source: trunk/src/series/civ_series.m @ 707

Last change on this file since 707 was 707, checked in by sommeria, 10 years ago

bug repaired for civ_series

File size: 48.3 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,ncfile)
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: input images and processing parameters
16%     .Civ1: for civ1
17%     .Fix1:
18%     .Patch1:
19%     .Civ2: for civ2
20%     .Fix2:
21%     .Patch2:
22% ncfile: name of a netcdf file to be created for the result (extension .nc)
23%
24%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
25%  Copyright  2011, LEGI / CNRS-UJF-INPG, joel.sommeria@legi.grenoble-inp.fr.
26%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
27%     This is part of the toolbox UVMAT.
28%
29%     UVMAT is free software; you can redistribute it and/or modify
30%     it under the terms of the GNU General Public License as published by
31%     the Free Software Foundation; either version 2 of the License, or
32%     (at your option) any later version.
33%
34%     UVMAT is distributed in the hope that it will be useful,
35%     but WITHOUT ANY WARRANTY; without even the implied warranty of
36%     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
37%     GNU General Public License (open UVMAT/COPYING.txt) for more details.
38%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
39
40function [Data,errormsg,result_conv]= civ_series(Param,ncfile)
41errormsg='';
42path_series=fileparts(which('series'));
43addpath(fullfile(path_series,'series'))
44%% set the input elements needed on the GUI series when the action is selected in the menu ActionName or InputTable refreshed
45if isstruct(Param) && isequal(Param.Action.RUN,0)
46    Data=civ_input(Param);% introduce the civ parameters using the GUI civ_input
47    if isempty(Data)
48        Data=Param;% if  civ_input has been cancelled, keep previous parameters
49    end
50    Data.Program=mfilename;%gives the name of the current function
51    Data.AllowInputSort='off';% allow alphabetic sorting of the list of input file SubDir (options 'off'/'on', 'off' by default)
52    Data.WholeIndexRange='off';% prescribes the file index ranges from min to max (options 'off'/'on', 'off' by default)
53    Data.NbSlice='off'; %nbre of slices ('off' by default)
54    Data.VelType='off';% menu for selecting the velocity type (options 'off'/'one'/'two',  'off' by default)
55    Data.FieldName='off';% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default)
56    Data.FieldTransform = 'off';%can use a transform function
57    Data.ProjObject='off';%can use projection object(option 'off'/'on',
58    Data.Mask='off';%can use mask option   (option 'off'/'on', 'off' by default)
59    Data.OutputDirExt='.civ';%set the output dir extension
60    Data.OutputFileMode='NbInput_i';% one output file expected per value of i index (used for waitbar)
61    filecell=get_file_series(Param);%check existence of the first input file
62    if ~exist(filecell{1,1},'file')
63        msgbox_uvmat('WARNING','the first input file does not exist')
64    else
65        FileType=get_file_type(filecell{1,1});
66        if isempty(find(strcmp(FileType,{'civdata','image','multimage','mmreader','video'})));% =1 for images
67            msgbox_uvmat('ERROR',['bad input file type for ' mfilename ': an image or civdata file is needed'])
68        end
69    end
70    return
71end
72
73%% read input parameters from an xml file if input is a file name (batch mode)
74checkrun=1;
75if ischar(Param)
76    Param=xml2struct(Param);% read Param as input file (batch case)
77    checkrun=0;
78end
79if ~isfield(Param,'ActionInput')
80     disp_uvmat('ERROR','no parameter set for PIV',checkrun)
81        return
82end
83hseries=findobj(allchild(0),'Tag','series');
84RUNHandle=findobj(hseries,'Tag','RUN');%handle of RUN button in GUI series
85WaitbarHandle=findobj(hseries,'Tag','Waitbar');%handle of waitbar in GUI series
86
87%% input files and indexing
88NbField=1;
89MaxIndex_i=Param.IndexRange.MaxIndex_i;
90MinIndex_i=Param.IndexRange.MinIndex_i;
91MaxIndex_j=1;MinIndex_j=1;
92if isfield(Param.IndexRange,'MaxIndex_j')&& isfield(Param.IndexRange,'MinIndex_j')
93    MaxIndex_j=Param.IndexRange.MaxIndex_j;
94    MinIndex_j=Param.IndexRange.MinIndex_j;
95end
96if isfield(Param,'InputTable')
97    [filecell,i_series,tild,j_series]=get_file_series(Param);
98    if ~exist(filecell{1,1},'file')
99        disp_uvmat('ERROR',' the first input file does not exist',checkrun)
100        return
101    else
102        FileType=get_file_type(filecell{1,1});
103        iview_nc=0;% series index (iview) for an input nc file (for civ2 or patch2)
104        iview_A=0;% series index (iview) for the first image series
105        iview_B=0;% series index (iview) for the second image series (only non zero for option 'shift' )
106        switch FileType
107            case 'civdata';% =1 for images
108                iview_nc=1;
109                if size(filecell,1)>=2
110                    iview_A=2;iview_B=2;
111                    if size(filecell,1)>=3
112                        iview_B=3;
113                    end
114                end
115            case {'image','multimage','mmreader','video'}
116                iview_A=1;
117                if size(filecell,1)>=2
118                    iview_B=2;
119                end
120        end
121    end
122    if iview_A~=0
123        [FileType_A,FileInfo_A,VideoObject_A]=get_file_type(filecell{1,1});
124        if isempty(strcmp(FileType_A,{'multimage','mmreader','video'}))
125            displ(['ERROR: the file line ' num2str(iview_A) ' must be an image'])
126        end
127        RootPath_A=Param.InputTable{1,1};
128        RootFile_A=Param.InputTable{1,3};
129        SubDir_A=Param.InputTable{1,2};
130        NomType_A=Param.InputTable{1,4};
131        FileExt_A=Param.InputTable{1,5};
132    end
133    if iview_B==0
134        FileType_B=FileType_A;
135        VideoObject_B=VideoObject_A;
136        RootPath_B=RootPath_A;
137        RootFile_B=RootFile_A;
138        SubDir_B=SubDir_A;
139        NomType_B=NomType_A;
140        FileExt_B=FileExt_A;
141        PairCiv2='';
142        switch Param.ActionInput.ListCompareMode
143            case 'PIV'
144                PairCiv1=Param.ActionInput.PairIndices.ListPairCiv1;
145                if isfield(Param.ActionInput.PairIndices,'ListPairCiv2')
146                    PairCiv2=Param.ActionInput.PairIndices.ListPairCiv2;
147                end
148                [i1_series_Civ1,i2_series_Civ1,j1_series_Civ1,j2_series_Civ1,check_bounds,NomTypeNc]=...
149                    find_pair_indices(PairCiv1,i_series{1},j_series{1},MinIndex_i,MaxIndex_i,MinIndex_j,MaxIndex_j);
150                if ~isempty(PairCiv2)
151                    [i1_series_Civ2,i2_series_Civ2,j1_series_Civ2,j2_series_Civ2,check_bounds_Civ2]=...
