source: trunk/src/civ.m @ 295

Last change on this file since 295 was 292, checked in by sommeria, 9 years ago

GUI civ patch2 corrected (SmoothingParam?).
uvmatand view_field updated with panels.
read_plot_param removed (replaced by the mostgeneral read_GUI)

File size: 219.1 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, 2011, LEGI / CNRS-UJF-INPG, sommeria@legi.grenoble-inp.fr
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%TODO: search range
24
25% Last Modified by GUIDE v2.5 21-Nov-2011 10:58:28
26% Begin initialization code - DO NOT EDIT
27gui_Singleton = 1;
28gui_State = struct('gui_Name',       mfilename, ...
29    'gui_Singleton',  gui_Singleton, ...
30    'gui_OpeningFcn', @civ_OpeningFcn, ...
31    'gui_OutputFcn',  @civ_OutputFcn, ...
32    'gui_LayoutFcn',  [] , ...
33    'gui_Callback',   []);
34if nargin && ischar(varargin{1})
35    gui_State.gui_Callback = str2func(varargin{1});
36end
37
38if nargout
39    [varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:});
40else
41    gui_mainfcn(gui_State, varargin{:});
42end
43% End initialization code - DO NOT EDIT
44
45%------------------------------------------------------------------------
46% --- Executes just before civ is made visible.
47function civ_OpeningFcn(hObject, eventdata, handles, param)
48%------------------------------------------------------------------------
49% This function has no output args, see OutputFcn.
50%filebase: root name
51%nom_type: nomencalture used ('png_old','_i_j'...)
52%list of field numbers to process
53%subdir: subdirectory of the opened netcdf file
54%ind_opening: operation number advised for beginning (1=checkciv1,2=checkfix1,3=checkpatch1,4=checkciv2,5=checkfix2,6=checkpatch2),
55%ind_a_opening ind_b_opening chosen pair from the opened netcdf file
56% Choose default command line output for civ
57handles.output = hObject;
58% Update handles structure
59guidata(hObject, handles);
60set(hObject,'WindowButtonDownFcn',{'mouse_alt_gui',handles}) % allows mouse action with right button (zoom for uicontrol display)
61%default initial parameters
62filebase=''; % root file name ('filebase'.civ)
63ext=[];
64
65%% read names of the .exe file to adjust the interface according to available binaries
66%path_uvmat=which('uvmat');% check the path detected for source file uvmat
67path_civ=fileparts(which('civ')); %path to civ
68addpath (path_civ) ; %add the path to UVMAT, (useful in case of change of working directory after civ has been s opened in the working directory)
69errormsg=[];%default error message
70xmlfile='PARAM.xml';
71if exist(xmlfile,'file')
72    try
73        t=xmltree(xmlfile);
74        sparam=convert(t);
75    catch
76        errormsg={' Unable to read the file PARAM.xml defining the civx binaries:'; lasterr};
77        return
78    end
79else
80    errormsg=[xmlfile ' not found: path to civx binaries undefined'];
81    return
82end
83if ~isempty(errormsg)
84    msgbox_uvmat('ERROR',errormsg);
85end
86
87test_batch=0;%default: ,no batch mode available
88if isfield(sparam,'BatchParam') && isfield(sparam.BatchParam,'BatchMode')
89    test_batch=strcmp(sparam.BatchParam.BatchMode,'sge'); %sge is currently the only implemented batch mod
90end
91if test_batch==0
92    set(handles.BATCH,'Enable','off')% put the BATCH button in grey (unactivated)
93    set(handles.BATCH,'BackgroundColor',[0.831 0.816 0.784])% put the BATCH button in grey (unactivated)
94end
95if isfield(sparam.RunParam,'CivBin')
96    if ~exist(sparam.RunParam.CivBin,'file')
97        sparam.RunParam.CivBin=fullfile(path_civ,sparam.RunParam.CivBin);
98    end
99else
100    sparam.RunParam.CivBin='';
101end
102
103%% load the list of previously browsed files in menu Open
104 dir_perso=prefdir; % path to the directory .matlab for personal data
105 profil_perso=fullfile(dir_perso,'uvmat_perso.mat');% personal data file uvmauvmat_perso.mat' in .matlab
106 if exist(profil_perso,'file')
107      h=load (profil_perso);
108      if isfield(h,'MenuFile')
109          set(handles.MenuFile_1,'Label',h.MenuFile{1})
110          %set(handles.MenuFile_1,'Label',h.MenuFile_1);
111      end
112%       if isfield(h,'MenuFile_2')
113%           set(handles.MenuFile_2,'Label',h.MenuFile_2);
114%       end
115%       if isfield(h,'MenuFile_3')
116%           set(handles.MenuFile_3,'Label',h.MenuFile_3);
117%       end
118%       if isfield(h,'MenuFile_4')
119%           set(handles.MenuFile_4,'Label',h.MenuFile_4);
120%       end
121%       if isfield(h,'MenuFile_5')
122%           set(handles.MenuFile_5,'Label',h.MenuFile_5);
123%       end
124end
125
126%default input parameters:
127num_i1=1; % set of field i numbers
128num_i2=1; % set of field i numbers
129num_j1=1; % set of field j numbers (fields a)
130num_j2=1; % second set of field j numbers (fields b)
131%subdir='A'; % subdir for the netcdf result files
132ind_opening=0; % proposed operation number (1=civ1,2=fix1,3=patch1,4=civ2,5=fix2,6=patch2)
133%load the initial parameters if the interface is started from uvmat
134if exist('param','var')&&isstruct(param)% the interface is opened from uvmat
135    filebase=param.RootName;
136    nom_type_read=param.NomType;
137    num_i1=param.num1;
138    if isnan(num_i1),num_i1=1;end
139    num_i2=param.num2;
140    if isnan(num_i2),num_i2=num_i1;end
141    num_j1=param.num_a;
142    if isnan(num_j1),num_j1=1;end
143    num_j2=param.num_b;
144    if isnan(num_j2),num_j2=num_j1;end
145    subdir=param.SubDir;
146    ind_opening=param.IndOpening;
147    ext=param.ImaExt;
148end
149browse.num_i1=num_i1;
150browse.num_i2=num_i2;
151browse.num_j1=num_j1;
152browse.num_j2=num_j2;
153if ~isempty(ext) && (~isempty(imformats(ext(2:end)))||strcmpi(ext,'.avi'));%if an image file has been opened by uvmat
154    set(handles.ImaExt,'String',ext)
155    browse.ext_ima=ext;
156    if exist('nom_type_read','var')
157        browse.nom_type_ima=nom_type_read; % the image nomenclature is stored
158    end
159elseif isequal(ext,'.nc')
160    if exist('nom_type_read','var')
161        browse.nom_type_nc=nom_type_read;% the netcdf  nomenclature is stored
162    end
163end
164set(handles.RootName,'String',filebase);
165set(handles.ImaDoc,'String',ext)
166
167%initiate advised operations
168enable_civ1(handles,0)
169enable_civ2(handles,0)
170%enable_pair1(handles,'on')
171enable_fix1(handles,0)
172enable_patch1(handles,0)
173enable_fix2(handles,0)
174enable_patch2(handles,0)
175set(handles.CheckCiv1,'Value',0)
176set(handles.CheckFix1,'Value',0)
177set(handles.CheckPatch1,'Value',0)
178set(handles.CheckCiv2,'Value',0)
179set(handles.CheckFix2,'Value',0)
180set(handles.CheckPatch2,'Value',0)
181%set(handles.frame_subdirciv2,'BackgroundColor',[0.831 0.816 0.784])
182if isequal(ind_opening,1)
183    set(handles.CheckCiv1,'Value',1)
184    enable_civ1(handles,1)
185elseif isequal(ind_opening,2)
186    set(handles.CheckFix1,'Value',1)
187    enable_fix1(handles,1)
188elseif isequal(ind_opening,3)
189    set(handles.CheckPatch1,'Value',1)
190    enable_patch1(handles,1)
191elseif isequal(ind_opening,4)
192    set(handles.CheckCiv2,'Value',1)
193    enable_civ2(handles,1)
194elseif isequal(ind_opening,5)
195    set(handles.CheckFix2,'Value',1)
196    enable_fix2(handles,1)
197    set(handles.frame_subdirciv2,'BackgroundColor',[1 1 0])
198    set(handles.ListPairCiv2,'Enable','On')
199    set(handles.ListPairCiv2,'Enable','On')
200    enable_pair1(handles,'off')
201elseif isequal(ind_opening,6)
202    set(handles.CheckPatch2,'Value',1)
203    enable_patch2(handles,1)
204    set(handles.frame_subdirciv2,'BackgroundColor',[1 1 0])
205    set(handles.ListPairCiv2,'Enable','On')
206    enable_pair1(handles,'off')
207end
208
209% set the range of fields (1:1 by default) and selected pair
210if isequal(num_i2,num_i1)
211    num_ref_i=num_i1;
212else
213    num_ref_i=floor((num_i1+num_i2)/2);
214    browse.incr_pair(1)=num_i2-num_i1;
215    browse.incr_pair(2)=0;
216end
217if isequal(num_j1,num_j2)
218    if isnan(num_j1)
219        num_ref_j=1;
220    else
221        num_ref_j=num_j1;
222    end
223else
224    num_ref_j=floor((num_j1+num_j2)/2);
225    browse.incr_pair(2)=num_j2-num_j1;
226end
227set(handles.first_i,'String',num2str(num_ref_i));
228set(handles.last_i,'String',num2str(num_ref_i));
229set(handles.first_j,'String',num2str(num_ref_j));
230set(handles.last_j,'String',num2str(num_ref_j));
231set(handles.ref_i,'String',num2str(num_ref_i));
232set(handles.ref_j,'String',num2str(num_ref_j));
233% set(handles.ref_i_civ2,'String',num2str(num_ref_i));
234% set(handles.ref_j_civ2,'String',num2str(num_ref_j));
235set(handles.RootName,'UserData',browse);
236if exist('param','var') && isfield(param,'RootName') && ~isempty(param.RootName)%varargin the interface is opened from uvmat
237    RootName_Callback(hObject, eventdata, handles);
238end
239
240%------------------------------------------------------------------------
241% --- Outputs from this function are returned to the command line.
242function varargout = civ_OutputFcn(hObject, eventdata, handles)
243%------------------------------------------------------------------------
244% varargout  cell array for returning output args (see VARARGOUT);
245% hObject    handle to figure
246% eventdata  reserved - to be defined in a future version of MATLAB
247% handles    structure with handles and user data (see GUIDATA)
248% Get default command line output from handles structure
249varargout{1} = handles.output;
250
251% --------------------------------------------------------------------
252function MenuBrowse_Callback(hObject, eventdata, handles)
253
254%get the input file properties
255filebase=get(handles.RootName,'String');
256oldfile=''; %default
257if isempty(filebase)|| isequal(filebase,'')%loads the previously stored file name and set it as default in the file_input box
258    dir_perso=prefdir;
259    profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
260    if exist(profil_perso,'file')
261        h=load (profil_perso);
262        if isfield(h,'filebase')&& ischar(h.filebase)
263            oldfile=h.filebase;
264        end
265        if isfield(h,'RootPath') && ischar(h.RootPath)
266            oldfile=h.RootPath;
267        end
268    end
269else
270    oldfile=filebase;
271end
272ind_opening=1;%default
273browse.incr_pair=[0 0]; %default
274menu={'*.xml;*.civ;*.png;*.jpg;*.tif;*.avi;*.AVI;*.nc;', ' (*.xml,*.civ,*.png,*.jpg ,.tif, *.avi,*.nc)';
275       '*.xml',  '.xml files '; ...
276        '*.civ',  '.civ files '; ...
277        '*.png','.png image files'; ...
278        '*.jpg',' jpeg image files'; ...
279        '*.tif','.tif image files'; ...
280        '*.avi;*.AVI','.avi movie files'; ...
281        '*.nc','.netcdf files'; ...
282        '*.*',  'All Files (*.*)'};
283[FileName, PathName, filtindex] = uigetfile( menu, 'Pick a file',oldfile);
284fileinput=[PathName FileName];%complete file name
285sizf=size(fileinput);
286if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end %stop if fileinput not a character string
287[path,name,ext]=fileparts(fileinput);
288testeditxml=0;
289if isequal(ext,'.xml')
290    testeditxml=1;
291    t_browse=xmltree(fileinput);
292    head_element=get(t_browse,1);
293    if isfield(head_element,'name')&& isequal(head_element.name,'ImaDoc')
294        testeditxml=0;
295    end
296end
297if testeditxml==1 || isequal(ext,'.xls')
298    heditxml=editxml({fileinput});
299    set(heditxml,'Tag','browser')
300    waitfor(heditxml,'Tag','idle')
301    if ~ishandle(heditxml)
302        return
303    end
304    attr=findobj(get(heditxml,'children'),'Tag','CurrentAttributes');
305    set(handles.browse,'UserData',fileinput)% store for future opening with browser
306    fileinput=get(attr,'UserData');
307    if ~exist(fileinput,'file')
308        return
309    end
310end
311[RootPath,RootFile,str1,str2,str_a,str_b,ext,nom_type,subdir]=name2display(fileinput);
312filebase=fullfile(RootPath,RootFile);
313num_i1=str2double(str1);
314if isnan(num_i1),num_i1=1;end
315num_i2=str2double(str2);
316if isnan(num_i2),num_i2=num_i1;end
317num_j1=stra2num(str_a);
318if isnan(num_j1),num_j1=1;end
319num_j2=stra2num(str_b);
320if isnan(num_j2),num_j2=num_j1;end
321if isequal(get(handles.ListCompareMode,'Value'),1)
322    browse=[];%initialisation
323else
324    browse=get(handlesRootName,'UserData');
325end
326browse.num_i1=num_i1;
327browse.num_i2=num_i2;
328browse.num_j1=num_j1;
329browse.num_j2=num_j2;
330if length(ext)>1 && (~isempty(imformats(ext(2:end)))||strcmpi(ext,'.avi'));%if an image file has been opened by uvmat
331    browse.nom_type_ima=nom_type;
332    browse.ext_ima=ext;
333    set(handles.ImaExt,'String',ext)
334end
335set(handles.ImaDoc,'String',ext);
336
337%%%%% read the state of the selected netcdf file to advise default operation
338if isequal(ext,'.nc')
339    browse.nom_type_nc=nom_type;
340    ind_opening=2;% propose 'fix' as the default option
341    Data=nc2struct(fileinput,'ListGlobalAttribute','CivStage','absolut_time_T0','fix','patch','civ2','fix2');
342    if ~isempty(Data.CivStage)%test for civ files
343        ind_opening=Data.CivStage;
344        set(handles.ListPairMode,'Value',3)
345    end
346    if ~isempty(Data.absolut_time_T0)%test for civx files
347        set(handles.ListPairMode,'Value',1)
348        if isfield(Data,'fix') && isequal(Data.fix,1)
349            ind_opening=3;
350        end
351        if isequal(Data.patch,1)
352            ind_opening=4;
353        end
354        if isequal(Data.civ2,1)
355            ind_opening=5;
356        end
357        if  isequal(Data.fix2,1)
358            ind_opening=6;
359        end
360        testciv=1; %TO SUPPRESS WITH NEW VERSION OF CIVX
361    else
362        ind_opening=3; %GUI used only for patch
363        testciv=0;
364    end
365    set(handles.txt_SubdirCiv1,'String',subdir);%set the default subdir directories for installing the .nc results
366    set(handles.txt_SubdirCiv2,'String',subdir);
367    browse.testciv=testciv;
368    browse.ind_opening=ind_opening;
369end
370set(handles.RootName,'String',filebase);
371set(handles.ImaDoc,'String',ext);
372if ~isempty(num_i1)
373    ref_i=num_i1;
374    if ~isempty(num_i2)
375        ref_i=floor((ref_i+num_i2)/2);% reference image number corresponding to the file
376        browse.incr_pair(1)=num_i2-num_i1;
377        browse.incr_pair(2)=0;
378    end
379    set(handles.first_i,'String',num2str(ref_i));
380    set(handles.last_i,'String',num2str(ref_i));
381    set(handles.ref_i,'String',num2str(ref_i));
382%     set(handles.ref_i_civ2,'String',num2str(ref_i))
383end
384if isempty(num_j1)
385    set(handles.ref_j,'String','1');
386    set(handles.ref_j_civ2,'String','1');
387else
388    ref_j=num_j1;
389    if ~isempty(num_j2)
390        ref_j=floor((num_j1+num_j2)/2);
391        browse.incr_pair(2)=num_j2-num_j1;
392    end
393    set(handles.first_j,'String',num2str(ref_j));
394    set(handles.last_j,'String',num2str(ref_j));
395    set(handles.ref_j,'String',num2str(ref_j));
396%     set(handles.ref_j_civ2,'String',num2str(ref_j));
397end
398
399% set default operation options
400enable_civ1(handles,0)
401enable_civ2(handles,0')
402enable_pair1(handles,'on')
403enable_fix1(handles,0)
404enable_patch1(handles,0)
405enable_fix2(handles,0)
406enable_patch2(handles,0)
407set(handles.CheckCiv1,'Value',0)
408set(handles.CheckFix1,'Value',0)
409set(handles.CheckPatch1,'Value',0)
410set(handles.CheckCiv2,'Value',0)
411set(handles.CheckFix2,'Value',0)
412set(handles.CheckPatch2,'Value',0)
413% set(handles.frame_subdirciv2,'BackgroundColor',[0.831 0.816 0.784])
414if isequal(ind_opening,1)
415    set(handles.CheckCiv1,'Value',1)
416    enable_civ1(handles,'on')
417elseif isequal(ind_opening,2)
418    set(handles.CheckFix1,'Value',1)
419    enable_fix1(handles,'on')
420elseif isequal(ind_opening,3)
421    set(handles.CheckPatch1,'Value',1)
422    enable_patch1(handles)
423elseif isequal(ind_opening,4)
424    set(handles.CheckCiv2,'Value',1)
425    enable_civ2(handles,'on')
426elseif isequal(ind_opening,5)
427    enable_pair1(handles,'off')
428    set(handles.CheckFix2,'Value',1)
429    enable_fix2(handles)
430    set(handles.frame_subdirciv2,'BackgroundColor',[1 1 0])
431    set(handles.ListPairCiv2,'Enable','On')
432    set(handles.ListPairCiv2,'Enable','On')
433elseif isequal(ind_opening,6)
434    enable_pair1(handles,'off')
435    set(handles.CheckPatch2,'Value',1)
436    enable_patch2(handles)
437    set(handles.frame_subdirciv2,'BackgroundColor',[1 1 0])
438    set(handles.ListPairCiv2,'Enable','On')
439end
440set(handles.RootName,'UserData',browse);% store information from browser
441RootName_Callback(hObject, eventdata, handles);
442
443
444% -----------------------------------------------------------------------
445% --- Open again the file whose name has been recorded in MenuFile_1
446function MenuFile_1_Callback(hObject, eventdata, handles)
447%------------------------------------------------------------------------
448fileinput=get(handles.MenuFile_1,'Label');
449display_file_name(hObject, eventdata, handles,fileinput)
450
451% -----------------------------------------------------------------------
452% --- Open again the file whose name has been recorded in MenuFile_2
453function MenuFile_2_Callback(hObject, eventdata, handles)
454%------------------------------------------------------------------------
455fileinput=get(handles.MenuFile_2,'Label');
456display_file_name(hObject, eventdata, handles,fileinput)
457
458% -----------------------------------------------------------------------
459% --- Open again the file whose name has been recorded in MenuFile_3
460function MenuFile_3_Callback(hObject, eventdata, handles)
461%------------------------------------------------------------------------
462fileinput=get(handles.MenuFile_3,'Label');
463display_file_name(hObject, eventdata, handles,fileinput)
464
465% -----------------------------------------------------------------------
466% --- Open again the file whose name has been recorded in MenuFile_4
467function MenuFile_4_Callback(hObject, eventdata, handles)
468%------------------------------------------------------------------------
469fileinput=get(handles.MenuFile_4,'Label');
470display_file_name(hObject, eventdata, handles,fileinput)
471
472% -----------------------------------------------------------------------
473% --- Open again the file whose name has been recorded in MenuFile_5
474function MenuFile_5_Callback(hObject, eventdata, handles)
475%------------------------------------------------------------------------
476fileinput=get(handles.MenuFile_5,'Label');
477display_file_name(hObject, eventdata, handles,fileinput)
478
479%------------------------------------------------------------------------
480function ImaDoc_Callback(hObject, eventdata, handles)
481%------------------------------------------------------------------------
482RootName_Callback(hObject, eventdata, handles)
483
484%------------------------------------------------------------------------
485% --- function activated when a new filebase (image series) is introduced
486function RootName_Callback(hObject, eventdata, handles)
487%------------------------------------------------------------------------
488filebase=get(handles.RootName,'String');
489display_file_name(hObject, eventdata, handles,filebase)
490
491%------------------------------------------------------------------------
492function display_file_name(hObject, eventdata, handles,filebase)
493%------------------------------------------------------------------------
494set(handles.ListCompareMode,'Visible','on')
495ext_ima='';%default
496nom_type_ima=[];%default
497field_count=1;%default
498nom_type_nc=[];
499time=[];
500TimeUnit='frame'; %default
501CoordUnit='px';%default
502pxcmx_search=[];%default
503pxcmy_search=[];%default
504
505ext_imadoc=get(handles.ImaDoc,'String');
506browse=get(handles.RootName,'UserData');%default
507if isfield(browse,'nom_type_ima')
508    nom_type_ima=browse.nom_type_ima;% get an image nomenclature type already determined by an input image name
509end
510if isfield(browse,'ext_ima')
511    ext_ima=browse.ext_ima;
512end
513if isfield(browse,'nom_type_nc')
514    nom_type_nc=browse.nom_type_nc;% get an image nomenclature type already determined by an input image name
515end
516if isfield(browse,'num_i1')
517    field_count=browse.num_i1;% get an image index type already determined by an input file
518end
519set(handles.civ,'UserData',[]); %refresh list of previous civ files (for STATUS)
520
521%default first_i and j and increments
522first_i=str2double(get(handles.first_i,'String'));%value possibly set by uvmat_Opening
523if isnan(first_i)|| first_i < 1
524    first_i=1; %default first_i
525end
526last_i=str2double(get(handles.last_i,'String'));
527if isnan(last_i)|| last_i < first_i
528    last_i=first_i;  %default last_i
529end
530first_j=str2double(get(handles.first_j,'String'));
531if isnan(first_j)|| first_j < 1
532    first_j=1; %default first_j
533end
534last_j=str2double(get(handles.last_j,'String'));
535if isnan(last_j)|| last_j < first_j
536    last_j=first_j; %default last_j
537end
538incr_i=str2double(get(handles.incr_i,'String'));
539if isnan(incr_i) || incr_i < 1;
540    set(handles.incr_i,'String','1') %default incr_i
541end
542incr_j=str2double(get(handles.incr_j,'String'));
543if isnan(incr_j) || incr_j < 1;
544    set(handles.incr_j,'String','1') %default incr_j
545end
546dt=[];%default
547testmode=0;%default
548nbfield=[]; %default
549nburst=[];%default
550pxcmx=1;
551pxcmy=1;
552
553%look for an image documentation file
554if ~strcmp(ext_imadoc,'.xml') && ~strcmp(ext_imadoc,'.civ')&& ~strcmpi(ext_imadoc,'.avi')
555    if exist([filebase '.xml'],'file')
556        ext_imadoc='.xml';
557    elseif exist([filebase '.civxml'],'file')
558        ext_imadoc='.civxml';
559    elseif exist([filebase '.civ'],'file')
560        ext_imadoc='.civ';
561    elseif exist([filebase '.avi'],'file')
562        ext_imadoc='.avi';
563    elseif exist([filebase '.AVI'],'file')
564        ext_imadoc='.AVI';
565    end
566    set(handles.ImaDoc,'String',ext_imadoc)
567end
568
569%%%%%%%%   read image documentation file  %%%%%%%%%%%%%%%%%%%%%%%%%%%
570mode=''; %default
571set(handles.ImaDoc,'BackgroundColor',[1 1 0])
572drawnow
573if isequal(ext_imadoc,'.civxml') || isequal(ext_imadoc,'.xml')|| isequal(ext_imadoc,'.civ')
574    set(handles.ref_i,'Visible','On')%use a reference index
575    set(handles.ref_j,'Visible','On')
576elseif isequal(ext_imadoc,'.avi') || isequal(ext_imadoc,'.AVI')
577    set(handles.ref_j,'Visible','Off')
578else
579    set(handles.ref_i,'Visible','Off')
580    set(handles.ref_j,'Visible','Off')
581end
582testima_xml=0;
583if isequal(ext_imadoc,'.civxml')%TO ABANDON
584    [nbfield,nbfield2,time]=read_civxml([filebase '.civxml']);
585    mode='pair j1-j2';
586    if isempty(nom_type_ima)% dtermine types by default if not already selected by browser or uvmat
587        nom_type_ima='_i_j';
588    end
589elseif isequal(ext_imadoc,'.xml')
590    [XmlData,warntext]=imadoc2struct([filebase '.xml']);
591    ext_ima_read=[];
592    nom_type_read=[];
593    if isfield(XmlData,'Heading')&&isfield(XmlData.Heading','ImageName')&&ischar(XmlData.Heading.ImageName)% get image nom type and extension from the xml file
594        [PP,FF,fc,str2,str_a,str_b,ext_ima_read,nom_type_read]=name2display(XmlData.Heading.ImageName);
595        fullname=fullfile(fileparts(filebase),XmlData.Heading.ImageName); %full name (including path) of the first image defined by the xmle file,
596        if ~exist(fullname,'file')
597            msgbox_uvmat('WARNING',['FirstImage ' fullname ' defined in the xml file does not exist'])
598        end
599    end
600    if isfield(XmlData,'Time')
601        time=XmlData.Time;
602        nbfield=size(time,1);
603        nbfield2=size(time,2);
604        %transform .Time to a column vector if it is a line vector thenomenclature uses a single index: correct possible bug in xml
605        if isequal(nbfield,1) && ~isequal(nbfield2,1)% .Time is a line vector
606            if numel(nom_type_read)>=2 && isempty(regexp(nom_type_read(2:end),'\D'))
607                time=time';
608                nbfield=nbfield2;
609                nbfield2=1;
610            end
611        end
612    end
613    if isfield(XmlData,'TimeUnit')
614        TimeUnit=XmlData.TimeUnit;
615    end
616    if isfield(XmlData,'Npx')
617        npx=XmlData.Npx;
618        npy=XmlData.Npy;
619    end
620    pxcmx_search=1;
621    pxcmy_search=1;
622    if isfield(XmlData,'GeometryCalib')
623        tsai=XmlData.GeometryCalib;
624        if isfield(tsai,'f') && isfield(tsai,'Tz') && isfield(tsai,'dpx') && isfield(tsai,'dpy')&& isfield(tsai,'R')
625            rot2D=tsai.R(1:2,[1,2]);
626            pxcmx_search=tsai.f * sqrt(det(rot2D))/(tsai.Tz*tsai.dpx);
627            pxcmy_search=tsai.f * sqrt(det(rot2D))/(tsai.Tz*tsai.dpy);
628        end
629        if isfield(tsai,'CoordUnit')
630            CoordUnit=tsai.CoordUnit;
631        end
632    end
633elseif strcmp(ext_imadoc,'.civ')% case of .civ image documentation file
634    [error,time,TimeUnit,mode,npx,npy]=read_imatext([filebase '.civ']);
635    if error==2, msgbox_uvmat('WARNING',['no file ' filebase '.civ']);
636    elseif error==1, msgbox_uvmat('WARNING','inconsistent number of fields in the .civ file');
637    end
638    nom_type_ima='001a';
639elseif strcmpi(ext_imadoc,'.avi')
640    nom_type_ima='*';
641    ext_ima=ext_imadoc;
642    set(handles.ListPairMode,'Value',1);
643    set(handles.ListPairMode,'String',{'series(Di)'})
644    dt=0.04;%default
645    if exist([filebase ext_imadoc],'file')==2
646        info=aviinfo([filebase ext_imadoc]);%read infos on the avi movie
647        dt=1/info.FramesPerSecond;%time interval between successive frames
648        nbfield=info.NumFrames;%number of frames
649    end
650    time=(dt*(0:nbfield-1))';%list of image times
651end
652if isempty(time)
653    set(handles.ImaDoc,'String',''); %xml file not used for timing
654end
655set(handles.ImaDoc,'BackgroundColor',[1 1 1])
656
657%get the imabe nomenclature type if not defined by the input file nor by the xml file
658dirima=[];%default
659if isempty(nom_type_ima)
660    %look for double image series '_i_j'
661    dirima=dir([filebase '_' num2str(first_i) '_' num2str(first_j) '.*']);
662    if isempty(dirima)
663        % look for images series  with sub marker '_'
664        dirima=dir([filebase '_*' num2str(first_i) '.*']);
665        if isempty(dirima)
666            % look for other images series
667            dirima=dir([filebase '*' num2str(first_i) '.*']);
668            if isempty(dirima)
669                % look for other images series witth letter appendix
670                appendix=char(96+first_j);
671                dirima=dir([filebase '*' num2str(first_i) appendix '.*']);
672            end
673        end
674    end
675end
676for ilist=1:numel(dirima)
677    [pp,ff,fc,str2,str_a,str_b,ext_list,nom_type_list]=name2display(dirima(ilist).name);
678    form=imformats(ext_list(2:end));
679    if ~isempty(form)% if the extension corresponds to an image format recognized by Matlab
680        ext_ima=ext_list;
681        nom_type_ima=nom_type_list;
682            break
683    end
684end
685% no image documentation file found: look for a series of existing files,images by priority or .nc files
686if isempty(nom_type_ima)
687    ext_search=ext_imadoc;
688    nom_type_search=nom_type_nc;
689else
690    ext_search=ext_ima;
691    nom_type_search=nom_type_ima;
692end
693if isempty(time) && ~strcmp(nom_type_search,'none') && ~strcmp(nom_type_search,'') && ~strcmp(nom_type_search,'*')
694    subdir=get(handles.txt_SubdirCiv1,'String');
695    incr_pair=[0 0];%default
696    if isfield(browse,'incr_pair')
697        incr_pair=browse.incr_pair;
698    end
699    %     nbdetect=0;%test of detected images
700    field_i=browse.num_i2;
701    imagename=name_generator(filebase,field_i,1,ext_search,nom_type_search);
702    imagename_plus='';
703    idetect=1;
704    while idetect %look for the maximum file number in the series
705        imagename_plus=name_generator(filebase,field_i+1,1,ext_search,nom_type_search);
706        idetect=(exist(imagename_plus,'file')==2)&& ~strcmp(imagename,imagename_plus);
707        if idetect
708            field_i=field_i+1;
709        end
710        %SEE CASE OF NETCDF FILES
711        %             nbdetect=nbdetect+(exist(imagename,'file')==2);
712    end
713    nbfield=field_i;% last detected field number
714    field_i=browse.num_i1;%look for the minimum file number in the series
715    imagename_min='';
716    idetect=1;
717    while idetect==1
718        imagename_min=name_generator(filebase,field_i-1,1,ext_search,nom_type_search);
719        idetect=(exist(imagename_min,'file')==2)&& ~strcmp(imagename,imagename_min);
720        if idetect
721            field_i=field_i-1;
722        end
723    end
724    first_i=max(field_i,1);
725    if numel(regexp(nom_type_search,'\D'))>=1%two indices i and j
726        field_i=browse.num_i1;
727        field_j=browse.num_j2;
728        imagename=name_generator(filebase,field_i,field_j,ext_search,nom_type_search);
729        imagename_plus='';
730        jdetect=1;
731        while jdetect==1 %look for the maximum file number in the series
732            imagename_plus=name_generator(filebase,field_i,field_j+1,ext_search,nom_type_search);
733            jdetect=(exist(imagename_plus,'file')==2)&& ~strcmp(imagename,imagename_plus);
734            if jdetect
735                field_j=field_j+1;
736            end
737            %SEE CASE OF NETCDF FILES
738            %             nbdetect=nbdetect+(exist(imagename,'file')==2);
739        end
740        nbfield2=field_j;% last detected field number
741     end
742 
743    %determine the set of times and possible intervals for CIV
744    %   dt=(1/1000)*str2double(get(handles.dt,'String'));
745    time=(0:nbfield-1)';% time=file index -1  by default
746    if numel(regexp(nom_type_search,'\D'))>=1%two indices i and j
747        [x,y]=meshgrid(0:nbfield2-1,0:nbfield-1);
748        time=x+y;
749    end
750end
751
752if exist('time','var')
753    if size(time,1)+size(time,2)>=3 % if there are at least two time values to define dt
754        nbfield=size(time,1);
755        nbfield2=size(time,2);
756        set(handles.ImaDoc,'UserData',time); %store the set of times
757        set(handles.dt_unit,'String',['dt in m' TimeUnit]);
758%         set(handles.dt_unit_civ2,'String',['dt in m' TimeUnit]);
759        set(handles.TimeUnit,'String',TimeUnit);
760        set(handles.nb_field,'String',num2str(nbfield));
761        set(handles.nb_field2,'String',num2str(nbfield2));
762    end
763end
764set(handles.CoordUnit,'String',CoordUnit)
765set(handles.SearchRange,'UserData',[pxcmx_search pxcmy_search]);
766% npxy=[npy npx];
767set(handles.ImaExt,'String',ext_ima)
768set(handles.first_i,'String',num2str(first_i));
769set(handles.last_i,'String',num2str(last_i));%
770set(handles.first_j,'String',num2str(first_j));
771set(handles.last_j,'String',num2str(last_j));%
772browse.nom_type_ima=nom_type_ima;
773set(handles.RootName,'UserData',browse)% store the nomenclature type
774
775%%  set the menus of image pairs and default selection for civ   %%%%%%%%%%%%%%%%%%%
776test_ima_i=numel(nom_type_ima)>1 && isempty(regexp(nom_type_ima(2:end),'\D','once'));%images with single indexing
777if test_ima_i || isequal(nom_type_nc,'_i1-i2')||~(exist('nbfield2','var')&&(nbfield2~=1))
778    set(handles.ListPairMode,'Value',1)
779    set(handles.ListPairMode,'String',{'series(Di)'})   
780elseif (nbfield==1)% simple series in j
781    set(handles.ListPairMode,'Value',1)
782    set(handles.ListPairMode,'String',{'series(Dj)'})
783else
784    set(handles.ListPairMode,'String',{'pair j1-j2';'series(Dj)';'series(Di)'})%multiple choice
785    if nbfield2 <= 10
786        set(handles.ListPairMode,'Value',1)% advice 'pair j1-j2' for small burst
787    end
788end
789
790
791%% desable status and RUN button
792set(handles.RUN, 'Enable','On')
793set(handles.RUN,'BackgroundColor',[1 0 0])
794set(handles.BATCH,'Enable','On')
795set(handles.BATCH,'BackgroundColor',[1 0 0])
796if isfield(handles,'status')
797set(handles.status,'Value',0);%suppress status display
798status_Callback(hObject, eventdata, handles)
799end
800
801%% store the root input filename for future opening
802dir_perso=prefdir;
803profil_perso=fullfile(prefdir,'uvmat_perso.mat');
804RootPath=fileparts(filebase);
805if exist(profil_perso,'file')
806    save (profil_perso,'RootPath','-append'); %store the root name for future opening of uvmat
807else
808    txt=ver('MATLAB');
809    Release=txt.Release;
810    relnumb=str2double(Release(3:4));
811    if relnumb >= 14
812        save (profil_perso,'RootPath','-V6'); %store the root name for future opening of uvmat
813    else
814        save (profil_perso,'RootPath'); %store the root name for future opening of uvmat
815    end
816end
817
818%% update the subdir
819pathdir=fileparts(filebase);%path to the current xml file
820listot=dir(pathdir);
821idir=0;
822listdir={''};%default
823for ilist=1:length(listot)
824    if listot(ilist).isdir
825        name=listot(ilist).name;
826        if ~isequal(name,'.') && ~isequal(name,'..')
