source: trunk/src/series/civ_series.m @ 865

Last change on this file since 865 was 862, checked in by sommeria, 10 years ago

bugs repaired

File size: 61.0 KB
Line 
1%'civ_series': PIV function activated by the general GUI series
2% --- call the sub-functions:
3%   civ: PIV function itself
4%   fix: removes false vectors after detection by various criteria
5%   filter_tps: make interpolation-smoothing
6%------------------------------------------------------------------------
7% function [Data,errormsg,result_conv]= civ_series(Param)
8%
9%OUTPUT
10% Data=structure containing the PIV results and information on the processing parameters
11% errormsg=error message char string, default=''
12% resul_conv: image inter-correlation function for the last grid point (used for tests)
13%
14%INPUT:
15% Param: Matlab structure of input  parameters
16%     Param contains info of the GUI series using the fct read_GUI.
17%     Param.Action.RUN = 0 (to set the status of the GUI series) or =1 to RUN the computation
18%     Param.InputTable: sets the input file(s)
19%           if absent, the fct looks for input data in Param.ActionInput     (test mode)
20%     Param.OutputSubDir: sets the folder name of output file(s,
21%           if absent no file is produced, result in the output structure Data (test mode)
22%     Param.ActionInput: substructure with the parameters provided by the GUI civ_input
23%                      .Civ1: parameters for civ1
24%                      .Fix1: parameters for fix1
25%                      .Patch1:
26%                      .Civ2: for civ2
27%                      .Fix2:
28%                      .Patch2:
29
30%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
31%  Copyright 2011-2014, LEGI / CNRS UJF G-INP, Joel.Sommeria@legi.grenoble-inp.fr
32%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
33%     This is part of the toolbox UVMAT.
34%
35%     UVMAT is free software; you can redistribute it and/or modify
36%     it under the terms of the GNU General Public License as published by
37%     the Free Software Foundation; either version 2 of the License, or
38%     (at your option) any later version.
39%
40%     UVMAT is distributed in the hope that it will be useful,
41%     but WITHOUT ANY WARRANTY; without even the implied warranty of
42%     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
43%     GNU General Public License (open UVMAT/COPYING.txt) for more details.
44%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
45
46function [Data,errormsg,result_conv]= civ_series(Param)
47errormsg='';
48
49%% set the input elements needed on the GUI series when the action is selected in the menu ActionName or InputTable refreshed
50if isstruct(Param) && isequal(Param.Action.RUN,0)% function activated from the GUI series but not RUN
51    path_series=fileparts(which('series'));
52    addpath(fullfile(path_series,'series'))
53    Data=civ_input(Param);% introduce the civ parameters using the GUI civ_input
54    if isempty(Data)
55        Data=Param;% if  civ_input has been cancelled, keep previous parameters
56    end
57    Data.Program=mfilename;%gives the name of the current function
58    Data.AllowInputSort='off';% allow alphabetic sorting of the list of input file SubDir (options 'off'/'on', 'off' by default)
59    Data.WholeIndexRange='off';% prescribes the file index ranges from min to max (options 'off'/'on', 'off' by default)
60    if isfield(Data,'ActionInput') && isfield(Data.ActionInput,'PairIndices')&& strcmp(Data.ActionInput.PairIndices.ListPairMode,'pair j1-j2')
61        Data.Desable_j_index='on';% hide the j index in series (set by the pair choice in civ_input)
62    end
63    Data.NbSlice='off'; %nbre of slices ('off' by default)
64    Data.VelType='off';% menu for selecting the velocity type (options 'off'/'one'/'two',  'off' by default)
65    Data.FieldName='on';% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default)
66    Data.FieldTransform = 'off';%can use a transform function
67    Data.ProjObject='off';%can use projection object(option 'off'/'on',
68    Data.Mask='off';%can use mask option   (option 'off'/'on', 'off' by default)
69    Data.OutputDirExt='.civ';%set the output dir extension
70    Data.OutputSubDirMode='last'; %select the last subDir in the input table as root of the output subdir name (option 'all'/'first'/'last', 'all' by default)
71    Data.OutputFileMode='NbInput_i';% one output file expected per value of i index (used for waitbar)
72    return
73end
74
75%% read input parameters from an xml file if input is a file name (batch mode)
76checkrun=1;
77if ischar(Param)
78    Param=xml2struct(Param);% read Param as input file (batch case)
79    checkrun=0;
80end
81
82%% test input
83if ~isfield(Param,'ActionInput')
84    disp_uvmat('ERROR','no parameter set for PIV',checkrun)
85    return
86end
87iview_A=0;%default values
88NbField=1;
89RUNHandle=[];
90CheckInputFile=isfield(Param,'InputTable');%= 1 in test use for TestCiv (no nc file involved)
91CheckOutputFile=isfield(Param,'OutputSubDir');%= 1 in test use for TestPatch (no nc file produced)
92
93%% input files and indexing (skipped in Test mode)
94if CheckInputFile
95    hseries=findobj(allchild(0),'Tag','series');
96    RUNHandle=findobj(hseries,'Tag','RUN');%handle of RUN button in GUI series
97    WaitbarHandle=findobj(hseries,'Tag','Waitbar');%handle of waitbar in GUI series
98    MaxIndex_i=Param.IndexRange.MaxIndex_i;
99    MinIndex_i=Param.IndexRange.MinIndex_i;
100    MaxIndex_j=ones(size(MaxIndex_i));MinIndex_j=ones(size(MinIndex_i));
101    if isfield(Param.IndexRange,'MaxIndex_j')&& isfield(Param.IndexRange,'MinIndex_j')
102        MaxIndex_j=Param.IndexRange.MaxIndex_j;
103        MinIndex_j=Param.IndexRange.MinIndex_j;
104    end
105    if isfield(Param,'InputTable')
106        [tild,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param);
107        iview_A=0;% series index (iview) for the first image series
108        iview_B=0;% series index (iview) for the second image series (only non zero for option 'shift' comparing two image series )
109        if Param.ActionInput.CheckCiv1
110            iview_A=1;% usual PIV, the image series is on the first line of the table
111        elseif Param.ActionInput.CheckCiv2 % civ2 is performed without Civ1, a netcdf file series is needed in the first table line
112            iview_A=2;% the second line is used for the input images of Civ2
113        end
114        if strcmp(Param.ActionInput.ListCompareMode,'shift')
115            iview_B=iview_A+1; % the second image series is on the next line of the input table
116        end
117        if iview_A~=0
118            RootPath_A=Param.InputTable{iview_A,1};
119            RootFile_A=Param.InputTable{iview_A,3};
120            SubDir_A=Param.InputTable{iview_A,2};
121            NomType_A=Param.InputTable{iview_A,4};
122            FileExt_A=Param.InputTable{iview_A,5};
123            if iview_B==0
124                iview_B=iview_A;% the second image series is the same as the first
125            end
126            RootPath_B=Param.InputTable{iview_B,1};
127            RootFile_B=Param.InputTable{iview_B,3};
128            SubDir_B=Param.InputTable{iview_B,2};
129            NomType_B=Param.InputTable{iview_B,4};
130            FileExt_B=Param.InputTable{iview_B,5};
131        end
132       
133        PairCiv2='';
134        switch Param.ActionInput.ListCompareMode
135            case 'PIV'
136                PairCiv1=Param.ActionInput.PairIndices.ListPairCiv1;
137                if isfield(Param.ActionInput.PairIndices,'ListPairCiv2')
138                    PairCiv2=Param.ActionInput.PairIndices.ListPairCiv2;%string which determines the civ2 pair
139                end
140                if iview_A==1% if Civ1 is performed
141                    [i1_series_Civ1,i2_series_Civ1,j1_series_Civ1,j2_series_Civ1,check_bounds,NomTypeNc]=...
142                        find_pair_indices(PairCiv1,i1_series{1},j1_series{1},MinIndex_i,MaxIndex_i,MinIndex_j,MaxIndex_j);
143                    if ~isempty(PairCiv2)
144                        [i1_series_Civ2,i2_series_Civ2,j1_series_Civ2,j2_series_Civ2,check_bounds_Civ2]=...
145                            find_pair_indices(PairCiv2,i1_series{1},j1_series{1},MinIndex_i(1),MaxIndex_i(1),MinIndex_j(1),MaxIndex_j(1));
146                        check_bounds=check_bounds | check_bounds_Civ2;
147                    end
148                else% we start from an existing Civ1 file
149                    i1_series_Civ1=i1_series{1};
150                    i2_series_Civ1=i2_series{1};
151                    j1_series_Civ1=j1_series{1};
152                    j2_series_Civ1=j2_series{1};
153                    NomTypeNc=Param.InputTable{1,4};
154                    if ~isempty(PairCiv2)
155                        [i1_series_Civ2,i2_series_Civ2,j1_series_Civ2,j2_series_Civ2,check_bounds,NomTypeNc]=...
