ1_param{4+ilist})=Param.ActionInput.Civ1.(list_param{ilist});
433            end
434            Data.ListGlobalAttribute=[ListGlobalAttribute Civ1_param];
435            Data.CivStage=1;
436        end
437        % set the list of variables
438        Data.ListVarName={'Civ1_X','Civ1_Y','Civ1_U','Civ1_V','Civ1_F','Civ1_C'};%  cell array containing the names of the fields to record
439        Data.VarDimName={'nb_vec_1','nb_vec_1','nb_vec_1','nb_vec_1','nb_vec_1','nb_vec_1'};
440        Data.VarAttribute{1}.Role='coord_x';
441        Data.VarAttribute{2}.Role='coord_y';
442        Data.VarAttribute{3}.Role='vector_x';
443        Data.VarAttribute{4}.Role='vector_y';
444        Data.VarAttribute{5}.Role='warnflag';
445        % case of mask
446        if par_civ1.CheckMask&&~isempty(par_civ1.Mask)
447            if isfield(par_civ1,'NbSlice')
448                [RootPath_mask,SubDir_mask,RootFile_mask,i1_mask,i2_mask,j1_mask,j2_mask,Ext_mask]=fileparts_uvmat(Param.ActionInput.Civ1.Mask);
449                i1_mask=mod(i1-1,par_civ1.NbSlice)+1;
450                maskname=fullfile_uvmat(RootPath_mask,SubDir_mask,RootFile_mask,Ext_mask,'_1',i1_mask);
451            else
452                maskname=Param.ActionInput.Civ1.Mask;
453            end
454            if strcmp(maskoldname,maskname)% mask exist, not already read in civ1
455                par_civ1.Mask=mask; %use mask already opened
456            else
457                try
458                    par_civ1.Mask=imread(maskname);%update the mask, an store it for future use
459                catch ME
460                    if ~isempty(ME.message)
461                        errormsg=['error reading input image: ' ME.message];
462                        disp_uvmat('ERROR',errormsg,checkrun)
463                        return
464                    end
465                end
466                mask=par_civ1.Mask;
467                maskoldname=maskname;
468            end
469        end
470        if strcmp(Param.ActionInput.ListCompareMode, 'PIV volume')
471            Data.ListVarName=[Data.ListVarName 'Civ1_Z'];
472            Data.Civ1_X=[];Data.Civ1_Y=[];Data.Civ1_Z=[];
473            Data.Civ1_U=[];Data.Civ1_V=[];Data.Civ1_C=[];Data.Civ1_F=[];
474            for ivol=1:NbSlice
475                % caluclate velocity data (y and v in indices, reverse to y component)
476                [xtable, ytable, utable, vtable, ctable, F, result_conv, errormsg] = civ (par_civ1);
477                if ~isempty(errormsg)
478                    disp_uvmat('ERROR',errormsg,checkrun)
479                    return
480                end
481                Data.Civ1_X=[Data.Civ1_X reshape(xtable,[],1)];
482                Data.Civ1_Y=[Data.Civ1_Y reshape(Param.Civ1.ImageHeight-ytable+1,[],1)];
483                Data.Civ1_Z=[Data.Civ1_Z ivol*ones(numel(xtable),1)];% z=image index in image coordinates
484                Data.Civ1_U=[Data.Civ1_U reshape(utable,[],1)];
485                Data.Civ1_V=[Data.Civ1_V reshape(-vtable,[],1)];
486                Data.Civ1_C=[Data.Civ1_C reshape(ctable,[],1)];
487                Data.Civ1_F=[Data.Civ1_C reshape(F,[],1)];
488            end
489        else %usual PIV
490            % caluclate velocity data (y and v in indices, reverse to y component)
491            [xtable, ytable, utable, vtable, ctable, F, result_conv, errormsg] = civ (par_civ1);
492            if ~isempty(errormsg)
493                disp_uvmat('ERROR',errormsg,checkrun)
494                return
495            end
496            Data.Civ1_X=reshape(xtable,[],1);
497            Data.Civ1_Y=reshape(par_civ1.ImageHeight-ytable+1,[],1);
498            Data.Civ1_U=reshape(utable,[],1);
499            Data.Civ1_V=reshape(-vtable,[],1);
500            Data.Civ1_C=reshape(ctable,[],1);
501            Data.Civ1_F=reshape(F,[],1);
502        end
503    else% we use existing Civ1 data
504        if exist('ncfile','var')
505            CivFile=ncfile;
506            [Data,tild,tild,errormsg]=nc2struct(CivFile,'ListGlobalAttribute','absolut_time_T0'); %look for the constant 'absolut_time_T0' to detect old civx data format
507            if ~isempty(errormsg)
508                disp_uvmat('ERROR',errormsg,checkrun)
509                return
510            end
511            [Data,tild,tild,errormsg]=nc2struct(CivFile);%read civ1 and fix1 data in the existing netcdf file
512        elseif isfield(Param,'Civ1_X')
513            Data.ListGlobalAttribute={};
514            Data.ListVarName={};
515            Data.VarDimName={};
516            Data.Civ1_X=Param.Civ1_X;
517            Data.Civ1_Y=Param.Civ1_Y;
518            Data.Civ1_U=Param.Civ1_U;
519            Data.Civ1_V=Param.Civ1_V;
520            Data.Civ1_FF=Param.Civ1_FF;
521        end
522    end
523   
524    %% Fix1
525    if isfield (Param.ActionInput,'Fix1')
526        disp('fix1 started')
527        if ~isfield (Param.ActionInput,'Civ1')% if we use existing Civ1, remove previous data beyond Civ1
528            Fix1_attr=find(strcmp('Fix1',Data.ListGlobalAttribute));
529            Data.ListGlobalAttribute(Fix1_attr)=[];
530            for ilist=1:numel(Fix1_attr)
531                Data=rmfield(Data,Data.ListGlobalAttribute{Fix1_attr(ilist)});
532            end
533        end
534        list_param=fieldnames(Param.ActionInput.Fix1)';
535        Fix1_param=regexprep(list_param,'^.+','Fix1_$0');% insert 'Fix1_' before  each string in ListFixParam
536        %indicate the values of all the global attributes in the output data
537        for ilist=1:length(list_param)
538            Data.(Fix1_param{ilist})=Param.ActionInput.Fix1.(list_param{ilist});
539        end
540        Data.ListGlobalAttribute=[Data.ListGlobalAttribute Fix1_param];
541        Data.ListVarName=[Data.ListVarName {'Civ1_FF'}];
542        Data.VarDimName=[Data.VarDimName {'nb_vec_1'}];
543        nbvar=length(Data.ListVarName);
544        Data.VarAttribute{nbvar}.Role='errorflag';
545        Data.Civ1_FF=int8(fix(Param.ActionInput.Fix1,Data.Civ1_F,Data.Civ1_C,Data.Civ1_U,Data.Civ1_V));
546        Data.CivStage=2;
547    end
548    %% Patch1
549    if isfield (Param.ActionInput,'Patch1')
550        disp('patch1 started')
551        if check_civx
552            errormsg='Civ Matlab input needed for patch';
553            disp_uvmat('ERROR',errormsg,checkrun)
554            return
555        end
556       
557        % record the processing parameters of Patch1 as global attributes in the result nc file
558        list_param=fieldnames(Param.ActionInput.Patch1)';
559        list_param(strcmp('TestPatch1',list_param))=[];% remove 'TestPatch1' from the list of parameters
560        Patch1_param=regexprep(list_param,'^.+','Patch1_$0');% insert 'Patch1_' before  each parameter name
561        for ilist=1:length(list_param)
562            Data.(Patch1_param{ilist})=Param.ActionInput.Patch1.(list_param{ilist});
563        end
564        Data.CivStage=3;% record the new state of processing
565        Data.ListGlobalAttribute=[Data.ListGlobalAttribute Patch1_param];
566       
567        % list the variables to record
568        nbvar=length(Data.ListVarName);
569        Data.ListVarName=[Data.ListVarName {'Civ1_U_smooth','Civ1_V_smooth','Civ1_SubRange','Civ1_NbCentres','Civ1_Coord_tps','Civ1_U_tps','Civ1_V_tps'}];
570        Data.VarDimName=[Data.VarDimName {'nb_vec_1','nb_vec_1',{'nb_coord','nb_bounds','nb_subdomain_1'},'nb_subdomain_1',...
