source: trunk/src/civ.m @ 549

Last change on this file since 549 was 549, checked in by sommeria, 8 years ago

bug corrected in civ: multiple commands in .sh for civ_matlab
.m and .sh files recognized in get_file_type

File size: 194.3 KB
Line 
1
2%'civ': function associated with the interface 'civ.fig' for PIV, spline interpolation and stereo PIV (patch)
3%------------------------------------------------------------------------
4%  provides an interface for the software menucivx
5% function varargout = civ(varargin)
6% provides an interface for the software menucivx
7%
8%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
9%  Copyright Joel Sommeria, 2011, LEGI / CNRS-UJF-INPG, sommeria@legi.grenoble-inp.fr
10%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
11%     This file is part of the toolbox UVMAT.
12%
13%     UVMAT is free software; you can redistribute it and/or modify
14%     it under the terms of the GNU General Public License as published by
15%     the Free Software Foundation; either version 2 of the License, or
16%     (at your option) any later version.
17%
18%     UVMAT is distributed in the hope that it will be useful,
19%     but WITHOUT ANY WARRANTY; without even the implied warranty of
20%     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
21%     GNU General Public License (file UVMAT/COPYING.txt) for more details.
22%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
23function varargout = civ(varargin)
24%TODO: search range
25
26% Last Modified by GUIDE v2.5 24-Jul-2012 13:14:00
27% Begin initialization code - DO NOT EDIT
28gui_Singleton = 1;
29gui_State = struct('gui_Name',       mfilename, ...
30    'gui_Singleton',  gui_Singleton, ...
31    'gui_OpeningFcn', @civ_OpeningFcn, ...
32    'gui_OutputFcn',  @civ_OutputFcn, ...
33    'gui_LayoutFcn',  [] , ...
34    'gui_Callback',   []);
35if nargin && ischar(varargin{1}) && ~isempty(regexp(varargin{1},'_Callback$','once'))
36    gui_State.gui_Callback = str2func(varargin{1});
37end
38
39if nargout
40    [varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:});
41else
42    gui_mainfcn(gui_State, varargin{:});
43end
44% End initialization code - DO NOT EDIT
45
46%------------------------------------------------------------------------
47% --- Executes just before civ is made visible.
48function civ_OpeningFcn(hObject, eventdata, handles, fileinput)
49%------------------------------------------------------------------------
50% This function has no output args, see OutputFcn.
51
52%% General settings
53handles.output = hObject;
54guidata(hObject, handles); % Update handles structure
55set(hObject,'WindowButtonDownFcn',{'mouse_down'}) % allows mouse action with right button (zoom for uicontrol display)
56
57%% Adjust the GUI according to the binaries available in PARAM.xml
58path_civ=fileparts(which('civ')); %path to civ
59addpath (path_civ) ; %add the path to civ, (useful in case of change of working directory after civ has been s opened in the working directory)
60errormsg=[];%default error message
61xmlfile=fullfile(path_civ,'PARAM.xml');
62test_batch=0;%default: ,no batch mode available
63sparam=[];
64if ~exist(xmlfile,'file')
65    [success,message]=copyfile(fullfile(path_civ,'PARAM.xml.default'),xmlfile);
66end
67if exist(xmlfile,'file')
68    try
69        t=xmltree(xmlfile);
70        sparam=convert(t);
71    catch ME
72        errormsg={' Unable to read the file PARAM.xml defining the civx binaries:';ME.message};
73         msgbox_uvmat('WARNING',errormsg);
74    end
75else
76    [s,w]=system('oarstat');
77    if ~isequal(s,0)
78        [s,w]=system('qstat');
79    end
80    if isequal(s,0)
81        test_batch=1;
82    end           
83end
84if isfield(sparam,'BatchParam') && isfield(sparam.BatchParam,'BatchMode')
85    batch_mode=sparam.BatchParam.BatchMode; %sge is currently the only implemented batch mod
86    test_command='';
87    switch batch_mode
88        case 'sge'
89            test_command='qstat';
90        case 'oar'
91            test_command='oarstat';
92    end
93    if ~isempty(test_command)
94        [s,w]=system(test_command);
95        if isequal(s,0)
96            test_batch=1;
97        end
98    end
99end
100RUNVal=get(handles.RunMode,'Value');
101if test_batch==0
102   if RUNVal>2
103       set(handles.RunMode,'Value',1)
104   end
105   set(handles.RunMode,'String',{'local';'background'})
106else
107    set(handles.RunMode,'String',{'local';'background';'cluster'})
108end
109
110%% load the list of previously browsed files in the upper bar menu Open/
111dir_perso=prefdir; % path to the directory .matlab for personal data
112profil_perso=fullfile(dir_perso,'uvmat_perso.mat');% personal data file uvmauvmat_perso.mat' in .matlab
113if exist(profil_perso,'file')
114    h=load (profil_perso);
115    if isfield(h,'MenuFile')
116        for ifile=1:min(length(h.MenuFile),5)
117            eval(['set(handles.MenuFile_' num2str(ifile) ',''Label'',h.MenuFile{ifile});'])
118        end
119    end
120end
121
122%% prepare the GUI with parameters from the input file if opened from uvmat
123if exist('fileinput','var')% && isfield(param,'RootName') && ~isempty(param.RootName)
124    set(handles.RootPath,'BackgroundColor',[1 1 0])%paint RootName edit box in yellow to indicate that the file input is proceeding
125    errormsg=display_file_name(handles,fileinput);
126    if ~isempty(errormsg)
127        msgbox_uvmat('ERROR',errormsg)
128    end
129    set(handles.RootPath,'BackgroundColor',[1 1 1])%paint RootName back to white to indicate that the file input is finished
130end
131Program_Callback([],[], handles)
132
133%------------------------------------------------------------------------
134% --- Outputs from this function are returned to the command line.
135function varargout = civ_OutputFcn(hObject, eventdata, handles)
136%------------------------------------------------------------------------
137% Get default command line output from handles structure
138varargout{1} = handles.output;
139
140%------------------------------------------------------------------------
141% --- Function activated by the Open/Browse... option in the upper menu bar.
142function MenuBrowse_Callback(hObject, eventdata, handles)
143%------------------------------------------------------------------------
144%% get the current input root file name to initiate the browser
145filebase=get(handles.RootPath,'String');
146oldfile=''; %default
147if isempty(filebase)|| isequal(filebase,'')%loads the previously stored root file name
148    dir_perso=prefdir;
149    profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
150    if exist(profil_perso,'file')
151        h=load (profil_perso);
152        if isfield(h,'filebase')&& ischar(h.filebase)
153            oldfile=h.filebase;
154        end
155        if isfield(h,'RootPath') && ischar(h.RootPath)
156            oldfile=h.RootPath;
157        end
158    end
159else
160    oldfile=filebase;
161end
162
163%% get the new input file with the browser
164menu={'*.xml;*.civ;*.png;*.jpg;*.tif;*.avi;*.AVI;*.nc;', ' (*.xml,*.civ,*.png,*.jpg ,.tif, *.avi,*.nc)';
165    '*.xml',  '.xml files '; ...
166    '*.civ',  '.civ files '; ...
167    '*.png','.png image files'; ...
168    '*.jpg',' jpeg image files'; ...
169    '*.tif','.tif image files'; ...
170    '*.avi;*.AVI','.avi movie files'; ...
171    '*.nc','.netcdf files'; ...
172    '*.*',  'All Files (*.*)'};
173[FileName, PathName, filtindex] = uigetfile( menu, 'Pick a file',oldfile);
174fileinput=[PathName FileName];%complete file name
175sizf=size(fileinput);
176if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end %stop if fileinput not a character string
177
178%% case of the xml file opened as input (TODO: check and see whether it is useful)
179[path,name,ext]=fileparts(fileinput);
180testeditxml=0;
181% if isequal(ext,'.xml')
182%     testeditxml=1;
183%     t_browse=xmltree(fileinput);
184%     head_element=get(t_browse,1);
185%     if isfield(head_element,'name')&& isequal(head_element.name,'ImaDoc')
186%         testeditxml=0;
187%     end
188% end
189% if testeditxml==1 || isequal(ext,'.xls')
190%     heditxml=editxml({fileinput});
191%     set(heditxml,'Tag','browser')
192%     waitfor(heditxml,'Tag','idle')
193%     if ~ishandle(heditxml)
194%         return
195%     end
196%     attr=findobj(get(heditxml,'children'),'Tag','CurrentAttributes');
197%     set(handles.browse,'UserData',fileinput)% store for future opening with browser
198%     fileinput=get(attr,'UserData');
199%     if ~exist(fileinput,'file')
200%         return
201%     end
202% end
203[tild,tild,tild,i1,i2,j1,j2,FileExt,NomType]=fileparts_uvmat(fileinput);
204
205%% prepare the GUI with parameters from the input file
206set(handles.RootPath,'BackgroundColor',[1 1 0])%paint RootName edit box in yellow to indicate that the file input is proceeding
207errormsg=display_file_name(handles,fileinput);
208if ~isempty(errormsg)
209    msgbox_uvmat('ERROR',erromsg)
210end
211set(handles.RootPath,'BackgroundColor',[1 1 1])%paint RootName back to white to indicate that the file input is finished
212
213%------------------------------------------------------------------------
214% --- Open again the file whose name has been recorded in MenuFile_1
215function MenuFile_1_Callback(hObject, eventdata, handles)
216%------------------------------------------------------------------------
217set(handles.RootPath,'BackgroundColor',[1 1 0])%paint RootName edit box in yellow to indicate that the file input is proceeding
218fileinput=get(handles.MenuFile_1,'Label');
219errormsg=display_file_name(handles,fileinput);
220if ~isempty(errormsg)
221    msgbox_uvmat('ERROR',errormsg)
222end
223set(handles.RootPath,'BackgroundColor',[1 1 1])%paint RootName back to white to indicate that the file input is finished
224
225% -----------------------------------------------------------------------
226% --- Open again the file whose name has been recorded in MenuFile_2
227function MenuFile_2_Callback(hObject, eventdata, handles)
228%------------------------------------------------------------------------
229set(handles.RootPath,'BackgroundColor',[1 1 0])%paint RootName edit box in yellow to indicate that the file input is proceeding
230fileinput=get(handles.MenuFile_2,'Label');
231errormsg=display_file_name(handles,fileinput);
232if ~isempty(errormsg)
233    msgbox_uvmat('ERROR',errormsg)
234end
235set(handles.RootPath,'BackgroundColor',[1 1 1])%paint RootName back to white to indicate that the file input is finished
236
237% -----------------------------------------------------------------------
238% --- Open again the file whose name has been recorded in MenuFile_3
239function MenuFile_3_Callback(hObject, eventdata, handles)
240%------------------------------------------------------------------------
241set(handles.RootPath,'BackgroundColor',[1 1 0])%paint RootName edit box in yellow to indicate that the file input is proceeding
242fileinput=get(handles.MenuFile_3,'Label');
243errormsg=display_file_name(handles,fileinput);
244if ~isempty(errormsg)
245    msgbox_uvmat('ERROR',errormsg)
246end
247set(handles.RootPath,'BackgroundColor',[1 1 1])%paint RootName back to white to indicate that the file input is finished
248
249% -----------------------------------------------------------------------
250% --- Open again the file whose name has been recorded in MenuFile_4
251function MenuFile_4_Callback(hObject, eventdata, handles)
252%------------------------------------------------------------------------
253set(handles.RootPath,'BackgroundColor',[1 1 0])%paint RootName edit box in yellow to indicate that the file input is proceeding
254fileinput=get(handles.MenuFile_4,'Label');
255errormsg=display_file_name(handles,fileinput);
256if ~isempty(errormsg)
257    msgbox_uvmat('ERROR',errormsg)
258end
259set(handles.RootPath,'BackgroundColor',[1 1 1])%paint RootName back to white to indicate that the file input is finished
260
261% -----------------------------------------------------------------------
262% --- Open again the file whose name has been recorded in MenuFile_5
263function MenuFile_5_Callback(hObject, eventdata, handles)
264%------------------------------------------------------------------------
265set(handles.RootPath,'BackgroundColor',[1 1 0])%paint RootName edit box in yellow to indicate that the file input is proceeding
266fileinput=get(handles.MenuFile_5,'Label');
267errormsg=display_file_name(handles,fileinput);
268if ~isempty(errormsg)
269    msgbox_uvmat('ERROR',errormsg)
270end
271set(handles.RootPath,'BackgroundColor',[1 1 1])%paint RootName back to white to indicate that the file input is finished
272
273% -----------------------------------------------------------------------
274% -----------------------------------------------------------------------
275% --- Open the help html file
276function MenuHelp_Callback(hObject, eventdata, handles)
277% -----------------------------------------------------------------------
278path_civ=fileparts(which ('civ'));
279helpfile=fullfile(path_civ,'uvmat_doc','uvmat_doc.html');
280if isempty(dir(helpfile))
281    msgbox_uvmat('ERROR','Please put the help file uvmat_doc.html in the sub-directory /uvmat_doc of the UVMAT package')
282else
283    addpath (fullfile(path_civ,'uvmat_doc'))
284    web([helpfile '#civ'])
285end
286
287%------------------------------------------------------------------------
288% --- Function activated when a new filebase (image series) is introduced
289function RootPath_Callback(hObject, eventdata, handles)
290%------------------------------------------------------------------------
291set(handles.RootPath,'BackgroundColor',[1 1 0])%paint RootName edit box in yellow to indicate that the file input is proceeding
292RootPath=get(handles.RootPath,'String');
293SubDirImages=get(handles.SubDirImages,'String');
294RootFile=get(handles.RootFile,'String');
295ref_i=str2num(get(handles.ref_i,'String'));
296ref_j=str2num(get(handles.ref_j,'String'));
297NomType=get(handles.NomType,'String');
298ImaExt=get(handles.ImaExt,'String');
299fileinput=fullfile_uvmat(RootPath,SubDirImages,RootFile,ImaExt,NomType,ref_i,[],ref_j);
300errormsg=display_file_name(handles,fileinput);
301if ~isempty(errormsg)
302    msgbox_uvmat('ERROR',errormsg)
303end
304set(handles.RootPath,'BackgroundColor',[1 1 1])%paint RootName back to white to indicate that the file input is finished
305
306%------------------------------------------------------------------------
307% --- general function activated for an input file series
308function errormsg=display_file_name(handles,fileinput)
309%------------------------------------------------------------------------
310set(handles.ListCompareMode,'Visible','on')
311errormsg='';%default empty error message
312drawnow
313
314%% enable RUN, BATCH button and 'status' display
315set(handles.RUN, 'Enable','On')
316set(handles.RUN,'BackgroundColor',[1 0 0])%set RUN button to red color
317if isfield(handles,'status')
318    set(handles.status,'Value',0);       %suppress the 'status' display
319    status_Callback([], [], handles)
320end
321
322%% determine nomenclature types and extension of the input files
323[RootPath,SubDir,RootFile,i1,i2,j1,j2,ExtInput,NomTypeInput]=fileparts_uvmat(fileinput);
324NomTypeNc='';%default
325
326%% case of xml file as input, read the civ parameters
327ind_opening=0;%default
328if strcmp(ExtInput,'.xml')
329    %reinitialise menus
330        set(handles.ListPairMode,'Value',1)
331    set(handles.ListPairMode,'String',{''})
332    set(handles.ListPairCiv1,'Value',1)
333    set(handles.ListPairCiv1,'String',{''})
334        set(handles.ListPairCiv2,'Value',1)
335    set(handles.ListPairCiv2,'String',{''})
336    Param=xml2struct(fileinput);  %read parameters from the xml input file
337    fill_GUI(Param,handles);%fill the GUI with the parameters retrieved from the xml file
338    return
339end
340
341%% case of netcdf file as input, get the civ processing stage and look for a coresponding image
342imageinput=fileinput;%default
343if strcmp(ExtInput,'.nc')
344    NomTypeNc=NomTypeInput;
345    if isempty(regexp(NomTypeInput,'[ab|AB|-]', 'once'))
346        set(handles.ListCompareMode,'Value',2) %mode displacement advised if the nomencalture does not involve index pairs
347        set(handles.RootFile_1,'Visible','On');
348    else
349        set(handles.ListCompareMode,'Value',1)
350        set(handles.RootFile_1,'Visible','Off');
351    end
352    imageinput='';
353    Data=nc2struct(fileinput,'ListGlobalAttribute','Conventions','absolut_time_T0','CivStage','Civ2_ImageA','Civ1_ImageA','Civ2_ImageB','Civ1_ImageB','fix','patch','civ2','fix2');
354    if isfield(Data,'Txt')
355        errormsg=Data.Txt;
356        return
357    end
358    % settings for  new civ data,
359    if strcmp(Data.Conventions,'uvmat/civdata')% case of new civ data,
360        set(handles.Program,'Value',1) %select civ/Matlab by default
361        Program_Callback([],[], handles)
362        if ~isempty(Data.CivStage)%test for civ files
363            ind_opening=Data.CivStage;
364        end
365        if  ~isempty(Data.Civ2_ImageB)%get the corresponding input image in the netcdf file
366            imageinput=Data.Civ2_ImageB;
367            [tild,ImaName,ImaExt]=fileparts(Data.Civ2_ImageA);
368            set(handles.RootFile_1,'String',[ImaName ImaExt])
369        elseif ~isempty(Data.Civ1_ImageB)
370            imageinput=Data.Civ1_ImageB;
371            [tild,ImaName,ImaExt]=fileparts(Data.Civ1_ImageA);
372            set(handles.RootFile_1,'String',[ImaName ImaExt])
373        end
374        % settings for civx data,
375    elseif ~isempty(Data.absolut_time_T0')% case of  civx data,
376        set(handles.Program,'Value',3) %select Cix by default
377        Program_Callback([],[], handles)
378        if ~isempty(Data.fix2)
379            ind_opening=5;
380        elseif ~isempty(Data.civ2)
381            ind_opening=4;
382        elseif ~isempty(Data.patch)
383            ind_opening=3;
384        elseif ~isempty(Data.fix)
385            ind_opening=2;
386        end
387    else
388        errormsg='the input netcdf file is not civ data';
389        return
390    end
391    % look for the corresponding input images
392    check_letter=~isempty(regexp(NomTypeInput,'[ab|AB]$','once'));%detect pair label by letter
393    NomTypeIma=NomTypeInput;
394    if check_letter
395        NomTypeIma=NomTypeInput(1:end-1);
396    else
397        r=regexp(NomTypeIma,'.-(?<num2>\d+)$','names');
398        if ~isempty(r)
399            NomTypeIma=regexprep(NomTypeIma,['-' r.num2],'');
400        end
401        r=regexp(NomTypeIma,'.-(?<num2>\d+)','names');
402        if ~isempty(r)
403            NomTypeIma=regexprep(NomTypeIma,['-' r.num2],'');
404        end
405    end
406    if ~exist(imageinput,'file')
407    imageinput=fullfile_uvmat(RootPath,regexprep(SubDir,'.civ(_?)(\d*)$',''),RootFile,'.png',NomTypeIma,i1,[],j1);
408    end
409end
410
411%% no corresponding image found, select manually with the browser
412ImaExt=ExtInput;
413if ~isempty(NomTypeNc)
414    %no corresponding image found, select manually with the browser
415    if ~exist(imageinput,'file')
416        menu={'*.png;*.jpg;*.tif;*.avi;*.AVI', '(*.png,*.jpg ,*.tif, *.avi,*.AVI)';
417            '*.png','.png image files'; ...
418            '*.jpg',' jpeg image files'; ...
419            '*.tif','.tif image files'; ...
420            '*.avi;*.AVI','.avi movie files'; ...
421            '*.*',  'All Files (*.*)'};
422        [FileName, PathName] = uigetfile( menu, 'Pick an input image file',fileparts(fileparts(fileinput)));
423        imageinput=[PathName FileName];%complete file name
424        if ~exist(imageinput,'file')
425            return %abandon of the browser is cancelled
426        end
427    end   
428    %fileinput=imageinput;
429end
430
431%% scan the image file series
432[FilePath,FileName,ImaExt]=fileparts(imageinput);
433% detect the file type, get the movie object if relevant, and look for the corresponding file series:
434% the root name and indices may be corrected by including the first index i1 if a corresponding xml file exists
435[RootPath,SubDirImages,RootFile,i1_series,tild,j1_series,tild,NomTypeIma,FileType,MovieObject]=find_file_series(FilePath,[FileName ImaExt]);
436switch FileType
437    case {'image','multimage','video','mmreader'}
438    otherwise
439        errormsg='invalid input file: enter an image, a movie or civ .nc file';
440        return
441end
442set(handles.RootPath,'String',RootPath)
443set(handles.SubDirImages,'String',SubDirImages)
444set(handles.RootFile,'String',RootFile)
445if strcmp(ExtInput,'.nc')
446    SubDirCiv=regexprep(SubDir,['^' SubDirImages],'');%suppress the root  SuddirImages;
447else
448    SubDirCiv= '.civ';
449end
450set(handles.SubdirCiv1,'String',SubDirCiv)
451set(handles.SubdirCiv2,'String',SubDirCiv)
452browse=get(handles.RootPath,'UserData');
453browse.incr_pair=[0 0];%default
454
455%% scan the images if a civ file has been opened
456MinIndex_i=min(i1_series(i1_series>0));
457MinIndex_j=min(j1_series(j1_series>0));
458MaxIndex_i=max(i1_series(i1_series>0));
459MaxIndex_j=max(j1_series(j1_series>0));
460
461%% look for an image documentation file
462XmlFileName=find_imadoc(RootPath,SubDir,RootFile,ImaExt);
463if isempty(XmlFileName)
464    if (strcmp(FileType,'video') || strcmp(FileType,'mmreader'))
465        ext_imadoc=ImaExt;% the timing from the video movie is used
466    else
467        ext_imadoc='';
468    end
469else
470    [tild,tild,ext_imadoc]=fileparts(XmlFileName);
471end
472set(handles.ImaDoc,'String',ext_imadoc)% display the extension name for the image documentation file used
473
474%%  read the time in the image documentation file 
475time=[];
476TimeUnit=''; %default
477CoordUnit='';%default
478pxcm_search=1;
479if ~isempty(XmlFileName)
480    set(handles.ImaDoc,'BackgroundColor',[1 1 0]) % set edit box to yellow cloro to indicate that the file reading is beginning
481    drawnow
482    [XmlData,warntext]=imadoc2struct(XmlFileName);
483    nom_type_read=[];
484    if isfield(XmlData,'Time') && ~isempty(XmlData.Time)
485        time=XmlData.Time;
486        %transform .Time to a column vector if it is a line vector thenomenclature uses a single index: correct possible bug in xml
487        if isequal(MaxIndex_i,1) && ~isequal(MaxIndex_j,1)% .Time is a line vector
488            if numel(nom_type_read)>=2 && isempty(regexp(nom_type_read(2:end),'\D','once'))
489                time=time';
490                MaxIndex_i=MaxIndex_j;
491                MaxIndex_j=1;
492            end
493        end
494    end
495    if isfield(XmlData,'TimeUnit')
496        TimeUnit=XmlData.TimeUnit;
497    end
498    if isfield(XmlData,'GeometryCalib')
499        tsai=XmlData.GeometryCalib;
500        if isfield(tsai,'fx_fy')
501            pxcm_search=max(tsai.fx_fy(1),tsai.fx_fy(2));%pixels:cm estimated for the search range
502        end
503        if isfield(tsai,'CoordUnit')
504            CoordUnit=tsai.CoordUnit;
505        end
506    end
507end
508if isempty(time) && (strcmp(FileType,'video') || strcmp(FileType,'mmreader'))
509    set(handles.ListPairMode,'Value',1);
510    dt=1/get(MovieObject,'FrameRate');%time interval between successive frames
511    if strcmp(NomTypeIma,'*')
512        set(handles.ListPairMode,'String',{'series(Di)'})
513        MaxIndex_i=get(MovieObject,'NumberOfFrames');
514        time=(dt*(0:MaxIndex_i-1))';%list of image times
515    else
516        set(handles.ListPairMode,'String',[{'series(Dj)'};{'series(Di)'}])
517        MaxIndex_i=max(i1_series(i1_series>0));
518        MaxIndex_j=get(MovieObject,'NumberOfFrames');
519        time=ones(MaxIndex_i,1)*(dt*(0:MaxIndex_j-1));%list of image times
520        enable_j(handles,'on')
521    end
522    TimeUnit='s';
523    set(handles.ImaDoc,'BackgroundColor',[1 1 1])% set display box back to whiter
524end
525
526%% timing display
527%show the reference image edit box if relevant (not needed for movies or in the absence of time information
528if numel(time)>=2 % if there are at least two time values to define dt
529    MaxIndex_i=min(size(time,1),MaxIndex_i);%possibly adjust the max index according to time data
530    MaxIndex_j=min(size(time,2),MaxIndex_j);
531    time=[zeros(size(time,1),1) time]; %insert a vertical line of zeros (to deal with zero file indices)
532    time=[zeros(1,size(time,2)); time]; %insert a horizontal line of zeros
533else
534    set(handles.ImaDoc,'String',''); %xml file not used for timing
535    time=(i1_series(:,1)+0:size(i1_series,3)-1);% time=index i
536    time=time'*ones(1,size(i1_series,2),1); %makes a time matrix with the same time for all j indices
537    TimeUnit='frame';
538end
539set(handles.ImaDoc,'UserData',time); %store the matrix of times
540set(handles.dt_unit,'String',['dt in m' TimeUnit]);%display dt in unit 10-3 of the time (e.g ms)
541set(handles.TimeUnit,'String',TimeUnit);
542set(handles.nb_field,'String',num2str(MaxIndex_i));
543set(handles.nb_field2,'String',num2str(MaxIndex_j));
544set(handles.CoordUnit,'String',CoordUnit)
545set(handles.SearchRange,'UserData', pxcm_search);
546set(handles.ImaExt,'String',ImaExt)
547set(handles.NomType,'String',NomTypeIma)
548
549%% set the reference indices from the input file indices
550num_ref_i=str2num(get(handles.ref_i,'String'));
551num_ref_j=str2num(get(handles.ref_j,'String'));
552% for movies don't modify except if the current ref is outside index bounds
553%if strcmp(ExtInput,'.nc')|| ~(strcmp(FileType,'mmreader')||strcmp(FileType,'VideoReader') && num_ref_i<=MaxIndex_i && num_ref_j<=MaxIndex_j)
554if ~isempty(i1)% if i1 has been selected by the input
555    num_ref_i=i1;%default ref index
556    if ~isempty(i2)
557        num_ref_i=floor((num_ref_i+i2)/2);
558    end
559    if ~isempty(j1)
560    num_ref_j=j1;
561    if ~isempty(j2)
562        num_ref_j=floor((num_ref_j+j2)/2);
563    end
564    end
565end
566if num_ref_i>MaxIndex_i||num_ref_i<MinIndex_i
567    num_ref_i=round((MinIndex_i+MaxIndex_i)/2);
568end
569if ~isempty(num_ref_j)&&~isempty(MaxIndex_j)&& ~isempty(MinIndex_j)
570    if (num_ref_j>MaxIndex_j||num_ref_j<MinIndex_j)
571        num_ref_j=round((MinIndex_j+MaxIndex_j)/2);
572    end
573end
574if isempty(num_ref_j)
575    num_ref_j=1;
576end
577
578%% update i and j index range if a nc file has been opened or pb withmin max image indices:
579% then set first and last to the inputfile index by default
580first_i=str2num(get(handles.first_i,'String'));
581last_i=str2num(get(handles.last_i,'String'));
582if isempty(first_i) || isempty(last_i)||isempty(MinIndex_i)||isempty(MaxIndex_i)||ind_opening~=0 || isempty(first_i) || isempty(last_i)|| first_i<MinIndex_i || last_i>MaxIndex_i
583   first_i=num_ref_i;
584   last_i=num_ref_i;
585    set(handles.first_i,'String',num2str(first_i));
586    set(handles.last_i,'String',num2str(last_i));%
587end
588
589%j index range
590first_j=str2num(get(handles.first_j,'String'));
591last_j=str2num(get(handles.last_j,'String'));
592if isempty(first_j) || isempty(last_j)||isempty(MinIndex_j)||isempty(MaxIndex_j)||ind_opening~=0 || first_j<MinIndex_j || last_j>MaxIndex_j
593       first_j=num_ref_j;
594   last_j=num_ref_j;
595    set(handles.first_j,'String',num2str(first_j));
596    set(handles.last_j,'String',num2str(last_j));%
597end
598if num_ref_i>last_i || num_ref_i<first_i
599    num_ref_i=round((first_i+last_i)/2);
600end
601if num_ref_j>last_j || num_ref_j<first_j
602    num_ref_j=round((first_j+last_j)/2);
603end
604set(handles.ref_i,'String',num2str(num_ref_i))
605set(handles.ref_j,'String',num2str(num_ref_j))
606
607%% set the civ options depending on the input file content when a nc file has been opened
608ListOptions={'CheckCiv1', 'CheckFix1' 'CheckPatch1', 'CheckCiv2', 'CheckFix2', 'CheckPatch2'};
609checkbox=zeros(size(ListOptions));%default
610if ind_opening==0%case of image opening, start with Civ1
611    for index=1:numel(ListOptions)
612        checkbox(index)=get(handles.(ListOptions{index}),'Value');
613    end
614    index_max=find(checkbox, 1, 'last' );
615    if isempty(index_max),index_max=1;end       
616    for index=1:index_max
617        set(handles.(ListOptions{index}),'Value',1)% select all operations starting from CIV1
618    end
619else
620    for index = 1:min(ind_opening,5)
621        set(handles.(ListOptions{index}),'value',0)
622    end
623    set(handles.(ListOptions{min(ind_opening+1,6)}),'value',1)
624    for index = ind_opening+2:6
625        set(handles.(ListOptions{index}),'value',0)
626    end
627end
628%list_operation={'CheckCiv1','CheckFix1','CheckPatch1','CheckCiv2','CheckFix2','CheckPatch2'};
629
630%set(handles.(ListOptions{min(ind_opening+1,6)}),'value',1)
631update_CivOptions(handles,ind_opening)
632
633%%  set the menus of image pairs and default selection for civ   %%%%%%%%%%%%%%%%%%%
634%check_letter=~isempty(regexp(NomTypeIma,'[ab|AB]$'));%detect pair label by letter
635if  isequal(NomTypeNc,'_1-2')||isempty(MaxIndex_j)|| (MaxIndex_j==1)
636    set(handles.ListPairMode,'Value',1)
637    set(handles.ListPairMode,'String',{'series(Di)'})   
638elseif  MaxIndex_i==1 && MaxIndex_j>1% simple series in j
639    set(handles.ListPairMode,'String',{'pair j1-j2';'series(Dj)'})
640    if  MaxIndex_j <= 10
641        set(handles.ListPairMode,'Value',1)% advice 'pair j1-j2' except in MaxIndex_j is large
642    end
643elseif ~(strcmp(FileType,'video') || strcmp(FileType,'mmreader'))
644    set(handles.ListPairMode,'String',{'pair j1-j2';'series(Dj)';'series(Di)'})%multiple choice
645    if strcmp(NomTypeNc,'_1-2_1')
646        set(handles.ListPairMode,'Value',3)% advise 'series(Di)'
647    elseif  MaxIndex_j <= 10
648        set(handles.ListPairMode,'Value',1)% advice 'pair j1-j2' except in MaxIndex_j is large
649    end
650end
651
652%% scan files to update the subdirectory list display
653listot=dir(RootPath);%directory of RootPath
654idir=0;
655listdir={''};%default
656% get the list of existing civ subdirectories in the path of theinput root  file
657for ilist=1:length(listot)
658    if listot(ilist).isdir
659        name=listot(ilist).name;
660        if ~isequal(name,'.') && ~isequal(name,'..')