827            idir=idir+1;
828            listdir{idir,1}=listot(ilist).name;
829        end
830    end
831end
832set(handles.ListSubdirCiv1,'Value',1)
833set(handles.ListSubdirCiv2,'Value',1)
834set(handles.ListSubdirCiv1,'String',[listdir;'new...'])
835set(handles.ListSubdirCiv2,'String',[listdir;'new...'])
836if isempty(listdir)
837    dirname=listdir{1};
838else
839    dirname='CIV'; %default civ directory name
840end
841set(handles.txt_SubdirCiv1,'String',dirname)
842set(handles.txt_SubdirCiv2,'String',dirname)
843%check wether the current subdir exists:
844% txt_SubdirCiv1=get(handles.txt_SubdirCiv1,'String');
845% txt_SubdirCiv2=get(handles.txt_SubdirCiv2,'String');
846
847ListPairMode_Callback(hObject, eventdata, handles)
848
849%------------------------------------------------------------------------
850% --- Executes on button press in ListPairMode.
851function ListPairMode_Callback(hObject, eventdata, handles)
852%------------------------------------------------------------------------
853browse=get(handles.RootName,'UserData');
854compare_list=get(handles.ListCompareMode,'String');
855val=get(handles.ListCompareMode,'Value');
856compare=compare_list{val};
857if strcmp(compare,'displacement')
858    mode='displacement';
859else
860    mode_list=get(handles.ListPairMode,'String');
861    if ischar(mode_list)
862        mode_list={mode_list};
863    end
864    mode_value=get(handles.ListPairMode,'Value');
865    mode=mode_list{mode_value};
866end
867displ_num=[];%default
868ref_i=str2double(get(handles.ref_i,'String'));
869% last_i=str2num(get(handles.last_i,'String'));
870time=get(handles.ImaDoc,'UserData'); %get the set of times
871siztime=size(time);
872nbfield=siztime(1);
873nbfield2=siztime(2);
874indchosen=1;  %%first pair selected by default
875if isequal(mode,'pair j1-j2')%| isequal(mode,'st_pair j1-j2')
876    dt=1;
877    displ='';
878    index=0;
879    numlist_a=[];
880    numlist_B=[];
881    %get all the time intervals in bursts
882    displ_dt=1;%default
883    nbfield2=min(nbfield2,10);%limitate the number of pairs to 10x10
884    for numod_a=1:nbfield2-1 %nbfield2 always >=2 for 'pair j1-j2' mode
885        for numod_b=(numod_a+1):nbfield2
886            index=index+1;
887            numlist_a(index)=numod_a;
888            numlist_b(index)=numod_b;
889            if ~isempty(time)
890                dt(numod_a,numod_b)=time(ref_i,numod_b)-time(ref_i,numod_a);%first time interval dt
891                displ_dt(index)=dt(numod_a,numod_b);
892            else
893                displ_dt(index)=1;
894            end
895        end
896    end
897    [dtsort,indsort]=sort(displ_dt);
898    if ~isempty(numlist_a)
899        displ_num(1,:)=numlist_a(indsort);
900        displ_num(2,:)=numlist_b(indsort);
901    end
902    displ_num(3,:)=0;
903    displ_num(4,:)=0;
904    set(handles.jtext,'Visible','Off')
905    set(handles.first_j,'Visible','Off')
906    set(handles.last_j,'Visible','Off')
907    set(handles.incr_j,'Visible','Off')
908    set(handles.nb_field2,'Visible','Off')
909    set(handles.ref_j,'Visible','Off')
910elseif isequal(mode,'series(Dj)') %| isequal(mode,'st_series(Dj)')
911    for index=1:min(nbfield2-1,200)
912        displ_num(1,index)=-floor(index/2);
913        displ_num(2,index)=ceil(index/2);
914        displ_num(3,index)=0;
915        displ_num(4,index)=0;
916    end
917    set(handles.jtext,'Visible','On')
918    set(handles.first_j,'Visible','On')
919    set(handles.last_j,'Visible','On')
920    set(handles.incr_j,'Visible','On')
921    set(handles.nb_field2,'Visible','On')
922    set(handles.ref_j,'Visible','On')
923    if nbfield > 1
924        set(handles.itext,'Visible','On')
925        set(handles.first_i,'Visible','On')
926        set(handles.last_i,'Visible','On')
927        set(handles.incr_i,'Visible','On')
928        set(handles.nb_field,'Visible','On')
929        set(handles.ref_i,'Visible','On')
930    else
931        set(handles.itext,'Visible','Off')
932        set(handles.first_i,'Visible','Off')
933        set(handles.last_i,'Visible','Off')
934        set(handles.incr_i,'Visible','Off')
935        set(handles.nb_field,'Visible','Off')
936        set(handles.ref_i,'Visible','Off')
937    end
938elseif isequal(mode,'series(Di)') %| isequal(mode,'st_series(Di)')
939    for index=1:200%min(nbfield-1,200)
940        displ_num(1,index)=0;
941        displ_num(2,index)=0;
942        displ_num(3,index)=-floor(index/2);
943        displ_num(4,index)=ceil(index/2);
944    end
945    set(handles.itext,'Visible','On')
946    set(handles.first_i,'Visible','On')
947    set(handles.last_i,'Visible','On')
948    set(handles.incr_i,'Visible','On')
949    set(handles.nb_field,'Visible','On')
950    set(handles.ref_i,'Visible','On')
951    if nbfield2 > 1
952        set(handles.jtext,'Visible','On')
953        set(handles.first_j,'Visible','On')
954        set(handles.last_j,'Visible','On')
955        set(handles.incr_j,'Visible','On')
956        set(handles.nb_field2,'Visible','On')
957        set(handles.ref_j,'Visible','On')
958    else
959        set(handles.jtext,'Visible','Off')
960        set(handles.first_j,'Visible','Off')
961        set(handles.last_j,'Visible','Off')
962        set(handles.incr_j,'Visible','Off')
963        set(handles.nb_field2,'Visible','Off')
964        set(handles.ref_j,'Visible','Off')
965    end
966elseif isequal(mode,'displacement')%the pairs have the same indices
967    displ_num(1,1)=0;
968    displ_num(2,1)=0;
969    displ_num(3,1)=0;
970    displ_num(4,1)=0;
971    if nbfield > 1
972        set(handles.itext,'Visible','On')
973        set(handles.first_i,'Visible','On')
974        set(handles.last_i,'Visible','On')
975        set(handles.incr_i,'Visible','On')
976        set(handles.nb_field,'Visible','On')
977        set(handles.ref_i,'Visible','On')
978    else
979        set(handles.itext,'Visible','Off')
980        set(handles.first_i,'Visible','Off')
981        set(handles.last_i,'Visible','Off')
982        set(handles.incr_i,'Visible','Off')
983        set(handles.nb_field,'Visible','Off')
984        set(handles.ref_i,'Visible','Off')
985    end
986    if nbfield2 > 1
987        set(handles.jtext,'Visible','On')
988        set(handles.first_j,'Visible','On')
989        set(handles.last_j,'Visible','On')
990        set(handles.incr_j,'Visible','On')
991        set(handles.nb_field2,'Visible','On')
992        set(handles.ref_j,'Visible','On')
993    else
994        set(handles.jtext,'Visible','Off')
995        set(handles.first_j,'Visible','Off')
996        set(handles.last_j,'Visible','Off')
997        set(handles.incr_j,'Visible','Off')
998        set(handles.nb_field2,'Visible','Off')
999        set(handles.ref_j,'Visible','Off')
1000    end
1001end
1002set(handles.ListPairCiv1,'UserData',displ_num);
1003find_netcpair_civ1(hObject, eventdata, handles)
1004find_netcpair_civ2(hObject, eventdata, handles)
1005
1006%------------------------------------------------------------------------
1007% determine the menu for checkciv1 pairs depending on existing netcdf file at the middle of
1008% the field series set by first_i, incr, last_i
1009function find_netcpair_civ1(handles)
1010%------------------------------------------------------------------------
1011set(gcf,'Pointer','watch')
1012%nomenclature types
1013filebase=get(handles.RootName,'String');
1014[filepath,Nme,ext_dir]=fileparts(filebase);
1015browse=get(handles.RootName,'UserData');
1016compare_list=get(handles.ListCompareMode,'String');
1017val=get(handles.ListCompareMode,'Value');
1018compare=compare_list{val};
1019if strcmp(compare,'displacement')
1020    mode='displacement';
1021else
1022    mode_list=get(handles.ListPairMode,'String');
1023    mode_value=get(handles.ListPairMode,'Value');
1024    if isempty(mode_list)
1025        return
1026    end
1027    mode=mode_list{mode_value};
1028end
1029
1030% nomenclature type of the .nc files
1031nom_type_ima=[];%default
1032if isfield(browse,'nom_type_ima')
1033    nom_type_ima=browse.nom_type_ima;
1034end
1035
1036%determine nom_type_nc:
1037nom_type_nc=[];%default
1038if isfield(browse,'nom_type_nc')
1039    nom_type_nc=browse.nom_type_nc;
1040end
1041if isempty(nom_type_nc)
1042    [nom_type_nc]=nomtype2pair(nom_type_ima,isequal(mode,'series(Di)'),isequal(mode,'series(Dj)'));
1043end
1044browse.nom_type_nc=nom_type_nc;
1045set(handles.RootName,'UserData',browse)
1046
1047%reads .nc subdirectoy and image numbers from the interface
1048subdir_civ1=get(handles.txt_SubdirCiv1,'String');%subdirectory subdir_civ1 for the netcdf data
1049ref_i=str2double(get(handles.ref_i,'String'));
1050if isequal(mode,'pair j1-j2')%|isequal(mode,'st_pair j1-j2')
1051    ref_j=0;
1052else
1053    ref_j=str2double(get(handles.ref_j,'String'));
1054end
1055time=get(handles.ImaDoc,'UserData');%get the set of times
1056if isempty(time)
1057    time=[0 1];
1058end
1059dt_unit=1000;%default
1060displ_num=get(handles.ListPairCiv1,'UserData');
1061
1062%eliminate the first pairs inconsistent with the position
1063if isempty(displ_num)
1064    nbpair=0;
1065else
1066    nbpair=length(displ_num(1,:));%nbre of displayed pairs
1067    if  isequal(mode,'series(Di)')  %| isequal(mode,'st_series(Di)')
1068        nbpair=min(2*ref_i-1,nbpair);%limit the number of pairs with positive first index
1069    elseif  isequal(mode,'series(Dj)')% | isequal(mode,'st_series(Dj)')
1070        nbpair=min(2*ref_j-1,nbpair);%limit the number of pairs with positive first index
1071    end
1072end
1073nbpair=min(200,nbpair);%limit the number of displayed pairs to 200
1074
1075%look for existing processed pairs involving the field at the middle of the series if checkciv1 will not
1076% be performed, while the result is needed for next steps.
1077displ_pair={''};
1078select=ones(size(1:nbpair));%flag for displayed pairs =1 for display
1079testpair=0;
1080% case with no checkciv1 operation, netcdf files need to exist for reading
1081if get(handles.CheckCiv1,'Value')==0 %
1082    if ~exist(fullfile(filepath,subdir_civ1,ext_dir),'dir')
1083        msgbox_uvmat('ERROR',['no civ1 file available: subdirectory ' subdir_civ1 ' does not exist']);
1084        set(handles.ListPairCiv1,'String',{});
1085        return
1086    end
1087    for ipair=1:nbpair
1088        filename=name_generator(filebase,ref_i+displ_num(3,ipair),ref_j+displ_num(1,ipair),'.nc',nom_type_nc,1,...
1089            ref_i+displ_num(4,ipair),ref_j+displ_num(2,ipair),subdir_civ1);
1090        select(ipair)=exist(filename,'file')==2;% put flag to 0 if the file does not exist
1091    end   
1092    % case of no displayed pair
1093    if isequal(select,zeros(size(1:nbpair)))
1094        if isfield(browse,'incr_pair') && ~isequal(browse.incr_pair,[0 0])
1095            num_i1=ref_i-floor(browse.incr_pair(1)/2);
1096            num_i2=ref_i+ceil(browse.incr_pair(1)/2);
1097            num_j1=ref_j-floor(browse.incr_pair(2)/2);
1098            num_j2=ref_j+ceil(browse.incr_pair(2)/2);
1099            filename=name_generator(filebase,num_i1,num_j1,'.nc',nom_type_nc,1,num_i2,num_j2,subdir_civ1);
1100            select(1)=exist(filename,'file')==2;
1101            testpair=1;
1102        else
1103            if  isequal(mode,'series(Dj)')% | isequal(mode,'st_series(Dj)')
1104                msgbox_uvmat('ERROR',['no civ1 file available for the selected reference index j=' num2str(ref_j) ' and subdirectory ' subdir_civ1]);
1105            else
1106                msgbox_uvmat('ERROR',['no civ1 file available for the selected reference index i=' num2str(ref_i) ' and subdirectory ' subdir_civ1]);
1107            end
1108            set(handles.ListPairCiv1,'String',{''});
1109            %COMPLETER CAS STEREO
1110            return
1111        end
1112    end
1113end
1114if isequal(mode,'series(Di)') %| isequal(mode,'st_series(Di)')
1115    if testpair
1116        displ_pair{1}=['Di= ' num2str(-floor(browse.incr_pair(1)/2)) '|' num2str(ceil(browse.incr_pair(1)/2))];
1117    else
1118        for ipair=1:nbpair
1119            if select(ipair)
1120                if size(time,1)>=ref_i+displ_num(4,ipair) && size(time,2)>=ref_j+displ_num(2,ipair)
1121                    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
1122                    displ_pair{ipair}=['Di= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2)) ' :dt= ' num2str(dt*1000)];
1123                else
1124                    displ_pair{ipair}='...'; %pair not displayed in the menu
1125                end
1126            end
1127        end
1128    end
1129elseif isequal(mode,'series(Dj)')%|isequal(mode,'st_series(Dj)')% series on the j index
1130    if testpair
1131        displ_pair{1}=['Dj= ' num2str(-floor(browse.incr_pair(1)/2)) '|' num2str(ceil(browse.incr_pair(1)/2))];
1132    else
1133        for ipair=1:nbpair
1134            if select(ipair)
1135                if size(time,1)>=ref_i+displ_num(4,ipair) && size(time,2)>=ref_j+displ_num(2,ipair)
1136                    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
1137                    displ_pair{ipair}=['Dj= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2)) ' :dt= ' num2str(dt*1000)];
1138                end
1139            elseif testpair
1140                displ_pair{1}=['Dj= ' num2str(-floor(browse.incr_pair(2)/2)) '|' num2str(ceil(browse.incr_pair(2)/2))];
1141            else
1142                displ_pair{ipair}='...'; %pair not displayed in the menu
1143            end
1144        end
1145    end
1146elseif isequal(mode,'pair j1-j2')%|isequal(mode,'st_pair j1-j2')%case of pairs
1147    for ipair=1:nbpair
1148        if select(ipair)
1149            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
1150            displ_pair{ipair}=['j= ' num2stra(displ_num(1,ipair),nom_type_ima) '-' num2stra(displ_num(2,ipair),nom_type_ima) ...
1151                ' :dt= ' num2str(dt*1000)];
1152        else
1153            displ_pair{ipair}='...'; %pair not displayed in the menu
1154        end
1155    end
1156elseif isequal(mode,'displacement')
1157    displ_pair={'Di=Dj=0'};
1158end
1159set(handles.ListPairCiv1,'String',displ_pair');
1160ichoice=find(select,1);
1161if (isempty(ichoice) || ichoice < 1); ichoice=1; end;
1162initial=get(handles.ListPairCiv1,'Value');%initial choice of pair
1163if initial>nbpair
1164    set(handles.ListPairCiv1,'Value',ichoice);% first valid pair proposed by default in the menu
1165end
1166if numel(select)>=initial && ~isequal(select(initial),1)
1167    set(handles.ListPairCiv1,'Value',ichoice);% first valid pair proposed by default in the menu
1168end
1169
1170%set(handles.ListPairCiv2,'String',displ_pair');
1171initial=get(handles.ListPairCiv2,'Value');
1172if initial>length(displ_pair')%|~isequal(select(initial),1)
1173    if ichoice <= length(displ_pair')
1174        set(handles.ListPairCiv2,'Value',ichoice);% same pair proposed by default for civ2
1175    else
1176        set(handles.ListPairCiv2,'Value',1);% same pair proposed by default for civ2
1177    end
1178end
1179set(handles.ListPairCiv2,'String',displ_pair');
1180set(gcf,'Pointer','arrow')
1181
1182%------------------------------------------------------------------------
1183% determine the menu for checkciv2 pairs depending on the existing netcdf file at the
1184%middle of the series set by first_i, incr, last_i
1185function find_netcpair_civ2(handles)
1186%------------------------------------------------------------------------
1187set(gcf,'Pointer','watch')
1188%nomenclature types
1189filebase=get(handles.RootName,'String');
1190[filepath,Nme,ext_dir]=fileparts(filebase);
1191browse=get(handles.RootName,'UserData');
1192compare_list=get(handles.ListCompareMode,'String');
1193val=get(handles.ListCompareMode,'Value');
1194compare=compare_list{val};
1195if strcmp(compare,'displacement')
1196    mode='displacement';
1197else
1198    mode_list=get(handles.ListPairMode,'String');
1199    if isempty(mode_list)
1200        msgbox_uvmat('ERROR','please enter an input image or netcdf file')
1201        return
1202    end
1203    mode_value=get(handles.ListPairMode,'Value');
1204    mode=mode_list{mode_value};
1205end
1206
1207% nomenclature type of the .nc files
1208nom_type_ima='ima_num';%default
1209if isfield(browse,'nom_type_ima')
1210    nom_type_ima=browse.nom_type_ima;
1211end
1212nom_type_nc='_i1-i2';%default
1213if isfield(browse,'nom_type_nc')
1214    nom_type_nc=browse.nom_type_nc;
1215end
1216if isequal(nom_type_ima,'png_old') || isequal(nom_type_ima,'netc_old')|| isequal(nom_type_ima,'raw_SMD')|| isequal(nom_type_nc,'netc_old')
1217    nom_type_nc='netc_old';%nom_type for the netcdf files
1218elseif isequal(nom_type_ima,'none')||isequal(nom_type_nc,'none')
1219    nom_type_nc='none';
1220elseif isequal(nom_type_ima,'avi')||isequal(nom_type_ima,'_i')||isequal(nom_type_ima,'ima_num')||isequal(nom_type_nc,'_i1-i2')
1221    nom_type_nc='_i1-i2';
1222else
1223    if  isequal(mode,'series(Di)')%|isequal(mode,'st_series(Di)')
1224        nom_type_nc='_i1-i2_j'; % PIV in volume
1225    else
1226        nom_type_nc='_i_j1-j2';
1227    end
1228end
1229browse.nom_type_nc=nom_type_nc;
1230set(handles.RootName,'UserData',browse)
1231
1232%reads .nc subdirectory and image numbers from the interface
1233subdir_civ1=get(handles.txt_SubdirCiv1,'String');%subdirectory subdir_civ1 for the netcdf data
1234subdir_civ2=get(handles.txt_SubdirCiv2,'String');%subdirectory subdir_civ2 for the netcdf data
1235% first_i=str2num(get(handles.first_i,'String'));
1236% last_i=str2num(get(handles.last_i,'String'));
1237% incr=str2num(get(handles.incr_i,'String'));
1238% num1=first_i:incr:last_i;
1239% if isempty(num1)
1240%     set(handles.ListPairCiv2,'Value',1);
1241%     set(handles.ListPairCiv2,'String',{''});
1242%     return
1243% end
1244ref_i=str2double(get(handles.ref_i,'String'));
1245if isequal(mode,'pair j1-j2')%|isequal(mode,'st_pair j1-j2')
1246    ref_j=0;
1247else
1248    ref_j=str2double(get(handles.ref_j,'String'));
1249end
1250time=get(handles.ImaDoc,'UserData'); %get the set of times
1251if isempty(time)
1252    time=[0 1];%default
1253end
1254%dt_unit=str2num(get(handles.dt,'String'));% used when there is no image documentation file
1255%dt_unit=1000;
1256displ_num=get(handles.ListPairCiv1,'UserData');
1257
1258
1259%eliminate the first pairs inconsistent with the position
1260if isempty(displ_num)
1261    nbpair=0;
1262else
1263    nbpair=length(displ_num(1,:));%nbre of displayed pairs
1264    if  isequal(mode,'series(Di)')% | isequal(mode,'st_series(Di)')
1265        nbpair=min(2*ref_i-1,nbpair);%limit the number of pairs with positive first index
1266    elseif  isequal(mode,'series(Dj)')% | isequal(mode,'st_series(Dj)')
1267        nbpair=min(2*ref_j-1,nbpair);%limit the number of pairs with positive first index
1268    end
1269end
1270nbpair=min(200,nbpair);%limit the number of displayed pairs to 200
1271
1272%look for existing processed pairs involving the field at the middle of the series if checkciv1 will not
1273% be performed, while the result is needed for next steps.
1274displ_pair={''}; %default
1275select=ones(size(1:nbpair));%default =1 for numbers of displayed pairs
1276if get(handles.CheckCiv2,'Value')==0 & get(handles.CheckCiv1,'Value')==0 & get(handles.CheckFix1,'Value')==0 & get(handles.CheckPatch1,'Value')==0%&...
1277    if ~exist(fullfile(filepath,subdir_civ2,ext_dir),'dir')
1278        errordlg(['no civ2 file available: subdirectory ' subdir_civ2 ' does not exist'])
1279        set(handles.ListPairCiv2,'Value',1);
1280        set(handles.ListPairCiv2,'String',{''});
1281        return
1282    end
1283    for ipair=1:nbpair
1284        filename=name_generator(filebase,ref_i+displ_num(3,ipair),ref_j+displ_num(1,ipair),'.nc',nom_type_nc,1,...
1285            ref_i+displ_num(4,ipair),ref_j+displ_num(2,ipair),subdir_civ1);
1286        select(ipair)=exist(filename,'file')==2;
1287    end
1288    if  isequal(select,zeros(size(1:nbpair)))
1289        if isfield(browse,'incr_pair')
1290            num_i1=ref_i-floor(browse.incr_pair(1)/2);
1291            num_i2=ref_i+floor((browse.incr_pair(1)+1)/2);
1292            num_j1=ref_j-floor(browse.incr_pair(2)/2);
1293            num_j2=ref_j+floor((browse.incr_pair(2)+1)/2);
1294            filename=name_generator(filebase,num_i1,num_j1,'.nc',nom_type_nc,1,num_i2,num_j2,subdir_civ2);
1295            select(1)=exist(filename,'file')==2;
1296        else
1297            if  isequal(mode,'series(Dj)')% | isequal(mode,'st_series(Dj)')
1298                errordlg(['no civ2 file available for the selected reference index j=' num2str(ref_j) ' and subdirectory ' subdir_civ2])
1299            else
1300                errordlg(['no civ2 file available for the selected reference index i=' num2str(ref_i) ' and subdirectory ' subdir_civ2])
1301            end
1302            set(handles.ListPairCiv2,'Value',1);
1303            set(handles.ListPairCiv2,'String',{''});
1304            return
1305        end
1306    end
1307end
1308if isequal(mode,'series(Di)') % | isequal(mode,'st_series(Di)')
1309    for ipair=1:nbpair
1310        if select(ipair)
1311            if size(time,1)>=ref_i+displ_num(4,ipair) && size(time,2)>=ref_j+displ_num(2,ipair)
1312                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
1313                displ_pair{ipair}=['Di= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2)) ' :dt= ' num2str(dt*1000)];
1314            end
1315        else
1316            displ_pair{ipair}='...'; %pair not displayed in the menu
1317        end
1318    end
1319elseif isequal(mode,'series(Dj)') %| isequal(mode,'st_series(Dj)') % series on the j index
1320    for ipair=1:nbpair
1321        if select(ipair)
1322            if size(time,1)>=ref_i+displ_num(4,ipair) && size(time,2)>=ref_j+displ_num(2,ipair)
1323                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
1324                displ_pair{ipair}=['Dj= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2)) ' :dt= ' num2str(dt*1000)];
1325            end
1326        else
1327            displ_pair{ipair}='...'; %pair not displayed in the menu
1328        end
1329    end
1330elseif isequal(mode,'pair j1-j2')% | isequal(mode,'st_pair j1-j2') %case of pairs
1331    for ipair=1:nbpair
1332        if select(ipair)
1333            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
1334            displ_pair{ipair}=['j= ' num2stra(displ_num(1,ipair),nom_type_ima) '-' num2stra(displ_num(2,ipair),nom_type_ima) ...
1335                ' :dt= ' num2str(dt*1000)];
1336        else
1337            displ_pair{ipair}='...'; %pair not displayed in the menu
1338        end
1339    end
1340elseif isequal(mode,'displacement')
1341    displ_pair={'Di=Dj=0'};
1342end
1343val=get(handles.ListPairCiv2,'Value');
1344ichoice=find(select,1);
1345if (isempty(ichoice) || ichoice < 1); ichoice=1; end;
1346if get(handles.CheckCiv2,'Value')==0 && get(handles.CheckCiv1,'Value')==0 && get(handles.CheckFix1,'Value')==0 && get(handles.CheckPatch1,'Value')==0
1347    val=ichoice;% first valid pair proposed by default in the menu
1348end
1349if val>length(displ_pair')
1350    set(handles.ListPairCiv2,'Value',1);% first valid pair proposed by default in the menu
1351else
1352    set(handles.ListPairCiv2,'Value',val);
1353end
1354set(handles.ListPairCiv2,'String',displ_pair');
1355set(gcf,'Pointer','arrow')
1356
1357
1358
1359
1360%------------------------------------------------------------------------
1361% --- Executes on selection change in ListPairCiv1.
1362function ListPairCiv1_Callback(hObject, eventdata, handles)
1363%------------------------------------------------------------------------
1364%reproduce by default the chosen pair in the checkciv2 menu
1365list_pair=get(handles.ListPairCiv1,'String');%get the menu of image pairs
1366index_pair=get(handles.ListPairCiv1,'Value');
1367displ_num=get(handles.ListPairCiv1,'UserData');
1368% num_a=displ_num(1,index_pair);
1369% num_b=displ_num(2,index_pair);
1370list_pair2=get(handles.ListPairCiv2,'String');%get the menu of image pairs
1371if index_pair<=length(list_pair2)
1372    set(handles.ListPairCiv2,'Value',index_pair);
1373end
1374
1375%update first_i and last_i according to the chosen image pairs
1376mode_list=get(handles.ListPairMode,'String');
1377mode_value=get(handles.ListPairMode,'Value');
1378mode=mode_list{mode_value};
1379if isequal(mode,'series(Di)')
1380    first_i=str2double(get(handles.first_i,'String'));
1381    last_i=str2double(get(handles.last_i,'String'));
1382    incr_i=str2double(get(handles.incr_i,'String'));
1383    num1=first_i:incr_i:last_i;
1384    lastfield=str2double(get(handles.nb_field,'String'));
1385    if ~isnan(lastfield)
1386        test_find=(num1-floor(index_pair/2)*ones(size(num1))>0)& ...
1387            (num1+ceil(index_pair/2)*ones(size(num1))<=lastfield);
1388        num1=num1(test_find);
1389    end
1390    set(handles.first_i,'String',num2str(num1(1)));
1391    set(handles.last_i,'String',num2str(num1(end)));
1392elseif isequal(mode,'series(Dj)')
1393    first_j=str2double(get(handles.first_j,'String'));
1394    last_j=str2double(get(handles.last_j,'String'));
1395    incr_j=str2double(get(handles.incr_j,'String'));
1396    num_j=first_j:incr_j:last_j;
1397    lastfield2=str2double(get(handles.nb_field2,'String'));
1398    if ~isnan(lastfield2)
1399        test_find=(num_j-floor(index_pair/2)*ones(size(num_j))>0)& ...
1400            (num_j+ceil(index_pair/2)*ones(size(num_j))<=lastfield2);
1401        num1=num_j(test_find);
1402    end
1403    set(handles.first_j,'String',num2str(num1(1)));
1404    set(handles.last_j,'String',num2str(num1(end)));
1405end
1406
1407%------------------------------------------------------------------------
1408% --- Executes on selection change in ListPairCiv2.
1409function ListPairCiv2_Callback(hObject, eventdata, handles)
1410%------------------------------------------------------------------------
1411index_pair=get(handles.ListPairCiv2,'Value');%get the selected position index in the menu
1412
1413%update first_i and last_i according to the chosen image pairs
1414mode_list=get(handles.ListPairMode,'String');
1415mode_value=get(handles.ListPairMode,'Value');
1416mode=mode_list{mode_value};
1417if isequal(mode,'series(Di)')
1418    first_i=str2double(get(handles.first_i,'String'));
1419    last_i=str2double(get(handles.last_i,'String'));
1420    incr_i=str2double(get(handles.incr_i,'String'));
1421    num1=first_i:incr_i:last_i;
1422    lastfield=str2double(get(handles.nb_field,'String'));
1423    if ~isnan(lastfield)
1424        test_find=(num1-floor(index_pair/2)*ones(size(num1))>0)& ...
1425            (num1+ceil(index_pair/2)*ones(size(num1))<=lastfield);
1426        num1=num1(test_find);
1427    end
1428    set(handles.first_i,'String',num2str(num1(1)));
1429    set(handles.last_i,'String',num2str(num1(end)));
1430elseif isequal(mode,'series(Dj)')
1431    first_j=str2double(get(handles.first_j,'String'));
1432    last_j=str2double(get(handles.last_j,'String'));
1433    incr_j=str2double(get(handles.incr_j,'String'));
1434    num_j=first_j:incr_j:last_j;
1435    lastfield2=str2double(get(handles.nb_field2,'String'));
1436    if ~isnan(lastfield2)
1437        test_find=(num_j-floor(index_pair/2)*ones(size(num_j))>0)& ...
