source: trunk/src/series/civ_series.m @ 908

Last change on this file since 908 was 908, checked in by g7moreau, 6 years ago
  • Update Copyright to 2015
File size: 64.8 KB
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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, default=''
12% resul_conv: image inter-correlation function for the last grid point (used for tests)
13%
14%INPUT:
15% Param: Matlab structure of input  parameters
16%     Param contains info of the GUI series using the fct read_GUI.
17%     Param.Action.RUN = 0 (to set the status of the GUI series) or =1 to RUN the computation
18%     Param.InputTable: sets the input file(s)
19%           if absent, the fct looks for input data in Param.ActionInput     (test mode)
20%     Param.OutputSubDir: sets the folder name of output file(s,
21%           if absent no file is produced, result in the output structure Data (test mode)
22%     Param.ActionInput: substructure with the parameters provided by the GUI civ_input
23%                      .Civ1: parameters for civ1
24%                      .Fix1: parameters for fix1
25%                      .Patch1:
26%                      .Civ2: for civ2
27%                      .Fix2:
28%                      .Patch2:
29
30%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
31%  Copyright 2011-2015, LEGI / CNRS UJF G-INP, Joel.Sommeria@legi.grenoble-inp.fr
32%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
33%     This is part of the toolbox UVMAT.
34%
35%     UVMAT is free software; you can redistribute it and/or modify
36%     it under the terms of the GNU General Public License as published by
37%     the Free Software Foundation; either version 2 of the License, or
38%     (at your option) any later version.
39%
40%     UVMAT is distributed in the hope that it will be useful,
41%     but WITHOUT ANY WARRANTY; without even the implied warranty of
42%     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
43%     GNU General Public License (open UVMAT/COPYING.txt) for more details.
44%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
45
46function [Data,errormsg,result_conv]= civ_series(Param)
47errormsg='';
48
49%% set the input elements needed on the GUI series when the action is selected in the menu ActionName or InputTable refreshed
50if isstruct(Param) && isequal(Param.Action.RUN,0)% function activated from the GUI series but not RUN
51    path_series=fileparts(which('series'));
52    addpath(fullfile(path_series,'series'))
53    Data=civ_input(Param);% introduce the civ parameters using the GUI civ_input
54    if isempty(Data)
55        Data=Param;% if  civ_input has been cancelled, keep previous parameters
56    end
57    Data.Program=mfilename;%gives the name of the current function
58    Data.AllowInputSort='off';% allow alphabetic sorting of the list of input file SubDir (options 'off'/'on', 'off' by default)
59    Data.WholeIndexRange='off';% prescribes the file index ranges from min to max (options 'off'/'on', 'off' by default)
60    if isfield(Data,'ActionInput') && isfield(Data.ActionInput,'PairIndices')&& strcmp(Data.ActionInput.PairIndices.ListPairMode,'pair j1-j2')
61        Data.Desable_j_index='on';% hide the j index in series (set by the pair choice in civ_input)
62    end
63    Data.NbSlice='off'; %nbre of slices ('off' by default)
64    Data.VelType='off';% menu for selecting the velocity type (options 'off'/'one'/'two',  'off' by default)
65    Data.FieldName='on';% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default)
66    Data.FieldTransform = 'off';%can use a transform function
67    Data.ProjObject='off';%can use projection object(option 'off'/'on',
68    Data.Mask='off';%can use mask option   (option 'off'/'on', 'off' by default)
69    Data.OutputDirExt='.civ';%set the output dir extension
70    Data.OutputSubDirMode='last'; %select the last subDir in the input table as root of the output subdir name (option 'all'/'first'/'last', 'all' by default)
71    Data.OutputFileMode='NbInput_i';% one output file expected per value of i index (used for waitbar)
72    Data.CheckOverwriteVisible='on'; % manage the overwrite of existing files (default=1)
73    return
74end
75
76%% read input parameters from an xml file if input is a file name (batch mode)
77checkrun=1;
78if ischar(Param)
79    Param=xml2struct(Param);% read Param as input file (batch case)
80    checkrun=0;
81end
82
83%% test input
84if ~isfield(Param,'ActionInput')
85    disp_uvmat('ERROR','no parameter set for PIV',checkrun)
86    return
87end
88iview_A=0;%default values
89NbField=1;
90RUNHandle=[];
91CheckInputFile=isfield(Param,'InputTable');%= 1 in test use for TestCiv (no nc file involved)
92CheckOutputFile=isfield(Param,'OutputSubDir');%= 1 in test use for TestPatch (no nc file produced)
93
94%% input files and indexing (skipped in Test mode)
95if CheckInputFile
96    hseries=findobj(allchild(0),'Tag','series');
97    RUNHandle=findobj(hseries,'Tag','RUN');%handle of RUN button in GUI series
98    WaitbarHandle=findobj(hseries,'Tag','Waitbar');%handle of waitbar in GUI series
99    MaxIndex_i=Param.IndexRange.MaxIndex_i;
100    MinIndex_i=Param.IndexRange.MinIndex_i;
101    MaxIndex_j=ones(size(MaxIndex_i));MinIndex_j=ones(size(MinIndex_i));
102    if isfield(Param.IndexRange,'MaxIndex_j')&& isfield(Param.IndexRange,'MinIndex_j')
103        MaxIndex_j=Param.IndexRange.MaxIndex_j;
104        MinIndex_j=Param.IndexRange.MinIndex_j;
105    end
106    if isfield(Param,'InputTable')
107        [tild,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param);
108        iview_A=0;% series index (iview) for the first image series
109        iview_B=0;% series index (iview) for the second image series (only non zero for option 'shift' comparing two image series )
110        if Param.ActionInput.CheckCiv1
111            iview_A=1;% usual PIV, the image series is on the first line of the table
112        elseif Param.ActionInput.CheckCiv2 % civ2 is performed without Civ1, a netcdf file series is needed in the first table line
113            iview_A=2;% the second line is used for the input images of Civ2
114        end
115        if strcmp(Param.ActionInput.ListCompareMode,'shift')
116            iview_B=iview_A+1; % the second image series is on the next line of the input table
117        end
118        if iview_A~=0
119            RootPath_A=Param.InputTable{iview_A,1};
120            RootFile_A=Param.InputTable{iview_A,3};
121            SubDir_A=Param.InputTable{iview_A,2};
122            NomType_A=Param.InputTable{iview_A,4};
123            FileExt_A=Param.InputTable{iview_A,5};
124            if iview_B==0
125                iview_B=iview_A;% the second image series is the same as the first
126            end
127            RootPath_B=Param.InputTable{iview_B,1};
128            RootFile_B=Param.InputTable{iview_B,3};
129            SubDir_B=Param.InputTable{iview_B,2};
130            NomType_B=Param.InputTable{iview_B,4};
131            FileExt_B=Param.InputTable{iview_B,5};
132        end
133       
134        PairCiv2='';
135        switch Param.ActionInput.ListCompareMode
136            case 'PIV'
137                PairCiv1=Param.ActionInput.PairIndices.ListPairCiv1;
138                if isfield(Param.ActionInput.PairIndices,'ListPairCiv2')
139                    PairCiv2=Param.ActionInput.PairIndices.ListPairCiv2;%string which determines the civ2 pair
140                end
141                if iview_A==1% if Civ1 is performed
142                    [i1_series_Civ1,i2_series_Civ1,j1_series_Civ1,j2_series_Civ1,check_bounds,NomTypeNc]=...
143                        find_pair_indices(PairCiv1,i1_series{1},j1_series{1},MinIndex_i,MaxIndex_i,MinIndex_j,MaxIndex_j);
144                    if ~isempty(PairCiv2)
145                        [i1_series_Civ2,i2_series_Civ2,j1_series_Civ2,j2_series_Civ2,check_bounds_Civ2]=...
146                            find_pair_indices(PairCiv2,i1_series{1},j1_series{1},MinIndex_i(1),MaxIndex_i(1),MinIndex_j(1),MaxIndex_j(1));
147                        check_bounds=check_bounds | check_bounds_Civ2;
148                    end
149                else% we start from an existing Civ1 file
150                    i1_series_Civ1=i1_series{1};
151                    i2_series_Civ1=i2_series{1};
152                    j1_series_Civ1=j1_series{1};
153                    j2_series_Civ1=j2_series{1};
154                    NomTypeNc=Param.InputTable{1,4};
155                    if ~isempty(PairCiv2)
156                        [i1_series_Civ2,i2_series_Civ2,j1_series_Civ2,j2_series_Civ2,check_bounds,NomTypeNc]=...