661            idir=idir+1;
662            listdir{idir,1}=listot(ilist).name;
663        end
664    end
665end
666
667%% store info
668set(handles.RootPath,'UserData',browse)% store the nomenclature type
669
670%% list the possible index pairs, depending on the option set in ListPairMode
671ListPairMode_Callback([], [], handles)
672
673%% store the root input filename for future opening
674profil_perso=fullfile(prefdir,'uvmat_perso.mat');
675if exist(profil_perso,'file')
676    save (profil_perso,'RootPath','-append'); %store the root name for future opening of uvmat
677else
678    txt=ver('MATLAB');
679    Release=txt.Release;
680    relnumb=str2double(Release(3:4));
681    if relnumb >= 14
682        save (profil_perso,'RootPath','-V6'); %store the root name for future opening of uvmat
683    else
684        save (profil_perso,'RootPath'); %store the root name for future opening of uvmat
685    end
686end
687set(handles.RootPath,'BackgroundColor',[1 1 1])
688
689%------------------------------------------------------------------------
690% --- Executes on carriage return on the subdir checkciv1 edit window
691function SubdirCiv1_Callback(hObject, eventdata, handles)
692%------------------------------------------------------------------------
693SubDir=get(handles.SubdirCiv1,'String');
694menu_str=get(handles.ListSubdirCiv1,'String');% read the list of subdirectories for update
695ichoice=find(strcmp(SubDir,menu_str),1);
696if isempty(ichoice)
697    ilist=numel(menu_str); %select 'new...' in the menu
698else
699    ilist=ichoice;
700end
701set(handles.ListSubdirCiv1,'Value',ilist)% select the selected subdir in the menu
702if get(handles.CheckCiv1,'Value')% if Civ1 is performed
703    set(handles.SubdirCiv2,'String',SubDir);% set by default civ2 directory the same as civ1
704%     set(handles.ListSubdirCiv2,'Value',ilist)
705else % if Civ1 data already exist
706    errormsg=find_netcpair_civ(handles,1); %update the list of available pairs from netcdf files in the new directory
707    if ~isempty(errormsg)
708    msgbox_uvmat('ERROR',errormsg)
709    end
710end
711
712%------------------------------------------------------------------------
713% --- Executes on carriage return on the SubDir checkciv1 edit window
714function SubdirCiv2_Callback(hObject, eventdata, handles)
715%------------------------------------------------------------------------
716SubDir=get(handles.SubdirCiv1,'String');
717menu_str=get(handles.ListSubdirCiv2,'String');% read the list of subdirectories for update
718ichoice=find(strcmp(SubDir,menu_str),1);
719if isempty(ichoice)
720    ilist=numel(menu_str); %select 'new...' in the menu
721else
722    ilist=ichoice;
723end
724set(handles.ListSubdirCiv2,'Value',ilist)% select the selected subdir in the menu
725%update the list of available pairs from netcdf files in the new directory
726if ~get(handles.CheckCiv2,'Value') && ~get(handles.CheckCiv1,'Value') && ~get(handles.CheckFix1,'Value') && ~get(handles.CheckPatch1,'Value')
727    errormsg=find_netcpair_civ(handles,2);
728        if ~isempty(errormsg)
729    msgbox_uvmat('ERROR',errormsg)
730    end
731end
732
733%------------------------------------------------------------------------
734% --- Executes on button press in CheckCiv1.
735function CheckCiv1_Callback(hObject, eventdata, handles)
736%------------------------------------------------------------------------
737update_CivOptions(handles,0)
738
739%------------------------------------------------------------------------
740% --- Executes on button press in CheckFix1.
741function CheckFix1_Callback(hObject, eventdata, handles)
742%------------------------------------------------------------------------
743update_CivOptions(handles,0)
744
745%------------------------------------------------------------------------
746% --- Executes on button press in CheckPatch1.
747function CheckPatch1_Callback(hObject, eventdata, handles)
748%------------------------------------------------------------------------
749update_CivOptions(handles,0)
750
751%------------------------------------------------------------------------
752% --- Executes on button press in CheckCiv2.
753function CheckCiv2_Callback(hObject, eventdata, handles)
754%------------------------------------------------------------------------
755update_CivOptions(handles,0)
756
757%------------------------------------------------------------------------
758% --- Executes on button press in CheckFix2.
759function CheckFix2_Callback(hObject, eventdata, handles)
760%------------------------------------------------------------------------
761update_CivOptions(handles,0)
762
763%------------------------------------------------------------------------
764% --- Executes on button press in CheckPatch2.
765function CheckPatch2_Callback(hObject, eventdata, handles)
766%------------------------------------------------------------------------
767update_CivOptions(handles,0)
768
769%------------------------------------------------------------------------
770% --- activated by any checkbox controling the selection of Civ1,Fix1,Patch1,Civ2,Fix2,Patch2
771function update_CivOptions(handles,opening)
772%------------------------------------------------------------------------
773checkbox=zeros(1,6);
774checkbox(1)=get(handles.CheckCiv1,'Value');
775checkbox(2)=get(handles.CheckFix1,'Value');
776checkbox(3)=get(handles.CheckPatch1,'Value');
777checkbox(4)=get(handles.CheckCiv2,'Value');
778checkbox(5)=get(handles.CheckFix2,'Value');
779checkbox(6)=get(handles.CheckPatch2,'Value');
780ind_selected=find(checkbox,1);
781if ~isempty(ind_selected)
782    RootPath=get(handles.RootPath,'String');
783    if isempty(RootPath)
784        msgbox_uvmat('ERROR','Please open an image or PIV .nc file with the upper bar menu Open/Browse...')
785        return
786    end
787end
788set(handles.PairIndices,'Visible','on')
789set(handles.SubdirCiv1,'Visible','on')
790set(handles.TitleSubdirCiv1,'Visible','on')
791if opening==0
792    errormsg=find_netcpair_civ(handles,1); % select the available netcdf files
793    if ~isempty(errormsg)
794        msgbox_uvmat('ERROR',errormsg)
795    end
796end
797if max(checkbox(4:6))% case of civ2 pair choice needed
798    set(handles.TitlePairCiv2,'Visible','on')
799    set(handles.TitleSubdirCiv2,'Visible','on')
800    set(handles.SubdirCiv2,'Visible','on')
801    %set(handles.ListSubdirCiv2,'Visible','on')
802    set(handles.ListPairCiv2,'Visible','on')
803    if ~opening
804        errormsg=find_netcpair_civ(handles,2); % select the available netcdf files
805        if ~isempty(errormsg)
806            msgbox_uvmat('ERROR',errormsg)
807        end
808    end
809else
810    set(handles.TitleSubdirCiv2,'Visible','off')
811    set(handles.SubdirCiv2,'Visible','off')
812    set(handles.ListPairCiv2,'Visible','off')
813end
814options={'Civ1','Fix1','Patch1','Civ2','Fix2','Patch2'};
815for ilist=1:length(options)
816    if checkbox(ilist)
817        set(handles.(options{ilist}),'Visible','on')
818    else
819        set(handles.(options{ilist}),'Visible','off')
820    end
821end
822
823%------------------------------------------------------------------------
824% --- Executes on button press in RUN: processing on local computer
825function RUN_Callback(hObject, eventdata, handles)
826%------------------------------------------------------------------------
827set(handles.RUN, 'Enable','Off')
828set(handles.RUN,'BackgroundColor',[0.831 0.816 0.784])
829set(handles.RUN,'UserData',now)% record the time of launch
830errormsg=launch_jobs(hObject, eventdata, handles);
831set(handles.RUN, 'Enable','On')
832set(handles.RUN,'BackgroundColor',[1 0 0])
833
834% display errors or start status callback to visualise results
835if ~isempty(errormsg)
836    display(errormsg)
837    msgbox_uvmat('ERROR',errormsg)
838elseif  isfield(handles,'status') %&& ~isequal(get(handles.ListPairMode,'Value'),3)
839    set(handles.status,'Value',1);%suppress status display
840    status_Callback(hObject, eventdata, handles)
841end
842
843%-------------------------------------------------------------------
844% --- Executes on button press in status.
845function status_Callback(hObject, eventdata, handles)
846%-------------------------------------------------------------------
847val=get(handles.status,'Value');
848if val==0
849    set(handles.status,'BackgroundColor',[0 1 0])
850    hfig=findobj(allchild(0),'name','civ_status');
851    if ~isempty(hfig)
852        delete(hfig)
853    end
854    return
855end
856set(handles.status,'BackgroundColor',[1 1 0])
857drawnow
858listtype={'civ1','fix1','patch1','civ2','fix2','patch2'};
859Param.CheckCiv1=get(handles.CheckCiv1,'Value');
860Param.CheckFix1=get(handles.CheckFix1,'Value');
861Param.CheckPatch1=get(handles.CheckPatch1,'Value');
862Param.CheckCiv2=get(handles.CheckCiv2,'Value');
863Param.CheckFix2=get(handles.CheckFix2,'Value');
864Param.CheckPatch2=get(handles.CheckPatch2,'Value');
865box_test=[Param.CheckCiv1 Param.CheckFix1 Param.CheckPatch1 Param.CheckCiv2 Param.CheckFix2 Param.CheckPatch2];
866
867option_civ=find(box_test,1,'last');%last selected option (non-zero index of box_test)
868filecell=get(handles.civ,'UserData');%retrieve the list of output files expected for PIV
869test_new=0;
870if ~isfield(filecell,'nc')
871    test_new=1;
872    [ref_i,ref_j,errormsg]=find_ref_indices(handles);
873    if ~isempty(errormsg)
874        msgbox_uvmat('ERROR',errormsg)
875        return
876    end
877    filecell=set_civ_filenames(handles,ref_i,ref_j,box_test);%determine the output file expected from the GUI status
878end
879if ~isequal(box_test(4:6),[0 0 0])
880    civ_files=filecell.nc.civ2;%case of civ2 operations
881else
882    civ_files=filecell.nc.civ1;
883end
884[root,filename,ext]=fileparts(civ_files{1});
885[rootroot,SubDir,extdir]=fileparts(root);
886hfig=findobj(allchild(0),'name','civ_status');
887if isempty(hfig)
888    hfig=figure('DeleteFcn',@stop_status);
889    set(hfig,'MenuBar','none')% suppress the menu bar
890    set(hfig,'NumberTitle','off')%suppress the fig number in the title
891    set(hfig,'name','civ_status')
892    set(hfig,'tag','civ_status')
893    set(hfig,'UserData',civ_files)
894    hlist= uicontrol('Style','listbox','Units','normalized', 'Position',[0.05 0.09 0.9 0.71], 'Callback', {'open_uvmat'},'tag','list');
895    uicontrol('Style','edit','Units','normalized', 'Position', [0.05 0.87 0.9 0.1],'tag','msgbox','Max',2,'String','checking files...');
896    uicontrol('Style','frame','Units','normalized', 'Position', [0.05 0.81 0.9 0.05]);
897    uicontrol('Style','pushbutton','Units','normalized', 'Position', [0.7 0.01 0.2 0.07],'String','Close','FontWeight','bold','FontUnits','normalized','FontSize',0.9,'Callback',@close_GUI);
898    hrefresh=uicontrol('Style','pushbutton','Units','normalized', 'Position', [0.1 0.01 0.2 0.07],'String','Refresh','FontWeight','bold','FontUnits','normalized','FontSize',0.9,'Callback',@refresh_GUI);
899    BarPosition=[0.05 0.81 0.01 0.05];
900    uicontrol('Style','frame','Units','normalized', 'Position',BarPosition ,'BackgroundColor',[1 0 0],'tag','waitbar');
901    drawnow
902end
903StatusData.time_ref=get(handles.RUN,'UserData');% get the time of launch
904StatusData.option_civ=option_civ;
905set(hrefresh,'UserData',StatusData)
906filepath=fileparts(civ_files{1});
907set(hlist,'UserData',fileparts(filepath))
908refresh_GUI(hrefresh,[])
909
910%------------------------------------------------------------------------   
911% launched by refreshing the status figure
912function refresh_GUI(hObject, eventdata)
913%------------------------------------------------------------------------
914Tabchar={};
915BarPosition=[0.05 0.81 0.01 0.05];
916hfig=get(hObject,'parent');
917StatusData=get(hObject,'UserData');
918civ_files=get(hfig,'UserData');
919[filepath,filename,ext]=fileparts(civ_files{1});
920[tild,SubDir,extdir]=fileparts(filepath);
921SubDir=[SubDir extdir];
922option_civ=StatusData.option_civ;
923nbfiles=numel(civ_files);
924testrecent=0;
925count=0;
926datnum=zeros(1,nbfiles);
927filefound=cell(1,nbfiles);
928for ifile=1:nbfiles
929    detect=exist(civ_files{ifile},'file'); % check the existence of the file
930    option=0;
931    if detect==0
932        option_str='not created';
933    else
934        datfile=dir(civ_files{ifile});
935        if isfield(datfile,'datenum')
936            datnum(ifile)=datfile.datenum;%only available in recent matlab versions
937            testrecent=1;
938        end
939        filefound(ifile)={datfile.name};
940       
941        % check the content  netcdf file
942        Data=nc2struct(civ_files{ifile},'ListGlobalAttribute','CivStage','patch2','fix2','civ2','patch','fix');
943        option_list={'civ1','fix1','patch1','civ2','fix2','patch2'};
944        if ~isempty(Data.CivStage)
945            option=Data.CivStage;%case of Matlab civ
946        else
947            if ~isempty(Data.patch2) && isequal(Data.patch2,1)
948                option=6;
949            elseif ~isempty(Data.fix2) && isequal(Data.fix2,1)
950                option=5;
951            elseif ~isempty(Data.civ2) && isequal(Data.civ2,1);
952                option=4;
953            elseif ~isempty(Data.patch) && isequal(Data.patch,1);
954                option=3;
955            elseif ~isempty(Data.fix) && isequal(Data.fix,1);
956                option=2;
957            else
958                option=1;
959            end
960        end
961        option_str=option_list{option};
962        if datnum(ifile)<StatusData.time_ref
963            option_str=[option_str '  --OLD--'];
964        end
965    end
966    if option >= option_civ
967        count=count+1;
968    end
969    [filepath,filename,ext]=fileparts(civ_files{ifile});
970    Tabchar{ifile,1}=[fullfile(SubDir,filename) ext  '...' option_str];
971end
972datnum=datnum(datnum~=0);%keep the non zero values corresponding to existing files
973if isempty(datnum)
974    if testrecent
975        message='no civ result created yet';
976    else
977        message='';
978    end
979else
980    datnum=datnum(datnum~=0);%keep the non zero values corresponding to existing files
981    [first,ind]=min(datnum);
982    [last,indlast]=max(datnum);
983    message={[num2str(count) ' file(s) done over ' num2str(nbfiles)] ;['oldest modification:  ' cell2mat(filefound(ind)) ' : ' datestr(first)];...
984        ['latest modification:  ' cell2mat(filefound(indlast)) ' : ' datestr(last)]};
985end
986hlist=findobj(hfig,'tag','list');
987hmsgbox=findobj(hfig,'tag','msgbox');
988hwaitbar=findobj(hfig,'tag','waitbar');
989set(hlist,'String',Tabchar)
990set(hmsgbox,'String', message)
991if count>0 %&& ~test_new
992    BarPosition(3)=0.9*count/nbfiles;
993    set(hwaitbar,'Position',BarPosition)
994end
995
996
997%------------------------------------------------------------------------   
998% launched by deleting the status figure
999function stop_status(hObject, eventdata)
1000%------------------------------------------------------------------------
1001hciv=findobj(allchild(0),'tag','civ');
1002hhciv=guidata(hciv);
1003set(hhciv.status,'value',0) %reset the status uicontrol in the GUI civ
1004set(hhciv.status,'BackgroundColor',[0 1 0])
1005
1006%------------------------------------------------------------------------   
1007% launched by pressing OK on the status figure
1008function close_GUI(hObject, eventdata)
1009%------------------------------------------------------------------------
1010    delete(gcbf)
1011
1012
1013%------------------------------------------------------------------------
1014% --- Main lauch command, called by RUN and BATCH
1015function errormsg=launch_jobs(hObject, eventdata, handles)
1016%------------------------------------------------------------------------
1017errormsg='';%default
1018
1019%% read the input parameters from the  GUI civ
1020Param=read_GUI(handles.civ);
1021
1022%% check the selected list of operations:
1023operations={'Civ1','Fix1','Patch1','Civ2','Fix2','Patch2'};
1024box_test=[Param.CheckCiv1 Param.CheckFix1 Param.CheckPatch1 Param.CheckCiv2 Param.CheckFix2 Param.CheckPatch2];
1025index_first=find(box_test==1,1);
1026if isempty(index_first)
1027    errormsg='no selected operation';
1028    return
1029end
1030index_last=find(box_test==1,1,'last');
1031box_used=box_test(index_first : index_last);
1032[box_missing,ind_missing]=min(box_used);
1033if isequal(box_missing,0); %there is a missing step in the sequence of operations
1034    errormsg=['missing' cell2mat(operations(ind_missing))];
1035    return
1036end
1037
1038%% check mask if selecetd
1039%could be included in get_mask callback ?
1040if isequal(get(handles.CheckMask,'Value'),1)
1041    maskname=get(handles.Mask,'String');
1042    if ~exist(maskname,'file')
1043        get_mask_civ1_Callback(hObject, eventdata, handles);
1044    end
1045end
1046if isequal(get(handles.CheckMask,'Value'),1)
1047    maskname=get(handles.Mask,'String');
1048    if ~exist(maskname,'file')
1049        get_mask_fix1_Callback(hObject, eventdata, handles);
1050    end
1051end
1052if isequal(get(handles.CheckMask,'Value'),1)
1053    maskname=get(handles.Mask,'String');
1054    if ~exist(maskname,'file')
1055        get_mask_civ2_Callback(hObject, eventdata, handles);
1056    end
1057end
1058if isequal(get(handles.CheckMask,'Value'),1)
1059    maskname=get(handles.Mask,'String');
1060    if ~exist(maskname,'file')
1061        get_mask_fix2_Callback(hObject, eventdata, handles);
1062    end
1063end
1064
1065%% reinitialise status callback
1066if isfield(handles,'status')
1067    set(handles.status,'Value',0);%suppress status display
1068    status_Callback([], [], handles)
1069end
1070
1071%% read the PARAM.xml file to get the binaries (and batch_mode if batch)
1072path_civ=fileparts(which('civ')); %path to the source directory of uvmat
1073xmlfile=fullfile(path_civ,'PARAM.xml');
1074s=[];
1075if exist(xmlfile,'file')% search parameter xml file in the whole matlab path
1076    t=xmltree(xmlfile);
1077    s=convert(t);
1078end% default configuration
1079if ~isfield(s,'RunParam')
1080    Param.xml.Civ1Bin=fullfile('bin','civ1');
1081    Param.xml.Civ2Bin=fullfile('bin','civ2');
1082    Param.xml.FixBin=fullfile('bin','fix_flag');
1083    Param.xml.PatchBin=fullfile('bin','patch_up');
1084end
1085if strcmp(Param.RunMode,'cluster') %computation dispatched on a cluster
1086    if isfield(s,'BatchParam')
1087        Param.xml=s.BatchParam;
1088        if isfield(Param.xml,'BatchMode')
1089            batch_mode=Param.xml.BatchMode;
1090            if ~ismember(batch_mode,{'sge','oar'})
1091                errormsg=['batch mode ' batch_mode ' not supported by UVMAT'];
1092                return
1093            end
1094        end
1095    else
1096        %default configuration
1097        Param.xml.Civ1Bin=fullfile('bin','civ1');
1098        Param.xml.Civ2Bin=fullfile('bin','civ2');
1099        Param.xml.FixBin=fullfile('bin','fix_flag');
1100        Param.xml.PatchBin=fullfile('bin','patch_up');
1101   %     Param.xml.CivmBin=fullfile('bin','civ_matlab');
1102        Param.xml.BatchMode='oar';% TODO : allow choice for sge
1103    end
1104else % run
1105    if isfield(s,'RunParam')
1106        Param.xml=s.RunParam;
1107    else %default configuration
1108        Param.xml.Civ1Bin=fullfile('bin','civ1');
1109        Param.xml.Civ2Bin=fullfile('bin','civ2');
1110        Param.xml.FixBin=fullfile('bin','fix_flag');
1111        Param.xml.PatchBin=fullfile('bin','patch_up');
1112    end
1113end
1114%Param.xml.CivmBin=fullfile('bin','civ_matlab');
1115
1116%% check if the binaries exist : to move in civ_opening
1117binary_list={};
1118switch Param.Program
1119    case 'CivX'
1120        binary_list={'Civ1Bin','Civ2Bin','PatchBin','FixBin'};
1121    case 'CivAll'% desactivated option
1122        binary_list={'Civ'};
1123%     case 'civ_matlab.sh'% compiled version of civ_matlab
1124%         binary_list={'CivmBin'};         
1125end
1126for bin_name=binary_list %loop on the list of binaries
1127    if isfield(Param.xml,bin_name{1})% bin_name{1} =current name in the list
1128        if ~isunix
1129        Param.xml.(bin_name{1})=[regexprep(Param.xml.(bin_name{1}),'/','\') '.exe'];
1130        end
1131        if exist(Param.xml.(bin_name{1}),'file')
1132            [path,name,ext]=fileparts(Param.xml.(bin_name{1}));
1133            currentdir=pwd;
1134            if isempty(path)
1135                path=fileparts(which('civ.m'));
1136            end
1137            if exist(path,'dir')
1138                cd(path);
1139                binpath=pwd;%path of the binary
1140                Param.xml.(bin_name{1})=fullfile(binpath,[name ext]);
1141                cd(currentdir);
1142            else
1143                errormsg=['path ' path ' for binaries specified in PARAM.xml does not exist'];
1144                return
1145            end         
1146        else  %look for the full path if the file name has been defined with a relative path in PARAM.xm
1147            fullname=fullfile(path_civ,Param.xml.(bin_name{1}));
1148            if exist(fullname,'file')
1149                Param.xml.(bin_name{1})=fullname;
1150            else
1151                errormsg=['Binary ' Param.xml.(bin_name{1}) ' specified in PARAM.xml does not exist'];
1152                return
1153            end
1154        end
1155    end
1156end
1157if strcmp(Param.Program,'civ_matlab.sh')
1158    if ~exist(fullfile(path_civ,'civ_matlab.sh'),'file')
1159        errormsg=[{'no file civ_matlab.sh found'}; {'run compile_functions.m to create it by compiling civ_matlab.m'}];
1160            return
1161    end
1162end
1163
1164%% set the list of files and check them
1165display('checking the files...')
1166[ref_i,ref_j,errormsg]=find_ref_indices(handles);
1167if ~isempty(errormsg)
1168    return
1169end
1170[filecell,i1_civ1,i2_civ1,j1_civ1,j2_civ1,i1_civ2,i2_civ2,j1_civ2,j2_civ2,nom_type_nc,tild,tild,compare,errormsg]=...
1171    set_civ_filenames(handles,ref_i,ref_j,box_test);
1172if ~isempty(errormsg)
1173    return
1174end
1175set(handles.civ,'UserData',filecell);%store for futur use of status callback
1176display('files OK, processing...')
