source: trunk/src/series/civ_series.m @ 1128

Last change on this file since 1128 was 1127, checked in by g7moreau, 5 months ago

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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 2008-2024, LEGI UMR 5519 / CNRS UGA G-INP, Grenoble, France
32%   http://www.legi.grenoble-inp.fr
33%   Joel.Sommeria - Joel.Sommeria (A) univ-grenoble-alpes.fr
34%
35%     This file is part of the toolbox UVMAT.
36%
37%     UVMAT is free software; you can redistribute it and/or modify
38%     it under the terms of the GNU General Public License as published
39%     by the Free Software Foundation; either version 2 of the license,
40%     or (at your option) any later version.
41%
42%     UVMAT is distributed in the hope that it will be useful,
43%     but WITHOUT ANY WARRANTY; without even the implied warranty of
44%     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
45%     GNU General Public License (see LICENSE.txt) for more details.
46%=======================================================================
47
48function [Data,errormsg,result_conv]= civ_series(Param)
49errormsg='';
50
51%% set the input elements needed on the GUI series when the action is selected in the menu ActionName or InputTable refreshed
52if isstruct(Param) && isequal(Param.Action.RUN,0)% function activated from the GUI series but not RUN
53    path_series=fileparts(which('series'));
54    addpath(fullfile(path_series,'series'))
55    Data=civ_input(Param);% introduce the civ parameters using the GUI civ_input
56    %Data=civ_input_App(Param);% introduce the civ parameters using the GUI civ_input
57    if isempty(Data)
58        Data=Param;% if  civ_input has been cancelled, keep previous parameters
59    end
60    Data.Program=mfilename;%gives the name of the current function
61    Data.AllowInputSort='off';% allow alphabetic sorting of the list of input file SubDir (options 'off'/'on', 'off' by default)
62    Data.WholeIndexRange='off';% prescribes the file index ranges from min to max (options 'off'/'on', 'off' by default)
63    Data.NbSlice='off'; %nbre of slices ('off' by default)
64    Data.VelType='off';% menu for selecting the velocity type (options 'off'/'one'/'two',  'off' by default)
65    Data.FieldName='on';% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default)
66    Data.FieldTransform = 'off';%can use a transform function
67    Data.ProjObject='off';%can use projection object(option 'off'/'on',
68    Data.Mask='off';%can use mask option   (option 'off'/'on', 'off' by default)
69    Data.OutputDirExt='.civ';%set the output dir extension
70    Data.OutputSubDirMode='last'; %select the last subDir in the input table as root of the output subdir name (option 'all'/'first'/'last', 'all' by default)
71    Data.OutputFileMode='NbInput_i';% one output file expected per value of i index (used for waitbar)
72    Data.CheckOverwriteVisible='on'; % manage the overwrite of existing files (default=1)
73    if isfield(Data,'ActionInput') && isfield(Data.ActionInput,'PairIndices') && strcmp(Data.ActionInput.PairIndices.ListPairMode,'pair j1-j2')
74        if isfield(Data.ActionInput.PairIndices,'ListPairCiv2')
75            str_civ=Data.ActionInput.PairIndices.ListPairCiv2;
76        else
77            str_civ=Data.ActionInput.PairIndices.ListPairCiv1;
78        end
79        r=regexp(str_civ,'^j= (?<num1>[a-z])-(?<num2>[a-z])','names');
80        if isempty(r)
81            r=regexp(str_civ,'^j= (?<num1>[A-Z])-(?<num2>[A-Z])','names');
82            if isempty(r)
83                r=regexp(str_civ,'^j= (?<num1>\d+)-(?<num2>\d+)','names');
84            end
85        end
86        if ~isempty(r)
87            Data.j_index_1=stra2num(r.num1);
88            Data.j_index_2=stra2num(r.num2);
89        end
90    end
91    return
92end
93
94%% read input parameters from an xml file if input is a file name (batch mode)
95checkrun=1;
96if ischar(Param)
97    Param=xml2struct(Param);% read Param as input file (batch case)
98    checkrun=0;
99end
100
101%% test input
102if ~isfield(Param,'ActionInput')
103    disp_uvmat('ERROR','no parameter set for PIV',checkrun)
104    return
105end
106iview_A=0;%default values
107NbField=1;
108RUNHandle=[];
109CheckInputFile=isfield(Param,'InputTable');%= 1 in test use for TestCiv (no nc file involved)
110CheckOutputFile=isfield(Param,'OutputSubDir');%= 1 in test use for TestPatch (no nc file produced)
111
112%% input files and indexing (skipped in Test mode)
113if CheckInputFile
114    hseries=findobj(allchild(0),'Tag','series');
115    RUNHandle=findobj(hseries,'Tag','RUN');%handle of RUN button in GUI series
116    WaitbarHandle=findobj(hseries,'Tag','Waitbar');%handle of waitbar in GUI series
117    MaxIndex_i=Param.IndexRange.MaxIndex_i;
118    MinIndex_i=Param.IndexRange.MinIndex_i;
119    MaxIndex_j=ones(size(MaxIndex_i));MinIndex_j=ones(size(MinIndex_i));
120    if isfield(Param.IndexRange,'MaxIndex_j')&& isfield(Param.IndexRange,'MinIndex_j')
121        MaxIndex_j=Param.IndexRange.MaxIndex_j;
122        MinIndex_j=Param.IndexRange.MinIndex_j;
123    end
124    if isfield(Param,'InputTable')
125        [tild,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param);
126        iview_A=0;% series index (iview) for the first image series
127        iview_B=0;% series index (iview) for the second image series (only non zero for option 'shift' comparing two image series )
128        if Param.ActionInput.CheckCiv1
129            iview_A=1;% usual PIV, the image series is on the first line of the table
130        elseif Param.ActionInput.CheckCiv2 % civ2 is performed without Civ1, a netcdf file series is needed in the first table line
131            iview_A=2;% the second line is used for the input images of Civ2
132        end
133%         if strcmp(Param.ActionInput.ListCompareMode,'shift')
134%             iview_B=iview_A+1; % the second image series is on the next line of the input table
135%         end
136        if iview_A~=0
137            RootPath_A=Param.InputTable{iview_A,1};
138            RootFile_A=Param.InputTable{iview_A,3};
139            SubDir_A=Param.InputTable{iview_A,2};
140            NomType_A=Param.InputTable{iview_A,4};
141            FileExt_A=Param.InputTable{iview_A,5};
142            if iview_B==0
143                iview_B=iview_A;% the second image series is the same as the first
144            end
145            RootPath_B=Param.InputTable{iview_B,1};
146            RootFile_B=Param.InputTable{iview_B,3};
147            SubDir_B=Param.InputTable{iview_B,2};
148            NomType_B=Param.InputTable{iview_B,4};
149            FileExt_B=Param.InputTable{iview_B,5};
150        end
151       
152        PairCiv2='';
153        switch Param.ActionInput.ListCompareMode
154            case 'PIV'
155                PairCiv1=Param.ActionInput.PairIndices.ListPairCiv1;
156                if isfield(Param.ActionInput.PairIndices,'ListPairCiv2')
157                    PairCiv2=Param.ActionInput.PairIndices.ListPairCiv2;%string which determines the civ2 pair
158                end
159                if iview_A==1% if Civ1 is performed
160                    [i1_series_Civ1,i2_series_Civ1,j1_series_Civ1,j2_series_Civ1,check_bounds,NomTypeNc]=...
161                        find_pair_indices(PairCiv1,i1_series{1},j1_series{1},MinIndex_i,MaxIndex_i,MinIndex_j,MaxIndex_j);
162                    if ~isempty(PairCiv2)
163                        [i1_series_Civ2,i2_series_Civ2,j1_series_Civ2,j2_series_Civ2,check_bounds_Civ2]=...
164                            find_pair_indices(PairCiv2,i1_series{1},j1_series{1},MinIndex_i(1),MaxIndex_i(1),MinIndex_j(1),MaxIndex_j(1));
165                        check_bounds=check_bounds | check_bounds_Civ2;
166                    end
167                else% we start from an existing Civ1 file
168                    i1_series_Civ1=i1_series{1};
169                    i2_series_Civ1=i2_series{1};
170                    j1_series_Civ1=j1_series{1};
171                    j2_series_Civ1=j2_series{1};
172                    NomTypeNc=Param.InputTable{1,4};
173                    if ~isempty(PairCiv2)
174                        [i1_series_Civ2,i2_series_Civ2,j1_series_Civ2,j2_series_Civ2,check_bounds,NomTypeNc]=...