157                            find_pair_indices(PairCiv2,i1_series{2},j1_series{2},MinIndex_i(2),MaxIndex_i(2),MinIndex_j(2),MaxIndex_j(2));
158                    end
159                end
160            case 'displacement'
161                i1_series_Civ1=Param.ActionInput.OriginIndex*ones(size(i1_series{1}));
162                i2_series_Civ1=i1_series{1};i2_series_Civ2=i1_series{1};
163                j1_series_Civ1=ones(size(i1_series{1}));% first j index is 1
164                if isempty(j1_series_Civ1)
165                    j2_series_Civ1=ones(size(i1_series{1}));
166                else
167                    j2_series_Civ1=j1_series_Civ1;
168                end
169                i1_series_Civ2=i1_series_Civ1;
170                j1_series_Civ2=j1_series_Civ1;
171                j2_series_Civ2=j2_series_Civ1;
172                NomTypeNc=Param.InputTable{1,4};
173            case 'PIV volume'
174                % TODO, TODO
175        end
176        if isempty(j1_series_Civ1)
177            FrameIndex_A_Civ1=i1_series_Civ1;
178            FrameIndex_B_Civ1=i2_series_Civ1;
179            j1_series_Civ1=ones(size(i1_series_Civ1));
180            j2_series_Civ1=ones(size(i1_series_Civ1));
181        else
182            FrameIndex_A_Civ1=j1_series_Civ1;
183            FrameIndex_B_Civ1=j2_series_Civ1;
184        end
185        if isempty(PairCiv2)
186            FrameIndex_A_Civ2=FrameIndex_A_Civ1;
187            FrameIndex_B_Civ2=FrameIndex_B_Civ1;
188        else
189            if isempty(j1_series_Civ2)
190                FrameIndex_A_Civ2=i1_series_Civ2;
191                FrameIndex_B_Civ2=i2_series_Civ2;
192                j1_series_Civ2=ones(size(i1_series_Civ2));
193                j2_series_Civ2=ones(size(i1_series_Civ2));
194            else
195                FrameIndex_A_Civ2=j1_series_Civ2;
196                FrameIndex_B_Civ2=j2_series_Civ2;
197            end
198        end
199        if isempty(i1_series_Civ1)||(~isempty(PairCiv2) && isempty(i1_series_Civ2))
200            disp_uvmat('ERROR','no image pair fo civ in the input file index range',checkrun)
201            return
202        end
203    end
204   
205    %% check the first image pair
206    try
207        if Param.ActionInput.CheckCiv1% Civ1 is performed
208            ImageName_A=fullfile_uvmat(RootPath_A,SubDir_A,RootFile_A,FileExt_A,NomType_A,i1_series_Civ1(1),[],j1_series_Civ1(1));
209            if ~exist(ImageName_A,'file')
210                disp_uvmat('ERROR',['first input image ' ImageName_A ' does not exist'],checkrun)
211                return
212            end
213            [FileInfo_A,VideoObject_A]=get_file_info(ImageName_A);
214            FileType_A=FileInfo_A.FileType;
215            if strcmp(FileInfo_A.FileType,'netcdf')
216                FieldName_A=Param.InputFields.FieldName;
217                [DataIn,tild,tild,errormsg]=nc2struct(ImageName_A,{FieldName_A});
218                par_civ1.ImageA=DataIn.(FieldName_A);
219            else
220                [par_civ1.ImageA,VideoObject_A] = read_image(ImageName_A,FileType_A,VideoObject_A,FrameIndex_A_Civ1(1));
221            end
222            ImageName_B=fullfile_uvmat(RootPath_B,SubDir_B,RootFile_B,FileExt_B,NomType_B,i2_series_Civ1(1),[],j2_series_Civ1(1));
223            if ~exist(ImageName_B,'file')
224                disp_uvmat('ERROR',['first input image ' ImageName_B ' does not exist'],checkrun)
225                return
226            end
227            [FileInfo_B,VideoObject_B]=get_file_info(ImageName_B);
228            FileType_B=FileInfo_B.FileType;
229            if strcmp(FileInfo_B.FileType,'netcdf')
230                FieldName_B=Param.InputFields.FieldName;
231                [DataIn,tild,tild,errormsg]=nc2struct(ImageName_B,{FieldName_B});
232                par_civ1.ImageB=DataIn.(FieldName_B);
233            else
234                [par_civ1.ImageB,VideoObject_B] = read_image(ImageName_B,FileType_B,VideoObject_B,FrameIndex_B_Civ1(1));
235            end
236            NbField=numel(i1_series_Civ1);
237        elseif Param.ActionInput.CheckCiv2 % Civ2 is performed without Civ1
238            ImageName_A=fullfile_uvmat(RootPath_A,SubDir_A,RootFile_A,FileExt_A,NomType_A,i1_series_Civ2(1),[],j1_series_Civ2(1));
239            if ~exist(ImageName_A,'file')
240                disp_uvmat('ERROR',['first input image ' ImageName_A ' does not exist'],checkrun)
241                return
242            end
243            [FileInfo_A,VideoObject_A]=get_file_info(ImageName_A);
244            FileType_A=FileInfo_A.FileType;
245            [par_civ1.ImageA,VideoObject_A] = read_image(ImageName_A,FileInfo_A.FileType,VideoObject_A,FrameIndex_A_Civ2(1));
246            ImageName_B=fullfile_uvmat(RootPath_B,SubDir_B,RootFile_B,FileExt_B,NomType_B,i2_series_Civ2(1),[],j2_series_Civ2(1));
247            if ~exist(ImageName_B,'file')
248                disp_uvmat('ERROR',['first input image ' ImageName_B ' does not exist'],checkrun)
249                return
250            end
251            [FileInfo_B,VideoObject_B]=get_file_info(ImageName_B);
252            FileType_B=FileInfo_B.FileType;
253            [par_civ1.ImageB,VideoObject_B] = read_image(ImageName_B,FileType_B,VideoObject_B,FrameIndex_B_Civ2(1));
254            NbField=numel(i1_series_Civ2);
255        else
256            NbField=numel(i1_series_Civ1);% no image used (only fix or patch) TO CHECK
257        end
258    catch ME
259        if ~isempty(ME.message)
260            disp_uvmat('ERROR', ['error reading input image: ' ME.message],checkrun)
261            return
262        end
263    end
264   
265   
266    %% Output directory
267    OutputDir='';
268    if CheckOutputFile
269        OutputDir=[Param.OutputSubDir Param.OutputDirExt];
270    end
271end
272
273%% prepare output Data
274ListGlobalAttribute={'Conventions','Program','CivStage'};
275Data.Conventions='uvmat/civdata';% states the conventions used for the description of field variables and attributes
276Data.Program='civ_series';
277Data.CivStage=0;%default
278check_civx=0;%default
279
280%% get timing from the ImaDoc file or input video
281if iview_A~=0
282    XmlFileName=find_imadoc(RootPath_A,SubDir_A,RootFile_A,FileExt_A);
283    time=[];
284    if ~isempty(XmlFileName)
285        XmlData=imadoc2struct(XmlFileName);
286        if isfield(XmlData,'Time')
287            time=XmlData.Time;
288            TimeSource='xml';
289        end
290        if isfield(XmlData,'Camera')
291            if isfield(XmlData.Camera,'NbSlice')&& ~isempty(XmlData.Camera.NbSlice)
292                NbSlice_calib{iview}=XmlData.Camera.NbSlice;% Nbre of slices for Zindex in phys transform
293                if ~isequal(NbSlice_calib{iview},NbSlice_calib{1})
294                    msgbox_uvmat('WARNING','inconsistent number of Z indices for the two field series');
295                end
296            end
297            if isfield(XmlData.Camera,'TimeUnit')&& ~isempty(XmlData.Camera.TimeUnit)
298                TimeUnit=XmlData.Camera.TimeUnit;
299            end
300        end
301    end
302    if isempty(time) && ~isempty(find(strcmp(FileType_A,{'mmreader','video'})))% case of video input
303        time=zeros(FileInfo_A.NumberOfFrames+1,2);
304        time(:,2)=(0:1/FileInfo_A.FrameRate:(FileInfo_A.NumberOfFrames)/FileInfo_A.FrameRate)';
305        TimeSource='video';
306        ColorType='truecolor';
307    end
308    if isempty(time)% time = index i +0.001 index j by default
309        %MinIndex_i=min(i1_series_Civ1);
310        MaxIndex_i=max(i2_series_Civ1);
311        %MinIndex_j=min(j1_series_Civ1);
312        MaxIndex_j=max(j2_series_Civ1);
313        time=(1:MaxIndex_i)'*ones(1,MaxIndex_j);
314        time=time+0.001*ones(MaxIndex_i,1)*(1:MaxIndex_j);
315        time=[zeros(1,MaxIndex_j);time];% insert a first line of zeros
316        time=[zeros(MaxIndex_i+1,1) time];% insert a first column of zeros
317    end
318   
319    if length(FileInfo_A) >1 %case of image with multiple frames
320        nbfield=length(FileInfo_A);
321        nbfield_j=1;
322    end
323end
324
325%%%%% MAIN LOOP %%%%%%
326maskname='';% initiate the mask name
327tic;
328CheckOverwrite=1;%default
329if isfield(Param,'CheckOverwrite')
330    CheckOverwrite=Param.CheckOverwrite;
331end
332for ifield=1:NbField
333    if ~isempty(RUNHandle)% update the waitbar in interactive mode with GUI series  (checkrun=1)
334        update_waitbar(WaitbarHandle,ifield/NbField)
335        if  checkrun && ~strcmp(get(RUNHandle,'BusyAction'),'queue')
336            disp('program stopped by user')
337            break
338        end
339    end
340    if CheckInputFile
341        if iview_A==0 % no nc file has been entered
342            ncfile=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},Param.InputTable{1,5},...
343                NomTypeNc,i1_series_Civ1(ifield),i2_series_Civ1(ifield),j1_series_Civ1(ifield),j2_series_Civ1(ifield));
344        else% an existing nc file has been entered
345            if iview_A==1% if Civ1 is performed
346                Civ1Dir=OutputDir;
347            else
348                Civ1Dir=Param.InputTable{1,2};
349            end
350            if strcmp(Param.ActionInput.ListCompareMode,'PIV')
351                ncfile=fullfile_uvmat(RootPath_A,Civ1Dir,RootFile_A,'.nc',NomTypeNc,i1_series_Civ1(ifield),i2_series_Civ1(ifield),...
352                    j1_series_Civ1(ifield),j2_series_Civ1(ifield));
353            else
354                ncfile=fullfile_uvmat(RootPath_A,Civ1Dir,RootFile_A,'.nc',NomTypeNc,i2_series_Civ1(ifield),[],...
