source: trunk/src/civ.m @ 444

Last change on this file since 444 was 444, checked in by sommeria, 12 years ago

masks and calibration updated to fit with the new conventions on file organisation.
bug corrected in mouse_up (object creation)
bug corrected in civ in mode TESTciv

File size: 193.0 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 03-Jun-2012 22:16:42
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='PARAM.xml';
62if exist(xmlfile,'file')
63    try
64        t=xmltree(xmlfile);
65        sparam=convert(t);
66    catch ME
67        errormsg={' Unable to read the file PARAM.xml defining the civx binaries:';ME.message};
68    end
69else
70    errormsg=[xmlfile ' not found: path to civx binaries undefined'];
71end
72if ~isempty(errormsg)
73    msgbox_uvmat('WARNING',errormsg);
74end
75test_batch=0;%default: ,no batch mode available
76if isfield(sparam,'BatchParam') && isfield(sparam.BatchParam,'BatchMode')
77    test_batch=strcmp(sparam.BatchParam.BatchMode,'sge'); %sge is currently the only implemented batch mod
78end
79if test_batch==0
80    set(handles.BATCH,'Enable','off')% put the BATCH button in grey (unactivated)
81    set(handles.BATCH,'BackgroundColor',[0.831 0.816 0.784])% put the BATCH button in grey (unactivated)
82end
83if isfield(sparam.RunParam,'CivBin')
84    if ~exist(sparam.RunParam.CivBin,'file')
85        sparam.RunParam.CivBin=fullfile(path_civ,sparam.RunParam.CivBin);
86    end
87else
88    sparam.RunParam.CivBin='';
89end
90
91%% load the list of previously browsed files in the upper bar menu Open/
92dir_perso=prefdir; % path to the directory .matlab for personal data
93profil_perso=fullfile(dir_perso,'uvmat_perso.mat');% personal data file uvmauvmat_perso.mat' in .matlab
94if exist(profil_perso,'file')
95    h=load (profil_perso);
96    if isfield(h,'MenuFile')
97        for ifile=1:min(length(h.MenuFile),5)
98            eval(['set(handles.MenuFile_' num2str(ifile) ',''Label'',h.MenuFile{ifile});'])
99        end
100    end
101end
102
103%% prepare the GUI with parameters from the input file if opened from uvmat
104if exist('fileinput','var')% && isfield(param,'RootName') && ~isempty(param.RootName)
105    set(handles.RootPath,'BackgroundColor',[1 1 0])%paint RootName edit box in yellow to indicate that the file input is proceeding
106    errormsg=display_file_name(handles,fileinput);
107    if ~isempty(errormsg)
108        msgbox_uvmat('ERROR',errormsg)
109    end
110    set(handles.RootPath,'BackgroundColor',[1 1 1])%paint RootName back to white to indicate that the file input is finished
111end
112
113%------------------------------------------------------------------------
114% --- Outputs from this function are returned to the command line.
115function varargout = civ_OutputFcn(hObject, eventdata, handles)
116%------------------------------------------------------------------------
117% Get default command line output from handles structure
118varargout{1} = handles.output;
119
120%------------------------------------------------------------------------
121% --- Function activated by the Open/Browse... option in the upper menu bar.
122function MenuBrowse_Callback(hObject, eventdata, handles)
123%------------------------------------------------------------------------
124%% get the current input root file name to initiate the browser
125filebase=get(handles.RootPath,'String');
126oldfile=''; %default
127if isempty(filebase)|| isequal(filebase,'')%loads the previously stored root file name
128    dir_perso=prefdir;
129    profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
130    if exist(profil_perso,'file')
131        h=load (profil_perso);
132        if isfield(h,'filebase')&& ischar(h.filebase)
133            oldfile=h.filebase;
134        end
135        if isfield(h,'RootPath') && ischar(h.RootPath)
136            oldfile=h.RootPath;
137        end
138    end
139else
140    oldfile=filebase;
141end
142
143%% get the new input file with the browser
144menu={'*.xml;*.civ;*.png;*.jpg;*.tif;*.avi;*.AVI;*.nc;', ' (*.xml,*.civ,*.png,*.jpg ,.tif, *.avi,*.nc)';
145    '*.xml',  '.xml files '; ...
146    '*.civ',  '.civ files '; ...
147    '*.png','.png image files'; ...
148    '*.jpg',' jpeg image files'; ...
149    '*.tif','.tif image files'; ...
150    '*.avi;*.AVI','.avi movie files'; ...
151    '*.nc','.netcdf files'; ...
152    '*.*',  'All Files (*.*)'};
153[FileName, PathName, filtindex] = uigetfile( menu, 'Pick a file',oldfile);
154fileinput=[PathName FileName];%complete file name
155sizf=size(fileinput);
156if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end %stop if fileinput not a character string
157
158%% case of the xml file opened as input (TODO: check and see whether it is useful)
159[path,name,ext]=fileparts(fileinput);
160testeditxml=0;
161% if isequal(ext,'.xml')
162%     testeditxml=1;
163%     t_browse=xmltree(fileinput);
164%     head_element=get(t_browse,1);
165%     if isfield(head_element,'name')&& isequal(head_element.name,'ImaDoc')
166%         testeditxml=0;
167%     end
168% end
169% if testeditxml==1 || isequal(ext,'.xls')
170%     heditxml=editxml({fileinput});
171%     set(heditxml,'Tag','browser')
172%     waitfor(heditxml,'Tag','idle')
173%     if ~ishandle(heditxml)
174%         return
175%     end
176%     attr=findobj(get(heditxml,'children'),'Tag','CurrentAttributes');
177%     set(handles.browse,'UserData',fileinput)% store for future opening with browser
178%     fileinput=get(attr,'UserData');
179%     if ~exist(fileinput,'file')
180%         return
181%     end
182% end
183[tild,tild,tild,i1,i2,j1,j2,FileExt,NomType]=fileparts_uvmat(fileinput);
184
185%% prepare the GUI with parameters from the input file
186set(handles.RootPath,'BackgroundColor',[1 1 0])%paint RootName edit box in yellow to indicate that the file input is proceeding
187errormsg=display_file_name(handles,fileinput);
188if ~isempty(errormsg)
189    msgbox_uvmat('ERROR',erromsg)
190end
191set(handles.RootPath,'BackgroundColor',[1 1 1])%paint RootName back to white to indicate that the file input is finished
192
193%------------------------------------------------------------------------
194% --- Open again the file whose name has been recorded in MenuFile_1
195function MenuFile_1_Callback(hObject, eventdata, handles)
196%------------------------------------------------------------------------
197set(handles.RootPath,'BackgroundColor',[1 1 0])%paint RootName edit box in yellow to indicate that the file input is proceeding
198fileinput=get(handles.MenuFile_1,'Label');
199errormsg=display_file_name(handles,fileinput);
200if ~isempty(errormsg)
201    msgbox_uvmat('ERROR',errormsg)
202end
203set(handles.RootPath,'BackgroundColor',[1 1 1])%paint RootName back to white to indicate that the file input is finished
204
205% -----------------------------------------------------------------------
206% --- Open again the file whose name has been recorded in MenuFile_2
207function MenuFile_2_Callback(hObject, eventdata, handles)
208%------------------------------------------------------------------------
209set(handles.RootPath,'BackgroundColor',[1 1 0])%paint RootName edit box in yellow to indicate that the file input is proceeding
210fileinput=get(handles.MenuFile_2,'Label');
211errormsg=display_file_name(handles,fileinput);
212if ~isempty(errormsg)
213    msgbox_uvmat('ERROR',errormsg)
214end
215set(handles.RootPath,'BackgroundColor',[1 1 1])%paint RootName back to white to indicate that the file input is finished
216
217% -----------------------------------------------------------------------
218% --- Open again the file whose name has been recorded in MenuFile_3
219function MenuFile_3_Callback(hObject, eventdata, handles)
220%------------------------------------------------------------------------
221set(handles.RootPath,'BackgroundColor',[1 1 0])%paint RootName edit box in yellow to indicate that the file input is proceeding
222fileinput=get(handles.MenuFile_3,'Label');
223errormsg=display_file_name(handles,fileinput);
224if ~isempty(errormsg)
225    msgbox_uvmat('ERROR',errormsg)
226end
227set(handles.RootPath,'BackgroundColor',[1 1 1])%paint RootName back to white to indicate that the file input is finished
228
229% -----------------------------------------------------------------------
230% --- Open again the file whose name has been recorded in MenuFile_4
231function MenuFile_4_Callback(hObject, eventdata, handles)
232%------------------------------------------------------------------------
233set(handles.RootPath,'BackgroundColor',[1 1 0])%paint RootName edit box in yellow to indicate that the file input is proceeding
234fileinput=get(handles.MenuFile_4,'Label');
235errormsg=display_file_name(handles,fileinput);
236if ~isempty(errormsg)
237    msgbox_uvmat('ERROR',errormsg)
238end
239set(handles.RootPath,'BackgroundColor',[1 1 1])%paint RootName back to white to indicate that the file input is finished
240
241% -----------------------------------------------------------------------
242% --- Open again the file whose name has been recorded in MenuFile_5
243function MenuFile_5_Callback(hObject, eventdata, handles)
244%------------------------------------------------------------------------
245set(handles.RootPath,'BackgroundColor',[1 1 0])%paint RootName edit box in yellow to indicate that the file input is proceeding
246fileinput=get(handles.MenuFile_5,'Label');
247errormsg=display_file_name(handles,fileinput);
248if ~isempty(errormsg)
249    msgbox_uvmat('ERROR',errormsg)
250end
251set(handles.RootPath,'BackgroundColor',[1 1 1])%paint RootName back to white to indicate that the file input is finished
252
253% -----------------------------------------------------------------------
254% -----------------------------------------------------------------------
255% --- Open the help html file
256function MenuHelp_Callback(hObject, eventdata, handles)
257% -----------------------------------------------------------------------
258path_civ=fileparts(which ('civ'));
259helpfile=fullfile(path_civ,'uvmat_doc','uvmat_doc.html');
260if isempty(dir(helpfile))
261    msgbox_uvmat('ERROR','Please put the help file uvmat_doc.html in the sub-directory /uvmat_doc of the UVMAT package')
262else
263    addpath (fullfile(path_civ,'uvmat_doc'))
264    web([helpfile '#civ'])
265end
266
267%------------------------------------------------------------------------
268% --- Function activated when a new filebase (image series) is introduced
269function RootPath_Callback(hObject, eventdata, handles)
270%------------------------------------------------------------------------
271set(handles.RootPath,'BackgroundColor',[1 1 0])%paint RootName edit box in yellow to indicate that the file input is proceeding
272RootPath=get(handles.RootPath,'String');
273SubdirImages=get(handles.SubdirImages,'String');
274RootFile=get(handles.RootFile,'String');
275ref_i=str2num(get(handles.ref_i,'String'));
276ref_j=str2num(get(handles.ref_j,'String'));
277NomType=get(handles.NomType,'String');
278ImaExt=get(handles.ImaExt,'String');
279fileinput=fullfile_uvmat(RootPath,SubdirImages,RootFile,ImaExt,NomType,ref_i,[],ref_j);
280errormsg=display_file_name(handles,fileinput);
281if ~isempty(errormsg)
282    msgbox_uvmat('ERROR',errormsg)
283end
284set(handles.RootPath,'BackgroundColor',[1 1 1])%paint RootName back to white to indicate that the file input is finished
285
286%------------------------------------------------------------------------
287% --- general function activated for an input file series
288function errormsg=display_file_name(handles,fileinput)
289%------------------------------------------------------------------------
290set(handles.ListCompareMode,'Visible','on')
291errormsg='';%default empty error message
292drawnow
293
294%% enable RUN, BATCH button and 'status' display
295set(handles.RUN, 'Enable','On')
296set(handles.RUN,'BackgroundColor',[1 0 0])%set RUN button to red color
297set(handles.BATCH,'Enable','On')
298set(handles.BATCH,'BackgroundColor',[1 0 0])%set BATCH button to red color
299if isfield(handles,'status')
300    set(handles.status,'Value',0);       %suppress the 'status' display
301    status_Callback([], [], handles)
302end
303
304%% determine nomenclature types and extension of the input files
305[RootPath,SubDir,RootFile,i1,i2,j1,j2,ExtInput,NomTypeInput]=fileparts_uvmat(fileinput);
306NomTypeNc='';%default
307
308%% case of xml file as input, read the civ parameters
309ind_opening=0;%default
310if strcmp(ExtInput,'.xml')
311    Param=xml2struct(fileinput);
312    fill_GUI(Param,handles);%fill the GUI with the parameters retrieved from the xml file
313    return
314end
315
316%% case of netcdf file as input, get the civ processing stage and look for a coresponding image
317if strcmp(ExtInput,'.nc')
318    NomTypeNc=NomTypeInput;
319    if isempty(regexp(NomTypeInput,'[ab|AB|-]'))
320        set(handles.ListCompareMode,'Value',2) %mode displacement advised if the nomencalture does not involve index pairs
321      %  [RootPath,SubDir]=fileparts(RootPath);
322        set(handles.RootFile_1,'Visible','On');
323    else
324        set(handles.ListCompareMode,'Value',1)
325        set(handles.RootFile_1,'Visible','Off');
326    end
327    Data=nc2struct(fileinput,'ListGlobalAttribute','Conventions','absolut_time_T0','CivStage','Civ2_ImageA','Civ1_ImageA','Civ2_ImageB','Civ1_ImageB','fix','patch','civ2','fix2');
328    if isfield(Data,'Txt')
329        errormsg=Data.Txt;
330        return
331    end
332    % settings for  new civ data,
333    if strcmp(Data.Conventions,'uvmat/civdata')% case of new civ data,
334        set(handles.ListProgram,'Value',2) %select civ/Matlab by default
335        ListProgram_Callback([],[], handles)
336        if ~isempty(Data.CivStage)%test for civ files
337            ind_opening=Data.CivStage;
338        end
339        if  ~isempty(Data.Civ2_ImageB)%get the corresponding input image in the netcdf file
340            imageinput=Data.Civ2_ImageB;
341            [tild,ImaName,ImaExt]=fileparts(Data.Civ2_ImageA);
342            set(handles.RootFile_1,'String',[ImaName ImaExt])
343        elseif ~isempty(Data.Civ1_ImageB)
344            imageinput=Data.Civ1_ImageB;
345            [tild,ImaName,ImaExt]=fileparts(Data.Civ1_ImageA);
346            set(handles.RootFile_1,'String',[ImaName ImaExt])
347        end
348        % settings for civx data,
349    elseif ~isempty(Data.absolut_time_T0')% case of  civx data,
350        set(handles.ListProgram,'Value',1) %select Cix by default
351        ListProgram_Callback([],[], handles)
352        if ~isempty(Data.fix2)
353            ind_opening=5;
354        elseif ~isempty(Data.civ2)
355            ind_opening=4;
356        elseif ~isempty(Data.patch)
357            ind_opening=3;
358        elseif ~isempty(Data.fix)
359            ind_opening=2;
360        end
361    else
362        errormsg='the input netcdf file is not civ data';
363        return
364    end
365    % look for the corresponding input images
366    check_letter=~isempty(regexp(NomTypeInput,'[ab|AB]$','once'));%detect pair label by letter
367    NomTypeIma=NomTypeInput;
368    if check_letter
369        NomTypeIma=NomTypeInput(1:end-1);
370    else
371        r=regexp(NomTypeIma,'.-(?<num2>\d+)$','names');
372        if ~isempty(r)
373            NomTypeIma=regexprep(NomTypeIma,['-' r.num2],'');
374        end
375        r=regexp(NomTypeIma,'.-(?<num2>\d+)','names');
376        if ~isempty(r)
377            NomTypeIma=regexprep(NomTypeIma,['-' r.num2],'');
378        end
379    end
380    imageinput=fullfile_uvmat(RootPath,regexprep(SubDir,'.civ(_?)(\d*)$',''),RootFile,'.png',NomTypeIma,i1,[],j1);
381end
382
383%no corresponding image found, select manually with the browser
384ImaExt=ExtInput;
385if ~isempty(NomTypeNc)
386    %no corresponding image found, select manually with the browser
387    if ~exist(imageinput,'file')
388        menu={'*.png;*.jpg;*.tif;*.avi;*.AVI', '(*.png,*.jpg ,*.tif, *.avi,*.AVI)';
389            '*.png','.png image files'; ...
390            '*.jpg',' jpeg image files'; ...
391            '*.tif','.tif image files'; ...
392            '*.avi;*.AVI','.avi movie files'; ...
393            '*.*',  'All Files (*.*)'};
394        [FileName, PathName] = uigetfile( menu, 'Pick an input image file',fileparts(fileparts(fileinput)));
395        imageinput=[PathName FileName];%complete file name
396     
397    end   
398    fileinput=imageinput;
399end
400
401%% scan the image file series
402[FilePath,FileName,ImaExt]=fileparts(fileinput);
403% detect the file type, get the movie object if relevant, and look for the corresponding file series:
404% the root name and indices may be corrected by including the first index i1 if a corresponding xml file exists
405[RootPath,SubdirImages,RootFile,i1_series,tild,j1_series,tild,NomTypeIma,FileType,Object,i1,i2,j1,j2]=find_file_series(FilePath,[FileName ImaExt]);
406
407switch FileType
408    case {'image','multimage','video','mmreader'}
409    otherwise
410        errormsg='invalid input file: enter an image, a movie or civ .nc file';
411        return
412end
413set(handles.RootPath,'String',RootPath)
414set(handles.SubdirImages,'String',SubdirImages)
415set(handles.RootFile,'String',RootFile)
416if strcmp(ExtInput,'.nc')
417    SubDirCiv=regexprep(SubDir,[SuddirImages '^'],'');%suppress the root  SuddirImages;
418else
419    SubDirCiv= '.civ';
420end
421set(handles.SubdirCiv1,'String',SubDirCiv)
422set(handles.SubdirCiv2,'String',SubDirCiv)
423browse=get(handles.RootPath,'UserData');
424browse.incr_pair=[0 0];%default
425
426%% fill reference indices from the input file indices
427num_ref_i=i1;%efaulmt ref index
428if ~isempty(i2)
429    num_ref_i=floor((num_ref_i+i2)/2);
430end
431num_ref_j=j1;
432if ~isempty(j2)
433    num_ref_j=floor((num_ref_j+j2)/2);
434end
435
436%% scan the images if a civ file has been opened
437MinIndex_i=min(i1_series(i1_series>0));
438MinIndex_j=min(j1_series(j1_series>0));
439MaxIndex_i=max(i1_series(i1_series>0));
440MaxIndex_j=max(j1_series(j1_series>0));
441
442%% look for an image documentation file
443ext_imadoc='';%default
444SubDirBase=regexprep(SubDir,'\..*','');%take the root part of SubDir, before the first dot '.'
445filexml=fullfile(RootPath,[SubDirBase '.xml']);% new convention: xml above the image dir
446if ~exist(filexml,'file')
447    filexml=fullfile(RootPath,SubDir,[RootFile '.xml']);%old convention: xml within the image directroy
448end
449RootName=fullfile(RootPath,RootFile);
450if exist(filexml,'file')
451    ext_imadoc='.xml';
452elseif exist(fullfile(RootPath,SubDir,[RootFile '.civ']),'file')
453    ext_imadoc='.civ';
454    fileciv=fullfile(RootPath,SubDir,[RootFile '.civ']);
455elseif exist([RootName '.avi'],'file')
456    ext_imadoc='.avi';
457elseif exist([RootName '.AVI'],'file')
458    ext_imadoc='.AVI';
459end
460set(handles.ImaDoc,'String',ext_imadoc)% display the extension name for the image documentation file used
461
462%%  read the time in the image documentation file 
463time=[];
464TimeUnit=''; %default
465CoordUnit='';%default
466pxcm_search=1;
467if ~isempty(ext_imadoc)
468    set(handles.ImaDoc,'BackgroundColor',[1 1 0]) % set edit box to yellow cloro to indicate that the file reading is beginning
469    drawnow
470    switch ext_imadoc
471        case '.xml'
472            [XmlData,warntext]=imadoc2struct(filexml);
473            ext_ima_read=[];
474            nom_type_read=[];
475            if isfield(XmlData,'Heading')&&isfield(XmlData.Heading','ImageName')&&ischar(XmlData.Heading.ImageName)% get image nom type and extension from the xml file
476                %[PP,FF,fc,str2,str_a,str_b,ext_ima_read,nom_type_read]=name2display(XmlData.Heading.ImageName);
477                [tild,tild,tild,tild,tild,tild,tild,tild,nom_type_read]=fileparts_uvmat(XmlData.Heading.ImageName);
478                fullname=fullfile(fileparts(RootName),XmlData.Heading.ImageName); %full name (including path) of the first image defined by the xmle file,
479                if ~exist(fullname,'file')
480                    msgbox_uvmat('WARNING',['FirstImage ' fullname ' defined in the xml file does not exist'])
481                end
482            end
483            if isfield(XmlData,'Time')
484                time=XmlData.Time;
485                %transform .Time to a column vector if it is a line vector thenomenclature uses a single index: correct possible bug in xml
486                if isequal(MaxIndex_i,1) && ~isequal(MaxIndex_j,1)% .Time is a line vector
487                    if numel(nom_type_read)>=2 && isempty(regexp(nom_type_read(2:end),'\D','once'))
488                        time=time';
489                        MaxIndex_i=MaxIndex_j;
490                        MaxIndex_j=1;
491                    end
492                end
493            end
494            if isfield(XmlData,'TimeUnit')
495                TimeUnit=XmlData.TimeUnit;
496            end
497
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
507        case '.civ'% OBSOLETE: case of .civ image documentation file
508            [error,time,TimeUnit,mode,npx,npy]=read_imatext(fileciv);
509            if error==2, msgbox_uvmat('WARNING',['no file ' fileciv]);
510            elseif error==1, msgbox_uvmat('WARNING','inconsistent number of fields in the .civ file');
511            end
512            nom_type_ima='001a';
513        case {'.avi','.AVI'}
514            nom_type_ima='*';
515            ImaExt=ext_imadoc;
516            set(handles.ListPairMode,'Value',1);
517            set(handles.ListPairMode,'String',{'series(Di)'})
518            dt=0.04;%default
519            if exist([RootName ext_imadoc],'file')==2
520                hhh=which('videoreader');
521                if isempty(hhh)%use old video function of matlab
522                    imainfo=aviinfo([RootName ext_imadoc]);%read infos on the avi movie TO REPLACE mmreader
523                    dt=1/imainfo.FramesPerSecond;%time interval between successive frames
524                    MaxIndex_i=imainfo.NumFrames;%number of frames
525                    %         XmlData.Time=(0:1/imainfo.FramesPerSecond:(imainfo.NumFrames-1)/imainfo.FramesPerSecond)';
526                    %         nbfield=imainfo.NumFrames;
527                    %         set(handles.Dt_txt,'String',['Dt=' num2str(1000/imainfo.FramesPerSecond) 'ms']);%display the elementary time interval in millisec
528                    %         ColorType=imainfo.ImageType;%='truecolor' for color images
529                else %use video function videoreader of matlab
530                    imainfo=get(videoreader([RootName ext_imadoc]));%read infos on the avi movie
531                    dt=1/imainfo.FrameRate;%time interval between successive frames
532                    MaxIndex_i=imainfo.NumberOfFrames;%number of frames
533                    %         XmlData.Time=(0:1/imainfo.FrameRate:(imainfo.NumberOfFrames-1)/imainfo.FrameRate)';
534                    %         nbfield=imainfo.NumberOfFrames;
535                    %         set(handles.Dt_txt,'String',['Dt=' num2str(1000/imainfo.FrameRate) 'ms']);%display the elementary time interval in millisec
536                    %         ColorType='truecolor';
537                end
538               
539                time=(dt*(0:MaxIndex_i-1))';%list of image times
540                TimeUnit='s';
541            end
542            set(handles.ImaDoc,'BackgroundColor',[1 1 1])% set display box back to whiter
543    end
544end
545%% timing display
546%show the reference image edit box if relevant (not needed for movies or in the absence of time information
547if numel(time)>=2 % if there are at least two time values to define dt
548    MaxIndex_i=min(size(time,1),MaxIndex_i);
549    MaxIndex_j=min(size(time,2),MaxIndex_j);
550    time=[zeros(size(time,1),1) time]; %insert a vertical line of zeros (to deal with zero file indices)
551    time=[zeros(1,size(time,2)); time]; %insert a horizontal line of zeros
552    set(handles.ImaDoc,'UserData',time); %store the matrix of times
553    set(handles.dt_unit,'String',['dt in m' TimeUnit]);
554    set(handles.TimeUnit,'String',TimeUnit);
555else
556    set(handles.ImaDoc,'String',''); %xml file not used for timing
557    time=(i1_series(:,1)+0:size(i1_series,1)-1);% time=index i
558    time=time'*ones(1,size(i1_series,2),1); %makes a time matrix with the same time for all j indices
559    TimeUnit='frame';
560end
561set(handles.ImaDoc,'UserData',time); %store the matrix of times
562set(handles.dt_unit,'String',['dt in m' TimeUnit]);%display dt in unit 10-3 of the time (e.g ms)
563set(handles.TimeUnit,'String',TimeUnit);
564set(handles.nb_field,'String',num2str(MaxIndex_i));
565set(handles.nb_field2,'String',num2str(MaxIndex_j));
566set(handles.CoordUnit,'String',CoordUnit)
567set(handles.SearchRange,'UserData', pxcm_search);
568set(handles.ImaExt,'String',ImaExt)
569set(handles.NomType,'String',NomTypeIma)
570set(handles.ref_i,'String',num2str(num_ref_i))
571set(handles.ref_j,'String',num2str(num_ref_j))
572
573%% update i and j index range if a nc file has been opened or pb withmin max image indices:
574% then set first and last to the inputfile index by default
575first_i=str2num(get(handles.first_i,'String'));
576last_i=str2num(get(handles.last_i,'String'));
577if isempty(first_i) || isempty(last_i)||isempty(MinIndex_i)||isempty(MaxIndex_i)
578    set(handles.first_i,'String',num2str(num_ref_i));
579    set(handles.last_i,'String',num2str(num_ref_i));%
580end
581if ind_opening~=0 || isempty(first_i) || isempty(last_i)|| first_i<MinIndex_i || last_i>MaxIndex_i
582    set(handles.first_i,'String',num2str(num_ref_i));
583    set(handles.last_i,'String',num2str(num_ref_i));%
584end
585
586%j index range
587first_j=str2num(get(handles.first_j,'String'));
588last_j=str2num(get(handles.last_i,'String'));
589if isempty(first_j) || isempty(last_j)||isempty(MinIndex_j)||isempty(MaxIndex_j)
590    set(handles.first_j,'String',num2str(num_ref_j));
591    set(handles.last_j,'String',num2str(num_ref_j));%
592elseif ind_opening~=0 || first_j<MinIndex_j || last_j>MaxIndex_j
593    set(handles.first_j,'String',num2str(num_ref_j));
594set(handles.last_j,'String',num2str(num_ref_j));%
595end
596
597%% set the civ options depending on the input file content when a nc file has been opened
598ListOptions={'CheckCiv1', 'CheckFix1' 'CheckPatch1', 'CheckCiv2', 'CheckFix2', 'CheckPatch2'};
599if ind_opening~=0
600    for index = 1:ind_opening
601        set(handles.(ListOptions{index}),'value',0)
602    end
603end
604for index = ind_opening+2:6
605    set(handles.(ListOptions{index}),'value',0)
606end
607set(handles.(ListOptions{min(ind_opening+1,6)}),'value',1)
608update_CivOptions(handles,ind_opening)
609
610%%  set the menus of image pairs and default selection for civ   %%%%%%%%%%%%%%%%%%%
611%check_letter=~isempty(regexp(NomTypeIma,'[ab|AB]$'));%detect pair label by letter
612if  isequal(NomTypeNc,'_1-2')||isempty(MaxIndex_j)|| (MaxIndex_j==1)
613    set(handles.ListPairMode,'Value',1)
614    set(handles.ListPairMode,'String',{'series(Di)'})   
615elseif  MaxIndex_i==1 && MaxIndex_j>1% simple series in j
616    set(handles.ListPairMode,'String',{'pair j1-j2';'series(Dj)'})
617    if  MaxIndex_j <= 10
618        set(handles.ListPairMode,'Value',1)% advice 'pair j1-j2' except in MaxIndex_j is large
619    end
620else
621    set(handles.ListPairMode,'String',{'pair j1-j2';'series(Dj)';'series(Di)'})%multiple choice
622    if strcmp(NomTypeNc,'_1-2_1')
623        set(handles.ListPairMode,'Value',3)% advise 'series(Di)'
624    elseif  MaxIndex_j <= 10
625        set(handles.ListPairMode,'Value',1)% advice 'pair j1-j2' except in MaxIndex_j is large
626    end
627end
628
629%% scan files to update the subdirectory list display
630listot=dir(RootPath);%directory of RootPath
631idir=0;
632listdir={''};%default
633% get the list of existing civ subdirectories in the path of theinput root  file
634for ilist=1:length(listot)
635    if listot(ilist).isdir
636        name=listot(ilist).name;
637        if ~isequal(name,'.') && ~isequal(name,'..')