175                            find_pair_indices(PairCiv2,i1_series{2},j1_series{2},MinIndex_i(2),MaxIndex_i(2),MinIndex_j(2),MaxIndex_j(2));
176                    end
177                end
178            case 'displacement'
179                if isfield(Param.ActionInput,'OriginIndex')
180                i1_series_Civ1=Param.ActionInput.OriginIndex*ones(size(i1_series{1}));
181                else
182                    i1_series_Civ1=ones(size(i1_series{1}));
183                end
184                i1_series_Civ2=i1_series_Civ1;
185                i2_series_Civ1=i1_series{1};
186                i2_series_Civ2=i1_series{1};
187                j1_series_Civ1=[];% no j index variation for the ref image
188                j1_series_Civ2=[];
189                if isempty(j1_series{1})
190                    j2_series_Civ1=ones(size(i1_series_Civ1));
191                else
192                    j2_series_Civ1=j1_series{1};% if j index exist 
193                end
194                j2_series_Civ2=j2_series_Civ1;
195                NomTypeNc='_1';
196            case 'PIV volume'
197                % TODO, TODO
198        end
199        %determine frame indices for input with movie or other multiframe input file
200        if isempty(j1_series_Civ1)% simple movie with index i
201            FrameIndex_A_Civ1=i1_series_Civ1;
202            FrameIndex_B_Civ1=i2_series_Civ1;
203            j1_series_Civ1=ones(size(i1_series_Civ1));
204            if strcmp(Param.ActionInput.ListCompareMode,'PIV')
205            j2_series_Civ1=ones(size(i1_series_Civ1));
206            end
207        else % movie for each burst or volume (index j)
208            FrameIndex_A_Civ1=j1_series_Civ1;
209            FrameIndex_B_Civ1=j2_series_Civ1;
210        end
211        if isempty(PairCiv2)
212            FrameIndex_A_Civ2=FrameIndex_A_Civ1;
213            FrameIndex_B_Civ2=FrameIndex_B_Civ1;
214        else
215            if isempty(j1_series_Civ2)
216                FrameIndex_A_Civ2=i1_series_Civ2;
217                FrameIndex_B_Civ2=i2_series_Civ2;
218                j1_series_Civ2=ones(size(i1_series_Civ2));
219                if strcmp(Param.ActionInput.ListCompareMode,'PIV')
220                j2_series_Civ2=ones(size(i1_series_Civ2));
221                end
222            else
223                FrameIndex_A_Civ2=j1_series_Civ2;
224                FrameIndex_B_Civ2=j2_series_Civ2;
225            end
226        end
227        if isempty(i1_series_Civ1)||(~isempty(PairCiv2) && isempty(i1_series_Civ2))
228            disp_uvmat('ERROR','no image pair for civ in the input file index range',checkrun)
229            return
230        end
231    end
232   
233    %% check the first image pair
234        if Param.ActionInput.CheckCiv1% Civ1 is performed
235            NbField=numel(i1_series_Civ1);
236        elseif Param.ActionInput.CheckCiv2 % Civ2 is performed without Civ1
237            NbField=numel(i1_series_Civ2);
238        else
239            NbField=numel(i1_series_Civ1);% no image used (only fix or patch) TO CHECK
240        end
241
242    %% Output directory
243    OutputDir='';
244    if CheckOutputFile
245        OutputDir=[Param.OutputSubDir Param.OutputDirExt];
246    end
247end
248
249%% prepare output Data
250ListGlobalAttribute={'Conventions','Program','CivStage'};
251Data.Conventions='uvmat/civdata';% states the conventions used for the description of field variables and attributes
252Data.Program='civ_series';
253Data.CivStage=0;%default
254check_civx=0;%default
255
256%% get timing from the ImaDoc file or input video
257if iview_A~=0
258    XmlFileName=find_imadoc(RootPath_A,SubDir_A,RootFile_A,FileExt_A);
259    Time=[];
260    if ~isempty(XmlFileName)
261        XmlData=imadoc2struct(XmlFileName);
262        if isfield(XmlData,'Time')
263            Time=XmlData.Time;
264        end
265        if isfield(XmlData,'Camera')
266            if isfield(XmlData.Camera,'NbSlice')&& ~isempty(XmlData.Camera.NbSlice)
267                NbSlice_calib{iview}=XmlData.Camera.NbSlice;% Nbre of slices for Zindex in phys transform
268                if ~isequal(NbSlice_calib{iview},NbSlice_calib{1})
269                    msgbox_uvmat('WARNING','inconsistent number of Z indices for the two field series');
270                end
271            end
272            if isfield(XmlData.Camera,'TimeUnit')&& ~isempty(XmlData.Camera.TimeUnit)
273                TimeUnit=XmlData.Camera.TimeUnit;
274            end
275        end
276    end
277end
278
279%%%%% MAIN LOOP %%%%%%
280maskoldname='';% initiate the mask name
281FileType_A='';
282FileType_B='';
283CheckOverwrite=1;%default
284if isfield(Param,'CheckOverwrite')
285    CheckOverwrite=Param.CheckOverwrite;
286end
287for ifield=1:NbField
288    tic
289    if ~isempty(RUNHandle)% update the waitbar in interactive mode with GUI series  (checkrun=1)
290        update_waitbar(WaitbarHandle,ifield/NbField)
291        if  checkrun && ~strcmp(get(RUNHandle,'BusyAction'),'queue')
292            disp('program stopped by user')
293            break
294        end
295    end
296    if CheckInputFile
297        OutputPath=fullfile(Param.OutputPath,num2str(Param.Experiment),num2str(Param.Device));
298        if iview_A==0 % no nc file has been entered
299            ncfile=fullfile_uvmat(OutputPath,Param.InputTable{1,2},Param.InputTable{1,3},Param.InputTable{1,5},...
300                NomTypeNc,i1_series_Civ1(ifield),i2_series_Civ1(ifield),j1_series_Civ1(ifield),j2_series_Civ1(ifield));
301        else% an existing nc file has been entered
302            if iview_A==1% if Civ1 is performed
303                Civ1Dir=OutputDir;
304            else
305                Civ1Dir=Param.InputTable{1,2};
306            end
307            if strcmp(Param.ActionInput.ListCompareMode,'PIV')
308                ncfile=fullfile_uvmat(OutputPath,Civ1Dir,RootFile_A,'.nc',NomTypeNc,i1_series_Civ1(ifield),i2_series_Civ1(ifield),...
309                    j1_series_Civ1(ifield),j2_series_Civ1(ifield));
310            else
311                ncfile=fullfile_uvmat(OutputPath,Civ1Dir,RootFile_A,'.nc',NomTypeNc,i2_series_Civ1(ifield),[],...
312                    j1_series_Civ1(ifield),j2_series_Civ1(ifield));
313            end
314        end
315        ncfile_out=ncfile;% by default
316       
317        if isfield (Param.ActionInput,'Civ2')
318            i1_civ2=i1_series_Civ2(ifield);
319            i2_civ2=i1_civ2;
320            if ~isempty(i2_series_Civ2)
321                i2_civ2=i2_series_Civ2(ifield);
322            end
323            j1_civ2=1;
324            if ~isempty(j1_series_Civ2)
325                j1_civ2=j1_series_Civ2(ifield);
326            end
327            j2_civ2=i1_civ2;
328            if ~isempty(j2_series_Civ2)
329                j2_civ2=j2_series_Civ2(ifield);
330            end
331            if strcmp(Param.ActionInput.ListCompareMode,'PIV')
332                ncfile_out=fullfile_uvmat(OutputPath,OutputDir,RootFile_A,'.nc',NomTypeNc,i1_civ2,i2_civ2,j1_civ2,j2_civ2);
333%                 ncfile_out=fullfile_uvmat(RootPath_A,OutputDir,RootFile_A,'.nc',NomTypeNc,i1_civ2,i2_civ2,j1_civ2,j2_civ2);
334            else % displacement
335                ncfile_out=fullfile_uvmat(OutputPath,OutputDir,RootFile_A,'.nc',NomTypeNc,i2_civ2,[],j2_civ2);
336            end
337        end
338        if ~CheckOverwrite && exist(ncfile_out,'file')
339            disp(['existing output file ' ncfile_out ' already exists, skip to next field'])
340            continue% skip iteration if the mode overwrite is desactivated and the result file already exists
341        end
342    end
343    ImageName_A='';ImageName_B='';%default
344    VideoObject_A=[];VideoObject_B=[];
345    %% Civ1
346    % if Civ1 computation is requested
347    if isfield (Param.ActionInput,'Civ1')
348        if CheckInputFile
349            disp('civ1 started')
350        end
351        par_civ1=Param.ActionInput.Civ1;% parameters for civ1
352        if CheckInputFile % read input images (except in mode Test where it is introduced directly in Param.ActionInput.Civ1.ImageNameA and B)
353            try
354                if strcmp(Param.ActionInput.ListCompareMode,'displacement')
355                    ImageName_A=Param.ActionInput.RefFile;
356                else
357                ImageName_A=fullfile_uvmat(RootPath_A,SubDir_A,RootFile_A,FileExt_A,NomType_A,i1_series_Civ1(ifield),[],j1_series_Civ1(ifield));
358                end
359                if strcmp(FileExt_A,'.nc')% case of input images in format netcdf
360                    FieldName_A=Param.InputFields.FieldName;
361                    [DataIn,tild,tild,errormsg]=nc2struct(ImageName_A,{FieldName_A});
362                    par_civ1.ImageA=DataIn.(FieldName_A);
363                else % usual image formats for image A
364                    if isempty(FileType_A)% open the image object if not already done in case of movie input
365                        [FileInfo_A,VideoObject_A]=get_file_info(ImageName_A);
366                        FileType_A=FileInfo_A.FileType;
367                        if isempty(Time) && ~isempty(find(strcmp(FileType_A,{'mmreader','video','cine_phantom'})))% case of video input
368                            Time=zeros(FileInfo_A.NumberOfFrames+1,2);
369                            Time(:,2)=(0:1/FileInfo_A.FrameRate:(FileInfo_A.NumberOfFrames)/FileInfo_A.FrameRate)';
370                        end
371                        if ~isempty(FileType_A) && isempty(Time)% Time = index i +0.001 index j by default
372                            MaxIndex_i=max(i2_series_Civ1);
373                            MaxIndex_j=max(j2_series_Civ1);
374                            Time=(1:MaxIndex_i)'*ones(1,MaxIndex_j);
375                            Time=Time+0.001*ones(MaxIndex_i,1)*(1:MaxIndex_j);
376                            Time=[zeros(1,MaxIndex_j);Time];% insert a first line of zeros
377                            Time=[zeros(MaxIndex_i+1,1) Time];% insert a first column of zeros
378                        end
379                    end
380                    if isempty(regexp(ImageName_A,'(^http://)|(^https://)')) && ~exist(ImageName_A,'file')
381                        disp([ImageName_A ' missing'])
382                        continue
383                    end
384                    [par_civ1.ImageA,VideoObject_A] = read_image(ImageName_A,FileType_A,VideoObject_A,FrameIndex_A_Civ1(ifield));
385                end
386                ImageName_B=fullfile_uvmat(RootPath_B,SubDir_B,RootFile_B,FileExt_B,NomType_B,i2_series_Civ1(ifield),[],j2_series_Civ1(ifield));