355                    j1_series_Civ1(ifield),j2_series_Civ1(ifield));
356            end
357        end
358        if ~CheckOverwrite && exist(ncfile,'file')         
359        continue% skip iteration if the mode overwrite is desactivated and the result file already exists
360        end
361    end
362    %% Civ1
363    % if Civ1 computation is requested
364    if isfield (Param.ActionInput,'Civ1')
365        if CheckInputFile
366        disp('civ1 started')
367        end
368        par_civ1=Param.ActionInput.Civ1;
369        if CheckInputFile % read input images (except in mode Test where it is introduced directly in Param.ActionInput.Civ1.ImageNameA and B)
370            try
371                ImageName_A=fullfile_uvmat(RootPath_A,SubDir_A,RootFile_A,FileExt_A,NomType_A,i1_series_Civ1(ifield),[],j1_series_Civ1(ifield));
372                if strcmp(FileInfo_A.FileType,'netcdf')% case of input images in format netcdf
373                    FieldName_A=Param.InputFields.FieldName;
374                    [DataIn,tild,tild,errormsg]=nc2struct(ImageName_A,{FieldName_A});
375                    par_civ1.ImageA=DataIn.(FieldName_A);
376                else % usual image formats for image A
377                    [par_civ1.ImageA,VideoObject_A] = read_image(ImageName_A,FileType_A,VideoObject_A,FrameIndex_A_Civ1(ifield));
378                end
379                ImageName_B=fullfile_uvmat(RootPath_B,SubDir_B,RootFile_B,FileExt_B,NomType_B,i2_series_Civ1(ifield),[],j2_series_Civ1(ifield));
380                if strcmp(FileInfo_B.FileType,'netcdf') % case of input images in format netcdf
381                    FieldName_B=Param.InputFields.FieldName;
382                    [DataIn,tild,tild,errormsg]=nc2struct(ImageName_B,{FieldName_B});
383                    par_civ1.ImageB=DataIn.(FieldName_B);
384                else % usual image formats for image B
385                    [par_civ1.ImageB,VideoObject_B] = read_image(ImageName_B,FileType_B,VideoObject_B,FrameIndex_B_Civ1(ifield));
386                end
387            catch ME % display errors in reading input images
388                if ~isempty(ME.message)
389                    disp_uvmat('ERROR', ['error reading input image: ' ME.message],checkrun)
390                    return
391                end
392            end
393            par_civ1.ImageWidth=size(par_civ1.ImageA,2);%FileInfo_A.Width;
394            par_civ1.ImageHeight=size(par_civ1.ImageA,1);%FileInfo_A.Height;
395            list_param=(fieldnames(Param.ActionInput.Civ1))';
396            list_param(strcmp('TestCiv1',list_param))=[];% remove the parameter TestCiv1 from the list
397            Civ1_param=regexprep(list_param,'^.+','Civ1_$0');% insert 'Civ1_' before  each string in list_param
398            Civ1_param=[{'Civ1_ImageA','Civ1_ImageB','Civ1_Time','Civ1_Dt'} Civ1_param]; %insert the names of the two input images
399            %indicate the values of all the global attributes in the output data
400            Data.Civ1_ImageA=ImageName_A;
401            Data.Civ1_ImageB=ImageName_B;
402            i1=i1_series_Civ1(ifield);
403            i2=i1;
404            if ~isempty(i2_series_Civ1)
405                i2=i2_series_Civ1(ifield);
406            end
407            j1=1;
408            if ~isempty(j1_series_Civ1)
409                j1=j1_series_Civ1(ifield);
410            end
411            j2=j1;
412            if ~isempty(j2_series_Civ1)
413                j2=j2_series_Civ1(ifield);
414            end
415            if strcmp(Param.ActionInput.ListCompareMode,'displacement')
416                Data.Civ1_Time=time(i2+1,j2+1);% the time is the time of the secodn image
417                Data.Civ1_Dt=1;% time interval is 1, to yield displacement instead of velocity=displacement/Dt at reading
418            else
419            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
420            Data.Civ1_Dt=time(i2+1,j2+1)-time(i1+1,j1+1);
421            end
422            for ilist=1:length(list_param)
423                Data.(Civ1_param{4+ilist})=Param.ActionInput.Civ1.(list_param{ilist});
424            end
425            Data.ListGlobalAttribute=[ListGlobalAttribute Civ1_param];
426            Data.CivStage=1;
427        end
428        % set the list of variables
429        Data.ListVarName={'Civ1_X','Civ1_Y','Civ1_U','Civ1_V','Civ1_F','Civ1_C'};%  cell array containing the names of the fields to record
430        Data.VarDimName={'nb_vec_1','nb_vec_1','nb_vec_1','nb_vec_1','nb_vec_1','nb_vec_1'};
431        Data.VarAttribute{1}.Role='coord_x';
432        Data.VarAttribute{2}.Role='coord_y';
433        Data.VarAttribute{3}.Role='vector_x';
434        Data.VarAttribute{4}.Role='vector_y';
435        Data.VarAttribute{5}.Role='warnflag';
436        if par_civ1.CheckMask&&~isempty(par_civ1.Mask)
437            if strcmp(maskname,par_civ1.Mask)% mask exist, not already read in civ1
438                par_civ1.Mask=mask; %use mask already opened
439            else
440                try
441                    par_civ1.Mask=imread(par_civ1.Mask);%update the mask, an store it for future use
442                catch ME
443                    if ~isempty(ME.message)
444                        errormsg=['error reading input image: ' ME.message];
445                        disp_uvmat('ERROR',errormsg,checkrun)
446                        return
447                    end
448                end
449                mask=par_civ1.Mask;
450                maskname=par_civ1.Mask;
451            end
452        end
453        if strcmp(Param.ActionInput.ListCompareMode, 'PIV volume')
454            Data.ListVarName=[Data.ListVarName 'Civ1_Z'];
455            Data.Civ1_X=[];Data.Civ1_Y=[];Data.Civ1_Z=[];
456            Data.Civ1_U=[];Data.Civ1_V=[];Data.Civ1_C=[];Data.Civ1_F=[];
457            for ivol=1:NbSlice
458                % caluclate velocity data (y and v in indices, reverse to y component)
459                [xtable, ytable, utable, vtable, ctable, F, result_conv, errormsg] = civ (par_civ1);
460                if ~isempty(errormsg)
461                    disp_uvmat('ERROR',errormsg,checkrun)
462                    return
463                end
464                Data.Civ1_X=[Data.Civ1_X reshape(xtable,[],1)];
465                Data.Civ1_Y=[Data.Civ1_Y reshape(Param.Civ1.ImageHeight-ytable+1,[],1)];
466                Data.Civ1_Z=[Data.Civ1_Z ivol*ones(numel(xtable),1)];% z=image index in image coordinates
467                Data.Civ1_U=[Data.Civ1_U reshape(utable,[],1)];
468                Data.Civ1_V=[Data.Civ1_V reshape(-vtable,[],1)];
469                Data.Civ1_C=[Data.Civ1_C reshape(ctable,[],1)];
470                Data.Civ1_F=[Data.Civ1_C reshape(F,[],1)];
471            end
472        else %usual PIV
473            % caluclate velocity data (y and v in indices, reverse to y component)
474            [xtable, ytable, utable, vtable, ctable, F, result_conv, errormsg] = civ (par_civ1);
475            if ~isempty(errormsg)
476                disp_uvmat('ERROR',errormsg,checkrun)
477                return
478            end
479            Data.Civ1_X=reshape(xtable,[],1);
480            Data.Civ1_Y=reshape(par_civ1.ImageHeight-ytable+1,[],1);
481            Data.Civ1_U=reshape(utable,[],1);
482            Data.Civ1_V=reshape(-vtable,[],1);
483            Data.Civ1_C=reshape(ctable,[],1);
484            Data.Civ1_F=reshape(F,[],1);
485        end
486    else% we use existing Civ1 data
487        if exist('ncfile','var')
488            CivFile=ncfile;
489            [Data,tild,tild,errormsg]=nc2struct(CivFile,'ListGlobalAttribute','absolut_time_T0'); %look for the constant 'absolut_time_T0' to detect old civx data format
490            if ~isempty(errormsg)
491                disp_uvmat('ERROR',errormsg,checkrun)
492                return
493            end
494            [Data,tild,tild,errormsg]=nc2struct(CivFile);%read civ1 and fix1 data in the existing netcdf file
495        elseif isfield(Param,'Civ1_X')
496            Data.ListGlobalAttribute={};
497            Data.ListVarName={};
498            Data.VarDimName={};
499            Data.Civ1_X=Param.Civ1_X;
500            Data.Civ1_Y=Param.Civ1_Y;
501            Data.Civ1_U=Param.Civ1_U;
502            Data.Civ1_V=Param.Civ1_V;
503            Data.Civ1_FF=Param.Civ1_FF;
504        end
505    end
506   
507    %% Fix1
508    if isfield (Param.ActionInput,'Fix1')
509         disp('fix1 started')
510        if ~isfield (Param.ActionInput,'Civ1')% if we use existing Civ1, remove previous data beyond Civ1
511            Fix1_attr=find(strcmp('Fix1',Data.ListGlobalAttribute));
512            Data.ListGlobalAttribute(Fix1_attr)=[];
513            for ilist=1:numel(Fix1_attr)
514                Data=rmfield(Data,Data.ListGlobalAttribute{Fix1_attr(ilist)});
515            end
516        end
517        list_param=fieldnames(Param.ActionInput.Fix1)';
518        Fix1_param=regexprep(list_param,'^.+','Fix1_$0');% insert 'Fix1_' before  each string in ListFixParam
519        %indicate the values of all the global attributes in the output data
520        for ilist=1:length(list_param)
521            Data.(Fix1_param{ilist})=Param.ActionInput.Fix1.(list_param{ilist});
522        end
523        Data.ListGlobalAttribute=[Data.ListGlobalAttribute Fix1_param];
524        Data.ListVarName=[Data.ListVarName {'Civ1_FF'}];
525        Data.VarDimName=[Data.VarDimName {'nb_vec_1'}];
526        nbvar=length(Data.ListVarName);
527        Data.VarAttribute{nbvar}.Role='errorflag';
528        Data.Civ1_FF=fix(Param.ActionInput.Fix1,Data.Civ1_F,Data.Civ1_C,Data.Civ1_U,Data.Civ1_V);
529        Data.CivStage=2;
530    end
531    %% Patch1
532    if isfield (Param.ActionInput,'Patch1')
533        disp('patch1 started')
534        if check_civx
535            errormsg='Civ Matlab input needed for patch';
536            disp_uvmat('ERROR',errormsg,checkrun)
537            return
538        end
539       
540        % record the processing parameters of Patch1 as global attributes in the result nc file
541        list_param=fieldnames(Param.ActionInput.Patch1)';
542        list_param(strcmp('TestPatch1',list_param))=[];% remove 'TestPatch1' from the list of parameters
543        Patch1_param=regexprep(list_param,'^.+','Patch1_$0');% insert 'Patch1_' before  each parameter name
544        for ilist=1:length(list_param)
545            Data.(Patch1_param{ilist})=Param.ActionInput.Patch1.(list_param{ilist});
546        end
547        Data.CivStage=3;% record the new state of processing
548        Data.ListGlobalAttribute=[Data.ListGlobalAttribute Patch1_param];
549       
550        % list the variables to record
551        nbvar=length(Data.ListVarName);
552        Data.ListVarName=[Data.ListVarName {'Civ1_U_smooth','Civ1_V_smooth','Civ1_SubRange','Civ1_NbCentres','Civ1_Coord_tps','Civ1_U_tps','Civ1_V_tps'}];
553        Data.VarDimName=[Data.VarDimName {'nb_vec_1','nb_vec_1',{'nb_coord','nb_bounds','nb_subdomain_1'},'nb_subdomain_1',...