1438            (num_j+ceil(index_pair/2)*ones(size(num_j))<=lastfield2);
1439        num1=num_j(test_find);
1440    end
1441    set(handles.first_j,'String',num2str(num1(1)));
1442    set(handles.last_j,'String',num2str(num1(end)));
1443end
1444
1445%------------------------------------------------------------------------
1446% --- Executes on button press in RUN: processing on local computer
1447function RUN_Callback(hObject, eventdata, handles)
1448%------------------------------------------------------------------------
1449set(handles.RUN, 'Enable','Off')
1450set(handles.RUN,'BackgroundColor',[0.831 0.816 0.784])
1451batch=0;
1452errormsg=launch_jobs(hObject, eventdata, handles,batch);
1453set(handles.RUN, 'Enable','On')
1454set(handles.RUN,'BackgroundColor',[1 0 0])
1455
1456% start status callback to visualise results
1457if ~isempty(errormsg)
1458    display(errormsg)
1459    msgbox_uvmat('ERROR',errormsg)
1460elseif  isfield(handles,'status') %&& ~isequal(get(handles.ListPairMode,'Value'),3)
1461    set(handles.status,'Value',1);%suppress status display
1462    status_Callback(hObject, eventdata, handles)
1463end
1464
1465%------------------------------------------------------------------------
1466% --- Executes on button press in BATCH: remote processing
1467function BATCH_Callback(hObject, eventdata, handles)
1468% -----------------------------------------------------------------------
1469set(handles.BATCH, 'Enable','Off')
1470set(handles.BATCH,'BackgroundColor',[0.831 0.816 0.784])
1471batch=1;
1472errormsg=launch_jobs(hObject, eventdata, handles, batch);
1473set(handles.BATCH, 'Enable','On')
1474set(handles.BATCH,'BackgroundColor',[1 0 0])
1475
1476% start status callback to visualise results
1477if ~isempty(errormsg)
1478    display(errormsg)
1479    msgbox_uvmat('ERROR',errormsg)
1480elseif isfield(handles,'status')
1481    set(handles.status,'Value',1);%suppress status display
1482    status_Callback(hObject, eventdata, handles)
1483end
1484
1485%------------------------------------------------------------------------
1486% --- Lauch command called by RUN and BATCH: remote processing
1487function errormsg=launch_jobs(hObject, eventdata, handles, batch)
1488%-----------------------------------------------------------------------
1489errormsg='';%default
1490
1491%%read the civ GUI
1492Param=read_GUI(handles.civ);
1493%% check the selected list of operations:
1494operations={'Civ1','Fix1','Patch1','Civ2','Fix2','Patch2'};
1495box_test=[Param.CheckCiv1 Param.CheckFix1 Param.CheckPatch1 Param.CheckCiv2 Param.CheckFix2 Param.CheckPatch2];
1496
1497index_first=find(box_test==1,1);
1498if isempty(index_first)
1499    errormsg='no selected operation';
1500    return
1501end
1502index_last=find(box_test==1,1,'last');
1503box_used=box_test(index_first : index_last);
1504[box_missing,ind_missing]=min(box_used);
1505if isequal(box_missing,0); %there is a missing step in the sequence of operations
1506    errormsg=['missing' cell2mat(operations(ind_missing))];
1507    return
1508end
1509
1510%% check mask if selecetd
1511%could be included in get_mask callback ?
1512if isequal(get(handles.CheckMask,'Value'),1)
1513    maskname=get(handles.txt_MaskName,'String');
1514    if ~exist(maskname,'file')
1515        get_mask_civ1_Callback(hObject, eventdata, handles);
1516    end
1517end
1518if isequal(get(handles.CheckMask,'Value'),1)
1519    maskname=get(handles.txt_MaskName,'String');
1520    if ~exist(maskname,'file')
1521        get_mask_fix1_Callback(hObject, eventdata, handles);
1522    end
1523end
1524if isequal(get(handles.CheckMask,'Value'),1)
1525    maskname=get(handles.txt_Mask,'String');
1526    if ~exist(maskname,'file')
1527        get_mask_civ2_Callback(hObject, eventdata, handles);
1528    end
1529end
1530if isequal(get(handles.CheckMask,'Value'),1)
1531    maskname=get(handles.txt_MaskName,'String');
1532    if ~exist(maskname,'file')
1533        get_mask_fix2_Callback(hObject, eventdata, handles);
1534    end
1535end
1536
1537%% reinitialise status callback
1538if isfield(handles,'status')
1539    set(handles.status,'Value',0);%suppress status display
1540    status_Callback(hObject, eventdata, handles)
1541end
1542
1543%% set the list of files and check them
1544display('checking the files...')
1545[ref_i,ref_j,errormsg]=find_ref_indices(handles);
1546if ~isempty(errormsg)
1547    return
1548end
1549[filecell,num1_civ1,num2_civ1,num_a_civ1,num_b_civ1,num1_civ2,num2_civ2,num_a_civ2,num_b_civ2,nom_type_nc,xx,yy,compare]=...
1550    set_civ_filenames(handles,ref_i,ref_j,box_test);
1551% ADDED
1552   [Rootbat,Filebat]=fileparts(filecell.nc.civ1{1,1});%output netcdf file (without extention)
1553%ADDED
1554set(handles.civ,'UserData',filecell);%store for futur use of status callback
1555if isempty(filecell)% (error message displayed in fct set_civ_filenames)
1556    return
1557end
1558nbfield=numel(num1_civ1);
1559nbslice=numel(num_a_civ1);
1560
1561%% read the PARAM.xml file to get the binaries (and batch_mode if batch)
1562path_civ=fileparts(which('civ')); %path to the source directory of uvmat
1563xmlfile='PARAM.xml';
1564if exist(xmlfile,'file')% search parameter xml file in the whole matlab path
1565    t=xmltree(xmlfile);
1566    s=convert(t);
1567else
1568    errormsg=['no file ' xmlfile];
1569    return
1570end
1571
1572test_interp=0; %eviter les variables test_ (LG)
1573
1574if batch
1575    if isfield(s,'BatchParam')
1576        Param.xml=s.BatchParam;
1577        if isfield(Param.xml,'BatchMode')
1578            batch_mode=Param.xml.BatchMode;
1579            if ~ismember(batch_mode,{'sge','oar'})
1580                errormsg=['batch mode ' batch_mode ' not supported by UVMAT'];
1581                return
1582            end
1583        end
1584    else
1585        errormsg='no batch civ binaries defined in PARAM.xml';
1586        return
1587    end
1588else % run
1589    if isfield(s,'RunParam')
1590        Param.xml=s.RunParam;
1591    else
1592        msgbox_uvmat('ERROR','no run civ binaries defined in PARAM.xml')
1593        return
1594    end
1595end
1596
1597%% check batch mode supported
1598if batch
1599    switch batch_mode
1600        case 'sge'
1601            test_command='qstat';
1602        case 'oar'
1603            test_command='oarstat';
1604    end   
1605    [s,w]=system(test_command);
1606    if ~isequal(s,0)
1607        msgbox_uvmat('ERROR',[batch_mode ' batch system not available'])
1608        return
1609    end
1610end
1611
1612%% check if the binaries exist
1613if isequal(get(handles.Matlab,'checked'),'on')
1614    CivMode='Matlab';
1615else
1616    CivMode='CivX';
1617end
1618binary_list={};
1619switch CivMode
1620    case 'CivX'
1621        binary_list={'Civ1Bin','Civ2Bin','PatchBin','FixBin'};
1622    case 'CivAll'
1623        binary_list={'Civ'};
1624    case 'Matlab'
1625        if batch
1626            % vérifier Matlab installé sur le cluster
1627            % difficile a faire a priori
1628        end         
1629end
1630for bin_name=binary_list
1631    if isfield(Param.xml,bin_name{1})
1632        if ~exist(Param.xml.(bin_name{1}),'file')%look for the full path if the file name has been defined with a relative path in PARAM.xml
1633            fullname=fullfile(path_civ,Param.xml.(bin_name{1}));
1634            if exist(fullname,'file')
1635                Param.xml.(bin_name{1})=fullname;
1636            else
1637                msgbox_uvmat('ERROR',['Binary ' Param.xml.(bin_name{1}) ' defined in PARAM.xml does not exist'])
1638                return
1639            end
1640        else
1641            [path,name,ext]=fileparts(Param.xml.(bin_name{1}));
1642            currentdir=pwd;
1643            cd(path);
1644            binpath=pwd;%path of the binary
1645            Param.xml.(bin_name{1})=fullfile(binpath,[name ext]);
1646            %                      display(Param.xml.(bin_name{1}));
1647            cd(currentdir);
1648        end
1649       
1650    end
1651end
1652
1653display('files OK, processing...')
1654
1655
1656%% MAIN LOOP
1657time=get(handles.ImaDoc,'UserData'); %get the set of times
1658
1659super_cmd=[];
1660batch_file_list=[];
1661   
1662for ifile=1:nbfield
1663    for j=1:nbslice
1664        % initiate system command
1665        switch CivMode
1666            case 'CivX'
1667                if isunix % check: necessaire aussi en RUN?
1668                    cmd=['#!/bin/bash \n '...
1669                        '#$ -cwd \n '...
1670                        'hostname && date \n '...
1671                        'umask 002 \n'];%allow writting access to created files for user group
1672                else
1673                    cmd=[];
1674                end
1675            case 'CivAll'
1676                %         if CivAll
1677                CivAllxml=xmltree;% xml contents,  all parameters
1678                CivAllCmd='';
1679                CivAllxml=set(CivAllxml,1,'name','CivDoc');
1680        end
1681       
1682       
1683        % define output file name
1684        if Param.CheckCiv2==1 || Param.CheckFix2==1 || Param.CheckPatch2==1
1685            OutputFile=filecell.nc.civ2{ifile,j};
1686        else
1687            OutputFile=filecell.nc.civ1{ifile,j};
1688        end
1689        OutputFile=regexprep(OutputFile,'.nc','');
1690
1691        if Param.CheckCiv1
1692            % read image-dependent parameters
1693            Param.Civ1.filename_ima_a=filecell.ima1.civ1{ifile,j};
1694            Param.Civ1.filename_ima_b=filecell.ima2.civ1{ifile,j};
1695            Param.Civ1.Dt=(time(num2_civ1(ifile),num_b_civ1(j))-time(num1_civ1(ifile),num_a_civ1(j)));
1696            Param.Civ1.T0=((time(num2_civ1(ifile),num_b_civ1(j))+time(num1_civ1(ifile),num_a_civ1(j)))/2);
1697            Param.Civ1.term_a=num2stra(num_a_civ1(j),nom_type_nc);%UTILITE?
1698            Param.Civ1.term_b=num2stra(num_b_civ1(j),nom_type_nc);%
1699            Param.Civ1.pxcmx=1; %velocities are expressed in pixel dispalcement
1700            Param.Civ1.pxcmy=1;
1701
1702            A=imread(filecell.ima1.civ1{1,1});%read the first image to get the size
1703            sizim=size(A);
1704            Param.Civ1.npx=(sizim(2));
1705            Param.Civ1.npy=(sizim(1));
1706            %TODO : civ should not need npx and npy
1707
1708            % read mask parameters
1709            if Param.Civ1.CheckMask % the lines below should be changed with the new gui
1710                %matbe they when check_mask the Maskname is read
1711                if exist(Param.Civ1.MaskName,'file')
1712                    Param.Civ1.MaskFlag='y';
1713                else
1714                    maskbase=[filecell.filebase '_' Param.Civ1.MaskName]; %
1715                    nbslice_mask=str2double(maskdispl(1:end-4)); %
1716                    num1_mask=mod(num1_civ1(ifile)-1,nbslice_mask)+1;
1717                    Param.Civ1.MaskName=name_generator(maskbase,num1_mask,1,'.png','_i');
1718                    if exist(Param.Civ1.MaskName,'file')
1719                        Param.Civ1.maskflag='y';
1720                    else
1721                        Param.Civ1.MaskName='noFile use default';
1722                        Param.Civ1.MaskFlag='n';
1723                    end
1724                end
1725            else
1726                Param.Civ1.MaskName='noFile use default';
1727                Param.Civ1.MaskFlag='n';
1728            end
1729           
1730            % read grid parameters=
1731            if Param.Civ1.CheckGrid
1732                Param.Civ1.GridFlag='y';
1733                if isequal(Param.Civ1.GridName(end-3:end),'grid')
1734                    nbslice_grid=str2double(Param.Civ1.GridName(1:end-4)); %
1735                    if ~isnan(nbslice_grid)
1736                        num1_grid=mod(num1_civ1(ifile)-1,nbslice_grid)+1;
1737                        Param.Civ1.GridName=[filecell.filebase '_' name_generator(gridname,num1_grid,1,'.grid','_i')];
1738                        if ~exist(Param.Civ1.GridName,'file')
1739                            msgbox_uvmat('ERROR','grid file absent for civ1')
1740                        end
1741                    elseif ~exist(Param.Civ1.GridName,'file')
1742                        msgbox_uvmat('ERROR','grid file absent for civ1')
1743                    end
1744                end
1745            else
1746                Param.Civ1.GridName='noFile use default';
1747                Param.Civ1.GridFlag='n';
1748            end
1749           
1750            % send command
1751            switch CivMode
1752                case 'CivX'
1753                    cmd=[cmd...
1754                        cmd_civ1(filecell.nc.civ1{ifile,j},Param) '\n'];
1755                case 'CivAll'
1756                    CivAllCmd=[CivAllCmd ' civ1 '];
1757                    str=CIV1_CMD_Unified(filecell.nc.civ1{ifile,j},'',Param.Civ1);
1758                    fieldnames=fields(str);
1759                    [CivAllxml,uid_civ1]=add(CivAllxml,1,'element','civ1');
1760                    for ilist=1:length(fieldnames)
1761                        val=eval(['str.' fieldnames{ilist}]);
1762                        if ischar(val)
1763                            [CivAllxml,uid_t]=add(CivAllxml,uid_civ1,'element',fieldnames{ilist});
1764                            [CivAllxml,uid_t2]=add(CivAllxml,uid_t,'chardata',val);
1765                        end
1766                    end
1767            end
1768        end
1769       
1770        if Param.CheckFix1
1771           switch CivMode
1772                case 'CivX'
1773                    cmd=[cmd...
1774                        cmd_fix(filecell.nc.civ1{ifile,j},Param,'Fix1') '\n'];
1775                case 'CivAll'
1776                    fix1.inputFileName=filecell.nc.civ1{ifile,j} ;
1777                    fix1.fi1=num2str(param.fix1.flagindex1(1));
1778                    fix1.fi2=num2str(param.fix1.flagindex1(2));
1779                    fix1.fi3=num2str(param.fix1.flagindex1(3));
1780                    fix1.threshC=num2str(param.fix1.thresh_vecC1);
1781                    fix1.threshV=num2str(param.fix1.thresh_vel1);
1782                    fieldnames=fields(fix1);
1783                    [CivAllxml,uid_fix1]=add(CivAllxml,1,'element','fix1');
1784                    for ilist=1:length(fieldnames)
1785                        val=eval(['fix1.' fieldnames{ilist}]);
1786                        if ischar(val)
1787                            [CivAllxml,uid_t]=add(CivAllxml,uid_fix1,'element',fieldnames{ilist});
1788                            [CivAllxml,uid_t2]=add(CivAllxml,uid_t,'chardata',val);
1789                        end
1790                    end
1791                    CivAllCmd=[CivAllCmd ' fix1 '];
1792            end
1793        end
1794       
1795        %CheckPatch1
1796        if Param.CheckPatch1==1
1797            switch CivMode
1798                case 'CivX'
1799                    cmd=[cmd...
1800                        cmd_patch(filecell.nc.civ1{ifile,j},Param,'Patch1') '\n'];
1801                case 'CivAll'
1802                    patch1.inputFileName=filecell.nc.civ1{ifile,j} ;
1803                    patch1.nopt=subdomain_patch1;
1804                    patch1.maxdiff=thresh_patch1;
1805                    patch1.ro=rho_patch1;
1806                    test_grid=get(handles.get_gridpatch1,'Value');
1807                    if test_grid
1808                        patch1.gridflag='y';
1809                        gridname=get(handles.grid_patch1,'String');
1810                        if isequal(gridname(end-3:end),'grid')
1811                            nbslice_grid=str2double(gridname(1:end-4)); %
1812                            if ~isnan(nbslice_grid)
1813                                num1_grid=mod(num1_civ1(ifile)-1,nbslice_grid)+1;
1814                                patch1.gridPatch=[filecell.filebase '_' name_generator(gridname,num1_grid,1,'.grid','_i')];
1815                                if ~exist(patch1.gridPatch,'file')
1816                                    msgbox_uvmat('ERROR','grid file absent for patch1')
1817                                end
1818                            elseif exist(gridname,'file')
1819                                patch1.gridPatch=gridname;
1820                            else
1821                                msgbox_uvmat('ERROR','grid file absent for patch1')
1822                            end
1823                        end
1824                    else
1825                        patch1.gridPatch='none';
1826                        patch1.gridflag='n';
1827                        patch1.m=nx_patch1;
1828                        patch1.n=ny_patch1;
1829                    end
1830                    patch1.convectFlow='n';
1831                    fieldnames=fields(patch1);
1832                    [CivAllxml,uid_patch1]=add(CivAllxml,1,'element','patch1');
1833                    for ilist=1:length(fieldnames)
1834                        val=eval(['patch1.' fieldnames{ilist}]);
1835                        if ischar(val)
1836                            [CivAllxml,uid_t]=add(CivAllxml,uid_patch1,'element',fieldnames{ilist});
1837                            [CivAllxml,uid_t2]=add(CivAllxml,uid_t,'chardata',val);
1838                        end
1839                    end
1840                    CivAllCmd=[CivAllCmd ' patch1 '];
1841            end
1842        end
1843        if Param.CheckCiv2==1
1844            Param.Civ2.filename_ima_a=filecell.ima1.civ2{ifile,j};
1845            Param.Civ2.filename_ima_b=filecell.ima2.civ2{ifile,j};
1846            Param.Civ2.Dt=num2str(time(num2_civ2(ifile),num_b_civ2(j))-time(num1_civ2(ifile),num_a_civ2(j)));
1847            Param.Civ2.T0=num2str((time(num2_civ1(ifile),num_b_civ2(j))+time(num1_civ2(ifile),num_a_civ2(j)))/2);
1848            Param.Civ2.term_a=num2stra(num_a_civ2(j),nom_type_nc);
1849            Param.Civ2.term_b=num2stra(num_b_civ2(j),nom_type_nc);
1850            Param.Civ2.filename_nc1=filecell.nc.civ1{ifile,j};
1851            Param.Civ2.filename_nc1(end-2:end)=[]; % remove '.nc'
1852            Param.Civ2.pxcmx=1; %velocities are expressed in pixel dispalcement
1853            Param.Civ2.pxcmy=1;
1854            if Param.Civ2.CheckMask
1855                maskdispl=get(handles.txt_Mask,'String');
1856                if exist(maskdispl,'file')
1857                    Param.Civ2.MaskName=maskdispl;
1858                    Param.Civ2.MaskFlag='y';
1859                else
1860                    maskbase=[filecell.filebase '_' maskdispl]; %
1861                    nbslice_mask=str2double(maskdispl(1:end-4)); %
1862                    num1_mask=mod(num1_civ2(ifile)-1,nbslice_mask)+1;
1863                    Param.Civ2.MaskName=name_generator(maskbase,num1_mask,1,'.png','_i');
1864                    if exist(Param.Civ2.MaskName,'file')
1865                        Param.Civ2.MaskFlag='y';
1866                    else
1867                        Param.Civ2.MaskName='noFile use default';
1868                        Param.Civ2.MaskFlag='n';
1869                    end
1870                end
1871            else
1872                Param.Civ2.MaskName='noFile use default';
1873                Param.Civ2.MaskFlag='n';
1874            end
1875            gridname=get(handles.txt_GridName,'String');
1876            if numel(gridname)>=4 && isequal(gridname(end-3:end),'grid')
1877                nbslice_grid=str2double(gridname(1:end-4)); %
1878                if ~isnan(nbslice_grid)
1879                    Param.Civ2.GridFlag='y';
1880                    num1_grid=mod(num1_civ2(ifile)-1,nbslice_grid)+1;
1881                    Param.Civ2.GridName=[filecell.filebase '_' name_generator(gridname,num1_grid,1,'.grid','_i')];
1882                    if exist(Param.Civ2.GridName,'file')
1883                        Param.Civ2.GridFlag='y';
1884                    else
1885                        Param.Civ2.GridName='noFile use default';
1886                        Param.Civ2.GridFlag='n';
1887                    end
1888                elseif exist(gridname,'file')
1889                    Param.Civ2.GridFlag='y';
1890                else
1891                    Param.Civ2.GridName='noFile use default';
1892                    Param.Civ2.GridFlag='n';
1893                end
1894            else
1895                Param.Civ2.GridName='noFile use default';
1896                Param.Civ2.GridFlag='n';
1897            end
1898            A=imread(filecell.ima1.civ2{1,1});%read the first image to get the size
1899            sizim=size(A);
1900            Param.Civ2.npx=(sizim(2));
1901            Param.Civ2.npy=(sizim(1));
1902                 
1903            switch CivMode
1904                case 'CivX'
1905                     cmd=[cmd...
1906                        cmd_civ2(filecell.nc.civ2{ifile,j},Param) '\n'];
1907                case 'CivAll'
1908                    CivAllCmd=[CivAllCmd ' civ2 '];
1909                    str=CIV2_CMD_Unified(filecell.nc.civ2{ifile,j},'',Param.Civ2);
1910                    fieldnames=fields(str);
1911                    [CivAllxml,uid_civ2]=add(CivAllxml,1,'element','civ2');
1912                    for ilist=1:length(fieldnames)
1913                        val=eval(['str.' fieldnames{ilist}]);
1914                        if ischar(val)
1915                            [CivAllxml,uid_t]=add(CivAllxml,uid_civ2,'element',fieldnames{ilist});
1916                            [CivAllxml,uid_t2]=add(CivAllxml,uid_t,'chardata',val);
1917                        end
1918                    end
1919            end
1920        end
1921       
1922        % CheckFix2
1923        if Param.CheckFix2==1
1924            switch CivMode
1925                case 'CivX'
1926                    cmd=[cmd...
1927                        cmd_fix(filecell.nc.civ2{ifile,j},Param,'Fix2') '\n'];
1928                case 'CivAll'
1929                    fix2.inputFileName=filecell.nc.civ2{ifile,j} ;
1930                    fix2.fi1=num2str(flagindex2(1));
1931                    fix2.fi2=num2str(flagindex2(2));
1932                    fix2.fi3=num2str(flagindex2(3));
1933                    fix2.threshC=num2str(thresh_vec2C);
1934                    fix2.threshV=num2str(thresh_vel2);
1935                    fieldnames=fields(fix2);
1936                    [CivAllxml,uid_fix2]=add(CivAllxml,1,'element','fix2');
1937                    for ilist=1:length(fieldnames)
1938                        val=eval(['fix2.' fieldnames{ilist}]);
1939                        if ischar(val)
1940                            [CivAllxml,uid_t]=add(CivAllxml,uid_fix2,'element',fieldnames{ilist});
1941                            [CivAllxml,uid_t2]=add(CivAllxml,uid_t,'chardata',val);
1942                        end
1943                    end
1944                    CivAllCmd=[CivAllCmd ' fix2 '];
1945            end
1946        end
1947       
1948        %CheckPatch2
1949        if Param.CheckPatch2==1
1950            switch CivMode
1951                case 'CivX'
1952                    cmd=[cmd...
1953                        cmd_patch(filecell.nc.civ1{ifile,j},Param,'Patch2') '\n'];
1954                case 'CivAll'
1955                    patch2.inputFileName=filecell.nc.civ1{ifile,j} ;
1956                    patch2.nopt=subdomain_patch2;
1957                    patch2.maxdiff=thresh_patch2;
1958                    patch2.ro=rho_patch2;
1959                    test_grid=get(handles.get_gridpatch2,'Value');
1960                    if test_grid
1961                        patch2.gridflag='y';
1962                        gridname=get(handles.grid_patch2,'String');
1963                        if isequal(gridname(end-3:end),'grid')
1964                            nbslice_grid=str2double(gridname(1:end-4)); %
1965                            if ~isnan(nbslice_grid)
1966                                num1_grid=mod(num1_civ2(ifile)-1,nbslice_grid)+1;
1967                                patch2.gridPatch=[filecell.filebase '_' name_generator(gridname,num1_grid,1,'.grid','_i')];
1968                                if ~exist(patch2.gridPatch,'file')
1969                                    msgbox_uvmat('ERROR','grid file absent for patch2')
1970                                end
1971                            elseif exist(gridname,'file')
1972                                patch2.gridPatch=gridname;
1973                            else
1974                                msgbox_uvmat('ERROR','grid file absent for patch2')
1975                            end
1976                        end
1977                    else
1978                        patch2.gridPatch='none';
1979                        patch2.gridflag='n';
1980                        patch2.m=nx_patch2;
1981                        patch2.n=ny_patch2;
1982                    end
1983                    patch2.convectFlow='n';
1984                    fieldnames=fields(patch2);
1985                    [CivAllxml,uid_patch2]=add(CivAllxml,1,'element','patch2');
1986                    for ilist=1:length(fieldnames)
1987                        val=eval(['patch2.' fieldnames{ilist}]);
1988                        if ischar(val)
1989                            [CivAllxml,uid_t]=add(CivAllxml,uid_patch2,'element',fieldnames{ilist});
1990                            [CivAllxml,uid_t2]=add(CivAllxml,uid_t,'chardata',val);
1991                        end
1992                    end
1993                    CivAllCmd=[CivAllCmd ' patch2 '];
1994            end
1995        end
1996 
1997        switch CivMode
1998            case {'CivX','CivAll'}
1999                if isequal(CivMode,'CivAll')
2000                    save(CivAllxml,[OutputFile '.xml']);
2001                    cmd=[cmd sparam.CivBin ' -f ' OutputFile '.xml '  CivAllCmd ' >' OutputFile '.log' '\n'];
2002                end
2003               
2004                % create the .bat file used in run or batch
2005                filename_bat=[OutputFile '.bat'];
2006                [fid,message]=fopen(filename_bat,'w');
2007                if isequal(fid,-1)
2008                    msgbox_uvmat('ERROR', ['creation of .bat file: ' message])
2009                    return
2010                end
2011                fprintf(fid,cmd);
2012                fclose(fid);
2013               
2014                if isunix
2015                    system(['chmod +x ' filename_bat]);
2016                end
2017               
2018                batch_file_list{length(batch_file_list)+1}=filename_bat;
2019               
2020%                 if batch
2021%                     switch batch_mode
2022%                         case 'sge'                           
2023%                             display(['!qsub -p ' pvalue ' -q civ.q -e ' flname '.errors -o ' flname '.log' ' ' filename_bat]);
2024%                             eval(  ['!qsub -p ' pvalue ' -q civ.q -e ' flname '.errors -o ' flname '.log' ' ' filename_bat]);
2025%                         case 'oar'
2026% %                             eval(  ['!chmod +x ' filename_bat]);
2027% %                             %eval(  ['!oarsub -n CIVX -l /core=1,walltime=00:10:00  ' filename_bat]);                   
2028% %                             eval(  ['!oarsub -n CIVX -l "/core=1+{type = ''smalljob''}/licence=1,walltime=00:10:00"   ' filename_bat]);
2029%
2030%                     cmd_str=['sh ' filename_bat];
2031%                     super_cmd{length(super_cmd)+1}=cmd_str;
2032%                           
2033%                     end
2034%                 else
2035%                     %% to lauch the jobs locally :
2036%                     if(isunix)
2037%                         cmd_str=['. ' filename_bat];
2038%                     else %case of Windows
2039%                         cmd_str=['@call "' regexprep(filename_bat,'\\','\\\\') '"'];
2040%                     end
2041%                     super_cmd=[super_cmd cmd_str '\n'];
2042%                     disp(cmd_str);
2043%                 end
2044            case 'Matlab'
2045                drawnow
2046                if Param.CheckCiv1==1
2047                    Param.Civ1=Param.Civ1;
2048                end
2049                if Param.CheckFix1==1
2050                    fix1.WarnFlags=[];
2051                    if get(handles.CheckFmin2,'Value')
2052                        fix1.WarnFlags=[fix1.WarnFlags -2];
2053                    end
2054                    if get(handles.CheckF3,'Value')
2055                        fix1.WarnFlags=[fix1.WarnFlags 3];
2056                    end
2057                    fix1.LowerBoundCorr=thresh_vecC1;
2058                    if get(handles.num_MinVel,'Value')
2059                        fix1.UppperBoundVel=thresh_vel1;
2060                    else
2061                        fix1.LowerBoundVel=thresh_vel1;
2062                    end
2063                    if get(handles.CheckMask,'Value')
2064                        fix1.MaskName=maskname;
2065                    end
2066                    Param.Fix1=fix1;
2067                end
2068                if Param.CheckPatch1==1
2069                    if strcmp(compare,'stereo PIV')
2070                        filebase_A=filecell.filebase;
2071                        [pp,ff]=fileparts(filebase_A);
2072                        filebase_B=fullfile(pp,get(handles.RootName_1,'String'));
2073                        RUN_STLIN(filecell.ncA.civ1{ifile,j},filecell.nc.civ1{ifile,j},'civ1',filecell.st{ifile,j},...
2074                            str2num(nx_patch1),str2num(ny_patch1),str2num(thresh_patch1),[filebase_A '.xml'],[filebase_B '.xml'])
2075                    else
2076                        Param.Patch1.Rho=rho_patch1;
2077                        Param.Patch1.Threshold=thresh_patch1;
2078                        Param.Patch1.SubDomain=subdomain_patch1;
2079                    end
2080                end
2081                if Param.CheckCiv2==1
2082                    Param.Civ2=Param.Civ2;
2083                end
2084                if Param.CheckFix2==1
2085                    fix2.WarnFlags=[];
2086                    if get(handles.CheckFmin2,'Value')
2087                        fix2.WarnFlags=[fix2.WarnFlags -2];
2088                    end
2089                    if get(handles.CheckF4,'Value')
2090                        fix2.WarnFlags=[fix2.WarnFlags 4];
2091                    end
2092                    if get(handles.CheckF3,'Value')
2093                        fix2.WarnFlags=[fix2.WarnFlags 3];
2094                    end
2095                    fix2.LowerBoundCorr=thresh_vec2C;
2096                    if get(handles.num_MinVel,'Value')
2097                        fix2.UppperBoundVel=thresh_vel2;
2098                    else
2099                        fix2.LowerBoundVel=thresh_vel2;
2100                    end
2101                    if get(handles.CheckMask,'Value')
2102                        fix2.MaskName=maskname;
2103                    end
2104                    Param.Fix2=fix2;
2105                end
2106                if Param.CheckPatch2==1
2107                    if strcmp(compare,'stereo PIV')
2108                        filebase_A=filecell.filebase;
2109                        [pp,ff]=fileparts(filebase_A);
2110                        filebase_B=fullfile(pp,get(handles.RootName_1,'String'));
2111                        RUN_STLIN(filecell.ncA.civ2{ifile,j},filecell.nc.civ2{ifile,j},'civ2',filecell.st{ifile,j},...
2112                            str2num(nx_patch2),str2num(ny_patch2),str2num(thresh_patch2),[filebase_A '.xml'],[filebase_B '.xml'])
2113                    else
2114                        Param.Patch2.Rho=rho_patch2;
2115                        Param.Patch2.Threshold=thresh_patch2;
2116                        Param.Patch2.SubDomain=subdomain_patch2;
2117                    end
2118                end
2119                if ~strcmp(compare,'stereo PIV')
2120                    [Data,erromsg]=civ_uvmat(Param,filecell.nc.civ1{ifile,j});
2121                    if isempty(errormsg)
2122                        display([filecell.nc.civ1{ifile,j} ' written'])
2123                    else
2124                        msgbox_uvmat('ERROR',errormsg)
2125                    end
2126
2127                end
2128        end
2129    end
2130end
2131
2132if batch
2133    switch batch_mode                       
2134        case 'sge'
2135            for p=1:length(batch_file_list)
2136                cmd=['!qsub -p ' pvalue ' -q civ.q -e ' flname '.errors -o ' flname '.log' ' ' batch_file_list{p}];
2137                display(cmd);eval(cmd);
2138            end
2139        case 'oar_old'
2140                for p=1:length(batch_file_list)
2141                    oar_command=['!oarsub -n CIVX -q nicejob '...
2142                   '-E ' regexprep(batch_file_list{p},'.bat','.errors') ' -O ' regexprep(batch_file_list{p},'.bat','.log ')...