638            idir=idir+1;
639            listdir{idir,1}=listot(ilist).name;
640        end
641    end
642end
643
644%% store info
645set(handles.RootPath,'UserData',browse)% store the nomenclature type
646
647%% list the possible index pairs, depending on the option set in ListPairMode
648ListPairMode_Callback([], [], handles)
649
650%% store the root input filename for future opening
651profil_perso=fullfile(prefdir,'uvmat_perso.mat');
652if exist(profil_perso,'file')
653    save (profil_perso,'RootPath','-append'); %store the root name for future opening of uvmat
654else
655    txt=ver('MATLAB');
656    Release=txt.Release;
657    relnumb=str2double(Release(3:4));
658    if relnumb >= 14
659        save (profil_perso,'RootPath','-V6'); %store the root name for future opening of uvmat
660    else
661        save (profil_perso,'RootPath'); %store the root name for future opening of uvmat
662    end
663end
664set(handles.RootPath,'BackgroundColor',[1 1 1])
665
666%------------------------------------------------------------------------
667% --- Executes on carriage return on the subdir checkciv1 edit window
668function SubdirCiv1_Callback(hObject, eventdata, handles)
669%------------------------------------------------------------------------
670SubDir=get(handles.SubdirCiv1,'String');
671menu_str=get(handles.ListSubdirCiv1,'String');% read the list of subdirectories for update
672ichoice=find(strcmp(SubDir,menu_str),1);
673if isempty(ichoice)
674    ilist=numel(menu_str); %select 'new...' in the menu
675else
676    ilist=ichoice;
677end
678set(handles.ListSubdirCiv1,'Value',ilist)% select the selected subdir in the menu
679if get(handles.CheckCiv1,'Value')% if Civ1 is performed
680    set(handles.SubdirCiv2,'String',SubDir);% set by default civ2 directory the same as civ1
681%     set(handles.ListSubdirCiv2,'Value',ilist)
682else % if Civ1 data already exist
683    errormsg=find_netcpair_civ(handles,1); %update the list of available pairs from netcdf files in the new directory
684    if ~isempty(errormsg)
685    msgbox_uvmat('ERROR',errormsg)
686    end
687end
688
689%------------------------------------------------------------------------
690% --- Executes on carriage return on the SubDir checkciv1 edit window
691function SubdirCiv2_Callback(hObject, eventdata, handles)
692%------------------------------------------------------------------------
693SubDir=get(handles.SubdirCiv1,'String');
694menu_str=get(handles.ListSubdirCiv2,'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.ListSubdirCiv2,'Value',ilist)% select the selected subdir in the menu
702%update the list of available pairs from netcdf files in the new directory
703if ~get(handles.CheckCiv2,'Value') && ~get(handles.CheckCiv1,'Value') && ~get(handles.CheckFix1,'Value') && ~get(handles.CheckPatch1,'Value')
704    errormsg=find_netcpair_civ(handles,2);
705        if ~isempty(errormsg)
706    msgbox_uvmat('ERROR',errormsg)
707    end
708end
709
710%------------------------------------------------------------------------
711% --- Executes on button press in CheckCiv1.
712function CheckCiv1_Callback(hObject, eventdata, handles)
713%------------------------------------------------------------------------
714update_CivOptions(handles,0)
715
716%------------------------------------------------------------------------
717% --- Executes on button press in CheckFix1.
718function CheckFix1_Callback(hObject, eventdata, handles)
719%------------------------------------------------------------------------
720update_CivOptions(handles,0)
721
722%------------------------------------------------------------------------
723% --- Executes on button press in CheckPatch1.
724function CheckPatch1_Callback(hObject, eventdata, handles)
725%------------------------------------------------------------------------
726update_CivOptions(handles,0)
727
728%------------------------------------------------------------------------
729% --- Executes on button press in CheckCiv2.
730function CheckCiv2_Callback(hObject, eventdata, handles)
731%------------------------------------------------------------------------
732update_CivOptions(handles,0)
733
734%------------------------------------------------------------------------
735% --- Executes on button press in CheckFix2.
736function CheckFix2_Callback(hObject, eventdata, handles)
737%------------------------------------------------------------------------
738update_CivOptions(handles,0)
739
740%------------------------------------------------------------------------
741% --- Executes on button press in CheckPatch2.
742function CheckPatch2_Callback(hObject, eventdata, handles)
743%------------------------------------------------------------------------
744update_CivOptions(handles,0)
745
746%------------------------------------------------------------------------
747% --- activated by any checkbox controling the selection of Civ1,Fix1,Patch1,Civ2,Fix2,Patch2
748function update_CivOptions(handles,opening)
749%------------------------------------------------------------------------
750checkbox=zeros(1,6);
751checkbox(1)=get(handles.CheckCiv1,'Value');
752checkbox(2)=get(handles.CheckFix1,'Value');
753checkbox(3)=get(handles.CheckPatch1,'Value');
754checkbox(4)=get(handles.CheckCiv2,'Value');
755checkbox(5)=get(handles.CheckFix2,'Value');
756checkbox(6)=get(handles.CheckPatch2,'Value');
757ind_selected=find(checkbox,1);
758if ~isempty(ind_selected)
759    RootPath=get(handles.RootPath,'String');
760    if isempty(RootPath)
761        msgbox_uvmat('ERROR','Please open an image or PIV .nc file with the upper bar menu Open/Browse...')
762        return
763    end
764end
765set(handles.PairIndices,'Visible','on')
766set(handles.SubdirCiv1,'Visible','on')
767set(handles.TitleSubdirCiv1,'Visible','on')
768if opening==0
769    errormsg=find_netcpair_civ(handles,1); % select the available netcdf files
770    if ~isempty(errormsg)
771        msgbox_uvmat('ERROR',errormsg)
772    end
773end
774if max(checkbox(4:6))% case of civ2 pair choice needed
775    set(handles.TitlePairCiv2,'Visible','on')
776    set(handles.TitleSubdirCiv2,'Visible','on')
777    set(handles.SubdirCiv2,'Visible','on')
778    %set(handles.ListSubdirCiv2,'Visible','on')
779    set(handles.ListPairCiv2,'Visible','on')
780    if ~opening
781        errormsg=find_netcpair_civ(handles,2); % select the available netcdf files
782        if ~isempty(errormsg)
783            msgbox_uvmat('ERROR',errormsg)
784        end
785    end
786else
787    set(handles.TitleSubdirCiv2,'Visible','off')
788    set(handles.SubdirCiv2,'Visible','off')
789    set(handles.ListPairCiv2,'Visible','off')
790end
791options={'Civ1','Fix1','Patch1','Civ2','Fix2','Patch2'};
792for ilist=1:length(options)
793    if checkbox(ilist)
794        set(handles.(options{ilist}),'Visible','on')
795    else
796        set(handles.(options{ilist}),'Visible','off')
797    end
798end
799
800%------------------------------------------------------------------------
801% --- Executes on button press in RUN: processing on local computer
802function RUN_Callback(hObject, eventdata, handles)
803%------------------------------------------------------------------------
804set(handles.RUN, 'Enable','Off')
805set(handles.RUN,'BackgroundColor',[0.831 0.816 0.784])
806batch=0;
807errormsg=launch_jobs(hObject, eventdata, handles,batch);
808set(handles.RUN, 'Enable','On')
809set(handles.RUN,'BackgroundColor',[1 0 0])
810
811% display errors or start status callback to visualise results
812if ~isempty(errormsg)
813    display(errormsg)
814    msgbox_uvmat('ERROR',errormsg)
815elseif  isfield(handles,'status') %&& ~isequal(get(handles.ListPairMode,'Value'),3)
816    set(handles.status,'Value',1);%suppress status display
817    status_Callback(hObject, eventdata, handles)
818end
819
820%------------------------------------------------------------------------
821% --- Executes on button press in BATCH: remote processing
822function BATCH_Callback(hObject, eventdata, handles)
823% -----------------------------------------------------------------------
824set(handles.BATCH, 'Enable','Off')
825set(handles.BATCH,'BackgroundColor',[0.831 0.816 0.784])
826batch=1;
827errormsg=launch_jobs(hObject, eventdata, handles, batch);
828set(handles.BATCH, 'Enable','On')
829set(handles.BATCH,'BackgroundColor',[1 0 0])
830
831% display errors or start status callback to visualise results
832if ~isempty(errormsg)
833    display(errormsg)
834    msgbox_uvmat('ERROR',errormsg)
835elseif isfield(handles,'status')
836    set(handles.status,'Value',1);%suppress status display
837    status_Callback(hObject, eventdata, handles)
838end
839
840%-------------------------------------------------------------------
841% --- Executes on button press in status.
842function status_Callback(hObject, eventdata, handles)
843%-------------------------------------------------------------------
844val=get(handles.status,'Value');
845if val==0
846    set(handles.status,'BackgroundColor',[0 1 0])
847    hfig=findobj(allchild(0),'name','civ_status');
848    if ~isempty(hfig)
849        delete(hfig)
850    end
851    return
852end
853set(handles.status,'BackgroundColor',[1 1 0])
854drawnow
855listtype={'civ1','fix1','patch1','civ2','fix2','patch2'};
856Param.CheckCiv1=get(handles.CheckCiv1,'Value');
857Param.CheckFix1=get(handles.CheckFix1,'Value');
858Param.CheckPatch1=get(handles.CheckPatch1,'Value');
859Param.CheckCiv2=get(handles.CheckCiv2,'Value');
860Param.CheckFix2=get(handles.CheckFix2,'Value');
861Param.CheckPatch2=get(handles.CheckPatch2,'Value');
862box_test=[Param.CheckCiv1 Param.CheckFix1 Param.CheckPatch1 Param.CheckCiv2 Param.CheckFix2 Param.CheckPatch2];
863
864option_civ=find(box_test,1,'last');%last selected option (non-zero index of box_test)
865filecell=get(handles.civ,'UserData');%retrieve the list of output files expected for PIV
866test_new=0;
867if ~isfield(filecell,'nc')
868    test_new=1;
869    [ref_i,ref_j,errormsg]=find_ref_indices(handles);
870    if ~isempty(errormsg)
871        msgbox_uvmat('ERROR',errormsg)
872        return
873    end
874    filecell=set_civ_filenames(handles,ref_i,ref_j,box_test);%determine the output file expected from the GUI status
875end
876if ~isequal(box_test(4:6),[0 0 0])
877    civ_files=filecell.nc.civ2;%case of civ2 operations
878else
879    civ_files=filecell.nc.civ1;
880end
881[root,filename,ext]=fileparts(civ_files{1});
882[rootroot,SubDir,extdir]=fileparts(root);
883hfig=findobj(allchild(0),'name','civ_status');
884if isempty(hfig)
885    hfig=figure('DeleteFcn',@stop_status);
886    set(hfig,'MenuBar','none')% suppress the menu bar
887    set(hfig,'NumberTitle','off')%suppress the fig number in the title
888    set(hfig,'name','civ_status')
889    set(hfig,'tag','civ_status')
890    set(hfig,'UserData',civ_files)
891    hlist= uicontrol('Style','listbox','Units','normalized', 'Position',[0.05 0.09 0.9 0.71], 'Callback', {'open_uvmat'},'tag','list');
892    uicontrol('Style','edit','Units','normalized', 'Position', [0.05 0.87 0.9 0.1],'tag','msgbox','Max',2,'String','checking files...');
893    uicontrol('Style','frame','Units','normalized', 'Position', [0.05 0.81 0.9 0.05]);
894    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);
895    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);
896    BarPosition=[0.05 0.81 0.01 0.05];
897    uicontrol('Style','frame','Units','normalized', 'Position',BarPosition ,'BackgroundColor',[1 0 0],'tag','waitbar');
898    drawnow
899end
900set(hrefresh,'UserData',option_civ)
901        filepath=fileparts(civ_files{1});
902set(hlist,'UserData',fileparts(filepath))
903refresh_GUI(hrefresh,[])
904
905%------------------------------------------------------------------------   
906% launched by refreshing the status figure
907function refresh_GUI(hObject, eventdata)
908%------------------------------------------------------------------------
909Tabchar={};
910BarPosition=[0.05 0.81 0.01 0.05];
911hfig=get(hObject,'parent');
912civ_files=get(hfig,'UserData');
913        [filepath,filename,ext]=fileparts(civ_files{1});
914        [tild,SubDir,extdir]=fileparts(filepath);
915        SubDir=[SubDir extdir];
916option_civ=get(hObject,'UserData');
917nbfiles=numel(civ_files);
918count=0;
919testrecent=0;
920% while count<nbfiles
921    count=0;
922    datnum=zeros(1,nbfiles);
923    for ifile=1:nbfiles
924        detect=exist(civ_files{ifile},'file'); % check the existence of the file
925        option=0;
926        if detect==0
927            option_str='not created';
928        else
929            datfile=dir(civ_files{ifile});
930            if isfield(datfile,'datenum')
931                datnum(ifile)=datfile.datenum;%only available in recent matlab versions
932                testrecent=1;
933            end
934            filefound(ifile)={datfile.name};
935            lastfield='';
936            % check the content  netcdf file
937            Data=nc2struct(civ_files{ifile},'ListGlobalAttribute','CivStage','patch2','fix2','civ2','patch','fix');
938            option_list={'civ1','fix1','patch1','civ2','fix2','patch2'};
939            if ~isempty(Data.CivStage)
940                option=Data.CivStage;%case of Matlab civ
941            else
942                if ~isempty(Data.patch2) && isequal(Data.patch2,1)
943                    option=6;
944                elseif ~isempty(Data.fix2) && isequal(Data.fix2,1)
945                    option=5;
946                elseif ~isempty(Data.civ2) && isequal(Data.civ2,1);
947                    option=4;
948                elseif ~isempty(Data.patch) && isequal(Data.patch,1);
949                    option=3;
950                elseif ~isempty(Data.fix) && isequal(Data.fix,1);
951                    option=2;
952                else
953                    option=1;
954                end
955            end
956            option_str=option_list{option};
957        end
958        if option >= option_civ
959            count=count+1;
960        end
961        [filepath,filename,ext]=fileparts(civ_files{ifile});
962        Tabchar{ifile,1}=[fullfile(SubDir,filename) ext  '...' option_str];
963    end
964    datnum=datnum(datnum~=0);%keep the non zero values corresponding to existing files
965    if isempty(datnum)
966        if testrecent
967            message='no civ result created yet';
968        else
969            message='';
970        end
971    else
972        datnum=datnum(datnum~=0);%keep the non zero values corresponding to existing files
973        [first,ind]=min(datnum);
974        [last,indlast]=max(datnum);
975%         if test_new
976%             message='existing file status, no processing launched yet';
977%         else
978        message={[num2str(count) ' file(s) done over ' num2str(nbfiles)] ;['oldest modification:  ' cell2mat(filefound(ind)) ' : ' datestr(first)];...
979            ['latest modification:  ' cell2mat(filefound(indlast)) ' : ' datestr(last)]};
980%         end
981    end
982    %hfig=findobj(allchild(0),'name','civ_status');
983%     if isempty(hfig)% the status list has been deleted
984%         return
985%     else
986        hlist=findobj(hfig,'tag','list');
987        hmsgbox=findobj(hfig,'tag','msgbox');
988        hwaitbar=findobj(hfig,'tag','waitbar');
989        set(hlist,'String',Tabchar)
990        set(hmsgbox,'String', message)
991        if count>0 %&& ~test_new
992            BarPosition(3)=0.9*count/nbfiles;
993            set(hwaitbar,'Position',BarPosition)
994        end
995%     end
996%     [root,filename,ext]=fileparts(civ_files{1});
997% [rootroot,SubDir,extdir]=fileparts(root);
998%
999%     set(hlist,'UserData',rootroot)
1000%     if count<10||(nbfiles-count)<10
1001%     pause(.5)% wait 0.5 seconds for next check
1002%     else
1003%         pause(10)% wait 10 seconds for next check
1004%     end
1005% end
1006
1007%------------------------------------------------------------------------   
1008% launched by deleting the status figure
1009function stop_status(hObject, eventdata)
1010%------------------------------------------------------------------------
1011hciv=findobj(allchild(0),'tag','civ');
1012hhciv=guidata(hciv);
1013set(hhciv.status,'value',0) %reset the status uicontrol in the GUI civ
1014set(hhciv.status,'BackgroundColor',[0 1 0])
1015
1016%------------------------------------------------------------------------   
1017% launched by pressing OK on the status figure
1018function close_GUI(hObject, eventdata)
1019%------------------------------------------------------------------------
1020    delete(gcbf)
1021
1022
1023%--------------orm----------------------------------------------------------
1024% --- Main lauch command, called by RUN and BATCH
1025function errormsg=launch_jobs(hObject, eventdata, handles, batch)
1026%-----------------------------------------------------------------------
1027errormsg='';%default
1028
1029%% read the input parameters from the  GUI civ
1030Param=read_GUI(handles.civ);
1031
1032%% check the selected list of operations:
1033operations={'Civ1','Fix1','Patch1','Civ2','Fix2','Patch2'};
1034box_test=[Param.CheckCiv1 Param.CheckFix1 Param.CheckPatch1 Param.CheckCiv2 Param.CheckFix2 Param.CheckPatch2];
1035index_first=find(box_test==1,1);
1036if isempty(index_first)
1037    errormsg='no selected operation';
1038    return
1039end
1040index_last=find(box_test==1,1,'last');
1041box_used=box_test(index_first : index_last);
1042[box_missing,ind_missing]=min(box_used);
1043if isequal(box_missing,0); %there is a missing step in the sequence of operations
1044    errormsg=['missing' cell2mat(operations(ind_missing))];
1045    return
1046end
1047
1048%% check mask if selecetd
1049%could be included in get_mask callback ?
1050if isequal(get(handles.CheckMask,'Value'),1)
1051    maskname=get(handles.Mask,'String');
1052    if ~exist(maskname,'file')
1053        get_mask_civ1_Callback(hObject, eventdata, handles);
1054    end
1055end
1056if isequal(get(handles.CheckMask,'Value'),1)
1057    maskname=get(handles.Mask,'String');
1058    if ~exist(maskname,'file')
1059        get_mask_fix1_Callback(hObject, eventdata, handles);
1060    end
1061end
1062if isequal(get(handles.CheckMask,'Value'),1)
1063    maskname=get(handles.Mask,'String');
1064    if ~exist(maskname,'file')
1065        get_mask_civ2_Callback(hObject, eventdata, handles);
1066    end
1067end
1068if isequal(get(handles.CheckMask,'Value'),1)
1069    maskname=get(handles.Mask,'String');
1070    if ~exist(maskname,'file')
1071        get_mask_fix2_Callback(hObject, eventdata, handles);
1072    end
1073end
1074
1075%% reinitialise status callback
1076if isfield(handles,'status')
1077    set(handles.status,'Value',0);%suppress status display
1078    status_Callback(hObject, eventdata, handles)
1079end
1080
1081%% read the PARAM.xml file to get the binaries (and batch_mode if batch)
1082path_civ=fileparts(which('civ')); %path to the source directory of uvmat
1083xmlfile='PARAM.xml';
1084if exist(xmlfile,'file')% search parameter xml file in the whole matlab path
1085    t=xmltree(xmlfile);
1086    s=convert(t);
1087else
1088    errormsg=['no file ' xmlfile];
1089    return
1090end
1091test_interp=0; %eviter les variables test_ (LG)
1092if batch
1093    if isfield(s,'BatchParam')
1094        Param.xml=s.BatchParam;
1095        if isfield(Param.xml,'BatchMode')
1096            batch_mode=Param.xml.BatchMode;
1097            if ~ismember(batch_mode,{'sge','oar'})
1098                errormsg=['batch mode ' batch_mode ' not supported by UVMAT'];
1099                return
1100            end
1101        end
1102    else
1103        errormsg='no batch civ binaries defined in PARAM.xml';
1104        return
1105    end
1106else % run
1107    if isfield(s,'RunParam')
1108        Param.xml=s.RunParam;
1109    else
1110        errormsg='no run civ binaries defined in PARAM.xml';
1111        return
1112    end
1113end
1114
1115%% check batch mode supported
1116if batch
1117    switch batch_mode
1118        case 'sge'
1119            test_command='qstat';
1120        case 'oar'
1121            test_command='oarstat';
1122    end   
1123    [s,w]=system(test_command);
1124    if ~isequal(s,0)
1125        errormsg=[batch_mode ' batch system not available'];
1126        return
1127    end
1128end
1129
1130%% check if the binaries exist
1131ListProgram=get(handles.ListProgram,'String');
1132CivMode=ListProgram{get(handles.ListProgram,'Value')};
1133binary_list={};
1134switch CivMode
1135    case 'CivX'
1136        binary_list={'Civ1Bin','Civ2Bin','PatchBin','FixBin'};
1137    case 'CivAll'% desactivated option
1138        binary_list={'Civ'};
1139    case 'Matlab'
1140        if batch
1141            binary_list={'CivmBin'};
1142            % verifier MenuMatlab installe sur le cluster
1143            % difficile a faire a priori
1144        end         
1145end
1146for bin_name=binary_list %loop on the list of binaries
1147    if isfield(Param.xml,bin_name{1})% bin_name{1} =current name in the list
1148        if exist(Param.xml.(bin_name{1}),'file')
1149            [path,name,ext]=fileparts(Param.xml.(bin_name{1}));
1150            currentdir=pwd;
1151            if exist(path,'dir')
1152                cd(path);
1153                binpath=pwd;%path of the binary
1154                Param.xml.(bin_name{1})=fullfile(binpath,[name ext]);
1155                cd(currentdir)
1156            else
1157                errormsg=['path ' path ' for binaries defined in PARAM.xml does not exist'];
1158                return
1159            end
1160        else  %look for the full path if the file name has been defined with a relative path in PARAM.xm
1161            fullname=fullfile(path_civ,Param.xml.(bin_name{1}));
1162            if exist(fullname,'file')
1163                Param.xml.(bin_name{1})=fullname;
1164            else
1165                errormsg=['Binary ' Param.xml.(bin_name{1}) ' defined in PARAM.xml does not exist'];
1166                return
1167            end
1168        end
1169    end
1170end
1171display('files OK, processing...')
1172
1173%% set the list of files and check them
1174display('checking the files...')
1175[ref_i,ref_j,errormsg]=find_ref_indices(handles);
1176if ~isempty(errormsg)
1177    return
1178end
1179[filecell,i1_civ1,i2_civ1,j1_civ1,j2_civ1,i1_civ2,i2_civ2,j1_civ2,j2_civ2,nom_type_nc,tild,tild,compare,errormsg]=...
1180    set_civ_filenames(handles,ref_i,ref_j,box_test);
1181if ~isempty(errormsg)
1182    return
1183end
1184% if isempty(filecell)% (error message displayed in fct set_civ_filenames)
1185%     return
1186% end
1187Rootbat=fileparts(filecell.nc.civ1{1,1});%output netcdf file (without extention)
1188set(handles.civ,'UserData',filecell);%store for futur use of status callback
1189nbfield=numel(i1_civ1);
1190nbslice=numel(j1_civ1);
1191if ~strcmp(CivMode,'CivX')
1192    if Param.CheckCiv1
1193        [Param.Civ1.FileTypeA,FileInfo,Param.Civ1.ImageA]=get_file_type(filecell.ima1.civ1{1});
1194        [Param.Civ1.FileTypeB,FileInfo,Param.Civ1.ImageB]=get_file_type(filecell.ima2.civ1{1});
1195    end
1196    if Param.CheckCiv2
1197        [Param.Civ2.FileTypeA,FileInfo,Param.Civ2.ImageA]=get_file_type(filecell.ima1.civ2{1});
1198        [Param.Civ2.FileTypeB,FileInfo,Param.Civ2.ImageB]=get_file_type(filecell.ima2.civ2{1});
1199    end
1200end
1201
1202%% MAIN LOOP
1203time=get(handles.ImaDoc,'UserData'); %get the set of times
1204TimeUnit=get(handles.TimeUnit,'String');
1205checkframe=strcmp(TimeUnit,'frame');
1206batch_file_list=[];%should be renamed file_list, can be used for xml or bash files
1207 
1208for ifile=1:nbfield
1209    for j=1:nbslice
1210        % initiate system command
1211        switch CivMode
1212            case 'CivX'
1213                if isunix % check: necessaire aussi en RUN?
1214                    cmd=['#!/bin/bash \n '...
1215                        '#$ -cwd \n '...
1216                        'hostname && date \n '...