554            {'nb_tps_1','nb_coord','nb_subdomain_1'},{'nb_tps_1','nb_subdomain_1'},{'nb_tps_1','nb_subdomain_1'}}];
555        Data.VarAttribute{nbvar+1}.Role='vector_x';
556        Data.VarAttribute{nbvar+2}.Role='vector_y';
557        Data.VarAttribute{nbvar+5}.Role='coord_tps';
558        Data.VarAttribute{nbvar+6}.Role='vector_x';
559        Data.VarAttribute{nbvar+7}.Role='vector_y';
560        Data.Civ1_U_smooth=Data.Civ1_U; % zeros(size(Data.Civ1_X));
561        Data.Civ1_V_smooth=Data.Civ1_V; %zeros(size(Data.Civ1_X));
562        if isfield(Data,'Civ1_FF')
563            ind_good=find(Data.Civ1_FF==0);
564        else
565            ind_good=1:numel(Data.Civ1_X);
566        end
567       
568        % perform Patch calculation using the UVMAT fct 'filter_tps'
569        [Data.Civ1_SubRange,Data.Civ1_NbCentres,Data.Civ1_Coord_tps,Data.Civ1_U_tps,Data.Civ1_V_tps,tild,Ures, Vres,tild,FFres]=...
570            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);
571        Data.Civ1_U_smooth(ind_good)=Ures;% take the interpolated (smoothed) velocity values for good vectors, keep 0 for the others
572        Data.Civ1_V_smooth(ind_good)=Vres;
573        Data.Civ1_FF(ind_good)=FFres;
574        disp('patch1 performed')
575    end
576   
577    %% Civ2
578    if isfield (Param.ActionInput,'Civ2')
579        disp('civ2 started')
580        par_civ2=Param.ActionInput.Civ2;
581        if CheckInputFile % read input images (except in mode Test where it is introduced directly in Param.ActionInput.Civ1.ImageNameA and B)
582            par_civ2.ImageA=[];
583            par_civ2.ImageB=[];
584            i1=i1_series_Civ2(ifield);
585            i2=i1;
586            if ~isempty(i2_series_Civ2)
587                i2=i2_series_Civ2(ifield);
588            end
589            j1=1;
590            if ~isempty(j1_series_Civ2)
591                j1=j1_series_Civ2(ifield);
592            end
593            j2=j1;
594            if ~isempty(j2_series_Civ2)
595                j2=j2_series_Civ2(ifield);
596            end
597            ImageName_A_Civ2=fullfile_uvmat(RootPath_A,SubDir_A,RootFile_A,FileExt_A,NomType_A,i1,[],j1);
598           
599            if strcmp(ImageName_A_Civ2,ImageName_A) && isequal(FrameIndex_A_Civ1(ifield),FrameIndex_A_Civ2(ifield))
600                par_civ2.ImageA=par_civ1.ImageA;
601            else
602                [par_civ2.ImageA,VideoObject_A] = read_image(ImageName_A_Civ2,FileType_A,VideoObject_A,FrameIndex_A_Civ2(ifield));
603            end
604            ImageName_B_Civ2=fullfile_uvmat(RootPath_B,SubDir_B,RootFile_B,FileExt_B,NomType_B,i2,[],j2);
605            if strcmp(ImageName_B_Civ2,ImageName_B) && isequal(FrameIndex_B_Civ1(ifield),FrameIndex_B_Civ2)
606                par_civ2.ImageB=par_civ1.ImageB;
607            else
608                [par_civ2.ImageB,VideoObject_B] = read_image(ImageName_B_Civ2,FileType_B,VideoObject_B,FrameIndex_B_Civ2(ifield));
609            end
610            if strcmp(Param.ActionInput.ListCompareMode,'PIV')
611                ncfile=fullfile_uvmat(RootPath_A,OutputDir,RootFile_A,'.nc',NomTypeNc,i1,i2,j1,j2);
612            else % displacement
613                ncfile=fullfile_uvmat(RootPath_A,OutputDir,RootFile_A,'.nc',NomTypeNc,i2,[],j2);
614            end
615            par_civ2.ImageWidth=FileInfo_A.Width;
616            par_civ2.ImageHeight=FileInfo_A.Height;
617            if isfield(par_civ2,'Grid')% grid points set as input file
618                if ischar(par_civ2.Grid)%read the grid file if the input is a file name
619                    par_civ2.Grid=dlmread(par_civ2.Grid);
620                    par_civ2.Grid(1,:)=[];%the first line must be removed (heading in the grid file)
621                end
622            else% automatic grid
623                minix=floor(par_civ2.Dx/2)-0.5;
624                maxix=minix+par_civ2.Dx*floor((par_civ2.ImageWidth-1)/par_civ2.Dx);
625                miniy=floor(par_civ2.Dy/2)-0.5;
626                maxiy=minix+par_civ2.Dy*floor((par_civ2.ImageHeight-1)/par_civ2.Dy);
627                [GridX,GridY]=meshgrid(minix:par_civ2.Dx:maxix,miniy:par_civ2.Dy:maxiy);
628                par_civ2.Grid(:,1)=reshape(GridX,[],1);
629                par_civ2.Grid(:,2)=reshape(GridY,[],1);
630            end
631        end
632       
633        % get the guess from patch1 or patch2 (case 'CheckCiv3')
634        if CheckInputFile % read input images (except in mode Test where it is introduced directly in Param.ActionInput.Civ1.ImageNameA and B)
635            if isfield (par_civ2,'CheckCiv3') && par_civ2.CheckCiv3 %get the guess from  patch2
636                SubRange= Data.Civ2_SubRange;
637                NbCentres=Data.Civ2_NbCentres;
638                Coord_tps=Data.Civ2_Coord_tps;
639                U_tps=Data.Civ2_U_tps;
640                V_tps=Data.Civ2_V_tps;
641                CivStage=Data.CivStage;%store the current CivStage
642                Civ1_Dt=Data.Civ2_Dt;
643                Data=[];%reinitialise the result structure Data
644                Data.ListGlobalAttribute={'Conventions','Program','CivStage'};
645                Data.Conventions='uvmat/civdata';% states the conventions used for the description of field variables and attributes
646                Data.Program='civ_series';
647                Data.CivStage=CivStage+1;%update the current civStage after reinitialisation of Data
648                Data.ListVarName={};
649                Data.VarDimName={};
650            else % get the guess from patch1
651                SubRange= Data.Civ1_SubRange;
652                NbCentres=Data.Civ1_NbCentres;
653                Coord_tps=Data.Civ1_Coord_tps;
654                U_tps=Data.Civ1_U_tps;
655                V_tps=Data.Civ1_V_tps;
656                Civ1_Dt=Data.Civ1_Dt;
657                Data.CivStage=4;
658            end
659        else
660            SubRange= par_civ2.Civ1_SubRange;
661            NbCentres=par_civ2.Civ1_NbCentres;
662            Coord_tps=par_civ2.Civ1_Coord_tps;
663            U_tps=par_civ2.Civ1_U_tps;
664            V_tps=par_civ2.Civ1_V_tps;
665            Civ1_Dt=par_civ2.Civ1_Dt;
666            Civ2_Dt=par_civ2.Civ1_Dt;
667            Data.ListVarName={};
668            Data.VarDimName={};
669        end
670        Shiftx=zeros(size(par_civ2.Grid,1),1);% shift expected from civ1 data
671        Shifty=zeros(size(par_civ2.Grid,1),1);
672        nbval=zeros(size(par_civ2.Grid,1),1);% nbre of interpolated values at each grid point (from the different patch subdomains)
673        if par_civ2.CheckDeformation
674            DUDX=zeros(size(par_civ2.Grid,1),1);
675            DUDY=zeros(size(par_civ2.Grid,1),1);
676            DVDX=zeros(size(par_civ2.Grid,1),1);
677            DVDY=zeros(size(par_civ2.Grid,1),1);
678        end
679        NbSubDomain=size(SubRange,3);
680        for isub=1:NbSubDomain% for each sub-domain of Patch1
681            nbvec_sub=NbCentres(isub);% nbre of Civ vectors in the subdomain
682            ind_sel=find(par_civ2.Grid(:,1)>=SubRange(1,1,isub) & par_civ2.Grid(:,1)<=SubRange(1,2,isub) &...