156                            find_pair_indices(PairCiv2,i1_series{2},j1_series{2},MinIndex_i(2),MaxIndex_i(2),MinIndex_j(2),MaxIndex_j(2));
157                    end
158                end
159            case 'displacement'
160                i1_series_Civ1=Param.ActionInput.OriginIndex*ones(size(i1_series{1}));
161                i2_series_Civ1=i1_series{1};i2_series_Civ2=i1_series{1};
162                j1_series_Civ1=ones(size(i1_series{1}));% first j index is 1
163                if isempty(j1_series_Civ1)
164                    j2_series_Civ1=ones(size(i1_series{1}));
165                else
166                    j2_series_Civ1=j1_series_Civ1;
167                end
168                i1_series_Civ2=i1_series_Civ1;
169                j1_series_Civ2=j1_series_Civ1;
170                j2_series_Civ2=j2_series_Civ1;
171                NomTypeNc=Param.InputTable{1,4};
172            case 'PIV volume'
173                % TODO, TODO
174        end
175        if isempty(j1_series_Civ1)
176            FrameIndex_A_Civ1=i1_series_Civ1;
177            FrameIndex_B_Civ1=i2_series_Civ1;
178            j1_series_Civ1=ones(size(i1_series_Civ1));
179            j2_series_Civ1=ones(size(i1_series_Civ1));
180        else
181            FrameIndex_A_Civ1=j1_series_Civ1;
182            FrameIndex_B_Civ1=j2_series_Civ1;
183        end
184        if isempty(PairCiv2)
185            FrameIndex_A_Civ2=FrameIndex_A_Civ1;
186            FrameIndex_B_Civ2=FrameIndex_B_Civ1;
187        else
188            if isempty(j1_series_Civ2)
189                FrameIndex_A_Civ2=i1_series_Civ2;
190                FrameIndex_B_Civ2=i2_series_Civ2;
191                j1_series_Civ2=ones(size(i1_series_Civ2));
192                j2_series_Civ2=ones(size(i1_series_Civ2));
193            else
194                FrameIndex_A_Civ2=j1_series_Civ2;
195                FrameIndex_B_Civ2=j2_series_Civ2;
196            end
197        end
198        if isempty(i1_series_Civ1)||(~isempty(PairCiv2) && isempty(i1_series_Civ2))
199            disp_uvmat('ERROR','no image pair fo civ in the input file index range',checkrun)
200            return
201        end
202    end
203   
204    %% check the first image pair
205    try
206        if Param.ActionInput.CheckCiv1% Civ1 is performed
207            ImageName_A=fullfile_uvmat(RootPath_A,SubDir_A,RootFile_A,FileExt_A,NomType_A,i1_series_Civ1(1),[],j1_series_Civ1(1));
208            if ~exist(ImageName_A,'file')
209                disp_uvmat('ERROR',['first input image ' ImageName_A ' does not exist'],checkrun)
210                return
211            end
212            [FileInfo_A,VideoObject_A]=get_file_info(ImageName_A);
213            FileType_A=FileInfo_A.FileType;
214            if strcmp(FileInfo_A.FileType,'netcdf')
215                FieldName_A=Param.InputFields.FieldName;
216                [DataIn,tild,tild,errormsg]=nc2struct(ImageName_A,{FieldName_A});
217                par_civ1.ImageA=DataIn.(FieldName_A);
218            else
219                [par_civ1.ImageA,VideoObject_A] = read_image(ImageName_A,FileType_A,VideoObject_A,FrameIndex_A_Civ1(1));
220            end
221            ImageName_B=fullfile_uvmat(RootPath_B,SubDir_B,RootFile_B,FileExt_B,NomType_B,i2_series_Civ1(1),[],j2_series_Civ1(1));
222            if ~exist(ImageName_B,'file')
223                disp_uvmat('ERROR',['first input image ' ImageName_B ' does not exist'],checkrun)
224                return
225            end
226            [FileInfo_B,VideoObject_B]=get_file_info(ImageName_B);
227            FileType_B=FileInfo_B.FileType;
228            if strcmp(FileInfo_B.FileType,'netcdf')
229                FieldName_B=Param.InputFields.FieldName;
230                [DataIn,tild,tild,errormsg]=nc2struct(ImageName_B,{FieldName_B});
231                par_civ1.ImageB=DataIn.(FieldName_B);
232            else
233                [par_civ1.ImageB,VideoObject_B] = read_image(ImageName_B,FileType_B,VideoObject_B,FrameIndex_B_Civ1(1));
234            end
235            NbField=numel(i1_series_Civ1);
236        elseif Param.ActionInput.CheckCiv2 % Civ2 is performed without Civ1
237            ImageName_A=fullfile_uvmat(RootPath_A,SubDir_A,RootFile_A,FileExt_A,NomType_A,i1_series_Civ2(1),[],j1_series_Civ2(1));
238            if ~exist(ImageName_A,'file')
239                disp_uvmat('ERROR',['first input image ' ImageName_A ' does not exist'],checkrun)
240                return
241            end
242            [FileInfo_A,VideoObject_A]=get_file_info(ImageName_A);
243            FileType_A=FileInfo_A.FileType;
244            [par_civ1.ImageA,VideoObject_A] = read_image(ImageName_A,FileInfo_A.FileType,VideoObject_A,FrameIndex_A_Civ2(1));
245            ImageName_B=fullfile_uvmat(RootPath_B,SubDir_B,RootFile_B,FileExt_B,NomType_B,i2_series_Civ2(1),[],j2_series_Civ2(1));
246            if ~exist(ImageName_B,'file')
247                disp_uvmat('ERROR',['first input image ' ImageName_B ' does not exist'],checkrun)
248                return
249            end
250            [FileInfo_B,VideoObject_B]=get_file_info(ImageName_B);
251            FileType_B=FileInfo_B.FileType;
252            [par_civ1.ImageB,VideoObject_B] = read_image(ImageName_B,FileType_B,VideoObject_B,FrameIndex_B_Civ2(1));
253            NbField=numel(i1_series_Civ2);
254        else
255            NbField=numel(i1_series_Civ1);% no image used (only fix or patch) TO CHECK
256        end
257    catch ME
258        if ~isempty(ME.message)
259            disp_uvmat('ERROR', ['error reading input image: ' ME.message],checkrun)
260            return
261        end
262    end
263   
264   
265    %% Output directory
266    OutputDir='';
267    if CheckOutputFile
268        OutputDir=[Param.OutputSubDir Param.OutputDirExt];
269    end
270end
271
272%% prepare output Data
273Data.ListGlobalAttribute={'Conventions','Program','CivStage'};
274Data.Conventions='uvmat/civdata';% states the conventions used for the description of field variables and attributes
275Data.Program='civ_series';
276Data.CivStage=0;%default
277check_civx=0;%default
278
279%% get timing from the ImaDoc file or input video
280if iview_A~=0
281    XmlFileName=find_imadoc(RootPath_A,SubDir_A,RootFile_A,FileExt_A);
282    time=[];
283    if ~isempty(XmlFileName)
284        XmlData=imadoc2struct(XmlFileName);
285        if isfield(XmlData,'Time')
286            time=XmlData.Time;
287            TimeSource='xml';
288        end
289        if isfield(XmlData,'Camera')
290            if isfield(XmlData.Camera,'NbSlice')&& ~isempty(XmlData.Camera.NbSlice)
291                NbSlice_calib{iview}=XmlData.Camera.NbSlice;% Nbre of slices for Zindex in phys transform
292                if ~isequal(NbSlice_calib{iview},NbSlice_calib{1})
293                    msgbox_uvmat('WARNING','inconsistent number of Z indices for the two field series');
294                end
295            end
296            if isfield(XmlData.Camera,'TimeUnit')&& ~isempty(XmlData.Camera.TimeUnit)
297                TimeUnit=XmlData.Camera.TimeUnit;
298            end
299        end
300    end
301    if isempty(time) && ~isempty(find(strcmp(FileType_A,{'mmreader','video'})))% case of video input
302        time=zeros(FileInfo_A.NumberOfFrames+1,2);
303        time(:,2)=(0:1/FileInfo_A.FrameRate:(FileInfo_A.NumberOfFrames)/FileInfo_A.FrameRate)';
304        TimeSource='video';
305        ColorType='truecolor';
306    end
307    if isempty(time)% time = index i +0.001 index j by default
308        %MinIndex_i=min(i1_series_Civ1);
309        MaxIndex_i=max(i2_series_Civ1);
310        %MinIndex_j=min(j1_series_Civ1);
311        MaxIndex_j=max(j2_series_Civ1);
312        time=(1:MaxIndex_i)'*ones(1,MaxIndex_j);
313        time=time+0.001*ones(MaxIndex_i,1)*(1:MaxIndex_j);
314        time=[zeros(1,MaxIndex_j);time];% insert a first line of zeros
315        time=[zeros(MaxIndex_i+1,1) time];% insert a first column of zeros
316    end
317   
318    if length(FileInfo_A) >1 %case of image with multiple frames
319        nbfield=length(FileInfo_A);
320        nbfield_j=1;
321    end
322end
323
324%%%%% MAIN LOOP %%%%%%
325maskname='';% initiate the mask name
326for ifield=1:NbField
327    if ~isempty(RUNHandle)% update the waitbar in interactive mode with GUI series  (checkrun=1)
328        update_waitbar(WaitbarHandle,ifield/NbField)
329        if  get(RUNHandle,'Value')&& ~strcmp(get(RUNHandle,'BusyAction'),'queue')
330            disp('program stopped by user')
331            break
332        end
333    end
334    if CheckInputFile
335        if iview_A==0 % no nc file has been entered
336            ncfile=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},Param.InputTable{1,5},...