152                        find_pair_indices(PairCiv2,i_series{1},j_series{1},MinIndex_i,MaxIndex_i,MinIndex_j,MaxIndex_j);
153                    check_bounds=check_bounds | check_bounds_Civ2;
154                end
155                i1_series_Civ1=i1_series_Civ1(~check_bounds);
156                i2_series_Civ1=i2_series_Civ1(~check_bounds);
157                j1_series_Civ1=j1_series_Civ1(~check_bounds);
158                j2_series_Civ1=j2_series_Civ1(~check_bounds);
159            case 'displacement'
160                i1_series_Civ1=Param.ActionInput.OriginIndex*ones(size(i_series{1}));
161                i2_series_Civ1=i_series{1};i2_series_Civ2=i_series{1};
162                j1_series_Civ1=ones(size(i_series{1}));% first j index is 1
163                if isempty(j_series{1})
164                    j2_series_Civ1=ones(size(i_series{1}));
165                else
166                    j2_series_Civ1=j_series{1};
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=NomType;
172        end
173        if ~isempty(PairCiv2)
174            i1_series_Civ2=i1_series_Civ2(~check_bounds);
175            i2_series_Civ2=i2_series_Civ2(~check_bounds);
176            j1_series_Civ2=j1_series_Civ2(~check_bounds);
177            j2_series_Civ2=j2_series_Civ2(~check_bounds);
178            if isempty(j_series{1})
179                FrameIndex_A_Civ2=i1_series_Civ2;
180                FrameIndex_B_Civ2=i2_series_Civ2;
181            else
182                FrameIndex_A_Civ2=j1_series_Civ2;
183                FrameIndex_B_Civ2=j2_series_Civ2;
184            end
185        end
186    else
187        [FileType_B,FileInfo,VideoObject_B]=get_file_type(filecell{2,1});
188        if ~ismember(FileType_B,{'image','multimage','mmreader','video'})
189            disp_uvmat('ERROR',['the file line ' num2str(iview_B) ' must be an image'],checkrun)
190        end
191        i1_series_Civ1=i_series{1};i1_series_Civ2=i_series{1};
192        i2_series_Civ1=i_series{1};i2_series_Civ2=i_series{1};
193        if isempty(j_series{1})
194            j1_series_Civ1=ones(size(i_series{1}));
195            j2_series_Civ1=ones(size(i_series{1}));
196        else
197            j1_series_Civ1=j_series{1};
198            j2_series_Civ1=j_series{1};
199        end
200        j1_series_Civ2=j1_series_Civ1;
201        j2_series_Civ2=j2_series_Civ1;
202        NomTypeNc=NomType_A;
203        RootPath_B=Param.InputTable{2,1};
204        RootFile_B=Param.InputTable{2,3};
205        SubDir_B=Param.InputTable{2,2};
206        NomType_B=Param.InputTable{2,4};
207        FileExt_B=Param.InputTable{2,5};
208    end
209    if isempty(j_series{1})
210        FrameIndex_A_Civ1=i1_series_Civ1;
211        FrameIndex_B_Civ1=i2_series_Civ1;
212    else
213        FrameIndex_A_Civ1=j1_series_Civ1;
214        FrameIndex_B_Civ1=j2_series_Civ1;
215    end
216end
217NbField=numel(i1_series_Civ1);
218
219%% Output directory
220OutputDir=[Param.OutputSubDir Param.OutputDirExt];
221
222Data.ListGlobalAttribute={'Conventions','Program','CivStage'};
223Data.Conventions='uvmat/civdata';% states the conventions used for the description of field variables and attributes
224Data.Program='civ_series';
225Data.CivStage=0;%default
226ListVarCiv1={'Civ1_X','Civ1_Y','Civ1_U','Civ1_V','Civ1_C','Civ1_F'}; %variables to read
227ListVarFix1={'Civ1_X','Civ1_Y','Civ1_U','Civ1_V','Civ1_C','Civ1_F','Civ1_FF'};
228mask='';
229maskname='';%default
230check_civx=0;%default
231check_civ1=0;%default
232check_patch1=0;%default
233
234%% get timing from the ImaDoc file or input video
235XmlFileName=find_imadoc(RootPath_A,SubDir_A,RootFile_A,FileExt_A);
236time=[];
237if ~isempty(XmlFileName)
238    XmlData=imadoc2struct(XmlFileName);
239        if isfield(XmlData,'Time')
240            time=XmlData.Time;
241            TimeSource='xml';
242        end
243        if isfield(XmlData,'Camera')
244            if isfield(XmlData.Camera,'NbSlice')&& ~isempty(XmlData.Camera.NbSlice)
245                NbSlice_calib{iview}=XmlData.Camera.NbSlice;% Nbre of slices for Zindex in phys transform
246                if ~isequal(NbSlice_calib{iview},NbSlice_calib{1})
247                    msgbox_uvmat('WARNING','inconsistent number of Z indices for the two field series');
248                end
249            end
250            if isfield(XmlData.Camera,'TimeUnit')&& ~isempty(XmlData.Camera.TimeUnit)
251                TimeUnit=XmlData.Camera.TimeUnit;
252            end
253        end
254end
255if isempty(time) && ~isempty(find(strcmp(FileType_A,{'mmreader','video'})))% case of video input
256    time=zeros(2,FileInfo_A.NumberOfFrames+1);
257    time(2,:)=(0:1/FileInfo_A.FrameRate:(FileInfo_A.NumberOfFrames)/FileInfo_A.FrameRate);
258    TimeSource='video';
259    % set(han:dles.Dt_txt,'String',['Dt=' num2str(1000/imainfo.FrameRate) 'ms']);%display the elementary time interval in millisec
260    ColorType='truecolor';
261end
262if isempty(time)% time = index i +0.001 index j by default
263    time=(MinIndex_i:MaxIndex_i)'*ones(1,MaxIndex_j-MinIndex_j+1);
264    time=time+0.001*ones(MaxIndex_i-MinIndex_i+1,1)*(MinIndex_j:MaxIndex_j);
265    time=[zeros(1,MaxIndex_j-MinIndex_j+1);time];% insert a first line of zeros
266    time=[zeros(MaxIndex_i-MinIndex_i+2,1) time];% insert a first column of zeros
267end
268   
269if length(FileInfo_A) >1 %case of image with multiple frames
270    nbfield=length(FileInfo_A);
271    nbfield_j=1;
272end
273
274%%%%% MAIN LOOP %%%%%%
275for ifield=1:NbField
276    update_waitbar(WaitbarHandle,ifield/NbField)
277    if ~isempty(RUNHandle) && ~strcmp(get(RUNHandle,'BusyAction'),'queue')
278        disp('program stopped by user')
279        break
280    end
281    if strcmp(Param.ActionInput.ListCompareMode,'PIV')
282        ncfile=fullfile_uvmat(RootPath_A,OutputDir,RootFile_A,'.nc',NomTypeNc,i1_series_Civ1(ifield),i2_series_Civ1(ifield),...
283            j1_series_Civ1(ifield),j2_series_Civ1(ifield));
284    else
285        ncfile=fullfile_uvmat(RootPath_A,OutputDir,RootFile_A,'.nc',NomTypeNc,i2_series_Civ1(ifield),[],...
