source: trunk/src/series/civ_series.m @ 645

Last change on this file since 645 was 645, checked in by sommeria, 8 years ago

various improvements

File size: 45.2 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    Data.Program=mfilename;%gives the name of the current function
48    Data.AllowInputSort='off';% allow alphabetic sorting of the list of input file SubDir (options 'off'/'on', 'off' by default)
49    Data.WholeIndexRange='off';% prescribes the file index ranges from min to max (options 'off'/'on', 'off' by default)
50    Data.NbSlice='off'; %nbre of slices ('off' by default)
51    Data.VelType='off';% menu for selecting the velocity type (options 'off'/'one'/'two',  'off' by default)
52    Data.FieldName='off';% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default)
53    Data.FieldTransform = 'off';%can use a transform function
54    Data.ProjObject='off';%can use projection object(option 'off'/'on',
55    Data.Mask='off';%can use mask option   (option 'off'/'on', 'off' by default)
56    Data.OutputDirExt='.civ';%set the output dir extension
57    Data.OutputFileMode='NbInput_i';% one output file expected per value of i index (used for waitbar)
58    filecell=get_file_series(Param);%check existence of the first input file
59    if ~exist(filecell{1,1},'file')
60        msgbox_uvmat('WARNING','the first input file does not exist')
61    else
62        FileType=get_file_type(filecell{1,1});
63        if isempty(find(strcmp(FileType,{'civdata','image','multimage','mmreader','video'})));% =1 for images
64            msgbox_uvmat('ERROR',['bad input file type for ' mfilename ': an image or civdata file is needed'])
65        end
66    end
67    return
68end
69
70%% read input parameters from an xml file if input is a file name (batch mode)
71checkrun=1;
72if ischar(Param)
73    Param=xml2struct(Param);% read Param as input file (batch case)
74    checkrun=0;
75end
76hseries=findobj(allchild(0),'Tag','series');
77RUNHandle=findobj(hseries,'Tag','RUN');%handle of RUN button in GUI series
78WaitbarHandle=findobj(hseries,'Tag','Waitbar');%handle of waitbar in GUI series
79
80%% input files and indexing
81NbField=1;
82MaxIndex_i=Param.IndexRange.MaxIndex_i;
83MinIndex_i=Param.IndexRange.MinIndex_i;
84MaxIndex_j=1;MinIndex_j=1;
85if isfield(Param.IndexRange,'MaxIndex_j')&& isfield(Param.IndexRange,'MinIndex_j')
86    MaxIndex_j=Param.IndexRange.MaxIndex_j;
87    MinIndex_j=Param.IndexRange.MinIndex_j;
88end
89if isfield(Param,'InputTable')
90    [filecell,i_series,tild,j_series]=get_file_series(Param);
91    if ~exist(filecell{1,1},'file')
92        displ_uvmat('ERROR',' the first input file does not exist')
93        return
94    else
95        FileType=get_file_type(filecell{1,1});
96        iview_nc=0;
97        iview_A=0;
98        iview_B=0;
99        switch FileType
100            case 'civdata';% =1 for images
101                iview_nc=1;
102                if size(filecell,1)>=2
103                    iview_A=2;iview_B=2;
104                    if size(filecell,1)>=3
105                        iview_B=3;
106                    end
107                end
108            case {'image','multimage','mmreader','video'}
109                iview_A=1;
110                if size(filecell,1)>=2
111                    iview_B=2;
112                end
113        end
114    end
115    if iview_A~=0
116        [FileType_A,FileInfo_A,VideoObject_A]=get_file_type(filecell{1,1});
117        if isempty(strcmp(FileType_A,{'multimage','mmreader','video'}))
118            displ(['ERROR: the file line ' num2str(iview_A) ' must be an image'])
119        end
120        RootPath=Param.InputTable{1,1};
121        RootFile=Param.InputTable{1,3};
122        SubDir=Param.InputTable{1,2};
123        NomType=Param.InputTable{1,4};
124        FileExt=Param.InputTable{1,5};
125    end
126    if iview_B==0
127        FileType_B=FileType_A;
128        VideoObject_B=VideoObject_A;
129        PairCiv1=Param.ActionInput.PairIndices.ListPairCiv1;
130        PairCiv2='';
131        if isfield(Param.ActionInput.PairIndices,'ListPairCiv2')
132            PairCiv2=Param.ActionInput.PairIndices.ListPairCiv2;
133        end
134        [i1_series_Civ1,i2_series_Civ1,j1_series_Civ1,j2_series_Civ1,check_bounds,NomTypeNc]=...
135            find_pair_indices(PairCiv1,i_series{1},j_series{1},MinIndex_i,MaxIndex_i,MinIndex_j,MaxIndex_j);
136        if ~isempty(PairCiv2)
137            [i1_series_Civ2,i2_series_Civ2,j1_series_Civ2,j2_series_Civ2,check_bounds_Civ2]=...