337                NomTypeNc,i1_series_Civ1(ifield),i2_series_Civ1(ifield),j1_series_Civ1(ifield),j2_series_Civ1(ifield));
338        else% an existing nc file has been entered
339            if iview_A==1% if Civ1 is performed
340                Civ1Dir=OutputDir;
341            else
342                Civ1Dir=Param.InputTable{1,2};
343            end
344            if strcmp(Param.ActionInput.ListCompareMode,'PIV')
345                ncfile=fullfile_uvmat(RootPath_A,Civ1Dir,RootFile_A,'.nc',NomTypeNc,i1_series_Civ1(ifield),i2_series_Civ1(ifield),...
346                    j1_series_Civ1(ifield),j2_series_Civ1(ifield));
347            else
348                ncfile=fullfile_uvmat(RootPath_A,Civ1Dir,RootFile_A,'.nc',NomTypeNc,i2_series_Civ1(ifield),[],...
349                    j1_series_Civ1(ifield),j2_series_Civ1(ifield));
350            end
351        end
352    end
353    %% Civ1
354    % if Civ1 computation is requested
355    if isfield (Param.ActionInput,'Civ1')
356        par_civ1=Param.ActionInput.Civ1;
357        if CheckInputFile % read input images (except in mode Test where it is introduced directly in Param.ActionInput.Civ1.ImageNameA and B)
358            try
359                ImageName_A=fullfile_uvmat(RootPath_A,SubDir_A,RootFile_A,FileExt_A,NomType_A,i1_series_Civ1(ifield),[],j1_series_Civ1(ifield));
360                if strcmp(FileInfo_A.FileType,'netcdf')% case of input images in format netcdf
361                    FieldName_A=Param.InputFields.FieldName;
362                    [DataIn,tild,tild,errormsg]=nc2struct(ImageName_A,{FieldName_A});
363                    par_civ1.ImageA=DataIn.(FieldName_A);
364                else % usual image formats for image A
365                    [par_civ1.ImageA,VideoObject_A] = read_image(ImageName_A,FileType_A,VideoObject_A,FrameIndex_A_Civ1(ifield));
366                end
367                ImageName_B=fullfile_uvmat(RootPath_B,SubDir_B,RootFile_B,FileExt_B,NomType_B,i2_series_Civ1(ifield),[],j2_series_Civ1(ifield));
368                if strcmp(FileInfo_B.FileType,'netcdf') % case of input images in format netcdf
369                    FieldName_B=Param.InputFields.FieldName;
370                    [DataIn,tild,tild,errormsg]=nc2struct(ImageName_B,{FieldName_B});
371                    par_civ1.ImageB=DataIn.(FieldName_B);
372                else % usual image formats for image B
373                    [par_civ1.ImageB,VideoObject_B] = read_image(ImageName_B,FileType_B,VideoObject_B,FrameIndex_B_Civ1(ifield));
374                end
375            catch ME % display errors in reading input images
376                if ~isempty(ME.message)
377                    disp_uvmat('ERROR', ['error reading input image: ' ME.message],checkrun)
378                    return
379                end
380            end
381            par_civ1.ImageWidth=size(par_civ1.ImageA,2);%FileInfo_A.Width;
382            par_civ1.ImageHeight=size(par_civ1.ImageA,1);%FileInfo_A.Height;
383            list_param=(fieldnames(Param.ActionInput.Civ1))';
384            list_param(strcmp('TestCiv1',list_param))=[];% remove the parameter TestCiv1 from the list
385            Civ1_param=regexprep(list_param,'^.+','Civ1_$0');% insert 'Civ1_' before  each string in list_param
386            Civ1_param=[{'Civ1_ImageA','Civ1_ImageB','Civ1_Time','Civ1_Dt'} Civ1_param]; %insert the names of the two input images
387            %indicate the values of all the global attributes in the output data
388            Data.Civ1_ImageA=ImageName_A;
389            Data.Civ1_ImageB=ImageName_B;
390            i1=i1_series_Civ1(ifield);
391            i2=i1;
392            if ~isempty(i2_series_Civ1)
393                i2=i2_series_Civ1(ifield);
394            end
395            j1=1;
396            if ~isempty(j1_series_Civ1)
397                j1=j1_series_Civ1(ifield);
398            end
399            j2=j1;
400            if ~isempty(j2_series_Civ1)
401                j2=j2_series_Civ1(ifield);
402            end
403            if strcmp(Param.ActionInput.ListCompareMode,'displacement')
404                Data.Civ1_Time=time(i2+1,j2+1);% the time is the time of the secodn image
405                Data.Civ1_Dt=1;% time interval is 1, to yield displacement instead of velocity=displacement/Dt at reading
406            else
407            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
408            Data.Civ1_Dt=time(i2+1,j2+1)-time(i1+1,j1+1);
409            end
410            for ilist=1:length(list_param)
411                Data.(Civ1_param{4+ilist})=Param.ActionInput.Civ1.(list_param{ilist});
412            end
413            Data.ListGlobalAttribute=[Data.ListGlobalAttribute Civ1_param];
414            Data.CivStage=1;
415        end
416        % set the list of variables
417        Data.ListVarName={'Civ1_X','Civ1_Y','Civ1_U','Civ1_V','Civ1_F','Civ1_C'};%  cell array containing the names of the fields to record
418        Data.VarDimName={'nb_vec_1','nb_vec_1','nb_vec_1','nb_vec_1','nb_vec_1','nb_vec_1'};
419        Data.VarAttribute{1}.Role='coord_x';
420        Data.VarAttribute{2}.Role='coord_y';
421        Data.VarAttribute{3}.Role='vector_x';
422        Data.VarAttribute{4}.Role='vector_y';
423        Data.VarAttribute{5}.Role='warnflag';
424        if par_civ1.CheckMask&&~isempty(par_civ1.Mask)
425            if strcmp(maskname,par_civ1.Mask)% mask exist, not already read in civ1
426                par_civ1.Mask=mask; %use mask already opened
427            else
428                try
429                    par_civ1.Mask=imread(par_civ1.Mask);%update the mask, an store it for future use
430                catch ME
431                    if ~isempty(ME.message)
432                        errormsg=['error reading input image: ' ME.message];
433                        disp_uvmat('ERROR',errormsg,checkrun)
434                        return
435                    end
436                end
437                mask=par_civ1.Mask;
438                maskname=par_civ1.Mask;
439            end
440        end
441        if strcmp(Param.ActionInput.ListCompareMode, 'PIV volume')
442            Data.ListVarName=[Data.ListVarName 'Civ1_Z'];
443            Data.Civ1_X=[];Data.Civ1_Y=[];Data.Civ1_Z=[];
444            Data.Civ1_U=[];Data.Civ1_V=[];Data.Civ1_C=[];Data.Civ1_F=[];
445            for ivol=1:NbSlice
446                % caluclate velocity data (y and v in indices, reverse to y component)
447                [xtable, ytable, utable, vtable, ctable, F, result_conv, errormsg] = civ (par_civ1);
448                if ~isempty(errormsg)
449                    disp_uvmat('ERROR',errormsg,checkrun)
450                    return
451                end
452                Data.Civ1_X=[Data.Civ1_X reshape(xtable,[],1)];
453                Data.Civ1_Y=[Data.Civ1_Y reshape(Param.Civ1.ImageHeight-ytable+1,[],1)];
454                Data.Civ1_Z=[Data.Civ1_Z ivol*ones(numel(xtable),1)];% z=image index in image coordinates
455                Data.Civ1_U=[Data.Civ1_U reshape(utable,[],1)];
456                Data.Civ1_V=[Data.Civ1_V reshape(-vtable,[],1)];
457                Data.Civ1_C=[Data.Civ1_C reshape(ctable,[],1)];
458                Data.Civ1_F=[Data.Civ1_C reshape(F,[],1)];
459            end
460        else %usual PIV
461            % caluclate velocity data (y and v in indices, reverse to y component)
462            [xtable, ytable, utable, vtable, ctable, F, result_conv, errormsg] = civ (par_civ1);
463            if ~isempty(errormsg)
464                disp_uvmat('ERROR',errormsg,checkrun)
465                return
466            end
467            Data.Civ1_X=reshape(xtable,[],1);
468            Data.Civ1_Y=reshape(par_civ1.ImageHeight-ytable+1,[],1);
469            Data.Civ1_U=reshape(utable,[],1);
470            Data.Civ1_V=reshape(-vtable,[],1);
471            Data.Civ1_C=reshape(ctable,[],1);
472            Data.Civ1_F=reshape(F,[],1);
473        end
474    else% we use existing Civ1 data
475        if exist('ncfile','var')
476            CivFile=ncfile;
477            [Data,tild,tild,errormsg]=nc2struct(CivFile,'ListGlobalAttribute','absolut_time_T0'); %look for the constant 'absolut_time_T0' to detect old civx data format
478            if ~isempty(errormsg)
479                disp_uvmat('ERROR',errormsg,checkrun)
480                return
481            end
482            [Data,tild,tild,errormsg]=nc2struct(CivFile);%read civ1 and fix1 data in the existing netcdf file
483        elseif isfield(Param,'Civ1_X')
484            Data.ListGlobalAttribute={};
485            Data.ListVarName={};
486            Data.VarDimName={};
487            Data.Civ1_X=Param.Civ1_X;
488            Data.Civ1_Y=Param.Civ1_Y;
489            Data.Civ1_U=Param.Civ1_U;
490            Data.Civ1_V=Param.Civ1_V;
491            Data.Civ1_FF=Param.Civ1_FF;
492        end
493    end
494   
495    %% Fix1
496    if isfield (Param.ActionInput,'Fix1')
497        if ~isfield (Param.ActionInput,'Civ1')% if we use existing Civ1, remove previous data beyond Civ1
498            Fix1_attr=find(strcmp('Fix1',Data.ListGlobalAttribute));
499            Data.ListGlobalAttribute(Fix1_attr)=[];
500            for ilist=1:numel(Fix1_attr)
501                Data=rmfield(Data,Data.ListGlobalAttribute{Fix1_attr(ilist)});