1217                        'umask 002 \n'];%allow writting access to created files for user group
1218                else
1219                    cmd=[];
1220                end
1221            case 'CivAll'
1222                CivAllxml=xmltree;% xml contents,  all parameters
1223                CivAllCmd='';
1224                CivAllxml=set(CivAllxml,1,'name','CivDoc');
1225        end
1226           
1227        % define output file name
1228        if Param.CheckCiv2==1 || Param.CheckFix2==1 || Param.CheckPatch2==1
1229            OutputFile=filecell.nc.civ2{ifile,j};
1230        else
1231            OutputFile=filecell.nc.civ1{ifile,j};
1232        end
1233        OutputFile=regexprep(OutputFile,'.nc','');
1234       
1235        if Param.CheckCiv1
1236            % read image-dependent parameters
1237           
1238            if ~checkframe% && size(time,1)>=i2_civ1(ifile) && size(time,2)>=j2_civ1(j)
1239                Param.Civ1.Dt=(time(i2_civ1(ifile)+1,j2_civ1(j)+1)-time(i1_civ1(ifile)+1,j1_civ1(j)+1));
1240            else
1241                Param.Civ1.Dt=1;
1242            end
1243            Param.Civ1.Time=((time(i2_civ1(ifile)+1,j2_civ1(j)+1)+time(i1_civ1(ifile)+1,j1_civ1(j)+1))/2);
1244            if strcmp(CivMode,'CivX')
1245                Param.Civ1.term_a=num2stra(j1_civ1(j),nom_type_nc);%UTILITE?
1246                Param.Civ1.term_b=num2stra(j2_civ1(j),nom_type_nc);%
1247            end
1248            if isfield(Param.Civ1,'FileTypeA')&&(strcmp(Param.Civ1.FileTypeA,'video')|| strcmp(Param.Civ1.FileTypeA,'mmreader'))
1249                %   ImageInfo=get(VideoReader(fullfile(Param.RootPath,[Param.RootFile Param.ImaExt])));
1250                ImageInfo=get(Param.Civ1.ImageA);
1251                %                 elseif strcmp(Param.Civ1.FileTypeA,'mmreader')
1252                %                     ImageInfo=get(mmreader(fullfile(Param.RootPath,[Param.RootFile Param.ImaExt])));
1253                Param.Civ1.ImageBitDepth=ImageInfo.BitsPerPixel/3;
1254                if batch
1255                    Param.Civ1.ImageA=filecell.ima1.civ1{ifile,j};%file name must be used for batch instead of video object
1256                    Param.Civ1.ImageB=filecell.ima2.civ1{ifile,j};
1257                end
1258            else
1259                Param.Civ1.ImageA=filecell.ima1.civ1{ifile,j};
1260                Param.Civ1.ImageB=filecell.ima2.civ1{ifile,j};
1261               % form=imformats(regexprep(get(handles.ImaExt,'String'),'^.',''));%look for image formats
1262                ImageInfo=imfinfo(filecell.ima1.civ1{1,1});%read the first image to get the size
1263                Param.Civ1.ImageBitDepth=ImageInfo.BitDepth;
1264            end
1265            Param.Civ1.ImageWidth=ImageInfo.Width;
1266            Param.Civ1.ImageHeight=ImageInfo.Height;
1267            Param.Civ1.FrameIndexA=i1_civ1(ifile);
1268            Param.Civ1.FrameIndexB=i2_civ1(ifile);
1269            % read mask )parameters
1270            if Param.Civ1.CheckMask % the lines below should be changed with the new gui
1271                if ~exist(Param.Civ1.Mask,'file')
1272                    maskbase=[filecell.filebase '_' Param.Civ1.Mask]; %
1273                    nbslice_mask=str2double(Param.Civ1.Mask(1:end-4)); %
1274                    i1_mask=mod(i1_civ1(ifile)-1,nbslice_mask)+1;
1275                    [RootPathMask,RootFileMask]=fileparts(maskbase);
1276                    Param.Civ1.Mask=fullfile_uvmat(RootPathMask,[],RootFileMask,'.png','_1',i1_mask);
1277                end
1278            end
1279            % read grid parameters
1280            if Param.Civ1.CheckGrid
1281                if numel(Param.Civ1.Grid)>=4 && isequal(Param.Civ1.Grid(end-3:end),'grid')
1282                    nbslice_grid=str2double(Param.Civ1.Grid(1:end-4)); %
1283                    if ~isnan(nbslice_grid)
1284                        i1_grid=mod(i1_civ1(ifile)-1,nbslice_grid)+1;
1285                        Param.Civ1.Grid=[filecell.filebase '_' fullfile_uvmat('','',Param.Civ1.Grid,'.grid','_1',i1_grid)];
1286                        %                         Param.Civ1.Grid=[filecell.filebase '_' name_generator(Param.Civ1.Grid,i1_grid,1,'.grid','_i')];
1287                        if ~exist(Param.Civ1.GridName,'file')
1288                            errormsg='grid file absent for civ1';
1289                            return
1290                        end
1291                    elseif ~exist(Param.Civ1.Grid,'file')
1292                        errormsg='grid file absent for civ1';
1293                        return
1294                    end
1295                end
1296            end
1297           
1298            % send command
1299            switch CivMode
1300                case 'CivX'
1301                    [cmd_civ,errormsg]=cmd_civ1(filecell.nc.civ1{ifile,j},Param);
1302                    cmd=[cmd cmd_civ '\n'];
1303                    if ~isempty(errormsg)
1304                        return
1305                    end
1306                case 'CivAll'
1307                    CivAllCmd=[CivAllCmd ' civ1 '];
1308                    str=CIV1_CMD_Unified(filecell.nc.civ1{ifile,j},'',Param.Civ1);
1309                    fieldnames=fields(str);
1310                    [CivAllxml,uid_civ1]=add(CivAllxml,1,'element','civ1');
1311                    for ilist=1:length(fieldnames)
1312                        val=eval(['str.' fieldnames{ilist}]);
1313                        if ischar(val)
1314                            [CivAllxml,uid_t]=add(CivAllxml,uid_civ1,'element',fieldnames{ilist});
1315                            [CivAllxml,uid_t2]=add(CivAllxml,uid_t,'chardata',val);
1316                        end
1317                    end
1318            end
1319        end
1320       
1321        if Param.CheckFix1
1322            switch CivMode
1323                case 'CivX'
1324                    cmd=[cmd...
1325                        cmd_fix(filecell.nc.civ1{ifile,j},Param,'Fix1') '\n'];
1326                case 'CivAll'%to abandon
1327                    fix1.inputFileName=filecell.nc.civ1{ifile,j} ;
1328                    fix1.fi1=num2str(param.fix1.flagindex1(1));
1329                    fix1.fi2=num2str(param.fix1.flagindex1(2));
1330                    fix1.fi3=num2str(param.fix1.flagindex1(3));
1331                    fix1.threshC=num2str(param.fix1.thresh_vecC1);
1332                    fix1.threshV=num2str(param.fix1.thresh_vel1);
1333                    fieldnames=fields(fix1);
1334                    [CivAllxml,uid_fix1]=add(CivAllxml,1,'element','fix1');
1335                    for ilist=1:length(fieldnames)
1336                        val=eval(['fix1.' fieldnames{ilist}]);
1337                        if ischar(val)
1338                            [CivAllxml,uid_t]=add(CivAllxml,uid_fix1,'element',fieldnames{ilist});
1339                            [CivAllxml,uid_t2]=add(CivAllxml,uid_t,'chardata',val);
1340                        end
1341                    end
1342                    CivAllCmd=[CivAllCmd ' fix1 '];
1343            end
1344        end
1345       
1346        %CheckPatch1
1347        if Param.CheckPatch1==1
1348            switch CivMode
1349                case 'CivX'
1350                    cmd=[cmd...
1351                        cmd_patch(filecell.nc.civ1{ifile,j},Param,'Patch1') '\n'];
1352                case 'CivAll'
1353                    patch1.inputFileName=filecell.nc.civ1{ifile,j} ;
1354                    patch1.nopt=subdomain_patch1;
1355                    patch1.maxdiff=thresh_patch1;
1356                    patch1.ro=rho_patch1;
1357                    test_grid=get(handles.get_gridpatch1,'Value');
1358                    if test_grid
1359                        patch1.gridflag='y';
1360                        gridname=get(handles.grid_patch1,'String');
1361                        if isequal(gridname(end-3:end),'grid')
1362                            nbslice_grid=str2double(gridname(1:end-4)); %
1363                            if ~isnan(nbslice_grid)
1364                                i1_grid=mod(i1_civ1(ifile)-1,nbslice_grid)+1;
1365                                patch1.gridPatch=[filecell.filebase '_' fullfile_uvmat('','',gridname,'.grid','_1',i1_grid)];
1366%                                 patch1.gridPatch=[filecell.filebase '_' name_generator(gridname,i1_grid,1,'.grid','_i')];
1367                                if ~exist(patch1.gridPatch,'file')
1368                                    errormsg='grid file absent for patch1';
1369                                    return
1370                                end
1371                            elseif exist(gridname,'file')
1372                                patch1.gridPatch=gridname;
1373                            else
1374                                errormsg='grid file absent for patch1';
1375                                return
1376                            end
1377                        end
1378                    else
1379                        patch1.gridPatch='none';
1380                        patch1.gridflag='n';
1381                        patch1.m=nx_patch1;
1382                        patch1.n=ny_patch1;
1383                    end
1384                    patch1.convectFlow='n';
1385                    fieldnames=fields(patch1);
1386                    [CivAllxml,uid_patch1]=add(CivAllxml,1,'element','patch1');
1387                    for ilist=1:length(fieldnames)
1388                        val=eval(['patch1.' fieldnames{ilist}]);
1389                        if ischar(val)
1390                            [CivAllxml,uid_t]=add(CivAllxml,uid_patch1,'element',fieldnames{ilist});
1391                            [CivAllxml,uid_t2]=add(CivAllxml,uid_t,'chardata',val);
1392                        end
1393                    end
1394                    CivAllCmd=[CivAllCmd ' patch1 '];
1395            end
1396        end
1397        if Param.CheckCiv2==1
1398            if isfield(Param.Civ2,'FileTypeA') &&(strcmp(Param.Civ2.FileTypeA,'video')|| strcmp(Param.Civ2.FileTypeA,'mmreader'))
1399                %   ImageInfo=get(VideoReader(fullfile(Param.RootPath,[Param.RootFile Param.ImaExt])));
1400                ImageInfo=get(Param.Civ2.ImageA);
1401                %                 elseif strcmp(Param.Civ1.FileTypeA,'mmreader')
1402                %                     ImageInfo=get(mmreader(fullfile(Param.RootPath,[Param.RootFile Param.ImaExt])));
1403                Param.Civ2.ImageBitDepth=ImageInfo.BitsPerPixel/3;
1404                if batch
1405                    Param.Civ2.ImageA=filecell.ima1.civ2{ifile,j};%file name must be used for batch instead of video object
1406                    Param.Civ2.ImageB=filecell.ima2.civ2{ifile,j};
1407                end
1408            else
1409                Param.Civ2.ImageA=filecell.ima1.civ2{ifile,j};
1410                Param.Civ2.ImageB=filecell.ima2.civ2{ifile,j};
1411                form=imformats(regexprep(get(handles.ImaExt,'String'),'^.',''));%look for image formats
1412                ImageInfo=imfinfo(filecell.ima1.civ2{1,1});%read the first image to get the size
1413                Param.Civ2.ImageBitDepth=ImageInfo.BitDepth;
1414            end
1415           
1416            if ~checkframe %&& size(time,1)>=i2_civ2(ifile) && size(time,2)>=j2_civ2(j)
1417                Param.Civ2.Dt=time(i2_civ2(ifile)+1,j2_civ2(j)+1)-time(i1_civ2(ifile)+1,j1_civ2(j)+1);
1418            else
1419                Param.Civ2.Dt=1;
1420            end
1421            Param.Civ2.Time=(time(i2_civ2(ifile)+1,j2_civ2(j)+1)+time(i1_civ2(ifile)+1,j1_civ2(j)+1))/2;
1422            if strcmp(CivMode,'CivX')
1423            Param.Civ2.term_a=num2stra(j1_civ2(j),nom_type_nc);
1424            Param.Civ2.term_b=num2stra(j2_civ2(j),nom_type_nc);
1425            end
1426            Param.Civ2.filename_nc1=filecell.nc.civ1{ifile,j};
1427            Param.Civ2.filename_nc1(end-2:end)=[]; % remove '.nc'
1428           
1429            % mask
1430            if Param.Civ2.CheckMask
1431                if ~exist(Param.Civ2.Mask,'file')
1432                    maskbase=[filecell.filebase '_' Param.Civ2.Mask]; %
1433                    nbslice_mask=str2double(Param.Civ2.Mask(1:end-4)); %
1434                    i1_mask=mod(i1_civ2(ifile)-1,nbslice_mask)+1;
1435                    [RootPathMask,RootFileMask]=fileparts(maskbase);
1436                    Param.Civ2.Mask=fullfile_uvmat(RootPathMask,[],RootFileMask,'.png','_1',i1_mask);
1437%                     Param.Civ2.Mask=name_generator(maskbase,i1_mask,1,'.png','_i');
1438                end
1439            end
1440            %grid
1441            if Param.Civ2.CheckGrid
1442                if numel(Param.Civ2.Grid)>=4 && isequal(Param.Civ2.Grid(end-3:end),'grid')
1443                    nbslice_grid=str2double(Param.Civ2.Grid(1:end-4)); %
1444                    if ~isnan(nbslice_grid)
1445                        i1_grid=mod(i1_civ2(ifile)-1,nbslice_grid)+1;
1446                        Param.Civ2.Grid=[filecell.filebase '_' fullfile_uvmat('','',gridname,'.grid','_1',i1_grid)];
1447%                         Param.Civ2.Grid=[filecell.filebase '_' name_generator(gridname,i1_grid,1,'.grid','_i')];
1448                    end
1449                end
1450            end
1451            form=imformats(regexprep(get(handles.ImaExt,'String'),'^.',''));%look for image formats
1452            if isempty(form)
1453               % ImageInfo=get(VideoReader(fullfile());
1454                Param.Civ2.ImageBitDepth=ImageInfo.BitsPerPixel/3;
1455            else
1456                ImageInfo=imfinfo(filecell.ima1.civ2{1,1});%read the first image to get the size
1457                Param.Civ2.ImageBitDepth=ImageInfo.BitDepth;
1458            end
1459            Param.Civ2.ImageWidth=ImageInfo.Width;
1460            Param.Civ2.ImageHeight=ImageInfo.Height;
1461            Param.Civ2.FrameIndexA=i1_civ2(ifile);
1462             Param.Civ2.FrameIndexB=i2_civ2(ifile);
1463%             Param.Civ2.i1=i1_civ2(ifile);
1464%             Param.Civ2.i2=i2_civ2(ifile);
1465            switch CivMode
1466                case 'CivX'
1467                    cmd=[cmd...
1468                        cmd_civ2(filecell.nc.civ2{ifile,j},Param) '\n'];
1469                case 'CivAll'
1470                    CivAllCmd=[CivAllCmd ' civ2 '];
1471                    str=CIV2_CMD_Unified(filecell.nc.civ2{ifile,j},'',Param.Civ2);
1472                    fieldnames=fields(str);
1473                    [CivAllxml,uid_civ2]=add(CivAllxml,1,'element','civ2');
1474                    for ilist=1:length(fieldnames)
1475                        val=eval(['str.' fieldnames{ilist}]);
1476                        if ischar(val)
1477                            [CivAllxml,uid_t]=add(CivAllxml,uid_civ2,'element',fieldnames{ilist});
1478                            [CivAllxml,uid_t2]=add(CivAllxml,uid_t,'chardata',val);
1479                        end
1480                    end
1481            end
1482        end
1483       
1484        % CheckFix2
1485        if Param.CheckFix2==1
1486            switch CivMode
1487                case 'CivX'
1488                    cmd=[cmd...
1489                        cmd_fix(filecell.nc.civ2{ifile,j},Param,'Fix2') '\n'];
1490                case 'CivAll'
1491                    fix2.inputFileName=filecell.nc.civ2{ifile,j} ;
1492                    fix2.fi1=num2str(flagindex2(1));
1493                    fix2.fi2=num2str(flagindex2(2));
1494                    fix2.fi3=num2str(flagindex2(3));
1495                    fix2.threshC=num2str(thresh_vec2C);
1496                    fix2.threshV=num2str(thresh_vel2);
1497                    fieldnames=fields(fix2);
1498                    [CivAllxml,uid_fix2]=add(CivAllxml,1,'element','fix2');
1499                    for ilist=1:length(fieldnames)
1500                        val=eval(['fix2.' fieldnames{ilist}]);
1501                        if ischar(val)
1502                            [CivAllxml,uid_t]=add(CivAllxml,uid_fix2,'element',fieldnames{ilist});
1503                            [CivAllxml,uid_t2]=add(CivAllxml,uid_t,'chardata',val);
1504                        end
1505                    end
1506                    CivAllCmd=[CivAllCmd ' fix2 '];
1507            end
1508        end
1509       
1510        %CheckPatch2
1511        if Param.CheckPatch2==1
1512           
1513            switch CivMode
1514               
1515                case 'CivX'
1516                    cmd=[cmd...
1517                        cmd_patch(filecell.nc.civ1{ifile,j},Param,'Patch2') '\n'];
1518                   
1519                case 'CivAll'
1520                    patch2.inputFileName=filecell.nc.civ1{ifile,j} ;
1521                    patch2.nopt=subdomain_patch2;
1522                    patch2.maxdiff=thresh_patch2;
1523                    patch2.ro=rho_patch2;
1524                    test_grid=get(handles.get_gridpatch2,'Value');
1525                    if test_grid
1526                        patch2.gridflag='y';
1527                        gridname=get(handles.grid_patch2,'String');
1528                        if isequal(gridname(end-3:end),'grid')
1529                            nbslice_grid=str2double(gridname(1:end-4)); %
1530                            if ~isnan(nbslice_grid)
1531                                i1_grid=mod(i1_civ2(ifile)-1,nbslice_grid)+1;
1532                                patch2.gridPatch=[filecell.filebase '_' fullfile_uvmat('','',gridname,'.grid','_1',i1_grid)];
1533%                                 patch2.gridPatch=[filecell.filebase '_' name_generator(gridname,i1_grid,1,'.grid','_i')];
1534                                if ~exist(patch2.gridPatch,'file')
1535                                    errormsg='grid file absent for patch2';
1536                                    return
1537                                end
1538                            elseif exist(gridname,'file')
1539                                patch2.gridPatch=gridname;
1540                            else
1541                                errormsg='grid file absent for patch2';
1542                                return
1543                            end
1544                        end
1545                    else
1546                        patch2.gridPatch='none';
1547                        patch2.gridflag='n';
1548                        patch2.m=nx_patch2;
1549                        patch2.n=ny_patch2;
1550                    end
1551                    patch2.convectFlow='n';
1552                    fieldnames=fields(patch2);
1553                    [CivAllxml,uid_patch2]=add(CivAllxml,1,'element','patch2');
1554                    for ilist=1:length(fieldnames)
1555                        val=eval(['patch2.' fieldnames{ilist}]);
1556                        if ischar(val)
1557                            [CivAllxml,uid_t]=add(CivAllxml,uid_patch2,'element',fieldnames{ilist});
1558                            [CivAllxml,uid_t2]=add(CivAllxml,uid_t,'chardata',val);
1559                        end
1560                    end
1561                    CivAllCmd=[CivAllCmd ' patch2 '];
1562            end
1563        end
1564       
1565        switch CivMode
1566           
1567            case {'CivX','CivAll'}
1568                if isequal(CivMode,'CivAll')
1569                    save(CivAllxml,[OutputFile '.xml']);
1570                    cmd=[cmd sparam.CivBin ' -f ' OutputFile '.xml '  CivAllCmd ' >' OutputFile '.log' '\n'];
1571                end             
1572                % create the .bat file used in run or batch
1573                filename_bat=[OutputFile '.bat'];
1574                [fid,message]=fopen(filename_bat,'w');
1575                if isequal(fid,-1)
1576                    errormsg=['creation of .bat file: ' message];
1577                    return
1578                end
1579                fprintf(fid,cmd);
1580                fclose(fid);           
1581                if isunix
1582                    system(['chmod +x ' filename_bat]);
1583                end             
1584                batch_file_list{length(batch_file_list)+1}=filename_bat;
1585               
1586            case 'Matlab'
1587                drawnow
1588                if ~strcmp(compare,'stereo PIV')
1589                    filename_xml=[OutputFile '.civ.xml'];
1590                    t=struct2xml(Param);           
1591                    save(t,filename_xml)
1592                    if batch   
1593                        path_civ=fileparts(which('civ'));
1594                        filename_bat=[OutputFile '.bat'];
1595                        [fid,message]=fopen(filename_bat,'w');
1596                        if isequal(fid,-1)
1597                            errormsg= ['creation of .bat file: ' message];
1598                            return
1599                        end
1600%                         text_matlabscript=[...
1601%                         '#!/bin/bash \n'...
1602%                         '. /etc/sysprofile \n'...
1603%                         'matlab -nodisplay -nosplash -nojvm <<END_MATLAB \n'...
1604%                         'cd(''' path_civ '''); \n'...
1605%                         'civ_matlab(''' filename_xml ''',''' OutputFile '.nc''); \n'...
1606%                         'exit \n'...
1607%                         'END_MATLAB \n'];
1608                        cmd=['#!/bin/bash \n '...
1609                        '#$ -cwd \n '...
1610                        'hostname && date \n '...
1611                        'umask 002 \n'...
1612                         Param.xml.CivmBin ' ' Param.xml.RunTime ' ' filename_xml ' ' OutputFile '.nc'];%allow writting access to created files for user group
1613                   
1614                        fprintf(fid,cmd);
1615                        fclose(fid);
1616                        if isunix
1617                            system(['chmod +x ' filename_bat]);
1618                        end
1619                        batch_file_list{length(batch_file_list)+1}=filename_bat;
1620                    else
1621                        [tild,errormsg]=civ_matlab(Param,filecell.nc.civ1{ifile,j});
1622                        if isempty(errormsg)
1623                            display([filecell.nc.civ1{ifile,j} ' written'])
1624                        end
1625                    end
1626                end
1627        end
1628    end
1629end
1630
1631if batch 
1632    switch batch_mode   
1633       
1634        case 'sge' %at the moment only psmn ENS Lyon uses it
1635            for p=1:length(batch_file_list)
1636                %cmd=['!qsub -p ' pvalue ' -q civ.q -e ' flname '.errors -o ' flname '.log' ' ' batch_file_list{p}];
1637                cmd=['!qsub -q piv1,piv2,piv3 '...
1638                    '-e ' regexprep(batch_file_list{p},'.bat','.errors') ' -o ' regexprep(batch_file_list{p},'.bat','.log ')...
1639                    ' -v ' 'LD_LIBRARY_PATH=/home/sjoubaud/matlab_sylvain/civx/lib ' batch_file_list{p}];               
1640                display(cmd);eval(cmd);
1641            end           
1642        case 'oar_old'
1643                for p=1:length(batch_file_list)
1644                    oar_command=['!oarsub -n CIVX -q nicejob '...
1645                   '-E ' regexprep(batch_file_list{p},'.bat','.errors') ' -O ' regexprep(batch_file_list{p},'.bat','.log ')...
1646                    '-l "/core=1+{type = ''smalljob''}/licence=1,walltime=00:60:00"   ' batch_file_list{p}];
1647                display(oar_command);eval(oar_command);
1648                end               
1649        case 'oar'
1650           
1651            max_walltime=3600*12; % 12h max
1652            oar_modes={'oar-parexec','oar-dispatch','mpilauncher'};
1653            text={'Batch processing on servcalcul3 LEGI';...
1654                'Please choose one of the followint modes';...
1655                '* oar-parexec : default and best choice';...
1656                '* oar-dispatch : jobs in a container of several cores';...
1657                '* mpilauncher : one single parallel mpi job using several cores';...
1658                '**********************************'...
1659                };
1660            [S,v]=listdlg('PromptString',text,'ListString',oar_modes,...
1661                'SelectionMode','single','ListSize',[400 100],'Name','LEGI job mode');
1662            switch oar_modes{S}
1663                case 'oar-parexec' %oar-dispatch.pl
1664                    answer=inputdlg({'Number of cores (max 36)','extra oar options'},'oarsub parameter',1,{'12',''});
1665                    ncores=str2double(answer{1});
1666                    extra_oar=answer{2};
1667                    walltime_onejob=600;%seconds
1668                    filename_joblist=fullfile(Rootbat,'job_list.txt');
1669                    fid=fopen(filename_joblist,'w');
1670                    for p=1:length(batch_file_list)
1671                        fprintf(fid,[batch_file_list{p} '\n']);
1672                    end
1673                    fclose(fid)
1674                    oar_command=['oarsub -n CIVX '...
1675                        '-t idempotent --checkpoint ' num2str(walltime_onejob+60) ' '...
1676                        '-l /core=' num2str(ncores) ','...
1677                            'walltime=' datestr(min(1.05*walltime_onejob/86400*max(length(batch_file_list),ncores)/ncores,max_walltime/86400),13) ' '...
1678                        '-E ' regexprep(filename_joblist,'\.txt\>','.stderr') ' '...
1679                        '-O ' regexprep(filename_joblist,'\.txt\>','.stdout') ' '...
1680                        extra_oar ' '...
1681                        '"oar-parexec -s -f ' filename_joblist ' '...
1682                            '-l ' filename_joblist '.log"'];
1683                    filename_oarcommand=fullfile(Rootbat,'oar_command');
1684                    fid=fopen(filename_oarcommand,'w');
1685                    fprintf(fid,[oar_command '\n']);
1686                    fclose(fid);
1687                    display(oar_command);
1688                    eval(['! . ' filename_oarcommand])
1689                case 'oar-dispatch' %oar-dispatch.pl
1690                    ncores=str2double(...
1691                        inputdlg('Number of cores (max 36)','oarsub parameter',1,{'6'})...
1692                        );
1693                    walltime_onejob=600;%seconds
1694                    filename_joblist=fullfile(Rootbat,'job_list.txt');
1695                    fid=fopen(filename_joblist,'w');
1696                    for p=1:length(batch_file_list)
1697                        oar_command=['oarsub -n CIVX '...
1698                            '-E ' regexprep(batch_file_list{p},'\.bat\>','.stderr') ' -O ' regexprep(batch_file_list{p},'\.bat\>','.stdout ')...
1699                            '-l "/core=1,walltime=' datestr(walltime_onejob/86400,13) '"   ' batch_file_list{p}];
1700                        fprintf(fid,[oar_command '\n']);
1701                    end
1702                    fclose(fid);
1703                    oar_command=['oarsub -t container -n civx-container '...
1704                        '-l /core=' num2str(ncores)...
1705                        ',walltime=' datestr(1.05*walltime_onejob/86400*max(length(batch_file_list),ncores)/ncores,13) ' '...
1706                        '-E ' regexprep(filename_joblist,'\.txt\>','.stderr') ' '...
1707                        '-O ' regexprep(filename_joblist,'\.txt\>','.stdout') ' '...
1708                        '"oar-dispatch -f ' filename_joblist '"'];
1709                    filename_oarcommand=fullfile(Rootbat,'oar_command');
1710                    fid=fopen(filename_oarcommand,'w');
1711                    fprintf(fid,[oar_command '\n']);
1712                    fclose(fid);
1713                    display(oar_command);
1714                    eval(['! . ' filename_oarcommand])
1715                case 'mpilauncher'
1716                    filename_joblist=fullfile(Rootbat,'job_list.txt');
1717                    fid=fopen(filename_joblist,'w');
1718                   
1719                    for p=1:length(batch_file_list)
1720                        fprintf(fid,[batch_file_list{p} '\n']);
1721                    end
1722                    fclose(fid)
1723                    text_oarscript=[...
1724                        '#!/bin/bash \n'...
1725                        '#OAR -n Mylauncher \n'...
1726                        '#OAR -l node=4/core=5,walltime=0:15:00 \n'...
1727                        '#OAR -E ' fullfile(Rootbat,'stderrfile.log') ' \n'...
1728                        '#OAR -O ' fullfile(Rootbat,'stdoutfile.log') ' \n'...
1729                        '# ========================================================= \n'...
1730                        '# This simple program launch a multinode parallel OpenMPI mpilauncher \n'...
1731                        '# application for coriolis PIV post-processing. \n'...
1732                        '# OAR uses oarshmost wrapper to propagate the user environement. \n'...
1733                        '# This wrapper assert that the user has the same environment on all the \n'...
1734                        '# allocated nodes (basic behavior needed by most MPI applications).  \n'...
1735                        '# \n'...
1736                        '# REQUIREMENT: \n'...
1737                        '# the oarshmost wrapper should be installed in $HOME/bin directory. \n'...
1738                        '# If a different location is used, change the line following the comment "Bidouille" \n'...
1739                        '# ========================================================= \n'...
1740                        '#   USER should only modify these 2 lines  \n'...
1741                        'WORKDIR=' pwd ' \n'...
1742                        'COMMANDE="mpilauncher  -f ' filename_joblist '" \n'...
1743                        '# ========================================================= \n'...
1744                        '# DO NOT MODIFY the FOLOWING LINES. (or be carefull) \n'...
1745                        'echo "job starting on: "`hostname` \n'...
1746                        'MPINODES="-host `tr [\\\\\\n] [,] <$OAR_NODEFILE |sed -e "s/,$/ /"`" \n'...
1747                        'NCPUS=`cat $OAR_NODEFILE |wc -l` \n'...
1748                        '#========== Bidouille ============== \n'...
1749                        'export OMPI_MCA_plm_rsh_agent=oar-envsh \n'...%                     'cd $WORKDIR \n'...
1750                        'CMD="mpirun -np $NCPUS -wdir $WORKDIR $MPINODES $COMMANDE" \n'...
1751                        'echo "I run: $CMD"  \n'...
1752                        '$CMD \n'...
1753                        'echo "job ending" \n'...