138                find_pair_indices(PairCiv2,i_series{1},j_series{1},MinIndex_i,MaxIndex_i,MinIndex_j,MaxIndex_j);
139            check_bounds=check_bounds | check_bounds_Civ2;
140        end
141        i1_series_Civ1=i1_series_Civ1(~check_bounds);
142        i2_series_Civ1=i2_series_Civ1(~check_bounds);
143        j1_series_Civ1=j1_series_Civ1(~check_bounds);
144        j2_series_Civ1=j2_series_Civ1(~check_bounds);
145        if isempty(j_series{1})
146            FrameIndex_A_Civ1=i1_series_Civ1;
147            FrameIndex_B_Civ1=i2_series_Civ1;
148        else
149            FrameIndex_A_Civ1=j1_series_Civ1;
150            FrameIndex_B_Civ1=j2_series_Civ1;
151        end
152        if ~isempty(PairCiv2)
153            i1_series_Civ2=i1_series_Civ2(~check_bounds);
154            i2_series_Civ2=i2_series_Civ2(~check_bounds);
155            j1_series_Civ2=j1_series_Civ2(~check_bounds);
156            j2_series_Civ2=j2_series_Civ2(~check_bounds);
157            if isempty(j_series{1})
158                FrameIndex_A_Civ2=i1_series_Civ2;
159                FrameIndex_B_Civ2=i2_series_Civ2;
160            else
161                FrameIndex_A_Civ2=j1_series_Civ2;
162                FrameIndex_B_Civ2=j2_series_Civ2;
163            end
164        end
165    else
166        [FileType_B,FileInfo,VideoObject_B]=get_file_type(filecell{2,1});
167        if isempty(find(strcmp(FileType_B,{'multimage','mmreader','video'})))
168            displ(['ERROR: the file line ' num2str(iview_B) ' must be an image'])
169        end
170        %TODO : introduce the second file series if relevant: case %displacement
171    end
172end
173NbField=numel(i1_series_Civ1);
174
175%% Output directory
176OutputDir=[Param.OutputSubDir Param.OutputDirExt];
177
178Data.ListGlobalAttribute={'Conventions','Program','CivStage'};
179Data.Conventions='uvmat/civdata';% states the conventions used for the description of field variables and attributes
180Data.Program='civ_series';
181Data.CivStage=0;%default
182ListVarCiv1={'Civ1_X','Civ1_Y','Civ1_U','Civ1_V','Civ1_C','Civ1_F'}; %variables to read
183ListVarFix1={'Civ1_X','Civ1_Y','Civ1_U','Civ1_V','Civ1_C','Civ1_F','Civ1_FF'};
184mask='';
185maskname='';%default
186check_civx=0;%default
187check_civ1=0;%default
188check_patch1=0;%default
189
190%% get timing from the ImaDoc file or input video
191XmlFileName=find_imadoc(RootPath,SubDir,RootFile,FileExt);
192time=[];
193if ~isempty(XmlFileName)
194    XmlData=imadoc2struct(XmlFileName);
195        if isfield(XmlData,'Time')
196            time=XmlData.Time;
197            TimeSource='xml';
198        end
199        if isfield(XmlData,'Camera')
200            if isfield(XmlData.Camera,'NbSlice')&& ~isempty(XmlData.Camera.NbSlice)
201                NbSlice_calib{iview}=XmlData.Camera.NbSlice;% Nbre of slices for Zindex in phys transform
202                if ~isequal(NbSlice_calib{iview},NbSlice_calib{1})
203                    msgbox_uvmat('WARNING','inconsistent number of Z indices for the two field series');
204                end
205            end
206            if isfield(XmlData.Camera,'TimeUnit')&& ~isempty(XmlData.Camera.TimeUnit)
207                TimeUnit=XmlData.Camera.TimeUnit;
208            end
209        end
210end
211if isempty(time) && ~isempty(find(strcmp(FileType_A,{'mmreader','video'})))% case of video input
212    time=zeros(2,FileInfo_A.NumberOfFrames+1);
213    time(2,:)=(0:1/FileInfo_A.FrameRate:(FileInfo_A.NumberOfFrames)/FileInfo_A.FrameRate);
214    TimeSource='video';
215    % set(han:dles.Dt_txt,'String',['Dt=' num2str(1000/imainfo.FrameRate) 'ms']);%display the elementary time interval in millisec
216    ColorType='truecolor';
217end
218if isempty(time)% time = index i +0.001 index j by default
219    time=(MinIndex_i:MaxIndex_i)'*ones(1,MaxIndex_j-MinIndex_j+1);
220    time=time+0.001*ones(MaxIndex_i-MinIndex_i+1,1)*(MinIndex_j:MaxIndex_j);
221    time=[zeros(1,MaxIndex_j-MinIndex_j+1);time];% insert a first line of zeros
222    time=[zeros(MaxIndex_i-MinIndex_i+2,1) time];% insert a first column of zeros
223end
224   
225if length(FileInfo_A) >1 %case of image with multiple frames
226    nbfield=length(FileInfo_A);
227    nbfield_j=1;
228end
229
230%%%%% MAIN LOOP %%%%%%
231for ifield=1:NbField
232    update_waitbar(WaitbarHandle,ifield/NbField)
233    if ~isempty(RUNHandle) && ~strcmp(get(RUNHandle,'BusyAction'),'queue')
234        disp('program stopped by user')
235        break
236    end
237    %% Civ1
238    if isfield (Param.ActionInput,'Civ1')
239        par_civ1=Param.ActionInput.Civ1;
240        if isfield(par_civ1,'reverse_pair')% A REVOIR
241            if par_civ1.reverse_pair
242                if ischar(par_civ1.ImageB)
243                    temp=par_civ1.ImageA;
244                    par_civ1.ImageA=imread(par_civ1.ImageB);
245                end
246                if ischar(temp)
247                    par_civ1.ImageB=imread(temp);
248                end
249            end
250        else
251            ImageName_A=fullfile_uvmat(RootPath,SubDir,RootFile,FileExt,NomType,i1_series_Civ1(ifield),[],j1_series_Civ1(ifield));
252            [par_civ1.ImageA,VideoObject_A] = read_image(ImageName_A,FileType_A,VideoObject_A,FrameIndex_A_Civ1(ifield));
253            ImageName_B=fullfile_uvmat(RootPath,SubDir,RootFile,FileExt,NomType,i2_series_Civ1(ifield),[],j2_series_Civ1(ifield));
254            [par_civ1.ImageB,VideoObject_B] = read_image(ImageName_B,FileType_B,VideoObject_B,FrameIndex_B_Civ1(ifield));
255        end
256        ncfile=fullfile_uvmat(RootPath,OutputDir,RootFile,'.nc',NomTypeNc,i1_series_Civ1(ifield),i2_series_Civ1(ifield),...