502            end
503        end
504        list_param=fieldnames(Param.ActionInput.Fix1)';
505        Fix1_param=regexprep(list_param,'^.+','Fix1_$0');% insert 'Fix1_' before  each string in ListFixParam
506        %indicate the values of all the global attributes in the output data
507        for ilist=1:length(list_param)
508            Data.(Fix1_param{ilist})=Param.ActionInput.Fix1.(list_param{ilist});
509        end
510        Data.ListGlobalAttribute=[Data.ListGlobalAttribute Fix1_param];
511        Data.ListVarName=[Data.ListVarName {'Civ1_FF'}];
512        Data.VarDimName=[Data.VarDimName {'nb_vec_1'}];
513        nbvar=length(Data.ListVarName);
514        Data.VarAttribute{nbvar}.Role='errorflag';
515        Data.Civ1_FF=fix(Param.ActionInput.Fix1,Data.Civ1_F,Data.Civ1_C,Data.Civ1_U,Data.Civ1_V);
516        Data.CivStage=2;
517    end
518    %% Patch1
519    if isfield (Param.ActionInput,'Patch1')
520        if check_civx
521            errormsg='Civ Matlab input needed for patch';
522            disp_uvmat('ERROR',errormsg,checkrun)
523            return
524        end
525       
526        % record the processing parameters of Patch1 as global attributes in the result nc file
527        list_param=fieldnames(Param.ActionInput.Patch1)';
528        list_param(strcmp('TestPatch1',list_param))=[];% remove 'TestPatch1' from the list of parameters
529        Patch1_param=regexprep(list_param,'^.+','Patch1_$0');% insert 'Patch1_' before  each parameter name
530        for ilist=1:length(list_param)
531            Data.(Patch1_param{ilist})=Param.ActionInput.Patch1.(list_param{ilist});
532        end
533        Data.CivStage=3;% record the new state of processing
534        Data.ListGlobalAttribute=[Data.ListGlobalAttribute Patch1_param];
535       
536        % list the variables to record
537        nbvar=length(Data.ListVarName);
538        Data.ListVarName=[Data.ListVarName {'Civ1_U_smooth','Civ1_V_smooth','Civ1_SubRange','Civ1_NbCentres','Civ1_Coord_tps','Civ1_U_tps','Civ1_V_tps'}];
539        Data.VarDimName=[Data.VarDimName {'nb_vec_1','nb_vec_1',{'nb_coord','nb_bounds','nb_subdomain_1'},'nb_subdomain_1',...
540            {'nb_tps_1','nb_coord','nb_subdomain_1'},{'nb_tps_1','nb_subdomain_1'},{'nb_tps_1','nb_subdomain_1'}}];
541        Data.VarAttribute{nbvar+1}.Role='vector_x';
542        Data.VarAttribute{nbvar+2}.Role='vector_y';
543        Data.VarAttribute{nbvar+5}.Role='coord_tps';
544        Data.VarAttribute{nbvar+6}.Role='vector_x';
545        Data.VarAttribute{nbvar+7}.Role='vector_y';
546        Data.Civ1_U_smooth=Data.Civ1_U; % zeros(size(Data.Civ1_X));
547        Data.Civ1_V_smooth=Data.Civ1_V; %zeros(size(Data.Civ1_X));
548        if isfield(Data,'Civ1_FF')
549            ind_good=find(Data.Civ1_FF==0);
550        else
551            ind_good=1:numel(Data.Civ1_X);
552        end
553       
554        % perform Patch calculation using the UVMAT fct 'filter_tps'
555        [Data.Civ1_SubRange,Data.Civ1_NbCentres,Data.Civ1_Coord_tps,Data.Civ1_U_tps,Data.Civ1_V_tps,tild,Ures, Vres,tild,FFres]=...
556            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);
557        Data.Civ1_U_smooth(ind_good)=Ures;% take the interpolated (smoothed) velocity values for good vectors, keep 0 for the others
558        Data.Civ1_V_smooth(ind_good)=Vres;
559        Data.Civ1_FF(ind_good)=FFres;
560    end
561   
562    %% Civ2
563    if isfield (Param.ActionInput,'Civ2')
564        par_civ2=Param.ActionInput.Civ2;
565        if CheckInputFile % read input images (except in mode Test where it is introduced directly in Param.ActionInput.Civ1.ImageNameA and B)
566            par_civ2.ImageA=[];
567            par_civ2.ImageB=[];
568            i1=i1_series_Civ2(ifield);
569            i2=i1;
570            if ~isempty(i2_series_Civ2)
571                i2=i2_series_Civ2(ifield);
572            end
573            j1=1;
574            if ~isempty(j1_series_Civ2)
575                j1=j1_series_Civ2(ifield);
576            end
577            j2=j1;
578            if ~isempty(j2_series_Civ2)
579                j2=j2_series_Civ2(ifield);
580            end
581            ImageName_A_Civ2=fullfile_uvmat(RootPath_A,SubDir_A,RootFile_A,FileExt_A,NomType_A,i1,[],j1);
582           
583            if strcmp(ImageName_A_Civ2,ImageName_A) && isequal(FrameIndex_A_Civ1(ifield),FrameIndex_A_Civ2(ifield))
584                par_civ2.ImageA=par_civ1.ImageA;
585            else
586                [par_civ2.ImageA,VideoObject_A] = read_image(ImageName_A_Civ2,FileType_A,VideoObject_A,FrameIndex_A_Civ2(ifield));
587            end
588            ImageName_B_Civ2=fullfile_uvmat(RootPath_B,SubDir_B,RootFile_B,FileExt_B,NomType_B,i2,[],j2);
589            if strcmp(ImageName_B_Civ2,ImageName_B) && isequal(FrameIndex_B_Civ1(ifield),FrameIndex_B_Civ2)
590                par_civ2.ImageB=par_civ1.ImageB;
591            else
592                [par_civ2.ImageB,VideoObject_B] = read_image(ImageName_B_Civ2,FileType_B,VideoObject_B,FrameIndex_B_Civ2(ifield));
593            end
594            if strcmp(Param.ActionInput.ListCompareMode,'PIV')
595                ncfile=fullfile_uvmat(RootPath_A,OutputDir,RootFile_A,'.nc',NomTypeNc,i1,i2,j1,j2);
596            else % displacement
597                ncfile=fullfile_uvmat(RootPath_A,OutputDir,RootFile_A,'.nc',NomTypeNc,i2,[],j2);
598            end
599            par_civ2.ImageWidth=FileInfo_A.Width;
600            par_civ2.ImageHeight=FileInfo_A.Height;
601            if isfield(par_civ2,'Grid')% grid points set as input file
602                if ischar(par_civ2.Grid)%read the grid file if the input is a file name
603                    par_civ2.Grid=dlmread(par_civ2.Grid);
604                    par_civ2.Grid(1,:)=[];%the first line must be removed (heading in the grid file)
605                end
606            else% automatic grid
607                minix=floor(par_civ2.Dx/2)-0.5;
608                maxix=minix+par_civ2.Dx*floor((par_civ2.ImageWidth-1)/par_civ2.Dx);
609                miniy=floor(par_civ2.Dy/2)-0.5;
610                maxiy=minix+par_civ2.Dy*floor((par_civ2.ImageHeight-1)/par_civ2.Dy);
611                [GridX,GridY]=meshgrid(minix:par_civ2.Dx:maxix,miniy:par_civ2.Dy:maxiy);
612                par_civ2.Grid(:,1)=reshape(GridX,[],1);
613                par_civ2.Grid(:,2)=reshape(GridY,[],1);
614            end
615        end
616       
617        % get the guess from patch1 or patch2 (case 'CheckCiv3')
618        if CheckInputFile % read input images (except in mode Test where it is introduced directly in Param.ActionInput.Civ1.ImageNameA and B)
619            if isfield (par_civ2,'CheckCiv3') && par_civ2.CheckCiv3 %get the guess from  patch2
620                SubRange= Data.Civ2_SubRange;
621                NbCentres=Data.Civ2_NbCentres;
622                Coord_tps=Data.Civ2_Coord_tps;
623                U_tps=Data.Civ2_U_tps;
624                V_tps=Data.Civ2_V_tps;
625                CivStage=Data.CivStage;%store the current CivStage
626                Civ1_Dt=Data.Civ2_Dt;
627                Data=[];%reinitialise the result structure Data
628                Data.ListGlobalAttribute={'Conventions','Program','CivStage'};
629                Data.Conventions='uvmat/civdata';% states the conventions used for the description of field variables and attributes
630                Data.Program='civ_series';
631                Data.CivStage=CivStage+1;%update the current civStage after reinitialisation of Data
632                Data.ListVarName={};
633                Data.VarDimName={};
634            else % get the guess from patch1
635                SubRange= Data.Civ1_SubRange;
636                NbCentres=Data.Civ1_NbCentres;
637                Coord_tps=Data.Civ1_Coord_tps;
638                U_tps=Data.Civ1_U_tps;
639                V_tps=Data.Civ1_V_tps;
640                Civ1_Dt=Data.Civ1_Dt;
641                Data.CivStage=4;
642            end
643        else
644            SubRange= par_civ2.Civ1_SubRange;
645            NbCentres=par_civ2.Civ1_NbCentres;
646            Coord_tps=par_civ2.Civ1_Coord_tps;
647            U_tps=par_civ2.Civ1_U_tps;
648            V_tps=par_civ2.Civ1_V_tps;
649            Civ1_Dt=par_civ2.Civ1_Dt;
650            Civ2_Dt=par_civ2.Civ1_Dt;
651            Data.ListVarName={};
652            Data.VarDimName={};
653        end
654        Shiftx=zeros(size(par_civ2.Grid,1),1);% shift expected from civ1 data
655        Shifty=zeros(size(par_civ2.Grid,1),1);
656        nbval=zeros(size(par_civ2.Grid,1),1);% nbre of interpolated values at each grid point (from the different patch subdomains)
657        if par_civ2.CheckDeformation
658            DUDX=zeros(size(par_civ2.Grid,1),1);
659            DUDY=zeros(size(par_civ2.Grid,1),1);
660            DVDX=zeros(size(par_civ2.Grid,1),1);
661            DVDY=zeros(size(par_civ2.Grid,1),1);
662        end
663        NbSubDomain=size(SubRange,3);
664        for isub=1:NbSubDomain% for each sub-domain of Patch1
665            nbvec_sub=NbCentres(isub);% nbre of Civ vectors in the subdomain
666            ind_sel=find(par_civ2.Grid(:,1)>=SubRange(1,1,isub) & par_civ2.Grid(:,1)<=SubRange(1,2,isub) &...