387                if strcmp(FileExt_B,'.nc') % case of input images in format netcdf
388                    FieldName_B=Param.InputFields.FieldName;
389                    [DataIn,tild,tild,errormsg]=nc2struct(ImageName_B,{FieldName_B});
390                    par_civ1.ImageB=DataIn.(FieldName_B);
391                else % usual image formats for image B
392                    if isempty(FileType_B)
393                        [FileInfo_B,VideoObject_B]=get_file_info(ImageName_B);
394                        FileType_B=FileInfo_B.FileType;
395                    end
396                    if isempty(regexp(ImageName_B,'(^http://)|(^https://)')) && ~exist(ImageName_B,'file')
397                        disp([ImageName_B ' missing'])
398                        continue
399                    end
400                    [par_civ1.ImageB,VideoObject_B] = read_image(ImageName_B,FileType_B,VideoObject_B,FrameIndex_B_Civ1(ifield));
401                end
402            catch ME % display errors in reading input images
403                if ~isempty(ME.message)
404                    disp_uvmat('ERROR', ['error reading input image: ' ME.message],checkrun)
405                    continue
406                end
407            end
408            par_civ1.ImageWidth=size(par_civ1.ImageA,2);
409            par_civ1.ImageHeight=size(par_civ1.ImageA,1);
410            list_param=(fieldnames(Param.ActionInput.Civ1))';
411            list_param(strcmp('TestCiv1',list_param))=[];% remove the parameter TestCiv1 from the list
412            Civ1_param=regexprep(list_param,'^.+','Civ1_$0');% insert 'Civ1_' before  each string in list_param
413            Civ1_param=[{'Civ1_ImageA','Civ1_ImageB','Civ1_Time','Civ1_Dt'} Civ1_param]; %insert the names of the two input images
414            %indicate the values of all the global attributes in the output data
415            Data.Civ1_ImageA=ImageName_A;
416            Data.Civ1_ImageB=ImageName_B;
417            i1=i1_series_Civ1(ifield);
418            i2=i1;
419            if ~isempty(i2_series_Civ1)
420                i2=i2_series_Civ1(ifield);
421            end
422            j1=1;
423            if ~isempty(j1_series_Civ1)
424                j1=j1_series_Civ1(ifield);
425            end
426            j2=j1;
427            if ~isempty(j2_series_Civ1)
428                j2=j2_series_Civ1(ifield);
429            end
430            if strcmp(Param.ActionInput.ListCompareMode,'displacement')
431                Data.Civ1_Time=Time(i2+1,j2+1);% the Time is the Time of the secodn image
432                Data.Civ1_Dt=1;% Time interval is 1, to yield displacement instead of velocity=displacement/Dt at reading
433            else
434                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
435                Data.Civ1_Dt=Time(i2+1,j2+1)-Time(i1+1,j1+1);
436            end
437            for ilist=1:length(list_param)
438                Data.(Civ1_param{4+ilist})=Param.ActionInput.Civ1.(list_param{ilist});
439            end
440            Data.ListGlobalAttribute=[ListGlobalAttribute Civ1_param];
441            Data.CivStage=1;
442        else
443            i1=Param.ActionInput.PairIndices.ref_i; %case of TESTmode
444        end
445        % set the list of variables
446        Data.ListVarName={'Civ1_X','Civ1_Y','Civ1_U','Civ1_V','Civ1_F','Civ1_C'};%  cell array containing the names of the fields to record
447        Data.VarDimName={'nb_vec_1','nb_vec_1','nb_vec_1','nb_vec_1','nb_vec_1','nb_vec_1'};
448        Data.VarAttribute{1}.Role='coord_x';
449        Data.VarAttribute{2}.Role='coord_y';
450        Data.VarAttribute{3}.Role='vector_x';
451        Data.VarAttribute{4}.Role='vector_y';
452        Data.VarAttribute{5}.Role='warnflag';
453        % case of mask
454        if par_civ1.CheckMask&&~isempty(par_civ1.Mask)
455            if isfield(par_civ1,'NbSlice')
456                [RootPath_mask,SubDir_mask,RootFile_mask,i1_mask,i2_mask,j1_mask,j2_mask,Ext_mask]=fileparts_uvmat(Param.ActionInput.Civ1.Mask);
457                i1_mask=mod(i1-1,par_civ1.NbSlice)+1;
458                maskname=fullfile_uvmat(RootPath_mask,SubDir_mask,RootFile_mask,Ext_mask,'_1',i1_mask);
459            else
460                maskname=Param.ActionInput.Civ1.Mask;
461            end
462            if strcmp(maskoldname,maskname)% mask exist, not already read in civ1
463                par_civ1.Mask=mask; %use mask already opened
464            else
465                if ~isempty(regexp(maskname,'(^http://)|(^https://)'))|| exist(maskname,'file')
466                    try
467                        par_civ1.Mask=imread(maskname);%update the mask, an store it for future use
468                    catch ME
469                        if ~isempty(ME.message)
470                            errormsg=['error reading input image: ' ME.message];
471                            disp_uvmat('ERROR',errormsg,checkrun)
472                            return
473                        end
474                    end
475                else
476                    par_civ1.Mask=[];
477                end
478                mask=par_civ1.Mask;
479                maskoldname=maskname;
480            end
481        end
482        if strcmp(Param.ActionInput.ListCompareMode, 'PIV volume')
483            Data.ListVarName=[Data.ListVarName 'Civ1_Z'];
484            Data.Civ1_X=[];Data.Civ1_Y=[];Data.Civ1_Z=[];
485            Data.Civ1_U=[];Data.Civ1_V=[];Data.Civ1_C=[];Data.Civ1_F=[];
486            for ivol=1:NbSlice
487                % caluclate velocity data (y and v in indices, reverse to y component)
488                [xtable, ytable, utable, vtable, ctable, F, result_conv, errormsg] = civ (par_civ1);
489                if ~isempty(errormsg)
490                    disp_uvmat('ERROR',errormsg,checkrun)
491                    return
492                end
493                Data.Civ1_X=[Data.Civ1_X reshape(xtable,[],1)];
494                Data.Civ1_Y=[Data.Civ1_Y reshape(Param.Civ1.ImageHeight-ytable+1,[],1)];
495                Data.Civ1_Z=[Data.Civ1_Z ivol*ones(numel(xtable),1)];% z=image index in image coordinates
496                Data.Civ1_U=[Data.Civ1_U reshape(utable,[],1)];
497                Data.Civ1_V=[Data.Civ1_V reshape(-vtable,[],1)];
498                Data.Civ1_C=[Data.Civ1_C reshape(ctable,[],1)];
499                Data.Civ1_F=[Data.Civ1_C reshape(F,[],1)];
500            end
501        else %usual PIV
502            % caluclate velocity data (y and v in indices, reverse to y component)
503            [xtable, ytable, utable, vtable, ctable, F, result_conv, errormsg] = civ (par_civ1);
504            if ~isempty(errormsg)
505                disp_uvmat('ERROR',errormsg,checkrun)
506                return
507            end
508            Data.Civ1_X=reshape(xtable,[],1);
509            Data.Civ1_Y=reshape(par_civ1.ImageHeight-ytable+1,[],1);
510            Data.Civ1_U=reshape(utable,[],1);
511            Data.Civ1_V=reshape(-vtable,[],1);
512            Data.Civ1_C=reshape(ctable,[],1);
513            Data.Civ1_F=reshape(F,[],1);
514        end
515    else% we use existing Civ1 data
516        if exist('ncfile','var')
517            CivFile=ncfile;
518            [Data,tild,tild,errormsg]=nc2struct(CivFile,'ListGlobalAttribute','absolut_time_T0'); %look for the constant 'absolut_time_T0' to detect old civx data format
519            if ~isempty(errormsg)
520                disp_uvmat('ERROR',errormsg,checkrun)
521                return
522            end
523            [Data,tild,tild,errormsg]=nc2struct(CivFile);%read civ1 and fix1 data in the existing netcdf file
524        elseif isfield(Param,'Civ1_X')
525            Data.ListGlobalAttribute={};
526            Data.ListVarName={};
527            Data.VarDimName={};
528            Data.Civ1_X=Param.Civ1_X;
529            Data.Civ1_Y=Param.Civ1_Y;
530            Data.Civ1_U=Param.Civ1_U;
531            Data.Civ1_V=Param.Civ1_V;
532            Data.Civ1_FF=Param.Civ1_FF;
533        end
534    end
535   
536    %% Fix1
537    if isfield (Param.ActionInput,'Fix1')
538        disp('fix1 started')
539        if ~isfield (Param.ActionInput,'Civ1')% if we use existing Civ1, remove previous data beyond Civ1
540            Fix1_attr=find(strcmp('Fix1',Data.ListGlobalAttribute));
541            Data.ListGlobalAttribute(Fix1_attr)=[];
542            for ilist=1:numel(Fix1_attr)
543                Data=rmfield(Data,Data.ListGlobalAttribute{Fix1_attr(ilist)});
544            end
545        end
546        list_param=fieldnames(Param.ActionInput.Fix1)';
547        Fix1_param=regexprep(list_param,'^.+','Fix1_$0');% insert 'Fix1_' before  each string in ListFixParam
548        %indicate the values of all the global attributes in the output data
549        for ilist=1:length(list_param)
550            Data.(Fix1_param{ilist})=Param.ActionInput.Fix1.(list_param{ilist});
551        end
552        Data.ListGlobalAttribute=[Data.ListGlobalAttribute Fix1_param];
553        Data.ListVarName=[Data.ListVarName {'Civ1_FF'}];
554        Data.VarDimName=[Data.VarDimName {'nb_vec_1'}];
555        nbvar=length(Data.ListVarName);
556        Data.VarAttribute{nbvar}.Role='errorflag';
557        Data.Civ1_FF=int8(fix(Param.ActionInput.Fix1,Data.Civ1_F,Data.Civ1_C,Data.Civ1_U,Data.Civ1_V));
558        Data.CivStage=2;
559    end
560    %% Patch1
561    if isfield (Param.ActionInput,'Patch1')
562        disp('patch1 started')
563        if check_civx
564            errormsg='Civ Matlab input needed for patch';
565            disp_uvmat('ERROR',errormsg,checkrun)
566            return
567        end
568       
569        % record the processing parameters of Patch1 as global attributes in the result nc file
570        list_param=fieldnames(Param.ActionInput.Patch1)';
571        list_param(strcmp('TestPatch1',list_param))=[];% remove 'TestPatch1' from the list of parameters
572        Patch1_param=regexprep(list_param,'^.+','Patch1_$0');% insert 'Patch1_' before  each parameter name
573        for ilist=1:length(list_param)
574            Data.(Patch1_param{ilist})=Param.ActionInput.Patch1.(list_param{ilist});
575        end
576        Data.CivStage=3;% record the new state of processing
577        Data.ListGlobalAttribute=[Data.ListGlobalAttribute Patch1_param];
578       
579        % list the variables to record
580        nbvar=length(Data.ListVarName);
581        Data.ListVarName=[Data.ListVarName {'Civ1_U_smooth','Civ1_V_smooth','Civ1_SubRange','Civ1_NbCentres','Civ1_Coord_tps','Civ1_U_tps','Civ1_V_tps'}];
582        Data.VarDimName=[Data.VarDimName {'nb_vec_1','nb_vec_1',{'nb_coord','nb_bounds','nb_subdomain_1'},'nb_subdomain_1',...
