source: trunk/src/civ.m @ 174

Last change on this file since 174 was 174, checked in by sommeria, 13 years ago

civ.m : clarification of .cmx : creation of .civ1.cmx and .civ2.cmx
uvmat: reading and projecting volume images (not yet successfull)

File size: 184.3 KB
Line 
1%'civ': function associated with the interface 'civ.fig' for PIV, spline interpolation and stereo PIV (patch)
2%------------------------------------------------------------------------
3%  provides an interface for the software CIVx
4% function varargout = civ(varargin)
5% provides an interface for the software CIVx
6%
7%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
8%  Copyright Joel Sommeria, 2008, LEGI / CNRS-UJF-INPG, sommeria@coriolis-legi.org.
9%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
10%     This file is part of the toolbox UVMAT.
11%
12%     UVMAT is free software; you can redistribute it and/or modify
13%     it under the terms of the GNU General Public License as published by
14%     the Free Software Foundation; either version 2 of the License, or
15%     (at your option) any later version.
16%
17%     UVMAT is distributed in the hope that it will be useful,
18%     but WITHOUT ANY WARRANTY; without even the implied warranty of
19%     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
20%     GNU General Public License (file UVMAT/COPYING.txt) for more details.
21%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
22function varargout = civ(varargin)
23
24% Last Modified by GUIDE v2.5 01-Dec-2010 23:19:15
25% Begin initialization code - DO NOT EDIT
26gui_Singleton = 1;
27gui_State = struct('gui_Name',       mfilename, ...
28    'gui_Singleton',  gui_Singleton, ...
29    'gui_OpeningFcn', @civ_OpeningFcn, ...
30    'gui_OutputFcn',  @civ_OutputFcn, ...
31    'gui_LayoutFcn',  [] , ...
32    'gui_Callback',   []);
33if nargin && ischar(varargin{1})
34    gui_State.gui_Callback = str2func(varargin{1});
35end
36
37if nargout
38    [varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:});
39else
40    gui_mainfcn(gui_State, varargin{:});
41end
42% End initialization code - DO NOT EDIT
43
44%------------------------------------------------------------------------
45% --- Executes just before civ is made visible.
46function civ_OpeningFcn(hObject, eventdata, handles, param)
47%------------------------------------------------------------------------
48% This function has no output args, see OutputFcn.
49% hObject    handle to figure
50% eventdata  reserved - to be defined in a future version of MATLAB
51% handles    structure with handles and user data (see GUIDATA)
52% varargin   command line arguments to civ (see VARARGIN)
53global patch_newBin %=1 if new patch processing available
54%filebase: root name
55%nom_type: nomencalture used ('png_old','_i_j'...)
56%list of field numbers to process
57%subdir: subdirectory of the opened netcdf file
58%ind_opening: operation number advised for beginning (1=civ1,2=fix1,3=patch1,4=civ2,5=fix2,6=patch2),
59%ind_a_opening ind_b_opening chosen pair from the opened netcdf file
60% Choose default command line output for civ
61handles.output = hObject;
62% Update handles structure
63guidata(hObject, handles);
64
65%default initial parameters
66filebase=''; % root file name ('filebase'.civ)
67ext=[];
68testall=0;
69%default input parameters:
70num_i1=1; % set of field i numbers
71num_i2=1; % set of field i numbers
72num_j1=1; % set of field j numbers (fields a)
73num_j2=1; % second set of field j numbers (fields b)
74subdir='A'; % subdir for the netcdf result files
75ind_opening=1; % proposed operation number (1=civ1,2=fix1,3=patch1,4=civ2,5=fix2,6=patch2)
76%load the initial parameters if the interface is started from uvmat
77if exist('param','var')&&isstruct(param)% the interface is opened from uvmat
78    filebase=param.RootName;
79    nom_type_read=param.NomType;
80    num_i1=param.num1;
81    if isnan(num_i1),num_i1=1;end
82    num_i2=param.num2;
83    if isnan(num_i2),num_i2=num_i1;end
84    num_j1=param.num_a;
85    if isnan(num_j1),num_j1=1;end
86    num_j2=param.num_b;
87    if isnan(num_j2),num_j2=num_j1;end
88    subdir=param.SubDir;
89    ind_opening=param.IndOpening;
90    ext=param.ImaExt;
91end
92browse.num_i1=num_i1;
93browse.num_i2=num_i2;
94browse.num_j1=num_j1;
95browse.num_j2=num_j2;
96if ~isempty(ext) && (~isempty(imformats(ext(2:end)))||strcmpi(ext,'.avi'));%if an image file has been opened by uvmat
97    set(handles.ImaExt,'String',ext)
98    browse.ext_ima=ext;
99    if exist('nom_type_read','var')
100        browse.nom_type_ima=nom_type_read; % the image nomenclature is stored
101    end
102elseif isequal(ext,'.nc')
103    if exist('nom_type_read','var')
104        browse.nom_type_nc=nom_type_read;% the netcdf  nomenclature is stored
105    end
106end
107set(handles.RootName,'String',filebase);
108set(handles.ImaDoc,'UserData',testall);
109set(handles.ImaDoc,'String',ext)
110
111%read names of the .exe file to adjust the interface according to available binaries
112path_uvmat=which('uvmat');% check the path detected for source file uvmat
113path_UVMAT=fileparts(path_uvmat); %path to UVMAT
114errormsg=[];%default error message
115% xmlfile=fullfile(path_UVMAT,'PARAM.xml');
116% if ~exist(xmlfile,'file')
117xmlfile='PARAM.xml';
118% end
119if exist(xmlfile,'file')
120    try
121        t=xmltree(xmlfile);
122        sparam=convert(t);
123    catch
124        errormsg={' Unable to read the file PARAM.xml defining the civx binaries:'; lasterr};
125    end
126else
127    errormsg=[xmlfile ' not found: path to civx binaries undefined'];
128end
129
130
131if ~isempty(errormsg)
132    msgbox_uvmat('ERROR',errormsg);
133end
134% patch_newBin='';
135test_batch=0;%default: ,no batch mode available
136if isfield(sparam,'BatchParam') && isfield(sparam.BatchParam,'BatchMode')
137    test_batch=strcmp(sparam.BatchParam.BatchMode,'sge'); %sge is currently the only implemented batch mod
138end
139if test_batch==0
140    set(handles.BATCH,'Enable','off')% put the BATCH button in grey (unactivated)
141    set(handles.BATCH,'BackgroundColor',[0.831 0.816 0.784])% put the BATCH button in grey (unactivated)
142end
143if isfield(sparam.RunParam,'CivBin')
144    if ~exist(sparam.RunParam.CivBin,'file')
145        sparam.RunParam.CivBin=fullfile(path_UVMAT,sparam.RunParam.CivBin);
146    end
147else
148    sparam.RunParam.CivBin='';
149end
150patch_newBin=exist(sparam.RunParam.CivBin,'file');
151set(handles.subdir_civ1,'String',subdir)%default subdir on which uvmat was working
152set(handles.subdir_civ2,'String',subdir)%default subdir on which uvmat was working
153
154%initiate advised operations
155if isequal(ind_opening,[])
156    ind_opening=1; % default
157end
158% set default operation options
159enable_civ1(handles,'off')
160enable_civ2(handles,'off')
161enable_pair1(handles,'on')
162enable_fix1(handles,'off')
163desable_patch1(handles)
164desable_fix2(handles)
165desable_patch2(handles)
166set(handles.CIV1,'Value',0)
167set(handles.FIX1,'Value',0)
168set(handles.PATCH1,'Value',0)
169set(handles.CIV2,'Value',0)
170set(handles.FIX2,'Value',0)
171set(handles.PATCH2,'Value',0)
172set(handles.frame_subdirciv2,'BackgroundColor',[0.831 0.816 0.784])
173if isequal(ind_opening,1)
174    set(handles.CIV1,'Value',1)
175    enable_civ1(handles,'on')
176elseif isequal(ind_opening,2)
177    set(handles.FIX1,'Value',1)
178    enable_fix1(handles,'on')
179elseif isequal(ind_opening,3)
180    set(handles.PATCH1,'Value',1)
181    enable_patch1(handles)
182elseif isequal(ind_opening,4)
183    set(handles.CIV2,'Value',1)
184    enable_civ2(handles,1)
185elseif isequal(ind_opening,5)
186    set(handles.FIX2,'Value',1)
187    enable_fix2(handles)
188    set(handles.frame_subdirciv2,'BackgroundColor',[1 1 0])
189    set(handles.list_pair_civ2,'Enable','On')
190    set(handles.list_pair_civ2,'Enable','On')
191    enable_pair1(handles,'off')
192elseif isequal(ind_opening,6)
193    set(handles.PATCH2,'Value',1)
194    enable_patch2(handles)
195    set(handles.frame_subdirciv2,'BackgroundColor',[1 1 0])
196    set(handles.list_pair_civ2,'Enable','On')
197    enable_pair1(handles,'off')
198end
199
200% set the range of fields (1:1 by default) and selected pair
201if isequal(num_i2,num_i1)
202    num_ref_i=num_i1;
203else
204    num_ref_i=floor((num_i1+num_i2)/2);
205    browse.incr_pair(1)=num_i2-num_i1;
206    browse.incr_pair(2)=0;
207end
208if isequal(num_j1,num_j2)
209    if isnan(num_j1)
210        num_ref_j=1;
211    else
212        num_ref_j=num_j1;
213    end
214else
215    num_ref_j=floor((num_j1+num_j2)/2);
216    browse.incr_pair(2)=num_j2-num_j1;
217end
218set(handles.first_i,'String',num2str(num_ref_i));
219set(handles.last_i,'String',num2str(num_ref_i));
220set(handles.first_j,'String',num2str(num_ref_j));
221set(handles.last_j,'String',num2str(num_ref_j));
222set(handles.ref_i,'String',num2str(num_ref_i));
223set(handles.ref_j,'String',num2str(num_ref_j));
224set(handles.ref_i_civ2,'String',num2str(num_ref_i));
225set(handles.ref_j_civ2,'String',num2str(num_ref_j));
226set(handles.browse_root,'UserData',browse);
227if exist('param','var')%varargin the interface is opened from uvmat
228    RootName_Callback(hObject, eventdata, handles);
229end
230
231% set(handles.waitbar_1,'Position',[0.946 0.877 0.03 0.001])
232% set(handles.waitbar_patch1,'Position',[0.946 0.626 0.03 0.001])
233% set(handles.waitbar_civ2,'Position',[0.946 0.406 0.03 0.001])
234% set(handles.waitbar_patch2,'Position',[0.946 0.187 0.03 0.001])
235
236%------------------------------------------------------------------------
237% --- Outputs from this function are returned to the command line.
238function varargout = civ_OutputFcn(hObject, eventdata, handles)
239%------------------------------------------------------------------------
240% varargout  cell array for returning output args (see VARARGOUT);
241% hObject    handle to figure
242% eventdata  reserved - to be defined in a future version of MATLAB
243% handles    structure with handles and user data (see GUIDATA)
244% Get default command line output from handles structure
245varargout{1} = handles.output;
246
247%------------------------------------------------------------------------
248% --- Executes on button press in browse_root.
249function browse_root_Callback(hObject, eventdata, handles)
250%------------------------------------------------------------------------
251%get the input file properties
252filebase=get(handles.RootName,'String');
253oldfile=''; %default
254if isempty(filebase)|| isequal(filebase,'')%loads the previously stored file name and set it as default in the file_input box
255    dir_perso=prefdir;
256    profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
257    if exist(profil_perso,'file')
258        h=load (profil_perso);
259        if isfield(h,'filebase')&& ischar(h.filebase)
260            oldfile=h.filebase;
261        end
262        if isfield(h,'RootPath') && ischar(h.RootPath)
263            oldfile=h.RootPath;
264        end
265    end
266else
267    oldfile=filebase;
268end
269% testall=get(handles.ImaDoc,'UserData');
270ind_opening=1;%default
271browse.incr_pair=[0 0]; %default
272% if testall
273%     menu={'*.*', 'All Files (*.*)'; '*.xml; *.avi;*.AVI;*.nc','(*.xml,*.avi,*.nc)'; ...
274%         '*.xml', '.xml files';'*.avi;*.AVI', '.avi files';'*.nc','.nc files'};
275% else % menu selecting only .civ or .avi files
276 menu={'*.xml;*.civ;*.png;*.jpg;*.tif;*.avi;*.AVI;*.nc;', ' (*.xml,*.civ,*.png,*.jpg ,.tif, *.avi,*.nc)';
277       '*.xml',  '.xml files '; ...
278        '*.civ',  '.civ files '; ...
279        '*.png','.png image files'; ...
280        '*.jpg',' jpeg image files'; ...
281        '*.tif','.tif image files'; ...
282        '*.avi;*.AVI','.avi movie files'; ...
283        '*.nc','.netcdf files'; ...
284        '*.*',  'All Files (*.*)'};
285   % menu={'*.xml;*.avi;*.AVI;*.nc','(*.xml,*.avi,*.nc)'; ...
286     %   '*.xml', '.xml files';'*.avi;*.AVI', '.avi files';'*.nc', '.nc files';...
287    %    '*.*', 'All Files (*.*)'};
288% end
289[FileName, PathName, filtindex] = uigetfile( menu, 'Pick a file',oldfile);
290fileinput=[PathName FileName];%complete file name
291sizf=size(fileinput);
292if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end %stop if fileinput not a character string
293[path,name,ext]=fileparts(fileinput);
294testeditxml=0;
295if isequal(ext,'.xml')
296    testeditxml=1;
297    t_browse=xmltree(fileinput);
298    head_element=get(t_browse,1);
299    if isfield(head_element,'name')&& isequal(head_element.name,'ImaDoc')
300        testeditxml=0;
301    end
302end
303if testeditxml==1 || isequal(ext,'.xls')
304    heditxml=editxml({fileinput});
305    set(heditxml,'Tag','browser')
306    waitfor(heditxml,'Tag','idle')
307    if ~ishandle(heditxml)
308        return
309    end
310    attr=findobj(get(heditxml,'children'),'Tag','CurrentAttributes');
311    set(handles.browse,'UserData',fileinput)% store for future opening with browser
312    fileinput=get(attr,'UserData');
313    if ~exist(fileinput,'file')
314        return
315    end
316end
317[RootPath,RootFile,str1,str2,str_a,str_b,ext,nom_type,subdir]=name2display(fileinput);
318filebase=fullfile(RootPath,RootFile);
319num_i1=str2double(str1);
320if isnan(num_i1),num_i1=1;end
321num_i2=str2double(str2);
322if isnan(num_i2),num_i2=num_i1;end
323num_j1=stra2num(str_a);
324if isnan(num_j1),num_j1=1;end
325num_j2=stra2num(str_b);
326if isnan(num_j2),num_j2=num_j1;end
327if isequal(get(handles.compare,'Value'),1)
328    browse=[];%initialisation
329else
330    browse=get(handles.browse_root,'UserData');
331end
332browse.num_i1=num_i1;
333browse.num_i2=num_i2;
334browse.num_j1=num_j1;
335browse.num_j2=num_j2;
336if length(ext)>1 && (~isempty(imformats(ext(2:end)))||strcmpi(ext,'.avi'));%if an image file has been opened by uvmat
337%     set(handles.ImaExt,'String',ext)
338    browse.nom_type_ima=nom_type;
339    browse.ext_ima=ext;
340end
341set(handles.ImaDoc,'String',ext);
342
343%%%%% read the state of the selected netcdf file to advise default operation
344if isequal(ext,'.nc')
345    browse.nom_type_nc=nom_type;
346    ind_opening=2;% propose 'fix' as the default option
347    Data=nc2struct(fileinput,[]);
348    if isfield(Data,'absolut_time_T0')%test for civx files
349        if isfield(Data,'fix') && isequal(Data.fix,1)
350            ind_opening=3;
351        end
352        if isfield(Data,'patch') && isequal(Data.patch,1)
353            ind_opening=4;
354        end
355        if isfield(Data,'civ2') && isequal(Data.civ2,1)
356            ind_opening=5;
357        end
358        if isfield(Data,'fix2') && isequal(Data.fix2,1)
359            ind_opening=6;
360        end
361        testciv=1; %TO SUPPRESS WITH NEW VERSION OF CIVX
362    else
363        ind_opening=3; %GUI used only for patch
364        testciv=0;
365    end
366    set(handles.subdir_civ1,'String',subdir);%set the default subdir directories for installing the .nc results
367    set(handles.subdir_civ2,'String',subdir);
368    browse.testciv=testciv;
369    browse.ind_opening=ind_opening;
370end
371set(handles.RootName,'String',filebase);
372set(handles.ImaDoc,'String',ext);
373if ~isempty(num_i1)
374    ref_i=num_i1;
375    if ~isempty(num_i2)
376        ref_i=floor((ref_i+num_i2)/2);% reference image number corresponding to the file
377        browse.incr_pair(1)=num_i2-num_i1;
378        browse.incr_pair(2)=0;
379    end
380    set(handles.first_i,'String',num2str(ref_i));
381    set(handles.last_i,'String',num2str(ref_i));
382    set(handles.ref_i,'String',num2str(ref_i));
383    set(handles.ref_i_civ2,'String',num2str(ref_i))
384end
385if isempty(num_j1)
386    set(handles.ref_j,'String','1');
387    set(handles.ref_j_civ2,'String','1');
388else
389    ref_j=num_j1;
390    if ~isempty(num_j2)
391        ref_j=floor((num_j1+num_j2)/2);
392        browse.incr_pair(2)=num_j2-num_j1;
393    end
394    set(handles.first_j,'String',num2str(ref_j));
395    set(handles.last_j,'String',num2str(ref_j));
396    set(handles.ref_j,'String',num2str(ref_j));
397    set(handles.ref_j_civ2,'String',num2str(ref_j));
398end
399
400% set default operation options
401enable_civ1(handles,'off')
402enable_civ2(handles,'off')
403enable_pair1(handles,'on')
404enable_fix1(handles,'off')
405desable_patch1(handles)
406desable_fix2(handles)
407desable_patch2(handles)
408set(handles.CIV1,'Value',0)
409set(handles.FIX1,'Value',0)
410set(handles.PATCH1,'Value',0)
411set(handles.CIV2,'Value',0)
412set(handles.FIX2,'Value',0)
413set(handles.PATCH2,'Value',0)
414set(handles.frame_subdirciv2,'BackgroundColor',[0.831 0.816 0.784])
415if isequal(ind_opening,1)
416    set(handles.CIV1,'Value',1)
417    enable_civ1(handles,'on')
418elseif isequal(ind_opening,2)
419    set(handles.FIX1,'Value',1)
420    enable_fix1(handles,'on')
421elseif isequal(ind_opening,3)
422    set(handles.PATCH1,'Value',1)
423    enable_patch1(handles)
424elseif isequal(ind_opening,4)
425    set(handles.CIV2,'Value',1)
426    enable_civ2(handles,1)
427elseif isequal(ind_opening,5)
428    enable_pair1(handles,'off')
429    set(handles.FIX2,'Value',1)
430    enable_fix2(handles)
431    set(handles.frame_subdirciv2,'BackgroundColor',[1 1 0])
432    set(handles.list_pair_civ2,'Enable','On')
433    set(handles.list_pair_civ2,'Enable','On')
434elseif isequal(ind_opening,6)
435    enable_pair1(handles,'off')
436    set(handles.PATCH2,'Value',1)
437    enable_patch2(handles)
438    set(handles.frame_subdirciv2,'BackgroundColor',[1 1 0])
439    set(handles.list_pair_civ2,'Enable','On')
440end
441set(handles.browse_root,'UserData',browse);% store information from browser
442% testall=isequal(menu(filtindex,1),{'*.*'});
443% set(handles.ImaDoc,'UserData',testall);
444
445RootName_Callback(hObject, eventdata, handles);
446
447%------------------------------------------------------------------------
448function ImaDoc_Callback(hObject, eventdata, handles)
449%------------------------------------------------------------------------
450RootName_Callback(hObject, eventdata, handles)
451
452%------------------------------------------------------------------------
453% --- function activated when a new filebase (image series) is introduced
454function RootName_Callback(hObject, eventdata, handles)
455%------------------------------------------------------------------------
456set(handles.compare,'Visible','on')
457%ext_ima=get(handles.ImaExt,'String');
458ext_ima='';%default
459nom_type_ima=[];%default
460field_count=1;%default
461nom_type_nc=[];
462time=[];
463TimeUnit='frame'; %default
464CoordUnit='px';%default
465pxcmx_search=[];%default
466pxcmy_search=[];%default
467filebase=get(handles.RootName,'String');
468ext_imadoc=get(handles.ImaDoc,'String');
469browse=get(handles.browse_root,'UserData');%default
470if isfield(browse,'nom_type_ima')
471    nom_type_ima=browse.nom_type_ima;% get an image nomenclature type already determined by an input image name
472end
473if isfield(browse,'ext_ima')
474    ext_ima=browse.ext_ima;
475end
476if isfield(browse,'nom_type_nc')
477    nom_type_nc=browse.nom_type_nc;% get an image nomenclature type already determined by an input image name
478end
479if isfield(browse,'num_i1')
480    field_count=browse.num_i1;% get an image index type already determined by an input file
481end
482
483%default first_i and j and increments
484first_i=str2double(get(handles.first_i,'String'));%value possibly set by uvmat_Opening
485if isnan(first_i)|| first_i < 1
486    first_i=1; %default first_i
487end
488last_i=str2double(get(handles.last_i,'String'));
489if isnan(last_i)|| last_i < first_i
490    last_i=first_i;  %default last_i
491end
492first_j=str2double(get(handles.first_j,'String'));
493if isnan(first_j)|| first_j < 1
494    first_j=1; %default first_j
495end
496last_j=str2double(get(handles.last_j,'String'));
497if isnan(last_j)|| last_j < first_j
498    last_j=first_j; %default last_j
499end
500incr_i=str2double(get(handles.incr_i,'String'));
501if isnan(incr_i) || incr_i < 1;
502    set(handles.incr_i,'String','1') %default incr_i
503end
504incr_j=str2double(get(handles.incr_j,'String'));
505if isnan(incr_j) || incr_j < 1;
506    set(handles.incr_j,'String','1') %default incr_j
507end
508dt=[];%default
509testmode=0;%default
510nbfield=[]; %default
511nburst=[];%default
512pxcmx=1;
513pxcmy=1;
514
515%look for an image documentation file
516if ~strcmp(ext_imadoc,'.xml') && ~strcmp(ext_imadoc,'.civ')&& ~strcmpi(ext_imadoc,'.avi')
517    if exist([filebase '.xml'],'file')
518        ext_imadoc='.xml';
519    elseif exist([filebase '.civxml'],'file')
520        ext_imadoc='.civxml';
521    elseif exist([filebase '.civ'],'file')
522        ext_imadoc='.civ';
523    elseif exist([filebase '.avi'],'file')
524        ext_imadoc='.avi';
525    elseif exist([filebase '.AVI'],'file')
526        ext_imadoc='.AVI';
527    end
528    set(handles.ImaDoc,'String',ext_imadoc)
529end
530
531%%%%%%%%   read image documentation file  %%%%%%%%%%%%%%%%%%%%%%%%%%%
532mode=''; %default
533set(handles.ImaDoc,'BackgroundColor',[1 1 0])
534drawnow
535if isequal(ext_imadoc,'.civxml') || isequal(ext_imadoc,'.xml')|| isequal(ext_imadoc,'.civ')
536    set(handles.ref_i,'Visible','On')%use a reference index
537    set(handles.ref_j,'Visible','On')
538elseif isequal(ext_imadoc,'.avi') || isequal(ext_imadoc,'.AVI')
539    set(handles.ref_j,'Visible','Off')
540else
541    set(handles.ref_i,'Visible','Off')
542    set(handles.ref_j,'Visible','Off')
543end
544testima_xml=0;
545if isequal(ext_imadoc,'.civxml')%TO ABANDON
546    [nbfield,nbfield2,time]=read_civxml([filebase '.civxml']);
547    mode='pair j1-j2';
548    if isempty(nom_type_ima)% dtermine types by default if not already selected by browser or uvmat
549        nom_type_ima='_i_j';
550    end
551elseif isequal(ext_imadoc,'.xml')
552    [XmlData,warntext]=imadoc2struct([filebase '.xml']);
553    ext_ima_read=[];
554    nom_type_read=[];
555    if isfield(XmlData,'Heading')&&isfield(XmlData.Heading','ImageName')&&ischar(XmlData.Heading.ImageName)% get image nom type and extension from the xml file
556        [PP,FF,fc,str2,str_a,str_b,ext_ima_read,nom_type_read]=name2display(XmlData.Heading.ImageName);
557        fullname=fullfile(fileparts(filebase),XmlData.Heading.ImageName); %full name (including path) of the first image defined by the xmle file,
558        if ~exist(fullname,'file')
559            msgbox_uvmat('WARNING',['FirstImage ' fullname ' defined in the xml file does not exist'])
560        end
561    end
562    if isfield(XmlData,'Time')
563        time=XmlData.Time;
564        nbfield=size(time,1);
565        nbfield2=size(time,2);
566        %transform .Time to a column vector if it is a line vector thenomenclature uses a single index: correct possible bug in xml
567        if isequal(nbfield,1) && ~isequal(nbfield2,1)% .Time is a line vector
568            if numel(nom_type_read)>=2 && isempty(regexp(nom_type_read(2:end),'\D'))
569                time=time';
570                nbfield=nbfield2;
571                nbfield2=1;
572            end
573        end
574    end
575    if isfield(XmlData,'TimeUnit')
576        TimeUnit=XmlData.TimeUnit;
577    end
578    if isfield(XmlData,'Npx')
579        npx=XmlData.Npx;
580        npy=XmlData.Npy;
581    end
582    pxcmx_search=1;
583    pxcmy_search=1;
584    if isfield(XmlData,'GeometryCalib')
585        tsai=XmlData.GeometryCalib;
586        if isfield(tsai,'f') && isfield(tsai,'Tz') && isfield(tsai,'dpx') && isfield(tsai,'dpy')&& isfield(tsai,'R')
587            rot2D=tsai.R(1:2,[1,2]);
588            pxcmx_search=tsai.f * sqrt(det(rot2D))/(tsai.Tz*tsai.dpx);
589            pxcmy_search=tsai.f * sqrt(det(rot2D))/(tsai.Tz*tsai.dpy);
590        end
591        if isfield(tsai,'CoordUnit')
592            CoordUnit=tsai.CoordUnit;
593        end
594    end
595%     if ~isempty(ext_ima_read) && ~isempty(nom_type_read)
596% %         if isempty(ext_ima)
597% %             ext_ima=ext_ima_read;% define image extension from the xml file if an image has not been opened previously
598% %         else   %keep the image extension
599% %             if  ~strcmp(ext_ima_read,ext_ima)
600% %                 msgbox_uvmat('WARNING',['FirtsImage extension ' ext_ima_read ' announced in the xml file inconsistent with the selected image'])
601% %             end
602% %         end
603%         nom_type_ima=nom_type_read;
604%     end
605elseif strcmp(ext_imadoc,'.civ')% case of .civ image documentation file
606    [error,time,TimeUnit,mode,npx,npy]=read_imatext([filebase '.civ']);
607    if error==2, msgbox_uvmat('WARNING',['no file ' filebase '.civ']);
608    elseif error==1, msgbox_uvmat('WARNING','inconsistent number of fields in the .civ file');
609    end
610    nom_type_ima='001a';
611elseif strcmpi(ext_imadoc,'.avi')
612    nom_type_ima='*';
613    ext_ima=ext_imadoc;
614    set(handles.mode,'String',{'series(Di)'})
615    dt=0.04;%default
616    if exist([filebase ext_imadoc],'file')==2
617        info=aviinfo([filebase ext_imadoc]);%read infos on the avi movie
618        dt=1/info.FramesPerSecond;%time interval between successive frames
619        nbfield=info.NumFrames;%number of frames
620    end
621    time=(dt*(0:nbfield-1))';%list of image times
622    %set(handles.dt,'String',num2str(dt*1000));%store the time interval between successive images
623end
624if isempty(time)
625    set(handles.ImaDoc,'String',''); %xml file not used for timing
626end
627set(handles.ImaDoc,'BackgroundColor',[1 1 1])
628
629%get the imabe nomenclature type if not defined by the input file nor by the xml file
630dirima=[];%default
631if isempty(nom_type_ima)
632    %look for double image series '_i_j'
633    dirima=dir([filebase '_' num2str(first_i) '_' num2str(first_j) '.*']);
634    if isempty(dirima)
635        % look for images series  with sub marker '_'
636        dirima=dir([filebase '_*' num2str(first_i) '.*']);
637        if isempty(dirima)
638            % look for other images series
639            dirima=dir([filebase '*' num2str(first_i) '.*']);
640            if isempty(dirima)
641                % look for other images series witth letter appendix
642                appendix=char(96+first_j);
643                dirima=dir([filebase '*' num2str(first_i) appendix '.*']);
644            end
645        end
646    end
647end
648for ilist=1:numel(dirima)
649    [pp,ff,fc,str2,str_a,str_b,ext_list,nom_type_list]=name2display(dirima(ilist).name);
650    form=imformats(ext_list(2:end));
651    if ~isempty(form)% if the extension corresponds to an image format recognized by Matlab
652        ext_ima=ext_list;
653        nom_type_ima=nom_type_list;
654            break
655    end
656end
657% no image documentation file found: look for a series of existing files,images by priority or .nc files
658if isempty(nom_type_ima)
659    ext_search=ext_imadoc;
660    nom_type_search=nom_type_nc;
661else
662    ext_search=ext_ima;
663    nom_type_search=nom_type_ima;
664end
665if isempty(time) && ~strcmp(nom_type_search,'none') && ~strcmp(nom_type_search,'') && ~strcmp(nom_type_search,'*')
666    subdir=get(handles.subdir_civ1,'String');
667    incr_pair=[0 0];%default
668    if isfield(browse,'incr_pair')
669        incr_pair=browse.incr_pair;
670    end
671    %     nbdetect=0;%test of detected images
672    field_i=browse.num_i2;
673    imagename=name_generator(filebase,field_i,1,ext_search,nom_type_search);
674    imagename_plus='';
675    idetect=1;
676    while idetect %look for the maximum file number in the series
677        imagename_plus=name_generator(filebase,field_i+1,1,ext_search,nom_type_search);
678        idetect=(exist(imagename_plus,'file')==2)&& ~strcmp(imagename,imagename_plus);
679        if idetect
680            field_i=field_i+1;
681        end
682        %SEE CASE OF NETCDF FILES
683        %             nbdetect=nbdetect+(exist(imagename,'file')==2);
684    end
685    nbfield=field_i;% last detected field number
686    field_i=browse.num_i1;%look for the minimum file number in the series
687    imagename_min='';
688    idetect=1;
689    while idetect==1
690        imagename_min=name_generator(filebase,field_i-1,1,ext_search,nom_type_search);
691        idetect=(exist(imagename_min,'file')==2)&& ~strcmp(imagename,imagename_min);
692        if idetect
693            field_i=field_i-1;
694        end
695    end
696    first_i=max(field_i,1);
697    if numel(regexp(nom_type_search,'\D'))>=1%two indices i and j
698        field_i=browse.num_i1;
699        field_j=browse.num_j2;
700        imagename_plus='';
701        jdetect=1;
702        while jdetect==1 %look for the maximum file number in the series
703            imagename_plus=name_generator(filebase,field_i,field_j+1,ext_search,nom_type_search);
704            jdetect=(exist(imagename_plus,'file')==2)&& ~strcmp(imagename,imagename_plus);
705            if jdetect
706                field_j=field_j+1;
707            end
708            %SEE CASE OF NETCDF FILES
709            %             nbdetect=nbdetect+(exist(imagename,'file')==2);
710        end
711        nbfield2=field_j;% last detected field number
712     end
713 
714    %determine the set of times and possible intervals for CIV
715    %   dt=(1/1000)*str2double(get(handles.dt,'String'));
716    time=(0:nbfield-1)';% time=file index -1  by default
717    if numel(regexp(nom_type_search,'\D'))>=1%two indices i and j
718%     switch nom_type_search 
719%         case {'_i_j','%01dA','%02dA','%03dA','%04dA'}
720        % time=[0:nb_field-1]'*ones(1,nb_field_j);% time=file index -1  by default
721        [x,y]=meshgrid(0:nbfield2-1,0:nbfield-1);
722        time=x+y;
723%         time=[0:nb_field-1]'*[0:nb_field_j-1];% time=file index -1  by default
724    end
725%     set(handles.mode,'String',{'series(Di)'})
726end
727
728if exist('time','var')
729    if size(time,1)+size(time,2)>=3 % if there are at least two time values to define dt
730        nbfield=size(time,1);
731        nbfield2=size(time,2);
732        set(handles.RootName,'UserData',time); %store the set of times
733        set(handles.dt_unit,'String',['dt in m' TimeUnit]);
734        set(handles.dt_unit_civ2,'String',['dt in m' TimeUnit]);
735        set(handles.TimeUnit,'String',TimeUnit);
736        set(handles.nb_field,'String',num2str(nbfield));
737        set(handles.nb_field2,'String',num2str(nbfield2));
738    end
739end
740set(handles.CoordUnit,'String',CoordUnit)
741set(handles.calcul_search,'UserData',[pxcmx_search pxcmy_search]);
742% npxy=[npy npx];
743set(handles.ImaExt,'String',ext_ima)
744set(handles.first_i,'String',num2str(first_i));
745set(handles.last_i,'String',num2str(last_i));%
746set(handles.first_j,'String',num2str(first_j));
747set(handles.last_j,'String',num2str(last_j));%
748browse.nom_type_ima=nom_type_ima;
749set(handles.browse_root,'UserData',browse)% store the nomenclature type
750
751%%%%%%%%%%%  set the menus of image pairs and default selection for civ   %%%%%%%%%%%%%%%%%%%
752test_ima_i=numel(nom_type_ima)>1 && isempty(regexp(nom_type_ima(2:end),'\D'));%images with single indexing
753if test_ima_i || isequal(nom_type_nc,'_i1-i2')||~(exist('nbfield2','var')&&(nbfield2~=1))
754    set(handles.mode,'String',{'series(Di)'})
755    set(handles.mode,'Value',1)
756elseif (nbfield==1)% simple series in j
757    set(handles.mode,'String',{'series(Dj)'})
758    set(handles.mode,'Value',1)
759else
760    set(handles.mode,'String',{'pair j1-j2';'series(Dj)';'series(Di)'})%multiple choice
761    if nbfield2 <= 10
762        set(handles.mode,'Value',1)% advice 'pair j1-j2' for small burst
763    end
764end
765
766%update the subdir
767pathdir=fileparts(filebase);%path to the current xml file
768listot=dir(pathdir);
769idir=0;
770listdir={''};%default
771for ilist=1:length(listot)
772    if listot(ilist).isdir
773        name=listot(ilist).name;
774        if ~isequal(name,'.') && ~isequal(name,'..')
