source: trunk/src/civ.m @ 257

Last change on this file since 257 was 257, checked in by sommeria, 13 years ago

launch_jobs clarified to deal with different systems and PIV in matlab

File size: 200.9 KB
Line 
1%'civ': function associated with the interface 'civ.fig' for PIV, spline interpolation and stereo PIV (patch)
2%------------------------------------------------------------------------
3%  provides an interface for the software CIVx
4% function varargout = civ(varargin)
5% provides an interface for the software CIVx
6%
7%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
8%  Copyright Joel Sommeria, 2008, LEGI / CNRS-UJF-INPG, sommeria@coriolis-legi.org.
9%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
10%     This file is part of the toolbox UVMAT.
11%
12%     UVMAT is free software; you can redistribute it and/or modify
13%     it under the terms of the GNU General Public License as published by
14%     the Free Software Foundation; either version 2 of the License, or
15%     (at your option) any later version.
16%
17%     UVMAT is distributed in the hope that it will be useful,
18%     but WITHOUT ANY WARRANTY; without even the implied warranty of
19%     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
20%     GNU General Public License (file UVMAT/COPYING.txt) for more details.
21%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
22function varargout = civ(varargin)
23
24% Last Modified by GUIDE v2.5 27-May-2011 17:55:50
25% Begin initialization code - DO NOT EDIT
26gui_Singleton = 1;
27gui_State = struct('gui_Name',       mfilename, ...
28    'gui_Singleton',  gui_Singleton, ...
29    'gui_OpeningFcn', @civ_OpeningFcn, ...
30    'gui_OutputFcn',  @civ_OutputFcn, ...
31    'gui_LayoutFcn',  [] , ...
32    'gui_Callback',   []);
33if nargin && ischar(varargin{1})
34    gui_State.gui_Callback = str2func(varargin{1});
35end
36
37if nargout
38    [varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:});
39else
40    gui_mainfcn(gui_State, varargin{:});
41end
42% End initialization code - DO NOT EDIT
43
44%------------------------------------------------------------------------
45% --- Executes just before civ is made visible.
46function civ_OpeningFcn(hObject, eventdata, handles, param)
47%------------------------------------------------------------------------
48% This function has no output args, see OutputFcn.
49% hObject    handle to figure
50% eventdata  reserved - to be defined in a future version of MATLAB
51% handles    structure with handles and user data (see GUIDATA)
52% varargin   command line arguments to civ (see VARARGIN)
53global patch_newBin %=1 if new patch processing available
54%filebase: root name
55%nom_type: nomencalture used ('png_old','_i_j'...)
56%list of field numbers to process
57%subdir: subdirectory of the opened netcdf file
58%ind_opening: operation number advised for beginning (1=civ1,2=fix1,3=patch1,4=civ2,5=fix2,6=patch2),
59%ind_a_opening ind_b_opening chosen pair from the opened netcdf file
60% Choose default command line output for civ
61handles.output = hObject;
62% Update handles structure
63guidata(hObject, handles);
64set(hObject,'WindowButtonDownFcn',{'mouse_alt_gui',handles}) % allows mouse action with right button (zoom for uicontrol display)
65%default initial parameters
66filebase=''; % root file name ('filebase'.civ)
67ext=[];
68
69%default input parameters:
70num_i1=1; % set of field i numbers
71num_i2=1; % set of field i numbers
72num_j1=1; % set of field j numbers (fields a)
73num_j2=1; % second set of field j numbers (fields b)
74subdir='A'; % subdir for the netcdf result files
75ind_opening=1; % proposed operation number (1=civ1,2=fix1,3=patch1,4=civ2,5=fix2,6=patch2)
76%load the initial parameters if the interface is started from uvmat
77if exist('param','var')&&isstruct(param)% the interface is opened from uvmat
78    filebase=param.RootName;
79    nom_type_read=param.NomType;
80    num_i1=param.num1;
81    if isnan(num_i1),num_i1=1;end
82    num_i2=param.num2;
83    if isnan(num_i2),num_i2=num_i1;end
84    num_j1=param.num_a;
85    if isnan(num_j1),num_j1=1;end
86    num_j2=param.num_b;
87    if isnan(num_j2),num_j2=num_j1;end
88    subdir=param.SubDir;
89    ind_opening=param.IndOpening;
90    ext=param.ImaExt;
91end
92browse.num_i1=num_i1;
93browse.num_i2=num_i2;
94browse.num_j1=num_j1;
95browse.num_j2=num_j2;
96if ~isempty(ext) && (~isempty(imformats(ext(2:end)))||strcmpi(ext,'.avi'));%if an image file has been opened by uvmat
97    set(handles.ImaExt,'String',ext)
98    browse.ext_ima=ext;
99    if exist('nom_type_read','var')
100        browse.nom_type_ima=nom_type_read; % the image nomenclature is stored
101    end
102elseif isequal(ext,'.nc')
103    if exist('nom_type_read','var')
104        browse.nom_type_nc=nom_type_read;% the netcdf  nomenclature is stored
105    end
106end
107set(handles.RootName,'String',filebase);
108set(handles.ImaDoc,'String',ext)
109
110%read names of the .exe file to adjust the interface according to available binaries
111path_uvmat=which('uvmat');% check the path detected for source file uvmat
112path_UVMAT=fileparts(path_uvmat); %path to UVMAT
113errormsg=[];%default error message
114xmlfile='PARAM.xml';
115if exist(xmlfile,'file')
116    try
117        t=xmltree(xmlfile);
118        sparam=convert(t);
119    catch
120        errormsg={' Unable to read the file PARAM.xml defining the civx binaries:'; lasterr};
121        return
122    end
123else
124    errormsg=[xmlfile ' not found: path to civx binaries undefined'];
125    return
126end
127
128
129if ~isempty(errormsg)
130    msgbox_uvmat('ERROR',errormsg);
131end
132% patch_newBin='';
133test_batch=0;%default: ,no batch mode available
134if isfield(sparam,'BatchParam') && isfield(sparam.BatchParam,'BatchMode')
135    test_batch=strcmp(sparam.BatchParam.BatchMode,'sge'); %sge is currently the only implemented batch mod
136end
137if test_batch==0
138    set(handles.BATCH,'Enable','off')% put the BATCH button in grey (unactivated)
139    set(handles.BATCH,'BackgroundColor',[0.831 0.816 0.784])% put the BATCH button in grey (unactivated)
140end
141if isfield(sparam.RunParam,'CivBin')
142    if ~exist(sparam.RunParam.CivBin,'file')
143        sparam.RunParam.CivBin=fullfile(path_UVMAT,sparam.RunParam.CivBin);
144    end
145else
146    sparam.RunParam.CivBin='';
147end
148patch_newBin=exist(sparam.RunParam.CivBin,'file');
149set(handles.subdir_civ1,'String',subdir)%default subdir on which uvmat was working
150set(handles.subdir_civ2,'String',subdir)%default subdir on which uvmat was working
151
152%initiate advised operations
153if isequal(ind_opening,[])
154    ind_opening=1; % default
155end
156% set default operation options
157enable_civ1(handles,'off')
158enable_civ2(handles,'off')
159enable_pair1(handles,'on')
160enable_fix1(handles,'off')
161desable_patch1(handles)
162desable_fix2(handles)
163desable_patch2(handles)
164set(handles.CIV1,'Value',0)
165set(handles.FIX1,'Value',0)
166set(handles.PATCH1,'Value',0)
167set(handles.CIV2,'Value',0)
168set(handles.FIX2,'Value',0)
169set(handles.PATCH2,'Value',0)
170set(handles.frame_subdirciv2,'BackgroundColor',[0.831 0.816 0.784])
171if isequal(ind_opening,1)
172    set(handles.CIV1,'Value',1)
173    enable_civ1(handles,'on')
174elseif isequal(ind_opening,2)
175    set(handles.FIX1,'Value',1)
176    enable_fix1(handles,'on')
177elseif isequal(ind_opening,3)
178    set(handles.PATCH1,'Value',1)
179    enable_patch1(handles)
180elseif isequal(ind_opening,4)
181    set(handles.CIV2,'Value',1)
182    enable_civ2(handles,'on')
183elseif isequal(ind_opening,5)
184    set(handles.FIX2,'Value',1)
185    enable_fix2(handles)
186    set(handles.frame_subdirciv2,'BackgroundColor',[1 1 0])
187    set(handles.list_pair_civ2,'Enable','On')
188    set(handles.list_pair_civ2,'Enable','On')
189    enable_pair1(handles,'off')
190elseif isequal(ind_opening,6)
191    set(handles.PATCH2,'Value',1)
192    enable_patch2(handles)
193    set(handles.frame_subdirciv2,'BackgroundColor',[1 1 0])
194    set(handles.list_pair_civ2,'Enable','On')
195    enable_pair1(handles,'off')
196end
197
198% set the range of fields (1:1 by default) and selected pair
199if isequal(num_i2,num_i1)
200    num_ref_i=num_i1;
201else
202    num_ref_i=floor((num_i1+num_i2)/2);
203    browse.incr_pair(1)=num_i2-num_i1;
204    browse.incr_pair(2)=0;
205end
206if isequal(num_j1,num_j2)
207    if isnan(num_j1)
208        num_ref_j=1;
209    else
210        num_ref_j=num_j1;
211    end
212else
213    num_ref_j=floor((num_j1+num_j2)/2);
214    browse.incr_pair(2)=num_j2-num_j1;
215end
216set(handles.first_i,'String',num2str(num_ref_i));
217set(handles.last_i,'String',num2str(num_ref_i));
218set(handles.first_j,'String',num2str(num_ref_j));
219set(handles.last_j,'String',num2str(num_ref_j));
220set(handles.ref_i,'String',num2str(num_ref_i));
221set(handles.ref_j,'String',num2str(num_ref_j));
222set(handles.ref_i_civ2,'String',num2str(num_ref_i));
223set(handles.ref_j_civ2,'String',num2str(num_ref_j));
224set(handles.browse_root,'UserData',browse);
225if exist('param','var') && isfield(param,'RootName') && ~isempty(param.RootName)%varargin the interface is opened from uvmat
226    RootName_Callback(hObject, eventdata, handles);
227end
228
229% set(handles.waitbar_1,'Position',[0.946 0.877 0.03 0.001])
230% set(handles.waitbar_patch1,'Position',[0.946 0.626 0.03 0.001])
231% set(handles.waitbar_civ2,'Position',[0.946 0.406 0.03 0.001])
232% set(handles.waitbar_patch2,'Position',[0.946 0.187 0.03 0.001])
233
234%------------------------------------------------------------------------
235% --- Outputs from this function are returned to the command line.
236function varargout = civ_OutputFcn(hObject, eventdata, handles)
237%------------------------------------------------------------------------
238% varargout  cell array for returning output args (see VARARGOUT);
239% hObject    handle to figure
240% eventdata  reserved - to be defined in a future version of MATLAB
241% handles    structure with handles and user data (see GUIDATA)
242% Get default command line output from handles structure
243varargout{1} = handles.output;
244
245%------------------------------------------------------------------------
246% --- Executes on button press in browse_root.
247function browse_root_Callback(hObject, eventdata, handles)
248%------------------------------------------------------------------------
249%get the input file properties
250filebase=get(handles.RootName,'String');
251oldfile=''; %default
252if isempty(filebase)|| isequal(filebase,'')%loads the previously stored file name and set it as default in the file_input box
253    dir_perso=prefdir;
254    profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
255    if exist(profil_perso,'file')
256        h=load (profil_perso);
257        if isfield(h,'filebase')&& ischar(h.filebase)
258            oldfile=h.filebase;
259        end
260        if isfield(h,'RootPath') && ischar(h.RootPath)
261            oldfile=h.RootPath;
262        end
263    end
264else
265    oldfile=filebase;
266end
267ind_opening=1;%default
268browse.incr_pair=[0 0]; %default
269menu={'*.xml;*.civ;*.png;*.jpg;*.tif;*.avi;*.AVI;*.nc;', ' (*.xml,*.civ,*.png,*.jpg ,.tif, *.avi,*.nc)';
270       '*.xml',  '.xml files '; ...
271        '*.civ',  '.civ files '; ...
272        '*.png','.png image files'; ...
273        '*.jpg',' jpeg image files'; ...
274        '*.tif','.tif image files'; ...
275        '*.avi;*.AVI','.avi movie files'; ...
276        '*.nc','.netcdf files'; ...
277        '*.*',  'All Files (*.*)'};
278[FileName, PathName, filtindex] = uigetfile( menu, 'Pick a file',oldfile);
279fileinput=[PathName FileName];%complete file name
280sizf=size(fileinput);
281if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end %stop if fileinput not a character string
282[path,name,ext]=fileparts(fileinput);
283testeditxml=0;
284if isequal(ext,'.xml')
285    testeditxml=1;
286    t_browse=xmltree(fileinput);
287    head_element=get(t_browse,1);
288    if isfield(head_element,'name')&& isequal(head_element.name,'ImaDoc')
289        testeditxml=0;
290    end
291end
292if testeditxml==1 || isequal(ext,'.xls')
293    heditxml=editxml({fileinput});
294    set(heditxml,'Tag','browser')
295    waitfor(heditxml,'Tag','idle')
296    if ~ishandle(heditxml)
297        return
298    end
299    attr=findobj(get(heditxml,'children'),'Tag','CurrentAttributes');
300    set(handles.browse,'UserData',fileinput)% store for future opening with browser
301    fileinput=get(attr,'UserData');
302    if ~exist(fileinput,'file')
303        return
304    end
305end
306[RootPath,RootFile,str1,str2,str_a,str_b,ext,nom_type,subdir]=name2display(fileinput);
307filebase=fullfile(RootPath,RootFile);
308num_i1=str2double(str1);
309if isnan(num_i1),num_i1=1;end
310num_i2=str2double(str2);
311if isnan(num_i2),num_i2=num_i1;end
312num_j1=stra2num(str_a);
313if isnan(num_j1),num_j1=1;end
314num_j2=stra2num(str_b);
315if isnan(num_j2),num_j2=num_j1;end
316if isequal(get(handles.compare,'Value'),1)
317    browse=[];%initialisation
318else
319    browse=get(handles.browse_root,'UserData');
320end
321browse.num_i1=num_i1;
322browse.num_i2=num_i2;
323browse.num_j1=num_j1;
324browse.num_j2=num_j2;
325if length(ext)>1 && (~isempty(imformats(ext(2:end)))||strcmpi(ext,'.avi'));%if an image file has been opened by uvmat
326    browse.nom_type_ima=nom_type;
327    browse.ext_ima=ext;
328    set(handles.ImaExt,'String',ext)
329end
330set(handles.ImaDoc,'String',ext);
331
332%%%%% read the state of the selected netcdf file to advise default operation
333if isequal(ext,'.nc')
334    browse.nom_type_nc=nom_type;
335    ind_opening=2;% propose 'fix' as the default option
336    Data=nc2struct(fileinput,'ListGlobalAttribute','CivStage','absolut_time_T0','fix','patch','civ2','fix2');
337    if ~isempty(Data.CivStage)%test for civ files
338        ind_opening=Data.CivStage;
339        set(handles.CivMode,'Value',3)
340    end
341    if ~isempty(Data.absolut_time_T0)%test for civx files
342        set(handles.CivMode,'Value',1)
343        if isfield(Data,'fix') && isequal(Data.fix,1)
344            ind_opening=3;
345        end
346        if isequal(Data.patch,1)
347            ind_opening=4;
348        end
349        if isequal(Data.civ2,1)
350            ind_opening=5;
351        end
352        if  isequal(Data.fix2,1)
353            ind_opening=6;
354        end
355        testciv=1; %TO SUPPRESS WITH NEW VERSION OF CIVX
356    else
357        ind_opening=3; %GUI used only for patch
358        testciv=0;
359    end
360    set(handles.subdir_civ1,'String',subdir);%set the default subdir directories for installing the .nc results
361    set(handles.subdir_civ2,'String',subdir);
362    browse.testciv=testciv;
363    browse.ind_opening=ind_opening;
364end
365set(handles.RootName,'String',filebase);
366set(handles.ImaDoc,'String',ext);
367if ~isempty(num_i1)
368    ref_i=num_i1;
369    if ~isempty(num_i2)
370        ref_i=floor((ref_i+num_i2)/2);% reference image number corresponding to the file
371        browse.incr_pair(1)=num_i2-num_i1;
372        browse.incr_pair(2)=0;
373    end
374    set(handles.first_i,'String',num2str(ref_i));
375    set(handles.last_i,'String',num2str(ref_i));
376    set(handles.ref_i,'String',num2str(ref_i));
377    set(handles.ref_i_civ2,'String',num2str(ref_i))
378end
379if isempty(num_j1)
380    set(handles.ref_j,'String','1');
381    set(handles.ref_j_civ2,'String','1');
382else
383    ref_j=num_j1;
384    if ~isempty(num_j2)
385        ref_j=floor((num_j1+num_j2)/2);
386        browse.incr_pair(2)=num_j2-num_j1;
387    end
388    set(handles.first_j,'String',num2str(ref_j));
389    set(handles.last_j,'String',num2str(ref_j));
390    set(handles.ref_j,'String',num2str(ref_j));
391    set(handles.ref_j_civ2,'String',num2str(ref_j));
392end
393
394% set default operation options
395enable_civ1(handles,'off')
396enable_civ2(handles,'off')
397enable_pair1(handles,'on')
398enable_fix1(handles,'off')
399desable_patch1(handles)
400desable_fix2(handles)
401desable_patch2(handles)
402set(handles.CIV1,'Value',0)
403set(handles.FIX1,'Value',0)
404set(handles.PATCH1,'Value',0)
405set(handles.CIV2,'Value',0)
406set(handles.FIX2,'Value',0)
407set(handles.PATCH2,'Value',0)
408set(handles.frame_subdirciv2,'BackgroundColor',[0.831 0.816 0.784])
409if isequal(ind_opening,1)
410    set(handles.CIV1,'Value',1)
411    enable_civ1(handles,'on')
412elseif isequal(ind_opening,2)
413    set(handles.FIX1,'Value',1)
414    enable_fix1(handles,'on')
415elseif isequal(ind_opening,3)
416    set(handles.PATCH1,'Value',1)
417    enable_patch1(handles)
418elseif isequal(ind_opening,4)
419    set(handles.CIV2,'Value',1)
420    enable_civ2(handles,'on')
421elseif isequal(ind_opening,5)
422    enable_pair1(handles,'off')
423    set(handles.FIX2,'Value',1)
424    enable_fix2(handles)
425    set(handles.frame_subdirciv2,'BackgroundColor',[1 1 0])
426    set(handles.list_pair_civ2,'Enable','On')
427    set(handles.list_pair_civ2,'Enable','On')
428elseif isequal(ind_opening,6)
429    enable_pair1(handles,'off')
430    set(handles.PATCH2,'Value',1)
431    enable_patch2(handles)
432    set(handles.frame_subdirciv2,'BackgroundColor',[1 1 0])
433    set(handles.list_pair_civ2,'Enable','On')
434end
435set(handles.browse_root,'UserData',browse);% store information from browser
436
437RootName_Callback(hObject, eventdata, handles);
438
439%------------------------------------------------------------------------
440function ImaDoc_Callback(hObject, eventdata, handles)
441%------------------------------------------------------------------------
442RootName_Callback(hObject, eventdata, handles)
443
444%------------------------------------------------------------------------
445% --- function activated when a new filebase (image series) is introduced
446function RootName_Callback(hObject, eventdata, handles)
447%------------------------------------------------------------------------
448set(handles.compare,'Visible','on')
449ext_ima='';%default
450nom_type_ima=[];%default
451field_count=1;%default
452nom_type_nc=[];
453time=[];
454TimeUnit='frame'; %default
455CoordUnit='px';%default
456pxcmx_search=[];%default
457pxcmy_search=[];%default
458filebase=get(handles.RootName,'String');
459ext_imadoc=get(handles.ImaDoc,'String');
460browse=get(handles.browse_root,'UserData');%default
461if isfield(browse,'nom_type_ima')
462    nom_type_ima=browse.nom_type_ima;% get an image nomenclature type already determined by an input image name
463end
464if isfield(browse,'ext_ima')
465    ext_ima=browse.ext_ima;
466end
467if isfield(browse,'nom_type_nc')
468    nom_type_nc=browse.nom_type_nc;% get an image nomenclature type already determined by an input image name
469end
470if isfield(browse,'num_i1')
471    field_count=browse.num_i1;% get an image index type already determined by an input file
472end
473set(handles.civ,'UserData',[]); %refresh list of previous civ files (for STATUS)
474
475%default first_i and j and increments
476first_i=str2double(get(handles.first_i,'String'));%value possibly set by uvmat_Opening
477if isnan(first_i)|| first_i < 1
478    first_i=1; %default first_i
479end
480last_i=str2double(get(handles.last_i,'String'));
481if isnan(last_i)|| last_i < first_i
482    last_i=first_i;  %default last_i
483end
484first_j=str2double(get(handles.first_j,'String'));
485if isnan(first_j)|| first_j < 1
486    first_j=1; %default first_j
487end
488last_j=str2double(get(handles.last_j,'String'));
489if isnan(last_j)|| last_j < first_j
490    last_j=first_j; %default last_j
491end
492incr_i=str2double(get(handles.incr_i,'String'));
493if isnan(incr_i) || incr_i < 1;
494    set(handles.incr_i,'String','1') %default incr_i
495end
496incr_j=str2double(get(handles.incr_j,'String'));
497if isnan(incr_j) || incr_j < 1;
498    set(handles.incr_j,'String','1') %default incr_j
499end
500dt=[];%default
501testmode=0;%default
502nbfield=[]; %default
503nburst=[];%default
504pxcmx=1;
505pxcmy=1;
506
507%look for an image documentation file
508if ~strcmp(ext_imadoc,'.xml') && ~strcmp(ext_imadoc,'.civ')&& ~strcmpi(ext_imadoc,'.avi')
509    if exist([filebase '.xml'],'file')
510        ext_imadoc='.xml';
511    elseif exist([filebase '.civxml'],'file')
512        ext_imadoc='.civxml';
513    elseif exist([filebase '.civ'],'file')
514        ext_imadoc='.civ';
515    elseif exist([filebase '.avi'],'file')
516        ext_imadoc='.avi';
517    elseif exist([filebase '.AVI'],'file')
518        ext_imadoc='.AVI';
519    end
520    set(handles.ImaDoc,'String',ext_imadoc)
521end
522
523%%%%%%%%   read image documentation file  %%%%%%%%%%%%%%%%%%%%%%%%%%%
524mode=''; %default
525set(handles.ImaDoc,'BackgroundColor',[1 1 0])
526drawnow
527if isequal(ext_imadoc,'.civxml') || isequal(ext_imadoc,'.xml')|| isequal(ext_imadoc,'.civ')
528    set(handles.ref_i,'Visible','On')%use a reference index
529    set(handles.ref_j,'Visible','On')
530elseif isequal(ext_imadoc,'.avi') || isequal(ext_imadoc,'.AVI')
531    set(handles.ref_j,'Visible','Off')
532else
533    set(handles.ref_i,'Visible','Off')
534    set(handles.ref_j,'Visible','Off')
535end
536testima_xml=0;
537if isequal(ext_imadoc,'.civxml')%TO ABANDON
538    [nbfield,nbfield2,time]=read_civxml([filebase '.civxml']);
539    mode='pair j1-j2';
540    if isempty(nom_type_ima)% dtermine types by default if not already selected by browser or uvmat
541        nom_type_ima='_i_j';
542    end
543elseif isequal(ext_imadoc,'.xml')
544    [XmlData,warntext]=imadoc2struct([filebase '.xml']);
545    ext_ima_read=[];
546    nom_type_read=[];
547    if isfield(XmlData,'Heading')&&isfield(XmlData.Heading','ImageName')&&ischar(XmlData.Heading.ImageName)% get image nom type and extension from the xml file
548        [PP,FF,fc,str2,str_a,str_b,ext_ima_read,nom_type_read]=name2display(XmlData.Heading.ImageName);
549        fullname=fullfile(fileparts(filebase),XmlData.Heading.ImageName); %full name (including path) of the first image defined by the xmle file,
550        if ~exist(fullname,'file')
551            msgbox_uvmat('WARNING',['FirstImage ' fullname ' defined in the xml file does not exist'])
552        end
553    end
554    if isfield(XmlData,'Time')
555        time=XmlData.Time;
556        nbfield=size(time,1);
557        nbfield2=size(time,2);
558        %transform .Time to a column vector if it is a line vector thenomenclature uses a single index: correct possible bug in xml
559        if isequal(nbfield,1) && ~isequal(nbfield2,1)% .Time is a line vector
560            if numel(nom_type_read)>=2 && isempty(regexp(nom_type_read(2:end),'\D'))
561                time=time';
562                nbfield=nbfield2;
563                nbfield2=1;
564            end
565        end
566    end
567    if isfield(XmlData,'TimeUnit')
568        TimeUnit=XmlData.TimeUnit;
569    end
570    if isfield(XmlData,'Npx')
571        npx=XmlData.Npx;
572        npy=XmlData.Npy;
573    end
574    pxcmx_search=1;
575    pxcmy_search=1;
576    if isfield(XmlData,'GeometryCalib')
577        tsai=XmlData.GeometryCalib;
578        if isfield(tsai,'f') && isfield(tsai,'Tz') && isfield(tsai,'dpx') && isfield(tsai,'dpy')&& isfield(tsai,'R')