1177
1178%% create subfolders for log, cmx, nml, xml, bat
1179RootBat=fileparts(filecell.nc.civ1{1,1});
1180switch(Param.Program)
1181    case {'CivX','CivAll'}
1182dir_list={'0_BAT','0_CMX','0_LOG'};
1183    case {'civ_matlab','civ_matlab.sh'}
1184        dir_list={'0_BAT','0_XML'};
1185end
1186for k=1:length(dir_list)
1187    if ~exist(fullfile(RootBat,dir_list{k}),'dir')
1188        mkdir(fullfile(RootBat,dir_list{k}));
1189    end
1190end
1191
1192%% get information on input images or movies
1193nbfield=numel(i1_civ1);
1194nbslice=numel(j1_civ1);
1195% if strcmp(Param.Program,'civ_matlab')
1196    if Param.CheckCiv1
1197        [Param.Civ1.FileTypeA,ImageInfoA_civ1,Param.Civ1.ImageA]=get_file_type(filecell.ima1.civ1{1});
1198        [Param.Civ1.FileTypeB,ImageInfoB_civ1,Param.Civ1.ImageB]=get_file_type(filecell.ima2.civ1{1});
1199    end
1200    if Param.CheckCiv2
1201        [Param.Civ2.FileTypeA,ImageInfoA_civ2,Param.Civ2.ImageA]=get_file_type(filecell.ima1.civ2{1});
1202        [Param.Civ2.FileTypeB,ImageInfoB_civ2,Param.Civ2.ImageB]=get_file_type(filecell.ima2.civ2{1});
1203    end
1204% end
1205
1206%% MAIN LOOP
1207time=get(handles.ImaDoc,'UserData'); %get the set of times
1208TimeUnit=get(handles.TimeUnit,'String');
1209checkframe=strcmp(TimeUnit,'frame');
1210batch_file_list=[];%should be renamed file_list, can be used for xml or bash files
1211NomTypeIma=get(handles.NomType,'String');
1212for ifile=1:nbfield
1213    for j=1:nbslice
1214           
1215        % define output file name
1216        if Param.CheckCiv2==1 || Param.CheckFix2==1 || Param.CheckPatch2==1
1217            Param.OutputFile=filecell.nc.civ2{ifile,j};
1218        else
1219            Param.OutputFile=filecell.nc.civ1{ifile,j};
1220        end
1221        Param.OutputFile=regexprep(Param.OutputFile,'.nc','');
1222
1223        if Param.CheckCiv1
1224            % read image-dependent parameters         
1225            if ~checkframe% && size(time,1)>=i2_civ1(ifile) && size(time,2)>=j2_civ1(j)
1226                Param.Civ1.Dt=(time(i2_civ1(ifile)+1,j2_civ1(j)+1)-time(i1_civ1(ifile)+1,j1_civ1(j)+1));
1227            else
1228                Param.Civ1.Dt=1;
1229            end
1230            Param.Civ1.Time=((time(i2_civ1(ifile)+1,j2_civ1(j)+1)+time(i1_civ1(ifile)+1,j1_civ1(j)+1))/2);
1231            if strcmp(Param.Program,'CivX')
1232                Param.Civ1.term_a=num2stra(j1_civ1(j),nom_type_nc);%UTILITE?
1233                Param.Civ1.term_b=num2stra(j2_civ1(j),nom_type_nc);%
1234            end
1235            Param.Civ1.ImageA=filecell.ima1.civ1{ifile,j};
1236            Param.Civ1.ImageB=filecell.ima2.civ1{ifile,j};
1237            Param.Civ1.ImageBitDepth=ImageInfoA_civ1.BitDepth;
1238            Param.Civ1.ImageWidth=ImageInfoA_civ1.Width;
1239            Param.Civ1.ImageHeight=ImageInfoA_civ1.Height;
1240            if strcmp(NomTypeIma,'*')
1241                Param.Civ1.FrameIndexA=i1_civ1(ifile);
1242                Param.Civ1.FrameIndexB=i2_civ1(ifile);
1243            else% case of movies indexed with i, the frame index is then in j
1244                Param.Civ1.FrameIndexA=j1_civ1(j);
1245                Param.Civ1.FrameIndexB=j2_civ1(j);
1246            end
1247            % read mask )parameters
1248            if Param.Civ1.CheckMask % the lines below should be changed with the new gui
1249                if ~exist(Param.Civ1.Mask,'file')
1250                    maskbase=[filecell.filebase '_' Param.Civ1.Mask]; %
1251                    nbslice_mask=str2double(Param.Civ1.Mask(1:end-4)); %
1252                    i1_mask=mod(i1_civ1(ifile)-1,nbslice_mask)+1;
1253                    [RootPathMask,RootFileMask]=fileparts(maskbase);
1254                    Param.Civ1.Mask=fullfile_uvmat(RootPathMask,[],RootFileMask,'.png','_1',i1_mask);
1255                end
1256            end
1257            % read grid parameters
1258            if Param.Civ1.CheckGrid
1259                if numel(Param.Civ1.Grid)>=4 && isequal(Param.Civ1.Grid(end-3:end),'grid')
1260                    nbslice_grid=str2double(Param.Civ1.Grid(1:end-4)); %
1261                    if ~isnan(nbslice_grid)
1262                        i1_grid=mod(i1_civ1(ifile)-1,nbslice_grid)+1;
1263                        Param.Civ1.Grid=[filecell.filebase '_' fullfile_uvmat('','',Param.Civ1.Grid,'.grid','_1',i1_grid)];
1264                        if ~exist(Param.Civ1.GridName,'file')
1265                            errormsg='grid file absent for civ1';
1266                            return
1267                        end
1268                    elseif ~exist(Param.Civ1.Grid,'file')
1269                        errormsg='grid file absent for civ1';
1270                        return
1271                    end
1272                end
1273            end
1274           
1275        end
1276       
1277        if Param.CheckCiv2==1
1278            Param.Civ2.ImageA=filecell.ima1.civ2{ifile,j};
1279            Param.Civ2.ImageB=filecell.ima2.civ2{ifile,j};         
1280            if ~checkframe %&& size(time,1)>=i2_civ2(ifile) && size(time,2)>=j2_civ2(j)
1281                Param.Civ2.Dt=time(i2_civ2(ifile)+1,j2_civ2(j)+1)-time(i1_civ2(ifile)+1,j1_civ2(j)+1);
1282            else
1283                Param.Civ2.Dt=1;
1284            end
1285            Param.Civ2.Time=(time(i2_civ2(ifile)+1,j2_civ2(j)+1)+time(i1_civ2(ifile)+1,j1_civ2(j)+1))/2;
1286            if strcmp(Param.Program,'CivX')
1287                Param.Civ2.term_a=num2stra(j1_civ2(j),nom_type_nc);
1288                Param.Civ2.term_b=num2stra(j2_civ2(j),nom_type_nc);
1289            end
1290            Param.Civ2.filename_nc1=filecell.nc.civ1{ifile,j};
1291            Param.Civ2.filename_nc1(end-2:end)=[]; % remove '.nc'
1292           
1293            % mask
1294            if Param.Civ2.CheckMask
1295                if ~exist(Param.Civ2.Mask,'file')
1296                    maskbase=[filecell.filebase '_' Param.Civ2.Mask]; %
1297                    nbslice_mask=str2double(Param.Civ2.Mask(1:end-4)); %
1298                    i1_mask=mod(i1_civ2(ifile)-1,nbslice_mask)+1;
1299                    [RootPathMask,RootFileMask]=fileparts(maskbase);
1300                    Param.Civ2.Mask=fullfile_uvmat(RootPathMask,[],RootFileMask,'.png','_1',i1_mask);
1301                    %                     Param.Civ2.Mask=name_generator(maskbase,i1_mask,1,'.png','_i');
1302                end
1303            end
1304            %grid
1305            if Param.Civ2.CheckGrid
1306                if numel(Param.Civ2.Grid)>=4 && isequal(Param.Civ2.Grid(end-3:end),'grid')
1307                    nbslice_grid=str2double(Param.Civ2.Grid(1:end-4)); %
1308                    if ~isnan(nbslice_grid)
1309                        i1_grid=mod(i1_civ2(ifile)-1,nbslice_grid)+1;
1310                        Param.Civ2.Grid=[filecell.filebase '_' fullfile_uvmat('','',gridname,'.grid','_1',i1_grid)];
1311                        %                         Param.Civ2.Grid=[filecell.filebase '_' name_generator(gridname,i1_grid,1,'.grid','_i')];
1312                    end
1313                end
1314            end
1315
1316            Param.Civ2.ImageBitDepth=ImageInfoA_civ2.BitDepth;
1317            Param.Civ2.ImageWidth=ImageInfoA_civ2.Width;
1318            Param.Civ2.ImageHeight=ImageInfoA_civ2.Height;
1319            if strcmp(NomTypeIma,'*')
1320                Param.Civ2.FrameIndexA=i1_civ2(ifile);
1321                Param.Civ2.FrameIndexB=i2_civ2(ifile);
1322            else% case of movies indexed with i, the frame index is then in j
1323                Param.Civ2.FrameIndexA=j1_civ2(j);
1324                Param.Civ2.FrameIndexB=j2_civ2(j);
1325            end
1326        end
1327       
1328        % write the command and eventually the cmx, xml or nml files
1329        cmd=write_cmd(Param);
1330        write_param(Param);
1331             
1332        % create the file used in run or batch
1333        switch Param.Program
1334            case {'civ_matlab'}
1335                filename_bat=regexprep(Param.OutputFile,'(.+)([/\\])(.+$)','$1$20_BAT$2$3.m');           
1336                [BatRoot,BatFile]=fileparts(filename_bat);
1337                 BatFile=regexprep(BatFile,'-','__');%transform name to suppress'-' (not valid for .m files)
1338                 filename_bat=[fullfile(BatRoot,BatFile) '.m'];
1339            case {'CivX','CivAll','civ_matlab.sh'}
1340                switch computer
1341                    case {'PCWIN','PCWIN64'}
1342                        filename_bat=regexprep(Param.OutputFile,'(.+)([/\\])(.+$)','$1$20_BAT$2$3.bat');
1343                    case {'GLNX86','GLNXA64','MACI64'}
1344                        filename_bat=regexprep(Param.OutputFile,'(.+)([/\\])(.+$)','$1$20_BAT$2$3.sh');
1345                end
1346        end
1347       
1348        % print the command in the bat file
1349        [fid,message]=fopen(filename_bat,'w');
1350        if isequal(fid,-1)
1351            errormsg=['creation of .bat file: ' message];
1352            return
1353        end
1354        fprintf(fid,cmd);
1355        fclose(fid);
1356       
1357        % special case for civ_matlab on cluster
1358        if strcmp(Param.Program,'civ_matlab') && strcmp(Param.RunMode,'cluster')
1359            filename_bat2=regexprep(Param.OutputFile,'(.+)([/\\])(.+$)','$1$20_BAT$2$3.sh');
1360            [fid,message]=fopen(filename_bat2,'w');
1361            if isequal(fid,-1)
1362                errormsg=['creation of .bat file: ' message];
1363                return
1364            end
1365            fprintf(fid,['#!/bin/bash \n' ...
1366                '/etc/sysprofile \n'...
1367                'matlab -nodisplay -nosplash -nojvm <<END_MATLAB \n'...
1368                'addpath(''' path_civ ''');\n']);
1369%             for p=1:length(batch_file_list)
1370                fprintf(fid,['run ' filename_bat '\n']);
1371%             end
1372            fprintf(fid, 'exit\nEND_MATLAB\n');
1373            fclose(fid);
1374            filename_bat=filename_bat2;
1375        end
1376       
1377        switch computer
1378            case {'GLNX86','GLNXA64','MACI64'}
1379                system(['chmod +x ' filename_bat]);
1380        end
1381        batch_file_list{length(batch_file_list)+1}=filename_bat;
1382    end
1383end
1384
1385%% start calculation
1386%computation on cluster
1387%if batch ==3
1388switch Param.RunMode,
1389    case 'cluster'
1390        switch batch_mode
1391            case 'sge' %at the moment only psmn ENS Lyon uses it
1392                for p=1:length(batch_file_list)
1393                    %cmd=['!qsub -p ' pvalue ' -q civ.q -e ' flname '.errors -o ' flname '.log' ' ' batch_file_list{p}];
1394                    cmd=['!qsub -q piv1,piv2,piv3 '...
1395                        '-e ' regexprep(batch_file_list{p},'.bat','.errors') ' -o ' regexprep(batch_file_list{p},'.bat','.log ')...
1396                        ' -v ' 'LD_LIBRARY_PATH=/home/sjoubaud/matlab_sylvain/civx/lib ' batch_file_list{p}];
1397                    display(cmd);eval(cmd);
1398                end
1399            case 'oar_old' % to remove
1400                for p=1:length(batch_file_list)
1401                    oar_command=['!oarsub -n CIVX -q nicejob '...
1402                        '-E ' regexprep(batch_file_list{p},'.bat','.errors') ' -O ' regexprep(batch_file_list{p},'.bat','.log ')...
1403                        '-l "/core=1+{type = ''smalljob''}/licence=1,walltime=00:60:00"   ' batch_file_list{p}];
1404                    display(oar_command);eval(oar_command);
1405                end
1406            case 'oar'
1407                max_walltime=3600*12; % 12h max
1408                oar_modes={'oar-parexec','oar-dispatch','mpilauncher'};
1409                text={'Batch processing on servcalcul3 LEGI';...
1410                    'Please choose one of the followint modes';...
1411                    '* oar-parexec : default and best choice';...
1412                    '* oar-dispatch : jobs in a container of several cores';...
1413                    '* mpilauncher : one single parallel mpi job using several cores';...
1414                    '**********************************'...
1415                    };
1416                [S,v]=listdlg('PromptString',text,'ListString',oar_modes,...
1417                    'SelectionMode','single','ListSize',[400 100],'Name','LEGI job mode');
1418                switch oar_modes{S}
1419                    case 'oar-parexec' %oar-dispatch.pl
1420                        answer=inputdlg({'Number of cores (max 36)','extra oar options'},'oarsub parameter',1,{'12',''});
1421                        ncores=str2double(answer{1});
1422                        if strcmp(Param.Program,'civ_matlab')
1423                            ncores=1;
1424                        end
1425                        extra_oar=answer{2};
1426                        walltime_onejob=600;%seconds
1427                        filename_joblist=fullfile(RootBat,'job_list.txt');
1428                        fid=fopen(filename_joblist,'w');
1429                        for p=1:length(batch_file_list)
1430                            fprintf(fid,[batch_file_list{p} '\n']);
1431                        end
1432                        fclose(fid);
1433                        oar_command=['oarsub -n CIVX '...
1434                            '-t idempotent --checkpoint ' num2str(walltime_onejob+60) ' '...
1435                            '-l /core=' num2str(ncores) ','...
1436                            'walltime=' datestr(min(1.05*walltime_onejob/86400*max(length(batch_file_list),ncores)/ncores,max_walltime/86400),13) ' '...
1437                            '-E ' regexprep(filename_joblist,'\.txt\>','.stderr') ' '...
1438                            '-O ' regexprep(filename_joblist,'\.txt\>','.stdout') ' '...
1439                            extra_oar ' '...
1440                            '"oar-parexec -s -f ' filename_joblist ' '...
1441                            '-l ' filename_joblist '.log"\n'];
1442                        filename_oarcommand=fullfile(RootBat,'oar_command');
1443                        fid=fopen(filename_oarcommand,'w');
1444                        fprintf(fid,oar_command);
1445                        fclose(fid);
1446                        fprintf(oar_command);% display in command line
1447                        system(oar_command);
1448%                         eval(['! . ' filename
1449%                             _oarcommand])
1450                    case 'oar-dispatch' %oar-dispatch.pl
1451                        ncores=str2double(...
1452                            inputdlg('Number of cores (max 36)','oarsub parameter',1,{'6'})...
1453                            );
1454                        walltime_onejob=600;%seconds
1455                        filename_joblist=fullfile(RootBat,'job_list.txt');
1456                        fid=fopen(filename_joblist,'w');
1457                        for p=1:length(batch_file_list)
1458                            oar_command=['oarsub -n CIVX '...
1459                                '-E ' regexprep(batch_file_list{p},'\.bat\>','.stderr') ' -O ' regexprep(batch_file_list{p},'\.bat\>','.stdout ')...
1460                                '-l "/core=1,walltime=' datestr(walltime_onejob/86400,13) '"   ' batch_file_list{p}];
1461                            fprintf(fid,[oar_command '\n']);
1462                        end
1463                        fclose(fid);
1464                        oar_command=['oarsub -t container -n civx-container '...
1465                            '-l /core=' num2str(ncores)...
1466                            ',walltime=' datestr(1.05*walltime_onejob/86400*max(length(batch_file_list),ncores)/ncores,13) ' '...
1467                            '-E ' regexprep(filename_joblist,'\.txt\>','.stderr') ' '...
1468                            '-O ' regexprep(filename_joblist,'\.txt\>','.stdout') ' '...
1469                            '"oar-dispatch -f ' filename_joblist '"'];
1470                        filename_oarcommand=fullfile(RootBat,'oar_command');
1471                        fid=fopen(filename_oarcommand,'w');
1472                        fprintf(fid,[oar_command '\n']);
1473                        fclose(fid);
1474                        display(oar_command);
1475                        eval(['! . ' filename_oarcommand])
1476                    case 'mpilauncher'
1477                        filename_joblist=fullfile(RootBat,'job_list.txt');
1478                        fid=fopen(filename_joblist,'w');
1479                       
1480                        for p=1:length(batch_file_list)
1481                            fprintf(fid,[batch_file_list{p} '\n']);
1482                        end
1483                        fclose(fid)
1484                        text_oarscript=[...
1485                            '#!/bin/bash \n'...
1486                            '#OAR -n Mylauncher \n'...
1487                            '#OAR -l node=4/core=5,walltime=0:15:00 \n'...
1488                            '#OAR -E ' fullfile(RootBat,'stderrfile.log') ' \n'...
1489                            '#OAR -O ' fullfile(RootBat,'stdoutfile.log') ' \n'...
1490                            '# ========================================================= \n'...
1491                            '# This simple program launch a multinode parallel OpenMPI mpilauncher \n'...
1492                            '# application for coriolis PIV post-processing. \n'...
1493                            '# OAR uses oarshmost wrapper to propagate the user environement. \n'...
1494                            '# This wrapper assert that the user has the same environment on all the \n'...
1495                            '# allocated nodes (basic behavior needed by most MPI applications).  \n'...
1496                            '# \n'...
1497                            '# REQUIREMENT: \n'...
1498                            '# the oarshmost wrapper should be installed in $HOME/bin directory. \n'...
1499                            '# If a different location is used, change the line following the comment "Bidouille" \n'...
1500                            '# ========================================================= \n'...
1501                            '#   USER should only modify these 2 lines  \n'...
1502                            'WORKDIR=' pwd ' \n'...
1503                            'COMMANDE="mpilauncher  -f ' filename_joblist '" \n'...
1504                            '# ========================================================= \n'...
1505                            '# DO NOT MODIFY the FOLOWING LINES. (or be carefull) \n'...
1506                            'echo "job starting on: "`hostname` \n'...
1507                            'MPINODES="-host `tr [\\\\\\n] [,] <$OAR_NODEFILE |sed -e "s/,$/ /"`" \n'...
1508                            'NCPUS=`cat $OAR_NODEFILE |wc -l` \n'...
1509                            '#========== Bidouille ============== \n'...
1510                            'export OMPI_MCA_plm_rsh_agent=oar-envsh \n'...%                     'cd $WORKDIR \n'...
1511                            'CMD="mpirun -np $NCPUS -wdir $WORKDIR $MPINODES $COMMANDE" \n'...
1512                            'echo "I run: $CMD"  \n'...
1513                            '$CMD \n'...
1514                            'echo "job ending" \n'...
1515                            ];
1516                        %                 oarsub -S ./oar.sub
1517                        filename_oarscript=fullfile(RootBat,'oar_command');
1518                        fid=fopen(filename_oarscript,'w');
1519                        fprintf(fid,[text_oarscript]);
1520                        fclose(fid);
1521                        eval(['!chmod +x  ' filename_oarscript]);
1522                        eval(['!oarsub -S ' filename_oarscript]);
1523                end
1524        end
1525    case {'background','local'}
1526        switch Param.Program
1527            case {'civ_matlab'}
1528                switch Param.RunMode
1529                    case 'background'
1530                        switch computer
1531                            case {'PCWIN','PCWIN64'}
1532                                filename_superbat=fullfile(RootBat,'job_list.bat');
1533                                fid=fopen(filename_superbat,'w');
1534                                if fid==-1
1535                                    msgbox_uvmat('ERROR',['cannot create the command file ' filename_superbat])
1536                                    return
1537                                end
1538                                 fprintf(fid,['matlab -automation '...
1539                                     '-r "addpath(''' regexprep(path_civ,'\\','\\\\') ''');']);
1540                                for p=1:length(batch_file_list)
1541                                    fprintf(fid,['run ' regexprep(batch_file_list{p},'\\','\\\\') ';']);
1542                                end
1543                                 fprintf(fid, 'exit"');
1544                                fclose(fid);
1545                                dos([filename_superbat ' &']);
1546                            case {'GLNX86','GLNXA64','MACI64'}
1547                                filename_superbat=fullfile(RootBat,'job_list.sh');
1548                                fid=fopen(filename_superbat,'w');
1549                                if fid==-1
1550                                    msgbox_uvmat('ERROR',['cannot create the command file ' filename_superbat])
1551                                    return
1552                                end
1553                                fprintf(fid,['#!/bin/bash \n' ...
1554                                    '/etc/sysprofile \n'...
1555                                    'matlab -nodisplay -nosplash -nojvm -logfile  <<END_MATLAB \n'...
1556                                    'addpath(''' path_civ ''');\n']);
1557                                for p=1:length(batch_file_list)
1558                                    fprintf(fid,['run ' batch_file_list{p} '\n']);
1559                                end
1560                                fprintf(fid, 'exit\nEND_MATLAB\n');
1561                                fclose(fid);
1562                                system(['chmod +x ' filename_superbat]);
1563                                system([filename_superbat ' &']);
1564                        end
1565                    case 'local'
1566                        for p=1:length(batch_file_list)
1567                            fid=fopen(batch_file_list{p});
1568                            eval(fscanf(fid,'%s'));
1569                            fclose(fid);
1570                        end
1571                end
1572            case {'CivX','CivAll','civ_matlab.sh'}
1573                    switch computer
1574                        case {'PCWIN','PCWIN64'}
1575                            filename_superbat=fullfile(RootBat,'job_list.bat');
1576                            fid=fopen(filename_superbat,'w');
1577                            if fid==-1
1578                                msgbox_uvmat('ERROR',['cannot create the command file ' filename_superbat])
1579                                return
1580                            end
1581                            for p=1:length(batch_file_list)
1582                                fprintf(fid,['@call "' regexprep(batch_file_list{p},'\\','\\\\') '"' '\n']);
1583                            end
1584                            fclose(fid);
1585                            system(['chmod +x ' filename_superbat]);
1586                        case {'GLNX86','GLNXA64','MACI64'}
1587                            filename_superbat=fullfile(RootBat,'job_list.bat');
1588                            fid=fopen(filename_superbat,'w');
1589                            if fid==-1
1590                                msgbox_uvmat('ERROR',['cannot create the command file ' filename_superbat])
1591                                return
1592                            end
1593                            for p=1:length(batch_file_list)
1594                                fprintf(fid,['sh ' batch_file_list{p} '\n']);
1595                            end
1596                            fclose(fid);
1597                            system(['chmod +x ' filename_superbat]);
1598                    end
1599                switch Param.RunMode
1600                    case 'background'
1601                        system([filename_superbat ' &']);% execute main commmand see what it does in dos ?
1602                    case 'local'
1603                        system(filename_superbat);
1604                end
1605        end
1606end
1607
1608
1609%% save interface state
1610if isfield(filecell,'nc')
1611    if isfield(filecell.nc,'civ2')
1612        fileresu=filecell.nc.civ2{1,1};
1613    else
1614        fileresu=filecell.nc.civ1{1,1};
1615    end
1616end
1617[RootPath,SubDir,RootFile]=fileparts_uvmat(fileresu);
1618namedoc=fullfile(RootPath,SubDir,RootFile);
1619detect=1;
1620while detect==1
1621    namefigfull=[namedoc '.fig'];
1622    hh=dir(namefigfull);
1623    if ~isempty(hh)
1624        detect=1;
1625        namedoc=[namedoc '.0'];
1626    else
1627        detect=0;
1628    end
1629end
1630Param=rmfield(Param,'status');
1631Param=rmfield(Param,'xml');
1632t=struct2xml(Param);
1633t=set(t,1,'name','Civ');% set the head label
1634save(t,[namedoc '.civ.xml']); %save GUI  parameters as xml file
1635% saveas(gcbf,namefigfull);%save the interface with name namefigfull (A CHANGER EN FICHIER  .xml)
1636
1637%Save info in personal profile (initiate browser next time) TODO
1638MenuFile={};
1639dir_perso=prefdir;
1640profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
1641if exist(profil_perso,'file')
1642    hh=load (profil_perso);
1643      if isfield(hh,'MenuFile')
1644          MenuFile=hh.MenuFile;
1645      end
1646      if isfield(filecell.nc,'civ2')
1647          MenuFile=[filecell.nc.civ2{1,1}; MenuFile];
1648      else
1649           MenuFile=[filecell.nc.civ1{1,1}; MenuFile];
1650      end
1651      save (profil_perso,'MenuFile','-append'); %store the file names for future opening of uvmat
1652else
1653    MenuFile=filecell.ima1.civ1(1,1);
1654    save (profil_perso,'MenuFile')
1655end
1656
1657%------------------------------------------------------------------------
1658% --- determine the list of reference indices of processing file
1659function [ref_i,ref_j,errormsg]=find_ref_indices(handles)
1660%------------------------------------------------------------------------
1661errormsg=''; %default error message
1662first_i=str2double(get(handles.first_i,'String'));%first index i
1663last_i=str2double(get(handles.last_i,'String'));%last index i
1664incr_i=str2double(get(handles.incr_i,'String'));% increment
1665if isequal(get(handles.first_j,'Visible'),'on')
1666    first_j=str2double(get(handles.first_j,'String'));%first index j
1667    last_j=str2double(get(handles.last_j,'String'));%last index j
1668    incr_j=str2double(get(handles.incr_j,'String'));% increment
1669else
1670    first_j=1;
1671    last_j=1;
1672    incr_j=1;
1673end
1674ref_i=first_i:incr_i:last_i;% list of i indices (reference values for each pair)
1675ref_j=first_j:incr_j:last_j;% list of j indices (reference values for each pair)
1676if isnan(first_i)||isnan(first_j)
1677    errormsg='first field number not defined';
1678elseif isnan(last_i)||isnan(last_j)
1679    errormsg='last field number not defined';
1680elseif isnan(incr_i)||isnan(incr_j)
1681    errormsg='increment in field number not defined';
1682elseif last_i < first_i || last_j < first_j
1683    errormsg='last field number must be larger than the first one';
1684end
1685
1686%------------------------------------------------------------------------
1687% --- determine the list of filenames and indices needed for launch_job
1688%------------------------------------------------------------------------
1689% OUTPUT:
1690% filecell: structure of cell arrays {ref_i,ref_j} containing all the filenames involved in the civ process
1691%    the indices ref_i and ref_j correspond to the list of reference indices
1692%       .filebase=fullfile(RootPath,RootFile) used to construct mask names, grid names, CivDoc xml file
1693%       .ima1.civ1,.ima1.civ2: first image for civ1 and civ2 respectively (possibly different)
1694%       .ima2.civ1,.ima2.civ2: second image for civ1 and civ2 respectively (possibly different)
1695%       .nc.civ1,.nc.civ2: netcdf files containing civ1 and civ2 data respectively (possibly different)
1696% i1_civ1,i2_civ1,j1_civ1,j2_civ1,i1_civ2,i2_civ2,j1_civ2,j2_civ2: arrays of files indices, needed for timing records
1697function [filecell,i1_civ1,i2_civ1,j1_civ1,j2_civ1,i1_civ2,i2_civ2,j1_civ2,j2_civ2,NomType_nc,file_ref_fix1,file_ref_fix2,compare,errormsg]=...
1698    set_civ_filenames(handles,ref_i,ref_j,checkbox)
1699%------------------------------------------------------------------------
1700filecell=[];%default
1701errormsg='';
1702ListProgram=get(handles.Program,'String');
1703CivMode=ListProgram{get(handles.Program,'Value')};%Program to use , CivX or Matlab
1704
1705%% get the root name and check dir
1706RootPath=get(handles.RootPath,'String');
1707SubDirImages=get(handles.SubDirImages,'String');
1708RootFile=get(handles.RootFile,'String');
1709filecell.filebase=fullfile(RootPath,SubDirImages,RootFile);
1710if isempty(filecell.filebase)
1711    errormsg='please open an image with the upper menu option Open/Browse...';
1712    return
1713end
1714if ~exist(RootPath,'dir')
1715    errormsg=['path to images ' RootPath ' not found'];
1716    return
1717end
1718[tild,message]=fileattrib(RootPath);
1719if ~isempty(message) && ~isequal(message.UserWrite,1)
1720    errormsg=['No writting access to ' RootPath];
1721    return
1722end
1723%check result directory
1724subdir_civ1=regexprep(get(handles.SubdirCiv1,'String'),'^.','');%subdirectory subdir_civ1 for the netcdf output data
1725subdir_civ2=regexprep(get(handles.SubdirCiv2,'String'),'^.','');
1726if isequal(subdir_civ1,''),subdir_civ1='civ'; end% put default subdir
1727% subdir_civ1=[ '.' subdir_civ1];
1728% subdir_civ2=[ '.' subdir_civ2];
1729if isequal(subdir_civ2,''),subdir_civ2=subdir_civ1; end% put default subdir
1730subdir_civ1=[SubDirImages '.' subdir_civ1];
1731subdir_civ2=[SubDirImages '.' subdir_civ2];
1732
1733%% choose root names depending on ListCompareMode =displacement, shift, PIV or stereo PIV
1734ListCompareMode=get(handles.ListCompareMode,'String');
1735compare=ListCompareMode{get(handles.ListCompareMode,'Value')};
1736
1737% set the nomenclature type of the nc files depending on the pair mode
1738if strcmp(compare,'displacement')||strcmp(compare,'shift')
1739    mode='displacement';
1740else
1741    mode_list=get(handles.ListPairMode,'String');
1742    mode_value=get(handles.ListPairMode,'Value');
1743    mode=mode_list{mode_value};
1744end
1745NomType_ima2=get(handles.NomType,'String');
1746NomType_nc=nomtype2pair(NomType_ima2,mode);
1747
1748% set the rootfile and image indexing
1749RootFile_ima2=get(handles.RootFile,'String');%root file for the second image series
1750ext_ima=get(handles.ImaExt,'String'); % image extension (the same for all images)
1751switch compare
1752    case 'PIV'
1753       RootFile_ima1=RootFile_ima2;% root name of the two image series is the same
1754       NomType_ima1=NomType_ima2;% the index of the first image follows the index of the second one
1755       RootFile_nc=RootFile_ima2;
1756    case 'displacement'
1757       RootFile_ima1=get(handles.RootFile_1,'String');% root name of the first image series set by handles.RootFile_1
1758       NomType_ima1='';% no indexing of the first image, a fixed reference for the whole series
1759       RootFile_nc=RootFile_ima2;
1760    case 'shift'
1761       RootFile_ima1=get(handles.RootFile_1,'String');% root name of the first image series set by handles.RootFile_1
1762       NomType_ima1=NomType_ima2;% the index of the first image follows the index of the second one
1763       RootFile_nc=[RootFile_ima1 '-' RootFile_ima2];
1764end
1765
1766%determine the list of file indices involved
1767[i1_civ1,i2_civ1,j1_civ1,j2_civ1,i1_civ2,i2_civ2,j1_civ2,j2_civ2]=...