583            {'nb_tps_1','nb_coord','nb_subdomain_1'},{'nb_tps_1','nb_subdomain_1'},{'nb_tps_1','nb_subdomain_1'}}];
584        Data.VarAttribute{nbvar+1}.Role='vector_x';
585        Data.VarAttribute{nbvar+2}.Role='vector_y';
586        Data.VarAttribute{nbvar+5}.Role='coord_tps';
587        Data.VarAttribute{nbvar+6}.Role='vector_x';
588        Data.VarAttribute{nbvar+7}.Role='vector_y';
589        Data.Civ1_U_smooth=Data.Civ1_U; % zeros(size(Data.Civ1_X));
590        Data.Civ1_V_smooth=Data.Civ1_V; %zeros(size(Data.Civ1_X));
591        if isfield(Data,'Civ1_FF')
592            ind_good=find(Data.Civ1_FF==0);
593        else
594            ind_good=1:numel(Data.Civ1_X);
595        end
596        if isempty(ind_good)
597                        disp_uvmat('ERROR','all vectors of civ1 are bad, check input parameters' ,checkrun)
598                        return
599        end
600
601        % perform Patch calculation using the UVMAT fct 'filter_tps'
602        [Data.Civ1_SubRange,Data.Civ1_NbCentres,Data.Civ1_Coord_tps,Data.Civ1_U_tps,Data.Civ1_V_tps,tild,Ures, Vres,tild,FFres]=...
603            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);
604        Data.Civ1_U_smooth(ind_good)=Ures;% take the interpolated (smoothed) velocity values for good vectors, keep civ1 data for the other
605        Data.Civ1_V_smooth(ind_good)=Vres;
606        Data.Civ1_FF(ind_good)=int8(FFres);
607        disp('patch1 performed')
608    end
609   
610    %% Civ2
611    if isfield (Param.ActionInput,'Civ2')
612        disp('civ2 started')
613        par_civ2=Param.ActionInput.Civ2;
614        if CheckInputFile % read input images (except in mode Test where it is introduced directly in Param.ActionInput.Civ1.ImageNameA and B)
615            par_civ2.ImageA=[];
616            par_civ2.ImageB=[];
617            if strcmp(Param.ActionInput.ListCompareMode,'displacement')
618                ImageName_A_Civ2=Param.ActionInput.RefFile;
619            else
620                ImageName_A_Civ2=fullfile_uvmat(RootPath_A,SubDir_A,RootFile_A,FileExt_A,NomType_A,i1_civ2,[],j1_civ2);
621            end
622            if strcmp(ImageName_A_Civ2,ImageName_A) && isequal(FrameIndex_A_Civ1(ifield),FrameIndex_A_Civ2(ifield))
623                par_civ2.ImageA=par_civ1.ImageA;
624            else
625                [par_civ2.ImageA,VideoObject_A] = read_image(ImageName_A_Civ2,FileType_A,VideoObject_A,FrameIndex_A_Civ2(ifield));
626            end
627            ImageName_B_Civ2=fullfile_uvmat(RootPath_B,SubDir_B,RootFile_B,FileExt_B,NomType_B,i2_civ2,[],j2_civ2);
628            if strcmp(ImageName_B_Civ2,ImageName_B) && isequal(FrameIndex_B_Civ1(ifield),FrameIndex_B_Civ2)
629                par_civ2.ImageB=par_civ1.ImageB;
630            else
631                [par_civ2.ImageB,VideoObject_B] = read_image(ImageName_B_Civ2,FileType_B,VideoObject_B,FrameIndex_B_Civ2(ifield));
632            end
633            [FileInfo_A,VideoObject_A]=get_file_info(ImageName_A_Civ2);
634            par_civ2.ImageWidth=FileInfo_A.Width;
635            par_civ2.ImageHeight=FileInfo_A.Height;
636            if isfield(par_civ2,'Grid')% grid points set as input file
637                if ischar(par_civ2.Grid)%read the grid file if the input is a file name
638                    par_civ2.Grid=dlmread(par_civ2.Grid);
639                    par_civ2.Grid(1,:)=[];%the first line must be removed (heading in the grid file)
640                end
641            else% automatic grid
642                minix=floor(par_civ2.Dx/2)-0.5;
643                maxix=minix+par_civ2.Dx*floor((par_civ2.ImageWidth-1)/par_civ2.Dx);
644                miniy=floor(par_civ2.Dy/2)-0.5;
645                maxiy=minix+par_civ2.Dy*floor((par_civ2.ImageHeight-1)/par_civ2.Dy);
646                [GridX,GridY]=meshgrid(minix:par_civ2.Dx:maxix,miniy:par_civ2.Dy:maxiy);
647                par_civ2.Grid(:,1)=reshape(GridX,[],1);
648                par_civ2.Grid(:,2)=reshape(GridY,[],1);
649            end
650        end
651       
652        % get the guess from patch1 or patch2 (case 'CheckCiv3')
653        if CheckInputFile % read input images (except in mode Test where it is introduced directly in Param.ActionInput.Civ1.ImageNameA and B)
654            if isfield (par_civ2,'CheckCiv3') && par_civ2.CheckCiv3 %get the guess from  patch2
655                SubRange= Data.Civ2_SubRange;
656                NbCentres=Data.Civ2_NbCentres;
657                Coord_tps=Data.Civ2_Coord_tps;
658                U_tps=Data.Civ2_U_tps;
659                V_tps=Data.Civ2_V_tps;
660                CivStage=Data.CivStage;%store the current CivStage
661                Civ1_Dt=Data.Civ2_Dt;
662                Data=[];%reinitialise the result structure Data
663                Data.ListGlobalAttribute={'Conventions','Program','CivStage'};
664                Data.Conventions='uvmat/civdata';% states the conventions used for the description of field variables and attributes
665                Data.Program='civ_series';
666                Data.CivStage=CivStage+1;%update the current civStage after reinitialisation of Data
667                Data.ListVarName={};
668                Data.VarDimName={};
669            else % get the guess from patch1
670                SubRange= Data.Civ1_SubRange;
671                NbCentres=Data.Civ1_NbCentres;
672                Coord_tps=Data.Civ1_Coord_tps;
673                U_tps=Data.Civ1_U_tps;
674                V_tps=Data.Civ1_V_tps;
675                Civ1_Dt=Data.Civ1_Dt;
676                Data.CivStage=4;
677            end
678        else
679            SubRange= par_civ2.Civ1_SubRange;
680            NbCentres=par_civ2.Civ1_NbCentres;
681            Coord_tps=par_civ2.Civ1_Coord_tps;
682            U_tps=par_civ2.Civ1_U_tps;
683            V_tps=par_civ2.Civ1_V_tps;
684            Civ1_Dt=par_civ2.Civ1_Dt;
685            Civ2_Dt=par_civ2.Civ1_Dt;
686            Data.ListVarName={};
687            Data.VarDimName={};
688        end
689        Shiftx=zeros(size(par_civ2.Grid,1),1);% shift expected from civ1 data
690        Shifty=zeros(size(par_civ2.Grid,1),1);
691        nbval=zeros(size(par_civ2.Grid,1),1);% nbre of interpolated values at each grid point (from the different patch subdomains)
692        if par_civ2.CheckDeformation
693            DUDX=zeros(size(par_civ2.Grid,1),1);
694            DUDY=zeros(size(par_civ2.Grid,1),1);
695            DVDX=zeros(size(par_civ2.Grid,1),1);
696            DVDY=zeros(size(par_civ2.Grid,1),1);
697        end
698        NbSubDomain=size(SubRange,3);
699        for isub=1:NbSubDomain% for each sub-domain of Patch1
700            nbvec_sub=NbCentres(isub);% nbre of Civ vectors in the subdomain
701            ind_sel=find(par_civ2.Grid(:,1)>=SubRange(1,1,isub) & par_civ2.Grid(:,1)<=SubRange(1,2,isub) &...