2143                    '-l "/core=1+{type = ''smalljob''}/licence=1,walltime=00:60:00"   ' batch_file_list{p}];
2144                display(oar_command);eval(oar_command);
2145                end         
2146       case 'oar' %oar-dispatch.pl
2147                filename_joblist=fullfile(Rootbat,'job_list.txt');
2148                fid=fopen(filename_joblist,'w');
2149
2150                for p=1:length(batch_file_list)
2151                    oar_command=['oarsub -n CIVX '...
2152                        '-l "/core=1,walltime=00:10:00"   ' batch_file_list{p}];
2153                    fprintf(fid,[oar_command '\n']);
2154                end
2155                fclose(fid);
2156                walltime=datestr(length(batch_file_list)*10/24/60,13);
2157                oar_command=['oarsub -t container -n civx-container -l /core=24,walltime=' walltime ' "/fsnet/data/legi/calcul9/home/gostiaux/Documents/MATLAB/uvmat_dev/oar-dispatch -f '...
2158                    filename_joblist '"'];
2159                filename_oarcommand=fullfile(Rootbat,'oar_command');
2160                fid=fopen(filename_oarcommand,'w');
2161                fprintf(fid,[oar_command '\n']);
2162                fclose(fid);
2163                display(oar_command);
2164                eval(['! . ' filename_oarcommand])
2165        case 'oar_mpi'
2166                filename_joblist=fullfile(Rootbat,'job_list.txt');
2167                fid=fopen(filename_joblist,'w');
2168
2169                for p=1:length(batch_file_list)
2170                    fprintf(fid,[batch_file_list{p} '\n']);
2171                end
2172                fclose(fid)
2173               
2174               
2175%                 oarsub -S ./oar.sub
2176
2177               
2178               
2179
2180               
2181        case 'oar_new' % to be develloped with Patrick Begou
2182                filename_joblist=fullfile(Rootbat,'job_list.txt');
2183                fid=fopen(filename_superbat,'w');
2184                if fid==-1
2185                    msgbox_uvmat('ERROR',['cannot create the command file ' filename_superbat])
2186                    return
2187                end
2188                for p=1:length(batch_file_list)
2189                    fprintf(fid,[batch_file_list{p} '\n']);
2190                end
2191                fclose(fid);
2192                walltime=datestr(length(super_cmd)*10/24/60,13);
2193                eval(  ['!oarsub -n CIVX -q nicejob -l "/core=1+{type = ''smalljob''}/licence=1,walltime=' walltime '"   ' filename_superbat]);
2194    end
2195else
2196    if ~isequal(CivMode,'Matlab')
2197        filename_superbat=fullfile(Rootbat,'job_list.bat');
2198        fid=fopen(filename_superbat,'w');
2199        if fid==-1
2200            msgbox_uvmat('ERROR',['cannot create the command file ' filename_superbat])
2201            return
2202        end
2203        for p=1:length(batch_file_list)
2204            if isunix
2205                fprintf(fid,['sh ' batch_file_list{p} '\n']);
2206            else
2207                fprintf(fid,['@call "' regexprep(filename_bat,'\\','\\\\') '"' '\n']);
2208            end
2209        end
2210        fclose(fid);
2211        if(isunix)
2212            system(['chmod +x ' filename_superbat]);
2213        end
2214        system([filename_superbat ' &']);% execute main commmand
2215    end
2216   
2217end
2218
2219
2220%% save interface state
2221if isfield(filecell,'nc')
2222    if isfield(filecell.nc,'civ2')
2223        fileresu=filecell.nc.civ2{1,1};
2224    else
2225        fileresu=filecell.nc.civ1{1,1};
2226    end
2227end
2228[RootPath,RootFile,field_count,str2,str_a,str_b,ext,nom_type,subdir]=name2display(fileresu);
2229namedoc=fullfile(RootPath,subdir,RootFile);
2230detect=1;
2231while detect==1
2232    namefigfull=[namedoc '.fig'];
2233    hh=dir(namefigfull);
2234    if ~isempty(hh)
2235        detect=1;
2236        namedoc=[namedoc '.0'];
2237    else
2238        detect=0;
2239    end
2240end
2241saveas(gcbf,namefigfull);%save the interface with name namefigfull (A CHANGER EN FICHIER  .xml)
2242
2243%Save info in personal profile (initiate browser next time) TODO
2244MenuFile={};
2245dir_perso=prefdir;
2246profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
2247if exist(profil_perso,'file')
2248    hh=load (profil_perso);
2249      if isfield(hh,'MenuFile')
2250          MenuFile=hh.MenuFile;
2251      end
2252      if isfield(filecell.nc,'civ2')
2253          MenuFile=[filecell.nc.civ2{1,1}; MenuFile];
2254      else
2255           MenuFile=[filecell.nc.civ1{1,1}; MenuFile];
2256      end
2257      save (profil_perso,'MenuFile','-append'); %store the file names for future opening of uvmat
2258else
2259    MenuFile=filecell.ima1.civ1(1,1);
2260    save (profil_perso,'MenuFile')
2261end
2262
2263
2264%------------------------------------------------------------------------
2265% --- determine the list of reference indices of processing file
2266function [ref_i,ref_j,errormsg]=find_ref_indices(handles)
2267%------------------------------------------------------------------------
2268errormsg=''; %default error message
2269first_i=str2double(get(handles.first_i,'String'));%first index i
2270last_i=str2double(get(handles.last_i,'String'));%last index i
2271incr_i=str2double(get(handles.incr_i,'String'));% increment
2272if isequal(get(handles.first_j,'Visible'),'on')
2273    first_j=str2double(get(handles.first_j,'String'));%first index j
2274    last_j=str2double(get(handles.last_j,'String'));%last index j
2275    incr_j=str2double(get(handles.incr_j,'String'));% increment
2276else
2277    first_j=1;
2278    last_j=1;
2279    incr_j=1;
2280end
2281ref_i=first_i:incr_i:last_i;% list of i indices (reference values for each pair)
2282ref_j=first_j:incr_j:last_j;% list of j indices (reference values for each pair)
2283if isnan(first_i)||isnan(first_j)
2284    errormsg='first field number not defined';
2285elseif isnan(last_i)||isnan(last_j)
2286    errormsg='last field number not defined';
2287elseif isnan(incr_i)||isnan(incr_j)
2288    errormsg='increment in field number not defined';
2289elseif last_i < first_i || last_j < first_j
2290    errormsg='last field number must be larger than the first one';
2291end
2292
2293%------------------------------------------------------------------------
2294% --- determine the list of filenames and indices needed for launch_job
2295function [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,compare]=...
2296    set_civ_filenames(handles,ref_i,ref_j,checkbox)
2297%------------------------------------------------------------------------
2298filecell=[];%default
2299
2300%% get the root names nomenclature and numbers
2301filebase=get(handles.RootName,'String');
2302
2303if isempty(filebase)||isequal(filebase,'')
2304    msgbox_uvmat('ERROR','no input files')
2305    return
2306end
2307
2308%filebase=regexprep(filebase,'\.fsnet','fsnet');% temporary fix for cluster Coriolis
2309filecell.filebase=filebase;
2310
2311browse=get(handles.RootName,'UserData');
2312compare_list=get(handles.ListCompareMode,'String');
2313val=get(handles.ListCompareMode,'Value');
2314compare=compare_list{val};
2315if strcmp(compare,'displacement')
2316    mode='displacement';
2317else
2318    mode_list=get(handles.ListPairMode,'String');
2319    mode_value=get(handles.ListPairMode,'Value');
2320    mode=mode_list{mode_value};
2321end
2322%time=get(handles.RootName,'UserData'); %get the set of times
2323ext_ima=get(handles.ImaExt,'String');
2324nom_type_nc=browse.nom_type_nc;
2325if isfield(browse,'nom_type_ima')
2326    nom_type_ima2=browse.nom_type_ima;
2327end
2328if isempty(nom_type_ima2),nom_type_ima2='1';end; %default
2329if isempty(nom_type_nc),nom_type_nc='_i1-i2';end; %default
2330[num1_civ1,num2_civ1,num_a_civ1,num_b_civ1,num1_civ2,num2_civ2,num_a_civ2,num_b_civ2]=...
2331    find_pair_indices(handles,ref_i,ref_j,mode);
2332%determine the new filebase for 'displacement' ListPairMode (comparison of two series)
2333filebase_B=filebase;% root name of the second field series for stereo
2334if strcmp(compare,'displacement') || strcmp(compare,'stereo PIV')
2335%     test_disp=1;
2336    nom_type_ima1=browse.nom_type_ima_1; %nomenclature type of the second file series
2337    [Path2,Name2]=fileparts(filebase_B);
2338    Path1=Path2;
2339    Name1=get(handles.RootName_1,'String');% root name of the first field series for stereo
2340    filebase_A=fullfile(Path1,Name1);
2341    if length(Name1)>6
2342        Name1=Name1(end-5:end);
2343    end
2344    if length(Name2)>6
2345        Name2=Name2(end-5:end);
2346    end
2347    filebase_AB=fullfile(Path2,[Name2 '-' Name1]);
2348else
2349%     test_disp=0;
2350    filebase_A=filebase;
2351    nom_type_ima1=nom_type_ima2;
2352    filebase_AB=filebase;
2353end
2354if strcmp(compare,'displacement')
2355    filebase_ima1=filebase_A;
2356    filebase_ima2=filebase_B;
2357    filebase_nc=filebase_AB; %root name for the result of civ2
2358else
2359    filebase_ima1=filebase_B;
2360    filebase_ima2=filebase_B;
2361    filebase_nc=filebase_B;
2362end
2363
2364%determine reference files for fix:
2365file_ref_fix1={};%default
2366file_ref_fix2={};
2367nbfield=length(num1_civ1);
2368nbslice=length(num_a_civ1);
2369if checkbox(2)==1% fix1 performed
2370    ref=get(handles.ref_fix1,'UserData');%read data on the ref file stored by get_ref_fix1_Callback
2371    if ~isempty(ref)
2372        first_i=str2double(get(handles.first_i,'String'));
2373        last_i=str2double(get(handles.last_i,'String'));
2374        incr_i=str2double(get(handles.incr_i,'String'));
2375        first_j=str2double(get(handles.first_j,'String'));
2376        last_j=str2double(get(handles.last_j,'String'));
2377        incr_j=str2double(get(handles.incr_j,'String'));
2378        num_i_ref=first_i:incr_i:last_i;
2379        num_j_ref=first_j:incr_j:last_j;
2380        if isequal(mode,'displacement')
2381            num_i1=num_i_ref;
2382            num_i2=num_i_ref;
2383            num_j1=num_j_ref;
2384            num_j2=num_j_ref;
2385        elseif isequal(mode,'pair j1-j2')% isequal(mode,'st_pair j1-j2')
2386            num_i1=num_i_ref;
2387            num_i2=num_i1;
2388            num_j1=ref.num_a*ones(size(num_i_ref));
2389            num_j2=ref.num_b*ones(size(num_i_ref));
2390        elseif isequal(mode,'series(Di)') % isequal(mode,'st_series(Di)')
2391            delta1=floor((ref.num2-ref.num1)/2);
2392            delta2=ceil((ref.num2-ref.num1)/2);
2393            num_i1=num_i_ref-delta1*ones(size(num_i_ref));
2394            num_i2=num_i_ref+delta2*ones(size(num_i_ref));
2395            if isempty(ref.num_a)
2396                ref.num_a=1;
2397            end
2398            num_j1=ref.num_a*ones(size(num_i1));
2399            num_j2=num_j1;
2400        elseif isequal(mode,'series(Dj)')%| isequal(mode,'st_series(Dj)')
2401            delta1=floor((ref.num_b-ref.num_a)/2);
2402            delta2=ceil((ref.num_b-ref.num_a)/2);
2403            num_i1=ref.num1*ones(size(num_i_ref));
2404            num_i2=num_i1;
2405            num_j1=num_j_ref-delta1*ones(size(num_j_ref));
2406            num_j2=num_j_ref+delta2*ones(size(num_j_ref));
2407        end
2408        for ifile=1:nbfield
2409            for j=1:nbslice
2410                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);%
2411                file_ref_fix1(ifile,j)={file_ref};
2412                if ~exist(file_ref,'file')
2413                    msgbox_uvmat('ERROR',['reference file ' file_ref ' not found for fix1'])
2414                    filecell=[];
2415                    return
2416                end
2417            end
2418        end
2419    end
2420end
2421
2422%determine reference files for checkfix2:
2423if checkbox(5)==1% fix2 performed
2424    ref=get(handles.ref_fix2,'UserData');
2425    if ~isempty(ref)
2426        first_i=str2double(get(handles.first_i,'String'));
2427        last_i=str2double(get(handles.last_i,'String'));
2428        incr_i=str2double(get(handles.incr_i,'String'));
2429        first_j=str2double(get(handles.first_j,'String'));
2430        last_j=str2double(get(handles.last_j,'String'));
2431        incr_j=str2double(get(handles.incr_j,'String'));
2432        num_i_ref=first_i:incr_i:last_i;
2433        num_j_ref=first_j:incr_j:last_j;
2434        if isequal(mode,'displacement')
2435            num_i1=num_i_ref;
2436            num_i2=num_i_ref;
2437            num_j1=num_j_ref;
2438            num_j2=num_j_ref;
2439        elseif isequal(mode,'pair j1-j2')
2440            num_i1=num_i_ref;
2441            num_i2=num_i1;
2442            num_j1=ref.num_a;
2443            num_j2=ref.num_b;
2444        elseif isequal(mode,'series(Di)')
2445            delta1=floor((ref.num2-ref.num1)/2);
2446            delta2=ceil((ref.num2-ref.num1)/2);
2447            num_i1=num_i_ref-delta1*ones(size(num_i_ref));
2448            num_i2=num_i_ref+delta2*ones(size(num_i_ref));
2449            num_j1=ref.num_a*ones(size(num_i1));
2450            num_j2=num_j1;
2451        elseif isequal(mode,'series(Dj)')
2452            delta1=floor((ref.num_b-ref.num_a)/2);
2453            delta2=ceil((ref.num_b-ref.num_a)/2);
2454            num_i1=ref.num1*ones(size(num_i_ref));
2455            num_i2=num_i1;
2456            num_j1=num_j_ref-delta1*ones(size(num_j_ref));
2457            num_j2=num_j_ref+delta2*ones(size(num_j_ref));
2458        end
2459        for ifile=1:nbfield
2460            for j=1:nbslice
2461                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);%
2462                file_ref_fix2(ifile,j)={file_ref};
2463                if ~exist(file_ref,'file')
2464                    msgbox_uvmat('ERROR',['reference file ' file_ref ' not found for fix2'])
2465                    filecell={};
2466                    return
2467                end
2468            end
2469        end
2470    end
2471end
2472
2473%check dir
2474subdir_civ1=get(handles.txt_SubdirCiv1,'String');%subdirectory subdir_civ1 for the netcdf output data
2475subdir_civ2=get(handles.txt_SubdirCiv2,'String');
2476if isequal(subdir_civ1,''),subdir_civ1='CIV'; end% put default subdir
2477if isequal(subdir_civ2,''),subdir_civ2=subdir_civ1; end% put default subdir
2478% currentdir=pwd;%store the current working directory
2479[Path_ima,Name]=fileparts(filebase);%Path of the image files (.civ)
2480if ~exist(Path_ima,'dir')
2481    msgbox_uvmat('ERROR',['path to images ' Path_ima ' not found'])
2482    filecell={};
2483    return
2484end
2485[xx,message]=fileattrib(Path_ima);
2486if ~isempty(message) && ~isequal(message.UserWrite,1)
2487    msgbox_uvmat('ERROR',['No writting access to ' Path_ima])
2488    filecell={};
2489%     cd(currentdir);
2490    return
2491end
2492
2493%check the existence of the netcdf and image files involved
2494% %%%%%%%%%%%%  case CheckCiv1 activated   %%%%%%%%%%%%%
2495if checkbox(1)==1;
2496    detect=1;
2497    vers=0;
2498    subdir_civ1_new=subdir_civ1;
2499    while detect==1 %create a new subdir if the netcdf files already exist
2500        for ifile=1:nbfield
2501            for j=1:nbslice
2502                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);
2503                detect=exist(filename,'file')==2;
2504                if detect% if a netcdf file already exists
2505                    indstr=regexp(subdir_civ1_new,'\D');
2506                    if indstr(end)<length(subdir_civ1_new) %subdir_civ1 ends by a number
2507                        vers=str2double(subdir_civ1_new(indstr(end)+1:end))+1;
2508                        subdir_civ1_new=[subdir_civ1_new(1:indstr(end)) num2str(vers)];
2509                    else
2510                        vers=vers+1;
2511                        subdir_civ1_new=[subdir_civ1_new(1:indstr(end)) '_' num2str(vers)];       
2512                    end
2513                    subdir_civ2=subdir_civ1_new;
2514                    break
2515                end
2516                filecell.nc.civ1(ifile,j)={filename};
2517            end
2518            if detect% if a netcdf file already exists
2519                break
2520            end
2521        end
2522 
2523        %create the new txt_SubdirCiv1
2524        if ~exist(fullfile(Path_ima,subdir_civ1_new),'dir')
2525%             cd(Path_ima);         
2526            [xx,msg1]=mkdir(fullfile(Path_ima,subdir_civ1_new));
2527
2528            if ~strcmp(msg1,'')
2529                msgbox_uvmat('ERROR',['cannot create ' subdir_civ1_new ': ' msg1])%error message for directory creation
2530                filecell={};
2531                return
2532            elseif isunix         
2533                [xx,msg2] = fileattrib(fullfile(Path_ima,subdir_civ1_new),'+w','g'); %yield writing access (+w) to user group (g)
2534                if ~strcmp(msg2,'')
2535                    msgbox_uvmat('ERROR',['pb of permission for  ' fullfile(Path_ima,subdir_civ1_new) ': ' msg2])%error message for directory creation
2536                    filecell={};
2537                    return
2538                end
2539            end
2540%             cd(currentdir);
2541        end
2542        if strcmp(compare,'stereo PIV')&&(strcmp(mode,'pair j1-j2')||strcmp(mode,'series(Dj)')||strcmp(mode,'series(Di)'))%check second nc series
2543            for ifile=1:nbfield
2544                for j=1:nbslice
2545                    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);%
2546                    detect=exist(filename,'file')==2;
2547                    if detect% if a netcdf file already exists
2548                       indstr=regexp(subdir_civ1_new,'\D');
2549                       if indstr(end)<length(subdir_civ1_new) %subdir_civ1 ends by a number
2550                           vers=str2double(subdir_civ1_new(indstr(end)+1:end))+1;
2551                           subdir_civ1_new=[subdir_civ1_new(1:indstr(end)) num2str(vers)];
2552                       else
2553                           vers=vers+1;
2554                           subdir_civ1_new=[subdir_civ1_new '_' num2str(vers)];
2555                       end
2556                       subdir_civ2=subdir_civ1;
2557                       break
2558                    end
2559                    filecell.ncA.civ1(ifile,j)={filename};
2560                end
2561                if detect% if a netcdf file already exists
2562                    break
2563                end
2564            end
2565            %create the new txt_SubdirCiv1
2566            if ~exist(fullfile(Path_ima,subdir_civ1_new),'dir')
2567%                    cd(Path_ima);         
2568                [xx,msg1]=mkdir(fullfile(Path_ima,subdir_civ1_new));
2569%                             cd(currentdir);
2570                if ~strcmp(msg1,'')
2571                    msgbox_uvmat('ERROR',['cannot create ' subdir_civ1_new ': ' msg1])
2572%                     cd(currentdir)
2573                    filecell={};
2574                    return
2575                else
2576                    [xx,msg2] = fileattrib(fullfile(Path_ima,subdir_civ1_new),'+w','g'); %yield writing access (+w) to user group (g)
2577                    if ~strcmp(msg2,'')
2578                        msgbox_uvmat('ERROR',['pb of permission for ' subdir_civ1_new ': ' msg2])%error message for directory creation
2579%                         cd(currentdir)
2580                        filecell={};
2581                        return
2582                    end
2583                end
2584            end
2585        end
2586    end
2587    subdir_civ1=subdir_civ1_new;
2588    % get image names
2589    for ifile=1:nbfield
2590        for j=1:nbslice
2591            filename=name_generator(filebase_ima1, num1_civ1(ifile),num_a_civ1(j),ext_ima,nom_type_ima1);
2592            idetect(j)=exist(filename,'file')==2;
2593            filecell.ima1.civ1(ifile,j)={filename}; %first image
2594            filename=name_generator(filebase_ima2, num2_civ1(ifile),num_b_civ1(j),ext_ima,nom_type_ima2);
2595            idetect_1(j)=exist(filename,'file')==2;
2596            filecell.ima2.civ1(ifile,j)={filename};%second image
2597        end
2598        [idetectmin,indexj]=min(idetect);
2599        if idetectmin==0,
2600            msgbox_uvmat('ERROR',[filecell.ima1.civ1{ifile,indexj} ' not found'])
2601            filecell={};
2602           % cd(currentdir)
2603            return
2604        end
2605        [idetectmin,indexj]=min(idetect_1);
2606        if idetectmin==0,
2607            msgbox_uvmat('ERROR',[filecell.ima2.civ1{ifile,indexj} ' not found'])
2608            filecell={};
2609            %cd(currentdir)
2610            return
2611        end
2612    end
2613    if strcmp(compare,'stereo PIV') && (strcmp(mode,'pair j1-j2') || strcmp(mode,'series(Dj)') || strcmp(mode,'series(Di)'))
2614        for ifile=1:nbfield
2615            for j=1:nbslice
2616                filename=name_generator(filebase_A, num1_civ1(ifile),num_a_civ1(j),ext_ima,nom_type_ima1);
2617                idetect(j)=exist(filename,'file')==2;
2618                filecell.imaA1.civ1(ifile,j)={filename} ;%first image
2619                filename=name_generator(filebase_A, num2_civ1(ifile),num_b_civ1(j),ext_ima,nom_type_ima2);
2620                idetect_1(j)=exist(filename,'file')==2;
2621                filecell.imaA2.civ1(ifile,j)={filename};%second image
2622            end
2623            [idetectmin,indexj]=min(idetect);
2624            if idetectmin==0,
2625                msgbox_uvmat('ERROR',[filecell.imaA1.civ1{ifile,indexj} ' not found'])
2626                filecell={};
2627               % cd(currentdir)
2628                return
2629            end
2630            [idetectmin,indexj]=min(idetect_1);
2631            if idetectmin==0,
2632                msgbox_uvmat('ERROR',[filecell.imaA2.civ1{ifile,indexj} ' not found'])
2633                filecell={};
2634               % cd(currentdir)
2635                return
2636            end
2637        end
2638    end
2639   
2640    %%%%%%%%%%%%%  checkfix1 or checkpatch1 activated but no checkciv1   %%%%%%%%%%%%%
2641elseif (checkbox(2)==1 || checkbox(3)==1);
2642    for ifile=1:nbfield
2643        for j=1:nbslice
2644            filename=name_generator(filebase_nc,num1_civ1(ifile),num_a_civ1(j),'.nc',...
2645                nom_type_nc,1,num2_civ1(ifile),num_b_civ1(j),subdir_civ1);%
2646            detect=exist(filename,'file')==2;
2647            if detect==0
2648                msgbox_uvmat('ERROR',[filename ' not found'])
2649                filecell={};
2650               % cd(currentdir)
2651                return
2652            end
2653            filecell.nc.civ1(ifile,j)={filename};
2654        end
2655    end
2656    if strcmp(compare,'stereo PIV')
2657        for ifile=1:nbfield
2658            for j=1:nbslice
2659                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);%
2660                filecell.ncA.civ1(ifile,j)={filename};
2661                if ~exist(filename,'file')
2662                    msgbox_uvmat('ERROR',['input file ' filename ' not found'])
2663                    set(handles.RUN, 'Enable','On')
2664                    set(handles.RUN,'BackgroundColor',[1 0 0])
2665                    filecell={};
2666                    %cd(currentdir)
2667                    return
2668                end
2669            end
2670        end
2671    end
2672end
2673
2674%%%%%%%%%%%%%  if checkciv2 performed with pairs different than checkciv1  %%%%%%%%%%%%%
2675testdiff=0;
2676if (checkbox(4)==1)&&...
2677        ((get(handles.ListPairCiv1,'Value')~=get(handles.ListPairCiv2,'Value'))||~strcmp(subdir_civ2,subdir_civ1))
2678    testdiff=1;
2679    detect=1;
2680    vers=0;
2681    subdir_civ2_new=subdir_civ2;
2682    while detect==1 %create a new subdir if the netcdf files already exist
2683        for ifile=1:nbfield
2684            for j=1:nbslice
2685                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);%
2686                detect=exist(filename,'file')==2;
2687                if detect% if a netcdf file already exists
2688                    indstr=regexp(subdir_civ2,'\D');
2689                    if indstr(end)<length(subdir_civ2) %subdir_civ1 ends by a number
2690                        vers=str2double(subdir_civ2(indstr(end)+1:end))+1;
2691                        subdir_civ2_new=[subdir_civ2(1:indstr(end)) num2str(vers)];
2692                    else
2693                        vers=vers+1;
2694                        subdir_civ2_new=[subdir_civ1 '_' num2str(vers)];
2695                    end
2696                    break
2697                end
2698                filecell.nc.civ2(ifile,j)={filename};
2699            end
2700            if detect% if a netcdf file already exists
2701                break
2702            end
2703        end
2704        %create the new subdir_civ2_new
2705        if ~exist(fullfile(Path_ima,subdir_civ2_new),'dir')
2706            [xx,m2]=mkdir(fullfile(Path_ima,subdir_civ2_new));
2707            [xx,msg2] = fileattrib(fullfile(Path_ima,subdir_civ2_new),'+w','g'); %yield writing access (+w) to user group (g)
2708            if ~isequal(m2,'')
2709                msgbox_uvmat('ERROR',['cannot create ' fullfile(Path_ima,subdir_civ2_new) ': ' m2])
2710                filecell={};
2711               % cd(currentdir)
2712                return
2713            end
2714        end
2715        if strcmp(compare,'stereo PIV')%check second nc series
2716            for ifile=1:nbfield
2717                for j=1:nbslice
2718                    filename=name_generator(filebase_A,num1_civ2(ifile),num_a_civ2(j),'.nc',...
2719                        nom_type_nc,1,num2_civ2(ifile),num_b_civ1(j),subdir_civ2_new);%
2720                    detect=exist(filename,'file')==2;
2721                    if detect% if a netcdf file already exists
2722                        indstr=regexp(subdir_civ2,'\D');
2723                        if indstr(end)<length(subdir_civ2) %subdir_civ1 ends by a number
2724                           vers=str2double(subdir_civ2(indstr(end)+1:end))+1;
2725                           subdir_civ2_new=[subdir_civ2(1:indstr(end)) num2str(vers)];
2726                        else
2727                           vers=vers+1;
2728                           subdir_civ2_new=[subdir_civ1 '_' num2str(vers)];
2729                        end
2730                        break
2731                    end
2732                    filecell.ncA.civ2(ifile,j)={filename};
2733                end
2734                if detect% if a netcdf file already exists
2735                    break
2736                end
2737            end
2738            subdir_civ2=subdir_civ2_new;
2739            %create the new txt_SubdirCiv1
2740            if ~exist(fullfile(Path_ima,subdir_civ2_new),'dir')
2741                [xx,m2]=mkdir(subdir_civ2_new);
2742                 [xx,msg2] = fileattrib(fullfile(Path_ima,subdir_civ2_new),'+w','g'); %yield writing access (+w) to user group (g)
2743                if ~isequal(m2,'')
2744                    msgbox_uvmat('ERROR', ['cannot create ' fullfile(Path_ima,subdir_civ2_new) ': ' m2])%error message for directory creation
2745                  %  cd(currentdir)
2746                    filecell={};
2747                    return
2748                end
2749            end
2750        end
2751    end
2752    subdir_civ2=subdir_civ2_new;
2753end
2754%cd(currentdir);%come back to the current working directory
2755
2756%%%%%%%%%%%%%  if checkciv2 results are obtained or used  %%%%%%%%%%%%%
2757if checkbox(4)==1 || checkbox(5)==1 || checkbox(6)==1 %civ2
2758    %check source netcdf file of checkciv1 estimates
2759    if checkbox(1)==0; %no civ1 performed
2760        for ifile=1:nbfield
2761            for j=1:nbslice
2762                filename=name_generator(filebase_nc,num1_civ1(ifile),num_a_civ1(j),'.nc',...
2763                    nom_type_nc,1,num2_civ1(ifile),num_b_civ1(j),subdir_civ1);%
2764                filecell.nc.civ1(ifile,j)={filename};% name of the civ1 file
2765                if ~exist(filename,'file')
2766                    msgbox_uvmat('ERROR',['input file ' filename ' not found'])
2767                    filecell={};
2768                    return
2769                end
2770                if ~testdiff % civ2 or patch2 are written in the same file as civ1
2771                    if checkbox(4)==0 ; %check the existence of civ2 if it is not calculated
2772                        Data=nc2struct(filename,'ListGlobalAttribute','CivStage','civ2');
2773                        if ~isempty(Data.CivStage) && Data.CivStage<4 %test for civ files
2774                            msgbox_uvmat('ERROR',['no civ2 data in ' filename])
2775                            filecell=[];
2776                            return
2777                        elseif isempty(Data.civ2)||isequal(Data.civ2,0)
2778                            msgbox_uvmat('ERROR',['no civ2 data in ' filename])
2779                            filecell=[];
2780                            return
2781                        end
2782                    elseif checkbox(3)==0; %check the existence of patch if it is not calculated
2783                        Data=nc2struct(filename,'ListGlobalAttribute','CivStage','patch');
2784                        if ~isempty(Data.CivStage)
2785                            if Data.CivStage<3 %test for civ files
2786                                msgbox_uvmat('ERROR',['no patch data in ' filename])
2787                                filecell=[];
2788                                return
2789                            end
2790                        elseif isempty(Data.patch)||isequal(Data.patch,0)
2791                            msgbox_uvmat('ERROR',['no patch data in ' filename])
2792                            filecell=[];
2793                            return
2794                        end
2795                    end
2796                end
2797            end
2798        end
2799        if strcmp(compare,'stereo PIV')
2800            for ifile=1:nbfield
2801                for j=1:nbslice
2802                    filename=name_generator(filebase_A,num1_civ2(ifile),num_a_civ2(j),'.nc',...
2803                        nom_type_nc,1,num2_civ2(ifile),num_b_civ2(j),subdir_civ2);%
2804                    filecell.ncA.civ2(ifile,j)={filename};
2805                    if ~exist(filename,'file')
2806                        msgbox_uvmat('ERROR',['input file ' filename ' not found'])
2807                        set(handles.RUN, 'Enable','On')
2808                        set(handles.RUN,'BackgroundColor',[1 0 0])
2809                        return
2810                    end
2811                end
2812            end
2813        end
2814    end
2815   
2816    detect=1;
2817    %     while detect==1%creates a new subdir if the netcdf files already contain checkciv2 data
2818    for ifile=1:nbfield
2819        for j=1:nbslice
2820            filename=name_generator(filebase_nc,num1_civ2(ifile),num_a_civ2(j),'.nc',...
2821                nom_type_nc,1,num2_civ2(ifile),num_b_civ2(j),subdir_civ2);
2822            detect=exist(filename,'file')==2;
2823            filecell.nc.civ2(ifile,j)={filename};
2824        end
2825    end
2826    %get first image names for checkciv2
2827    if checkbox(1)==1 && isequal(num1_civ1,num1_civ2) && isequal(num_a_civ1,num_a_civ2)
2828        filecell.ima1.civ2=filecell.ima1.civ1;
2829    elseif checkbox(4)==1
2830        for ifile=1:nbfield
2831            for j=1:nbslice
2832                filename=name_generator(filebase_ima1, num1_civ2(ifile),num_a_civ2(j),ext_ima,nom_type_ima1);
2833                idetect_2(j)=exist(filename,'file')==2;
2834                filecell.ima1.civ2(ifile,j)={filename};%first image
2835            end
2836            [idetectmin,indexj]=min(idetect_2);
2837            if idetectmin==0,
2838                msgbox_uvmat('ERROR',['input image ' filecell.ima1.civ2{ifile,indexj} ' not found'])
2839                filecell=[];
2840                return
2841            end
2842        end
2843    end
2844   
2845    %get second image names for checkciv2
2846    if checkbox(1)==1 && isequal(num2_civ1,num2_civ2) && isequal(num_b_civ1,num_b_civ2)
2847        filecell.ima2.civ2=filecell.ima2.civ1;
2848    elseif checkbox(4)==1
2849        for ifile=1:nbfield
2850            for j=1:nbslice
2851                filename=name_generator(filebase_ima2, num2_civ2(ifile),num_b_civ2(j),ext_ima,nom_type_ima2);
2852                idetect_3(j)=exist(filename,'file')==2;
2853                filecell.ima2.civ2(ifile,j)={filename};%first image
2854            end
2855            [idetectmin,indexj]=min(idetect_3);
2856            if idetectmin==0,
2857                msgbox_uvmat('ERROR',['input image ' filecell.ima2.civ2{ifile,indexj} ' not found'])
2858                filecell=[];
2859                return
2860            end
2861        end
2862    end
2863end
2864if (checkbox(5) || checkbox(6)) && ~checkbox(4)  % need to read an existing netcdf civ2 file
2865    if ~testdiff
2866        filecell.nc.civ2=filecell.nc.civ1;% file already checked
2867    else     % check the civ2 files
2868        for ifile=1:nbfield
2869            for j=1:nbslice
2870                filename=name_generator(filebase_nc,num1_civ2(ifile),num_a_civ2(j),'.nc',...