286            j1_series_Civ1(ifield),j2_series_Civ1(ifield));
287    end
288
289    %% Civ1
290    % if Civ1 computation is requested
291    if isfield (Param.ActionInput,'Civ1')
292        par_civ1=Param.ActionInput.Civ1;
293        if isfield(par_civ1,'reverse_pair')% A REVOIR
294            if par_civ1.reverse_pair
295                if ischar(par_civ1.ImageB)
296                    temp=par_civ1.ImageA;
297                    par_civ1.ImageA=imread(par_civ1.ImageB);
298                end
299                if ischar(temp)
300                    par_civ1.ImageB=imread(temp);
301                end
302            end
303        else
304            ImageName_A=fullfile_uvmat(RootPath_A,SubDir_A,RootFile_A,FileExt_A,NomType_A,i1_series_Civ1(ifield),[],j1_series_Civ1(ifield));
305            [par_civ1.ImageA,VideoObject_A] = read_image(ImageName_A,FileType_A,VideoObject_A,FrameIndex_A_Civ1(ifield));
306            ImageName_B=fullfile_uvmat(RootPath_B,SubDir_B,RootFile_B,FileExt_B,NomType_B,i2_series_Civ1(ifield),[],j2_series_Civ1(ifield));
307            [par_civ1.ImageB,VideoObject_B] = read_image(ImageName_B,FileType_B,VideoObject_B,FrameIndex_B_Civ1(ifield));
308        end
309        par_civ1.ImageWidth=FileInfo_A.Width;
310        par_civ1.ImageHeight=FileInfo_A.Height;
311        list_param=(fieldnames(Param.ActionInput.Civ1))';
312        Civ1_param=regexprep(list_param,'^.+','Civ1_$0');% insert 'Civ1_' before  each string in list_param
313        Civ1_param=[{'Civ1_ImageA','Civ1_ImageB','Civ1_Time','Civ1_Dt'} Civ1_param]; %insert the names of the two input images
314        %indicate the values of all the global attributes in the output data
315        Data.Civ1_ImageA=ImageName_A;
316        Data.Civ1_ImageB=ImageName_B;
317        i1=i1_series_Civ1(ifield);
318        i2=i1;
319        if ~isempty(i2_series_Civ1)
320            i2=i2_series_Civ1(ifield);
321        end
322        j1=1;
323        if ~isempty(j1_series_Civ1)
324            j1=j1_series_Civ1(ifield);
325        end
326        j2=j1;
327        if ~isempty(j2_series_Civ1)
328            j2=j2_series_Civ1(ifield);
329        end
330        Data.Civ1_Time=(time(i2+1,j2+1)+time(i1+1,j1+1))/2;
331        Data.Civ1_Dt=time(i2+1,j2+1)-time(i1+1,j1+1);
332        for ilist=1:length(list_param)
333            Data.(Civ1_param{4+ilist})=Param.ActionInput.Civ1.(list_param{ilist});
334        end
335        Data.ListGlobalAttribute=[Data.ListGlobalAttribute Civ1_param];
336        Data.CivStage=1;
337       
338        % set the list of variables
339        Data.ListVarName={'Civ1_X','Civ1_Y','Civ1_U','Civ1_V','Civ1_F','Civ1_C'};%  cell array containing the names of the fields to record
340        Data.VarDimName={'nb_vec_1','nb_vec_1','nb_vec_1','nb_vec_1','nb_vec_1','nb_vec_1'};
341        Data.VarAttribute{1}.Role='coord_x';
342        Data.VarAttribute{2}.Role='coord_y';
343        Data.VarAttribute{3}.Role='vector_x';
344        Data.VarAttribute{4}.Role='vector_y';
345        Data.VarAttribute{5}.Role='warnflag';
346       
347        if strcmp(Param.ActionInput.ListCompareMode, 'PIV volume')
348            Data.ListVarName=[Data.ListVarName 'Civ1_Z'];
349            Data.Civ1_X=[];Data.Civ1_Y=[];Data.Civ1_Z=[];
350            Data.Civ1_U=[];Data.Civ1_V=[];Data.Civ1_C=[];Data.Civ1_F=[];
351            for ivol=1:NbSlice
352                % caluclate velocity data (y and v in indices, reverse to y component)
353                [xtable ytable utable vtable ctable F result_conv errormsg] = civ (par_civ1);
354                if ~isempty(errormsg)
355                     disp_uvmat('ERROR',errormsg,checkrun)
356                    return
357                end
358                Data.Civ1_X=[Data.Civ1_X reshape(xtable,[],1)];
359                Data.Civ1_Y=[Data.Civ1_Y reshape(Param.Civ1.ImageHeight-ytable+1,[],1)];
360                Data.Civ1_Z=[Data.Civ1_Z ivol*ones(numel(xtable),1)];% z=image index in image coordinates
361                Data.Civ1_U=[Data.Civ1_U reshape(utable,[],1)];
362                Data.Civ1_V=[Data.Civ1_V reshape(-vtable,[],1)];
363                Data.Civ1_C=[Data.Civ1_C reshape(ctable,[],1)];
364                Data.Civ1_F=[Data.Civ1_C reshape(F,[],1)];
365            end
366        else %usual PIV
367            % caluclate velocity data (y and v in indices, reverse to y component)
368            [xtable ytable utable vtable ctable F result_conv errormsg] = civ (par_civ1);
369            if ~isempty(errormsg)
370                disp_uvmat('ERROR',errormsg,checkrun)
371                return
372            end
373            Data.Civ1_X=reshape(xtable,[],1);
374            Data.Civ1_Y=reshape(par_civ1.ImageHeight-ytable+1,[],1);
375            Data.Civ1_U=reshape(utable,[],1);
376            Data.Civ1_V=reshape(-vtable,[],1);
377            Data.Civ1_C=reshape(ctable,[],1);
378            Data.Civ1_F=reshape(F,[],1);
379        end
380    else% we use existing Civ1 data
381        if exist('ncfile','var')
382            CivFile=ncfile;
383        elseif isfield(Param.Patch1,'CivFile')
384            CivFile=Param.Patch1.CivFile;
385        end
386        Data=nc2struct(CivFile,'ListGlobalAttribute','absolut_time_T0'); %look for the constant 'absolut_time_T0' to detect old civx data format
387        if isfield(Data,'Txt')
388            errormsg=Data.Txt;
389            disp_uvmat('ERROR',errormsg,checkrun)
390            return
391        end
392        if ~isempty(Data.absolut_time_T0')%read civx file
393            check_civx=1;% test for old civx data format
394            [Data,vardetect,ichoice]=nc2struct(CivFile);%read the variables in the netcdf file
395        else
396            Data=nc2struct(CivFile);%read civ1 and fix1 data in the existing netcdf file
397        end
398    end
399   
400    %% Fix1
401    if isfield (Param.ActionInput,'Fix1')
402        ListFixParam=fieldnames(Param.ActionInput.Fix1);
403        for ilist=1:length(ListFixParam)
404            ParamName=ListFixParam{ilist};
405            ListName=['Fix1_' ParamName];
406            eval(['Data.ListGlobalAttribute=[Data.ListGlobalAttribute ''' ParamName '''];'])
407            eval(['Data.' ListName '=Param.ActionInput.Fix1.' ParamName ';'])
408        end
409        if check_civx
410            if ~isfield(Data,'fix')
411                Data.ListGlobalAttribute=[Data.ListGlobalAttribute 'fix'];
412                Data.fix=1;
413                Data.ListVarName=[Data.ListVarName {'vec_FixFlag'}];
414                Data.VarDimName=[Data.VarDimName {'nb_vectors'}];
415            end
416            Data.vec_FixFlag=fix(Param.ActionInput.Fix1,Data.vec_F,Data.vec_C,Data.vec_U,Data.vec_V,Data.vec_X,Data.vec_Y);
417        else
418            Data.ListVarName=[Data.ListVarName {'Civ1_FF'}];
419            Data.VarDimName=[Data.VarDimName {'nb_vec_1'}];
420            nbvar=length(Data.ListVarName);
421            Data.VarAttribute{nbvar}.Role='errorflag';
422            Data.Civ1_FF=fix(Param.ActionInput.Fix1,Data.Civ1_F,Data.Civ1_C,Data.Civ1_U,Data.Civ1_V);
423            Data.CivStage=2;
424        end
425    end
426    %% Patch1
427    if isfield (Param.ActionInput,'Patch1')
428        if check_civx
429            errormsg='Civ Matlab input needed for patch';
430            disp_uvmat('ERROR',errormsg,checkrun)
431            return
432        end
433       
434        Data.ListGlobalAttribute=[Data.ListGlobalAttribute {'Patch1_Rho','Patch1_Threshold','Patch1_SubDomain'}];
435        Data.Patch1_FieldSmooth=Param.ActionInput.Patch1.FieldSmooth;
436        Data.Patch1_MaxDiff=Param.ActionInput.Patch1.MaxDiff;
437        Data.Patch1_SubDomainSize=Param.ActionInput.Patch1.SubDomainSize;
438        nbvar=length(Data.ListVarName);
439        Data.ListVarName=[Data.ListVarName {'Civ1_U_smooth','Civ1_V_smooth','Civ1_SubRange','Civ1_NbCentres','Civ1_Coord_tps','Civ1_U_tps','Civ1_V_tps'}];
440        Data.VarDimName=[Data.VarDimName {'nb_vec_1','nb_vec_1',{'nb_coord','nb_bounds','nb_subdomain_1'},'nb_subdomain_1',...