702                par_civ2.Grid(:,2)>=SubRange(2,1,isub) & par_civ2.Grid(:,2)<=SubRange(2,2,isub));% grid points in the subdomain
703            if ~isempty(ind_sel)
704                epoints = par_civ2.Grid(ind_sel,:);% coordinates of interpolation sites (measurement grids)
705                ctrs=Coord_tps(1:nbvec_sub,:,isub) ;%(=initial points) ctrs
706                nbval(ind_sel)=nbval(ind_sel)+1;% records the number of values for each interpolation point (in case of subdomain overlap)
707                EM = tps_eval(epoints,ctrs);% thin plate spline (tps) coefficient
708                Shiftx(ind_sel)=Shiftx(ind_sel)+EM*U_tps(1:nbvec_sub+3,isub);%velocity shift estimated by tps from civ1
709                Shifty(ind_sel)=Shifty(ind_sel)+EM*V_tps(1:nbvec_sub+3,isub);
710                if par_civ2.CheckDeformation
711                    [EMDX,EMDY] = tps_eval_dxy(epoints,ctrs);%2D matrix of distances between extrapolation points epoints and spline centres (=site points) ctrs
712                    DUDX(ind_sel)=DUDX(ind_sel)+EMDX*U_tps(1:nbvec_sub+3,isub);
713                    DUDY(ind_sel)=DUDY(ind_sel)+EMDY*U_tps(1:nbvec_sub+3,isub);
714                    DVDX(ind_sel)=DVDX(ind_sel)+EMDX*V_tps(1:nbvec_sub+3,isub);
715                    DVDY(ind_sel)=DVDY(ind_sel)+EMDY*V_tps(1:nbvec_sub+3,isub);
716                end
717            end
718        end
719        if par_civ2.CheckMask&&~isempty(par_civ2.Mask)       
720            if isfield(par_civ2,'NbSlice')
721                [RootPath_mask,SubDir_mask,RootFile_mask,i1_mask,i2_mask,j1_mask,j2_mask,Ext_mask]=fileparts_uvmat(Param.ActionInput.Civ2.Mask);
722                i1_mask=mod(i1-1,par_civ2.NbSlice)+1;
723                maskname=fullfile_uvmat(RootPath_mask,SubDir_mask,RootFile_mask,Ext_mask,'_1',i1_mask);
724            else
725                maskname=Param.ActionInput.Civ2.Mask;
726            end
727            if strcmp(maskoldname,maskname)% mask exist, not already read in civ1
728                par_civ2.Mask=mask; %use mask already opened
729            else
730                if exist(maskname,'file')
731                try
732                    par_civ2.Mask=imread(maskname);%update the mask, an store it for future use
733                catch ME
734                    if ~isempty(ME.message)
735                        errormsg=['error reading input image: ' ME.message];
736                        disp_uvmat('ERROR',errormsg,checkrun)
737                        return
738                    end
739                end
740                else
741                    par_civ2.Mask=[];
742                end
743                mask=par_civ2.Mask;
744                maskoldname=maskname;
745            end
746        end
747
748        if CheckInputFile % else Dt given by par_civ2
749            if strcmp(Param.ActionInput.ListCompareMode,'displacement')
750                Civ1_Dt=1;
751                Civ2_Dt=1;
752            else
753                Civ2_Dt=Time(i2_civ2+1,j2_civ2+1)-Time(i1_civ2+1,j1_civ2+1);
754            end
755        end
756        par_civ2.SearchBoxShift=(Civ2_Dt/Civ1_Dt)*[Shiftx(nbval>=1)./nbval(nbval>=1) Shifty(nbval>=1)./nbval(nbval>=1)];
757        % shift the grid points by half the expected shift to provide the correlation box position in image A
758        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];
759        if par_civ2.CheckDeformation
760            par_civ2.DUDX=DUDX(nbval>=1)./nbval(nbval>=1);
761            par_civ2.DUDY=DUDY(nbval>=1)./nbval(nbval>=1);
762            par_civ2.DVDX=DVDX(nbval>=1)./nbval(nbval>=1);
763            par_civ2.DVDY=DVDY(nbval>=1)./nbval(nbval>=1);
764        end
765       
766        % calculate velocity data (y and v in image indices, reverse to y component)
767        [xtable, ytable, utable, vtable, ctable, F,result_conv,errormsg] = civ (par_civ2);
768       
769        list_param=(fieldnames(Param.ActionInput.Civ2))';
770        list_param(strcmp('TestCiv2',list_param))=[];% remove the parameter TestCiv2 from the list
771        Civ2_param=regexprep(list_param,'^.+','Civ2_$0');% insert 'Civ2_' before  each string in list_param
772        Civ2_param=[{'Civ2_ImageA','Civ2_ImageB','Civ2_Time','Civ2_Dt'} Civ2_param]; %insert the names of the two input images
773        %indicate the values of all the global attributes in the output data
774        if exist('ImageName_A','var')
775            Data.Civ2_ImageA=ImageName_A;
776            Data.Civ2_ImageB=ImageName_B;
777            if strcmp(Param.ActionInput.ListCompareMode,'displacement')
778                Data.Civ2_Time=Time(i2_civ2+1,j2_civ2+1);% the Time is the Time of the secodn image
779                Data.Civ2_Dt=1;% Time interval is 1, to yield displacement instead of velocity=displacement/Dt at reading
780            else
781                Data.Civ2_Time=(Time(i2_civ2+1,j2_civ2+1)+Time(i1_civ2+1,j1_civ2+1))/2;
782                Data.Civ2_Dt=Civ2_Dt;
783            end
784        end
785        for ilist=1:length(list_param)
786            Data.(Civ2_param{4+ilist})=Param.ActionInput.Civ2.(list_param{ilist});
787        end
788        Data.ListGlobalAttribute=[Data.ListGlobalAttribute Civ2_param];
789       
790        nbvar=numel(Data.ListVarName);
791        % define the Civ2 variable (if Civ2 data are not replaced from previous calculation)
792        if isempty(find(strcmp('Civ2_X',Data.ListVarName),1))
793            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
794            Data.VarDimName=[Data.VarDimName {'nb_vec_2','nb_vec_2','nb_vec_2','nb_vec_2','nb_vec_2','nb_vec_2'}];
795            Data.VarAttribute{nbvar+1}.Role='coord_x';
796            Data.VarAttribute{nbvar+2}.Role='coord_y';
797            Data.VarAttribute{nbvar+3}.Role='vector_x';
798            Data.VarAttribute{nbvar+4}.Role='vector_y';
799            Data.VarAttribute{nbvar+5}.Role='warnflag';
800        end
801        Data.Civ2_X=reshape(xtable,[],1);
802        Data.Civ2_Y=reshape(size(par_civ2.ImageA,1)-ytable+1,[],1);
803        Data.Civ2_U=reshape(utable,[],1);
804        Data.Civ2_V=reshape(-vtable,[],1);
805        Data.Civ2_C=reshape(ctable,[],1);
806        Data.Civ2_F=reshape(F,[],1);
807        disp('civ2 performed')
808    elseif ~isfield(Data,'ListVarName') % we start there, using existing Civ2 data
809        if exist('ncfile','var')
810            CivFile=ncfile;
811            [Data,tild,tild,errormsg]=nc2struct(CivFile);%read civ1 and fix1 data in the existing netcdf file
812            if ~isempty(errormsg)
813                disp_uvmat('ERROR',errormsg,checkrun)
814                return
815            end
816        elseif isfield(Param,'Civ2_X')% use Civ2 data as input in Param (test mode)
817            Data.ListGlobalAttribute={};
818            Data.ListVarName={};
819            Data.VarDimName={};
820            Data.Civ2_X=Param.Civ2_X;
821            Data.Civ2_Y=Param.Civ2_Y;
822            Data.Civ2_U=Param.Civ2_U;
823            Data.Civ2_V=Param.Civ2_V;
824            Data.Civ2_FF=Param.Civ2_FF;
825        end
826    end
827   
828    %% Fix2
829    if isfield (Param.ActionInput,'Fix2')
830        disp('fix2 started')
831        list_param=fieldnames(Param.ActionInput.Fix2)';
832        Fix2_param=regexprep(list_param,'^.+','Fix2_$0');% insert 'Fix1_' before  each string in ListFixParam
833        %indicate the values of all the global attributes in the output data
834        for ilist=1:length(list_param)
835            Data.(Fix2_param{ilist})=Param.ActionInput.Fix2.(list_param{ilist});
836        end
837        Data.ListGlobalAttribute=[Data.ListGlobalAttribute Fix2_param];
838        %
839        %         ListFixParam=fieldnames(Param.ActionInput.Fix2);
840        %         for ilist=1:length(ListFixParam)
841        %             ParamName=ListFixParam{ilist};
842        %             ListName=['Fix2_' ParamName];
843        %             eval(['Data.ListGlobalAttribute=[Data.ListGlobalAttribute ''' ParamName '''];'])
844        %             eval(['Data.' ListName '=Param.ActionInput.Fix2.' ParamName ';'])
845        %         end
846        if check_civx
847            if ~isfield(Data,'fix2')
848                Data.ListGlobalAttribute=[Data.ListGlobalAttribute 'fix2'];
849                Data.fix2=1;
850                Data.ListVarName=[Data.ListVarName {'vec2_FixFlag'}];
851                Data.VarDimName=[Data.VarDimName {'nb_vectors2'}];
852            end
853            Data.vec_FixFlag=fix(Param.Fix2,Data.vec2_F,Data.vec2_C,Data.vec2_U,Data.vec2_V,Data.vec2_X,Data.vec2_Y);
854        else
855            Data.ListVarName=[Data.ListVarName {'Civ2_FF'}];
856            Data.VarDimName=[Data.VarDimName {'nb_vec_2'}];
857            nbvar=length(Data.ListVarName);
858            Data.VarAttribute{nbvar}.Role='errorflag';
859            Data.Civ2_FF=double(fix(Param.ActionInput.Fix2,Data.Civ2_F,Data.Civ2_C,Data.Civ2_U,Data.Civ2_V));
860            Data.CivStage=Data.CivStage+1;
861        end
862    end
863   
864    %% Patch2
865    if isfield (Param.ActionInput,'Patch2')
866        disp('patch2 started')
867        list_param=fieldnames(Param.ActionInput.Patch2)';
868        list_param(strcmp('TestPatch2',list_param))=[];% remove the parameter TestCiv1 from the list
869        Patch2_param=regexprep(list_param,'^.+','Patch2_$0');% insert 'Fix1_' before  each string in ListFixParam
870        %indicate the values of all the global attributes in the output data
871        for ilist=1:length(list_param)
872            Data.(Patch2_param{ilist})=Param.ActionInput.Patch2.(list_param{ilist});
873        end
874        Data.ListGlobalAttribute=[Data.ListGlobalAttribute Patch2_param];
875       
876        nbvar=length(Data.ListVarName);
877        Data.ListVarName=[Data.ListVarName {'Civ2_U_smooth','Civ2_V_smooth','Civ2_SubRange','Civ2_NbCentres','Civ2_Coord_tps','Civ2_U_tps','Civ2_V_tps'}];
878        Data.VarDimName=[Data.VarDimName {'nb_vec_2','nb_vec_2',{'nb_coord','nb_bounds','nb_subdomain_2'},{'nb_subdomain_2'},...