2871                    nom_type_nc,1,num2_civ2(ifile),num_b_civ2(j),subdir_civ2);%
2872                filecell.nc.civ2(ifile,j)={filename};
2873                if ~exist(filename,'file')
2874                    msgbox_uvmat('ERROR',['input file ' filename ' not found'])
2875                    filecell=[];
2876                    return
2877                else
2878                    Data=nc2struct(filename,'ListGlobalAttribute','CivStage','civ2');
2879                    if ~isempty(Data.CivStage) && Data.CivStage<4 %test for civ files
2880                            msgbox_uvmat('ERROR',['no civ2 data in ' filename])
2881                            filecell=[];
2882                            return
2883                    elseif isempty(Data.civ2)||isequal(Data.civ2,0)
2884                        msgbox_uvmat('ERROR',['no civ2 data in ' filename])
2885                        filecell=[];
2886                        return
2887                    end
2888                end
2889            end
2890        end
2891    end
2892end
2893
2894%%%%%%%%%%%%%  if stereo fields are calculated by PATCH %%%%%%%%%%%%%
2895if strcmp(compare,'stereo PIV')
2896    if  checkbox(3) && isequal(get(handles.test_stereo1,'Value'),1)
2897        for ifile=1:nbfield
2898            for j=1:nbslice
2899                filename=name_generator(filebase_AB,num1_civ1(ifile),num_a_civ1(j),'.nc',...
2900                    nom_type_nc,1,num2_civ1(ifile),num_b_civ1(j),subdir_civ1);%
2901                filecell.st(ifile,j)={filename};
2902            end
2903        end
2904    end
2905    if  checkbox(6) && isequal(get(handles.CheckStereo,'Value'),1)
2906        for ifile=1:nbfield
2907            for j=1:nbslice
2908                filename=name_generator(filebase_AB,num1_civ2(ifile),num_a_civ2(j),'.nc',...
2909                    nom_type_nc,1,num2_civ2(ifile),num_b_civ2(j),subdir_civ2);%
2910                filecell.st(ifile,j)={filename};
2911            end
2912        end
2913    end
2914end
2915set(handles.txt_SubdirCiv1,'String',subdir_civ1);%update the edit box
2916set(handles.txt_SubdirCiv2,'String',subdir_civ2);%update the edit box
2917browse.nom_type_nc=nom_type_nc;
2918set(handles.RootName,'UserData',browse); %update the nomenclature type for uvmat
2919
2920
2921%COPY IMAGES TO THE FORMAT .png IF NEEDED
2922if isequal(nom_type_ima1,'*')%case of movie files
2923    nom_type_imanew1='_i';
2924else
2925    nom_type_imanew1=nom_type_ima1;
2926end
2927if isequal(nom_type_ima2,'*')%case of movie files
2928    nom_type_imanew2='_i';
2929else
2930    nom_type_imanew2=nom_type_ima2;
2931end
2932if ~isequal(ext_ima,'.png')
2933    %%type of image file
2934    type_ima1='none';%default
2935    movieobject1=[];%default
2936    if strcmpi(ext_ima,'.avi')
2937        hhh=which('mmreader');
2938        if ~isequal(hhh,'')&& mmreader.isPlatformSupported()% if the mmreader function is found (recent version of matlab)
2939            type_ima1='movie';
2940            movieobject1=mmreader([filebase_ima2 ext_ima]);
2941        else
2942            type_ima1='avi';
2943        end
2944    elseif ischar(ext_ima) && ~isempty(ext_ima(2:end))
2945        form=imformats(ext_ima(2:end));
2946        if ~isempty(form)% if the extension corresponds to an image format recognized by Matlab
2947            if isequal(nom_type_ima1,'*');
2948                type_ima1='multimage';%image series in a single image file
2949            else
2950                type_ima1='image';
2951            end
2952        end
2953    end
2954    type_ima2='none';%default
2955    movieobject2=[];
2956    if strcmpi(ext_ima,'.avi')
2957        hhh=which('mmreader');
2958        if ~isequal(hhh,'')&& mmreader.isPlatformSupported()% if the mmreader function is found (recent version of matlab)
2959            type_ima2='movie';
2960            movieobject2=mmreader([filebase_ima2 ext_ima]);
2961        else
2962            type_ima2='avi';
2963        end
2964    elseif ischar(ext_ima) && ~isempty(ext_ima(2:end))
2965        form=imformats(ext_ima(2:end));
2966        if ~isempty(form)% if the extension corresponds to an image format recognized by Matlab
2967            if isequal(nom_type_ima1,'*');
2968                type_ima2='multimage';%image series in a single image file
2969            else
2970                type_ima2='image';
2971            end
2972        end
2973    end
2974    %npxy=get(handles.ImaExt,'UserData');
2975    % %     if numel(npxy)<2
2976    %
2977    %         filename=name_generator(filebase_ima1,num1_civ1(1),num_a_civ1(1),ImaExt,nom_type_ima1);
2978    %         A=imread(filename);
2979    %         npxy=size(A);
2980    % %     end
2981    %     npy=npxy(1);
2982    %     npx=npxy(2);
2983    if checkbox(1) %if civ1 is performed
2984        h = waitbar(0,'copy images to the .png format for civ1');% display a wait bar
2985        for ifile=1:nbfield
2986            waitbar(ifile/nbfield);
2987            for j=1:nbslice
2988                filename=name_generator(filebase_ima1,num1_civ1(ifile),num_a_civ1(j),'.png',nom_type_imanew1);
2989                if ~exist(filename,'file')
2990                    A=read_image(filecell.ima1.civ1{ifile,j},type_ima1,num1_civ1(ifile),movieobject1);
2991                    imwrite(A,filename,'BitDepth',16);
2992                end
2993                filecell.ima1.civ1(ifile,j)={filename};
2994                filename=name_generator(filebase_ima2, num2_civ1(ifile),num_b_civ1(j),'.png',nom_type_imanew2);
2995                if ~exist(filename,'file')
2996                    A=read_image(filecell.ima2.civ1{ifile,j},type_ima2,num2_civ1(ifile),movieobject2);
2997                    imwrite(A,filename,'BitDepth',16);
2998                end
2999                filecell.ima2.civ1(ifile,j)={filename};
3000            end
3001        end
3002        close(h)
3003    end
3004    if checkbox(4) %if civ2 is performed
3005        h = waitbar(0,'copy images to the .png format for civ2');% display a wait bar
3006        for ifile=1:nbfield
3007            waitbar(ifile/nbfield);
3008            for j=1:nbslice
3009                filename=name_generator(filebase_ima1,num1_civ2(ifile),num_a_civ2(j),'.png',nom_type_imanew1);
3010                if ~exist(filename,'file')
3011                    A=read_image(cell2mat(filecell.ima1.civ2(ifile,j)),type_ima2,num1_civ2(ifile));
3012                    imwrite(A,filename,'BitDepth',16);
3013                end
3014                filecell.ima1.civ2(ifile,j)={filename};
3015                filename=name_generator(filebase_ima2, num2_civ2(ifile),num_b_civ2(j),'.png',nom_type_imanew2);
3016                if ~exist(filename,'file')
3017                    A=read_image(cell2mat(filecell.ima2.civ2(ifile,j)),type_ima2,num2_civ2(ifile));
3018                    imwrite(A,filename,'BitDepth',16);
3019                end
3020                filecell.ima2.civ2(ifile,j)={filename};
3021            end
3022        end
3023        close(h);
3024    end
3025end
3026
3027%------------------------------------------------------------------------
3028% --- determine the list of index pairs of processing file
3029function [num1_civ1,num2_civ1,num_a_civ1,num_b_civ1,num1_civ2,num2_civ2,num_a_civ2,num_b_civ2]=...
3030    find_pair_indices(handles,ref_i,ref_j,mode)
3031%------------------------------------------------------------------------
3032
3033list_civ1=get(handles.ListPairCiv1,'String');
3034index_civ1=get(handles.ListPairCiv1,'Value');
3035str_civ1=list_civ1{index_civ1};%string defining the image pairs for civ1
3036if isempty(str_civ1)||isequal(str_civ1,'')
3037    msgbox_uvmat('ERROR','no image pair selected for civ1')
3038    return
3039end
3040list_civ2=get(handles.ListPairCiv2,'String');
3041index_civ2=get(handles.ListPairCiv2,'Value');
3042if index_civ2>length(list_civ2)
3043    list_civ2=list_civ1;
3044    index_civ2=index_civ1;
3045end
3046str_civ2=list_civ2{index_civ2};%string defining the image pairs for civ2
3047
3048if isequal (mode,'series(Di)')
3049    lastfield=str2double(get(handles.nb_field,'String'));
3050    num1_civ1=ref_i-floor(index_civ1/2)*ones(size(ref_i));% set of first image numbers
3051    num2_civ1=ref_i+ceil(index_civ1/2)*ones(size(ref_i));
3052    num_a_civ1=ref_j;
3053    num_b_civ1=ref_j;
3054    num1_civ2=ref_i-floor(index_civ2/2)*ones(size(ref_i));
3055    num2_civ2=ref_i+ceil(index_civ2/2)*ones(size(ref_i));
3056    num_a_civ2=ref_j;
3057    num_b_civ2=ref_j;   
3058   
3059    % adjust the first and last field number
3060    lastfield=str2double(get(handles.nb_field,'String'));
3061    if isnan(lastfield)
3062        indsel=find((num1_civ1 >= 1)&(num1_civ2 >= 1));
3063    else
3064        indsel=find((num2_civ1 <= lastfield)&(num2_civ2 <= lastfield)&(num1_civ1 >= 1)&(num1_civ2 >= 1));
3065    end
3066    if length(indsel)>=1
3067        firstind=indsel(1);
3068        lastind=indsel(end);
3069        set(handles.first_i,'String',num2str(ref_i(firstind)))%update the display of first and last fields
3070        set(handles.last_i,'String',num2str(ref_i(lastind)))
3071        ref_i=ref_i(indsel);
3072        num1_civ1=num1_civ1(indsel);
3073        num1_civ2=num1_civ2(indsel);
3074        num2_civ1=num2_civ1(indsel);
3075        num2_civ2=num2_civ2(indsel);
3076    end
3077elseif isequal (mode,'series(Dj)')
3078    lastfield_j=str2double(get(handles.nb_field2,'String'));
3079    num1_civ1=ref_i;% set of first image numbers
3080    num2_civ1=ref_i;
3081    num_a_civ1=ref_j-floor(index_civ1/2)*ones(size(ref_j));
3082    num_b_civ1=ref_j+ceil(index_civ1/2)*ones(size(ref_j));
3083    num1_civ2=ref_i;
3084    num2_civ2=ref_i;
3085    num_a_civ2=ref_j-floor(index_civ2/2)*ones(size(ref_j));
3086    num_b_civ2=ref_j+ceil(index_civ2/2)*ones(size(ref_j));
3087    % adjust the first and last field number
3088    if isnan(lastfield_j)
3089        indsel=find((num_a_civ1 >= 1)&(num_a_civ2 >= 1));
3090    else
3091        indsel=find((num_b_civ1 <= lastfield_j)&(num_b_civ2 <= lastfield_j)&(num_a_civ1 >= 1)&(num_a_civ2 >= 1));
3092    end
3093    if length(indsel)>=1
3094        firstind=indsel(1);
3095        lastind=indsel(end);
3096        set(handles.first_j,'String',num2str(ref_j(firstind)))%update the display of first and last fields
3097        set(handles.last_j,'String',num2str(ref_j(lastind)))
3098        ref_j=ref_j(indsel);
3099        num_a_civ1=num_a_civ1(indsel);
3100        num_b_civ1=num_b_civ1(indsel);
3101        num_a_civ2=num_a_civ2(indsel);
3102        num_b_civ2=num_b_civ2(indsel);
3103    end
3104elseif isequal(mode,'pair j1-j2') %case of bursts (png_old or png_2D)
3105    displ_num=get(handles.ListPairCiv1,'UserData');
3106    num1_civ1=ref_i;
3107    num2_civ1=ref_i;
3108    num_a_civ1=displ_num(1,index_civ1);
3109    num_b_civ1=displ_num(2,index_civ1);
3110    num1_civ2=ref_i;
3111    num2_civ2=ref_i;
3112    num_a_civ2=displ_num(1,index_civ2);
3113    num_b_civ2=displ_num(2,index_civ2);
3114elseif isequal(mode,'displacement')
3115    num1_civ1=ref_i;
3116    num2_civ1=ref_i;
3117    num_a_civ1=ref_j;
3118    num_b_civ1=ref_j;
3119    num1_civ2=ref_i;
3120    num2_civ2=ref_i;
3121    num_a_civ2=ref_j;
3122    num_b_civ2=ref_j;
3123end
3124
3125
3126%------------------------------------------------------------------------
3127% --- STEREO Interp
3128function cmd=RUN_STINTERP(stinterpBin,filename_A_nc,filename_B_nc,filename_nc,nx_patch,ny_patch,rho_patch,subdomain_patch,thresh_value,xmlA,xmlB)
3129%------------------------------------------------------------------------
3130namelog=[filename_nc(1:end-3) '_stinterp.log'];
3131cmd=[stinterpBin ' -f1 ' filename_A_nc  ' -f2 ' filename_B_nc ' -f  ' filename_nc ...
3132    ' -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
3133
3134%------------------------------------------------------------------------
3135% --- Executes on button press in CheckCiv1.
3136function CheckCiv1_Callback(hObject, eventdata, handles)
3137%------------------------------------------------------------------------
3138update_CivOptions(handles)
3139
3140%------------------------------------------------------------------------
3141% --- Executes on button press in CheckFix1.
3142function CheckFix1_Callback(hObject, eventdata, handles)
3143%------------------------------------------------------------------------
3144update_CivOptions(handles)
3145
3146%------------------------------------------------------------------------
3147% --- Executes on button press in CheckPatch1.
3148function CheckPatch1_Callback(hObject, eventdata, handles)
3149%------------------------------------------------------------------------
3150update_CivOptions(handles)
3151
3152%------------------------------------------------------------------------
3153% --- Executes on button press in CheckCiv2.
3154function CheckCiv2_Callback(hObject, eventdata, handles)
3155%------------------------------------------------------------------------
3156update_CivOptions(handles)
3157
3158%------------------------------------------------------------------------
3159% --- Executes on button press in CheckFix2.
3160function CheckFix2_Callback(hObject, eventdata, handles)
3161%------------------------------------------------------------------------
3162update_CivOptions(handles)
3163
3164%------------------------------------------------------------------------
3165% --- Executes on button press in CheckPatch2.
3166function CheckPatch2_Callback(hObject, eventdata, handles)
3167%------------------------------------------------------------------------
3168update_CivOptions(handles)
3169
3170%------------------------------------------------------------------------
3171% --- activated by any checkbox controling the selection of Civ1,Fix1,Patch1,Civ2,Fix2,Patch2
3172function update_CivOptions(handles)
3173%------------------------------------------------------------------------
3174checkbox=zeros(1,6);
3175checkbox(1)=get(handles.CheckCiv1,'Value');
3176checkbox(2)=get(handles.CheckFix1,'Value');
3177checkbox(3)=get(handles.CheckPatch1,'Value');
3178checkbox(4)=get(handles.CheckCiv2,'Value');
3179checkbox(5)=get(handles.CheckFix2,'Value');
3180checkbox(6)=get(handles.CheckPatch2,'Value');
3181ind_selected=find(checkbox);
3182if ~isempty(ind_selected)
3183  RootName=get(handles.RootName,'String');
3184    if isempty(RootName)
3185         msgbox_uvmat('ERROR','No input file')
3186        return
3187    end
3188end
3189set(handles.PairIndices,'Visible','on')
3190set(handles.txt_SubdirCiv1,'Visible','on')
3191set(handles.ListSubdirCiv1,'Visible','on')
3192find_netcpair_civ1(handles) % select the available netcdf files
3193% check_civ2pair=ind_selected(4;6);
3194if max(checkbox(4:6))% case of civ2 pair choice needed
3195    set(handles.TitlePairCiv2,'Visible','on')
3196    set(handles.TitleSubdirCiv2,'Visible','on')
3197    set(handles.txt_SubdirCiv2,'Visible','on')
3198    set(handles.ListSubdirCiv2,'Visible','on')
3199    set(handles.ListPairCiv2,'Visible','on')
3200    find_netcpair_civ2(handles) % select the available netcdf files
3201else
3202    set(handles.TitleSubdirCiv2,'Visible','off')
3203    set(handles.txt_SubdirCiv2,'Visible','off')
3204    set(handles.ListSubdirCiv2,'Visible','off')
3205    set(handles.ListPairCiv2,'Visible','off')
3206end
3207%index_last=find(checkbox,1,'last');%last selected button
3208options={'Civ1','Fix1','Patch1','Civ2','Fix2','Patch2'};
3209for ilist=1:length(options)
3210    if checkbox(ilist)
3211        set(handles.(options{ilist}),'Visible','on')
3212    else
3213        set(handles.(options{ilist}),'Visible','off')
3214    end
3215end
3216
3217% end
3218
3219% set(handles.(operations(ind_selected)),'Visible','on')
3220%
3221% if state
3222%     RootName=get(handles.RootName,'String');
3223%     if isempty(RootName)
3224%          msgbox_uvmat('ERROR','No input file')
3225%         return
3226%     end
3227%     set(handles.Civ1,'Visible','on')   
3228%     set(handles.PairIndices,'Visible','on')
3229% else
3230%     set(handles.Civ1,'Visible','off') 
3231% end
3232
3233
3234%------------------------------------------------------------------------
3235function first_i_Callback(hObject, eventdata, handles)
3236%------------------------------------------------------------------------
3237% last_i_Callback(hObject, eventdata, handles)
3238first_i=str2double(get(handles.first_i,'String'));
3239% last_i=str2num(get(handles.last_i,'String'));
3240% ref_i=ceil((first_i+last_i)/2);
3241set(handles.ref_i,'String', num2str(first_i))% reference index for pair dt = first index
3242%set(handles.ref_i_civ2,'String', num2str(first_i))% reference index for pair dt = first index
3243ref_i_Callback(hObject, eventdata, handles)%refresh dispaly of dt for pairs (in case of non constant dt)
3244
3245%------------------------------------------------------------------------
3246function first_j_Callback(hObject, eventdata, handles)
3247%------------------------------------------------------------------------
3248first_j=str2num(get(handles.first_j,'String'));
3249set(handles.ref_j,'String', num2str(first_j))% reference index for pair dt = first index
3250ref_j_Callback(hObject, eventdata, handles)%refresh dispaly of dt for pairs (in case of non constant dt)
3251
3252%------------------------------------------------------------------------
3253% --- Executes on button press in SearchRange: determine the search range num_Searchx,num_Searchy
3254function SearchRange_Callback(hObject, eventdata, handles)
3255%------------------------------------------------------------------------
3256%determine pair numbers
3257if strcmp(get(handles.umin,'Visible'),'off')
3258    set(handles.u_title,'Visible','on')
3259    set(handles.v_title,'Visible','on')
3260    set(handles.umin,'Visible','on')
3261    set(handles.umax,'Visible','on')
3262    set(handles.vmin,'Visible','on')
3263    set(handles.vmax,'Visible','on')
3264    set(handles.CoordUnit,'Visible','on')
3265    set(handles.TimeUnit,'Visible','on')
3266    set(handles.slash_title,'Visible','on')
3267    set(handles.min_title,'Visible','on')
3268    set(handles.max_title,'Visible','on')
3269    set(handles.unit_title,'Visible','on')
3270else
3271    get_search_range(hObject, eventdata, handles)
3272end
3273
3274%------------------------------------------------------------------------
3275% ---  determine the search range num_Searchx,num_Searchy and shift
3276function get_search_range(hObject, eventdata, handles)
3277umin=str2double(get(handles.umin,'String'));
3278umax=str2double(get(handles.umax,'String'));
3279vmin=str2double(get(handles.umin,'String'));
3280vmax=str2double(get(handles.vmax,'String'));
3281%switch min_title and max_title in case of error
3282if umax<=umin
3283    umin_old=umin;
3284    umin=umax;
3285    umax=umin_old;
3286    set(handles.umin,'String', num2str(umin))
3287    set(handles.umax,'String', num2str(umax))
3288end
3289if vmax<=vmin
3290    vmin_old=vmin;
3291    vmin=vmax;
3292    vmax=vmin_old;
3293    set(handles.vmin,'String', num2str(vmin))
3294    set(handles.vmax,'String', num2str(vmax))
3295end   
3296if ~(isnan(umin)||isnan(umax)||isnan(vmin)||isnan(vmax))
3297    list_pair=get(handles.ListPairCiv1,'String');%get the menu of image pairs
3298    index=get(handles.ListPairCiv1,'Value');
3299    displ_num=get(handles.ListPairCiv1,'UserData');
3300    time=get(handles.ImaDoc,'UserData'); %get the set of times
3301    pxcm_xy=get(handles.SearchRange,'UserData');
3302    pxcmx=pxcm_xy(1);
3303    pxcmy=pxcm_xy(2);
3304    mode_list=get(handles.ListPairMode,'String');
3305    mode_value=get(handles.ListPairMode,'Value');
3306    mode=mode_list{mode_value};
3307    if isequal (mode, 'series(Di)' )
3308        ref_i=str2double(get(handles.ref_i,'String'));
3309        num1=ref_i-floor(index/2);%  first image numbers
3310        num2=ref_i+ceil(index/2);
3311        num_a=1;
3312        num_b=1;
3313    elseif isequal (mode, 'series(Dj)')
3314        num1=1;
3315        num2=1;
3316        ref_j=str2double(get(handles.ref_j,'String'));
3317        num_a=ref_j-floor(index/2);%  first image numbers
3318        num_b=ref_j+ceil(index/2);
3319    elseif isequal(mode,'pair j1-j2') %case of bursts (png_old or png_2D)
3320        ref_i=str2double(get(handles.ref_i,'String'));
3321        num1=ref_i;
3322        num2=ref_i;
3323        num_a=displ_num(1,index);
3324        num_b=displ_num(2,index);
3325    end
3326    dt=time(num2,num_b)-time(num1,num_a);
3327    ibx=str2double(get(handles.num_Bx,'String'));
3328    iby=str2double(get(handles.num_By,'String'));
3329    umin=dt*pxcmx*umin;
3330    umax=dt*pxcmx*umax;
3331    vmin=dt*pxcmy*vmin;
3332    vmax=dt*pxcmy*vmax;
3333    shiftx=round((umin+umax)/2);
3334    shifty=round((vmin+vmax)/2);
3335    isx=(umax+2-shiftx)*2+ibx;
3336    isx=2*ceil(isx/2)+1;
3337    isy=(vmax+2-shifty)*2+iby;
3338    isy=2*ceil(isy/2)+1;
3339    set(handles.num_Shiftx,'String',num2str(shiftx));
3340    set(handles.num_Shifty,'String',num2str(shifty));
3341    set(handles.num_Searchx,'String',num2str(isx));
3342    set(handles.num_Searchy,'String',num2str(isy));
3343end
3344
3345%------------------------------------------------------------------------
3346% --- Executes on carriage return on the subdir checkciv1 edit window
3347function txt_SubdirCiv1_Callback(hObject, eventdata, handles)
3348%------------------------------------------------------------------------
3349subdir=get(handles.txt_SubdirCiv1,'String');
3350set(handles.txt_SubdirCiv2,'String',subdir);% set civ2 directory the same as civ1 by default
3351menu_str=get(handles.ListSubdirCiv1,'String');% read the list of subdirectories for update
3352ichoice=find(strcmp(subdir,menu_str),1);
3353if isempty(ichoice)
3354    ilist=numel(menu_str); %select 'new...' in the menu
3355else
3356    ilist=ichoice;
3357end
3358set(handles.ListSubdirCiv1,'Value',ilist)% select the selected subdir in the menu
3359if get(handles.CheckCiv1,'Value')==0
3360    find_netcpair_civ1(hObject, eventdata, handles); %update the list of available pairs from netcdf files in the new directory
3361end
3362
3363%------------------------------------------------------------------------
3364% --- Executes on carriage return on the subdir checkciv1 edit window
3365function txt_SubdirCiv2_Callback(hObject, eventdata, handles)
3366%------------------------------------------------------------------------
3367subdir=get(handles.txt_SubdirCiv1,'String');
3368menu_str=get(handles.ListSubdirCiv2,'String');% read the list of subdirectories for update
3369ichoice=find(strcmp(subdir,menu_str),1);
3370if isempty(ichoice)
3371    ilist=numel(menu_str); %select 'new...' in the menu
3372else
3373    ilist=ichoice;
3374end
3375set(handles.ListSubdirCiv2,'Value',ilist)% select the selected subdir in the menu
3376%update the list of available pairs from netcdf files in the new directory
3377if ~get(handles.CheckCiv2,'Value') && ~get(handles.CheckCiv1,'Value') && ~get(handles.CheckFix1,'Value') && ~get(handles.CheckPatch1,'Value')
3378    find_netcpair_civ2(hObject, eventdata, handles);
3379end
3380
3381% %------------------------------------------------------------------------
3382% % --- Executes on button press in CheckMask: select box for mask option
3383% function check_Mask_Callback(hObject, eventdata, handles)
3384% %------------------------------------------------------------------------
3385% maskval=get(handles.CheckMask,'Value');
3386% if isequal(maskval,0)
3387%     set(handles.txt_MaskName,'Visible','off')
3388% %     set(handles.txt_MaskName,'String','')
3389% else
3390%     mask_displ='no mask'; %default
3391%     filebase=get(handles.RootName,'String');
3392%     [ nbslice_mask, flag_mask]=get_mask(filebase,handles);
3393%     if isequal(flag_mask,1)
3394%         mask_displ=[num2str(nbslice_mask) 'mask'];
3395%     elseif get(handles.ListCompareMode,'Value')>1 & ~isequal(mask_displ,'no mask')% look for the second mask series
3396%         common_path=fileparts(filebase);
3397%         filebase_a=fullfile(common_path,get(handles.RootName_1,'String'));
3398%         [nbslice_a, flag_mask_a]=get_mask(filebase_a,handles);
3399%         if isequal(flag_mask_a,0) || ~isequal(nbslice_a,nbslice_mask)
3400%             mask_displ='no mask';
3401%         end
3402%     end
3403%     if isequal(mask_displ,'no mask')
3404%         [FileName, PathName, filterindex] = uigetfile( ...
3405%             {'*.png', ' (*.png)';
3406%             '*.png',  '.png files '; ...
3407%             '*.*', 'All Files (*.*)'}, ...
3408%             'Pick a mask file *.png',filebase);
3409%         mask_displ=fullfile(PathName,FileName);
3410%         if exist(mask_displ,'file')
3411%             set(handles.txt_MaskName,'Visible','on')
3412%             set(handles.txt_MaskName,'String',mask_displ)
3413% %             mask_displ='no mask';
3414%         end
3415%     end
3416%     if isequal(mask_displ,'no mask')
3417%         set(handles.CheckMask,'Value',0)
3418%         set(handles.CheckMask,'Value',0)
3419%         set(handles.CheckMask,'Value',0)
3420%         set(handles.CheckMask,'Value',0)
3421%     else
3422%         set(handles.CheckMask,'Value',1)
3423%         set(handles.CheckMask,'Value',1)
3424%     end
3425%     set(handles.txt_MaskName,'String',mask_displ)
3426%     set(handles.txt_MaskName,'String',mask_displ)
3427%     set(handles.txt_Mask,'String',mask_displ)
3428%     set(handles.txt_MaskName,'String',mask_displ)
3429% end
3430% set(handles.CheckMask,'Value',maskval)%update the checkciv2 mask with the same option as checkciv1
3431
3432%------------------------------------------------------------------------
3433% --- Executes on button press in CheckMask.
3434function get_mask_fix1_Callback(hObject, eventdata, handles)
3435%------------------------------------------------------------------------
3436maskval=get(handles.CheckMask,'Value');
3437if isequal(maskval,0)
3438    set(handles.txt_MaskName,'String','')
3439else
3440    mask_displ='no mask'; %default
3441    filebase=get(handles.RootName,'String');
3442    [nbslice, flag_mask]=get_mask(filebase,handles);
3443    if isequal(flag_mask,1)
3444        mask_displ=[num2str(nbslice) 'mask'];
3445    elseif get(handles.ListCompareMode,'Value')>1 & ~isequal(mask_displ,'no mask')% look for the second mask series
3446        filebase_a=get(handles.RootName_1,'String');
3447        [nbslice_a, flag_mask_a]=get_mask(filebase_a,handles);
3448        if isequal(flag_mask_a,0) || ~isequal(nbslice_a,nbslice)
3449            mask_displ='no mask';
3450        end
3451    end
3452    if isequal(mask_displ,'no mask')
3453        [FileName, PathName, filterindex] = uigetfile( ...
3454            {'*.png', ' (*.png)';
3455            '*.png',  '.png files '; ...
3456            '*.*', 'All Files (*.*)'}, ...
3457            'Pick a mask file *.png',filebase);
3458        mask_displ=fullfile(PathName,FileName);
3459        if ~exist(mask_displ,'file')
3460            mask_displ='no mask';
3461        end
3462    end
3463    if isequal(mask_displ,'no mask')
3464        set(handles.CheckMask,'Value',0)
3465        set(handles.CheckMask,'Value',0)
3466        set(handles.CheckMask,'Value',0)
3467    else
3468        %set(handles.CheckMask,'Value',1)
3469        set(handles.CheckMask,'Value',1)
3470    end
3471    set(handles.txt_MaskName,'String',mask_displ)
3472    set(handles.txt_Mask,'String',mask_displ)
3473    set(handles.txt_MaskName,'String',mask_displ)
3474end
3475
3476%------------------------------------------------------------------------
3477% --- Executes on button press in CheckMask: select box for mask option
3478function get_mask_civ2_Callback(hObject, eventdata, handles)
3479%------------------------------------------------------------------------
3480maskval=get(handles.CheckMask,'Value');
3481if isequal(maskval,0)
3482    set(handles.txt_Mask,'String','')
3483else
3484    mask_displ='no mask'; %default
3485    filebase=get(handles.RootName,'String');
3486    [nbslice, flag_mask]=get_mask(filebase,handles);
3487    if isequal(flag_mask,1)
3488        mask_displ=[num2str(nbslice) 'mask'];
3489    elseif get(handles.ListCompareMode,'Value')>1 & ~isequal(mask_displ,'no mask')% look for the second mask series
3490        filebase_a=get(handles.RootName_1,'String');
3491        [nbslice_a, flag_mask_a]=get_mask(filebase_a,handles);
3492        if isequal(flag_mask_a,0) || ~isequal(nbslice_a,nbslice)
3493            mask_displ='no mask';
3494        end
3495    end
3496    if isequal(mask_displ,'no mask')
3497        [FileName, PathName, filterindex] = uigetfile( ...
3498            {'*.png', ' (*.png)';
3499            '*.png',  '.png files '; ...
3500            '*.*', 'All Files (*.*)'}, ...
3501            'Pick a mask file *.png',filebase);
3502        mask_displ=fullfile(PathName,FileName);
3503        if ~exist(mask_displ,'file')
3504            mask_displ='no mask';
3505        end
3506    end
3507    if isequal(mask_displ,'no mask')
3508        set(handles.CheckMask,'Value',0)
3509        set(handles.CheckMask,'Value',0)
3510    else
3511        set(handles.CheckMask,'Value',1)
3512    end
3513    set(handles.txt_Mask,'String',mask_displ)
3514    set(handles.txt_MaskName,'String',mask_displ)
3515end
3516
3517%------------------------------------------------------------------------
3518% --- Executes on button press in CheckMask.
3519function get_mask_fix2_Callback(hObject, eventdata, handles)
3520%------------------------------------------------------------------------
3521maskval=get(handles.CheckMask,'Value');
3522if isequal(maskval,0)
3523    set(handles.txt_MaskName,'String','')
3524else
3525    mask_displ='no mask'; %default
3526    filebase=get(handles.RootName,'String');
3527    [nbslice, flag_mask]=get_mask(filebase,handles);
3528    if isequal(flag_mask,1)
3529        mask_displ=[num2str(nbslice) 'mask'];
3530    elseif get(handles.ListCompareMode,'Value')>1 & ~isequal(mask_displ,'no mask')% look for the second mask series
3531        filebase_a=get(handles.RootName_1,'String');
3532        [nbslice_a, flag_mask_a]=get_mask(filebase_a,handles);
3533        if isequal(flag_mask_a,0) || ~isequal(nbslice_a,nbslice)
3534            mask_displ='no mask';
3535        end
3536    end
3537    if isequal(mask_displ,'no mask')
3538        [FileName, PathName, filterindex] = uigetfile( ...