683                par_civ2.Grid(:,2)>=SubRange(2,1,isub) & par_civ2.Grid(:,2)<=SubRange(2,2,isub));% grid points in the subdomain
684            if ~isempty(ind_sel)
685                epoints = par_civ2.Grid(ind_sel,:);% coordinates of interpolation sites (measurement grids)
686                ctrs=Coord_tps(1:nbvec_sub,:,isub) ;%(=initial points) ctrs
687                nbval(ind_sel)=nbval(ind_sel)+1;% records the number of values for each interpolation point (in case of subdomain overlap)
688                EM = tps_eval(epoints,ctrs);% thin plate spline (tps) coefficient
689                Shiftx(ind_sel)=Shiftx(ind_sel)+EM*U_tps(1:nbvec_sub+3,isub);%velocity shift estimated by tps from civ1
690                Shifty(ind_sel)=Shifty(ind_sel)+EM*V_tps(1:nbvec_sub+3,isub);
691                if par_civ2.CheckDeformation
692                    [EMDX,EMDY] = tps_eval_dxy(epoints,ctrs);%2D matrix of distances between extrapolation points epoints and spline centres (=site points) ctrs
693                    DUDX(ind_sel)=DUDX(ind_sel)+EMDX*U_tps(1:nbvec_sub+3,isub);
694                    DUDY(ind_sel)=DUDY(ind_sel)+EMDY*U_tps(1:nbvec_sub+3,isub);
695                    DVDX(ind_sel)=DVDX(ind_sel)+EMDX*V_tps(1:nbvec_sub+3,isub);
696                    DVDY(ind_sel)=DVDY(ind_sel)+EMDY*V_tps(1:nbvec_sub+3,isub);
697                end
698            end
699        end
700        if par_civ2.CheckMask&&~isempty(par_civ2.Mask)
701            if strcmp(maskname,par_civ2.Mask)% mask exist, not already read in civ1
702                par_civ2.Mask=mask; %use mask already opened
703            else
704                par_civ2.Mask=imread(par_civ2.Mask);%update the mask, and store it for future use
705                mask=par_civ2.Mask;
706                maskname=par_civ2.Mask;
707            end
708        end
709        if CheckInputFile % else Dt given by par_civ2
710            if strcmp(Param.ActionInput.ListCompareMode,'displacement')
711                Civ1_Dt=1;
712                Civ2_Dt=1;
713            else
714                Civ2_Dt=time(i2+1,j2+1)-time(i1+1,j1+1);
715            end
716        end
717        par_civ2.SearchBoxShift=(Civ2_Dt/Civ1_Dt)*[Shiftx(nbval>=1)./nbval(nbval>=1) Shifty(nbval>=1)./nbval(nbval>=1)];
718        % shift the grid points by half the expected shift to provide the correlation box position in image A
719        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];
720        if par_civ2.CheckDeformation
721            par_civ2.DUDX=DUDX(nbval>=1)./nbval(nbval>=1);
722            par_civ2.DUDY=DUDY(nbval>=1)./nbval(nbval>=1);
723            par_civ2.DVDX=DVDX(nbval>=1)./nbval(nbval>=1);
724            par_civ2.DVDY=DVDY(nbval>=1)./nbval(nbval>=1);
725        end
726       
727        % calculate velocity data (y and v in image indices, reverse to y component)
728        [xtable, ytable, utable, vtable, ctable, F,result_conv,errormsg] = civ (par_civ2);
729       
730        list_param=(fieldnames(Param.ActionInput.Civ2))';
731        list_param(strcmp('TestCiv2',list_param))=[];% remove the parameter TestCiv2 from the list
732        Civ2_param=regexprep(list_param,'^.+','Civ2_$0');% insert 'Civ2_' before  each string in list_param
733        Civ2_param=[{'Civ2_ImageA','Civ2_ImageB','Civ2_Time','Civ2_Dt'} Civ2_param]; %insert the names of the two input images
734        %indicate the values of all the global attributes in the output data
735        if exist('ImageName_A','var')
736            Data.Civ2_ImageA=ImageName_A;
737            Data.Civ2_ImageB=ImageName_B;
738             if strcmp(Param.ActionInput.ListCompareMode,'displacement')
739                Data.Civ2_Time=time(i2+1,j2+1);% the time is the time of the secodn image
740                Data.Civ2_Dt=1;% time interval is 1, to yield displacement instead of velocity=displacement/Dt at reading
741             else
742            Data.Civ2_Time=(time(i2+1,j2+1)+time(i1+1,j1+1))/2;
743            Data.Civ2_Dt=Civ2_Dt;
744             end
745        end
746        for ilist=1:length(list_param)
747            Data.(Civ2_param{4+ilist})=Param.ActionInput.Civ2.(list_param{ilist});
748        end
749        Data.ListGlobalAttribute=[Data.ListGlobalAttribute Civ2_param];
750       
751        nbvar=numel(Data.ListVarName);
752        % define the Civ2 variable (if Civ2 data are not replaced from previous calculation)
753        if isempty(find(strcmp('Civ2_X',Data.ListVarName),1))
754            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
755            Data.VarDimName=[Data.VarDimName {'nb_vec_2','nb_vec_2','nb_vec_2','nb_vec_2','nb_vec_2','nb_vec_2'}];
756            Data.VarAttribute{nbvar+1}.Role='coord_x';
757            Data.VarAttribute{nbvar+2}.Role='coord_y';
758            Data.VarAttribute{nbvar+3}.Role='vector_x';
759            Data.VarAttribute{nbvar+4}.Role='vector_y';
760            Data.VarAttribute{nbvar+5}.Role='warnflag';
761        end
762        Data.Civ2_X=reshape(xtable,[],1);
763        Data.Civ2_Y=reshape(size(par_civ2.ImageA,1)-ytable+1,[],1);
764        Data.Civ2_U=reshape(utable,[],1);
765        Data.Civ2_V=reshape(-vtable,[],1);
766        Data.Civ2_C=reshape(ctable,[],1);
767        Data.Civ2_F=reshape(F,[],1);
768        disp('civ2 performed')
769    elseif ~isfield(Data,'ListVarName') % we start there, using existing Civ2 data
770        if exist('ncfile','var')
771            CivFile=ncfile;
772            [Data,tild,tild,errormsg]=nc2struct(CivFile);%read civ1 and fix1 data in the existing netcdf file
773            if ~isempty(errormsg)
774                disp_uvmat('ERROR',errormsg,checkrun)
775                return
776            end         
777        elseif isfield(Param,'Civ2_X')% use Civ2 data as input in Param (test mode)
778            Data.ListGlobalAttribute={};
779            Data.ListVarName={};
780            Data.VarDimName={};
781            Data.Civ2_X=Param.Civ2_X;
782            Data.Civ2_Y=Param.Civ2_Y;
783            Data.Civ2_U=Param.Civ2_U;
784            Data.Civ2_V=Param.Civ2_V;
785            Data.Civ2_FF=Param.Civ2_FF;
786        end
787    end
788   
789    %% Fix2
790    if isfield (Param.ActionInput,'Fix2')
791        disp('fix2 started')
792        list_param=fieldnames(Param.ActionInput.Fix2)';
793        Fix2_param=regexprep(list_param,'^.+','Fix2_$0');% insert 'Fix1_' before  each string in ListFixParam
794        %indicate the values of all the global attributes in the output data
795        for ilist=1:length(list_param)
796            Data.(Fix2_param{ilist})=Param.ActionInput.Fix2.(list_param{ilist});
797        end
798        Data.ListGlobalAttribute=[Data.ListGlobalAttribute Fix2_param];
799        %
800        %         ListFixParam=fieldnames(Param.ActionInput.Fix2);
801        %         for ilist=1:length(ListFixParam)
802        %             ParamName=ListFixParam{ilist};
803        %             ListName=['Fix2_' ParamName];
804        %             eval(['Data.ListGlobalAttribute=[Data.ListGlobalAttribute ''' ParamName '''];'])
805        %             eval(['Data.' ListName '=Param.ActionInput.Fix2.' ParamName ';'])
806        %         end
807        if check_civx
808            if ~isfield(Data,'fix2')
809                Data.ListGlobalAttribute=[Data.ListGlobalAttribute 'fix2'];
810                Data.fix2=1;
811                Data.ListVarName=[Data.ListVarName {'vec2_FixFlag'}];
812                Data.VarDimName=[Data.VarDimName {'nb_vectors2'}];
813            end
814            Data.vec_FixFlag=fix(Param.Fix2,Data.vec2_F,Data.vec2_C,Data.vec2_U,Data.vec2_V,Data.vec2_X,Data.vec2_Y);
815        else
816            Data.ListVarName=[Data.ListVarName {'Civ2_FF'}];
817            Data.VarDimName=[Data.VarDimName {'nb_vec_2'}];
818            nbvar=length(Data.ListVarName);
819            Data.VarAttribute{nbvar}.Role='errorflag';
820            Data.Civ2_FF=double(fix(Param.ActionInput.Fix2,Data.Civ2_F,Data.Civ2_C,Data.Civ2_U,Data.Civ2_V));
821            Data.CivStage=Data.CivStage+1;
822        end
823    end
824   
825    %% Patch2
826    if isfield (Param.ActionInput,'Patch2')
827        disp('patch2 started')
828        list_param=fieldnames(Param.ActionInput.Patch2)';
829        list_param(strcmp('TestPatch2',list_param))=[];% remove the parameter TestCiv1 from the list
830        Patch2_param=regexprep(list_param,'^.+','Patch2_$0');% insert 'Fix1_' before  each string in ListFixParam
831        %indicate the values of all the global attributes in the output data
832        for ilist=1:length(list_param)
833            Data.(Patch2_param{ilist})=Param.ActionInput.Patch2.(list_param{ilist});
834        end
835        Data.ListGlobalAttribute=[Data.ListGlobalAttribute Patch2_param];
836       
837        nbvar=length(Data.ListVarName);
838        Data.ListVarName=[Data.ListVarName {'Civ2_U_smooth','Civ2_V_smooth','Civ2_SubRange','Civ2_NbCentres','Civ2_Coord_tps','Civ2_U_tps','Civ2_V_tps'}];
839        Data.VarDimName=[Data.VarDimName {'nb_vec_2','nb_vec_2',{'nb_coord','nb_bounds','nb_subdomain_2'},{'nb_subdomain_2'},...