257            j1_series_Civ1(ifield),j2_series_Civ1(ifield));
258        par_civ1.ImageWidth=FileInfo_A.Width;
259        par_civ1.ImageHeight=FileInfo_A.Height;
260        list_param=(fieldnames(Param.ActionInput.Civ1))';
261        Civ1_param=regexprep(list_param,'^.+','Civ1_$0');% insert 'Civ1_' before  each string in list_param
262        Civ1_param=[{'Civ1_ImageA','Civ1_ImageB','Civ1_Time','Civ1_Dt'} Civ1_param]; %insert the names of the two input images
263        %indicate the values of all the global attributes in the output data
264        Data.Civ1_ImageA=ImageName_A;
265        Data.Civ1_ImageB=ImageName_B;
266        i1=i1_series_Civ1(ifield);
267        i2=i1;
268        if ~isempty(i2_series_Civ1)
269            i2=i2_series_Civ1(ifield);
270        end
271        j1=1;
272        if ~isempty(j1_series_Civ1)
273            j1=j1_series_Civ1(ifield);
274        end
275        j2=j1;
276        if ~isempty(j2_series_Civ1)
277            j2=j2_series_Civ1(ifield);
278        end
279        Data.Civ1_Time=(time(i2+1,j2+1)+time(i1+1,j1+1))/2;
280        Data.Civ1_Dt=time(i2+1,j2+1)-time(i1+1,j1+1);
281        for ilist=1:length(list_param)
282            Data.(Civ1_param{4+ilist})=Param.ActionInput.Civ1.(list_param{ilist});
283        end
284        Data.ListGlobalAttribute=[Data.ListGlobalAttribute Civ1_param];
285        Data.CivStage=1;
286       
287        % set the list of variables
288        Data.ListVarName={'Civ1_X','Civ1_Y','Civ1_U','Civ1_V','Civ1_F','Civ1_C'};%  cell array containing the names of the fields to record
289        Data.VarDimName={'nb_vec_1','nb_vec_1','nb_vec_1','nb_vec_1','nb_vec_1','nb_vec_1'};
290        Data.VarAttribute{1}.Role='coord_x';
291        Data.VarAttribute{2}.Role='coord_y';
292        Data.VarAttribute{3}.Role='vector_x';
293        Data.VarAttribute{4}.Role='vector_y';
294        Data.VarAttribute{5}.Role='warnflag';
295       
296        if strcmp(Param.ActionInput.ListCompareMode, 'PIV volume')
297            Data.ListVarName=[Data.ListVarName 'Civ1_Z'];
298            Data.Civ1_X=[];Data.Civ1_Y=[];Data.Civ1_Z=[];
299            Data.Civ1_U=[];Data.Civ1_V=[];Data.Civ1_C=[];Data.Civ1_F=[];
300            for ivol=1:NbSlice
301                % caluclate velocity data (y and v in indices, reverse to y component)
302                [xtable ytable utable vtable ctable F result_conv errormsg] = civ (par_civ1);
303                if ~isempty(errormsg)
304                    return
305                end
306                Data.Civ1_X=[Data.Civ1_X reshape(xtable,[],1)];
307                Data.Civ1_Y=[Data.Civ1_Y reshape(Param.Civ1.ImageHeight-ytable+1,[],1)];
308                Data.Civ1_Z=[Data.Civ1_Z ivol*ones(numel(xtable),1)];% z=image index in image coordinates
309                Data.Civ1_U=[Data.Civ1_U reshape(utable,[],1)];
310                Data.Civ1_V=[Data.Civ1_V reshape(-vtable,[],1)];
311                Data.Civ1_C=[Data.Civ1_C reshape(ctable,[],1)];
312                Data.Civ1_F=[Data.Civ1_C reshape(F,[],1)];
313            end
314        else %usual PIV
315            % caluclate velocity data (y and v in indices, reverse to y component)
316            [xtable ytable utable vtable ctable F result_conv errormsg] = civ (par_civ1);
317            if ~isempty(errormsg)
318                return
319            end
320            Data.Civ1_X=reshape(xtable,[],1);
321            Data.Civ1_Y=reshape(par_civ1.ImageHeight-ytable+1,[],1);
322            Data.Civ1_U=reshape(utable,[],1);
323            Data.Civ1_V=reshape(-vtable,[],1);
324            Data.Civ1_C=reshape(ctable,[],1);
325            Data.Civ1_F=reshape(F,[],1);
326        end
327    else
328        if exist('ncfile','var')
329            CivFile=ncfile;
330        elseif isfield(Param.Patch1,'CivFile')
331            CivFile=Param.Patch1.CivFile;
332        end
333        Data=nc2struct(CivFile,'ListGlobalAttribute','absolut_time_T0'); %look for the constant 'absolut_time_T0' to detect old civx data format
334        if isfield(Data,'Txt')
335            errormsg=Data.Txt;
336            return
337        end
338        if ~isempty(Data.absolut_time_T0')%read civx file
339            check_civx=1;% test for old civx data format
340            [Data,vardetect,ichoice]=nc2struct(CivFile);%read the variables in the netcdf file
341        else
342            Data=nc2struct(CivFile);%read civ1 and fix1 data in the existing netcdf file
343        end
344    end
345   
346    %% Fix1
347    if isfield (Param.ActionInput,'Fix1')
348        ListFixParam=fieldnames(Param.ActionInput.Fix1);
349        for ilist=1:length(ListFixParam)
350            ParamName=ListFixParam{ilist};
351            ListName=['Fix1_' ParamName];
352            eval(['Data.ListGlobalAttribute=[Data.ListGlobalAttribute ''' ParamName '''];'])
353            eval(['Data.' ListName '=Param.ActionInput.Fix1.' ParamName ';'])
354        end
355        if check_civx
356            if ~isfield(Data,'fix')
357                Data.ListGlobalAttribute=[Data.ListGlobalAttribute 'fix'];
358                Data.fix=1;
359                Data.ListVarName=[Data.ListVarName {'vec_FixFlag'}];
360                Data.VarDimName=[Data.VarDimName {'nb_vectors'}];
361            end
362            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);
363        else
364            Data.ListVarName=[Data.ListVarName {'Civ1_FF'}];
365            Data.VarDimName=[Data.VarDimName {'nb_vec_1'}];
366            nbvar=length(Data.ListVarName);
367            Data.VarAttribute{nbvar}.Role='errorflag';
368            Data.Civ1_FF=fix(Param.ActionInput.Fix1,Data.Civ1_F,Data.Civ1_C,Data.Civ1_U,Data.Civ1_V);
369            Data.CivStage=2;
370        end
371    end
372    %% Patch1
373    if isfield (Param.ActionInput,'Patch1')
374        if check_civx
375            errormsg='Civ Matlab input needed for patch';
376            return
377        end
378       
379        Data.ListGlobalAttribute=[Data.ListGlobalAttribute {'Patch1_Rho','Patch1_Threshold','Patch1_SubDomain'}];
380        Data.Patch1_FieldSmooth=Param.ActionInput.Patch1.FieldSmooth;
381        Data.Patch1_MaxDiff=Param.ActionInput.Patch1.MaxDiff;
382        Data.Patch1_SubDomainSize=Param.ActionInput.Patch1.SubDomainSize;
383        nbvar=length(Data.ListVarName);
384        Data.ListVarName=[Data.ListVarName {'Civ1_U_smooth','Civ1_V_smooth','Civ1_SubRange','Civ1_NbCentres','Civ1_Coord_tps','Civ1_U_tps','Civ1_V_tps'}];
385        Data.VarDimName=[Data.VarDimName {'nb_vec_1','nb_vec_1',{'nb_coord','nb_bounds','nb_subdomain_1'},'nb_subdomain_1',...
386            {'nb_tps_1','nb_coord','nb_subdomain_1'},{'nb_tps_1','nb_subdomain_1'},{'nb_tps_1','nb_subdomain_1'}}];
387        Data.VarAttribute{nbvar+1}.Role='vector_x';
388        Data.VarAttribute{nbvar+2}.Role='vector_y';
389        Data.VarAttribute{nbvar+5}.Role='coord_tps';
390        Data.VarAttribute{nbvar+6}.Role='vector_x';
391        Data.VarAttribute{nbvar+7}.Role='vector_y';
392        Data.Civ1_U_smooth=zeros(size(Data.Civ1_X));
393        Data.Civ1_V_smooth=zeros(size(Data.Civ1_X));
394        if isfield(Data,'Civ1_FF')
395            ind_good=find(Data.Civ1_FF==0);
396        else
397            ind_good=1:numel(Data.Civ1_X);
398        end
399        [Data.Civ1_SubRange,Data.Civ1_NbCentres,Data.Civ1_Coord_tps,Data.Civ1_U_tps,Data.Civ1_V_tps,tild,Ures, Vres,tild,FFres]=...