775            idir=idir+1;
776            listdir{idir,1}=listot(ilist).name;
777        end
778    end
779end
780set(handles.list_subdir_civ1,'Value',1)
781set(handles.list_subdir_civ2,'Value',1)
782set(handles.list_subdir_civ1,'String',[{'browse...'};listdir])
783set(handles.list_subdir_civ2,'String',[{'browse...'};listdir])
784%check wether the current subdir exists:
785subdir_civ1=get(handles.subdir_civ1,'String');
786subdir_civ2=get(handles.subdir_civ2,'String');
787
788mode_Callback(hObject, eventdata, handles)
789
790%%%%%% initialize waitbars and RUN button
791% set(handles.waitbar_1,'Position',[0.946 0.876 0.03 0.001])
792% set(handles.waitbar_patch1,'Position',[0.946 0.439 0.03 0.001])
793% set(handles.waitbar_civ2,'Position',[0.946 0.219 0.03 0.001])
794% set(handles.waitbar_patch2,'Position',[0.946 0.0 0.03 0.001])
795set(handles.RUN, 'Enable','On')
796set(handles.RUN,'BackgroundColor',[1 0 0])
797set(handles.BATCH,'Enable','On')
798set(handles.BATCH,'BackgroundColor',[1 0 0])
799
800%%%%% store the root input filename for future opening
801dir_perso=prefdir;
802profil_perso=fullfile(prefdir,'uvmat_perso.mat');
803RootPath=fileparts(filebase);
804if exist(profil_perso,'file')
805    save (profil_perso,'RootPath','-append'); %store the root name for future opening of uvmat
806else
807    txt=ver('MATLAB');
808    Release=txt.Release;
809    relnumb=str2double(Release(3:4));
810    if relnumb >= 14
811        save (profil_perso,'RootPath','-V6'); %store the root name for future opening of uvmat
812    else
813        save (profil_perso,'RootPath'); %store the root name for future opening of uvmat
814    end
815end
816% save(profil_perso, 'filebase'); %store the root name for future opening of uvmat
817set(gcf,'Pointer','arrow')
818
819%------------------------------------------------------------------------
820% --- Executes on button press in mode.
821function mode_Callback(hObject, eventdata, handles)
822%------------------------------------------------------------------------
823browse=get(handles.browse_root,'UserData');
824compare_list=get(handles.compare,'String');
825val=get(handles.compare,'Value');
826compare=compare_list{val};
827if strcmp(compare,'displacement')
828    mode='displacement';
829else
830    mode_list=get(handles.mode,'String');
831    mode_value=get(handles.mode,'Value');
832    mode=mode_list{mode_value};
833end
834displ_num=[];%default
835ref_i=str2double(get(handles.ref_i,'String'));
836% last_i=str2num(get(handles.last_i,'String'));
837time=get(handles.RootName,'UserData'); %get the set of times
838siztime=size(time);
839nbfield=siztime(1);
840nbfield2=siztime(2);
841indchosen=1;  %%first pair selected by default
842if isequal(mode,'pair j1-j2')%| isequal(mode,'st_pair j1-j2')
843    dt=1;
844    displ='';
845    index=0;
846    numlist_a=[];
847    numlist_B=[];
848    %get all the time intervals in bursts
849    displ_dt=1;%default
850    nbfield2=min(nbfield2,10);%limitate the number of pairs to 10x10
851    for numod_a=1:nbfield2-1 %nbfield2 always >=2 for 'pair j1-j2' mode
852        for numod_b=(numod_a+1):nbfield2
853            index=index+1;
854            numlist_a(index)=numod_a;
855            numlist_b(index)=numod_b;
856            if ~isempty(time)
857                dt(numod_a,numod_b)=time(ref_i,numod_b)-time(ref_i,numod_a);%first time interval dt
858                displ_dt(index)=dt(numod_a,numod_b);
859            else
860                displ_dt(index)=1;
861            end
862        end
863    end
864    [dtsort,indsort]=sort(displ_dt);
865    if ~isempty(numlist_a)
866        displ_num(1,:)=numlist_a(indsort);
867        displ_num(2,:)=numlist_b(indsort);
868    end
869    displ_num(3,:)=0;
870    displ_num(4,:)=0;
871    set(handles.jtext,'Visible','Off')
872    set(handles.first_j,'Visible','Off')
873    set(handles.last_j,'Visible','Off')
874    set(handles.incr_j,'Visible','Off')
875    set(handles.nb_field2,'Visible','Off')
876    set(handles.ref_j,'Visible','Off')
877elseif isequal(mode,'series(Dj)') %| isequal(mode,'st_series(Dj)')
878    for index=1:min(nbfield2-1,200)
879        displ_num(1,index)=-floor(index/2);
880        displ_num(2,index)=ceil(index/2);
881        displ_num(3,index)=0;
882        displ_num(4,index)=0;
883    end
884    set(handles.jtext,'Visible','On')
885    set(handles.first_j,'Visible','On')
886    set(handles.last_j,'Visible','On')
887    set(handles.incr_j,'Visible','On')
888    set(handles.nb_field2,'Visible','On')
889    set(handles.ref_j,'Visible','On')
890    if nbfield > 1
891        set(handles.itext,'Visible','On')
892        set(handles.first_i,'Visible','On')
893        set(handles.last_i,'Visible','On')
894        set(handles.incr_i,'Visible','On')
895        set(handles.nb_field,'Visible','On')
896        set(handles.ref_i,'Visible','On')
897    else
898        set(handles.itext,'Visible','Off')
899        set(handles.first_i,'Visible','Off')
900        set(handles.last_i,'Visible','Off')
901        set(handles.incr_i,'Visible','Off')
902        set(handles.nb_field,'Visible','Off')
903        set(handles.ref_i,'Visible','Off')
904    end
905elseif isequal(mode,'series(Di)') %| isequal(mode,'st_series(Di)')
906    for index=1:200%min(nbfield-1,200)
907        displ_num(1,index)=0;
908        displ_num(2,index)=0;
909        displ_num(3,index)=-floor(index/2);
910        displ_num(4,index)=ceil(index/2);
911    end
912    set(handles.itext,'Visible','On')
913    set(handles.first_i,'Visible','On')
914    set(handles.last_i,'Visible','On')
915    set(handles.incr_i,'Visible','On')
916    set(handles.nb_field,'Visible','On')
917    set(handles.ref_i,'Visible','On')
918    if nbfield2 > 1
919        set(handles.jtext,'Visible','On')
920        set(handles.first_j,'Visible','On')
921        set(handles.last_j,'Visible','On')
922        set(handles.incr_j,'Visible','On')
923        set(handles.nb_field2,'Visible','On')
924        set(handles.ref_j,'Visible','On')
925    else
926        set(handles.jtext,'Visible','Off')
927        set(handles.first_j,'Visible','Off')
928        set(handles.last_j,'Visible','Off')
929        set(handles.incr_j,'Visible','Off')
930        set(handles.nb_field2,'Visible','Off')
931        set(handles.ref_j,'Visible','Off')
932    end
933elseif isequal(mode,'displacement')%the pairs have the same indices
934    displ_num(1,1)=0;
935    displ_num(2,1)=0;
936    displ_num(3,1)=0;
937    displ_num(4,1)=0;
938    if nbfield > 1
939        set(handles.itext,'Visible','On')
940        set(handles.first_i,'Visible','On')
941        set(handles.last_i,'Visible','On')
942        set(handles.incr_i,'Visible','On')
943        set(handles.nb_field,'Visible','On')
944        set(handles.ref_i,'Visible','On')
945    else
946        set(handles.itext,'Visible','Off')
947        set(handles.first_i,'Visible','Off')
948        set(handles.last_i,'Visible','Off')
949        set(handles.incr_i,'Visible','Off')
950        set(handles.nb_field,'Visible','Off')
951        set(handles.ref_i,'Visible','Off')
952    end
953    if nbfield2 > 1
954        set(handles.jtext,'Visible','On')
955        set(handles.first_j,'Visible','On')
956        set(handles.last_j,'Visible','On')
957        set(handles.incr_j,'Visible','On')
958        set(handles.nb_field2,'Visible','On')
959        set(handles.ref_j,'Visible','On')
960    else
961        set(handles.jtext,'Visible','Off')
962        set(handles.first_j,'Visible','Off')
963        set(handles.last_j,'Visible','Off')
964        set(handles.incr_j,'Visible','Off')
965        set(handles.nb_field2,'Visible','Off')
966        set(handles.ref_j,'Visible','Off')
967    end
968end
969set(handles.list_pair_civ1,'UserData',displ_num);
970find_netcpair_civ1(hObject, eventdata, handles)
971find_netcpair_civ2(hObject, eventdata, handles)
972
973%------------------------------------------------------------------------
974% determine the menu for civ1 pairs depending on existing netcdf file at the middle of
975% the field series set by first_i, incr, last_i
976function find_netcpair_civ1(hObject, eventdata, handles)
977%------------------------------------------------------------------------
978set(gcf,'Pointer','watch')
979%nomenclature types
980filebase=get(handles.RootName,'String');
981[filepath,Nme,ext_dir]=fileparts(filebase);
982browse=get(handles.browse_root,'UserData');
983compare_list=get(handles.compare,'String');
984val=get(handles.compare,'Value');
985compare=compare_list{val};
986if strcmp(compare,'displacement')
987    mode='displacement';
988else
989    mode_list=get(handles.mode,'String');
990    mode_value=get(handles.mode,'Value');
991    mode=mode_list{mode_value};
992end
993
994% nomenclature type of the .nc files
995nom_type_ima=[];%default
996if isfield(browse,'nom_type_ima')
997    nom_type_ima=browse.nom_type_ima;
998end
999
1000%determine nom_type_nc:
1001nom_type_nc=[];%default
1002if isfield(browse,'nom_type_nc')
1003    nom_type_nc=browse.nom_type_nc;
1004end
1005if isempty(nom_type_nc)
1006    [nom_type_nc]=nomtype2pair(nom_type_ima,isequal(mode,'series(Di)'),isequal(mode,'series(Dj)'));
1007end
1008browse.nom_type_nc=nom_type_nc;
1009set(handles.browse_root,'UserData',browse)
1010
1011%reads .nc subdirectoy and image numbers from the interface
1012subdir_civ1=get(handles.subdir_civ1,'String');%subdirectory subdir_civ1 for the netcdf data
1013% first_i=str2num(get(handles.first_i,'String'));
1014% last_i=str2num(get(handles.last_i,'String'));
1015% incr=str2num(get(handles.incr_i,'String'));
1016% num1=first_i:incr:last_i;
1017% if isempty(num1)
1018%     set(handles.list_pair_civ1,'String',{''});
1019%     return
1020% end
1021ref_i=str2double(get(handles.ref_i,'String'));
1022if isequal(mode,'pair j1-j2')%|isequal(mode,'st_pair j1-j2')
1023    ref_j=0;
1024else
1025    ref_j=str2double(get(handles.ref_j,'String'));
1026end
1027time=get(handles.RootName,'UserData');%get the set of times
1028if isempty(time)
1029    time=[0 1];
1030end
1031%dt_unit=str2double(get(handles.dt,'String'));% used when there is no image documentation file
1032dt_unit=1000;%default
1033displ_num=get(handles.list_pair_civ1,'UserData');
1034
1035%eliminate the first pairs inconsistent with the position
1036if isempty(displ_num)
1037    nbpair=0;
1038else
1039    nbpair=length(displ_num(1,:));%nbre of displayed pairs
1040    if  isequal(mode,'series(Di)')  %| isequal(mode,'st_series(Di)')
1041        nbpair=min(2*ref_i-1,nbpair);%limit the number of pairs with positive first index
1042    elseif  isequal(mode,'series(Dj)')% | isequal(mode,'st_series(Dj)')
1043        nbpair=min(2*ref_j-1,nbpair);%limit the number of pairs with positive first index
1044    end
1045end
1046nbpair=min(200,nbpair);%limit the number of displayed pairs to 200
1047
1048%look for existing processed pairs involving the field at the middle of the series if civ1 will not
1049% be performed, while the result is needed for next steps.
1050displ_pair={''};
1051select=ones(size(1:nbpair));%default =1 for numbers of displayed pairs
1052testpair=0;
1053if get(handles.CIV1,'Value')==0 %
1054    if ~exist(fullfile(filepath,subdir_civ1,ext_dir),'dir')
1055        msgbox_uvmat('ERROR',['no civ1 file available: subdirectory ' subdir_civ1 ' does not exist']);
1056        set(handles.list_pair_civ1,'String',{});
1057        return
1058    end
1059    for ipair=1:nbpair
1060        filename=name_generator(filebase,ref_i+displ_num(3,ipair),ref_j+displ_num(1,ipair),'.nc',nom_type_nc,1,...
1061            ref_i+displ_num(4,ipair),ref_j+displ_num(2,ipair),subdir_civ1);
1062        select(ipair)=exist(filename,'file')==2;
1063    end
1064    if ~exist('select','var') || isequal(select,zeros(size(1:nbpair)))
1065        if isfield(browse,'incr_pair')
1066            num_i1=ref_i-floor(browse.incr_pair(1)/2);
1067            num_i2=ref_i+ceil(browse.incr_pair(1)/2);
1068            num_j1=ref_j-floor(browse.incr_pair(2)/2);
1069            num_j2=ref_j+ceil(browse.incr_pair(2)/2);
1070            filename=name_generator(filebase,num_i1,num_j1,'.nc',nom_type_nc,1,num_i2,num_j2,subdir_civ1);
1071            select(1)=exist(filename,'file')==2;
1072            testpair=1;
1073        else
1074            if  isequal(mode,'series(Dj)')% | isequal(mode,'st_series(Dj)')
1075                msgbox_uvmat('ERROR',['no civ1 file available for the selected reference index j=' num2str(ref_j) ' and subdirectory ' subdir_civ1]);
1076            else
1077                msgbox_uvmat('ERROR',['no civ1 file available for the selected reference index i=' num2str(ref_i) ' and subdirectory ' subdir_civ1]);
1078            end
1079            set(handles.list_pair_civ1,'String',{''});
1080            %COMPLETER CAS STEREO
1081            return
1082        end
1083    end
1084end
1085if isequal(mode,'series(Di)') %| isequal(mode,'st_series(Di)')
1086    if testpair
1087        displ_pair{1}=['Di= ' num2str(-floor(browse.incr_pair(1)/2)) '|' num2str(ceil(browse.incr_pair(1)/2))];
1088        %     elseif ~isequal(get(handles.root_txt,'String'),'dt(ms)=')
1089        %        for ipair=1:nbpair
1090        %           if select(ipair)
1091        %               if size(time,1)>=ref_i+displ_num(4,ipair) && size(time,2)>=ref_j+displ_num(2,ipair)
1092        %               dt=time(ref_i+displ_num(4,ipair),ref_j+displ_num(2,ipair))-time(ref_i+displ_num(3,ipair),ref_j+displ_num(1,ipair));%time interval dt
1093        %               displ_pair{ipair}=['Di= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2)) ' :dt= ' num2str(dt*1000)];
1094        %               end
1095        %           else
1096        %              displ_pair{ipair}='...'; %pair not displayed in the menu
1097        %           end
1098        %        end
1099    else
1100        for ipair=1:nbpair
1101            if select(ipair)
1102                if size(time,1)>=ref_i+displ_num(4,ipair) && size(time,2)>=ref_j+displ_num(2,ipair)
1103                    dt=time(ref_i+displ_num(4,ipair),ref_j+displ_num(2,ipair))-time(ref_i+displ_num(3,ipair),ref_j+displ_num(1,ipair));%time interval dt
1104                    displ_pair{ipair}=['Di= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2)) ' :dt= ' num2str(dt*1000)];
1105                else
1106                    displ_pair{ipair}='...'; %pair not displayed in the menu
1107                end
1108            end
1109        end
1110    end
1111elseif isequal(mode,'series(Dj)')%|isequal(mode,'st_series(Dj)')% series on the j index
1112    if testpair
1113        displ_pair{1}=['Dj= ' num2str(-floor(browse.incr_pair(1)/2)) '|' num2str(ceil(browse.incr_pair(1)/2))];
1114    else
1115        for ipair=1:nbpair
1116            if select(ipair)
1117                if size(time,1)>=ref_i+displ_num(4,ipair) && size(time,2)>=ref_j+displ_num(2,ipair)
1118                    dt=time(ref_i+displ_num(4,ipair),ref_j+displ_num(2,ipair))-time(ref_i+displ_num(3,ipair),ref_j+displ_num(1,ipair));%time interval dt
1119                    displ_pair{ipair}=['Dj= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2)) ' :dt= ' num2str(dt*1000)];
1120                end
1121            elseif testpair
1122                displ_pair{1}=['Dj= ' num2str(-floor(browse.incr_pair(2)/2)) '|' num2str(ceil(browse.incr_pair(2)/2))];
1123            else
1124                displ_pair{ipair}='...'; %pair not displayed in the menu
1125            end
1126        end
1127    end
1128elseif isequal(mode,'pair j1-j2')%|isequal(mode,'st_pair j1-j2')%case of pairs
1129    for ipair=1:nbpair
1130        if select(ipair)
1131            dt=time(ref_i+displ_num(4,ipair),displ_num(2,ipair))-time(ref_i+displ_num(3,ipair),displ_num(1,ipair));%time interval dt
1132            displ_pair{ipair}=['j= ' num2stra(displ_num(1,ipair),nom_type_ima) '-' num2stra(displ_num(2,ipair),nom_type_ima) ...
1133                ' :dt= ' num2str(dt*1000)];
1134        else
1135            displ_pair{ipair}='...'; %pair not displayed in the menu
1136        end
1137    end
1138elseif isequal(mode,'displacement')
1139    displ_pair={'Di=Dj=0'};
1140end
1141set(handles.list_pair_civ1,'String',displ_pair');
1142ichoice=min(find(select));
1143if (isempty(ichoice) || ichoice < 1); ichoice=1; end;
1144initial=get(handles.list_pair_civ1,'Value');%initial choice of pair
1145if initial>nbpair
1146    set(handles.list_pair_civ1,'Value',ichoice);% first valid pair proposed by default in the menu
1147end
1148if numel(select)>=initial && ~isequal(select(initial),1)
1149    set(handles.list_pair_civ1,'Value',ichoice);% first valid pair proposed by default in the menu
1150end
1151
1152%set(handles.list_pair_civ2,'String',displ_pair');
1153initial=get(handles.list_pair_civ2,'Value');
1154if initial>length(displ_pair')%|~isequal(select(initial),1)
1155    if ichoice <= length(displ_pair')
1156        set(handles.list_pair_civ2,'Value',ichoice);% same pair proposed by default for civ2
1157    else
1158        set(handles.list_pair_civ2,'Value',1);% same pair proposed by default for civ2
1159    end
1160end
1161set(handles.list_pair_civ2,'String',displ_pair');
1162set(gcf,'Pointer','arrow')
1163
1164%------------------------------------------------------------------------
1165% determine the menu for civ2 pairs depending on the existing netcdf file at the
1166%middle of the series set by first_i, incr, last_i
1167function find_netcpair_civ2(hObject, eventdata, handles)
1168%------------------------------------------------------------------------
1169set(gcf,'Pointer','watch')
1170%nomenclature types
1171filebase=get(handles.RootName,'String');
1172[filepath,Nme,ext_dir]=fileparts(filebase);
1173browse=get(handles.browse_root,'UserData');
1174compare_list=get(handles.compare,'String');
1175val=get(handles.compare,'Value');
1176compare=compare_list{val};
1177if strcmp(compare,'displacement')
1178    mode='displacement';
1179else
1180    mode_list=get(handles.mode,'String');
1181    mode_value=get(handles.mode,'Value');
1182    mode=mode_list{mode_value};
1183end
1184
1185% nomenclature type of the .nc files
1186nom_type_ima='ima_num';%default
1187if isfield(browse,'nom_type_ima')
1188    nom_type_ima=browse.nom_type_ima;
1189end
1190nom_type_nc='_i1-i2';%default
1191if isfield(browse,'nom_type_nc')
1192    nom_type_nc=browse.nom_type_nc;
1193end
1194if isequal(nom_type_ima,'png_old') || isequal(nom_type_ima,'netc_old')|| isequal(nom_type_ima,'raw_SMD')|| isequal(nom_type_nc,'netc_old')
1195    nom_type_nc='netc_old';%nom_type for the netcdf files
1196elseif isequal(nom_type_ima,'none')||isequal(nom_type_nc,'none')
1197    nom_type_nc='none';
1198elseif isequal(nom_type_ima,'avi')||isequal(nom_type_ima,'_i')||isequal(nom_type_ima,'ima_num')||isequal(nom_type_nc,'_i1-i2')
1199    nom_type_nc='_i1-i2';
1200else
1201    if  isequal(mode,'series(Di)')%|isequal(mode,'st_series(Di)')
1202        nom_type_nc='_i1-i2_j'; % PIV in volume
1203    else
1204        nom_type_nc='_i_j1-j2';
1205    end
1206end
1207browse.nom_type_nc=nom_type_nc;
1208set(handles.browse_root,'UserData',browse)
1209
1210%reads .nc subdirectory and image numbers from the interface
1211subdir_civ1=get(handles.subdir_civ1,'String');%subdirectory subdir_civ1 for the netcdf data
1212subdir_civ2=get(handles.subdir_civ2,'String');%subdirectory subdir_civ2 for the netcdf data
1213% first_i=str2num(get(handles.first_i,'String'));
1214% last_i=str2num(get(handles.last_i,'String'));
1215% incr=str2num(get(handles.incr_i,'String'));
1216% num1=first_i:incr:last_i;
1217% if isempty(num1)
1218%     set(handles.list_pair_civ2,'Value',1);
1219%     set(handles.list_pair_civ2,'String',{''});
1220%     return
1221% end
1222ref_i=str2double(get(handles.ref_i_civ2,'String'));
1223if isequal(mode,'pair j1-j2')%|isequal(mode,'st_pair j1-j2')
1224    ref_j=0;
1225else
1226    ref_j=str2double(get(handles.ref_j_civ2,'String'));
1227end
1228time=get(handles.RootName,'UserData'); %get the set of times
1229if isempty(time)
1230    time=[0 1];%default
1231end
1232%dt_unit=str2num(get(handles.dt,'String'));% used when there is no image documentation file
1233%dt_unit=1000;
1234displ_num=get(handles.list_pair_civ1,'UserData');
1235
1236
1237%eliminate the first pairs inconsistent with the position
1238if isempty(displ_num)
1239    nbpair=0;
1240else
1241    nbpair=length(displ_num(1,:));%nbre of displayed pairs
1242    if  isequal(mode,'series(Di)')% | isequal(mode,'st_series(Di)')
1243        nbpair=min(2*ref_i-1,nbpair);%limit the number of pairs with positive first index
1244    elseif  isequal(mode,'series(Dj)')% | isequal(mode,'st_series(Dj)')
1245        nbpair=min(2*ref_j-1,nbpair);%limit the number of pairs with positive first index
1246    end
1247end
1248nbpair=min(200,nbpair);%limit the number of displayed pairs to 200
1249
1250%look for existing processed pairs involving the field at the middle of the series if civ1 will not
1251% be performed, while the result is needed for next steps.