579            rot2D=tsai.R(1:2,[1,2]);
580            pxcmx_search=tsai.f * sqrt(det(rot2D))/(tsai.Tz*tsai.dpx);
581            pxcmy_search=tsai.f * sqrt(det(rot2D))/(tsai.Tz*tsai.dpy);
582        end
583        if isfield(tsai,'CoordUnit')
584            CoordUnit=tsai.CoordUnit;
585        end
586    end
587elseif strcmp(ext_imadoc,'.civ')% case of .civ image documentation file
588    [error,time,TimeUnit,mode,npx,npy]=read_imatext([filebase '.civ']);
589    if error==2, msgbox_uvmat('WARNING',['no file ' filebase '.civ']);
590    elseif error==1, msgbox_uvmat('WARNING','inconsistent number of fields in the .civ file');
591    end
592    nom_type_ima='001a';
593elseif strcmpi(ext_imadoc,'.avi')
594    nom_type_ima='*';
595    ext_ima=ext_imadoc;
596    set(handles.mode,'Value',1);
597    set(handles.mode,'String',{'series(Di)'})
598    dt=0.04;%default
599    if exist([filebase ext_imadoc],'file')==2
600        info=aviinfo([filebase ext_imadoc]);%read infos on the avi movie
601        dt=1/info.FramesPerSecond;%time interval between successive frames
602        nbfield=info.NumFrames;%number of frames
603    end
604    time=(dt*(0:nbfield-1))';%list of image times
605end
606if isempty(time)
607    set(handles.ImaDoc,'String',''); %xml file not used for timing
608end
609set(handles.ImaDoc,'BackgroundColor',[1 1 1])
610
611%get the imabe nomenclature type if not defined by the input file nor by the xml file
612dirima=[];%default
613if isempty(nom_type_ima)
614    %look for double image series '_i_j'
615    dirima=dir([filebase '_' num2str(first_i) '_' num2str(first_j) '.*']);
616    if isempty(dirima)
617        % look for images series  with sub marker '_'
618        dirima=dir([filebase '_*' num2str(first_i) '.*']);
619        if isempty(dirima)
620            % look for other images series
621            dirima=dir([filebase '*' num2str(first_i) '.*']);
622            if isempty(dirima)
623                % look for other images series witth letter appendix
624                appendix=char(96+first_j);
625                dirima=dir([filebase '*' num2str(first_i) appendix '.*']);
626            end
627        end
628    end
629end
630for ilist=1:numel(dirima)
631    [pp,ff,fc,str2,str_a,str_b,ext_list,nom_type_list]=name2display(dirima(ilist).name);
632    form=imformats(ext_list(2:end));
633    if ~isempty(form)% if the extension corresponds to an image format recognized by Matlab
634        ext_ima=ext_list;
635        nom_type_ima=nom_type_list;
636            break
637    end
638end
639% no image documentation file found: look for a series of existing files,images by priority or .nc files
640if isempty(nom_type_ima)
641    ext_search=ext_imadoc;
642    nom_type_search=nom_type_nc;
643else
644    ext_search=ext_ima;
645    nom_type_search=nom_type_ima;
646end
647if isempty(time) && ~strcmp(nom_type_search,'none') && ~strcmp(nom_type_search,'') && ~strcmp(nom_type_search,'*')
648    subdir=get(handles.subdir_civ1,'String');
649    incr_pair=[0 0];%default
650    if isfield(browse,'incr_pair')
651        incr_pair=browse.incr_pair;
652    end
653    %     nbdetect=0;%test of detected images
654    field_i=browse.num_i2;
655    imagename=name_generator(filebase,field_i,1,ext_search,nom_type_search);
656    imagename_plus='';
657    idetect=1;
658    while idetect %look for the maximum file number in the series
659        imagename_plus=name_generator(filebase,field_i+1,1,ext_search,nom_type_search);
660        idetect=(exist(imagename_plus,'file')==2)&& ~strcmp(imagename,imagename_plus);
661        if idetect
662            field_i=field_i+1;
663        end
664        %SEE CASE OF NETCDF FILES
665        %             nbdetect=nbdetect+(exist(imagename,'file')==2);
666    end
667    nbfield=field_i;% last detected field number
668    field_i=browse.num_i1;%look for the minimum file number in the series
669    imagename_min='';
670    idetect=1;
671    while idetect==1
672        imagename_min=name_generator(filebase,field_i-1,1,ext_search,nom_type_search);
673        idetect=(exist(imagename_min,'file')==2)&& ~strcmp(imagename,imagename_min);
674        if idetect
675            field_i=field_i-1;
676        end
677    end
678    first_i=max(field_i,1);
679    if numel(regexp(nom_type_search,'\D'))>=1%two indices i and j
680        field_i=browse.num_i1;
681        field_j=browse.num_j2;
682        imagename=name_generator(filebase,field_i,field_j,ext_search,nom_type_search);
683        imagename_plus='';
684        jdetect=1;
685        while jdetect==1 %look for the maximum file number in the series
686            imagename_plus=name_generator(filebase,field_i,field_j+1,ext_search,nom_type_search);
687            jdetect=(exist(imagename_plus,'file')==2)&& ~strcmp(imagename,imagename_plus);
688            if jdetect
689                field_j=field_j+1;
690            end
691            %SEE CASE OF NETCDF FILES
692            %             nbdetect=nbdetect+(exist(imagename,'file')==2);
693        end
694        nbfield2=field_j;% last detected field number
695     end
696 
697    %determine the set of times and possible intervals for CIV
698    %   dt=(1/1000)*str2double(get(handles.dt,'String'));
699    time=(0:nbfield-1)';% time=file index -1  by default
700    if numel(regexp(nom_type_search,'\D'))>=1%two indices i and j
701        [x,y]=meshgrid(0:nbfield2-1,0:nbfield-1);
702        time=x+y;
703    end
704end
705
706if exist('time','var')
707    if size(time,1)+size(time,2)>=3 % if there are at least two time values to define dt
708        nbfield=size(time,1);
709        nbfield2=size(time,2);
710        set(handles.RootName,'UserData',time); %store the set of times
711        set(handles.dt_unit,'String',['dt in m' TimeUnit]);
712        set(handles.dt_unit_civ2,'String',['dt in m' TimeUnit]);
713        set(handles.TimeUnit,'String',TimeUnit);
714        set(handles.nb_field,'String',num2str(nbfield));
715        set(handles.nb_field2,'String',num2str(nbfield2));
716    end
717end
718set(handles.CoordUnit,'String',CoordUnit)
719set(handles.calcul_search,'UserData',[pxcmx_search pxcmy_search]);
720% npxy=[npy npx];
721set(handles.ImaExt,'String',ext_ima)
722set(handles.first_i,'String',num2str(first_i));
723set(handles.last_i,'String',num2str(last_i));%
724set(handles.first_j,'String',num2str(first_j));
725set(handles.last_j,'String',num2str(last_j));%
726browse.nom_type_ima=nom_type_ima;
727set(handles.browse_root,'UserData',browse)% store the nomenclature type
728
729%%%%%%%%%%%  set the menus of image pairs and default selection for civ   %%%%%%%%%%%%%%%%%%%
730test_ima_i=numel(nom_type_ima)>1 && isempty(regexp(nom_type_ima(2:end),'\D','once'));%images with single indexing
731if test_ima_i || isequal(nom_type_nc,'_i1-i2')||~(exist('nbfield2','var')&&(nbfield2~=1))
732    set(handles.mode,'Value',1)
733    set(handles.mode,'String',{'series(Di)'})   
734elseif (nbfield==1)% simple series in j
735    set(handles.mode,'Value',1)
736    set(handles.mode,'String',{'series(Dj)'})
737else
738    set(handles.mode,'String',{'pair j1-j2';'series(Dj)';'series(Di)'})%multiple choice
739    if nbfield2 <= 10
740        set(handles.mode,'Value',1)% advice 'pair j1-j2' for small burst
741    end
742end
743
744%update the subdir
745pathdir=fileparts(filebase);%path to the current xml file
746listot=dir(pathdir);
747idir=0;
748listdir={''};%default
749for ilist=1:length(listot)
750    if listot(ilist).isdir
751        name=listot(ilist).name;
752        if ~isequal(name,'.') && ~isequal(name,'..')
753            idir=idir+1;
754            listdir{idir,1}=listot(ilist).name;
755        end
756    end
757end
758set(handles.list_subdir_civ1,'Value',1)
759set(handles.list_subdir_civ2,'Value',1)
760set(handles.list_subdir_civ1,'String',[{'browse...'};listdir])
761set(handles.list_subdir_civ2,'String',[{'browse...'};listdir])
762%check wether the current subdir exists:
763subdir_civ1=get(handles.subdir_civ1,'String');
764subdir_civ2=get(handles.subdir_civ2,'String');
765
766mode_Callback(hObject, eventdata, handles)
767
768%% desable status and RUN button
769% set(handles.waitbar_1,'Position',[0.946 0.876 0.03 0.001])
770% set(handles.waitbar_patch1,'Position',[0.946 0.439 0.03 0.001])
771% set(handles.waitbar_civ2,'Position',[0.946 0.219 0.03 0.001])
772% set(handles.waitbar_patch2,'Position',[0.946 0.0 0.03 0.001])
773set(handles.RUN, 'Enable','On')
774set(handles.RUN,'BackgroundColor',[1 0 0])
775set(handles.BATCH,'Enable','On')
776set(handles.BATCH,'BackgroundColor',[1 0 0])
777if isfield(handles,'status')
778set(handles.status,'Value',0);%suppress status display
779status_Callback(hObject, eventdata, handles)
780end
781
782%% store the root input filename for future opening
783dir_perso=prefdir;
784profil_perso=fullfile(prefdir,'uvmat_perso.mat');
785RootPath=fileparts(filebase);
786if exist(profil_perso,'file')
787    save (profil_perso,'RootPath','-append'); %store the root name for future opening of uvmat
788else
789    txt=ver('MATLAB');
790    Release=txt.Release;
791    relnumb=str2double(Release(3:4));
792    if relnumb >= 14
793        save (profil_perso,'RootPath','-V6'); %store the root name for future opening of uvmat
794    else
795        save (profil_perso,'RootPath'); %store the root name for future opening of uvmat
796    end
797end
798
799%------------------------------------------------------------------------
800% --- Executes on button press in mode.
801function mode_Callback(hObject, eventdata, handles)
802%------------------------------------------------------------------------
803browse=get(handles.browse_root,'UserData');
804compare_list=get(handles.compare,'String');
805val=get(handles.compare,'Value');
806compare=compare_list{val};
807if strcmp(compare,'displacement')
808    mode='displacement';
809else
810    mode_list=get(handles.mode,'String');
811    if ischar(mode_list)
812        mode_list={mode_list};
813    end
814    mode_value=get(handles.mode,'Value');
815    mode=mode_list{mode_value};
816end
817displ_num=[];%default
818ref_i=str2double(get(handles.ref_i,'String'));
819% last_i=str2num(get(handles.last_i,'String'));
820time=get(handles.RootName,'UserData'); %get the set of times
821siztime=size(time);
822nbfield=siztime(1);
823nbfield2=siztime(2);
824indchosen=1;  %%first pair selected by default
825if isequal(mode,'pair j1-j2')%| isequal(mode,'st_pair j1-j2')
826    dt=1;
827    displ='';
828    index=0;
829    numlist_a=[];
830    numlist_B=[];
831    %get all the time intervals in bursts
832    displ_dt=1;%default
833    nbfield2=min(nbfield2,10);%limitate the number of pairs to 10x10
834    for numod_a=1:nbfield2-1 %nbfield2 always >=2 for 'pair j1-j2' mode
835        for numod_b=(numod_a+1):nbfield2
836            index=index+1;
837            numlist_a(index)=numod_a;
838            numlist_b(index)=numod_b;
839            if ~isempty(time)
840                dt(numod_a,numod_b)=time(ref_i,numod_b)-time(ref_i,numod_a);%first time interval dt
841                displ_dt(index)=dt(numod_a,numod_b);
842            else
843                displ_dt(index)=1;
844            end
845        end
846    end
847    [dtsort,indsort]=sort(displ_dt);
848    if ~isempty(numlist_a)
849        displ_num(1,:)=numlist_a(indsort);
850        displ_num(2,:)=numlist_b(indsort);
851    end
852    displ_num(3,:)=0;
853    displ_num(4,:)=0;
854    set(handles.jtext,'Visible','Off')
855    set(handles.first_j,'Visible','Off')
856    set(handles.last_j,'Visible','Off')
857    set(handles.incr_j,'Visible','Off')
858    set(handles.nb_field2,'Visible','Off')
859    set(handles.ref_j,'Visible','Off')
860elseif isequal(mode,'series(Dj)') %| isequal(mode,'st_series(Dj)')
861    for index=1:min(nbfield2-1,200)
862        displ_num(1,index)=-floor(index/2);
863        displ_num(2,index)=ceil(index/2);
864        displ_num(3,index)=0;
865        displ_num(4,index)=0;
866    end
867    set(handles.jtext,'Visible','On')
868    set(handles.first_j,'Visible','On')
869    set(handles.last_j,'Visible','On')
870    set(handles.incr_j,'Visible','On')
871    set(handles.nb_field2,'Visible','On')
872    set(handles.ref_j,'Visible','On')
873    if nbfield > 1
874        set(handles.itext,'Visible','On')
875        set(handles.first_i,'Visible','On')
876        set(handles.last_i,'Visible','On')
877        set(handles.incr_i,'Visible','On')
878        set(handles.nb_field,'Visible','On')
879        set(handles.ref_i,'Visible','On')
880    else
881        set(handles.itext,'Visible','Off')
882        set(handles.first_i,'Visible','Off')
883        set(handles.last_i,'Visible','Off')
884        set(handles.incr_i,'Visible','Off')
885        set(handles.nb_field,'Visible','Off')
886        set(handles.ref_i,'Visible','Off')
887    end
888elseif isequal(mode,'series(Di)') %| isequal(mode,'st_series(Di)')
889    for index=1:200%min(nbfield-1,200)
890        displ_num(1,index)=0;
891        displ_num(2,index)=0;
892        displ_num(3,index)=-floor(index/2);
893        displ_num(4,index)=ceil(index/2);
894    end
895    set(handles.itext,'Visible','On')
896    set(handles.first_i,'Visible','On')
897    set(handles.last_i,'Visible','On')
898    set(handles.incr_i,'Visible','On')
899    set(handles.nb_field,'Visible','On')
900    set(handles.ref_i,'Visible','On')
901    if nbfield2 > 1
902        set(handles.jtext,'Visible','On')
903        set(handles.first_j,'Visible','On')
904        set(handles.last_j,'Visible','On')
905        set(handles.incr_j,'Visible','On')
906        set(handles.nb_field2,'Visible','On')
907        set(handles.ref_j,'Visible','On')
908    else
909        set(handles.jtext,'Visible','Off')
910        set(handles.first_j,'Visible','Off')
911        set(handles.last_j,'Visible','Off')
912        set(handles.incr_j,'Visible','Off')
913        set(handles.nb_field2,'Visible','Off')
914        set(handles.ref_j,'Visible','Off')
915    end
916elseif isequal(mode,'displacement')%the pairs have the same indices
917    displ_num(1,1)=0;
918    displ_num(2,1)=0;
919    displ_num(3,1)=0;
920    displ_num(4,1)=0;
921    if nbfield > 1
922        set(handles.itext,'Visible','On')
923        set(handles.first_i,'Visible','On')
924        set(handles.last_i,'Visible','On')
925        set(handles.incr_i,'Visible','On')
926        set(handles.nb_field,'Visible','On')
927        set(handles.ref_i,'Visible','On')
928    else
929        set(handles.itext,'Visible','Off')
930        set(handles.first_i,'Visible','Off')
931        set(handles.last_i,'Visible','Off')
932        set(handles.incr_i,'Visible','Off')
933        set(handles.nb_field,'Visible','Off')
934        set(handles.ref_i,'Visible','Off')
935    end
936    if nbfield2 > 1
937        set(handles.jtext,'Visible','On')
938        set(handles.first_j,'Visible','On')
939        set(handles.last_j,'Visible','On')
940        set(handles.incr_j,'Visible','On')
941        set(handles.nb_field2,'Visible','On')
942        set(handles.ref_j,'Visible','On')
943    else
944        set(handles.jtext,'Visible','Off')
945        set(handles.first_j,'Visible','Off')
946        set(handles.last_j,'Visible','Off')
947        set(handles.incr_j,'Visible','Off')
948        set(handles.nb_field2,'Visible','Off')
949        set(handles.ref_j,'Visible','Off')
950    end
951end
952set(handles.list_pair_civ1,'UserData',displ_num);
953find_netcpair_civ1(hObject, eventdata, handles)
954find_netcpair_civ2(hObject, eventdata, handles)
955
956%------------------------------------------------------------------------
957% determine the menu for civ1 pairs depending on existing netcdf file at the middle of
958% the field series set by first_i, incr, last_i
959function find_netcpair_civ1(hObject, eventdata, handles)
960%------------------------------------------------------------------------
961set(gcf,'Pointer','watch')
962%nomenclature types
963filebase=get(handles.RootName,'String');
964[filepath,Nme,ext_dir]=fileparts(filebase);
965browse=get(handles.browse_root,'UserData');
966compare_list=get(handles.compare,'String');
967val=get(handles.compare,'Value');
968compare=compare_list{val};
969if strcmp(compare,'displacement')
970    mode='displacement';
971else
972    mode_list=get(handles.mode,'String');
973    mode_value=get(handles.mode,'Value');
974    mode=mode_list{mode_value};
975end
976
977% nomenclature type of the .nc files
978nom_type_ima=[];%default
979if isfield(browse,'nom_type_ima')
980    nom_type_ima=browse.nom_type_ima;
981end
982
983%determine nom_type_nc:
984nom_type_nc=[];%default
985if isfield(browse,'nom_type_nc')
986    nom_type_nc=browse.nom_type_nc;
987end
988if isempty(nom_type_nc)
989    [nom_type_nc]=nomtype2pair(nom_type_ima,isequal(mode,'series(Di)'),isequal(mode,'series(Dj)'));
990end
991browse.nom_type_nc=nom_type_nc;
992set(handles.browse_root,'UserData',browse)
993
994%reads .nc subdirectoy and image numbers from the interface
995subdir_civ1=get(handles.subdir_civ1,'String');%subdirectory subdir_civ1 for the netcdf data
996% first_i=str2num(get(handles.first_i,'String'));
997% last_i=str2num(get(handles.last_i,'String'));
998% incr=str2num(get(handles.incr_i,'String'));
999% num1=first_i:incr:last_i;
1000% if isempty(num1)
1001%     set(handles.list_pair_civ1,'String',{''});
1002%     return
1003% end
1004ref_i=str2double(get(handles.ref_i,'String'));
1005if isequal(mode,'pair j1-j2')%|isequal(mode,'st_pair j1-j2')
1006    ref_j=0;
1007else
1008    ref_j=str2double(get(handles.ref_j,'String'));
1009end
1010time=get(handles.RootName,'UserData');%get the set of times
1011if isempty(time)
1012    time=[0 1];
1013end
1014%dt_unit=str2double(get(handles.dt,'String'));% used when there is no image documentation file
1015dt_unit=1000;%default
1016displ_num=get(handles.list_pair_civ1,'UserData');
1017
1018%eliminate the first pairs inconsistent with the position
1019if isempty(displ_num)
1020    nbpair=0;
1021else
1022    nbpair=length(displ_num(1,:));%nbre of displayed pairs
1023    if  isequal(mode,'series(Di)')  %| isequal(mode,'st_series(Di)')
1024        nbpair=min(2*ref_i-1,nbpair);%limit the number of pairs with positive first index
1025    elseif  isequal(mode,'series(Dj)')% | isequal(mode,'st_series(Dj)')
1026        nbpair=min(2*ref_j-1,nbpair);%limit the number of pairs with positive first index
1027    end
1028end
1029nbpair=min(200,nbpair);%limit the number of displayed pairs to 200
1030
1031%look for existing processed pairs involving the field at the middle of the series if civ1 will not
1032% be performed, while the result is needed for next steps.
1033displ_pair={''};
1034select=ones(size(1:nbpair));%default =1 for numbers of displayed pairs
1035testpair=0;
1036if get(handles.CIV1,'Value')==0 %
1037    if ~exist(fullfile(filepath,subdir_civ1,ext_dir),'dir')
1038        msgbox_uvmat('ERROR',['no civ1 file available: subdirectory ' subdir_civ1 ' does not exist']);
1039        set(handles.list_pair_civ1,'String',{});
1040        return
1041    end
1042    for ipair=1:nbpair
1043        filename=name_generator(filebase,ref_i+displ_num(3,ipair),ref_j+displ_num(1,ipair),'.nc',nom_type_nc,1,...
1044            ref_i+displ_num(4,ipair),ref_j+displ_num(2,ipair),subdir_civ1);
1045        select(ipair)=exist(filename,'file')==2;
1046    end
1047    if ~exist('select','var') || isequal(select,zeros(size(1:nbpair)))
1048        if isfield(browse,'incr_pair')
1049            num_i1=ref_i-floor(browse.incr_pair(1)/2);
1050            num_i2=ref_i+ceil(browse.incr_pair(1)/2);
1051            num_j1=ref_j-floor(browse.incr_pair(2)/2);
1052            num_j2=ref_j+ceil(browse.incr_pair(2)/2);
1053            filename=name_generator(filebase,num_i1,num_j1,'.nc',nom_type_nc,1,num_i2,num_j2,subdir_civ1);
1054            select(1)=exist(filename,'file')==2;
1055            testpair=1;
1056        else
1057            if  isequal(mode,'series(Dj)')% | isequal(mode,'st_series(Dj)')
1058                msgbox_uvmat('ERROR',['no civ1 file available for the selected reference index j=' num2str(ref_j) ' and subdirectory ' subdir_civ1]);
1059            else
1060                msgbox_uvmat('ERROR',['no civ1 file available for the selected reference index i=' num2str(ref_i) ' and subdirectory ' subdir_civ1]);
1061            end
1062            set(handles.list_pair_civ1,'String',{''});
1063            %COMPLETER CAS STEREO
1064            return
1065        end
1066    end
1067end
1068if isequal(mode,'series(Di)') %| isequal(mode,'st_series(Di)')
1069    if testpair
1070        displ_pair{1}=['Di= ' num2str(-floor(browse.incr_pair(1)/2)) '|' num2str(ceil(browse.incr_pair(1)/2))];
1071        %     elseif ~isequal(get(handles.root_txt,'String'),'dt(ms)=')
1072        %        for ipair=1:nbpair
1073        %           if select(ipair)
1074        %               if size(time,1)>=ref_i+displ_num(4,ipair) && size(time,2)>=ref_j+displ_num(2,ipair)
1075        %               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
1076        %               displ_pair{ipair}=['Di= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2)) ' :dt= ' num2str(dt*1000)];
1077        %               end
1078        %           else
1079        %              displ_pair{ipair}='...'; %pair not displayed in the menu
1080        %           end
1081        %        end
1082    else
1083        for ipair=1:nbpair
1084            if select(ipair)
1085                if size(time,1)>=ref_i+displ_num(4,ipair) && size(time,2)>=ref_j+displ_num(2,ipair)
1086                    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
1087                    displ_pair{ipair}=['Di= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2)) ' :dt= ' num2str(dt*1000)];
1088                else
1089                    displ_pair{ipair}='...'; %pair not displayed in the menu
1090                end
1091            end
1092        end
1093    end
1094elseif isequal(mode,'series(Dj)')%|isequal(mode,'st_series(Dj)')% series on the j index
1095    if testpair
1096        displ_pair{1}=['Dj= ' num2str(-floor(browse.incr_pair(1)/2)) '|' num2str(ceil(browse.incr_pair(1)/2))];
1097    else
1098        for ipair=1:nbpair
1099            if select(ipair)
1100                if size(time,1)>=ref_i+displ_num(4,ipair) && size(time,2)>=ref_j+displ_num(2,ipair)
1101                    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
1102                    displ_pair{ipair}=['Dj= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2)) ' :dt= ' num2str(dt*1000)];
1103                end
1104            elseif testpair
1105                displ_pair{1}=['Dj= ' num2str(-floor(browse.incr_pair(2)/2)) '|' num2str(ceil(browse.incr_pair(2)/2))];
1106            else
1107                displ_pair{ipair}='...'; %pair not displayed in the menu
1108            end
1109        end
1110    end
1111elseif isequal(mode,'pair j1-j2')%|isequal(mode,'st_pair j1-j2')%case of pairs
1112    for ipair=1:nbpair
1113        if select(ipair)
1114            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
1115            displ_pair{ipair}=['j= ' num2stra(displ_num(1,ipair),nom_type_ima) '-' num2stra(displ_num(2,ipair),nom_type_ima) ...