400            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);
401        Data.Civ1_U_smooth(ind_good)=Ures;
402        Data.Civ1_V_smooth(ind_good)=Vres;
403        Data.Civ1_FF(ind_good)=FFres;
404        Data.CivStage=3;
405    end
406   
407    %% Civ2
408    if isfield (Param.ActionInput,'Civ2')
409        par_civ2=Param.ActionInput.Civ2;
410        par_civ2.ImageA=[];
411        par_civ2.ImageB=[];
412        %         if ~isfield(Param.Civ1,'ImageA')
413        ImageName_A_Civ2=fullfile_uvmat(RootPath,SubDir,RootFile,FileExt,NomType,i1_series_Civ2(ifield),[],j1_series_Civ2(ifield));
414
415        if strcmp(ImageName_A_Civ2,ImageName_A) && isequal(FrameIndex_A_Civ1(ifield),FrameIndex_A_Civ2(ifield))
416            par_civ2.ImageA=par_civ1.ImageA;
417        else
418            [par_civ2.ImageA,VideoObject_A] = read_image(ImageName_A,FileType_A,VideoObject_A,FrameIndex_A_Civ2(ifield));
419        end
420        ImageName_B_Civ2=fullfile_uvmat(RootPath,SubDir,RootFile,FileExt,NomType,i2_series_Civ2(ifield),[],j2_series_Civ2(ifield));
421        if strcmp(ImageName_B_Civ2,ImageName_B) && isequal(FrameIndex_B_Civ1(ifield),FrameIndex_B_Civ2)
422            par_civ2.ImageB=par_civ1.ImageB;
423        else
424            [par_civ2.ImageB,VideoObject_B] = read_image(ImageName_B,FileType_B,VideoObject_B,FrameIndex_B_Civ2(ifield));
425        end     
426       
427        ncfile=fullfile_uvmat(RootPath,OutputDir,RootFile,'.nc',NomTypeNc,i1_series_Civ2(ifield),i2_series_Civ2(ifield),...
428            j1_series_Civ2(ifield),j2_series_Civ2(ifield));
429        par_civ2.ImageWidth=FileInfo_A.Width;
430        par_civ2.ImageHeight=FileInfo_A.Height;
431       
432        if isfield(par_civ2,'Grid')% grid points set as input file
433            if ischar(par_civ2.Grid)%read the grid file if the input is a file name
434                par_civ2.Grid=dlmread(par_civ2.Grid);
435                par_civ2.Grid(1,:)=[];%the first line must be removed (heading in the grid file)
436            end
437        else% automatic grid
438            minix=floor(par_civ2.Dx/2)-0.5;
439            maxix=minix+par_civ2.Dx*floor((par_civ2.ImageWidth-1)/par_civ2.Dx);
440            miniy=floor(par_civ2.Dy/2)-0.5;
441            maxiy=minix+par_civ2.Dy*floor((par_civ2.ImageHeight-1)/par_civ2.Dy);
442            [GridX,GridY]=meshgrid(minix:par_civ2.Dx:maxix,miniy:par_civ2.Dy:maxiy);
443            par_civ2.Grid(:,1)=reshape(GridX,[],1);
444            par_civ2.Grid(:,2)=reshape(GridY,[],1);
445        end
446        Shiftx=zeros(size(par_civ2.Grid,1),1);% shift expected from civ1 data
447        Shifty=zeros(size(par_civ2.Grid,1),1);
448        nbval=zeros(size(par_civ2.Grid,1),1);
449        if par_civ2.CheckDeformation
450            DUDX=zeros(size(par_civ2.Grid,1),1);
451            DUDY=zeros(size(par_civ2.Grid,1),1);
452            DVDX=zeros(size(par_civ2.Grid,1),1);
453            DVDY=zeros(size(par_civ2.Grid,1),1);
454        end
455        NbSubDomain=size(Data.Civ1_SubRange,3);
456        % get the guess from patch1
457        for isub=1:NbSubDomain
458            nbvec_sub=Data.Civ1_NbCentres(isub);
459            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));
460            epoints = [GridX(ind_sel) GridY(ind_sel)];% coordinates of interpolation sites
461            ctrs=Data.Civ1_Coord_tps(1:nbvec_sub,:,isub) ;%(=initial points) ctrs
462            nbval(ind_sel)=nbval(ind_sel)+1;% records the number of values for eacn interpolation point (in case of subdomain overlap)
463            EM = tps_eval(epoints,ctrs);
464            Shiftx(ind_sel)=Shiftx(ind_sel)+EM*Data.Civ1_U_tps(1:nbvec_sub+3,isub);
465            Shifty(ind_sel)=Shifty(ind_sel)+EM*Data.Civ1_V_tps(1:nbvec_sub+3,isub);
466            if par_civ2.CheckDeformation
467                [EMDX,EMDY] = tps_eval_dxy(epoints,ctrs);%2D matrix of distances between extrapolation points epoints and spline centres (=site points) ctrs
468                DUDX(ind_sel)=DUDX(ind_sel)+EMDX*Data.Civ1_U_tps(1:nbvec_sub+3,isub);
469                DUDY(ind_sel)=DUDY(ind_sel)+EMDY*Data.Civ1_U_tps(1:nbvec_sub+3,isub);
470                DVDX(ind_sel)=DVDX(ind_sel)+EMDX*Data.Civ1_V_tps(1:nbvec_sub+3,isub);
471                DVDY(ind_sel)=DVDY(ind_sel)+EMDY*Data.Civ1_V_tps(1:nbvec_sub+3,isub);
472            end
473        end
474        mask='';
475        if par_civ2.CheckMask&&~isempty(par_civ2.Mask)&& ~strcmp(maskname,par_civ2.Mask)% mask exist, not already read in civ1
476            mask=imread(par_civ2.Mask);
477        end
478        ibx2=ceil(par_civ2.CorrBoxSize(1)/2);
479        iby2=ceil(par_civ2.CorrBoxSize(2)/2);
480        par_civ2.SearchBoxSize(1)=2*ibx2+9;% search ara +-4 pixels around the guess
481        par_civ2.SearchBoxSize(2)=2*iby2+9;
482        par_civ2.SearchBoxShift=[Shiftx(nbval>=1)./nbval(nbval>=1) Shifty(nbval>=1)./nbval(nbval>=1)];
483        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
484        if par_civ2.CheckDeformation
485            par_civ2.DUDX=DUDX./nbval;
486            par_civ2.DUDY=DUDY./nbval;
487            par_civ2.DVDX=DVDX./nbval;
488            par_civ2.DVDY=DVDY./nbval;
489        end
490        % caluclate velocity data (y and v in indices, reverse to y component)
491        [xtable ytable utable vtable ctable F] = civ (par_civ2);
492
493        list_param=(fieldnames(Param.ActionInput.Civ2))';
494        Civ2_param=regexprep(list_param,'^.+','Civ2_$0');% insert 'Civ2_' before  each string in list_param
495        Civ2_param=[{'Civ2_ImageA','Civ2_ImageB','Civ2_Time','Civ2_Dt'} Civ2_param]; %insert the names of the two input images
496        %indicate the values of all the global attributes in the output data
497        Data.Civ2_ImageA=ImageName_A;
498        Data.Civ2_ImageB=ImageName_B;
499        Data.Civ2_Time=1;
500        Data.Civ2_Dt=1;
501        for ilist=1:length(list_param)
502            Data.(Civ2_param{4+ilist})=Param.ActionInput.Civ2.(list_param{ilist});
503        end