1252displ_pair={''}; %default
1253select=ones(size(1:nbpair));%default =1 for numbers of displayed pairs
1254if get(handles.CIV2,'Value')==0 & get(handles.CIV1,'Value')==0 & get(handles.FIX1,'Value')==0 & get(handles.PATCH1,'Value')==0%&...
1255    if ~exist(fullfile(filepath,subdir_civ2,ext_dir),'dir')
1256        errordlg(['no civ2 file available: subdirectory ' subdir_civ2 ' does not exist'])
1257        set(handles.list_pair_civ2,'Value',1);
1258        set(handles.list_pair_civ2,'String',{''});
1259        return
1260    end
1261    for ipair=1:nbpair
1262        filename=name_generator(filebase,ref_i+displ_num(3,ipair),ref_j+displ_num(1,ipair),'.nc',nom_type_nc,1,...
1263            ref_i+displ_num(4,ipair),ref_j+displ_num(2,ipair),subdir_civ1);
1264        select(ipair)=exist(filename,'file')==2;
1265    end
1266    if  isequal(select,zeros(size(1:nbpair)))
1267        if isfield(browse,'incr_pair')
1268            num_i1=ref_i-floor(browse.incr_pair(1)/2);
1269            num_i2=ref_i+floor((browse.incr_pair(1)+1)/2);
1270            num_j1=ref_j-floor(browse.incr_pair(2)/2);
1271            num_j2=ref_j+floor((browse.incr_pair(2)+1)/2);
1272            filename=name_generator(filebase,num_i1,num_j1,'.nc',nom_type_nc,1,num_i2,num_j2,subdir_civ2);
1273            select(1)=exist(filename,'file')==2;
1274        else
1275            if  isequal(mode,'series(Dj)')% | isequal(mode,'st_series(Dj)')
1276                errordlg(['no civ2 file available for the selected reference index j=' num2str(ref_j) ' and subdirectory ' subdir_civ2])
1277            else
1278                errordlg(['no civ2 file available for the selected reference index i=' num2str(ref_i) ' and subdirectory ' subdir_civ2])
1279            end
1280            set(handles.list_pair_civ2,'Value',1);
1281            set(handles.list_pair_civ2,'String',{''});
1282            return
1283        end
1284    end
1285end
1286if isequal(mode,'series(Di)') % | isequal(mode,'st_series(Di)')
1287    for ipair=1:nbpair
1288        if select(ipair)
1289            if size(time,1)>=ref_i+displ_num(4,ipair) && size(time,2)>=ref_j+displ_num(2,ipair)
1290                dt=time(ref_i+displ_num(4,ipair),ref_j+displ_num(2,ipair))-time(ref_i+displ_num(3,ipair),ref_j+displ_num(1,ipair));%time interval dt
1291                displ_pair{ipair}=['Di= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2)) ' :dt= ' num2str(dt*1000)];
1292            end
1293        else
1294            displ_pair{ipair}='...'; %pair not displayed in the menu
1295        end
1296    end
1297elseif isequal(mode,'series(Dj)') %| isequal(mode,'st_series(Dj)') % series on the j index
1298    for ipair=1:nbpair
1299        if select(ipair)
1300            if size(time,1)>=ref_i+displ_num(4,ipair) && size(time,2)>=ref_j+displ_num(2,ipair)
1301                dt=time(ref_i+displ_num(4,ipair),ref_j+displ_num(2,ipair))-time(ref_i+displ_num(3,ipair),ref_j+displ_num(1,ipair));%time interval dt
1302                displ_pair{ipair}=['Dj= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2)) ' :dt= ' num2str(dt*1000)];
1303            end
1304        else
1305            displ_pair{ipair}='...'; %pair not displayed in the menu
1306        end
1307    end
1308elseif isequal(mode,'pair j1-j2')% | isequal(mode,'st_pair j1-j2') %case of pairs
1309    for ipair=1:nbpair
1310        if select(ipair)
1311            dt=time(ref_i+displ_num(4,ipair),displ_num(2,ipair))-time(ref_i+displ_num(3,ipair),displ_num(1,ipair));%time interval dt
1312            displ_pair{ipair}=['j= ' num2stra(displ_num(1,ipair),nom_type_ima) '-' num2stra(displ_num(2,ipair),nom_type_ima) ...
1313                ' :dt= ' num2str(dt*1000)];
1314        else
1315            displ_pair{ipair}='...'; %pair not displayed in the menu
1316        end
1317    end
1318elseif isequal(mode,'displacement')
1319    displ_pair={'Di=Dj=0'};
1320end
1321val=get(handles.list_pair_civ2,'Value');
1322ichoice=min(find(select));
1323if (isempty(ichoice) || ichoice < 1); ichoice=1; end;
1324if get(handles.CIV2,'Value')==0 && get(handles.CIV1,'Value')==0 && get(handles.FIX1,'Value')==0 && get(handles.PATCH1,'Value')==0
1325    val=ichoice;% first valid pair proposed by default in the menu
1326end
1327if val>length(displ_pair')
1328    set(handles.list_pair_civ2,'Value',1);% first valid pair proposed by default in the menu
1329else
1330    set(handles.list_pair_civ2,'Value',val);
1331end
1332set(handles.list_pair_civ2,'String',displ_pair');
1333set(gcf,'Pointer','arrow')
1334
1335%------------------------------------------------------------------------
1336%  determine the list of index pairs of processing file
1337function [num1_civ1,num2_civ1,num_a_civ1,num_b_civ1,num1_civ2,num2_civ2,num_a_civ2,num_b_civ2]=...
1338    find_pair_indices(handles,mode)
1339%------------------------------------------------------------------------
1340first_i=str2double(get(handles.first_i,'String'));%first index i
1341last_i=str2double(get(handles.last_i,'String'));%last index i
1342incr=str2double(get(handles.incr_i,'String'));% increment
1343num_i=first_i:incr:last_i;% list of i indices (reference values for each pair)
1344if isequal(get(handles.first_j,'Visible'),'on')
1345    first_j=str2double(get(handles.first_j,'String'));%first index j
1346    last_j=str2double(get(handles.last_j,'String'));%last index j
1347    incr_j=str2double(get(handles.incr_j,'String'));% increment
1348else
1349    first_j=1;
1350    last_j=1;
1351    incr_j=1;
1352end
1353num_j=[first_j:incr_j:last_j];% list of j indices (reference values for each pair)
1354list_civ1=get(handles.list_pair_civ1,'String');
1355index_civ1=get(handles.list_pair_civ1,'Value');
1356str_civ1=list_civ1{index_civ1};%string defining the image pairs for civ1
1357if isempty(str_civ1)||isequal(str_civ1,'')
1358    msgbox_uvmat('ERROR','no image pair selected for civ1')
1359    return
1360end
1361list_civ2=get(handles.list_pair_civ2,'String');
1362index_civ2=get(handles.list_pair_civ2,'Value');
1363if index_civ2>length(list_civ2)
1364    list_civ2=list_civ1;
1365    index_civ2=index_civ1;
1366end
1367str_civ2=list_civ2{index_civ2};%string defining the image pairs for civ2
1368if isempty(first_i)||isempty(first_j), msgbox_uvmat('ERROR','first field number not defined'),...
1369        return,end;
1370if isequal(last_i,[])|| isequal(last_j,[]),msgbox_uvmat('ERROR','last field number not defined'),...
1371        return,end;
1372if isequal(incr,[])|| isequal(incr_j,[]),msgbox_uvmat('ERROR','increment in field number not defined'),...
1373        return,end;
1374if last_i < first_i || last_j < first_j , msgbox_uvmat('ERROR','last field number must be larger than the first one'),...
1375        return,end;
1376if isequal (mode,'series(Di)')
1377    %recognize the pair civ1 from the display
1378    indsel=find((double(str_civ1)<48)|(double(str_civ1)>57));% character indices of non numerical characters
1379    str_raw=str_civ1(indsel);
1380    indsepar=find(str_raw=='|'); %character index of the separator
1381    d1=str2double(str_civ1(indsel(indsepar-1)+1:indsel(indsepar)-1));
1382    if indsepar==length(str_raw)
1383        d2=str2double(str_civ1(indsel(indsepar)+1:end));
1384    else
1385        d2=str2double(str_civ1(indsel(indsepar)+1:indsel(indsepar+1)-1));
1386    end
1387    num1_civ1=num_i-d1;% set of first image numbers
1388    num2_civ1=num_i+d2;
1389    num_a_civ1=num_j;
1390    num_b_civ1=num_j;
1391   
1392    %recognize the pair civ2 from the display
1393    indsel=find((double(str_civ2)<48)|(double(str_civ2)>57));% character indices of non numerical characters
1394    str_raw=str_civ2(indsel);
1395    indsepar=find(str_raw=='|'); %character index of the separator
1396    d1=str2double(str_civ2(indsel(indsepar-1)+1:indsel(indsepar)-1));
1397    if indsepar==length(str_raw)
1398        d2=str2double(str_civ2(indsel(indsepar)+1:end));
1399    else
1400        d2=str2double(str_civ2(indsel(indsepar)+1:indsel(indsepar+1)-1));
1401    end
1402    if isnan(d1)
1403        num1_civ2=num_i;
1404    else
1405        num1_civ2=num_i-d1;% set of first image numbers
1406    end
1407    if isnan(d2)
1408        num2_civ2=num_i;
1409    else
1410        num2_civ2=num_i+d2;
1411    end
1412    num_a_civ2=num_j;
1413    num_b_civ2=num_j;
1414   
1415    % adjust the first and last field number
1416    lastfield=str2double(get(handles.nb_field,'String'));
1417    if isequal(lastfield,[])
1418        indsel=find((num1_civ1 >= 1)&(num1_civ2 >= 1));
1419    else
1420        indsel=find((num2_civ1 <= lastfield)&(num2_civ2 <= lastfield)&(num1_civ1 >= 1)&(num1_civ2 >= 1));
1421    end
1422    if length(indsel)>=1
1423        firstind=indsel(1);
1424        lastind=indsel(end);
1425        set(handles.first_i,'String',num2str(num_i(firstind)))%update the display of first and last fields
1426        set(handles.last_i,'String',num2str(num_i(lastind)))
1427        num_i=num_i(indsel);
1428        num1_civ1=num1_civ1(indsel);
1429        num1_civ2=num1_civ2(indsel);
1430        num2_civ1=num2_civ1(indsel);
1431        num2_civ2=num2_civ2(indsel);
1432    end
1433elseif isequal (mode,'series(Dj)')
1434    lastfield_j=str2double(get(handles.nb_field2,'String'));
1435    num1_civ1=num_i;% set of first image numbers
1436    num2_civ1=num_i;
1437    num_a_civ1=num_j-floor(index_civ1/2)*ones(size(num_j));
1438    num_b_civ1=num_j+ceil(index_civ1/2)*ones(size(num_j));
1439    num1_civ2=num_i;
1440    num2_civ2=num_i;
1441    num_a_civ2=num_j-floor(index_civ2/2)*ones(size(num_j));
1442    num_b_civ2=num_j+ceil(index_civ2/2)*ones(size(num_j));
1443    % adjust the first and last field number
1444    if isnan(lastfield_j)
1445        indsel=find((num_a_civ1 >= 1)&(num_a_civ2 >= 1));
1446    else
1447        indsel=find((num_b_civ1 <= lastfield_j)&(num_b_civ2 <= lastfield_j)&(num_a_civ1 >= 1)&(num_a_civ2 >= 1));
1448    end
1449    if length(indsel)>=1
1450        firstind=indsel(1);
1451        lastind=indsel(end);
1452        set(handles.first_j,'String',num2str(num_j(firstind)))%update the display of first and last fields
1453        set(handles.last_j,'String',num2str(num_j(lastind)))
1454        num_j=num_j(indsel);
1455        num_a_civ1=num_a_civ1(indsel);
1456        num_a_civ2=num_a_civ2(indsel);
1457        num_b_civ1=num_b_civ1(indsel);
1458        num_b_civ2=num_b_civ2(indsel);
1459    end
1460elseif isequal(mode,'pair j1-j2') %case of bursts (png_old or png_2D)
1461    num1_civ1=num_i;
1462    num1_civ2=num_i;
1463    displ_num=get(handles.list_pair_civ1,'UserData');
1464    num2_civ1=num_i;
1465    num_a_civ1=displ_num(1,index_civ1);
1466    num_b_civ1=displ_num(2,index_civ1);
1467    num2_civ2=num_i;
1468    num_a_civ2=displ_num(1,index_civ2);
1469    num_b_civ2=displ_num(2,index_civ2);
1470elseif isequal(mode,'displacement')
1471    num1_civ1=num_i;
1472    num2_civ1=num_i;
1473    num_a_civ1=num_j;
1474    num_b_civ1=num_j;
1475    num1_civ2=num_i;
1476    num2_civ2=num_i;
1477    num_a_civ2=num_j;
1478    num_b_civ2=num_j;
1479end
1480
1481
1482%------------------------------------------------------------------------
1483% --- Executes on selection change in list_pair_civ1.
1484function list_pair_civ1_Callback(hObject, eventdata, handles)
1485%------------------------------------------------------------------------
1486%reproduce by default the chosen pair in the civ2 menu
1487list_pair=get(handles.list_pair_civ1,'String');%get the menu of image pairs
1488index_pair=get(handles.list_pair_civ1,'Value');
1489displ_num=get(handles.list_pair_civ1,'UserData');
1490% num_a=displ_num(1,index_pair);
1491% num_b=displ_num(2,index_pair);
1492list_pair2=get(handles.list_pair_civ2,'String');%get the menu of image pairs
1493if index_pair<=length(list_pair2)
1494    set(handles.list_pair_civ2,'Value',index_pair);
1495end
1496
1497%update first_i and last_i according to the chosen image pairs
1498mode_list=get(handles.mode,'String');
1499mode_value=get(handles.mode,'Value');
1500mode=mode_list{mode_value};
1501if isequal(mode,'series(Di)')
1502    first_i=str2double(get(handles.first_i,'String'));
1503    last_i=str2double(get(handles.last_i,'String'));
1504    incr_i=str2double(get(handles.incr_i,'String'));
1505    num1=first_i:incr_i:last_i;
1506    lastfield=str2double(get(handles.nb_field,'String'));
1507    if ~isnan(lastfield)
1508        ind=find((num1-floor(index_pair/2)*ones(size(num1))>0)& ...
1509            (num1+ceil(index_pair/2)*ones(size(num1))<=lastfield));
1510        num1=num1(ind);
1511    end
1512    set(handles.first_i,'String',num2str(num1(1)));
1513    set(handles.last_i,'String',num2str(num1(end)));
1514elseif isequal(mode,'series(Dj)')
1515    first_j=str2double(get(handles.first_j,'String'));
1516    last_j=str2double(get(handles.last_j,'String'));
1517    incr_j=str2double(get(handles.incr_j,'String'));
1518    num_j=first_j:incr_j:last_j;
1519    lastfield2=str2double(get(handles.nb_field2,'String'));
1520    if ~isnan(lastfield2)
1521        ind=find((num_j-floor(index_pair/2)*ones(size(num_j))>0)& ...
1522            (num_j+ceil(index_pair/2)*ones(size(num_j))<=lastfield2));
1523        num1=num_j(ind);
1524    end
1525    set(handles.first_j,'String',num2str(num1(1)));
1526    set(handles.last_j,'String',num2str(num1(end)));
1527end
1528
1529%------------------------------------------------------------------------
1530% --- Executes on selection change in list_pair_civ2.
1531function list_pair_civ2_Callback(hObject, eventdata, handles)
1532%------------------------------------------------------------------------
1533index_pair=get(handles.list_pair_civ2,'Value');%get the selected position index in the menu
1534
1535%update first_i and last_i according to the chosen image pairs
1536mode_list=get(handles.mode,'String');
1537mode_value=get(handles.mode,'Value');
1538mode=mode_list{mode_value};
1539if isequal(mode,'series(Di)')
1540    first_i=str2double(get(handles.first_i,'String'));
1541    last_i=str2double(get(handles.last_i,'String'));
1542    incr_i=str2double(get(handles.incr_i,'String'));
1543    num1=first_i:incr_i:last_i;
1544    lastfield=str2double(get(handles.nb_field,'String'));
1545    if ~isnan(lastfield)
1546        ind=find((num1-floor(index_pair/2)*ones(size(num1))>0)& ...
1547            (num1+ceil(index_pair/2)*ones(size(num1))<=lastfield));
1548        num1=num1(ind);
1549    end
1550    set(handles.first_i,'String',num2str(num1(1)));
1551    set(handles.last_i,'String',num2str(num1(end)));
1552elseif isequal(mode,'series(Dj)')
1553    first_j=str2double(get(handles.first_j,'String'));
1554    last_j=str2double(get(handles.last_j,'String'));
1555    incr_j=str2double(get(handles.incr_j,'String'));
1556    num_j=first_j:incr_j:last_j;
1557    lastfield2=str2double(get(handles.nb_field2,'String'));
1558    if ~isnan(lastfield2)
1559        ind=find((num_j-floor(index_pair/2)*ones(size(num_j))>0)& ...
1560            (num_j+ceil(index_pair/2)*ones(size(num_j))<=lastfield2));
1561        num1=num_j(ind);
1562    end
1563    set(handles.first_j,'String',num2str(num1(1)));
1564    set(handles.last_j,'String',num2str(num1(end)));
1565end
1566
1567function RUN_Callback(hObject, eventdata, handles)
1568%------------------------------------------------------------------------
1569% global civ1_exe civ2_exe patch_exe patch_new_exe sge
1570set(handles.RUN, 'Enable','Off')
1571set(handles.RUN,'BackgroundColor',[0.831 0.816 0.784])
1572batch=0;
1573launch_jobs(hObject, eventdata, handles,batch);
1574set(handles.RUN, 'Enable','On')
1575set(handles.RUN,'BackgroundColor',[1 0 0])
1576
1577%------------------------------------------------------------------------
1578% --- Executes on button press in BATCH: remote processing
1579function BATCH_Callback(hObject, eventdata, handles)
1580%% -----------------------------------------------------------------------
1581%global civ1_exe civ2_exe patch_exe patch_new_exe fix_exe todo_path sge Civ_exe % probabely to remove
1582set(handles.BATCH, 'Enable','Off')
1583set(handles.BATCH,'BackgroundColor',[0.831 0.816 0.784])
1584batch=1;
1585launch_jobs(hObject, eventdata, handles, batch)
1586set(handles.BATCH, 'Enable','On')
1587set(handles.BATCH,'BackgroundColor',[1 0 0])
1588
1589%------------------------------------------------------------------------
1590% --- Lauch command called by RUN and BATCH: remote processing
1591function launch_jobs(hObject, eventdata, handles, batch)
1592%-----------------------------------------------------------------------
1593%% check the selected list of operations:
1594operations={'CIV1','FIX1','PATCH1','CIV2','FIX2','PATCH2'};
1595box_test(1)=get(handles.CIV1,'Value');
1596box_test(2)=get(handles.FIX1,'Value');
1597box_test(3)=get(handles.PATCH1,'Value');
1598box_test(4)=get(handles.CIV2,'Value');
1599box_test(5)=get(handles.FIX2,'Value');
1600box_test(6)=get(handles.PATCH2,'Value');
1601index=find(box_test==1);
1602if isempty(index)
1603    msgbox_uvmat('ERROR','no selected operation')
1604    return
1605end
1606index_first=min(index);
1607index_last=max(index);
1608box_used=box_test(index_first : index_last);
1609[box_missing,ind_missing]=min(box_used);
1610if isequal(box_missing,0)
1611    msgbox_uvmat('ERROR',['missing' cell2mat(operations(ind_missing))]);
1612    return
1613end
1614
1615%check mask if selecetd
1616if isequal(get(handles.get_mask_civ1,'Value'),1)
1617    maskname=get(handles.mask_civ1,'String');
1618    if ~exist(maskname,'file')
1619        get_mask_civ1_Callback(hObject, eventdata, handles);
1620    end
1621end
1622if isequal(get(handles.get_mask_fix1,'Value'),1)
1623    maskname=get(handles.mask_fix1,'String');
1624    if ~exist(maskname,'file')
1625        get_mask_fix1_Callback(hObject, eventdata, handles);
1626    end
1627end
1628if isequal(get(handles.get_mask_civ2,'Value'),1)
1629    maskname=get(handles.mask_civ2,'String');
1630    if ~exist(maskname,'file')
1631        get_mask_civ2_Callback(hObject, eventdata, handles);
1632    end
1633end
1634if isequal(get(handles.get_mask_fix2,'Value'),1)
1635    maskname=get(handles.mask_fix2,'String');
1636    if ~exist(maskname,'file')
1637        get_mask_fix2_Callback(hObject, eventdata, handles);
1638    end
1639end
1640
1641%% initialize the waitbars: TO suppress, waitbar not used
1642% set(handles.waitbar_1,'Position',[0.946 0.876 0.03 0.001])
1643% set(handles.waitbar_patch1,'Position',[0.946 0.439 0.03 0.001])
1644% set(handles.waitbar_civ2,'Position',[0.946 0.219 0.03 0.001])
1645% set(handles.waitbar_patch2,'Position',[0.946 0.0 0.03 0.001])
1646% drawnow
1647
1648%% set the list of files and check them
1649display('checking the files...')
1650%compare=get(handles.compare,'Value');%test for usual PIV (compare=1) or displacement (=2) or stereo PIV (=3)
1651[filecell,num1_civ1,num2_civ1,num_a_civ1,num_b_civ1,num1_civ2,num2_civ2,num_a_civ2,num_b_civ2,nom_type_nc]=...
1652    set_civ_filenames(handles,box_test);
1653if isempty(filecell)% (error message displayed in fct set_civ_filenames)
1654    return
1655end
1656nbfield=numel(num1_civ1);
1657nbslice=numel(num_a_civ1);
1658
1659%% choice of batch priority
1660ind_answer=2;
1661if batch
1662    [s,w]=unix('qstat -q civ.q|grep job_| wc -l'); %check the waiting list (command unix)
1663    if isequal(s,0)
1664        w(end)=[];
1665        str_displ={[w ' jobs in the waiting list'];'Select a priority:'};
1666        str={'urgent';'normal';'low'};
1667        [ind_answer,v] = listdlg('PromptString',str_displ,...
1668            'SelectionMode','single',...
1669            'ListString',str,'ListSize',[200 200],'Name','job priority','InitialValue',3);
1670        if isequal(v,0) % to handle Cancel button and figure close,
1671            return % a better way should be create
1672        end
1673    else
1674        msgbox_uvmat('ERROR','batch system not available')
1675        return
1676    end
1677else
1678    if isunix
1679        [xx,w]=unix('ps faux |grep civ|wc -l');
1680        w(end)=[];
1681        if str2double(w)+numel(num1_civ1)> 50
1682            msgbox_uvmat('ERROR',{['There are already ' w ' civ processes running locally'];'Use BATCH or submit RUN later'})
1683            return
1684        end
1685    end
1686end
1687
1688
1689%% read names of the .exe files for PIV and patch
1690path_UVMAT=fileparts(which('uvmat')); %path to the source directory of uvmat
1691xmlfile='PARAM.xml';
1692if exist(xmlfile,'file')% search parameter xml file in the whole matlab path
1693    t=xmltree(xmlfile);
1694    s=convert(t);
1695end
1696test_interp=0;
1697if batch
1698    if isfield(s,'BatchParam')
1699        sparam=s.BatchParam;
1700        if ~ismember(sparam.BatchMode,{'sge'})
1701            msgbox_uvmat('ERROR',['batch mode ' sparam.BatchMode ' not supported by UVMAT'])
1702        end
1703    else
1704        msgbox_uvmat('ERROR','no batch mode defined in PARAM.xml')
1705        return
1706    end
1707else
1708    if isfield(s,'RunParam')
1709        sparam=s.RunParam;
1710    else
1711        msgbox_uvmat('ERROR','no civ binaries defined in PARAM.xml')
1712        return
1713    end
1714    if isfield(sparam,'CivBin')
1715        if ~exist(sparam.CivBin,'file')
1716            sparam.CivBin=fullfile(path_UVMAT,sparam.CivBin);
1717        end
1718    end
1719    if isfield(sparam,'Civ1Bin')
1720        if ~exist(sparam.Civ1Bin,'file')
1721            sparam.Civ1Bin=fullfile(path_UVMAT,sparam.Civ1Bin);
1722        end
1723    end
1724    if isfield(sparam,'Civ2Bin')
1725        if ~exist(sparam.Civ2Bin,'file')
1726            sparam.Civ2Bin=fullfile(path_UVMAT,sparam.Civ2Bin);
1727        end
1728    end
1729    %test_interp=get(handles.test_interp,'Value');
1730
1731    if  isfield(sparam,'PatchBin')
1732        if ~exist(sparam.PatchBin,'file')
1733            sparam.PatchBin=fullfile(path_UVMAT,sparam.PatchBin);
1734        end
1735    end
1736    % if test_interp && isfield(sparam,'PatchNewBin')
1737    %     if ~exist(sparam.PatchNewBin,'file')
1738    %          sparam.PatchNewBin=fullfile(path_UVMAT,sparam.PatchNewBin);
1739    %     end
1740    % end
1741    if isfield(sparam,'FixBin')
1742        if ~exist(sparam.FixBin,'file')
1743            sparam.FixBin=fullfile(path_UVMAT,sparam.FixBin);
1744        end
1745    end
1746end
1747if batch
1748    if isfield(sparam,'BatchMode')
1749        batch_mode=sparam.BatchMode;
1750    end
1751else
1752%     MaxCivProcesses=50;
1753%     if isfield(sparam,'MaxCivProcesses')
1754%         MaxCivProcesses=str2double(sparam.MaxCivProcesses);
1755%     end
1756end
1757
1758
1759%% get civ1 parameters:
1760display('files OK, processing...')