667                par_civ2.Grid(:,2)>=SubRange(2,1,isub) & par_civ2.Grid(:,2)<=SubRange(2,2,isub));% grid points in the subdomain
668            if ~isempty(ind_sel)
669                epoints = par_civ2.Grid(ind_sel,:);% coordinates of interpolation sites (measurement grids)
670                ctrs=Coord_tps(1:nbvec_sub,:,isub) ;%(=initial points) ctrs
671                nbval(ind_sel)=nbval(ind_sel)+1;% records the number of values for each interpolation point (in case of subdomain overlap)
672                EM = tps_eval(epoints,ctrs);% thin plate spline (tps) coefficient
673                Shiftx(ind_sel)=Shiftx(ind_sel)+EM*U_tps(1:nbvec_sub+3,isub);%velocity shift estimated by tps from civ1
674                Shifty(ind_sel)=Shifty(ind_sel)+EM*V_tps(1:nbvec_sub+3,isub);
675                if par_civ2.CheckDeformation
676                    [EMDX,EMDY] = tps_eval_dxy(epoints,ctrs);%2D matrix of distances between extrapolation points epoints and spline centres (=site points) ctrs
677                    DUDX(ind_sel)=DUDX(ind_sel)+EMDX*U_tps(1:nbvec_sub+3,isub);
678                    DUDY(ind_sel)=DUDY(ind_sel)+EMDY*U_tps(1:nbvec_sub+3,isub);
679                    DVDX(ind_sel)=DVDX(ind_sel)+EMDX*V_tps(1:nbvec_sub+3,isub);
680                    DVDY(ind_sel)=DVDY(ind_sel)+EMDY*V_tps(1:nbvec_sub+3,isub);
681                end
682            end
683        end
684        if par_civ2.CheckMask&&~isempty(par_civ2.Mask)
685            if strcmp(maskname,par_civ2.Mask)% mask exist, not already read in civ1
686                par_civ2.Mask=mask; %use mask already opened
687            else
688                par_civ2.Mask=imread(par_civ2.Mask);%update the mask, and store it for future use
689                mask=par_civ2.Mask;
690                maskname=par_civ2.Mask;
691            end
692        end
693%         ibx2=ceil(par_civ2.CorrBoxSize(1)/2);
694%         iby2=ceil(par_civ2.CorrBoxSize(2)/2);
695       % par_civ2.SearchBoxSize(1)=2*ibx2+9;% search ara +-4 pixels around the guess
696        %par_civ2.SearchBoxSize(2)=2*iby2+9;
697        if CheckInputFile % else Dt given by par_civ2
698            if strcmp(Param.ActionInput.ListCompareMode,'displacement')
699                Civ1_Dt=1;
700                Civ2_Dt=1;
701            else
702                Civ2_Dt=time(i2+1,j2+1)-time(i1+1,j1+1);
703            end
704        end
705        par_civ2.SearchBoxShift=(Civ2_Dt/Civ1_Dt)*[Shiftx(nbval>=1)./nbval(nbval>=1) Shifty(nbval>=1)./nbval(nbval>=1)];
706        % shift the grid points by half the expected shift to provide the correlation box position in image A
707        par_civ2.Grid=[par_civ2.Grid(nbval>=1,1)-par_civ2.SearchBoxShift(nbval>=1,1)/2 par_civ2.Grid(nbval>=1,2)-par_civ2.SearchBoxShift(nbval>=1,2)/2];
708        if par_civ2.CheckDeformation
709            par_civ2.DUDX=DUDX./nbval;
710            par_civ2.DUDY=DUDY./nbval;
711            par_civ2.DVDX=DVDX./nbval;
712            par_civ2.DVDY=DVDY./nbval;
713        end
714       
715        % calculate velocity data (y and v in image indices, reverse to y component)
716        [xtable, ytable, utable, vtable, ctable, F,result_conv,errormsg] = civ (par_civ2);
717       
718        list_param=(fieldnames(Param.ActionInput.Civ2))';
719        list_param(strcmp('TestCiv2',list_param))=[];% remove the parameter TestCiv2 from the list
720        Civ2_param=regexprep(list_param,'^.+','Civ2_$0');% insert 'Civ2_' before  each string in list_param
721        Civ2_param=[{'Civ2_ImageA','Civ2_ImageB','Civ2_Time','Civ2_Dt'} Civ2_param]; %insert the names of the two input images
722        %indicate the values of all the global attributes in the output data
723        if exist('ImageName_A','var')
724            Data.Civ2_ImageA=ImageName_A;
725            Data.Civ2_ImageB=ImageName_B;
726             if strcmp(Param.ActionInput.ListCompareMode,'displacement')
727                Data.Civ2_Time=time(i2+1,j2+1);% the time is the time of the secodn image
728                Data.Civ2_Dt=1;% time interval is 1, to yield displacement instead of velocity=displacement/Dt at reading
729             else
730            Data.Civ2_Time=(time(i2+1,j2+1)+time(i1+1,j1+1))/2;
731            Data.Civ2_Dt=Civ2_Dt;
732             end
733        end
734        %         Data.Civ2_Time=1;
735        %         Data.Civ2_Dt=1;
736        for ilist=1:length(list_param)
737            Data.(Civ2_param{4+ilist})=Param.ActionInput.Civ2.(list_param{ilist});
738        end
739        Data.ListGlobalAttribute=[Data.ListGlobalAttribute Civ2_param];
740       
741        nbvar=numel(Data.ListVarName);
742        % define the Civ2 variable (if Civ2 data are not replaced from previous calculation)
743        if isempty(find(strcmp('Civ2_X',Data.ListVarName),1))
744            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
745            Data.VarDimName=[Data.VarDimName {'nb_vec_2','nb_vec_2','nb_vec_2','nb_vec_2','nb_vec_2','nb_vec_2'}];
746            Data.VarAttribute{nbvar+1}.Role='coord_x';
747            Data.VarAttribute{nbvar+2}.Role='coord_y';
748            Data.VarAttribute{nbvar+3}.Role='vector_x';
749            Data.VarAttribute{nbvar+4}.Role='vector_y';
750            Data.VarAttribute{nbvar+5}.Role='warnflag';
751        end
752        Data.Civ2_X=reshape(xtable,[],1);
753        Data.Civ2_Y=reshape(size(par_civ2.ImageA,1)-ytable+1,[],1);
754        Data.Civ2_U=reshape(utable,[],1);
755        Data.Civ2_V=reshape(-vtable,[],1);
756        Data.Civ2_C=reshape(ctable,[],1);
757        Data.Civ2_F=reshape(F,[],1);
758    elseif ~isfield(Data,'ListVarName') % we start there, using existing Civ2 data
759        if exist('ncfile','var')
760            CivFile=ncfile;
761            [Data,tild,tild,errormsg]=nc2struct(CivFile);%read civ1 and fix1 data in the existing netcdf file
762            if ~isempty(errormsg)
763                disp_uvmat('ERROR',errormsg,checkrun)
764                return
765            end         
766        elseif isfield(Param,'Civ2_X')% use Civ2 data as input in Param (test mode)
767            Data.ListGlobalAttribute={};
768            Data.ListVarName={};
769            Data.VarDimName={};
770            Data.Civ2_X=Param.Civ2_X;
771            Data.Civ2_Y=Param.Civ2_Y;
772            Data.Civ2_U=Param.Civ2_U;
773            Data.Civ2_V=Param.Civ2_V;
774            Data.Civ2_FF=Param.Civ2_FF;
775        end
776    end
777   
778    %% Fix2
779    if isfield (Param.ActionInput,'Fix2')
780        list_param=fieldnames(Param.ActionInput.Fix2)';
781        Fix2_param=regexprep(list_param,'^.+','Fix2_$0');% insert 'Fix1_' before  each string in ListFixParam
782        %indicate the values of all the global attributes in the output data
783        for ilist=1:length(list_param)
784            Data.(Fix2_param{ilist})=Param.ActionInput.Fix2.(list_param{ilist});
785        end
786        Data.ListGlobalAttribute=[Data.ListGlobalAttribute Fix2_param];
787        %
788        %         ListFixParam=fieldnames(Param.ActionInput.Fix2);
789        %         for ilist=1:length(ListFixParam)
790        %             ParamName=ListFixParam{ilist};
791        %             ListName=['Fix2_' ParamName];
792        %             eval(['Data.ListGlobalAttribute=[Data.ListGlobalAttribute ''' ParamName '''];'])
793        %             eval(['Data.' ListName '=Param.ActionInput.Fix2.' ParamName ';'])
794        %         end
795        if check_civx
796            if ~isfield(Data,'fix2')
797                Data.ListGlobalAttribute=[Data.ListGlobalAttribute 'fix2'];
798                Data.fix2=1;
799                Data.ListVarName=[Data.ListVarName {'vec2_FixFlag'}];