504        Data.ListGlobalAttribute=[Data.ListGlobalAttribute Civ2_param];
505       
506        nbvar=numel(Data.ListVarName);
507        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
508        Data.VarDimName=[Data.VarDimName {'nb_vec_2','nb_vec_2','nb_vec_2','nb_vec_2','nb_vec_2','nb_vec_2'}];
509        Data.VarAttribute{nbvar+1}.Role='coord_x';
510        Data.VarAttribute{nbvar+2}.Role='coord_y';
511        Data.VarAttribute{nbvar+3}.Role='vector_x';
512        Data.VarAttribute{nbvar+4}.Role='vector_y';
513        Data.VarAttribute{nbvar+5}.Role='warnflag';
514        Data.Civ2_X=reshape(xtable,[],1);
515        Data.Civ2_Y=reshape(size(par_civ2.ImageA,1)-ytable+1,[],1);
516        Data.Civ2_U=reshape(utable,[],1);
517        Data.Civ2_V=reshape(-vtable,[],1);
518        Data.Civ2_C=reshape(ctable,[],1);
519        Data.Civ2_F=reshape(F,[],1);
520        Data.CivStage=Data.CivStage+1;
521    end
522   
523    %% Fix2
524    if isfield (Param.ActionInput,'Fix2')
525        ListFixParam=fieldnames(Param.ActionInput.Fix2);
526        for ilist=1:length(ListFixParam)
527            ParamName=ListFixParam{ilist};
528            ListName=['Fix2_' ParamName];
529            eval(['Data.ListGlobalAttribute=[Data.ListGlobalAttribute ''' ParamName '''];'])
530            eval(['Data.' ListName '=Param.ActionInput.Fix2.' ParamName ';'])
531        end
532        if check_civx
533            if ~isfield(Data,'fix2')
534                Data.ListGlobalAttribute=[Data.ListGlobalAttribute 'fix2'];
535                Data.fix2=1;
536                Data.ListVarName=[Data.ListVarName {'vec2_FixFlag'}];
537                Data.VarDimName=[Data.VarDimName {'nb_vectors2'}];
538            end
539            Data.vec_FixFlag=fix(Param.Fix2,Data.vec2_F,Data.vec2_C,Data.vec2_U,Data.vec2_V,Data.vec2_X,Data.vec2_Y);
540        else
541            Data.ListVarName=[Data.ListVarName {'Civ2_FF'}];
542            Data.VarDimName=[Data.VarDimName {'nb_vec_2'}];
543            nbvar=length(Data.ListVarName);
544            Data.VarAttribute{nbvar}.Role='errorflag';
545            Data.Civ2_FF=fix(Param.ActionInput.Fix2,Data.Civ2_F,Data.Civ2_C,Data.Civ2_U,Data.Civ2_V);
546            Data.CivStage=Data.CivStage+1;
547        end
548       
549    end
550   
551    %% Patch2
552    if isfield (Param.ActionInput,'Patch2')
553        Data.ListGlobalAttribute=[Data.ListGlobalAttribute {'Patch2_Rho','Patch2_Threshold','Patch2_SubDomain'}];
554        Data.Patch2_FieldSmooth=Param.ActionInput.Patch2.FieldSmooth;
555        Data.Patch2_MaxDiff=Param.ActionInput.Patch2.MaxDiff;
556        Data.Patch2_SubDomainSize=Param.ActionInput.Patch2.SubDomainSize;
557        nbvar=length(Data.ListVarName);
558        Data.ListVarName=[Data.ListVarName {'Civ2_U_smooth','Civ2_V_smooth','Civ2_SubRange','Civ2_NbCentres','Civ2_Coord_tps','Civ2_U_tps','Civ2_V_tps'}];
559        Data.VarDimName=[Data.VarDimName {'nb_vec_2','nb_vec_2',{'nb_coord','nb_bounds','nb_subdomain_2'},{'nb_subdomain_2'},...
560            {'nb_tps_2','nb_coord','nb_subdomain_2'},{'nb_tps_2','nb_subdomain_2'},{'nb_tps_2','nb_subdomain_2'}}];
561       
562        Data.VarAttribute{nbvar+1}.Role='vector_x';
563        Data.VarAttribute{nbvar+2}.Role='vector_y';
564        Data.VarAttribute{nbvar+5}.Role='coord_tps';
565        Data.VarAttribute{nbvar+6}.Role='vector_x';
566        Data.VarAttribute{nbvar+7}.Role='vector_y';
567        Data.Civ2_U_smooth=zeros(size(Data.Civ2_X));
568        Data.Civ2_V_smooth=zeros(size(Data.Civ2_X));
569        if isfield(Data,'Civ2_FF')
570            ind_good=find(Data.Civ2_FF==0);
571        else
572            ind_good=1:numel(Data.Civ2_X);
573        end
574        [Data.Civ2_SubRange,Data.Civ2_NbCentres,Data.Civ2_Coord_tps,Data.Civ2_U_tps,Data.Civ2_V_tps,tild,Ures, Vres,tild,FFres]=...
575            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);
576        Data.Civ2_U_smooth(ind_good)=Ures;
577        Data.Civ2_V_smooth(ind_good)=Vres;
578        Data.Civ2_FF(ind_good)=FFres;
579        Data.CivStage=Data.CivStage+1;
580    end
581   
582    %% write result in a netcdf file if requested
583    if exist('ncfile','var')
584        errormsg=struct2nc(ncfile,Data);
585        if isempty(errormsg)
586            disp([ncfile ' written'])
587        else
588            disp(errormsg)
589        end
590    end
591end
592
593% 'civ': function piv.m adapted from PIVlab http://pivlab.blogspot.com/
594%--------------------------------------------------------------------------
595% function [xtable ytable utable vtable typevector] = civ (image1,image2,ibx,iby step, subpixfinder, mask, roi)
596%
597% OUTPUT:
598% xtable: set of x coordinates
599% ytable: set of y coordiantes
600% utable: set of u displacements (along x)
601% vtable: set of v displacements (along y)
602% ctable: max image correlation for each vector
603% typevector: set of flags, =1 for good, =0 for NaN vectors
604%
605%INPUT:
606% par_civ: structure of input parameters, with fields:
607%  .CorrBoxSize
608%  .SearchBoxSize
609%  .SearchBoxShift
610%  .ImageHeight
611%  .ImageWidth
612%  .Dx, Dy
613%  .Grid
614%  .Mask
615%  .MinIma
616%  .MaxIma
617%  .image1:first image (matrix)
618% image2: second image (matrix)
619% ibx2,iby2: half size of the correlation box along x and y, in px (size=(2*iby2+1,2*ibx2+1)
620% isx2,isy2: half size of the search box along x and y, in px (size=(2*isy2+1,2*isx2+1)
621% shiftx, shifty: shift of the search box (in pixel index, yshift reversed)
622% step: mesh of the measurement points (in px)
623% subpixfinder=1 or 2 controls the curve fitting of the image correlation
624% mask: =[] for no mask
625% roi: 4 element vector defining a region of interest: x position, y position, width, height, (in image indices), for the whole image, roi=[];
626function [xtable ytable utable vtable ctable F result_conv errormsg] = civ (par_civ)
627%this funtion performs the DCC PIV analysis. Recent window-deformation
628%methods perform better and will maybe be implemented in the future.