441            {'nb_tps_1','nb_coord','nb_subdomain_1'},{'nb_tps_1','nb_subdomain_1'},{'nb_tps_1','nb_subdomain_1'}}];
442        Data.VarAttribute{nbvar+1}.Role='vector_x';
443        Data.VarAttribute{nbvar+2}.Role='vector_y';
444        Data.VarAttribute{nbvar+5}.Role='coord_tps';
445        Data.VarAttribute{nbvar+6}.Role='vector_x';
446        Data.VarAttribute{nbvar+7}.Role='vector_y';
447        Data.Civ1_U_smooth=zeros(size(Data.Civ1_X));
448        Data.Civ1_V_smooth=zeros(size(Data.Civ1_X));
449        if isfield(Data,'Civ1_FF')
450            ind_good=find(Data.Civ1_FF==0);
451        else
452            ind_good=1:numel(Data.Civ1_X);
453        end
454        [Data.Civ1_SubRange,Data.Civ1_NbCentres,Data.Civ1_Coord_tps,Data.Civ1_U_tps,Data.Civ1_V_tps,tild,Ures, Vres,tild,FFres]=...
455            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);
456        Data.Civ1_U_smooth(ind_good)=Ures;
457        Data.Civ1_V_smooth(ind_good)=Vres;
458        Data.Civ1_FF(ind_good)=FFres;
459        Data.CivStage=3;
460    end
461   
462    %% Civ2
463    if isfield (Param.ActionInput,'Civ2')
464        par_civ2=Param.ActionInput.Civ2;
465        par_civ2.ImageA=[];
466        par_civ2.ImageB=[];
467        %         if ~isfield(Param.Civ1,'ImageA')
468        ImageName_A_Civ2=fullfile_uvmat(RootPath_A,SubDir_A,RootFile_A,FileExt_A,NomType_A,i1_series_Civ2(ifield),[],j1_series_Civ2(ifield));
469
470        if strcmp(ImageName_A_Civ2,ImageName_A) && isequal(FrameIndex_A_Civ1(ifield),FrameIndex_A_Civ2(ifield))
471            par_civ2.ImageA=par_civ1.ImageA;
472        else
473            [par_civ2.ImageA,VideoObject_A] = read_image(ImageName_A,FileType_A,VideoObject_A,FrameIndex_A_Civ2(ifield));
474        end
475        ImageName_B_Civ2=fullfile_uvmat(RootPath_B,SubDir_B,RootFile_B,FileExt_B,NomType_B,i2_series_Civ2(ifield),[],j2_series_Civ2(ifield));
476        if strcmp(ImageName_B_Civ2,ImageName_B) && isequal(FrameIndex_B_Civ1(ifield),FrameIndex_B_Civ2)
477            par_civ2.ImageB=par_civ1.ImageB;
478        else
479            [par_civ2.ImageB,VideoObject_B] = read_image(ImageName_B,FileType_B,VideoObject_B,FrameIndex_B_Civ2(ifield));
480        end     
481       
482        ncfile=fullfile_uvmat(RootPath_A,OutputDir,RootFile_A,'.nc',NomTypeNc,i1_series_Civ2(ifield),i2_series_Civ2(ifield),...
483            j1_series_Civ2(ifield),j2_series_Civ2(ifield));
484        par_civ2.ImageWidth=FileInfo_A.Width;
485        par_civ2.ImageHeight=FileInfo_A.Height;
486       
487        if isfield(par_civ2,'Grid')% grid points set as input file
488            if ischar(par_civ2.Grid)%read the grid file if the input is a file name
489                par_civ2.Grid=dlmread(par_civ2.Grid);
490                par_civ2.Grid(1,:)=[];%the first line must be removed (heading in the grid file)
491            end
492        else% automatic grid
493            minix=floor(par_civ2.Dx/2)-0.5;
494            maxix=minix+par_civ2.Dx*floor((par_civ2.ImageWidth-1)/par_civ2.Dx);
495            miniy=floor(par_civ2.Dy/2)-0.5;
496            maxiy=minix+par_civ2.Dy*floor((par_civ2.ImageHeight-1)/par_civ2.Dy);
497            [GridX,GridY]=meshgrid(minix:par_civ2.Dx:maxix,miniy:par_civ2.Dy:maxiy);
498            par_civ2.Grid(:,1)=reshape(GridX,[],1);
499            par_civ2.Grid(:,2)=reshape(GridY,[],1);
500        end
501        Shiftx=zeros(size(par_civ2.Grid,1),1);% shift expected from civ1 data
502        Shifty=zeros(size(par_civ2.Grid,1),1);
503        nbval=zeros(size(par_civ2.Grid,1),1);
504        if par_civ2.CheckDeformation
505            DUDX=zeros(size(par_civ2.Grid,1),1);
506            DUDY=zeros(size(par_civ2.Grid,1),1);
507            DVDX=zeros(size(par_civ2.Grid,1),1);
508            DVDY=zeros(size(par_civ2.Grid,1),1);
509        end
510        NbSubDomain=size(Data.Civ1_SubRange,3);
511        % get the guess from patch1
512        for isub=1:NbSubDomain
513            nbvec_sub=Data.Civ1_NbCentres(isub);
514            ind_sel=find(GridX>=Data.Civ1_SubRange(1,1,isub) & GridX<=Data.Civ1_SubRange(1,2,isub) & GridY>=Data.Civ1_SubRange(2,1,isub) & GridY<=Data.Civ1_SubRange(2,2,isub));
515            epoints = [GridX(ind_sel) GridY(ind_sel)];% coordinates of interpolation sites
516            ctrs=Data.Civ1_Coord_tps(1:nbvec_sub,:,isub) ;%(=initial points) ctrs
517            nbval(ind_sel)=nbval(ind_sel)+1;% records the number of values for eacn interpolation point (in case of subdomain overlap)
518            EM = tps_eval(epoints,ctrs);
519            Shiftx(ind_sel)=Shiftx(ind_sel)+EM*Data.Civ1_U_tps(1:nbvec_sub+3,isub);
520            Shifty(ind_sel)=Shifty(ind_sel)+EM*Data.Civ1_V_tps(1:nbvec_sub+3,isub);
521            if par_civ2.CheckDeformation
522                [EMDX,EMDY] = tps_eval_dxy(epoints,ctrs);%2D matrix of distances between extrapolation points epoints and spline centres (=site points) ctrs
523                DUDX(ind_sel)=DUDX(ind_sel)+EMDX*Data.Civ1_U_tps(1:nbvec_sub+3,isub);
524                DUDY(ind_sel)=DUDY(ind_sel)+EMDY*Data.Civ1_U_tps(1:nbvec_sub+3,isub);
525                DVDX(ind_sel)=DVDX(ind_sel)+EMDX*Data.Civ1_V_tps(1:nbvec_sub+3,isub);
526                DVDY(ind_sel)=DVDY(ind_sel)+EMDY*Data.Civ1_V_tps(1:nbvec_sub+3,isub);
527            end
528        end
529        mask='';
530        if par_civ2.CheckMask&&~isempty(par_civ2.Mask)&& ~strcmp(maskname,par_civ2.Mask)% mask exist, not already read in civ1
531            mask=imread(par_civ2.Mask);
532        end
533        ibx2=ceil(par_civ2.CorrBoxSize(1)/2);
534        iby2=ceil(par_civ2.CorrBoxSize(2)/2);
535        par_civ2.SearchBoxSize(1)=2*ibx2+9;% search ara +-4 pixels around the guess