571            {'nb_tps_1','nb_coord','nb_subdomain_1'},{'nb_tps_1','nb_subdomain_1'},{'nb_tps_1','nb_subdomain_1'}}];
572        Data.VarAttribute{nbvar+1}.Role='vector_x';
573        Data.VarAttribute{nbvar+2}.Role='vector_y';
574        Data.VarAttribute{nbvar+5}.Role='coord_tps';
575        Data.VarAttribute{nbvar+6}.Role='vector_x';
576        Data.VarAttribute{nbvar+7}.Role='vector_y';
577        Data.Civ1_U_smooth=Data.Civ1_U; % zeros(size(Data.Civ1_X));
578        Data.Civ1_V_smooth=Data.Civ1_V; %zeros(size(Data.Civ1_X));
579        if isfield(Data,'Civ1_FF')
580            ind_good=find(Data.Civ1_FF==0);
581        else
582            ind_good=1:numel(Data.Civ1_X);
583        end
584       
585        % perform Patch calculation using the UVMAT fct 'filter_tps'
586        [Data.Civ1_SubRange,Data.Civ1_NbCentres,Data.Civ1_Coord_tps,Data.Civ1_U_tps,Data.Civ1_V_tps,tild,Ures, Vres,tild,FFres]=...
587            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);
588        Data.Civ1_U_smooth(ind_good)=Ures;% take the interpolated (smoothed) velocity values for good vectors, keep civ1 data for the other
589        Data.Civ1_V_smooth(ind_good)=Vres;
590        Data.Civ1_FF(ind_good)=int8(FFres);
591        disp('patch1 performed')
592    end
593   
594    %% Civ2
595    if isfield (Param.ActionInput,'Civ2')
596        disp('civ2 started')
597        par_civ2=Param.ActionInput.Civ2;
598        if CheckInputFile % read input images (except in mode Test where it is introduced directly in Param.ActionInput.Civ1.ImageNameA and B)
599            par_civ2.ImageA=[];
600            par_civ2.ImageB=[];
601            if strcmp(Param.ActionInput.ListCompareMode,'displacement')
602                    ImageName_A_Civ2=Param.ActionInput.RefFile;
603                else
604            ImageName_A_Civ2=fullfile_uvmat(RootPath_A,SubDir_A,RootFile_A,FileExt_A,NomType_A,i1_civ2,[],j1_civ2);
605            end
606            if strcmp(ImageName_A_Civ2,ImageName_A) && isequal(FrameIndex_A_Civ1(ifield),FrameIndex_A_Civ2(ifield))
607                par_civ2.ImageA=par_civ1.ImageA;
608            else
609                [par_civ2.ImageA,VideoObject_A] = read_image(ImageName_A_Civ2,FileType_A,VideoObject_A,FrameIndex_A_Civ2(ifield));
610            end
611            ImageName_B_Civ2=fullfile_uvmat(RootPath_B,SubDir_B,RootFile_B,FileExt_B,NomType_B,i2_civ2,[],j2_civ2);
612            if strcmp(ImageName_B_Civ2,ImageName_B) && isequal(FrameIndex_B_Civ1(ifield),FrameIndex_B_Civ2)
613                par_civ2.ImageB=par_civ1.ImageB;
614            else
615                [par_civ2.ImageB,VideoObject_B] = read_image(ImageName_B_Civ2,FileType_B,VideoObject_B,FrameIndex_B_Civ2(ifield));
616            end
617            par_civ2.ImageWidth=FileInfo_A.Width;
618            par_civ2.ImageHeight=FileInfo_A.Height;
619            if isfield(par_civ2,'Grid')% grid points set as input file
620                if ischar(par_civ2.Grid)%read the grid file if the input is a file name
621                    par_civ2.Grid=dlmread(par_civ2.Grid);
622                    par_civ2.Grid(1,:)=[];%the first line must be removed (heading in the grid file)
623                end
624            else% automatic grid
625                minix=floor(par_civ2.Dx/2)-0.5;
626                maxix=minix+par_civ2.Dx*floor((par_civ2.ImageWidth-1)/par_civ2.Dx);
627                miniy=floor(par_civ2.Dy/2)-0.5;
628                maxiy=minix+par_civ2.Dy*floor((par_civ2.ImageHeight-1)/par_civ2.Dy);
629                [GridX,GridY]=meshgrid(minix:par_civ2.Dx:maxix,miniy:par_civ2.Dy:maxiy);
630                par_civ2.Grid(:,1)=reshape(GridX,[],1);
631                par_civ2.Grid(:,2)=reshape(GridY,[],1);
632            end
633        end
634       
635        % get the guess from patch1 or patch2 (case 'CheckCiv3')
636        if CheckInputFile % read input images (except in mode Test where it is introduced directly in Param.ActionInput.Civ1.ImageNameA and B)
637            if isfield (par_civ2,'CheckCiv3') && par_civ2.CheckCiv3 %get the guess from  patch2
638                SubRange= Data.Civ2_SubRange;
639                NbCentres=Data.Civ2_NbCentres;
640                Coord_tps=Data.Civ2_Coord_tps;
641                U_tps=Data.Civ2_U_tps;
642                V_tps=Data.Civ2_V_tps;
643                CivStage=Data.CivStage;%store the current CivStage
644                Civ1_Dt=Data.Civ2_Dt;
645                Data=[];%reinitialise the result structure Data
646                Data.ListGlobalAttribute={'Conventions','Program','CivStage'};
647                Data.Conventions='uvmat/civdata';% states the conventions used for the description of field variables and attributes
648                Data.Program='civ_series';
649                Data.CivStage=CivStage+1;%update the current civStage after reinitialisation of Data
650                Data.ListVarName={};
651                Data.VarDimName={};
652            else % get the guess from patch1
653                SubRange= Data.Civ1_SubRange;
654                NbCentres=Data.Civ1_NbCentres;
655                Coord_tps=Data.Civ1_Coord_tps;
656                U_tps=Data.Civ1_U_tps;
657                V_tps=Data.Civ1_V_tps;
658                Civ1_Dt=Data.Civ1_Dt;
659                Data.CivStage=4;
660            end
661        else
662            SubRange= par_civ2.Civ1_SubRange;
663            NbCentres=par_civ2.Civ1_NbCentres;
664            Coord_tps=par_civ2.Civ1_Coord_tps;