1754                        ];
1755                    %                 oarsub -S ./oar.sub
1756                    filename_oarscript=fullfile(Rootbat,'oar_command');
1757                    fid=fopen(filename_oarscript,'w');
1758                    fprintf(fid,[text_oarscript]);
1759                    fclose(fid);
1760                    eval(['!chmod +x  ' filename_oarscript]);
1761                    eval(['!oarsub -S ' filename_oarscript]);
1762            end
1763    end
1764else
1765    if ~isequal(CivMode,'Matlab')
1766        filename_superbat=fullfile(Rootbat,'job_list.bat');
1767        fid=fopen(filename_superbat,'w');
1768        if fid==-1
1769            msgbox_uvmat('ERROR',['cannot create the command file ' filename_superbat])
1770            return
1771        end
1772        for p=1:length(batch_file_list)
1773            if isunix
1774                fprintf(fid,['sh ' batch_file_list{p} '\n']);
1775            else
1776                fprintf(fid,['@call "' regexprep(batch_file_list{p},'\\','\\\\') '"' '\n']);
1777            end
1778        end
1779        fclose(fid);
1780        if(isunix)
1781            system(['chmod +x ' filename_superbat]);
1782        end
1783        system([filename_superbat ' &']);% execute main commmand
1784    end
1785end
1786
1787
1788%% save interface state
1789if isfield(filecell,'nc')
1790    if isfield(filecell.nc,'civ2')
1791        fileresu=filecell.nc.civ2{1,1};
1792    else
1793        fileresu=filecell.nc.civ1{1,1};
1794    end
1795end
1796[RootPath,SubDir,RootFile]=fileparts_uvmat(fileresu);
1797namedoc=fullfile(RootPath,SubDir,RootFile);
1798detect=1;
1799while detect==1
1800    namefigfull=[namedoc '.fig'];
1801    hh=dir(namefigfull);
1802    if ~isempty(hh)
1803        detect=1;
1804        namedoc=[namedoc '.0'];
1805    else
1806        detect=0;
1807    end
1808end
1809Param=rmfield(Param,'status');
1810Param=rmfield(Param,'xml');
1811t=struct2xml(Param);
1812t=set(t,1,'name','Civ');% set the head label
1813save(t,[namedoc '.civ.xml']); %save GUI  parameters as xml file
1814saveas(gcbf,namefigfull);%save the interface with name namefigfull (A CHANGER EN FICHIER  .xml)
1815
1816%Save info in personal profile (initiate browser next time) TODO
1817MenuFile={};
1818dir_perso=prefdir;
1819profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
1820if exist(profil_perso,'file')
1821    hh=load (profil_perso);
1822      if isfield(hh,'MenuFile')
1823          MenuFile=hh.MenuFile;
1824      end
1825      if isfield(filecell.nc,'civ2')
1826          MenuFile=[filecell.nc.civ2{1,1}; MenuFile];
1827      else
1828           MenuFile=[filecell.nc.civ1{1,1}; MenuFile];
1829      end
1830      save (profil_perso,'MenuFile','-append'); %store the file names for future opening of uvmat
1831else
1832    MenuFile=filecell.ima1.civ1(1,1);
1833    save (profil_perso,'MenuFile')
1834end
1835
1836%------------------------------------------------------------------------
1837% --- determine the list of reference indices of processing file
1838function [ref_i,ref_j,errormsg]=find_ref_indices(handles)
1839%------------------------------------------------------------------------
1840errormsg=''; %default error message
1841first_i=str2double(get(handles.first_i,'String'));%first index i
1842last_i=str2double(get(handles.last_i,'String'));%last index i
1843incr_i=str2double(get(handles.incr_i,'String'));% increment
1844if isequal(get(handles.first_j,'Visible'),'on')
1845    first_j=str2double(get(handles.first_j,'String'));%first index j
1846    last_j=str2double(get(handles.last_j,'String'));%last index j
1847    incr_j=str2double(get(handles.incr_j,'String'));% increment
1848else
1849    first_j=1;
1850    last_j=1;
1851    incr_j=1;
1852end
1853ref_i=first_i:incr_i:last_i;% list of i indices (reference values for each pair)
1854ref_j=first_j:incr_j:last_j;% list of j indices (reference values for each pair)
1855if isnan(first_i)||isnan(first_j)
1856    errormsg='first field number not defined';
1857elseif isnan(last_i)||isnan(last_j)
1858    errormsg='last field number not defined';
1859elseif isnan(incr_i)||isnan(incr_j)
1860    errormsg='increment in field number not defined';
1861elseif last_i < first_i || last_j < first_j
1862    errormsg='last field number must be larger than the first one';
1863end
1864
1865%------------------------------------------------------------------------
1866% --- determine the list of filenames and indices needed for launch_job
1867%------------------------------------------------------------------------
1868% OUTPUT:
1869% filecell: structure of cell arrays {ref_i,ref_j} containing all the filenames involved in the civ process
1870%    the indices ref_i and ref_j correspond to the list of reference indices
1871%       .filebase=fullfile(RootPath,RootFile) used to construct mask names, grid names, CivDoc xml file
1872%       .ima1.civ1,.ima1.civ2: first image for civ1 and civ2 respectively (possibly different)
1873%       .ima2.civ1,.ima2.civ2: second image for civ1 and civ2 respectively (possibly different)
1874%       .nc.civ1,.nc.civ2: netcdf files containing civ1 and civ2 data respectively (possibly different)
1875% i1_civ1,i2_civ1,j1_civ1,j2_civ1,i1_civ2,i2_civ2,j1_civ2,j2_civ2: arrays of files indices, needed for timing records
1876function [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]=...
1877    set_civ_filenames(handles,ref_i,ref_j,checkbox)
1878%------------------------------------------------------------------------
1879filecell=[];%default
1880errormsg='';
1881ListProgram=get(handles.ListProgram,'String');
1882CivMode=ListProgram{get(handles.ListProgram,'Value')};%Program to use , CivX or Matlab
1883
1884%% get the root name and check dir
1885RootPath=get(handles.RootPath,'String');
1886SubdirImages=get(handles.SubdirImages,'String');
1887RootFile=get(handles.RootFile,'String');
1888filecell.filebase=fullfile(RootPath,SubdirImages,RootFile);
1889if isempty(filecell.filebase)
1890    errormsg='please open an image with the upper menu option Open/Browse...';
1891    return
1892end
1893if ~exist(RootPath,'dir')
1894    errormsg=['path to images ' RootPath ' not found'];
1895    return
1896end
1897[tild,message]=fileattrib(RootPath);
1898if ~isempty(message) && ~isequal(message.UserWrite,1)
1899    errormsg=['No writting access to ' RootPath];
1900    return
1901end
1902%check result directory
1903subdir_civ1=regexprep(get(handles.SubdirCiv1,'String'),'^.','');%subdirectory subdir_civ1 for the netcdf output data
1904subdir_civ2=regexprep(get(handles.SubdirCiv2,'String'),'^.','');
1905if isequal(subdir_civ1,''),subdir_civ1='civ'; end% put default subdir
1906% subdir_civ1=[ '.' subdir_civ1];
1907% subdir_civ2=[ '.' subdir_civ2];
1908if isequal(subdir_civ2,''),subdir_civ2=subdir_civ1; end% put default subdir
1909subdir_civ1=[SubdirImages '.' subdir_civ1];
1910subdir_civ2=[SubdirImages '.' subdir_civ2];
1911
1912%% choose root names depending on ListCompareMode =displacement, shift, PIV or stereo PIV
1913ListCompareMode=get(handles.ListCompareMode,'String');
1914compare=ListCompareMode{get(handles.ListCompareMode,'Value')};
1915
1916% set the nomenclature type of the nc files depending on the pair mode
1917if strcmp(compare,'displacement')||strcmp(compare,'shift')
1918    mode='displacement';
1919else
1920    mode_list=get(handles.ListPairMode,'String');
1921    mode_value=get(handles.ListPairMode,'Value');
1922    mode=mode_list{mode_value};
1923end
1924NomType_ima2=get(handles.NomType,'String');
1925NomType_nc=nomtype2pair(NomType_ima2,mode);
1926
1927% set the rootfile and image indexing
1928RootFile_ima2=get(handles.RootFile,'String');%root file for the second image series
1929ext_ima=get(handles.ImaExt,'String'); % image extension (the same for all images)
1930switch compare
1931    case 'PIV'
1932       RootFile_ima1=RootFile_ima2;% root name of the two image series is the same
1933       NomType_ima1=NomType_ima2;% the index of the first image follows the index of the second one
1934       RootFile_nc=RootFile_ima2;
1935    case 'displacement'
1936       RootFile_ima1=get(handles.RootFile_1,'String');% root name of the first image series set by handles.RootFile_1
1937       NomType_ima1='';% no indexing of the first image, a fixed reference for the whole series
1938       RootFile_nc=RootFile_ima2;
1939    case 'shift'
1940       RootFile_ima1=get(handles.RootFile_1,'String');% root name of the first image series set by handles.RootFile_1
1941       NomType_ima1=NomType_ima2;% the index of the first image follows the index of the second one
1942       RootFile_nc=[RootFile_ima1 '-' RootFile_ima2];
1943end
1944
1945%determine the list of file indices involved
1946[i1_civ1,i2_civ1,j1_civ1,j2_civ1,i1_civ2,i2_civ2,j1_civ2,j2_civ2]=...
1947    find_pair_indices(handles,ref_i,ref_j,mode);
1948
1949%determine the new filebase for 'displacement' ListPairMode (comparison of two series)
1950%filebase_B=filebase;% root name of the second field series for stereo
1951% filebase_A=filebase;%default
1952% if strcmp(compare,'PIV')
1953%     filebase_AB=filebase;
1954% else
1955%     [Path2,Name2]=fileparts(filebase_B);
1956%     Name1=RootFile_ima1;
1957%     filebase_AB=fullfile(Path2,[Name2 '-' Name1]);   
1958% end
1959% [RootPath_AB,RootFile_AB]=fileparts(filebase_AB);
1960% % [RootPath_ima1,RootFile_ima1]=fileparts(filebase_B);
1961% [RootPath_ima2,RootFile_ima2]=fileparts(filebase_B);
1962% [RootPath_nc,RootFile_nc]=fileparts(filebase_B);%default
1963% if strcmp(compare,'displacement')
1964% %     [RootPath_ima1,RootFile_ima1]=fileparts(filebase_B);
1965% %     [RootPath_ima2,RootFile_ima2]=fileparts(filebase_B);
1966%     [RootPath_nc,RootFile_nc]=fileparts(filebase_B);
1967% elseif strcmp(compare,'shift')
1968%     RootPath_nc=RootPath_AB;
1969%     RootFile_nc=RootFile_AB;
1970% end
1971% else
1972%     filebase_ima1=filebase_B;
1973%     filebase_ima2=filebase_B;
1974%     filebase_nc=filebase_B;
1975% [RootPath_ima1,RootFile_ima1]=fileparts(filebase_ima1);
1976% [RootPath_ima2,RootFile_ima2]=fileparts(filebase_ima2);
1977% [RootPath_nc,RootFile_nc]=fileparts(filebase_nc);
1978% [RootPath_A,RootFile_A]=fileparts(filebase_A);
1979
1980   
1981%% determine reference files for fix:
1982file_ref_fix1={};%default
1983file_ref_fix2={};
1984nbfield=length(i1_civ1);
1985nbslice=length(j1_civ1);
1986if checkbox(2)==1% fix1 performed
1987    ref=get(handles.ref_fix1,'UserData');%read data on the ref file stored by get_ref_fix1_Callback
1988    if ~isempty(ref)
1989        first_i=str2double(get(handles.first_i,'String'));
1990        last_i=str2double(get(handles.last_i,'String'));
1991        incr_i=str2double(get(handles.incr_i,'String'));
1992        first_j=str2double(get(handles.first_j,'String'));
1993        last_j=str2double(get(handles.last_j,'String'));
1994        incr_j=str2double(get(handles.incr_j,'String'));
1995        num_i_ref=first_i:incr_i:last_i;
1996        num_j_ref=first_j:incr_j:last_j;
1997        if isequal(mode,'displacement')
1998            num_i1=num_i_ref;
1999            num_i2=num_i_ref;
2000            num_j1=num_j_ref;
2001            num_j2=num_j_ref;
2002        elseif isequal(mode,'pair j1-j2')% isequal(mode,'st_pair j1-j2')
2003            num_i1=num_i_ref;
2004            num_i2=num_i1;
2005            num_j1=ref.num_a*ones(size(num_i_ref));
2006            num_j2=ref.num_b*ones(size(num_i_ref));
2007        elseif isequal(mode,'series(Di)') % isequal(mode,'st_series(Di)')
2008            delta1=floor((ref.num2-ref.num1)/2);
2009            delta2=ceil((ref.num2-ref.num1)/2);
2010            num_i1=num_i_ref-delta1*ones(size(num_i_ref));
2011            num_i2=num_i_ref+delta2*ones(size(num_i_ref));
2012            if isempty(ref.num_a)
2013                ref.num_a=1;
2014            end
2015            num_j1=ref.num_a*ones(size(num_i1));
2016            num_j2=num_j1;
2017        elseif isequal(mode,'series(Dj)')%| isequal(mode,'st_series(Dj)')
2018            delta1=floor((ref.num_b-ref.num_a)/2);
2019            delta2=ceil((ref.num_b-ref.num_a)/2);
2020            num_i1=ref.num1*ones(size(num_i_ref));
2021            num_i2=num_i1;
2022            num_j1=num_j_ref-delta1*ones(size(num_j_ref));
2023            num_j2=num_j_ref+delta2*ones(size(num_j_ref));
2024        end
2025        for ifile=1:nbfield
2026            for j=1:nbslice
2027                [RootPathRef,RootFile]=fileparts(ref.filebase);
2028                file_ref=fullfile_uvmat(RootPathRef,ref.subdir,RootFile,'.nc',ref.NomType,num_i1(ifile),num_i2(ifile),num_j1(j),num_j2(j));
2029                file_ref_fix1(ifile,j)={file_ref};
2030                if ~exist(file_ref,'file')
2031                    errormsg=['reference file ' file_ref ' not found for fix1'];
2032                    return
2033                end
2034            end
2035        end
2036    end
2037end
2038
2039%% determine reference files for fix2:
2040if checkbox(5)==1% fix2 performed
2041    ref=get(handles.ref_fix2,'UserData');
2042    if ~isempty(ref)
2043        first_i=str2double(get(handles.first_i,'String'));
2044        last_i=str2double(get(handles.last_i,'String'));
2045        incr_i=str2double(get(handles.incr_i,'String'));
2046        first_j=str2double(get(handles.first_j,'String'));
2047        last_j=str2double(get(handles.last_j,'String'));
2048        incr_j=str2double(get(handles.incr_j,'String'));
2049        num_i_ref=first_i:incr_i:last_i;
2050        num_j_ref=first_j:incr_j:last_j;
2051        if isequal(mode,'displacement')
2052            num_i1=num_i_ref;
2053            num_i2=num_i_ref;
2054            num_j1=num_j_ref;
2055            num_j2=num_j_ref;
2056        elseif isequal(mode,'pair j1-j2')
2057            num_i1=num_i_ref;
2058            num_i2=num_i1;
2059            num_j1=ref.num_a;
2060            num_j2=ref.num_b;
2061        elseif isequal(mode,'series(Di)')
2062            delta1=floor((ref.num2-ref.num1)/2);
2063            delta2=ceil((ref.num2-ref.num1)/2);
2064            num_i1=num_i_ref-delta1*ones(size(num_i_ref));
2065            num_i2=num_i_ref+delta2*ones(size(num_i_ref));
2066            num_j1=ref.num_a*ones(size(num_i1));
2067            num_j2=num_j1;
2068        elseif isequal(mode,'series(Dj)')
2069            delta1=floor((ref.num_b-ref.num_a)/2);
2070            delta2=ceil((ref.num_b-ref.num_a)/2);
2071            num_i1=ref.num1*ones(size(num_i_ref));
2072            num_i2=num_i1;
2073            num_j1=num_j_ref-delta1*ones(size(num_j_ref));
2074            num_j2=num_j_ref+delta2*ones(size(num_j_ref));
2075        end
2076        for ifile=1:nbfield
2077            for j=1:nbslice
2078                [RootPathRef,RootFile]=fileparts(ref.filebase);
2079                file_ref=fullfile_uvmat(RootPathRef,ref.subdir,RootFile,'.nc',ref.NomType,num_i1(ifile),num_i2(ifile),num_j1(j),num_j2(j));
2080                file_ref_fix2(ifile,j)={file_ref};
2081                if ~exist(file_ref,'file')
2082                    errormsg=['reference file ' file_ref ' not found for fix2'];
2083                    return
2084                end
2085            end
2086        end
2087    end
2088end
2089
2090%% check the existence of the netcdf and image files involved
2091% %%%%%%%%%%%%  case CheckCiv1 activated   %%%%%%%%%%%%%
2092if checkbox(1)==1;
2093    detect=1;
2094    vers=0;
2095    subdir_civ1_new=subdir_civ1;
2096    while detect==1 %create a new subdir if the netcdf files already exist
2097        for ifile=1:nbfield
2098            for j=1:nbslice
2099                filename=fullfile_uvmat(RootPath,subdir_civ1_new,RootFile_nc,'.nc',NomType_nc,i1_civ1(ifile),i2_civ1(ifile),j1_civ1(j),j2_civ1(j));
2100                detect=exist(filename,'file')==2;
2101                if detect% if a netcdf file already exists
2102                    r=regexp(subdir_civ1_new,'(?<root>.*\D)(?<num1>\d+)$','names');%detect whether name ends by a number
2103                    if isempty(r)
2104                        r(1).root=[subdir_civ1_new '_'];
2105                        r(1).num1='0';
2106                    end
2107                    subdir_civ1_new=[r(1).root num2str(str2num(r(1).num1)+1)];%increment the index by 1 or put 1
2108%                     indstr=regexp(subdir_civ1_new,'\D');
2109%                     if indstr(end)<length(subdir_civ1_new) %subdir_civ1 ends by a number
2110%                         vers=str2double(subdir_civ1_new(indstr(end)+1:end))+1;
2111%                         subdir_civ1_new=[subdir_civ1_new(1:indstr(end)) num2str(vers)];
2112%                     else
2113%                         vers=vers+1;
2114%                         subdir_civ1_new=[subdir_civ1_new(1:indstr(end)) '_' num2str(vers)];       
2115%                     end
2116                    subdir_civ2=subdir_civ1_new;
2117                    break
2118                end
2119                filecell.nc.civ1(ifile,j)={filename};
2120            end
2121            if detect% if a netcdf file already exists
2122                break
2123            end
2124        end
2125 
2126        %create the new SubdirCiv1
2127        if ~exist(fullfile(RootPath,subdir_civ1_new),'dir')     
2128            [xx,msg1]=mkdir(fullfile(RootPath,subdir_civ1_new));
2129            if ~strcmp(msg1,'')
2130                errormsg=['cannot create ' subdir_civ1_new ': ' msg1];%error message for directory creation
2131                return
2132            elseif isunix         
2133                [xx,msg2] = fileattrib(fullfile(RootPath,subdir_civ1_new),'+w','g'); %yield writing access (+w) to user group (g)
2134                if ~strcmp(msg2,'')
2135                    errormsg=['pb of permission for  ' fullfile(RootPath,subdir_civ1_new) ': ' msg2];%error message for directory creation
2136                    return
2137                end
2138            end
2139        end
2140        if strcmp(compare,'stereo PIV')&&(strcmp(mode,'pair j1-j2')||strcmp(mode,'series(Dj)')||strcmp(mode,'series(Di)'))%check second nc series
2141            for ifile=1:nbfield
2142                for j=1:nbslice
2143                     filename=fullfile_uvmat(RootPath,subdir_civ1_new,RootFile_A,'.nc',NomType_nc,i1_civ1(ifile),i2_civ1(ifile),j1_civ1(j),j2_civ1(j));
2144                   % filename=name_generator(filebase_A,i1_civ1(ifile),j1_civ1(j),'.nc',NomType_nc,1,i2_civ1(ifile),j2_civ1(j),subdir_civ1_new);%
2145                    detect=exist(filename,'file')==2;
2146                    if detect% if a netcdf file already exists
2147                       indstr=regexp(subdir_civ1_new,'\D');
2148                       if indstr(end)<length(subdir_civ1_new) %subdir_civ1 ends by a number
2149                           vers=str2double(subdir_civ1_new(indstr(end)+1:end))+1;
2150                           subdir_civ1_new=[subdir_civ1_new(1:indstr(end)) num2str(vers)];
2151                       else
2152                           vers=vers+1;
2153                           subdir_civ1_new=[subdir_civ1_new '_' num2str(vers)];
2154                       end
2155                       subdir_civ2=subdir_civ1;
2156                       break
2157                    end
2158                    filecell.ncA.civ1(ifile,j)={filename};
2159                end
2160                if detect% if a netcdf file already exists
2161                    break
2162                end
2163            end
2164            %create the new SubdirCiv1
2165            if ~exist(fullfile(RootPath,subdir_civ1_new),'dir')       
2166                [xx,msg1]=mkdir(fullfile(RootPath,subdir_civ1_new));
2167                if ~strcmp(msg1,'')
2168                    errormsg=['cannot create ' subdir_civ1_new ': ' msg1];
2169                    return
2170                else
2171                    [xx,msg2] = fileattrib(fullfile(RootPath,subdir_civ1_new),'+w','g'); %yield writing access (+w) to user group (g)
2172                    if ~strcmp(msg2,'')
2173                        errormsg=['pb of permission for ' subdir_civ1_new ': ' msg2];%error message for directory creation
2174                        return
2175                    end
2176                end
2177            end
2178        end
2179    end
2180    subdir_civ1=subdir_civ1_new;
2181    % get image names
2182    for ifile=1:nbfield
2183        for j=1:nbslice
2184             filename=fullfile_uvmat(RootPath,SubdirImages,RootFile_ima1,ext_ima,NomType_ima1,i1_civ1(ifile),[],j1_civ1(j));
2185            idetect(j)=exist(filename,'file')==2;
2186            filecell.ima1.civ1(ifile,j)={filename}; %first image
2187            filename=fullfile_uvmat(RootPath,SubdirImages,RootFile_ima2,ext_ima,NomType_ima2,i2_civ1(ifile),[],j2_civ1(j));
2188            idetect_1(j)=exist(filename,'file')==2;
2189            filecell.ima2.civ1(ifile,j)={filename};%second image
2190        end
2191        [idetectmin,indexj]=min(idetect);
2192        if idetectmin==0,
2193            errormsg=[filecell.ima1.civ1{ifile,indexj} ' not found'];
2194            return
2195        end
2196        [idetectmin,indexj]=min(idetect_1);
2197        if idetectmin==0,
2198            errormsg=[filecell.ima2.civ1{ifile,indexj} ' not found'];
2199            return
2200        end
2201    end
2202    if strcmp(compare,'stereo PIV') && (strcmp(mode,'pair j1-j2') || strcmp(mode,'series(Dj)') || strcmp(mode,'series(Di)'))
2203        for ifile=1:nbfield
2204            for j=1:nbslice
2205                filename=fullfile_uvmat(RootPath,'',RootFile_A,ext_ima,NomType_ima1,i1_civ1(ifile),[],j1_civ1(j));
2206                idetect(j)=exist(filename,'file')==2;
2207                filecell.imaA1.civ1(ifile,j)={filename} ;%first image
2208                filename=fullfile_uvmat(RootPath,'',RootFile_A,ext_ima,NomType_ima2,i2_civ1(ifile),[],j2_civ1(j));
2209                idetect_1(j)=exist(filename,'file')==2;
2210                filecell.imaA2.civ1(ifile,j)={filename};%second image
2211            end
2212            [idetectmin,indexj]=min(idetect);
2213            if idetectmin==0,
2214                errormsg=[filecell.imaA1.civ1{ifile,indexj} ' not found'];
2215                return
2216            end
2217            [idetectmin,indexj]=min(idetect_1);
2218            if idetectmin==0,
2219                errormsg=[filecell.imaA2.civ1{ifile,indexj} ' not found'];
2220                return
2221            end
2222        end
2223    end
2224   
2225    %%%%%%%%%%%%%  checkfix1 or checkpatch1 activated but no checkciv1   %%%%%%%%%%%%%
2226elseif (checkbox(2)==1 || checkbox(3)==1);
2227    for ifile=1:nbfield
2228        for j=1:nbslice
2229            filename=fullfile_uvmat(RootPath,subdir_civ1,RootFile_nc,'.nc',NomType_nc,i1_civ1(ifile),i2_civ1(ifile),j1_civ1(j),j2_civ1(j));
2230            detect=exist(filename,'file')==2;
2231            if detect==0
2232                errormsg=[filename ' not found'];
2233                return
2234            end
2235            filecell.nc.civ1(ifile,j)={filename};
2236        end
2237    end
2238    if strcmp(compare,'stereo PIV')
2239        for ifile=1:nbfield
2240            for j=1:nbslice
2241                filename=fullfile_uvmat(RootPath,subdir_civ1,RootFile_A,'.nc',NomType_nc,i1_civ1(ifile),i2_civ1(ifile),j1_civ1(j),j2_civ1(j));
2242                filecell.ncA.civ1(ifile,j)={filename};
2243                if ~exist(filename,'file')
2244                    errormsg=['input file ' filename ' not found'];
2245                    return
2246                end
2247            end
2248        end
2249    end
2250end
2251
2252%%%%%%%%%%%%%  if checkciv2 performed with pairs different than checkciv1  %%%%%%%%%%%%%
2253testdiff=0;
2254if (checkbox(4)==1)&&...