1768    find_pair_indices(handles,ref_i,ref_j,mode);
1769
1770%determine the new filebase for 'displacement' ListPairMode (comparison of two series)
1771%filebase_B=filebase;% root name of the second field series for stereo
1772% filebase_A=filebase;%default
1773% if strcmp(compare,'PIV')
1774%     filebase_AB=filebase;
1775% else
1776%     [Path2,Name2]=fileparts(filebase_B);
1777%     Name1=RootFile_ima1;
1778%     filebase_AB=fullfile(Path2,[Name2 '-' Name1]);   
1779% end
1780% [RootPath_AB,RootFile_AB]=fileparts(filebase_AB);
1781% % [RootPath_ima1,RootFile_ima1]=fileparts(filebase_B);
1782% [RootPath_ima2,RootFile_ima2]=fileparts(filebase_B);
1783% [RootPath_nc,RootFile_nc]=fileparts(filebase_B);%default
1784% if strcmp(compare,'displacement')
1785% %     [RootPath_ima1,RootFile_ima1]=fileparts(filebase_B);
1786% %     [RootPath_ima2,RootFile_ima2]=fileparts(filebase_B);
1787%     [RootPath_nc,RootFile_nc]=fileparts(filebase_B);
1788% elseif strcmp(compare,'shift')
1789%     RootPath_nc=RootPath_AB;
1790%     RootFile_nc=RootFile_AB;
1791% end
1792% else
1793%     filebase_ima1=filebase_B;
1794%     filebase_ima2=filebase_B;
1795%     filebase_nc=filebase_B;
1796% [RootPath_ima1,RootFile_ima1]=fileparts(filebase_ima1);
1797% [RootPath_ima2,RootFile_ima2]=fileparts(filebase_ima2);
1798% [RootPath_nc,RootFile_nc]=fileparts(filebase_nc);
1799% [RootPath_A,RootFile_A]=fileparts(filebase_A);
1800
1801   
1802%% determine reference files for fix:
1803file_ref_fix1={};%default
1804file_ref_fix2={};
1805nbfield=length(i1_civ1);
1806nbslice=length(j1_civ1);
1807if checkbox(2)==1% fix1 performed
1808    ref=get(handles.ref_fix1,'UserData');%read data on the ref file stored by get_ref_fix1_Callback
1809    if ~isempty(ref)
1810        first_i=str2double(get(handles.first_i,'String'));
1811        last_i=str2double(get(handles.last_i,'String'));
1812        incr_i=str2double(get(handles.incr_i,'String'));
1813        first_j=str2double(get(handles.first_j,'String'));
1814        last_j=str2double(get(handles.last_j,'String'));
1815        incr_j=str2double(get(handles.incr_j,'String'));
1816        num_i_ref=first_i:incr_i:last_i;
1817        num_j_ref=first_j:incr_j:last_j;
1818        if isequal(mode,'displacement')
1819            num_i1=num_i_ref;
1820            num_i2=num_i_ref;
1821            num_j1=num_j_ref;
1822            num_j2=num_j_ref;
1823        elseif isequal(mode,'pair j1-j2')% isequal(mode,'st_pair j1-j2')
1824            num_i1=num_i_ref;
1825            num_i2=num_i1;
1826            num_j1=ref.num_a*ones(size(num_i_ref));
1827            num_j2=ref.num_b*ones(size(num_i_ref));
1828        elseif isequal(mode,'series(Di)') % isequal(mode,'st_series(Di)')
1829            delta1=floor((ref.num2-ref.num1)/2);
1830            delta2=ceil((ref.num2-ref.num1)/2);
1831            num_i1=num_i_ref-delta1*ones(size(num_i_ref));
1832            num_i2=num_i_ref+delta2*ones(size(num_i_ref));
1833            if isempty(ref.num_a)
1834                ref.num_a=1;
1835            end
1836            num_j1=ref.num_a*ones(size(num_i1));
1837            num_j2=num_j1;
1838        elseif isequal(mode,'series(Dj)')%| isequal(mode,'st_series(Dj)')
1839            delta1=floor((ref.num_b-ref.num_a)/2);
1840            delta2=ceil((ref.num_b-ref.num_a)/2);
1841            num_i1=ref.num1*ones(size(num_i_ref));
1842            num_i2=num_i1;
1843            num_j1=num_j_ref-delta1*ones(size(num_j_ref));
1844            num_j2=num_j_ref+delta2*ones(size(num_j_ref));
1845        end
1846        for ifile=1:nbfield
1847            for j=1:nbslice
1848                [RootPathRef,RootFile]=fileparts(ref.filebase);
1849                file_ref=fullfile_uvmat(RootPathRef,ref.subdir,RootFile,'.nc',ref.NomType,num_i1(ifile),num_i2(ifile),num_j1(j),num_j2(j));
1850                file_ref_fix1(ifile,j)={file_ref};
1851                if ~exist(file_ref,'file')
1852                    errormsg=['reference file ' file_ref ' not found for fix1'];
1853                    return
1854                end
1855            end
1856        end
1857    end
1858end
1859
1860%% determine reference files for fix2:
1861if checkbox(5)==1% fix2 performed
1862    ref=get(handles.ref_fix2,'UserData');
1863    if ~isempty(ref)
1864        first_i=str2double(get(handles.first_i,'String'));
1865        last_i=str2double(get(handles.last_i,'String'));
1866        incr_i=str2double(get(handles.incr_i,'String'));
1867        first_j=str2double(get(handles.first_j,'String'));
1868        last_j=str2double(get(handles.last_j,'String'));
1869        incr_j=str2double(get(handles.incr_j,'String'));
1870        num_i_ref=first_i:incr_i:last_i;
1871        num_j_ref=first_j:incr_j:last_j;
1872        if isequal(mode,'displacement')
1873            num_i1=num_i_ref;
1874            num_i2=num_i_ref;
1875            num_j1=num_j_ref;
1876            num_j2=num_j_ref;
1877        elseif isequal(mode,'pair j1-j2')
1878            num_i1=num_i_ref;
1879            num_i2=num_i1;
1880            num_j1=ref.num_a;
1881            num_j2=ref.num_b;
1882        elseif isequal(mode,'series(Di)')
1883            delta1=floor((ref.num2-ref.num1)/2);
1884            delta2=ceil((ref.num2-ref.num1)/2);
1885            num_i1=num_i_ref-delta1*ones(size(num_i_ref));
1886            num_i2=num_i_ref+delta2*ones(size(num_i_ref));
1887            num_j1=ref.num_a*ones(size(num_i1));
1888            num_j2=num_j1;
1889        elseif isequal(mode,'series(Dj)')
1890            delta1=floor((ref.num_b-ref.num_a)/2);
1891            delta2=ceil((ref.num_b-ref.num_a)/2);
1892            num_i1=ref.num1*ones(size(num_i_ref));
1893            num_i2=num_i1;
1894            num_j1=num_j_ref-delta1*ones(size(num_j_ref));
1895            num_j2=num_j_ref+delta2*ones(size(num_j_ref));
1896        end
1897        for ifile=1:nbfield
1898            for j=1:nbslice
1899                [RootPathRef,RootFile]=fileparts(ref.filebase);
1900                file_ref=fullfile_uvmat(RootPathRef,ref.subdir,RootFile,'.nc',ref.NomType,num_i1(ifile),num_i2(ifile),num_j1(j),num_j2(j));
1901                file_ref_fix2(ifile,j)={file_ref};
1902                if ~exist(file_ref,'file')
1903                    errormsg=['reference file ' file_ref ' not found for fix2'];
1904                    return
1905                end
1906            end
1907        end
1908    end
1909end
1910
1911%% check the existence of the netcdf and image files involved
1912% %%%%%%%%%%%%  case CheckCiv1 activated   %%%%%%%%%%%%%
1913if checkbox(1)==1;
1914    detect=1;
1915    vers=0;
1916    subdir_civ1_new=subdir_civ1;
1917    answer='No';
1918    while detect==1 %create a new subdir if the netcdf files already exist
1919        for ifile=1:nbfield
1920            for j=1:nbslice
1921                filename=fullfile_uvmat(RootPath,subdir_civ1_new,RootFile_nc,'.nc',NomType_nc,i1_civ1(ifile),i2_civ1(ifile),j1_civ1(j),j2_civ1(j));
1922                detect=exist(filename,'file')==2;
1923                if detect% if a netcdf file already exists
1924                    if strcmp(answer,'No')
1925                        answer=msgbox_uvmat('INPUT_Y-N',['overwrite existing civ files in ' subdir_civ1_new]);
1926                    end
1927                    if strcmp(answer,'Yes')
1928                        detect=0;
1929                        filecell.nc.civ1(ifile,j)={filename};
1930                    else
1931                        r=regexp(subdir_civ1_new,'(?<root>.*\D)(?<num1>\d+)$','names');%detect whether name ends by a number
1932                        if isempty(r)
1933                            r(1).root=[subdir_civ1_new '_'];
1934                            r(1).num1='0';
1935                        end
1936                        subdir_civ1_new=[r(1).root num2str(str2num(r(1).num1)+1)];%increment the index by 1 or put 1
1937                        subdir_civ2=subdir_civ1_new;
1938                    end
1939                    break
1940                end
1941                filecell.nc.civ1(ifile,j)={filename};
1942            end
1943            if detect% if a netcdf file already exists
1944                break
1945            end
1946        end
1947 
1948        %create the new SubdirCiv1
1949        if ~exist(fullfile(RootPath,subdir_civ1_new),'dir')     
1950            [xx,msg1]=mkdir(fullfile(RootPath,subdir_civ1_new));
1951            if ~strcmp(msg1,'')
1952                errormsg=['cannot create ' subdir_civ1_new ': ' msg1];%error message for directory creation
1953                return
1954            elseif isunix         
1955                [xx,msg2] = fileattrib(fullfile(RootPath,subdir_civ1_new),'+w','g'); %yield writing access (+w) to user group (g)
1956                if ~strcmp(msg2,'')
1957                    errormsg=['pb of permission for  ' fullfile(RootPath,subdir_civ1_new) ': ' msg2];%error message for directory creation
1958                    return
1959                end
1960            end
1961        end
1962        if strcmp(compare,'stereo PIV')&&(strcmp(mode,'pair j1-j2')||strcmp(mode,'series(Dj)')||strcmp(mode,'series(Di)'))%check second nc series
1963            for ifile=1:nbfield
1964                for j=1:nbslice
1965                     filename=fullfile_uvmat(RootPath,subdir_civ1_new,RootFile_A,'.nc',NomType_nc,i1_civ1(ifile),i2_civ1(ifile),j1_civ1(j),j2_civ1(j));
1966                    detect=exist(filename,'file')==2;
1967                    if detect% if a netcdf file already exists
1968                       indstr=regexp(subdir_civ1_new,'\D');
1969                       if indstr(end)<length(subdir_civ1_new) %subdir_civ1 ends by a number
1970                           vers=str2double(subdir_civ1_new(indstr(end)+1:end))+1;
1971                           subdir_civ1_new=[subdir_civ1_new(1:indstr(end)) num2str(vers)];
1972                       else
1973                           vers=vers+1;
1974                           subdir_civ1_new=[subdir_civ1_new '_' num2str(vers)];
1975                       end
1976                       subdir_civ2=subdir_civ1;
1977                       break
1978                    end
1979                    filecell.ncA.civ1(ifile,j)={filename};
1980                end
1981                if detect% if a netcdf file already exists
1982                    break
1983                end
1984            end
1985            %create the new SubdirCiv1
1986            if ~exist(fullfile(RootPath,subdir_civ1_new),'dir')       
1987                [xx,msg1]=mkdir(fullfile(RootPath,subdir_civ1_new));
1988                if ~strcmp(msg1,'')
1989                    errormsg=['cannot create ' subdir_civ1_new ': ' msg1];
1990                    return
1991                else
1992                    [xx,msg2] = fileattrib(fullfile(RootPath,subdir_civ1_new),'+w','g'); %yield writing access (+w) to user group (g)
1993                    if ~strcmp(msg2,'')
1994                        errormsg=['pb of permission for ' subdir_civ1_new ': ' msg2];%error message for directory creation
1995                        return
1996                    end
1997                end
1998            end
1999        end
2000    end
2001    subdir_civ1=subdir_civ1_new;
2002    % get image names
2003    for ifile=1:nbfield
2004        for j=1:nbslice
2005             filename=fullfile_uvmat(RootPath,SubDirImages,RootFile_ima1,ext_ima,NomType_ima1,i1_civ1(ifile),[],j1_civ1(j));
2006            idetect(j)=exist(filename,'file')==2;
2007            filecell.ima1.civ1(ifile,j)={filename}; %first image
2008            filename=fullfile_uvmat(RootPath,SubDirImages,RootFile_ima2,ext_ima,NomType_ima2,i2_civ1(ifile),[],j2_civ1(j));
2009            idetect_1(j)=exist(filename,'file')==2;
2010            filecell.ima2.civ1(ifile,j)={filename};%second image
2011        end
2012        [idetectmin,indexj]=min(idetect);
2013        if idetectmin==0,
2014            errormsg=[filecell.ima1.civ1{ifile,indexj} ' not found'];
2015            return
2016        end
2017        [idetectmin,indexj]=min(idetect_1);
2018        if idetectmin==0,
2019            errormsg=[filecell.ima2.civ1{ifile,indexj} ' not found'];
2020            return
2021        end
2022    end
2023    if strcmp(compare,'stereo PIV') && (strcmp(mode,'pair j1-j2') || strcmp(mode,'series(Dj)') || strcmp(mode,'series(Di)'))
2024        for ifile=1:nbfield
2025            for j=1:nbslice
2026                filename=fullfile_uvmat(RootPath,'',RootFile_A,ext_ima,NomType_ima1,i1_civ1(ifile),[],j1_civ1(j));
2027                idetect(j)=exist(filename,'file')==2;
2028                filecell.imaA1.civ1(ifile,j)={filename} ;%first image
2029                filename=fullfile_uvmat(RootPath,'',RootFile_A,ext_ima,NomType_ima2,i2_civ1(ifile),[],j2_civ1(j));
2030                idetect_1(j)=exist(filename,'file')==2;
2031                filecell.imaA2.civ1(ifile,j)={filename};%second image
2032            end
2033            [idetectmin,indexj]=min(idetect);
2034            if idetectmin==0,
2035                errormsg=[filecell.imaA1.civ1{ifile,indexj} ' not found'];
2036                return
2037            end
2038            [idetectmin,indexj]=min(idetect_1);
2039            if idetectmin==0,
2040                errormsg=[filecell.imaA2.civ1{ifile,indexj} ' not found'];
2041                return
2042            end
2043        end
2044    end
2045   
2046    %%%%%%%%%%%%%  checkfix1 or checkpatch1 activated but no checkciv1   %%%%%%%%%%%%%
2047elseif (checkbox(2)==1 || checkbox(3)==1);
2048    for ifile=1:nbfield
2049        for j=1:nbslice
2050            filename=fullfile_uvmat(RootPath,subdir_civ1,RootFile_nc,'.nc',NomType_nc,i1_civ1(ifile),i2_civ1(ifile),j1_civ1(j),j2_civ1(j));
2051            detect=exist(filename,'file')==2;
2052            if detect==0
2053                errormsg=[filename ' not found'];
2054                return
2055            end
2056            filecell.nc.civ1(ifile,j)={filename};
2057        end
2058    end
2059    if strcmp(compare,'stereo PIV')
2060        for ifile=1:nbfield
2061            for j=1:nbslice
2062                filename=fullfile_uvmat(RootPath,subdir_civ1,RootFile_A,'.nc',NomType_nc,i1_civ1(ifile),i2_civ1(ifile),j1_civ1(j),j2_civ1(j));
2063                filecell.ncA.civ1(ifile,j)={filename};
2064                if ~exist(filename,'file')
2065                    errormsg=['input file ' filename ' not found'];
2066                    return
2067                end
2068            end
2069        end
2070    end
2071end
2072
2073%%%%%%%%%%%%%  if checkciv2 performed with pairs different than checkciv1  %%%%%%%%%%%%%
2074testdiff=0;
2075if (checkbox(4)==1)&&...
2076        ((get(handles.ListPairCiv1,'Value')~=get(handles.ListPairCiv2,'Value'))||~strcmp(subdir_civ2,subdir_civ1))
2077    testdiff=1;
2078    detect=1;
2079    vers=0;
2080    subdir_civ2_new=subdir_civ2;
2081    while detect==1 %create a new subdir if the netcdf files already exist
2082        for ifile=1:nbfield
2083            for j=1:nbslice
2084                filename=fullfile_uvmat(RootPath,subdir_civ2_new,RootFile_nc,'.nc',NomType_nc,i1_civ2(ifile),i2_civ2(ifile),j1_civ2(j),j2_civ2(j));
2085                detect=exist(filename,'file')==2;
2086                if detect% if a netcdf file already exists
2087                    indstr=regexp(subdir_civ2,'\D');
2088                    if indstr(end)<length(subdir_civ2) %subdir_civ1 ends by a number
2089                        vers=str2double(subdir_civ2(indstr(end)+1:end))+1;
2090                        subdir_civ2_new=[subdir_civ2(1:indstr(end)) num2str(vers)];
2091                    else
2092                        vers=vers+1;
2093                        subdir_civ2_new=[subdir_civ1 '_' num2str(vers)];
2094                    end
2095                    break
2096                end
2097                filecell.nc.civ2(ifile,j)={filename};
2098            end
2099            if detect% if a netcdf file already exists
2100                break
2101            end
2102        end
2103        %create the new subdir_civ2_new
2104        if ~exist(fullfile(RootPath,subdir_civ2_new),'dir')
2105            [xx,m2]=mkdir(fullfile(RootPath,subdir_civ2_new));
2106            [xx,msg2] = fileattrib(fullfile(RootPath,subdir_civ2_new),'+w','g'); %yield writing access (+w) to user group (g)
2107            if ~isequal(m2,'')
2108                errormsg=['cannot create ' fullfile(RootPath,subdir_civ2_new) ': ' m2];
2109                return
2110            end
2111        end
2112        if strcmp(compare,'stereo PIV')%check second nc series
2113            for ifile=1:nbfield
2114                for j=1:nbslice
2115                    filename=fullfile_uvmat(RootPath,subdir_civ2_new,RootFile_A,'.nc',NomType_nc,i1_civ2(ifile),i2_civ2(ifile),j1_civ2(j),j2_civ2(j));
2116                    detect=exist(filename,'file')==2;
2117                    if detect% if a netcdf file already exists
2118                        indstr=regexp(subdir_civ2,'\D');
2119                        if indstr(end)<length(subdir_civ2) %subdir_civ1 ends by a number
2120                           vers=str2double(subdir_civ2(indstr(end)+1:end))+1;
2121                           subdir_civ2_new=[subdir_civ2(1:indstr(end)) num2str(vers)];
2122                        else
2123                           vers=vers+1;
2124                           subdir_civ2_new=[subdir_civ1 '_' num2str(vers)];
2125                        end
2126                        break
2127                    end
2128                    filecell.ncA.civ2(ifile,j)={filename};
2129                end
2130                if detect% if a netcdf file already exists
2131                    break
2132                end
2133            end
2134            subdir_civ2=subdir_civ2_new;
2135            %create the new SubdirCiv1
2136            if ~exist(fullfile(RootPath,subdir_civ2_new),'dir')
2137                [xx,m2]=mkdir(subdir_civ2_new);
2138                 [xx,msg2] = fileattrib(fullfile(RootPath,subdir_civ2_new),'+w','g'); %yield writing access (+w) to user group (g)
2139                if ~isequal(m2,'')
2140                    errormsg= ['cannot create ' fullfile(RootPath,subdir_civ2_new) ': ' m2];%error message for directory creation
2141                    return
2142                end
2143            end
2144        end
2145    end
2146    subdir_civ2=subdir_civ2_new;
2147end
2148
2149%%%%%%%%%%%%%  if checkciv2 results are obtained or used  %%%%%%%%%%%%%
2150if checkbox(4)==1 || checkbox(5)==1 || checkbox(6)==1 %civ2
2151    %check source netcdf file of checkciv1 estimates
2152    if checkbox(1)==0; %no civ1 performed
2153        for ifile=1:nbfield
2154            for j=1:nbslice
2155                filename=fullfile_uvmat(RootPath,subdir_civ1,RootFile_nc,'.nc',NomType_nc,i1_civ1(ifile),i2_civ1(ifile),j1_civ1(j),j2_civ1(j));%
2156                filecell.nc.civ1(ifile,j)={filename};% name of the civ1 file
2157                if ~exist(filename,'file')
2158                    errormsg=['input file ' filename ' not found'];
2159                    return
2160                end
2161                if ~testdiff % civ2 or patch2 are written in the same file as civ1
2162                    if checkbox(4)==0 ; %check the existence of civ2 if it is not calculated
2163                        Data=nc2struct(filename,'ListGlobalAttribute','CivStage','civ2');
2164                        if isfield(Data,'Txt')
2165                            errormsg=Data.Txt;
2166                            return
2167                        elseif ~isempty(Data.CivStage)% case of new civ files
2168                            if Data.CivStage<4 %test for civ files
2169                            errormsg=['no civ2 data in ' filename];
2170                            return
2171                            end
2172                        elseif isempty(Data.civ2)||isequal(Data.civ2,0)
2173                            errormsg=['no civ2 data in ' filename];
2174                            return
2175                        end
2176                    elseif checkbox(3)==0; %check the existence of patch if it is not calculated
2177                        Data=nc2struct(filename,'ListGlobalAttribute','CivStage','patch');
2178                        if isfield(Data,'Txt')
2179                            errormsg=Data.Txt;
2180                            return
2181                        elseif ~isempty(Data.CivStage)
2182                            if Data.CivStage<3 %test for civ files
2183                                errormsg=['no patch data in ' filename];
2184                                return
2185                            end
2186                        elseif isempty(Data.patch)||isequal(Data.patch,0)
2187                            errormsg=['no patch data in ' filename];
2188                            return
2189                        end
2190                    end
2191                end
2192            end
2193        end
2194        if strcmp(compare,'stereo PIV')
2195            for ifile=1:nbfield
2196                for j=1:nbslice
2197                    filename=fullfile_uvmat(RootPath,subdir_civ2,RootFile_A,'.nc',NomType_nc,i1_civ2(ifile),i2_civ2(ifile),j1_civ2(j),j2_civ2(j));
2198                    filecell.ncA.civ2(ifile,j)={filename};
2199                    if ~exist(filename,'file')
2200                        errormsg=['input file ' filename ' not found'];
2201                        return
2202                    end
2203                end
2204            end
2205        end
2206    end
2207   
2208    detect=1;
2209    %     while detect==1%creates a new subdir if the netcdf files already contain checkciv2 data
2210    for ifile=1:nbfield
2211        for j=1:nbslice
2212            filename=fullfile_uvmat(RootPath,subdir_civ2,RootFile_nc,'.nc',NomType_nc,i1_civ2(ifile),i2_civ2(ifile),j1_civ2(j),j2_civ2(j));
2213            detect=exist(filename,'file')==2;
2214            filecell.nc.civ2(ifile,j)={filename};
2215        end
2216    end
2217    %get first image names for checkciv2
2218    if checkbox(1)==1 && isequal(i1_civ1,i1_civ2) && isequal(j1_civ1,j1_civ2)
2219        filecell.ima1.civ2=filecell.ima1.civ1;
2220    elseif checkbox(4)==1
2221        for ifile=1:nbfield
2222            for j=1:nbslice
2223                filename=fullfile_uvmat(RootPath,SubDirImages,RootFile_ima1,ext_ima,NomType_ima1,i1_civ2(ifile),[],j1_civ2(j));
2224                idetect_2(j)=exist(filename,'file')==2;
2225                filecell.ima1.civ2(ifile,j)={filename};%first image
2226            end
2227            [idetectmin,indexj]=min(idetect_2);
2228            if idetectmin==0,
2229               errormsg=['input image ' filecell.ima1.civ2{ifile,indexj} ' not found'];
2230                return
2231            end
2232        end
2233    end
2234   
2235    %get second image names for checkciv2
2236    if checkbox(1)==1 && isequal(i2_civ1,i2_civ2) && isequal(j2_civ1,j2_civ2)
2237        filecell.ima2.civ2=filecell.ima2.civ1;
2238    elseif checkbox(4)==1
2239        for ifile=1:nbfield
2240            for j=1:nbslice
2241                filename=fullfile_uvmat(RootPath,SubDirImages,RootFile_ima2,ext_ima,NomType_ima2,i2_civ2(ifile),[],j2_civ2(j));
2242                idetect_3(j)=exist(filename,'file')==2;
2243                filecell.ima2.civ2(ifile,j)={filename};%first image
2244            end
2245            [idetectmin,indexj]=min(idetect_3);
2246            if idetectmin==0,
2247                errormsg=['input image ' filecell.ima2.civ2{ifile,indexj} ' not found'];
2248                return
2249            end
2250        end
2251    end
2252end
2253if (checkbox(5) || checkbox(6)) && ~checkbox(4)  % need to read an existing netcdf civ2 file
2254    if ~testdiff
2255        filecell.nc.civ2=filecell.nc.civ1;% file already checked
2256    else     % check the civ2 files
2257        for ifile=1:nbfield
2258            for j=1:nbslice
2259                 filename=fullfile_uvmat(RootPath,subdir_civ2,RootFile_nc,'.nc',NomType_nc,i1_civ2(ifile),i2_civ2(ifile),j1_civ2(j),j2_civ2(j));
2260                filecell.nc.civ2(ifile,j)={filename};
2261                if ~exist(filename,'file')
2262                    errormsg=['input file ' filename ' not found'];
2263                    return
2264                else
2265                    Data=nc2struct(filename,'ListGlobalAttribute','CivStage','civ2');
2266                    if ~isempty(Data.CivStage) && Data.CivStage<4 %test for civ files
2267                            errormsg=['no civ2 data in ' filename];
2268                            return
2269                    elseif isempty(Data.civ2)||isequal(Data.civ2,0)
2270                        errormsg=['no civ2 data in ' filename];
2271                        return
2272                    end
2273                end
2274            end
2275        end
2276    end
2277end
2278
2279%%%%%%%%%%%%%  if stereo fields are calculated by PATCH %%%%%%%%%%%%%
2280if strcmp(compare,'stereo PIV')
2281    if  checkbox(3) && isequal(get(handles.test_stereo1,'Value'),1)
2282        for ifile=1:nbfield
2283            for j=1:nbslice
2284                 filename=fullfile_uvmat(RootPath,subdir_civ1,RootFile_AB,'.nc',NomType_nc,i1_civ1(ifile),i2_civ1(ifile),j1_civ1(j),j2_civ1(j));
2285                filecell.st(ifile,j)={filename};
2286            end
2287        end
2288    end
2289    if  checkbox(6) && isequal(get(handles.CheckStereo,'Value'),1)
2290        for ifile=1:nbfield
2291            for j=1:nbslice
2292                 filename=fullfile_uvmat(RootPath,subdir_civ2,RootFile_AB,'.nc',NomType_nc,i1_civ2(ifile),i2_civ2(ifile),j1_civ2(j),j2_civ2(j));
2293                filecell.st(ifile,j)={filename};
2294            end
2295        end
2296    end
2297end
2298set(handles.SubdirCiv1,'String',regexprep(subdir_civ1,['^' SubDirImages],''));%suppress the root  SuddirImages;);%update the edit box
2299set(handles.SubdirCiv2,'String',regexprep(subdir_civ2,['^' SubDirImages],''));%update the edit box
2300
2301% For CivX COPY IMAGES TO THE FORMAT .png IF NEEDED
2302if strcmp(CivMode,'CivX')
2303    NomType_imanew1=NomType_ima1;
2304    NomType_imanew2=NomType_ima2;
2305    if ~isequal(ext_ima,'.png')
2306        if checkbox(1) %if civ1 is performed
2307             [FileType,FileInfo,MovieObject]=get_file_type(filecell.ima1.civ1{1});
2308            check_j=0;
2309            if strcmp(FileType,'mmreader')||strcmp(FileType,'VideoReader')||strcmp(FileType,'multimage')
2310                if max(j1_civ1)>1
2311                    check_j=1;
2312                    NomType_imanew1='_1_1';
2313                else
2314                    NomType_imanew1='_1';
2315                end
2316            end
2317            h = waitbar(0,'copy images to the .png format for civ1');% display a wait bar
2318            for ifile=1:nbfield
2319                waitbar(ifile/nbfield);
2320                for j=1:nbslice
2321                    filename=fullfile_uvmat(RootPath,SubDirImages,RootFile_ima1,'.png',NomType_imanew1,i1_civ1(ifile),[],j1_civ1(j));
2322                    if ~exist(filename,'file')
2323                        if check_j
2324                        A=read_image(filecell.ima1.civ1{ifile,j},FileType,MovieObject,j1_civ1(j));
2325                        else
2326                            A=read_image(filecell.ima1.civ1{ifile,j},FileType,MovieObject,i1_civ1(ifile));
2327                        end
2328                        imwrite(uint16(sum(A,3)),filename,'BitDepth',16);
2329                    end
2330                    filecell.ima1.civ1(ifile,j)={filename};
2331                    filename=fullfile_uvmat(RootPath,SubDirImages,RootFile_ima2,'.png',NomType_imanew1,i2_civ1(ifile),[],j2_civ1(j));
2332                    if ~exist(filename,'file')
2333                         if check_j
2334                            A=read_image(filecell.ima1.civ1{ifile,j},FileType,MovieObject,j2_civ1(j));
2335                        else
2336                            A=read_image(filecell.ima1.civ1{ifile,j},FileType,MovieObject,i2_civ1(ifile));
2337                         end
2338                        imwrite(uint16(sum(A,3)),filename,'BitDepth',16);
2339                    end
2340                    filecell.ima2.civ1(ifile,j)={filename};
2341                end
2342            end
2343            close(h)
2344        end
2345        if checkbox(4) %if civ2 is performed
2346             [FileType,FileInfo,MovieObject]=get_file_type(filecell.ima1.civ2{1});
2347            check_j=0;
2348            if strcmp(FileType,'mmreader')||strcmp(FileType,'VideoReader')||strcmp(FileType,'multimage')
2349                if max(j1_civ2)>1
2350                    check_j=1;
2351                    NomType_imanew1='_1_1';
2352                else
2353                    NomType_imanew1='_1';
2354                end
2355            end
2356            h = waitbar(0,'copy images to the .png format for civ2');% display a wait bar
2357            for ifile=1:nbfield
2358                waitbar(ifile/nbfield);
2359                for j=1:nbslice
2360                    filename=fullfile_uvmat(RootPath,SubDirImages,RootFile_ima1,'.png',NomType_imanew1,i1_civ2(ifile),[],j1_civ2(j));
2361                    if ~exist(filename,'file')
2362                        if check_j
2363                        A=read_image(filecell.ima1.civ1{ifile,j},FileType,MovieObject,j1_civ2(j));
2364                        else
2365                            A=read_image(filecell.ima1.civ1{ifile,j},FileType,MovieObject,i1_civ2(ifile));
2366                        end
2367                        imwrite(uint16(sum(A,3)),filename,'BitDepth',16);
2368                    end
2369                    filecell.ima1.civ2(ifile,j)={filename};
2370                    filename=fullfile_uvmat(RootPath,SubDirImages,RootFile_ima2,'.png',NomType_imanew2,i2_civ2(ifile),[],j2_civ2(j));
2371                    if ~exist(filename,'file')
2372                        if check_j
2373                        A=read_image(filecell.ima1.civ1{ifile,j},FileType,MovieObject,j1_civ2(j));
2374                        else
2375                            A=read_image(filecell.ima1.civ1{ifile,j},FileType,MovieObject,i1_civ2(ifile));
2376                        end
2377                        imwrite(uint16(sum(A,3)),filename,'BitDepth',16);
2378                    end
2379                    filecell.ima2.civ2(ifile,j)={filename};
2380                end
2381            end
2382            close(h);
2383        end
2384    end
2385end
2386
2387%------------------------------------------------------------------------
2388% --- determine the list of index pairs of processing file
2389function [i1_civ1,i2_civ1,j1_civ1,j2_civ1,i1_civ2,i2_civ2,j1_civ2,j2_civ2]=...