1116                ' :dt= ' num2str(dt*1000)];
1117        else
1118            displ_pair{ipair}='...'; %pair not displayed in the menu
1119        end
1120    end
1121elseif isequal(mode,'displacement')
1122    displ_pair={'Di=Dj=0'};
1123end
1124set(handles.list_pair_civ1,'String',displ_pair');
1125ichoice=find(select,1);
1126if (isempty(ichoice) || ichoice < 1); ichoice=1; end;
1127initial=get(handles.list_pair_civ1,'Value');%initial choice of pair
1128if initial>nbpair
1129    set(handles.list_pair_civ1,'Value',ichoice);% first valid pair proposed by default in the menu
1130end
1131if numel(select)>=initial && ~isequal(select(initial),1)
1132    set(handles.list_pair_civ1,'Value',ichoice);% first valid pair proposed by default in the menu
1133end
1134
1135%set(handles.list_pair_civ2,'String',displ_pair');
1136initial=get(handles.list_pair_civ2,'Value');
1137if initial>length(displ_pair')%|~isequal(select(initial),1)
1138    if ichoice <= length(displ_pair')
1139        set(handles.list_pair_civ2,'Value',ichoice);% same pair proposed by default for civ2
1140    else
1141        set(handles.list_pair_civ2,'Value',1);% same pair proposed by default for civ2
1142    end
1143end
1144set(handles.list_pair_civ2,'String',displ_pair');
1145set(gcf,'Pointer','arrow')
1146
1147%------------------------------------------------------------------------
1148% determine the menu for civ2 pairs depending on the existing netcdf file at the
1149%middle of the series set by first_i, incr, last_i
1150function find_netcpair_civ2(hObject, eventdata, handles)
1151%------------------------------------------------------------------------
1152set(gcf,'Pointer','watch')
1153%nomenclature types
1154filebase=get(handles.RootName,'String');
1155[filepath,Nme,ext_dir]=fileparts(filebase);
1156browse=get(handles.browse_root,'UserData');
1157compare_list=get(handles.compare,'String');
1158val=get(handles.compare,'Value');
1159compare=compare_list{val};
1160if strcmp(compare,'displacement')
1161    mode='displacement';
1162else
1163    mode_list=get(handles.mode,'String')
1164    mode_value=get(handles.mode,'Value')
1165    mode=mode_list{mode_value};
1166end
1167
1168% nomenclature type of the .nc files
1169nom_type_ima='ima_num';%default
1170if isfield(browse,'nom_type_ima')
1171    nom_type_ima=browse.nom_type_ima;
1172end
1173nom_type_nc='_i1-i2';%default
1174if isfield(browse,'nom_type_nc')
1175    nom_type_nc=browse.nom_type_nc;
1176end
1177if isequal(nom_type_ima,'png_old') || isequal(nom_type_ima,'netc_old')|| isequal(nom_type_ima,'raw_SMD')|| isequal(nom_type_nc,'netc_old')
1178    nom_type_nc='netc_old';%nom_type for the netcdf files
1179elseif isequal(nom_type_ima,'none')||isequal(nom_type_nc,'none')
1180    nom_type_nc='none';
1181elseif isequal(nom_type_ima,'avi')||isequal(nom_type_ima,'_i')||isequal(nom_type_ima,'ima_num')||isequal(nom_type_nc,'_i1-i2')
1182    nom_type_nc='_i1-i2';
1183else
1184    if  isequal(mode,'series(Di)')%|isequal(mode,'st_series(Di)')
1185        nom_type_nc='_i1-i2_j'; % PIV in volume
1186    else
1187        nom_type_nc='_i_j1-j2';
1188    end
1189end
1190browse.nom_type_nc=nom_type_nc;
1191set(handles.browse_root,'UserData',browse)
1192
1193%reads .nc subdirectory and image numbers from the interface
1194subdir_civ1=get(handles.subdir_civ1,'String');%subdirectory subdir_civ1 for the netcdf data
1195subdir_civ2=get(handles.subdir_civ2,'String');%subdirectory subdir_civ2 for the netcdf data
1196% first_i=str2num(get(handles.first_i,'String'));
1197% last_i=str2num(get(handles.last_i,'String'));
1198% incr=str2num(get(handles.incr_i,'String'));
1199% num1=first_i:incr:last_i;
1200% if isempty(num1)
1201%     set(handles.list_pair_civ2,'Value',1);
1202%     set(handles.list_pair_civ2,'String',{''});
1203%     return
1204% end
1205ref_i=str2double(get(handles.ref_i_civ2,'String'));
1206if isequal(mode,'pair j1-j2')%|isequal(mode,'st_pair j1-j2')
1207    ref_j=0;
1208else
1209    ref_j=str2double(get(handles.ref_j_civ2,'String'));
1210end
1211time=get(handles.RootName,'UserData'); %get the set of times
1212if isempty(time)
1213    time=[0 1];%default
1214end
1215%dt_unit=str2num(get(handles.dt,'String'));% used when there is no image documentation file
1216%dt_unit=1000;
1217displ_num=get(handles.list_pair_civ1,'UserData');
1218
1219
1220%eliminate the first pairs inconsistent with the position
1221if isempty(displ_num)
1222    nbpair=0;
1223else
1224    nbpair=length(displ_num(1,:));%nbre of displayed pairs
1225    if  isequal(mode,'series(Di)')% | isequal(mode,'st_series(Di)')
1226        nbpair=min(2*ref_i-1,nbpair);%limit the number of pairs with positive first index
1227    elseif  isequal(mode,'series(Dj)')% | isequal(mode,'st_series(Dj)')
1228        nbpair=min(2*ref_j-1,nbpair);%limit the number of pairs with positive first index
1229    end
1230end
1231nbpair=min(200,nbpair);%limit the number of displayed pairs to 200
1232
1233%look for existing processed pairs involving the field at the middle of the series if civ1 will not
1234% be performed, while the result is needed for next steps.
1235displ_pair={''}; %default
1236select=ones(size(1:nbpair));%default =1 for numbers of displayed pairs
1237if get(handles.CIV2,'Value')==0 & get(handles.CIV1,'Value')==0 & get(handles.FIX1,'Value')==0 & get(handles.PATCH1,'Value')==0%&...
1238    if ~exist(fullfile(filepath,subdir_civ2,ext_dir),'dir')
1239        errordlg(['no civ2 file available: subdirectory ' subdir_civ2 ' does not exist'])
1240        set(handles.list_pair_civ2,'Value',1);
1241        set(handles.list_pair_civ2,'String',{''});
1242        return
1243    end
1244    for ipair=1:nbpair
1245        filename=name_generator(filebase,ref_i+displ_num(3,ipair),ref_j+displ_num(1,ipair),'.nc',nom_type_nc,1,...
1246            ref_i+displ_num(4,ipair),ref_j+displ_num(2,ipair),subdir_civ1);
1247        select(ipair)=exist(filename,'file')==2;
1248    end
1249    if  isequal(select,zeros(size(1:nbpair)))
1250        if isfield(browse,'incr_pair')
1251            num_i1=ref_i-floor(browse.incr_pair(1)/2);
1252            num_i2=ref_i+floor((browse.incr_pair(1)+1)/2);
1253            num_j1=ref_j-floor(browse.incr_pair(2)/2);
1254            num_j2=ref_j+floor((browse.incr_pair(2)+1)/2);
1255            filename=name_generator(filebase,num_i1,num_j1,'.nc',nom_type_nc,1,num_i2,num_j2,subdir_civ2);
1256            select(1)=exist(filename,'file')==2;
1257        else
1258            if  isequal(mode,'series(Dj)')% | isequal(mode,'st_series(Dj)')
1259                errordlg(['no civ2 file available for the selected reference index j=' num2str(ref_j) ' and subdirectory ' subdir_civ2])
1260            else
1261                errordlg(['no civ2 file available for the selected reference index i=' num2str(ref_i) ' and subdirectory ' subdir_civ2])
1262            end
1263            set(handles.list_pair_civ2,'Value',1);
1264            set(handles.list_pair_civ2,'String',{''});
1265            return
1266        end
1267    end
1268end
1269if isequal(mode,'series(Di)') % | isequal(mode,'st_series(Di)')
1270    for ipair=1:nbpair
1271        if select(ipair)
1272            if size(time,1)>=ref_i+displ_num(4,ipair) && size(time,2)>=ref_j+displ_num(2,ipair)
1273                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
1274                displ_pair{ipair}=['Di= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2)) ' :dt= ' num2str(dt*1000)];
1275            end
1276        else
1277            displ_pair{ipair}='...'; %pair not displayed in the menu
1278        end
1279    end
1280elseif isequal(mode,'series(Dj)') %| isequal(mode,'st_series(Dj)') % series on the j index
1281    for ipair=1:nbpair
1282        if select(ipair)
1283            if size(time,1)>=ref_i+displ_num(4,ipair) && size(time,2)>=ref_j+displ_num(2,ipair)
1284                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
1285                displ_pair{ipair}=['Dj= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2)) ' :dt= ' num2str(dt*1000)];
1286            end
1287        else
1288            displ_pair{ipair}='...'; %pair not displayed in the menu
1289        end
1290    end
1291elseif isequal(mode,'pair j1-j2')% | isequal(mode,'st_pair j1-j2') %case of pairs
1292    for ipair=1:nbpair
1293        if select(ipair)
1294            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
1295            displ_pair{ipair}=['j= ' num2stra(displ_num(1,ipair),nom_type_ima) '-' num2stra(displ_num(2,ipair),nom_type_ima) ...
1296                ' :dt= ' num2str(dt*1000)];
1297        else
1298            displ_pair{ipair}='...'; %pair not displayed in the menu
1299        end
1300    end
1301elseif isequal(mode,'displacement')
1302    displ_pair={'Di=Dj=0'};
1303end
1304val=get(handles.list_pair_civ2,'Value');
1305ichoice=find(select,1);
1306if (isempty(ichoice) || ichoice < 1); ichoice=1; end;
1307if get(handles.CIV2,'Value')==0 && get(handles.CIV1,'Value')==0 && get(handles.FIX1,'Value')==0 && get(handles.PATCH1,'Value')==0
1308    val=ichoice;% first valid pair proposed by default in the menu
1309end
1310if val>length(displ_pair')
1311    set(handles.list_pair_civ2,'Value',1);% first valid pair proposed by default in the menu
1312else
1313    set(handles.list_pair_civ2,'Value',val);
1314end
1315set(handles.list_pair_civ2,'String',displ_pair');
1316set(gcf,'Pointer','arrow')
1317
1318
1319
1320
1321%------------------------------------------------------------------------
1322% --- Executes on selection change in list_pair_civ1.
1323function list_pair_civ1_Callback(hObject, eventdata, handles)
1324%------------------------------------------------------------------------
1325%reproduce by default the chosen pair in the civ2 menu
1326list_pair=get(handles.list_pair_civ1,'String');%get the menu of image pairs
1327index_pair=get(handles.list_pair_civ1,'Value');
1328displ_num=get(handles.list_pair_civ1,'UserData');
1329% num_a=displ_num(1,index_pair);
1330% num_b=displ_num(2,index_pair);
1331list_pair2=get(handles.list_pair_civ2,'String');%get the menu of image pairs
1332if index_pair<=length(list_pair2)
1333    set(handles.list_pair_civ2,'Value',index_pair);
1334end
1335
1336%update first_i and last_i according to the chosen image pairs
1337mode_list=get(handles.mode,'String');
1338mode_value=get(handles.mode,'Value');
1339mode=mode_list{mode_value};
1340if isequal(mode,'series(Di)')
1341    first_i=str2double(get(handles.first_i,'String'));
1342    last_i=str2double(get(handles.last_i,'String'));
1343    incr_i=str2double(get(handles.incr_i,'String'));
1344    num1=first_i:incr_i:last_i;
1345    lastfield=str2double(get(handles.nb_field,'String'));
1346    if ~isnan(lastfield)
1347        test_find=(num1-floor(index_pair/2)*ones(size(num1))>0)& ...
1348            (num1+ceil(index_pair/2)*ones(size(num1))<=lastfield);
1349        num1=num1(test_find);
1350    end
1351    set(handles.first_i,'String',num2str(num1(1)));
1352    set(handles.last_i,'String',num2str(num1(end)));
1353elseif isequal(mode,'series(Dj)')
1354    first_j=str2double(get(handles.first_j,'String'));
1355    last_j=str2double(get(handles.last_j,'String'));
1356    incr_j=str2double(get(handles.incr_j,'String'));
1357    num_j=first_j:incr_j:last_j;
1358    lastfield2=str2double(get(handles.nb_field2,'String'));
1359    if ~isnan(lastfield2)
1360        test_find=(num_j-floor(index_pair/2)*ones(size(num_j))>0)& ...
1361            (num_j+ceil(index_pair/2)*ones(size(num_j))<=lastfield2);
1362        num1=num_j(test_find);
1363    end
1364    set(handles.first_j,'String',num2str(num1(1)));
1365    set(handles.last_j,'String',num2str(num1(end)));
1366end
1367
1368%------------------------------------------------------------------------
1369% --- Executes on selection change in list_pair_civ2.
1370function list_pair_civ2_Callback(hObject, eventdata, handles)
1371%------------------------------------------------------------------------
1372index_pair=get(handles.list_pair_civ2,'Value');%get the selected position index in the menu
1373
1374%update first_i and last_i according to the chosen image pairs
1375mode_list=get(handles.mode,'String');
1376mode_value=get(handles.mode,'Value');
1377mode=mode_list{mode_value};
1378if isequal(mode,'series(Di)')
1379    first_i=str2double(get(handles.first_i,'String'));
1380    last_i=str2double(get(handles.last_i,'String'));
1381    incr_i=str2double(get(handles.incr_i,'String'));
1382    num1=first_i:incr_i:last_i;
1383    lastfield=str2double(get(handles.nb_field,'String'));
1384    if ~isnan(lastfield)
1385        test_find=(num1-floor(index_pair/2)*ones(size(num1))>0)& ...
1386            (num1+ceil(index_pair/2)*ones(size(num1))<=lastfield);
1387        num1=num1(test_find);
1388    end
1389    set(handles.first_i,'String',num2str(num1(1)));
1390    set(handles.last_i,'String',num2str(num1(end)));
1391elseif isequal(mode,'series(Dj)')
1392    first_j=str2double(get(handles.first_j,'String'));
1393    last_j=str2double(get(handles.last_j,'String'));
1394    incr_j=str2double(get(handles.incr_j,'String'));
1395    num_j=first_j:incr_j:last_j;
1396    lastfield2=str2double(get(handles.nb_field2,'String'));
1397    if ~isnan(lastfield2)
1398        test_find=(num_j-floor(index_pair/2)*ones(size(num_j))>0)& ...
1399            (num_j+ceil(index_pair/2)*ones(size(num_j))<=lastfield2);
1400        num1=num_j(test_find);
1401    end
1402    set(handles.first_j,'String',num2str(num1(1)));
1403    set(handles.last_j,'String',num2str(num1(end)));
1404end
1405
1406%------------------------------------------------------------------------
1407% --- Executes on button press in RUN: processing on local computer
1408function RUN_Callback(hObject, eventdata, handles)
1409%------------------------------------------------------------------------
1410set(handles.RUN, 'Enable','Off')
1411set(handles.RUN,'BackgroundColor',[0.831 0.816 0.784])
1412batch=0;
1413errormsg=launch_jobs(hObject, eventdata, handles,batch);
1414set(handles.RUN, 'Enable','On')
1415set(handles.RUN,'BackgroundColor',[1 0 0])
1416
1417% start status callback to visualise results
1418if ~isempty(errormsg)
1419    display(errormsg)
1420    msgbox_uvmat('ERROR',errormsg)
1421elseif  isfield(handles,'status') %&& ~isequal(get(handles.CivMode,'Value'),3)
1422    set(handles.status,'Value',1);%suppress status display
1423    status_Callback(hObject, eventdata, handles)
1424end
1425
1426%------------------------------------------------------------------------
1427% --- Executes on button press in BATCH: remote processing
1428function BATCH_Callback(hObject, eventdata, handles)
1429% -----------------------------------------------------------------------
1430set(handles.BATCH, 'Enable','Off')
1431set(handles.BATCH,'BackgroundColor',[0.831 0.816 0.784])
1432batch=1;
1433errormsg=launch_jobs(hObject, eventdata, handles, batch);
1434set(handles.BATCH, 'Enable','On')
1435set(handles.BATCH,'BackgroundColor',[1 0 0])
1436
1437% start status callback to visualise results
1438if ~isempty(errormsg)
1439    display(errormsg)
1440    msgbox_uvmat('ERROR',errormsg)
1441elseif isfield(handles,'status')
1442    set(handles.status,'Value',1);%suppress status display
1443    status_Callback(hObject, eventdata, handles)
1444end
1445
1446%------------------------------------------------------------------------
1447% --- Lauch command called by RUN and BATCH: remote processing
1448function errormsg=launch_jobs(hObject, eventdata, handles, batch)
1449%-----------------------------------------------------------------------
1450errormsg='';%default
1451%% check the selected list of operations:
1452operations={'CIV1','FIX1','PATCH1','CIV2','FIX2','PATCH2'};
1453box_test(1)=get(handles.CIV1,'Value');
1454box_test(2)=get(handles.FIX1,'Value');
1455box_test(3)=get(handles.PATCH1,'Value');
1456box_test(4)=get(handles.CIV2,'Value');
1457box_test(5)=get(handles.FIX2,'Value');
1458box_test(6)=get(handles.PATCH2,'Value');
1459index_first=find(box_test==1,1);
1460if isempty(index_first)
1461    errormsg='no selected operation';
1462    return
1463end
1464index_last=find(box_test==1,1,'last');
1465box_used=box_test(index_first : index_last);
1466[box_missing,ind_missing]=min(box_used);
1467if isequal(box_missing,0); %there is a missing step in the sequence of operations
1468    errormsg=['missing' cell2mat(operations(ind_missing))];
1469    return
1470end
1471
1472%% check mask if selecetd
1473if isequal(get(handles.get_mask_civ1,'Value'),1)
1474    maskname=get(handles.mask_civ1,'String');
1475    if ~exist(maskname,'file')
1476        get_mask_civ1_Callback(hObject, eventdata, handles);
1477    end
1478end
1479if isequal(get(handles.get_mask_fix1,'Value'),1)
1480    maskname=get(handles.mask_fix1,'String');
1481    if ~exist(maskname,'file')
1482        get_mask_fix1_Callback(hObject, eventdata, handles);
1483    end
1484end
1485if isequal(get(handles.get_mask_civ2,'Value'),1)
1486    maskname=get(handles.mask_civ2,'String');
1487    if ~exist(maskname,'file')
1488        get_mask_civ2_Callback(hObject, eventdata, handles);
1489    end
1490end
1491if isequal(get(handles.get_mask_fix2,'Value'),1)
1492    maskname=get(handles.mask_fix2,'String');
1493    if ~exist(maskname,'file')
1494        get_mask_fix2_Callback(hObject, eventdata, handles);
1495    end
1496end
1497
1498%% reinitialise status callback
1499if isfield(handles,'status')
1500    set(handles.status,'Value',0);%suppress status display
1501    status_Callback(hObject, eventdata, handles)
1502end
1503
1504%% set the list of files and check them
1505display('checking the files...')
1506[ref_i,ref_j,errormsg]=find_ref_indices(handles);
1507if ~isempty(errormsg)
1508    return
1509end
1510[filecell,num1_civ1,num2_civ1,num_a_civ1,num_b_civ1,num1_civ2,num2_civ2,num_a_civ2,num_b_civ2,nom_type_nc]=...
1511    set_civ_filenames(handles,ref_i,ref_j,box_test);
1512set(handles.civ,'UserData',filecell);%store for futur use of status callback
1513if isempty(filecell)% (error message displayed in fct set_civ_filenames)
1514    return
1515end
1516nbfield=numel(num1_civ1);
1517nbslice=numel(num_a_civ1);
1518
1519%% choose the batch or run mode
1520path_UVMAT=fileparts(which('uvmat')); %path to the source directory of uvmat
1521xmlfile='PARAM.xml';
1522if exist(xmlfile,'file')% search parameter xml file in the whole matlab path
1523    t=xmltree(xmlfile);
1524    s=convert(t);
1525end
1526test_interp=0;
1527if batch
1528    if isfield(s,'BatchParam')
1529        sparam=s.BatchParam;
1530        if isfield(sparam,'BatchMode')
1531            batch_mode=sparam.BatchMode;
1532            if ~ismember(batch_mode,{'sge','oar'})
1533                errormsg=['batch mode ' batch_mode ' not supported by UVMAT'];
1534                return
1535            end
1536        end
1537    else
1538        errormsg='no batch civ binaries defined in PARAM.xml';
1539        return
1540    end
1541   
1542    switch batch_mode
1543        case 'sge'
1544            % choice of batch priority:
1545            ind_answer=2;
1546            [s,w]=unix('qstat -q civ.q|grep job_| wc -l'); %check the waiting list (command unix)
1547            if isequal(s,0)
1548                w(end)=[];
1549                str_displ={[w ' jobs in the waiting list'];...
1550                    '***********************';...
1551                    'JOBS PRIORITY POLICY';...
1552                    '- urgent = less than 100 images pairs';...
1553                    '- normal = during the experiments';...
1554                    '- low = post processing';...
1555                    '***********************';...
1556                    'Select a priority:'};
1557                ' ';...
1558                    str={'urgent';'normal';'low'};
1559                [ind_answer,v] = listdlg('PromptString',str_displ,...
1560                    'SelectionMode','single',...