3539            {'*.png', ' (*.png)';
3540            '*.png',  '.png files '; ...
3541            '*.*', 'All Files (*.*)'}, ...
3542            'Pick a mask file *.png',filebase);
3543        mask_displ=fullfile(PathName,FileName);
3544        if ~exist(mask_displ,'file')
3545            mask_displ='no mask';
3546        end
3547    end
3548    if isequal(mask_displ,'no mask')
3549        set(handles.CheckMask,'Value',0)
3550    end
3551    set(handles.txt_MaskName,'String',mask_displ)
3552end
3553
3554%------------------------------------------------------------------------
3555% --- function called to look for mask files
3556function [nbslice, flag_mask]=get_mask(filebase,handles)
3557%------------------------------------------------------------------------
3558%detect mask files, images with appropriate file base
3559%[filebase '_' xx 'mask'], xx=nbslice
3560%flag_mask=1 indicates detection
3561
3562flag_mask=0;%default
3563nbslice=1;
3564
3565% subdir=get(handles.txt_SubdirCiv1,'String');
3566[Path,Name]=fileparts(filebase);
3567if ~isdir(Path)
3568    msgbox_uvmat('ERROR','no path for input files')
3569    return
3570end
3571% currentdir=pwd;
3572% cd(Path);%move in the dir of the root name filebase
3573maskfiles=dir(fullfile(Path,[Name '_*mask_*.png']));%look for mask files
3574% cd(currentdir);%come back to the current working directory
3575if ~isempty(maskfiles)
3576    %     msgbox_uvmat('ERROR','no mask available, to create it use Tools/Make mask in the upper menu bar of uvmat')
3577    % else
3578    flag_mask=1;
3579    maskname=maskfiles(1).name;% take the first mask file in the list
3580    [Path2,Name,ext]=fileparts(maskname);
3581    Namedouble=double(Name);
3582    val=(48>Namedouble)|(Namedouble>57);% select the non-numerical characters
3583    ind_mask=findstr('mask',Name);
3584    i=ind_mask-1;
3585    while val(i)==0 && i>0
3586        i=i-1;
3587    end
3588    nbslice=str2double(Name(i+1:ind_mask-1));
3589    if ~isnan(nbslice) && Name(i)=='_'
3590        flag_mask=1;
3591    else
3592        msgbox_uvmat('ERROR',['bad mask file ' Name ext ' found in ' Path2])
3593        return
3594        nbslice=1;
3595    end
3596end
3597
3598%------------------------------------------------------------------------
3599% --- function called to look for grid files
3600function [nbslice, flag_mask]=get_grid(filebase,handles)
3601%------------------------------------------------------------------------
3602flag_mask=0;%default
3603nbslice=1;
3604[Path,Name]=fileparts(filebase);
3605currentdir=pwd;
3606cd(Path);%move in the dir of the root name filebase
3607maskfiles=dir([Name '_*grid_*.grid']);%look for mask files
3608cd(currentdir);%come back to the current working directory
3609if ~isempty(maskfiles)
3610    flag_mask=1;
3611    maskname=maskfiles(1).name;% take the first mask file in the list
3612    [Path2,Name,ext]=fileparts(maskname);
3613    Namedouble=double(Name);
3614    val=(48>Namedouble)|(Namedouble>57);% select the non-numerical characters
3615    ind_mask=findstr('grid',Name);
3616    i=ind_mask-1;
3617    while val(i)==0 && i>0
3618        i=i-1;
3619    end
3620    nbslice=str2double(Name(i+1:ind_mask-1));
3621    if ~isnan(nbslice) && Name(i)=='_'
3622        flag_mask=1;
3623    else
3624        msgbox_uvmat('ERROR',['bad grid file ' Name ext ' found in ' Path2])
3625        return
3626        nbslice=1;
3627    end
3628end
3629
3630%------------------------------------------------------------------------
3631% --- transform numbers to letters
3632function str=num2stra(num,nom_type)
3633%------------------------------------------------------------------------
3634if isempty(nom_type)
3635    str='';
3636elseif strcmp(nom_type(end),'a')
3637    str=char(96+num);
3638elseif strcmp(nom_type(end),'A')
3639    str=char(96+num);
3640elseif isempty(nom_type(2:end))%a single index
3641    str='';
3642else
3643    str=num2str(num);
3644end
3645
3646%------------------------------------------------------------------------
3647% --- Executes on button press in ListSubdirCiv1.
3648function ListSubdirCiv1_Callback(hObject, eventdata, handles)
3649%------------------------------------------------------------------------
3650list_subdir_civ1=get(handles.ListSubdirCiv1,'String');
3651val=get(handles.ListSubdirCiv1,'Value');
3652subdir=list_subdir_civ1{val};
3653if strcmp(subdir,'new...')
3654    subdir='CIV'; %default subdirectory
3655end
3656set(handles.txt_SubdirCiv1,'String',subdir);
3657find_netcpair_civ1(hObject, eventdata, handles)
3658% end
3659
3660%------------------------------------------------------------------------
3661% --- Executes on button press in ListSubdirCiv2.
3662function ListSubdirCiv2_Callback(hObject, eventdata, handles)
3663%------------------------------------------------------------------------
3664list_subdir_civ2=get(handles.ListSubdirCiv2,'String');
3665val=get(handles.ListSubdirCiv2,'Value');
3666subdir=list_subdir_civ2{val};
3667if strcmp(subdir,'new...')
3668    subdir='CIV'; %default subdirectory
3669end
3670set(handles.txt_SubdirCiv2,'String',subdir);
3671%     set(handles.ListSubdirCiv2,'Value',1);
3672
3673
3674%------------------------------------------------------------------------
3675% --- Executes on button press in CheckGrid.
3676function CheckGrid_Callback(hObject, eventdata, handles)
3677%------------------------------------------------------------------------
3678value=get(hObject,'Value');
3679hparent=get(hObject,'parent');
3680hchildren=get(hparent,'children');
3681handle_txtbox=findobj(hchildren,'tag','txt_GridName');
3682handle_dx=findobj(hchildren,'tag','num_Dx');
3683handle_dy=findobj(hchildren,'tag','num_Dy');
3684testgrid=0;
3685filegrid='';
3686if value
3687    filebase=get(handles.RootName,'String');
3688    [nbslice, flag_grid]=get_grid(filebase,handles);% look for a grid with appropriate name
3689    if isequal(flag_grid,1)
3690        filegrid=[num2str(nbslice) 'grid'];
3691        testgrid=1;
3692    else % browse for a grid
3693        filegrid=get(hObject,'UserData');%look for previous grid name stored as UserData
3694        if exist(filegrid,'file')
3695            filebase=filegrid;
3696        end
3697        [FileName, PathName, filterindex] = uigetfile( ...
3698            {'*.grid', ' (*.grid)';
3699            '*.grid',  '.grid files '; ...
3700            '*.*', 'All Files (*.*)'}, ...
3701            'Pick a file',filebase);
3702        filegrid=fullfile(PathName,FileName);
3703        set(hObject,'UserData',filegrid);%store for future use
3704        if ~(isempty(FileName)||isempty(PathName)||isequal(FileName,0)||~exist(filegrid,'file'))
3705            testgrid=1;
3706        end
3707    end
3708end
3709if testgrid
3710    set(handle_dx,'Visible','off');
3711    set(handle_dy,'Visible','off');
3712    set(handle_txtbox,'Visible','on')
3713    set(handle_txtbox,'String',filegrid)
3714else
3715    set(hObject,'Value',0);
3716    set(handle_dx,'Visible','on');
3717    set(handle_dy,'Visible','on');
3718    set(handle_txtbox,'Visible','off')
3719end
3720
3721%% if hObject is on the checkciv1 frame, duplicate action for checkciv2 frame
3722PanelName=get(hparent,'tag');
3723if strcmp(PanelName,'panel_Civ1')
3724    hchildren=get(handles.Civ2,'children');
3725    handle_checkbox=findobj(hchildren,'tag','check_Grid');
3726    handle_txtbox=findobj(hchildren,'tag','txt_GridName');
3727    handle_dx=findobj(hchildren,'tag','num_Dx');
3728    handle_dy=findobj(hchildren,'tag','num_Dy');
3729    set(handle_checkbox,'UserData',filegrid);%store for future use
3730    if testgrid
3731        set(handle_checkbox,'Value',1);
3732        set(handle_dx,'Visible','off');
3733        set(handle_dy,'Visible','off');
3734        set(handle_txtbox,'Visible','on')
3735        set(handle_txtbox,'String',filegrid)
3736    else
3737        set(handle_checkbox,'Value',0);
3738        set(handles.CheckGrid,'Value',0);
3739        set(handle_dx,'Visible','on');
3740        set(handle_dy,'Visible','on');
3741        set(handle_txtbox,'Visible','off')
3742    end
3743end
3744%------------------------------------------------------------------------
3745% --- Executes on button press in CheckMask.
3746function CheckMask_Callback(hObject, eventdata, handles)
3747%------------------------------------------------------------------------
3748value=get(hObject,'Value');
3749testmask=0;
3750if value
3751    filebase=get(handles.RootName,'String');
3752    [nbslice, flag_mask]=get_mask(filebase,handles);% look for a mask with appropriate name
3753    if isequal(flag_mask,1)
3754        filemask=[num2str(nbslice) 'mask'];
3755        testmask=1;
3756    else % browse for a mask
3757        filemask=get(handles.CheckMask,'UserData');%look for previous mask name stored as UserData
3758        if exist(filemask,'file')
3759            filebase=filemask;
3760        end
3761        [FileName, PathName, filterindex] = uigetfile( ...
3762            {'*.png', ' (*.png)';
3763            '*.png',  '.png files '; ...
3764            '*.*', 'All Files (*.*)'}, ...
3765            'Pick a mask file *.png',filebase);
3766        filemask=fullfile(PathName,FileName);
3767        set(handles.CheckMask,'UserData',filemask);%store for future use
3768        if ~(isempty(FileName)||isempty(PathName)||isequal(FileName,0)||~exist(filemask,'file'))
3769            testmask=1;
3770        end
3771    end
3772end
3773if testmask
3774    set(handles.num_Dx,'Visible','off');
3775    set(handles.num_Dy,'Visible','off');
3776    set(handles.num_Dx,'Visible','off');
3777    set(handles.num_Dy,'Visible','off');
3778    set(handles.txt_MaskName,'Visible','on')
3779    set(handles.txt_MaskName,'String',filemask)
3780else
3781    set(handles.CheckMask,'Value',0);
3782    set(handles.CheckGrid,'Value',0);
3783    set(handles.num_Dx,'Visible','on');
3784    set(handles.num_Dy,'Visible','on');
3785    set(handles.num_Dx,'Visible','on');
3786    set(handles.num_Dy,'Visible','on');
3787    set(handles.txt_MaskName,'Visible','off')
3788end
3789
3790%------------------------------------------------------------------------
3791% --- Executes on button press in CheckGrid.
3792function browse_gridciv2_Callback(hObject, eventdata, handles)
3793%------------------------------------------------------------------------
3794value=get(handles.CheckGrid,'Value');
3795if value
3796    filebase=get(handles.RootName,'String');
3797    [nbslice, flag_grid]=get_grid(filebase,handles);
3798    if isequal(flag_grid,1)
3799        mask_displ=[num2str(nbslice) 'grid'];
3800        set(handles.txt_GridName,'String',mask_displ)
3801        set(handles.num_Dx,'Visible','off');
3802        set(handles.num_Dy,'Visible','off');
3803    else
3804        [FileName, PathName, filterindex] = uigetfile( ...
3805            {'*.grid', ' (*.grid)';
3806            '*.grid',  '.grid files '; ...
3807            '*.*', 'All Files (*.*)'}, ...
3808            'Pick a file',filebase);
3809        filegrid=fullfile(PathName,FileName);
3810        if isempty(FileName)||isempty(PathName)||isequal(FileName,0)||~exist(filegrid,'file')
3811            set(handles.CheckGrid,'Value',0);
3812            set(handles.txt_GridName,'string','');
3813            set(handles.num_Dx,'Visible','on');
3814            set(handles.num_Dy,'Visible','on');
3815            set(handles.txt_GridName,'string','');
3816        else
3817            set(handles.txt_GridName,'string',filegrid);
3818            set(handles.num_Dx,'Visible','off');
3819            set(handles.num_Dy,'Visible','off');
3820            set(handles.txt_GridName,'string',filegrid);
3821        end
3822    end
3823else
3824    set(handles.txt_GridName,'string','');
3825    set(handles.num_Dx,'Visible','on');
3826    set(handles.num_Dy,'Visible','on');
3827    set(handles.txt_GridName,'string','');
3828end
3829
3830% % --- Executes on button press in CheckGrid.
3831% function browse_gridciv2_Callback(hObject, eventdata, handles)
3832%
3833% filebase=get(handles.RootName,'String');
3834% [FileName, PathName, filterindex] = uigetfile( ...
3835%        {'*.grid', ' (*.grid)';
3836%         '*.grid',  '.grid files '; ...
3837%         '*.*', 'All Files (*.*)'}, ...
3838%         'Pick a file',filebase);
3839% filegrid=fullfile(PathName,FileName);
3840% set(handles.txt_GridName,'string',filegrid);
3841% set(handles.num_Dx,'String',' ');
3842% set(handles.num_Dy,'String',' ');
3843% % set(handles.grid_patch2,'string',filegrid);
3844
3845% --- Executes on button press in get_gridpatch1.
3846function get_gridpatch1_Callback(hObject, eventdata, handles)
3847% hObject    handle to get_gridpatch1 (see GCBO)
3848% eventdata  reserved - to be defined in a future version of MATLAB
3849% handles    structure with handles and user data (see GUIDATA)
3850
3851filebase=get(handles.RootName,'String');
3852[FileName, PathName, filterindex] = uigetfile( ...
3853    {'*.grid', ' (*.grid)';
3854    '*.grid',  '.grid files '; ...
3855    '*.*', 'All Files (*.*)'}, ...
3856    'Pick a file',filebase);
3857filegrid=fullfile(PathName,FileName);
3858set(handles.grid_patch1,'string',filegrid);
3859% set(handles.grid_patch2,'string',filegrid
3860
3861%------------------------------------------------------------------------
3862% --- Executes on button press in get_gridpatch2.
3863function get_gridpatch2_Callback(hObject, eventdata, handles)
3864%------------------------------------------------------------------------
3865
3866%------------------------------------------------------------------------
3867function enable_civ1(handles,state)
3868%------------------------------------------------------------------------
3869if state
3870    RootName=get(handles.RootName,'String');
3871    if isempty(RootName)
3872         msgbox_uvmat('ERROR','No input file')
3873        return
3874    end
3875    set(handles.Civ1,'Visible','on')   
3876    set(handles.PairIndices,'Visible','on')
3877%     set(handles.frame_civ1,'BackgroundColor',[1 1 0])
3878%     set(handles.frame_para_civ1,'BackgroundColor',[1 1 0])
3879%     set(handles.frame_grid_civ1,'BackgroundColor',[1 1 0])
3880else
3881    set(handles.Civ1,'Visible','off') 
3882%     set(handles.frame_civ1,'BackgroundColor',[0.831 0.816 0.784])
3883%     set(handles.frame_para_civ1,'BackgroundColor',[0.831 0.816 0.784])
3884%     set(handles.frame_grid_civ1,'BackgroundColor',[0.831 0.816 0.784])
3885end
3886
3887% set(handles.num_Bx,'Visible',state)
3888% set(handles.num_By,'Visible',state)
3889% set(handles.num_Searchx,'Visible',state)
3890% set(handles.num_Searchy,'Visible',state)
3891% set(handles.num_Shiftx,'Visible',state)
3892% set(handles.num_Shifty,'Visible',state)
3893% set(handles.num_Rho,'Visible',state)
3894% set(handles.num_Dx,'Visible',state)
3895% set(handles.num_Dy,'Visible',state)
3896% set(handles.SearchRange,'Visible',state)
3897% set(handles.u_title,'Visible',state)
3898% set(handles.v_title,'Visible',state)
3899% set(handles.min_title,'Visible',state)
3900% set(handles.max_title,'Visible',state)
3901% set(handles.umin,'Visible',state)
3902% set(handles.umax,'Visible',state)
3903% set(handles.vmin,'Visible',state)
3904% set(handles.vmax,'Visible',state)
3905% set(handles.txt_GridName,'Visible',state)
3906% set(handles.txt_MaskName,'Visible',state)
3907% set(handles.CheckGrid,'Visible',state)
3908% set(handles.CheckMask,'Visible',state)
3909% set(handles.parameters,'Visible',state)
3910% set(handles.grid,'Visible',state)
3911% set(handles.num_Dx,'Visible',state)
3912% set(handles.num_Dy,'Visible',state)
3913% set(handles.check_Threshold,'Visible',state)
3914% if isequal(state,'off')
3915%     set(handles.num_MinIma,'Visible','off')
3916%     set(handles.num_MaxIma,'Visible','off')
3917%     set(handles.check_Threshold,'Value',0)
3918% end
3919% set(handles.dx_civ1_title,'Visible',state)
3920% set(handles.dy_civ1_title,'Visible',state)
3921% set(handles.ImaThreshold_title,'Visible',state)
3922% set(handles.ib_title,'Visible',state)
3923% set(handles.is_title,'Visible',state)
3924% set(handles.shift_title,'Visible',state)
3925% set(handles.rho_title,'Visible',state)
3926% set(handles.TestCiv1,'Visible',state)
3927%set(handles.ListPairMode,'Visible',state)
3928
3929%------------------------------------------------------------------------
3930function enable_fix1(handles,state)
3931%------------------------------------------------------------------------
3932
3933if isequal(state,0)
3934    state='off';
3935end
3936if isequal(state,1)
3937    state='on';
3938    RootName=get(handles.RootName,'String');
3939    if isempty(RootName)
3940         msgbox_uvmat('ERROR','No input file')
3941        return
3942    end
3943end
3944if isequal(state,'on')
3945    set(handles.Fix1,'Visible','on')
3946%     set(handles.frame_fix1,'BackgroundColor',[1 1 0])
3947else
3948    set(handles.Fix1,'Visible','off')
3949    %set(handles.frame_fix1,'BackgroundColor',[0.7 0.7 0.7])
3950end
3951% % set(handles.REMOVE,'Visible',state)
3952% set(handles.CheckFmin2,'Visible',state)
3953% set(handles.CheckF2,'Visible',state)
3954% set(handles.CheckF3,'Visible',state)
3955% set(handles.num_MinCorr,'Visible',state)
3956% set(handles.thresh_vecC_title,'Visible',state)
3957% set(handles.num_MinVel,'Visible',state)
3958% set(handles.TitleMinVel,'Visible',state)
3959% set(handles.txt_MaskName,'Visible',state)
3960% set(handles.CheckMask,'Visible',state)
3961% set(handles.get_ref_fix1,'Visible',state)
3962% set(handles.ref_fix1,'Visible',state)
3963% set(handles.num_MinVel,'Visible',state)
3964% set(handles.field_ref1,'Visible',state)
3965
3966%------------------------------------------------------------------------
3967function enable_patch1(handles,state)
3968%------------------------------------------------------------------------
3969if state
3970    RootName=get(handles.RootName,'String');
3971    if isempty(RootName)
3972        msgbox_uvmat('ERROR','No input file')
3973        return
3974    end
3975    set(handles.Patch1,'Visible','on')
3976else
3977    set(handles.Patch1,'Visible','off')
3978end
3979return
3980set(handles.frame_patch1,'BackgroundColor',[1 1 0])
3981set(handles.rho_patch1,'Visible','on')
3982set(handles.rho_text1,'Visible','on')
3983if get(handles.ListPairMode,'Value')==2
3984    set(handles.thresh_patch1,'Visible','on')
3985    set(handles.thresh_text1,'Visible','on')
3986end
3987set(handles.subdomain_patch1,'Visible','on')
3988set(handles.subdomain_text1,'Visible','on')
3989set(handles.nx_patch1,'Visible','on')
3990set(handles.num_Ny,'Visible','on')
3991set(handles.nx_patch1_title,'Visible','on')
3992set(handles.ny_patch1_title,'Visible','on')
3993% if ~isempty(patch_newBin)
3994set(handles.test_interp,'Visible','off');
3995stereo_test=get(handles.ListCompareMode,'Value');
3996if stereo_test==3
3997    set(handles.test_stereo1,'Visible','on')
3998end
3999% end
4000%set(handles.get_gridpatch1,'Visible','on')
4001%set(handles.grid_patch1,'string','none');
4002%set(handles.grid_patch1,'Visible','on')
4003
4004% %------------------------------------------------------------------------
4005% function desable_patch1(handles)
4006% %------------------------------------------------------------------------
4007% return
4008% set(handles.frame_patch1,'BackgroundColor',[0.831 0.816 0.784])
4009% set(handles.rho_patch1,'Visible','off')
4010% set(handles.rho_text1,'Visible','off')
4011% set(handles.thresh_patch1,'Visible','off')
4012% set(handles.thresh_text1,'Visible','off')
4013% set(handles.subdomain_patch1,'Visible','off')
4014% set(handles.subdomain_text1,'Visible','off')
4015% set(handles.nx_patch1,'Visible','off')
4016% set(handles.num_Ny,'Visible','off')
4017% set(handles.nx_patch1_title,'Visible','off')
4018% set(handles.ny_patch1_title,'Visible','off')
4019% set(handles.test_stereo1,'Visible','off')
4020% %set(handles.test_interp,'Visible','off')
4021% %set(handles.get_gridpatch1,'Visible','off')
4022% %set(handles.grid_patch1,'Visible','off')
4023
4024%------------------------------------------------------------------------
4025function enable_civ2(handles,state)
4026%------------------------------------------------------------------------
4027if state
4028    RootName=get(handles.RootName,'String');
4029    if isempty(RootName)
4030         msgbox_uvmat('ERROR','No input file')
4031        return
4032    end
4033    set(handles.Civ2,'Visible','on')
4034    set(handles.ListSubdirCiv2,'Visible','on')
4035    set(handles.SubdirCiv2,'Visible','on')
4036    set(handles.TitleSubdirCiv2,'Visible','on')
4037else
4038    set(handles.Civ2,'Visible','off')
4039end
4040
4041%
4042% set(handles.num_Bx,'Visible',state)
4043% set(handles.num_By,'Visible',state)
4044% set(handles.CheckDecimal,'Visible',state)
4045% set(handles.CheckDeformation,'Visible',state)
4046% set(handles.num_Rho,'Visible',state)
4047% set(handles.num_Dx,'Visible',state)
4048% set(handles.num_Dy,'Visible',state)
4049% set(handles.CheckGrid,'Visible',state)
4050% set(handles.CheckMask,'Visible',state)
4051% set(handles.parameters,'Visible',state)
4052% set(handles.grid,'Visible',state)
4053% set(handles.parameters_text,'Visible',state)
4054% set(handles.grid_text,'Visible',state)
4055% set(handles.txt_GridName,'Visible',state)
4056% set(handles.txt_Mask,'Visible',state)
4057% set(handles.dx_civ2_title,'Visible',state)
4058% set(handles.dy_civ2_title,'Visible',state)
4059% set(handles.ibx_civ2_text,'Visible',state)
4060% set(handles.rho_civ2_title,'Visible',state)
4061% set(handles.ImaThreshold2,'Visible',state)
4062% set(handles.ImaThreshold_title2,'Visible',state)
4063% if isequal(state,'off')
4064%     set(handles.num_MinIma,'Visible','off')
4065%     set(handles.num_MaxIma,'Visible','off')
4066%     set(handles.ImaThreshold2,'Value',0)
4067%     if isequal(get(handles.CheckFix2,'Value'),0) & isequal(get(handles.CheckPatch2,'Value'),0)
4068%         set(handles.ListPairCiv2,'Visible','off')
4069%         set(handles.txt_SubdirCiv2,'Visible','off')
4070%         set(handles.TitleSubdirCiv2,'Visible','off')
4071%         set(handles.dt_unit_civ2,'Visible','off')
4072%         %set(handles.ref_i_civ2,'Visible','off')
4073%         set(handles.i_ref_civ2_title,'Visible','off')
4074%         set(handles.j_ref_civ2_title,'Visible','off')
4075%         set(handles.ref_j_civ2,'Visible','off')
4076%     end
4077% else
4078%     set(handles.ListPairCiv2,'Visible','on')
4079%     set(handles.txt_SubdirCiv2,'Visible','on')
4080%     set(handles.TitleSubdirCiv2,'Visible','on')
4081%     set(handles.dt_unit_civ2,'Visible','on')
4082%   %  set(handles.ref_i_civ2,'Visible','on')
4083%     set(handles.i_ref_civ2_title,'Visible','on')
4084%     set(handles.j_ref_civ2_title,'Visible','on')
4085%     set(handles.ref_j_civ2,'Visible','on')
4086% end
4087% set(handles.rho_civ2_title,'Visible',state)
4088
4089%------------------------------------------------------------------------
4090function enable_fix2(handles,state)
4091%------------------------------------------------------------------------
4092% if isequal(state,'on')
4093%     set(handles.Fix2,'Visible','on') 
4094%     
4095% %     set(handles.frame_civ2,'BackgroundColor',[1 1 0])
4096% %     set(handles.frame_para_civ2,'BackgroundColor',[1 1 0])
4097% %     set(handles.frame_grid_civ2,'BackgroundColor',[1 1 0])
4098% %     set(handles.frame_subdirciv2,'BackgroundColor',[1 1 0])
4099% else
4100if state
4101    RootName=get(handles.RootName,'String');
4102    if isempty(RootName)
4103         msgbox_uvmat('ERROR','No input file')
4104        return
4105    end
4106    set(handles.Fix2,'Visible','on')
4107else
4108    set(handles.Fix2,'Visible','off')
4109end
4110
4111% set(handles.frame_fix2,'BackgroundColor',[1 1 0])
4112% set(handles.REMOVE2,'Visible','on')
4113% set(handles.CheckFmin2,'Visible','on')
4114% set(handles.CheckF4,'Visible','on')
4115% set(handles.CheckF3,'Visible','on')
4116% set(handles.num_MinCorr,'Visible','on')
4117% set(handles.thresh_vec2C_text,'Visible','on')
4118% set(handles.num_MinVel,'Visible','on')
4119% set(handles.TitleMinVel,'Visible','on')
4120% set(handles.txt_MaskName,'Visible','on')
4121% set(handles.CheckMask,'Visible','on')
4122% set(handles.ListPairCiv2,'Visible','on')
4123% set(handles.txt_SubdirCiv2,'Visible','on')
4124% set(handles.TitleSubdirCiv2,'Visible','on')
4125% set(handles.get_ref_fix2,'Visible','on')
4126% set(handles.ref_fix2,'Visible','on')
4127% set(handles.num_MinVel,'Visible','on')
4128% set(handles.field_ref2,'Visible','on')
4129
4130% %------------------------------------------------------------------------
4131% function desable_fix2(handles)
4132% %------------------------------------------------------------------------
4133% set(handles.frame_fix2,'BackgroundColor',[0.831 0.816 0.784])
4134% set(handles.REMOVE2,'Visible','off')
4135% set(handles.CheckFmin2,'Visible','off')
4136% set(handles.CheckF4,'Visible','off')
4137% set(handles.CheckF3,'Visible','off')
4138% set(handles.num_MinCorr,'Visible','off')
4139% set(handles.thresh_vec2C_text,'Visible','off')
4140% set(handles.num_MinVel,'Visible','off')
4141% set(handles.TitleMinVel,'Visible','off')
4142% set(handles.txt_MaskName,'Visible','off')
4143% set(handles.CheckMask,'Visible','off')
4144% set(handles.get_ref_fix2,'Visible','off')
4145% set(handles.ref_fix2,'Visible','off')
4146% set(handles.num_MinVel,'Visible','off')
4147% set(handles.field_ref2,'Visible','off')
4148% if isequal(get(handles.CheckCiv2,'Value'),0) & isequal(get(handles.CheckPatch2,'Value'),0)
4149%     set(handles.ListPairCiv2,'Visible','off')
4150%     set(handles.txt_SubdirCiv2,'Visible','off')
4151%     set(handles.TitleSubdirCiv2,'Visible','off')
4152% end
4153
4154%------------------------------------------------------------------------
4155function enable_patch2(handles,state)
4156%------------------------------------------------------------------------
4157if state
4158RootName=get(handles.RootName,'String');
4159    if isempty(RootName)
4160         msgbox_uvmat('ERROR','No input file')
4161        return
4162    end
4163    set(handles.Patch2,'Visible','on')
4164else
4165set(handles.Patch2,'Visible','off')
4166end
4167% set(handles.frame_patch2,'BackgroundColor',[1 1 0])
4168% set(handles.num_SmoothingParam,'Visible','on')
4169% set(handles.num_SmoothingParam,'Visible','on')
4170% set(handles.num_MaxDiff,'Visible','on')
4171% set(handles.thresh_text2,'Visible','on')
4172% set(handles.num_SubdomainSize,'Visible','on')
4173% set(handles.subdomain_text2,'Visible','on')
4174% set(handles.num_Nx,'Visible','on')
4175% set(handles.num_Ny,'Visible','on')
4176% set(handles.nx_patch2_title,'Visible','on')
4177% set(handles.ny_patch2_title,'Visible','on')
4178% % set(handles.get_gridpatch2,'Visible','on')
4179% % set(handles.grid_patch2,'Visible','on')
4180% set(handles.ListPairCiv2,'Visible','on')
4181% set(handles.txt_SubdirCiv2,'Visible','on')
4182% set(handles.TitleSubdirCiv2,'Visible','on')
4183% stereo_test=get(handles.ListCompareMode,'Value');
4184% if stereo_test==3
4185%     set(handles.CheckStereo,'Visible','on')
4186% end
4187
4188% %------------------------------------------------------------------------
4189% function desable_patch2(handles)
4190% %------------------------------------------------------------------------
4191% %set(handles.checkpatch2,'Visible','off')
4192% return
4193% set(handles.frame_patch2,'BackgroundColor',[0.831 0.816 0.784])
4194% set(handles.num_SmoothingParam,'Visible','off')
4195% set(handles.num_SmoothingParam,'Visible','off')
4196% set(handles.num_MaxDiff,'Visible','off')
4197% set(handles.thresh_text2,'Visible','off')
4198% set(handles.num_SubdomainSize,'Visible','off')
4199% set(handles.subdomain_text2,'Visible','off')
4200% set(handles.num_Nx,'Visible','off')
4201% set(handles.num_Ny,'Visible','off')
4202% set(handles.nx_patch2_title,'Visible','off')
4203% set(handles.ny_patch2_title,'Visible','off')
4204% % set(handles.get_gridpatch2,'Visible','off')
4205% % set(handles.grid_patch2,'Visible','off')
4206% if isequal(get(handles.CheckCiv2,'Value'),0) & isequal(get(handles.CheckFix2,'Value'),0)
4207%     set(handles.ListPairCiv2,'Visible','off')
4208%     set(handles.txt_SubdirCiv2,'Visible','off')
4209%     set(handles.TitleSubdirCiv2,'Visible','off')
4210% end
4211% set(handles.CheckStereo,'Visible','off')
4212%------------------------------------------------------------------------
4213function enable_pair1(handles,state)
4214%------------------------------------------------------------------------
4215set(handles.txt_SubdirCiv1,'Visible',state)
4216set(handles.ListSubdirCiv1,'Visible',state)
4217set(handles.TitleSubdirCiv1,'Visible',state)
4218%set(handles.frame_subdirciv1,'Visible',state)
4219set(handles.ListPairCiv1,'Visible',state)
4220set(handles.TitlePairCiv1,'Visible',state)
4221%set(handles.dt_unit,'Visible',state)
4222%set(handles.PAIR_frame,'Visible',state)
4223
4224%------------------------------------------------------------------------
4225% --- Read the parameters for checkciv1 on the interface
4226% function par=read_param_civ1(handles,filecell)
4227% % not deeden anymore
4228% %------------------------------------------------------------------------
4229% ibx_val=str2double(get(handles.num_Bx,'String'));
4230% par.ibx=num2str(ibx_val);
4231% iby_val=str2double(get(handles.num_By,'String'));
4232% par.iby=num2str(iby_val);
4233% isx=get(handles.num_Searchx,'String');
4234% if isnan(str2double(isx)), isx='41'; set(handles.num_Searchx,'String','41'), end; %default
4235% if str2double(isx)<ibx_val+8,isx=num2str(ibx_val+8); set(handles.num_Searchx,'String',num2str(ibx_val+8)); end
4236% isy=get(handles.num_Searchy,'String');
4237% if isnan(str2double(isy)), isy='41'; set(handles.num_Searchy,'String','41'), end;%default
4238% if str2double(isy)<iby_val+8,isy=num2str(iby_val+8); set(handles.num_Searchy,'String',num2str(iby_val+8)); end
4239% par.isx=get(handles.num_Searchx,'String');
4240% par.isy=get(handles.num_Searchy,'String');
4241% par.shiftx=get(handles.num_Shiftx,'String');
4242% par.shifty=get(handles.num_Shifty,'String');
4243% if isnan(str2double(par.isx))
4244%     par.isx='41';%default
4245%     set(handles.num_Searchx,'String','41');
4246% end
4247% if isnan(str2double(par.isy))
4248%     par.isy='41'; %default
4249%     set(handles.num_Searchy,'String','41');
4250% end
4251% if isnan(str2double(par.shiftx))
4252%     par.shiftx='0';%default
4253%     set(handles.num_Shiftx,'String','0');
4254% end
4255% if isnan(str2double(par.shifty))
4256%     par.shifty='0'; %default
4257%     set(handles.num_Shifty,'String','0');
4258% end
4259% par.rho=get(handles.num_Rho,'String');
4260% if isequal(get(handles.num_Rho,'Style'),'popupmenu')
4261%     index=get(handles.num_Rho,'Value');
4262%     par.rho=par.rho{index};
4263% end
4264% dummy=get(handles.num_Dx,'String');
4265% par.dx=dummy{1};
4266% dummy=get(handles.num_Dy,'String');
4267% par.dy=dummy{1};
4268% if isnan(str2double(par.dx))
4269%     if isempty(get(handles.txt_GridName,'String'));
4270%         par.dx='0'; %just read by civ program, not used
4271%     else
4272%         par.dx='20';%default
4273%         set(handles.num_Dx,'String','20');
4274%     end
4275% end
4276% if isnan(str2double(par.dy))
4277%     if isempty(get(handles.txt_GridName,'String'));
4278%         par.dy='0';%just read by civ program, not used
4279%     else
4280%         par.dy='20';%default
4281%         set(handles.dy_civ1_title,'String','20');
4282%     end
4283% end
4284% par.pxcmx='1'; %velocities are expressed in pixel dispalcement
4285% par.pxcmy='1';
4286% % if exist('file_ima','var')
4287% A=imread(filecell.ima1.civ1{1,1});%read the first image to get the size
4288% sizim=size(A);
4289% par.npx=num2str(sizim(2));
4290% par.npy=num2str(sizim(1));
4291% %TODO : civ should not need npx and npy
4292%
4293%
4294% % end
4295% %time=get(handles.RootName,'UserData'); %get the set of times
4296% dummy=get(handles.txt_GridName,'String');
4297% par.gridname=dummy{1};
4298% par.gridflag='y';
4299% if strcmp(par.gridname,'')|| isempty(par.gridname)
4300%     par.gridname='nogrid';
4301%     par.gridflag='n';
4302% end
4303%
4304 
4305           
4306%------------------------------------------------------------------------
4307function par=read_param_civ2(handles,file_ima)
4308%------------------------------------------------------------------------
4309par.ibx=get(handles.num_Bx,'String');
4310par.iby=get(handles.num_By,'String');
4311par.rho=get(handles.num_Rho,'String');
4312par.decimal=int2str(get(handles.CheckDecimal,'Value'));
4313par.deformation=int2str(get(handles.CheckDeformation,'Value'));
4314par.dx=get(handles.num_Dx,'String');
4315par.dy=get(handles.num_Dy,'String');
4316if isnan(str2double(par.dx))
4317    if isempty(get(handles.txt_GridName,'String'));
4318        par.dx='0'; %just read by civ program, not used
4319    else
4320        par.dx='20';%default
4321        set(handles.num_Dx,'String','20');
4322    end
4323end
4324if isnan(str2double(par.dy))
4325    if isempty(get(handles.txt_GridName,'String'));
4326        par.dy='0';%just read by civ program, not used
4327    else
4328        par.dy='20';%default
4329        set(handles.num_Dy,'String','20');
4330    end
4331end
4332par.pxcmx='1';
4333par.pxcmy='1';
4334A=imread(file_ima);%read the first image to get the size
4335sizim=size(A);
4336par.npx=num2str(sizim(2));
4337par.npy=num2str(sizim(1));
4338%time=get(handles.RootName,'UserData'); %get the set of times
4339par.gridname=get(handles.txt_GridName,'String');
4340par.gridflag='y';
4341if strcmp(par.gridname,'')|| isempty(par.gridname)
4342    par.gridname='nogrid';
4343    par.gridflag='n';
4344end
4345
4346function cmd_CIV1=CIV1_CMD(filename,param)
4347%TODO : include filename in par_civ1
4348%------------------------------------------------------------------------
4349%pixels per cm and matrix of the image times, read from the .civ file by uvmat
4350
4351%changes : filename_cmx -> filename ( no extension )
4352
4353filename=regexprep(filename,'.nc','');
4354
4355if isequal(Param.Civ1.Dt,'0')
4356    Param.Civ1.Dt='1' ;%case of 'displacement' mode
4357end
4358Param.Civ1.filename_ima_a=regexprep(Param.Civ1.filename_ima_a,'.png','');
4359Param.Civ1.filename_ima_b=regexprep(Param.Civ1.filename_ima_b,'.png','');
4360fid=fopen([filename '.civ1.cmx'],'w');
4361fprintf(fid,['##############   CMX file' '\n' ]);
4362fprintf(fid,   ['FirstImage ' regexprep(Param.Civ1.filename_ima_a,'\\','\\\\') '\n' ]);% for windows compatibility
4363fprintf(fid,   ['LastImage  ' regexprep(Param.Civ1.filename_ima_b,'\\','\\\\') '\n' ]);% for windows compatibility
4364fprintf(fid,  ['XX' '\n' ]);
4365fprintf(fid,  ['Mask ' Param.Civ1.maskflag '\n' ]);
4366fprintf(fid,  ['MaskName ' regexprep(Param.Civ1.maskname,'\\','\\\\') '\n' ]);
4367fprintf(fid,   ['ImageSize ' Param.Civ1.npx ' ' Param.Civ1.npy '\n' ]);   %VERIFIER CAS GENERAL ?