536        par_civ2.SearchBoxSize(2)=2*iby2+9;
537        par_civ2.SearchBoxShift=[Shiftx(nbval>=1)./nbval(nbval>=1) Shifty(nbval>=1)./nbval(nbval>=1)];
538        par_civ2.Grid=[GridX(nbval>=1)-par_civ2.SearchBoxShift(:,1)/2 GridY(nbval>=1)-par_civ2.SearchBoxShift(:,2)/2];% grid taken at the extrapolated origin of the displacement vectors
539        if par_civ2.CheckDeformation
540            par_civ2.DUDX=DUDX./nbval;
541            par_civ2.DUDY=DUDY./nbval;
542            par_civ2.DVDX=DVDX./nbval;
543            par_civ2.DVDY=DVDY./nbval;
544        end
545        % caluclate velocity data (y and v in indices, reverse to y component)
546        [xtable ytable utable vtable ctable F] = civ (par_civ2);
547
548        list_param=(fieldnames(Param.ActionInput.Civ2))';
549        Civ2_param=regexprep(list_param,'^.+','Civ2_$0');% insert 'Civ2_' before  each string in list_param
550        Civ2_param=[{'Civ2_ImageA','Civ2_ImageB','Civ2_Time','Civ2_Dt'} Civ2_param]; %insert the names of the two input images
551        %indicate the values of all the global attributes in the output data
552        Data.Civ2_ImageA=ImageName_A;
553        Data.Civ2_ImageB=ImageName_B;
554        i1=i1_series_Civ2(ifield);
555        i2=i1;
556        if ~isempty(i2_series_Civ2)
557            i2=i2_series_Civ2(ifield);
558        end
559        j1=1;
560        if ~isempty(j1_series_Civ2)
561            j1=j1_series_Civ2(ifield);
562        end
563        j2=j1;
564        if ~isempty(j2_series_Civ1)
565            j2=j2_series_Civ2(ifield);
566        end
567        Data.Civ2_Time=(time(i2+1,j2+1)+time(i1+1,j1+1))/2;
568        Data.Civ2_Dt=time(i2+1,j2+1)-time(i1+1,j1+1);
569%         Data.Civ2_Time=1;
570%         Data.Civ2_Dt=1;
571        for ilist=1:length(list_param)
572            Data.(Civ2_param{4+ilist})=Param.ActionInput.Civ2.(list_param{ilist});
573        end
574        Data.ListGlobalAttribute=[Data.ListGlobalAttribute Civ2_param];
575       
576        nbvar=numel(Data.ListVarName);
577        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
578        Data.VarDimName=[Data.VarDimName {'nb_vec_2','nb_vec_2','nb_vec_2','nb_vec_2','nb_vec_2','nb_vec_2'}];
579        Data.VarAttribute{nbvar+1}.Role='coord_x';
580        Data.VarAttribute{nbvar+2}.Role='coord_y';
581        Data.VarAttribute{nbvar+3}.Role='vector_x';
582        Data.VarAttribute{nbvar+4}.Role='vector_y';
583        Data.VarAttribute{nbvar+5}.Role='warnflag';
584        Data.Civ2_X=reshape(xtable,[],1);
585        Data.Civ2_Y=reshape(size(par_civ2.ImageA,1)-ytable+1,[],1);
586        Data.Civ2_U=reshape(utable,[],1);
587        Data.Civ2_V=reshape(-vtable,[],1);
588        Data.Civ2_C=reshape(ctable,[],1);
589        Data.Civ2_F=reshape(F,[],1);
590        Data.CivStage=Data.CivStage+1;
591    end
592   
593    %% Fix2
594    if isfield (Param.ActionInput,'Fix2')
595        ListFixParam=fieldnames(Param.ActionInput.Fix2);
596        for ilist=1:length(ListFixParam)
597            ParamName=ListFixParam{ilist};
598            ListName=['Fix2_' ParamName];
599            eval(['Data.ListGlobalAttribute=[Data.ListGlobalAttribute ''' ParamName '''];'])
600            eval(['Data.' ListName '=Param.ActionInput.Fix2.' ParamName ';'])
601        end
602        if check_civx
603            if ~isfield(Data,'fix2')
604                Data.ListGlobalAttribute=[Data.ListGlobalAttribute 'fix2'];
605                Data.fix2=1;
606                Data.ListVarName=[Data.ListVarName {'vec2_FixFlag'}];
607                Data.VarDimName=[Data.VarDimName {'nb_vectors2'}];
608            end
609            Data.vec_FixFlag=fix(Param.Fix2,Data.vec2_F,Data.vec2_C,Data.vec2_U,Data.vec2_V,Data.vec2_X,Data.vec2_Y);
610        else
611            Data.ListVarName=[Data.ListVarName {'Civ2_FF'}];
612            Data.VarDimName=[Data.VarDimName {'nb_vec_2'}];
613            nbvar=length(Data.ListVarName);
614            Data.VarAttribute{nbvar}.Role='errorflag';
615            Data.Civ2_FF=fix(Param.ActionInput.Fix2,Data.Civ2_F,Data.Civ2_C,Data.Civ2_U,Data.Civ2_V);
616            Data.CivStage=Data.CivStage+1;
617        end
618       
619    end
620   
621    %% Patch2
622    if isfield (Param.ActionInput,'Patch2')
623        Data.ListGlobalAttribute=[Data.ListGlobalAttribute {'Patch2_Rho','Patch2_Threshold','Patch2_SubDomain'}];
624        Data.Patch2_FieldSmooth=Param.ActionInput.Patch2.FieldSmooth;
625        Data.Patch2_MaxDiff=Param.ActionInput.Patch2.MaxDiff;
626        Data.Patch2_SubDomainSize=Param.ActionInput.Patch2.SubDomainSize;
627        nbvar=length(Data.ListVarName);
628        Data.ListVarName=[Data.ListVarName {'Civ2_U_smooth','Civ2_V_smooth','Civ2_SubRange','Civ2_NbCentres','Civ2_Coord_tps','Civ2_U_tps','Civ2_V_tps'}];
629        Data.VarDimName=[Data.VarDimName {'nb_vec_2','nb_vec_2',{'nb_coord','nb_bounds','nb_subdomain_2'},{'nb_subdomain_2'},...
630            {'nb_tps_2','nb_coord','nb_subdomain_2'},{'nb_tps_2','nb_subdomain_2'},{'nb_tps_2','nb_subdomain_2'}}];
631       
632        Data.VarAttribute{nbvar+1}.Role='vector_x';
633        Data.VarAttribute{nbvar+2}.Role='vector_y';
634        Data.VarAttribute{nbvar+5}.Role='coord_tps';
635        Data.VarAttribute{nbvar+6}.Role='vector_x';
636        Data.VarAttribute{nbvar+7}.Role='vector_y';
637        Data.Civ2_U_smooth=zeros(size(Data.Civ2_X));
638        Data.Civ2_V_smooth=zeros(size(Data.Civ2_X));
639        if isfield(Data,'Civ2_FF')
640            ind_good=find(Data.Civ2_FF==0);
641        else
642            ind_good=1:numel(Data.Civ2_X);
643        end
644        [Data.Civ2_SubRange,Data.Civ2_NbCentres,Data.Civ2_Coord_tps,Data.Civ2_U_tps,Data.Civ2_V_tps,tild,Ures, Vres,tild,FFres]=...