840            {'nb_tps_2','nb_coord','nb_subdomain_2'},{'nb_tps_2','nb_subdomain_2'},{'nb_tps_2','nb_subdomain_2'}}];
841       
842        Data.VarAttribute{nbvar+1}.Role='vector_x';
843        Data.VarAttribute{nbvar+2}.Role='vector_y';
844        Data.VarAttribute{nbvar+5}.Role='coord_tps';
845        Data.VarAttribute{nbvar+6}.Role='vector_x';
846        Data.VarAttribute{nbvar+7}.Role='vector_y';
847        Data.Civ2_U_smooth=Data.Civ2_U; % zeros(size(Data.Civ2_X));
848        Data.Civ2_V_smooth=Data.Civ2_V; %zeros(size(Data.Civ2_X));
849        if isfield(Data,'Civ2_FF')
850            ind_good=find(Data.Civ2_FF==0);
851        else
852            ind_good=1:numel(Data.Civ2_X);
853        end
854        [Data.Civ2_SubRange,Data.Civ2_NbCentres,Data.Civ2_Coord_tps,Data.Civ2_U_tps,Data.Civ2_V_tps,tild,Ures, Vres,tild,FFres]=...
855            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);
856        Data.Civ2_U_smooth(ind_good)=Ures;
857        Data.Civ2_V_smooth(ind_good)=Vres;
858        Data.Civ2_FF(ind_good)=FFres;
859        Data.CivStage=Data.CivStage+1;
860        disp('patch2 performed')
861    end
862   
863    %% write result in a netcdf file if requested
864    if CheckOutputFile
865        errormsg=struct2nc(ncfile,Data);
866        if isempty(errormsg)
867            disp([ncfile ' written'])
868        else
869            disp(errormsg)
870        end
871        disp(['ellapsed time ' num2str(toc/60,2) ' minutes'])
872    end
873end
874
875
876% 'civ': function piv.m adapted from PIVlab http://pivlab.blogspot.com/
877%--------------------------------------------------------------------------
878% function [xtable ytable utable vtable typevector] = civ (image1,image2,ibx,iby step, subpixfinder, mask, roi)
879%
880% OUTPUT:
881% xtable: set of x coordinates
882% ytable: set of y coordiantes
883% utable: set of u displacements (along x)
884% vtable: set of v displacements (along y)
885% ctable: max image correlation for each vector
886% typevector: set of flags, =1 for good, =0 for NaN vectors
887%
888%INPUT:
889% par_civ: structure of input parameters, with fields:
890%  .ImageA: first image for correlation (matrix)
891%  .ImageB: second image for correlation(matrix)
892%  .CorrBoxSize: 1,2 vector giving the size of the correlation box in x and y
893%  .SearchBoxSize:  1,2 vector giving the size of the search box in x and y
894%  .SearchBoxShift: 1,2 vector or 2 column matrix (for civ2) giving the shift of the search box in x and y
895%  .CorrSmooth: =1 or 2 determines the choice of the sub-pixel determination of the correlation max
896%  .ImageWidth: nb of pixels of the image in x
897%  .Dx, Dy: mesh for the PIV calculation
898%  .Grid: grid giving the PIV calculation points (alternative to .Dx .Dy): centres of the correlation boxes in Image A
899%  .Mask: name of a mask file or mask image matrix itself
900%  .MinIma: thresholds for image luminosity
901%  .MaxIma
902%  .CheckDeformation=1 for subpixel interpolation and image deformation (linear transform)
903%  .DUDX: matrix of deformation obtained from patch at each grid point
904%  .DUDY
905%  .DVDX:
906%  .DVDY
907
908function [xtable,ytable,utable,vtable,ctable,F,result_conv,errormsg] = civ (par_civ)
909
910%% prepare measurement grid
911if isfield(par_civ,'Grid')% grid points set as input, central positions of the sub-images in image A
912    if ischar(par_civ.Grid)%read the grid file if the input is a file name (grid in x, y image coordinates)
913        par_civ.Grid=dlmread(par_civ.Grid);
914        par_civ.Grid(1,:)=[];%the first line must be removed (heading in the grid file)
915    end
916    % else par_civ.Grid is already an array, no action here
917else% automatic grid in x, y image coordinates
918    minix=floor(par_civ.Dx/2)-0.5;
919    maxix=minix+par_civ.Dx*floor((par_civ.ImageWidth-1)/par_civ.Dx);
920    miniy=floor(par_civ.Dy/2)-0.5;% first automatic grid point at half the mesh Dy
921    maxiy=minix+par_civ.Dy*floor((par_civ.ImageHeight-1)/par_civ.Dy);
922    [GridX,GridY]=meshgrid(minix:par_civ.Dx:maxix,miniy:par_civ.Dy:maxiy);
923    par_civ.Grid(:,1)=reshape(GridX,[],1);
924    par_civ.Grid(:,2)=reshape(GridY,[],1);% increases with array index
925end
926nbvec=size(par_civ.Grid,1);
927
928%% prepare correlation and search boxes
929ibx2=floor(par_civ.CorrBoxSize(1)/2);
930iby2=floor(par_civ.CorrBoxSize(2)/2);
931isx2=floor(par_civ.SearchBoxSize(1)/2);
932isy2=floor(par_civ.SearchBoxSize(2)/2);
933shiftx=round(par_civ.SearchBoxShift(:,1));%use the input shift estimate, rounded to the next integer value
934shifty=-round(par_civ.SearchBoxShift(:,2));% sign minus because image j index increases when y decreases
935if numel(shiftx)==1% case of a unique shift for the whole field( civ1)
936    shiftx=shiftx*ones(nbvec,1);
937    shifty=shifty*ones(nbvec,1);
938end
939
940%% Array initialisation and default output  if par_civ.CorrSmooth=0 (just the grid calculated, no civ computation)
941xtable=round(par_civ.Grid(:,1)+0.5)-0.5;
942ytable=round(par_civ.ImageHeight-par_civ.Grid(:,2)+0.5)-0.5;% y index corresponding to the position in image coordiantes
943utable=shiftx;%zeros(nbvec,1);
944vtable=shifty;%zeros(nbvec,1);
945ctable=zeros(nbvec,1);
946F=zeros(nbvec,1);
947result_conv=[];
948errormsg='';
949
950%% prepare mask
951if isfield(par_civ,'Mask') && ~isempty(par_civ.Mask)
952    if strcmp(par_civ.Mask,'all')
953        return    % get the grid only, no civ calculation
954    elseif ischar(par_civ.Mask)
955        par_civ.Mask=imread(par_civ.Mask);% read the mask if not allready done
956    end
957end
958check_MinIma=isfield(par_civ,'MinIma');% test for image luminosity threshold
959check_MaxIma=isfield(par_civ,'MaxIma') && ~isempty(par_civ.MaxIma);
960
961par_civ.ImageA=sum(double(par_civ.ImageA),3);%sum over rgb component for color images
962par_civ.ImageB=sum(double(par_civ.ImageB),3);
963[npy_ima npx_ima]=size(par_civ.ImageA);
964if ~isequal(size(par_civ.ImageB),[npy_ima npx_ima])
965    errormsg='image pair with unequal size';
966    return
967end
968
969%% Apply mask
970% Convention for mask IDEAS TO IMPLEMENT ?