1561                    'ListString',str,'ListSize',[200 100],'Name','job priority','InitialValue',3);
1562                if isequal(v,0) % to handle Cancel button and figure close,
1563                    errormsg='job cancelled';
1564                    return % a better way should be create
1565                end
1566            else
1567                msgbox_uvmat('ERROR','sge batch system not available')
1568                return
1569            end
1570    end
1571else % run
1572    if isfield(s,'RunParam')
1573        sparam=s.RunParam;
1574    else
1575        msgbox_uvmat('ERROR','no run civ binaries defined in PARAM.xml')
1576        return
1577    end
1578end
1579
1580%% choose the civ program
1581ProgList=get(handles.CivMode,'String');
1582index=get(handles.CivMode,'Value');
1583% CivX=isequal(ProgList{index},'CivX');
1584% CivAll=isequal(ProgList{index},'CivAll');
1585% CivUvmat=isequal(ProgList{index},'CivUvmat');
1586CivMode=ProgList{index};
1587%CivMode=isequal(get(handles.CivMode,'Value'),2); % Boolean for new civ programs
1588
1589switch CivMode
1590    case 'CivAll'
1591        if isfield(sparam,'CivBin')
1592            CivBin=sparam.CivBin;
1593            if ~exist(CivBin,'file') || ~isempty(which(CivBin))% if path defined as relative to uvmat
1594                sparam.CivBin=fullfile(path_UVMAT,CivBin);
1595                if ~exist(sparam.CivBin,'file')
1596                    msgbox_uvmat('ERROR',['CIVx binary ' CivBin ' defined in PARAM.xm does not exist'])
1597                    return
1598                end
1599            end
1600        end
1601    case 'CivX'
1602        if isfield(sparam,'Civ1Bin')
1603            Civ1Bin=sparam.Civ1Bin;
1604            if ~exist(Civ1Bin,'file')||~isempty(which(Civ1Bin))% if path defined as relative to uvmat
1605                sparam.Civ1Bin=fullfile(path_UVMAT,Civ1Bin);
1606                if ~exist(sparam.Civ1Bin,'file')
1607                    msgbox_uvmat('ERROR',['civ1 binary ' Civ1Bin ' defined in PARAM.xm does not exist'])
1608                    return
1609                end
1610            end
1611        end
1612        if isfield(sparam,'Civ2Bin')
1613            Civ2Bin=sparam.Civ2Bin;
1614            if ~exist(Civ2Bin,'file')||~isempty(which(Civ2Bin))% if path defined as relative to uvmat
1615                sparam.Civ2Bin=fullfile(path_UVMAT,Civ2Bin);
1616                if ~exist(sparam.Civ2Bin,'file')
1617                    msgbox_uvmat('ERROR',['civ2 binary ' Civ2Bin ' defined in PARAM.xm does not exist'])
1618                    return
1619                end
1620            end
1621        end
1622        if  isfield(sparam,'PatchBin')
1623            if ~exist(sparam.PatchBin,'file')||~isempty(which(sparam.PatchBin))% if path defined as relative to uvmat
1624                sparam.PatchBin=fullfile(path_UVMAT,sparam.PatchBin);
1625            end
1626        end
1627        if isfield(sparam,'FixBin')
1628            if ~exist(sparam.FixBin,'file')||~isempty(which(sparam.FixBin))% if path defined as relative to uvmat
1629                sparam.FixBin=fullfile(path_UVMAT,sparam.FixBin);
1630            end
1631        end
1632    case 'Matlab'
1633        if batch
1634            %% vérifier Mtlab installé sur le cluster
1635        end         
1636end
1637
1638
1639
1640%% get civ1 parameters:
1641display('files OK, processing...')
1642if box_test(1)==1
1643    par_civ1=read_param_civ1(handles,filecell.ima1.civ1{1,1});
1644end
1645
1646%% get fix1 parameters TODO : par_fix1=read_param_fix1(handles);
1647if box_test(2)==1
1648    flagindex1(1)=get(handles.vec_Fmin2, 'Value');
1649    flagindex1(2)=get(handles.vec_F3, 'Value');
1650    flagindex1(3)=get(handles.vec_F2, 'Value');
1651    thresh_vecC1=str2double(get(handles.thresh_vecC,'String'));%threshold on image correlation vec_C
1652    thresh_vel1=str2double(get(handles.thresh_vel,'String'));%threshold on velocity modulus
1653    test_mask=get(handles.get_mask_fix1,'Value');
1654    nbslice_mask=get(handles.mask_fix1,'UserData'); % get the number of slices (= number of masks)
1655    %%%%%%%%%%%%%COMPLETER LE PROGRAMME FIX
1656    %     inf_sup=get(handles.inf_sup1,'Value');80
1657    %     fileref=get(handles.ref_fix1,'String');
1658    %     refpath=get(handles.ref_fix1,'UserData');
1659    %     fileref=fullfile(refpath,fileref);
1660    menu=get(handles.field_ref1,'String');
1661    index=get(handles.field_ref1,'Value');
1662    if isempty(menu)
1663        fieldchoice='';
1664    else
1665        fieldchoice=menu{index};
1666        msgbox_uvmat('WARNING','reference field is not used presently with batch, use RUN option')
1667    end
1668end
1669
1670%% get patch1 parameters
1671if box_test(3)==1
1672    rho_patch1=str2double(get(handles.rho_patch1,'String'));
1673    if isnan(rho_patch1)
1674        rho_patch1='1000';
1675        set(handles.rho_patch1,'String','1')
1676    else
1677        rho_patch1=num2str(1000*rho_patch1);
1678    end
1679    nx_patch1=get(handles.nx_patch1,'String');
1680    ny_patch1=get(handles.ny_patch1,'String');
1681    if isnan(str2double(nx_patch1))
1682        nx_patch1='50' ;%default
1683        set(handles.nx_patch1,'String','50');
1684    end
1685    if isnan(str2double(ny_patch1))
1686        ny_patch1='50' ;%default
1687        set(handles.ny_patch1,'String','50');
1688    end
1689    subdomain_patch1=get(handles.subdomain_patch1,'String');
1690    thresh_patch1=get(handles.thresh_patch1,'String');
1691end
1692
1693%% get civ2 parameters:
1694if box_test(4)==1
1695    par_civ2=read_param_civ2(handles,cell2mat(filecell.ima1.civ2(1,1)));
1696end
1697
1698%% get fix2 parameters
1699if box_test(5)==1
1700    flagindex2(1)=get(handles.vec_Fmin2_2, 'Value');
1701    flagindex2(2)=get(handles.vec_F3_2, 'Value');
1702    flagindex2(3)=get(handles.vec_F4, 'Value');
1703    thresh_vec2C=str2double(get(handles.thresh_vec2C,'String'));%threshold on image correlation vec_C
1704    thresh_vel2=str2double(get(handles.thresh_vel2,'String'));%threshold on velocity modulus
1705    test_mask=get(handles.get_mask_fix2,'Value');
1706    nbslice_mask=get(handles.mask_fix2,'UserData'); % get the number of slices (= number of masks)
1707    %%%%%%%%%%%%%COMPLETER LE PROGRAMME FIX AVEC REF FILE ET OPTION inf_sup=2
1708    %     inf_sup=get(handles.inf_sup2,'Value');
1709    %     ref=get(handles.ref_fix2,'UserData');
1710   
1711    %%%%%%%%%%%%%%%%%%%
1712end
1713
1714%% get patch2 parameters
1715if box_test(6)==1
1716    rho_patch2=str2double(get(handles.rho_patch2,'String'));
1717    if isnan(rho_patch2)
1718        rho_patch2='1000';
1719        set(handles.rho_patch2,'String','1')
1720    else
1721        rho_patch2=num2str(1000*rho_patch2);
1722    end
1723    nx_patch2=get(handles.nx_patch2,'String');
1724    ny_patch2=get(handles.ny_patch2,'String');
1725    if isnan(str2double(nx_patch2))
1726        nx_patch2='50' ;%default
1727        set(handles.nx_patch2,'String','50');
1728    end
1729    if isnan(str2double(ny_patch2))
1730        ny_patch2='50' ;%default
1731        set(handles.ny_patch2,'String','50');
1732    end
1733    subdomain_patch2=get(handles.subdomain_patch2,'String');
1734    thresh_patch2=get(handles.thresh_patch2,'String');
1735end
1736
1737%% MAIN LOOP
1738time=get(handles.RootName,'UserData'); %get the set of times
1739super_cmd=[];
1740
1741for ifile=1:nbfield
1742    for j=1:nbslice
1743        % initiate system command
1744        i_cmd=0;
1745        switch CivMode
1746            case 'CivX'
1747                cmd='';
1748                if isunix % check: necessaire aussi en RUN?
1749                    cmd='#!/bin/bash \n';
1750                    cmd=[cmd '#$ -cwd \n'];
1751                    cmd=[cmd 'hostname && date \n'];
1752                    cmd=[cmd 'umask 002 \n'];%allow writting access to created files for user group
1753                end
1754            case 'CivAll'
1755                %         if CivAll
1756                CivAllxml=xmltree;% xml contents,  all parameters
1757                CivAllCmd='';
1758                CivAllxml=set(CivAllxml,1,'name','CivDoc');
1759        end
1760        [Rootbat,Filebat]=fileparts(filecell.nc.civ1{ifile,j});%output netcdf file (without extention)
1761        flname=fullfile(Rootbat,Filebat);
1762        if batch
1763            filename_bat=fullfile(Rootbat,['job_' Filebat]);
1764        else
1765            filename_bat=flname;
1766        end
1767        filename_bat=[filename_bat '.bat'];
1768       
1769        %CIV1
1770        if box_test(1)==1
1771            par_civ1.filename_ima_a=filecell.ima1.civ1{ifile,j};
1772            par_civ1.filename_ima_b=filecell.ima2.civ1{ifile,j};
1773            par_civ1.Dt=num2str(time(num2_civ1(ifile),num_b_civ1(j))-time(num1_civ1(ifile),num_a_civ1(j)));
1774            par_civ1.T0=num2str((time(num2_civ1(ifile),num_b_civ1(j))+time(num1_civ1(ifile),num_a_civ1(j)))/2);
1775            par_civ1.term_a=num2stra(num_a_civ1(j),nom_type_nc);%UTILITE?
1776            par_civ1.term_b=num2stra(num_b_civ1(j),nom_type_nc);%
1777            test_mask=get(handles.get_mask_civ1,'Value');
1778            if test_mask==0
1779                par_civ1.maskname='noFile use default';
1780                par_civ1.maskflag='n';
1781            else
1782                maskdispl=get(handles.mask_civ1,'String');
1783                if exist(maskdispl,'file')
1784                    par_civ1.maskname=maskdispl;
1785                    par_civ1.maskflag='y';
1786                else
1787                    maskbase=[filecell.filebase '_' maskdispl]; %
1788                    nbslice_mask=str2double(maskdispl(1:end-4)); %
1789                    num1_mask=mod(num1_civ1(ifile)-1,nbslice_mask)+1;
1790                    par_civ1.maskname=name_generator(maskbase,num1_mask,1,'.png','_i');
1791                    if exist(par_civ1.maskname,'file')
1792                        par_civ1.maskflag='y';
1793                    else
1794                        par_civ1.maskname='noFile use default';
1795                        par_civ1.maskflag='n';
1796                    end
1797                end
1798            end
1799            test_grid=get(handles.browse_gridciv1,'Value');
1800            if test_grid
1801                par_civ1.gridflag='y';
1802                gridname=get(handles.grid_civ1,'String');
1803                if isequal(gridname(end-3:end),'grid')
1804                    nbslice_grid=str2double(gridname(1:end-4)); %
1805                    if ~isnan(nbslice_grid)
1806                        num1_grid=mod(num1_civ1(ifile)-1,nbslice_grid)+1;
1807                        par_civ1.gridname=[filecell.filebase '_' name_generator(gridname,num1_grid,1,'.grid','_i')];
1808                        if ~exist(par_civ1.gridname,'file')
1809                            msgbox_uvmat('ERROR','grid file absent for civ1')
1810                        end
1811                    elseif exist(gridname,'file')
1812                        par_civ1.gridname=gridname;
1813                    else
1814                        msgbox_uvmat('ERROR','grid file absent for civ1')
1815                    end
1816                end
1817            else
1818                par_civ1.gridname='noFile use default';
1819                par_civ1.gridflag='n';
1820            end
1821           
1822            i_cmd=i_cmd+1;
1823            switch CivMode
1824                case 'CivX'
1825                    civ1_exe=CIV1_CMD(fullfile(Rootbat,Filebat),'',par_civ1,handles,sparam);%create the parameter file .civ1.cmx and set the execution string civ1_exe
1826                    cmd=[cmd civ1_exe '\n'];
1827                case 'CivAll'
1828                    CivAllCmd=[CivAllCmd ' civ1 '];
1829                    str=CIV1_CMD_Unified(fullfile(Rootbat,Filebat),'',par_civ1);
1830                    fieldnames=fields(str);
1831                    [CivAllxml,uid_civ1]=add(CivAllxml,1,'element','civ1');
1832                    for ilist=1:length(fieldnames)
1833                        val=eval(['str.' fieldnames{ilist}]);
1834                        if ischar(val)
1835                            [CivAllxml,uid_t]=add(CivAllxml,uid_civ1,'element',fieldnames{ilist});
1836                            [CivAllxml,uid_t2]=add(CivAllxml,uid_t,'chardata',val);
1837                        end
1838                    end
1839            end
1840        end
1841       
1842        % FIX1
1843        if box_test(2)==1
1844            test_mask=get(handles.get_mask_fix1,'Value');
1845            if test_mask==0
1846                maskname='';
1847            else
1848                maskdispl=get(handles.mask_fix1,'String');
1849                nbslice_mask=str2double(maskdispl(1:end-4)); %
1850                num1_mask=mod(num1_civ1(ifile)-1,nbslice_mask)+1;
1851                maskbase=[filecell.filebase '_' maskdispl];
1852                maskname=name_generator(maskbase,num1_mask,1,'.png','_i');
1853            end
1854            switch CivMode
1855                %             if CivX
1856                case 'CivX'
1857                    if isunix %unix system
1858                        cmd_FIX=[sparam.FixBin ' -f ' filecell.nc.civ1{ifile,j} ' -fi1 ' num2str(flagindex1(1)) ...
1859                            ' -fi2 ' num2str(flagindex1(2)) ' -fi3 ' num2str(flagindex1(3)) ...
1860                            ' -threshC ' num2str(thresh_vecC1) ' -threshV ' num2str(thresh_vel1) ' -maskName ' maskname];
1861                    else %windows system
1862                        cmd_FIX=['"' sparam.FixBin '" -f "' filecell.nc.civ1{ifile,j} '" -fi1 ' num2str(flagindex1(1)) ...
1863                            ' -fi2 ' num2str(flagindex1(2)) ' -fi3 ' num2str(flagindex1(3)) ...
1864                            ' -threshC ' num2str(thresh_vecC1) ' -threshV ' num2str(thresh_vel1) ' -maskName "' maskname '"'];
1865                        cmd_FIX=regexprep(cmd_FIX,'\\','\\\\');
1866                    end
1867                    cmd=[cmd cmd_FIX '\n'];
1868                case 'CivAll'
1869                    fix1.inputFileName=filecell.nc.civ1{ifile,j} ;
1870                    fix1.fi1=num2str(flagindex1(1));
1871                    fix1.fi2=num2str(flagindex1(2));
1872                    fix1.fi3=num2str(flagindex1(3));
1873                    fix1.threshC=num2str(thresh_vecC1);
1874                    fix1.threshV=num2str(thresh_vel1);
1875                    fieldnames=fields(fix1);
1876                    [CivAllxml,uid_fix1]=add(CivAllxml,1,'element','fix1');
1877                    for ilist=1:length(fieldnames)
1878                        val=eval(['fix1.' fieldnames{ilist}]);
1879                        if ischar(val)
1880                            [CivAllxml,uid_t]=add(CivAllxml,uid_fix1,'element',fieldnames{ilist});
1881                            [CivAllxml,uid_t2]=add(CivAllxml,uid_t,'chardata',val);
1882                        end
1883                    end
1884                    CivAllCmd=[CivAllCmd ' fix1 '];
1885            end
1886        end
1887       
1888        %PATCH1
1889        if box_test(3)==1
1890            switch CivMode
1891                case 'CivX'
1892                    cmd_PATCH=PATCH_CMD(filecell.nc.civ1{ifile,j},nx_patch1,ny_patch1,rho_patch1,subdomain_patch1,thresh_patch1,test_interp,sparam.PatchBin);
1893                    cmd=[cmd cmd_PATCH '\n'];
1894                case 'CivAll'
1895                    patch1.inputFileName=filecell.nc.civ1{ifile,j} ;
1896                    patch1.nopt=subdomain_patch1;
1897                    patch1.maxdiff=thresh_patch1;
1898                    patch1.ro=rho_patch1;
1899                    test_grid=get(handles.get_gridpatch1,'Value');
1900                    if test_grid
1901                        patch1.gridflag='y';
1902                        gridname=get(handles.grid_patch1,'String');
1903                        if isequal(gridname(end-3:end),'grid')
1904                            nbslice_grid=str2double(gridname(1:end-4)); %
1905                            if ~isnan(nbslice_grid)
1906                                num1_grid=mod(num1_civ1(ifile)-1,nbslice_grid)+1;
1907                                patch1.gridPatch=[filecell.filebase '_' name_generator(gridname,num1_grid,1,'.grid','_i')];
1908                                if ~exist(patch1.gridPatch,'file')
1909                                    msgbox_uvmat('ERROR','grid file absent for patch1')
1910                                end
1911                            elseif exist(gridname,'file')
1912                                patch1.gridPatch=gridname;
1913                            else
1914                                msgbox_uvmat('ERROR','grid file absent for patch1')
1915                            end
1916                        end
1917                    else
1918                        patch1.gridPatch='none';
1919                        patch1.gridflag='n';
1920                        patch1.m=nx_patch1;
1921                        patch1.n=ny_patch1;
1922                    end
1923                    patch1.convectFlow='n';
1924                    fieldnames=fields(patch1);
1925                    [CivAllxml,uid_patch1]=add(CivAllxml,1,'element','patch1');
1926                    for ilist=1:length(fieldnames)
1927                        val=eval(['patch1.' fieldnames{ilist}]);
1928                        if ischar(val)
1929                            [CivAllxml,uid_t]=add(CivAllxml,uid_patch1,'element',fieldnames{ilist});
1930                            [CivAllxml,uid_t2]=add(CivAllxml,uid_t,'chardata',val);
1931                        end
1932                    end
1933                    CivAllCmd=[CivAllCmd ' patch1 '];
1934            end
1935        end
1936        if box_test(4)==1 || box_test(5)==1 || box_test(6)==1
1937            filename_cmx=filecell.nc.civ2{ifile,j};%output netcdf file
1938            filename_cmx(end-1:end+1)='cmx';%name of cmx file
1939        end
1940        if box_test(4)==1
1941            par_civ2.filename_ima_a=filecell.ima1.civ2{ifile,j};
1942            par_civ2.filename_ima_b=filecell.ima2.civ2{ifile,j};
1943            [Rootbat,Filebat]=fileparts(filecell.nc.civ2{ifile,j});%output netcdf file (without extention)
1944            par_civ2.Dt=num2str(time(num2_civ2(ifile),num_b_civ2(j))-time(num1_civ2(ifile),num_a_civ2(j)));
1945            par_civ2.T0=num2str((time(num2_civ1(ifile),num_b_civ2(j))+time(num1_civ2(ifile),num_a_civ2(j)))/2);
1946            par_civ2.term_a=num2stra(num_a_civ2(j),nom_type_nc);
1947            par_civ2.term_b=num2stra(num_b_civ2(j),nom_type_nc);
1948            par_civ2.filename_nc1=filecell.nc.civ1{ifile,j};
1949            par_civ2.filename_nc1(end-2:end)=[]; % remove '.nc'
1950            test_mask=get(handles.get_mask_civ2,'Value');
1951            if test_mask==0
1952                par_civ2.maskname='noFile use default';
1953                par_civ2.maskflag='n';
1954            else
1955                maskdispl=get(handles.mask_civ2,'String');
1956                if exist(maskdispl,'file')
1957                    par_civ2.maskname=maskdispl;
1958                    par_civ2.maskflag='y';
1959                else
1960                    maskbase=[filecell.filebase '_' maskdispl]; %
1961                    nbslice_mask=str2double(maskdispl(1:end-4)); %
1962                    num1_mask=mod(num1_civ2(ifile)-1,nbslice_mask)+1;
1963                    par_civ2.maskname=name_generator(maskbase,num1_mask,1,'.png','_i');
1964                    if exist(par_civ2.maskname,'file')
1965                        par_civ2.maskflag='y';
1966                    else
1967                        par_civ2.maskname='noFile use default';
1968                        par_civ2.maskflag='n';
1969                    end
1970                end
1971            end
1972            gridname=get(handles.grid_civ2,'String');
1973            if numel(gridname)>=4 && isequal(gridname(end-3:end),'grid')
1974                nbslice_grid=str2double(gridname(1:end-4)); %
1975                if ~isnan(nbslice_grid)
1976                    par_civ2.gridflag='y';
1977                    num1_grid=mod(num1_civ2(ifile)-1,nbslice_grid)+1;
1978                    par_civ2.gridname=[filecell.filebase '_' name_generator(gridname,num1_grid,1,'.grid','_i')];
1979                    if exist(par_civ2.gridname,'file')
1980                        par_civ2.gridflag='y';
1981                    else
1982                        par_civ2.gridname='noFile use default';
1983                        par_civ2.gridflag='n';
1984                    end
1985                elseif exist(gridname,'file')
1986                    par_civ2.gridflag='y';
1987                else
1988                    par_civ2.gridname='noFile use default';
1989                    par_civ2.gridflag='n';
1990                end
1991            end
1992            i_cmd=i_cmd+1;
1993            flname=fullfile(Rootbat,Filebat);
1994            switch CivMode
1995                case 'CivX'
1996                    cmd_CIV2=CIV2_CMD(flname,[],par_civ2,sparam);%creates the cmx file [fullfile(Rootbat,Filebat) '.civ2.cmx]
1997                    cmd=[cmd cmd_CIV2 '\n'];
1998                case 'CivAll'
1999                    CivAllCmd=[CivAllCmd ' civ2 '];
2000                    str=CIV2_CMD_Unified(flname,'',par_civ2);
2001                    fieldnames=fields(str);
2002                    [CivAllxml,uid_civ2]=add(CivAllxml,1,'element','civ2');
2003                    for ilist=1:length(fieldnames)
2004                        val=eval(['str.' fieldnames{ilist}]);
2005                        if ischar(val)
2006                            [CivAllxml,uid_t]=add(CivAllxml,uid_civ2,'element',fieldnames{ilist});
2007                            [CivAllxml,uid_t2]=add(CivAllxml,uid_t,'chardata',val);
2008                        end
2009                    end
2010            end
2011        end
2012       
2013        % FIX2
2014        if box_test(5)==1
2015            test_mask=get(handles.get_mask_fix2,'Value');
2016            if test_mask==0
2017                maskname=''; %no mask used
2018            else
2019                maskdispl=get(handles.mask_fix2,'String');
2020                maskbase=[filecell.filebase '_' maskdispl]; %
2021                nbslice_mask=str2double(maskdispl(1:end-4)); %
2022                num1_mask=mod(num1_civ2(ifile)-1,nbslice_mask)+1;
2023                maskname =name_generator(maskbase,num1_mask,1,'.png','_i');
2024            end
2025            switch CivMode
2026                case 'CivX'
2027                    if isunix
2028                        cmd_FIX=[sparam.FixBin ' -f ' filecell.nc.civ2{ifile,j} ' -fi1 ' num2str(flagindex2(1)) ...
2029                            ' -fi2 ' num2str(flagindex2(2)) ' -fi3 ' num2str(flagindex2(3)) ...
2030                            ' -threshC ' num2str(thresh_vec2C) ' -threshV ' num2str(thresh_vel2) ' -maskName ' maskname];
2031                    else
2032                        cmd_FIX=['"' sparam.FixBin '" -f "' filecell.nc.civ2{ifile,j} '" -fi1 ' num2str(flagindex2(1)) ...
2033                            ' -fi2 ' num2str(flagindex2(2)) ' -fi3 ' num2str(flagindex2(3)) ...