645            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);
646        Data.Civ2_U_smooth(ind_good)=Ures;
647        Data.Civ2_V_smooth(ind_good)=Vres;
648        Data.Civ2_FF(ind_good)=FFres;
649        Data.CivStage=Data.CivStage+1;
650    end
651   
652    %% write result in a netcdf file if requested
653    if exist('ncfile','var')
654        errormsg=struct2nc(ncfile,Data);
655        if isempty(errormsg)
656            disp([ncfile ' written'])
657        else
658            disp(errormsg)
659        end
660    end
661end
662
663% 'civ': function piv.m adapted from PIVlab http://pivlab.blogspot.com/
664%--------------------------------------------------------------------------
665% function [xtable ytable utable vtable typevector] = civ (image1,image2,ibx,iby step, subpixfinder, mask, roi)
666%
667% OUTPUT:
668% xtable: set of x coordinates
669% ytable: set of y coordiantes
670% utable: set of u displacements (along x)
671% vtable: set of v displacements (along y)
672% ctable: max image correlation for each vector
673% typevector: set of flags, =1 for good, =0 for NaN vectors
674%
675%INPUT:
676% par_civ: structure of input parameters, with fields:
677%  .CorrBoxSize
678%  .SearchBoxSize
679%  .SearchBoxShift
680%  .ImageHeight
681%  .ImageWidth
682%  .Dx, Dy
683%  .Grid
684%  .Mask
685%  .MinIma
686%  .MaxIma
687%  .image1:first image (matrix)
688% image2: second image (matrix)
689% ibx2,iby2: half size of the correlation box along x and y, in px (size=(2*iby2+1,2*ibx2+1)
690% isx2,isy2: half size of the search box along x and y, in px (size=(2*isy2+1,2*isx2+1)
691% shiftx, shifty: shift of the search box (in pixel index, yshift reversed)
692% step: mesh of the measurement points (in px)
693% subpixfinder=1 or 2 controls the curve fitting of the image correlation
694% mask: =[] for no mask
695% roi: 4 element vector defining a region of interest: x position, y position, width, height, (in image indices), for the whole image, roi=[];
696function [xtable ytable utable vtable ctable F result_conv errormsg] = civ (par_civ)
697%this funtion performs the DCC PIV analysis. Recent window-deformation
698%methods perform better and will maybe be implemented in the future.
699
700%% prepare measurement grid
701if isfield(par_civ,'Grid')% grid points set as input
702    if ischar(par_civ.Grid)%read the drid file if the input is a file name
703        par_civ.Grid=dlmread(par_civ.Grid);
704        par_civ.Grid(1,:)=[];%the first line must be removed (heading in the grid file)
705    end
706else% automatic grid
707    minix=floor(par_civ.Dx/2)-0.5;
708    maxix=minix+par_civ.Dx*floor((par_civ.ImageWidth-1)/par_civ.Dx);
709    miniy=floor(par_civ.Dy/2)-0.5;
710    maxiy=minix+par_civ.Dy*floor((par_civ.ImageHeight-1)/par_civ.Dy);
711    [GridX,GridY]=meshgrid(minix:par_civ.Dx:maxix,miniy:par_civ.Dy:maxiy);
712    par_civ.Grid(:,1)=reshape(GridX,[],1);
713    par_civ.Grid(:,2)=reshape(GridY,[],1);
714end
715nbvec=size(par_civ.Grid,1);
716
717%% prepare correlation and search boxes
718ibx2=ceil(par_civ.CorrBoxSize(1)/2);
719iby2=ceil(par_civ.CorrBoxSize(2)/2);
720isx2=ceil(par_civ.SearchBoxSize(1)/2);
721isy2=ceil(par_civ.SearchBoxSize(2)/2);
722shiftx=round(par_civ.SearchBoxShift(:,1));
723shifty=-round(par_civ.SearchBoxShift(:,2));% sign minus because image j index increases when y decreases
724if numel(shiftx)==1% case of a unique shift for the whole field( civ1)
725    shiftx=shiftx*ones(nbvec,1);
726    shifty=shifty*ones(nbvec,1);
727end
728
729%% Default output
730xtable=par_civ.Grid(:,1);
731ytable=par_civ.Grid(:,2);
732utable=zeros(nbvec,1);
733vtable=zeros(nbvec,1);
734ctable=zeros(nbvec,1);
735F=zeros(nbvec,1);
736result_conv=[];
737errormsg='';
738
739%% prepare mask
740if isfield(par_civ,'Mask') && ~isempty(par_civ.Mask)
741    if strcmp(par_civ.Mask,'all')
742        return    % get the grid only, no civ calculation
743    elseif ischar(par_civ.Mask)
744        par_civ.Mask=imread(par_civ.Mask);
745    end
746end
747check_MinIma=isfield(par_civ,'MinIma');% test for image luminosity threshold
748check_MaxIma=isfield(par_civ,'MaxIma') && ~isempty(par_civ.MaxIma);
749
750% %% prepare images
751% if isfield(par_civ,'reverse_pair')
752%     if par_civ.reverse_pair
753%         if ischar(par_civ.ImageB)
754%             temp=par_civ.ImageA;
755%             par_civ.ImageA=imread(par_civ.ImageB);
756%         end
757%         if ischar(temp)
758%             par_civ.ImageB=imread(temp);
759%         end
760%     end
761% else
762%     if ischar(par_civ.ImageA)
763%         par_civ.ImageA=imread(par_civ.ImageA);
764%     end
765%     if ischar(par_civ.ImageB)
766%         par_civ.ImageB=imread(par_civ.ImageB);
767%     end
768% end
769par_civ.ImageA=sum(double(par_civ.ImageA),3);%sum over rgb component for color images
770par_civ.ImageB=sum(double(par_civ.ImageB),3);
771[npy_ima npx_ima]=size(par_civ.ImageA);
772if ~isequal(size(par_civ.ImageB),[npy_ima npx_ima])
773    errormsg='image pair with unequal size';
774    return
775end
776
777%% Apply mask
778    % Convention for mask IDEAS TO IMPLEMENT ?