1761%get civ parameters
1762if box_test(1)==1
1763    par_civ1=read_param_civ1(handles,filecell.ima1.civ1{1,1});
1764end
1765
1766%% get fix1 parameters
1767if box_test(2)==1
1768    flagindex1(1)=get(handles.vec_Fmin2, 'Value');
1769    flagindex1(2)=get(handles.vec_F3, 'Value');
1770    flagindex1(3)=get(handles.vec_F2, 'Value');
1771    thresh_vecC1=str2double(get(handles.thresh_vecC,'String'));%threshold on image correlation vec_C
1772    thresh_vel1=str2double(get(handles.thresh_vel,'String'));%threshold on velocity modulus
1773    test_mask=get(handles.get_mask_fix1,'Value');
1774    nbslice_mask=get(handles.mask_fix1,'UserData'); % get the number of slices (= number of masks)
1775    %%%%%%%%%%%%%COMPLETER LE PROGRAMME FIX
1776    %     inf_sup=get(handles.inf_sup1,'Value');80
1777    %     fileref=get(handles.ref_fix1,'String');
1778    %     refpath=get(handles.ref_fix1,'UserData');
1779    %     fileref=fullfile(refpath,fileref);
1780    menu=get(handles.field_ref1,'String');
1781    index=get(handles.field_ref1,'Value');
1782    if isempty(menu)
1783        fieldchoice='';
1784    else
1785        fieldchoice=menu{index};
1786        msgbox_uvmat('WARNING','reference field is not used presently with batch, use RUN option')
1787    end
1788end
1789
1790%% get patch1 parameters
1791if box_test(3)==1
1792    rho_patch1=str2double(get(handles.rho_patch1,'String'));
1793    if isnan(rho_patch1)
1794        rho_patch1='1000';
1795        set(handles.rho_patch1,'String','1')
1796    else
1797        rho_patch1=num2str(1000*rho_patch1);
1798    end
1799    nx_patch1=get(handles.nx_patch1,'String');
1800    ny_patch1=get(handles.ny_patch1,'String');
1801    if isnan(str2double(nx_patch1))
1802        nx_patch1='50' ;%default
1803        set(handles.nx_patch1,'String','50');
1804    end
1805    if isnan(str2double(ny_patch1))
1806        ny_patch1='50' ;%default
1807        set(handles.ny_patch1,'String','50');
1808    end
1809    subdomain_patch1=get(handles.subdomain_patch1,'String');
1810    thresh_patch1=get(handles.thresh_patch1,'String');
1811end
1812
1813%% get civ2 parameters:
1814if box_test(4)==1
1815    par_civ2=read_param_civ2(handles,cell2mat(filecell.ima1.civ2(1,1)));
1816end
1817
1818%% get fix2 parameters
1819if box_test(5)==1
1820    flagindex2(1)=get(handles.vec_Fmin2_2, 'Value');
1821    flagindex2(2)=get(handles.vec_F3_2, 'Value');
1822    flagindex2(3)=get(handles.vec_F4, 'Value');
1823    thresh_vec2C=str2double(get(handles.thresh_vec2C,'String'));%threshold on image correlation vec_C
1824    thresh_vel2=str2double(get(handles.thresh_vel2,'String'));%threshold on velocity modulus
1825    test_mask=get(handles.get_mask_fix2,'Value');
1826    nbslice_mask=get(handles.mask_fix2,'UserData'); % get the number of slices (= number of masks)
1827    %%%%%%%%%%%%%COMPLETER LE PROGRAMME FIX AVEC REF FILE ET OPTION inf_sup=2
1828    %     inf_sup=get(handles.inf_sup2,'Value');
1829    %     ref=get(handles.ref_fix2,'UserData');
1830   
1831    %%%%%%%%%%%%%%%%%%%
1832end
1833
1834%% get patch2 parameters
1835if box_test(6)==1
1836    rho_patch2=str2double(get(handles.rho_patch2,'String'));
1837    if isnan(rho_patch2)
1838        rho_patch2='1000';
1839        set(handles.rho_patch2,'String','1')
1840    else
1841        rho_patch2=num2str(1000*rho_patch2);
1842    end
1843    nx_patch2=get(handles.nx_patch2,'String');
1844    ny_patch2=get(handles.ny_patch2,'String');
1845    if isnan(str2double(nx_patch2))
1846        nx_patch2='50' ;%default
1847        set(handles.nx_patch2,'String','50');
1848    end
1849    if isnan(str2double(ny_patch2))
1850        ny_patch2='50' ;%default
1851        set(handles.ny_patch2,'String','50');
1852    end
1853    subdomain_patch2=get(handles.subdomain_patch2,'String');
1854    thresh_patch2=get(handles.thresh_patch2,'String');
1855    %              test_interp=get(handles.test_interp,'Value');
1856end
1857
1858%% MAIN LOOP
1859time=get(handles.RootName,'UserData'); %get the set of times
1860civAll=get(handles.Experimental,'Value'); % Boolean for new civ excution method
1861super_cmd=[];
1862
1863for ifile=1:nbfield
1864    for j=1:nbslice
1865        i_cmd=0;
1866        cmd='';
1867        if isunix % check: necessaire aussi en RUN?
1868            %fid=fopen([filename '.cmx'],'w')
1869            cmd='#!/bin/bash \n';
1870            cmd=[cmd '#$ -cwd \n'];
1871            cmd=[cmd 'hostname && date \n'];
1872            cmd=[cmd 'umask 002 \n'];%allow writting access for user group for created files
1873        end
1874        if civAll
1875            civAllxml=xmltree;% xml contents,  all parameters
1876            civAllCmd='';
1877            civAllxml=set(civAllxml,1,'name','CivDoc');
1878        end
1879        %filename_cur=filecell.nc.civ1{ifile,j};%output netcdf file
1880        [Rootbat,Filebat]=fileparts(filecell.nc.civ1{ifile,j});%output netcdf file (without extention)
1881        %filename_cmx(end-1:end+6)='civ1.cmx';%name of cmx file
1882        if batch
1883%             [Rootbat,Filebat,extbat]=fileparts(filename_cmx);
1884            filename_bat=fullfile(Rootbat,['job_' Filebat]);
1885         else
1886            filename_bat=fullfile(Rootbat,Filebat);
1887        end
1888        filename_bat=[filename_bat '.bat'];
1889       
1890        %CIV1
1891        if box_test(1)==1
1892            par_civ1.filename_ima_a=filecell.ima1.civ1{ifile,j};
1893            par_civ1.filename_ima_b=filecell.ima2.civ1{ifile,j};
1894            namelog=[fullfile(Rootbat,Filebat) '.civ1.log'];
1895            par_civ1.Dt=num2str(time(num2_civ1(ifile),num_b_civ1(j))-time(num1_civ1(ifile),num_a_civ1(j)));
1896            par_civ1.T0=num2str((time(num2_civ1(ifile),num_b_civ1(j))+time(num1_civ1(ifile),num_a_civ1(j)))/2);
1897            par_civ1.term_a=num2stra(num_a_civ1(j),nom_type_nc);%UTILITE?
1898            par_civ1.term_b=num2stra(num_b_civ1(j),nom_type_nc);%
1899            test_mask=get(handles.get_mask_civ1,'Value');
1900            if test_mask==0
1901                par_civ1.maskname='noFile use default';
1902                par_civ1.maskflag='n';
1903            else
1904                maskdispl=get(handles.mask_civ1,'String');
1905                if exist(maskdispl,'file')
1906                    par_civ1.maskname=maskdispl;
1907                    par_civ1.maskflag='y';
1908                else
1909                    maskbase=[filecell.filebase '_' maskdispl]; %
1910                    nbslice_mask=str2double(maskdispl(1:end-4)); %
1911                    num1_mask=mod(num1_civ1(ifile)-1,nbslice_mask)+1;
1912                    par_civ1.maskname=name_generator(maskbase,num1_mask,1,'.png','_i');
1913                    if exist(par_civ1.maskname,'file')
1914                        par_civ1.maskflag='y';
1915                    else
1916                        par_civ1.maskname='noFile use default';
1917                        par_civ1.maskflag='n';
1918                    end
1919                end
1920            end
1921           
1922            test_grid=get(handles.browse_gridciv1,'Value');
1923            if test_grid
1924                par_civ1.gridflag='y';
1925                gridname=get(handles.grid_civ1,'String');
1926                if isequal(gridname(end-3:end),'grid')
1927                    nbslice_grid=str2double(gridname(1:end-4)); %
1928                    if ~isnan(nbslice_grid)
1929                        num1_grid=mod(num1_civ1(ifile)-1,nbslice_grid)+1;
1930                        par_civ1.gridname=[filecell.filebase '_' name_generator(gridname,num1_grid,1,'.grid','_i')];
1931                        if ~exist(par_civ1.gridname,'file')
1932                            msgbox_uvmat('ERROR','grid file absent for civ1')
1933                        end
1934                    elseif exist(gridname,'file')
1935                        par_civ1.gridname=gridname;
1936                    else
1937                        msgbox_uvmat('ERROR','grid file absent for civ1')
1938                    end
1939                end
1940            else
1941                par_civ1.gridname='noFile use default';
1942                par_civ1.gridflag='n';
1943            end
1944            %
1945            i_cmd=i_cmd+1;
1946            if isequal(civAll,0)
1947                cmd=[cmd CIV1_CMD(fullfile(Rootbat,Filebat),'',par_civ1,handles,sparam) '\n'];
1948            else
1949                civAllCmd=[civAllCmd ' civ1 '];
1950                str=CIV1_CMD_Unified(fullfile(Rootbat,Filebat),'',par_civ1);
1951                fieldnames=fields(str);
1952                [civAllxml,uid_civ1]=add(civAllxml,1,'element','civ1');
1953                for ilist=1:length(fieldnames)
1954                    val=eval(['str.' fieldnames{ilist}]);
1955                    if ischar(val)
1956                        [civAllxml,uid_t]=add(civAllxml,uid_civ1,'element',fieldnames{ilist});
1957                        [civAllxml,uid_t2]=add(civAllxml,uid_t,'chardata',val);
1958                    end
1959                end
1960            end
1961        end
1962       
1963        % FIX1
1964        if box_test(2)==1
1965            test_mask=get(handles.get_mask_fix1,'Value');
1966            if test_mask==0
1967                maskname='';
1968            else
1969                maskdispl=get(handles.mask_fix1,'String');
1970                nbslice_mask=str2double(maskdispl(1:end-4)); %
1971                num1_mask=mod(num1_civ1(ifile)-1,nbslice_mask)+1;
1972                maskbase=[filecell.filebase '_' maskdispl];
1973                maskname=name_generator(maskbase,num1_mask,1,'.png','_i');
1974            end
1975            if isequal(civAll,0)
1976                if isunix %unix system
1977                cmd_FIX=[sparam.FixBin ' -f ' filecell.nc.civ1{ifile,j} ' -fi1 ' num2str(flagindex1(1)) ...
1978                    ' -fi2 ' num2str(flagindex1(2)) ' -fi3 ' num2str(flagindex1(3)) ...
1979                    ' -threshC ' num2str(thresh_vecC1) ' -threshV ' num2str(thresh_vel1) ' -maskName ' maskname];
1980                else %windows system
1981                    cmd_FIX=['"' sparam.FixBin '" -f "' filecell.nc.civ1{ifile,j} '" -fi1 ' num2str(flagindex1(1)) ...
1982                    ' -fi2 ' num2str(flagindex1(2)) ' -fi3 ' num2str(flagindex1(3)) ...
1983                    ' -threshC ' num2str(thresh_vecC1) ' -threshV ' num2str(thresh_vel1) ' -maskName "' maskname '"'];
1984                    cmd_FIX=regexprep(cmd_FIX,'\\','\\\\');
1985                end
1986                cmd=[cmd cmd_FIX '\n'];
1987            else
1988                fix1.inputFileName=filecell.nc.civ1{ifile,j} ;
1989                fix1.fi1=num2str(flagindex1(1));
1990                fix1.fi2=num2str(flagindex1(2));
1991                fix1.fi3=num2str(flagindex1(3));
1992                fix1.threshC=num2str(thresh_vecC1);
1993                fix1.threshV=num2str(thresh_vel1);
1994                fieldnames=fields(fix1);
1995                [civAllxml,uid_fix1]=add(civAllxml,1,'element','fix1');
1996                for ilist=1:length(fieldnames)
1997                    val=eval(['fix1.' fieldnames{ilist}]);
1998                    if ischar(val)
1999                        [civAllxml,uid_t]=add(civAllxml,uid_fix1,'element',fieldnames{ilist});
2000                        [civAllxml,uid_t2]=add(civAllxml,uid_t,'chardata',val);
2001                    end
2002                end
2003                civAllCmd=[civAllCmd ' fix1 '];
2004            end
2005        end
2006       
2007        %PATCH1
2008        if box_test(3)==1
2009            if isequal(civAll,0)
2010                cmd_PATCH=PATCH_CMD(filecell.nc.civ1{ifile,j},nx_patch1,ny_patch1,rho_patch1,subdomain_patch1,thresh_patch1,test_interp,sparam.PatchBin);
2011                cmd=[cmd cmd_PATCH '\n'];
2012            else
2013                patch1.inputFileName=filecell.nc.civ1{ifile,j} ;
2014                patch1.nopt=subdomain_patch1;
2015                patch1.maxdiff=thresh_patch1;
2016                patch1.ro=rho_patch1;
2017                test_grid=get(handles.get_gridpatch1,'Value');
2018                if test_grid
2019                    patch1.gridflag='y';
2020                    gridname=get(handles.grid_patch1,'String');
2021                    if isequal(gridname(end-3:end),'grid')
2022                        nbslice_grid=str2double(gridname(1:end-4)); %
2023                        if ~isnan(nbslice_grid)
2024                            num1_grid=mod(num1_civ1(ifile)-1,nbslice_grid)+1;
2025                            patch1.gridPatch=[filecell.filebase '_' name_generator(gridname,num1_grid,1,'.grid','_i')];
2026                            if ~exist(patch1.gridPatch,'file')
2027                                msgbox_uvmat('ERROR','grid file absent for patch1')
2028                            end
2029                        elseif exist(gridname,'file')
2030                            patch1.gridPatch=gridname;
2031                        else
2032                            msgbox_uvmat('ERROR','grid file absent for patch1')
2033                        end
2034                    end
2035                else
2036                    patch1.gridPatch='none';
2037                    patch1.gridflag='n';
2038                    patch1.m=nx_patch1;
2039                    patch1.n=ny_patch1;
2040                end
2041                patch1.convectFlow='n';
2042                fieldnames=fields(patch1);
2043                [civAllxml,uid_patch1]=add(civAllxml,1,'element','patch1');
2044                for ilist=1:length(fieldnames)
2045                    val=eval(['patch1.' fieldnames{ilist}]);
2046                    if ischar(val)
2047                        [civAllxml,uid_t]=add(civAllxml,uid_patch1,'element',fieldnames{ilist});
2048                        [civAllxml,uid_t2]=add(civAllxml,uid_t,'chardata',val);
2049                    end
2050                end
2051                civAllCmd=[civAllCmd ' patch1 '];
2052            end
2053        end
2054       
2055        if box_test(4)==1 || box_test(5)==1 || box_test(6)==1
2056            filename_cmx=filecell.nc.civ2{ifile,j};%output netcdf file
2057            filename_cmx([end-1:end+1])=[ 'cmx'];%name of cmx file
2058%             filename_cmx=[filename_cmx 'x'];
2059        end
2060       
2061        if box_test(4)==1
2062            par_civ2.filename_ima_a=filecell.ima1.civ2{ifile,j};
2063            %par_civ2.filename_ima_a([end-3:end])=[];%remove .png extension
2064            par_civ2.filename_ima_b=filecell.ima2.civ2{ifile,j};
2065            %par_civ2.filename_ima_b([end-3:end])=[];%remove .png extension
2066            [Rootbat,Filebat]=fileparts(filecell.nc.civ2{ifile,j});%output netcdf file (without extention)
2067            namelog=[fullfile(Rootbat,Filebat) '.civ2.log'];
2068            par_civ2.Dt=num2str(time(num2_civ2(ifile),num_b_civ2(j))-time(num1_civ2(ifile),num_a_civ2(j)));
2069            par_civ2.T0=num2str((time(num2_civ1(ifile),num_b_civ2(j))+time(num1_civ2(ifile),num_a_civ2(j)))/2);
2070            par_civ2.term_a=num2stra(num_a_civ2(j),nom_type_nc);
2071            par_civ2.term_b=num2stra(num_b_civ2(j),nom_type_nc);
2072            par_civ2.filename_nc1=filecell.nc.civ1{ifile,j};
2073            par_civ2.filename_nc1([end-2:end])=[]; % remove '.nc'
2074            test_mask=get(handles.get_mask_civ2,'Value');
2075            if test_mask==0
2076                par_civ2.maskname='noFile use default';
2077                par_civ2.maskflag='n';
2078            else
2079                maskdispl=get(handles.mask_civ2,'String');
2080                if exist(maskdispl,'file')
2081                    par_civ2.maskname=maskdispl;
2082                    par_civ2.maskflag='y';
2083                else
2084                    maskbase=[filecell.filebase '_' maskdispl]; %
2085                    nbslice_mask=str2double(maskdispl(1:end-4)); %
2086                    num1_mask=mod(num1_civ2(ifile)-1,nbslice_mask)+1;
2087                    par_civ2.maskname=name_generator(maskbase,num1_mask,1,'.png','_i');
2088                    if exist(par_civ2.maskname,'file')
2089                        par_civ2.maskflag='y';
2090                    else
2091                        par_civ2.maskname='noFile use default';
2092                        par_civ2.maskflag='n';
2093                    end
2094                end
2095            end
2096            %TESTgrid
2097            %test_grid=get(handles.browse_gridciv2,'Value');
2098            gridname=get(handles.grid_civ2,'String');
2099            %gridflag='y';
2100            if numel(gridname)>=4 && isequal(gridname(end-3:end),'grid')
2101                nbslice_grid=str2double(gridname(1:end-4)); %
2102                if ~isnan(nbslice_grid)
2103                    par_civ2.gridflag='y';
2104                    num1_grid=mod(num1_civ2(ifile)-1,nbslice_grid)+1;
2105                    par_civ2.gridname=[filecell.filebase '_' name_generator(gridname,num1_grid,1,'.grid','_i')];
2106                    if exist(par_civ2.gridname,'file')
2107                        par_civ2.gridflag='y';
2108                    else
2109                        par_civ2.gridname='noFile use default';
2110                        par_civ2.gridflag='n';
2111                    end
2112                elseif exist(gridname,'file')
2113                    par_civ2.gridflag='y';
2114                else
2115                    par_civ2.gridname='noFile use default';
2116                    par_civ2.gridflag='n';
2117                end
2118            end
2119            %endTESTgrid
2120            i_cmd=i_cmd+1;
2121            cmd_CIV2=CIV2_CMD(fullfile(Rootbat,Filebat),[],par_civ2,sparam);%creates the cmx file [fullfile(Rootbat,Filebat) '.civ2.cmx]
2122            if isequal(civAll,0)
2123                flname=fullfile(Rootbat,Filebat);
2124                if(isunix)
2125                     cmd=[cmd 'cp -f ' flname '.civ2.cmx ' flname '.cmx\n' cmd_CIV2 '\n'];
2126                else
2127                    flname=regexprep(flname,'\\','\\\\');
2128                    cmd=[cmd 'copy /Y "' flname '.civ2.cmx" "' flname '.cmx"\n' cmd_CIV2 '\n'];
2129                end
2130            else
2131                civAllCmd=[civAllCmd ' civ2 '];
2132                str=CIV2_CMD_Unified(filename_cmx([1:end-4]),namelog,par_civ2);
2133                fieldnames=fields(str);
2134                [civAllxml,uid_civ2]=add(civAllxml,1,'element','civ2');
2135                for ilist=1:length(fieldnames)
2136                    val=eval(['str.' fieldnames{ilist}]);
2137                    if ischar(val)
2138                        [civAllxml,uid_t]=add(civAllxml,uid_civ2,'element',fieldnames{ilist});
2139                        [civAllxml,uid_t2]=add(civAllxml,uid_t,'chardata',val);
2140                    end
2141                end
2142            end
2143        end
2144       
2145        % FIX2
2146        if box_test(5)==1
2147            test_mask=get(handles.get_mask_fix2,'Value');
2148            if test_mask==0
2149                maskname=''; %no mask used
2150            else
2151                maskdispl=get(handles.mask_fix2,'String');
2152                maskbase=[filecell.filebase '_' maskdispl]; %
2153                nbslice_mask=str2double(maskdispl(1:end-4)); %
2154                num1_mask=mod(num1_civ2(ifile)-1,nbslice_mask)+1;
2155                maskname =name_generator(maskbase,num1_mask,1,'.png','_i');
2156            end
2157            if isequal(civAll,0)
2158                if isunix
2159                cmd_FIX=[sparam.FixBin ' -f ' filecell.nc.civ2{ifile,j} ' -fi1 ' num2str(flagindex2(1)) ...
2160                    ' -fi2 ' num2str(flagindex2(2)) ' -fi3 ' num2str(flagindex2(3)) ...
2161                    ' -threshC ' num2str(thresh_vec2C) ' -threshV ' num2str(thresh_vel2) ' -maskName ' maskname];
2162                else
2163                    cmd_FIX=['"' sparam.FixBin '" -f "' filecell.nc.civ2{ifile,j} '" -fi1 ' num2str(flagindex2(1)) ...
2164                    ' -fi2 ' num2str(flagindex2(2)) ' -fi3 ' num2str(flagindex2(3)) ...
2165                    ' -threshC ' num2str(thresh_vec2C) ' -threshV ' num2str(thresh_vel2) ' -maskName "' maskname '"'];
2166                    cmd_FIX=regexprep(cmd_FIX,'\\','\\\\');
2167                end
2168                cmd=[cmd cmd_FIX '\n'];
2169            else
2170                fix2.inputFileName=filecell.nc.civ2{ifile,j} ;
2171                fix2.fi1=num2str(flagindex2(1));
2172                fix2.fi2=num2str(flagindex2(2));
2173                fix2.fi3=num2str(flagindex2(3));
2174                fix2.threshC=num2str(thresh_vec2C);
2175                fix2.threshV=num2str(thresh_vel2);
2176                fieldnames=fields(fix2);
2177                [civAllxml,uid_fix2]=add(civAllxml,1,'element','fix2');
2178                for ilist=1:length(fieldnames)
2179                    val=eval(['fix2.' fieldnames{ilist}]);
2180                    if ischar(val)
2181                        [civAllxml,uid_t]=add(civAllxml,uid_fix2,'element',fieldnames{ilist});
2182                        [civAllxml,uid_t2]=add(civAllxml,uid_t,'chardata',val);
2183                    end
2184                end
2185                civAllCmd=[civAllCmd ' fix2 '];
2186            end
2187        end
2188       
2189        %PATCH2
2190        if box_test(6)==1
2191            if isequal(civAll,0)
2192                cmd_PATCH=PATCH_CMD(filecell.nc.civ2{ifile,j},nx_patch2,ny_patch2,rho_patch2,subdomain_patch2,thresh_patch2,test_interp,sparam.PatchBin);
2193                cmd=[cmd cmd_PATCH '\n'];
2194            else
2195                patch2.inputFileName=filecell.nc.civ1{ifile,j} ;
2196                patch2.nopt=subdomain_patch1;
2197                patch2.maxdiff=thresh_patch1;
2198                patch2.ro=rho_patch1;
2199                test_grid=get(handles.get_gridpatch2,'Value');
2200                if test_grid
2201                    patch2.gridflag='y';
2202                    gridname=get(handles.grid_patch2,'String');
2203                    if isequal(gridname(end-3:end),'grid')
2204                        nbslice_grid=str2double(gridname(1:end-4)); %
2205                        if ~isnan(nbslice_grid)
2206                            num1_grid=mod(num1_civ2(ifile)-1,nbslice_grid)+1;
2207                            patch2.gridPatch=[filecell.filebase '_' name_generator(gridname,num1_grid,1,'.grid','_i')];
2208                            if ~exist(patch2.gridPatch,'file')
2209                                msgbox_uvmat('ERROR','grid file absent for patch2')
2210                            end
2211                        elseif exist(gridname,'file')
2212                            patch2.gridPatch=gridname;
2213                        else
2214                            msgbox_uvmat('ERROR','grid file absent for patch2')
2215                        end
2216                    end
2217                else
2218                    patch2.gridPatch='none';
2219                    patch2.gridflag='n';
2220                    patch2.m=nx_patch2;
2221                    patch2.n=ny_patch2;
2222                end
2223                patch2.convectFlow='n';
2224                fieldnames=fields(patch2);
2225                [civAllxml,uid_patch2]=add(civAllxml,1,'element','patch2');
2226                for ilist=1:length(fieldnames)
2227                    val=eval(['patch2.' fieldnames{ilist}]);
2228                    if ischar(val)
2229                        [civAllxml,uid_t]=add(civAllxml,uid_patch2,'element',fieldnames{ilist});
2230                        [civAllxml,uid_t2]=add(civAllxml,uid_t,'chardata',val);
2231                    end
2232                end
2233                civAllCmd=[civAllCmd ' patch2 '];
2234            end
2235        end
2236        if isequal(civAll,1)
2237            save(civAllxml,[filename_cmx([1:end-4]) '.xml']);
2238            %cmd=char({cmd;[CivBin ' -f ' [filename_cmx([1:end-4]) '.xml'] ' ' civAllCmd]});
2239            cmd=[cmd CivBin ' -f ' filename_cmx(1:end-4) '.xml '  civAllCmd  '\n'];
2240        end
2241        % create the .bat file:
2242        [fid,message]=fopen(filename_bat,'w');
2243        if isequal(fid,-1)
2244            msgbox_uvmat('ERROR', ['creation of .bat file: ' message])
2245            return
2246        end
2247        fprintf(fid,cmd);
2248        fclose(fid);
2249        %dlmwrite(filename_bat,cmd,'');%write commands in filename_bat
2250        if batch
2251            switch batch_mode
2252                case 'sge'
2253                    pvalue=num2str((1-ind_answer)*500);
2254                    %namelog=[filename_bat '.patch.log'];
2255                    display(['!qsub -p ' pvalue ' -q civ.q -e ' filename_cmx(1:end-4) '.errors -o ' filename_cmx(1:end-4) '.log' ' ' filename_bat]);
2256                    eval(  ['!qsub -p ' pvalue ' -q civ.q -e ' filename_cmx(1:end-4) '.errors -o ' filename_cmx(1:end-4) '.log' ' ' filename_bat]);
2257            end
2258        else
2259            %% to lauch the jobs locally :
2260            if(isunix)
2261                cmd_str=['. ' filename_bat];
2262                % cmd_str=['!at -qb now -f ' filename_bat ' &']; %ou at -qb now -f bad idea...
2263            else %case of Windows
2264                cmd_str=['@call "' regexprep(filename_bat,'\\','\\\\') '"'];
2265            end
2266            super_cmd=[super_cmd cmd_str '\n'];         
2267            disp(cmd_str);
2268        end
2269    end
2270end
2271
2272if ~batch
2273    [Rootbat,Filebat,extbat]=fileparts(filename_bat);
2274    filename_superbat=fullfile(Rootbat,['job_list.bat']);
2275    fid=fopen(filename_superbat,'w');
2276    fprintf(fid,super_cmd');
2277    fclose(fid);
2278    if(isunix)
2279        eval(['!. ' filename_superbat ' &']);
2280    else
2281        eval(['!' filename_superbat ' &']);
2282    end
2283end
2284
2285%% save interface state
2286if isfield(filecell,'nc')
2287    if isfield(filecell.nc,'civ2')
2288        fileresu=filecell.nc.civ2{1,1};
2289    else
2290        fileresu=filecell.nc.civ1{1,1};
2291    end
2292end
2293[RootPath,RootFile,field_count,str2,str_a,str_b,ext,nom_type,subdir]=name2display(fileresu);
2294namedoc=fullfile(RootPath,subdir,RootFile);
2295detect=1;
2296while detect==1
2297    namefigfull=[namedoc '.fig'];
2298    hh=dir(namefigfull);
2299    if ~isempty(hh)
2300        detect=1;
2301        namedoc=[namedoc '.0'];
2302    else
2303        detect=0;
2304    end
2305end
2306saveas(gcbf,namefigfull);%save the interface with name namefigfull (A CHANGER EN FICHIER  .xml)
2307
2308
2309
2310function [filecell,num1_civ1,num2_civ1,num_a_civ1,num_b_civ1,num1_civ2,num2_civ2,num_a_civ2,num_b_civ2,nom_type_nc,file_ref_fix1,file_ref_fix2]=...