665            U_tps=par_civ2.Civ1_U_tps;
666            V_tps=par_civ2.Civ1_V_tps;
667            Civ1_Dt=par_civ2.Civ1_Dt;
668            Civ2_Dt=par_civ2.Civ1_Dt;
669            Data.ListVarName={};
670            Data.VarDimName={};
671        end
672        Shiftx=zeros(size(par_civ2.Grid,1),1);% shift expected from civ1 data
673        Shifty=zeros(size(par_civ2.Grid,1),1);
674        nbval=zeros(size(par_civ2.Grid,1),1);% nbre of interpolated values at each grid point (from the different patch subdomains)
675        if par_civ2.CheckDeformation
676            DUDX=zeros(size(par_civ2.Grid,1),1);
677            DUDY=zeros(size(par_civ2.Grid,1),1);
678            DVDX=zeros(size(par_civ2.Grid,1),1);
679            DVDY=zeros(size(par_civ2.Grid,1),1);
680        end
681        NbSubDomain=size(SubRange,3);
682        for isub=1:NbSubDomain% for each sub-domain of Patch1
683            nbvec_sub=NbCentres(isub);% nbre of Civ vectors in the subdomain
684            ind_sel=find(par_civ2.Grid(:,1)>=SubRange(1,1,isub) & par_civ2.Grid(:,1)<=SubRange(1,2,isub) &...
685                par_civ2.Grid(:,2)>=SubRange(2,1,isub) & par_civ2.Grid(:,2)<=SubRange(2,2,isub));% grid points in the subdomain
686            if ~isempty(ind_sel)
687                epoints = par_civ2.Grid(ind_sel,:);% coordinates of interpolation sites (measurement grids)
688                ctrs=Coord_tps(1:nbvec_sub,:,isub) ;%(=initial points) ctrs
689                nbval(ind_sel)=nbval(ind_sel)+1;% records the number of values for each interpolation point (in case of subdomain overlap)
690                EM = tps_eval(epoints,ctrs);% thin plate spline (tps) coefficient
691                Shiftx(ind_sel)=Shiftx(ind_sel)+EM*U_tps(1:nbvec_sub+3,isub);%velocity shift estimated by tps from civ1
692                Shifty(ind_sel)=Shifty(ind_sel)+EM*V_tps(1:nbvec_sub+3,isub);
693                if par_civ2.CheckDeformation
694                    [EMDX,EMDY] = tps_eval_dxy(epoints,ctrs);%2D matrix of distances between extrapolation points epoints and spline centres (=site points) ctrs
695                    DUDX(ind_sel)=DUDX(ind_sel)+EMDX*U_tps(1:nbvec_sub+3,isub);
696                    DUDY(ind_sel)=DUDY(ind_sel)+EMDY*U_tps(1:nbvec_sub+3,isub);
697                    DVDX(ind_sel)=DVDX(ind_sel)+EMDX*V_tps(1:nbvec_sub+3,isub);
698                    DVDY(ind_sel)=DVDY(ind_sel)+EMDY*V_tps(1:nbvec_sub+3,isub);
699                end
700            end
701        end
702        if par_civ2.CheckMask&&~isempty(par_civ2.Mask)       
703            if isfield(par_civ2,'NbSlice')
704                [RootPath_mask,SubDir_mask,RootFile_mask,i1_mask,i2_mask,j1_mask,j2_mask,Ext_mask]=fileparts_uvmat(Param.ActionInput.Civ2.Mask);
705                i1_mask=mod(i1-1,par_civ2.NbSlice)+1;
706                maskname=fullfile_uvmat(RootPath_mask,SubDir_mask,RootFile_mask,Ext_mask,'_1',i1_mask);
707            else
708                maskname=Param.ActionInput.Civ2.Mask;
709            end
710            if strcmp(maskoldname,maskname)% mask exist, not already read in civ1
711                par_civ2.Mask=mask; %use mask already opened
712            else
713                try
714                    par_civ2.Mask=imread(maskname);%update the mask, an store it for future use
715                catch ME
716                    if ~isempty(ME.message)
717                        errormsg=['error reading input image: ' ME.message];
718                        disp_uvmat('ERROR',errormsg,checkrun)
719                        return
720                    end
721                end
722                mask=par_civ2.Mask;
723                maskoldname=maskname;
724            end
725        end
726
727        if CheckInputFile % else Dt given by par_civ2
728            if strcmp(Param.ActionInput.ListCompareMode,'displacement')
729                Civ1_Dt=1;
730                Civ2_Dt=1;
731            else
732                Civ2_Dt=Time(i2_civ2+1,j2_civ2+1)-Time(i1_civ2+1,j1_civ2+1);
733            end
734        end
735        par_civ2.SearchBoxShift=(Civ2_Dt/Civ1_Dt)*[Shiftx(nbval>=1)./nbval(nbval>=1) Shifty(nbval>=1)./nbval(nbval>=1)];
736        % shift the grid points by half the expected shift to provide the correlation box position in image A
737        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];
738        if par_civ2.CheckDeformation
739            par_civ2.DUDX=DUDX(nbval>=1)./nbval(nbval>=1);
740            par_civ2.DUDY=DUDY(nbval>=1)./nbval(nbval>=1);
741            par_civ2.DVDX=DVDX(nbval>=1)./nbval(nbval>=1);
742            par_civ2.DVDY=DVDY(nbval>=1)./nbval(nbval>=1);
743        end
744       
745        % calculate velocity data (y and v in image indices, reverse to y component)
746        [xtable, ytable, utable, vtable, ctable, F,result_conv,errormsg] = civ (par_civ2);
747       
748        list_param=(fieldnames(Param.ActionInput.Civ2))';
749        list_param(strcmp('TestCiv2',list_param))=[];% remove the parameter TestCiv2 from the list
750        Civ2_param=regexprep(list_param,'^.+','Civ2_$0');% insert 'Civ2_' before  each string in list_param
751        Civ2_param=[{'Civ2_ImageA','Civ2_ImageB','Civ2_Time','Civ2_Dt'} Civ2_param]; %insert the names of the two input images
752        %indicate the values of all the global attributes in the output data
753        if exist('ImageName_A','var')
754            Data.Civ2_ImageA=ImageName_A;
755            Data.Civ2_ImageB=ImageName_B;
756            if strcmp(Param.ActionInput.ListCompareMode,'displacement')