2255        ((get(handles.ListPairCiv1,'Value')~=get(handles.ListPairCiv2,'Value'))||~strcmp(subdir_civ2,subdir_civ1))
2256    testdiff=1;
2257    detect=1;
2258    vers=0;
2259    subdir_civ2_new=subdir_civ2;
2260    while detect==1 %create a new subdir if the netcdf files already exist
2261        for ifile=1:nbfield
2262            for j=1:nbslice
2263                filename=fullfile_uvmat(RootPath,subdir_civ2_new,RootFile_nc,'.nc',NomType_nc,i1_civ2(ifile),i2_civ2(ifile),j1_civ2(j),j2_civ2(j));
2264                detect=exist(filename,'file')==2;
2265                if detect% if a netcdf file already exists
2266                    indstr=regexp(subdir_civ2,'\D');
2267                    if indstr(end)<length(subdir_civ2) %subdir_civ1 ends by a number
2268                        vers=str2double(subdir_civ2(indstr(end)+1:end))+1;
2269                        subdir_civ2_new=[subdir_civ2(1:indstr(end)) num2str(vers)];
2270                    else
2271                        vers=vers+1;
2272                        subdir_civ2_new=[subdir_civ1 '_' num2str(vers)];
2273                    end
2274                    break
2275                end
2276                filecell.nc.civ2(ifile,j)={filename};
2277            end
2278            if detect% if a netcdf file already exists
2279                break
2280            end
2281        end
2282        %create the new subdir_civ2_new
2283        if ~exist(fullfile(RootPath,subdir_civ2_new),'dir')
2284            [xx,m2]=mkdir(fullfile(RootPath,subdir_civ2_new));
2285            [xx,msg2] = fileattrib(fullfile(RootPath,subdir_civ2_new),'+w','g'); %yield writing access (+w) to user group (g)
2286            if ~isequal(m2,'')
2287                errormsg=['cannot create ' fullfile(RootPath,subdir_civ2_new) ': ' m2];
2288                return
2289            end
2290        end
2291        if strcmp(compare,'stereo PIV')%check second nc series
2292            for ifile=1:nbfield
2293                for j=1:nbslice
2294                    filename=fullfile_uvmat(RootPath,subdir_civ2_new,RootFile_A,'.nc',NomType_nc,i1_civ2(ifile),i2_civ2(ifile),j1_civ2(j),j2_civ2(j));
2295                    detect=exist(filename,'file')==2;
2296                    if detect% if a netcdf file already exists
2297                        indstr=regexp(subdir_civ2,'\D');
2298                        if indstr(end)<length(subdir_civ2) %subdir_civ1 ends by a number
2299                           vers=str2double(subdir_civ2(indstr(end)+1:end))+1;
2300                           subdir_civ2_new=[subdir_civ2(1:indstr(end)) num2str(vers)];
2301                        else
2302                           vers=vers+1;
2303                           subdir_civ2_new=[subdir_civ1 '_' num2str(vers)];
2304                        end
2305                        break
2306                    end
2307                    filecell.ncA.civ2(ifile,j)={filename};
2308                end
2309                if detect% if a netcdf file already exists
2310                    break
2311                end
2312            end
2313            subdir_civ2=subdir_civ2_new;
2314            %create the new SubdirCiv1
2315            if ~exist(fullfile(RootPath,subdir_civ2_new),'dir')
2316                [xx,m2]=mkdir(subdir_civ2_new);
2317                 [xx,msg2] = fileattrib(fullfile(RootPath,subdir_civ2_new),'+w','g'); %yield writing access (+w) to user group (g)
2318                if ~isequal(m2,'')
2319                    errormsg= ['cannot create ' fullfile(RootPath,subdir_civ2_new) ': ' m2];%error message for directory creation
2320                    return
2321                end
2322            end
2323        end
2324    end
2325    subdir_civ2=subdir_civ2_new;
2326end
2327
2328%%%%%%%%%%%%%  if checkciv2 results are obtained or used  %%%%%%%%%%%%%
2329if checkbox(4)==1 || checkbox(5)==1 || checkbox(6)==1 %civ2
2330    %check source netcdf file of checkciv1 estimates
2331    if checkbox(1)==0; %no civ1 performed
2332        for ifile=1:nbfield
2333            for j=1:nbslice
2334                filename=fullfile_uvmat(RootPath,subdir_civ1,RootFile_nc,'.nc',NomType_nc,i1_civ1(ifile),i2_civ1(ifile),j1_civ1(j),j2_civ1(j));%
2335                filecell.nc.civ1(ifile,j)={filename};% name of the civ1 file
2336                if ~exist(filename,'file')
2337                    errormsg=['input file ' filename ' not found'];
2338                    return
2339                end
2340                if ~testdiff % civ2 or patch2 are written in the same file as civ1
2341                    if checkbox(4)==0 ; %check the existence of civ2 if it is not calculated
2342                        Data=nc2struct(filename,'ListGlobalAttribute','CivStage','civ2');
2343                        if isfield(Data,'Txt')
2344                            errormsg=Data.Txt;
2345                            return
2346                        elseif ~isempty(Data.CivStage)% case of new civ files
2347                            if Data.CivStage<4 %test for civ files
2348                            errormsg=['no civ2 data in ' filename];
2349                            return
2350                            end
2351                        elseif isempty(Data.civ2)||isequal(Data.civ2,0)
2352                            errormsg=['no civ2 data in ' filename];
2353                            return
2354                        end
2355                    elseif checkbox(3)==0; %check the existence of patch if it is not calculated
2356                        Data=nc2struct(filename,'ListGlobalAttribute','CivStage','patch');
2357                        if isfield(Data,'Txt')
2358                            errormsg=Data.Txt;
2359                            return
2360                        elseif ~isempty(Data.CivStage)
2361                            if Data.CivStage<3 %test for civ files
2362                                errormsg=['no patch data in ' filename];
2363                                return
2364                            end
2365                        elseif isempty(Data.patch)||isequal(Data.patch,0)
2366                            errormsg=['no patch data in ' filename];
2367                            return
2368                        end
2369                    end
2370                end
2371            end
2372        end
2373        if strcmp(compare,'stereo PIV')
2374            for ifile=1:nbfield
2375                for j=1:nbslice
2376                    filename=fullfile_uvmat(RootPath,subdir_civ2,RootFile_A,'.nc',NomType_nc,i1_civ2(ifile),i2_civ2(ifile),j1_civ2(j),j2_civ2(j));
2377                    filecell.ncA.civ2(ifile,j)={filename};
2378                    if ~exist(filename,'file')
2379                        errormsg=['input file ' filename ' not found'];
2380                        return
2381                    end
2382                end
2383            end
2384        end
2385    end
2386   
2387    detect=1;
2388    %     while detect==1%creates a new subdir if the netcdf files already contain checkciv2 data
2389    for ifile=1:nbfield
2390        for j=1:nbslice
2391            filename=fullfile_uvmat(RootPath,subdir_civ2,RootFile_nc,'.nc',NomType_nc,i1_civ2(ifile),i2_civ2(ifile),j1_civ2(j),j2_civ2(j));
2392            detect=exist(filename,'file')==2;
2393            filecell.nc.civ2(ifile,j)={filename};
2394        end
2395    end
2396    %get first image names for checkciv2
2397    if checkbox(1)==1 && isequal(i1_civ1,i1_civ2) && isequal(j1_civ1,j1_civ2)
2398        filecell.ima1.civ2=filecell.ima1.civ1;
2399    elseif checkbox(4)==1
2400        for ifile=1:nbfield
2401            for j=1:nbslice
2402                filename=fullfile_uvmat(RootPath,[],RootFile_ima1,ext_ima,NomType_ima1,i1_civ2(ifile),[],j1_civ2(j));
2403                idetect_2(j)=exist(filename,'file')==2;
2404                filecell.ima1.civ2(ifile,j)={filename};%first image
2405            end
2406            [idetectmin,indexj]=min(idetect_2);
2407            if idetectmin==0,
2408               errormsg=['input image ' filecell.ima1.civ2{ifile,indexj} ' not found'];
2409                return
2410            end
2411        end
2412    end
2413   
2414    %get second image names for checkciv2
2415    if checkbox(1)==1 && isequal(i2_civ1,i2_civ2) && isequal(j2_civ1,j2_civ2)
2416        filecell.ima2.civ2=filecell.ima2.civ1;
2417    elseif checkbox(4)==1
2418        for ifile=1:nbfield
2419            for j=1:nbslice
2420                filename=fullfile_uvmat(RootPath,[],RootFile_ima2,ext_ima,NomType_ima2,i2_civ2(ifile),[],j2_civ2(j));
2421                idetect_3(j)=exist(filename,'file')==2;
2422                filecell.ima2.civ2(ifile,j)={filename};%first image
2423            end
2424            [idetectmin,indexj]=min(idetect_3);
2425            if idetectmin==0,
2426                errormsg=['input image ' filecell.ima2.civ2{ifile,indexj} ' not found'];
2427                return
2428            end
2429        end
2430    end
2431end
2432if (checkbox(5) || checkbox(6)) && ~checkbox(4)  % need to read an existing netcdf civ2 file
2433    if ~testdiff
2434        filecell.nc.civ2=filecell.nc.civ1;% file already checked
2435    else     % check the civ2 files
2436        for ifile=1:nbfield
2437            for j=1:nbslice
2438                 filename=fullfile_uvmat(RootPath,subdir_civ2,RootFile_nc,'.nc',NomType_nc,i1_civ2(ifile),i2_civ2(ifile),j1_civ2(j),j2_civ2(j));
2439                filecell.nc.civ2(ifile,j)={filename};
2440                if ~exist(filename,'file')
2441                    errormsg=['input file ' filename ' not found'];
2442                    return
2443                else
2444                    Data=nc2struct(filename,'ListGlobalAttribute','CivStage','civ2');
2445                    if ~isempty(Data.CivStage) && Data.CivStage<4 %test for civ files
2446                            errormsg=['no civ2 data in ' filename];
2447                            return
2448                    elseif isempty(Data.civ2)||isequal(Data.civ2,0)
2449                        errormsg=['no civ2 data in ' filename];
2450                        return
2451                    end
2452                end
2453            end
2454        end
2455    end
2456end
2457
2458%%%%%%%%%%%%%  if stereo fields are calculated by PATCH %%%%%%%%%%%%%
2459if strcmp(compare,'stereo PIV')
2460    if  checkbox(3) && isequal(get(handles.test_stereo1,'Value'),1)
2461        for ifile=1:nbfield
2462            for j=1:nbslice
2463                 filename=fullfile_uvmat(RootPath,subdir_civ1,RootFile_AB,'.nc',NomType_nc,i1_civ1(ifile),i2_civ1(ifile),j1_civ1(j),j2_civ1(j));
2464                filecell.st(ifile,j)={filename};
2465            end
2466        end
2467    end
2468    if  checkbox(6) && isequal(get(handles.CheckStereo,'Value'),1)
2469        for ifile=1:nbfield
2470            for j=1:nbslice
2471                 filename=fullfile_uvmat(RootPath,subdir_civ2,RootFile_AB,'.nc',NomType_nc,i1_civ2(ifile),i2_civ2(ifile),j1_civ2(j),j2_civ2(j));
2472                filecell.st(ifile,j)={filename};
2473            end
2474        end
2475    end
2476end
2477set(handles.SubdirCiv1,'String',regexprep(subdir_civ1,['^' SubdirImages],''));%suppress the root  SuddirImages;);%update the edit box
2478set(handles.SubdirCiv2,'String',regexprep(subdir_civ2,['^' SubdirImages],''));%update the edit box
2479
2480% For CivX COPY IMAGES TO THE FORMAT .png IF NEEDED
2481if strcmp(CivMode,'CivX')
2482    if isequal(NomType_ima1,'*')%case of movie files
2483        NomType_imanew1='_i';
2484    else
2485        NomType_imanew1=NomType_ima1;
2486    end
2487    if isequal(NomType_ima2,'*')%case of movie files
2488        NomType_imanew2='_i';
2489    else
2490        NomType_imanew2=NomType_ima2;
2491    end
2492    if ~isequal(ext_ima,'.png')
2493        %%type of image file
2494        type_ima1='none';%default
2495        movieobject1=[];%default
2496        if strcmpi(ext_ima,'.avi')
2497            if ~isempty(which('mmreader'))% if the mmreader function is found (recent version of matlab)
2498                type_ima1='movie';
2499                movieobject1=mmreader([filecell.filebase ext_ima]);
2500            else
2501                type_ima1='avi';
2502            end
2503        elseif ischar(ext_ima) && ~isempty(ext_ima(2:end))
2504            form=imformats(ext_ima(2:end));
2505            if ~isempty(form)% if the extension corresponds to an image format recognized by Matlab
2506                if isequal(NomType_ima1,'*');
2507                    type_ima1='multimage';%image series in a single image file
2508                else
2509                    type_ima1='image';
2510                end
2511            end
2512        end
2513        type_ima2='none';%default
2514        movieobject2=[];
2515        if strcmpi(ext_ima,'.avi')
2516            if ~isempty(which('mmreader'))% if the mmreader function is found (recent version of matlab)
2517                type_ima2='movie';
2518                movieobject2=mmreader([filecell.filebase ext_ima]);
2519            else
2520                type_ima2='avi';
2521            end
2522        elseif ischar(ext_ima) && ~isempty(ext_ima(2:end))
2523            form=imformats(ext_ima(2:end));
2524            if ~isempty(form)% if the extension corresponds to an image format recognized by Matlab
2525                if isequal(NomType_ima1,'*');
2526                    type_ima2='multimage';%image series in a single image file
2527                else
2528                    type_ima2='image';
2529                end
2530            end
2531        end
2532        if checkbox(1) %if civ1 is performed
2533            h = waitbar(0,'copy images to the .png format for civ1');% display a wait bar
2534            for ifile=1:nbfield
2535                waitbar(ifile/nbfield);
2536                for j=1:nbslice
2537                    filename=fullfile_uvmat(RootPath,[],RootFile_ima1,'.png',NomType_imanew1,i1_civ1(ifile),[],j1_civ1(j));
2538                    if ~exist(filename,'file')
2539                        A=read_image(filecell.ima1.civ1{ifile,j},type_ima1,i1_civ1(ifile),movieobject1);
2540                        imwrite(A,filename,'BitDepth',16);
2541                    end
2542                    filecell.ima1.civ1(ifile,j)={filename};
2543                    filename=fullfile_uvmat(RootPath,[],RootFile_ima2,'.png',NomType_imanew2,i2_civ1(ifile),[],j2_civ1(j));
2544                    if ~exist(filename,'file')
2545                        A=read_image(filecell.ima2.civ1{ifile,j},type_ima2,i2_civ1(ifile),movieobject2);
2546                        imwrite(A,filename,'BitDepth',16);
2547                    end
2548                    filecell.ima2.civ1(ifile,j)={filename};
2549                end
2550            end
2551            close(h)
2552        end
2553        if checkbox(4) %if civ2 is performed
2554            h = waitbar(0,'copy images to the .png format for civ2');% display a wait bar
2555            for ifile=1:nbfield
2556                waitbar(ifile/nbfield);
2557                for j=1:nbslice
2558                    filename=fullfile_uvmat(RootPath,[],RootFile_ima1,'.png',NomType_imanew1,i1_civ2(ifile),[],j1_civ2(j));
2559                    if ~exist(filename,'file')
2560                        A=read_image(cell2mat(filecell.ima1.civ2(ifile,j)),type_ima2,i1_civ2(ifile));
2561                        imwrite(A,filename,'BitDepth',16);
2562                    end
2563                    filecell.ima1.civ2(ifile,j)={filename};
2564                    filename=fullfile_uvmat(RootPath,[],RootFile_ima2,'.png',NomType_imanew2,i2_civ2(ifile),[],j2_civ2(j));
2565                    if ~exist(filename,'file')
2566                        A=read_image(cell2mat(filecell.ima2.civ2(ifile,j)),type_ima2,i2_civ2(ifile));
2567                        imwrite(A,filename,'BitDepth',16);
2568                    end
2569                    filecell.ima2.civ2(ifile,j)={filename};
2570                end
2571            end
2572            close(h);
2573        end
2574    end
2575end
2576
2577%------------------------------------------------------------------------
2578% --- determine the list of index pairs of processing file
2579function [num1_civ1,num2_civ1,num_a_civ1,num_b_civ1,num1_civ2,num2_civ2,num_a_civ2,num_b_civ2]=...
2580    find_pair_indices(handles,ref_i,ref_j,mode)
2581%------------------------------------------------------------------------
2582
2583list_civ1=get(handles.ListPairCiv1,'String');
2584index_civ1=get(handles.ListPairCiv1,'Value');
2585str_civ1=list_civ1{index_civ1};%string defining the image pairs for civ1
2586if isempty(str_civ1)||isequal(str_civ1,'')
2587    msgbox_uvmat('ERROR','no image pair selected for civ1')
2588    return
2589end
2590list_civ2=get(handles.ListPairCiv2,'String');
2591index_civ2=get(handles.ListPairCiv2,'Value');
2592if index_civ2>length(list_civ2)
2593    list_civ2=list_civ1;
2594    index_civ2=index_civ1;
2595end
2596str_civ2=list_civ2{index_civ2};%string defining the image pairs for civ2
2597
2598if isequal (mode,'series(Di)')
2599    lastfield=str2double(get(handles.nb_field,'String'));
2600    num1_civ1=ref_i-floor(index_civ1/2)*ones(size(ref_i));% set of first image numbers
2601    num2_civ1=ref_i+ceil(index_civ1/2)*ones(size(ref_i));
2602    num_a_civ1=ref_j;
2603    num_b_civ1=ref_j;
2604    num1_civ2=ref_i-floor(index_civ2/2)*ones(size(ref_i));
2605    num2_civ2=ref_i+ceil(index_civ2/2)*ones(size(ref_i));
2606    num_a_civ2=ref_j;
2607    num_b_civ2=ref_j;   
2608   
2609    % adjust the first and last field number
2610    lastfield=str2double(get(handles.nb_field,'String'));
2611    if isnan(lastfield)
2612        indsel=find((num1_civ1 >= 1)&(num1_civ2 >= 1));
2613    else
2614        indsel=find((num2_civ1 <= lastfield)&(num2_civ2 <= lastfield)&(num1_civ1 >= 1)&(num1_civ2 >= 1));
2615    end
2616    if length(indsel)>=1
2617        firstind=indsel(1);
2618        lastind=indsel(end);
2619        set(handles.first_i,'String',num2str(ref_i(firstind)))%update the display of first and last fields
2620        set(handles.last_i,'String',num2str(ref_i(lastind)))
2621        ref_i=ref_i(indsel);
2622        num1_civ1=num1_civ1(indsel);
2623        num1_civ2=num1_civ2(indsel);
2624        num2_civ1=num2_civ1(indsel);
2625        num2_civ2=num2_civ2(indsel);
2626    end
2627elseif isequal (mode,'series(Dj)')
2628    lastfield_j=str2double(get(handles.nb_field2,'String'));
2629    num1_civ1=ref_i;% set of first image numbers
2630    num2_civ1=ref_i;
2631    num_a_civ1=ref_j-floor(index_civ1/2)*ones(size(ref_j));
2632    num_b_civ1=ref_j+ceil(index_civ1/2)*ones(size(ref_j));
2633    num1_civ2=ref_i;
2634    num2_civ2=ref_i;
2635    num_a_civ2=ref_j-floor(index_civ2/2)*ones(size(ref_j));
2636    num_b_civ2=ref_j+ceil(index_civ2/2)*ones(size(ref_j));
2637    % adjust the first and last field number
2638    if isnan(lastfield_j)
2639        indsel=find((num_a_civ1 >= 1)&(num_a_civ2 >= 1));
2640    else
2641        indsel=find((num_b_civ1 <= lastfield_j)&(num_b_civ2 <= lastfield_j)&(num_a_civ1 >= 1)&(num_a_civ2 >= 1));
2642    end
2643    if length(indsel)>=1
2644        firstind=indsel(1);
2645        lastind=indsel(end);
2646        set(handles.first_j,'String',num2str(ref_j(firstind)))%update the display of first and last fields
2647        set(handles.last_j,'String',num2str(ref_j(lastind)))
2648        ref_j=ref_j(indsel);
2649        num_a_civ1=num_a_civ1(indsel);
2650        num_b_civ1=num_b_civ1(indsel);
2651        num_a_civ2=num_a_civ2(indsel);
2652        num_b_civ2=num_b_civ2(indsel);
2653    end
2654elseif isequal(mode,'pair j1-j2') %case of bursts (png_old or png_2D)
2655    displ_num=get(handles.ListPairCiv1,'UserData');
2656    num1_civ1=ref_i;
2657    num2_civ1=ref_i;
2658    num_a_civ1=displ_num(1,index_civ1);
2659    num_b_civ1=displ_num(2,index_civ1);
2660    num1_civ2=ref_i;
2661    num2_civ2=ref_i;
2662    num_a_civ2=displ_num(1,index_civ2);
2663    num_b_civ2=displ_num(2,index_civ2);
2664elseif isequal(mode,'displacement')
2665    num1_civ1=ref_i;
2666    num2_civ1=ref_i;
2667    num_a_civ1=ref_j;
2668    num_b_civ1=ref_j;
2669    num1_civ2=ref_i;
2670    num2_civ2=ref_i;
2671    num_a_civ2=ref_j;
2672    num_b_civ2=ref_j;
2673end
2674
2675%------------------------------------------------------------------------
2676% --- Executes on button press in ListCompareMode.
2677function ListCompareMode_Callback(hObject, eventdata, handles)
2678%------------------------------------------------------------------------
2679ListCompareMode=get(handles.ListCompareMode,'String');
2680option=ListCompareMode{get(handles.ListCompareMode,'Value')};
2681if ~strcmp(option,'PIV') % case 'displacement' or 'stereo PIV'
2682    filebase=get(handles.RootPath,'String');
2683    set(handles.sub_txt,'Visible','on')
2684    set(handles.RootFile_1,'Visible','On');%mkes the second file input window visible
2685    mode_store=get(handles.ListPairMode,'String');%get the present 'mode'
2686    set(handles.ListCompareMode,'UserData',mode_store);%store the mode display
2687    set(handles.ListPairMode,'Visible','off')
2688   
2689    %% open an image file with the browser
2690    ind_opening=1;%default
2691    browse.incr_pair=[0 0]; %default
2692    oldfile=get(handles.RootPath,'String');
2693    menu={'*.png;*.jpg;*.tif;*.avi;*.AVI;', ' (*.png,*.jpg ,.tif, *.avi,*.AVI)';
2694        '*.png','.png image files'; ...
2695        '*.jpg',' jpeg image files'; ...
2696        '*.tif','.tif image files'; ...
2697        '*.avi;*.AVI','.avi movie files'; ...
2698        '*.*',  'All Files (*.*)'};
2699    if strcmp(option,'displacement')
2700        comment='Pick the reference file for displacements';
2701    else
2702        comment='Pick a file of the second series';
2703    end
2704    [FileName, PathName] = uigetfile( menu, comment,oldfile);
2705    fileinput=[PathName FileName];%complete file name
2706    sizf=size(fileinput);
2707    if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end %stop if fileinput not a character string
2708    [path,name,ext]=fileparts(fileinput);
2709    [path1]=fileparts(filebase);
2710    if isunix
2711        [status,path]=system(['readlink ' path]);
2712        [status,path1]=system(['readlink ' path1]);% look for the true path in case of symbolic paths
2713    end
2714    if ~strcmp(path1,path)
2715        msgbox_uvmat('ERROR','The second image or series must be in the same directory as the first one')
2716        return
2717    end
2718    if strcmp(option,'displacement')
2719        [tild,RootFile_1]=fileparts(name);
2720    else
2721        [FilePath,FileName,Ext]=fileparts(fileinput);
2722% detect the file type, get the movie object if relevant, and look for the corresponding file series:
2723% the root name and indices may be corrected by including the first index i1 if a corresponding xml file exists
2724[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]);
2725       
2726       % [tild,tild,RootFile_1,tild,tild,tild,tild,tild,nom_type_1]=fileparts_uvmat(fileinput);
2727        %[RootFile_1,i1_series,tild,j1_series,tild,nom_type_1,FileType,Object]=find_file_series(PathName,FileName);
2728        %check image nom type
2729        if ~strcmp(nom_type_1,get(handles.NomType,'String'))
2730        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')
2731        return
2732        end
2733    end   
2734    %check image  extension
2735    if ~strcmp(ext,get(handles.ImaExt,'String'))
2736        msgbox_uvmat('ERROR','The second image series must have the same extension name as the first one')
2737        return
2738    end
2739    set(handles.RootFile_1,'String',RootFile_1);
2740else
2741    set(handles.ListPairMode,'Visible','on')
2742    set(handles.RootFile_1,'Visible','Off');
2743    set(handles.sub_txt,'Visible','off')
2744    set(handles.RootFile_1,'String',[]);
2745    mode_store=get(handles.ListCompareMode,'UserData');
2746    set(handles.ListPairMode,'Value',1)
2747    set(handles.ListPairMode,'String',mode_store)
2748    set(handles.CheckStereo,'Value',0)
2749    set(handles.ListPairMode,'Value',1) % mode 'civX' selected by default
2750end
2751% if strcmp(option,'stereo PIV') && get(handles.CheckPatch1,'Value')
2752%     set(handles.CheckStereo,'Visible','on')
2753% else
2754%     set(handles.CheckStereo,'Visible','off')
2755% end
2756% if strcmp(option,'stereo PIV') && get(handles.CheckPatch2,'Value')
2757%     set(handles.CheckStereo,'Visible','on')
2758% else
2759%     set(handles.CheckStereo,'Visible','off')
2760% end
2761ListPairMode_Callback(hObject, eventdata, handles)
2762
2763
2764%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
2765% Callbacks in the uipanel Pair Indices
2766%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
2767%------------------------------------------------------------------------
2768% --- Executes on button press in ListPairMode.
2769function ListPairMode_Callback(hObject, eventdata, handles)
2770%------------------------------------------------------------------------
2771compare_list=get(handles.ListCompareMode,'String');
2772val=get(handles.ListCompareMode,'Value');
2773compare=compare_list{val};
2774if strcmp(compare,'displacement')||strcmp(compare,'shift')
2775    mode='displacement';
2776else
2777    mode_list=get(handles.ListPairMode,'String');
2778    if ischar(mode_list)
2779        mode_list={mode_list};
2780    end
2781    mode_value=get(handles.ListPairMode,'Value');
2782    mode=mode_list{mode_value};
2783end
2784displ_num=[];%default
2785ref_i=str2double(get(handles.ref_i,'String'));
2786% last_i=str2num(get(handles.last_i,'String'));
2787time=get(handles.ImaDoc,'UserData'); %get the set of times
2788TimeUnit=get(handles.TimeUnit,'String');
2789checkframe=strcmp(TimeUnit,'frame');
2790siztime=size(time);
2791nbfield=siztime(1)-1;
2792nbfield2=siztime(2)-1;
2793indchosen=1;  %%first pair selected by default
2794%displ_num used to define the indices of the civ pairs
2795% in mode 'pair j1-j2', j1 and j2 are the file indices, else the indices
2796% are relative to the reference indices ref_i and ref_j respectively.
2797if isequal(mode,'pair j1-j2')%| isequal(mode,'st_pair j1-j2')
2798    dt=1;
2799    displ='';
2800    index=0;
2801    numlist_a=[];
2802    numlist_B=[];
2803    %get all the time intervals in bursts
2804    displ_dt=1;%default
2805    nbfield2=min(nbfield2,10);%limitate the number of pairs to 10x10
2806    for numod_a=1:nbfield2-1 %nbfield2 always >=2 for 'pair j1-j2' mode
2807        for numod_b=(numod_a+1):nbfield2
2808            index=index+1;
2809            numlist_a(index)=numod_a;
2810            numlist_b(index)=numod_b;
2811            if size(time,2)>1 && ~checkframe
2812                dt(numod_a,numod_b)=time(ref_i+1,numod_b+1)-time(ref_i+1,numod_a+1);%first time interval dt
2813                displ_dt(index)=dt(numod_a,numod_b);
2814            else
2815                displ_dt(index)=1;
2816            end
2817        end
2818    end
2819    [dtsort,indsort]=sort(displ_dt);
2820    if ~isempty(numlist_a)
2821        displ_num(1,:)=numlist_a(indsort);
2822        displ_num(2,:)=numlist_b(indsort);
2823    end
2824    displ_num(3,:)=0;
2825    displ_num(4,:)=0;
2826    enable_j(handles, 'off')
2827elseif isequal(mode,'series(Dj)') %| isequal(mode,'st_series(Dj)')
2828    index=1:200;
2829    displ_num(1,index)=-floor(index/2);
2830    displ_num(2,index)=ceil(index/2);
2831    displ_num(3:4,index)=zeros(2,200);
2832    enable_j(handles, 'on')
2833elseif isequal(mode,'series(Di)') %| isequal(mode,'st_series(Di)')
2834    index=1:200;
2835    displ_num(1:2,index)=zeros(2,200);
2836    displ_num(3,index)=-floor(index/2);
2837    displ_num(4,index)=ceil(index/2);
2838    enable_i(handles, 'on')
2839    if nbfield2 > 1
2840        enable_j(handles, 'on')
2841    else
2842        enable_j(handles, 'off')
2843    end
2844elseif isequal(mode,'displacement')%the pairs have the same indices
2845    displ_num(1,1)=0;
2846    displ_num(2,1)=0;
2847    displ_num(3,1)=0;
2848    displ_num(4,1)=0;
2849    if nbfield > 1 || nbfield==0
2850        enable_i(handles, 'on')
2851    else
2852        enable_j(handles, 'off')
2853    end
2854    if nbfield2 > 1
2855        enable_j(handles, 'on')
2856    else
2857        enable_j(handles, 'off')
2858    end
2859end
2860set(handles.ListPairCiv1,'UserData',displ_num);
2861errormsg=find_netcpair_civ( handles,1);
2862    if ~isempty(errormsg)
2863    msgbox_uvmat('ERROR',errormsg)
2864    end
2865% find_netcpair_civ2(handles)
2866
2867function enable_i(handles, state)
2868set(handles.itext,'Visible',state)
2869set(handles.first_i,'Visible',state)
2870set(handles.last_i,'Visible',state)
2871set(handles.incr_i,'Visible',state)
2872set(handles.nb_field,'Visible',state)
2873set(handles.ref_i,'Visible',state)
2874
2875function enable_j(handles, state)
2876set(handles.jtext,'Visible',state)
2877set(handles.first_j,'Visible',state)
2878set(handles.last_j,'Visible',state)
2879set(handles.incr_j,'Visible',state)
2880set(handles.nb_field2,'Visible',state)
2881set(handles.ref_j,'Visible',state)
2882
2883
2884%------------------------------------------------------------------------
2885% --- Executes on selection change in ListPairCiv1.