879            {'nb_tps_2','nb_coord','nb_subdomain_2'},{'nb_tps_2','nb_subdomain_2'},{'nb_tps_2','nb_subdomain_2'}}];
880       
881        Data.VarAttribute{nbvar+1}.Role='vector_x';
882        Data.VarAttribute{nbvar+2}.Role='vector_y';
883        Data.VarAttribute{nbvar+5}.Role='coord_tps';
884        Data.VarAttribute{nbvar+6}.Role='vector_x';
885        Data.VarAttribute{nbvar+7}.Role='vector_y';
886        Data.Civ2_U_smooth=Data.Civ2_U;
887        Data.Civ2_V_smooth=Data.Civ2_V;
888        if isfield(Data,'Civ2_FF')
889            ind_good=find(Data.Civ2_FF==0);
890        else
891            ind_good=1:numel(Data.Civ2_X);
892        end
893                if isempty(ind_good)
894                        disp_uvmat('ERROR','all vectors of civ2 are bad, check input parameters' ,checkrun)
895                        return
896        end
897        [Data.Civ2_SubRange,Data.Civ2_NbCentres,Data.Civ2_Coord_tps,Data.Civ2_U_tps,Data.Civ2_V_tps,tild,Ures,Vres,tild,FFres]=...
898            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);
899        Data.Civ2_U_smooth(ind_good)=Ures;
900        Data.Civ2_V_smooth(ind_good)=Vres;
901        Data.Civ2_FF(ind_good)=FFres;
902        Data.CivStage=Data.CivStage+1;
903        disp('patch2 performed')
904    end
905   
906    %% write result in a netcdf file if requested
907    if CheckOutputFile
908        errormsg=struct2nc(ncfile_out,Data);
909        if isempty(errormsg)
910            disp([ncfile_out ' written'])
911            %[success,msg] = fileattrib(ncfile_out ,'+w','g');% done in struct2nc
912        else
913            disp(errormsg)
914        end
915        disp(['ellapsed time ' num2str(toc/60,2) ' minutes'])
916    end
917end
918
919
920% 'civ': function piv.m adapted from PIVlab http://pivlab.blogspot.com/
921%--------------------------------------------------------------------------
922% function [xtable ytable utable vtable typevector] = civ (image1,image2,ibx,iby step, subpixfinder, mask, roi)
923%
924% OUTPUT:
925% xtable: set of x coordinates
926% ytable: set of y coordiantes
927% utable: set of u displacements (along x)
928% vtable: set of v displacements (along y)
929% ctable: max image correlation for each vector
930% typevector: set of flags, =1 for good, =0 for NaN vectors
931%
932%INPUT:
933% par_civ: structure of input parameters, with fields:
934%  .ImageA: first image for correlation (matrix)
935%  .ImageB: second image for correlation(matrix)
936%  .CorrBoxSize: 1,2 vector giving the size of the correlation box in x and y
937%  .SearchBoxSize:  1,2 vector giving the size of the search box in x and y
938%  .SearchBoxShift: 1,2 vector or 2 column matrix (for civ2) giving the shift of the search box in x and y
939%  .CorrSmooth: =1 or 2 determines the choice of the sub-pixel determination of the correlation max
940%  .ImageWidth: nb of pixels of the image in x
941%  .Dx, Dy: mesh for the PIV calculation
942%  .Grid: grid giving the PIV calculation points (alternative to .Dx .Dy): centres of the correlation boxes in Image A
943%  .Mask: name of a mask file or mask image matrix itself
944%  .MinIma: thresholds for image luminosity
945%  .MaxIma
946%  .CheckDeformation=1 for subpixel interpolation and image deformation (linear transform)
947%  .DUDX: matrix of deformation obtained from patch at each grid point
948%  .DUDY
949%  .DVDX:
950%  .DVDY
951
952function [xtable,ytable,utable,vtable,ctable,F,result_conv,errormsg] = civ (par_civ)
953
954%% prepare measurement grid
955if isfield(par_civ,'Grid')% grid points set as input, central positions of the sub-images in image A
956    if ischar(par_civ.Grid)%read the grid file if the input is a file name (grid in x, y image coordinates)
957        par_civ.Grid=dlmread(par_civ.Grid);
958        par_civ.Grid(1,:)=[];%the first line must be removed (heading in the grid file)
959    end
960    % else par_civ.Grid is already an array, no action here
961else% automatic grid in x, y image coordinates
962    minix=floor(par_civ.Dx/2)-0.5;
963    maxix=minix+par_civ.Dx*floor((par_civ.ImageWidth-1)/par_civ.Dx);
964    miniy=floor(par_civ.Dy/2)-0.5;% first automatic grid point at half the mesh Dy
965    maxiy=minix+par_civ.Dy*floor((par_civ.ImageHeight-1)/par_civ.Dy);
966    [GridX,GridY]=meshgrid(minix:par_civ.Dx:maxix,miniy:par_civ.Dy:maxiy);
967    par_civ.Grid(:,1)=reshape(GridX,[],1);
968    par_civ.Grid(:,2)=reshape(GridY,[],1);% increases with array index
969end
970nbvec=size(par_civ.Grid,1);
971
972%% prepare correlation and search boxes
973ibx2=floor(par_civ.CorrBoxSize(1)/2);
974iby2=floor(par_civ.CorrBoxSize(2)/2);
975isx2=floor(par_civ.SearchBoxSize(1)/2);
976isy2=floor(par_civ.SearchBoxSize(2)/2);
977shiftx=round(par_civ.SearchBoxShift(:,1));%use the input shift estimate, rounded to the next integer value
978shifty=-round(par_civ.SearchBoxShift(:,2));% sign minus because image j index increases when y decreases
979if numel(shiftx)==1% case of a unique shift for the whole field( civ1)
980    shiftx=shiftx*ones(nbvec,1);
981    shifty=shifty*ones(nbvec,1);
982end
983
984%% Array initialisation and default output  if par_civ.CorrSmooth=0 (just the grid calculated, no civ computation)
985xtable=round(par_civ.Grid(:,1)+0.5)-0.5;
986ytable=round(par_civ.ImageHeight-par_civ.Grid(:,2)+0.5)-0.5;% y index corresponding to the position in image coordiantes
987utable=shiftx;%zeros(nbvec,1);
988vtable=shifty;%zeros(nbvec,1);
989ctable=zeros(nbvec,1);
990F=zeros(nbvec,1);
991result_conv=[];
992errormsg='';
993
994%% prepare mask
995if isfield(par_civ,'Mask') && ~isempty(par_civ.Mask)
996    if strcmp(par_civ.Mask,'all')
997        return    % get the grid only, no civ calculation
998    elseif ischar(par_civ.Mask)
999        par_civ.Mask=imread(par_civ.Mask);% read the mask if not allready done
1000    end
1001end
1002check_MinIma=isfield(par_civ,'MinIma');% test for image luminosity threshold
1003check_MaxIma=isfield(par_civ,'MaxIma') && ~isempty(par_civ.MaxIma);
1004
1005par_civ.ImageA=sum(double(par_civ.ImageA),3);%sum over rgb component for color images
1006par_civ.ImageB=sum(double(par_civ.ImageB),3);
1007[npy_ima npx_ima]=size(par_civ.ImageA);
1008if ~isequal(size(par_civ.ImageB),[npy_ima npx_ima])
1009    errormsg='image pair with unequal size';
1010    return
1011end
1012
1013%% Apply mask
1014% Convention for mask IDEAS TO IMPLEMENT ?