757                Data.Civ2_Time=Time(i2_civ2+1,j2_civ2+1);% the Time is the Time of the secodn image
758                Data.Civ2_Dt=1;% Time interval is 1, to yield displacement instead of velocity=displacement/Dt at reading
759            else
760                Data.Civ2_Time=(Time(i2_civ2+1,j2_civ2+1)+Time(i1_civ2+1,j1_civ2+1))/2;
761                Data.Civ2_Dt=Civ2_Dt;
762            end
763        end
764        for ilist=1:length(list_param)
765            Data.(Civ2_param{4+ilist})=Param.ActionInput.Civ2.(list_param{ilist});
766        end
767        Data.ListGlobalAttribute=[Data.ListGlobalAttribute Civ2_param];
768       
769        nbvar=numel(Data.ListVarName);
770        % define the Civ2 variable (if Civ2 data are not replaced from previous calculation)
771        if isempty(find(strcmp('Civ2_X',Data.ListVarName),1))
772            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
773            Data.VarDimName=[Data.VarDimName {'nb_vec_2','nb_vec_2','nb_vec_2','nb_vec_2','nb_vec_2','nb_vec_2'}];
774            Data.VarAttribute{nbvar+1}.Role='coord_x';
775            Data.VarAttribute{nbvar+2}.Role='coord_y';
776            Data.VarAttribute{nbvar+3}.Role='vector_x';
777            Data.VarAttribute{nbvar+4}.Role='vector_y';
778            Data.VarAttribute{nbvar+5}.Role='warnflag';
779        end
780        Data.Civ2_X=reshape(xtable,[],1);
781        Data.Civ2_Y=reshape(size(par_civ2.ImageA,1)-ytable+1,[],1);
782        Data.Civ2_U=reshape(utable,[],1);
783        Data.Civ2_V=reshape(-vtable,[],1);
784        Data.Civ2_C=reshape(ctable,[],1);
785        Data.Civ2_F=reshape(F,[],1);
786        disp('civ2 performed')
787    elseif ~isfield(Data,'ListVarName') % we start there, using existing Civ2 data
788        if exist('ncfile','var')
789            CivFile=ncfile;
790            [Data,tild,tild,errormsg]=nc2struct(CivFile);%read civ1 and fix1 data in the existing netcdf file
791            if ~isempty(errormsg)
792                disp_uvmat('ERROR',errormsg,checkrun)
793                return
794            end
795        elseif isfield(Param,'Civ2_X')% use Civ2 data as input in Param (test mode)
796            Data.ListGlobalAttribute={};
797            Data.ListVarName={};
798            Data.VarDimName={};
799            Data.Civ2_X=Param.Civ2_X;
800            Data.Civ2_Y=Param.Civ2_Y;
801            Data.Civ2_U=Param.Civ2_U;
802            Data.Civ2_V=Param.Civ2_V;
803            Data.Civ2_FF=Param.Civ2_FF;
804        end
805    end
806   
807    %% Fix2
808    if isfield (Param.ActionInput,'Fix2')
809        disp('fix2 started')
810        list_param=fieldnames(Param.ActionInput.Fix2)';
811        Fix2_param=regexprep(list_param,'^.+','Fix2_$0');% insert 'Fix1_' before  each string in ListFixParam
812        %indicate the values of all the global attributes in the output data
813        for ilist=1:length(list_param)
814            Data.(Fix2_param{ilist})=Param.ActionInput.Fix2.(list_param{ilist});
815        end
816        Data.ListGlobalAttribute=[Data.ListGlobalAttribute Fix2_param];
817        %
818        %         ListFixParam=fieldnames(Param.ActionInput.Fix2);
819        %         for ilist=1:length(ListFixParam)
820        %             ParamName=ListFixParam{ilist};
821        %             ListName=['Fix2_' ParamName];
822        %             eval(['Data.ListGlobalAttribute=[Data.ListGlobalAttribute ''' ParamName '''];'])
823        %             eval(['Data.' ListName '=Param.ActionInput.Fix2.' ParamName ';'])
824        %         end
825        if check_civx
826            if ~isfield(Data,'fix2')
827                Data.ListGlobalAttribute=[Data.ListGlobalAttribute 'fix2'];
828                Data.fix2=1;
829                Data.ListVarName=[Data.ListVarName {'vec2_FixFlag'}];
830                Data.VarDimName=[Data.VarDimName {'nb_vectors2'}];
831            end
832            Data.vec_FixFlag=fix(Param.Fix2,Data.vec2_F,Data.vec2_C,Data.vec2_U,Data.vec2_V,Data.vec2_X,Data.vec2_Y);
833        else
834            Data.ListVarName=[Data.ListVarName {'Civ2_FF'}];
835            Data.VarDimName=[Data.VarDimName {'nb_vec_2'}];
836            nbvar=length(Data.ListVarName);
837            Data.VarAttribute{nbvar}.Role='errorflag';
838            Data.Civ2_FF=double(fix(Param.ActionInput.Fix2,Data.Civ2_F,Data.Civ2_C,Data.Civ2_U,Data.Civ2_V));
839            Data.CivStage=Data.CivStage+1;
840        end
841    end
842   
843    %% Patch2
844    if isfield (Param.ActionInput,'Patch2')
845        disp('patch2 started')
846        list_param=fieldnames(Param.ActionInput.Patch2)';
847        list_param(strcmp('TestPatch2',list_param))=[];% remove the parameter TestCiv1 from the list
848        Patch2_param=regexprep(list_param,'^.+','Patch2_$0');% insert 'Fix1_' before  each string in ListFixParam
849        %indicate the values of all the global attributes in the output data
850        for ilist=1:length(list_param)
851            Data.(Patch2_param{ilist})=Param.ActionInput.Patch2.(list_param{ilist});
852        end
853        Data.ListGlobalAttribute=[Data.ListGlobalAttribute Patch2_param];
854       
855        nbvar=length(Data.ListVarName);
856        Data.ListVarName=[Data.ListVarName {'Civ2_U_smooth','Civ2_V_smooth','Civ2_SubRange','Civ2_NbCentres','Civ2_Coord_tps','Civ2_U_tps','Civ2_V_tps'}];
857        Data.VarDimName=[Data.VarDimName {'nb_vec_2','nb_vec_2',{'nb_coord','nb_bounds','nb_subdomain_2'},{'nb_subdomain_2'},...