971% mask >200 : velocity calculated
972%  200 >=mask>150;velocity not calculated, interpolation allowed (bad spots)
973% 150>=mask >100: velocity not calculated, nor interpolated
974%  100>=mask> 20: velocity not calculated, impermeable (no flux through mask boundaries)
975%  20>=mask: velocity=0
976checkmask=0;
977MinA=min(min(par_civ.ImageA));
978%MinB=min(min(par_civ.ImageB));
979%check_undefined=false(size(par_civ.ImageA));
980if isfield(par_civ,'Mask') && ~isempty(par_civ.Mask)
981    checkmask=1;
982    if ~isequal(size(par_civ.Mask),[npy_ima npx_ima])
983        errormsg='mask must be an image with the same size as the images';
984        return
985    end
986    check_undefined=(par_civ.Mask<200 & par_civ.Mask>=20 );
987%     par_civ.ImageA(check_undefined)=0;% put image A to zero (i.e. the min image value) in the undefined  area
988%     par_civ.ImageB(check_undefined)=0;% put image B to zero (i.e. the min image value) in the undefined  area
989end
990
991%% compute image correlations: MAINLOOP on velocity vectors
992corrmax=0;
993sum_square=1;% default
994mesh=1;% default
995CheckDeformation=isfield(par_civ,'CheckDeformation')&& par_civ.CheckDeformation==1;
996if CheckDeformation
997    mesh=0.25;%mesh in pixels for subpixel image interpolation (x 4 in each direction)
998    par_civ.CorrSmooth=2;% use SUBPIX2DGAUSS (take into account more points near the max)
999end
1000
1001if par_civ.CorrSmooth~=0 % par_civ.CorrSmooth=0 implies no civ computation (just input image and grid points given)
1002    for ivec=1:nbvec
1003        iref=round(par_civ.Grid(ivec,1)+0.5);% xindex on the image A for the middle of the correlation box
1004        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
1005        F(ivec)=0;
1006        subrange1_x=iref-ibx2:iref+ibx2;% x indices defining the first subimage
1007        subrange1_y=jref-iby2:jref+iby2;% y indices defining the first subimage
1008        subrange2_x=iref+shiftx(ivec)-isx2:iref+shiftx(ivec)+isx2;%x indices defining the second subimage
1009        subrange2_y=jref+shifty(ivec)-isy2:jref+shifty(ivec)+isy2;%y indices defining the second subimage
1010        image1_crop=MinA*ones(numel(subrange1_y),numel(subrange1_x));% default value=min of image A
1011        image2_crop=MinA*ones(numel(subrange2_y),numel(subrange2_x));% default value=min of image A
1012        check1_x=subrange1_x>=1 & subrange1_x<=par_civ.ImageWidth;% check which points in the subimage 1 are contained in the initial image 1
1013        check1_y=subrange1_y>=1 & subrange1_y<=par_civ.ImageHeight;
1014        check2_x=subrange2_x>=1 & subrange2_x<=par_civ.ImageWidth;% check which points in the subimage 2 are contained in the initial image 2
1015        check2_y=subrange2_y>=1 & subrange2_y<=par_civ.ImageHeight;
1016        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
1017        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
1018        if checkmask
1019            mask1_crop=ones(numel(subrange1_y),numel(subrange1_x));% default value=1 for mask
1020            mask2_crop=ones(numel(subrange2_y),numel(subrange2_x));% default value=1 for mask
1021            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
1022            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
1023            sizemask=sum(sum(mask1_crop))/(numel(subrange1_y)*numel(subrange1_x));%size of the masked part relative to the correlation sub-image
1024            if sizemask > 1/2% eliminate point if more than half of the correlation box is masked
1025                F(ivec)=3; %
1026            else
1027                image1_crop=image1_crop.*~mask1_crop;% put to zero the masked pixels (mask1_crop='true'=1)
1028                image2_crop=image2_crop.*~mask2_crop;
1029                image1_mean=mean(mean(image1_crop))/(1-sizemask);
1030                image2_mean=mean(mean(image2_crop))/(1-sizemask);
1031            end
1032        else
1033            image1_mean=mean(mean(image1_crop));
1034            image2_mean=mean(mean(image2_crop));
1035        end
1036        %threshold on image minimum
1037        if F(ivec)~=3
1038            if check_MinIma && (image1_mean < par_civ.MinIma || image2_mean < par_civ.MinIma)
1039                F(ivec)=3;
1040                %threshold on image maximum
1041            elseif check_MaxIma && (image1_mean > par_civ.MaxIma || image2_mean > par_civ.MaxIma)
1042                F(ivec)=3;
1043            end
1044            if F(ivec)~=3
1045                %mask
1046                if checkmask
1047                    image1_crop=(image1_crop-image1_mean).*~mask1_crop;%substract the mean, put to zero the masked parts
1048                    image2_crop=(image2_crop-image2_mean).*~mask2_crop;
1049                else
1050                    image1_crop=(image1_crop-image1_mean);
1051                    image2_crop=(image2_crop-image2_mean);
1052                end
1053                %deformation
1054                if CheckDeformation
1055                    xi=(1:mesh:size(image1_crop,2));
1056                    yi=(1:mesh:size(image1_crop,1))';
1057                    [XI,YI]=meshgrid(xi-ceil(size(image1_crop,2)/2),yi-ceil(size(image1_crop,1)/2));
1058                    XIant=XI-par_civ.DUDX(ivec)*XI+par_civ.DUDY(ivec)*YI+ceil(size(image1_crop,2)/2);
1059                    YIant=YI+par_civ.DVDX(ivec)*XI-par_civ.DVDY(ivec)*YI+ceil(size(image1_crop,1)/2);
1060                    image1_crop=interp2(image1_crop,XIant,YIant);
1061                    image1_crop(isnan(image1_crop))=0;
1062                    xi=(1:mesh:size(image2_crop,2));
1063                    yi=(1:mesh:size(image2_crop,1))';
1064                    image2_crop=interp2(image2_crop,xi,yi,'*spline');
1065                    image2_crop(isnan(image2_crop))=0;
1066                end
1067                sum_square=sum(sum(image1_crop.*image1_crop));
1068                %reference: Oliver Pust, PIV: Direct Cross-Correlation
1069                result_conv= conv2(image2_crop,flipdim(flipdim(image1_crop,2),1),'valid');
1070                corrmax= max(max(result_conv));
1071                result_conv=(result_conv/corrmax)*255; %normalize, peak=always 255
1072                %Find the correlation max, at 255
1073                [y,x] = find(result_conv==255,1);
1074                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
1075                sum_square=sum_square*sum(sum(subimage2_crop.*subimage2_crop));% product of variances of image 1 and 2
1076                sum_square=sqrt(sum_square);% srt of the variance product to normalise correlation
1077                if ~isempty(y) && ~isempty(x)
1078                    try
1079                        if par_civ.CorrSmooth==1
1080                            [vector,F(ivec)] = SUBPIXGAUSS (result_conv,x,y);
1081                        elseif par_civ.CorrSmooth==2
1082                            [vector,F(ivec)] = SUBPIX2DGAUSS (result_conv,x,y);
1083                        else
1084                            [vector,F(ivec)] = quadr_fit(result_conv,x,y);
1085                        end
1086                        utable(ivec)=vector(1)*mesh+shiftx(ivec);
1087                        vtable(ivec)=vector(2)*mesh+shifty(ivec);
1088                        xtable(ivec)=iref+utable(ivec)/2-0.5;% convec flow (velocity taken at the point middle from imgae 1 and 2)
1089                        ytable(ivec)=jref+vtable(ivec)/2-0.5;% and position of pixel 1=0.5 (convention for image coordinates=0 at the edge)
1090                        iref=round(xtable(ivec));% nearest image index for the middle of the vector
1091                        jref=round(ytable(ivec));
1092                        % eliminate vectors located in the mask
1093                        if checkmask && par_civ.Mask(jref,iref)<200 && par_civ.Mask(jref,iref)>=100
1094                            utable(ivec)=0;
1095                            vtable(ivec)=0;
1096                            F(ivec)=3;
1097                        end
1098                        ctable(ivec)=corrmax/sum_square;% correlation value
1099                    catch ME
1100                        F(ivec)=3;
1101                    end
1102                else
1103                    F(ivec)=3;
1104                end
1105            end
1106        end
1107    end
1108end
1109result_conv=result_conv*corrmax/(255*sum_square);% keep the last correlation matrix for output
1110
1111%------------------------------------------------------------------------
1112% --- Find the maximum of the correlation function after interpolation
1113% OUPUT:
1114% vector = optimum displacement vector with subpixel correction
1115% F =flag: =0 OK
1116%           =-2 , warning: max too close to the edge of the search box (1 pixel margin)
1117% INPUT:
1118% x,y: position of the maximum correlation at integer values
1119
1120function [vector,F] = SUBPIXGAUSS (result_conv,x,y)