2034                            ' -threshC ' num2str(thresh_vec2C) ' -threshV ' num2str(thresh_vel2) ' -maskName "' maskname '"'];
2035                        cmd_FIX=regexprep(cmd_FIX,'\\','\\\\');
2036                    end
2037                    cmd=[cmd cmd_FIX '\n'];
2038                case 'CivAll'
2039                    fix2.inputFileName=filecell.nc.civ2{ifile,j} ;
2040                    fix2.fi1=num2str(flagindex2(1));
2041                    fix2.fi2=num2str(flagindex2(2));
2042                    fix2.fi3=num2str(flagindex2(3));
2043                    fix2.threshC=num2str(thresh_vec2C);
2044                    fix2.threshV=num2str(thresh_vel2);
2045                    fieldnames=fields(fix2);
2046                    [CivAllxml,uid_fix2]=add(CivAllxml,1,'element','fix2');
2047                    for ilist=1:length(fieldnames)
2048                        val=eval(['fix2.' fieldnames{ilist}]);
2049                        if ischar(val)
2050                            [CivAllxml,uid_t]=add(CivAllxml,uid_fix2,'element',fieldnames{ilist});
2051                            [CivAllxml,uid_t2]=add(CivAllxml,uid_t,'chardata',val);
2052                        end
2053                    end
2054                    CivAllCmd=[CivAllCmd ' fix2 '];
2055            end
2056        end
2057       
2058        %PATCH2
2059        if box_test(6)==1
2060            switch CivMode
2061                case 'CivX'
2062                    cmd_PATCH=PATCH_CMD(filecell.nc.civ2{ifile,j},nx_patch2,ny_patch2,rho_patch2,subdomain_patch2,thresh_patch2,test_interp,sparam.PatchBin);
2063                    cmd=[cmd cmd_PATCH '\n'];
2064                case 'CivAll'
2065                    patch2.inputFileName=filecell.nc.civ1{ifile,j} ;
2066                    patch2.nopt=subdomain_patch2;
2067                    patch2.maxdiff=thresh_patch2;
2068                    patch2.ro=rho_patch2;
2069                    test_grid=get(handles.get_gridpatch2,'Value');
2070                    if test_grid
2071                        patch2.gridflag='y';
2072                        gridname=get(handles.grid_patch2,'String');
2073                        if isequal(gridname(end-3:end),'grid')
2074                            nbslice_grid=str2double(gridname(1:end-4)); %
2075                            if ~isnan(nbslice_grid)
2076                                num1_grid=mod(num1_civ2(ifile)-1,nbslice_grid)+1;
2077                                patch2.gridPatch=[filecell.filebase '_' name_generator(gridname,num1_grid,1,'.grid','_i')];
2078                                if ~exist(patch2.gridPatch,'file')
2079                                    msgbox_uvmat('ERROR','grid file absent for patch2')
2080                                end
2081                            elseif exist(gridname,'file')
2082                                patch2.gridPatch=gridname;
2083                            else
2084                                msgbox_uvmat('ERROR','grid file absent for patch2')
2085                            end
2086                        end
2087                    else
2088                        patch2.gridPatch='none';
2089                        patch2.gridflag='n';
2090                        patch2.m=nx_patch2;
2091                        patch2.n=ny_patch2;
2092                    end
2093                    patch2.convectFlow='n';
2094                    fieldnames=fields(patch2);
2095                    [CivAllxml,uid_patch2]=add(CivAllxml,1,'element','patch2');
2096                    for ilist=1:length(fieldnames)
2097                        val=eval(['patch2.' fieldnames{ilist}]);
2098                        if ischar(val)
2099                            [CivAllxml,uid_t]=add(CivAllxml,uid_patch2,'element',fieldnames{ilist});
2100                            [CivAllxml,uid_t2]=add(CivAllxml,uid_t,'chardata',val);
2101                        end
2102                    end
2103                    CivAllCmd=[CivAllCmd ' patch2 '];
2104            end
2105        end
2106 
2107        switch CivMode
2108            case {'CivX','CivAll'}
2109                if isequal(CivMode,'CivAll')
2110                    save(CivAllxml,[flname '.xml']);
2111                    cmd=[cmd sparam.CivBin ' -f ' flname '.xml '  CivAllCmd ' >' flname '.log' '\n'];
2112                end
2113                % create the .bat file:
2114                [fid,message]=fopen(filename_bat,'w');
2115                if isequal(fid,-1)
2116                    msgbox_uvmat('ERROR', ['creation of .bat file: ' message])
2117                    return
2118                end
2119                fprintf(fid,cmd);
2120                fclose(fid);
2121                if batch
2122                    switch batch_mode
2123                        case 'sge'
2124                            pvalue=num2str((1-ind_answer)*500);
2125                            display(['!qsub -p ' pvalue ' -q civ.q -e ' flname '.errors -o ' flname '.log' ' ' filename_bat]);
2126                            eval(  ['!qsub -p ' pvalue ' -q civ.q -e ' flname '.errors -o ' flname '.log' ' ' filename_bat]);
2127                        case 'oar'
2128                            eval(  ['!chmod +x ' filename_bat]);
2129                            eval(  ['!oarsub -l /nodes=1/cpu=1,walltime=00:10:00  ' filename_bat]);
2130                    end
2131                else
2132                    %% to lauch the jobs locally :
2133                    if(isunix)
2134                        cmd_str=['. ' filename_bat];
2135                    else %case of Windows
2136                        cmd_str=['@call "' regexprep(filename_bat,'\\','\\\\') '"'];
2137                    end
2138                    super_cmd=[super_cmd cmd_str '\n'];
2139                    disp(cmd_str);
2140                end
2141            case 'Matlab'
2142                drawnow
2143                if box_test(1)==1
2144                    Param.Civ1=par_civ1;
2145                end
2146                if box_test(2)==1
2147                    fix1.WarnFlags=[];
2148                    if get(handles.vec_Fmin2,'Value')
2149                        fix1.WarnFlags=[fix1.WarnFlags -2];
2150                    end
2151                    if get(handles.vec_F3,'Value')
2152                        fix1.WarnFlags=[fix1.WarnFlags 3];
2153                    end
2154                    fix1.LowerBoundCorr=thresh_vecC1;
2155                    if get(handles.inf_sup1,'Value')
2156                        fix1.UppperBoundVel=thresh_vel1;
2157                    else
2158                        fix1.LowerBoundVel=thresh_vel1;
2159                    end
2160                    if get(handles.get_mask_fix1,'Value')
2161                        fix1.MaskName=maskname;
2162                    end
2163                    Param.Fix1=fix1;
2164                end
2165                if box_test(3)==1
2166                    Param.Patch1.Rho=rho_patch1;
2167                    Param.Patch1.Threshold=thresh_patch1;
2168                    Param.Patch1.SubDomain=subdomain_patch1;
2169                end
2170                if box_test(4)==1
2171                    Param.Civ2=par_civ2;
2172                end
2173                if box_test(5)==1
2174                    fix2.WarnFlags=[];
2175                    if get(handles.vec_Fmin2_2,'Value')
2176                        fix2.WarnFlags=[fix2.WarnFlags -2];
2177                    end
2178                    if get(handles.vec_F4,'Value')
2179                        fix2.WarnFlags=[fix2.WarnFlags 4];
2180                    end
2181                    if get(handles.vec_F3_2,'Value')
2182                        fix2.WarnFlags=[fix2.WarnFlags 3];
2183                    end
2184                    fix2.LowerBoundCorr=thresh_vec2C;
2185                    if get(handles.inf_sup2,'Value')
2186                        fix2.UppperBoundVel=thresh_vel2;
2187                    else
2188                        fix2.LowerBoundVel=thresh_vel2;
2189                    end
2190                    if get(handles.get_mask_fix2,'Value')
2191                        fix2.MaskName=maskname;
2192                    end
2193                    Param.Fix2=fix2;
2194                end
2195                [Data,erromsg]=civ_uvmat(Param,filecell.nc.civ1{ifile,j});
2196                if isempty(errormsg)
2197                    display([filecell.nc.civ1{ifile,j} ' written'])
2198                else
2199                    msgbox_uvmat('ERROR',errormsg)
2200                end
2201        end
2202    end
2203end
2204
2205if ~batch && ~isequal(CivMode,'Matlab')
2206    [Rootbat,Filebat,extbat]=fileparts(filename_bat);
2207    filename_superbat=fullfile(Rootbat,'job_list.bat');
2208    fid=fopen(filename_superbat,'w');
2209    if fid==-1
2210        msgbox_uvmat('ERROR',['cannot create the command file ' filename_superbat])
2211        return
2212    end
2213    fprintf(fid,super_cmd');
2214    fclose(fid);
2215    if(isunix)
2216        system(['chmod +x ' filename_superbat])
2217    end
2218    system([filename_superbat ' &'])% execute main commmand
2219end
2220
2221%% save interface state
2222if isfield(filecell,'nc')
2223    if isfield(filecell.nc,'civ2')
2224        fileresu=filecell.nc.civ2{1,1};
2225    else
2226        fileresu=filecell.nc.civ1{1,1};
2227    end
2228end
2229[RootPath,RootFile,field_count,str2,str_a,str_b,ext,nom_type,subdir]=name2display(fileresu);
2230namedoc=fullfile(RootPath,subdir,RootFile);
2231detect=1;
2232while detect==1
2233    namefigfull=[namedoc '.fig'];
2234    hh=dir(namefigfull);
2235    if ~isempty(hh)
2236        detect=1;
2237        namedoc=[namedoc '.0'];
2238    else
2239        detect=0;
2240    end
2241end
2242saveas(gcbf,namefigfull);%save the interface with name namefigfull (A CHANGER EN FICHIER  .xml)
2243
2244%------------------------------------------------------------------------
2245% --- determine the list of reference indices of processing file
2246function [ref_i,ref_j,errormsg]=find_ref_indices(handles)
2247%------------------------------------------------------------------------
2248errormsg=''; %default error message
2249first_i=str2double(get(handles.first_i,'String'));%first index i
2250last_i=str2double(get(handles.last_i,'String'));%last index i
2251incr_i=str2double(get(handles.incr_i,'String'));% increment
2252if isequal(get(handles.first_j,'Visible'),'on')
2253    first_j=str2double(get(handles.first_j,'String'));%first index j
2254    last_j=str2double(get(handles.last_j,'String'));%last index j
2255    incr_j=str2double(get(handles.incr_j,'String'));% increment
2256else
2257    first_j=1;
2258    last_j=1;
2259    incr_j=1;
2260end
2261ref_i=first_i:incr_i:last_i;% list of i indices (reference values for each pair)
2262ref_j=first_j:incr_j:last_j;% list of j indices (reference values for each pair)
2263if isnan(first_i)||isnan(first_j)
2264    errormsg='first field number not defined';
2265elseif isnan(last_i)||isnan(last_j)
2266    errormsg='last field number not defined';
2267elseif isnan(incr_i)||isnan(incr_j)
2268    errormsg='increment in field number not defined';
2269elseif last_i < first_i || last_j < first_j
2270    errormsg='last field number must be larger than the first one';
2271end
2272
2273%------------------------------------------------------------------------
2274% --- determine the list of filenames and indices needed for launch_job
2275function [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]=...
2276    set_civ_filenames(handles,ref_i,ref_j,box_test)
2277%------------------------------------------------------------------------
2278filecell=[];%default
2279
2280%% get the root names nomenclature and numbers
2281filebase=get(handles.RootName,'String');
2282
2283if isempty(filebase)||isequal(filebase,'')
2284    msgbox_uvmat('ERROR','no input files')
2285    return
2286end
2287
2288%filebase=regexprep(filebase,'\.fsnet','fsnet');% temporary fix for cluster Coriolis
2289filecell.filebase=filebase;
2290
2291browse=get(handles.browse_root,'UserData');
2292compare_list=get(handles.compare,'String');
2293val=get(handles.compare,'Value');
2294compare=compare_list{val};
2295if strcmp(compare,'displacement')
2296    mode='displacement';
2297else
2298    mode_list=get(handles.mode,'String');
2299    mode_value=get(handles.mode,'Value');
2300    mode=mode_list{mode_value};
2301end
2302%time=get(handles.RootName,'UserData'); %get the set of times
2303ext_ima=get(handles.ImaExt,'String');
2304nom_type_nc=browse.nom_type_nc;
2305if isfield(browse,'nom_type_ima')
2306    nom_type_ima2=browse.nom_type_ima;
2307end
2308if isempty(nom_type_ima2),nom_type_ima2='1';end; %default
2309if isempty(nom_type_nc),nom_type_nc='_i1-i2';end; %default
2310[num1_civ1,num2_civ1,num_a_civ1,num_b_civ1,num1_civ2,num2_civ2,num_a_civ2,num_b_civ2]=...
2311    find_pair_indices(handles,ref_i,ref_j,mode);
2312%determine the new filebase for 'displacement' mode (comparison of two series)
2313filebase_B=filebase;% root name of the second field series for stereo
2314if strcmp(compare,'displacement') || strcmp(compare,'stereo PIV')
2315%     test_disp=1;
2316    nom_type_ima1=browse.nom_type_ima_1; %nomenclature type of the second file series
2317    [Path2,Name2]=fileparts(filebase_B);
2318    Path1=Path2;
2319    Name1=get(handles.RootName_1,'String');% root name of the first field series for stereo
2320    filebase_A=fullfile(Path1,Name1);
2321    if length(Name1)>6
2322        Name1=Name1(end-5:end);
2323    end
2324    if length(Name2)>6
2325        Name2=Name2(end-5:end);
2326    end
2327    filebase_AB=fullfile(Path2,[Name2 '-' Name1]);
2328else
2329%     test_disp=0;
2330    filebase_A=filebase;
2331    nom_type_ima1=nom_type_ima2;
2332    filebase_AB=filebase;
2333end
2334if strcmp(compare,'displacement')
2335    filebase_ima1=filebase_A;
2336    filebase_ima2=filebase_B;
2337    filebase_nc=filebase_AB; %root name for the result of civ2
2338else
2339    filebase_ima1=filebase_B;
2340    filebase_ima2=filebase_B;
2341    filebase_nc=filebase_B;
2342end
2343
2344%determine reference files for fix:
2345file_ref_fix1={};%default
2346file_ref_fix2={};
2347nbfield=length(num1_civ1);
2348nbslice=length(num_a_civ1);
2349if box_test(2)==1% fix1 performed
2350    ref=get(handles.ref_fix1,'UserData');%read data on the ref file stored by get_ref_fix1_Callback
2351    if ~isempty(ref)
2352        first_i=str2double(get(handles.first_i,'String'));
2353        last_i=str2double(get(handles.last_i,'String'));
2354        incr_i=str2double(get(handles.incr_i,'String'));
2355        first_j=str2double(get(handles.first_j,'String'));
2356        last_j=str2double(get(handles.last_j,'String'));
2357        incr_j=str2double(get(handles.incr_j,'String'));
2358        num_i_ref=first_i:incr_i:last_i;
2359        num_j_ref=first_j:incr_j:last_j;
2360        if isequal(mode,'displacement')
2361            num_i1=num_i_ref;
2362            num_i2=num_i_ref;
2363            num_j1=num_j_ref;
2364            num_j2=num_j_ref;
2365        elseif isequal(mode,'pair j1-j2')% isequal(mode,'st_pair j1-j2')
2366            num_i1=num_i_ref;
2367            num_i2=num_i1;
2368            num_j1=ref.num_a*ones(size(num_i_ref));
2369            num_j2=ref.num_b*ones(size(num_i_ref));
2370        elseif isequal(mode,'series(Di)') % isequal(mode,'st_series(Di)')
2371            delta1=floor((ref.num2-ref.num1)/2);
2372            delta2=ceil((ref.num2-ref.num1)/2);
2373            num_i1=num_i_ref-delta1*ones(size(num_i_ref));
2374            num_i2=num_i_ref+delta2*ones(size(num_i_ref));
2375            if isempty(ref.num_a)
2376                ref.num_a=1;
2377            end
2378            num_j1=ref.num_a*ones(size(num_i1));
2379            num_j2=num_j1;
2380        elseif isequal(mode,'series(Dj)')%| isequal(mode,'st_series(Dj)')
2381            delta1=floor((ref.num_b-ref.num_a)/2);
2382            delta2=ceil((ref.num_b-ref.num_a)/2);
2383            num_i1=ref.num1*ones(size(num_i_ref));
2384            num_i2=num_i1;
2385            num_j1=num_j_ref-delta1*ones(size(num_j_ref));
2386            num_j2=num_j_ref+delta2*ones(size(num_j_ref));
2387        end
2388        for ifile=1:nbfield
2389            for j=1:nbslice
2390                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);%
2391                file_ref_fix1(ifile,j)={file_ref};
2392                if ~exist(file_ref,'file')
2393                    msgbox_uvmat('ERROR',['reference file ' file_ref ' not found for fix1'])
2394                    filecell=[];
2395                    return
2396                end
2397            end
2398        end
2399    end
2400end
2401
2402%determine reference files for fix2:
2403if box_test(5)==1% fix2 performed
2404    ref=get(handles.ref_fix2,'UserData');
2405    if ~isempty(ref)
2406        first_i=str2double(get(handles.first_i,'String'));
2407        last_i=str2double(get(handles.last_i,'String'));
2408        incr_i=str2double(get(handles.incr_i,'String'));
2409        first_j=str2double(get(handles.first_j,'String'));
2410        last_j=str2double(get(handles.last_j,'String'));
2411        incr_j=str2double(get(handles.incr_j,'String'));
2412        num_i_ref=first_i:incr_i:last_i;
2413        num_j_ref=first_j:incr_j:last_j;
2414        if isequal(mode,'displacement')
2415            num_i1=num_i_ref;
2416            num_i2=num_i_ref;
2417            num_j1=num_j_ref;
2418            num_j2=num_j_ref;
2419        elseif isequal(mode,'pair j1-j2')
2420            num_i1=num_i_ref;
2421            num_i2=num_i1;
2422            num_j1=ref.num_a;
2423            num_j2=ref.num_b;
2424        elseif isequal(mode,'series(Di)')
2425            delta1=floor((ref.num2-ref.num1)/2);
2426            delta2=ceil((ref.num2-ref.num1)/2);
2427            num_i1=num_i_ref-delta1*ones(size(num_i_ref));
2428            num_i2=num_i_ref+delta2*ones(size(num_i_ref));
2429            num_j1=ref.num_a*ones(size(num_i1));
2430            num_j2=num_j1;
2431        elseif isequal(mode,'series(Dj)')
2432            delta1=floor((ref.num_b-ref.num_a)/2);
2433            delta2=ceil((ref.num_b-ref.num_a)/2);
2434            num_i1=ref.num1*ones(size(num_i_ref));
2435            num_i2=num_i1;
2436            num_j1=num_j_ref-delta1*ones(size(num_j_ref));
2437            num_j2=num_j_ref+delta2*ones(size(num_j_ref));
2438        end
2439        for ifile=1:nbfield
2440            for j=1:nbslice
2441                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);%
2442                file_ref_fix2(ifile,j)={file_ref};
2443                if ~exist(file_ref,'file')
2444                    msgbox_uvmat('ERROR',['reference file ' file_ref ' not found for fix2'])
2445                    filecell={};
2446                    return
2447                end
2448            end
2449        end
2450    end
2451end
2452
2453%check dir
2454subdir_civ1=get(handles.subdir_civ1,'String');%subdirectory subdir_civ1 for the netcdf output data
2455subdir_civ2=get(handles.subdir_civ2,'String');
2456if isequal(subdir_civ1,''),subdir_civ1='CIV'; end% put default subdir
2457if isequal(subdir_civ2,''),subdir_civ2=subdir_civ1; end% put default subdir
2458currentdir=pwd;%store the current working directory
2459[Path_ima,Name]=fileparts(filebase);%Path of the image files (.civ)
2460if ~exist(Path_ima,'dir')
2461    msgbox_uvmat('ERROR',['path to images ' Path_ima ' not found'])
2462    filecell={};
2463    return
2464end
2465[xx,message]=fileattrib(Path_ima);
2466if ~isempty(message) && ~isequal(message.UserWrite,1)
2467    msgbox_uvmat('ERROR',['No writting access to ' Path_ima])
2468    filecell={};
2469    cd(currentdir);
2470    return
2471end
2472
2473%check the existence of the netcdf and image files involved
2474% %%%%%%%%%%%%  case CIV1 activated   %%%%%%%%%%%%%
2475if box_test(1)==1;
2476    detect=1;
2477    vers=0;
2478    subdir_civ1_new=subdir_civ1;
2479    while detect==1 %create a new subdir if the netcdf files already exist
2480        for ifile=1:nbfield
2481            for j=1:nbslice
2482                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);
2483                detect=exist(filename,'file')==2;
2484                if detect% if a netcdf file already exists
2485                    indstr=regexp(subdir_civ1_new,'\D');
2486                    if indstr(end)<length(subdir_civ1_new) %subdir_civ1 ends by a number
2487                        vers=str2double(subdir_civ1_new(indstr(end)+1:end))+1;
2488                        subdir_civ1_new=[subdir_civ1_new(1:indstr(end)) num2str(vers)];
2489                    else
2490                        vers=vers+1;
2491                        subdir_civ1_new=[subdir_civ1_new(1:indstr(end)) '_' num2str(vers)];       
2492                    end
2493                    subdir_civ2=subdir_civ1_new;
2494                    break
2495                end
2496                filecell.nc.civ1(ifile,j)={filename};
2497            end
2498            if detect% if a netcdf file already exists
2499                break
2500            end
2501        end
2502 
2503        %create the new subdir_civ1
2504        if ~exist(fullfile(Path_ima,subdir_civ1_new),'dir')
2505            cd(Path_ima);         
2506            [xx,msg1]=mkdir(subdir_civ1_new);
2507
2508            if ~strcmp(msg1,'')
2509                msgbox_uvmat('ERROR',['cannot create ' subdir_civ1_new ': ' msg1])%error message for directory creation
2510                filecell={};
2511                return
2512            elseif isunix         
2513                [xx,msg2] = fileattrib(subdir_civ1_new,'+w','g'); %yield writing access (+w) to user group (g)
2514                if ~strcmp(msg2,'')
2515                    msgbox_uvmat('ERROR',['pb of permission for  ' subdir_civ1_new ': ' msg2])%error message for directory creation
2516                    filecell={};
2517                    return
2518                end
2519            end
2520            cd(currentdir);
2521        end
2522        if strcmp(compare,'stereo PIV')&&(strcmp(mode,'pair j1-j2')||strcmp(mode,'series(Dj)')||strcmp(mode,'series(Di)'))%check second nc series
2523            for ifile=1:nbfield
2524                for j=1:nbslice
2525                    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);%
2526                    detect=exist(filename,'file')==2;
2527                    if detect% if a netcdf file already exists
2528                       indstr=regexp(subdir_civ1_new,'\D');
2529                       if indstr(end)<length(subdir_civ1_new) %subdir_civ1 ends by a number
2530                           vers=str2double(subdir_civ1_new(indstr(end)+1:end))+1;
2531                           subdir_civ1_new=[subdir_civ1_new(1:indstr(end)) num2str(vers)];
2532                       else
2533                           vers=vers+1;
2534                           subdir_civ1_new=[subdir_civ1_new '_' num2str(vers)];
2535                       end
2536                       subdir_civ2=subdir_civ1;
2537                       break
2538                    end
2539                    filecell.ncA.civ1(ifile,j)={filename};
2540                end
2541                if detect% if a netcdf file already exists
2542                    break
2543                end
2544            end
2545            %create the new subdir_civ1
2546            if exist(fullfile(Path_ima,subdir_civ1_new),'dir')
2547                   cd(Path_ima);         
2548                [xx,msg1]=mkdir(subdir_civ1_new);
2549                            cd(currentdir);
2550                if ~strcmp(msg1,'')
2551                    msgbox_uvmat('ERROR',['cannot create ' subdir_civ1_new ': ' msg1])
2552                    cd(currentdir)
2553                    filecell={};
2554                    return
2555                else
2556                    [xx,msg2] = fileattrib(subdir_civ1_new,'+w','g'); %yield writing access (+w) to user group (g)
2557                    if ~strcmp(msg2,'')
2558                        msgbox_uvmat('ERROR',['pb of permission for ' subdir_civ1_new ': ' msg2])%error message for directory creation
2559                        cd(currentdir)
2560                        filecell={};
2561                        return
2562                    end
2563                end
2564            end
2565        end
2566    end
2567    subdir_civ1=subdir_civ1_new;
2568    % get image names
2569    for ifile=1:nbfield
2570        for j=1:nbslice
2571            filename=name_generator(filebase_ima1, num1_civ1(ifile),num_a_civ1(j),ext_ima,nom_type_ima1);
2572            idetect(j)=exist(filename,'file')==2;
2573            filecell.ima1.civ1(ifile,j)={filename}; %first image
2574            filename=name_generator(filebase_ima2, num2_civ1(ifile),num_b_civ1(j),ext_ima,nom_type_ima2);
2575            idetect_1(j)=exist(filename,'file')==2;
2576            filecell.ima2.civ1(ifile,j)={filename};%second image
2577        end
2578        [idetectmin,indexj]=min(idetect);
2579        if idetectmin==0,
2580            msgbox_uvmat('ERROR',[filecell.ima1.civ1{ifile,indexj} ' not found'])
2581            filecell={};
2582            cd(currentdir)
2583            return
2584        end
2585        [idetectmin,indexj]=min(idetect_1);
2586        if idetectmin==0,
2587            msgbox_uvmat('ERROR',[filecell.ima2.civ1{ifile,indexj} ' not found'])
2588            filecell={};
2589            cd(currentdir)
2590            return
2591        end
2592    end
2593    if strcmp(compare,'stereo PIV') && (strcmp(mode,'pair j1-j2') || strcmp(mode,'series(Dj)') || strcmp(mode,'series(Di)'))
2594        for ifile=1:nbfield
2595            for j=1:nbslice
2596                filename=name_generator(filebase_A, num1_civ1(ifile),num_a_civ1(j),ext_ima,nom_type_ima1);
2597                idetect(j)=exist(filename,'file')==2;
2598                filecell.imaA1.civ1(ifile,j)={filename} ;%first image
2599                filename=name_generator(filebase_A, num2_civ1(ifile),num_b_civ1(j),ext_ima,nom_type_ima2);
2600                idetect_1(j)=exist(filename,'file')==2;
2601                filecell.imaA2.civ1(ifile,j)={filename};%second image
2602            end
2603            [idetectmin,indexj]=min(idetect);
2604            if idetectmin==0,
2605                msgbox_uvmat('ERROR',[filecell.imaA1.civ1{ifile,indexj} ' not found'])
2606                filecell={};
2607                cd(currentdir)
2608                return
2609            end
2610            [idetectmin,indexj]=min(idetect_1);
2611            if idetectmin==0,
2612                msgbox_uvmat('ERROR',[filecell.imaA2.civ1{ifile,indexj} ' not found'])
2613                filecell={};
2614                cd(currentdir)
2615                return
2616            end
2617        end
2618    end
2619   
2620    %%%%%%%%%%%%%  fix1 or patch1 activated but no civ1   %%%%%%%%%%%%%
2621elseif (box_test(2)==1 || box_test(3)==1);
2622    for ifile=1:nbfield
2623        for j=1:nbslice
2624            filename=name_generator(filebase_nc,num1_civ1(ifile),num_a_civ1(j),'.nc',...