858            {'nb_tps_2','nb_coord','nb_subdomain_2'},{'nb_tps_2','nb_subdomain_2'},{'nb_tps_2','nb_subdomain_2'}}];
859       
860        Data.VarAttribute{nbvar+1}.Role='vector_x';
861        Data.VarAttribute{nbvar+2}.Role='vector_y';
862        Data.VarAttribute{nbvar+5}.Role='coord_tps';
863        Data.VarAttribute{nbvar+6}.Role='vector_x';
864        Data.VarAttribute{nbvar+7}.Role='vector_y';
865        Data.Civ2_U_smooth=Data.Civ2_U;
866        Data.Civ2_V_smooth=Data.Civ2_V;
867        if isfield(Data,'Civ2_FF')
868            ind_good=find(Data.Civ2_FF==0);
869        else
870            ind_good=1:numel(Data.Civ2_X);
871        end
872        [Data.Civ2_SubRange,Data.Civ2_NbCentres,Data.Civ2_Coord_tps,Data.Civ2_U_tps,Data.Civ2_V_tps,tild,Ures,Vres,tild,FFres]=...
873            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);
874        Data.Civ2_U_smooth(ind_good)=Ures;
875        Data.Civ2_V_smooth(ind_good)=Vres;
876        Data.Civ2_FF(ind_good)=FFres;
877        Data.CivStage=Data.CivStage+1;
878        disp('patch2 performed')
879    end
880   
881    %% write result in a netcdf file if requested
882    if CheckOutputFile
883        errormsg=struct2nc(ncfile_out,Data);
884        if isempty(errormsg)
885            disp([ncfile_out ' written'])
886            %[success,msg] = fileattrib(ncfile_out ,'+w','g');% done in struct2nc
887        else
888            disp(errormsg)
889        end
890        disp(['ellapsed time ' num2str(toc/60,2) ' minutes'])
891    end
892end
893
894
895% 'civ': function piv.m adapted from PIVlab http://pivlab.blogspot.com/
896%--------------------------------------------------------------------------
897% function [xtable ytable utable vtable typevector] = civ (image1,image2,ibx,iby step, subpixfinder, mask, roi)
898%
899% OUTPUT:
900% xtable: set of x coordinates
901% ytable: set of y coordiantes
902% utable: set of u displacements (along x)
903% vtable: set of v displacements (along y)
904% ctable: max image correlation for each vector
905% typevector: set of flags, =1 for good, =0 for NaN vectors
906%
907%INPUT:
908% par_civ: structure of input parameters, with fields:
909%  .ImageA: first image for correlation (matrix)
910%  .ImageB: second image for correlation(matrix)
911%  .CorrBoxSize: 1,2 vector giving the size of the correlation box in x and y
912%  .SearchBoxSize:  1,2 vector giving the size of the search box in x and y
913%  .SearchBoxShift: 1,2 vector or 2 column matrix (for civ2) giving the shift of the search box in x and y
914%  .CorrSmooth: =1 or 2 determines the choice of the sub-pixel determination of the correlation max
915%  .ImageWidth: nb of pixels of the image in x
916%  .Dx, Dy: mesh for the PIV calculation
917%  .Grid: grid giving the PIV calculation points (alternative to .Dx .Dy): centres of the correlation boxes in Image A
918%  .Mask: name of a mask file or mask image matrix itself
919%  .MinIma: thresholds for image luminosity
920%  .MaxIma
921%  .CheckDeformation=1 for subpixel interpolation and image deformation (linear transform)
922%  .DUDX: matrix of deformation obtained from patch at each grid point
923%  .DUDY
924%  .DVDX:
925%  .DVDY
926
927function [xtable,ytable,utable,vtable,ctable,F,result_conv,errormsg] = civ (par_civ)
928
929%% prepare measurement grid
930if isfield(par_civ,'Grid')% grid points set as input, central positions of the sub-images in image A
931    if ischar(par_civ.Grid)%read the grid file if the input is a file name (grid in x, y image coordinates)
932        par_civ.Grid=dlmread(par_civ.Grid);
933        par_civ.Grid(1,:)=[];%the first line must be removed (heading in the grid file)
934    end
935    % else par_civ.Grid is already an array, no action here
936else% automatic grid in x, y image coordinates
937    minix=floor(par_civ.Dx/2)-0.5;
938    maxix=minix+par_civ.Dx*floor((par_civ.ImageWidth-1)/par_civ.Dx);
939    miniy=floor(par_civ.Dy/2)-0.5;% first automatic grid point at half the mesh Dy
940    maxiy=minix+par_civ.Dy*floor((par_civ.ImageHeight-1)/par_civ.Dy);
941    [GridX,GridY]=meshgrid(minix:par_civ.Dx:maxix,miniy:par_civ.Dy:maxiy);
942    par_civ.Grid(:,1)=reshape(GridX,[],1);
943    par_civ.Grid(:,2)=reshape(GridY,[],1);% increases with array index
944end
945nbvec=size(par_civ.Grid,1);
946
947%% prepare correlation and search boxes
948ibx2=floor(par_civ.CorrBoxSize(1)/2);
949iby2=floor(par_civ.CorrBoxSize(2)/2);
950isx2=floor(par_civ.SearchBoxSize(1)/2);
951isy2=floor(par_civ.SearchBoxSize(2)/2);
952shiftx=round(par_civ.SearchBoxShift(:,1));%use the input shift estimate, rounded to the next integer value
953shifty=-round(par_civ.SearchBoxShift(:,2));% sign minus because image j index increases when y decreases
954if numel(shiftx)==1% case of a unique shift for the whole field( civ1)
955    shiftx=shiftx*ones(nbvec,1);
956    shifty=shifty*ones(nbvec,1);
957end
958
959%% Array initialisation and default output  if par_civ.CorrSmooth=0 (just the grid calculated, no civ computation)
960xtable=round(par_civ.Grid(:,1)+0.5)-0.5;
961ytable=round(par_civ.ImageHeight-par_civ.Grid(:,2)+0.5)-0.5;% y index corresponding to the position in image coordiantes
962utable=shiftx;%zeros(nbvec,1);
963vtable=shifty;%zeros(nbvec,1);
964ctable=zeros(nbvec,1);
965F=zeros(nbvec,1);
966result_conv=[];
967errormsg='';
968
969%% prepare mask
970if isfield(par_civ,'Mask') && ~isempty(par_civ.Mask)
971    if strcmp(par_civ.Mask,'all')
972        return    % get the grid only, no civ calculation
973    elseif ischar(par_civ.Mask)
974        par_civ.Mask=imread(par_civ.Mask);% read the mask if not allready done
975    end
976end
977check_MinIma=isfield(par_civ,'MinIma');% test for image luminosity threshold
978check_MaxIma=isfield(par_civ,'MaxIma') && ~isempty(par_civ.MaxIma);
979
980par_civ.ImageA=sum(double(par_civ.ImageA),3);%sum over rgb component for color images
981par_civ.ImageB=sum(double(par_civ.ImageB),3);
982[npy_ima npx_ima]=size(par_civ.ImageA);
983if ~isequal(size(par_civ.ImageB),[npy_ima npx_ima])
984    errormsg='image pair with unequal size';
985    return
986end
987
988%% Apply mask
989% Convention for mask IDEAS TO IMPLEMENT ?