800                Data.VarDimName=[Data.VarDimName {'nb_vectors2'}];
801            end
802            Data.vec_FixFlag=fix(Param.Fix2,Data.vec2_F,Data.vec2_C,Data.vec2_U,Data.vec2_V,Data.vec2_X,Data.vec2_Y);
803        else
804            Data.ListVarName=[Data.ListVarName {'Civ2_FF'}];
805            Data.VarDimName=[Data.VarDimName {'nb_vec_2'}];
806            nbvar=length(Data.ListVarName);
807            Data.VarAttribute{nbvar}.Role='errorflag';
808            Data.Civ2_FF=double(fix(Param.ActionInput.Fix2,Data.Civ2_F,Data.Civ2_C,Data.Civ2_U,Data.Civ2_V));
809            Data.CivStage=Data.CivStage+1;
810        end
811       
812    end
813   
814    %% Patch2
815    if isfield (Param.ActionInput,'Patch2')
816        list_param=fieldnames(Param.ActionInput.Patch2)';
817        list_param(strcmp('TestPatch2',list_param))=[];% remove the parameter TestCiv1 from the list
818        Patch2_param=regexprep(list_param,'^.+','Patch2_$0');% insert 'Fix1_' before  each string in ListFixParam
819        %indicate the values of all the global attributes in the output data
820        for ilist=1:length(list_param)
821            Data.(Patch2_param{ilist})=Param.ActionInput.Patch2.(list_param{ilist});
822        end
823        Data.ListGlobalAttribute=[Data.ListGlobalAttribute Patch2_param];
824       
825        nbvar=length(Data.ListVarName);
826        Data.ListVarName=[Data.ListVarName {'Civ2_U_smooth','Civ2_V_smooth','Civ2_SubRange','Civ2_NbCentres','Civ2_Coord_tps','Civ2_U_tps','Civ2_V_tps'}];
827        Data.VarDimName=[Data.VarDimName {'nb_vec_2','nb_vec_2',{'nb_coord','nb_bounds','nb_subdomain_2'},{'nb_subdomain_2'},...
828            {'nb_tps_2','nb_coord','nb_subdomain_2'},{'nb_tps_2','nb_subdomain_2'},{'nb_tps_2','nb_subdomain_2'}}];
829       
830        Data.VarAttribute{nbvar+1}.Role='vector_x';
831        Data.VarAttribute{nbvar+2}.Role='vector_y';
832        Data.VarAttribute{nbvar+5}.Role='coord_tps';
833        Data.VarAttribute{nbvar+6}.Role='vector_x';
834        Data.VarAttribute{nbvar+7}.Role='vector_y';
835        Data.Civ2_U_smooth=Data.Civ2_U; % zeros(size(Data.Civ2_X));
836        Data.Civ2_V_smooth=Data.Civ2_V; %zeros(size(Data.Civ2_X));
837        if isfield(Data,'Civ2_FF')
838            ind_good=find(Data.Civ2_FF==0);
839        else
840            ind_good=1:numel(Data.Civ2_X);
841        end
842        [Data.Civ2_SubRange,Data.Civ2_NbCentres,Data.Civ2_Coord_tps,Data.Civ2_U_tps,Data.Civ2_V_tps,tild,Ures, Vres,tild,FFres]=...
843            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);
844        Data.Civ2_U_smooth(ind_good)=Ures;
845        Data.Civ2_V_smooth(ind_good)=Vres;
846        Data.Civ2_FF(ind_good)=FFres;
847        Data.CivStage=Data.CivStage+1;
848    end
849   
850    %% write result in a netcdf file if requested
851    if CheckOutputFile
852        errormsg=struct2nc(ncfile,Data);
853        if isempty(errormsg)
854            disp([ncfile ' written'])
855        else
856            disp(errormsg)
857        end
858    end
859end
860
861% 'civ': function piv.m adapted from PIVlab http://pivlab.blogspot.com/
862%--------------------------------------------------------------------------
863% function [xtable ytable utable vtable typevector] = civ (image1,image2,ibx,iby step, subpixfinder, mask, roi)
864%
865% OUTPUT:
866% xtable: set of x coordinates
867% ytable: set of y coordiantes
868% utable: set of u displacements (along x)
869% vtable: set of v displacements (along y)
870% ctable: max image correlation for each vector
871% typevector: set of flags, =1 for good, =0 for NaN vectors
872%
873%INPUT:
874% par_civ: structure of input parameters, with fields:
875%  .ImageA: first image for correlation (matrix)
876%  .ImageB: second image for correlation(matrix)
877%  .CorrBoxSize: 1,2 vector giving the size of the correlation box in x and y
878%  .SearchBoxSize:  1,2 vector giving the size of the search box in x and y
879%  .SearchBoxShift: 1,2 vector or 2 column matrix (for civ2) giving the shift of the search box in x and y
880%  .CorrSmooth: =1 or 2 determines the choice of the sub-pixel determination of the correlation max
881%  .ImageWidth: nb of pixels of the image in x
882%  .Dx, Dy: mesh for the PIV calculation
883%  .Grid: grid giving the PIV calculation points (alternative to .Dx .Dy): centres of the correlation boxes in Image A
884%  .Mask: name of a mask file or mask image matrix itself
885%  .MinIma: thresholds for image luminosity
886%  .MaxIma
887%  .CheckDeformation=1 for subpixel interpolation and image deformation (linear transform)
888%  .DUDX: matrix of deformation obtained from patch at each grid point
889%  .DUDY
890%  .DVDX:
891%  .DVDY
892
893function [xtable,ytable,utable,vtable,ctable,F,result_conv,errormsg] = civ (par_civ)
894
895%% prepare measurement grid
896if isfield(par_civ,'Grid')% grid points set as input, central positions of the sub-images in image A
897    if ischar(par_civ.Grid)%read the grid file if the input is a file name (grid in x, y image coordinates)
898        par_civ.Grid=dlmread(par_civ.Grid);
899        par_civ.Grid(1,:)=[];%the first line must be removed (heading in the grid file)
900    end
901    % else par_civ.Grid is already an array, no action here
902else% automatic grid in x, y image coordinates
903    minix=floor(par_civ.Dx/2)-0.5;
904    maxix=minix+par_civ.Dx*floor((par_civ.ImageWidth-1)/par_civ.Dx);
905    miniy=floor(par_civ.Dy/2)-0.5;% first automatic grid point at half the mesh Dy
906    maxiy=minix+par_civ.Dy*floor((par_civ.ImageHeight-1)/par_civ.Dy);
907    [GridX,GridY]=meshgrid(minix:par_civ.Dx:maxix,miniy:par_civ.Dy:maxiy);
908    par_civ.Grid(:,1)=reshape(GridX,[],1);
909    par_civ.Grid(:,2)=reshape(GridY,[],1);% increases with array index
910end
911nbvec=size(par_civ.Grid,1);
912
913%% prepare correlation and search boxes
914ibx2=ceil(par_civ.CorrBoxSize(1)/2);
915iby2=ceil(par_civ.CorrBoxSize(2)/2);
916isx2=ceil(par_civ.SearchBoxSize(1)/2);
917isy2=ceil(par_civ.SearchBoxSize(2)/2);
918shiftx=round(par_civ.SearchBoxShift(:,1));%use the input shift estimate, rounded to the next integer value
919shifty=-round(par_civ.SearchBoxShift(:,2));% sign minus because image j index increases when y decreases
920if numel(shiftx)==1% case of a unique shift for the whole field( civ1)
921    shiftx=shiftx*ones(nbvec,1);
922    shifty=shifty*ones(nbvec,1);
923end
924
925%% Array initialisation and default output  if par_civ.CorrSmooth=0 (just the grid calculated, no civ computation)
926xtable=round(par_civ.Grid(:,1)+0.5)-0.5;
927ytable=round(par_civ.ImageHeight-par_civ.Grid(:,2)+0.5)-0.5;% y index corresponding to the position in image coordiantes
928utable=shiftx;%zeros(nbvec,1);
929vtable=shifty;%zeros(nbvec,1);
930ctable=zeros(nbvec,1);
931F=zeros(nbvec,1);
932result_conv=[];
933errormsg='';
934
935%% prepare mask
936if isfield(par_civ,'Mask') && ~isempty(par_civ.Mask)
937    if strcmp(par_civ.Mask,'all')
938        return    % get the grid only, no civ calculation
939    elseif ischar(par_civ.Mask)
940        par_civ.Mask=imread(par_civ.Mask);% read the mask if not allready done
941    end
942end
943check_MinIma=isfield(par_civ,'MinIma');% test for image luminosity threshold
944check_MaxIma=isfield(par_civ,'MaxIma') && ~isempty(par_civ.MaxIma);
945
946par_civ.ImageA=sum(double(par_civ.ImageA),3);%sum over rgb component for color images
947par_civ.ImageB=sum(double(par_civ.ImageB),3);
948[npy_ima npx_ima]=size(par_civ.ImageA);
949if ~isequal(size(par_civ.ImageB),[npy_ima npx_ima])
950    errormsg='image pair with unequal size';
951    return
952end
953
954%% Apply mask
955% Convention for mask IDEAS TO IMPLEMENT ?