629
630%% prepare measurement grid
631if isfield(par_civ,'Grid')% grid points set as input
632    if ischar(par_civ.Grid)%read the drid file if the input is a file name
633        par_civ.Grid=dlmread(par_civ.Grid);
634        par_civ.Grid(1,:)=[];%the first line must be removed (heading in the grid file)
635    end
636else% automatic grid
637    minix=floor(par_civ.Dx/2)-0.5;
638    maxix=minix+par_civ.Dx*floor((par_civ.ImageWidth-1)/par_civ.Dx);
639    miniy=floor(par_civ.Dy/2)-0.5;
640    maxiy=minix+par_civ.Dy*floor((par_civ.ImageHeight-1)/par_civ.Dy);
641    [GridX,GridY]=meshgrid(minix:par_civ.Dx:maxix,miniy:par_civ.Dy:maxiy);
642    par_civ.Grid(:,1)=reshape(GridX,[],1);
643    par_civ.Grid(:,2)=reshape(GridY,[],1);
644end
645nbvec=size(par_civ.Grid,1);
646
647%% prepare correlation and search boxes
648ibx2=ceil(par_civ.CorrBoxSize(1)/2);
649iby2=ceil(par_civ.CorrBoxSize(2)/2);
650isx2=ceil(par_civ.SearchBoxSize(1)/2);
651isy2=ceil(par_civ.SearchBoxSize(2)/2);
652shiftx=round(par_civ.SearchBoxShift(:,1));
653shifty=-round(par_civ.SearchBoxShift(:,2));% sign minus because image j index increases when y decreases
654if numel(shiftx)==1% case of a unique shift for the whole field( civ1)
655    shiftx=shiftx*ones(nbvec,1);
656    shifty=shifty*ones(nbvec,1);
657end
658
659%% Default output
660xtable=par_civ.Grid(:,1);
661ytable=par_civ.Grid(:,2);
662utable=zeros(nbvec,1);
663vtable=zeros(nbvec,1);
664ctable=zeros(nbvec,1);
665F=zeros(nbvec,1);
666result_conv=[];
667errormsg='';
668
669%% prepare mask
670if isfield(par_civ,'Mask') && ~isempty(par_civ.Mask)
671    if strcmp(par_civ.Mask,'all')
672        return    % get the grid only, no civ calculation
673    elseif ischar(par_civ.Mask)
674        par_civ.Mask=imread(par_civ.Mask);
675    end
676end
677check_MinIma=isfield(par_civ,'MinIma');% test for image luminosity threshold
678check_MaxIma=isfield(par_civ,'MaxIma') && ~isempty(par_civ.MaxIma);
679
680% %% prepare images
681% if isfield(par_civ,'reverse_pair')
682%     if par_civ.reverse_pair
683%         if ischar(par_civ.ImageB)
684%             temp=par_civ.ImageA;
685%             par_civ.ImageA=imread(par_civ.ImageB);
686%         end
687%         if ischar(temp)
688%             par_civ.ImageB=imread(temp);
689%         end
690%     end
691% else
692%     if ischar(par_civ.ImageA)
693%         par_civ.ImageA=imread(par_civ.ImageA);
694%     end
695%     if ischar(par_civ.ImageB)
696%         par_civ.ImageB=imread(par_civ.ImageB);
697%     end
698% end
699par_civ.ImageA=sum(double(par_civ.ImageA),3);%sum over rgb component for color images
700par_civ.ImageB=sum(double(par_civ.ImageB),3);
701[npy_ima npx_ima]=size(par_civ.ImageA);
702if ~isequal(size(par_civ.ImageB),[npy_ima npx_ima])
703    errormsg='image pair with unequal size';
704    return
705end
706
707%% Apply mask
708    % Convention for mask IDEAS TO IMPLEMENT ?
709    % mask >200 : velocity calculated
710    %  200 >=mask>150;velocity not calculated, interpolation allowed (bad spots)
711    % 150>=mask >100: velocity not calculated, nor interpolated
712    %  100>=mask> 20: velocity not calculated, impermeable (no flux through mask boundaries)
713    %  20>=mask: velocity=0
714checkmask=0;
715MinA=min(min(par_civ.ImageA));
716MinB=min(min(par_civ.ImageB));
717if isfield(par_civ,'Mask') && ~isempty(par_civ.Mask)
718   checkmask=1;
719   if ~isequal(size(par_civ.Mask),[npy_ima npx_ima])
720        errormsg='mask must be an image with the same size as the images';
721        return
722   end
723  %  check_noflux=(par_civ.Mask<100) ;%TODO: to implement
724    check_undefined=(par_civ.Mask<200 & par_civ.Mask>=20 );
725    par_civ.ImageA(check_undefined)=MinA;% put image A to zero (i.e. the min image value) in the undefined  area
726    par_civ.ImageB(check_undefined)=MinB;% put image B to zero (i.e. the min image value) in the undefined  area
727end
728
729%% compute image correlations: MAINLOOP on velocity vectors
730corrmax=0;
731sum_square=1;% default
732mesh=1;% default
733CheckDecimal=isfield(par_civ,'CheckDecimal')&& par_civ.CheckDecimal==1;
734if CheckDecimal
735    mesh=0.2;%mesh in pixels for subpixel image interpolation
736    CheckDeformation=isfield(par_civ,'CheckDeformation')&& par_civ.CheckDeformation==1;
737end
738% vector=[0 0];%default
739for ivec=1:nbvec
740    iref=round(par_civ.Grid(ivec,1)+0.5);% xindex on the image A for the middle of the correlation box
741    jref=round(par_civ.ImageHeight-par_civ.Grid(ivec,2)+0.5);% yindex on the image B for the middle of the correlation box
742    %if ~(checkmask && par_civ.Mask(jref,iref)<=20) %velocity not set to zero by the black mask
743    %         if jref-iby2<1 || jref+iby2>par_civ.ImageHeight|| iref-ibx2<1 || iref+ibx2>par_civ.ImageWidth||...