2625                nom_type_nc,1,num2_civ1(ifile),num_b_civ1(j),subdir_civ1);%
2626            detect=exist(filename,'file')==2;
2627            if detect==0
2628                msgbox_uvmat('ERROR',[filename ' not found'])
2629                filecell={};
2630                cd(currentdir)
2631                return
2632            end
2633            filecell.nc.civ1(ifile,j)={filename};
2634        end
2635    end
2636    if strcmp(compare,'stereo PIV')
2637        for ifile=1:nbfield
2638            for j=1:nbslice
2639                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);%
2640                filecell.ncA.civ1(ifile,j)={filename};
2641                if ~exist(filename,'file')
2642                    msgbox_uvmat('ERROR',['input file ' filename ' not found'])
2643                    set(handles.RUN, 'Enable','On')
2644                    set(handles.RUN,'BackgroundColor',[1 0 0])
2645                    filecell={};
2646                    cd(currentdir)
2647                    return
2648                end
2649            end
2650        end
2651    end
2652end
2653
2654%%%%%%%%%%%%%  if civ2 performed with pairs different than civ1  %%%%%%%%%%%%%
2655testdiff=0;
2656if (box_test(4)==1)&&...
2657        ((get(handles.list_pair_civ1,'Value')~=get(handles.list_pair_civ2,'Value'))||~strcmp(subdir_civ2,subdir_civ1))
2658    testdiff=1;
2659    detect=1;
2660    vers=0;
2661    subdir_civ2_new=subdir_civ2;
2662    while detect==1 %create a new subdir if the netcdf files already exist
2663        for ifile=1:nbfield
2664            for j=1:nbslice
2665                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);%
2666                detect=exist(filename,'file')==2;
2667                if detect% if a netcdf file already exists
2668                    indstr=regexp(subdir_civ2,'\D');
2669                    if indstr(end)<length(subdir_civ2) %subdir_civ1 ends by a number
2670                        vers=str2double(subdir_civ2(indstr(end)+1:end))+1;
2671                        subdir_civ2_new=[subdir_civ2(1:indstr(end)) num2str(vers)];
2672                    else
2673                        vers=vers+1;
2674                        subdir_civ2_new=[subdir_civ1 '_' num2str(vers)];
2675                    end
2676                    break
2677                end
2678                filecell.nc.civ2(ifile,j)={filename};
2679            end
2680            if detect% if a netcdf file already exists
2681                break
2682            end
2683        end
2684        %create the new subdir_civ2_new
2685        if ~exist(fullfile(Path_ima,subdir_civ2_new),'dir')
2686            [xx,m2]=mkdir(fullfile(Path_ima,subdir_civ2_new));
2687            [xx,msg2] = fileattrib(subdir_civ2_new,'+w','g'); %yield writing access (+w) to user group (g)
2688            if ~isequal(m2,'')
2689                msgbox_uvmat('ERROR',['cannot create ' subdir_civ2_new ': ' m2])
2690                filecell={};
2691                cd(currentdir)
2692                return
2693            end
2694        end
2695        if strcmp(compare,'stereo PIV')%check second nc series
2696            for ifile=1:nbfield
2697                for j=1:nbslice
2698                    filename=name_generator(filebase_A,num1_civ2(ifile),num_a_civ2(j),'.nc',...
2699                        nom_type_nc,1,num2_civ2(ifile),num_b_civ1(j),subdir_civ2_new);%
2700                    detect=exist(filename,'file')==2;
2701                    if detect% if a netcdf file already exists
2702                        indstr=regexp(subdir_civ2,'\D');
2703                        if indstr(end)<length(subdir_civ2) %subdir_civ1 ends by a number
2704                           vers=str2double(subdir_civ2(indstr(end)+1:end))+1;
2705                           subdir_civ2_new=[subdir_civ2(1:indstr(end)) num2str(vers)];
2706                        else
2707                           vers=vers+1;
2708                           subdir_civ2_new=[subdir_civ1 '_' num2str(vers)];
2709                        end
2710                        break
2711                    end
2712                    filecell.ncA.civ2(ifile,j)={filename};
2713                end
2714                if detect% if a netcdf file already exists
2715                    break
2716                end
2717            end
2718            subdir_civ2=subdir_civ2_new;
2719            %create the new subdir_civ1
2720            if ~exist(fullfile(Path_ima,subdir_civ2_new),'dir')
2721                [xx,m2]=mkdir(subdir_civ2_new);
2722                 [xx,msg2] = fileattrib(subdir_civ2_new,'+w','g'); %yield writing access (+w) to user group (g)
2723                if ~isequal(m2,'')
2724                    msgbox_uvmat('ERROR', ['cannot create ' subdir_civ2_new ': ' m2])%error message for directory creation
2725                    cd(currentdir)
2726                    filecell={};
2727                    return
2728                end
2729            end
2730        end
2731    end
2732    subdir_civ2=subdir_civ2_new;
2733end
2734cd(currentdir);%come back to the current working directory
2735
2736%%%%%%%%%%%%%  if civ2 results are obtained or used  %%%%%%%%%%%%%
2737if box_test(4)==1 || box_test(5)==1 || box_test(6)==1 %civ2
2738    %check source netcdf file of civ1 estimates
2739    if box_test(1)==0; %no civ1 performed
2740        for ifile=1:nbfield
2741            for j=1:nbslice
2742                filename=name_generator(filebase_nc,num1_civ1(ifile),num_a_civ1(j),'.nc',...
2743                    nom_type_nc,1,num2_civ1(ifile),num_b_civ1(j),subdir_civ1);%
2744                filecell.nc.civ1(ifile,j)={filename};% name of the civ1 file
2745                if ~exist(filename,'file')
2746                    msgbox_uvmat('ERROR',['input file ' filename ' not found'])
2747                    filecell={};
2748                    return
2749                end
2750                if ~testdiff % civ2 or patch2 are written in the same file as civ1
2751                    if box_test(4)==0 ; %check the existence of civ2 if it is not calculated
2752                        Data=nc2struct(filename,'ListGlobalAttribute','CivStage','civ2');
2753                        if ~isempty(Data.CivStage) && Data.CivStage<4 %test for civ files
2754                            msgbox_uvmat('ERROR',['no civ2 data in ' filename])
2755                            filecell=[];
2756                            return
2757                        elseif isempty(Data.civ2)||isequal(Data.civ2,0)
2758                            msgbox_uvmat('ERROR',['no civ2 data in ' filename])
2759                            filecell=[];
2760                            return
2761                        end
2762                    elseif box_test(3)==0; %check the existence of patch if it is not calculated
2763                        Data=nc2struct(filename,'ListGlobalAttribute','CivStage','patch')
2764                        if ~isempty(Data.CivStage)
2765                            if Data.CivStage<3 %test for civ files
2766                                msgbox_uvmat('ERROR',['no patch data in ' filename])
2767                                filecell=[];
2768                                return
2769                            end
2770                        elseif isempty(Data.patch)||isequal(Data.patch,0)
2771                            msgbox_uvmat('ERROR',['no patch data in ' filename])
2772                            filecell=[];
2773                            return
2774                        end
2775                    end
2776                end
2777            end
2778        end
2779        if strcmp(compare,'stereo PIV')
2780            for ifile=1:nbfield
2781                for j=1:nbslice
2782                    filename=name_generator(filebase_A,num1_civ2(ifile),num_a_civ2(j),'.nc',...
2783                        nom_type_nc,1,num2_civ2(ifile),num_b_civ2(j),subdir_civ2);%
2784                    filecell.ncA.civ2(ifile,j)={filename};
2785                    if ~exist(filename,'file')
2786                        msgbox_uvmat('ERROR',['input file ' filename ' not found'])
2787                        set(handles.RUN, 'Enable','On')
2788                        set(handles.RUN,'BackgroundColor',[1 0 0])
2789                        return
2790                    end
2791                end
2792            end
2793        end
2794    end
2795   
2796    detect=1;
2797    %     while detect==1%creates a new subdir if the netcdf files already contain civ2 data
2798    for ifile=1:nbfield
2799        for j=1:nbslice
2800            filename=name_generator(filebase_nc,num1_civ2(ifile),num_a_civ2(j),'.nc',...
2801                nom_type_nc,1,num2_civ2(ifile),num_b_civ2(j),subdir_civ2);
2802            detect=exist(filename,'file')==2;
2803            filecell.nc.civ2(ifile,j)={filename};
2804        end
2805    end
2806    %get first image names for civ2
2807    if box_test(1)==1 & isequal(num1_civ1,num1_civ2) & isequal(num_a_civ1,num_a_civ2)
2808        filecell.ima1.civ2=filecell.ima1.civ1;
2809    elseif box_test(4)==1
2810        for ifile=1:nbfield
2811            for j=1:nbslice
2812                filename=name_generator(filebase_ima1, num1_civ2(ifile),num_a_civ2(j),ext_ima,nom_type_ima1);
2813                idetect_2(j)=exist(filename,'file')==2;
2814                filecell.ima1.civ2(ifile,j)={filename};%first image
2815            end
2816            [idetectmin,indexj]=min(idetect_2);
2817            if idetectmin==0,
2818                msgbox_uvmat('ERROR',['input image ' filecell.ima1.civ2{ifile,indexj} ' not found'])
2819                filecell=[];
2820                return
2821            end
2822        end
2823    end
2824   
2825    %get second image names for civ2
2826    if box_test(1)==1 & isequal(num2_civ1,num2_civ2) & isequal(num_b_civ1,num_b_civ2)
2827        filecell.ima2.civ2=filecell.ima2.civ1;
2828    elseif box_test(4)==1
2829        for ifile=1:nbfield
2830            for j=1:nbslice
2831                filename=name_generator(filebase_ima2, num2_civ2(ifile),num_b_civ2(j),ext_ima,nom_type_ima2);
2832                idetect_3(j)=exist(filename,'file')==2;
2833                filecell.ima2.civ2(ifile,j)={filename};%first image
2834            end
2835            [idetectmin,indexj]=min(idetect_3);
2836            if idetectmin==0,
2837                msgbox_uvmat('ERROR',['input image ' filecell.ima2.civ2{ifile,indexj} ' not found'])
2838                filecell=[];
2839                return
2840            end
2841        end
2842    end
2843end
2844if (box_test(5)==1 || box_test(6)==1 ) && box_test(4)==0  % need to read an existing netcdf civ2 file
2845    if ~testdiff
2846        filecell.nc.civ2=filecell.nc.civ1;% file already checked
2847    else     % check the civ2 files
2848        for ifile=1:nbfield
2849            for j=1:nbslice
2850                filename=name_generator(filebase_nc,num1_civ2(ifile),num_a_civ2(j),'.nc',...
2851                    nom_type_nc,1,num2_civ2(ifile),num_b_civ2(j),subdir_civ2);%
2852                filecell.nc.civ2(ifile,j)={filename};
2853                if ~exist(filename,'file')
2854                    msgbox_uvmat('ERROR',['input file ' filename ' not found'])
2855                    filecell=[];
2856                    return
2857                else
2858                    Data=nc2struct(filename,'ListGlobalAttribute','CivStage','civ2');
2859                    if ~isempty(Data.CivStage) && Data.CivStage<4 %test for civ files
2860                            msgbox_uvmat('ERROR',['no civ2 data in ' filename])
2861                            filecell=[];
2862                            return
2863                    elseif isempty(Data.civ2)||isequal(Data.civ2,0)
2864                        msgbox_uvmat('ERROR',['no civ2 data in ' filename])
2865                        filecell=[];
2866                        return
2867                    end
2868                end
2869            end
2870        end
2871    end
2872end
2873
2874%%%%%%%%%%%%%  if stereo fields are calculated by PATCH %%%%%%%%%%%%%
2875if strcmp(compare,'stereo PIV')
2876    if  box_test(3)==1 && isequal(get(handles.test_stereo1,'Value'),1)
2877        for ifile=1:nbfield
2878            for j=1:nbslice
2879                filename=name_generator(filebase_AB,num1_civ1(ifile),num_a_civ1(j),'.nc',...
2880                    nom_type_nc,1,num2_civ1(ifile),num_b_civ1(j),subdir_civ1);%
2881                filecell.st(ifile,j)={filename};
2882            end
2883        end
2884    end
2885    if  box_test(6)==1 && isequal(get(handles.test_stereo2,'Value'),1)
2886        for ifile=1:nbfield
2887            for j=1:nbslice
2888                filename=name_generator(filebase_AB,num1_civ2(ifile),num_a_civ2(j),'.nc',...
2889                    nom_type_nc,1,num2_civ2(ifile),num_b_civ2(j),subdir_civ2);%
2890                filecell.st(ifile,j)={filename};
2891            end
2892        end
2893    end
2894end
2895set(handles.subdir_civ1,'String',subdir_civ1);%update the edit box
2896set(handles.subdir_civ2,'String',subdir_civ2);%update the edit box
2897browse.nom_type_nc=nom_type_nc;
2898set(handles.browse_root,'UserData',browse); %update the nomenclature type for uvmat
2899
2900
2901%COPY IMAGES TO THE FORMAT .png IF NEEDED
2902if isequal(nom_type_ima1,'*')%case of movie files
2903    nom_type_imanew1='_i';
2904else
2905    nom_type_imanew1=nom_type_ima1;
2906end
2907if isequal(nom_type_ima2,'*')%case of movie files
2908    nom_type_imanew2='_i';
2909else
2910    nom_type_imanew2=nom_type_ima2;
2911end
2912if ~isequal(ext_ima,'.png')
2913    %%type of image file
2914    type_ima1='none';%default
2915    movieobject1=[];%default
2916    if strcmpi(ext_ima,'.avi')
2917        hhh=which('mmreader');
2918        if ~isequal(hhh,'')&& mmreader.isPlatformSupported()% if the mmreader function is found (recent version of matlab)
2919            type_ima1='movie';
2920            movieobject1=mmreader([filebase_ima2 ext_ima]);
2921        else
2922            type_ima1='avi';
2923        end
2924    elseif ischar(ext_ima) && ~isempty(ext_ima(2:end))
2925        form=imformats(ext_ima(2:end));
2926        if ~isempty(form)% if the extension corresponds to an image format recognized by Matlab
2927            if isequal(nom_type_ima1,'*');
2928                type_ima1='multimage';%image series in a single image file
2929            else
2930                type_ima1='image';
2931            end
2932        end
2933    end
2934    type_ima2='none';%default
2935    movieobject2=[];
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_ima2='movie';
2940            movieobject2=mmreader([filebase_ima2 ext_ima]);
2941        else
2942            type_ima2='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_ima2='multimage';%image series in a single image file
2949            else
2950                type_ima2='image';
2951            end
2952        end
2953    end
2954    %npxy=get(handles.ImaExt,'UserData');
2955    % %     if numel(npxy)<2
2956    %
2957    %         filename=name_generator(filebase_ima1,num1_civ1(1),num_a_civ1(1),ImaExt,nom_type_ima1);
2958    %         A=imread(filename);
2959    %         npxy=size(A);
2960    % %     end
2961    %     npy=npxy(1);
2962    %     npx=npxy(2);
2963    if box_test(1)==1 %if civ1 is performed
2964        h = waitbar(0,'copy images to the .png format for civ1');% display a wait bar
2965        for ifile=1:nbfield
2966            waitbar(ifile/nbfield);
2967            for j=1:nbslice
2968                filename=name_generator(filebase_ima1,num1_civ1(ifile),num_a_civ1(j),'.png',nom_type_imanew1);
2969                if ~exist(filename,'file')
2970                    A=read_image(filecell.ima1.civ1{ifile,j},type_ima1,num1_civ1(ifile),movieobject1);
2971                    imwrite(A,filename,'BitDepth',16);
2972                end
2973                filecell.ima1.civ1(ifile,j)={filename};
2974                filename=name_generator(filebase_ima2, num2_civ1(ifile),num_b_civ1(j),'.png',nom_type_imanew2);
2975                if ~exist(filename,'file')
2976                    A=read_image(filecell.ima2.civ1{ifile,j},type_ima2,num2_civ1(ifile),movieobject2);
2977                    imwrite(A,filename,'BitDepth',16);
2978                end
2979                filecell.ima2.civ1(ifile,j)={filename};
2980            end
2981        end
2982        close(h)
2983    end
2984    if box_test(4)==1 %if civ2 is performed
2985        h = waitbar(0,'copy images to the .png format for civ2');% display a wait bar
2986        for ifile=1:nbfield
2987            waitbar(ifile/nbfield);
2988            for j=1:nbslice
2989                filename=name_generator(filebase_ima1,num1_civ2(ifile),num_a_civ2(j),'.png',nom_type_imanew1);
2990                if ~exist(filename,'file')
2991                    A=read_image(cell2mat(filecell.ima1.civ2(ifile,j)),type_ima2,num1_civ2(ifile));
2992                    imwrite(A,filename,'BitDepth',16);
2993                end
2994                filecell.ima1.civ2(ifile,j)={filename};
2995                filename=name_generator(filebase_ima2, num2_civ2(ifile),num_b_civ2(j),'.png',nom_type_imanew2);
2996                if ~exist(filename,'file')
2997                    A=read_image(cell2mat(filecell.ima2.civ2(ifile,j)),type_ima2,num2_civ2(ifile));
2998                    imwrite(A,filename,'BitDepth',16);
2999                end
3000                filecell.ima2.civ2(ifile,j)={filename};
3001            end
3002        end
3003        close(h);
3004    end
3005end
3006
3007%------------------------------------------------------------------------
3008% --- determine the list of index pairs of processing file
3009function [num1_civ1,num2_civ1,num_a_civ1,num_b_civ1,num1_civ2,num2_civ2,num_a_civ2,num_b_civ2]=...
3010    find_pair_indices(handles,ref_i,ref_j,mode)
3011%------------------------------------------------------------------------
3012
3013list_civ1=get(handles.list_pair_civ1,'String');
3014index_civ1=get(handles.list_pair_civ1,'Value');
3015str_civ1=list_civ1{index_civ1};%string defining the image pairs for civ1
3016if isempty(str_civ1)||isequal(str_civ1,'')
3017    msgbox_uvmat('ERROR','no image pair selected for civ1')
3018    return
3019end
3020list_civ2=get(handles.list_pair_civ2,'String');
3021index_civ2=get(handles.list_pair_civ2,'Value');
3022if index_civ2>length(list_civ2)
3023    list_civ2=list_civ1;
3024    index_civ2=index_civ1;
3025end
3026str_civ2=list_civ2{index_civ2};%string defining the image pairs for civ2
3027
3028if isequal (mode,'series(Di)')
3029    lastfield=str2double(get(handles.nb_field,'String'));
3030    num1_civ1=ref_i-floor(index_civ1/2)*ones(size(ref_i));% set of first image numbers
3031    num2_civ1=ref_i+ceil(index_civ1/2)*ones(size(ref_i));
3032    num_a_civ1=ref_j;
3033    num_b_civ1=ref_j;
3034    num1_civ2=ref_i-floor(index_civ2/2)*ones(size(ref_i));
3035    num2_civ2=ref_i+ceil(index_civ2/2)*ones(size(ref_i));
3036    num_a_civ2=ref_j;
3037    num_b_civ2=ref_j;   
3038   
3039    % adjust the first and last field number
3040    lastfield=str2double(get(handles.nb_field,'String'));
3041    if isnan(lastfield)
3042        indsel=find((num1_civ1 >= 1)&(num1_civ2 >= 1));
3043    else
3044        indsel=find((num2_civ1 <= lastfield)&(num2_civ2 <= lastfield)&(num1_civ1 >= 1)&(num1_civ2 >= 1));
3045    end
3046    if length(indsel)>=1
3047        firstind=indsel(1);
3048        lastind=indsel(end);
3049        set(handles.first_i,'String',num2str(ref_i(firstind)))%update the display of first and last fields
3050        set(handles.last_i,'String',num2str(ref_i(lastind)))
3051        ref_i=ref_i(indsel);
3052        num1_civ1=num1_civ1(indsel);
3053        num1_civ2=num1_civ2(indsel);
3054        num2_civ1=num2_civ1(indsel);
3055        num2_civ2=num2_civ2(indsel);
3056    end
3057elseif isequal (mode,'series(Dj)')
3058    lastfield_j=str2double(get(handles.nb_field2,'String'));
3059    num1_civ1=ref_i;% set of first image numbers
3060    num2_civ1=ref_i;
3061    num_a_civ1=ref_j-floor(index_civ1/2)*ones(size(ref_j));
3062    num_b_civ1=ref_j+ceil(index_civ1/2)*ones(size(ref_j));
3063    num1_civ2=ref_i;
3064    num2_civ2=ref_i;
3065    num_a_civ2=ref_j-floor(index_civ2/2)*ones(size(ref_j));
3066    num_b_civ2=ref_j+ceil(index_civ2/2)*ones(size(ref_j));
3067    % adjust the first and last field number
3068    if isnan(lastfield_j)
3069        indsel=find((num_a_civ1 >= 1)&(num_a_civ2 >= 1));
3070    else
3071        indsel=find((num_b_civ1 <= lastfield_j)&(num_b_civ2 <= lastfield_j)&(num_a_civ1 >= 1)&(num_a_civ2 >= 1));
3072    end
3073    if length(indsel)>=1
3074        firstind=indsel(1);
3075        lastind=indsel(end);
3076        set(handles.first_j,'String',num2str(ref_j(firstind)))%update the display of first and last fields
3077        set(handles.last_j,'String',num2str(ref_j(lastind)))
3078        ref_j=ref_j(indsel);
3079        num_a_civ1=num_a_civ1(indsel);
3080        num_b_civ1=num_b_civ1(indsel);
3081        num_a_civ2=num_a_civ2(indsel);
3082        num_b_civ2=num_b_civ2(indsel);
3083    end
3084elseif isequal(mode,'pair j1-j2') %case of bursts (png_old or png_2D)
3085    displ_num=get(handles.list_pair_civ1,'UserData');
3086    num1_civ1=ref_i;
3087    num2_civ1=ref_i;
3088    num_a_civ1=displ_num(1,index_civ1);
3089    num_b_civ1=displ_num(2,index_civ1);
3090    num1_civ2=ref_i;
3091    num2_civ2=ref_i;
3092    num_a_civ2=displ_num(1,index_civ2);
3093    num_b_civ2=displ_num(2,index_civ2);
3094elseif isequal(mode,'displacement')
3095    num1_civ1=ref_i;
3096    num2_civ1=ref_i;
3097    num_a_civ1=ref_j;
3098    num_b_civ1=ref_j;
3099    num1_civ2=ref_i;
3100    num2_civ2=ref_i;
3101    num_a_civ2=ref_j;
3102    num_b_civ2=ref_j;
3103end
3104
3105
3106%------------------------------------------------------------------------
3107% --- PATCH
3108function cmd_PATCH=PATCH_CMD(filename_nc,nx_patch,ny_patch,rho_patch,subdomain_patch,thresh_value,test_interp,PatchBin)
3109%------------------------------------------------------------------------
3110namelog=[filename_nc(1:end-3) '_patch.log'];
3111if test_interp==0
3112    if isunix
3113    cmd_PATCH=[PatchBin ' -f ' filename_nc ' -m ' nx_patch  ' -n ' ny_patch ' -ro ' rho_patch ' -nopt ' subdomain_patch ...