2390    find_pair_indices(handles,ref_i,ref_j,mode)
2391%------------------------------------------------------------------------
2392
2393list_civ1=get(handles.ListPairCiv1,'String');
2394index_civ1=get(handles.ListPairCiv1,'Value');
2395str_civ1=list_civ1{index_civ1};%string defining the image pairs for civ1
2396if isempty(str_civ1)||isequal(str_civ1,'')
2397    msgbox_uvmat('ERROR','no image pair selected for civ1')
2398    return
2399end
2400list_civ2=get(handles.ListPairCiv2,'String');
2401index_civ2=get(handles.ListPairCiv2,'Value');
2402if index_civ2>length(list_civ2)
2403    list_civ2=list_civ1;
2404    index_civ2=index_civ1;
2405end
2406str_civ2=list_civ2{index_civ2};%string defining the image pairs for civ2
2407
2408if isequal (mode,'series(Di)')
2409    lastfield=str2double(get(handles.nb_field,'String'));
2410    i1_civ1=ref_i-floor(index_civ1/2)*ones(size(ref_i));% set of first image numbers
2411    i2_civ1=ref_i+ceil(index_civ1/2)*ones(size(ref_i));
2412    j1_civ1=ref_j;
2413    j2_civ1=ref_j;
2414    i1_civ2=ref_i-floor(index_civ2/2)*ones(size(ref_i));
2415    i2_civ2=ref_i+ceil(index_civ2/2)*ones(size(ref_i));
2416    j1_civ2=ref_j;
2417    j2_civ2=ref_j;   
2418   
2419    % adjust the first and last field number
2420    lastfield=str2double(get(handles.nb_field,'String'));
2421    if isnan(lastfield)
2422        indsel=find((i1_civ1 >= 1)&(i1_civ2 >= 1));
2423    else
2424        indsel=find((i2_civ1 <= lastfield)&(i2_civ2 <= lastfield)&(i1_civ1 >= 1)&(i1_civ2 >= 1));
2425    end
2426    if length(indsel)>=1
2427        firstind=indsel(1);
2428        lastind=indsel(end);
2429        set(handles.first_i,'String',num2str(ref_i(firstind)))%update the display of first and last fields
2430        set(handles.last_i,'String',num2str(ref_i(lastind)))
2431        ref_i=ref_i(indsel);
2432        i1_civ1=i1_civ1(indsel);
2433        i1_civ2=i1_civ2(indsel);
2434        i2_civ1=i2_civ1(indsel);
2435        i2_civ2=i2_civ2(indsel);
2436    end
2437elseif isequal (mode,'series(Dj)')
2438    lastfield_j=str2double(get(handles.nb_field2,'String'));
2439    i1_civ1=ref_i;% set of first image numbers
2440    i2_civ1=ref_i;
2441    j1_civ1=ref_j-floor(index_civ1/2)*ones(size(ref_j));
2442    j2_civ1=ref_j+ceil(index_civ1/2)*ones(size(ref_j));
2443    i1_civ2=ref_i;
2444    i2_civ2=ref_i;
2445    j1_civ2=ref_j-floor(index_civ2/2)*ones(size(ref_j));
2446    j2_civ2=ref_j+ceil(index_civ2/2)*ones(size(ref_j));
2447    % adjust the first and last field number
2448    if isnan(lastfield_j)
2449        indsel=find((j1_civ1 >= 1)&(j1_civ2 >= 1));
2450    else
2451        indsel=find((j2_civ1 <= lastfield_j)&(j2_civ2 <= lastfield_j)&(j1_civ1 >= 1)&(j1_civ2 >= 1));
2452    end
2453    if length(indsel)>=1
2454        firstind=indsel(1);
2455        lastind=indsel(end);
2456        set(handles.first_j,'String',num2str(ref_j(firstind)))%update the display of first and last fields
2457        set(handles.last_j,'String',num2str(ref_j(lastind)))
2458        ref_j=ref_j(indsel);
2459        j1_civ1=j1_civ1(indsel);
2460        j2_civ1=j2_civ1(indsel);
2461        j1_civ2=j1_civ2(indsel);
2462        j2_civ2=j2_civ2(indsel);
2463    end
2464elseif isequal(mode,'pair j1-j2') %case of bursts (png_old or png_2D)
2465    displ_num=get(handles.ListPairCiv1,'UserData');
2466    i1_civ1=ref_i;
2467    i2_civ1=ref_i;
2468    j1_civ1=displ_num(1,index_civ1);
2469    j2_civ1=displ_num(2,index_civ1);
2470    i1_civ2=ref_i;
2471    i2_civ2=ref_i;
2472    j1_civ2=displ_num(1,index_civ2);
2473    j2_civ2=displ_num(2,index_civ2);
2474elseif isequal(mode,'displacement')
2475    i1_civ1=ref_i;
2476    i2_civ1=ref_i;
2477    j1_civ1=ref_j;
2478    j2_civ1=ref_j;
2479    i1_civ2=ref_i;
2480    i2_civ2=ref_i;
2481    j1_civ2=ref_j;
2482    j2_civ2=ref_j;
2483end
2484
2485%------------------------------------------------------------------------
2486% --- Executes on button press in ListCompareMode.
2487function ListCompareMode_Callback(hObject, eventdata, handles)
2488%------------------------------------------------------------------------
2489ListCompareMode=get(handles.ListCompareMode,'String');
2490option=ListCompareMode{get(handles.ListCompareMode,'Value')};
2491if ~strcmp(option,'PIV') % case 'displacement' or 'stereo PIV'
2492    filebase=get(handles.RootPath,'String');
2493    set(handles.sub_txt,'Visible','on')
2494    set(handles.RootFile_1,'Visible','On');%mkes the second file input window visible
2495    mode_store=get(handles.ListPairMode,'String');%get the present 'mode'
2496    set(handles.ListCompareMode,'UserData',mode_store);%store the mode display
2497    set(handles.ListPairMode,'Visible','off')
2498   
2499    %% open an image file with the browser
2500    ind_opening=1;%default
2501    browse.incr_pair=[0 0]; %default
2502    oldfile=get(handles.RootPath,'String');
2503    menu={'*.png;*.jpg;*.tif;*.avi;*.AVI;', ' (*.png,*.jpg ,.tif, *.avi,*.AVI)';
2504        '*.png','.png image files'; ...
2505        '*.jpg',' jpeg image files'; ...
2506        '*.tif','.tif image files'; ...
2507        '*.avi;*.AVI','.avi movie files'; ...
2508        '*.*',  'All Files (*.*)'};
2509    if strcmp(option,'displacement')
2510        comment='Pick the reference file for displacements';
2511    else
2512        comment='Pick a file of the second series';
2513    end
2514    [FileName, PathName] = uigetfile( menu, comment,oldfile);
2515    fileinput=[PathName FileName];%complete file name
2516    sizf=size(fileinput);
2517    if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end %stop if fileinput not a character string
2518    [path,name,ext]=fileparts(fileinput);
2519    [path1]=fileparts(filebase);
2520    if isunix
2521        [status,path]=system(['readlink ' path]);
2522        [status,path1]=system(['readlink ' path1]);% look for the true path in case of symbolic paths
2523    end
2524    if ~strcmp(path1,path)
2525        msgbox_uvmat('ERROR','The second image or series must be in the same directory as the first one')
2526        return
2527    end
2528    if strcmp(option,'displacement')
2529        [tild,RootFile_1]=fileparts(name);
2530    else
2531        [FilePath,FileName,Ext]=fileparts(fileinput);
2532% detect the file type, get the movie object if relevant, and look for the corresponding file series:
2533% the root name and indices may be corrected by including the first index i1 if a corresponding xml file exists
2534[RootPath,SubDir,RootFile_1,i1_series,i2_series,j1_series,j2_series,nom_type_1,FileType,Object,i1,i2,j1,j2]=find_file_series(FilePath,[FileName Ext]);
2535
2536        %check image nom type
2537        if ~strcmp(nom_type_1,get(handles.NomType,'String'))
2538        msgbox_uvmat('ERROR','The second image series must have the same indexing type as the first one, or use the option displacement for a fixed image')
2539        return
2540        end
2541    end   
2542    %check image  extension
2543    if ~strcmp(ext,get(handles.ImaExt,'String'))
2544        msgbox_uvmat('ERROR','The second image series must have the same extension name as the first one')
2545        return
2546    end
2547    set(handles.RootFile_1,'String',RootFile_1);
2548else
2549    set(handles.ListPairMode,'Visible','on')
2550    set(handles.RootFile_1,'Visible','Off');
2551    set(handles.sub_txt,'Visible','off')
2552    set(handles.RootFile_1,'String',[]);
2553    mode_store=get(handles.ListCompareMode,'UserData');
2554    set(handles.ListPairMode,'Value',1)
2555    set(handles.ListPairMode,'String',mode_store)
2556    set(handles.CheckStereo,'Value',0)
2557    set(handles.ListPairMode,'Value',1) % mode 'civX' selected by default
2558end
2559ListPairMode_Callback(hObject, eventdata, handles)
2560
2561
2562%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
2563% Callbacks in the uipanel Pair Indices
2564%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
2565%------------------------------------------------------------------------
2566% --- Executes on button press in ListPairMode.
2567function ListPairMode_Callback(hObject, eventdata, handles)
2568%------------------------------------------------------------------------
2569compare_list=get(handles.ListCompareMode,'String');
2570val=get(handles.ListCompareMode,'Value');
2571compare=compare_list{val};
2572if strcmp(compare,'displacement')||strcmp(compare,'shift')
2573    mode='displacement';
2574else
2575    mode_list=get(handles.ListPairMode,'String');
2576    if ischar(mode_list)
2577        mode_list={mode_list};
2578    end
2579    mode_value=get(handles.ListPairMode,'Value');
2580    mode=mode_list{mode_value};
2581end
2582displ_num=[];%default
2583ref_i=str2double(get(handles.ref_i,'String'));
2584% last_i=str2num(get(handles.last_i,'String'));
2585time=get(handles.ImaDoc,'UserData'); %get the set of times
2586TimeUnit=get(handles.TimeUnit,'String');
2587checkframe=strcmp(TimeUnit,'frame');
2588siztime=size(time);
2589nbfield=siztime(1)-1;
2590nbfield2=siztime(2)-1;
2591indchosen=1;  %%first pair selected by default
2592%displ_num used to define the indices of the civ pairs
2593% in mode 'pair j1-j2', j1 and j2 are the file indices, else the indices
2594% are relative to the reference indices ref_i and ref_j respectively.
2595if isequal(mode,'pair j1-j2')%| isequal(mode,'st_pair j1-j2')
2596    dt=1;
2597    displ='';
2598    index=0;
2599    numlist_a=[];
2600    numlist_B=[];
2601    %get all the time intervals in bursts
2602    displ_dt=1;%default
2603    nbfield2=min(nbfield2,10);%limitate the number of pairs to 10x10
2604    for numod_a=1:nbfield2-1 %nbfield2 always >=2 for 'pair j1-j2' mode
2605        for numod_b=(numod_a+1):nbfield2
2606            index=index+1;
2607            numlist_a(index)=numod_a;
2608            numlist_b(index)=numod_b;
2609            if size(time,2)>1 && ~checkframe
2610                dt(numod_a,numod_b)=time(ref_i+1,numod_b+1)-time(ref_i+1,numod_a+1);%first time interval dt
2611                displ_dt(index)=dt(numod_a,numod_b);
2612            else
2613                displ_dt(index)=1;
2614            end
2615        end
2616    end
2617    [dtsort,indsort]=sort(displ_dt);
2618    if ~isempty(numlist_a)
2619        displ_num(1,:)=numlist_a(indsort);
2620        displ_num(2,:)=numlist_b(indsort);
2621    end
2622    displ_num(3,:)=0;
2623    displ_num(4,:)=0;
2624    enable_j(handles, 'off')
2625elseif isequal(mode,'series(Dj)') %| isequal(mode,'st_series(Dj)')
2626    index=1:200;
2627    displ_num(1,index)=-floor(index/2);
2628    displ_num(2,index)=ceil(index/2);
2629    displ_num(3:4,index)=zeros(2,200);
2630    enable_j(handles, 'on')
2631elseif isequal(mode,'series(Di)') %| isequal(mode,'st_series(Di)')
2632    index=1:200;
2633    displ_num(1:2,index)=zeros(2,200);
2634    displ_num(3,index)=-floor(index/2);
2635    displ_num(4,index)=ceil(index/2);
2636    enable_i(handles, 'on')
2637    if nbfield2 > 1
2638        enable_j(handles, 'on')
2639    else
2640        enable_j(handles, 'off')
2641    end
2642elseif isequal(mode,'displacement')%the pairs have the same indices
2643    displ_num(1,1)=0;
2644    displ_num(2,1)=0;
2645    displ_num(3,1)=0;
2646    displ_num(4,1)=0;
2647    if nbfield > 1 || nbfield==0
2648        enable_i(handles, 'on')
2649    else
2650        enable_j(handles, 'off')
2651    end
2652    if nbfield2 > 1
2653        enable_j(handles, 'on')
2654    else
2655        enable_j(handles, 'off')
2656    end
2657end
2658set(handles.ListPairCiv1,'UserData',displ_num);
2659errormsg=find_netcpair_civ( handles,1);
2660    if ~isempty(errormsg)
2661    msgbox_uvmat('ERROR',errormsg)
2662    end
2663% find_netcpair_civ2(handles)
2664
2665function enable_i(handles, state)
2666set(handles.itext,'Visible',state)
2667set(handles.first_i,'Visible',state)
2668set(handles.last_i,'Visible',state)
2669set(handles.incr_i,'Visible',state)
2670set(handles.nb_field,'Visible',state)
2671set(handles.ref_i,'Visible',state)
2672
2673function enable_j(handles, state)
2674set(handles.jtext,'Visible',state)
2675set(handles.first_j,'Visible',state)
2676set(handles.last_j,'Visible',state)
2677set(handles.incr_j,'Visible',state)
2678set(handles.nb_field2,'Visible',state)
2679set(handles.ref_j,'Visible',state)
2680
2681
2682%------------------------------------------------------------------------
2683% --- Executes on selection change in ListPairCiv1.
2684function ListPairCiv1_Callback(hObject, eventdata, handles)
2685%------------------------------------------------------------------------
2686%reproduce by default the chosen pair in the checkciv2 menu
2687list_pair=get(handles.ListPairCiv1,'String');%get the menu of image pairs
2688index_pair=get(handles.ListPairCiv1,'Value');
2689displ_num=get(handles.ListPairCiv1,'UserData');
2690list_pair2=get(handles.ListPairCiv2,'String');%get the menu of image pairs
2691if index_pair<=length(list_pair2)
2692    set(handles.ListPairCiv2,'Value',index_pair);
2693end
2694
2695%update first_i and last_i according to the chosen image pairs
2696mode_list=get(handles.ListPairMode,'String');
2697mode_value=get(handles.ListPairMode,'Value');
2698mode=mode_list{mode_value};
2699if isequal(mode,'series(Di)')
2700    first_i=str2double(get(handles.first_i,'String'));
2701    last_i=str2double(get(handles.last_i,'String'));
2702    incr_i=str2double(get(handles.incr_i,'String'));
2703    num1=first_i:incr_i:last_i;
2704    lastfield=str2double(get(handles.nb_field,'String'));
2705    if ~isnan(lastfield)
2706        test_find=(num1-floor(index_pair/2)*ones(size(num1))>0)& ...
2707            (num1+ceil(index_pair/2)*ones(size(num1))<=lastfield);
2708        num1=num1(test_find);
2709    end
2710    set(handles.first_i,'String',num2str(num1(1)));
2711    set(handles.last_i,'String',num2str(num1(end)));
2712elseif isequal(mode,'series(Dj)')
2713    first_j=str2double(get(handles.first_j,'String'));
2714    last_j=str2double(get(handles.last_j,'String'));
2715    incr_j=str2double(get(handles.incr_j,'String'));
2716    num_j=first_j:incr_j:last_j;
2717    lastfield2=str2double(get(handles.nb_field2,'String'));
2718    if ~isnan(lastfield2)
2719        test_find=(num_j-floor(index_pair/2)*ones(size(num_j))>0)& ...
2720            (num_j+ceil(index_pair/2)*ones(size(num_j))<=lastfield2);
2721        num1=num_j(test_find);
2722    end
2723    set(handles.first_j,'String',num2str(num1(1)));
2724    set(handles.last_j,'String',num2str(num1(end)));
2725end
2726
2727%------------------------------------------------------------------------
2728% --- Executes on selection change in ListPairCiv2.
2729function ListPairCiv2_Callback(hObject, eventdata, handles)
2730%------------------------------------------------------------------------
2731index_pair=get(handles.ListPairCiv2,'Value');%get the selected position index in the menu
2732
2733%update first_i and last_i according to the chosen image pairs
2734mode_list=get(handles.ListPairMode,'String');
2735mode_value=get(handles.ListPairMode,'Value');
2736mode=mode_list{mode_value};
2737if isequal(mode,'series(Di)')
2738    first_i=str2double(get(handles.first_i,'String'));
2739    last_i=str2double(get(handles.last_i,'String'));
2740    incr_i=str2double(get(handles.incr_i,'String'));
2741    num1=first_i:incr_i:last_i;
2742    lastfield=str2double(get(handles.nb_field,'String'));
2743    if ~isnan(lastfield)
2744        test_find=(num1-floor(index_pair/2)*ones(size(num1))>0)& ...
2745            (num1+ceil(index_pair/2)*ones(size(num1))<=lastfield);
2746        num1=num1(test_find);
2747    end
2748    set(handles.first_i,'String',num2str(num1(1)));
2749    set(handles.last_i,'String',num2str(num1(end)));
2750elseif isequal(mode,'series(Dj)')
2751    first_j=str2double(get(handles.first_j,'String'));
2752    last_j=str2double(get(handles.last_j,'String'));
2753    incr_j=str2double(get(handles.incr_j,'String'));
2754    num_j=first_j:incr_j:last_j;
2755    lastfield2=str2double(get(handles.nb_field2,'String'));
2756    if ~isnan(lastfield2)
2757        test_find=(num_j-floor(index_pair/2)*ones(size(num_j))>0)& ...
2758            (num_j+ceil(index_pair/2)*ones(size(num_j))<=lastfield2);
2759        num1=num_j(test_find);
2760    end
2761    set(handles.first_j,'String',num2str(num1(1)));
2762    set(handles.last_j,'String',num2str(num1(end)));
2763end
2764
2765%------------------------------------------------------------------------
2766function ref_i_Callback(hObject, eventdata, handles)
2767%------------------------------------------------------------------------
2768mode_list=get(handles.ListPairMode,'String');
2769mode_value=get(handles.ListPairMode,'Value');
2770mode=mode_list{mode_value};
2771errormsg=find_netcpair_civ(handles,1);% update the menu of pairs depending on the available netcdf files
2772if isequal(mode,'series(Di)') || ...% we do patch2 only
2773        (get(handles.CheckCiv2,'Value')==0 && get(handles.CheckCiv1,'Value')==0 && get(handles.CheckFix1,'Value')==0 && get(handles.CheckPatch1,'Value')==0)
2774    errormsg=find_netcpair_civ( handles,2);
2775end
2776    if ~isempty(errormsg)
2777    msgbox_uvmat('ERROR',errormsg)
2778    end
2779
2780%------------------------------------------------------------------------
2781function ref_j_Callback(hObject, eventdata, handles)
2782%------------------------------------------------------------------------
2783mode_list=get(handles.ListPairMode,'String');
2784mode_value=get(handles.ListPairMode,'Value');
2785mode=mode_list{mode_value};
2786if isequal(get(handles.CheckCiv1,'Value'),0)|| isequal(mode,'series(Dj)')
2787    errormsg=find_netcpair_civ(handles,1);% update the menu of pairs depending on the available netcdf files
2788end
2789if isequal(mode,'series(Dj)') || ...
2790        (get(handles.CheckCiv2,'Value')==0 && get(handles.CheckCiv1,'Value')==0 && get(handles.CheckFix1,'Value')==0 && get(handles.CheckPatch1,'Value')==0)
2791    errormsg=find_netcpair_civ(handles,2);
2792end
2793    if ~isempty(errormsg)
2794    msgbox_uvmat('ERROR',errormsg)
2795    end
2796
2797%------------------------------------------------------------------------
2798% determine the menu for checkciv1 pairs depending on existing netcdf file at the middle of
2799% the field series set by first_i, incr, last_i
2800% index=1: look for pairs for civ1
2801% index=2: look for pairs for civ2
2802function errormsg=find_netcpair_civ(handles,index)
2803%------------------------------------------------------------------------
2804set(gcf,'Pointer','watch')% set the mouse pointer to 'watch' (clock)
2805
2806%% initialisation
2807errormsg='';
2808browse=get(handles.RootPath,'UserData');
2809compare_list=get(handles.ListCompareMode,'String');
2810val=get(handles.ListCompareMode,'Value');
2811compare=compare_list{val};
2812if strcmp(compare,'displacement')||strcmp(compare,'shift')
2813    mode='displacement';
2814else
2815    mode_list=get(handles.ListPairMode,'String');
2816    mode_value=get(handles.ListPairMode,'Value');
2817    if isempty(mode_list)
2818        return
2819    end
2820    mode=mode_list{mode_value};
2821end
2822nom_type_ima=get(handles.NomType,'String');
2823
2824%% determine nom_type_nc, nomenclature type of the .nc files:
2825[nom_type_nc]=nomtype2pair(nom_type_ima,mode);
2826
2827%% reads .nc subdirectoy and image numbers from the interface
2828SubDirImages=get(handles.SubDirImages,'String');
2829subdir_civ1=[SubDirImages get(handles.SubdirCiv1,'String')];%subdirectory subdir_civ1 for the netcdf data
2830subdir_civ2=[SubDirImages get(handles.SubdirCiv2,'String')];%subdirectory subdir_civ2 for the netcdf data
2831ref_i=str2double(get(handles.ref_i,'String'));
2832ref_j=[];
2833if isequal(mode,'pair j1-j2')%|isequal(mode,'st_pair j1-j2')
2834    ref_j=0;
2835elseif strcmp(get(handles.ref_j,'Visible'),'on')
2836    ref_j=str2double(get(handles.ref_j,'String'));
2837end
2838if isempty(ref_j)
2839    ref_j=1;
2840end
2841time=get(handles.ImaDoc,'UserData');%get the set of times
2842TimeUnit=get(handles.TimeUnit,'String');
2843checkframe=strcmp(TimeUnit,'frame');
2844displ_num=get(handles.ListPairCiv1,'UserData');
2845
2846%% eliminate the first pairs inconsistent with the position
2847if isempty(displ_num)
2848    nbpair=0;
2849else
2850    nbpair=length(displ_num(1,:));%nbre of displayed pairs
2851    if  isequal(mode,'series(Di)')  %| isequal(mode,'st_series(Di)')
2852        nbpair=min(2*ref_i-1,nbpair);%limit the number of pairs with positive first index
2853    elseif  isequal(mode,'series(Dj)')% | isequal(mode,'st_series(Dj)')
2854        nbpair=min(2*ref_j-1,nbpair);%limit the number of pairs with positive first index
2855    end
2856end
2857nbpair=min(200,nbpair);%limit the number of displayed pairs to 200
2858
2859%% case with no Civ1 operation, netcdf files need to exist for reading
2860displ_pair={''};
2861select=ones(size(1:nbpair));%flag for displayed pairs =1 for display
2862testpair=0;
2863RootPath=get(handles.RootPath,'String');
2864RootFile=get(handles.RootFile,'String');
2865if index==1 % case civ1
2866    if ~get(handles.CheckCiv1,'Value') %
2867        if ~exist(fullfile(RootPath,subdir_civ1),'dir')
2868            errormsg=['no civ1 file available: subdirectory ' subdir_civ1 ' does not exist'];
2869            set(handles.ListPairCiv1,'String',{});
2870            return
2871        end
2872        for ipair=1:nbpair
2873            filename=fullfile_uvmat(RootPath,subdir_civ1,RootFile,'.nc',nom_type_nc,...
2874                ref_i+displ_num(3,ipair),ref_i+displ_num(4,ipair),ref_j+displ_num(1,ipair),ref_j+displ_num(2,ipair));
2875            select(ipair)=exist(filename,'file')==2;% put flag to 0 if the file does not exist
2876        end
2877        % case of no displayed pair
2878        if isequal(select,zeros(size(1:nbpair)))
2879            if isfield(browse,'incr_pair') && ~isequal(browse.incr_pair,[0 0])
2880                num_i1=ref_i-floor(browse.incr_pair(1)/2);
2881                num_i2=ref_i+ceil(browse.incr_pair(1)/2);
2882                num_j1=ref_j-floor(browse.incr_pair(2)/2);
2883                num_j2=ref_j+ceil(browse.incr_pair(2)/2);
2884                filename=fullfile_uvmat(RootPath,subdir_civ1,RootFile,'.nc',nom_type_nc,num_i1,num_i2,num_j1,num_j2);
2885                select(1)=exist(filename,'file')==2;
2886                testpair=1;
2887            else
2888%                 if  isequal(mode,'series(Dj)')% | isequal(mode,'st_series(Dj)')
2889%                     errormsg=['no civ1 file available for the selected reference index j=' num2str(ref_j) ' and subdirectory ' subdir_civ1];
2890%                 else
2891                    errormsg=['no civ1 file available for the selected reference indices (i,j)= ' num2str(ref_i) ', ' num2str(ref_j) ' and subdirectory ' subdir_civ1];
2892%                 end
2893                set(handles.ListPairCiv1,'String',{''});
2894                %COMPLETER CAS STEREO
2895                return
2896            end
2897        end
2898    end
2899else %case civ2 alone
2900    if ~get(handles.CheckCiv2,'Value') && ~get(handles.CheckCiv1,'Value') && ~get(handles.CheckFix1,'Value') && ~get(handles.CheckPatch1,'Value')
2901        if ~exist(fullfile(RootPath,subdir_civ2),'dir')
2902            msgbox_uvmat('ERROR',['no civ2 file available: subdirectory ' subdir_civ2 ' does not exist'])
2903            set(handles.ListPairCiv2,'Value',1);
2904            set(handles.ListPairCiv2,'String',{''});
2905            return
2906        end
2907        for ipair=1:nbpair
2908            filename=fullfile_uvmat(RootPath,subdir_civ1,RootFile,'.nc',nom_type_nc,...