1121%------------------------------------------------------------------------
1122% vector=[0 0]; %default
1123F=0;
1124[npy,npx]=size(result_conv);
1125result_conv(result_conv<1)=1; %set to 1 correlation values smaller than 1 (to avoid divergence in the log)
1126%the following 8 lines are copyright (c) 1998, Uri Shavit, Roi Gurka, Alex Liberzon, Technion ᅵ Israel Institute of Technology
1127%http://urapiv.wordpress.com
1128peaky = y;
1129if y <= npy-1 && y >= 1
1130    f0 = log(result_conv(y,x));
1131    f1 = log(result_conv(y-1,x));
1132    f2 = log(result_conv(y+1,x));
1133    peaky = peaky+ (f1-f2)/(2*f1-4*f0+2*f2);
1134else
1135    F=-2; % warning flag for vector truncated by the limited search box
1136end
1137peakx=x;
1138if x <= npx-1 && x >= 1
1139    f0 = log(result_conv(y,x));
1140    f1 = log(result_conv(y,x-1));
1141    f2 = log(result_conv(y,x+1));
1142    peakx = peakx+ (f1-f2)/(2*f1-4*f0+2*f2);
1143else
1144    F=-2; % warning flag for vector truncated by the limited search box
1145end
1146vector=[peakx-floor(npx/2)-1 peaky-floor(npy/2)-1];
1147
1148%------------------------------------------------------------------------
1149% --- Find the maximum of the correlation function after interpolation
1150function [vector,F] = SUBPIX2DGAUSS (result_conv,x,y)
1151%------------------------------------------------------------------------
1152% vector=[0 0]; %default
1153F=-2;
1154peaky=y;
1155peakx=x;
1156result_conv(result_conv<1)=1; %set to 1 correlation values smaller than 1 (to avoid divergence in the log)
1157[npy,npx]=size(result_conv);
1158if (x <= npx-1) && (y <= npy-1) && (x >= 1) && (y >= 1)
1159    F=0;
1160    for i=-1:1
1161        for j=-1:1
1162            %following 15 lines based on
1163            %H. Nobach ï¿œ M. Honkanen (2005)
1164            %Two-dimensional Gaussian regression for sub-pixel displacement
1165            %estimation in particle image velocimetry or particle position
1166            %estimation in particle tracking velocimetry
1167            %Experiments in Fluids (2005) 38: 511ï¿œ515
1168            c10(j+2,i+2)=i*log(result_conv(y+j, x+i));
1169            c01(j+2,i+2)=j*log(result_conv(y+j, x+i));
1170            c11(j+2,i+2)=i*j*log(result_conv(y+j, x+i));
1171            c20(j+2,i+2)=(3*i^2-2)*log(result_conv(y+j, x+i));
1172            c02(j+2,i+2)=(3*j^2-2)*log(result_conv(y+j, x+i));
1173        end
1174    end
1175    c10=(1/6)*sum(sum(c10));
1176    c01=(1/6)*sum(sum(c01));
1177    c11=(1/4)*sum(sum(c11));
1178    c20=(1/6)*sum(sum(c20));
1179    c02=(1/6)*sum(sum(c02));
1180    deltax=(c11*c01-2*c10*c02)/(4*c20*c02-c11^2);
1181    deltay=(c11*c10-2*c01*c20)/(4*c20*c02-c11^2);
1182    if abs(deltax)<1
1183        peakx=x+deltax;
1184    end
1185    if abs(deltay)<1
1186        peaky=y+deltay;
1187    end
1188end
1189vector=[peakx-floor(npx/2)-1 peaky-floor(npy/2)-1];
1190
1191%------------------------------------------------------------------------
1192% --- Find the maximum of the correlation function after quadratic interpolation
1193function [vector,F] = quadr_fit(result_conv,x,y)
1194[npy,npx]=size(result_conv);
1195if x<4 || y<4 || npx-x<4 ||npy-y <4
1196    F=-2;
1197    vector=[x y];
1198else
1199    F=0;
1200    x_ind=x-4:x+4;
1201    y_ind=y-4:y+4;
1202    x_vec=0.25*(x_ind-x);
1203    y_vec=0.25*(y_ind-y);
1204    [X,Y]=meshgrid(x_vec,y_vec);
1205    coord=[reshape(X,[],1) reshape(Y,[],1)];
1206    result_conv=reshape(result_conv(y_ind,x_ind),[],1);
1207   
1208   
1209    % n=numel(X);
1210    % x=[X Y];
1211    % X=X-0.5;
1212    % Y=Y+0.5;
1213    % y = (X.*X+2*Y.*Y+X.*Y+6) + 0.1*rand(n,1);
1214    p = polyfitn(coord,result_conv,2);
1215    A(1,1)=2*p.Coefficients(1);
1216    A(1,2)=p.Coefficients(2);
1217    A(2,1)=p.Coefficients(2);
1218    A(2,2)=2*p.Coefficients(4);
1219    vector=[x y]'-A\[p.Coefficients(3) p.Coefficients(5)]';
1220    vector=vector'-[floor(npx/2) floor(npy/2)]-1 ;
1221    % zg = polyvaln(p,coord);
1222    % figure
1223    % surf(x_vec,y_vec,reshape(zg,9,9))
1224    % hold on
1225    % plot3(X,Y,reshape(result_conv,9,9),'o')
1226    % hold off
1227end
1228
1229%'RUN_FIX': function for fixing velocity fields:
1230%-----------------------------------------------
1231% RUN_FIX(filename,field,flagindex,thresh_vecC,thresh_vel,iter,flag_mask,maskname,fileref,fieldref)
1232%
1233%filename: name of the netcdf file (used as input and output)
1234%field: structure specifying the names of the fields to fix (depending on civ1 or civ2)
1235%.vel_type='civ1' or 'civ2';
1236%.nb=name of the dimension common to the field to fix ('nb_vectors' for civ1);
1237%.fixflag=name of fix flag variable ('vec_FixFlag' for civ1)
1238%flagindex: flag specifying which values of vec_f are removed:
1239% if flagindex(1)=1: vec_f=-2 vectors are removed
1240% if flagindex(2)=1: vec_f=3 vectors are removed
1241% if flagindex(3)=1: vec_f=2 vectors are removed (if iter=1) or vec_f=4 vectors are removed (if iter=2)
1242%iter=1 for civ1 fields and iter=2 for civ2 fields
1243%thresh_vecC: threshold in the image correlation vec_C
1244%flag_mask: =1 mask used to remove vectors (0 else)
1245%maskname: name of the mask image file for fix
1246%thresh_vel: threshold on velocity, or on the difference with the reference file fileref if exists
1247%inf_sup=1: remove values smaller than threshold thresh_vel, =2, larger than threshold
1248%fileref: .nc file name for a reference velocity (='': refrence 0 used)
1249%fieldref: 'civ1','filter1'...feld used in fileref
1250
1251function FF=fix(Param,F,C,U,V,X,Y)
1252FF=zeros(size(F));%default
1253
1254%criterium on warn flags
1255FlagName={'CheckFmin2','CheckF2','CheckF3','CheckF4'};
1256FlagVal=[-2 2 3 4];
1257for iflag=1:numel(FlagName)
1258    if isfield(Param,FlagName{iflag}) && Param.(FlagName{iflag})
1259        FF=(FF==1| F==FlagVal(iflag));
1260    end
1261end
1262%criterium on correlation values
1263if isfield (Param,'MinCorr')
1264    FF=FF==1 | C<Param.MinCorr;
1265end
1266if (isfield(Param,'MinVel')&&~isempty(Param.MinVel))||(isfield (Param,'MaxVel')&&~isempty(Param.MaxVel))
1267    Umod= U.*U+V.*V;
1268    if isfield (Param,'MinVel')&&~isempty(Param.MinVel)
1269        FF=FF==1 | Umod<(Param.MinVel*Param.MinVel);
1270    end
1271    if isfield (Param,'MaxVel')&&~isempty(Param.MaxVel)
1272        FF=FF==1 | Umod>(Param.MaxVel*Param.MaxVel);
1273    end
1274end
1275
1276
1277%------------------------------------------------------------------------
1278% --- determine the list of index pairs of processing file
1279function [i1_series,i2_series,j1_series,j2_series,check_bounds,NomTypeNc]=...
1280    find_pair_indices(str_civ,i_series,j_series,MinIndex_i,MaxIndex_i,MinIndex_j,MaxIndex_j)
1281%------------------------------------------------------------------------
1282i1_series=i_series;% set of first image indexes
1283i2_series=i_series;
1284j1_series=j_series;%ones(size(i_series));% set of first image numbers
1285j2_series=j_series;%ones(size(i_series));
1286r=regexp(str_civ,'^\D(?<ind>[i|j])=( -| )(?<num1>\d+)\|(?<num2>\d+)','names');
1287if ~isempty(r)
1288    mode=['D' r.ind];
1289    ind1=str2num(r.num1);
1290    ind2=str2num(r.num2);
1291else
1292    mode='j1-j2';
1293    r=regexp(str_civ,'^j= (?<num1>[a-z])-(?<num2>[a-z])','names');
1294    if ~isempty(r)
1295        NomTypeNc='_1ab';
1296    else
1297        r=regexp(str_civ,'^j= (?<num1>[A-Z])-(?<num2>[A-Z])','names');
1298        if ~isempty(r)
1299            NomTypeNc='_1AB';
1300        else
1301            r=regexp(str_civ,'^j= (?<num1>\d+)-(?<num2>\d+)','names');
1302            if ~isempty(r)
1303                NomTypeNc='_1_1-2';
1304            end
1305        end
1306    end
1307    if isempty(r)
1308        display('wrong pair mode input option')
1309    else
1310        ind1=stra2num(r.num1);
1311        ind2=stra2num(r.num2);
1312    end
1313end
1314switch mode
1315    case 'Di'
1316        i1_series=i_series-ind1;% set of first image numbers
1317        i2_series=i_series+ind2;
1318        check_bounds=i1_series<MinIndex_i | i2_series>MaxIndex_i;
1319        if isempty(j_series)
1320            NomTypeNc='_1-2';
1321        else
1322            j1_series=j_series;
1323            j2_series=j_series;
1324            NomTypeNc='_1-2_1';
1325        end
1326    case 'Dj'
1327        j1_series=j_series-ind1;
1328        j2_series=j_series+ind2;
1329        check_bounds=j1_series<MinIndex_j | j2_series>MaxIndex_j;
1330        NomTypeNc='_1_1-2';
1331    otherwise %bursts
1332        i1_series=i_series(1,:);% do not sweep the j index
1333        i2_series=i_series(1,:);
1334        j1_series=ind1*ones(1,size(i_series,2));% j index is fixed by pair choice
1335        j2_series=ind2*ones(1,size(i_series,2));
1336        check_bounds=zeros(size(i1_series));% no limitations due to min-max indices
1337end
1338
1339
1340
1341
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