956% mask >200 : velocity calculated
957%  200 >=mask>150;velocity not calculated, interpolation allowed (bad spots)
958% 150>=mask >100: velocity not calculated, nor interpolated
959%  100>=mask> 20: velocity not calculated, impermeable (no flux through mask boundaries)
960%  20>=mask: velocity=0
961checkmask=0;
962MinA=min(min(par_civ.ImageA));
963MinB=min(min(par_civ.ImageB));
964if isfield(par_civ,'Mask') && ~isempty(par_civ.Mask)
965    checkmask=1;
966    if ~isequal(size(par_civ.Mask),[npy_ima npx_ima])
967        errormsg='mask must be an image with the same size as the images';
968        return
969    end
970    %  check_noflux=(par_civ.Mask<100) ;%TODO: to implement
971    check_undefined=(par_civ.Mask<200 & par_civ.Mask>=20 );
972    par_civ.ImageA(check_undefined)=MinA;% put image A to zero (i.e. the min image value) in the undefined  area
973    par_civ.ImageB(check_undefined)=MinB;% put image B to zero (i.e. the min image value) in the undefined  area
974end
975
976%% compute image correlations: MAINLOOP on velocity vectors
977corrmax=0;
978sum_square=1;% default
979mesh=1;% default
980CheckDeformation=isfield(par_civ,'CheckDeformation')&& par_civ.CheckDeformation==1;
981if CheckDeformation
982    mesh=0.25;%mesh in pixels for subpixel image interpolation (x 4 in each direction)
983end
984
985if par_civ.CorrSmooth~=0 % par_civ.CorrSmooth=0 implies no civ computation (just input image and grid points given)
986    for ivec=1:nbvec
987        iref=round(par_civ.Grid(ivec,1)+0.5);% xindex on the image A for the middle of the correlation box
988        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
989        F(ivec)=0;
990        subrange1_x=iref-ibx2:iref+ibx2;% x indices defining the first subimage
991        subrange1_y=jref-iby2:jref+iby2;% y indices defining the first subimage
992        subrange2_x=iref+shiftx(ivec)-isx2:iref+shiftx(ivec)+isx2;%x indices defining the second subimage
993        subrange2_y=jref+shifty(ivec)-isy2:jref+shifty(ivec)+isy2;%y indices defining the second subimage
994        image1_crop=MinA*ones(numel(subrange1_y),numel(subrange1_x));% default value=min of image A
995        image2_crop=MinA*ones(numel(subrange2_y),numel(subrange2_x));% default value=min of image A
996        check1_x=subrange1_x>=1 & subrange1_x<=par_civ.ImageWidth;% check which points in the subimage 1 are contained in the initial image 1
997        check1_y=subrange1_y>=1 & subrange1_y<=par_civ.ImageHeight;
998        check2_x=subrange2_x>=1 & subrange2_x<=par_civ.ImageWidth;% check which points in the subimage 2 are contained in the initial image 2
999        check2_y=subrange2_y>=1 & subrange2_y<=par_civ.ImageHeight;
1000        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
1001        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
1002        image1_mean=mean(mean(image1_crop));
1003        image2_mean=mean(mean(image2_crop));
1004        %threshold on image minimum
1005        if check_MinIma && (image1_mean < par_civ.MinIma || image2_mean < par_civ.MinIma)
1006            F(ivec)=3;
1007        end
1008        %threshold on image maximum
1009        if check_MaxIma && (image1_mean > par_civ.MaxIma || image2_mean > par_civ.MaxIma)
1010            F(ivec)=3;
1011        end
1012       
1013        if F(ivec)~=3
1014            image1_crop=image1_crop-image1_mean;%substract the mean
1015            image2_crop=image2_crop-image2_mean;
1016            if CheckDeformation
1017                xi=(1:mesh:size(image1_crop,2));
1018                yi=(1:mesh:size(image1_crop,1))';
1019                [XI,YI]=meshgrid(xi-ceil(size(image1_crop,2)/2),yi-ceil(size(image1_crop,1)/2));
1020                XIant=XI-par_civ.DUDX(ivec)*XI-par_civ.DUDY(ivec)*YI+ceil(size(image1_crop,2)/2);
1021                YIant=YI-par_civ.DVDX(ivec)*XI-par_civ.DVDY(ivec)*YI+ceil(size(image1_crop,1)/2);
1022                image1_crop=interp2(image1_crop,XIant,YIant);
1023                image1_crop(isnan(image1_crop))=0;
1024                xi=(1:mesh:size(image2_crop,2));
1025                yi=(1:mesh:size(image2_crop,1))';
1026                image2_crop=interp2(image2_crop,xi,yi);
1027                image2_crop(isnan(image2_crop))=0;
1028                %%
1029            end
1030            sum_square=sum(sum(image1_crop.*image1_crop));
1031            %reference: Oliver Pust, PIV: Direct Cross-Correlation
1032            result_conv= conv2(image2_crop,flipdim(flipdim(image1_crop,2),1),'valid');
1033            corrmax= max(max(result_conv));
1034            result_conv=(result_conv/corrmax)*255; %normalize, peak=always 255
1035            %Find the correlation max, at 255
1036            [y,x] = find(result_conv==255,1);
1037            if ~isempty(y) && ~isempty(x)
1038                try
1039                    if par_civ.CorrSmooth==1
1040                        [vector,F(ivec)] = SUBPIXGAUSS (result_conv,x,y);
1041                    elseif par_civ.CorrSmooth==2
1042                        [vector,F(ivec)] = SUBPIX2DGAUSS (result_conv,x,y);
1043                    end
1044                    utable(ivec)=vector(1)*mesh+shiftx(ivec);
1045                    vtable(ivec)=vector(2)*mesh+shifty(ivec);
1046                    xtable(ivec)=iref+utable(ivec)/2-0.5;% convec flow (velocity taken at the point middle from imgae 1 and 2)
1047                    ytable(ivec)=jref+vtable(ivec)/2-0.5;% and position of pixel 1=0.5 (convention for image coordinates=0 at the edge)
1048                    iref=round(xtable(ivec));% image index for the middle of the vector
1049                    jref=round(ytable(ivec));
1050                    if checkmask && par_civ.Mask(jref,iref)<200 && par_civ.Mask(jref,iref)>=100
1051                        utable(ivec)=0;
1052                        vtable(ivec)=0;
1053                        F(ivec)=3;
1054                    end
1055                    ctable(ivec)=corrmax/sum_square;% correlation value
1056                catch ME
1057                    F(ivec)=3;
1058                end
1059            else
1060                F(ivec)=3;
1061            end
1062        end
1063    end
1064end
1065result_conv=result_conv*corrmax/(255*sum_square);% keep the last correlation matrix for output
1066
1067%------------------------------------------------------------------------
1068% --- Find the maximum of the correlation function after interpolation
1069% OUPUT:
1070% vector = optimum displacement vector with subpixel correction
1071% F =flag: =0 OK
1072%           =-2 , warning: max too close to the edge of the search box (1 pixel margin)
1073% INPUT:
1074% x,y: position of the maximum correlation at integer values
1075
1076function [vector,F] = SUBPIXGAUSS (result_conv,x,y)
1077%------------------------------------------------------------------------
1078% vector=[0 0]; %default
1079F=0;
1080[npy,npx]=size(result_conv);
1081result_conv(result_conv<1)=1; %set to 1 correlation values smaller than 1 (to avoid divergence in the log)
1082%the following 8 lines are copyright (c) 1998, Uri Shavit, Roi Gurka, Alex Liberzon, Technion ᅵ Israel Institute of Technology
1083%http://urapiv.wordpress.com
1084peaky = y;
1085if y <= npy-1 && y >= 1