2886function ListPairCiv1_Callback(hObject, eventdata, handles)
2887%------------------------------------------------------------------------
2888%reproduce by default the chosen pair in the checkciv2 menu
2889list_pair=get(handles.ListPairCiv1,'String');%get the menu of image pairs
2890index_pair=get(handles.ListPairCiv1,'Value');
2891displ_num=get(handles.ListPairCiv1,'UserData');
2892% num_a=displ_num(1,index_pair);
2893% num_b=displ_num(2,index_pair);
2894list_pair2=get(handles.ListPairCiv2,'String');%get the menu of image pairs
2895if index_pair<=length(list_pair2)
2896    set(handles.ListPairCiv2,'Value',index_pair);
2897end
2898
2899%update first_i and last_i according to the chosen image pairs
2900mode_list=get(handles.ListPairMode,'String');
2901mode_value=get(handles.ListPairMode,'Value');
2902mode=mode_list{mode_value};
2903if isequal(mode,'series(Di)')
2904    first_i=str2double(get(handles.first_i,'String'));
2905    last_i=str2double(get(handles.last_i,'String'));
2906    incr_i=str2double(get(handles.incr_i,'String'));
2907    num1=first_i:incr_i:last_i;
2908    lastfield=str2double(get(handles.nb_field,'String'));
2909    if ~isnan(lastfield)
2910        test_find=(num1-floor(index_pair/2)*ones(size(num1))>0)& ...
2911            (num1+ceil(index_pair/2)*ones(size(num1))<=lastfield);
2912        num1=num1(test_find);
2913    end
2914    set(handles.first_i,'String',num2str(num1(1)));
2915    set(handles.last_i,'String',num2str(num1(end)));
2916elseif isequal(mode,'series(Dj)')
2917    first_j=str2double(get(handles.first_j,'String'));
2918    last_j=str2double(get(handles.last_j,'String'));
2919    incr_j=str2double(get(handles.incr_j,'String'));
2920    num_j=first_j:incr_j:last_j;
2921    lastfield2=str2double(get(handles.nb_field2,'String'));
2922    if ~isnan(lastfield2)
2923        test_find=(num_j-floor(index_pair/2)*ones(size(num_j))>0)& ...
2924            (num_j+ceil(index_pair/2)*ones(size(num_j))<=lastfield2);
2925        num1=num_j(test_find);
2926    end
2927    set(handles.first_j,'String',num2str(num1(1)));
2928    set(handles.last_j,'String',num2str(num1(end)));
2929end
2930
2931%------------------------------------------------------------------------
2932% --- Executes on selection change in ListPairCiv2.
2933function ListPairCiv2_Callback(hObject, eventdata, handles)
2934%------------------------------------------------------------------------
2935index_pair=get(handles.ListPairCiv2,'Value');%get the selected position index in the menu
2936
2937%update first_i and last_i according to the chosen image pairs
2938mode_list=get(handles.ListPairMode,'String');
2939mode_value=get(handles.ListPairMode,'Value');
2940mode=mode_list{mode_value};
2941if isequal(mode,'series(Di)')
2942    first_i=str2double(get(handles.first_i,'String'));
2943    last_i=str2double(get(handles.last_i,'String'));
2944    incr_i=str2double(get(handles.incr_i,'String'));
2945    num1=first_i:incr_i:last_i;
2946    lastfield=str2double(get(handles.nb_field,'String'));
2947    if ~isnan(lastfield)
2948        test_find=(num1-floor(index_pair/2)*ones(size(num1))>0)& ...
2949            (num1+ceil(index_pair/2)*ones(size(num1))<=lastfield);
2950        num1=num1(test_find);
2951    end
2952    set(handles.first_i,'String',num2str(num1(1)));
2953    set(handles.last_i,'String',num2str(num1(end)));
2954elseif isequal(mode,'series(Dj)')
2955    first_j=str2double(get(handles.first_j,'String'));
2956    last_j=str2double(get(handles.last_j,'String'));
2957    incr_j=str2double(get(handles.incr_j,'String'));
2958    num_j=first_j:incr_j:last_j;
2959    lastfield2=str2double(get(handles.nb_field2,'String'));
2960    if ~isnan(lastfield2)
2961        test_find=(num_j-floor(index_pair/2)*ones(size(num_j))>0)& ...
2962            (num_j+ceil(index_pair/2)*ones(size(num_j))<=lastfield2);
2963        num1=num_j(test_find);
2964    end
2965    set(handles.first_j,'String',num2str(num1(1)));
2966    set(handles.last_j,'String',num2str(num1(end)));
2967end
2968
2969%------------------------------------------------------------------------
2970function ref_i_Callback(hObject, eventdata, handles)
2971%------------------------------------------------------------------------
2972mode_list=get(handles.ListPairMode,'String');
2973mode_value=get(handles.ListPairMode,'Value');
2974mode=mode_list{mode_value};
2975errormsg=find_netcpair_civ(handles,1);% update the menu of pairs depending on the available netcdf files
2976if isequal(mode,'series(Di)') || ...% we do patch2 only
2977        (get(handles.CheckCiv2,'Value')==0 && get(handles.CheckCiv1,'Value')==0 && get(handles.CheckFix1,'Value')==0 && get(handles.CheckPatch1,'Value')==0)
2978    errormsg=find_netcpair_civ( handles,2);
2979end
2980    if ~isempty(errormsg)
2981    msgbox_uvmat('ERROR',errormsg)
2982    end
2983
2984%------------------------------------------------------------------------
2985function ref_j_Callback(hObject, eventdata, handles)
2986%------------------------------------------------------------------------
2987mode_list=get(handles.ListPairMode,'String');
2988mode_value=get(handles.ListPairMode,'Value');
2989mode=mode_list{mode_value};
2990if isequal(get(handles.CheckCiv1,'Value'),0)|| isequal(mode,'series(Dj)')
2991    errormsg=find_netcpair_civ(handles,1);% update the menu of pairs depending on the available netcdf files
2992end
2993if isequal(mode,'series(Dj)') || ...
2994        (get(handles.CheckCiv2,'Value')==0 && get(handles.CheckCiv1,'Value')==0 && get(handles.CheckFix1,'Value')==0 && get(handles.CheckPatch1,'Value')==0)
2995    errormsg=find_netcpair_civ(handles,2);
2996end
2997    if ~isempty(errormsg)
2998    msgbox_uvmat('ERROR',errormsg)
2999    end
3000
3001%------------------------------------------------------------------------
3002% determine the menu for checkciv1 pairs depending on existing netcdf file at the middle of
3003% the field series set by first_i, incr, last_i
3004% index=1: look for pairs for civ1
3005% index=2: look for pairs for civ2
3006function errormsg=find_netcpair_civ(handles,index)
3007%------------------------------------------------------------------------
3008set(gcf,'Pointer','watch')% set the mouse pointer to 'watch' (clock)
3009
3010%% initialisation
3011errormsg='';
3012browse=get(handles.RootPath,'UserData');
3013compare_list=get(handles.ListCompareMode,'String');
3014val=get(handles.ListCompareMode,'Value');
3015compare=compare_list{val};
3016if strcmp(compare,'displacement')||strcmp(compare,'shift')
3017    mode='displacement';
3018else
3019    mode_list=get(handles.ListPairMode,'String');
3020    mode_value=get(handles.ListPairMode,'Value');
3021    if isempty(mode_list)
3022        return
3023    end
3024    mode=mode_list{mode_value};
3025end
3026nom_type_ima=get(handles.NomType,'String');
3027
3028%% determine nom_type_nc, nomenclature type of the .nc files:
3029[nom_type_nc]=nomtype2pair(nom_type_ima,mode);
3030
3031%% reads .nc subdirectoy and image numbers from the interface
3032subdir_civ1=get(handles.SubdirCiv1,'String');%subdirectory subdir_civ1 for the netcdf data
3033subdir_civ2=get(handles.SubdirCiv2,'String');%subdirectory subdir_civ2 for the netcdf data
3034ref_i=str2double(get(handles.ref_i,'String'));
3035if isequal(mode,'pair j1-j2')%|isequal(mode,'st_pair j1-j2')
3036    ref_j=0;
3037else
3038    ref_j=str2double(get(handles.ref_j,'String'));
3039    if isnan(ref_j)
3040        ref_j=1;
3041    end
3042end
3043time=get(handles.ImaDoc,'UserData');%get the set of times
3044TimeUnit=get(handles.TimeUnit,'String');
3045checkframe=strcmp(TimeUnit,'frame');
3046displ_num=get(handles.ListPairCiv1,'UserData');
3047
3048%% eliminate the first pairs inconsistent with the position
3049if isempty(displ_num)
3050    nbpair=0;
3051else
3052    nbpair=length(displ_num(1,:));%nbre of displayed pairs
3053    if  isequal(mode,'series(Di)')  %| isequal(mode,'st_series(Di)')
3054        nbpair=min(2*ref_i-1,nbpair);%limit the number of pairs with positive first index
3055    elseif  isequal(mode,'series(Dj)')% | isequal(mode,'st_series(Dj)')
3056        nbpair=min(2*ref_j-1,nbpair);%limit the number of pairs with positive first index
3057    end
3058end
3059nbpair=min(200,nbpair);%limit the number of displayed pairs to 200
3060
3061%% case with no Civ1 operation, netcdf files need to exist for reading
3062displ_pair={''};
3063select=ones(size(1:nbpair));%flag for displayed pairs =1 for display
3064testpair=0;
3065RootPath=get(handles.RootPath,'String');
3066RootFile=get(handles.RootFile,'String');
3067if index==1 % case civ1
3068    if ~get(handles.CheckCiv1,'Value') %
3069        if ~exist(fullfile(RootPath,subdir_civ1),'dir')
3070            errormsg=['no civ1 file available: subdirectory ' subdir_civ1 ' does not exist'];
3071            set(handles.ListPairCiv1,'String',{});
3072            return
3073        end
3074        for ipair=1:nbpair
3075            filename=fullfile_uvmat(RootPath,subdir_civ1,RootFile,'.nc',nom_type_nc,...
3076                ref_i+displ_num(3,ipair),ref_i+displ_num(4,ipair),ref_j+displ_num(1,ipair),ref_j+displ_num(2,ipair));
3077            select(ipair)=exist(filename,'file')==2;% put flag to 0 if the file does not exist
3078        end
3079        % case of no displayed pair
3080        if isequal(select,zeros(size(1:nbpair)))
3081            if isfield(browse,'incr_pair') && ~isequal(browse.incr_pair,[0 0])
3082                num_i1=ref_i-floor(browse.incr_pair(1)/2);
3083                num_i2=ref_i+ceil(browse.incr_pair(1)/2);
3084                num_j1=ref_j-floor(browse.incr_pair(2)/2);
3085                num_j2=ref_j+ceil(browse.incr_pair(2)/2);
3086                filename=fullfile_uvmat(RootPath,subdir_civ1,RootFile,'.nc',nom_type_nc,num_i1,num_i2,num_j1,num_j2);
3087                select(1)=exist(filename,'file')==2;
3088                testpair=1;
3089            else
3090                if  isequal(mode,'series(Dj)')% | isequal(mode,'st_series(Dj)')
3091                    errormsg=['no civ1 file available for the selected reference index j=' num2str(ref_j) ' and subdirectory ' subdir_civ1];
3092                else
3093                    errormsg=['no civ1 file available for the selected reference indices (i,j)= ' num2str(ref_i) ', ' num2str(ref_j) ' and subdirectory ' subdir_civ1];
3094                end
3095                set(handles.ListPairCiv1,'String',{''});
3096                %COMPLETER CAS STEREO
3097                return
3098            end
3099        end
3100    end
3101else %case civ2 alone
3102    if ~get(handles.CheckCiv2,'Value') && ~get(handles.CheckCiv1,'Value') && ~get(handles.CheckFix1,'Value') && ~get(handles.CheckPatch1,'Value')
3103        if ~exist(fullfile(RootPath,subdir_civ2),'dir')
3104            msgbox_uvmat('ERROR',['no civ2 file available: subdirectory ' subdir_civ2 ' does not exist'])
3105            set(handles.ListPairCiv2,'Value',1);
3106            set(handles.ListPairCiv2,'String',{''});
3107            return
3108        end
3109        for ipair=1:nbpair
3110            filename=fullfile_uvmat(RootPath,subdir_civ1,RootFile,'.nc',nom_type_nc,...
3111                ref_i+displ_num(3,ipair),ref_i+displ_num(4,ipair),ref_j+displ_num(1,ipair),ref_j+displ_num(2,ipair));
3112            select(ipair)=exist(filename,'file')==2;
3113        end
3114        if  isequal(select,zeros(size(1:nbpair)))
3115            if isfield(browse,'incr_pair')
3116                num_i1=ref_i-floor(browse.incr_pair(1)/2);
3117                num_i2=ref_i+floor((browse.incr_pair(1)+1)/2);
3118                num_j1=ref_j-floor(browse.incr_pair(2)/2);
3119                num_j2=ref_j+floor((browse.incr_pair(2)+1)/2);
3120                filename=fullfile_uvmat(RootPath,subdir_civ2,RootFile,'.nc',nom_type_nc,num_i1,num_i2,num_j1,num_j2);
3121                select(1)=exist(filename,'file')==2;
3122            else
3123                if  isequal(mode,'series(Dj)')% | isequal(mode,'st_series(Dj)')
3124                    errormsg=['no civ2 file available for the selected reference index j=' num2str(ref_j) ' and subdirectory ' subdir_civ2];
3125                else
3126                    errormsg=['no civ2 file available for the selected reference index i=' num2str(ref_i) ' and subdirectory ' subdir_civ2];
3127                end
3128                set(handles.ListPairCiv2,'Value',1);
3129                set(handles.ListPairCiv2,'String',{''});
3130                return
3131            end
3132        end
3133    end
3134end
3135
3136%% determine the menu display in .ListPairCiv1
3137% the menu depends on the mode defined in ListPairMode_callback through the array displ_num:
3138% displ_num(1,:)=indices j1
3139% displ_num(2,:)=indices j2
3140% displ_num(3,:)=indices i1
3141% displ_num(4,:)=indices i2
3142% in mode 'pair j1-j2', j1 and j2 are the file indices, else the indices
3143% are relative to the reference indices ref_i and ref_j respectively.
3144if isequal(mode,'series(Di)')
3145    if testpair
3146        displ_pair{1}=['Di= ' num2str(-floor(browse.incr_pair(1)/2)) '|' num2str(ceil(browse.incr_pair(1)/2))];
3147    else
3148        for ipair=1:nbpair
3149            if select(ipair)
3150                displ_pair{ipair}=['Di= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2))];
3151                %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
3152                 %   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
3153               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
3154                 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
3155                else
3156                    dt=1;
3157                end
3158                 displ_pair{ipair}=[displ_pair{ipair} ' :dt= ' num2str(dt*1000)];
3159            else
3160                displ_pair{ipair}='...'; %pair not displayed in the menu
3161            end
3162        end
3163    end
3164elseif isequal(mode,'series(Dj)')
3165    if testpair
3166        displ_pair{1}=['Dj= ' num2str(-floor(browse.incr_pair(1)/2)) '|' num2str(ceil(browse.incr_pair(1)/2))];
3167    else
3168        for ipair=1:nbpair
3169            if select(ipair)
3170                displ_pair{ipair}=['Dj= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2))];
3171                if ~checkframe && size(time,1)>=ref_i+1+displ_num(4,ipair) && size(time,2)>=ref_j+1+displ_num(2,ipair)
3172                    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
3173                    displ_pair{ipair}=[displ_pair{ipair} ' :dt= ' num2str(dt*1000)];
3174                end
3175            else
3176                displ_pair{ipair}='...'; %pair not displayed in the menu
3177            end
3178        end
3179    end
3180elseif isequal(mode,'pair j1-j2')%case of pairs
3181    for ipair=1:nbpair
3182        if select(ipair)
3183            if ~checkframe && size(time,2)>1
3184            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
3185            else % time set by default to i index
3186                dt=1;
3187            end
3188            displ_pair{ipair}=['j= ' num2stra(displ_num(1,ipair),nom_type_ima) '-' num2stra(displ_num(2,ipair),nom_type_ima) ...
3189                ' :dt= ' num2str(dt*1000)];
3190        else
3191            displ_pair{ipair}='...'; %pair not displayed in the menu
3192        end
3193    end
3194elseif isequal(mode,'displacement')
3195    displ_pair={'Di=Dj=0'};
3196end
3197if index==1
3198set(handles.ListPairCiv1,'String',displ_pair');
3199end
3200
3201%% determine the default selection in the pair menu
3202ichoice=find(select,1);% index of selected pair
3203if (isempty(ichoice) || ichoice < 1); ichoice=1; end;
3204initial=get(handles.ListPairCiv1,'Value');%initial choice of pair
3205if initial>nbpair || (numel(select)>=initial && ~isequal(select(initial),1))
3206    set(handles.ListPairCiv1,'Value',ichoice);% first valid pair proposed by default in the menu
3207end
3208initial=get(handles.ListPairCiv2,'Value');
3209if initial>length(displ_pair')%|~isequal(select(initial),1)
3210    if ichoice <= length(displ_pair')
3211        set(handles.ListPairCiv2,'Value',ichoice);% same pair proposed by default for civ2
3212    else
3213        set(handles.ListPairCiv2,'Value',1);% same pair proposed by default for civ2
3214    end
3215end
3216set(handles.ListPairCiv2,'String',displ_pair');
3217set(gcf,'Pointer','arrow')
3218
3219
3220   
3221% %------------------------------------------------------------------------   
3222% % call 'view_field.fig' to display the  field selected in the list of 'status'
3223% function open_view_field(hObject, eventdata)
3224% %------------------------------------------------------------------------
3225% list=get(hObject,'String');
3226% index=get(hObject,'Value');
3227% rootroot=get(hObject,'UserData');
3228% filename=list{index};
3229% ind_dot=strfind(filename,'...');
3230% filename=filename(1:ind_dot-1);
3231% filename=fullfile(rootroot,filename);
3232% delete(get(hObject,'parent'))%delete the display figure to stop the check process
3233% if exist(filename,'file')%visualise the vel field if it exists
3234%     uvmat(filename)
3235%     set(gcbo,'Value',1)
3236% end
3237
3238
3239%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3240% Callbacks in the uipanel Reference Indices
3241%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3242%------------------------------------------------------------------------
3243function first_i_Callback(hObject, eventdata, handles)
3244%------------------------------------------------------------------------
3245first_i=str2double(get(handles.first_i,'String'));
3246set(handles.ref_i,'String', num2str(first_i))% reference index for pair dt = first index
3247ref_i_Callback(hObject, eventdata, handles)%refresh dispaly of dt for pairs (in case of non constant dt)
3248
3249%------------------------------------------------------------------------
3250function first_j_Callback(hObject, eventdata, handles)
3251%------------------------------------------------------------------------
3252first_j=str2num(get(handles.first_j,'String'));
3253set(handles.ref_j,'String', num2str(first_j))% reference index for pair dt = first index
3254ref_j_Callback(hObject, eventdata, handles)%refresh dispaly of dt for pairs (in case of non constant dt)
3255
3256%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3257% Callbacks in the uipanel Civ1
3258%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3259%------------------------------------------------------------------------
3260% --- Executes on button press in SearchRange: determine the search range num_SearchBoxSize_1,num_SearchBoxSize_2
3261function SearchRange_Callback(hObject, eventdata, handles)
3262%------------------------------------------------------------------------
3263%determine pair numbers
3264if strcmp(get(handles.num_UMin,'Visible'),'off')
3265    set(handles.u_title,'Visible','on')
3266    set(handles.v_title,'Visible','on')
3267    set(handles.num_UMin,'Visible','on')
3268    set(handles.num_UMax,'Visible','on')
3269    set(handles.num_VMin,'Visible','on')
3270    set(handles.num_VMax,'Visible','on')
3271    set(handles.CoordUnit,'Visible','on')
3272    set(handles.TimeUnit,'Visible','on')
3273    set(handles.slash_title,'Visible','on')
3274    set(handles.min_title,'Visible','on')
3275    set(handles.max_title,'Visible','on')
3276    set(handles.unit_title,'Visible','on')
3277else
3278    get_search_range(hObject, eventdata, handles)
3279end
3280
3281%------------------------------------------------------------------------
3282% ---  determine the search range num_SearchBoxSize_1,num_SearchBoxSize_2 and shift
3283function get_search_range(hObject, eventdata, handles)
3284%------------------------------------------------------------------------
3285param_civ1=read_GUI(handles.Civ1);
3286umin=param_civ1.UMin;
3287umax=param_civ1.UMax;
3288vmin=param_civ1.VMin;
3289vmax=param_civ1.VMax;
3290%switch min_title and max_title in case of error
3291if umax<=umin
3292    umin_old=umin;
3293    umin=umax;
3294    umax=umin_old;
3295    set(handles.num_UMin,'String', num2str(umin))
3296    set(handles.num_UMax,'String', num2str(umax))
3297end
3298if vmax<=vmin
3299    vmin_old=vmin;
3300    vmin=vmax;
3301    vmax=vmin_old;
3302    set(handles.num_VMin,'String', num2str(vmin))
3303    set(handles.num_VMax,'String', num2str(vmax))
3304end   
3305if ~(isempty(umin)||isempty(umax)||isempty(vmin)||isempty(vmax))
3306    list_pair=get(handles.ListPairCiv1,'String');%get the menu of image pairs
3307    index=get(handles.ListPairCiv1,'Value');
3308    pair_string=list_pair{index};
3309    time=get(handles.ImaDoc,'UserData'); %get the set of times
3310    pxcm=get(handles.SearchRange,'UserData');
3311    mode_list=get(handles.ListPairMode,'String');
3312    mode_value=get(handles.ListPairMode,'Value');
3313    mode=mode_list{mode_value};     
3314    if isequal (mode, 'series(Di)' )
3315        ref_i=str2double(get(handles.ref_i,'String'));
3316        num1=ref_i-floor(index/2);%  first image numbers
3317        num2=ref_i+ceil(index/2);
3318        num_a=1;
3319        num_b=1;
3320    elseif isequal (mode, 'series(Dj)')
3321        num1=1;
3322        num2=1;
3323        ref_j=str2double(get(handles.ref_j,'String'));
3324        num_a=ref_j-floor(index/2);%  first image numbers
3325        num_b=ref_j+ceil(index/2);
3326    elseif isequal(mode,'pair j1-j2') %case of bursts (png_old or png_2D)     
3327        ref_i=str2double(get(handles.ref_i,'String'));
3328        num1=ref_i;
3329        num2=ref_i;
3330                r=regexp(pair_string,'(?<mode>(Di=)|(Dj=)) -*(?<num1>\d+)\|(?<num2>\d+)','names');
3331        if isempty(r)
3332            r=regexp(pair_string,'(?<num1>\d+)(?<mode>-)(?<num2>\d+)','names');
3333        end 
3334        num_a=str2num(r.num1);
3335        num_b=str2num(r.num2);
3336    end
3337    dt=time(num2+1,num_b+1)-time(num1+1,num_a+1);
3338    ibx=str2double(get(handles.num_CorrBoxSize_1,'String'));
3339    iby=str2double(get(handles.num_CorrBoxSize_2,'String'));
3340    umin=dt*pxcm*umin;
3341    umax=dt*pxcm*umax;
3342    vmin=dt*pxcm*vmin;
3343    vmax=dt*pxcm*vmax;
3344    shiftx=round((umin+umax)/2);
3345    shifty=round((vmin+vmax)/2);
3346    isx=(umax+2-shiftx)*2+param_civ1.Bx;
3347    isx=2*ceil(isx/2)+1;
3348    isy=(vmax+2-shifty)*2+param_civ1.Bx;
3349    isy=2*ceil(isy/2)+1;
3350    set(handles.num_SearchBoxShift_1,'String',num2str(shiftx));
3351    set(handles.num_SearchBoxShift_2,'String',num2str(shifty));
3352    set(handles.num_SearchBoxSize_1,'String',num2str(isx));
3353    set(handles.num_SearchBoxSize_2,'String',num2str(isy));
3354end
3355
3356%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3357% Callbacks in the uipanel Fix1
3358%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3359%------------------------------------------------------------------------
3360% --- Executes on button press in CheckMask.
3361function get_mask_fix1_Callback(hObject, eventdata, handles)
3362%------------------------------------------------------------------------
3363maskval=get(handles.CheckMask,'Value');
3364if isequal(maskval,0)
3365    set(handles.Mask,'String','')
3366else
3367    mask_displ='no mask'; %default
3368    filebase=get(handles.RootPath,'String');
3369    [nbslice, flag_mask]=get_mask(filebase,handles);
3370    if isequal(flag_mask,1)
3371        mask_displ=[num2str(nbslice) 'mask'];
3372    elseif get(handles.ListCompareMode,'Value')>1 & ~isequal(mask_displ,'no mask')% look for the second mask series
3373        filebase_a=get(handles.RootFile_1,'String');
3374        [nbslice_a, flag_mask_a]=get_mask(filebase_a,handles);
3375        if isequal(flag_mask_a,0) || ~isequal(nbslice_a,nbslice)
3376            mask_displ='no mask';
3377        end
3378    end
3379    if isequal(mask_displ,'no mask')
3380        [FileName, PathName, filterindex] = uigetfile( ...
3381            {'*.png', ' (*.png)';
3382            '*.png',  '.png files '; ...
3383            '*.*', 'All Files (*.*)'}, ...
3384            'Pick a mask file *.png',filebase);
3385        mask_displ=fullfile(PathName,FileName);
3386        if ~exist(mask_displ,'file')
3387            mask_displ='no mask';
3388        end
3389    end
3390    if isequal(mask_displ,'no mask')
3391        set(handles.CheckMask,'Value',0)
3392        set(handles.CheckMask,'Value',0)
3393        set(handles.CheckMask,'Value',0)
3394    else
3395        %set(handles.CheckMask,'Value',1)
3396        set(handles.CheckMask,'Value',1)
3397    end
3398    set(handles.Mask,'String',mask_displ)
3399    set(handles.Mask,'String',mask_displ)
3400    set(handles.Mask,'String',mask_displ)
3401end
3402
3403%------------------------------------------------------------------------
3404% --- Executes on button press in CheckMask: select box for mask option
3405function get_mask_civ2_Callback(hObject, eventdata, handles)
3406%------------------------------------------------------------------------
3407maskval=get(handles.CheckMask,'Value');
3408if isequal(maskval,0)
3409    set(handles.Mask,'String','')
3410else
3411    mask_displ='no mask'; %default
3412    filebase=get(handles.RootPath,'String');
3413    [nbslice, flag_mask]=get_mask(filebase,handles);
3414    if isequal(flag_mask,1)
3415        mask_displ=[num2str(nbslice) 'mask'];
3416    elseif get(handles.ListCompareMode,'Value')>1 & ~isequal(mask_displ,'no mask')% look for the second mask series
3417        filebase_a=get(handles.RootFile_1,'String');
3418        [nbslice_a, flag_mask_a]=get_mask(filebase_a,handles);
3419        if isequal(flag_mask_a,0) || ~isequal(nbslice_a,nbslice)
3420            mask_displ='no mask';
3421        end
3422    end
3423    if isequal(mask_displ,'no mask')
3424        [FileName, PathName, filterindex] = uigetfile( ...
3425            {'*.png', ' (*.png)';
3426            '*.png',  '.png files '; ...
3427            '*.*', 'All Files (*.*)'}, ...
3428            'Pick a mask file *.png',filebase);
3429        mask_displ=fullfile(PathName,FileName);
3430        if ~exist(mask_displ,'file')
3431            mask_displ='no mask';
3432        end
3433    end
3434    if isequal(mask_displ,'no mask')
3435        set(handles.CheckMask,'Value',0)
3436        set(handles.CheckMask,'Value',0)
3437    else
3438        set(handles.CheckMask,'Value',1)
3439    end
3440    set(handles.Mask,'String',mask_displ)
3441    set(handles.Mask,'String',mask_displ)
3442end
3443
3444%------------------------------------------------------------------------
3445% --- Executes on button press in CheckMask.