2909                ref_i+displ_num(3,ipair),ref_i+displ_num(4,ipair),ref_j+displ_num(1,ipair),ref_j+displ_num(2,ipair));
2910            select(ipair)=exist(filename,'file')==2;
2911        end
2912        if  isequal(select,zeros(size(1:nbpair)))
2913            if isfield(browse,'incr_pair')
2914                num_i1=ref_i-floor(browse.incr_pair(1)/2);
2915                num_i2=ref_i+floor((browse.incr_pair(1)+1)/2);
2916                num_j1=ref_j-floor(browse.incr_pair(2)/2);
2917                num_j2=ref_j+floor((browse.incr_pair(2)+1)/2);
2918                filename=fullfile_uvmat(RootPath,subdir_civ2,RootFile,'.nc',nom_type_nc,num_i1,num_i2,num_j1,num_j2);
2919                select(1)=exist(filename,'file')==2;
2920            else
2921                if  isequal(mode,'series(Dj)')% | isequal(mode,'st_series(Dj)')
2922                    errormsg=['no civ2 file available for the selected reference index j=' num2str(ref_j) ' and subdirectory ' subdir_civ2];
2923                else
2924                    errormsg=['no civ2 file available for the selected reference index i=' num2str(ref_i) ' and subdirectory ' subdir_civ2];
2925                end
2926                set(handles.ListPairCiv2,'Value',1);
2927                set(handles.ListPairCiv2,'String',{''});
2928                return
2929            end
2930        end
2931    end
2932end
2933
2934%% determine the menu display in .ListPairCiv1
2935% the menu depends on the mode defined in ListPairMode_callback through the array displ_num:
2936% displ_num(1,:)=indices j1
2937% displ_num(2,:)=indices j2
2938% displ_num(3,:)=indices i1
2939% displ_num(4,:)=indices i2
2940% in mode 'pair j1-j2', j1 and j2 are the file indices, else the indices
2941% are relative to the reference indices ref_i and ref_j respectively.
2942if isequal(mode,'series(Di)')
2943    if testpair
2944        displ_pair{1}=['Di= ' num2str(-floor(browse.incr_pair(1)/2)) '|' num2str(ceil(browse.incr_pair(1)/2))];
2945    else
2946        for ipair=1:nbpair
2947            if select(ipair)
2948                displ_pair{ipair}=['Di= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2))];
2949                %if ~checkframe && size(time,1)>=ref_i+1+displ_num(4,ipair) && size(time,2)>=ref_j+1+displ_num(2,ipair)&&displ_num(2,ipair)>=1 &&displ_num(1,ipair)>=1
2950                 %   dt=time(ref_i+1+displ_num(4,ipair),ref_j+1+displ_num(2,ipair))-time(ref_i+1+displ_num(3,ipair),ref_j+1+displ_num(1,ipair));%time interval dt
2951               if ~checkframe && size(time,1)>=ref_i+1+ceil(ipair/2) && size(time,2)>=ref_j+1&& ref_i-floor(ipair/2)>=0 && ref_j>=0
2952                 dt=time(ref_i+1+ceil(ipair/2),ref_j+1)-time(ref_i+1-floor(ipair/2),ref_j+1);%time interval dtref_j+1
2953                else
2954                    dt=1;
2955                end
2956                 displ_pair{ipair}=[displ_pair{ipair} ' :dt= ' num2str(dt*1000)];
2957            else
2958                displ_pair{ipair}='...'; %pair not displayed in the menu
2959            end
2960        end
2961    end
2962elseif isequal(mode,'series(Dj)')
2963    if testpair
2964        displ_pair{1}=['Dj= ' num2str(-floor(browse.incr_pair(1)/2)) '|' num2str(ceil(browse.incr_pair(1)/2))];
2965    else
2966        for ipair=1:nbpair
2967            if select(ipair)
2968                displ_pair{ipair}=['Dj= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2))];
2969                if ~checkframe && size(time,1)>=ref_i+1+displ_num(4,ipair) && size(time,2)>=ref_j+1+displ_num(2,ipair)
2970                    dt=time(ref_i+1+displ_num(4,ipair),ref_j+1+displ_num(2,ipair))-time(ref_i+1+displ_num(3,ipair),ref_j+1+displ_num(1,ipair));%time interval dt
2971                    displ_pair{ipair}=[displ_pair{ipair} ' :dt= ' num2str(dt*1000)];
2972                end
2973            else
2974                displ_pair{ipair}='...'; %pair not displayed in the menu
2975            end
2976        end
2977    end
2978elseif isequal(mode,'pair j1-j2')%case of pairs
2979    for ipair=1:nbpair
2980        if select(ipair)
2981            if ~checkframe && size(time,2)>1
2982            dt=time(ref_i+1+displ_num(4,ipair),displ_num(2,ipair)+1)-time(ref_i+1+displ_num(3,ipair),displ_num(1,ipair)+1);%time interval dt
2983            else % time set by default to i index
2984                dt=1;
2985            end
2986            displ_pair{ipair}=['j= ' num2stra(displ_num(1,ipair),nom_type_ima) '-' num2stra(displ_num(2,ipair),nom_type_ima) ...
2987                ' :dt= ' num2str(dt*1000)];
2988        else
2989            displ_pair{ipair}='...'; %pair not displayed in the menu
2990        end
2991    end
2992elseif isequal(mode,'displacement')
2993    displ_pair={'Di=Dj=0'};
2994end
2995if index==1
2996set(handles.ListPairCiv1,'String',displ_pair');
2997end
2998
2999%% determine the default selection in the pair menu
3000ichoice=find(select,1);% index of selected pair
3001if (isempty(ichoice) || ichoice < 1); ichoice=1; end;
3002initial=get(handles.ListPairCiv1,'Value');%initial choice of pair
3003if initial>nbpair || (numel(select)>=initial && ~isequal(select(initial),1))
3004    set(handles.ListPairCiv1,'Value',ichoice);% first valid pair proposed by default in the menu
3005end
3006initial=get(handles.ListPairCiv2,'Value');
3007if initial>length(displ_pair')%|~isequal(select(initial),1)
3008    if ichoice <= length(displ_pair')
3009        set(handles.ListPairCiv2,'Value',ichoice);% same pair proposed by default for civ2
3010    else
3011        set(handles.ListPairCiv2,'Value',1);% same pair proposed by default for civ2
3012    end
3013end
3014set(handles.ListPairCiv2,'String',displ_pair');
3015set(gcf,'Pointer','arrow')
3016
3017
3018   
3019% %------------------------------------------------------------------------   
3020% % call 'view_field.fig' to display the  field selected in the list of 'status'
3021% function open_view_field(hObject, eventdata)
3022% %------------------------------------------------------------------------
3023% list=get(hObject,'String');
3024% index=get(hObject,'Value');
3025% rootroot=get(hObject,'UserData');
3026% filename=list{index};
3027% ind_dot=strfind(filename,'...');
3028% filename=filename(1:ind_dot-1);
3029% filename=fullfile(rootroot,filename);
3030% delete(get(hObject,'parent'))%delete the display figure to stop the check process
3031% if exist(filename,'file')%visualise the vel field if it exists
3032%     uvmat(filename)
3033%     set(gcbo,'Value',1)
3034% end
3035
3036
3037%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3038% Callbacks in the uipanel Reference Indices
3039%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3040%------------------------------------------------------------------------
3041function first_i_Callback(hObject, eventdata, handles)
3042%------------------------------------------------------------------------
3043first_i=str2double(get(handles.first_i,'String'));
3044set(handles.ref_i,'String', num2str(first_i))% reference index for pair dt = first index
3045ref_i_Callback(hObject, eventdata, handles)%refresh dispaly of dt for pairs (in case of non constant dt)
3046
3047%------------------------------------------------------------------------
3048function first_j_Callback(hObject, eventdata, handles)
3049%------------------------------------------------------------------------
3050first_j=str2num(get(handles.first_j,'String'));
3051set(handles.ref_j,'String', num2str(first_j))% reference index for pair dt = first index
3052ref_j_Callback(hObject, eventdata, handles)%refresh dispaly of dt for pairs (in case of non constant dt)
3053
3054%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3055% Callbacks in the uipanel Civ1
3056%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3057%------------------------------------------------------------------------
3058% --- Executes on button press in SearchRange: determine the search range num_SearchBoxSize_1,num_SearchBoxSize_2
3059function SearchRange_Callback(hObject, eventdata, handles)
3060%------------------------------------------------------------------------
3061%determine pair numbers
3062if strcmp(get(handles.num_UMin,'Visible'),'off')
3063    set(handles.u_title,'Visible','on')
3064    set(handles.v_title,'Visible','on')
3065    set(handles.num_UMin,'Visible','on')
3066    set(handles.num_UMax,'Visible','on')
3067    set(handles.num_VMin,'Visible','on')
3068    set(handles.num_VMax,'Visible','on')
3069    set(handles.CoordUnit,'Visible','on')
3070    set(handles.TimeUnit,'Visible','on')
3071    set(handles.slash_title,'Visible','on')
3072    set(handles.min_title,'Visible','on')
3073    set(handles.max_title,'Visible','on')
3074    set(handles.unit_title,'Visible','on')
3075else
3076    get_search_range(hObject, eventdata, handles)
3077end
3078
3079%------------------------------------------------------------------------
3080% ---  determine the search range num_SearchBoxSize_1,num_SearchBoxSize_2 and shift
3081function get_search_range(hObject, eventdata, handles)
3082%------------------------------------------------------------------------
3083param_civ1=read_GUI(handles.Civ1);
3084umin=param_civ1.UMin;
3085umax=param_civ1.UMax;
3086vmin=param_civ1.VMin;
3087vmax=param_civ1.VMax;
3088%switch min_title and max_title in case of error
3089if umax<=umin
3090    umin_old=umin;
3091    umin=umax;
3092    umax=umin_old;
3093    set(handles.num_UMin,'String', num2str(umin))
3094    set(handles.num_UMax,'String', num2str(umax))
3095end
3096if vmax<=vmin
3097    vmin_old=vmin;
3098    vmin=vmax;
3099    vmax=vmin_old;
3100    set(handles.num_VMin,'String', num2str(vmin))
3101    set(handles.num_VMax,'String', num2str(vmax))
3102end   
3103if ~(isempty(umin)||isempty(umax)||isempty(vmin)||isempty(vmax))
3104    list_pair=get(handles.ListPairCiv1,'String');%get the menu of image pairs
3105    index=get(handles.ListPairCiv1,'Value');
3106    pair_string=list_pair{index};
3107    time=get(handles.ImaDoc,'UserData'); %get the set of times
3108    pxcm=get(handles.SearchRange,'UserData');
3109    mode_list=get(handles.ListPairMode,'String');
3110    mode_value=get(handles.ListPairMode,'Value');
3111    mode=mode_list{mode_value};     
3112    if isequal (mode, 'series(Di)' )
3113        ref_i=str2double(get(handles.ref_i,'String'));
3114        num1=ref_i-floor(index/2);%  first image numbers
3115        num2=ref_i+ceil(index/2);
3116        num_a=1;
3117        num_b=1;
3118    elseif isequal (mode, 'series(Dj)')
3119        num1=1;
3120        num2=1;
3121        ref_j=str2double(get(handles.ref_j,'String'));
3122        num_a=ref_j-floor(index/2);%  first image numbers
3123        num_b=ref_j+ceil(index/2);
3124    elseif isequal(mode,'pair j1-j2') %case of bursts (png_old or png_2D)     
3125        ref_i=str2double(get(handles.ref_i,'String'));
3126        num1=ref_i;
3127        num2=ref_i;
3128                r=regexp(pair_string,'(?<mode>(Di=)|(Dj=)) -*(?<num1>\d+)\|(?<num2>\d+)','names');
3129        if isempty(r)
3130            r=regexp(pair_string,'(?<num1>\d+)(?<mode>-)(?<num2>\d+)','names');
3131        end 
3132        num_a=str2num(r.num1);
3133        num_b=str2num(r.num2);
3134    end
3135    dt=time(num2+1,num_b+1)-time(num1+1,num_a+1);
3136    ibx=str2double(get(handles.num_CorrBoxSize_1,'String'));
3137    iby=str2double(get(handles.num_CorrBoxSize_2,'String'));
3138    umin=dt*pxcm*umin;
3139    umax=dt*pxcm*umax;
3140    vmin=dt*pxcm*vmin;
3141    vmax=dt*pxcm*vmax;
3142    shiftx=round((umin+umax)/2);
3143    shifty=round((vmin+vmax)/2);
3144    isx=(umax+2-shiftx)*2+param_civ1.Bx;
3145    isx=2*ceil(isx/2)+1;
3146    isy=(vmax+2-shifty)*2+param_civ1.Bx;
3147    isy=2*ceil(isy/2)+1;
3148    set(handles.num_SearchBoxShift_1,'String',num2str(shiftx));
3149    set(handles.num_SearchBoxShift_2,'String',num2str(shifty));
3150    set(handles.num_SearchBoxSize_1,'String',num2str(isx));
3151    set(handles.num_SearchBoxSize_2,'String',num2str(isy));
3152end
3153
3154%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3155% Callbacks in the uipanel Fix1
3156%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3157%------------------------------------------------------------------------
3158% --- Executes on button press in CheckMask.
3159function get_mask_fix1_Callback(hObject, eventdata, handles)
3160%------------------------------------------------------------------------
3161maskval=get(handles.CheckMask,'Value');
3162if isequal(maskval,0)
3163    set(handles.Mask,'String','')
3164else
3165    mask_displ='no mask'; %default
3166    filebase=get(handles.RootPath,'String');
3167    [nbslice, flag_mask]=get_mask(filebase,handles);
3168    if isequal(flag_mask,1)
3169        mask_displ=[num2str(nbslice) 'mask'];
3170    elseif get(handles.ListCompareMode,'Value')>1 & ~isequal(mask_displ,'no mask')% look for the second mask series
3171        filebase_a=get(handles.RootFile_1,'String');
3172        [nbslice_a, flag_mask_a]=get_mask(filebase_a,handles);
3173        if isequal(flag_mask_a,0) || ~isequal(nbslice_a,nbslice)
3174            mask_displ='no mask';
3175        end
3176    end
3177    if isequal(mask_displ,'no mask')
3178        [FileName, PathName, filterindex] = uigetfile( ...
3179            {'*.png', ' (*.png)';
3180            '*.png',  '.png files '; ...
3181            '*.*', 'All Files (*.*)'}, ...
3182            'Pick a mask file *.png',filebase);
3183        mask_displ=fullfile(PathName,FileName);
3184        if ~exist(mask_displ,'file')
3185            mask_displ='no mask';
3186        end
3187    end
3188    if isequal(mask_displ,'no mask')
3189        set(handles.CheckMask,'Value',0)
3190        set(handles.CheckMask,'Value',0)
3191        set(handles.CheckMask,'Value',0)
3192    else
3193        %set(handles.CheckMask,'Value',1)
3194        set(handles.CheckMask,'Value',1)
3195    end
3196    set(handles.Mask,'String',mask_displ)
3197    set(handles.Mask,'String',mask_displ)
3198    set(handles.Mask,'String',mask_displ)
3199end
3200
3201%------------------------------------------------------------------------
3202% --- Executes on button press in CheckMask: select box for mask option
3203function get_mask_civ2_Callback(hObject, eventdata, handles)
3204%------------------------------------------------------------------------
3205maskval=get(handles.CheckMask,'Value');
3206if isequal(maskval,0)
3207    set(handles.Mask,'String','')
3208else
3209    mask_displ='no mask'; %default
3210    filebase=get(handles.RootPath,'String');
3211    [nbslice, flag_mask]=get_mask(filebase,handles);
3212    if isequal(flag_mask,1)
3213        mask_displ=[num2str(nbslice) 'mask'];
3214    elseif get(handles.ListCompareMode,'Value')>1 & ~isequal(mask_displ,'no mask')% look for the second mask series
3215        filebase_a=get(handles.RootFile_1,'String');
3216        [nbslice_a, flag_mask_a]=get_mask(filebase_a,handles);
3217        if isequal(flag_mask_a,0) || ~isequal(nbslice_a,nbslice)
3218            mask_displ='no mask';
3219        end
3220    end
3221    if isequal(mask_displ,'no mask')
3222        [FileName, PathName, filterindex] = uigetfile( ...
3223            {'*.png', ' (*.png)';
3224            '*.png',  '.png files '; ...
3225            '*.*', 'All Files (*.*)'}, ...
3226            'Pick a mask file *.png',filebase);
3227        mask_displ=fullfile(PathName,FileName);
3228        if ~exist(mask_displ,'file')
3229            mask_displ='no mask';
3230        end
3231    end
3232    if isequal(mask_displ,'no mask')
3233        set(handles.CheckMask,'Value',0)
3234        set(handles.CheckMask,'Value',0)
3235    else
3236        set(handles.CheckMask,'Value',1)
3237    end
3238    set(handles.Mask,'String',mask_displ)
3239    set(handles.Mask,'String',mask_displ)
3240end
3241
3242%------------------------------------------------------------------------
3243% --- Executes on button press in CheckMask.
3244function get_mask_fix2_Callback(hObject, eventdata, handles)
3245%------------------------------------------------------------------------
3246maskval=get(handles.CheckMask,'Value');
3247if isequal(maskval,0)
3248    set(handles.Mask,'String','')
3249else
3250    mask_displ='no mask'; %default
3251    filebase=get(handles.RootPath,'String');
3252    [nbslice, flag_mask]=get_mask(filebase,handles);
3253    if isequal(flag_mask,1)
3254        mask_displ=[num2str(nbslice) 'mask'];
3255    elseif get(handles.ListCompareMode,'Value')>1 & ~isequal(mask_displ,'no mask')% look for the second mask series
3256        filebase_a=get(handles.RootFile_1,'String');
3257        [nbslice_a, flag_mask_a]=get_mask(filebase_a,handles);
3258        if isequal(flag_mask_a,0) || ~isequal(nbslice_a,nbslice)
3259            mask_displ='no mask';
3260        end
3261    end
3262    if isequal(mask_displ,'no mask')
3263        [FileName, PathName, filterindex] = uigetfile( ...
3264            {'*.png', ' (*.png)';
3265            '*.png',  '.png files '; ...
3266            '*.*', 'All Files (*.*)'}, ...
3267            'Pick a mask file *.png',filebase);
3268        mask_displ=fullfile(PathName,FileName);
3269        if ~exist(mask_displ,'file')
3270            mask_displ='no mask';
3271        end
3272    end
3273    if isequal(mask_displ,'no mask')
3274        set(handles.CheckMask,'Value',0)
3275    end
3276    set(handles.Mask,'String',mask_displ)
3277end
3278
3279%------------------------------------------------------------------------
3280% --- function called to look for mask files
3281function [nbslice, flag_mask]=get_mask(filebase,handles)
3282%------------------------------------------------------------------------
3283%detect mask files, images with appropriate file base
3284%[filebase '_' xx 'mask'], xx=nbslice
3285%flag_mask=1 indicates detection
3286
3287flag_mask=0;%default
3288nbslice=1;
3289
3290% subdir=get(handles.SubdirCiv1,'String');
3291[Path,Name]=fileparts(filebase);
3292if ~isdir(Path)
3293    msgbox_uvmat('ERROR','no path for input files')
3294    return
3295end
3296% currentdir=pwd;
3297% cd(Path);%move in the dir of the root name filebase
3298maskfiles=dir(fullfile(Path,[Name '_*mask_*.png']));%look for mask files
3299% cd(currentdir);%come back to the current working directory
3300if ~isempty(maskfiles)
3301    %     msgbox_uvmat('ERROR','no mask available, to create it use Tools/Make mask in the upper menu bar of uvmat')
3302    % else
3303    flag_mask=1;
3304    maskname=maskfiles(1).name;% take the first mask file in the list
3305    [Path2,Name,ext]=fileparts(maskname);
3306    Namedouble=double(Name);
3307    val=(48>Namedouble)|(Namedouble>57);% select the non-numerical characters
3308    ind_mask=findstr('mask',Name);
3309    i=ind_mask-1;
3310    while val(i)==0 && i>0
3311        i=i-1;
3312    end
3313    nbslice=str2double(Name(i+1:ind_mask-1));
3314    if ~isnan(nbslice) && Name(i)=='_'
3315        flag_mask=1;
3316    else
3317        msgbox_uvmat('ERROR',['bad mask file ' Name ext ' found in ' Path2])
3318        return
3319        nbslice=1;
3320    end
3321end
3322
3323%------------------------------------------------------------------------
3324% --- function called to look for grid files
3325function [nbslice, flag_mask]=get_grid(filebase,handles)
3326%------------------------------------------------------------------------
3327flag_mask=0;%default
3328nbslice=1;
3329[Path,Name]=fileparts(filebase);
3330currentdir=pwd;
3331cd(Path);%move in the dir of the root name filebase
3332maskfiles=dir([Name '_*grid_*.grid']);%look for mask files
3333cd(currentdir);%come back to the current working directory
3334if ~isempty(maskfiles)
3335    flag_mask=1;
3336    maskname=maskfiles(1).name;% take the first mask file in the list
3337    [Path2,Name,ext]=fileparts(maskname);
3338    Namedouble=double(Name);
3339    val=(48>Namedouble)|(Namedouble>57);% select the non-numerical characters
3340    ind_mask=findstr('grid',Name);
3341    i=ind_mask-1;
3342    while val(i)==0 && i>0
3343        i=i-1;
3344    end
3345    nbslice=str2double(Name(i+1:ind_mask-1));
3346    if ~isnan(nbslice) && Name(i)=='_'
3347        flag_mask=1;
3348    else
3349        msgbox_uvmat('ERROR',['bad grid file ' Name ext ' found in ' Path2])
3350        return
3351        nbslice=1;
3352    end
3353end
3354
3355%------------------------------------------------------------------------
3356% --- transform numbers to letters
3357function str=num2stra(num,nom_type)
3358%------------------------------------------------------------------------
3359if isempty(nom_type)
3360    str='';
3361elseif strcmp(nom_type(end),'a')
3362    str=char(96+num);
3363elseif strcmp(nom_type(end),'A')
3364    str=char(96+num);
3365elseif isempty(nom_type(2:end))%a single index
3366    str='';
3367else
3368    str=num2str(num);
3369end
3370
3371% %------------------------------------------------------------------------
3372% % --- Executes on button press in ListSubdirCiv1.
3373% function ListSubdirCiv1_Callback(hObject, eventdata, handles)
3374% %------------------------------------------------------------------------
3375% list_subdir_civ1=get(handles.ListSubdirCiv1,'String');
3376% val=get(handles.ListSubdirCiv1,'Value');
3377% SubDir=list_subdir_civ1{val};
3378% if strcmp(SubDir,'new...')
3379%     if get(handles.CheckCiv1,'Value')
3380%         SubDir='CIV'; %default subdirectory
3381%     else
3382%         msgbox_uvmat('ERROR','select CheckCiv1 to perform a new Civ operation')
3383%         return
3384%     end   
3385% end
3386% set(handles.SubdirCiv1,'String',SubDir);
3387% errormsg=find_netcpair_civ(handles,1);
3388% if ~isempty(errormsg)
3389%     msgbox_uvmat('ERROR',errormsg)
3390% end
3391%     
3392%------------------------------------------------------------------------
3393% % --- Executes on button press in ListSubdirCiv2.
3394% function ListSubdirCiv2_Callback(hObject, eventdata, handles)
3395% %------------------------------------------------------------------------
3396% list_subdir_civ2=get(handles.ListSubdirCiv2,'String');
3397% val=get(handles.ListSubdirCiv2,'Value');
3398% SubDir=list_subdir_civ2{val};
3399% if strcmp(SubDir,'new...')
3400%     if get(handles.CheckCiv2,'Value')
3401%         SubDir='CIV'; %default subdirectory
3402%     else
3403%         msgbox_uvmat('ERROR','select CheckCiv2 to perform a new Civ operation')
3404%         return
3405%     end
3406% end
3407% set(handles.SubdirCiv2,'String',SubDir);
3408
3409%------------------------------------------------------------------------
3410% --- Executes on button press in CheckGrid.
3411function CheckGrid_Callback(hObject, eventdata, handles)
3412%------------------------------------------------------------------------
3413value=get(hObject,'Value');
3414hparent=get(hObject,'parent');
3415hchildren=get(hparent,'children');
3416handle_txtbox=findobj(hchildren,'tag','txt_Grid');
3417handle_dx=findobj(hchildren,'tag','num_Dx');
3418handle_dy=findobj(hchildren,'tag','num_Dy');
3419handle_title_dx=findobj(hchildren,'tag','title_Dx');
3420handle_title_dy=findobj(hchildren,'tag','title_Dy');
3421testgrid=0;
3422filegrid='';
3423if value
3424    filebase=get(handles.RootPath,'String');
3425    [nbslice, flag_grid]=get_grid(filebase,handles);% look for a grid with appropriate name
3426    if isequal(flag_grid,1)
3427        filegrid=[num2str(nbslice) 'grid'];
3428        testgrid=1;
3429    else % browse for a grid
3430        filegrid=get(hObject,'UserData');%look for previous grid name stored as UserData
3431        if exist(filegrid,'file')
3432            filebase=filegrid;
3433        end
3434        [FileName, PathName, filterindex] = uigetfile( ...
3435            {'*.grid', ' (*.grid)';
3436            '*.grid',  '.grid files '; ...
3437            '*.*', 'All Files (*.*)'}, ...
3438            'Pick a file',filebase);
3439        filegrid=fullfile(PathName,FileName);
3440        set(hObject,'UserData',filegrid);%store for future use
3441        if ~(isempty(FileName)||isempty(PathName)||isequal(FileName,0)||~exist(filegrid,'file'))
3442            testgrid=1;
3443        end
3444    end
3445end
3446if testgrid
3447    set(handle_dx,'Visible','off');
3448    set(handle_dy,'Visible','off');
3449    set(handle_title_dy,'Visible','off');
3450    set(handle_title_dx,'Visible','off');
3451    set(handle_txtbox,'Visible','on')
3452    set(handle_txtbox,'String',filegrid)
3453else
3454    set(hObject,'Value',0);
3455    set(handle_dx,'Visible','on');
3456    set(handle_dy,'Visible','on');
3457    set(handle_title_dy,'Visible','on');
3458    set(handle_title_dx,'Visible','on');
3459    set(handle_txtbox,'Visible','off')
3460end
3461
3462%% if hObject is on the checkciv1 frame, duplicate action for checkciv2 frame
3463PanelName=get(hparent,'tag');
3464if strcmp(PanelName,'Civ1')
3465    hchildren=get(handles.Civ2,'children');
3466    handle_checkbox=findobj(hchildren,'tag','CheckGrid');
3467    handle_txtbox=findobj(hchildren,'tag','txt_Grid');
3468    handle_dx=findobj(hchildren,'tag','num_Dx');
3469    handle_dy=findobj(hchildren,'tag','num_Dy');
3470    handle_title_dx=findobj(hchildren,'tag','title_Dx');
3471    handle_title_dy=findobj(hchildren,'tag','title_Dy');
3472    set(handle_checkbox,'UserData',filegrid);%store for future use
3473    if testgrid
3474        set(handle_checkbox,'Value',1);
3475        set(handle_dx,'Visible','off');
3476        set(handle_dy,'Visible','off');
3477        set(handle_title_dx,'Visible','off');
3478        set(handle_title_dy,'Visible','off');
3479        set(handle_txtbox,'Visible','on')
3480        set(handle_txtbox,'String',filegrid)
3481%     else
3482%         set(handle_checkbox,'Value',0);
3483%         set(handles.CheckGrid,'Value',0);
3484%         set(handle_dx,'Visible','on');
3485%         set(handle_dy,'Visible','on');
3486%          set(handle_title_dx,'Visible','on');
3487%         set(handle_title_dy,'Visible','on');
3488%         set(handle_txtbox,'Visible','off')
3489    end
3490end
3491
3492%------------------------------------------------------------------------
3493% --- Executes on button press in CheckMask: common to all panels (civ1, Civ2..)