990% mask >200 : velocity calculated
991%  200 >=mask>150;velocity not calculated, interpolation allowed (bad spots)
992% 150>=mask >100: velocity not calculated, nor interpolated
993%  100>=mask> 20: velocity not calculated, impermeable (no flux through mask boundaries)
994%  20>=mask: velocity=0
995checkmask=0;
996MinA=min(min(par_civ.ImageA));
997%MinB=min(min(par_civ.ImageB));
998%check_undefined=false(size(par_civ.ImageA));
999if isfield(par_civ,'Mask') && ~isempty(par_civ.Mask)
1000    checkmask=1;
1001    if ~isequal(size(par_civ.Mask),[npy_ima npx_ima])
1002        errormsg='mask must be an image with the same size as the images';
1003        return
1004    end
1005    check_undefined=(par_civ.Mask<200 & par_civ.Mask>=20 );
1006    %     par_civ.ImageA(check_undefined)=0;% put image A to zero (i.e. the min image value) in the undefined  area
1007    %     par_civ.ImageB(check_undefined)=0;% put image B to zero (i.e. the min image value) in the undefined  area
1008end
1009
1010%% compute image correlations: MAINLOOP on velocity vectors
1011corrmax=0;
1012sum_square=1;% default
1013mesh=1;% default
1014CheckDeformation=isfield(par_civ,'CheckDeformation')&& par_civ.CheckDeformation==1;
1015if CheckDeformation
1016    mesh=0.25;%mesh in pixels for subpixel image interpolation (x 4 in each direction)
1017    par_civ.CorrSmooth=2;% use SUBPIX2DGAUSS (take into account more points near the max)
1018end
1019
1020if par_civ.CorrSmooth~=0 % par_civ.CorrSmooth=0 implies no civ computation (just input image and grid points given)
1021    for ivec=1:nbvec
1022        iref=round(par_civ.Grid(ivec,1)+0.5);% xindex on the image A for the middle of the correlation box
1023        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
1024        F(ivec)=0;
1025        subrange1_x=iref-ibx2:iref+ibx2;% x indices defining the first subimage
1026        subrange1_y=jref-iby2:jref+iby2;% y indices defining the first subimage
1027        subrange2_x=iref+shiftx(ivec)-isx2:iref+shiftx(ivec)+isx2;%x indices defining the second subimage
1028        subrange2_y=jref+shifty(ivec)-isy2:jref+shifty(ivec)+isy2;%y indices defining the second subimage
1029        image1_crop=MinA*ones(numel(subrange1_y),numel(subrange1_x));% default value=min of image A
1030        image2_crop=MinA*ones(numel(subrange2_y),numel(subrange2_x));% default value=min of image A
1031        check1_x=subrange1_x>=1 & subrange1_x<=par_civ.ImageWidth;% check which points in the subimage 1 are contained in the initial image 1
1032        check1_y=subrange1_y>=1 & subrange1_y<=par_civ.ImageHeight;
1033        check2_x=subrange2_x>=1 & subrange2_x<=par_civ.ImageWidth;% check which points in the subimage 2 are contained in the initial image 2
1034        check2_y=subrange2_y>=1 & subrange2_y<=par_civ.ImageHeight;
1035        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
1036        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
1037        if checkmask
1038            mask1_crop=ones(numel(subrange1_y),numel(subrange1_x));% default value=1 for mask
1039            mask2_crop=ones(numel(subrange2_y),numel(subrange2_x));% default value=1 for mask
1040            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
1041            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
1042            sizemask=sum(sum(mask1_crop))/(numel(subrange1_y)*numel(subrange1_x));%size of the masked part relative to the correlation sub-image
1043            if sizemask > 1/2% eliminate point if more than half of the correlation box is masked
1044                F(ivec)=3; %
1045                utable(ivec)=0;
1046                vtable(ivec)=0;
1047            else
1048                image1_crop=image1_crop.*~mask1_crop;% put to zero the masked pixels (mask1_crop='true'=1)
1049                image2_crop=image2_crop.*~mask2_crop;
1050                image1_mean=mean(mean(image1_crop))/(1-sizemask);
1051                image2_mean=mean(mean(image2_crop))/(1-sizemask);
1052            end
1053        else
1054            image1_mean=mean(mean(image1_crop));
1055            image2_mean=mean(mean(image2_crop));
1056        end
1057        %threshold on image minimum
1058        if F(ivec)~=3
1059            if check_MinIma && (image1_mean < par_civ.MinIma || image2_mean < par_civ.MinIma)
1060                F(ivec)=3;
1061                %threshold on image maximum
1062            elseif check_MaxIma && (image1_mean > par_civ.MaxIma || image2_mean > par_civ.MaxIma)
1063                F(ivec)=3;
1064            end
1065            if F(ivec)==3
1066                utable(ivec)=0;
1067                vtable(ivec)=0;
1068            else
1069                %mask
1070                if checkmask
1071                    image1_crop=(image1_crop-image1_mean).*~mask1_crop;%substract the mean, put to zero the masked parts
1072                    image2_crop=(image2_crop-image2_mean).*~mask2_crop;
1073                else
1074                    image1_crop=(image1_crop-image1_mean);
1075                    image2_crop=(image2_crop-image2_mean);
1076                end
1077                %deformation
1078                if CheckDeformation
1079                    xi=(1:mesh:size(image1_crop,2));
1080                    yi=(1:mesh:size(image1_crop,1))';
1081                    [XI,YI]=meshgrid(xi-ceil(size(image1_crop,2)/2),yi-ceil(size(image1_crop,1)/2));
1082                    XIant=XI-par_civ.DUDX(ivec)*XI+par_civ.DUDY(ivec)*YI+ceil(size(image1_crop,2)/2);
1083                    YIant=YI+par_civ.DVDX(ivec)*XI-par_civ.DVDY(ivec)*YI+ceil(size(image1_crop,1)/2);
1084                    image1_crop=interp2(image1_crop,XIant,YIant);
1085                    image1_crop(isnan(image1_crop))=0;
1086                    xi=(1:mesh:size(image2_crop,2));
1087                    yi=(1:mesh:size(image2_crop,1))';
1088                    image2_crop=interp2(image2_crop,xi,yi,'*spline');
1089                    image2_crop(isnan(image2_crop))=0;
1090                end
1091                sum_square=sum(sum(image1_crop.*image1_crop));