3446function get_mask_fix2_Callback(hObject, eventdata, handles)
3447%------------------------------------------------------------------------
3448maskval=get(handles.CheckMask,'Value');
3449if isequal(maskval,0)
3450    set(handles.Mask,'String','')
3451else
3452    mask_displ='no mask'; %default
3453    filebase=get(handles.RootPath,'String');
3454    [nbslice, flag_mask]=get_mask(filebase,handles);
3455    if isequal(flag_mask,1)
3456        mask_displ=[num2str(nbslice) 'mask'];
3457    elseif get(handles.ListCompareMode,'Value')>1 & ~isequal(mask_displ,'no mask')% look for the second mask series
3458        filebase_a=get(handles.RootFile_1,'String');
3459        [nbslice_a, flag_mask_a]=get_mask(filebase_a,handles);
3460        if isequal(flag_mask_a,0) || ~isequal(nbslice_a,nbslice)
3461            mask_displ='no mask';
3462        end
3463    end
3464    if isequal(mask_displ,'no mask')
3465        [FileName, PathName, filterindex] = uigetfile( ...
3466            {'*.png', ' (*.png)';
3467            '*.png',  '.png files '; ...
3468            '*.*', 'All Files (*.*)'}, ...
3469            'Pick a mask file *.png',filebase);
3470        mask_displ=fullfile(PathName,FileName);
3471        if ~exist(mask_displ,'file')
3472            mask_displ='no mask';
3473        end
3474    end
3475    if isequal(mask_displ,'no mask')
3476        set(handles.CheckMask,'Value',0)
3477    end
3478    set(handles.Mask,'String',mask_displ)
3479end
3480
3481%------------------------------------------------------------------------
3482% --- function called to look for mask files
3483function [nbslice, flag_mask]=get_mask(filebase,handles)
3484%------------------------------------------------------------------------
3485%detect mask files, images with appropriate file base
3486%[filebase '_' xx 'mask'], xx=nbslice
3487%flag_mask=1 indicates detection
3488
3489flag_mask=0;%default
3490nbslice=1;
3491
3492% subdir=get(handles.SubdirCiv1,'String');
3493[Path,Name]=fileparts(filebase);
3494if ~isdir(Path)
3495    msgbox_uvmat('ERROR','no path for input files')
3496    return
3497end
3498% currentdir=pwd;
3499% cd(Path);%move in the dir of the root name filebase
3500maskfiles=dir(fullfile(Path,[Name '_*mask_*.png']));%look for mask files
3501% cd(currentdir);%come back to the current working directory
3502if ~isempty(maskfiles)
3503    %     msgbox_uvmat('ERROR','no mask available, to create it use Tools/Make mask in the upper menu bar of uvmat')
3504    % else
3505    flag_mask=1;
3506    maskname=maskfiles(1).name;% take the first mask file in the list
3507    [Path2,Name,ext]=fileparts(maskname);
3508    Namedouble=double(Name);
3509    val=(48>Namedouble)|(Namedouble>57);% select the non-numerical characters
3510    ind_mask=findstr('mask',Name);
3511    i=ind_mask-1;
3512    while val(i)==0 && i>0
3513        i=i-1;
3514    end
3515    nbslice=str2double(Name(i+1:ind_mask-1));
3516    if ~isnan(nbslice) && Name(i)=='_'
3517        flag_mask=1;
3518    else
3519        msgbox_uvmat('ERROR',['bad mask file ' Name ext ' found in ' Path2])
3520        return
3521        nbslice=1;
3522    end
3523end
3524
3525%------------------------------------------------------------------------
3526% --- function called to look for grid files
3527function [nbslice, flag_mask]=get_grid(filebase,handles)
3528%------------------------------------------------------------------------
3529flag_mask=0;%default
3530nbslice=1;
3531[Path,Name]=fileparts(filebase);
3532currentdir=pwd;
3533cd(Path);%move in the dir of the root name filebase
3534maskfiles=dir([Name '_*grid_*.grid']);%look for mask files
3535cd(currentdir);%come back to the current working directory
3536if ~isempty(maskfiles)
3537    flag_mask=1;
3538    maskname=maskfiles(1).name;% take the first mask file in the list
3539    [Path2,Name,ext]=fileparts(maskname);
3540    Namedouble=double(Name);
3541    val=(48>Namedouble)|(Namedouble>57);% select the non-numerical characters
3542    ind_mask=findstr('grid',Name);
3543    i=ind_mask-1;
3544    while val(i)==0 && i>0
3545        i=i-1;
3546    end
3547    nbslice=str2double(Name(i+1:ind_mask-1));
3548    if ~isnan(nbslice) && Name(i)=='_'
3549        flag_mask=1;
3550    else
3551        msgbox_uvmat('ERROR',['bad grid file ' Name ext ' found in ' Path2])
3552        return
3553        nbslice=1;
3554    end
3555end
3556
3557%------------------------------------------------------------------------
3558% --- transform numbers to letters
3559function str=num2stra(num,nom_type)
3560%------------------------------------------------------------------------
3561if isempty(nom_type)
3562    str='';
3563elseif strcmp(nom_type(end),'a')
3564    str=char(96+num);
3565elseif strcmp(nom_type(end),'A')
3566    str=char(96+num);
3567elseif isempty(nom_type(2:end))%a single index
3568    str='';
3569else
3570    str=num2str(num);
3571end
3572
3573% %------------------------------------------------------------------------
3574% % --- Executes on button press in ListSubdirCiv1.
3575% function ListSubdirCiv1_Callback(hObject, eventdata, handles)
3576% %------------------------------------------------------------------------
3577% list_subdir_civ1=get(handles.ListSubdirCiv1,'String');
3578% val=get(handles.ListSubdirCiv1,'Value');
3579% SubDir=list_subdir_civ1{val};
3580% if strcmp(SubDir,'new...')
3581%     if get(handles.CheckCiv1,'Value')
3582%         SubDir='CIV'; %default subdirectory
3583%     else
3584%         msgbox_uvmat('ERROR','select CheckCiv1 to perform a new Civ operation')
3585%         return
3586%     end   
3587% end
3588% set(handles.SubdirCiv1,'String',SubDir);
3589% errormsg=find_netcpair_civ(handles,1);
3590% if ~isempty(errormsg)
3591%     msgbox_uvmat('ERROR',errormsg)
3592% end
3593%     
3594%------------------------------------------------------------------------
3595% % --- Executes on button press in ListSubdirCiv2.
3596% function ListSubdirCiv2_Callback(hObject, eventdata, handles)
3597% %------------------------------------------------------------------------
3598% list_subdir_civ2=get(handles.ListSubdirCiv2,'String');
3599% val=get(handles.ListSubdirCiv2,'Value');
3600% SubDir=list_subdir_civ2{val};
3601% if strcmp(SubDir,'new...')
3602%     if get(handles.CheckCiv2,'Value')
3603%         SubDir='CIV'; %default subdirectory
3604%     else
3605%         msgbox_uvmat('ERROR','select CheckCiv2 to perform a new Civ operation')
3606%         return
3607%     end
3608% end
3609% set(handles.SubdirCiv2,'String',SubDir);
3610
3611%------------------------------------------------------------------------
3612% --- Executes on button press in CheckGrid.
3613function CheckGrid_Callback(hObject, eventdata, handles)
3614%------------------------------------------------------------------------
3615value=get(hObject,'Value');
3616hparent=get(hObject,'parent');
3617hchildren=get(hparent,'children');
3618handle_txtbox=findobj(hchildren,'tag','txt_Grid');
3619handle_dx=findobj(hchildren,'tag','num_Dx');
3620handle_dy=findobj(hchildren,'tag','num_Dy');
3621handle_title_dx=findobj(hchildren,'tag','title_Dx');
3622handle_title_dy=findobj(hchildren,'tag','title_Dy');
3623testgrid=0;
3624filegrid='';
3625if value
3626    filebase=get(handles.RootPath,'String');
3627    [nbslice, flag_grid]=get_grid(filebase,handles);% look for a grid with appropriate name
3628    if isequal(flag_grid,1)
3629        filegrid=[num2str(nbslice) 'grid'];
3630        testgrid=1;
3631    else % browse for a grid
3632        filegrid=get(hObject,'UserData');%look for previous grid name stored as UserData
3633        if exist(filegrid,'file')
3634            filebase=filegrid;
3635        end
3636        [FileName, PathName, filterindex] = uigetfile( ...
3637            {'*.grid', ' (*.grid)';
3638            '*.grid',  '.grid files '; ...
3639            '*.*', 'All Files (*.*)'}, ...
3640            'Pick a file',filebase);
3641        filegrid=fullfile(PathName,FileName);
3642        set(hObject,'UserData',filegrid);%store for future use
3643        if ~(isempty(FileName)||isempty(PathName)||isequal(FileName,0)||~exist(filegrid,'file'))
3644            testgrid=1;
3645        end
3646    end
3647end
3648if testgrid
3649    set(handle_dx,'Visible','off');
3650    set(handle_dy,'Visible','off');
3651    set(handle_title_dy,'Visible','off');
3652    set(handle_title_dx,'Visible','off');
3653    set(handle_txtbox,'Visible','on')
3654    set(handle_txtbox,'String',filegrid)
3655else
3656    set(hObject,'Value',0);
3657    set(handle_dx,'Visible','on');
3658    set(handle_dy,'Visible','on');
3659    set(handle_title_dy,'Visible','on');
3660    set(handle_title_dx,'Visible','on');
3661    set(handle_txtbox,'Visible','off')
3662end
3663
3664%% if hObject is on the checkciv1 frame, duplicate action for checkciv2 frame
3665PanelName=get(hparent,'tag');
3666if strcmp(PanelName,'Civ1')
3667    hchildren=get(handles.Civ2,'children');
3668    handle_checkbox=findobj(hchildren,'tag','CheckGrid');
3669    handle_txtbox=findobj(hchildren,'tag','txt_Grid');
3670    handle_dx=findobj(hchildren,'tag','num_Dx');
3671    handle_dy=findobj(hchildren,'tag','num_Dy');
3672    handle_title_dx=findobj(hchildren,'tag','title_Dx');
3673    handle_title_dy=findobj(hchildren,'tag','title_Dy');
3674    set(handle_checkbox,'UserData',filegrid);%store for future use
3675    if testgrid
3676        set(handle_checkbox,'Value',1);
3677        set(handle_dx,'Visible','off');
3678        set(handle_dy,'Visible','off');
3679        set(handle_title_dx,'Visible','off');
3680        set(handle_title_dy,'Visible','off');
3681        set(handle_txtbox,'Visible','on')
3682        set(handle_txtbox,'String',filegrid)
3683%     else
3684%         set(handle_checkbox,'Value',0);
3685%         set(handles.CheckGrid,'Value',0);
3686%         set(handle_dx,'Visible','on');
3687%         set(handle_dy,'Visible','on');
3688%          set(handle_title_dx,'Visible','on');
3689%         set(handle_title_dy,'Visible','on');
3690%         set(handle_txtbox,'Visible','off')
3691    end
3692end
3693
3694%------------------------------------------------------------------------
3695% --- Executes on button press in CheckMask: common to all panels (civ1, Civ2..)
3696function CheckMask_Callback(hObject, eventdata, handles)
3697%------------------------------------------------------------------------
3698value=get(hObject,'Value');
3699hparent=get(hObject,'parent');
3700parent_tag=get(hparent,'Tag');
3701hchildren=get(hparent,'children');
3702handle_txtbox=findobj(hchildren,'tag','Mask');% look for the mask name box in the same panel
3703testmask=0;
3704if value
3705    filebase=get(handles.RootPath,'String');
3706    [nbslice, flag_mask]=get_mask(filebase,handles);% look for a mask with appropriate name
3707    if isequal(flag_mask,1)
3708        filemask=[num2str(nbslice) 'mask'];
3709        testmask=1;
3710    else % browse for a mask
3711        filemask=get(hObject,'UserData');%look for previous mask name stored as UserData
3712        if exist(filemask,'file')
3713            filebase=filemask;
3714        end
3715        [FileName, PathName] = uigetfile( ...
3716            {'*.png', ' (*.png)';
3717            '*.png',  '.png files '; ...
3718            '*.*', 'All Files (*.*)'}, ...
3719            'Pick a mask file *.png',filebase);
3720        filemask=fullfile(PathName,FileName);
3721        set(hObject,'UserData',filemask);%store for future use
3722        if ~(isempty(FileName)||isempty(PathName)||isequal(FileName,0)||~exist(filemask,'file'))
3723            testmask=1;
3724        end
3725    end
3726end
3727if testmask
3728    if strcmp(parent_tag,'Civ1')
3729        set(handles.Mask,'Visible','on')
3730        set(handles.Mask,'String',filemask)
3731    set(handles.CheckMask,'Value',1)
3732    end
3733%     switch parent_tag
3734% %         case 'Fix1'
3735% %             stage=2;
3736%         case 'Civ2'
3737%              stage=3;
3738% %         case 'Fix2'
3739% %             stage=4;
3740%     end
3741%     set(handles.Mask(stage:end),'Visible','on')
3742%     set(handles.Mask(stage:end),'String',filemask)
3743%     set(handles.CheckMask(stage:end),'Value',1)
3744else
3745    set(hObject,'Value',0);
3746    set(handle_txtbox,'Visible','off')
3747end
3748
3749
3750% --- Executes on button press in get_gridpatch1.
3751function get_gridpatch1_Callback(hObject, eventdata, handles)
3752filebase=get(handles.RootPath,'String');
3753[FileName, PathName, filterindex] = uigetfile( ...
3754    {'*.grid', ' (*.grid)';
3755    '*.grid',  '.grid files '; ...
3756    '*.*', 'All Files (*.*)'}, ...
3757    'Pick a file',filebase);
3758filegrid=fullfile(PathName,FileName);
3759set(handles.grid_patch1,'string',filegrid);
3760
3761
3762%------------------------------------------------------------------------
3763% --- Executes on button press in get_gridpatch2.
3764function get_gridpatch2_Callback(hObject, eventdata, handles)
3765%------------------------------------------------------------------------
3766
3767
3768%------------------------------------------------------------------------
3769% --- STEREO Interp
3770function cmd=RUN_STINTERP(stinterpBin,filename_A_nc,filename_B_nc,filename_nc,nx_patch,ny_patch,rho_patch,subdomain_patch,thresh_value,xmlA,xmlB)
3771%------------------------------------------------------------------------
3772namelog=[filename_nc(1:end-3) '_stinterp.log'];
3773cmd=[stinterpBin ' -f1 ' filename_A_nc  ' -f2 ' filename_B_nc ' -f  ' filename_nc ...
3774    ' -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
3775
3776%------------------------------------------------------------------------
3777%--read images and convert them to the uint16 format used for PIV
3778function A=read_image(filename,type_ima,num,movieobject)
3779%------------------------------------------------------------------------
3780%num is the view number needed for an avi movie
3781switch type_ima
3782    case 'movie'
3783        A=read(movieobject,num);
3784    case 'avi'
3785        mov=aviread(filename,num);
3786        A=frame2im(mov(1));
3787    case 'multimage'
3788        A=imread(filename,num);
3789    case 'image'
3790        A=imread(filename);
3791end
3792siz=size(A);
3793if length(siz)==3;%color images
3794    A=sum(double(A),3);
3795    A=uint16(A);
3796end
3797
3798
3799%------------------------------------------------------------------------
3800% --- Executes on button press in get_ref_fix1.
3801function get_ref_fix1_Callback(hObject, eventdata, handles)
3802%------------------------------------------------------------------------
3803filebase=get(handles.RootPath,'String');
3804[FileName, PathName, filterindex] = uigetfile( ...
3805    {'*.nc', ' (*.nc)';
3806    '*.nc',  'netcdf files '; ...
3807    '*.*', 'All Files (*.*)'}, ...
3808    'Pick a file',filebase);
3809
3810fileinput=[PathName FileName];
3811sizf=size(fileinput);
3812if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end %stop if fileinput not a character string
3813%[Path,File,field_count,str2,str_a,str_b,ref.ext,ref.nom_type,ref.subdir]=name2display(fileinput);
3814[Path,ref.subdir,File,ref.num1,ref.num2,ref.num_a,ref.num_b,ref.ext,ref.nom_type]=fileparts_uvmat(fileinput);
3815ref.filebase=fullfile(Path,File);
3816% ref.num_a=stra2num(str_a);
3817% ref.num_b=stra2num(str_b);
3818% ref.num1=str2double(field_count);
3819% ref.num2=str2double(str2);
3820browse=[];%initialisation
3821if ~isequal(ref.ext,'.nc')
3822    msgbox_uvmat('ERROR','the reference file must be in netcdf format (*.nc)')
3823    return
3824end
3825set(handles.ref_fix1,'String',[fullfile(ref.subdir,File) '....nc']);
3826set(handles.ref_fix1,'UserData',ref)
3827menu_field{1}='civ1';
3828Data=nc2struct(fileinput,[]);
3829if isfield(Data,'patch') && isequal(Data.patch,1)
3830    menu_field{2}='filter1';
3831end
3832if isfield(Data,'civ2') && isequal(Data.civ2,1)
3833    menu_field{3}='civ2';
3834end
3835if isfield(Data,'patch2') && isequal(Data.patch2,1)
3836    menu_field{4}='filter2';
3837end
3838set(handles.field_ref1,'String',menu_field);
3839set(handles.field_ref1,'Value',length(menu_field));
3840set(handles.num_MinVel,'Value',2);
3841set(handles.num_MinVel,'String','1');%default threshold
3842set(handles.ref_fix1,'Enable','on')
3843
3844%------------------------------------------------------------------------
3845% --- Executes on button press in get_ref_fix2.
3846function get_ref_fix2_Callback(hObject, eventdata, handles)
3847%------------------------------------------------------------------------
3848if isequal(get(handles.get_ref_fix2,'Value'),1)
3849    filebase=get(handles.RootPath,'String');
3850    [FileName, PathName, filterindex] = uigetfile( ...
3851        {'*.nc', ' (*.nc)';
3852        '*.nc',  'netcdf files '; ...
3853        '*.*', 'All Files (*.*)'}, ...
3854        'Pick a file',filebase);
3855    fileinput=[PathName FileName];
3856    sizf=size(fileinput);
3857    if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end %stop if fileinput not a character string
3858    %[Path,File,field_count,str2,str_a,str_b,ref.ext,ref.nom_type,ref.subdir]=name2display(fileinput);
3859    [Path,ref.subdir,File,ref.num1,ref.num2,ref.num_a,ref.num_b,ref.ext,ref.nom_type]=fileparts_uvmat(fileinput);
3860    ref.filebase=fullfile(Path,File);
3861%     ref.num_a=stra2num(str_a);
3862%     ref.num_b=stra2num(str_b);
3863%     ref.num1=str2num(field_count);
3864%     ref.num2=str2num(str2);
3865    browse=[];%initialisation
3866    if ~isequal(ref.ext,'.nc')
3867        msgbox_uvmat('ERROR','the reference file must be in netcdf format (*.nc)')
3868        return
3869    end
3870    set(handles.ref_fix2,'String',[fullfile(ref.subdir,File) '....nc']);
3871    set(handles.ref_fix2,'UserData',ref)
3872    menu_field{1}='civ1';
3873    Data=nc2struct(fileinput,[]);
3874    if isfield(Data,'patch') && isequal(Data.patch,1)
3875        menu_field{2}='filter1';
3876    end
3877    if isfield(Data,'civ2') && isequal(Data.civ2,1)
3878        menu_field{3}='civ2';
3879    end
3880    if isfield(Data,'patch2') && isequal(Data.patch2,1)
3881        menu_field{4}='filter2';
3882    end
3883    set(handles.field_ref2,'String',menu_field);
3884    set(handles.field_ref2,'Value',length(menu_field));
3885    set(handles.num_MinVel,'Value',2);
3886    set(handles.num_MinVel,'String','1');%default threshold
3887    set(handles.ref_fix2,'Enable','on')
3888    set(handles.ref_fix2,'Visible','on')
3889    set(handles.field_ref2,'Visible','on')
3890else
3891    set(handles.ref_fix2,'Visible','off')
3892    set(handles.field_ref2,'Visible','off')
3893end
3894
3895%------------------------------------------------------------------------
3896function ref_fix1_Callback(hObject, eventdata, handles)
3897%------------------------------------------------------------------------
3898set(handles.num_MinVel,'Value',1);
3899set(handles.field_ref1,'Value',1)
3900set(handles.field_ref1,'String',{' '})
3901set(handles.ref_fix1,'UserData',[]);
3902set(handles.ref_fix1,'String','');
3903set(handles.thresh_vel1,'String','0');
3904
3905%------------------------------------------------------------------------
3906function ref_fix2_Callback(hObject, eventdata, handles)
3907%------------------------------------------------------------------------
3908set(handles.num_MinVel,'Value',1);
3909set(handles.field_ref2,'Value',1)
3910set(handles.field_ref2,'String',{' '})
3911set(handles.ref_fix2,'UserData',[]);
3912set(handles.ref_fix2,'String','');
3913set(handles.num_MinVel,'String','0');
3914
3915%------------------------------------------------------------------------
3916% --- TO ABANDON Executes on button press in test_stereo1.
3917function CheckStereo_Callback(hObject, eventdata, handles)
3918%------------------------------------------------------------------------
3919hparent=get(hObject,'parent');
3920parent_tag=get(hparent,'Tag');
3921hchildren=get(hparent,'children');
3922handle_txtbox=findobj(hchildren,'tag','txt_Mask');
3923if isequal(get(hObject,'Value'),0)
3924    set(handles.num_SubdomainSize,'Visible','on')
3925    set(handles.num_FieldSmooth,'Visible','on')
3926else
3927    set(handles.num_SubdomainSize,'Visible','off')
3928    set(handles.num_FieldSmooth,'Visible','off')
3929end
3930
3931% %------------------------------------------------------------------------
3932% % --- Executes on button press in CheckStereo.
3933% function StereoCheck_Callback(hObject, eventdata, handles)
3934% %------------------------------------------------------------------------
3935% if isequal(get(handles.CheckStereo,'Value'),0)
3936%     set(handles.num_SubdomainSize,'Visible','on')
3937%     set(handles.num_FieldSmooth,'Visible','on')
3938% else
3939%     set(handles.num_SubdomainSize,'Visible','off')
3940%     set(handles.num_FieldSmooth,'Visible','off')
3941% end
3942
3943%------------------------------------------------------------------------
3944% --- Executes on button press in TestCiv1: prepare the image correlation function
3945% activated by mouse motion
3946function TestCiv1_Callback(hObject, eventdata, handles)
3947%------------------------------------------------------------------------
3948drawnow
3949if get(handles.TestCiv1,'Value')
3950    set(handles.TestCiv1,'BackgroundColor',[0.7 0.7 0.7])% paint TestCiv1 button to grey to confirm civ launch
3951    ref_i=str2double(get(handles.ref_i,'String'));% read reference i index
3952    if strcmp(get(handles.ref_j,'Visible'),'on')
3953        ref_j=str2double(get(handles.ref_j,'String'));% read reference j index if relevant
3954    else
3955        ref_j=1;%default j index
3956    end
3957    [filecell,i1,i2]=set_civ_filenames(handles,ref_i,ref_j,[1 0 0 0 0 0]);% get the corresponding file name and indices
3958    Data.ListVarName={'ny','nx','A'};
3959    Data.VarDimName= {'ny','nx',{'ny','nx'}};
3960
3961    Data.A=imread(filecell.ima1.civ1{1}); % read the first image
3962    if ndims(Data.A)==3 %case of color image
3963        Data.VarDimName= {'ny','nx',{'ny','nx','rgb'}};
3964    end
3965    Data.ny=[size(Data.A,1) 1];
3966    Data.nx=[1 size(Data.A,2)];
3967    Data.CoordUnit='pixel';% used to set equal scaling for x and y in image dispaly
3968    par_civ1=read_GUI(handles.Civ1);
3969    par_civ1.FileTypeA=get_file_type(filecell.ima1.civ1{1});
3970    par_civ1.ImageWidth=size(Data.A,2);
3971    par_civ1.ImageHeight=size(Data.A,1);
3972    par_civ1.Mask='all';% will provide only the grid set for PIV, no image correlation
3973    par_civ1.FrameIndexA=num2str(i1);
3974    par_civ1.FrameIndexB=num2str(i2);
3975    Param.Civ1=par_civ1;
3976    Grid=civ_matlab(Param);% get the grid of x, y positions set for PIV
3977    hview_field=view_field(Data); %view the image in the GUI view_field
3978    set(0,'CurrentFigure',hview_field)
3979    hhview_field=guihandles(hview_field);
3980    set(hview_field,'CurrentAxes',hhview_field.axes3)
3981    ViewData=get(hview_field,'UserData');
3982    ViewData.CivHandle=handles.civ;% indicate the handle of the civ GUI in view_field
3983    ViewData.axes3.B=imread(filecell.ima2.civ1{1});%store the second image in the UserData of the GUI view_field
3984    ViewData.axes3.X=Grid.Civ1_X; %keep the set of points in memeory
3985    ViewData.axes3.Y=Grid.Civ1_Y;
3986    set(hview_field,'UserData',ViewData)
3987    corrfig=findobj(allchild(0),'tag','corrfig');% look for a current figure for image correlation display
3988    if isempty(corrfig)
3989        corrfig=figure;
3990        set(corrfig,'tag','corrfig')
3991        set(corrfig,'name','image correlation')
3992        set(corrfig,'DeleteFcn',{@closeview_field})%
3993    end
3994    set(handles.TestCiv1,'BackgroundColor',[1 0 0])
3995else
3996    set(handles.TestCiv1,'BackgroundColor',[1 0 0])% paint button to red
3997    corrfig=findobj(allchild(0),'tag','corrfig');% look for a current figure for image correlation display
3998    if ~isempty(corrfig)
3999        delete(corrfig)
4000    end
4001    hview_field=findobj(allchild(0),'tag','view_field');% look for view_field   
4002    if ~isempty(hview_field)
4003        delete(hview_field)
4004    end
4005end
4006
4007%------------------------------------------------------------------------
4008%----function introduced for the correlation window figure, activated by deleting this window
4009function closeview_field(gcbo,eventdata)
4010%------------------------------------------------------------------------
4011hview_field=findobj(allchild(0),'tag','view_field');% look for view_field
4012if ~isempty(hview_field)
4013    delete(hview_field)
4014end
4015
4016%------------------------------------------------------------------------
4017% --- Executes on button press in CheckThreshold.
4018function CheckThreshold_Callback(hObject, eventdata, handles)
4019%------------------------------------------------------------------------
4020huipanel=get(hObject,'parent');
4021obj(1)=findobj(huipanel,'Tag','num_MinIma');
4022obj(2)=findobj(huipanel,'Tag','num_MaxIma');
4023obj(3)=findobj(huipanel,'Tag','title_Threshold');
4024if get(hObject,'Value')
4025    set(obj,'Visible','on')
4026else
4027    set(obj,'Visible','off')
4028end
4029
4030%------------------------------------------------------------------------
4031function [cmd,errormsg]=cmd_civ1(filename,Param)
4032%------------------------------------------------------------------------
4033%pixels per cm and matrix of the image times, read from the .civ file by uvmat
4034%changes : filename_cmx -> filename ( no extension )
4035cmd='';
4036filename=regexprep(filename,'.nc',''); %file name for the result
4037if isequal(Param.Civ1.Dt,0)
4038    Param.Civ1.Dt=1 ;%case of 'displacement' mode
4039end
4040Param.Civ1.ImageA=regexprep(Param.Civ1.ImageA,'.png','');
4041Param.Civ1.ImageB=regexprep(Param.Civ1.ImageB,'.png','');
4042[fid,errormsg]=fopen([filename '.civ1.cmx'],'w');
4043if isequal(fid,-1)
4044    errormsg=['cmd file ' filename ' cannot be created: ' errormsg];
4045    return
4046end
4047fprintf(fid,['##############   CMX file' '\n' ]);
4048fprintf(fid,   ['FirstImage ' regexprep(Param.Civ1.ImageA,'\\','\\\\') '\n' ]);% for windows compatibility
4049fprintf(fid,   ['LastImage  ' regexprep(Param.Civ1.ImageB,'\\','\\\\') '\n' ]);% for windows compatibility
4050fprintf(fid,  ['XX' '\n' ]);
4051if isfield(Param.Civ1,'Mask')
4052    fprintf(fid,  ['Mask ' 'y' '\n' ]);
4053    fprintf(fid,  ['MaskName ' regexprep(Param.Civ1.Mask,'\\','\\\\') '\n' ]);
4054else
4055    fprintf(fid,  ['Mask ' 'n' '\n' ]);
4056    fprintf(fid,  ['MaskName ' 'noFile use default' '\n' ]);
4057end
4058fprintf(fid,   ['ImageSize ' num2str(Param.Civ1.ImageWidth) ' ' num2str(Param.Civ1.ImageHeight) '\n' ]);   %VERIFIER CAS GENERAL ?