779    % mask >200 : velocity calculated
780    %  200 >=mask>150;velocity not calculated, interpolation allowed (bad spots)
781    % 150>=mask >100: velocity not calculated, nor interpolated
782    %  100>=mask> 20: velocity not calculated, impermeable (no flux through mask boundaries)
783    %  20>=mask: velocity=0
784checkmask=0;
785MinA=min(min(par_civ.ImageA));
786MinB=min(min(par_civ.ImageB));
787if isfield(par_civ,'Mask') && ~isempty(par_civ.Mask)
788   checkmask=1;
789   if ~isequal(size(par_civ.Mask),[npy_ima npx_ima])
790        errormsg='mask must be an image with the same size as the images';
791        return
792   end
793  %  check_noflux=(par_civ.Mask<100) ;%TODO: to implement
794    check_undefined=(par_civ.Mask<200 & par_civ.Mask>=20 );
795    par_civ.ImageA(check_undefined)=MinA;% put image A to zero (i.e. the min image value) in the undefined  area
796    par_civ.ImageB(check_undefined)=MinB;% put image B to zero (i.e. the min image value) in the undefined  area
797end
798
799%% compute image correlations: MAINLOOP on velocity vectors
800corrmax=0;
801sum_square=1;% default
802mesh=1;% default
803CheckDecimal=isfield(par_civ,'CheckDecimal')&& par_civ.CheckDecimal==1;
804if CheckDecimal
805    mesh=0.2;%mesh in pixels for subpixel image interpolation
806    CheckDeformation=isfield(par_civ,'CheckDeformation')&& par_civ.CheckDeformation==1;
807end
808% vector=[0 0];%default
809for ivec=1:nbvec
810    iref=round(par_civ.Grid(ivec,1)+0.5);% xindex on the image A for the middle of the correlation box
811    jref=round(par_civ.ImageHeight-par_civ.Grid(ivec,2)+0.5);% yindex on the image B for the middle of the correlation box
812    %if ~(checkmask && par_civ.Mask(jref,iref)<=20) %velocity not set to zero by the black mask
813    %         if jref-iby2<1 || jref+iby2>par_civ.ImageHeight|| iref-ibx2<1 || iref+ibx2>par_civ.ImageWidth||...
814    %               jref+shifty(ivec)-isy2<1||jref+shifty(ivec)+isy2>par_civ.ImageHeight|| iref+shiftx(ivec)-isx2<1 || iref+shiftx(ivec)+isx2>par_civ.ImageWidth  % we are outside the image
815    %             F(ivec)=3;
816    %         else
817    F(ivec)=0;
818    subrange1_x=iref-ibx2:iref+ibx2;% x indices defining the first subimage
819    subrange1_y=jref-iby2:jref+iby2;% y indices defining the first subimage
820    subrange2_x=iref+shiftx(ivec)-isx2:iref+shiftx(ivec)+isx2;%x indices defining the second subimage
821    subrange2_y=jref+shifty(ivec)-isy2:jref+shifty(ivec)+isy2;%y indices defining the second subimage
822    image1_crop=MinA*ones(numel(subrange1_y),numel(subrange1_x));% default value=min of image A
823    image2_crop=MinA*ones(numel(subrange2_y),numel(subrange2_x));% default value=min of image A
824    check1_x=subrange1_x>=1 & subrange1_x<=par_civ.ImageWidth;% check which points in the subimage 1 are contained in the initial image 1
825    check1_y=subrange1_y>=1 & subrange1_y<=par_civ.ImageHeight;
826    check2_x=subrange2_x>=1 & subrange2_x<=par_civ.ImageWidth;% check which points in the subimage 2 are contained in the initial image 2
827    check2_y=subrange2_y>=1 & subrange2_y<=par_civ.ImageHeight;
828   
829    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
830    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
831    image1_mean=mean(mean(image1_crop));
832    image2_mean=mean(mean(image2_crop));
833    %threshold on image minimum
834    if check_MinIma && (image1_mean < par_civ.MinIma || image2_mean < par_civ.MinIma)
835        F(ivec)=3;
836    end
837    %threshold on image maximum
838    if check_MaxIma && (image1_mean > par_civ.MaxIma || image2_mean > par_civ.MaxIma)
839        F(ivec)=3;
840    end
841    %         end
842    if F(ivec)~=3
843        image1_crop=image1_crop-image1_mean;%substract the mean
844        image2_crop=image2_crop-image2_mean;
845        if CheckDecimal
846            xi=(1:mesh:size(image1_crop,2));
847            yi=(1:mesh:size(image1_crop,1))';
848            if CheckDeformation
849                [XI,YI]=meshgrid(xi-ceil(size(image1_crop,2)/2),yi-ceil(size(image1_crop,1)/2));
850                XIant=XI-par_civ.DUDX(ivec)*XI-par_civ.DUDY(ivec)*YI+ceil(size(image1_crop,2)/2);
851                YIant=YI-par_civ.DVDX(ivec)*XI-par_civ.DVDY(ivec)*YI+ceil(size(image1_crop,1)/2);
852                image1_crop=interp2(image1_crop,XIant,YIant);
853            else
854                image1_crop=interp2(image1_crop,xi,yi);
855            end
856            xi=(1:mesh:size(image2_crop,2));
857            yi=(1:mesh:size(image2_crop,1))';
858            image2_crop=interp2(image2_crop,xi,yi);
859        end
860        sum_square=sum(sum(image1_crop.*image1_crop));
861        %reference: Oliver Pust, PIV: Direct Cross-Correlation
862        result_conv= conv2(image2_crop,flipdim(flipdim(image1_crop,2),1),'valid');
863        corrmax= max(max(result_conv));
864        result_conv=(result_conv/corrmax)*255; %normalize, peak=always 255
865        %Find the correlation max, at 255
866        [y,x] = find(result_conv==255,1);
867        if ~isempty(y) && ~isempty(x)
868            try
869                if par_civ.CorrSmooth==1
870                    [vector,F(ivec)] = SUBPIXGAUSS (result_conv,x,y);
871                elseif par_civ.CorrSmooth==2
872                    [vector,F(ivec)] = SUBPIX2DGAUSS (result_conv,x,y);
873                end
874                utable(ivec)=vector(1)*mesh+shiftx(ivec);
875                vtable(ivec)=vector(2)*mesh+shifty(ivec);
876                xtable(ivec)=iref+utable(ivec)/2-0.5;% convec flow (velocity taken at the point middle from imgae 1 and 2)
877                ytable(ivec)=jref+vtable(ivec)/2-0.5;% and position of pixel 1=0.5 (convention for image coordinates=0 at the edge)
878                iref=round(xtable(ivec));% image index for the middle of the vector
879                jref=round(ytable(ivec));
880                if checkmask && par_civ.Mask(jref,iref)<200 && par_civ.Mask(jref,iref)>=100
881                    utable(ivec)=0;
882                    vtable(ivec)=0;
883                    F(ivec)=3;
884                end
885                ctable(ivec)=corrmax/sum_square;% correlation value
886            catch ME
887                F(ivec)=3;
888            end
889        else
890            F(ivec)=3;
891        end
892    end
893end
894result_conv=result_conv*corrmax/(255*sum_square);% keep the last correlation matrix for output
895
896%------------------------------------------------------------------------
897% --- Find the maximum of the correlation function after interpolation
898function [vector,F] = SUBPIXGAUSS (result_conv,x,y)
899%------------------------------------------------------------------------
900vector=[0 0]; %default
901F=0;
902[npy,npx]=size(result_conv);
903
904% if (x <= (size(result_conv,1)-1)) && (y <= (size(result_conv,1)-1)) && (x >= 1) && (y >= 1)
905    %the following 8 lines are copyright (c) 1998, Uri Shavit, Roi Gurka, Alex Liberzon, Technion ï¿œ Israel Institute of Technology
906    %http://urapiv.wordpress.com
907    peaky = y;