3494function CheckMask_Callback(hObject, eventdata, handles)
3495%------------------------------------------------------------------------
3496value=get(hObject,'Value');
3497hparent=get(hObject,'parent');
3498parent_tag=get(hparent,'Tag');
3499hchildren=get(hparent,'children');
3500handle_txtbox=findobj(hchildren,'tag','Mask');% look for the mask name box in the same panel
3501testmask=0;
3502if value
3503    filebase=get(handles.RootPath,'String');
3504    [nbslice, flag_mask]=get_mask(filebase,handles);% look for a mask with appropriate name
3505    if isequal(flag_mask,1)
3506        filemask=[num2str(nbslice) 'mask'];
3507        testmask=1;
3508    else % browse for a mask
3509        filemask=get(hObject,'UserData');%look for previous mask name stored as UserData
3510        if exist(filemask,'file')
3511            filebase=filemask;
3512        end
3513        [FileName, PathName] = uigetfile( ...
3514            {'*.png', ' (*.png)';
3515            '*.png',  '.png files '; ...
3516            '*.*', 'All Files (*.*)'}, ...
3517            'Pick a mask file *.png',filebase);
3518        filemask=fullfile(PathName,FileName);
3519        set(hObject,'UserData',filemask);%store for future use
3520        if ~(isempty(FileName)||isempty(PathName)||isequal(FileName,0)||~exist(filemask,'file'))
3521            testmask=1;
3522        end
3523    end
3524end
3525if testmask
3526    if strcmp(parent_tag,'Civ1')
3527        set(handles.Mask,'Visible','on')
3528        set(handles.Mask,'String',filemask)
3529    set(handles.CheckMask,'Value',1)
3530    end
3531%     switch parent_tag
3532% %         case 'Fix1'
3533% %             stage=2;
3534%         case 'Civ2'
3535%              stage=3;
3536% %         case 'Fix2'
3537% %             stage=4;
3538%     end
3539%     set(handles.Mask(stage:end),'Visible','on')
3540%     set(handles.Mask(stage:end),'String',filemask)
3541%     set(handles.CheckMask(stage:end),'Value',1)
3542else
3543    set(hObject,'Value',0);
3544    set(handle_txtbox,'Visible','off')
3545end
3546
3547
3548% --- Executes on button press in get_gridpatch1.
3549function get_gridpatch1_Callback(hObject, eventdata, handles)
3550filebase=get(handles.RootPath,'String');
3551[FileName, PathName, filterindex] = uigetfile( ...
3552    {'*.grid', ' (*.grid)';
3553    '*.grid',  '.grid files '; ...
3554    '*.*', 'All Files (*.*)'}, ...
3555    'Pick a file',filebase);
3556filegrid=fullfile(PathName,FileName);
3557set(handles.grid_patch1,'string',filegrid);
3558
3559
3560%------------------------------------------------------------------------
3561% --- Executes on button press in get_gridpatch2.
3562function get_gridpatch2_Callback(hObject, eventdata, handles)
3563%------------------------------------------------------------------------
3564
3565
3566%------------------------------------------------------------------------
3567% --- STEREO Interp
3568function cmd=RUN_STINTERP(stinterpBin,filename_A_nc,filename_B_nc,filename_nc,nx_patch,ny_patch,rho_patch,subdomain_patch,thresh_value,xmlA,xmlB)
3569%------------------------------------------------------------------------
3570namelog=[filename_nc(1:end-3) '_stinterp.log'];
3571cmd=[stinterpBin ' -f1 ' filename_A_nc  ' -f2 ' filename_B_nc ' -f  ' filename_nc ...
3572    ' -m ' nx_patch  ' -n ' ny_patch ' -ro ' rho_patch ' -nopt ' subdomain_patch ' -c1 ' xmlA ' -c2 ' xmlB '  -xy  x -Nfy 1024 > ' namelog ' 2>&1']; % redirect standard output to the log file
3573
3574% %------------------------------------------------------------------------
3575% %--read images and convert them to the uint16 format used for PIV
3576% function A=read_image(filename,type_ima,num,movieobject)
3577% %------------------------------------------------------------------------
3578% %num is the view number needed for an avi movie
3579% switch type_ima
3580%     case 'movie'
3581%         A=read(movieobject,num);
3582%     case 'avi'
3583%         mov=aviread(filename,num);
3584%         A=frame2im(mov(1));
3585%     case 'multimage'
3586%         A=imread(filename,num);
3587%     case 'image'
3588%         A=imread(filename);
3589% end
3590% siz=size(A);
3591% if length(siz)==3;%color images
3592%     A=sum(double(A),3);
3593%     A=uint16(A);
3594% end
3595
3596
3597%------------------------------------------------------------------------
3598% --- Executes on button press in get_ref_fix1.
3599function get_ref_fix1_Callback(hObject, eventdata, handles)
3600%------------------------------------------------------------------------
3601filebase=get(handles.RootPath,'String');
3602[FileName, PathName, filterindex] = uigetfile( ...
3603    {'*.nc', ' (*.nc)';
3604    '*.nc',  'netcdf files '; ...
3605    '*.*', 'All Files (*.*)'}, ...
3606    'Pick a file',filebase);
3607
3608fileinput=[PathName FileName];
3609sizf=size(fileinput);
3610if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end %stop if fileinput not a character string
3611%[Path,File,field_count,str2,str_a,str_b,ref.ext,ref.nom_type,ref.subdir]=name2display(fileinput);
3612[Path,ref.subdir,File,ref.num1,ref.num2,ref.num_a,ref.num_b,ref.ext,ref.nom_type]=fileparts_uvmat(fileinput);
3613ref.filebase=fullfile(Path,File);
3614% ref.num_a=stra2num(str_a);
3615% ref.num_b=stra2num(str_b);
3616% ref.num1=str2double(field_count);
3617% ref.num2=str2double(str2);
3618browse=[];%initialisation
3619if ~isequal(ref.ext,'.nc')
3620    msgbox_uvmat('ERROR','the reference file must be in netcdf format (*.nc)')
3621    return
3622end
3623set(handles.ref_fix1,'String',[fullfile(ref.subdir,File) '....nc']);
3624set(handles.ref_fix1,'UserData',ref)
3625menu_field{1}='civ1';
3626Data=nc2struct(fileinput,[]);
3627if isfield(Data,'patch') && isequal(Data.patch,1)
3628    menu_field{2}='filter1';
3629end
3630if isfield(Data,'civ2') && isequal(Data.civ2,1)
3631    menu_field{3}='civ2';
3632end
3633if isfield(Data,'patch2') && isequal(Data.patch2,1)
3634    menu_field{4}='filter2';
3635end
3636set(handles.field_ref1,'String',menu_field);
3637set(handles.field_ref1,'Value',length(menu_field));
3638set(handles.num_MinVel,'Value',2);
3639set(handles.num_MinVel,'String','1');%default threshold
3640set(handles.ref_fix1,'Enable','on')
3641
3642%------------------------------------------------------------------------
3643% --- Executes on button press in get_ref_fix2.
3644function get_ref_fix2_Callback(hObject, eventdata, handles)
3645%------------------------------------------------------------------------
3646if isequal(get(handles.get_ref_fix2,'Value'),1)
3647    filebase=get(handles.RootPath,'String');
3648    [FileName, PathName, filterindex] = uigetfile( ...
3649        {'*.nc', ' (*.nc)';
3650        '*.nc',  'netcdf files '; ...
3651        '*.*', 'All Files (*.*)'}, ...
3652        'Pick a file',filebase);
3653    fileinput=[PathName FileName];
3654    sizf=size(fileinput);
3655    if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end %stop if fileinput not a character string
3656    %[Path,File,field_count,str2,str_a,str_b,ref.ext,ref.nom_type,ref.subdir]=name2display(fileinput);
3657    [Path,ref.subdir,File,ref.num1,ref.num2,ref.num_a,ref.num_b,ref.ext,ref.nom_type]=fileparts_uvmat(fileinput);
3658    ref.filebase=fullfile(Path,File);
3659%     ref.num_a=stra2num(str_a);
3660%     ref.num_b=stra2num(str_b);
3661%     ref.num1=str2num(field_count);
3662%     ref.num2=str2num(str2);
3663    browse=[];%initialisation
3664    if ~isequal(ref.ext,'.nc')
3665        msgbox_uvmat('ERROR','the reference file must be in netcdf format (*.nc)')
3666        return
3667    end
3668    set(handles.ref_fix2,'String',[fullfile(ref.subdir,File) '....nc']);
3669    set(handles.ref_fix2,'UserData',ref)
3670    menu_field{1}='civ1';
3671    Data=nc2struct(fileinput,[]);
3672    if isfield(Data,'patch') && isequal(Data.patch,1)
3673        menu_field{2}='filter1';
3674    end
3675    if isfield(Data,'civ2') && isequal(Data.civ2,1)
3676        menu_field{3}='civ2';
3677    end
3678    if isfield(Data,'patch2') && isequal(Data.patch2,1)
3679        menu_field{4}='filter2';
3680    end
3681    set(handles.field_ref2,'String',menu_field);
3682    set(handles.field_ref2,'Value',length(menu_field));
3683    set(handles.num_MinVel,'Value',2);
3684    set(handles.num_MinVel,'String','1');%default threshold
3685    set(handles.ref_fix2,'Enable','on')
3686    set(handles.ref_fix2,'Visible','on')
3687    set(handles.field_ref2,'Visible','on')
3688else
3689    set(handles.ref_fix2,'Visible','off')
3690    set(handles.field_ref2,'Visible','off')
3691end
3692
3693%------------------------------------------------------------------------
3694function ref_fix1_Callback(hObject, eventdata, handles)
3695%------------------------------------------------------------------------
3696set(handles.num_MinVel,'Value',1);
3697set(handles.field_ref1,'Value',1)
3698set(handles.field_ref1,'String',{' '})
3699set(handles.ref_fix1,'UserData',[]);
3700set(handles.ref_fix1,'String','');
3701set(handles.thresh_vel1,'String','0');
3702
3703%------------------------------------------------------------------------
3704function ref_fix2_Callback(hObject, eventdata, handles)
3705%------------------------------------------------------------------------
3706set(handles.num_MinVel,'Value',1);
3707set(handles.field_ref2,'Value',1)
3708set(handles.field_ref2,'String',{' '})
3709set(handles.ref_fix2,'UserData',[]);
3710set(handles.ref_fix2,'String','');
3711set(handles.num_MinVel,'String','0');
3712
3713%------------------------------------------------------------------------
3714% --- TO ABANDON Executes on button press in test_stereo1.
3715function CheckStereo_Callback(hObject, eventdata, handles)
3716%------------------------------------------------------------------------
3717hparent=get(hObject,'parent');
3718parent_tag=get(hparent,'Tag');
3719hchildren=get(hparent,'children');
3720handle_txtbox=findobj(hchildren,'tag','txt_Mask');
3721if isequal(get(hObject,'Value'),0)
3722    set(handles.num_SubdomainSize,'Visible','on')
3723    set(handles.num_FieldSmooth,'Visible','on')
3724else
3725    set(handles.num_SubdomainSize,'Visible','off')
3726    set(handles.num_FieldSmooth,'Visible','off')
3727end
3728
3729% %------------------------------------------------------------------------
3730% % --- Executes on button press in CheckStereo.
3731% function StereoCheck_Callback(hObject, eventdata, handles)
3732% %------------------------------------------------------------------------
3733% if isequal(get(handles.CheckStereo,'Value'),0)
3734%     set(handles.num_SubdomainSize,'Visible','on')
3735%     set(handles.num_FieldSmooth,'Visible','on')
3736% else
3737%     set(handles.num_SubdomainSize,'Visible','off')
3738%     set(handles.num_FieldSmooth,'Visible','off')
3739% end
3740
3741%------------------------------------------------------------------------
3742% --- Executes on button press in TestCiv1: prepare the image correlation function
3743% activated by mouse motion
3744function TestCiv1_Callback(hObject, eventdata, handles)
3745%------------------------------------------------------------------------
3746drawnow
3747if get(handles.TestCiv1,'Value')
3748    set(handles.TestCiv1,'BackgroundColor',[0.7 0.7 0.7])% paint TestCiv1 button to grey to confirm civ launch
3749    ref_i=str2double(get(handles.ref_i,'String'));% read reference i index
3750    if strcmp(get(handles.ref_j,'Visible'),'on')
3751        ref_j=str2double(get(handles.ref_j,'String'));% read reference j index if relevant
3752    else
3753        ref_j=1;%default j index
3754    end
3755    [filecell,i1,i2]=set_civ_filenames(handles,ref_i,ref_j,[1 0 0 0 0 0]);% get the corresponding file name and indices
3756    Data.ListVarName={'ny','nx','A'};
3757    Data.VarDimName= {'ny','nx',{'ny','nx'}};
3758
3759    Data.A=imread(filecell.ima1.civ1{1}); % read the first image
3760    if ndims(Data.A)==3 %case of color image
3761        Data.VarDimName= {'ny','nx',{'ny','nx','rgb'}};
3762    end
3763    Data.ny=[size(Data.A,1) 1];
3764    Data.nx=[1 size(Data.A,2)];
3765    Data.CoordUnit='pixel';% used to set equal scaling for x and y in image dispaly
3766    par_civ1=read_GUI(handles.Civ1);
3767    par_civ1.FileTypeA=get_file_type(filecell.ima1.civ1{1});
3768    par_civ1.ImageWidth=size(Data.A,2);
3769    par_civ1.ImageHeight=size(Data.A,1);
3770    par_civ1.Mask='all';% will provide only the grid set for PIV, no image correlation
3771    par_civ1.FrameIndexA=num2str(i1);
3772    par_civ1.FrameIndexB=num2str(i2);
3773    Param.Civ1=par_civ1;
3774    Grid=civ_matlab(Param);% get the grid of x, y positions set for PIV
3775    hview_field=view_field(Data); %view the image in the GUI view_field
3776    set(0,'CurrentFigure',hview_field)
3777    hhview_field=guihandles(hview_field);
3778    set(hview_field,'CurrentAxes',hhview_field.PlotAxes)
3779    ViewData=get(hview_field,'UserData');
3780    ViewData.CivHandle=handles.civ;% indicate the handle of the civ GUI in view_field
3781    ViewData.PlotAxes.B=imread(filecell.ima2.civ1{1});%store the second image in the UserData of the GUI view_field
3782    ViewData.PlotAxes.X=Grid.Civ1_X; %keep the set of points in memeory
3783    ViewData.PlotAxes.Y=Grid.Civ1_Y;
3784    set(hview_field,'UserData',ViewData)
3785    corrfig=findobj(allchild(0),'tag','corrfig');% look for a current figure for image correlation display
3786    if isempty(corrfig)
3787        corrfig=figure;
3788        set(corrfig,'tag','corrfig')
3789        set(corrfig,'name','image correlation')
3790        set(corrfig,'DeleteFcn',{@closeview_field})%
3791    end
3792    set(handles.TestCiv1,'BackgroundColor',[1 0 0])
3793else
3794    set(handles.TestCiv1,'BackgroundColor',[1 0 0])% paint button to red
3795    corrfig=findobj(allchild(0),'tag','corrfig');% look for a current figure for image correlation display
3796    if ~isempty(corrfig)
3797        delete(corrfig)
3798    end
3799    hview_field=findobj(allchild(0),'tag','view_field');% look for view_field   
3800    if ~isempty(hview_field)
3801        delete(hview_field)
3802    end
3803end
3804
3805%------------------------------------------------------------------------
3806%----function introduced for the correlation window figure, activated by deleting this window
3807function closeview_field(gcbo,eventdata)
3808%------------------------------------------------------------------------
3809hview_field=findobj(allchild(0),'tag','view_field');% look for view_field
3810if ~isempty(hview_field)
3811    delete(hview_field)
3812end
3813
3814%------------------------------------------------------------------------
3815% --- Executes on button press in CheckThreshold.
3816function CheckThreshold_Callback(hObject, eventdata, handles)
3817%------------------------------------------------------------------------
3818huipanel=get(hObject,'parent');
3819obj(1)=findobj(huipanel,'Tag','num_MinIma');
3820obj(2)=findobj(huipanel,'Tag','num_MaxIma');
3821obj(3)=findobj(huipanel,'Tag','title_Threshold');
3822if get(hObject,'Value')
3823    set(obj,'Visible','on')
3824else
3825    set(obj,'Visible','off')
3826end
3827
3828
3829
3830
3831%'nomtype2pair': creates nomencalture for index pairs knowing the image nomenclature
3832%---------------------------------------------------------------------
3833function NomTypeNc=nomtype2pair(NomTypeIma,mode)
3834%---------------------------------------------------------------------           
3835% OUTPUT:
3836% NomTypeNc
3837%---------------------------------------------------------------------
3838% INPUT:
3839% 'NomTypeIma': string defining the kind of nomenclature used for images
3840
3841NomTypeNc=NomTypeIma;%default
3842switch mode
3843    case 'pair j1-j2'     
3844    if ~isempty(regexp(NomTypeIma,'a$'))
3845        NomTypeNc=[NomTypeIma 'b'];
3846    elseif ~isempty(regexp(NomTypeIma,'A$'))
3847        NomTypeNc=[NomTypeIma 'B'];
3848    else
3849        r=regexp(NomTypeIma,'(?<num1>\d+)_(?<num2>\d+)$','names');
3850        if ~isempty(r)
3851            NomTypeNc='_1_1-2';
3852        end
3853    end
3854    case 'series(Dj)' 
3855%         r=regexp(NomTypeIma,'(?<num1>\d+)_(?<num2>\d+)$','names');
3856%         if ~isempty(r)
3857            NomTypeNc='_1_1-2';
3858%         end
3859   case 'series(Di)'
3860        r=regexp(NomTypeIma,'(?<num1>\d+)_(?<num2>\d+)$','names');
3861        if ~isempty(r)
3862            NomTypeNc='_1-2_1';
3863        else
3864            NomTypeNc='_1-2';
3865        end
3866end
3867
3868function NomType_Callback(hObject, eventdata, handles)
3869set(handles.RootPath,'BackgroundColor',[1 1 0])%paint RootName edit box in yellow to indicate that the file input is proceeding
3870RootPath=get(handles.RootPath,'String');
3871RootFile=get(handles.RootFile,'String');
3872SubDirImages=get(handles.SubDirImages,'String');
3873ref_i=str2num(get(handles.ref_i,'String'));
3874ref_j=str2num(get(handles.ref_j,'String'));
3875NomType=get(handles.NomType,'String');
3876ImaExt=get(handles.ImaExt,'String');
3877fileinput=fullfile_uvmat(RootPath,SubDirImages,RootFile,ImaExt,NomType,ref_i,[],ref_j);
3878errormsg=display_file_name(handles,fileinput);
3879if ~isempty(errormsg)
3880    msgbox_uvmat('ERROR',errormsg)
3881end
3882set(handles.RootPath,'BackgroundColor',[1 1 1])%paint RootName back to white to indicate that the file input is finished
3883
3884% --- Executes on selection change in Program.
3885function Program_Callback(hObject, eventdata, handles)
3886ListProgram=get(handles.Program,'String');
3887Program=ListProgram{get(handles.Program,'value')};
3888switch Program
3889    case 'CivX'
3890        set(handles.num_MaxDiff,'Visible','off')
3891        set(handles.num_MaxVel,'Visible','off')
3892        set(handles.title_MaxVel,'Visible','off')
3893        set(handles.num_Nx,'Visible','on')
3894        set(handles.num_Ny,'Visible','on')
3895        set(handles.title_Nx,'Visible','on')
3896        set(handles.title_Ny,'Visible','on')
3897        set(handles.title_MaxDiff,'Visible','off')
3898        set(handles.num_CorrSmooth,'Style','edit')
3899        set(handles.num_CorrSmooth,'String','1')
3900        set(handles.BATCH,'Enable','on')
3901        set(handles.CheckThreshold,'Visible','off')
3902        set(handles.CheckDeformation,'Value',1)
3903        set(handles.CheckDecimal,'Value',1)
3904    case {'civ_matlab','civ_matlab.sh'}
3905        set(handles.num_MaxDiff,'Visible','on')
3906        set(handles.num_MaxVel,'Visible','on')
3907        set(handles.title_MaxVel,'Visible','on')
3908        set(handles.title_MaxDiff,'Visible','on')
3909        set(handles.num_Nx,'Visible','off')
3910        set(handles.num_Ny,'Visible','off')
3911        set(handles.title_Nx,'Visible','off')
3912        set(handles.title_Ny,'Visible','off')
3913        set(handles.num_CorrSmooth,'Style','popupmenu')
3914        set(handles.num_CorrSmooth,'Value',1)
3915        set(handles.num_CorrSmooth,'String',{'1';'2'})
3916        set(handles.CheckThreshold,'Visible','on')
3917        set(handles.CheckDeformation,'Value',0)% desactivate (work in progress)
3918        set(handles.CheckDecimal,'Value',0)% desactivate (work in progress)
3919end
3920
3921% --- Executes on button press in TestPatch1.
3922function TestPatch1_Callback(hObject, eventdata, handles)
3923set(handles.TestPatch1,'BackgroundColor',[1 1 0])
3924drawnow
3925if get(handles.TestPatch1,'Value')
3926    ref_i=str2double(get(handles.ref_i,'String'));
3927    if strcmp(get(handles.ref_j,'Visible'),'on')
3928        ref_j=str2double(get(handles.ref_j,'String'));
3929    else
3930        ref_j=1;%default
3931    end
3932    filecell=set_civ_filenames(handles,ref_i,ref_j,[0 0 1 0 0 0]);   
3933    Data.ListVarName={'ny','nx','A'};
3934    Data.VarDimName= {'ny','nx',{'ny','nx'}};   
3935    param_patch1=read_GUI(handles.Patch1);
3936    param_patch1.CivFile=filecell.nc.civ1{1};
3937    Param.Patch1=param_patch1;
3938    for irho=1:7
3939        [Data,errormsg]=civ_matlab(Param);% get the grid of x, y positions set for PIV
3940        if ~isempty(errormsg)
3941            msgbox_uvmat('ERROR',errormsg)
3942            return
3943        end
3944        SmoothingParam(irho)=Param.Patch1.FieldSmooth;
3945        Data.Civ1_U_Diff=Data.Civ1_U_Diff(Data.Civ1_FF==0);
3946        Data.Civ1_V_Diff=Data.Civ1_V_Diff(Data.Civ1_FF==0);
3947        DiffVel(irho)=sqrt(mean(Data.Civ1_U_Diff.*Data.Civ1_U_Diff+Data.Civ1_V_Diff.*Data.Civ1_V_Diff))
3948        NbSites(irho,:)=Data.Civ1_NbSites*numel(Data.Civ1_NbSites)/numel(Data.Civ1_U_Diff);
3949        Param.Patch1.SmoothingParam=2*Param.Patch1.FieldSmooth;
3950    end
3951    figure
3952    plot(SmoothingParam,DiffVel,'b',SmoothingParam,NbSites,'r')
3953    set(handles.TestPatch1,'BackgroundColor',[1 0 0])
3954else
3955    corrfig=findobj(allchild(0),'tag','corrfig');% look for a current figure for image correlation display
3956    if ~isempty(corrfig)
3957        delete(corrfig)
3958    end
3959    hview_field=findobj(allchild(0),'tag','view_field');% look for view_field
3960    if ~isempty(hview_field)
3961        delete(hview_field)
3962    end
3963end
3964
3965
3966% --- Executes on button press in TestCiv2.
3967function TestCiv2_Callback(hObject, eventdata, handles)
3968
3969function RootFile_Callback(hObject, eventdata, handles)
3970
3971function SubDirImages_Callback(hObject, eventdata, handles)
3972
3973
3974
3975function errormsg=write_param(Param)
3976%------------------------------------------------------------------------
3977%pixels per cm and matrix of the image times, read from the .civ file by uvmat
3978%changes : filename_cmx -> filename ( no extension )
3979errormsg='';
3980switch Param.Program
3981    case 'CivX'
3982        if Param.CheckCiv1
3983            filename=regexprep(Param.OutputFile,'(.+)([/\\])(.+$)','$1$20_CMX$2$3.civ1.cmx');
3984            if isequal(Param.Civ1.Dt,0)
3985                Param.Civ1.Dt=1 ;%case of 'displacement' mode
3986            end
3987            Param.Civ1.ImageA=regexprep(Param.Civ1.ImageA,'.png','');
3988            Param.Civ1.ImageB=regexprep(Param.Civ1.ImageB,'.png','');
3989            [fid,errormsg]=fopen(filename,'w');
3990            if isequal(fid,-1)
3991                errormsg=['cmd file ' filename ' cannot be created: ' errormsg];
3992                return
3993            end
3994            fprintf(fid,['##############   CMX file' '\n' ]);
3995            fprintf(fid,   ['FirstImage ' regexprep(Param.Civ1.ImageA,'\\','\\\\') '\n' ]);% for windows compatibility
3996            fprintf(fid,   ['LastImage  ' regexprep(Param.Civ1.ImageB,'\\','\\\\') '\n' ]);% for windows compatibility
3997            fprintf(fid,  ['XX' '\n' ]);
3998            if isfield(Param.Civ1,'Mask')
3999                fprintf(fid,  ['Mask ' 'y' '\n' ]);
4000                fprintf(fid,  ['MaskName ' regexprep(Param.Civ1.Mask,'\\','\\\\') '\n' ]);
4001            else
4002                fprintf(fid,  ['Mask ' 'n' '\n' ]);
4003                fprintf(fid,  ['MaskName ' 'noFile use default' '\n' ]);
4004            end
4005            fprintf(fid,   ['ImageSize ' num2str(Param.Civ1.ImageWidth) ' ' num2str(Param.Civ1.ImageHeight) '\n' ]);   %VERIFIER CAS GENERAL ?
4006            fprintf(fid,   ['CorrelationBoxesSize ' num2str(Param.Civ1.CorrBoxSize(1)) ' ' num2str(Param.Civ1.CorrBoxSize(2)) '\n' ]);
4007            fprintf(fid,   ['SearchBoxeSize ' num2str(Param.Civ1.SearchBoxSize(1)) ' ' num2str(Param.Civ1.SearchBoxSize(2)) '\n' ]);
4008            fprintf(fid,   ['RO ' num2str(Param.Civ1.CorrSmooth) '\n' ]);
4009            if isfield(Param.Civ1,'Grid')
4010                fprintf(fid,   ['GridSpacing ' '25' ' ' '25' '\n' ]);
4011            else
4012                fprintf(fid,   ['GridSpacing ' num2str(Param.Civ1.Dx) ' ' num2str(Param.Civ1.Dy) '\n' ]);
4013            end
4014            fprintf(fid,   ['XX 1.0' '\n' ]);
4015            fprintf(fid,   ['Dt_TO ' num2str(Param.Civ1.Dt) ' ' num2str(Param.Civ1.Time) '\n' ]);
4016            fprintf(fid,  ['PixCmXY ' '1' ' ' '1' '\n' ]);
4017            fprintf(fid,  ['XX 1' '\n' ]);
4018            fprintf(fid,   ['ShiftXY ' num2str(Param.Civ1.SearchBoxShift(1)) ' '  num2str(Param.Civ1.SearchBoxShift(2)) '\n' ]);
4019            if isfield(Param.Civ1,'Grid')
4020                fprintf(fid,  ['Grid ' 'y' '\n' ]);
4021                fprintf(fid,   ['GridName ' regexprep(Param.Civ1.Grid,'\\','\\\\') '\n' ]);
4022            else
4023                fprintf(fid,  ['Grid ' 'n' '\n' ]);
4024                fprintf(fid,   ['GridName ' 'noFile use default' '\n' ]);
4025            end
4026            fprintf(fid,   ['XX 85' '\n' ]);
4027            fprintf(fid,   ['XX 1.0' '\n' ]);
4028            fprintf(fid,   ['XX 1.0' '\n' ]);
4029            fprintf(fid,   ['Hart 1' '\n' ]);
4030            fprintf(fid,  [ 'DecimalShift 0' '\n' ]);
4031            fprintf(fid,   ['Deformation 0' '\n' ]);
4032            fprintf(fid,  ['CorrelationMin 0' '\n' ]);
4033            fprintf(fid,   ['IntensityMin 0' '\n' ]);
4034            if ~isfield(Param.Civ1,'MinIma')% Image threshold not activated
4035                fprintf(fid,  ['SeuilImage n' '\n' ]);
4036                fprintf(fid,   ['SeuilImageValues 0 4096' '\n' ]);%not used in principle
4037            else% Image threshold  activated
4038                if isempty(Param.Civ1.MaxIma)||isnan(Param.Civ1.MaxIma)
4039                    Param.Civ1.MaxIma=2^Param.Civ1.ImageBitDepth;%take the max image value as upper bound by default
4040                end
4041                fprintf(fid,  ['SeuilImage y' '\n' ]);
4042                fprintf(fid,   ['SeuilImageValues ' num2str(Param.Civ1.MinIma) ' ' num2str(Param.Civ1.MaxIma) '\n' ]);
4043            end
4044            fprintf(fid,   ['ImageToUse ' Param.Civ1.term_a ' ' Param.Civ1.term_b '\n' ]); % VERIFIER ?