744    %               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
745    %             F(ivec)=3;
746    %         else
747    F(ivec)=0;
748    subrange1_x=iref-ibx2:iref+ibx2;% x indices defining the first subimage
749    subrange1_y=jref-iby2:jref+iby2;% y indices defining the first subimage
750    subrange2_x=iref+shiftx(ivec)-isx2:iref+shiftx(ivec)+isx2;%x indices defining the second subimage
751    subrange2_y=jref+shifty(ivec)-isy2:jref+shifty(ivec)+isy2;%y indices defining the second subimage
752    image1_crop=MinA*ones(numel(subrange1_y),numel(subrange1_x));% default value=min of image A
753    image2_crop=MinA*ones(numel(subrange2_y),numel(subrange2_x));% default value=min of image A
754    check1_x=subrange1_x>=1 & subrange1_x<=par_civ.ImageWidth;% check which points in the subimage 1 are contained in the initial image 1
755    check1_y=subrange1_y>=1 & subrange1_y<=par_civ.ImageHeight;
756    check2_x=subrange2_x>=1 & subrange2_x<=par_civ.ImageWidth;% check which points in the subimage 2 are contained in the initial image 2
757    check2_y=subrange2_y>=1 & subrange2_y<=par_civ.ImageHeight;
758   
759    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
760    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
761    image1_mean=mean(mean(image1_crop));
762    image2_mean=mean(mean(image2_crop));
763    %threshold on image minimum
764    if check_MinIma && (image1_mean < par_civ.MinIma || image2_mean < par_civ.MinIma)
765        F(ivec)=3;
766    end
767    %threshold on image maximum
768    if check_MaxIma && (image1_mean > par_civ.MaxIma || image2_mean > par_civ.MaxIma)
769        F(ivec)=3;
770    end
771    %         end
772    if F(ivec)~=3
773        image1_crop=image1_crop-image1_mean;%substract the mean
774        image2_crop=image2_crop-image2_mean;
775        if CheckDecimal
776            xi=(1:mesh:size(image1_crop,2));
777            yi=(1:mesh:size(image1_crop,1))';
778            if CheckDeformation
779                [XI,YI]=meshgrid(xi-ceil(size(image1_crop,2)/2),yi-ceil(size(image1_crop,1)/2));
780                XIant=XI-par_civ.DUDX(ivec)*XI-par_civ.DUDY(ivec)*YI+ceil(size(image1_crop,2)/2);
781                YIant=YI-par_civ.DVDX(ivec)*XI-par_civ.DVDY(ivec)*YI+ceil(size(image1_crop,1)/2);
782                image1_crop=interp2(image1_crop,XIant,YIant);
783            else
784                image1_crop=interp2(image1_crop,xi,yi);
785            end
786            xi=(1:mesh:size(image2_crop,2));
787            yi=(1:mesh:size(image2_crop,1))';
788            image2_crop=interp2(image2_crop,xi,yi);
789        end
790        sum_square=sum(sum(image1_crop.*image1_crop));
791        %reference: Oliver Pust, PIV: Direct Cross-Correlation
792        result_conv= conv2(image2_crop,flipdim(flipdim(image1_crop,2),1),'valid');
793        corrmax= max(max(result_conv));
794        result_conv=(result_conv/corrmax)*255; %normalize, peak=always 255
795        %Find the correlation max, at 255
796        [y,x] = find(result_conv==255,1);
797        if ~isempty(y) && ~isempty(x)
798            try
799                if par_civ.CorrSmooth==1
800                    [vector,F(ivec)] = SUBPIXGAUSS (result_conv,x,y);
801                elseif par_civ.CorrSmooth==2
802                    [vector,F(ivec)] = SUBPIX2DGAUSS (result_conv,x,y);
803                end
804                utable(ivec)=vector(1)*mesh+shiftx(ivec);
805                vtable(ivec)=vector(2)*mesh+shifty(ivec);
806                xtable(ivec)=iref+utable(ivec)/2-0.5;% convec flow (velocity taken at the point middle from imgae 1 and 2)
807                ytable(ivec)=jref+vtable(ivec)/2-0.5;% and position of pixel 1=0.5 (convention for image coordinates=0 at the edge)
808                iref=round(xtable(ivec));% image index for the middle of the vector
809                jref=round(ytable(ivec));
810                if checkmask && par_civ.Mask(jref,iref)<200 && par_civ.Mask(jref,iref)>=100
811                    utable(ivec)=0;
812                    vtable(ivec)=0;
813                    F(ivec)=3;
814                end
815                ctable(ivec)=corrmax/sum_square;% correlation value
816            catch ME
817                F(ivec)=3;
818            end
819        else
820            F(ivec)=3;
821        end
822    end
823end
824result_conv=result_conv*corrmax/(255*sum_square);% keep the last correlation matrix for output
825
826%------------------------------------------------------------------------
827% --- Find the maximum of the correlation function after interpolation
828function [vector,F] = SUBPIXGAUSS (result_conv,x,y)
829%------------------------------------------------------------------------
830vector=[0 0]; %default
831F=0;
832[npy,npx]=size(result_conv);
833
834% if (x <= (size(result_conv,1)-1)) && (y <= (size(result_conv,1)-1)) && (x >= 1) && (y >= 1)
835    %the following 8 lines are copyright (c) 1998, Uri Shavit, Roi Gurka, Alex Liberzon, Technion ï¿œ Israel Institute of Technology
836    %http://urapiv.wordpress.com
837    peaky = y;
838    if y <= npy-1 && y >= 1
839        f0 = log(result_conv(y,x));
840        f1 = real(log(result_conv(y-1,x)));
841        f2 = real(log(result_conv(y+1,x)));
842        peaky = peaky+ (f1-f2)/(2*f1-4*f0+2*f2);
843    else
844        F=-2; % warning flag for vector truncated by the limited search box
845    end
846    peakx=x;
847    if x <= npx-1 && x >= 1
848        f0 = log(result_conv(y,x));
849        f1 = real(log(result_conv(y,x-1)));
850        f2 = real(log(result_conv(y,x+1)));
851        peakx = peakx+ (f1-f2)/(2*f1-4*f0+2*f2);
852    else
853        F=-2; % warning flag for vector truncated by the limited search box
854    end
855    vector=[peakx-floor(npx/2)-1 peaky-floor(npy/2)-1];
856
857%------------------------------------------------------------------------
858% --- Find the maximum of the correlation function after interpolation