1092                %reference: Oliver Pust, PIV: Direct Cross-Correlation
1093                result_conv= conv2(image2_crop,flipdim(flipdim(image1_crop,2),1),'valid');
1094                corrmax= max(max(result_conv));
1095                result_conv=(result_conv/corrmax)*255; %normalize, peak=always 255
1096                %Find the correlation max, at 255
1097                [y,x] = find(result_conv==255,1);
1098                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
1099                sum_square=sum_square*sum(sum(subimage2_crop.*subimage2_crop));% product of variances of image 1 and 2
1100                sum_square=sqrt(sum_square);% srt of the variance product to normalise correlation
1101                if ~isempty(y) && ~isempty(x)
1102                    try
1103                        if par_civ.CorrSmooth==1
1104                            [vector,F(ivec)] = SUBPIXGAUSS (result_conv,x,y);
1105                        elseif par_civ.CorrSmooth==2
1106                            [vector,F(ivec)] = SUBPIX2DGAUSS (result_conv,x,y);
1107                        else
1108                            [vector,F(ivec)] = quadr_fit(result_conv,x,y);
1109                        end
1110                        utable(ivec)=vector(1)*mesh+shiftx(ivec);
1111                        vtable(ivec)=vector(2)*mesh+shifty(ivec);
1112                        xtable(ivec)=iref+utable(ivec)/2-0.5;% convec flow (velocity taken at the point middle from imgae 1 and 2)
1113                        ytable(ivec)=jref+vtable(ivec)/2-0.5;% and position of pixel 1=0.5 (convention for image coordinates=0 at the edge)
1114                        iref=round(xtable(ivec)+0.5);% nearest image index for the middle of the vector
1115                        jref=round(ytable(ivec)+0.5);
1116                        % eliminate vectors located in the mask
1117                        if  checkmask && (iref<1 || jref<1 ||iref>npx_ima || jref>npy_ima ||( par_civ.Mask(jref,iref)<200 && par_civ.Mask(jref,iref)>=100))
1118                            utable(ivec)=0;
1119                            vtable(ivec)=0;
1120                            F(ivec)=3;
1121                        end
1122                        ctable(ivec)=corrmax/sum_square;% correlation value
1123                    catch ME
1124                        F(ivec)=3;
1125                        disp(ME.message)
1126                    end
1127                else
1128                    F(ivec)=3;
1129                end
1130            end
1131        end
1132    end
1133end
1134result_conv=result_conv*corrmax/(255*sum_square);% keep the last correlation matrix for output
1135
1136%------------------------------------------------------------------------
1137% --- Find the maximum of the correlation function after interpolation
1138% OUPUT:
1139% vector = optimum displacement vector with subpixel correction
1140% F =flag: =0 OK
1141%           =-2 , warning: max too close to the edge of the search box (1 pixel margin)
1142% INPUT:
1143% x,y: position of the maximum correlation at integer values
1144
1145function [vector,F] = SUBPIXGAUSS (result_conv,x,y)
1146%------------------------------------------------------------------------
1147% vector=[0 0]; %default
1148F=0;
1149[npy,npx]=size(result_conv);
1150result_conv(result_conv<1)=1; %set to 1 correlation values smaller than 1  (=0 by discretisation, to avoid divergence in the log)
1151%the following 8 lines are copyright (c) 1998, Uri Shavit, Roi Gurka, Alex Liberzon, Technion ??? Israel Institute of Technology
1152%http://urapiv.wordpress.com
1153peaky = y;
1154if y < npy && y > 1
1155    f0 = log(result_conv(y,x));
1156    f1 = log(result_conv(y-1,x));
1157    f2 = log(result_conv(y+1,x));
1158    peaky = peaky+ (f1-f2)/(2*f1-4*f0+2*f2);
1159else
1160    F=-2; % warning flag for vector truncated by the limited search box
1161end
1162peakx=x;
1163if x < npx-1 && x > 1
1164    f0 = log(result_conv(y,x));
1165    f1 = log(result_conv(y,x-1));
1166    f2 = log(result_conv(y,x+1));
1167    peakx = peakx+ (f1-f2)/(2*f1-4*f0+2*f2);
1168else
1169    F=-2; % warning flag for vector truncated by the limited search box
1170end
1171vector=[peakx-floor(npx/2)-1 peaky-floor(npy/2)-1];
1172
1173%------------------------------------------------------------------------
1174% --- Find the maximum of the correlation function after interpolation
1175function [vector,F] = SUBPIX2DGAUSS (result_conv,x,y)
1176%------------------------------------------------------------------------
1177% vector=[0 0]; %default
1178F=-2;
1179peaky=y;
1180peakx=x;
1181result_conv(result_conv<1)=1; %set to 1 correlation values smaller than 1 (to avoid divergence in the log)
1182[npy,npx]=size(result_conv);
1183if (x < npx) && (y < npy) && (x > 1) && (y > 1)
1184    F=0;
1185    for i=-1:1
1186        for j=-1:1
1187            %following 15 lines based on
1188            %H. Nobach ??? M. Honkanen (2005)
1189            %Two-dimensional Gaussian regression for sub-pixel displacement
1190            %estimation in particle image velocimetry or particle position
1191            %estimation in particle tracking velocimetry
1192            %Experiments in Fluids (2005) 38: 511???515
1193            c10(j+2,i+2)=i*log(result_conv(y+j, x+i));
1194            c01(j+2,i+2)=j*log(result_conv(y+j, x+i));
1195            c11(j+2,i+2)=i*j*log(result_conv(y+j, x+i));
1196            c20(j+2,i+2)=(3*i^2-2)*log(result_conv(y+j, x+i));
1197            c02(j+2,i+2)=(3*j^2-2)*log(result_conv(y+j, x+i));
1198        end
1199    end
1200    c10=(1/6)*sum(sum(c10));
1201    c01=(1/6)*sum(sum(c01));
1202    c11=(1/4)*sum(sum(c11));
1203    c20=(1/6)*sum(sum(c20));
1204    c02=(1/6)*sum(sum(c02));
1205    deltax=(c11*c01-2*c10*c02)/(4*c20*c02-c11^2);
1206    deltay=(c11*c10-2*c01*c20)/(4*c20*c02-c11^2);
1207    if abs(deltax)<1
1208        peakx=x+deltax;
1209    end
1210    if abs(deltay)<1
1211        peaky=y+deltay;
1212    end
1213end
1214vector=[peakx-floor(npx/2)-1 peaky-floor(npy/2)-1];