4045            fprintf(fid,   ['ImageUsedBefore null null' '\n' ]);
4046            fclose(fid);
4047        end
4048       
4049        if Param.CheckCiv2
4050            filename=regexprep(Param.OutputFile,'(.+)([/\\])(.+$)','$1$20_CMX$2$3.civ2.cmx');
4051
4052            if isequal(Param.Civ2.Dt,'0')
4053                Param.Civ2.Dt='1' ;%case of 'displacement' mode
4054            end
4055            Param.Civ2.ImageA=regexprep(Param.Civ2.ImageA,'.png','');
4056            Param.Civ2.ImageB=regexprep(Param.Civ2.ImageB,'.png','');% bug : .png appears two times ?
4057            [fid,errormsg]=fopen(filename,'w');
4058            if isequal(fid,-1)
4059                return
4060            end
4061            fprintf(fid,['##############   CMX file' '\n' ]);
4062            fprintf(fid,   ['FirstImage ' regexprep(Param.Civ2.ImageA,'\\','\\\\') '\n' ]);% for windows compatibility
4063            fprintf(fid,   ['LastImage  ' regexprep(Param.Civ2.ImageB,'\\','\\\\') '\n' ]);% for windows compatibility
4064            fprintf(fid,  ['XX' '\n' ]);
4065            if isfield(Param.Civ2,'Mask')
4066                fprintf(fid,  ['Mask ' 'y' '\n' ]);
4067                fprintf(fid,  ['MaskName ' regexprep(Param.Civ2.Mask,'\\','\\\\') '\n' ]);
4068            else
4069                fprintf(fid,  ['Mask ' 'n' '\n' ]);
4070                fprintf(fid,  ['MaskName ' 'noFile use default' '\n' ]);
4071            end
4072            % fprintf(fid, ['Mask ' Param.Civ2.MaskFlag '\n' ]);
4073            % fprintf(fid, ['MaskName ' regexprep(Param.Civ2.MaskName,'\\','\\\\') '\n' ]);% for windows compatibility
4074            fprintf(fid,   ['ImageSize ' num2str(Param.Civ2.ImageWidth) ' ' num2str(Param.Civ2.ImageHeight) '\n' ]);
4075            % fprintf(fid, ['ImageSize ' num2str(Param.Civ2.npx) ' ' num2str(Param.Civ2.npy) '\n' ]);   %VERIFIER CAS GENERAL ?
4076            fprintf(fid, ['CorrelationBoxesSize ' num2str(Param.Civ2.CorrBoxSize(1)) ' ' num2str(Param.Civ2.CorrBoxSize(2)) '\n' ]);
4077            fprintf(fid, ['SearchBoxeSize ' num2str(Param.Civ2.CorrBoxSize(1)) ' ' num2str(Param.Civ2.CorrBoxSize(2)) '\n']);
4078            fprintf(fid, ['RO ' num2str(Param.Civ2.CorrSmooth) '\n']);
4079            if isfield(Param.Civ2,'Grid')
4080                fprintf(fid,   ['GridSpacing ' '25' ' ' '25' '\n' ]);
4081            else
4082                fprintf(fid,   ['GridSpacing ' num2str(Param.Civ2.Dx) ' ' num2str(Param.Civ2.Dy) '\n' ]);
4083            end
4084            % fprintf(fid, ['GridSpacing ' num2str(Param.Civ2.Dx) ' ' num2str(Param.Civ2.Dy) '\n']);
4085            fprintf(fid, ['XX 1.0' '\n' ]);
4086            fprintf(fid, ['Dt_TO ' num2str(Param.Civ2.Dt) ' ' num2str(Param.Civ2.Time) '\n' ]);
4087            fprintf(fid, ['PixCmXY ' '1' ' ' '1' '\n' ]);
4088            fprintf(fid, ['XX 1' '\n' ]);
4089            fprintf(fid, 'ShiftXY 0 0\n');
4090            if isfield(Param.Civ2,'Grid')
4091                fprintf(fid,  ['Grid ' 'y' '\n' ]);
4092                fprintf(fid,   ['GridName ' regexprep(Param.Civ2.Grid,'\\','\\\\') '\n' ]);
4093            else
4094                fprintf(fid,  ['Grid ' 'n' '\n' ]);
4095                fprintf(fid,   ['GridName ' 'noFile use default' '\n' ]);
4096            end
4097            % fprintf(fid, ['Grid ' Param.Civ2.GridFlag '\n' ]);
4098            % fprintf(fid, ['GridName ' regexprep(Param.Civ2.GridName,'\\','\\\\') '\n']);
4099            fprintf(fid, ['XX 85' '\n' ]);
4100            fprintf(fid, ['XX 1.0' '\n' ]);
4101            fprintf(fid, ['XX 1.0' '\n' ]);
4102            fprintf(fid, ['Hart 1' '\n' ]);
4103            fprintf(fid, ['DecimalShift ' num2str(Param.Civ2.CheckDecimal) '\n']);
4104            fprintf(fid, ['Deformation ' num2str(Param.Civ2.CheckDeformation) '\n']);
4105            fprintf(fid,  ['CorrelationMin 0' '\n' ]);
4106            fprintf(fid,   ['IntensityMin 0' '\n' ]);
4107           
4108            if ~isfield(Param.Civ2,'MinIma')% Image threshold not activated
4109                fprintf(fid,  ['SeuilImage n' '\n' ]);
4110                fprintf(fid,   ['SeuilImageValues 0 4096' '\n' ]);%not used in principle
4111            else% Image threshold  activated
4112                if isempty(Param.Civ2.MaxIma)||isnan(Param.Civ2.MaxIma)
4113                    Param.Civ2.MaxIma=2^Param.Civ2.ImageBitDepth;%take the max image value as upper bound by default
4114                end
4115                fprintf(fid,  ['SeuilImage y' '\n' ]);
4116                fprintf(fid,   ['SeuilImageValues ' num2str(Param.Civ2.MinIma) ' ' num2str(Param.Civ2.MaxIma) '\n' ]);
4117            end
4118            fprintf(fid,   ['ImageToUse ' Param.Civ2.term_a ' ' Param.Civ2.term_b '\n' ]); % VERIFIER ?
4119            fprintf(fid, ['ImageUsedBefore ' regexprep(Param.Civ2.filename_nc1,'\\','\\\\') '\n']);
4120            fclose(fid);
4121        end
4122    case {'civ_matlab','civ_matlab.sh'}
4123        filename=regexprep(Param.OutputFile,'(.+)([/\\])(.+$)','$1$20_XML$2$3.xml');
4124        save(struct2xml(Param),filename);
4125end
4126
4127
4128function cmd=write_cmd(Param)
4129
4130% initiate system command
4131cmd=[];
4132
4133switch Param.Program
4134    case 'CivX'
4135        if isunix % check: necessaire aussi en RUN?
4136            cmd=[cmd '#!/bin/bash \n'...
4137                '#$ -cwd \n'...
4138                'hostname && date \n'...
4139                'umask 002 \n'];%allow writting access to created files for user group
4140        end
4141    case 'CivAll'
4142        if isunix % check: necessaire aussi en RUN?
4143            cmd=[cmd '#!/bin/bash \n'...
4144                '#$ -cwd \n'...
4145                'hostname && date \n'...
4146                'umask 002 \n'];%allow writting access to created files for user group
4147        end
4148end
4149
4150filename=regexprep(Param.OutputFile,'.nc','');
4151
4152if Param.CheckCiv1
4153    switch Param.Program
4154        case 'CivX'
4155            if(isunix) %unix (or Mac) system
4156                cmd=[cmd 'cp -f ' regexprep(filename,'(.+)/(.+$)','$1/0_CMX/$2.civ1.cmx ') regexprep(filename,'(.+)/(.+$)','$1/$2.cmx \n')...% the cmx file gives the name to the nc file
4157                    Param.xml.Civ1Bin ' -f ' regexprep(filename,'(.+)/(.+$)','$1/$2.cmx >') regexprep(filename,'(.+)/(.+$)','$1/0_LOG/$2.civ1.log \n')... % redirect standard output to the log file, the result file is named [filename '.nc'] by CIVx
4158                    'rm ' regexprep(filename,'(.+)/(.+$)','$1/$2.cmx \n')];
4159            else %Windows system
4160                filename=regexprep(filename,'\\','\\\\');
4161                cmd=['copy /Y ' regexprep(filename,'(.+)\\\\(.+$)','"$1\\\\0_CMX\\\\$2.civ1.cmx" ') regexprep(filename,'(.+)\\\\(.+$)','"$1\\\\$2.cmx" \n')...
4162                    '"' regexprep(Param.xml.Civ1Bin,'\\','\\\\') '" -f ' regexprep(filename,'(.+)\\\\(.+$)','"$1\\\\$2.cmx" > ')...
4163                    regexprep(filename,'(.+)\\\\(.+$)','"$1\\\\0_LOG\\\\$2.civ1.log" \n')... % redirect standard output to the log file
4164                    'del ' regexprep(filename,'(.+)\\\\(.+$)','"$1\\\\$2.cmx" \n')];
4165            end
4166        case 'CivAll'
4167            CivAllCmd=[CivAllCmd ' civ1 '];
4168            str=CIV1_CMD_Unified(filecell.nc.civ1{ifile,j},'',Param.Civ1);
4169            fieldnames=fields(str);
4170            [CivAllxml,uid_civ1]=add(CivAllxml,1,'element','civ1');
4171            for ilist=1:length(fieldnames)
4172                val=eval(['str.' fieldnames{ilist}]);
4173                if ischar(val)
4174                    [CivAllxml,uid_t]=add(CivAllxml,uid_civ1,'element',fieldnames{ilist});
4175                    [CivAllxml,uid_t2]=add(CivAllxml,uid_t,'chardata',val);
4176                end
4177            end
4178    end
4179end
4180
4181if Param.CheckFix1
4182    switch Param.Program
4183        case 'CivX'
4184            cmd=[cmd...
4185                cmd_fix(Param,'Fix1') '\n'];
4186        case 'CivAll'%to abandon
4187            fix1.inputFileName=filecell.nc.civ1{ifile,j} ;
4188            fix1.fi1=num2str(param.fix1.flagindex1(1));
4189            fix1.fi2=num2str(param.fix1.flagindex1(2));
4190            fix1.fi3=num2str(param.fix1.flagindex1(3));
4191            fix1.threshC=num2str(param.fix1.thresh_vecC1);
4192            fix1.threshV=num2str(param.fix1.thresh_vel1);
4193            fieldnames=fields(fix1);
4194            [CivAllxml,uid_fix1]=add(CivAllxml,1,'element','fix1');
4195            for ilist=1:length(fieldnames)
4196                val=eval(['fix1.' fieldnames{ilist}]);
4197                if ischar(val)
4198                    [CivAllxml,uid_t]=add(CivAllxml,uid_fix1,'element',fieldnames{ilist});
4199                    [CivAllxml,uid_t2]=add(CivAllxml,uid_t,'chardata',val);
4200                end
4201            end
4202            CivAllCmd=[CivAllCmd ' fix1 '];
4203    end
4204end
4205
4206
4207%CheckPatch1
4208if Param.CheckPatch1
4209    switch Param.Program
4210        case 'CivX'
4211            cmd=[cmd...
4212                cmd_patch(Param,'Patch1') '\n'];
4213        case 'CivAll'
4214            patch1.inputFileName=filecell.nc.civ1{ifile,j} ;
4215            patch1.nopt=subdomain_patch1;
4216            patch1.maxdiff=thresh_patch1;
4217            patch1.ro=rho_patch1;
4218            test_grid=get(handles.get_gridpatch1,'Value');
4219            if test_grid
4220                patch1.gridflag='y';
4221                gridname=get(handles.grid_patch1,'String');
4222                if isequal(gridname(end-3:end),'grid')
4223                    nbslice_grid=str2double(gridname(1:end-4)); %
4224                    if ~isnan(nbslice_grid)
4225                        i1_grid=mod(i1_civ1(ifile)-1,nbslice_grid)+1;
4226                        patch1.gridPatch=[filecell.filebase '_' fullfile_uvmat('','',gridname,'.grid','_1',i1_grid)];
4227                        %                                 patch1.gridPatch=[filecell.filebase '_' name_generator(gridname,i1_grid,1,'.grid','_i')];
4228                        if ~exist(patch1.gridPatch,'file')
4229                            errormsg='grid file absent for patch1';
4230                            return
4231                        end
4232                    elseif exist(gridname,'file')
4233                        patch1.gridPatch=gridname;
4234                    else
4235                        errormsg='grid file absent for patch1';
4236                        return
4237                    end
4238                end
4239            else
4240                patch1.gridPatch='none';
4241                patch1.gridflag='n';
4242                patch1.m=nx_patch1;
4243                patch1.n=ny_patch1;
4244            end
4245            patch1.convectFlow='n';
4246            fieldnames=fields(patch1);
4247            [CivAllxml,uid_patch1]=add(CivAllxml,1,'element','patch1');
4248            for ilist=1:length(fieldnames)
4249                val=eval(['patch1.' fieldnames{ilist}]);
4250                if ischar(val)
4251                    [CivAllxml,uid_t]=add(CivAllxml,uid_patch1,'element',fieldnames{ilist});
4252                    [CivAllxml,uid_t2]=add(CivAllxml,uid_t,'chardata',val);
4253                end
4254            end
4255            CivAllCmd=[CivAllCmd ' patch1 '];
4256    end
4257end
4258
4259if Param.CheckCiv2
4260    switch Param.Program
4261        case 'CivX'
4262            if(isunix)
4263                cmd=[cmd 'cp -f '  regexprep(filename,'(.+)/(.+$)','$1/0_CMX/$2.civ2.cmx ') regexprep(filename,'(.+)/(.+$)','$1/$2.cmx \n')...
4264                    Param.xml.Civ2Bin ' -f ' regexprep(filename,'(.+)/(.+$)','$1/$2.cmx >') regexprep(filename,'(.+)/(.+$)','$1/0_LOG/$2.civ2.log \n')...% redirect standard output to the log file, the result file is named [filename '.nc'] by CIVx
4265                    'rm ' regexprep(filename,'(.+)/(.+$)','$1/$2.cmx \n')];%rename .cmx as .checkciv2.cmx, the result file is named [filename '.nc'] by CIVx
4266            else
4267                filename=regexprep(Param.OutputFile,'.nc','');
4268                filename=regexprep(filename,'\\','\\\\');
4269                cmd=[cmd 'copy /Y ' regexprep(filename,'(.+)\\\\(.+$)','"$1\\\\0_CMX\\\\$2.civ2.cmx" ') regexprep(filename,'(.+)\\\\(.+$)','"$1\\\\$2.cmx" \n')...
4270                    '"' regexprep(Param.xml.Civ2Bin,'\\','\\\\') '" -f ' regexprep(filename,'(.+)\\\\(.+$)','"$1\\\\$2.cmx" > ')...
4271                     regexprep(filename,'(.+)\\\\(.+$)','"$1\\\\0_LOG\\\\$2.civ2.log" \n')... % redirect standard output to the log file
4272                    'del ' regexprep(filename,'(.+)\\\\(.+$)','"$1\\\\$2.cmx" \n')];                       
4273            end
4274                 
4275        case 'CivAll'
4276            CivAllCmd=[CivAllCmd ' civ2 '];
4277            str=CIV2_CMD_Unified(filecell.nc.civ2{ifile,j},'',Param.Civ2);
4278            fieldnames=fields(str);
4279            [CivAllxml,uid_civ2]=add(CivAllxml,1,'element','civ2');
4280            for ilist=1:length(fieldnames)
4281                val=eval(['str.' fieldnames{ilist}]);
4282                if ischar(val)
4283                    [CivAllxml,uid_t]=add(CivAllxml,uid_civ2,'element',fieldnames{ilist});
4284                    [CivAllxml,uid_t2]=add(CivAllxml,uid_t,'chardata',val);
4285                end
4286            end
4287    end
4288end
4289
4290% CheckFix2
4291if Param.CheckFix2==1
4292    switch Param.Program
4293        case 'CivX'
4294            cmd=[cmd...
4295                cmd_fix(Param,'Fix2') '\n'];
4296        case 'CivAll'
4297            fix2.inputFileName=filecell.nc.civ2{ifile,j} ;
4298            fix2.fi1=num2str(flagindex2(1));
4299            fix2.fi2=num2str(flagindex2(2));
4300            fix2.fi3=num2str(flagindex2(3));
4301            fix2.threshC=num2str(thresh_vec2C);
4302            fix2.threshV=num2str(thresh_vel2);
4303            fieldnames=fields(fix2);
4304            [CivAllxml,uid_fix2]=add(CivAllxml,1,'element','fix2');
4305            for ilist=1:length(fieldnames)
4306                val=eval(['fix2.' fieldnames{ilist}]);
4307                if ischar(val)
4308                    [CivAllxml,uid_t]=add(CivAllxml,uid_fix2,'element',fieldnames{ilist});
4309                    [CivAllxml,uid_t2]=add(CivAllxml,uid_t,'chardata',val);
4310                end
4311            end
4312            CivAllCmd=[CivAllCmd ' fix2 '];
4313    end
4314end
4315
4316%CheckPatch2
4317if Param.CheckPatch2==1
4318   
4319    switch Param.Program
4320       
4321        case 'CivX'
4322            cmd=[cmd...
4323                cmd_patch(Param,'Patch2') '\n'];
4324        case 'CivAll'
4325            patch2.inputFileName=filecell.nc.civ1{ifile,j} ;
4326            patch2.nopt=subdomain_patch2;
4327            patch2.maxdiff=thresh_patch2;
4328            patch2.ro=rho_patch2;
4329            test_grid=get(handles.get_gridpatch2,'Value');
4330            if test_grid
4331                patch2.gridflag='y';
4332                gridname=get(handles.grid_patch2,'String');
4333                if isequal(gridname(end-3:end),'grid')
4334                    nbslice_grid=str2double(gridname(1:end-4)); %
4335                    if ~isnan(nbslice_grid)
4336                        i1_grid=mod(i1_civ2(ifile)-1,nbslice_grid)+1;
4337                        patch2.gridPatch=[filecell.filebase '_' fullfile_uvmat('','',gridname,'.grid','_1',i1_grid)];
4338                        %                                 patch2.gridPatch=[filecell.filebase '_' name_generator(gridname,i1_grid,1,'.grid','_i')];
4339                        if ~exist(patch2.gridPatch,'file')
4340                            errormsg='grid file absent for patch2';
4341                            return
4342                        end
4343                    elseif exist(gridname,'file')
4344                        patch2.gridPatch=gridname;
4345                    else
4346                        errormsg='grid file absent for patch2';
4347                        return
4348                    end
4349                end
4350            else
4351                patch2.gridPatch='none';
4352                patch2.gridflag='n';
4353                patch2.m=nx_patch2;
4354                patch2.n=ny_patch2;
4355            end
4356            patch2.convectFlow='n';
4357            fieldnames=fields(patch2);
4358            [CivAllxml,uid_patch2]=add(CivAllxml,1,'element','patch2');
4359            for ilist=1:length(fieldnames)
4360                val=eval(['patch2.' fieldnames{ilist}]);
4361                if ischar(val)
4362                    [CivAllxml,uid_t]=add(CivAllxml,uid_patch2,'element',fieldnames{ilist});
4363                    [CivAllxml,uid_t2]=add(CivAllxml,uid_t,'chardata',val);
4364                end
4365            end
4366            CivAllCmd=[CivAllCmd ' patch2 '];
4367    end
4368end
4369
4370switch Param.Program
4371    case 'CivAll'
4372        save(CivAllxml,[Param.OutputFile '.xml']);
4373        cmd=[cmd sparam.CivBin ' -f ' Param.OutputFile '.xml '  CivAllCmd ' >' Param.OutputFile '.log' '\n'];
4374    case 'civ_matlab'
4375                    switch computer
4376                        case {'PCWIN','PCWIN64'}                     
4377                            filename=regexprep(filename,'\\','\\\\');% add '\' so that '\' are left as characters
4378                                    cmd=['civ_matlab(''' regexprep(filename,'(.+)([/\\])(.+$)','$1$20_XML\\$2$3.xml') ''','''...
4379            filename '.nc'');'];
4380                        case {'GLNX86','GLNXA64','MACI64'}
4381                                    cmd=['civ_matlab(''' regexprep(filename,'(.+)([/\\])(.+$)','$1$20_XML$2$3.xml') ''','''...
4382            filename '.nc'');'];
4383                    end
4384
4385       
4386    case 'civ_matlab.sh'
4387        CivmBin=fullfile(fileparts(which('civ')),'civ_matlab.sh'); %path to the source directory of uvmat
4388        switch computer
4389            case {'PCWIN','PCWIN64'}
4390                filename=regexprep(filename,'\\','\\\\');% add '\' so that '\' are left as characters
4391                % TODO launch command in DOS
4392            case {'GLNX86','GLNXA64','MACI64'}
4393                cmd=['#!/bin/bash \n '...
4394                    '#$ -cwd \n '...
4395                    'hostname && date \n '...
4396                    'umask 002 \n'...
4397                    CivmBin ' ' Param.xml.RunTime ' ' regexprep(filename,'(.+)([/\\])(.+$)','$1$20_XML$2$3.xml') ' ' Param.OutputFile '.nc'];%allow writting access to created files for user group
4398        end
4399end   
4400   
4401
4402function cmd=cmd_fix(Param,fixname)
4403%%
4404switch fixname
4405    case 'Fix1'
4406        fi2_value=num2str(Param.(fixname).CheckF2);
4407        filename=regexprep(Param.OutputFile,'.nc','');
4408    case 'Fix2'
4409        fi2_value=num2str(Param.(fixname).CheckF4);%need to understand why...
4410        filename=regexprep(Param.OutputFile,'.nc','');       
4411end
4412
4413% filename=regexprep(Param.(fixname).OutFileName,'.nc','');
4414MaskName_string='';%default
4415MaxVel_string='';%default
4416if ~isempty(Param.(fixname).MinVel)
4417    MaxVel_string=[' -threshV ' num2str(Param.(fixname).MinVel)];
4418end
4419if isunix
4420    cmd=[Param.xml.FixBin ' -f ' filename '.nc -fi1 ' num2str(Param.(fixname).CheckFmin2) ...
4421        ' -fi2 ' fi2_value ' -fi3 ' num2str(Param.(fixname).CheckF3) ...
4422        ' -threshC ' num2str(Param.(fixname).MinCorr) MaxVel_string MaskName_string...
4423        ' >' regexprep(filename,'(.+)/(.+$)','$1/0_LOG/$2.')  lower(fixname) '.log 2>&1'];
4424else
4425    cmd=['"' Param.xml.FixBin '" -f "' filename '.nc" -fi1 ' num2str(Param.(fixname).CheckFmin2)...
4426        ' -fi2 ' fi2_value ' -fi3 ' num2str(Param.(fixname).CheckF3) ...
4427        ' -threshC ' num2str(Param.(fixname).MinCorr) MaxVel_string MaskName_string...
4428        ' > "' regexprep(filename,'(\w+)\\(\w+$)','$1\\0_LOG\\$2.') lower(fixname) '.log"'];
4429    cmd=regexprep(cmd,'\\','\\\\');
4430end
4431
4432
4433function cmd=cmd_patch(Param,patchname)
4434%% ------------------------------------------------------------------------
4435switch patchname
4436    case 'Patch1'
4437        filename=regexprep(Param.OutputFile,'.nc','');
4438    case 'Patch2'
4439        filename=regexprep(Param.OutputFile,'.nc','');       
4440end
4441% filename=regexprep(Param.(patchname).OutFileName,'.nc','');
4442if isunix
4443    cmd=[Param.xml.PatchBin...
4444        ' -f ' filename '.nc -m ' num2str(Param.(patchname).Nx)...
4445        ' -n ' num2str(Param.(patchname).Ny) ' -ro ' num2str(Param.(patchname).FieldSmooth)...
4446        ' -nopt ' num2str(Param.(patchname).SubdomainSize) ...
4447        '  > ' regexprep(filename,'(.+)/(.+$)','$1/0_LOG/$2.')  lower(patchname) '.log 2>&1']; % redirect standard output to the log file
4448else
4449    cmd=['"' Param.xml.PatchBin...
4450        '" -f "' filename '.nc" -m ' num2str(Param.(patchname).Nx)...
4451        ' -n ' num2str(Param.(patchname).Ny) ' -ro ' num2str(Param.(patchname).FieldSmooth)...
4452        ' -nopt ' num2str(Param.(patchname).SubdomainSize)...
4453        '  > "' filename '.' lower(patchname) '.log" 2>&1']; % redirect standard output to the log file
4454    cmd=regexprep(cmd,'\\','\\\\');
4455end
4456
4457
4458%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
4459% USELESS FUNCTIONS BELOW HERE,  TO CLEAN
4460%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
4461
4462%------------------------------------------------------------------------
4463% --- CheckCiv1  Unified: TO ABADON
4464function xml_civ1_parameters=CIV1_CMD_Unified(filename,namelog,par)
4465%------------------------------------------------------------------------
4466%pixels per cm and matrix of the image times, read from the .civ file by uvmat
4467%global CivBin%name of the executable for checkciv1 calculation
4468
4469civ1.image1=par.ImageA;
4470civ1.image2=par.ImageB;
4471civ1.imageSize_X=par.npx;
4472civ1.imageSize_Y=par.npy;
4473civ1.outputFileName=[filename '.nc'];
4474civ1.correlationBoxesSize_X=par.ibx;
4475civ1.correlationBoxesSize_Y=par.iby;
4476civ1.searchBoxesSize_X=par.isx;
4477civ1.searchBoxesSize_Y=par.isy;
4478civ1.globalShift_X=par.shiftx;
4479civ1.globalShift_Y=par.shifty;
4480civ1.ro=par.rho;
4481civ1.hart='y';
4482if isequal(par.gridflag,'y')
4483    civ1.grid=par.gridname;
4484else
4485    civ1.grid='n';
4486    civ1.gridSpacing_X=par.dx;
4487    civ1.gridSpacing_Y=par.dy;
4488end
4489if isequal(par.maskflag,'y')
4490    civ1.mask=par.maskname;
4491end
4492civ1.dt=par.Dt;
4493civ1.unit='pixel';
4494civ1.absolut_time_T0=par.Time;
4495civ1.pixcmx='1';
4496civ1.pixcmy='1';
4497civ1.convectFlow='n';
4498
4499xml_civ1_parameters=civ1;
4500
4501%------------------------------------------------------------------------
4502% --- CheckCiv2  Unified: TO ABADON
4503function civ2=CIV2_CMD_Unified(filename,namelog,par)
4504%------------------------------------------------------------------------
4505%pixels per cm and matrix of the image times, read from the .civ file by uvmat
4506%global CivBin%name of the executable for checkciv1 calculation
4507
4508filename=regexprep(filename,'.nc','');
4509
4510civ2.image1=par.ImageA;
4511civ2.image2=par.ImageB;
4512civ2.imageSize_X=par.npx;
4513civ2.imageSize_Y=par.npy;
4514civ2.inputFileName=[par.filename_nc1 '.nc'];
4515civ2.outputFileName=[filename '.nc'];
4516civ2.correlationBoxesSize_X=par.ibx;
4517civ2.correlationBoxesSize_Y=par.iby;
4518civ2.ro=par.rho;
4519%checkciv2.decimalShift=par.CheckDecimal;
4520%checkciv2.CheckDeformation=par.CheckDeformation;
4521if isequal(par.decimal,'1')
4522    civ2.decimalShift='y';
4523else
4524    civ2.decimalShift='n';
4525end
4526if isequal(par.deformation,'1')
4527    civ2.deformation='y';
4528else
4529    civ2.deformation='n';
4530end
4531if isequal(par.gridflag,'y')
4532    civ2.grid=par.gridname;
4533else
4534    civ2.grid='n';
4535    civ2.gridSpacing_X=par.dx;
4536    civ2.gridSpacing_Y=par.dy;
4537end
4538civ2.gridSpacing_X='10';
4539civ2.gridSpacing_Y='10';%NOTE: faut mettre gridSpacing pourque ca tourne, meme si c'est la grille qui est utilisee
4540if isequal(par.maskflag,'y')
4541    civ2.mask=par.maskname;
4542else
4543    civ2.mask='n';
4544end
4545civ2.dt=par.Dt;
4546civ2.unit='pixel';
4547civ2.absolut_time_T0=par.Time;
4548civ2.pixcmx='1';
4549civ2.pixcmy='1';
4550civ2.convectFlow='n';
4551
4552
4553% --- Executes on selection change in RunMode.
4554function RunMode_Callback(hObject, eventdata, handles)
4555
4556
4557function nb_field2_Callback(hObject, eventdata, handles)
4558
4559
4560function last_j_Callback(hObject, eventdata, handles)
4561
4562
4563function last_i_Callback(hObject, eventdata, handles)
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