2311    set_civ_filenames(handles,box_test)
2312%------------------------------------------------------------------------
2313filecell=[];%default
2314
2315%% get the root names nomenclature and numbers
2316filebase=get(handles.RootName,'String');
2317
2318if isempty(filebase)||isequal(filebase,'')
2319    msgbox_uvmat('ERROR','no input files')
2320    return
2321end
2322
2323%filebase=regexprep(filebase,'\.fsnet','fsnet');% temporary fix for cluster Coriolis
2324filecell.filebase=filebase;
2325
2326browse=get(handles.browse_root,'UserData');
2327compare_list=get(handles.compare,'String');
2328val=get(handles.compare,'Value');
2329compare=compare_list{val};
2330if strcmp(compare,'displacement')
2331    mode='displacement';
2332else
2333    mode_list=get(handles.mode,'String');
2334    mode_value=get(handles.mode,'Value');
2335    mode=mode_list{mode_value};
2336end
2337%time=get(handles.RootName,'UserData'); %get the set of times
2338ext_ima=get(handles.ImaExt,'String');
2339nom_type_nc=browse.nom_type_nc;
2340if isfield(browse,'nom_type_ima')
2341    nom_type_ima2=browse.nom_type_ima;
2342end
2343if isempty(nom_type_ima2),nom_type_ima2='1';end; %default
2344if isempty(nom_type_nc),nom_type_nc='_i1-i2';end; %default
2345[num1_civ1,num2_civ1,num_a_civ1,num_b_civ1,num1_civ2,num2_civ2,num_a_civ2,num_b_civ2]=...
2346    find_pair_indices(handles,mode);
2347%determine the new filebase for 'displacement' mode (comparison of two series)
2348filebase_B=filebase;% root name of the second field series for stereo
2349if strcmp(compare,'displacement') || strcmp(compare,'stereo PIV')
2350%     test_disp=1;
2351    nom_type_ima1=browse.nom_type_ima_1; %nomenclature type of the second file series
2352    [Path2,Name2]=fileparts(filebase_B);
2353    Path1=Path2;
2354    Name1=get(handles.RootName_1,'String');% root name of the first field series for stereo
2355    filebase_A=fullfile(Path1,Name1);
2356    if length(Name1)>6
2357        Name1=Name1(end-5:end);
2358    end
2359    if length(Name2)>6
2360        Name2=Name2(end-5:end);
2361    end
2362    filebase_AB=fullfile(Path2,[Name2 '-' Name1]);
2363else
2364%     test_disp=0;
2365    filebase_A=filebase;
2366    nom_type_ima1=nom_type_ima2;
2367    filebase_AB=filebase;
2368end
2369if strcmp(compare,'displacement')
2370    filebase_ima1=filebase_A;
2371    filebase_ima2=filebase_B;
2372    filebase_nc=filebase_AB; %root name for the result of civ2
2373else
2374    filebase_ima1=filebase_B;
2375    filebase_ima2=filebase_B;
2376    filebase_nc=filebase_B;
2377end
2378
2379%determine reference files for fix:
2380file_ref_fix1={};%default
2381file_ref_fix2={};
2382nbfield=length(num1_civ1);
2383nbslice=length(num_a_civ1);
2384if box_test(2)==1% fix1 performed
2385    ref=get(handles.ref_fix1,'UserData');%read data on the ref file stored by get_ref_fix1_Callback
2386    if ~isempty(ref)
2387        first_i=str2double(get(handles.first_i,'String'));
2388        last_i=str2double(get(handles.last_i,'String'));
2389        incr_i=str2double(get(handles.incr_i,'String'));
2390        first_j=str2double(get(handles.first_j,'String'));
2391        last_j=str2double(get(handles.last_j,'String'));
2392        incr_j=str2double(get(handles.incr_j,'String'));
2393        num_i_ref=first_i:incr_i:last_i;
2394        num_j_ref=first_j:incr_j:last_j;
2395        if isequal(mode,'displacement')
2396            num_i1=num_i_ref;
2397            num_i2=num_i_ref;
2398            num_j1=num_j_ref;
2399            num_j2=num_j_ref;
2400        elseif isequal(mode,'pair j1-j2')% isequal(mode,'st_pair j1-j2')
2401            num_i1=num_i_ref;
2402            num_i2=num_i1;
2403            num_j1=ref.num_a*ones(size(num_i_ref));
2404            num_j2=ref.num_b*ones(size(num_i_ref));
2405        elseif isequal(mode,'series(Di)') % isequal(mode,'st_series(Di)')
2406            delta1=floor((ref.num2-ref.num1)/2);
2407            delta2=ceil((ref.num2-ref.num1)/2);
2408            num_i1=num_i_ref-delta1*ones(size(num_i_ref));
2409            num_i2=num_i_ref+delta2*ones(size(num_i_ref));
2410            if isempty(ref.num_a)
2411                ref.num_a=1;
2412            end
2413            num_j1=ref.num_a*ones(size(num_i1));
2414            num_j2=num_j1;
2415        elseif isequal(mode,'series(Dj)')%| isequal(mode,'st_series(Dj)')
2416            delta1=floor((ref.num_b-ref.num_a)/2);
2417            delta2=ceil((ref.num_b-ref.num_a)/2);
2418            num_i1=ref.num1*ones(size(num_i_ref));
2419            num_i2=num_i1;
2420            num_j1=num_j_ref-delta1*ones(size(num_j_ref));
2421            num_j2=num_j_ref+delta2*ones(size(num_j_ref));
2422        end
2423        for ifile=1:nbfield
2424            for j=1:nbslice
2425                file_ref=name_generator(ref.filebase,num_i1(ifile),num_j1(j),'.nc',ref.nom_type,1,num_i2(ifile),num_j2(j),ref.subdir);%
2426                file_ref_fix1(ifile,j)={file_ref};
2427                if ~exist(file_ref,'file')
2428                    msgbox_uvmat('ERROR',['reference file ' file_ref ' not found for fix1'])
2429                    filecell=[];
2430                    return
2431                end
2432            end
2433        end
2434    end
2435end
2436
2437%determine reference files for fix2:
2438if box_test(5)==1% fix2 performed
2439    ref=get(handles.ref_fix2,'UserData');
2440    if ~isempty(ref)
2441        first_i=str2double(get(handles.first_i,'String'));
2442        last_i=str2double(get(handles.last_i,'String'));
2443        incr_i=str2double(get(handles.incr_i,'String'));
2444        first_j=str2double(get(handles.first_j,'String'));
2445        last_j=str2double(get(handles.last_j,'String'));
2446        incr_j=str2double(get(handles.incr_j,'String'));
2447        num_i_ref=[first_i:incr_i:last_i];
2448        num_j_ref=[first_j:incr_j:last_j];
2449        if isequal(mode,'displacement')
2450            num_i1=num_i_ref;
2451            num_i2=num_i_ref;
2452            num_j1=num_j_ref;
2453            num_j2=num_j_ref;
2454        elseif isequal(mode,'pair j1-j2')
2455            num_i1=num_i_ref;
2456            num_i2=num_i1;
2457            num_j1=ref.num_a;
2458            num_j2=ref.num_b;
2459        elseif isequal(mode,'series(Di)')
2460            delta1=floor((ref.num2-ref.num1)/2);
2461            delta2=ceil((ref.num2-ref.num1)/2);
2462            num_i1=num_i_ref-delta1*ones(size(num_i_ref));
2463            num_i2=num_i_ref+delta2*ones(size(num_i_ref));
2464            num_j1=ref.num_a*ones(size(num_i1));
2465            num_j2=num_j1;
2466        elseif isequal(mode,'series(Dj)')
2467            delta1=floor((ref.num_b-ref.num_a)/2);
2468            delta2=ceil((ref.num_b-ref.num_a)/2);
2469            num_i1=ref.num1*ones(size(num_i_ref));
2470            num_i2=num_i1;
2471            num_j1=num_j_ref-delta1*ones(size(num_j_ref));
2472            num_j2=num_j_ref+delta2*ones(size(num_j_ref));
2473        end
2474        for ifile=1:nbfield
2475            for j=1:nbslice
2476                file_ref=name_generator(ref.filebase,num_i1(ifile),num_j1(j),'.nc',ref.nom_type,1,num_i2(ifile),num_j2(j),ref.subdir);%
2477                file_ref_fix2(ifile,j)={file_ref};
2478                if ~exist(file_ref,'file')
2479                    msgbox_uvmat('ERROR',['reference file ' file_ref ' not found for fix2'])
2480                    filecell={};
2481                    return
2482                end
2483            end
2484        end
2485    end
2486end
2487
2488%check dir
2489subdir_civ1=get(handles.subdir_civ1,'String');%subdirectory subdir_civ1 for the netcdf output data
2490subdir_civ2=get(handles.subdir_civ2,'String');
2491if isequal(subdir_civ1,''),subdir_civ1='CIV'; end% put default subdir
2492if isequal(subdir_civ2,''),subdir_civ2=subdir_civ1; end% put default subdir
2493currentdir=pwd;%store the current working directory
2494[Path_ima,Name]=fileparts(filebase);%Path of the image files (.civ)
2495if ~exist(Path_ima,'dir')
2496    msgbox_uvmat('ERROR',['path to images ' Path_ima ' not found'])
2497    filecell={};
2498    return
2499end
2500[xx,message]=fileattrib(Path_ima);
2501if ~isempty(message) && ~isequal(message.UserWrite,1)
2502    msgbox_uvmat('ERROR',['No writting access to ' Path_ima])
2503    filecell={};
2504    cd(currentdir);
2505    return
2506end
2507
2508%check the existence of the netcdf and image files involved
2509% %%%%%%%%%%%%  case CIV1 activated   %%%%%%%%%%%%%
2510if box_test(1)==1;
2511    detect=1;
2512    vers=0;
2513    subdir_civ1_new=subdir_civ1;
2514    while detect==1 %create a new subdir if the netcdf files already exist
2515        for ifile=1:nbfield
2516            for j=1:nbslice
2517                filename=name_generator(filebase_nc,num1_civ1(ifile),num_a_civ1(j),'.nc',nom_type_nc,1,num2_civ1(ifile),num_b_civ1(j),subdir_civ1_new);
2518                detect=exist(filename,'file')==2;
2519                if detect% if a netcdf file already exists
2520                    indstr=regexp(subdir_civ1_new,'\D');
2521                    if indstr(end)<length(subdir_civ1_new) %subdir_civ1 ends by a number
2522                        vers=str2double(subdir_civ1_new(indstr(end)+1:end))+1;
2523                        subdir_civ1_new=[subdir_civ1_new(1:indstr(end)) num2str(vers)];
2524                    else
2525                        vers=vers+1;
2526                        subdir_civ1_new=[subdir_civ1_new(1:indstr(end)) '_' num2str(vers)];       
2527                    end
2528                    subdir_civ2=subdir_civ1_new;
2529                    break
2530                end
2531                filecell.nc.civ1(ifile,j)={filename};
2532            end
2533            if detect% if a netcdf file already exists
2534                break
2535            end
2536        end
2537 
2538        %create the new subdir_civ1
2539        if ~exist(fullfile(Path_ima,subdir_civ1_new),'dir')
2540            cd(Path_ima);         
2541            [xx,msg1]=mkdir(subdir_civ1_new);
2542
2543            if ~strcmp(msg1,'')
2544                msgbox_uvmat('ERROR',['cannot create ' subdir_civ1_new ': ' msg1])%error message for directory creation
2545                filecell={};
2546                return
2547            elseif isunix         
2548                [xx,msg2] = fileattrib(subdir_civ1_new,'+w','g'); %yield writing access (+w) to user group (g)
2549                if ~strcmp(msg2,'')
2550                    msgbox_uvmat('ERROR',['pb of permission for  ' subdir_civ1_new ': ' msg2])%error message for directory creation
2551                    filecell={};
2552                    return
2553                end
2554            end
2555            cd(currentdir);
2556        end
2557        if strcmp(compare,'stereo PIV')&&(strcmp(mode,'pair j1-j2')||strcmp(mode,'series(Dj)')||strcmp(mode,'series(Di)'))%check second nc series
2558            for ifile=1:nbfield
2559                for j=1:nbslice
2560                    filename=name_generator(filebase_A,num1_civ1(ifile),num_a_civ1(j),'.nc',nom_type_nc,1,num2_civ1(ifile),num_b_civ1(j),subdir_civ1_new);%
2561                    detect=exist(filename,'file')==2;
2562                    if detect% if a netcdf file already exists
2563                       indstr=regexp(subdir_civ1_new,'\D');
2564                       if indstr(end)<length(subdir_civ1_new) %subdir_civ1 ends by a number
2565                           vers=str2double(subdir_civ1_new(indstr(end)+1:end))+1;
2566                           subdir_civ1_new=[subdir_civ1_new(1:indstr(end)) num2str(vers)];
2567                       else
2568                           vers=vers+1;
2569                           subdir_civ1_new=[subdir_civ1_new '_' num2str(vers)];
2570                       end
2571                       subdir_civ2=subdir_civ1;
2572                       break
2573                    end
2574                    filecell.ncA.civ1(ifile,j)={filename};
2575                end
2576                if detect% if a netcdf file already exists
2577                    break
2578                end
2579            end
2580            %create the new subdir_civ1
2581            if exist(fullfile(Path_ima,subdir_civ1_new),'dir')
2582                   cd(Path_ima);         
2583                [xx,msg1]=mkdir(subdir_civ1_new);
2584                            cd(currentdir);
2585                if ~strcmpl(msg1,'')
2586                    msgbox_uvmat('ERROR',['cannot create ' subdir_civ1_new ': ' msg1])
2587                    cd(currentdir)
2588                    filecell={};
2589                    return
2590                else
2591                    [xx,msg2] = fileattrib(subdir_civ1_new,'+w','g'); %yield writing access (+w) to user group (g)
2592                    if ~strcmp(msg2,'')
2593                        msgbox_uvmat('ERROR',['pb of permission for ' subdir_civ1_new ': ' msg2])%error message for directory creation
2594                        cd(currentdir)
2595                        filecell={};
2596                        return
2597                    end
2598                end
2599            end
2600        end
2601    end
2602    subdir_civ1=subdir_civ1_new;
2603    % get image names
2604    for ifile=1:nbfield
2605        for j=1:nbslice
2606            filename=name_generator(filebase_ima1, num1_civ1(ifile),num_a_civ1(j),ext_ima,nom_type_ima1);
2607            idetect(j)=exist(filename,'file')==2;
2608            filecell.ima1.civ1(ifile,j)={filename}; %first image
2609            filename=name_generator(filebase_ima2, num2_civ1(ifile),num_b_civ1(j),ext_ima,nom_type_ima2);
2610            idetect_1(j)=exist(filename,'file')==2;
2611            filecell.ima2.civ1(ifile,j)={filename};%second image
2612        end
2613        [idetectmin,indexj]=min(idetect);
2614        if idetectmin==0,
2615            msgbox_uvmat('ERROR',[filecell.ima1.civ1{ifile,indexj} ' not found'])
2616            filecell={};
2617            cd(currentdir)
2618            return
2619        end
2620        [idetectmin,indexj]=min(idetect_1);
2621        if idetectmin==0,
2622            msgbox_uvmat('ERROR',[filecell.ima2.civ1{ifile,indexj} ' not found'])
2623            filecell={};
2624            cd(currentdir)
2625            return
2626        end
2627    end
2628    if strcmp(compare,'stereo PIV') && (strcmp(mode,'pair j1-j2') || strcmp(mode,'series(Dj)') || strcmp(mode,'series(Di)'))
2629        for ifile=1:nbfield
2630            for j=1:nbslice
2631                filename=name_generator(filebase_A, num1_civ1(ifile),num_a_civ1(j),ext_ima,nom_type_ima1);
2632                idetect(j)=exist(filename,'file')==2;
2633                filecell.imaA1.civ1(ifile,j)={filename} ;%first image
2634                filename=name_generator(filebase_A, num2_civ1(ifile),num_b_civ1(j),ext_ima,nom_type_ima2);
2635                idetect_1(j)=exist(filename,'file')==2;
2636                filecell.imaA2.civ1(ifile,j)={filename};%second image
2637            end
2638            [idetectmin,indexj]=min(idetect);
2639            if idetectmin==0,
2640                msgbox_uvmat('ERROR',[filecell.imaA1.civ1{ifile,indexj} ' not found'])
2641                filecell={};
2642                cd(currentdir)
2643                return
2644            end
2645            [idetectmin,indexj]=min(idetect_1);
2646            if idetectmin==0,
2647                msgbox_uvmat('ERROR',[filecell.imaA2.civ1{ifile,indexj} ' not found'])
2648                filecell={};
2649                cd(currentdir)
2650                return
2651            end
2652        end
2653    end
2654   
2655    %%%%%%%%%%%%%  fix1 or patch1 activated but no civ1   %%%%%%%%%%%%%
2656elseif (box_test(2)==1 || box_test(3)==1);
2657    for ifile=1:nbfield
2658        for j=1:nbslice
2659            filename=name_generator(filebase_nc,num1_civ1(ifile),num_a_civ1(j),'.nc',...
2660                nom_type_nc,1,num2_civ1(ifile),num_b_civ1(j),subdir_civ1);%
2661            detect=exist(filename,'file')==2;
2662            if detect==0
2663                msgbox_uvmat('ERROR',[filename ' not found'])
2664                filecell={};
2665                cd(currentdir)
2666                return
2667            end
2668            filecell.nc.civ1(ifile,j)={filename};
2669        end
2670    end
2671    if strcmp(compare,'stereo PIV')
2672        for ifile=1:nbfield
2673            for j=1:nbslice
2674                filename=name_generator(filebase_A,num1_civ1(ifile),num_a_civ1(j),'.nc',nom_type_nc,1,num2_civ1(ifile),num_b_civ1(j),subdir_civ1);%
2675                filecell.ncA.civ1(ifile,j)={filename};
2676                if ~exist(filename,'file')
2677                    msgbox_uvmat('ERROR',['input file ' filename ' not found'])
2678                    set(handles.RUN, 'Enable','On')
2679                    set(handles.RUN,'BackgroundColor',[1 0 0])
2680                    filecell={};
2681                    cd(currentdir)
2682                    return
2683                end
2684            end
2685        end
2686    end
2687end
2688
2689%%%%%%%%%%%%%  if civ2 performed with pairs different than civ1  %%%%%%%%%%%%%
2690testdiff=0;
2691if (box_test(4)==1)&&...
2692        ((get(handles.list_pair_civ1,'Value')~=get(handles.list_pair_civ2,'Value'))||~strcmp(subdir_civ2,subdir_civ1))
2693    testdiff=1;
2694    detect=1;
2695    vers=0;
2696    subdir_civ2_new=subdir_civ2;
2697    while detect==1 %create a new subdir if the netcdf files already exist
2698        for ifile=1:nbfield
2699            for j=1:nbslice
2700                filename=name_generator(filebase_nc,num1_civ2(ifile),num_a_civ2(j),'.nc',nom_type_nc,1,num2_civ2(ifile),num_b_civ2(j),subdir_civ2_new);%
2701                detect=exist(filename,'file')==2;
2702                if detect% if a netcdf file already exists
2703                    indstr=regexp(subdir_civ2,'\D');
2704                    if indstr(end)<length(subdir_civ2) %subdir_civ1 ends by a number
2705                        vers=str2double(subdir_civ2(indstr(end)+1:end))+1;
2706                        subdir_civ2_new=[subdir_civ2(1:indstr(end)) num2str(vers)];
2707                    else
2708                        vers=vers+1;
2709                        subdir_civ2_new=[subdir_civ1 '_' num2str(vers)];
2710                    end
2711                    break
2712                end
2713                filecell.nc.civ2(ifile,j)={filename};
2714            end
2715            if detect% if a netcdf file already exists
2716                break
2717            end
2718        end
2719        %create the new subdir_civ2_new
2720        if ~exist(fullfile(Path_ima,subdir_civ2_new),'dir')
2721            [xx,m2]=mkdir(fullfile(Path_ima,subdir_civ2_new));
2722            [xx,msg2] = fileattrib(subdir_civ2_new,'+w','g'); %yield writing access (+w) to user group (g)
2723            if ~isequal(m2,'')
2724                msgbox_uvmat('ERROR',['cannot create ' subdir_civ2_new ': ' m2])
2725                filecell={};
2726                cd(currentdir)
2727                return
2728            end
2729        end
2730        if strcmp(compare,'stereo PIV')%check second nc series
2731            for ifile=1:nbfield
2732                for j=1:nbslice
2733                    filename=name_generator(filebase_A,num1_civ2(ifile),num_a_civ2(j),'.nc',...
2734                        nom_type_nc,1,num2_civ2(ifile),num_b_civ1(j),subdir_civ2_new);%
2735                    detect=exist(filename,'file')==2;
2736                    if detect% if a netcdf file already exists
2737                        indstr=regexp(subdir_civ2,'\D');
2738                        if indstr(end)<length(subdir_civ2) %subdir_civ1 ends by a number
2739                           vers=str2double(subdir_civ2(indstr(end)+1:end))+1;
2740                           subdir_civ2_new=[subdir_civ2(1:indstr(end)) num2str(vers)];
2741                        else
2742                           vers=vers+1;
2743                           subdir_civ2_new=[subdir_civ1 '_' num2str(vers)];
2744                        end
2745                        break
2746                    end
2747                    filecell.ncA.civ2(ifile,j)={filename};
2748                end
2749                if detect% if a netcdf file already exists
2750                    break
2751                end
2752            end
2753            subdir_civ2=subdir_civ2_new;
2754            %create the new subdir_civ1
2755            if ~exist(fullfile(Path_ima,subdir_civ2_new),'dir')
2756                [xx,m2]=mkdir(subdir_civ2_new);
2757                 [xx,msg2] = fileattrib(subdir_civ2_new,'+w','g'); %yield writing access (+w) to user group (g)
2758                if ~isequal(m2,'')
2759                    msgbox_uvmat('ERROR', ['cannot create ' subdir_civ2_new ': ' m2])%error message for directory creation
2760                    cd(currentdir)
2761                    filecell={};
2762                    return
2763                end
2764            end
2765        end
2766    end
2767    subdir_civ2=subdir_civ2_new;
2768end
2769cd(currentdir);%come back to the current working directory
2770
2771%%%%%%%%%%%%%  if civ2 results are obtained or used  %%%%%%%%%%%%%
2772if box_test(4)==1 || box_test(5)==1 || box_test(6)==1 %civ2
2773    %check source netcdf file of civ1 estimates
2774    if box_test(1)==0; %no civ1 performed
2775        for ifile=1:nbfield
2776            for j=1:nbslice
2777                filename=name_generator(filebase_nc,num1_civ1(ifile),num_a_civ1(j),'.nc',...
2778                    nom_type_nc,1,num2_civ1(ifile),num_b_civ1(j),subdir_civ1);%
2779                filecell.nc.civ1(ifile,j)={filename};% name of the civ1 file
2780                if ~exist(filename,'file')
2781                    msgbox_uvmat('ERROR',['input file ' filename ' not found'])
2782                    filecell={};
2783                    return
2784                end
2785                if ~testdiff % civ2 or patch2 are written in the same file as civ1
2786                    if box_test(4)==0 ; %check the existence of civ2 if it is not calculated
2787                        Data=nc2struct(filename,'ListGlobalAttribute','civ2');
2788                        if isempty(Data.civ2)||isequal(Data.civ2,0)
2789                            msgbox_uvmat('ERROR',['no civ2 data in ' filename])
2790                            filecell=[];
2791                            return
2792                        end
2793                    elseif box_test(3)==0; %check the existence of patch if it is not calculated
2794                        Data=nc2struct(filename,'ListGlobalAttribute','patch');
2795                        if isempty(Data.patch)||isequal(Data.patch,0)
2796                            msgbox_uvmat('ERROR',['no patch data in ' filename])
2797                            filecell=[];
2798                            return
2799                        end
2800                    end
2801                end
2802            end
2803        end
2804        if strcmp(compare,'stereo PIV')
2805            for ifile=1:nbfield
2806                for j=1:nbslice
2807                    filename=name_generator(filebase_A,num1_civ2(ifile),num_a_civ2(j),'.nc',...
2808                        nom_type_nc,1,num2_civ2(ifile),num_b_civ2(j),subdir_civ2);%
2809                    filecell.ncA.civ2(ifile,j)={filename};
2810                    if ~exist(filename,'file')
2811                        msgbox_uvmat('ERROR',['input file ' filename ' not found'])
2812                        set(handles.RUN, 'Enable','On')
2813                        set(handles.RUN,'BackgroundColor',[1 0 0])
2814                        return
2815                    end
2816                end
2817            end
2818        end
2819    end
2820   
2821    detect=1;
2822    %     while detect==1%creates a new subdir if the netcdf files already contain civ2 data
2823    for ifile=1:nbfield
2824        for j=1:nbslice
2825            filename=name_generator(filebase_nc,num1_civ2(ifile),num_a_civ2(j),'.nc',...
2826                nom_type_nc,1,num2_civ2(ifile),num_b_civ2(j),subdir_civ2);
2827            detect=exist(filename,'file')==2;
2828            filecell.nc.civ2(ifile,j)={filename};
2829        end
2830    end
2831    %get first image names for civ2
2832    if box_test(1)==1 & isequal(num1_civ1,num1_civ2) & isequal(num_a_civ1,num_a_civ2)
2833        filecell.ima1.civ2=filecell.ima1.civ1;
2834    elseif box_test(4)==1
2835        for ifile=1:nbfield
2836            for j=1:nbslice
2837                filename=name_generator(filebase_ima1, num1_civ2(ifile),num_a_civ2(j),ext_ima,nom_type_ima1);
2838                idetect_2(j)=exist(filename,'file')==2;
2839                filecell.ima1.civ2(ifile,j)={filename};%first image
2840            end
2841            [idetectmin,indexj]=min(idetect_2);
2842            if idetectmin==0,
2843                msgbox_uvmat('ERROR',['input image ' filecell.ima1.civ2{ifile,indexj} ' not found'])
2844                filecell=[];
2845                return
2846            end
2847        end
2848    end
2849   
2850    %get second image names for civ2
2851    if box_test(1)==1 & isequal(num2_civ1,num2_civ2) & isequal(num_b_civ1,num_b_civ2)
2852        filecell.ima2.civ2=filecell.ima2.civ1;
2853    elseif box_test(4)==1
2854        for ifile=1:nbfield
2855            for j=1:nbslice
2856                filename=name_generator(filebase_ima2, num2_civ2(ifile),num_b_civ2(j),ext_ima,nom_type_ima2);
2857                idetect_3(j)=exist(filename,'file')==2;
2858                filecell.ima2.civ2(ifile,j)={filename};%first image
2859            end
2860            [idetectmin,indexj]=min(idetect_3);
2861            if idetectmin==0,
2862                msgbox_uvmat('ERROR',['input image ' filecell.ima2.civ2{ifile,indexj} ' not found'])
2863                filecell=[];
2864                return
2865            end
2866        end
2867    end
2868end
2869if (box_test(5)==1 || box_test(6)==1 ) && box_test(4)==0  % need to read an existing netcdf civ2 file
2870    if ~testdiff
2871        filecell.nc.civ2=filecell.nc.civ1;% file already checked
2872    else     % check the civ2 files
2873        for ifile=1:nbfield
2874            for j=1:nbslice
2875                filename=name_generator(filebase_nc,num1_civ2(ifile),num_a_civ2(j),'.nc',...
2876                    nom_type_nc,1,num2_civ2(ifile),num_b_civ2(j),subdir_civ2);%
2877                filecell.nc.civ2(ifile,j)={filename};
2878                if ~exist(filename,'file')
2879                    msgbox_uvmat('ERROR',['input file ' filename ' not found'])
2880                    filecell=[];
2881                    return
2882                else
2883                    Data=nc2struct(filename,'ListGlobalAttribute','civ2');
2884                    if isempty(Data.civ2)||isequal(Data.civ2,0)
2885                        msgbox_uvmat('ERROR',['no civ2 data in ' filename])
2886                        filecell=[];
2887                        return
2888                    end
2889                end
2890            end
2891        end
2892    end
2893end
2894
2895%%%%%%%%%%%%%  if stereo fields are calculated by PATCH %%%%%%%%%%%%%
2896if strcmp(compare,'stereo PIV')
2897    if  box_test(3)==1 && isequal(get(handles.test_stereo1,'Value'),1)
2898        for ifile=1:nbfield
2899            for j=1:nbslice
2900                filename=name_generator(filebase_AB,num1_civ1(ifile),num_a_civ1(j),'.nc',...