4368fprintf(fid,   ['CorrelationBoxesSize ' Param.Civ1.ibx ' ' Param.Civ1.iby '\n' ]);
4369fprintf(fid,   ['SearchBoxeSize ' Param.Civ1.isx ' ' Param.Civ1.isy '\n' ]);
4370fprintf(fid,   ['RO ' Param.Civ1.rho '\n' ]);
4371fprintf(fid,   ['GridSpacing ' Param.Civ1.dx ' ' Param.Civ1.dy '\n' ]);
4372fprintf(fid,   ['XX 1.0' '\n' ]);
4373fprintf(fid,   ['Dt_TO ' Param.Civ1.Dt ' ' Param.Civ1.T0 '\n' ]);
4374fprintf(fid,  ['PixCmXY ' Param.Civ1.pxcmx ' ' Param.Civ1.pxcmy '\n' ]);
4375fprintf(fid,  ['XX 1' '\n' ]);
4376fprintf(fid,   ['ShiftXY ' Param.Civ1.shiftx ' '  Param.Civ1.shifty '\n' ]);
4377fprintf(fid,  ['Grid ' Param.Civ1.gridflag '\n' ]);
4378fprintf(fid,   ['GridName ' regexprep(Param.Civ1.gridname,'\\','\\\\') '\n' ]);
4379fprintf(fid,   ['XX 85' '\n' ]);
4380fprintf(fid,   ['XX 1.0' '\n' ]);
4381fprintf(fid,   ['XX 1.0' '\n' ]);
4382fprintf(fid,   ['Hart 1' '\n' ]);
4383fprintf(fid,  [ 'DecimalShift 0' '\n' ]);
4384fprintf(fid,   ['Deformation 0' '\n' ]);
4385fprintf(fid,  ['CorrelationMin 0' '\n' ]);
4386fprintf(fid,   ['IntensityMin 0' '\n' ]);
4387fprintf(fid,  ['SeuilImage n' '\n' ]);
4388fprintf(fid,   ['SeuilImageValues 0 4096' '\n' ]);
4389fprintf(fid,   ['ImageToUse ' Param.Civ1.term_a ' ' Param.Civ1.term_b '\n' ]); % VERIFIER ?
4390fprintf(fid,   ['ImageUsedBefore null null' '\n' ]);
4391fclose(fid);
4392
4393% cmd_CIV1=[sparam.Civ1Bin ' -f ' filename '.cmx >' filename '.log' ]; % redirect standard output to the log file
4394% cmd_CIV1=regexprep(cmd_CIV1,'\\','\\\\');
4395% namelog=regexprep(namelog,'\\','\\\\');
4396if(isunix)
4397    cmd_CIV1=['cp -f ' filename '.civ1.cmx ' filename '.cmx'];
4398    cmd_CIV1=[cmd_CIV1 '\n'...
4399        Param.xml.Civ1Bin ' -f ' filename '.cmx >' filename '.log' ]; % redirect standard output to the log file, the result file is named [filename '.nc'] by CIVx
4400    cmd_CIV1=[cmd_CIV1 '\n' 'mv ' filename '.log' ' ' filename '.civ1.log' '\n' 'chmod g+w ' filename '.civ1.log' '\n' 'chmod g+w ' filename '.nc'];%rename .log as .civ1.log and set the netcdf result file for group user writting
4401   % cmd_CIV1=[cmd_CIV1 '\n' 'mv ' filename '.cmx' ' ' filename '.checkciv1.cmx' '\n'];%rename .cmx as .checkciv1.cmx
4402else %Windows system
4403%                     flname=regexprep(flname,'\\','\\\\');
4404%                     cmd=[cmd 'copy /Y "' flname '.checkciv1.cmx" "' flname '.cmx"\n'];
4405%     filename=regexprep(filename,'\\','\\\\');
4406    cmd_CIV1=['copy /Y "' filename '.civ1.cmx" "' filename '.cmx"'];% copy the .civ1.cmx parameter file to .cmx
4407    cmd_CIV1=[cmd_CIV1 '\n "' regexprep(Param.xml.Civ1Bin,'\\','\\\\') '" -f "' filename '.cmx" >"' filename '.log"' ]; % redirect standard output to the log file
4408%     namelog=regexprep(namelog,'\\','\\\\');
4409    cmd_CIV1=[cmd_CIV1 '\n ' 'copy /Y "' filename '.log' '" "' filename '.civ1.log"']; %preserve the log file as .civ1.log
4410
4411    %  cmd_CIV1=[cmd_CIV1 '\n' 'copy /Y "' filename '.cmx' '" "' filename '.checkciv1.cmx"'];
4412end
4413
4414%------------------------------------------------------------------------
4415% --- CheckCiv1  Unified
4416function xml_civ1_parameters=CIV1_CMD_Unified(filename,namelog,par)
4417%------------------------------------------------------------------------
4418%pixels per cm and matrix of the image times, read from the .civ file by uvmat
4419%global CivBin%name of the executable for checkciv1 calculation
4420
4421civ1.image1=par.filename_ima_a;
4422civ1.image2=par.filename_ima_b;
4423civ1.imageSize_X=par.npx;
4424civ1.imageSize_Y=par.npy;
4425civ1.outputFileName=[filename '.nc'];
4426civ1.correlationBoxesSize_X=par.ibx;
4427civ1.correlationBoxesSize_Y=par.iby;
4428civ1.searchBoxesSize_X=par.isx;
4429civ1.searchBoxesSize_Y=par.isy;
4430civ1.globalShift_X=par.shiftx;
4431civ1.globalShift_Y=par.shifty;
4432civ1.ro=par.rho;
4433civ1.hart='y';
4434if isequal(par.gridflag,'y')
4435    civ1.grid=par.gridname;
4436else
4437    civ1.grid='n';
4438    civ1.gridSpacing_X=par.dx;
4439    civ1.gridSpacing_Y=par.dy;
4440end
4441if isequal(par.maskflag,'y')
4442    civ1.mask=par.maskname;
4443end
4444civ1.dt=par.Dt;
4445civ1.unit='pixel';
4446civ1.absolut_time_T0=par.T0;
4447civ1.pixcmx=par.pxcmx;
4448civ1.pixcmy=par.pxcmy;
4449civ1.convectFlow='n';
4450
4451xml_civ1_parameters=civ1;
4452
4453%------------------------------------------------------------------------
4454% --- CheckCiv2  Unified
4455function civ2=CIV2_CMD_Unified(filename,namelog,par)
4456%------------------------------------------------------------------------
4457%pixels per cm and matrix of the image times, read from the .civ file by uvmat
4458%global CivBin%name of the executable for checkciv1 calculation
4459
4460filename=regexprep(filename,'.nc','');
4461
4462civ2.image1=par.filename_ima_a;
4463civ2.image2=par.filename_ima_b;
4464civ2.imageSize_X=par.npx;
4465civ2.imageSize_Y=par.npy;
4466civ2.inputFileName=[par.filename_nc1 '.nc'];
4467civ2.outputFileName=[filename '.nc'];
4468civ2.correlationBoxesSize_X=par.ibx;
4469civ2.correlationBoxesSize_Y=par.iby;
4470civ2.ro=par.rho;
4471%checkciv2.decimalShift=par.CheckDecimal;
4472%checkciv2.CheckDeformation=par.CheckDeformation;
4473if isequal(par.decimal,'1')
4474    civ2.decimalShift='y';
4475else
4476    civ2.decimalShift='n';
4477end
4478if isequal(par.deformation,'1')
4479    civ2.deformation='y';
4480else
4481    civ2.deformation='n';
4482end
4483if isequal(par.gridflag,'y')
4484    civ2.grid=par.gridname;
4485else
4486    civ2.grid='n';
4487    civ2.gridSpacing_X=par.dx;
4488    civ2.gridSpacing_Y=par.dy;
4489end
4490civ2.gridSpacing_X='10';
4491civ2.gridSpacing_Y='10';%NOTE: faut mettre gridSpacing pourque ca tourne, meme si c'est la grille qui est utilisee
4492if isequal(par.maskflag,'y')
4493    civ2.mask=par.maskname;
4494else
4495    civ2.mask='n';
4496end
4497civ2.dt=par.Dt;
4498civ2.unit='pixel';
4499civ2.absolut_time_T0=par.T0;
4500civ2.pixcmx=par.pxcmx;
4501civ2.pixcmy=par.pxcmy;
4502civ2.convectFlow='n';
4503civ2.pixcmx=par.pxcmx;
4504civ2.pixcmy=par.pxcmy;
4505civ2.convectFlow='n';
4506
4507%------------------------------------------------------------------------
4508% --- CheckCiv2  CheckCiv2  CheckCiv2 CheckCiv2
4509function cmd_CIV2=CIV2_CMD(filename,param)
4510%------------------------------------------------------------------------
4511%pixels per cm and matrix of the image times, read from the .civ file by uvmat
4512% global civ2Bin sge%name of the executable for checkciv1 calculation
4513filename=regexprep(filename,'.nc','');
4514if isequal(Param.Civ2.Dt,'0')
4515    Param.Civ2.Dt='1' ;%case of 'displacement' mode
4516end
4517Param.Civ2.filename_ima_a=regexprep(Param.Civ2.filename_ima_a,'.png','');
4518Param.Civ2.filename_ima_b=regexprep(Param.Civ2.filename_ima_b,'.png','');% bug : .png appears two times ?
4519[fid,errormsg]=fopen([filename '.civ2.cmx'],'w');
4520if isequal(fid,-1)
4521    msgbox_uvmat('ERROR',errormsg)
4522    cmd_CIV2='';
4523    return
4524end
4525fprintf(fid,['##############   CMX file' '\n' ]);
4526fprintf(fid,   ['FirstImage ' regexprep(Param.Civ2.filename_ima_a,'\\','\\\\') '\n' ]);% for windows compatibility
4527fprintf(fid,   ['LastImage  ' regexprep(Param.Civ2.filename_ima_b,'\\','\\\\') '\n' ]);% for windows compatibility
4528fprintf(fid,  ['XX' '\n' ]);
4529fprintf(fid, ['Mask ' Param.Civ2.MaskFlag '\n' ]);
4530fprintf(fid, ['MaskName ' regexprep(Param.Civ2.MaskName,'\\','\\\\') '\n' ]);% for windows compatibility
4531fprintf(fid, ['ImageSize ' Param.Civ2.npx ' ' Param.Civ2.npy '\n' ]);   %VERIFIER CAS GENERAL ?
4532fprintf(fid, ['CorrelationBoxesSize ' Param.Civ2.ibx ' ' Param.Civ2.iby '\n' ]);
4533fprintf(fid, ['SearchBoxeSize ' Param.Civ2.ibx ' ' Param.Civ2.iby '\n']);
4534fprintf(fid, ['RO ' Param.Civ2.rho '\n']);
4535fprintf(fid, ['GridSpacing ' Param.Civ2.dx ' ' Param.Civ2.dy '\n']);
4536fprintf(fid, ['XX 1.0' '\n' ]);
4537fprintf(fid, ['Dt_TO ' Param.Civ2.Dt ' ' Param.Civ2.T0 '\n' ]);
4538fprintf(fid, ['PixCmXY ' Param.Civ2.pxcmx ' ' Param.Civ2.pxcmy '\n' ]);
4539fprintf(fid, ['XX 1' '\n' ]);
4540fprintf(fid, 'ShiftXY 0 0\n');
4541fprintf(fid, ['Grid ' Param.Civ2.GridFlag '\n' ]);
4542fprintf(fid, ['GridName ' regexprep(Param.Civ2.GridName,'\\','\\\\') '\n']);
4543fprintf(fid, ['XX 85' '\n' ]);
4544fprintf(fid, ['XX 1.0' '\n' ]);
4545fprintf(fid, ['XX 1.0' '\n' ]);
4546fprintf(fid, ['Hart 1' '\n' ]);
4547fprintf(fid, ['DecimalShift ' Param.Civ2.decimal '\n']);
4548fprintf(fid, ['Deformation ' Param.Civ2.deformation '\n']);
4549fprintf(fid,  ['CorrelationMin 0' '\n' ]);
4550fprintf(fid,   ['IntensityMin 0' '\n' ]);
4551fprintf(fid,  ['SeuilImage n' '\n' ]);
4552fprintf(fid,   ['SeuilImageValues 0 4096' '\n' ]);
4553fprintf(fid,   ['ImageToUse ' Param.Civ2.term_a ' ' Param.Civ2.term_b '\n' ]); % VERIFIER ?
4554fprintf(fid, ['ImageUsedBefore ' regexprep(Param.Civ2.filename_nc1,'\\','\\\\') '\n']);
4555fclose(fid);
4556
4557if(isunix)
4558    cmd_CIV2=['cp -f ' filename '.civ2.cmx ' filename '.cmx\n'];
4559    cmd_CIV2=[cmd_CIV2 Param.xml.Civ2Bin ' -f ' filename  '.cmx >' filename '.log' ]; % redirect standard output to the log file, the result file is named [filename '.nc'] by CIVx
4560    cmd_CIV2=[cmd_CIV2 '\n' 'mv ' filename '.log' ' ' filename '.civ2.log' '\n' 'chmod g+w ' filename '.nc'];%preserve the log file as .civ2.log
4561%    cmd_CIV2=[cmd_CIV2 '\n' 'mv ' filename '.cmx' ' ' filename '.checkciv2.cmx' '\n'];%rename .cmx as .checkciv2.cmx, the result file is named [filename '.nc'] by CIVx
4562
4563else
4564    filename=regexprep(filename,'\\','\\\\');
4565    cmd_CIV2=['copy /Y "' filename '.civ2.cmx" "' filename '.cmx"'];
4566    cmd_CIV2=[cmd_CIV2 '\n "' regexprep(Param.xml.Civ2Bin,'\\','\\\\') '" -f "' filename  '.cmx" >"' filename '.log"' ]; % redirect standard output to the log file
4567    cmd_CIV2=[cmd_CIV2 '\n ' 'copy /Y "' filename '.log' '" "' filename '.civ2.log"'];
4568 %    cmd_CIV2=[cmd_CIV2 '\n' 'copy /Y "' filename '.cmx' '" "' filename '.checkciv2.cmx"'];
4569end
4570
4571
4572%------------------------------------------------------------------------
4573%--read images and convert them to the uint16 format used for PIV
4574function A=read_image(filename,type_ima,num,movieobject)
4575%------------------------------------------------------------------------
4576%num is the view number needed for an avi movie
4577switch type_ima
4578    case 'movie'
4579        A=read(movieobject,num);
4580    case 'avi'
4581        mov=aviread(filename,num);
4582        A=frame2im(mov(1));
4583    case 'multimage'
4584        A=imread(filename,num);
4585    case 'image'
4586        A=imread(filename);
4587end
4588siz=size(A);
4589if length(siz)==3;%color images
4590    A=sum(double(A),3);
4591    A=uint16(A);
4592end
4593
4594%------------------------------------------------------------------------
4595function ref_i_Callback(hObject, eventdata, handles)
4596%------------------------------------------------------------------------
4597mode_list=get(handles.ListPairMode,'String');
4598mode_value=get(handles.ListPairMode,'Value');
4599mode=mode_list{mode_value};
4600find_netcpair_civ1(hObject, eventdata, handles);% update the menu of pairs depending on the available netcdf files
4601if isequal(mode,'series(Di)') || ...% we do patch2 only
4602        (get(handles.CheckCiv2,'Value')==0 && get(handles.CheckCiv1,'Value')==0 && get(handles.CheckFix1,'Value')==0 && get(handles.CheckPatch1,'Value')==0)
4603    find_netcpair_civ2(hObject, eventdata, handles);
4604end
4605
4606%------------------------------------------------------------------------
4607function ref_j_Callback(hObject, eventdata, handles)
4608%------------------------------------------------------------------------
4609mode_list=get(handles.ListPairMode,'String');
4610mode_value=get(handles.ListPairMode,'Value');
4611mode=mode_list{mode_value};
4612if isequal(get(handles.CheckCiv1,'Value'),0)|| isequal(mode,'series(Dj)')
4613    find_netcpair_civ1(hObject, eventdata, handles);% update the menu of pairs depending on the available netcdf files
4614end
4615if isequal(mode,'series(Dj)') || ...
4616        (get(handles.CheckCiv2,'Value')==0 && get(handles.CheckCiv1,'Value')==0 && get(handles.CheckFix1,'Value')==0 && get(handles.CheckPatch1,'Value')==0)
4617    find_netcpair_civ2(hObject, eventdata, handles);
4618end
4619
4620%------------------------------------------------------------------------
4621function ref_i_civ2_Callback(hObject, eventdata, handles)
4622%------------------------------------------------------------------------
4623mode_list=get(handles.ListPairMode,'String');
4624mode_value=get(handles.ListPairMode,'Value');
4625mode=mode_list{mode_value};
4626find_netcpair_civ2(hObject, eventdata, handles);% update the menu of pairs depending on the available netcdf files
4627
4628%------------------------------------------------------------------------
4629function ref_j_civ2_Callback(hObject, eventdata, handles)
4630%------------------------------------------------------------------------
4631mode_list=get(handles.ListPairMode,'String');
4632mode_value=get(handles.ListPairMode,'Value');
4633mode=mode_list{mode_value};
4634if  isequal(mode,'series(Dj)')
4635    find_netcpair_civ2(hObject, eventdata, handles);% update the menu of pairs depending on the available netcdf files
4636end
4637
4638%------------------------------------------------------------------------
4639% --- Executes on button press in ListCompareMode.
4640function ListCompareMode_Callback(hObject, eventdata, handles)
4641%------------------------------------------------------------------------
4642test=get(handles.ListCompareMode,'Value');
4643if test==2 || test==3 % case 'dispalcemen' or 'stereo PIV'
4644    filebase=get(handles.RootName,'String');
4645    browse=get(handlesRootName,'Userdata');
4646    browse.nom_type_ima1=browse.nom_type_ima;
4647    set(handlesRootName,'UserData',browse);
4648    set(handles.sub_txt,'Visible','on')
4649    set(handles.RootName_1,'Visible','On');%mkes the second file input window visible
4650    mode_store=get(handles.ListPairMode,'String');%get the present 'mode'
4651    set(handles.ListCompareMode,'UserData',mode_store);%store the mode display
4652    set(handles.ListPairMode,'Visible','off')
4653    if test==2
4654        set(handles.ListPairMode,'Visible','off')
4655        set(handles.ListPairMode,'Value',1) % mode 'civX' selected by default
4656    else
4657        set(handles.ListPairMode,'Visible','on')
4658        set(handles.ListPairMode,'Value',3) % mode 'Matlab' selected for stereo
4659    end
4660   
4661    %% menuopen an image file with the browser
4662    ind_opening=1;%default
4663    browse.incr_pair=[0 0]; %default
4664    oldfile=get(handles.RootName,'String');
4665     menu={'*.xml;*.civ;*.png;*.jpg;*.tif;*.avi;*.AVI;*.nc;', ' (*.xml,*.civ,*.png,*.jpg ,.tif, *.avi,*.nc)';
4666       '*.xml',  '.xml files '; ...
4667        '*.civ',  '.civ files '; ...
4668        '*.png','.png image files'; ...
4669        '*.jpg',' jpeg image files'; ...
4670        '*.tif','.tif image files'; ...
4671        '*.avi;*.AVI','.avi movie files'; ...
4672        '*.nc','.netcdf files'; ...
4673        '*.*',  'All Files (*.*)'};
4674    [FileName, PathName, filtindex] = uigetfile( menu, 'Pick a file of the second series',oldfile);
4675    fileinput=[PathName FileName];%complete file name
4676    sizf=size(fileinput);
4677    if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end %stop if fileinput not a character string
4678    [path,name,ext]=fileparts(fileinput);
4679    [path1]=fileparts(filebase);
4680    if isunix
4681        [status,path]=system(['readlink ' path]);
4682        [status,path1]=system(['readlink ' path1]);% look for the true path in case of symbolic paths
4683    end
4684    if ~strcmp(path1,path)
4685        msgbox_uvmat('ERROR','The second image series must be in the same directory as the first one')
4686        return
4687     end
4688%     set(handles.RootName_1,'String',name);
4689    [RootPath,RootFile,field_count,str2,str_a,str_b,xx,nom_type,subdir]=name2display(name);
4690    set(handles.RootName_1,'String',RootFile);
4691    browse=get(handlesRootName,'UserData');
4692    browse.nom_type_ima_1=nom_type;
4693    set(handlesRootName,'UserData',browse)
4694   
4695    %check image extension
4696    if ~strcmp(ext,get(handles.ImaExt,'String'))
4697        msgbox_uvmat('ERROR','The second image series must have the same extension name as the first one')
4698        return
4699    end
4700   
4701    %% check coincidence of image sizes
4702%     ref_i=get(handles.ref_i,'string');
4703%     ref_j=get(handles.ref_j,'string');
4704%     [filecell,num1_civ1,num2_civ1,num_a_civ1,num_b_civ1,num1_civ2,num2_civ2,num_a_civ2,num_b_civ2,nom_type_nc]=set_civ_filenames(handles,ref_i,ref_j,[1 0 0 0 0 0]);
4705%     A=imread(filecell.ima1.checkciv1{1});
4706%     A_1=imread(fileinput);
4707%     npxy=size(A);
4708%     npxy_1=size(A_1);
4709%     if ~isequal(size(A),size(A_1))
4710%         msgbox_uvmat('ERROR','The two input image series do not have the same size')
4711%         return
4712%     end
4713else
4714    set(handles.ListPairMode,'Visible','on')
4715    set(handles.RootName_1,'Visible','Off');
4716    set(handles.sub_txt,'Visible','off')
4717    set(handles.RootName_1,'String',[]);
4718    mode_store=get(handles.ListCompareMode,'UserData');
4719    set(handles.ListPairMode,'Value',1)
4720    set(handles.ListPairMode,'String',mode_store)
4721    set(handles.test_stereo1,'Value',0)
4722    set(handles.CheckStereo,'Value',0)
4723    set(handles.ListPairMode,'Value',1) % mode 'civX' selected by default
4724end
4725if test==3 && get(handles.CheckPatch1,'Value')
4726    set(handles.test_stereo1,'Visible','on')
4727else
4728    set(handles.test_stereo1,'Visible','off')
4729end
4730if test==3 && get(handles.CheckPatch2,'Value')
4731    set(handles.CheckStereo,'Visible','on')
4732else
4733    set(handles.CheckStereo,'Visible','off')
4734end
4735mode_Callback(hObject, eventdata, handles)
4736
4737%------------------------------------------------------------------------
4738% --- Executes on button press in get_ref_fix1.
4739function get_ref_fix1_Callback(hObject, eventdata, handles)
4740%------------------------------------------------------------------------
4741filebase=get(handles.RootName,'String');
4742[FileName, PathName, filterindex] = uigetfile( ...
4743    {'*.nc', ' (*.nc)';
4744    '*.nc',  'netcdf files '; ...
4745    '*.*', 'All Files (*.*)'}, ...
4746    'Pick a file',filebase);
4747
4748fileinput=[PathName FileName];
4749sizf=size(fileinput);
4750if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end %stop if fileinput not a character string
4751[Path,File,field_count,str2,str_a,str_b,ref.ext,ref.nom_type,ref.subdir]=name2display(fileinput);
4752ref.filebase=fullfile(Path,File);
4753ref.num_a=stra2num(str_a);
4754ref.num_b=stra2num(str_b);
4755ref.num1=str2double(field_count);
4756ref.num2=str2double(str2);
4757browse=[];%initialisation
4758if ~isequal(ref.ext,'.nc')
4759    msgbox_uvmat('ERROR','the reference file must be in netcdf format (*.nc)')
4760    return
4761end
4762set(handles.ref_fix1,'String',[fullfile(ref.subdir,File) '....nc']);
4763set(handles.ref_fix1,'UserData',ref)
4764menu_field{1}='civ1';
4765Data=nc2struct(fileinput,[]);
4766if isfield(Data,'patch') && isequal(Data.patch,1)
4767    menu_field{2}='filter1';
4768end
4769if isfield(Data,'civ2') && isequal(Data.civ2,1)
4770    menu_field{3}='civ2';
4771end
4772if isfield(Data,'patch2') && isequal(Data.patch2,1)
4773    menu_field{4}='filter2';
4774end
4775set(handles.field_ref1,'String',menu_field);
4776set(handles.field_ref1,'Value',length(menu_field));
4777set(handles.num_MinVel,'Value',2);
4778set(handles.num_MinVel,'String','1');%default threshold
4779set(handles.ref_fix1,'Enable','on')
4780
4781%------------------------------------------------------------------------
4782% --- Executes on button press in get_ref_fix2.
4783function get_ref_fix2_Callback(hObject, eventdata, handles)
4784%------------------------------------------------------------------------
4785if isequal(get(handles.get_ref_fix2,'Value'),1)
4786    filebase=get(handles.RootName,'String');
4787    [FileName, PathName, filterindex] = uigetfile( ...
4788        {'*.nc', ' (*.nc)';
4789        '*.nc',  'netcdf files '; ...
4790        '*.*', 'All Files (*.*)'}, ...
4791        'Pick a file',filebase);
4792    fileinput=[PathName FileName];
4793    sizf=size(fileinput);
4794    if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end %stop if fileinput not a character string
4795    [Path,File,field_count,str2,str_a,str_b,ref.ext,ref.nom_type,ref.subdir]=name2display(fileinput);
4796    ref.filebase=fullfile(Path,File);
4797    ref.num_a=stra2num(str_a);
4798    ref.num_b=stra2num(str_b);
4799    ref.num1=str2num(field_count);
4800    ref.num2=str2num(str2);
4801    browse=[];%initialisation
4802    if ~isequal(ref.ext,'.nc')
4803        msgbox_uvmat('ERROR','the reference file must be in netcdf format (*.nc)')
4804        return
4805    end
4806    set(handles.ref_fix2,'String',[fullfile(ref.subdir,File) '....nc']);
4807    set(handles.ref_fix2,'UserData',ref)
4808    menu_field{1}='civ1';
4809    Data=nc2struct(fileinput,[]);
4810    if isfield(Data,'patch') & isequal(Data.patch,1)
4811        menu_field{2}='filter1';
4812    end
4813    if isfield(Data,'civ2') & isequal(Data.civ2,1)
4814        menu_field{3}='civ2';
4815    end
4816    if isfield(Data,'patch2') & isequal(Data.patch2,1)
4817        menu_field{4}='filter2';
4818    end
4819    set(handles.field_ref2,'String',menu_field);
4820    set(handles.field_ref2,'Value',length(menu_field));
4821    set(handles.num_MinVel,'Value',2);
4822    set(handles.num_MinVel,'String','1');%default threshold
4823    set(handles.ref_fix2,'Enable','on')
4824    set(handles.ref_fix2,'Visible','on')
4825    set(handles.field_ref2,'Visible','on')
4826else
4827    set(handles.ref_fix2,'Visible','off')
4828    set(handles.field_ref2,'Visible','off')
4829end
4830
4831%------------------------------------------------------------------------
4832function ref_fix1_Callback(hObject, eventdata, handles)
4833%------------------------------------------------------------------------
4834set(handles.num_MinVel,'Value',1);
4835set(handles.field_ref1,'Value',1)
4836set(handles.field_ref1,'String',{' '})
4837set(handles.ref_fix1,'UserData',[]);
4838set(handles.ref_fix1,'String','');
4839set(handles.thresh_vel1,'String','0');
4840
4841%------------------------------------------------------------------------
4842function ref_fix2_Callback(hObject, eventdata, handles)
4843%------------------------------------------------------------------------
4844set(handles.num_MinVel,'Value',1);
4845set(handles.field_ref2,'Value',1)
4846set(handles.field_ref2,'String',{' '})
4847set(handles.ref_fix2,'UserData',[]);
4848set(handles.ref_fix2,'String','');
4849set(handles.num_MinVel,'String','0');
4850
4851%------------------------------------------------------------------------
4852% --- Executes on button press in test_stereo1.