1015% mask >200 : velocity calculated
1016%  200 >=mask>150;velocity not calculated, interpolation allowed (bad spots)
1017% 150>=mask >100: velocity not calculated, nor interpolated
1018%  100>=mask> 20: velocity not calculated, impermeable (no flux through mask boundaries)
1019%  20>=mask: velocity=0
1020checkmask=0;
1021MinA=min(min(par_civ.ImageA));
1022%MinB=min(min(par_civ.ImageB));
1023%check_undefined=false(size(par_civ.ImageA));
1024if isfield(par_civ,'Mask') && ~isempty(par_civ.Mask)
1025    checkmask=1;
1026    if ~isequal(size(par_civ.Mask),[npy_ima npx_ima])
1027        errormsg='mask must be an image with the same size as the images';
1028        return
1029    end
1030    check_undefined=(par_civ.Mask<200 & par_civ.Mask>=20 );
1031    %     par_civ.ImageA(check_undefined)=0;% put image A to zero (i.e. the min image value) in the undefined  area
1032    %     par_civ.ImageB(check_undefined)=0;% put image B to zero (i.e. the min image value) in the undefined  area
1033end
1034
1035%% compute image correlations: MAINLOOP on velocity vectors
1036corrmax=0;
1037sum_square=1;% default
1038mesh=1;% default
1039CheckDeformation=isfield(par_civ,'CheckDeformation')&& par_civ.CheckDeformation==1;
1040if CheckDeformation
1041    mesh=0.25;%mesh in pixels for subpixel image interpolation (x 4 in each direction)
1042    par_civ.CorrSmooth=2;% use SUBPIX2DGAUSS (take into account more points near the max)
1043end
1044
1045if par_civ.CorrSmooth~=0 % par_civ.CorrSmooth=0 implies no civ computation (just input image and grid points given)
1046    for ivec=1:nbvec
1047        iref=round(par_civ.Grid(ivec,1)+0.5);% xindex on the image A for the middle of the correlation box
1048        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
1049        F(ivec)=0;
1050        subrange1_x=iref-ibx2:iref+ibx2;% x indices defining the first subimage
1051        subrange1_y=jref-iby2:jref+iby2;% y indices defining the first subimage
1052        subrange2_x=iref+shiftx(ivec)-isx2:iref+shiftx(ivec)+isx2;%x indices defining the second subimage
1053        subrange2_y=jref+shifty(ivec)-isy2:jref+shifty(ivec)+isy2;%y indices defining the second subimage
1054        image1_crop=MinA*ones(numel(subrange1_y),numel(subrange1_x));% default value=min of image A
1055        image2_crop=MinA*ones(numel(subrange2_y),numel(subrange2_x));% default value=min of image A
1056        check1_x=subrange1_x>=1 & subrange1_x<=par_civ.ImageWidth;% check which points in the subimage 1 are contained in the initial image 1
1057        check1_y=subrange1_y>=1 & subrange1_y<=par_civ.ImageHeight;
1058        check2_x=subrange2_x>=1 & subrange2_x<=par_civ.ImageWidth;% check which points in the subimage 2 are contained in the initial image 2
1059        check2_y=subrange2_y>=1 & subrange2_y<=par_civ.ImageHeight;
1060        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
1061        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
1062        if checkmask
1063            mask1_crop=ones(numel(subrange1_y),numel(subrange1_x));% default value=1 for mask
1064            mask2_crop=ones(numel(subrange2_y),numel(subrange2_x));% default value=1 for mask
1065            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
1066            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
1067            sizemask=sum(sum(mask1_crop))/(numel(subrange1_y)*numel(subrange1_x));%size of the masked part relative to the correlation sub-image
1068            if sizemask > 1/2% eliminate point if more than half of the correlation box is masked
1069                F(ivec)=3; %
1070                utable(ivec)=0;
1071                vtable(ivec)=0;
1072            else
1073                image1_crop=image1_crop.*~mask1_crop;% put to zero the masked pixels (mask1_crop='true'=1)
1074                image2_crop=image2_crop.*~mask2_crop;
1075                image1_mean=mean(mean(image1_crop))/(1-sizemask);
1076                image2_mean=mean(mean(image2_crop))/(1-sizemask);
1077            end
1078        else
1079            image1_mean=mean(mean(image1_crop));
1080            image2_mean=mean(mean(image2_crop));
1081        end
1082        %threshold on image minimum
1083        if F(ivec)~=3
1084            if check_MinIma && (image1_mean < par_civ.MinIma || image2_mean < par_civ.MinIma)
1085                F(ivec)=3;
1086                %threshold on image maximum
1087            elseif check_MaxIma && (image1_mean > par_civ.MaxIma || image2_mean > par_civ.MaxIma)
1088                F(ivec)=3;
1089            end
1090            if F(ivec)==3
1091                utable(ivec)=0;
1092                vtable(ivec)=0;
1093            else
1094                %mask
1095                if checkmask
1096                    image1_crop=(image1_crop-image1_mean).*~mask1_crop;%substract the mean, put to zero the masked parts
1097                    image2_crop=(image2_crop-image2_mean).*~mask2_crop;
1098                else
1099                    image1_crop=(image1_crop-image1_mean);
1100                    image2_crop=(image2_crop-image2_mean);
1101                end
1102                %deformation
1103                if CheckDeformation
1104                    xi=(1:mesh:size(image1_crop,2));
1105                    yi=(1:mesh:size(image1_crop,1))';
1106                    [XI,YI]=meshgrid(xi-ceil(size(image1_crop,2)/2),yi-ceil(size(image1_crop,1)/2));
1107                    XIant=XI-par_civ.DUDX(ivec)*XI+par_civ.DUDY(ivec)*YI+ceil(size(image1_crop,2)/2);
1108                    YIant=YI+par_civ.DVDX(ivec)*XI-par_civ.DVDY(ivec)*YI+ceil(size(image1_crop,1)/2);
1109                    image1_crop=interp2(image1_crop,XIant,YIant);
1110                    image1_crop(isnan(image1_crop))=0;
1111                    xi=(1:mesh:size(image2_crop,2));
1112                    yi=(1:mesh:size(image2_crop,1))';
1113                    image2_crop=interp2(image2_crop,xi,yi,'*spline');
1114                    image2_crop(isnan(image2_crop))=0;
1115                end
1116                sum_square=sum(sum(image1_crop.*image1_crop));
1117                %reference: Oliver Pust, PIV: Direct Cross-Correlation
1118                result_conv= conv2(image2_crop,flipdim(flipdim(image1_crop,2),1),'valid');
1119                corrmax= max(max(result_conv));
1120                result_conv=(result_conv/corrmax)*255; %normalize, peak=always 255
1121                %Find the correlation max, at 255
1122                [y,x] = find(result_conv==255,1);
1123                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
1124                sum_square=sum_square*sum(sum(subimage2_crop.*subimage2_crop));% product of variances of image 1 and 2
1125                sum_square=sqrt(sum_square);% srt of the variance product to normalise correlation
1126                if ~isempty(y) && ~isempty(x)
1127                    try
1128                        if par_civ.CorrSmooth==1
1129                            [vector,F(ivec)] = SUBPIXGAUSS (result_conv,x,y);
1130                        elseif par_civ.CorrSmooth==2
1131                            [vector,F(ivec)] = SUBPIX2DGAUSS (result_conv,x,y);
1132                        else
1133                            [vector,F(ivec)] = quadr_fit(result_conv,x,y);
1134                        end
1135                        utable(ivec)=vector(1)*mesh+shiftx(ivec);
1136                        vtable(ivec)=vector(2)*mesh+shifty(ivec);
1137                        xtable(ivec)=iref+utable(ivec)/2-0.5;% convec flow (velocity taken at the point middle from imgae 1 and 2)
1138                        ytable(ivec)=jref+vtable(ivec)/2-0.5;% and position of pixel 1=0.5 (convention for image coordinates=0 at the edge)
1139                        iref=round(xtable(ivec)+0.5);% nearest image index for the middle of the vector
1140                        jref=round(ytable(ivec)+0.5);
1141                        % eliminate vectors located in the mask
1142                        if  checkmask && (iref<1 || jref<1 ||iref>npx_ima || jref>npy_ima ||( par_civ.Mask(jref,iref)<200 && par_civ.Mask(jref,iref)>=100))
1143                            utable(ivec)=0;
1144                            vtable(ivec)=0;
1145                            F(ivec)=3;
1146                        end
1147                        ctable(ivec)=corrmax/sum_square;% correlation value
1148                    catch ME
1149                        F(ivec)=3;
1150                        disp(ME.message)
1151                    end
1152                else
1153                    F(ivec)=3;
1154                end
1155            end
1156        end
1157    end
1158end
1159result_conv=result_conv*corrmax/(255*sum_square);% keep the last correlation matrix for output
1160
1161%------------------------------------------------------------------------
1162% --- Find the maximum of the correlation function after interpolation
1163% OUPUT:
1164% vector = optimum displacement vector with subpixel correction
1165% F =flag: =0 OK
1166%           =-2 , warning: max too close to the edge of the search box (1 pixel margin)