4059fprintf(fid,   ['CorrelationBoxesSize ' num2str(Param.Civ1.CorrBoxSize(1)) ' ' num2str(Param.Civ1.CorrBoxSize(2)) '\n' ]);
4060fprintf(fid,   ['SearchBoxeSize ' num2str(Param.Civ1.SearchBoxSize(1)) ' ' num2str(Param.Civ1.SearchBoxSize(2)) '\n' ]);
4061fprintf(fid,   ['RO ' num2str(Param.Civ1.CorrSmooth) '\n' ]);
4062if isfield(Param.Civ1,'Grid')
4063    fprintf(fid,   ['GridSpacing ' '25' ' ' '25' '\n' ]);
4064else
4065    fprintf(fid,   ['GridSpacing ' num2str(Param.Civ1.Dx) ' ' num2str(Param.Civ1.Dy) '\n' ]);
4066end
4067fprintf(fid,   ['XX 1.0' '\n' ]);
4068fprintf(fid,   ['Dt_TO ' num2str(Param.Civ1.Dt) ' ' num2str(Param.Civ1.Time) '\n' ]);
4069fprintf(fid,  ['PixCmXY ' '1' ' ' '1' '\n' ]);
4070fprintf(fid,  ['XX 1' '\n' ]);
4071fprintf(fid,   ['ShiftXY ' num2str(Param.Civ1.SearchBoxShift(1)) ' '  num2str(Param.Civ1.SearchBoxShift(2)) '\n' ]);
4072if isfield(Param.Civ1,'Grid')
4073    fprintf(fid,  ['Grid ' 'y' '\n' ]);
4074    fprintf(fid,   ['GridName ' regexprep(Param.Civ1.Grid,'\\','\\\\') '\n' ]);
4075else
4076    fprintf(fid,  ['Grid ' 'n' '\n' ]);
4077    fprintf(fid,   ['GridName ' 'noFile use default' '\n' ]);
4078end
4079fprintf(fid,   ['XX 85' '\n' ]);
4080fprintf(fid,   ['XX 1.0' '\n' ]);
4081fprintf(fid,   ['XX 1.0' '\n' ]);
4082fprintf(fid,   ['Hart 1' '\n' ]);
4083fprintf(fid,  [ 'DecimalShift 0' '\n' ]);
4084fprintf(fid,   ['Deformation 0' '\n' ]);
4085fprintf(fid,  ['CorrelationMin 0' '\n' ]);
4086fprintf(fid,   ['IntensityMin 0' '\n' ]);
4087if ~isfield(Param.Civ1,'MinIma')% Image threshold not activated
4088    fprintf(fid,  ['SeuilImage n' '\n' ]);
4089    fprintf(fid,   ['SeuilImageValues 0 4096' '\n' ]);%not used in principle
4090else% Image threshold  activated
4091    if isempty(Param.Civ1.MaxIma)||isnan(Param.Civ1.MaxIma)
4092        Param.Civ1.MaxIma=2^Param.Civ1.ImageBitDepth;%take the max image value as upper bound by default
4093    end
4094    fprintf(fid,  ['SeuilImage y' '\n' ]);
4095    fprintf(fid,   ['SeuilImageValues ' num2str(Param.Civ1.MinIma) ' ' num2str(Param.Civ1.MaxIma) '\n' ]);
4096end
4097fprintf(fid,   ['ImageToUse ' Param.Civ1.term_a ' ' Param.Civ1.term_b '\n' ]); % VERIFIER ?
4098fprintf(fid,   ['ImageUsedBefore null null' '\n' ]);
4099fclose(fid);
4100
4101if(isunix) %unix (or Mac) system
4102    cmd=['cp -f ' filename '.civ1.cmx ' filename '.cmx \n '];% the cmx file gives the name to the nc file
4103    cmd=[cmd Param.xml.Civ1Bin ' -f ' filename '.cmx >' filename '.civ1.log \n ' ]; % redirect standard output to the log file, the result file is named [filename '.nc'] by CIVx
4104    cmd=[cmd 'rm ' filename '.cmx'];
4105else %Windows system
4106    filename=regexprep(filename,'\\','\\\\');
4107    cmd=['copy /Y "' filename '.civ1.cmx" "' filename '.cmx" \n '];
4108    cmd=[cmd '"' regexprep(Param.xml.Civ1Bin,'\\','\\\\')...
4109        '" -f "' filename '.cmx" >"' filename '.civ1.log" \n ' ]; % redirect standard output to the log file
4110    cmd=[cmd 'del "' filename '.cmx"'];
4111end
4112
4113
4114function cmd=cmd_fix(filename,Param,fixname)
4115%%
4116switch fixname
4117    case 'Fix1'
4118        fi2_value=num2str(Param.(fixname).CheckF2);
4119    case 'Fix2'
4120        fi2_value=num2str(Param.(fixname).CheckF4);%need to understand why...
4121end
4122filename=regexprep(filename,'.nc','');
4123MaskName_string='';%default
4124MaxVel_string='';%default
4125if ~isempty(Param.(fixname).MinVel)
4126    MaxVel_string=[' -threshV ' num2str(Param.(fixname).MinVel)];
4127end
4128if isunix
4129    cmd=[Param.xml.FixBin ' -f ' filename '.nc -fi1 ' num2str(Param.(fixname).CheckFmin2) ...
4130        ' -fi2 ' fi2_value ' -fi3 ' num2str(Param.(fixname).CheckF3) ...
4131        ' -threshC ' num2str(Param.(fixname).MinCorr) MaxVel_string MaskName_string...
4132        ' >' filename '.' lower(fixname) '.log 2>&1'];
4133else
4134    cmd=['"' Param.xml.FixBin '" -f "' filename '.nc" -fi1 ' num2str(Param.(fixname).CheckFmin2)...
4135        ' -fi2 ' fi2_value ' -fi3 ' num2str(Param.(fixname).CheckF3) ...
4136        ' -threshC ' num2str(Param.(fixname).MinCorr) MaxVel_string MaskName_string...
4137        ' > "' filename '.' lower(fixname) '.log"'];
4138    cmd=regexprep(cmd,'\\','\\\\');
4139end
4140
4141
4142function cmd=cmd_patch(filename,Param,patchname)
4143%% ------------------------------------------------------------------------
4144filename=regexprep(filename,'.nc','');
4145if isunix
4146    cmd=[Param.xml.PatchBin...
4147        ' -f ' filename '.nc -m ' num2str(Param.(patchname).Nx)...
4148        ' -n ' num2str(Param.(patchname).Ny) ' -ro ' num2str(Param.(patchname).FieldSmooth)...
4149        ' -nopt ' num2str(Param.(patchname).SubdomainSize) ...
4150        '  > ' filename '.' lower(patchname) '.log 2>&1']; % redirect standard output to the log file
4151else
4152    cmd=['"' Param.xml.PatchBin...
4153        '" -f "' filename '.nc" -m ' num2str(Param.(patchname).Nx)...
4154        ' -n ' num2str(Param.(patchname).Ny) ' -ro ' num2str(Param.(patchname).FieldSmooth)...
4155        ' -nopt ' num2str(Param.(patchname).SubdomainSize)...
4156        '  > "' filename '.' lower(patchname) '.log" 2>&1']; % redirect standard output to the log file
4157    cmd=regexprep(cmd,'\\','\\\\');
4158end
4159
4160%------------------------------------------------------------------------
4161% --- CheckCiv2  CheckCiv2  CheckCiv2 CheckCiv2
4162function [cmd,errormsg]=cmd_civ2(filename,Param)
4163%------------------------------------------------------------------------
4164%pixels per cm and matrix of the image times, read from the .civ file by uvmat
4165% global civ2Bin sge%name of the executable for checkciv1 calculation
4166 cmd='';
4167filename=regexprep(filename,'.nc','');
4168if isequal(Param.Civ2.Dt,'0')
4169    Param.Civ2.Dt='1' ;%case of 'displacement' mode
4170end
4171Param.Civ2.ImageA=regexprep(Param.Civ2.ImageA,'.png','');
4172Param.Civ2.ImageB=regexprep(Param.Civ2.ImageB,'.png','');% bug : .png appears two times ?
4173[fid,errormsg]=fopen([filename '.civ2.cmx'],'w');
4174if isequal(fid,-1)
4175    return
4176end
4177fprintf(fid,['##############   CMX file' '\n' ]);
4178fprintf(fid,   ['FirstImage ' regexprep(Param.Civ2.ImageA,'\\','\\\\') '\n' ]);% for windows compatibility
4179fprintf(fid,   ['LastImage  ' regexprep(Param.Civ2.ImageB,'\\','\\\\') '\n' ]);% for windows compatibility
4180fprintf(fid,  ['XX' '\n' ]);
4181if isfield(Param.Civ2,'Mask')
4182    fprintf(fid,  ['Mask ' 'y' '\n' ]);
4183    fprintf(fid,  ['MaskName ' regexprep(Param.Civ2.Mask,'\\','\\\\') '\n' ]);
4184else
4185    fprintf(fid,  ['Mask ' 'n' '\n' ]);
4186    fprintf(fid,  ['MaskName ' 'noFile use default' '\n' ]);
4187end
4188% fprintf(fid, ['Mask ' Param.Civ2.MaskFlag '\n' ]);
4189% fprintf(fid, ['MaskName ' regexprep(Param.Civ2.MaskName,'\\','\\\\') '\n' ]);% for windows compatibility
4190fprintf(fid,   ['ImageSize ' num2str(Param.Civ2.ImageWidth) ' ' num2str(Param.Civ2.ImageHeight) '\n' ]); 
4191% fprintf(fid, ['ImageSize ' num2str(Param.Civ2.npx) ' ' num2str(Param.Civ2.npy) '\n' ]);   %VERIFIER CAS GENERAL ?
4192fprintf(fid, ['CorrelationBoxesSize ' num2str(Param.Civ2.CorrBoxSize(1)) ' ' num2str(Param.Civ2.CorrBoxSize(2)) '\n' ]);
4193fprintf(fid, ['SearchBoxeSize ' num2str(Param.Civ2.CorrBoxSize(1)) ' ' num2str(Param.Civ2.CorrBoxSize(2)) '\n']);
4194fprintf(fid, ['RO ' num2str(Param.Civ2.CorrSmooth) '\n']);
4195if isfield(Param.Civ2,'Grid')
4196    fprintf(fid,   ['GridSpacing ' '25' ' ' '25' '\n' ]);
4197else
4198    fprintf(fid,   ['GridSpacing ' num2str(Param.Civ2.Dx) ' ' num2str(Param.Civ2.Dy) '\n' ]);
4199end
4200% fprintf(fid, ['GridSpacing ' num2str(Param.Civ2.Dx) ' ' num2str(Param.Civ2.Dy) '\n']);
4201fprintf(fid, ['XX 1.0' '\n' ]);
4202fprintf(fid, ['Dt_TO ' num2str(Param.Civ2.Dt) ' ' num2str(Param.Civ2.Time) '\n' ]);
4203fprintf(fid, ['PixCmXY ' '1' ' ' '1' '\n' ]);
4204fprintf(fid, ['XX 1' '\n' ]);
4205fprintf(fid, 'ShiftXY 0 0\n');
4206if isfield(Param.Civ2,'Grid')
4207    fprintf(fid,  ['Grid ' 'y' '\n' ]);
4208    fprintf(fid,   ['GridName ' regexprep(Param.Civ2.Grid,'\\','\\\\') '\n' ]);
4209else
4210    fprintf(fid,  ['Grid ' 'n' '\n' ]);
4211    fprintf(fid,   ['GridName ' 'noFile use default' '\n' ]);
4212end
4213% fprintf(fid, ['Grid ' Param.Civ2.GridFlag '\n' ]);
4214% fprintf(fid, ['GridName ' regexprep(Param.Civ2.GridName,'\\','\\\\') '\n']);
4215fprintf(fid, ['XX 85' '\n' ]);
4216fprintf(fid, ['XX 1.0' '\n' ]);
4217fprintf(fid, ['XX 1.0' '\n' ]);
4218fprintf(fid, ['Hart 1' '\n' ]);
4219fprintf(fid, ['DecimalShift ' num2str(Param.Civ2.CheckDecimal) '\n']);
4220fprintf(fid, ['Deformation ' num2str(Param.Civ2.CheckDeformation) '\n']);
4221fprintf(fid,  ['CorrelationMin 0' '\n' ]);
4222fprintf(fid,   ['IntensityMin 0' '\n' ]);
4223
4224if ~isfield(Param.Civ2,'MinIma')% Image threshold not activated
4225    fprintf(fid,  ['SeuilImage n' '\n' ]);
4226    fprintf(fid,   ['SeuilImageValues 0 4096' '\n' ]);%not used in principle
4227else% Image threshold  activated
4228    if isempty(Param.Civ2.MaxIma)||isnan(Param.Civ2.MaxIma)
4229        Param.Civ2.MaxIma=2^Param.Civ2.ImageBitDepth;%take the max image value as upper bound by default
4230    end
4231    fprintf(fid,  ['SeuilImage y' '\n' ]);
4232    fprintf(fid,   ['SeuilImageValues ' num2str(Param.Civ2.MinIma) ' ' num2str(Param.Civ2.MaxIma) '\n' ]);
4233end
4234fprintf(fid,   ['ImageToUse ' Param.Civ2.term_a ' ' Param.Civ2.term_b '\n' ]); % VERIFIER ?
4235fprintf(fid, ['ImageUsedBefore ' regexprep(Param.Civ2.filename_nc1,'\\','\\\\') '\n']);
4236fclose(fid);
4237
4238if(isunix)
4239    cmd=['cp -f ' filename '.civ2.cmx ' filename '.cmx\n'...
4240        Param.xml.Civ2Bin ' -f ' filename  '.cmx >' filename '.civ2.log \n '... % redirect standard output to the log file, the result file is named [filename '.nc'] by CIVx
4241        'rm ' filename '.cmx \n'];%rename .cmx as .checkciv2.cmx, the result file is named [filename '.nc'] by CIVx
4242else
4243    filename=regexprep(filename,'\\','\\\\');
4244    cmd=['copy /Y "' filename '.civ2.cmx" "' filename '.cmx" \n'...
4245        '"' regexprep(Param.xml.Civ2Bin,'\\','\\\\') '" -f "' filename  '.cmx" >"' filename '.civ2.log" \n'...
4246        'del "' filename '.cmx" \n'];
4247end
4248
4249%------------------------------------------------------------------------
4250% --- CheckCiv1  Unified: TO ABADON
4251function xml_civ1_parameters=CIV1_CMD_Unified(filename,namelog,par)
4252%------------------------------------------------------------------------
4253%pixels per cm and matrix of the image times, read from the .civ file by uvmat
4254%global CivBin%name of the executable for checkciv1 calculation
4255
4256civ1.image1=par.ImageA;
4257civ1.image2=par.ImageB;
4258civ1.imageSize_X=par.npx;
4259civ1.imageSize_Y=par.npy;
4260civ1.outputFileName=[filename '.nc'];
4261civ1.correlationBoxesSize_X=par.ibx;
4262civ1.correlationBoxesSize_Y=par.iby;
4263civ1.searchBoxesSize_X=par.isx;
4264civ1.searchBoxesSize_Y=par.isy;
4265civ1.globalShift_X=par.shiftx;
4266civ1.globalShift_Y=par.shifty;
4267civ1.ro=par.rho;
4268civ1.hart='y';
4269if isequal(par.gridflag,'y')
4270    civ1.grid=par.gridname;
4271else
4272    civ1.grid='n';
4273    civ1.gridSpacing_X=par.dx;
4274    civ1.gridSpacing_Y=par.dy;
4275end
4276if isequal(par.maskflag,'y')
4277    civ1.mask=par.maskname;
4278end
4279civ1.dt=par.Dt;
4280civ1.unit='pixel';
4281civ1.absolut_time_T0=par.Time;
4282civ1.pixcmx='1';
4283civ1.pixcmy='1';
4284civ1.convectFlow='n';
4285
4286xml_civ1_parameters=civ1;
4287
4288%------------------------------------------------------------------------
4289% --- CheckCiv2  Unified: TO ABADON
4290function civ2=CIV2_CMD_Unified(filename,namelog,par)
4291%------------------------------------------------------------------------
4292%pixels per cm and matrix of the image times, read from the .civ file by uvmat
4293%global CivBin%name of the executable for checkciv1 calculation
4294
4295filename=regexprep(filename,'.nc','');
4296
4297civ2.image1=par.ImageA;
4298civ2.image2=par.ImageB;
4299civ2.imageSize_X=par.npx;
4300civ2.imageSize_Y=par.npy;
4301civ2.inputFileName=[par.filename_nc1 '.nc'];
4302civ2.outputFileName=[filename '.nc'];
4303civ2.correlationBoxesSize_X=par.ibx;
4304civ2.correlationBoxesSize_Y=par.iby;
4305civ2.ro=par.rho;
4306%checkciv2.decimalShift=par.CheckDecimal;
4307%checkciv2.CheckDeformation=par.CheckDeformation;
4308if isequal(par.decimal,'1')
4309    civ2.decimalShift='y';
4310else
4311    civ2.decimalShift='n';
4312end
4313if isequal(par.deformation,'1')
4314    civ2.deformation='y';
4315else
4316    civ2.deformation='n';
4317end
4318if isequal(par.gridflag,'y')
4319    civ2.grid=par.gridname;
4320else
4321    civ2.grid='n';
4322    civ2.gridSpacing_X=par.dx;
4323    civ2.gridSpacing_Y=par.dy;
4324end
4325civ2.gridSpacing_X='10';
4326civ2.gridSpacing_Y='10';%NOTE: faut mettre gridSpacing pourque ca tourne, meme si c'est la grille qui est utilisee
4327if isequal(par.maskflag,'y')
4328    civ2.mask=par.maskname;
4329else
4330    civ2.mask='n';
4331end
4332civ2.dt=par.Dt;
4333civ2.unit='pixel';
4334civ2.absolut_time_T0=par.Time;
4335civ2.pixcmx='1';
4336civ2.pixcmy='1';
4337civ2.convectFlow='n';
4338
4339
4340% --- Executes on button press in TestPatch1.
4341function TestPatch1_Callback(hObject, eventdata, handles)
4342set(handles.TestPatch1,'BackgroundColor',[1 1 0])
4343drawnow
4344if get(handles.TestPatch1,'Value')
4345    ref_i=str2double(get(handles.ref_i,'String'));
4346    if strcmp(get(handles.ref_j,'Visible'),'on')
4347        ref_j=str2double(get(handles.ref_j,'String'));
4348    else
4349        ref_j=1;%default
4350    end
4351    filecell=set_civ_filenames(handles,ref_i,ref_j,[0 0 1 0 0 0]);   
4352    Data.ListVarName={'ny','nx','A'};
4353    Data.VarDimName= {'ny','nx',{'ny','nx'}};   
4354    param_patch1=read_GUI(handles.Patch1);
4355    param_patch1.CivFile=filecell.nc.civ1{1};
4356    Param.Patch1=param_patch1;
4357    for irho=1:7
4358        [Data,errormsg]=civ_matlab(Param);% get the grid of x, y positions set for PIV
4359        if ~isempty(errormsg)
4360            msgbox_uvmat('ERROR',errormsg)
4361            return
4362        end
4363        SmoothingParam(irho)=Param.Patch1.FieldSmooth;
4364        Data.Civ1_U_Diff=Data.Civ1_U_Diff(Data.Civ1_FF==0);
4365        Data.Civ1_V_Diff=Data.Civ1_V_Diff(Data.Civ1_FF==0);
4366        DiffVel(irho)=sqrt(mean(Data.Civ1_U_Diff.*Data.Civ1_U_Diff+Data.Civ1_V_Diff.*Data.Civ1_V_Diff))
4367        NbSites(irho,:)=Data.Civ1_NbSites*numel(Data.Civ1_NbSites)/numel(Data.Civ1_U_Diff);
4368        Param.Patch1.SmoothingParam=2*Param.Patch1.FieldSmooth;
4369    end
4370    figure
4371    plot(SmoothingParam,DiffVel,'b',SmoothingParam,NbSites,'r')
4372    set(handles.TestPatch1,'BackgroundColor',[1 0 0])
4373else
4374    corrfig=findobj(allchild(0),'tag','corrfig');% look for a current figure for image correlation display
4375    if ~isempty(corrfig)
4376        delete(corrfig)
4377    end
4378    hview_field=findobj(allchild(0),'tag','view_field');% look for view_field
4379    if ~isempty(hview_field)
4380        delete(hview_field)
4381    end
4382end
4383%'nomtype2pair': creates nomencalture for index pairs knowing the image nomenclature
4384%---------------------------------------------------------------------
4385% [nom_type_pair]=nomtype2pair(nom_type,Dti,Dtj);
4386%---------------------------------------------------------------------           
4387
4388% OUTPUT:
4389%nom_type_nc
4390
4391%---------------------------------------------------------------------
4392% INPUT:
4393% 'nom_type': string defining the kind of nomenclature used:
4394     %nom_type='': constant name [filebase ext] (default output if 'nom_type' is undefined)
4395     %nom_type='*': the same  file [filebase ext] contains successive fields (ex avi movies)
4396     %nom_type='_i': series of files with a single index i preceded by '_'(e.g. 'aa_45.png').
4397     %nom_type='#' series of indexed images wich is not series_i [filebase index ext], e.g. 'aa045.jpg' or 'aa45.tif'
4398     %nom_type='_i_j' matrix of files with two indices i and j separated by '_'(e.g. 'aa_45_2.png')
4399     %nom_type='_i1-i2' from pairs from a single index (e.g. 'aa_45-47.nc')
4400     %nom_type='_i_j1-j2'pairs of j indices (e.g. 'aa_45_2-3.nc')
4401     %nom_type='_i1-i2_j' pairs of i indices (e.g. 'aa_45-46_2.nc')
4402     %nom_type='#a','#A', with a numerical index and an index letter(e.g.'aa045b.png'), OBSOLETE (replaced by 'series_i_j')
4403     %nom_type='%03d' or '%04d', series of indexed images with numbers completed with zeros to 3 or 4 digits, e.g.'aa045.tif'
4404     %nom_type='_%03d', '_%04d', or '_%05d', series of indexed images with _ and numbers completed with zeros to 3, 4 or 5 digits, e.g.'aa_045.tif'
4405     %nom_type='raw_SMD', same as '#a' but with no extension ext='', OBSOLETE
4406     %nom_type='#_ab' from pairs of '#a' images (e.g. 'aa045bc.nc'), ext='.nc', OBSOLETE (replaced by 'netc_2D')
4407     %nom_type='%3dab' from pairs of '%3da' images (e.g. 'aa045bc.nc'), ext='.nc', OBSOLETE (replaced by 'netc_2D')
4408% Dti: ~=0 if i index pairs are used
4409% Dtj: ~=0 if i index pairs are used
4410
4411function NomTypeNc=nomtype2pair(NomTypeIma,mode)
4412
4413%determine nom_type_nc:
4414NomTypeNc=NomTypeIma;%default
4415switch mode
4416    case 'pair j1-j2'     
4417    if ~isempty(regexp(NomTypeIma,'a$'))
4418        NomTypeNc=[NomTypeIma 'b'];
4419    elseif ~isempty(regexp(NomTypeIma,'A$'))
4420        NomTypeNc=[NomTypeIma 'B'];
4421    else
4422        r=regexp(NomTypeIma,'(?<num1>\d+)_(?<num2>\d+)$','names');
4423        if ~isempty(r)
4424            NomTypeNc='_1_1-2';
4425        end
4426    end
4427    case 'series(Dj)' 
4428        r=regexp(NomTypeIma,'(?<num1>\d+)_(?<num2>\d+)$','names');
4429        if ~isempty(r)
4430            NomTypeNc='_1_1-2';
4431        end
4432   case 'series(Di)'
4433        r=regexp(NomTypeIma,'(?<num1>\d+)_(?<num2>\d+)$','names');
4434        if ~isempty(r)
4435            NomTypeNc='_1-2_1';
4436        else
4437            NomTypeNc='_1-2';
4438        end
4439end
4440
4441function NomType_Callback(hObject, eventdata, handles)
4442set(handles.RootPath,'BackgroundColor',[1 1 0])%paint RootName edit box in yellow to indicate that the file input is proceeding
4443RootPath=get(handles.RootPath,'String');
4444RootFile=get(handles.RootFile,'String');
4445ref_i=str2num(get(handles.ref_i,'String'));
4446ref_j=str2num(get(handles.ref_j,'String'));
4447NomType=get(handles.NomType,'String');
4448ImaExt=get(handles.ImaExt,'String');
4449fileinput=fullfile_uvmat(RootPath,'',RootFile,ImaExt,NomType,ref_i,[],ref_j);
4450errormsg=display_file_name(handles,fileinput);
4451if ~isempty(errormsg)
4452    msgbox_uvmat('ERROR',errormsg)
4453end
4454set(handles.RootPath,'BackgroundColor',[1 1 1])%paint RootName back to white to indicate that the file input is finished
4455
4456% --- Executes on selection change in ListProgram.
4457function ListProgram_Callback(hObject, eventdata, handles)
4458ListProgram=get(handles.ListProgram,'String');
4459Program=ListProgram{get(handles.ListProgram,'value')};
4460switch Program
4461    case 'CivX'
4462        set(handles.num_MaxDiff,'Visible','off')
4463        set(handles.num_MaxVel,'Visible','off')
4464        set(handles.title_MaxVel,'Visible','off')
4465        set(handles.num_Nx,'Visible','on')
4466        set(handles.num_Ny,'Visible','on')
4467        set(handles.title_Nx,'Visible','on')
4468        set(handles.title_Ny,'Visible','on')
4469        set(handles.title_MaxDiff,'Visible','off')
4470        set(handles.num_CorrSmooth,'Style','edit')
4471        set(handles.num_CorrSmooth,'String','1')
4472        set(handles.BATCH,'Enable','on')
4473        set(handles.CheckThreshold,'Visible','off')
4474        set(handles.CheckDeformation,'Value',1)
4475        set(handles.CheckDecimal,'Value',1)
4476    case 'Matlab'
4477        set(handles.num_MaxDiff,'Visible','on')
4478        set(handles.num_MaxVel,'Visible','on')
4479        set(handles.title_MaxVel,'Visible','on')
4480        set(handles.title_MaxDiff,'Visible','on')
4481        set(handles.num_Nx,'Visible','off')
4482        set(handles.num_Ny,'Visible','off')
4483        set(handles.title_Nx,'Visible','off')
4484        set(handles.title_Ny,'Visible','off')
4485        set(handles.num_CorrSmooth,'Style','popupmenu')
4486        set(handles.num_CorrSmooth,'Value',1)
4487        set(handles.num_CorrSmooth,'String',{'1';'2'})
4488        set(handles.CheckThreshold,'Visible','on')
4489        set(handles.CheckDeformation,'Value',0)% desactivate (work in progress)
4490        set(handles.CheckDecimal,'Value',0)% desactivate (work in progress)
4491end
4492
4493
4494% --- Executes on button press in TestCiv2.
4495function TestCiv2_Callback(hObject, eventdata, handles)
4496
4497
4498
4499function RootFile_Callback(hObject, eventdata, handles)
4500
4501
4502
4503function SubdirImages_Callback(hObject, eventdata, handles)
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