2901                    nom_type_nc,1,num2_civ1(ifile),num_b_civ1(j),subdir_civ1);%
2902                filecell.st(ifile,j)={filename};
2903            end
2904        end
2905    end
2906    if  box_test(6)==1 && isequal(get(handles.test_stereo2,'Value'),1)
2907        for ifile=1:nbfield
2908            for j=1:nbslice
2909                filename=name_generator(filebase_AB,num1_civ2(ifile),num_a_civ2(j),'.nc',...
2910                    nom_type_nc,1,num2_civ2(ifile),num_b_civ2(j),subdir_civ2);%
2911                filecell.st(ifile,j)={filename};
2912            end
2913        end
2914    end
2915end
2916set(handles.subdir_civ1,'String',subdir_civ1);%update the edit box
2917set(handles.subdir_civ2,'String',subdir_civ2);%update the edit box
2918browse.nom_type_nc=nom_type_nc;
2919set(handles.browse_root,'UserData',browse); %update the nomenclature type for uvmat
2920
2921
2922%COPY IMAGES TO THE FORMAT .png IF NEEDED
2923if isequal(nom_type_ima1,'*')%case of movie files
2924    nom_type_imanew1='_i';
2925else
2926    nom_type_imanew1=nom_type_ima1;
2927end
2928if isequal(nom_type_ima2,'*')%case of movie files
2929    nom_type_imanew2='_i';
2930else
2931    nom_type_imanew2=nom_type_ima2;
2932end
2933if ~isequal(ext_ima,'.png')
2934    %%type of image file
2935    type_ima1='none';%default
2936    movieobject1=[];%default
2937    if strcmpi(ext_ima,'.avi')
2938        hhh=which('mmreader');
2939        if ~isequal(hhh,'')&& mmreader.isPlatformSupported()% if the mmreader function is found (recent version of matlab)
2940            type_ima1='movie';
2941            movieobject1=mmreader([filebase_ima2 ext_ima]);
2942        else
2943            type_ima1='avi';
2944        end
2945    elseif ischar(ext_ima) && ~isempty(ext_ima(2:end))
2946        form=imformats(ext_ima(2:end));
2947        if ~isempty(form)% if the extension corresponds to an image format recognized by Matlab
2948            if isequal(nom_type_ima1,'*');
2949                type_ima1='multimage';%image series in a single image file
2950            else
2951                type_ima1='image';
2952            end
2953        end
2954    end
2955    type_ima2='none';%default
2956    movieobject2=[];
2957    if strcmpi(ext_ima,'.avi')
2958        hhh=which('mmreader');
2959        if ~isequal(hhh,'')&& mmreader.isPlatformSupported()% if the mmreader function is found (recent version of matlab)
2960            type_ima2='movie';
2961            movieobject2=mmreader([filebase_ima2 ext_ima]);
2962        else
2963            type_ima2='avi';
2964        end
2965    elseif ischar(ext_ima) && ~isempty(ext_ima(2:end))
2966        form=imformats(ext_ima(2:end));
2967        if ~isempty(form)% if the extension corresponds to an image format recognized by Matlab
2968            if isequal(nom_type_ima1,'*');
2969                type_ima2='multimage';%image series in a single image file
2970            else
2971                type_ima2='image';
2972            end
2973        end
2974    end
2975    %npxy=get(handles.ImaExt,'UserData');
2976    % %     if numel(npxy)<2
2977    %
2978    %         filename=name_generator(filebase_ima1,num1_civ1(1),num_a_civ1(1),ImaExt,nom_type_ima1);
2979    %         A=imread(filename);
2980    %         npxy=size(A);
2981    % %     end
2982    %     npy=npxy(1);
2983    %     npx=npxy(2);
2984    if box_test(1)==1 %if civ1 is performed
2985        h = waitbar(0,['copy images to the .png format for civ1']);% display a wait bar
2986        for ifile=1:nbfield
2987            waitbar(ifile/nbfield);
2988            for j=1:nbslice
2989                filename=name_generator(filebase_ima1,num1_civ1(ifile),num_a_civ1(j),'.png',nom_type_imanew1);
2990                if ~exist(filename,'file')
2991                    A=read_image(filecell.ima1.civ1{ifile,j},type_ima1,num1_civ1(ifile),movieobject1);
2992                    imwrite(A,filename,'BitDepth',16);
2993                end
2994                filecell.ima1.civ1(ifile,j)={filename};
2995                filename=name_generator(filebase_ima2, num2_civ1(ifile),num_b_civ1(j),'.png',nom_type_imanew2);
2996                if ~exist(filename,'file')
2997                    A=read_image(filecell.ima2.civ1{ifile,j},type_ima2,num2_civ1(ifile),movieobject2);
2998                    imwrite(A,filename,'BitDepth',16);
2999                end
3000                filecell.ima2.civ1(ifile,j)={filename};
3001            end
3002        end
3003        close(h)
3004    end
3005    if box_test(4)==1 %if civ2 is performed
3006        h = waitbar(0,['copy images to the .png format for civ2']);% display a wait bar
3007        for ifile=1:nbfield
3008            waitbar(ifile/nbfield);
3009            for j=1:nbslice
3010                filename=name_generator(filebase_ima1,num1_civ2(ifile),num_a_civ2(j),'.png',nom_type_imanew1);
3011                if ~exist(filename,'file')
3012                    A=read_image(cell2mat(filecell.ima1.civ2(ifile,j)),type_ima2,num1_civ2(ifile));
3013                    imwrite(A,filename,'BitDepth',16);
3014                end
3015                filecell.ima1.civ2(ifile,j)={filename};
3016                filename=name_generator(filebase_ima2, num2_civ2(ifile),num_b_civ2(j),'.png',nom_type_imanew2);
3017                if ~exist(filename,'file')
3018                    A=read_image(cell2mat(filecell.ima2.civ2(ifile,j)),type_ima2,num2_civ2(ifile));
3019                    imwrite(A,filename,'BitDepth',16);
3020                end
3021                filecell.ima2.civ2(ifile,j)={filename};
3022            end
3023        end
3024        close(h);
3025    end
3026end
3027
3028%------------------------------------------------------------------------
3029% --- PATCH
3030function cmd_PATCH=PATCH_CMD(filename_nc,nx_patch,ny_patch,rho_patch,subdomain_patch,thresh_value,test_interp,PatchBin)
3031%------------------------------------------------------------------------
3032namelog=[filename_nc([1:end-3]) '_patch.log'];
3033if test_interp==0
3034    if isunix
3035    cmd_PATCH=[PatchBin ' -f ' filename_nc ' -m ' nx_patch  ' -n ' ny_patch ' -ro ' rho_patch ' -nopt ' subdomain_patch ...
3036        '  > ' namelog ' 2>&1']; % redirect standard output to the log file
3037    else
3038      cmd_PATCH=['"' PatchBin '" -f "' filename_nc '" -m ' nx_patch  ' -n ' ny_patch ' -ro ' rho_patch ' -nopt ' subdomain_patch ...
3039        '  > "' namelog '" 2>&1']; % redirect standard output to the log file
3040    end
3041else %nouveau programme patch
3042    cmd_PATCH=[PatchBin ' -f ' filename_nc ' -m ' nx_patch  ' -n ' ny_patch ' -ro ' rho_patch ...
3043        ' -max ' thresh_value ' -nopt ' subdomain_patch  '  > ' namelog ' 2>&1']; % redirect standard output to the log file
3044end
3045cmd_PATCH=regexprep(cmd_PATCH,'\\','\\\\');
3046%------------------------------------------------------------------------
3047% --- STEREO Interp
3048function cmd=RUN_STINTERP(stinterpBin,filename_A_nc,filename_B_nc,filename_nc,nx_patch,ny_patch,rho_patch,subdomain_patch,thresh_value,xmlA,xmlB)
3049%------------------------------------------------------------------------
3050namelog=[filename_nc([1:end-3]) '_stinterp.log'];
3051cmd=[stinterpBin ' -f1 ' filename_A_nc  ' -f2 ' filename_B_nc ' -f  ' filename_nc ...
3052    ' -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
3053
3054%------------------------------------------------------------------------
3055% --- Executes on button press in CIV1.
3056function CIV1_Callback(hObject, eventdata, handles)
3057%------------------------------------------------------------------------
3058val=get(handles.CIV1,'Value');
3059if isequal(val,1)
3060    enable_civ1(handles,'on')
3061    enable_pair1(handles,'on')
3062else
3063    enable_civ1(handles,'off')
3064end
3065find_netcpair_civ1(hObject, eventdata, handles);
3066
3067%------------------------------------------------------------------------
3068% --- Executes on button press in FIX1.
3069function FIX1_Callback(hObject, eventdata, handles)
3070%------------------------------------------------------------------------
3071enable_fix1(handles,get(handles.FIX1,'Value'))
3072
3073%------------------------------------------------------------------------
3074% --- Executes on button press in PATCH1.
3075function PATCH1_Callback(hObject, eventdata, handles)
3076%------------------------------------------------------------------------
3077if get(handles.PATCH1,'Value')==1
3078    enable_patch1(handles)
3079else
3080    desable_patch1(handles)
3081end
3082
3083%------------------------------------------------------------------------
3084% --- Executes on button press in CIV2.
3085function CIV2_Callback(hObject, eventdata, handles)
3086%------------------------------------------------------------------------
3087state=get(handles.CIV2,'Value');
3088enable_civ2(handles,state)
3089if state
3090    find_netcpair_civ2(hObject, eventdata, handles)
3091    enable_pair1(handles,'on')
3092end
3093
3094%------------------------------------------------------------------------
3095% --- Executes on button press in FIX2.
3096function FIX2_Callback(hObject, eventdata, handles)
3097%------------------------------------------------------------------------
3098if get(handles.FIX2,'Value')==1
3099    enable_fix2(handles)
3100    if get(handles.CIV2,'Value')==0
3101        find_netcpair_civ2(hObject, eventdata, handles) % select the available netcdf files
3102    end
3103else
3104    desable_fix2(handles)
3105end
3106
3107%------------------------------------------------------------------------
3108% --- Executes on button press in PATCH2.
3109function PATCH2_Callback(hObject, eventdata, handles)
3110%------------------------------------------------------------------------
3111if get(handles.PATCH2,'Value')==1
3112    enable_patch2(handles)
3113    if get(handles.CIV2,'Value')==0
3114        find_netcpair_civ2(hObject, eventdata, handles) % select the available netcdf files
3115    end
3116else
3117    desable_patch2(handles)
3118end
3119
3120%------------------------------------------------------------------------
3121function first_i_Callback(hObject, eventdata, handles)
3122%------------------------------------------------------------------------
3123% last_i_Callback(hObject, eventdata, handles)
3124first_i=str2double(get(handles.first_i,'String'));
3125% last_i=str2num(get(handles.last_i,'String'));
3126% ref_i=ceil((first_i+last_i)/2);
3127set(handles.ref_i,'String', num2str(first_i))% reference index for pair dt = first index
3128set(handles.ref_i_civ2,'String', num2str(first_i))% reference index for pair dt = first index
3129ref_i_Callback(hObject, eventdata, handles)%refresh dispaly of dt for pairs (in case of non constant dt)
3130
3131%------------------------------------------------------------------------
3132function first_j_Callback(hObject, eventdata, handles)
3133%------------------------------------------------------------------------
3134first_j=str2num(get(handles.first_j,'String'));
3135set(handles.ref_j,'String', num2str(first_j))% reference index for pair dt = first index
3136ref_j_Callback(hObject, eventdata, handles)%refresh dispaly of dt for pairs (in case of non constant dt)
3137
3138%------------------------------------------------------------------------
3139% --- Executes on button press in calcul_search: determine the search range isx,isy
3140function calcul_search_Callback(hObject, eventdata, handles)
3141%------------------------------------------------------------------------
3142%determine pair numbers
3143list_pair=get(handles.list_pair_civ1,'String');%get the menu of image pairs
3144index=get(handles.list_pair_civ1,'Value');
3145displ_num=get(handles.list_pair_civ1,'UserData');
3146time=get(handles.RootName,'UserData'); %get the set of times
3147pxcm_xy=get(handles.calcul_search,'UserData');
3148pxcmx=pxcm_xy(1);
3149pxcmy=pxcm_xy(2);
3150mode_list=get(handles.mode,'String');
3151mode_value=get(handles.mode,'Value');
3152mode=mode_list{mode_value};
3153if isequal (mode, 'series(Di)' )
3154    ref_i=str2double(get(handles.ref_i,'String'));
3155    num1=ref_i-floor(index/2);%  first image numbers
3156    num2=ref_i+ceil(index/2);
3157    num_a=1;
3158    num_b=1;
3159elseif isequal (mode, 'series(Dj)')
3160    num1=1;
3161    num2=1;
3162    ref_j=str2double(get(handles.ref_j,'String'));
3163    num_a=ref_j-floor(index/2);%  first image numbers
3164    num_b=ref_j+ceil(index/2);
3165elseif isequal(mode,'pair j1-j2') %case of bursts (png_old or png_2D)
3166    ref_i=str2double(get(handles.ref_i,'String'));
3167    num1=ref_i;
3168    num2=ref_i;
3169    num_a=displ_num(1,index);
3170    num_b=displ_num(2,index);
3171end
3172dt=time(num2,num_b)-time(num1,num_a);
3173ibx=str2double(get(handles.ibx,'String'));
3174iby=str2double(get(handles.iby,'String'));
3175umin=dt*pxcmx*str2double(get(handles.umin,'String'));
3176umax=dt*pxcmx*str2double(get(handles.umax,'String'));
3177vmin=dt*pxcmy*str2double(get(handles.vmin,'String'));
3178vmax=dt*pxcmy*str2double(get(handles.vmax,'String'));
3179shiftx=round((umin+umax)/2);
3180shifty=round((vmin+vmax)/2);
3181isx=(umax+2-shiftx)*2+ibx;
3182isx=2*ceil(isx/2)+1;
3183isy=(vmax+2-shifty)*2+iby;
3184isy=2*ceil(isy/2)+1;
3185set(handles.shiftx,'String',num2str(shiftx));
3186set(handles.shifty,'String',num2str(shifty));
3187set(handles.isx,'String',num2str(isx));
3188set(handles.isy,'String',num2str(isy));
3189
3190%------------------------------------------------------------------------
3191% --- Executes on carriage return on the subdir civ1 edit window
3192function subdir_civ1_Callback(hObject, eventdata, handles)
3193%------------------------------------------------------------------------
3194subdir=get(handles.subdir_civ1,'String');
3195set(handles.subdir_civ2,'String',subdir);
3196if get(handles.CIV1,'Value')==0
3197    find_netcpair_civ1(hObject, eventdata, handles); %update the list of available pairs from netcdf files in the new directory
3198end
3199
3200%------------------------------------------------------------------------
3201% --- Executes on carriage return on the subdir civ1 edit window
3202function subdir_civ2_Callback(hObject, eventdata, handles)
3203%------------------------------------------------------------------------
3204%update the list of available pairs from netcdf files in the new directory
3205if get(handles.CIV2,'Value')==0 & get(handles.CIV1,'Value')==0 & get(handles.FIX1,'Value')==0 & get(handles.PATCH1,'Value')==0
3206    find_netcpair_civ2(hObject, eventdata, handles);
3207end
3208
3209%------------------------------------------------------------------------
3210% --- Executes on button press in get_mask_civ1: select box for mask option
3211function get_mask_civ1_Callback(hObject, eventdata, handles)
3212%------------------------------------------------------------------------
3213maskval=get(handles.get_mask_civ1,'Value');
3214if isequal(maskval,0)
3215    set(handles.mask_civ1,'String','')
3216else
3217    mask_displ='no mask'; %default
3218    filebase=get(handles.RootName,'String');
3219    [ nbslice_mask, flag_mask]=get_mask(filebase,handles);
3220    if isequal(flag_mask,1)
3221        mask_displ=[num2str(nbslice_mask) 'mask'];
3222    elseif get(handles.compare,'Value')>1 & ~isequal(mask_displ,'no mask')% look for the second mask series
3223        common_path=fileparts(filebase);
3224        filebase_a=fullfile(common_path,get(handles.RootName_1,'String'));
3225        [nbslice_a, flag_mask_a]=get_mask(filebase_a,handles);
3226        if isequal(flag_mask_a,0) || ~isequal(nbslice_a,nbslice_mask)
3227            mask_displ='no mask';
3228        end
3229    end
3230    if isequal(mask_displ,'no mask')
3231        [FileName, PathName, filterindex] = uigetfile( ...
3232            {'*.png', ' (*.png)';
3233            '*.png',  '.png files '; ...
3234            '*.*', 'All Files (*.*)'}, ...
3235            'Pick a mask file *.png',filebase);
3236        mask_displ=fullfile(PathName,FileName);
3237        if ~exist(mask_displ,'file')
3238            mask_displ='no mask';
3239        end
3240    end
3241    if isequal(mask_displ,'no mask')
3242        set(handles.get_mask_civ1,'Value',0)
3243        set(handles.get_mask_fix1,'Value',0)
3244        set(handles.get_mask_civ2,'Value',0)
3245        set(handles.get_mask_fix2,'Value',0)
3246    else
3247        set(handles.get_mask_fix1,'Value',1)
3248        set(handles.get_mask_fix2,'Value',1)
3249    end
3250    set(handles.mask_civ1,'String',mask_displ)
3251    set(handles.mask_fix1,'String',mask_displ)
3252    set(handles.mask_civ2,'String',mask_displ)
3253    set(handles.mask_fix2,'String',mask_displ)
3254end
3255set(handles.get_mask_civ2,'Value',maskval)%update the civ2 mask with the same option as civ1
3256
3257%------------------------------------------------------------------------
3258% --- Executes on button press in get_mask_fix1.
3259function get_mask_fix1_Callback(hObject, eventdata, handles)
3260%------------------------------------------------------------------------
3261maskval=get(handles.get_mask_fix1,'Value');
3262if isequal(maskval,0)
3263    set(handles.mask_fix1,'String','')
3264else
3265    mask_displ='no mask'; %default
3266    filebase=get(handles.RootName,'String');
3267    [nbslice, flag_mask]=get_mask(filebase,handles);
3268    if isequal(flag_mask,1)
3269        mask_displ=[num2str(nbslice) 'mask'];
3270    elseif get(handles.compare,'Value')>1 & ~isequal(mask_displ,'no mask')% look for the second mask series
3271        filebase_a=get(handles.RootName_1,'String');
3272        [nbslice_a, flag_mask_a]=get_mask(filebase_a,handles);
3273        if isequal(flag_mask_a,0) | ~isequal(nbslice_a,nbslice)
3274            mask_displ='no mask';
3275        end
3276    end
3277    if isequal(mask_displ,'no mask')
3278        [FileName, PathName, filterindex] = uigetfile( ...
3279            {'*.png', ' (*.png)';
3280            '*.png',  '.png files '; ...
3281            '*.*', 'All Files (*.*)'}, ...
3282            'Pick a mask file *.png',filebase);
3283        mask_displ=fullfile(PathName,FileName);
3284        if ~exist(mask_displ,'file')
3285            mask_displ='no mask';
3286        end
3287    end
3288    if isequal(mask_displ,'no mask')
3289        set(handles.get_mask_fix1,'Value',0)
3290        set(handles.get_mask_civ2,'Value',0)
3291        set(handles.get_mask_fix2,'Value',0)
3292    else
3293        %set(handles.get_mask_civ2,'Value',1)
3294        set(handles.get_mask_fix2,'Value',1)
3295    end
3296    set(handles.mask_fix1,'String',mask_displ)
3297    set(handles.mask_civ2,'String',mask_displ)
3298    set(handles.mask_fix2,'String',mask_displ)
3299end
3300
3301%------------------------------------------------------------------------
3302% --- Executes on button press in get_mask_civ2: select box for mask option
3303function get_mask_civ2_Callback(hObject, eventdata, handles)
3304%------------------------------------------------------------------------
3305maskval=get(handles.get_mask_civ2,'Value');
3306if isequal(maskval,0)
3307    set(handles.mask_civ2,'String','')
3308else
3309    mask_displ='no mask'; %default
3310    filebase=get(handles.RootName,'String');
3311    [nbslice, flag_mask]=get_mask(filebase,handles);
3312    if isequal(flag_mask,1)
3313        mask_displ=[num2str(nbslice) 'mask'];
3314    elseif get(handles.compare,'Value')>1 & ~isequal(mask_displ,'no mask')% look for the second mask series
3315        filebase_a=get(handles.RootName_1,'String');
3316        [nbslice_a, flag_mask_a]=get_mask(filebase_a,handles);
3317        if isequal(flag_mask_a,0) | ~isequal(nbslice_a,nbslice)
3318            mask_displ='no mask';
3319        end
3320    end
3321    if isequal(mask_displ,'no mask')
3322        [FileName, PathName, filterindex] = uigetfile( ...
3323            {'*.png', ' (*.png)';
3324            '*.png',  '.png files '; ...
3325            '*.*', 'All Files (*.*)'}, ...
3326            'Pick a mask file *.png',filebase);
3327        mask_displ=fullfile(PathName,FileName);
3328        if ~exist(mask_displ,'file')
3329            mask_displ='no mask';
3330        end
3331    end
3332    if isequal(mask_displ,'no mask')
3333        set(handles.get_mask_civ2,'Value',0)
3334        set(handles.get_mask_fix2,'Value',0)
3335    else
3336        set(handles.get_mask_fix2,'Value',1)
3337    end
3338    set(handles.mask_civ2,'String',mask_displ)
3339    set(handles.mask_fix2,'String',mask_displ)
3340end
3341
3342%------------------------------------------------------------------------
3343% --- Executes on button press in get_mask_fix2.
3344function get_mask_fix2_Callback(hObject, eventdata, handles)
3345%------------------------------------------------------------------------
3346maskval=get(handles.get_mask_fix2,'Value');
3347if isequal(maskval,0)
3348    set(handles.mask_fix2,'String','')
3349else
3350    mask_displ='no mask'; %default
3351    filebase=get(handles.RootName,'String');
3352    [nbslice, flag_mask]=get_mask(filebase,handles);
3353    if isequal(flag_mask,1)
3354        mask_displ=[num2str(nbslice) 'mask'];
3355    elseif get(handles.compare,'Value')>1 & ~isequal(mask_displ,'no mask')% look for the second mask series
3356        filebase_a=get(handles.RootName_1,'String');
3357        [nbslice_a, flag_mask_a]=get_mask(filebase_a,handles);
3358        if isequal(flag_mask_a,0) | ~isequal(nbslice_a,nbslice)
3359            mask_displ='no mask';
3360        end
3361    end
3362    if isequal(mask_displ,'no mask')
3363        [FileName, PathName, filterindex] = uigetfile( ...
3364            {'*.png', ' (*.png)';
3365            '*.png',  '.png files '; ...
3366            '*.*', 'All Files (*.*)'}, ...
3367            'Pick a mask file *.png',filebase);
3368        mask_displ=fullfile(PathName,FileName);
3369        if ~exist(mask_displ,'file')
3370            mask_displ='no mask';
3371        end
3372    end
3373    if isequal(mask_displ,'no mask')
3374        set(handles.get_mask_fix2,'Value',0)
3375    end
3376    set(handles.mask_fix2,'String',mask_displ)
3377end
3378
3379%------------------------------------------------------------------------
3380% --- function called to look for mask files
3381function [nbslice, flag_mask]=get_mask(filebase,handles)
3382%------------------------------------------------------------------------
3383%detect mask files, images with appropriate file base
3384%[filebase '_' xx 'mask'], xx=nbslice
3385%flag_mask=1 indicates detection
3386
3387flag_mask=0;%default
3388nbslice=1;
3389
3390% subdir=get(handles.subdir_civ1,'String');
3391[Path,Name]=fileparts(filebase);
3392if ~isdir(Path)
3393    msgbox_uvmat('ERROR','no path for input files')
3394    return
3395end
3396currentdir=pwd;
3397cd(Path);%move in the dir of the root name filebase
3398maskfiles=dir([Name '_*mask_*.png']);%look for mask files
3399cd(currentdir);%come back to the current working directory
3400if ~isempty(maskfiles)
3401    %     msgbox_uvmat('ERROR','no mask available, to create it use Tools/Make mask in the upper menu bar of uvmat')
3402    % else
3403    flag_mask=1;
3404    maskname=maskfiles(1).name;% take the first mask file in the list
3405    [Path2,Name,ext]=fileparts(maskname);
3406    Namedouble=double(Name);
3407    val=(48>Namedouble)|(Namedouble>57);% select the non-numerical characters
3408    ind_mask=findstr('mask',Name);
3409    i=ind_mask-1;
3410    while val(i)==0 && i>0
3411        i=i-1;
3412    end
3413    nbslice=str2double(Name(i+1:ind_mask-1));
3414    if ~isnan(nbslice) && Name(i)=='_'
3415        flag_mask=1;
3416    else
3417        msgbox_uvmat('ERROR',['bad mask file ' Name ext ' found in ' Path2])
3418        return
3419        nbslice=1;
3420    end
3421end
3422
3423%------------------------------------------------------------------------
3424% --- function called to look for grid files
3425function [nbslice, flag_mask]=get_grid(filebase,handles)
3426%------------------------------------------------------------------------
3427flag_mask=0;%default
3428nbslice=1;
3429[Path,Name]=fileparts(filebase);
3430currentdir=pwd;
3431cd(Path);%move in the dir of the root name filebase
3432maskfiles=dir([Name '_*grid_*.grid']);%look for mask files
3433cd(currentdir);%come back to the current working directory
3434if ~isempty(maskfiles)
3435    flag_mask=1;
3436    maskname=maskfiles(1).name;% take the first mask file in the list
3437    [Path2,Name,ext]=fileparts(maskname);
3438    Namedouble=double(Name);
3439    val=(48>Namedouble)|(Namedouble>57);% select the non-numerical characters
3440    ind_mask=findstr('grid',Name);
3441    i=ind_mask-1;
3442    while val(i)==0 && i>0
3443        i=i-1;
3444    end
3445    nbslice=str2double(Name(i+1:ind_mask-1));
3446    if ~isnan(nbslice) && Name(i)=='_'
3447        flag_mask=1;
3448    else
3449        msgbox_uvmat('ERROR',['bad grid file ' Name ext ' found in ' Path2])
3450        return
3451        nbslice=1;
3452    end
3453end
3454
3455%------------------------------------------------------------------------
3456% --- transform numbers to letters
3457function str=num2stra(num,nom_type)
3458%------------------------------------------------------------------------
3459if isempty(nom_type)
3460    str='';
3461elseif strcmp(nom_type(end),'a')
3462    str=char(96+num);
3463elseif strcmp(nom_type(end),'A')
3464    str=char(96+num);
3465elseif isempty(nom_type(2:end))%a single index
3466    str='';
3467else
3468    str=num2str(num);
3469end
3470
3471% %------------------------------------------------------------------------
3472% function mask_civ1_Callback(hObject, eventdata, handles)
3473% %------------------------------------------------------------------------
3474% set(handles.mask_civ1,'UserData',[])
3475% set(handles.mask_civ1,'String','')
3476%
3477% %------------------------------------------------------------------------
3478% function mask_civ2_Callback(hObject, eventdata, handles)
3479% %------------------------------------------------------------------------
3480% set(handles.mask_civ2,'UserData',[])
3481% set(handles.mask_civ2,'String','')
3482%
3483% %------------------------------------------------------------------------
3484% function mask_fix1_Callback(hObject, eventdata, handles)
3485% %------------------------------------------------------------------------
3486% set(handles.mask_fix1,'UserData',[])
3487% set(handles.mask_fix1,'String','')
3488%
3489% %------------------------------------------------------------------------
3490% function mask_fix2_Callback(hObject, eventdata, handles)
3491% %------------------------------------------------------------------------
3492% set(handles.mask_fix2,'UserData',[])
3493% set(handles.mask_fix2,'String','')
3494
3495%------------------------------------------------------------------------
3496% --- Executes on button press in list_subdir_civ1.
3497function list_subdir_civ1_Callback(hObject, eventdata, handles)
3498%------------------------------------------------------------------------
3499list_subdir_civ1=get(handles.list_subdir_civ1,'String');
3500val=get(handles.list_subdir_civ1,'Value');
3501if val>1
3502    subdir=list_subdir_civ1{val};
3503    set(handles.subdir_civ1,'String',subdir);
3504    set(handles.list_subdir_civ1,'Value',1);
3505end
3506
3507%------------------------------------------------------------------------
3508% --- Executes on button press in list_subdir_civ2.