1215
1216%------------------------------------------------------------------------
1217% --- Find the maximum of the correlation function after quadratic interpolation
1218function [vector,F] = quadr_fit(result_conv,x,y)
1219[npy,npx]=size(result_conv);
1220if x<4 || y<4 || npx-x<4 ||npy-y <4
1221    F=-2;
1222    vector=[x y];
1223else
1224    F=0;
1225    x_ind=x-4:x+4;
1226    y_ind=y-4:y+4;
1227    x_vec=0.25*(x_ind-x);
1228    y_vec=0.25*(y_ind-y);
1229    [X,Y]=meshgrid(x_vec,y_vec);
1230    coord=[reshape(X,[],1) reshape(Y,[],1)];
1231    result_conv=reshape(result_conv(y_ind,x_ind),[],1);
1232   
1233   
1234    % n=numel(X);
1235    % x=[X Y];
1236    % X=X-0.5;
1237    % Y=Y+0.5;
1238    % y = (X.*X+2*Y.*Y+X.*Y+6) + 0.1*rand(n,1);
1239    p = polyfitn(coord,result_conv,2);
1240    A(1,1)=2*p.Coefficients(1);
1241    A(1,2)=p.Coefficients(2);
1242    A(2,1)=p.Coefficients(2);
1243    A(2,2)=2*p.Coefficients(4);
1244    vector=[x y]'-A\[p.Coefficients(3) p.Coefficients(5)]';
1245    vector=vector'-[floor(npx/2) floor(npy/2)]-1 ;
1246    % zg = polyvaln(p,coord);
1247    % figure
1248    % surf(x_vec,y_vec,reshape(zg,9,9))
1249    % hold on
1250    % plot3(X,Y,reshape(result_conv,9,9),'o')
1251    % hold off
1252end
1253
1254%'RUN_FIX': function for fixing velocity fields:
1255%-----------------------------------------------
1256% RUN_FIX(filename,field,flagindex,thresh_vecC,thresh_vel,iter,flag_mask,maskname,fileref,fieldref)
1257%
1258%filename: name of the netcdf file (used as input and output)
1259%field: structure specifying the names of the fields to fix (depending on civ1 or civ2)
1260%.vel_type='civ1' or 'civ2';
1261%.nb=name of the dimension common to the field to fix ('nb_vectors' for civ1);
1262%.fixflag=name of fix flag variable ('vec_FixFlag' for civ1)
1263%flagindex: flag specifying which values of vec_f are removed:
1264% if flagindex(1)=1: vec_f=-2 vectors are removed
1265% if flagindex(2)=1: vec_f=3 vectors are removed
1266% if flagindex(3)=1: vec_f=2 vectors are removed (if iter=1) or vec_f=4 vectors are removed (if iter=2)
1267%iter=1 for civ1 fields and iter=2 for civ2 fields
1268%thresh_vecC: threshold in the image correlation vec_C
1269%flag_mask: =1 mask used to remove vectors (0 else)
1270%maskname: name of the mask image file for fix
1271%thresh_vel: threshold on velocity, or on the difference with the reference file fileref if exists
1272%inf_sup=1: remove values smaller than threshold thresh_vel, =2, larger than threshold
1273%fileref: .nc file name for a reference velocity (='': refrence 0 used)
1274%fieldref: 'civ1','filter1'...feld used in fileref
1275
1276function FF=fix(Param,F,C,U,V,X,Y)
1277FF=zeros(size(F));%default
1278
1279%criterium on warn flags
1280FlagName={'CheckFmin2','CheckF2','CheckF3','CheckF4'};
1281FlagVal=[-2 2 3 4];
1282for iflag=1:numel(FlagName)
1283    if isfield(Param,FlagName{iflag}) && Param.(FlagName{iflag})
1284        FF=(FF==1| F==FlagVal(iflag));
1285    end
1286end
1287%criterium on correlation values
1288if isfield (Param,'MinCorr')
1289    FF=FF==1 | C<Param.MinCorr;
1290end
1291if (isfield(Param,'MinVel')&&~isempty(Param.MinVel))||(isfield (Param,'MaxVel')&&~isempty(Param.MaxVel))
1292    Umod= U.*U+V.*V;
1293    if isfield (Param,'MinVel')&&~isempty(Param.MinVel)
1294        FF=FF==1 | Umod<(Param.MinVel*Param.MinVel);
1295    end
1296    if isfield (Param,'MaxVel')&&~isempty(Param.MaxVel)
1297        FF=FF==1 | Umod>(Param.MaxVel*Param.MaxVel);
1298    end
1299end
1300
1301
1302%------------------------------------------------------------------------
1303% --- determine the list of index pairs of processing file
1304function [i1_series,i2_series,j1_series,j2_series,check_bounds,NomTypeNc]=...
1305    find_pair_indices(str_civ,i_series,j_series,MinIndex_i,MaxIndex_i,MinIndex_j,MaxIndex_j)
1306%------------------------------------------------------------------------
1307i1_series=i_series;% set of first image indexes
1308i2_series=i_series;
1309j1_series=j_series;%ones(size(i_series));% set of first image numbers
1310j2_series=j_series;%ones(size(i_series));
1311r=regexp(str_civ,'^\D(?<ind>[i|j])=( -| )(?<num1>\d+)\|(?<num2>\d+)','names');
1312if ~isempty(r)
1313    mode=['D' r.ind];
1314    ind1=str2num(r.num1);
1315    ind2=str2num(r.num2);
1316else
1317    mode='j1-j2';
1318    r=regexp(str_civ,'^j= (?<num1>[a-z])-(?<num2>[a-z])','names');
1319    if ~isempty(r)
1320        NomTypeNc='_1ab';
1321    else
1322        r=regexp(str_civ,'^j= (?<num1>[A-Z])-(?<num2>[A-Z])','names');
1323        if ~isempty(r)
1324            NomTypeNc='_1AB';
1325        else
1326            r=regexp(str_civ,'^j= (?<num1>\d+)-(?<num2>\d+)','names');
1327            if ~isempty(r)
1328                NomTypeNc='_1_1-2';
1329            end
1330        end
1331    end
1332    if isempty(r)
1333        display('wrong pair mode input option')
1334    else
1335        ind1=stra2num(r.num1);
1336        ind2=stra2num(r.num2);
1337    end
1338end
1339switch mode
1340    case 'Di'
1341        i1_series=i_series-ind1;% set of first image numbers
1342        i2_series=i_series+ind2;
1343        check_bounds=i1_series<MinIndex_i | i2_series>MaxIndex_i;
1344        if isempty(j_series)
1345            NomTypeNc='_1-2';
1346        else
1347            j1_series=j_series;
1348            j2_series=j_series;
1349            NomTypeNc='_1-2_1';
1350        end
1351    case 'Dj'
1352        j1_series=j_series-ind1;
1353        j2_series=j_series+ind2;
1354        check_bounds=j1_series<MinIndex_j | j2_series>MaxIndex_j;
1355        NomTypeNc='_1_1-2';
1356    otherwise %bursts
1357        i1_series=i_series(1,:);% do not sweep the j index
1358        i2_series=i_series(1,:);
1359        j1_series=ind1*ones(1,size(i_series,2));% j index is fixed by pair choice
1360        j2_series=ind2*ones(1,size(i_series,2));
1361        check_bounds=zeros(size(i1_series));% no limitations due to min-max indices
1362end
1363
1364
1365
1366
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