859function [vector,F] = SUBPIX2DGAUSS (result_conv,x,y)
860%------------------------------------------------------------------------
861vector=[0 0]; %default
862F=-2;
863peaky=y;
864peakx=x;
865[npy,npx]=size(result_conv);
866if (x <= npx-1) && (y <= npy-1) && (x >= 1) && (y >= 1)
867    F=0;
868    for i=-1:1
869        for j=-1:1
870            %following 15 lines based on
871            %H. Nobach ï¿œ M. Honkanen (2005)
872            %Two-dimensional Gaussian regression for sub-pixel displacement
873            %estimation in particle image velocimetry or particle position
874            %estimation in particle tracking velocimetry
875            %Experiments in Fluids (2005) 38: 511ï¿œ515
876            c10(j+2,i+2)=i*log(result_conv(y+j, x+i));
877            c01(j+2,i+2)=j*log(result_conv(y+j, x+i));
878            c11(j+2,i+2)=i*j*log(result_conv(y+j, x+i));
879            c20(j+2,i+2)=(3*i^2-2)*log(result_conv(y+j, x+i));
880            c02(j+2,i+2)=(3*j^2-2)*log(result_conv(y+j, x+i));
881        end
882    end
883    c10=(1/6)*sum(sum(c10));
884    c01=(1/6)*sum(sum(c01));
885    c11=(1/4)*sum(sum(c11));
886    c20=(1/6)*sum(sum(c20));
887    c02=(1/6)*sum(sum(c02));
888    deltax=(c11*c01-2*c10*c02)/(4*c20*c02-c11^2);
889    deltay=(c11*c10-2*c01*c20)/(4*c20*c02-c11^2);
890    if abs(deltax)<1
891        peakx=x+deltax;
892    end
893    if abs(deltay)<1
894        peaky=y+deltay;
895    end
896end
897vector=[peakx-floor(npx/2)-1 peaky-floor(npy/2)-1];
898
899%'RUN_FIX': function for fixing velocity fields:
900%-----------------------------------------------
901% RUN_FIX(filename,field,flagindex,thresh_vecC,thresh_vel,iter,flag_mask,maskname,fileref,fieldref)
902%
903%filename: name of the netcdf file (used as input and output)
904%field: structure specifying the names of the fields to fix (depending on civ1 or civ2)
905    %.vel_type='civ1' or 'civ2';
906    %.nb=name of the dimension common to the field to fix ('nb_vectors' for civ1);
907    %.fixflag=name of fix flag variable ('vec_FixFlag' for civ1)
908%flagindex: flag specifying which values of vec_f are removed:
909        % if flagindex(1)=1: vec_f=-2 vectors are removed
910        % if flagindex(2)=1: vec_f=3 vectors are removed
911        % if flagindex(3)=1: vec_f=2 vectors are removed (if iter=1) or vec_f=4 vectors are removed (if iter=2)
912%iter=1 for civ1 fields and iter=2 for civ2 fields
913%thresh_vecC: threshold in the image correlation vec_C
914%flag_mask: =1 mask used to remove vectors (0 else)
915%maskname: name of the mask image file for fix
916%thresh_vel: threshold on velocity, or on the difference with the reference file fileref if exists
917%inf_sup=1: remove values smaller than threshold thresh_vel, =2, larger than threshold
918%fileref: .nc file name for a reference velocity (='': refrence 0 used)
919%fieldref: 'civ1','filter1'...feld used in fileref
920
921function FF=fix(Param,F,C,U,V,X,Y)
922FF=zeros(size(F));%default
923
924%criterium on warn flags
925FlagName={'CheckFmin2','CheckF2','CheckF3','CheckF4'};
926FlagVal=[-2 2 3 4];
927for iflag=1:numel(FlagName)
928    if isfield(Param,FlagName{iflag}) && Param.(FlagName{iflag})
929        FF=(FF==1| F==FlagVal(iflag));
930    end
931end
932%criterium on correlation values
933if isfield (Param,'MinCorr')
934    FF=FF==1 | C<Param.MinCorr;
935end
936if (isfield(Param,'MinVel')&&~isempty(Param.MinVel))||(isfield (Param,'MaxVel')&&~isempty(Param.MaxVel))
937    Umod= U.*U+V.*V;
938    if isfield (Param,'MinVel')&&~isempty(Param.MinVel)
939        FF=FF==1 | Umod<(Param.MinVel*Param.MinVel);
940    end
941    if isfield (Param,'MaxVel')&&~isempty(Param.MaxVel)
942        FF=FF==1 | Umod>(Param.MaxVel*Param.MaxVel);
943    end
944end
945
946
947%------------------------------------------------------------------------
948% --- determine the list of index pairs of processing file
949function [i1_series,i2_series,j1_series,j2_series,check_bounds,NomTypeNc]=...
950    find_pair_indices(str_civ,i_series,j_series,MinIndex_i,MaxIndex_i,MinIndex_j,MaxIndex_j)
951%------------------------------------------------------------------------
952i1_series=i_series;% set of first image indexes
953i2_series=i_series;
954j1_series=ones(size(i_series));% set of first image numbers
955j2_series=ones(size(i_series));
956check_bounds=false(size(i_series));
957r=regexp(str_civ,'^\D(?<ind>[i|j])=( -| )(?<num1>\d+)\|(?<num2>\d+)','names');
958if ~isempty(r)
959    mode=['D' r.ind];
960    ind1=str2num(r.num1);
961    ind2=str2num(r.num2);
962else
963    mode='burst';
964    r=regexp(str_civ,'^j= (?<num1>[a-z])-(?<num2>[a-z])','names');
965    if ~isempty(r)
966        NomTypeNc='_1ab';
967    else
968        r=regexp(str_civ,'^j= (?<num1>[A-Z])-(?<num2>[A-Z])','names');
969        if ~isempty(r)
970            NomTypeNc='_1AB';
971        else
972            r=regexp(str_civ,'^j= (?<num1>\d+)-(?<num2>\d+)','names');
973            if ~isempty(r)
974                NomTypeNc='_1_1-2';
975            end           
976        end
977    end
978    if isempty(r)
979        display('wrong pair mode input option')
980    else
981    ind1=stra2num(r.num1);
982    ind2=stra2num(r.num2);
983    end
984end
985if strcmp (mode,'Di')
986    i1_series=i_series-ind1;% set of first image numbers
987    i2_series=i_series+ind2;
988     check_bounds=i1_series<MinIndex_i | i2_series>MaxIndex_i;
989    if isempty(j_series)
990        NomTypeNc='_1-2';
991    else
992        j1_series=j_series;
993        j2_series=j_series;
994        NomTypeNc='_1-2_1';
995    end
996elseif strcmp (mode,'Dj')
997    j1_series=j_series-ind1;
998    j2_series=j_series+ind2;
999    check_bounds=j1_series<MinIndex_j | j2_series>MaxIndex_j;
1000    NomTypeNc='_1_1-2';
1001else  %bursts
1002    j1_series=ind1*ones(size(i_series));
1003    j2_series=ind2*ones(size(i_series));
1004end
1005
1006
1007
1008
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