3509function list_subdir_civ2_Callback(hObject, eventdata, handles)
3510%------------------------------------------------------------------------
3511list_subdir_civ2=get(handles.list_subdir_civ2,'String');
3512val=get(handles.list_subdir_civ2,'Value');
3513if val>1
3514    subdir=list_subdir_civ2{val};
3515    set(handles.subdir_civ2,'String',subdir);
3516    set(handles.list_subdir_civ2,'Value',1);
3517end
3518
3519%------------------------------------------------------------------------
3520% --- Executes on button press in browse_gridciv1.
3521function browse_gridciv1_Callback(hObject, eventdata, handles)
3522%------------------------------------------------------------------------
3523value=get(handles.browse_gridciv1,'Value');
3524testgrid=0;
3525if value
3526    filebase=get(handles.RootName,'String');
3527    [nbslice, flag_grid]=get_grid(filebase,handles);
3528    if isequal(flag_grid,1)
3529        filegrid=[num2str(nbslice) 'grid'];
3530        testgrid=1;
3531    else
3532        [FileName, PathName, filterindex] = uigetfile( ...
3533            {'*.grid', ' (*.grid)';
3534            '*.grid',  '.grid files '; ...
3535            '*.*', 'All Files (*.*)'}, ...
3536            'Pick a file',filebase);
3537        filegrid=fullfile(PathName,FileName);
3538        if ~(isempty(FileName)||isempty(PathName)||isequal(FileName,0)||~exist(filegrid,'file'))
3539            testgrid=1;
3540        end
3541    end
3542end
3543if testgrid
3544    set(handles.browse_gridciv2,'Value',1)
3545    set(handles.get_gridpatch1,'Value',1)
3546    set(handles.get_gridpatch2,'Value',1)
3547    set(handles.dx_civ1,'Visible','off');
3548    set(handles.dy_civ1,'Visible','off');
3549    set(handles.dx_civ2,'Visible','off');
3550    set(handles.dy_civ2,'Visible','off');
3551    set(handles.grid_civ1,'String',filegrid)
3552    set(handles.grid_patch1,'String',filegrid)
3553    set(handles.grid_civ2,'String',filegrid)
3554    set(handles.grid_patch2,'String',filegrid)
3555else
3556    set(handles.browse_gridciv1,'Value',0);
3557    set(handles.browse_gridciv2,'Value',0);
3558    set(handles.get_gridpatch1,'Value',0)
3559    set(handles.get_gridpatch2,'Value',0)
3560    set(handles.dx_civ1,'Visible','on');
3561    set(handles.dy_civ1,'Visible','on');
3562    set(handles.dx_civ2,'Visible','on');
3563    set(handles.dy_civ2,'Visible','on');
3564    set(handles.grid_civ1,'String','')
3565    set(handles.grid_patch1,'String','')
3566    set(handles.grid_civ2,'String','')
3567    set(handles.grid_patch2,'String','')
3568end
3569
3570%------------------------------------------------------------------------
3571% --- Executes on button press in browse_gridciv1.
3572function browse_gridciv2_Callback(hObject, eventdata, handles)
3573%------------------------------------------------------------------------
3574value=get(handles.browse_gridciv2,'Value');
3575if value
3576    filebase=get(handles.RootName,'String');
3577    [nbslice, flag_grid]=get_grid(filebase,handles);
3578    if isequal(flag_grid,1)
3579        mask_displ=[num2str(nbslice) 'grid'];
3580        set(handles.grid_civ2,'String',mask_displ)
3581        set(handles.dx_civ2,'Visible','off');
3582        set(handles.dy_civ2,'Visible','off');
3583    else
3584        [FileName, PathName, filterindex] = uigetfile( ...
3585            {'*.grid', ' (*.grid)';
3586            '*.grid',  '.grid files '; ...
3587            '*.*', 'All Files (*.*)'}, ...
3588            'Pick a file',filebase);
3589        filegrid=fullfile(PathName,FileName);
3590        if isempty(FileName)|isempty(PathName)|isequal(FileName,0)|~exist(filegrid,'file')
3591            set(handles.browse_gridciv2,'Value',0);
3592            set(handles.grid_civ2,'string','');
3593            set(handles.dx_civ2,'Visible','on');
3594            set(handles.dy_civ2,'Visible','on');
3595            set(handles.grid_civ2,'string','');
3596        else
3597            set(handles.grid_civ2,'string',filegrid);
3598            set(handles.dx_civ2,'Visible','off');
3599            set(handles.dy_civ2,'Visible','off');
3600            set(handles.grid_civ2,'string',filegrid);
3601        end
3602    end
3603else
3604    set(handles.grid_civ2,'string','');
3605    set(handles.dx_civ2,'Visible','on');
3606    set(handles.dy_civ2,'Visible','on');
3607    set(handles.grid_civ2,'string','');
3608end
3609
3610% % --- Executes on button press in browse_gridciv2.
3611% function browse_gridciv2_Callback(hObject, eventdata, handles)
3612%
3613% filebase=get(handles.RootName,'String');
3614% [FileName, PathName, filterindex] = uigetfile( ...
3615%        {'*.grid', ' (*.grid)';
3616%         '*.grid',  '.grid files '; ...
3617%         '*.*', 'All Files (*.*)'}, ...
3618%         'Pick a file',filebase);
3619% filegrid=fullfile(PathName,FileName);
3620% set(handles.grid_civ2,'string',filegrid);
3621% set(handles.dx_civ2,'String',' ');
3622% set(handles.dy_civ2,'String',' ');
3623% % set(handles.grid_patch2,'string',filegrid);
3624
3625% --- Executes on button press in get_gridpatch1.
3626function get_gridpatch1_Callback(hObject, eventdata, handles)
3627% hObject    handle to get_gridpatch1 (see GCBO)
3628% eventdata  reserved - to be defined in a future version of MATLAB
3629% handles    structure with handles and user data (see GUIDATA)
3630
3631filebase=get(handles.RootName,'String');
3632[FileName, PathName, filterindex] = uigetfile( ...
3633    {'*.grid', ' (*.grid)';
3634    '*.grid',  '.grid files '; ...
3635    '*.*', 'All Files (*.*)'}, ...
3636    'Pick a file',filebase);
3637filegrid=fullfile(PathName,FileName);
3638set(handles.grid_patch1,'string',filegrid);
3639% set(handles.grid_patch2,'string',filegrid
3640
3641%------------------------------------------------------------------------
3642% --- Executes on button press in get_gridpatch2.
3643function get_gridpatch2_Callback(hObject, eventdata, handles)
3644%------------------------------------------------------------------------
3645
3646%------------------------------------------------------------------------
3647function enable_civ1(handles,state)
3648%------------------------------------------------------------------------
3649if isequal(state,0)
3650    state='off';
3651end
3652if isequal(state,1)
3653    state='on';
3654end
3655if isequal(state,'on')
3656    set(handles.frame_civ1,'BackgroundColor',[1 1 0])
3657    set(handles.frame_para_civ1,'BackgroundColor',[1 1 0])
3658    set(handles.frame_grid_civ1,'BackgroundColor',[1 1 0])
3659else
3660    set(handles.frame_civ1,'BackgroundColor',[0.831 0.816 0.784])
3661    set(handles.frame_para_civ1,'BackgroundColor',[0.831 0.816 0.784])
3662    set(handles.frame_grid_civ1,'BackgroundColor',[0.831 0.816 0.784])
3663end
3664set(handles.ibx,'Visible',state)
3665set(handles.iby,'Visible',state)
3666set(handles.isx,'Visible',state)
3667set(handles.isy,'Visible',state)
3668set(handles.shiftx,'Visible',state)
3669set(handles.shifty,'Visible',state)
3670set(handles.rho,'Visible',state)
3671set(handles.dx_civ1,'Visible',state)
3672set(handles.dy_civ1,'Visible',state)
3673set(handles.calcul_search,'Visible',state)
3674set(handles.u_text,'Visible',state)
3675set(handles.v_text,'Visible',state)
3676set(handles.min,'Visible',state)
3677set(handles.max,'Visible',state)
3678set(handles.umin,'Visible',state)
3679set(handles.umax,'Visible',state)
3680set(handles.vmin,'Visible',state)
3681set(handles.vmax,'Visible',state)
3682set(handles.grid_civ1,'Visible',state)
3683set(handles.mask_civ1,'Visible',state)
3684set(handles.browse_gridciv1,'Visible',state)
3685set(handles.get_mask_civ1,'Visible',state)
3686set(handles.parameters,'Visible',state)
3687set(handles.grid,'Visible',state)
3688set(handles.dx_civ1,'Visible',state)
3689set(handles.dy_civ1,'Visible',state)
3690set(handles.ImaThreshold,'Visible',state)
3691if isequal(state,'off')
3692    set(handles.MinIma,'Visible','off')
3693    set(handles.MaxIma,'Visible','off')
3694    set(handles.ImaThreshold,'Value',0)
3695end
3696set(handles.dx_civ1_title,'Visible',state)
3697set(handles.dy_civ1_title,'Visible',state)
3698set(handles.ImaThreshold_title,'Visible',state)
3699set(handles.ib_title,'Visible',state)
3700set(handles.is_title,'Visible',state)
3701set(handles.shift_title,'Visible',state)
3702set(handles.rho_title,'Visible',state)
3703
3704%------------------------------------------------------------------------
3705function enable_fix1(handles,state)
3706%------------------------------------------------------------------------
3707if isequal(state,0)
3708    state='off';
3709end
3710if isequal(state,1)
3711    state='on';
3712end
3713if isequal(state,'on')
3714    set(handles.frame_fix1,'BackgroundColor',[1 1 0])
3715else
3716    set(handles.frame_fix1,'BackgroundColor',[0.7 0.7 0.7])
3717end
3718set(handles.REMOVE,'Visible',state)
3719set(handles.vec_Fmin2,'Visible',state)
3720set(handles.vec_F2,'Visible',state)
3721set(handles.vec_F3,'Visible',state)
3722set(handles.thresh_vecC,'Visible',state)
3723set(handles.thresh_vecC_title,'Visible',state)
3724set(handles.thresh_vel,'Visible',state)
3725set(handles.thresh_vel_text,'Visible',state)
3726set(handles.mask_fix1,'Visible',state)
3727set(handles.get_mask_fix1,'Visible',state)
3728set(handles.get_ref_fix1,'Visible',state)
3729set(handles.ref_fix1,'Visible',state)
3730set(handles.inf_sup1,'Visible',state)
3731set(handles.field_ref1,'Visible',state)
3732
3733%------------------------------------------------------------------------
3734function enable_patch1(handles)
3735%------------------------------------------------------------------------
3736global patch_newBin
3737set(handles.frame_patch1,'BackgroundColor',[1 1 0])
3738set(handles.rho_patch1,'Visible','on')
3739set(handles.rho_text1,'Visible','on')
3740set(handles.thresh_patch1,'Visible','on')
3741set(handles.thresh_text1,'Visible','on')
3742set(handles.subdomain_patch1,'Visible','on')
3743set(handles.subdomain_text1,'Visible','on')
3744set(handles.nx_patch1,'Visible','on')
3745set(handles.ny_patch1,'Visible','on')
3746set(handles.nx_patch1_title,'Visible','on')
3747set(handles.ny_patch1_title,'Visible','on')
3748% if ~isempty(patch_newBin)
3749%     set(handles.test_interp,'Visible','on');
3750% end
3751set(handles.get_gridpatch1,'Visible','on')
3752set(handles.grid_patch1,'string','none');
3753set(handles.grid_patch1,'Visible','on')
3754
3755%------------------------------------------------------------------------
3756function desable_patch1(handles)
3757%------------------------------------------------------------------------
3758set(handles.frame_patch1,'BackgroundColor',[0.831 0.816 0.784])
3759set(handles.rho_patch1,'Visible','off')
3760set(handles.rho_text1,'Visible','off')
3761set(handles.thresh_patch1,'Visible','off')
3762set(handles.thresh_text1,'Visible','off')
3763set(handles.subdomain_patch1,'Visible','off')
3764set(handles.subdomain_text1,'Visible','off')
3765set(handles.nx_patch1,'Visible','off')
3766set(handles.ny_patch1,'Visible','off')
3767set(handles.nx_patch1_title,'Visible','off')
3768set(handles.ny_patch1_title,'Visible','off')
3769%set(handles.test_interp,'Visible','off')
3770set(handles.get_gridpatch1,'Visible','off')
3771set(handles.grid_patch1,'Visible','off')
3772
3773%------------------------------------------------------------------------
3774function enable_civ2(handles,state)
3775%------------------------------------------------------------------------
3776if isequal(state,0)
3777    state='off';
3778end
3779if isequal(state,1)
3780    state='on';
3781end
3782if isequal(state,'on')
3783    set(handles.frame_civ2,'BackgroundColor',[1 1 0])
3784    set(handles.frame_para_civ2,'BackgroundColor',[1 1 0])
3785    set(handles.frame_grid_civ2,'BackgroundColor',[1 1 0])
3786    set(handles.frame_subdirciv2,'BackgroundColor',[1 1 0])
3787else
3788    set(handles.frame_civ2,'BackgroundColor',[0.831 0.816 0.784])
3789    set(handles.frame_para_civ2,'BackgroundColor',[0.831 0.816 0.784])
3790    set(handles.frame_grid_civ2,'BackgroundColor',[0.831 0.816 0.784])
3791    set(handles.frame_subdirciv2,'BackgroundColor',[0.831 0.816 0.784])
3792end
3793set(handles.ibx_civ2,'Visible',state)
3794set(handles.iby_civ2,'Visible',state)
3795set(handles.decimal,'Visible',state)
3796set(handles.deformation,'Visible',state)
3797set(handles.rho_civ2,'Visible',state)
3798set(handles.dx_civ2,'Visible',state)
3799set(handles.dy_civ2,'Visible',state)
3800set(handles.browse_gridciv2,'Visible',state)
3801set(handles.get_mask_civ2,'Visible',state)
3802set(handles.parameters,'Visible',state)
3803set(handles.grid,'Visible',state)
3804set(handles.parameters_text,'Visible',state)
3805set(handles.grid_text,'Visible',state)
3806set(handles.grid_civ2,'Visible',state)
3807set(handles.mask_civ2,'Visible',state)
3808set(handles.dx_civ2_title,'Visible',state)
3809set(handles.dy_civ2_title,'Visible',state)
3810set(handles.ibx_civ2_text,'Visible',state)
3811set(handles.rho_civ2_title,'Visible',state)
3812set(handles.ImaThreshold2,'Visible',state)
3813set(handles.ImaThreshold_title2,'Visible',state)
3814if isequal(state,'off')
3815    set(handles.MinIma2,'Visible','off')
3816    set(handles.MaxIma2,'Visible','off')
3817    set(handles.ImaThreshold2,'Value',0)
3818    if isequal(get(handles.FIX2,'Value'),0) & isequal(get(handles.PATCH2,'Value'),0)
3819        set(handles.list_pair_civ2,'Visible','off')
3820        set(handles.subdir_civ2,'Visible','off')
3821        set(handles.subdir_civ2_text,'Visible','off')
3822        set(handles.dt_unit_civ2,'Visible','off')
3823        set(handles.ref_i_civ2,'Visible','off')
3824        set(handles.i_ref_civ2_title,'Visible','off')
3825        set(handles.j_ref_civ2_title,'Visible','off')
3826        set(handles.ref_j_civ2,'Visible','off')
3827    end
3828else
3829    set(handles.list_pair_civ2,'Visible','on')
3830    set(handles.subdir_civ2,'Visible','on')
3831    set(handles.subdir_civ2_text,'Visible','on')
3832    set(handles.dt_unit_civ2,'Visible','on')
3833    set(handles.ref_i_civ2,'Visible','on')
3834    set(handles.i_ref_civ2_title,'Visible','on')
3835    set(handles.j_ref_civ2_title,'Visible','on')
3836    set(handles.ref_j_civ2,'Visible','on')
3837end
3838set(handles.rho_civ2_title,'Visible',state)
3839
3840%------------------------------------------------------------------------
3841function enable_fix2(handles)
3842%------------------------------------------------------------------------
3843set(handles.frame_fix2,'BackgroundColor',[1 1 0])
3844set(handles.REMOVE2,'Visible','on')
3845set(handles.vec_Fmin2_2,'Visible','on')
3846set(handles.vec_F4,'Visible','on')
3847set(handles.vec_F3_2,'Visible','on')
3848set(handles.thresh_vec2C,'Visible','on')
3849set(handles.thresh_vec2C_text,'Visible','on')
3850set(handles.thresh_vel2,'Visible','on')
3851set(handles.thresh_vel2_text,'Visible','on')
3852set(handles.mask_fix2,'Visible','on')
3853set(handles.get_mask_fix2,'Visible','on')
3854set(handles.list_pair_civ2,'Visible','on')
3855set(handles.subdir_civ2,'Visible','on')
3856set(handles.subdir_civ2_text,'Visible','on')
3857set(handles.get_ref_fix2,'Visible','on')
3858set(handles.ref_fix2,'Visible','on')
3859set(handles.inf_sup2,'Visible','on')
3860set(handles.field_ref2,'Visible','on')
3861
3862%------------------------------------------------------------------------
3863function desable_fix2(handles)
3864%------------------------------------------------------------------------
3865set(handles.frame_fix2,'BackgroundColor',[0.831 0.816 0.784])
3866set(handles.REMOVE2,'Visible','off')
3867set(handles.vec_Fmin2_2,'Visible','off')
3868set(handles.vec_F4,'Visible','off')
3869set(handles.vec_F3_2,'Visible','off')
3870set(handles.thresh_vec2C,'Visible','off')
3871set(handles.thresh_vec2C_text,'Visible','off')
3872set(handles.thresh_vel2,'Visible','off')
3873set(handles.thresh_vel2_text,'Visible','off')
3874set(handles.mask_fix2,'Visible','off')
3875set(handles.get_mask_fix2,'Visible','off')
3876set(handles.get_ref_fix2,'Visible','off')
3877set(handles.ref_fix2,'Visible','off')
3878set(handles.inf_sup2,'Visible','off')
3879set(handles.field_ref2,'Visible','off')
3880if isequal(get(handles.CIV2,'Value'),0) & isequal(get(handles.PATCH2,'Value'),0)
3881    set(handles.list_pair_civ2,'Visible','off')
3882    set(handles.subdir_civ2,'Visible','off')
3883    set(handles.subdir_civ2_text,'Visible','off')
3884end
3885
3886%------------------------------------------------------------------------
3887function enable_patch2(handles)
3888%------------------------------------------------------------------------
3889set(handles.frame_patch2,'BackgroundColor',[1 1 0])
3890set(handles.rho_patch2,'Visible','on')
3891set(handles.rho_text2,'Visible','on')
3892set(handles.thresh_patch2,'Visible','on')
3893set(handles.thresh_text2,'Visible','on')
3894set(handles.subdomain_patch2,'Visible','on')
3895set(handles.subdomain_text2,'Visible','on')
3896set(handles.nx_patch2,'Visible','on')
3897set(handles.ny_patch2,'Visible','on')
3898set(handles.nx_patch2_title,'Visible','on')
3899set(handles.ny_patch2_title,'Visible','on')
3900set(handles.get_gridpatch2,'Visible','on')
3901set(handles.grid_patch2,'Visible','on')
3902set(handles.list_pair_civ2,'Visible','on')
3903set(handles.subdir_civ2,'Visible','on')
3904set(handles.subdir_civ2_text,'Visible','on')
3905
3906%------------------------------------------------------------------------
3907function desable_patch2(handles)
3908%------------------------------------------------------------------------
3909set(handles.frame_patch2,'BackgroundColor',[0.831 0.816 0.784])
3910set(handles.rho_patch2,'Visible','off')
3911set(handles.rho_text2,'Visible','off')
3912set(handles.thresh_patch2,'Visible','off')
3913set(handles.thresh_text2,'Visible','off')
3914set(handles.subdomain_patch2,'Visible','off')
3915set(handles.subdomain_text2,'Visible','off')
3916set(handles.nx_patch2,'Visible','off')
3917set(handles.ny_patch2,'Visible','off')
3918set(handles.nx_patch2_title,'Visible','off')
3919set(handles.ny_patch2_title,'Visible','off')
3920set(handles.get_gridpatch2,'Visible','off')
3921set(handles.grid_patch2,'Visible','off')
3922if isequal(get(handles.CIV2,'Value'),0) & isequal(get(handles.FIX2,'Value'),0)
3923    set(handles.list_pair_civ2,'Visible','off')
3924    set(handles.subdir_civ2,'Visible','off')
3925    set(handles.subdir_civ2_text,'Visible','off')
3926end
3927
3928%------------------------------------------------------------------------
3929function enable_pair1(handles,state)
3930%------------------------------------------------------------------------
3931set(handles.subdir_civ1,'Visible',state)
3932set(handles.list_subdir_civ1,'Visible',state)
3933set(handles.SUBDIR_CIV1_txt,'Visible',state)
3934set(handles.frame_subdirciv1,'Visible',state)
3935set(handles.list_pair_civ1,'Visible',state)
3936set(handles.PAIR_txt,'Visible',state)
3937%set(handles.dt_unit,'Visible',state)
3938set(handles.PAIR_frame,'Visible',state)
3939
3940%------------------------------------------------------------------------
3941% --- Read the parameters for civ1 on the interface
3942function par=read_param_civ1(handles,file_ima)
3943%------------------------------------------------------------------------
3944ibx_val=str2double(get(handles.ibx,'String'));
3945par.ibx=num2str(ibx_val);
3946iby_val=str2double(get(handles.iby,'String'));
3947par.iby=num2str(iby_val);
3948isx=get(handles.isx,'String');
3949if isnan(str2double(isx)), isx='41'; set(handles.isx,'String','41'), end; %default
3950if str2double(isx)<ibx_val+8,isx=num2str(ibx_val+8); set(handles.isx,'String',num2str(ibx_val+8)); end
3951isy=get(handles.isy,'String');
3952if isnan(str2double(isy)), isy='41'; set(handles.isy,'String','41'), end;%default
3953if str2double(isy)<iby_val+8,isy=num2str(iby_val+8); set(handles.isy,'String',num2str(iby_val+8)); end
3954par.isx=get(handles.isx,'String');
3955par.isy=get(handles.isy,'String');
3956par.shiftx=get(handles.shiftx,'String');
3957par.shifty=get(handles.shifty,'String');
3958if isnan(str2double(par.isx))
3959    par.isx='41';%default
3960    set(handles.isx,'String','41');
3961end
3962if isnan(str2double(par.isy))
3963    par.isy='41'; %default
3964    set(handles.isy,'String','41');
3965end
3966if isnan(str2double(par.shiftx))
3967    par.shiftx='0';%default
3968    set(handles.shiftx,'String','0');
3969end
3970if isnan(str2double(par.shifty))
3971    par.shifty='0'; %default
3972    set(handles.shifty,'String','0');
3973end
3974par.rho=get(handles.rho,'String');
3975par.dx=get(handles.dx_civ1,'String');
3976par.dy=get(handles.dy_civ1,'String');
3977if isnan(str2double(par.dx))
3978    if isempty(get(handles.grid_civ1,'String'));
3979        par.dx='0'; %just read by civ program, not used
3980    else
3981        par.dx='20';%default
3982        set(handles.dx_civ1,'String','20');
3983    end
3984end
3985if isnan(str2double(par.dy))
3986    if isempty(get(handles.grid_civ1,'String'));
3987        par.dy='0';%just read by civ program, not used
3988    else
3989        par.dy='20';%default
3990        set(handles.dy_civ1_title,'String','20');
3991    end
3992end
3993par.pxcmx='1'; %velocities are expressed in pixel dispalcement
3994par.pxcmy='1';
3995if exist('file_ima','var')
3996A=imread(file_ima);%read the first image to get the size
3997sizim=size(A);
3998par.npx=num2str(sizim(2));
3999par.npy=num2str(sizim(1));
4000end
4001%time=get(handles.RootName,'UserData'); %get the set of times
4002par.gridname=get(handles.grid_civ1,'String');
4003par.gridflag='y';
4004if strcmp(par.gridname,'')|| isempty(par.gridname)
4005    par.gridname='nogrid';
4006    par.gridflag='n';
4007end
4008
4009%------------------------------------------------------------------------
4010function par=read_param_civ2(handles,file_ima)
4011%------------------------------------------------------------------------
4012par.ibx=get(handles.ibx_civ2,'String');
4013par.iby=get(handles.iby_civ2,'String');
4014par.rho=get(handles.rho_civ2,'String');
4015par.decimal=int2str(get(handles.decimal,'Value'));
4016par.deformation=int2str(get(handles.deformation,'Value'));
4017par.dx=get(handles.dx_civ2,'String');
4018par.dy=get(handles.dy_civ2,'String');
4019if isnan(str2double(par.dx))
4020    if isempty(get(handles.grid_civ2,'String'));
4021        par.dx='0'; %just read by civ program, not used
4022    else
4023        par.dx='20';%default
4024        set(handles.dx_civ2,'String','20');
4025    end
4026end
4027if isnan(str2double(par.dy))
4028    if isempty(get(handles.grid_civ2,'String'));
4029        par.dy='0';%just read by civ program, not used
4030    else
4031        par.dy='20';%default
4032        set(handles.dy_civ2,'String','20');
4033    end
4034end
4035par.pxcmx='1';
4036par.pxcmy='1';
4037A=imread(file_ima);%read the first image to get the size
4038sizim=size(A);
4039par.npx=num2str(sizim(2));
4040par.npy=num2str(sizim(1));
4041%time=get(handles.RootName,'UserData'); %get the set of times
4042par.gridname=get(handles.grid_civ2,'String');
4043par.gridflag='y';
4044if strcmp(par.gridname,'')|| isempty(par.gridname)
4045    par.gridname='nogrid';
4046    par.gridflag='n';
4047end
4048
4049%------------------------------------------------------------------------
4050% --- CIV1  CIV1  CIV1 CIV1
4051function cmd_CIV1=CIV1_CMD(filename,namelog,par,handles,sparam)
4052%------------------------------------------------------------------------
4053%pixels per cm and matrix of the image times, read from the .civ file by uvmat
4054
4055%changes : filename_cmx -> filename ( no extension )
4056% input namelog not used
4057if isequal(par.Dt,'0')
4058    par.Dt='1' ;%case of 'displacement' mode
4059end
4060par.filename_ima_a=regexprep(par.filename_ima_a,'.png','');
4061par.filename_ima_b=regexprep(par.filename_ima_b,'.png','');
4062fid=fopen([filename '.cmx'],'w');
4063fprintf(fid,['##############   CMX file' '\n' ]);
4064fprintf(fid,   ['FirstImage ' regexprep(par.filename_ima_a,'\\','\\\\') '\n' ]);% for windows compatibility
4065fprintf(fid,   ['LastImage  ' regexprep(par.filename_ima_b,'\\','\\\\') '\n' ]);% for windows compatibility
4066fprintf(fid,  ['XX' '\n' ]);
4067fprintf(fid,  ['Mask ' par.maskflag '\n' ]);
4068fprintf(fid,  ['MaskName ' regexprep(par.maskname,'\\','\\\\') '\n' ]);
4069fprintf(fid,   ['ImageSize ' par.npx ' ' par.npy '\n' ]);   %VERIFIER CAS GENERAL ?