3114        '  > ' namelog ' 2>&1']; % redirect standard output to the log file
3115    else
3116      cmd_PATCH=['"' PatchBin '" -f "' filename_nc '" -m ' nx_patch  ' -n ' ny_patch ' -ro ' rho_patch ' -nopt ' subdomain_patch ...
3117        '  > "' namelog '" 2>&1']; % redirect standard output to the log file
3118    end
3119else %nouveau programme patch
3120    cmd_PATCH=[PatchBin ' -f ' filename_nc ' -m ' nx_patch  ' -n ' ny_patch ' -ro ' rho_patch ...
3121        ' -max ' thresh_value ' -nopt ' subdomain_patch  '  > ' namelog ' 2>&1']; % redirect standard output to the log file
3122end
3123cmd_PATCH=regexprep(cmd_PATCH,'\\','\\\\');
3124%------------------------------------------------------------------------
3125% --- STEREO Interp
3126function cmd=RUN_STINTERP(stinterpBin,filename_A_nc,filename_B_nc,filename_nc,nx_patch,ny_patch,rho_patch,subdomain_patch,thresh_value,xmlA,xmlB)
3127%------------------------------------------------------------------------
3128namelog=[filename_nc(1:end-3) '_stinterp.log'];
3129cmd=[stinterpBin ' -f1 ' filename_A_nc  ' -f2 ' filename_B_nc ' -f  ' filename_nc ...
3130    ' -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
3131
3132%------------------------------------------------------------------------
3133% --- Executes on button press in CIV1.
3134function CIV1_Callback(hObject, eventdata, handles)
3135%------------------------------------------------------------------------
3136val=get(handles.CIV1,'Value');
3137if isequal(val,1)
3138    enable_civ1(handles,'on')
3139    enable_pair1(handles,'on')
3140else
3141    enable_civ1(handles,'off')
3142end
3143find_netcpair_civ1(hObject, eventdata, handles);
3144
3145%------------------------------------------------------------------------
3146% --- Executes on button press in FIX1.
3147function FIX1_Callback(hObject, eventdata, handles)
3148%------------------------------------------------------------------------
3149enable_fix1(handles,get(handles.FIX1,'Value'))
3150
3151%------------------------------------------------------------------------
3152% --- Executes on button press in PATCH1.
3153function PATCH1_Callback(hObject, eventdata, handles)
3154%------------------------------------------------------------------------
3155if get(handles.PATCH1,'Value')==1
3156    enable_patch1(handles)
3157else
3158    desable_patch1(handles)
3159end
3160
3161%------------------------------------------------------------------------
3162% --- Executes on button press in CIV2.
3163function CIV2_Callback(hObject, eventdata, handles)
3164%------------------------------------------------------------------------
3165state=get(handles.CIV2,'Value');
3166enable_civ2(handles,state)
3167if state
3168    find_netcpair_civ2(hObject, eventdata, handles)
3169    enable_pair1(handles,'on')
3170end
3171
3172%------------------------------------------------------------------------
3173% --- Executes on button press in FIX2.
3174function FIX2_Callback(hObject, eventdata, handles)
3175%------------------------------------------------------------------------
3176if get(handles.FIX2,'Value')==1
3177    enable_fix2(handles)
3178    if get(handles.CIV2,'Value')==0
3179        find_netcpair_civ2(hObject, eventdata, handles) % select the available netcdf files
3180    end
3181else
3182    desable_fix2(handles)
3183end
3184
3185%------------------------------------------------------------------------
3186% --- Executes on button press in PATCH2.
3187function PATCH2_Callback(hObject, eventdata, handles)
3188%------------------------------------------------------------------------
3189if get(handles.PATCH2,'Value')==1
3190    enable_patch2(handles)
3191    if get(handles.CIV2,'Value')==0
3192        find_netcpair_civ2(hObject, eventdata, handles) % select the available netcdf files
3193    end
3194else
3195    desable_patch2(handles)
3196end
3197
3198%------------------------------------------------------------------------
3199function first_i_Callback(hObject, eventdata, handles)
3200%------------------------------------------------------------------------
3201% last_i_Callback(hObject, eventdata, handles)
3202first_i=str2double(get(handles.first_i,'String'));
3203% last_i=str2num(get(handles.last_i,'String'));
3204% ref_i=ceil((first_i+last_i)/2);
3205set(handles.ref_i,'String', num2str(first_i))% reference index for pair dt = first index
3206set(handles.ref_i_civ2,'String', num2str(first_i))% reference index for pair dt = first index
3207ref_i_Callback(hObject, eventdata, handles)%refresh dispaly of dt for pairs (in case of non constant dt)
3208
3209%------------------------------------------------------------------------
3210function first_j_Callback(hObject, eventdata, handles)
3211%------------------------------------------------------------------------
3212first_j=str2num(get(handles.first_j,'String'));
3213set(handles.ref_j,'String', num2str(first_j))% reference index for pair dt = first index
3214ref_j_Callback(hObject, eventdata, handles)%refresh dispaly of dt for pairs (in case of non constant dt)
3215
3216%------------------------------------------------------------------------
3217% --- Executes on button press in calcul_search: determine the search range isx,isy
3218function calcul_search_Callback(hObject, eventdata, handles)
3219%------------------------------------------------------------------------
3220%determine pair numbers
3221list_pair=get(handles.list_pair_civ1,'String');%get the menu of image pairs
3222index=get(handles.list_pair_civ1,'Value');
3223displ_num=get(handles.list_pair_civ1,'UserData');
3224time=get(handles.RootName,'UserData'); %get the set of times
3225pxcm_xy=get(handles.calcul_search,'UserData');
3226pxcmx=pxcm_xy(1);
3227pxcmy=pxcm_xy(2);
3228mode_list=get(handles.mode,'String');
3229mode_value=get(handles.mode,'Value');
3230mode=mode_list{mode_value};
3231if isequal (mode, 'series(Di)' )
3232    ref_i=str2double(get(handles.ref_i,'String'));
3233    num1=ref_i-floor(index/2);%  first image numbers
3234    num2=ref_i+ceil(index/2);
3235    num_a=1;
3236    num_b=1;
3237elseif isequal (mode, 'series(Dj)')
3238    num1=1;
3239    num2=1;
3240    ref_j=str2double(get(handles.ref_j,'String'));
3241    num_a=ref_j-floor(index/2);%  first image numbers
3242    num_b=ref_j+ceil(index/2);
3243elseif isequal(mode,'pair j1-j2') %case of bursts (png_old or png_2D)
3244    ref_i=str2double(get(handles.ref_i,'String'));
3245    num1=ref_i;
3246    num2=ref_i;
3247    num_a=displ_num(1,index);
3248    num_b=displ_num(2,index);
3249end
3250dt=time(num2,num_b)-time(num1,num_a);
3251ibx=str2double(get(handles.ibx,'String'));
3252iby=str2double(get(handles.iby,'String'));
3253umin=dt*pxcmx*str2double(get(handles.umin,'String'));
3254umax=dt*pxcmx*str2double(get(handles.umax,'String'));
3255vmin=dt*pxcmy*str2double(get(handles.vmin,'String'));
3256vmax=dt*pxcmy*str2double(get(handles.vmax,'String'));
3257shiftx=round((umin+umax)/2);
3258shifty=round((vmin+vmax)/2);
3259isx=(umax+2-shiftx)*2+ibx;
3260isx=2*ceil(isx/2)+1;
3261isy=(vmax+2-shifty)*2+iby;
3262isy=2*ceil(isy/2)+1;
3263set(handles.shiftx,'String',num2str(shiftx));
3264set(handles.shifty,'String',num2str(shifty));
3265set(handles.isx,'String',num2str(isx));
3266set(handles.isy,'String',num2str(isy));
3267
3268%------------------------------------------------------------------------
3269% --- Executes on carriage return on the subdir civ1 edit window
3270function subdir_civ1_Callback(hObject, eventdata, handles)
3271%------------------------------------------------------------------------
3272subdir=get(handles.subdir_civ1,'String');
3273set(handles.subdir_civ2,'String',subdir);
3274if get(handles.CIV1,'Value')==0
3275    find_netcpair_civ1(hObject, eventdata, handles); %update the list of available pairs from netcdf files in the new directory
3276end
3277
3278%------------------------------------------------------------------------
3279% --- Executes on carriage return on the subdir civ1 edit window
3280function subdir_civ2_Callback(hObject, eventdata, handles)
3281%------------------------------------------------------------------------
3282%update the list of available pairs from netcdf files in the new directory
3283if get(handles.CIV2,'Value')==0 & get(handles.CIV1,'Value')==0 & get(handles.FIX1,'Value')==0 & get(handles.PATCH1,'Value')==0
3284    find_netcpair_civ2(hObject, eventdata, handles);
3285end
3286
3287%------------------------------------------------------------------------
3288% --- Executes on button press in get_mask_civ1: select box for mask option
3289function get_mask_civ1_Callback(hObject, eventdata, handles)
3290%------------------------------------------------------------------------
3291maskval=get(handles.get_mask_civ1,'Value')
3292if isequal(maskval,0)
3293    set(handles.mask_civ1,'String','')
3294else
3295    mask_displ='no mask'; %default
3296    filebase=get(handles.RootName,'String');
3297    [ nbslice_mask, flag_mask]=get_mask(filebase,handles);
3298    if isequal(flag_mask,1)
3299        mask_displ=[num2str(nbslice_mask) 'mask'];
3300    elseif get(handles.compare,'Value')>1 & ~isequal(mask_displ,'no mask')% look for the second mask series
3301        common_path=fileparts(filebase);
3302        filebase_a=fullfile(common_path,get(handles.RootName_1,'String'));
3303        [nbslice_a, flag_mask_a]=get_mask(filebase_a,handles);
3304        if isequal(flag_mask_a,0) || ~isequal(nbslice_a,nbslice_mask)
3305            mask_displ='no mask';
3306        end
3307    end
3308    if isequal(mask_displ,'no mask')
3309        [FileName, PathName, filterindex] = uigetfile( ...
3310            {'*.png', ' (*.png)';
3311            '*.png',  '.png files '; ...
3312            '*.*', 'All Files (*.*)'}, ...
3313            'Pick a mask file *.png',filebase);
3314        mask_displ=fullfile(PathName,FileName);
3315        if ~exist(mask_displ,'file')
3316            mask_displ='no mask';
3317        end
3318    end
3319    if isequal(mask_displ,'no mask')
3320        set(handles.get_mask_civ1,'Value',0)
3321        set(handles.get_mask_fix1,'Value',0)
3322        set(handles.get_mask_civ2,'Value',0)
3323        set(handles.get_mask_fix2,'Value',0)
3324    else
3325        set(handles.get_mask_fix1,'Value',1)
3326        set(handles.get_mask_fix2,'Value',1)
3327    end
3328    set(handles.mask_civ1,'String',mask_displ)
3329    set(handles.mask_fix1,'String',mask_displ)
3330    set(handles.mask_civ2,'String',mask_displ)
3331    set(handles.mask_fix2,'String',mask_displ)
3332end
3333set(handles.get_mask_civ2,'Value',maskval)%update the civ2 mask with the same option as civ1
3334
3335%------------------------------------------------------------------------
3336% --- Executes on button press in get_mask_fix1.
3337function get_mask_fix1_Callback(hObject, eventdata, handles)
3338%------------------------------------------------------------------------
3339maskval=get(handles.get_mask_fix1,'Value');
3340if isequal(maskval,0)
3341    set(handles.mask_fix1,'String','')
3342else
3343    mask_displ='no mask'; %default
3344    filebase=get(handles.RootName,'String');
3345    [nbslice, flag_mask]=get_mask(filebase,handles);
3346    if isequal(flag_mask,1)
3347        mask_displ=[num2str(nbslice) 'mask'];
3348    elseif get(handles.compare,'Value')>1 & ~isequal(mask_displ,'no mask')% look for the second mask series
3349        filebase_a=get(handles.RootName_1,'String');
3350        [nbslice_a, flag_mask_a]=get_mask(filebase_a,handles);
3351        if isequal(flag_mask_a,0) || ~isequal(nbslice_a,nbslice)
3352            mask_displ='no mask';
3353        end
3354    end
3355    if isequal(mask_displ,'no mask')
3356        [FileName, PathName, filterindex] = uigetfile( ...
3357            {'*.png', ' (*.png)';
3358            '*.png',  '.png files '; ...
3359            '*.*', 'All Files (*.*)'}, ...
3360            'Pick a mask file *.png',filebase);
3361        mask_displ=fullfile(PathName,FileName);
3362        if ~exist(mask_displ,'file')
3363            mask_displ='no mask';
3364        end
3365    end
3366    if isequal(mask_displ,'no mask')
3367        set(handles.get_mask_fix1,'Value',0)
3368        set(handles.get_mask_civ2,'Value',0)
3369        set(handles.get_mask_fix2,'Value',0)
3370    else
3371        %set(handles.get_mask_civ2,'Value',1)
3372        set(handles.get_mask_fix2,'Value',1)
3373    end
3374    set(handles.mask_fix1,'String',mask_displ)
3375    set(handles.mask_civ2,'String',mask_displ)
3376    set(handles.mask_fix2,'String',mask_displ)
3377end
3378
3379%------------------------------------------------------------------------
3380% --- Executes on button press in get_mask_civ2: select box for mask option
3381function get_mask_civ2_Callback(hObject, eventdata, handles)
3382%------------------------------------------------------------------------
3383maskval=get(handles.get_mask_civ2,'Value');
3384if isequal(maskval,0)
3385    set(handles.mask_civ2,'String','')
3386else
3387    mask_displ='no mask'; %default
3388    filebase=get(handles.RootName,'String');
3389    [nbslice, flag_mask]=get_mask(filebase,handles);
3390    if isequal(flag_mask,1)
3391        mask_displ=[num2str(nbslice) 'mask'];
3392    elseif get(handles.compare,'Value')>1 & ~isequal(mask_displ,'no mask')% look for the second mask series
3393        filebase_a=get(handles.RootName_1,'String');
3394        [nbslice_a, flag_mask_a]=get_mask(filebase_a,handles);
3395        if isequal(flag_mask_a,0) || ~isequal(nbslice_a,nbslice)
3396            mask_displ='no mask';
3397        end
3398    end
3399    if isequal(mask_displ,'no mask')
3400        [FileName, PathName, filterindex] = uigetfile( ...
3401            {'*.png', ' (*.png)';
3402            '*.png',  '.png files '; ...
3403            '*.*', 'All Files (*.*)'}, ...
3404            'Pick a mask file *.png',filebase);
3405        mask_displ=fullfile(PathName,FileName);
3406        if ~exist(mask_displ,'file')
3407            mask_displ='no mask';
3408        end
3409    end
3410    if isequal(mask_displ,'no mask')
3411        set(handles.get_mask_civ2,'Value',0)
3412        set(handles.get_mask_fix2,'Value',0)
3413    else
3414        set(handles.get_mask_fix2,'Value',1)
3415    end
3416    set(handles.mask_civ2,'String',mask_displ)
3417    set(handles.mask_fix2,'String',mask_displ)
3418end
3419
3420%------------------------------------------------------------------------
3421% --- Executes on button press in get_mask_fix2.
3422function get_mask_fix2_Callback(hObject, eventdata, handles)
3423%------------------------------------------------------------------------
3424maskval=get(handles.get_mask_fix2,'Value');
3425if isequal(maskval,0)
3426    set(handles.mask_fix2,'String','')
3427else
3428    mask_displ='no mask'; %default
3429    filebase=get(handles.RootName,'String');
3430    [nbslice, flag_mask]=get_mask(filebase,handles);
3431    if isequal(flag_mask,1)
3432        mask_displ=[num2str(nbslice) 'mask'];
3433    elseif get(handles.compare,'Value')>1 & ~isequal(mask_displ,'no mask')% look for the second mask series
3434        filebase_a=get(handles.RootName_1,'String');
3435        [nbslice_a, flag_mask_a]=get_mask(filebase_a,handles);
3436        if isequal(flag_mask_a,0) || ~isequal(nbslice_a,nbslice)
3437            mask_displ='no mask';
3438        end
3439    end
3440    if isequal(mask_displ,'no mask')
3441        [FileName, PathName, filterindex] = uigetfile( ...
3442            {'*.png', ' (*.png)';
3443            '*.png',  '.png files '; ...
3444            '*.*', 'All Files (*.*)'}, ...
3445            'Pick a mask file *.png',filebase);
3446        mask_displ=fullfile(PathName,FileName);
3447        if ~exist(mask_displ,'file')
3448            mask_displ='no mask';
3449        end
3450    end
3451    if isequal(mask_displ,'no mask')
3452        set(handles.get_mask_fix2,'Value',0)
3453    end
3454    set(handles.mask_fix2,'String',mask_displ)
3455end
3456
3457%------------------------------------------------------------------------
3458% --- function called to look for mask files
3459function [nbslice, flag_mask]=get_mask(filebase,handles)
3460%------------------------------------------------------------------------
3461%detect mask files, images with appropriate file base
3462%[filebase '_' xx 'mask'], xx=nbslice
3463%flag_mask=1 indicates detection
3464
3465flag_mask=0;%default
3466nbslice=1;
3467
3468% subdir=get(handles.subdir_civ1,'String');
3469[Path,Name]=fileparts(filebase);
3470if ~isdir(Path)
3471    msgbox_uvmat('ERROR','no path for input files')
3472    return
3473end
3474currentdir=pwd;
3475cd(Path);%move in the dir of the root name filebase
3476maskfiles=dir([Name '_*mask_*.png']);%look for mask files
3477cd(currentdir);%come back to the current working directory
3478if ~isempty(maskfiles)
3479    %     msgbox_uvmat('ERROR','no mask available, to create it use Tools/Make mask in the upper menu bar of uvmat')
3480    % else
3481    flag_mask=1;
3482    maskname=maskfiles(1).name;% take the first mask file in the list
3483    [Path2,Name,ext]=fileparts(maskname);
3484    Namedouble=double(Name);
3485    val=(48>Namedouble)|(Namedouble>57);% select the non-numerical characters
3486    ind_mask=findstr('mask',Name);
3487    i=ind_mask-1;
3488    while val(i)==0 && i>0
3489        i=i-1;
3490    end
3491    nbslice=str2double(Name(i+1:ind_mask-1));
3492    if ~isnan(nbslice) && Name(i)=='_'
3493        flag_mask=1;
3494    else
3495        msgbox_uvmat('ERROR',['bad mask file ' Name ext ' found in ' Path2])
3496        return
3497        nbslice=1;
3498    end
3499end
3500
3501%------------------------------------------------------------------------
3502% --- function called to look for grid files
3503function [nbslice, flag_mask]=get_grid(filebase,handles)
3504%------------------------------------------------------------------------
3505flag_mask=0;%default
3506nbslice=1;
3507[Path,Name]=fileparts(filebase);
3508currentdir=pwd;
3509cd(Path);%move in the dir of the root name filebase
3510maskfiles=dir([Name '_*grid_*.grid']);%look for mask files
3511cd(currentdir);%come back to the current working directory
3512if ~isempty(maskfiles)
3513    flag_mask=1;
3514    maskname=maskfiles(1).name;% take the first mask file in the list
3515    [Path2,Name,ext]=fileparts(maskname);
3516    Namedouble=double(Name);
3517    val=(48>Namedouble)|(Namedouble>57);% select the non-numerical characters
3518    ind_mask=findstr('grid',Name);
3519    i=ind_mask-1;
3520    while val(i)==0 && i>0
3521        i=i-1;
3522    end
3523    nbslice=str2double(Name(i+1:ind_mask-1));
3524    if ~isnan(nbslice) && Name(i)=='_'
3525        flag_mask=1;
3526    else
3527        msgbox_uvmat('ERROR',['bad grid file ' Name ext ' found in ' Path2])
3528        return
3529        nbslice=1;
3530    end
3531end
3532
3533%------------------------------------------------------------------------
3534% --- transform numbers to letters
3535function str=num2stra(num,nom_type)
3536%------------------------------------------------------------------------
3537if isempty(nom_type)
3538    str='';
3539elseif strcmp(nom_type(end),'a')
3540    str=char(96+num);
3541elseif strcmp(nom_type(end),'A')
3542    str=char(96+num);
3543elseif isempty(nom_type(2:end))%a single index
3544    str='';
3545else
3546    str=num2str(num);
3547end
3548
3549%------------------------------------------------------------------------
3550% --- Executes on button press in list_subdir_civ1.
3551function list_subdir_civ1_Callback(hObject, eventdata, handles)
3552%------------------------------------------------------------------------
3553list_subdir_civ1=get(handles.list_subdir_civ1,'String');
3554val=get(handles.list_subdir_civ1,'Value');
3555if val>1
3556    subdir=list_subdir_civ1{val};
3557    set(handles.subdir_civ1,'String',subdir);
3558    set(handles.list_subdir_civ1,'Value',1);
3559end
3560
3561%------------------------------------------------------------------------
3562% --- Executes on button press in list_subdir_civ2.
3563function list_subdir_civ2_Callback(hObject, eventdata, handles)
3564%------------------------------------------------------------------------
3565list_subdir_civ2=get(handles.list_subdir_civ2,'String');
3566val=get(handles.list_subdir_civ2,'Value');
3567if val>1
3568    subdir=list_subdir_civ2{val};
3569    set(handles.subdir_civ2,'String',subdir);
3570    set(handles.list_subdir_civ2,'Value',1);
3571end
3572
3573%------------------------------------------------------------------------
3574% --- Executes on button press in browse_gridciv1.
3575function browse_gridciv1_Callback(hObject, eventdata, handles)
3576%------------------------------------------------------------------------
3577value=get(handles.browse_gridciv1,'Value');
3578testgrid=0;
3579if value
3580    filebase=get(handles.RootName,'String');
3581    [nbslice, flag_grid]=get_grid(filebase,handles);
3582    if isequal(flag_grid,1)
3583        filegrid=[num2str(nbslice) 'grid'];
3584        testgrid=1;
3585    else
3586        [FileName, PathName, filterindex] = uigetfile( ...
3587            {'*.grid', ' (*.grid)';
3588            '*.grid',  '.grid files '; ...