1086    f0 = log(result_conv(y,x));
1087    f1 = log(result_conv(y-1,x));
1088    f2 = log(result_conv(y+1,x));
1089    peaky = peaky+ (f1-f2)/(2*f1-4*f0+2*f2);
1090else
1091    F=-2; % warning flag for vector truncated by the limited search box
1092end
1093peakx=x;
1094if x <= npx-1 && x >= 1
1095    f0 = log(result_conv(y,x));
1096    f1 = log(result_conv(y,x-1));
1097    f2 = log(result_conv(y,x+1));
1098    peakx = peakx+ (f1-f2)/(2*f1-4*f0+2*f2);
1099else
1100    F=-2; % warning flag for vector truncated by the limited search box
1101end
1102vector=[peakx-floor(npx/2)-1 peaky-floor(npy/2)-1];
1103
1104%------------------------------------------------------------------------
1105% --- Find the maximum of the correlation function after interpolation
1106function [vector,F] = SUBPIX2DGAUSS (result_conv,x,y)
1107%------------------------------------------------------------------------
1108% vector=[0 0]; %default
1109F=-2;
1110peaky=y;
1111peakx=x;
1112result_conv(result_conv<1)=1; %set to 1 correlation values smaller than 1 (to avoid divergence in the log)
1113[npy,npx]=size(result_conv);
1114if (x <= npx-1) && (y <= npy-1) && (x >= 1) && (y >= 1)
1115    F=0;
1116    for i=-1:1
1117        for j=-1:1
1118            %following 15 lines based on
1119            %H. Nobach ï¿œ M. Honkanen (2005)
1120            %Two-dimensional Gaussian regression for sub-pixel displacement
1121            %estimation in particle image velocimetry or particle position
1122            %estimation in particle tracking velocimetry
1123            %Experiments in Fluids (2005) 38: 511ï¿œ515
1124            c10(j+2,i+2)=i*log(result_conv(y+j, x+i));
1125            c01(j+2,i+2)=j*log(result_conv(y+j, x+i));
1126            c11(j+2,i+2)=i*j*log(result_conv(y+j, x+i));
1127            c20(j+2,i+2)=(3*i^2-2)*log(result_conv(y+j, x+i));
1128            c02(j+2,i+2)=(3*j^2-2)*log(result_conv(y+j, x+i));
1129        end
1130    end
1131    c10=(1/6)*sum(sum(c10));
1132    c01=(1/6)*sum(sum(c01));
1133    c11=(1/4)*sum(sum(c11));
1134    c20=(1/6)*sum(sum(c20));
1135    c02=(1/6)*sum(sum(c02));
1136    deltax=(c11*c01-2*c10*c02)/(4*c20*c02-c11^2);
1137    deltay=(c11*c10-2*c01*c20)/(4*c20*c02-c11^2);
1138    if abs(deltax)<1
1139        peakx=x+deltax;
1140    end
1141    if abs(deltay)<1
1142        peaky=y+deltay;
1143    end
1144end
1145vector=[peakx-floor(npx/2)-1 peaky-floor(npy/2)-1];
1146
1147%'RUN_FIX': function for fixing velocity fields:
1148%-----------------------------------------------
1149% RUN_FIX(filename,field,flagindex,thresh_vecC,thresh_vel,iter,flag_mask,maskname,fileref,fieldref)
1150%
1151%filename: name of the netcdf file (used as input and output)
1152%field: structure specifying the names of the fields to fix (depending on civ1 or civ2)
1153%.vel_type='civ1' or 'civ2';
1154%.nb=name of the dimension common to the field to fix ('nb_vectors' for civ1);
1155%.fixflag=name of fix flag variable ('vec_FixFlag' for civ1)
1156%flagindex: flag specifying which values of vec_f are removed:
1157% if flagindex(1)=1: vec_f=-2 vectors are removed
1158% if flagindex(2)=1: vec_f=3 vectors are removed
1159% if flagindex(3)=1: vec_f=2 vectors are removed (if iter=1) or vec_f=4 vectors are removed (if iter=2)
1160%iter=1 for civ1 fields and iter=2 for civ2 fields
1161%thresh_vecC: threshold in the image correlation vec_C
1162%flag_mask: =1 mask used to remove vectors (0 else)
1163%maskname: name of the mask image file for fix
1164%thresh_vel: threshold on velocity, or on the difference with the reference file fileref if exists
1165%inf_sup=1: remove values smaller than threshold thresh_vel, =2, larger than threshold
1166%fileref: .nc file name for a reference velocity (='': refrence 0 used)
1167%fieldref: 'civ1','filter1'...feld used in fileref
1168
1169function FF=fix(Param,F,C,U,V,X,Y)
1170FF=zeros(size(F));%default
1171
1172%criterium on warn flags
1173FlagName={'CheckFmin2','CheckF2','CheckF3','CheckF4'};
1174FlagVal=[-2 2 3 4];
1175for iflag=1:numel(FlagName)
1176    if isfield(Param,FlagName{iflag}) && Param.(FlagName{iflag})
1177        FF=(FF==1| F==FlagVal(iflag));
1178    end
1179end
1180%criterium on correlation values
1181if isfield (Param,'MinCorr')
1182    FF=FF==1 | C<Param.MinCorr;
1183end
1184if (isfield(Param,'MinVel')&&~isempty(Param.MinVel))||(isfield (Param,'MaxVel')&&~isempty(Param.MaxVel))
1185    Umod= U.*U+V.*V;
1186    if isfield (Param,'MinVel')&&~isempty(Param.MinVel)
1187        FF=FF==1 | Umod<(Param.MinVel*Param.MinVel);
1188    end
1189    if isfield (Param,'MaxVel')&&~isempty(Param.MaxVel)
1190        FF=FF==1 | Umod>(Param.MaxVel*Param.MaxVel);
1191    end
1192end
1193
1194
1195%------------------------------------------------------------------------
1196% --- determine the list of index pairs of processing file
1197function [i1_series,i2_series,j1_series,j2_series,check_bounds,NomTypeNc]=...
1198    find_pair_indices(str_civ,i_series,j_series,MinIndex_i,MaxIndex_i,MinIndex_j,MaxIndex_j)
1199%------------------------------------------------------------------------
1200i1_series=i_series;% set of first image indexes
1201i2_series=i_series;
1202j1_series=j_series;%ones(size(i_series));% set of first image numbers
1203j2_series=j_series;%ones(size(i_series));
1204r=regexp(str_civ,'^\D(?<ind>[i|j])=( -| )(?<num1>\d+)\|(?<num2>\d+)','names');
1205if ~isempty(r)
1206    mode=['D' r.ind];
1207    ind1=str2num(r.num1);
1208    ind2=str2num(r.num2);
1209else
1210    mode='j1-j2';
1211    r=regexp(str_civ,'^j= (?<num1>[a-z])-(?<num2>[a-z])','names');
1212    if ~isempty(r)
1213        NomTypeNc='_1ab';
1214    else
1215        r=regexp(str_civ,'^j= (?<num1>[A-Z])-(?<num2>[A-Z])','names');
1216        if ~isempty(r)
1217            NomTypeNc='_1AB';
1218        else
1219            r=regexp(str_civ,'^j= (?<num1>\d+)-(?<num2>\d+)','names');
1220            if ~isempty(r)
1221                NomTypeNc='_1_1-2';
1222            end
1223        end
1224    end
1225    if isempty(r)
1226        display('wrong pair mode input option')
1227    else
1228        ind1=stra2num(r.num1);
1229        ind2=stra2num(r.num2);
1230    end
1231end
1232switch mode
1233    case 'Di'
1234        i1_series=i_series-ind1;% set of first image numbers
1235        i2_series=i_series+ind2;
1236        check_bounds=i1_series<MinIndex_i | i2_series>MaxIndex_i;
1237        if isempty(j_series)
1238            NomTypeNc='_1-2';
1239        else
1240            j1_series=j_series;
1241            j2_series=j_series;
1242            NomTypeNc='_1-2_1';
1243        end
1244    case 'Dj'
1245        j1_series=j_series-ind1;
1246        j2_series=j_series+ind2;
1247        check_bounds=j1_series<MinIndex_j | j2_series>MaxIndex_j;
1248        NomTypeNc='_1_1-2';
1249    otherwise %bursts
1250        i1_series=i_series(1,:);% do not sweep the j index
1251        i2_series=i_series(1,:);
1252        j1_series=ind1*ones(1,size(i_series,2));% j index is fixed by pair choice
1253        j2_series=ind2*ones(1,size(i_series,2));
1254        check_bounds=zeros(size(i1_series));% no limitations due to min-max indices
1255end
1256
1257
1258
1259
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