908    if y <= npy-1 && y >= 1
909        f0 = log(result_conv(y,x));
910        f1 = real(log(result_conv(y-1,x)));
911        f2 = real(log(result_conv(y+1,x)));
912        peaky = peaky+ (f1-f2)/(2*f1-4*f0+2*f2);
913    else
914        F=-2; % warning flag for vector truncated by the limited search box
915    end
916    peakx=x;
917    if x <= npx-1 && x >= 1
918        f0 = log(result_conv(y,x));
919        f1 = real(log(result_conv(y,x-1)));
920        f2 = real(log(result_conv(y,x+1)));
921        peakx = peakx+ (f1-f2)/(2*f1-4*f0+2*f2);
922    else
923        F=-2; % warning flag for vector truncated by the limited search box
924    end
925    vector=[peakx-floor(npx/2)-1 peaky-floor(npy/2)-1];
926
927%------------------------------------------------------------------------
928% --- Find the maximum of the correlation function after interpolation
929function [vector,F] = SUBPIX2DGAUSS (result_conv,x,y)
930%------------------------------------------------------------------------
931vector=[0 0]; %default
932F=-2;
933peaky=y;
934peakx=x;
935[npy,npx]=size(result_conv);
936if (x <= npx-1) && (y <= npy-1) && (x >= 1) && (y >= 1)
937    F=0;
938    for i=-1:1
939        for j=-1:1
940            %following 15 lines based on
941            %H. Nobach ï¿œ M. Honkanen (2005)
942            %Two-dimensional Gaussian regression for sub-pixel displacement
943            %estimation in particle image velocimetry or particle position
944            %estimation in particle tracking velocimetry
945            %Experiments in Fluids (2005) 38: 511ï¿œ515
946            c10(j+2,i+2)=i*log(result_conv(y+j, x+i));
947            c01(j+2,i+2)=j*log(result_conv(y+j, x+i));
948            c11(j+2,i+2)=i*j*log(result_conv(y+j, x+i));
949            c20(j+2,i+2)=(3*i^2-2)*log(result_conv(y+j, x+i));
950            c02(j+2,i+2)=(3*j^2-2)*log(result_conv(y+j, x+i));
951        end
952    end
953    c10=(1/6)*sum(sum(c10));
954    c01=(1/6)*sum(sum(c01));
955    c11=(1/4)*sum(sum(c11));
956    c20=(1/6)*sum(sum(c20));
957    c02=(1/6)*sum(sum(c02));
958    deltax=(c11*c01-2*c10*c02)/(4*c20*c02-c11^2);
959    deltay=(c11*c10-2*c01*c20)/(4*c20*c02-c11^2);
960    if abs(deltax)<1
961        peakx=x+deltax;
962    end
963    if abs(deltay)<1
964        peaky=y+deltay;
965    end
966end
967vector=[peakx-floor(npx/2)-1 peaky-floor(npy/2)-1];
968
969%'RUN_FIX': function for fixing velocity fields:
970%-----------------------------------------------
971% RUN_FIX(filename,field,flagindex,thresh_vecC,thresh_vel,iter,flag_mask,maskname,fileref,fieldref)
972%
973%filename: name of the netcdf file (used as input and output)
974%field: structure specifying the names of the fields to fix (depending on civ1 or civ2)
975    %.vel_type='civ1' or 'civ2';
976    %.nb=name of the dimension common to the field to fix ('nb_vectors' for civ1);
977    %.fixflag=name of fix flag variable ('vec_FixFlag' for civ1)
978%flagindex: flag specifying which values of vec_f are removed:
979        % if flagindex(1)=1: vec_f=-2 vectors are removed
980        % if flagindex(2)=1: vec_f=3 vectors are removed
981        % if flagindex(3)=1: vec_f=2 vectors are removed (if iter=1) or vec_f=4 vectors are removed (if iter=2)
982%iter=1 for civ1 fields and iter=2 for civ2 fields
983%thresh_vecC: threshold in the image correlation vec_C
984%flag_mask: =1 mask used to remove vectors (0 else)
985%maskname: name of the mask image file for fix
986%thresh_vel: threshold on velocity, or on the difference with the reference file fileref if exists
987%inf_sup=1: remove values smaller than threshold thresh_vel, =2, larger than threshold
988%fileref: .nc file name for a reference velocity (='': refrence 0 used)
989%fieldref: 'civ1','filter1'...feld used in fileref
990
991function FF=fix(Param,F,C,U,V,X,Y)
992FF=zeros(size(F));%default
993
994%criterium on warn flags
995FlagName={'CheckFmin2','CheckF2','CheckF3','CheckF4'};
996FlagVal=[-2 2 3 4];
997for iflag=1:numel(FlagName)
998    if isfield(Param,FlagName{iflag}) && Param.(FlagName{iflag})
999        FF=(FF==1| F==FlagVal(iflag));
1000    end
1001end
1002%criterium on correlation values
1003if isfield (Param,'MinCorr')
1004    FF=FF==1 | C<Param.MinCorr;
1005end
1006if (isfield(Param,'MinVel')&&~isempty(Param.MinVel))||(isfield (Param,'MaxVel')&&~isempty(Param.MaxVel))
1007    Umod= U.*U+V.*V;
1008    if isfield (Param,'MinVel')&&~isempty(Param.MinVel)
1009        FF=FF==1 | Umod<(Param.MinVel*Param.MinVel);
1010    end
1011    if isfield (Param,'MaxVel')&&~isempty(Param.MaxVel)
1012        FF=FF==1 | Umod>(Param.MaxVel*Param.MaxVel);
1013    end
1014end
1015
1016
1017%------------------------------------------------------------------------
1018% --- determine the list of index pairs of processing file
1019function [i1_series,i2_series,j1_series,j2_series,check_bounds,NomTypeNc]=...
1020    find_pair_indices(str_civ,i_series,j_series,MinIndex_i,MaxIndex_i,MinIndex_j,MaxIndex_j)
1021%------------------------------------------------------------------------
1022i1_series=i_series;% set of first image indexes
1023i2_series=i_series;
1024j1_series=ones(size(i_series));% set of first image numbers
1025j2_series=ones(size(i_series));
1026r=regexp(str_civ,'^\D(?<ind>[i|j])=( -| )(?<num1>\d+)\|(?<num2>\d+)','names');
1027if ~isempty(r)
1028    mode=['D' r.ind];
1029    ind1=str2num(r.num1);
1030    ind2=str2num(r.num2);
1031else
1032    mode='j1-j2';
1033    r=regexp(str_civ,'^j= (?<num1>[a-z])-(?<num2>[a-z])','names');
1034    if ~isempty(r)
1035        NomTypeNc='_1ab';
1036    else
1037        r=regexp(str_civ,'^j= (?<num1>[A-Z])-(?<num2>[A-Z])','names');
1038        if ~isempty(r)
1039            NomTypeNc='_1AB';
1040        else
1041            r=regexp(str_civ,'^j= (?<num1>\d+)-(?<num2>\d+)','names');
1042            if ~isempty(r)
1043                NomTypeNc='_1_1-2';
1044            end           
1045        end
1046    end
1047    if isempty(r)
1048        display('wrong pair mode input option')
1049    else
1050    ind1=stra2num(r.num1);
1051    ind2=stra2num(r.num2);
1052    end
1053end
1054if strcmp (mode,'Di')
1055    i1_series=i_series-ind1;% set of first image numbers
1056    i2_series=i_series+ind2;
1057     check_bounds=i1_series<MinIndex_i | i2_series>MaxIndex_i;
1058    if isempty(j_series)
1059        NomTypeNc='_1-2';
1060    else
1061        j1_series=j_series;
1062        j2_series=j_series;
1063        NomTypeNc='_1-2_1';
1064    end
1065elseif strcmp (mode,'Dj')
1066    j1_series=j_series-ind1;
1067    j2_series=j_series+ind2;
1068    check_bounds=j1_series<MinIndex_j | j2_series>MaxIndex_j;
1069    NomTypeNc='_1_1-2';
1070else  %bursts
1071    i1_series=i_series(1,:);% do not sweep the j index
1072    i2_series=i_series(1,:);
1073    j1_series=ind1*ones(1,size(i_series,2));% j index is fixed by pair choice
1074    j2_series=ind2*ones(1,size(i_series,2));
1075    check_bounds=zeros(size(i1_series));% no limitations due to min-max indices
1076end
1077
1078
1079
1080
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