4070fprintf(fid,   ['CorrelationBoxesSize ' par.ibx ' ' par.iby '\n' ]);
4071fprintf(fid,   ['SearchBoxeSize ' par.isx ' ' par.isy '\n' ]);
4072fprintf(fid,   ['RO ' par.rho '\n' ]);
4073fprintf(fid,   ['GridSpacing ' par.dx ' ' par.dy '\n' ]);
4074fprintf(fid,   ['XX 1.0' '\n' ]);
4075fprintf(fid,   ['Dt_TO ' par.Dt ' ' par.T0 '\n' ]);
4076fprintf(fid,  ['PixCmXY ' par.pxcmx ' ' par.pxcmy '\n' ]);
4077fprintf(fid,  ['XX 1' '\n' ]);
4078fprintf(fid,   ['ShiftXY ' par.shiftx ' '  par.shifty '\n' ]);
4079fprintf(fid,  ['Grid ' par.gridflag '\n' ]);
4080fprintf(fid,   ['GridName ' regexprep(par.gridname,'\\','\\\\') '\n' ]);
4081fprintf(fid,   ['XX 85' '\n' ]);
4082fprintf(fid,   ['XX 1.0' '\n' ]);
4083fprintf(fid,   ['XX 1.0' '\n' ]);
4084fprintf(fid,   ['Hart 1' '\n' ]);
4085fprintf(fid,  [ 'DecimalShift 0' '\n' ]);
4086fprintf(fid,   ['Deformation 0' '\n' ]);
4087fprintf(fid,  ['CorrelationMin 0' '\n' ]);
4088fprintf(fid,   ['IntensityMin 0' '\n' ]);
4089fprintf(fid,  ['SeuilImage n' '\n' ]);
4090fprintf(fid,   ['SeuilImageValues 0 4096' '\n' ]);
4091fprintf(fid,   ['ImageToUse ' par.term_a ' ' par.term_b '\n' ]); % VERIFIER ?
4092fprintf(fid,   ['ImageUsedBefore null null' '\n' ]);
4093fclose(fid);
4094
4095% cmd_CIV1=[sparam.Civ1Bin ' -f ' filename '.cmx >' filename '.log' ]; % redirect standard output to the log file
4096% cmd_CIV1=regexprep(cmd_CIV1,'\\','\\\\');
4097% namelog=regexprep(namelog,'\\','\\\\');
4098if(isunix)
4099%     filename
4100%     namelog
4101%     
4102%     [Rootbat,Filebat,extbat]=fileparts(namelog);
4103%     ncName=fullfile(Rootbat,[ Filebat '.nc']);
4104    cmd_CIV1=[sparam.Civ1Bin ' -f ' filename '.cmx >' filename '.log' ]; % redirect standard output to the log file, the result file is named [filename '.nc'] by CIVx
4105    cmd_CIV1=[cmd_CIV1 '\n' 'mv ' filename '.log' ' ' filename '.civ1.log' '\n' 'chmod g+w ' filename '.nc'];%rename .log as .civ1.log and set the netcdf result file for group user writting
4106    cmd_CIV1=[cmd_CIV1 '\n' 'mv ' filename '.cmx' ' ' filename '.civ1.cmx' '\n'];%rename .cmx as .civ1.cmx
4107else %Windows system
4108    filename=regexprep(filename,'\\','\\\\');
4109    cmd_CIV1=['"' sparam.Civ1Bin '" -f "' filename '.cmx" >"' filename '.log"' ]; % redirect standard output to the log file
4110    cmd_CIV1=regexprep(cmd_CIV1,'\\','\\\\');
4111    namelog=regexprep(namelog,'\\','\\\\');
4112    cmd_CIV1=[cmd_CIV1 '\n' 'copy /Y "' filename '.log' '" "' filename '.civ1.log"'];
4113    cmd_CIV1=[cmd_CIV1 '\n' 'copy /Y "' filename '.cmx' '" "' filename '.civ1.cmx"'];
4114end
4115
4116%------------------------------------------------------------------------
4117% --- CIV1  Unified
4118function xml_civ1_parameters=CIV1_CMD_Unified(filename,namelog,par)
4119%------------------------------------------------------------------------
4120%pixels per cm and matrix of the image times, read from the .civ file by uvmat
4121%global CivBin%name of the executable for civ1 calculation
4122
4123civ1.image1=par.filename_ima_a;
4124civ1.image2=par.filename_ima_b;
4125civ1.imageSize_X=par.npx;
4126civ1.imageSize_Y=par.npy;
4127civ1.outputFileName=[filename '.nc'];
4128civ1.correlationBoxesSize_X=par.ibx;
4129civ1.correlationBoxesSize_Y=par.iby;
4130civ1.searchBoxesSize_X=par.isx;
4131civ1.searchBoxesSize_Y=par.isy;
4132civ1.globalShift_X=par.shiftx;
4133civ1.globalShift_Y=par.shifty;
4134civ1.ro=par.rho;
4135civ1.hart='y';
4136if isequal(par.gridflag,'y')
4137    civ1.grid=par.gridname;
4138else
4139    civ1.grid='n';
4140    civ1.gridSpacing_X=par.dx;
4141    civ1.gridSpacing_Y=par.dy;
4142end
4143if isequal(par.maskflag,'y')
4144    civ1.mask=par.maskname;
4145end
4146civ1.dt=par.Dt;
4147civ1.unit='pixel';
4148civ1.absolut_time_T0=par.T0;
4149civ1.pixcmx=par.pxcmx;
4150civ1.pixcmy=par.pxcmy;
4151civ1.convectFlow='n';
4152
4153xml_civ1_parameters=civ1;
4154
4155%------------------------------------------------------------------------
4156% --- CIV2  Unified
4157function civ2=CIV2_CMD_Unified(filename,namelog,par)
4158%------------------------------------------------------------------------
4159%pixels per cm and matrix of the image times, read from the .civ file by uvmat
4160%global CivBin%name of the executable for civ1 calculation
4161
4162civ2.image1=par.filename_ima_a;
4163civ2.image2=par.filename_ima_b;
4164civ2.imageSize_X=par.npx;
4165civ2.imageSize_Y=par.npy;
4166civ2.inputFileName=[par.filename_nc1 '.nc'];
4167civ2.outputFileName=[filename '.nc'];
4168civ2.correlationBoxesSize_X=par.ibx;
4169civ2.correlationBoxesSize_Y=par.iby;
4170civ2.ro=par.rho;
4171%civ2.decimalShift=par.decimal;
4172%civ2.deformation=par.deformation;
4173if isequal(par.decimal,'1')
4174    civ2.decimalShift='y';
4175else
4176    civ2.decimalShift='n';
4177end
4178if isequal(par.deformation,'1')
4179    civ2.deformation='y';
4180else
4181    civ2.deformation='n';
4182end
4183if isequal(par.gridflag,'y')
4184    civ2.grid=par.gridname;
4185else
4186    civ2.grid='n';
4187    civ2.gridSpacing_X=par.dx;
4188    civ2.gridSpacing_Y=par.dy;
4189end
4190civ2.gridSpacing_X='10';
4191civ2.gridSpacing_Y='10';%NOTE: faut mettre gridSpacing pourque ca tourne, meme si c'est la grille qui est utilisee
4192if isequal(par.maskflag,'y')
4193    civ2.mask=par.maskname;
4194else
4195    civ2.mask='n';
4196end
4197civ2.dt=par.Dt;
4198civ2.unit='pixel';
4199civ2.absolut_time_T0=par.T0;
4200civ2.pixcmx=par.pxcmx;
4201civ2.pixcmy=par.pxcmy;
4202civ2.convectFlow='n';
4203civ2.pixcmx=par.pxcmx;
4204civ2.pixcmy=par.pxcmy;
4205civ2.convectFlow='n';
4206
4207%------------------------------------------------------------------------
4208% --- CIV2  CIV2  CIV2 CIV2
4209function cmd_CIV2=CIV2_CMD(filename,namelog,par,sparam)
4210%------------------------------------------------------------------------
4211%pixels per cm and matrix of the image times, read from the .civ file by uvmat
4212% global civ2Bin sge%name of the executable for civ1 calculation
4213if isequal(par.Dt,'0')
4214    par.Dt='1' ;%case of 'displacement' mode
4215end
4216par.filename_ima_a=regexprep(par.filename_ima_a,'.png','');
4217par.filename_ima_b=regexprep(par.filename_ima_b,'.png','');% bug : .png appears two times ?
4218[fid,errormsg]=fopen([filename '.civ2.cmx'],'w');
4219if isequal(fid,-1)
4220    msgbox_uvmat('ERROR',errormsg)
4221    cmd_CIV2='';
4222    return
4223end
4224fprintf(fid,['##############   CMX file' '\n' ]);
4225fprintf(fid,   ['FirstImage ' regexprep(par.filename_ima_a,'\\','\\\\') '\n' ]);% for windows compatibility
4226fprintf(fid,   ['LastImage  ' regexprep(par.filename_ima_b,'\\','\\\\') '\n' ]);% for windows compatibility
4227fprintf(fid,  ['XX' '\n' ]);
4228fprintf(fid, ['Mask ' par.maskflag '\n' ]);
4229fprintf(fid, ['MaskName ' regexprep(par.maskname,'\\','\\\\') '\n' ]);% for windows compatibility
4230fprintf(fid, ['ImageSize ' par.npx ' ' par.npy '\n' ]);   %VERIFIER CAS GENERAL ?
4231fprintf(fid, ['CorrelationBoxesSize ' par.ibx ' ' par.iby '\n' ]);
4232fprintf(fid, ['SearchBoxeSize ' par.ibx ' ' par.iby '\n']);
4233fprintf(fid, ['RO ' par.rho '\n']);
4234fprintf(fid, ['GridSpacing ' par.dx ' ' par.dy '\n']);
4235fprintf(fid, ['XX 1.0' '\n' ]);
4236fprintf(fid, ['Dt_TO ' par.Dt ' ' par.T0 '\n' ]);
4237fprintf(fid, ['PixCmXY ' par.pxcmx ' ' par.pxcmy '\n' ]);
4238fprintf(fid, ['XX 1' '\n' ]);
4239fprintf(fid, 'ShiftXY 0 0\n');
4240fprintf(fid, ['Grid ' par.gridflag '\n' ]);
4241fprintf(fid, ['GridName ' regexprep(par.gridname,'\\','\\\\') '\n']);
4242fprintf(fid, ['XX 85' '\n' ]);
4243fprintf(fid, ['XX 1.0' '\n' ]);
4244fprintf(fid, ['XX 1.0' '\n' ]);
4245fprintf(fid, ['Hart 1' '\n' ]);
4246fprintf(fid, ['DecimalShift ' par.decimal '\n']);
4247fprintf(fid, ['Deformation ' par.deformation '\n']);
4248fprintf(fid,  ['CorrelationMin 0' '\n' ]);
4249fprintf(fid,   ['IntensityMin 0' '\n' ]);
4250fprintf(fid,  ['SeuilImage n' '\n' ]);
4251fprintf(fid,   ['SeuilImageValues 0 4096' '\n' ]);
4252fprintf(fid,   ['ImageToUse ' par.term_a ' ' par.term_b '\n' ]); % VERIFIER ?
4253fprintf(fid, ['ImageUsedBefore ' regexprep(par.filename_nc1,'\\','\\\\') '\n']);
4254fclose(fid);
4255
4256if(isunix)
4257%         cmd_CIV1=[sparam.Civ1Bin ' -f ' filename '.cmx >' filename '.log' ]; % redirect standard output to the log file, the result file is named [filename '.nc'] by CIVx
4258%     cmd_CIV1=[cmd_CIV1 '\n' 'mv ' filename '.log' ' ' filename '.civ1.log' '\n' 'chmod g+w ' filename '.nc'];
4259%     cmd_CIV1=[cmd_CIV1 '\n' 'mv ' filename '.cmx' ' ' filename '.civ1.cmx' '\n'];%rename .cmx as .civ1.cmx, the result file is named [filename '.nc'] by CIVx
4260   
4261    cmd_CIV2=[sparam.Civ2Bin ' -f ' filename  '.cmx >' filename '.log' ]; % redirect standard output to the log file, the result file is named [filename '.nc'] by CIVx
4262    cmd_CIV2=[cmd_CIV2 '\n' 'mv ' filename '.log' ' ' filename '.civ2.log' '\n' 'chmod g+w ' filename '.nc'];
4263    cmd_CIV2=[cmd_CIV2 '\n' 'mv ' filename '.cmx' ' ' filename '.civ2.cmx' '\n'];%rename .cmx as .civ2.cmx, the result file is named [filename '.nc'] by CIVx
4264%     [Rootbat,Filebat,extbat]=fileparts(namelog);
4265%     ncName=fullfile(Rootbat,[ Filebat '.nc']);
4266%    cmd_CIV2=[cmd_CIV2 '\n' 'mv ' namelog  ' ' regexprep(namelog,'\.log','') '.civ2.log' '\n' 'chmod g+w ' ncName];
4267else
4268    filename=regexprep(filename,'\\','\\\\');
4269    cmd_CIV2=['"' sparam.Civ2Bin '" -f "' filename  '.cmx" >"' filename '.log"' ]; % redirect standard output to the log file
4270    cmd_CIV2=regexprep(cmd_CIV2,'\\','\\\\');
4271    cmd_CIV2=[cmd_CIV2 '\n' 'copy /Y "' filename '.log' '" "' filename '.civ2.log"'];
4272     cmd_CIV2=[cmd_CIV2 '\n' 'copy /Y "' filename '.cmx' '" "' filename '.civ2.cmx"'];
4273end
4274
4275
4276
4277%------------------------------------------------------------------------
4278% --- Executes on button press in HELP.
4279function HELP_Callback(hObject, eventdata, handles)
4280%------------------------------------------------------------------------
4281path_to_uvmat=which ('uvmat');% check the path of uvmat
4282pathelp=fileparts(path_to_uvmat);
4283helpfile=fullfile(pathelp,'uvmat_doc','uvmat_doc.html');
4284if isempty(dir(helpfile)), msgbox_uvmat('ERROR','Please put the help file uvmat_doc.html in the sub-directory /uvmat_doc of the UVMAT package')
4285else
4286    addpath (fullfile(pathelp,'uvmat_doc'))
4287    web([helpfile '#civ'])
4288end
4289
4290%------------------------------------------------------------------------
4291%--read images and convert them to the uint16 format used for PIV
4292function A=read_image(filename,type_ima,num,movieobject)
4293%------------------------------------------------------------------------
4294%num is the view number needed for an avi movie
4295switch type_ima
4296    case 'movie'
4297        A=read(movieobject,num);
4298    case 'avi'
4299        mov=aviread(filename,num);
4300        A=frame2im(mov(1));
4301    case 'multimage'
4302        A=imread(filename,num);
4303    case 'image'
4304        A=imread(filename);
4305end
4306siz=size(A);
4307if length(siz)==3;%color images
4308    A=sum(double(A),3);
4309    A=uint16(A);
4310end
4311
4312%------------------------------------------------------------------------
4313function ref_i_Callback(hObject, eventdata, handles)
4314%------------------------------------------------------------------------
4315mode_list=get(handles.mode,'String');
4316mode_value=get(handles.mode,'Value');
4317mode=mode_list{mode_value};
4318find_netcpair_civ1(hObject, eventdata, handles);% update the menu of pairs depending on the available netcdf files
4319if isequal(mode,'series(Di)') || ...% we do patch2 only
4320        (get(handles.CIV2,'Value')==0 && get(handles.CIV1,'Value')==0 && get(handles.FIX1,'Value')==0 && get(handles.PATCH1,'Value')==0)
4321    find_netcpair_civ2(hObject, eventdata, handles);
4322end
4323
4324%------------------------------------------------------------------------
4325function ref_j_Callback(hObject, eventdata, handles)
4326%------------------------------------------------------------------------
4327mode_list=get(handles.mode,'String');
4328mode_value=get(handles.mode,'Value');
4329mode=mode_list{mode_value};
4330if isequal(get(handles.CIV1,'Value'),0)|| isequal(mode,'series(Dj)')
4331    find_netcpair_civ1(hObject, eventdata, handles);% update the menu of pairs depending on the available netcdf files
4332end
4333if isequal(mode,'series(Dj)') || ...
4334        (get(handles.CIV2,'Value')==0 && get(handles.CIV1,'Value')==0 && get(handles.FIX1,'Value')==0 && get(handles.PATCH1,'Value')==0)
4335    find_netcpair_civ2(hObject, eventdata, handles);
4336end
4337
4338%------------------------------------------------------------------------
4339function ref_i_civ2_Callback(hObject, eventdata, handles)
4340%------------------------------------------------------------------------
4341mode_list=get(handles.mode,'String');
4342mode_value=get(handles.mode,'Value');
4343mode=mode_list{mode_value};
4344find_netcpair_civ2(hObject, eventdata, handles);% update the menu of pairs depending on the available netcdf files
4345
4346%------------------------------------------------------------------------
4347function ref_j_civ2_Callback(hObject, eventdata, handles)
4348%------------------------------------------------------------------------
4349mode_list=get(handles.mode,'String');
4350mode_value=get(handles.mode,'Value');
4351mode=mode_list{mode_value};
4352if  isequal(mode,'series(Dj)')
4353    find_netcpair_civ2(hObject, eventdata, handles);% update the menu of pairs depending on the available netcdf files
4354end
4355
4356%------------------------------------------------------------------------
4357% --- Executes on button press in compare.
4358function compare_Callback(hObject, eventdata, handles)
4359%------------------------------------------------------------------------
4360test=get(handles.compare,'Value');
4361if test==2 || test==3
4362    filebase=get(handles.RootName,'String');
4363    browse=get(handles.browse_root,'Userdata');
4364    browse.nom_type_ima1=browse.nom_type_ima;
4365    set(handles.browse_root,'UserData',browse);
4366    set(handles.sub_txt,'Visible','on')
4367    set(handles.RootName_1,'Visible','On');%mkes the second file input window visible
4368    mode_store=get(handles.mode,'String');%get the present 'mode'
4369    set(handles.compare,'UserData',mode_store);%store the mode display
4370    set(handles.mode,'Visible','off')
4371    if test==2
4372        set(handles.mode,'Visible','off')
4373    else
4374        set(handles.mode,'Visible','on')
4375    end
4376   
4377    % open an image file with the browser
4378    ind_opening=1;%default
4379    browse.incr_pair=[0 0]; %default
4380    oldfile=get(handles.RootName,'String');
4381    menu={'*.xml;*.avi;*.AVI;*.nc','(*.xml,*.avi,*.nc)'; ...
4382        '*.xml', '.xml files';'*.avi;*.AVI', '.avi files';'*.nc', '.nc files';...
4383        '*.*', 'All Files (*.*)'};
4384    [FileName, PathName, filtindex] = uigetfile( menu, 'Pick a file',oldfile);
4385    fileinput=[PathName FileName];%complete file name
4386    sizf=size(fileinput);
4387    if (~ischar(fileinput)|~isequal(sizf(1),1)),return;end %stop if fileinput not a character string
4388    [path,name,ext]=fileparts(fileinput);
4389    [path1]=fileparts(filebase);
4390    if ~strcmp(path1,path)
4391        msgbox_uvmat('ERROR','The two  input image series must be in the same directory')
4392        return
4393    end
4394    set(handles.RootName_1,'String',name);
4395    [RootPath,RootFile,field_count,str2,str_a,str_b,xx,nom_type,subdir]=name2display(name);
4396    browse=get(handles.browse_root,'UserData');
4397    browse.nom_type_ima_1=nom_type;
4398    set(handles.browse_root,'UserData',browse)
4399   
4400    %check image extension
4401    if ~strcmp(ext,get(handles.ImaExt,'String'))
4402        msgbox_uvmat('ERROR','The two  input image series must have the same extenion name')
4403        return
4404    end
4405   
4406    %check image size
4407    A=imread(fileinput);
4408    npxy=get(handles.ImaExt,'UserData');
4409    if ~isequal(npxy(1),size(A,1))|| ~isequal(npxy(2),size(A,2))
4410        msgbox_uvmat('ERROR','The two input image series must have the same size')
4411        return
4412    end
4413else
4414    set(handles.mode,'Visible','on')
4415    set(handles.RootName_1,'Visible','Off');
4416    set(handles.sub_txt,'Visible','off')
4417    set(handles.RootName_1,'String',[]);
4418    mode_store=get(handles.compare,'UserData');
4419    set(handles.mode,'String',mode_store)
4420    set(handles.test_stereo1,'Value',0)
4421    set(handles.test_stereo2,'Value',0)
4422end
4423mode_Callback(hObject, eventdata, handles)
4424
4425%------------------------------------------------------------------------
4426% --- Executes on button press in get_ref_fix1.
4427function get_ref_fix1_Callback(hObject, eventdata, handles)
4428%------------------------------------------------------------------------
4429filebase=get(handles.RootName,'String');
4430[FileName, PathName, filterindex] = uigetfile( ...
4431    {'*.nc', ' (*.nc)';
4432    '*.nc',  'netcdf files '; ...
4433    '*.*', 'All Files (*.*)'}, ...
4434    'Pick a file',filebase);
4435
4436fileinput=[PathName FileName];
4437sizf=size(fileinput);
4438if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end %stop if fileinput not a character string
4439[Path,File,field_count,str2,str_a,str_b,ref.ext,ref.nom_type,ref.subdir]=name2display(fileinput);
4440ref.filebase=fullfile(Path,File);
4441ref.num_a=stra2num(str_a);
4442ref.num_b=stra2num(str_b);
4443ref.num1=str2double(field_count);
4444ref.num2=str2double(str2);
4445browse=[];%initialisation
4446if ~isequal(ref.ext,'.nc')
4447    msgbox_uvmat('ERROR','the reference file must be in netcdf format (*.nc)')
4448    return
4449end
4450set(handles.ref_fix1,'String',[fullfile(ref.subdir,File) '....nc']);
4451set(handles.ref_fix1,'UserData',ref)
4452menu_field{1}='civ1';
4453Data=nc2struct(fileinput,[]);
4454if isfield(Data,'patch') && isequal(Data.patch,1)
4455    menu_field{2}='filter1';
4456end
4457if isfield(Data,'civ2') && isequal(Data.civ2,1)
4458    menu_field{3}='civ2';
4459end
4460if isfield(Data,'patch2') && isequal(Data.patch2,1)
4461    menu_field{4}='filter2';
4462end
4463set(handles.field_ref1,'String',menu_field);
4464set(handles.field_ref1,'Value',length(menu_field));
4465set(handles.inf_sup1,'Value',2);
4466set(handles.thresh_vel,'String','1');%default threshold
4467set(handles.ref_fix1,'Enable','on')
4468
4469%------------------------------------------------------------------------
4470% --- Executes on button press in get_ref_fix2.
4471function get_ref_fix2_Callback(hObject, eventdata, handles)
4472%------------------------------------------------------------------------
4473if isequal(get(handles.get_ref_fix2,'Value'),1)
4474    filebase=get(handles.RootName,'String');
4475    [FileName, PathName, filterindex] = uigetfile( ...
4476        {'*.nc', ' (*.nc)';
4477        '*.nc',  'netcdf files '; ...
4478        '*.*', 'All Files (*.*)'}, ...
4479        'Pick a file',filebase);
4480    fileinput=[PathName FileName];
4481    sizf=size(fileinput);
4482    if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end %stop if fileinput not a character string
4483    [Path,File,field_count,str2,str_a,str_b,ref.ext,ref.nom_type,ref.subdir]=name2display(fileinput);
4484    ref.filebase=fullfile(Path,File);
4485    ref.num_a=stra2num(str_a);
4486    ref.num_b=stra2num(str_b);
4487    ref.num1=str2num(field_count);
4488    ref.num2=str2num(str2);
4489    browse=[];%initialisation
4490    if ~isequal(ref.ext,'.nc')
4491        msgbox_uvmat('ERROR','the reference file must be in netcdf format (*.nc)')
4492        return
4493    end
4494    set(handles.ref_fix2,'String',[fullfile(ref.subdir,File) '....nc']);
4495    set(handles.ref_fix2,'UserData',ref)
4496    menu_field{1}='civ1';
4497    Data=nc2struct(fileinput,[]);
4498    if isfield(Data,'patch') & isequal(Data.patch,1)
4499        menu_field{2}='filter1';
4500    end
4501    if isfield(Data,'civ2') & isequal(Data.civ2,1)
4502        menu_field{3}='civ2';
4503    end
4504    if isfield(Data,'patch2') & isequal(Data.patch2,1)
4505        menu_field{4}='filter2';
4506    end
4507    set(handles.field_ref2,'String',menu_field);
4508    set(handles.field_ref2,'Value',length(menu_field));
4509    set(handles.inf_sup2,'Value',2);
4510    set(handles.thresh_vel2,'String','1');%default threshold
4511    set(handles.ref_fix2,'Enable','on')
4512    set(handles.ref_fix2,'Visible','on')
4513    set(handles.field_ref2,'Visible','on')
4514else
4515    set(handles.ref_fix2,'Visible','off')
4516    set(handles.field_ref2,'Visible','off')
4517end
4518
4519%------------------------------------------------------------------------
4520function ref_fix1_Callback(hObject, eventdata, handles)
4521%------------------------------------------------------------------------
4522set(handles.inf_sup1,'Value',1);
4523set(handles.field_ref1,'Value',1)
4524set(handles.field_ref1,'String',{' '})
4525set(handles.ref_fix1,'UserData',[]);
4526set(handles.ref_fix1,'String','');
4527set(handles.thresh_vel1,'String','0');
4528
4529%------------------------------------------------------------------------
4530function ref_fix2_Callback(hObject, eventdata, handles)
4531%------------------------------------------------------------------------
4532set(handles.inf_sup2,'Value',1);
4533set(handles.field_ref2,'Value',1)
4534set(handles.field_ref2,'String',{' '})
4535set(handles.ref_fix2,'UserData',[]);
4536set(handles.ref_fix2,'String','');
4537set(handles.thresh_vel2,'String','0');
4538
4539%------------------------------------------------------------------------
4540% --- Executes on button press in test_stereo1.
4541function test_stereo1_Callback(hObject, eventdata, handles)
4542%------------------------------------------------------------------------
4543if isequal(get(handles.test_stereo1,'Value'),0)
4544    set(handles.subdomain_patch1,'Visible','on')
4545    set(handles.rho_patch1,'Visible','on')
4546else
4547    set(handles.subdomain_patch1,'Visible','off')
4548    set(handles.rho_patch1,'Visible','off')
4549end
4550
4551%------------------------------------------------------------------------
4552% --- Executes on button press in test_stereo2.
4553function test_stereo2_Callback(hObject, eventdata, handles)
4554%------------------------------------------------------------------------
4555if isequal(get(handles.test_stereo2,'Value'),0)
4556    set(handles.subdomain_patch2,'Visible','on')
4557    set(handles.rho_patch2,'Visible','on')
4558else
4559    set(handles.subdomain_patch2,'Visible','off')
4560    set(handles.rho_patch2,'Visible','off')
4561end
4562
4563%------------------------------------------------------------------------
4564% --- Executes on button press in ImaThreshold.
4565function ImaThreshold_Callback(hObject, eventdata, handles)
4566%------------------------------------------------------------------------
4567if isequal(get(handles.ImaThreshold,'Value'),1)
4568    set(handles.MinIma,'Visible','on')
4569    set(handles.MaxIma,'Visible','on')
4570else
4571    set(handles.MinIma,'Visible','off')
4572    set(handles.MaxIma,'Visible','off')
4573end
4574
4575%------------------------------------------------------------------------
4576% --- Executes on button press in ImaThreshold2.
4577function ImaThreshold2_Callback(hObject, eventdata, handles)
4578%------------------------------------------------------------------------
4579if isequal(get(handles.ImaThreshold2,'Value'),1)
4580    set(handles.MinIma2,'Visible','on')
4581    set(handles.MaxIma2,'Visible','on')
4582else
4583    set(handles.MinIma2,'Visible','off')
4584    set(handles.MaxIma2,'Visible','off')
4585end
4586
4587
4588% --- Executes on button press in TestCiv1.
4589function TestCiv1_Callback(hObject, eventdata, handles)
4590test_civ1=get(handles.TestCiv1,'Value');
4591if test_civ1
4592[filecell,num1_civ1,num2_civ1,num_a_civ1,num_b_civ1,num1_civ2,num2_civ2,num_a_civ2,num_b_civ2,nom_type_nc,file_ref_fix1,file_ref_fix2]=...
4593    set_civ_filenames(handles,[1 0 0 0 0 0]);
4594Data.ListVarName={'ny','nx','A'};
4595Data.VarDimName={'ny','nx',{'ny','nx'}};
4596Data.A=imread(filecell.ima1.civ1{1});
4597Data.ny=[size(Data.A,1) 1];
4598Data.nx=[1 size(Data.A,2)];
4599hh=view_field(Data);
4600ViewData=get(hh,'UserData');
4601ViewData.axes3.B=imread(filecell.ima2.civ1{1});
4602set(hh,'UserData',ViewData)
4603end
4604
4605
4606
4607
4608
4609
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