1167% INPUT:
1168% x,y: position of the maximum correlation at integer values
1169
1170function [vector,F] = SUBPIXGAUSS (result_conv,x,y)
1171%------------------------------------------------------------------------
1172% vector=[0 0]; %default
1173F=0;
1174[npy,npx]=size(result_conv);
1175result_conv(result_conv<1)=1; %set to 1 correlation values smaller than 1  (=0 by discretisation, to avoid divergence in the log)
1176%the following 8 lines are copyright (c) 1998, Uri Shavit, Roi Gurka, Alex Liberzon, Technion ??? Israel Institute of Technology
1177%http://urapiv.wordpress.com
1178peaky = y;
1179if y < npy && y > 1
1180    f0 = log(result_conv(y,x));
1181    f1 = log(result_conv(y-1,x));
1182    f2 = log(result_conv(y+1,x));
1183    peaky = peaky+ (f1-f2)/(2*f1-4*f0+2*f2);
1184else
1185    F=-2; % warning flag for vector truncated by the limited search box
1186end
1187peakx=x;
1188if x < npx-1 && x > 1
1189    f0 = log(result_conv(y,x));
1190    f1 = log(result_conv(y,x-1));
1191    f2 = log(result_conv(y,x+1));
1192    peakx = peakx+ (f1-f2)/(2*f1-4*f0+2*f2);
1193else
1194    F=-2; % warning flag for vector truncated by the limited search box
1195end
1196vector=[peakx-floor(npx/2)-1 peaky-floor(npy/2)-1];
1197
1198%------------------------------------------------------------------------
1199% --- Find the maximum of the correlation function after interpolation
1200function [vector,F] = SUBPIX2DGAUSS (result_conv,x,y)
1201%------------------------------------------------------------------------
1202% vector=[0 0]; %default
1203F=-2;
1204peaky=y;
1205peakx=x;
1206result_conv(result_conv<1)=1; %set to 1 correlation values smaller than 1 (to avoid divergence in the log)
1207[npy,npx]=size(result_conv);
1208if (x < npx) && (y < npy) && (x > 1) && (y > 1)
1209    F=0;
1210    for i=-1:1
1211        for j=-1:1
1212            %following 15 lines based on
1213            %H. Nobach ??? M. Honkanen (2005)
1214            %Two-dimensional Gaussian regression for sub-pixel displacement
1215            %estimation in particle image velocimetry or particle position
1216            %estimation in particle tracking velocimetry
1217            %Experiments in Fluids (2005) 38: 511???515
1218            c10(j+2,i+2)=i*log(result_conv(y+j, x+i));
1219            c01(j+2,i+2)=j*log(result_conv(y+j, x+i));
1220            c11(j+2,i+2)=i*j*log(result_conv(y+j, x+i));
1221            c20(j+2,i+2)=(3*i^2-2)*log(result_conv(y+j, x+i));
1222            c02(j+2,i+2)=(3*j^2-2)*log(result_conv(y+j, x+i));
1223        end
1224    end
1225    c10=(1/6)*sum(sum(c10));
1226    c01=(1/6)*sum(sum(c01));
1227    c11=(1/4)*sum(sum(c11));
1228    c20=(1/6)*sum(sum(c20));
1229    c02=(1/6)*sum(sum(c02));
1230    deltax=(c11*c01-2*c10*c02)/(4*c20*c02-c11^2);
1231    deltay=(c11*c10-2*c01*c20)/(4*c20*c02-c11^2);
1232    if abs(deltax)<1
1233        peakx=x+deltax;
1234    end
1235    if abs(deltay)<1
1236        peaky=y+deltay;
1237    end
1238end
1239vector=[peakx-floor(npx/2)-1 peaky-floor(npy/2)-1];
1240
1241%------------------------------------------------------------------------
1242% --- Find the maximum of the correlation function after quadratic interpolation
1243function [vector,F] = quadr_fit(result_conv,x,y)
1244[npy,npx]=size(result_conv);
1245if x<4 || y<4 || npx-x<4 ||npy-y <4
1246    F=-2;
1247    vector=[x y];
1248else
1249    F=0;
1250    x_ind=x-4:x+4;
1251    y_ind=y-4:y+4;
1252    x_vec=0.25*(x_ind-x);
1253    y_vec=0.25*(y_ind-y);
1254    [X,Y]=meshgrid(x_vec,y_vec);
1255    coord=[reshape(X,[],1) reshape(Y,[],1)];
1256    result_conv=reshape(result_conv(y_ind,x_ind),[],1);
1257   
1258   
1259    % n=numel(X);
1260    % x=[X Y];
1261    % X=X-0.5;
1262    % Y=Y+0.5;
1263    % y = (X.*X+2*Y.*Y+X.*Y+6) + 0.1*rand(n,1);
1264    p = polyfitn(coord,result_conv,2);
1265    A(1,1)=2*p.Coefficients(1);
1266    A(1,2)=p.Coefficients(2);
1267    A(2,1)=p.Coefficients(2);
1268    A(2,2)=2*p.Coefficients(4);
1269    vector=[x y]'-A\[p.Coefficients(3) p.Coefficients(5)]';
1270    vector=vector'-[floor(npx/2) floor(npy/2)]-1 ;
1271    % zg = polyvaln(p,coord);
1272    % figure
1273    % surf(x_vec,y_vec,reshape(zg,9,9))
1274    % hold on
1275    % plot3(X,Y,reshape(result_conv,9,9),'o')
1276    % hold off
1277end
1278
1279%'RUN_FIX': function for fixing velocity fields:
1280%-----------------------------------------------
1281% RUN_FIX(filename,field,flagindex,thresh_vecC,thresh_vel,iter,flag_mask,maskname,fileref,fieldref)
1282%
1283%filename: name of the netcdf file (used as input and output)
1284%field: structure specifying the names of the fields to fix (depending on civ1 or civ2)
1285%.vel_type='civ1' or 'civ2';
1286%.nb=name of the dimension common to the field to fix ('nb_vectors' for civ1);
1287%.fixflag=name of fix flag variable ('vec_FixFlag' for civ1)
1288%flagindex: flag specifying which values of vec_f are removed:
1289% if flagindex(1)=1: vec_f=-2 vectors are removed
1290% if flagindex(2)=1: vec_f=3 vectors are removed
1291% if flagindex(3)=1: vec_f=2 vectors are removed (if iter=1) or vec_f=4 vectors are removed (if iter=2)
1292%iter=1 for civ1 fields and iter=2 for civ2 fields
1293%thresh_vecC: threshold in the image correlation vec_C
1294%flag_mask: =1 mask used to remove vectors (0 else)
1295%maskname: name of the mask image file for fix
1296%thresh_vel: threshold on velocity, or on the difference with the reference file fileref if exists
1297%inf_sup=1: remove values smaller than threshold thresh_vel, =2, larger than threshold
1298%fileref: .nc file name for a reference velocity (='': refrence 0 used)
1299%fieldref: 'civ1','filter1'...feld used in fileref
1300
1301function FF=fix(Param,F,C,U,V,X,Y)
1302FF=zeros(size(F));%default
1303
1304%criterium on warn flags
1305FlagName={'CheckFmin2','CheckF2','CheckF3','CheckF4'};
1306FlagVal=[-2 2 3 4];
1307for iflag=1:numel(FlagName)
1308    if isfield(Param,FlagName{iflag}) && Param.(FlagName{iflag})
1309        FF=(FF==1| F==FlagVal(iflag));
1310    end
1311end
1312%criterium on correlation values
1313if isfield (Param,'MinCorr')
1314    FF=FF==1 | C<Param.MinCorr;
1315end
1316if (isfield(Param,'MinVel')&&~isempty(Param.MinVel))||(isfield (Param,'MaxVel')&&~isempty(Param.MaxVel))
1317    Umod= U.*U+V.*V;
1318    if isfield (Param,'MinVel')&&~isempty(Param.MinVel)
1319        FF=FF==1 | Umod<(Param.MinVel*Param.MinVel);
1320    end
1321    if isfield (Param,'MaxVel')&&~isempty(Param.MaxVel)
1322        FF=FF==1 | Umod>(Param.MaxVel*Param.MaxVel);
1323    end
1324end
1325
1326
1327%------------------------------------------------------------------------
1328% --- determine the list of index pairs of processing file
1329function [i1_series,i2_series,j1_series,j2_series,check_bounds,NomTypeNc]=...
1330    find_pair_indices(str_civ,i_series,j_series,MinIndex_i,MaxIndex_i,MinIndex_j,MaxIndex_j)
1331%------------------------------------------------------------------------
1332i1_series=i_series;% set of first image indexes
1333i2_series=i_series;
1334j1_series=j_series;%ones(size(i_series));% set of first image numbers
1335j2_series=j_series;%ones(size(i_series));
1336r=regexp(str_civ,'^\D(?<ind>[i|j])=( -| )(?<num1>\d+)\|(?<num2>\d+)','names');
1337if ~isempty(r)
1338    mode=['D' r.ind];
1339    ind1=str2num(r.num1);
1340    ind2=str2num(r.num2);
1341else
1342    mode='j1-j2';
1343    r=regexp(str_civ,'^j= (?<num1>[a-z])-(?<num2>[a-z])','names');
1344    if ~isempty(r)
1345        NomTypeNc='_1ab';
1346    else
1347        r=regexp(str_civ,'^j= (?<num1>[A-Z])-(?<num2>[A-Z])','names');
1348        if ~isempty(r)
1349            NomTypeNc='_1AB';
1350        else
1351            r=regexp(str_civ,'^j= (?<num1>\d+)-(?<num2>\d+)','names');
1352            if ~isempty(r)
1353                NomTypeNc='_1_1-2';
1354            end
1355        end
1356    end
1357    if isempty(r)
1358        display('wrong pair mode input option')
1359    else
1360        ind1=stra2num(r.num1);
1361        ind2=stra2num(r.num2);
1362    end
1363end
1364switch mode
1365    case 'Di'
1366        i1_series=i_series-ind1;% set of first image numbers
1367        i2_series=i_series+ind2;
1368        check_bounds=i1_series<MinIndex_i | i2_series>MaxIndex_i;
1369        if isempty(j_series)
1370            NomTypeNc='_1-2';
1371        else
1372            j1_series=j_series;
1373            j2_series=j_series;
1374            NomTypeNc='_1-2_1';
1375        end
1376    case 'Dj'
1377        j1_series=j_series-ind1;
1378        j2_series=j_series+ind2;
1379        check_bounds=j1_series<MinIndex_j | j2_series>MaxIndex_j;
1380        NomTypeNc='_1_1-2';
1381    otherwise %bursts
1382        i1_series=i_series(1,:);% do not sweep the j index
1383        i2_series=i_series(1,:);
1384        j1_series=ind1*ones(1,size(i_series,2));% j index is fixed by pair choice
1385        j2_series=ind2*ones(1,size(i_series,2));
1386        check_bounds=zeros(size(i1_series));% no limitations due to min-max indices
1387end
1388
1389
1390
1391
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