4853function test_stereo1_Callback(hObject, eventdata, handles)
4854%------------------------------------------------------------------------
4855if isequal(get(handles.test_stereo1,'Value'),0)
4856    set(handles.subdomain_patch1,'Visible','on')
4857    set(handles.rho_patch1,'Visible','on')
4858else
4859    set(handles.subdomain_patch1,'Visible','off')
4860    set(handles.rho_patch1,'Visible','off')
4861end
4862
4863%------------------------------------------------------------------------
4864% --- Executes on button press in CheckStereo.
4865function StereoCheck_Callback(hObject, eventdata, handles)
4866%------------------------------------------------------------------------
4867if isequal(get(handles.CheckStereo,'Value'),0)
4868    set(handles.num_SubdomainSize,'Visible','on')
4869    set(handles.num_SmoothingParam,'Visible','on')
4870else
4871    set(handles.num_SubdomainSize,'Visible','off')
4872    set(handles.num_SmoothingParam,'Visible','off')
4873end
4874
4875%------------------------------------------------------------------------
4876% --- Executes on button press in check_Threshold.
4877function ImaThreshold_Callback(hObject, eventdata, handles)
4878%------------------------------------------------------------------------
4879if isequal(get(handles.check_Threshold,'Value'),1)
4880    set(handles.num_MinIma,'Visible','on')
4881    set(handles.num_MaxIma,'Visible','on')
4882else
4883    set(handles.num_MinIma,'Visible','off')
4884    set(handles.num_MaxIma,'Visible','off')
4885end
4886
4887%------------------------------------------------------------------------
4888% --- Executes on button press in ImaThreshold2.
4889function ImaThreshold2_Callback(hObject, eventdata, handles)
4890%------------------------------------------------------------------------
4891if isequal(get(handles.ImaThreshold2,'Value'),1)
4892    set(handles.num_MinIma,'Visible','on')
4893    set(handles.num_MaxIma,'Visible','on')
4894else
4895    set(handles.num_MinIma,'Visible','off')
4896    set(handles.num_MaxIma,'Visible','off')
4897end
4898
4899%------------------------------------------------------------------------
4900% --- Executes on button press in TestCiv1: display image correlation function
4901function TestCiv1_Callback(hObject, eventdata, handles)
4902%------------------------------------------------------------------------
4903set(handles.TestCiv1,'BackgroundColor',[1 1 0])
4904drawnow
4905test_civ1=get(handles.TestCiv1,'Value');
4906if test_civ1
4907    ref_i=str2double(get(handles.ref_i,'String'));
4908    if strcmp(get(handles.ref_j,'Visible'),'on')
4909        ref_j=str2double(get(handles.ref_j,'String'));
4910    else
4911        ref_j=1;%default
4912    end
4913    [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]=...
4914        set_civ_filenames(handles,ref_i,ref_j,[1 0 0 0 0 0]);
4915    Data.ListVarName={'ny','nx','A'};
4916    Data.VarDimName={'ny','nx',{'ny','nx'}};
4917    Data.A=imread(filecell.ima1.civ1{1});
4918    Data.ny=[size(Data.A,1) 1];
4919    Data.nx=[1 size(Data.A,2)];
4920    par_civ1=read_param_civ1(handles,filecell.ima1.civ1{1});
4921    par_civ1.filename_ima_a=filecell.ima1.civ1{1};
4922    par_civ1.filename_ima_b=filecell.ima2.civ1{1};
4923    par_civ1.T0=0;
4924    par_civ1.Dt=1;
4925    Param.Civ1=par_civ1;
4926    Data=civ_uvmat(Param);
4927    Data.ListVarName=[Data.ListVarName {'ny','nx','A'}];
4928    Data.VarDimName=[Data.VarDimName {'ny','nx',{'ny','nx'}}];
4929    Data.A=imread(filecell.ima1.civ1{1});
4930    Data.ny=[size(Data.A,1) 1];
4931    Data.nx=[1 size(Data.A,2)];
4932    hview_field=view_field(Data);
4933    set(0,'CurrentFigure',hview_field)
4934    hhview_field=guihandles(hview_field);
4935    set(hview_field,'CurrentAxes',hhview_field.axes3)
4936    ViewData=get(hview_field,'UserData');
4937    ViewData.CivHandle=handles.civ;% indicate the handle of the civ GUI in view_field
4938    ViewData.axes3.B=imread(filecell.ima2.civ1{1});%store the second image in the UserData of the GUI view_field
4939    ViewData.axes3.X=Data.Civ1_X; %keep the set of points in memeory
4940    ViewData.axes3.Y=Data.Civ1_Y;
4941    set(hview_field,'UserData',ViewData)
4942    corrfig=findobj(allchild(0),'tag','corrfig');% look for a current figure for image correlation display
4943    if isempty(corrfig)
4944        corrfig=figure;
4945        set(corrfig,'tag','corrfig')
4946        set(corrfig,'name','image correlation')
4947        set(corrfig,'DeleteFcn',{@closeview_field})%
4948    end
4949    set(handles.TestCiv1,'BackgroundColor',[1 0 0])
4950else
4951    corrfig=findobj(allchild(0),'tag','corrfig');% look for a current figure for image correlation display
4952    if ~isempty(corrfig)
4953        delete(corrfig)
4954    end
4955    hview_field=findobj(allchild(0),'tag','view_field');% look for view_field   
4956    if ~isempty(hview_field)
4957        delete(hview_field)
4958    end
4959end
4960
4961function closeview_field(gcbo,eventdata)
4962hview_field=findobj(allchild(0),'tag','view_field');% look for view_field   
4963    if ~isempty(hview_field)
4964        delete(hview_field)
4965    end
4966%-------------------------------------------------------------------
4967% --- Executes on button press in status.
4968function status_Callback(hObject, eventdata, handles)
4969%-------------------------------------------------------------------
4970val=get(handles.status,'Value');
4971if val==0
4972    set(handles.status,'BackgroundColor',[0 1 0])
4973    hfig=findobj(allchild(0),'name','civ_status');
4974    if ~isempty(hfig)
4975        delete(hfig)
4976    end
4977    return
4978end
4979set(handles.status,'BackgroundColor',[1 1 0])
4980drawnow
4981listtype={'civ1','fix1','patch1','civ2','fix2','patch2'};
4982Param.CheckCiv1=get(handles.CheckCiv1,'Value');
4983Param.CheckFix1=get(handles.CheckFix1,'Value');
4984Param.CheckPatch1=get(handles.CheckPatch1,'Value');
4985Param.CheckCiv2=get(handles.CheckCiv2,'Value');
4986Param.CheckFix2=get(handles.CheckFix2,'Value');
4987Param.CheckPatch2=get(handles.CheckPatch2,'Value');
4988box_test=[Param.CheckCiv1 Param.CheckFix1 Param.CheckPatch1 Param.CheckCiv2 Param.CheckFix2 Param.CheckPatch2];
4989
4990option_civ=find(box_test,1,'last');%last selected option (non-zero index of box_test)
4991filecell=get(handles.civ,'UserData');%retrieve the list of output files expected for PIV
4992test_new=0;
4993if ~isfield(filecell,'nc')
4994    test_new=1;
4995    [ref_i,ref_j,errormsg]=find_ref_indices(handles);
4996    if ~isempty(errormsg)
4997        msgbox_uvmat('ERROR',errormsg)
4998        return
4999    end
5000    filecell=set_civ_filenames(handles,ref_i,ref_j,box_test);%determine the output file expected from the GUI status
5001end
5002if ~isequal(box_test(4:6),[0 0 0])
5003    civ_files=filecell.nc.civ2;%case of civ2 operations
5004else
5005    civ_files=filecell.nc.civ1;
5006end
5007[root,filename,ext]=fileparts(civ_files{1});
5008[rootroot,subdir,extdir]=fileparts(root);
5009hfig=findobj(allchild(0),'name','civ_status');
5010if isempty(hfig)
5011    hfig=figure('DeleteFcn',@stop_status);
5012    set(hfig,'name','civ_status')
5013    hlist=uicontrol('Style','listbox','Units','normalized', 'Position',[0.05 0.09 0.9 0.71], 'Callback', @open_view_field,'tag','list');
5014    uicontrol('Style','edit','Units','normalized', 'Position', [0.05 0.87 0.9 0.1],'tag','msgbox','Max',2,'String','checking files...');
5015    uicontrol('Style','frame','Units','normalized', 'Position', [0.05 0.81 0.9 0.05]);
5016    uicontrol('Style','pushbutton','Units','normalized', 'Position', [0.7 0.01 0.2 0.07],'String','OK','FontWeight','bold','FontUnits','normalized','FontSize',0.9,'Callback',@close_GUI);
5017    BarPosition=[0.05 0.81 0.01 0.05];
5018    hwaitbar=uicontrol('Style','frame','Units','normalized', 'Position',BarPosition ,'BackgroundColor',[1 0 0],'tag','waitbar');
5019    drawnow
5020end
5021% datnum=[];
5022Tabchar={};
5023nbfiles=numel(civ_files);
5024count=0;
5025testrecent=0;
5026while count<nbfiles
5027    count=0;
5028    datnum=zeros(1,nbfiles);
5029    for ifile=1:nbfiles
5030        detect=exist(civ_files{ifile},'file'); % check the existence of the file
5031        option=0;
5032        if detect==0
5033            option_str='not created';
5034        else
5035            datfile=dir(civ_files{ifile});
5036            if isfield(datfile,'datenum')
5037                datnum(ifile)=datfile.datenum;%only available in recent matlab versions
5038                testrecent=1;
5039            end
5040            filefound(ifile)={datfile.name};
5041            lastfield='';
5042            % check the content  netcdf file
5043            Data=nc2struct(civ_files{ifile},'ListGlobalAttribute','patch2','fix2','civ2','patch','fix');
5044            if ~isempty(Data.patch2) && isequal(Data.patch2,1)
5045                option=6;
5046                option_str='patch2';
5047            elseif ~isempty(Data.fix2) && isequal(Data.fix2,1)
5048                option=5;
5049                option_str='fix2';
5050            elseif ~isempty(Data.civ2) && isequal(Data.civ2,1);
5051                option=4;
5052                option_str='civ2';
5053            elseif ~isempty(Data.patch) && isequal(Data.patch,1);
5054                option=3;
5055                option_str='patch1';
5056            elseif ~isempty(Data.fix) && isequal(Data.fix,1);
5057                option=2;
5058                option_str='fix1';
5059            else
5060                option=1;
5061                option_str='civ1';
5062            end
5063        end
5064        if option >= option_civ
5065            count=count+1;
5066        end
5067        [rr,filename,ext]=fileparts(civ_files{ifile});
5068        Tabchar{ifile,1}=[fullfile([subdir extdir],filename) ext  '...' option_str];
5069    end
5070    datnum=datnum(datnum~=0);%keep the non zero values corresponding to existing files
5071    if isempty(datnum)
5072        if testrecent
5073            message='no civ result created yet';
5074        else
5075            message='';
5076        end
5077    else
5078        datnum=datnum(datnum~=0);%keep the non zero values corresponding to existing files
5079        [first,ind]=min(datnum);
5080        [last,indlast]=max(datnum);
5081        if test_new
5082            message='existing file status, no processing launched yet';
5083        else
5084        message={[num2str(count) ' file(s) done over ' num2str(nbfiles)] ;['oldest modification:  ' cell2mat(filefound(ind)) ' : ' datestr(first)];...
5085            ['latest modification:  ' cell2mat(filefound(indlast)) ' : ' datestr(last)]};
5086        end
5087    end
5088    hfig=findobj(allchild(0),'name','civ_status');
5089    if isempty(hfig)% the status list has been deleted
5090        return
5091    else
5092        hlist=findobj(hfig,'tag','list');
5093        hmsgbox=findobj(hfig,'tag','msgbox');
5094        hwaitbar=findobj(hfig,'tag','waitbar');
5095        set(hlist,'String',Tabchar)
5096        set(hmsgbox,'String', message)
5097        if count>0 && ~test_new
5098            BarPosition(3)=0.9*count/nbfiles;
5099            set(hwaitbar,'Position',BarPosition)
5100        end
5101    end
5102    set(hlist,'UserData',rootroot)
5103    pause(10)% wait 10 seconds for next check
5104end
5105
5106   
5107%------------------------------------------------------------------------   
5108% call 'view_field.fig' to display the  field selected in the list of 'status'
5109function open_view_field(hObject, eventdata)
5110%------------------------------------------------------------------------
5111list=get(hObject,'String');
5112index=get(hObject,'Value');
5113rootroot=get(hObject,'UserData');
5114filename=list{index};
5115ind_dot=findstr(filename,'...');
5116filename=filename(1:ind_dot-1);
5117filename=fullfile(rootroot,filename);
5118delete(get(hObject,'parent'))%delete the display figure to stop the check process
5119if exist(filename,'file')%visualise the vel field if it exists
5120    uvmat(filename)
5121    set(gcbo,'Value',1)
5122end
5123
5124%------------------------------------------------------------------------   
5125% launched by pressing OK on the status figure
5126function close_GUI(hObject, eventdata)
5127%------------------------------------------------------------------------
5128    delete(gcbf)
5129   
5130%------------------------------------------------------------------------   
5131% launched by deleting the status figure
5132function stop_status(hObject, eventdata)
5133%------------------------------------------------------------------------
5134hciv=findobj(allchild(0),'tag','civ');
5135hhciv=guidata(hciv);
5136set(hhciv.status,'value',0) %reset the status uicontrol in the GUI civ
5137set(hhciv.status,'BackgroundColor',[0 1 0])
5138
5139%------------------------------------------------------------------------
5140% % --- Executes on button press in ListPairMode.
5141% function CivMode_Callback(hObject, eventdata, handles)
5142% %------------------------------------------------------------------------
5143% Listprog=get(handles.ListPairMode,'String');
5144% index=get(handles.ListPairMode,'Value');
5145% prog=Listprog{index};
5146% switch prog
5147%     case 'CivX'
5148%         set(handles.thresh_patch1,'Visible','off')
5149%         set(handles.thresh_text1,'Visible','off')
5150%         set(handles.num_MaxDiff,'Visible','off')
5151%         set(handles.thresh_text2,'Visible','off')
5152%         set(handles.num_Rho,'Style','edit')
5153%         set(handles.num_Rho,'String','1')
5154%         set(handles.BATCH,'Enable','on')
5155%     case 'CivAll'
5156%         if get(handles.CheckPatch1,'Value')
5157%             set(handles.thresh_patch1,'Visible','on')
5158%             set(handles.thresh_text1,'Visible','on')
5159%         end
5160%         set(handles.num_Rho,'Style','edit')
5161%         set(handles.num_Rho,'String','1')
5162%         set(handles.BATCH,'Enable','on')
5163%     case 'CivUvmat'
5164%       
5165% end
5166
5167
5168% --------------------------------------------------------------------
5169function MenuHelp_Callback(hObject, eventdata, handles)
5170path_civ=fileparts(which ('civ'));
5171helpfile=fullfile(path_civ,'uvmat_doc','uvmat_doc.html');
5172if isempty(dir(helpfile))
5173    msgbox_uvmat('ERROR','Please put the help file uvmat_doc.html in the sub-directory /uvmat_doc of the UVMAT package')
5174else
5175    addpath (fullfile(path_civ,'uvmat_doc'))
5176    web([helpfile '#civ'])
5177end
5178
5179% --------------------------------------------------------------------
5180function CivX_Callback(hObject, eventdata, handles)
5181%set(handles.thresh_patch1,'Visible','off')
5182set(handles.thresh_text1,'Visible','off')
5183set(handles.num_MaxDiff,'Visible','off')
5184set(handles.thresh_text2,'Visible','off')
5185set(handles.num_Rho,'Style','edit')
5186set(handles.num_Rho,'String','1')
5187set(handles.BATCH,'Enable','on')
5188
5189% --------------------------------------------------------------------
5190function Matlab_Callback(hObject, eventdata, handles)
5191set(handles.Matlab,'checked','on')
5192set(handles.CivX,'checked','off')
5193if get(handles.CheckPatch1,'Value')
5194    set(handles.thresh_patch1,'Visible','on')
5195    set(handles.thresh_text1,'Visible','on')
5196end
5197if get(handles.CheckPatch2,'Value')
5198    set(handles.num_MaxDiff,'Visible','on')
5199    set(handles.thresh_text2,'Visible','on')
5200end
5201set(handles.num_Rho,'Style','popupmenu')
5202set(handles.num_Rho,'Value',1)
5203set(handles.num_Rho,'String',{'1';'2'})
5204set(handles.BATCH,'Enable','off')
5205
5206% --------------------------------------------------------------------
5207% --- read a panel with handle 'handle' producing a structure 'struct'
5208function struct=read_panel(handle)
5209hchild=get(handle,'children');
5210for ichild=1:numel(hchild)
5211    if strcmp(get(hchild(ichild),'Visible'),'on')
5212        object_style=get(hchild(ichild),'Style');
5213        tag=get(hchild(ichild),'tag');
5214        check_input=1;%default
5215        switch object_style
5216            case 'edit'
5217                switch(tag(1:4))
5218                    case 'num_'
5219                        input=str2double(get(hchild(ichild),'String'));
5220                        %deal with undefined input: retrieve the default value stored as UserData
5221                        if isnan(input)
5222                            input=get(hchild(ichild),'UserData');
5223                            set(hchild(ichild),'String',num2str(input))
5224                        end
5225                    case 'txt_'
5226                        input=get(hchild(ichild),'String');
5227                end
5228                key=tag(5:end);
5229            case 'checkbox'
5230                input=get(hchild(ichild),'Value');
5231                key=tag(7:end);
5232            otherwise
5233                check_input=0;
5234        end
5235        if check_input
5236            eval(['struct.' key '=input;'])
5237        end
5238    end
5239end
5240
5241
5242
5243function cmd=cmd_civ1(filename,Param)
5244%TODO : include filename in par_civ1
5245%------------------------------------------------------------------------
5246%pixels per cm and matrix of the image times, read from the .civ file by uvmat
5247
5248%changes : filename_cmx -> filename ( no extension )
5249
5250filename=regexprep(filename,'.nc','');
5251
5252if isequal(Param.Civ1.Dt,'0')
5253    Param.Civ1.Dt='1' ;%case of 'displacement' mode
5254end
5255Param.Civ1.filename_ima_a=regexprep(Param.Civ1.filename_ima_a,'.png','');
5256Param.Civ1.filename_ima_b=regexprep(Param.Civ1.filename_ima_b,'.png','');
5257fid=fopen([filename '.civ1.cmx'],'w');
5258fprintf(fid,['##############   CMX file' '\n' ]);
5259fprintf(fid,   ['FirstImage ' regexprep(Param.Civ1.filename_ima_a,'\\','\\\\') '\n' ]);% for windows compatibility
5260fprintf(fid,   ['LastImage  ' regexprep(Param.Civ1.filename_ima_b,'\\','\\\\') '\n' ]);% for windows compatibility
5261fprintf(fid,  ['XX' '\n' ]);
5262fprintf(fid,  ['Mask ' Param.Civ1.MaskFlag '\n' ]);
5263fprintf(fid,  ['MaskName ' regexprep(Param.Civ1.MaskName,'\\','\\\\') '\n' ]);
5264fprintf(fid,   ['ImageSize ' num2str(Param.Civ1.npx) ' ' num2str(Param.Civ1.npy) '\n' ]);   %VERIFIER CAS GENERAL ?
5265fprintf(fid,   ['CorrelationBoxesSize ' num2str(Param.Civ1.Bx) ' ' num2str(Param.Civ1.By) '\n' ]);
5266fprintf(fid,   ['SearchBoxeSize ' num2str(Param.Civ1.Searchx) ' ' num2str(Param.Civ1.Searchy) '\n' ]);
5267fprintf(fid,   ['RO ' num2str(Param.Civ1.Rho) '\n' ]);
5268fprintf(fid,   ['GridSpacing ' num2str(Param.Civ1.Dx) ' ' num2str(Param.Civ1.Dy) '\n' ]);
5269fprintf(fid,   ['XX 1.0' '\n' ]);
5270fprintf(fid,   ['Dt_TO ' num2str(Param.Civ1.Dt) ' ' num2str(Param.Civ1.T0) '\n' ]);
5271fprintf(fid,  ['PixCmXY ' num2str(Param.Civ1.pxcmx) ' ' num2str(Param.Civ1.pxcmy) '\n' ]);
5272fprintf(fid,  ['XX 1' '\n' ]);
5273fprintf(fid,   ['ShiftXY ' num2str(Param.Civ1.Shiftx) ' '  num2str(Param.Civ1.Shifty) '\n' ]);
5274fprintf(fid,  ['Grid ' Param.Civ1.GridFlag '\n' ]);
5275fprintf(fid,   ['GridName ' regexprep(Param.Civ1.GridName,'\\','\\\\') '\n' ]);
5276fprintf(fid,   ['XX 85' '\n' ]);
5277fprintf(fid,   ['XX 1.0' '\n' ]);
5278fprintf(fid,   ['XX 1.0' '\n' ]);
5279fprintf(fid,   ['Hart 1' '\n' ]);
5280fprintf(fid,  [ 'DecimalShift 0' '\n' ]);
5281fprintf(fid,   ['Deformation 0' '\n' ]);
5282fprintf(fid,  ['CorrelationMin 0' '\n' ]);
5283fprintf(fid,   ['IntensityMin 0' '\n' ]);
5284fprintf(fid,  ['SeuilImage n' '\n' ]);
5285fprintf(fid,   ['SeuilImageValues 0 4096' '\n' ]);
5286fprintf(fid,   ['ImageToUse ' Param.Civ1.term_a ' ' Param.Civ1.term_b '\n' ]); % VERIFIER ?
5287fprintf(fid,   ['ImageUsedBefore null null' '\n' ]);
5288fclose(fid);
5289
5290% cmd_CIV1=[sparam.Civ1Bin ' -f ' filename '.cmx >' filename '.log' ]; % redirect standard output to the log file
5291% cmd_CIV1=regexprep(cmd_CIV1,'\\','\\\\');
5292% namelog=regexprep(namelog,'\\','\\\\');
5293if(isunix)
5294    cmd=['cp -f ' filename '.civ1.cmx ' filename '.cmx \n '];% the cmx file gives the name to the nc file
5295    cmd=[cmd Param.xml.Civ1Bin ' -f ' filename '.cmx >' filename '.civ1.log \n ' ]; % redirect standard output to the log file, the result file is named [filename '.nc'] by CIVx
5296%     cmd=[cmd '\n' 'mv ' filename '.log' ' ' filename '.civ1.log' '\n' 'chmod g+w ' filename '.civ1.log' '\n' 'chmod g+w ' filename '.nc'];%rename .log as .civ1.log and set the netcdf result file for group user writting
5297%    cmd=[cmd '\n' 'mv ' filename '.cmx' ' ' filename '.civ1.cmx' '\n'];%rename .cmx as .civ1.cmx
5298    cmd=[cmd 'rm ' filename '.cmx'];
5299else %Windows system
5300    filename=regexprep(filename,'\\','\\\\');
5301    cmd=['copy /Y "' filename '.civ1.cmx" "' filename '.cmx" \n '];
5302    cmd=[cmd '"' regexprep(Param.xml.Civ1Bin,'\\','\\\\')...
5303        '" -f "' filename '.cmx" >"' filename '.civ1.log" \n ' ]; % redirect standard output to the log file
5304%     namelog=regexprep(namelog,'\\','\\\\');
5305%     cmd=[cmd '\n ' 'copy /Y "' filename '.log' '" "' filename '.civ1.log"']; %preserve the log file as .civ1.log
5306    cmd=[cmd 'del "' filename '.cmx"'];
5307end
5308
5309
5310function cmd=cmd_fix(filename,Param,fixname)
5311%%
5312switch fixname
5313    case 'Fix1'
5314        fi2_value=num2str(Param.(fixname).CheckF2);
5315    case 'Fix2'
5316        fi2_value=num2str(Param.(fixname).CheckF4);%need to understand why...
5317end
5318
5319
5320
5321filename=regexprep(filename,'.nc','');
5322MaskName_string='';%default
5323if Param.(fixname).CheckMask
5324    MaskName_string=[' -maskName "' Param.(fixname).MaskName '"'];
5325end
5326MaxVel_string='';%default
5327if ~isempty(Param.(fixname).MaxVel)
5328    MaxVel_string=[' -threshV ' num2str(Param.(fixname).MaxVel)];
5329end
5330if isunix
5331    cmd=[Param.xml.FixBin ' -f ' filename '.nc -fi1 ' num2str(Param.(fixname).CheckFmin2) ...
5332        ' -fi2 ' fi2_value ' -fi3 ' num2str(Param.(fixname).CheckF3) ...
5333        ' -threshC ' num2str(Param.(fixname).MinCorr) MaxVel_string MaskName_string...
5334        ' >' filename '.' lower(fixname) '.log 2>&1'];
5335else
5336    cmd=['"' Param.xml.FixBin '" -f "' filename '.nc" -fi1 ' num2str(Param.(fixname).CheckFmin2)...
5337        ' -fi2 ' fi2_value ' -fi3 ' num2str(Param.(fixname).CheckF3) ...
5338        ' -threshC ' num2str(Param.(fixname).MinCorr) MaxVel_string MaskName_string...
5339        ' > "' filename '.' lower(fixname) '.log"'];
5340    cmd=regexprep(cmd,'\\','\\\\');
5341end
5342
5343
5344function cmd=cmd_patch(filename,Param,patchname)
5345%% ------------------------------------------------------------------------
5346filename=regexprep(filename,'.nc','');
5347% if test_interp==0
5348if isunix
5349    cmd=[Param.xml.PatchBin...
5350        ' -f ' filename '.nc -m ' num2str(Param.(patchname).Nx)...
5351        ' -n ' num2str(Param.(patchname).Ny) ' -ro ' num2str(Param.(patchname).SmoothingParam)...
5352        ' -nopt ' num2str(Param.(patchname).SubdomainSize) ...
5353        '  > ' filename '.' lower(patchname) '.log 2>&1']; % redirect standard output to the log file
5354else
5355    cmd=['"' Param.xml.PatchBin...
5356        '" -f "' filename '.nc" -m ' num2str(Param.(patchname).Nx)...
5357        ' -n ' num2str(Param.(patchname).Ny) ' -ro ' num2str(Param.(patchname).SmoothingParam)...
5358        ' -nopt ' num2str(Param.(patchname).SubdomainSize)...
5359        '  > "' filename '.' lower(patchname) '.log" 2>&1']; % redirect standard output to the log file
5360    cmd=regexprep(cmd,'\\','\\\\');
5361end
5362% else %nouveau programme patch
5363%     cmd=[PatchBin ' -f ' filename_nc ' -m ' nx_patch  ' -n ' ny_patch ' -ro ' rho_patch ...
5364%         ' -max ' thresh_value ' -nopt ' subdomain_patch  '  > ' namelog ' 2>&1']; % redirect standard output to the log file
5365% end
5366
5367
5368%------------------------------------------------------------------------
5369% --- CheckCiv2  CheckCiv2  CheckCiv2 CheckCiv2
5370function cmd=cmd_civ2(filename,Param)
5371%------------------------------------------------------------------------
5372%pixels per cm and matrix of the image times, read from the .civ file by uvmat
5373% global civ2Bin sge%name of the executable for checkciv1 calculation
5374filename=regexprep(filename,'.nc','');
5375if isequal(Param.Civ2.Dt,'0')
5376    Param.Civ2.Dt='1' ;%case of 'displacement' mode
5377end
5378Param.Civ2.filename_ima_a=regexprep(Param.Civ2.filename_ima_a,'.png','');
5379Param.Civ2.filename_ima_b=regexprep(Param.Civ2.filename_ima_b,'.png','');% bug : .png appears two times ?
5380[fid,errormsg]=fopen([filename '.civ2.cmx'],'w');
5381if isequal(fid,-1)
5382    msgbox_uvmat('ERROR',errormsg)
5383    cmd='';
5384    return
5385end
5386fprintf(fid,['##############   CMX file' '\n' ]);
5387fprintf(fid,   ['FirstImage ' regexprep(Param.Civ2.filename_ima_a,'\\','\\\\') '\n' ]);% for windows compatibility
5388fprintf(fid,   ['LastImage  ' regexprep(Param.Civ2.filename_ima_b,'\\','\\\\') '\n' ]);% for windows compatibility
5389fprintf(fid,  ['XX' '\n' ]);
5390fprintf(fid, ['Mask ' Param.Civ2.MaskFlag '\n' ]);
5391fprintf(fid, ['MaskName ' regexprep(Param.Civ2.MaskName,'\\','\\\\') '\n' ]);% for windows compatibility
5392fprintf(fid, ['ImageSize ' num2str(Param.Civ2.npx) ' ' num2str(Param.Civ2.npy) '\n' ]);   %VERIFIER CAS GENERAL ?
5393fprintf(fid, ['CorrelationBoxesSize ' num2str(Param.Civ2.Bx) ' ' num2str(Param.Civ2.By) '\n' ]);
5394fprintf(fid, ['SearchBoxeSize ' num2str(Param.Civ2.Bx) ' ' num2str(Param.Civ2.By) '\n']);
5395fprintf(fid, ['RO ' num2str(Param.Civ2.Rho) '\n']);
5396fprintf(fid, ['GridSpacing ' num2str(Param.Civ2.Dx) ' ' num2str(Param.Civ2.Dy) '\n']);
5397fprintf(fid, ['XX 1.0' '\n' ]);
5398fprintf(fid, ['Dt_TO ' num2str(Param.Civ2.Dt) ' ' num2str(Param.Civ2.T0) '\n' ]);
5399fprintf(fid, ['PixCmXY ' num2str(Param.Civ2.pxcmx) ' ' num2str(Param.Civ2.pxcmy) '\n' ]);
5400fprintf(fid, ['XX 1' '\n' ]);
5401fprintf(fid, 'ShiftXY 0 0\n');
5402fprintf(fid, ['Grid ' Param.Civ2.GridFlag '\n' ]);
5403fprintf(fid, ['GridName ' regexprep(Param.Civ2.GridName,'\\','\\\\') '\n']);
5404fprintf(fid, ['XX 85' '\n' ]);
5405fprintf(fid, ['XX 1.0' '\n' ]);
5406fprintf(fid, ['XX 1.0' '\n' ]);
5407fprintf(fid, ['Hart 1' '\n' ]);
5408fprintf(fid, ['DecimalShift ' num2str(Param.Civ2.CheckDecimal) '\n']);
5409fprintf(fid, ['Deformation ' num2str(Param.Civ2.CheckDeformation) '\n']);
5410fprintf(fid,  ['CorrelationMin 0' '\n' ]);
5411fprintf(fid,   ['IntensityMin 0' '\n' ]);
5412fprintf(fid,  ['SeuilImage n' '\n' ]);
5413fprintf(fid,   ['SeuilImageValues 0 4096' '\n' ]);
5414fprintf(fid,   ['ImageToUse ' Param.Civ2.term_a ' ' Param.Civ2.term_b '\n' ]); % VERIFIER ?
5415fprintf(fid, ['ImageUsedBefore ' regexprep(Param.Civ2.filename_nc1,'\\','\\\\') '\n']);
5416fclose(fid);
5417
5418if(isunix)
5419    cmd=['cp -f ' filename '.civ2.cmx ' filename '.cmx\n'...
5420        Param.xml.Civ2Bin ' -f ' filename  '.cmx >' filename '.civ2.log \n '... % redirect standard output to the log file, the result file is named [filename '.nc'] by CIVx
5421        'rm ' filename '.cmx \n'];%rename .cmx as .checkciv2.cmx, the result file is named [filename '.nc'] by CIVx
5422else
5423    filename=regexprep(filename,'\\','\\\\');
5424    cmd=['copy /Y "' filename '.civ2.cmx" "' filename '.cmx" \n'...
5425        '"' regexprep(Param.xml.Civ2Bin,'\\','\\\\') '" -f "' filename  '.cmx" >"' filename '.civ2.log" \n'...
5426        'del "' filename '.cmx" \n'];
5427end
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