3589            '*.*', 'All Files (*.*)'}, ...
3590            'Pick a file',filebase);
3591        filegrid=fullfile(PathName,FileName);
3592        if ~(isempty(FileName)||isempty(PathName)||isequal(FileName,0)||~exist(filegrid,'file'))
3593            testgrid=1;
3594        end
3595    end
3596end
3597if testgrid
3598    set(handles.browse_gridciv2,'Value',1)
3599    set(handles.get_gridpatch1,'Value',1)
3600    set(handles.get_gridpatch2,'Value',1)
3601    set(handles.dx_civ1,'Visible','off');
3602    set(handles.dy_civ1,'Visible','off');
3603    set(handles.dx_civ2,'Visible','off');
3604    set(handles.dy_civ2,'Visible','off');
3605    set(handles.grid_civ1,'String',filegrid)
3606    set(handles.grid_patch1,'String',filegrid)
3607    set(handles.grid_civ2,'String',filegrid)
3608    set(handles.grid_patch2,'String',filegrid)
3609else
3610    set(handles.browse_gridciv1,'Value',0);
3611    set(handles.browse_gridciv2,'Value',0);
3612    set(handles.get_gridpatch1,'Value',0)
3613    set(handles.get_gridpatch2,'Value',0)
3614    set(handles.dx_civ1,'Visible','on');
3615    set(handles.dy_civ1,'Visible','on');
3616    set(handles.dx_civ2,'Visible','on');
3617    set(handles.dy_civ2,'Visible','on');
3618    set(handles.grid_civ1,'String','')
3619    set(handles.grid_patch1,'String','')
3620    set(handles.grid_civ2,'String','')
3621    set(handles.grid_patch2,'String','')
3622end
3623
3624%------------------------------------------------------------------------
3625% --- Executes on button press in browse_gridciv1.
3626function browse_gridciv2_Callback(hObject, eventdata, handles)
3627%------------------------------------------------------------------------
3628value=get(handles.browse_gridciv2,'Value');
3629if value
3630    filebase=get(handles.RootName,'String');
3631    [nbslice, flag_grid]=get_grid(filebase,handles);
3632    if isequal(flag_grid,1)
3633        mask_displ=[num2str(nbslice) 'grid'];
3634        set(handles.grid_civ2,'String',mask_displ)
3635        set(handles.dx_civ2,'Visible','off');
3636        set(handles.dy_civ2,'Visible','off');
3637    else
3638        [FileName, PathName, filterindex] = uigetfile( ...
3639            {'*.grid', ' (*.grid)';
3640            '*.grid',  '.grid files '; ...
3641            '*.*', 'All Files (*.*)'}, ...
3642            'Pick a file',filebase);
3643        filegrid=fullfile(PathName,FileName);
3644        if isempty(FileName)||isempty(PathName)||isequal(FileName,0)||~exist(filegrid,'file')
3645            set(handles.browse_gridciv2,'Value',0);
3646            set(handles.grid_civ2,'string','');
3647            set(handles.dx_civ2,'Visible','on');
3648            set(handles.dy_civ2,'Visible','on');
3649            set(handles.grid_civ2,'string','');
3650        else
3651            set(handles.grid_civ2,'string',filegrid);
3652            set(handles.dx_civ2,'Visible','off');
3653            set(handles.dy_civ2,'Visible','off');
3654            set(handles.grid_civ2,'string',filegrid);
3655        end
3656    end
3657else
3658    set(handles.grid_civ2,'string','');
3659    set(handles.dx_civ2,'Visible','on');
3660    set(handles.dy_civ2,'Visible','on');
3661    set(handles.grid_civ2,'string','');
3662end
3663
3664% % --- Executes on button press in browse_gridciv2.
3665% function browse_gridciv2_Callback(hObject, eventdata, handles)
3666%
3667% filebase=get(handles.RootName,'String');
3668% [FileName, PathName, filterindex] = uigetfile( ...
3669%        {'*.grid', ' (*.grid)';
3670%         '*.grid',  '.grid files '; ...
3671%         '*.*', 'All Files (*.*)'}, ...
3672%         'Pick a file',filebase);
3673% filegrid=fullfile(PathName,FileName);
3674% set(handles.grid_civ2,'string',filegrid);
3675% set(handles.dx_civ2,'String',' ');
3676% set(handles.dy_civ2,'String',' ');
3677% % set(handles.grid_patch2,'string',filegrid);
3678
3679% --- Executes on button press in get_gridpatch1.
3680function get_gridpatch1_Callback(hObject, eventdata, handles)
3681% hObject    handle to get_gridpatch1 (see GCBO)
3682% eventdata  reserved - to be defined in a future version of MATLAB
3683% handles    structure with handles and user data (see GUIDATA)
3684
3685filebase=get(handles.RootName,'String');
3686[FileName, PathName, filterindex] = uigetfile( ...
3687    {'*.grid', ' (*.grid)';
3688    '*.grid',  '.grid files '; ...
3689    '*.*', 'All Files (*.*)'}, ...
3690    'Pick a file',filebase);
3691filegrid=fullfile(PathName,FileName);
3692set(handles.grid_patch1,'string',filegrid);
3693% set(handles.grid_patch2,'string',filegrid
3694
3695%------------------------------------------------------------------------
3696% --- Executes on button press in get_gridpatch2.
3697function get_gridpatch2_Callback(hObject, eventdata, handles)
3698%------------------------------------------------------------------------
3699
3700%------------------------------------------------------------------------
3701function enable_civ1(handles,state)
3702%------------------------------------------------------------------------
3703if isequal(state,'on')
3704    set(handles.frame_civ1,'BackgroundColor',[1 1 0])
3705    set(handles.frame_para_civ1,'BackgroundColor',[1 1 0])
3706    set(handles.frame_grid_civ1,'BackgroundColor',[1 1 0])
3707else
3708    set(handles.frame_civ1,'BackgroundColor',[0.831 0.816 0.784])
3709    set(handles.frame_para_civ1,'BackgroundColor',[0.831 0.816 0.784])
3710    set(handles.frame_grid_civ1,'BackgroundColor',[0.831 0.816 0.784])
3711end
3712set(handles.ibx,'Visible',state)
3713set(handles.iby,'Visible',state)
3714set(handles.isx,'Visible',state)
3715set(handles.isy,'Visible',state)
3716set(handles.shiftx,'Visible',state)
3717set(handles.shifty,'Visible',state)
3718set(handles.rho,'Visible',state)
3719set(handles.dx_civ1,'Visible',state)
3720set(handles.dy_civ1,'Visible',state)
3721set(handles.calcul_search,'Visible',state)
3722set(handles.u_text,'Visible',state)
3723set(handles.v_text,'Visible',state)
3724set(handles.min,'Visible',state)
3725set(handles.max,'Visible',state)
3726set(handles.umin,'Visible',state)
3727set(handles.umax,'Visible',state)
3728set(handles.vmin,'Visible',state)
3729set(handles.vmax,'Visible',state)
3730set(handles.grid_civ1,'Visible',state)
3731set(handles.mask_civ1,'Visible',state)
3732set(handles.browse_gridciv1,'Visible',state)
3733set(handles.get_mask_civ1,'Visible',state)
3734set(handles.parameters,'Visible',state)
3735set(handles.grid,'Visible',state)
3736set(handles.dx_civ1,'Visible',state)
3737set(handles.dy_civ1,'Visible',state)
3738set(handles.ImaThreshold,'Visible',state)
3739if isequal(state,'off')
3740    set(handles.MinIma,'Visible','off')
3741    set(handles.MaxIma,'Visible','off')
3742    set(handles.ImaThreshold,'Value',0)
3743end
3744set(handles.dx_civ1_title,'Visible',state)
3745set(handles.dy_civ1_title,'Visible',state)
3746set(handles.ImaThreshold_title,'Visible',state)
3747set(handles.ib_title,'Visible',state)
3748set(handles.is_title,'Visible',state)
3749set(handles.shift_title,'Visible',state)
3750set(handles.rho_title,'Visible',state)
3751set(handles.TestCiv1,'Visible',state)
3752%set(handles.CivMode,'Visible',state)
3753
3754%------------------------------------------------------------------------
3755function enable_fix1(handles,state)
3756%------------------------------------------------------------------------
3757if isequal(state,0)
3758    state='off';
3759end
3760if isequal(state,1)
3761    state='on';
3762end
3763if isequal(state,'on')
3764    set(handles.frame_fix1,'BackgroundColor',[1 1 0])
3765else
3766    set(handles.frame_fix1,'BackgroundColor',[0.7 0.7 0.7])
3767end
3768set(handles.REMOVE,'Visible',state)
3769set(handles.vec_Fmin2,'Visible',state)
3770set(handles.vec_F2,'Visible',state)
3771set(handles.vec_F3,'Visible',state)
3772set(handles.thresh_vecC,'Visible',state)
3773set(handles.thresh_vecC_title,'Visible',state)
3774set(handles.thresh_vel,'Visible',state)
3775set(handles.thresh_vel_text,'Visible',state)
3776set(handles.mask_fix1,'Visible',state)
3777set(handles.get_mask_fix1,'Visible',state)
3778set(handles.get_ref_fix1,'Visible',state)
3779set(handles.ref_fix1,'Visible',state)
3780set(handles.inf_sup1,'Visible',state)
3781set(handles.field_ref1,'Visible',state)
3782
3783%------------------------------------------------------------------------
3784function enable_patch1(handles)
3785%------------------------------------------------------------------------
3786set(handles.frame_patch1,'BackgroundColor',[1 1 0])
3787set(handles.rho_patch1,'Visible','on')
3788set(handles.rho_text1,'Visible','on')
3789if get(handles.CivMode,'Value')==2
3790    set(handles.thresh_patch1,'Visible','on')
3791    set(handles.thresh_text1,'Visible','on')
3792end
3793set(handles.subdomain_patch1,'Visible','on')
3794set(handles.subdomain_text1,'Visible','on')
3795set(handles.nx_patch1,'Visible','on')
3796set(handles.ny_patch1,'Visible','on')
3797set(handles.nx_patch1_title,'Visible','on')
3798set(handles.ny_patch1_title,'Visible','on')
3799% if ~isempty(patch_newBin)
3800set(handles.test_interp,'Visible','off');
3801stereo_test=get(handles.compare,'Value');
3802if stereo_test==3
3803    set(handles.test_stereo1,'Visible','on')
3804end
3805% end
3806%set(handles.get_gridpatch1,'Visible','on')
3807%set(handles.grid_patch1,'string','none');
3808%set(handles.grid_patch1,'Visible','on')
3809
3810%------------------------------------------------------------------------
3811function desable_patch1(handles)
3812%------------------------------------------------------------------------
3813set(handles.frame_patch1,'BackgroundColor',[0.831 0.816 0.784])
3814set(handles.rho_patch1,'Visible','off')
3815set(handles.rho_text1,'Visible','off')
3816set(handles.thresh_patch1,'Visible','off')
3817set(handles.thresh_text1,'Visible','off')
3818set(handles.subdomain_patch1,'Visible','off')
3819set(handles.subdomain_text1,'Visible','off')
3820set(handles.nx_patch1,'Visible','off')
3821set(handles.ny_patch1,'Visible','off')
3822set(handles.nx_patch1_title,'Visible','off')
3823set(handles.ny_patch1_title,'Visible','off')
3824set(handles.test_stereo1,'Visible','off')
3825%set(handles.test_interp,'Visible','off')
3826%set(handles.get_gridpatch1,'Visible','off')
3827%set(handles.grid_patch1,'Visible','off')
3828
3829%------------------------------------------------------------------------
3830function enable_civ2(handles,state)
3831%------------------------------------------------------------------------
3832if isequal(state,0)
3833    state='off';
3834end
3835if isequal(state,1)
3836    state='on';
3837end
3838if isequal(state,'on')
3839    set(handles.frame_civ2,'BackgroundColor',[1 1 0])
3840    set(handles.frame_para_civ2,'BackgroundColor',[1 1 0])
3841    set(handles.frame_grid_civ2,'BackgroundColor',[1 1 0])
3842    set(handles.frame_subdirciv2,'BackgroundColor',[1 1 0])
3843else
3844    set(handles.frame_civ2,'BackgroundColor',[0.831 0.816 0.784])
3845    set(handles.frame_para_civ2,'BackgroundColor',[0.831 0.816 0.784])
3846    set(handles.frame_grid_civ2,'BackgroundColor',[0.831 0.816 0.784])
3847    set(handles.frame_subdirciv2,'BackgroundColor',[0.831 0.816 0.784])
3848end
3849set(handles.ibx_civ2,'Visible',state)
3850set(handles.iby_civ2,'Visible',state)
3851set(handles.decimal,'Visible',state)
3852set(handles.deformation,'Visible',state)
3853set(handles.rho_civ2,'Visible',state)
3854set(handles.dx_civ2,'Visible',state)
3855set(handles.dy_civ2,'Visible',state)
3856set(handles.browse_gridciv2,'Visible',state)
3857set(handles.get_mask_civ2,'Visible',state)
3858set(handles.parameters,'Visible',state)
3859set(handles.grid,'Visible',state)
3860set(handles.parameters_text,'Visible',state)
3861set(handles.grid_text,'Visible',state)
3862set(handles.grid_civ2,'Visible',state)
3863set(handles.mask_civ2,'Visible',state)
3864set(handles.dx_civ2_title,'Visible',state)
3865set(handles.dy_civ2_title,'Visible',state)
3866set(handles.ibx_civ2_text,'Visible',state)
3867set(handles.rho_civ2_title,'Visible',state)
3868set(handles.ImaThreshold2,'Visible',state)
3869set(handles.ImaThreshold_title2,'Visible',state)
3870if isequal(state,'off')
3871    set(handles.MinIma2,'Visible','off')
3872    set(handles.MaxIma2,'Visible','off')
3873    set(handles.ImaThreshold2,'Value',0)
3874    if isequal(get(handles.FIX2,'Value'),0) & isequal(get(handles.PATCH2,'Value'),0)
3875        set(handles.list_pair_civ2,'Visible','off')
3876        set(handles.subdir_civ2,'Visible','off')
3877        set(handles.subdir_civ2_text,'Visible','off')
3878        set(handles.dt_unit_civ2,'Visible','off')
3879        set(handles.ref_i_civ2,'Visible','off')
3880        set(handles.i_ref_civ2_title,'Visible','off')
3881        set(handles.j_ref_civ2_title,'Visible','off')
3882        set(handles.ref_j_civ2,'Visible','off')
3883    end
3884else
3885    set(handles.list_pair_civ2,'Visible','on')
3886    set(handles.subdir_civ2,'Visible','on')
3887    set(handles.subdir_civ2_text,'Visible','on')
3888    set(handles.dt_unit_civ2,'Visible','on')
3889    set(handles.ref_i_civ2,'Visible','on')
3890    set(handles.i_ref_civ2_title,'Visible','on')
3891    set(handles.j_ref_civ2_title,'Visible','on')
3892    set(handles.ref_j_civ2,'Visible','on')
3893end
3894set(handles.rho_civ2_title,'Visible',state)
3895
3896%------------------------------------------------------------------------
3897function enable_fix2(handles)
3898%------------------------------------------------------------------------
3899set(handles.frame_fix2,'BackgroundColor',[1 1 0])
3900set(handles.REMOVE2,'Visible','on')
3901set(handles.vec_Fmin2_2,'Visible','on')
3902set(handles.vec_F4,'Visible','on')
3903set(handles.vec_F3_2,'Visible','on')
3904set(handles.thresh_vec2C,'Visible','on')
3905set(handles.thresh_vec2C_text,'Visible','on')
3906set(handles.thresh_vel2,'Visible','on')
3907set(handles.thresh_vel2_text,'Visible','on')
3908set(handles.mask_fix2,'Visible','on')
3909set(handles.get_mask_fix2,'Visible','on')
3910set(handles.list_pair_civ2,'Visible','on')
3911set(handles.subdir_civ2,'Visible','on')
3912set(handles.subdir_civ2_text,'Visible','on')
3913set(handles.get_ref_fix2,'Visible','on')
3914set(handles.ref_fix2,'Visible','on')
3915set(handles.inf_sup2,'Visible','on')
3916set(handles.field_ref2,'Visible','on')
3917
3918%------------------------------------------------------------------------
3919function desable_fix2(handles)
3920%------------------------------------------------------------------------
3921set(handles.frame_fix2,'BackgroundColor',[0.831 0.816 0.784])
3922set(handles.REMOVE2,'Visible','off')
3923set(handles.vec_Fmin2_2,'Visible','off')
3924set(handles.vec_F4,'Visible','off')
3925set(handles.vec_F3_2,'Visible','off')
3926set(handles.thresh_vec2C,'Visible','off')
3927set(handles.thresh_vec2C_text,'Visible','off')
3928set(handles.thresh_vel2,'Visible','off')
3929set(handles.thresh_vel2_text,'Visible','off')
3930set(handles.mask_fix2,'Visible','off')
3931set(handles.get_mask_fix2,'Visible','off')
3932set(handles.get_ref_fix2,'Visible','off')
3933set(handles.ref_fix2,'Visible','off')
3934set(handles.inf_sup2,'Visible','off')
3935set(handles.field_ref2,'Visible','off')
3936if isequal(get(handles.CIV2,'Value'),0) & isequal(get(handles.PATCH2,'Value'),0)
3937    set(handles.list_pair_civ2,'Visible','off')
3938    set(handles.subdir_civ2,'Visible','off')
3939    set(handles.subdir_civ2_text,'Visible','off')
3940end
3941
3942%------------------------------------------------------------------------
3943function enable_patch2(handles)
3944%------------------------------------------------------------------------
3945set(handles.frame_patch2,'BackgroundColor',[1 1 0])
3946set(handles.rho_patch2,'Visible','on')
3947set(handles.rho_text2,'Visible','on')
3948set(handles.thresh_patch2,'Visible','on')
3949set(handles.thresh_text2,'Visible','on')
3950set(handles.subdomain_patch2,'Visible','on')
3951set(handles.subdomain_text2,'Visible','on')
3952set(handles.nx_patch2,'Visible','on')
3953set(handles.ny_patch2,'Visible','on')
3954set(handles.nx_patch2_title,'Visible','on')
3955set(handles.ny_patch2_title,'Visible','on')
3956% set(handles.get_gridpatch2,'Visible','on')
3957% set(handles.grid_patch2,'Visible','on')
3958set(handles.list_pair_civ2,'Visible','on')
3959set(handles.subdir_civ2,'Visible','on')
3960set(handles.subdir_civ2_text,'Visible','on')
3961stereo_test=get(handles.compare,'Value');
3962if stereo_test==3
3963    set(handles.test_stereo2,'Visible','on')
3964end
3965
3966%------------------------------------------------------------------------
3967function desable_patch2(handles)
3968%------------------------------------------------------------------------
3969set(handles.frame_patch2,'BackgroundColor',[0.831 0.816 0.784])
3970set(handles.rho_patch2,'Visible','off')
3971set(handles.rho_text2,'Visible','off')
3972set(handles.thresh_patch2,'Visible','off')
3973set(handles.thresh_text2,'Visible','off')
3974set(handles.subdomain_patch2,'Visible','off')
3975set(handles.subdomain_text2,'Visible','off')
3976set(handles.nx_patch2,'Visible','off')
3977set(handles.ny_patch2,'Visible','off')
3978set(handles.nx_patch2_title,'Visible','off')
3979set(handles.ny_patch2_title,'Visible','off')
3980% set(handles.get_gridpatch2,'Visible','off')
3981% set(handles.grid_patch2,'Visible','off')
3982if isequal(get(handles.CIV2,'Value'),0) & isequal(get(handles.FIX2,'Value'),0)
3983    set(handles.list_pair_civ2,'Visible','off')
3984    set(handles.subdir_civ2,'Visible','off')
3985    set(handles.subdir_civ2_text,'Visible','off')
3986end
3987set(handles.test_stereo2,'Visible','off')
3988%------------------------------------------------------------------------
3989function enable_pair1(handles,state)
3990%------------------------------------------------------------------------
3991set(handles.subdir_civ1,'Visible',state)
3992set(handles.list_subdir_civ1,'Visible',state)
3993set(handles.SUBDIR_CIV1_txt,'Visible',state)
3994set(handles.frame_subdirciv1,'Visible',state)
3995set(handles.list_pair_civ1,'Visible',state)
3996set(handles.PAIR_txt,'Visible',state)
3997%set(handles.dt_unit,'Visible',state)
3998set(handles.PAIR_frame,'Visible',state)
3999
4000%------------------------------------------------------------------------
4001% --- Read the parameters for civ1 on the interface
4002function par=read_param_civ1(handles,file_ima)
4003%------------------------------------------------------------------------
4004ibx_val=str2double(get(handles.ibx,'String'));
4005par.ibx=num2str(ibx_val);
4006iby_val=str2double(get(handles.iby,'String'));
4007par.iby=num2str(iby_val);
4008isx=get(handles.isx,'String');
4009if isnan(str2double(isx)), isx='41'; set(handles.isx,'String','41'), end; %default
4010if str2double(isx)<ibx_val+8,isx=num2str(ibx_val+8); set(handles.isx,'String',num2str(ibx_val+8)); end
4011isy=get(handles.isy,'String');
4012if isnan(str2double(isy)), isy='41'; set(handles.isy,'String','41'), end;%default
4013if str2double(isy)<iby_val+8,isy=num2str(iby_val+8); set(handles.isy,'String',num2str(iby_val+8)); end
4014par.isx=get(handles.isx,'String');
4015par.isy=get(handles.isy,'String');
4016par.shiftx=get(handles.shiftx,'String');
4017par.shifty=get(handles.shifty,'String');
4018if isnan(str2double(par.isx))
4019    par.isx='41';%default
4020    set(handles.isx,'String','41');
4021end
4022if isnan(str2double(par.isy))
4023    par.isy='41'; %default
4024    set(handles.isy,'String','41');
4025end
4026if isnan(str2double(par.shiftx))
4027    par.shiftx='0';%default
4028    set(handles.shiftx,'String','0');
4029end
4030if isnan(str2double(par.shifty))
4031    par.shifty='0'; %default
4032    set(handles.shifty,'String','0');
4033end
4034par.rho=get(handles.rho,'String');
4035if isequal(get(handles.rho,'Style'),'popupmenu')
4036    index=get(handles.rho,'Value');
4037    par.rho=par.rho{index};
4038end
4039par.dx=get(handles.dx_civ1,'String');
4040par.dy=get(handles.dy_civ1,'String');
4041if isnan(str2double(par.dx))
4042    if isempty(get(handles.grid_civ1,'String'));
4043        par.dx='0'; %just read by civ program, not used
4044    else
4045        par.dx='20';%default
4046        set(handles.dx_civ1,'String','20');
4047    end
4048end
4049if isnan(str2double(par.dy))
4050    if isempty(get(handles.grid_civ1,'String'));
4051        par.dy='0';%just read by civ program, not used
4052    else
4053        par.dy='20';%default
4054        set(handles.dy_civ1_title,'String','20');
4055    end
4056end
4057par.pxcmx='1'; %velocities are expressed in pixel dispalcement
4058par.pxcmy='1';
4059if exist('file_ima','var')
4060A=imread(file_ima);%read the first image to get the size
4061sizim=size(A);
4062par.npx=num2str(sizim(2));
4063par.npy=num2str(sizim(1));
4064end
4065%time=get(handles.RootName,'UserData'); %get the set of times
4066par.gridname=get(handles.grid_civ1,'String');
4067par.gridflag='y';
4068if strcmp(par.gridname,'')|| isempty(par.gridname)
4069    par.gridname='nogrid';
4070    par.gridflag='n';
4071end
4072
4073%------------------------------------------------------------------------
4074function par=read_param_civ2(handles,file_ima)
4075%------------------------------------------------------------------------
4076par.ibx=get(handles.ibx_civ2,'String');
4077par.iby=get(handles.iby_civ2,'String');
4078par.rho=get(handles.rho_civ2,'String');
4079par.decimal=int2str(get(handles.decimal,'Value'));
4080par.deformation=int2str(get(handles.deformation,'Value'));
4081par.dx=get(handles.dx_civ2,'String');
4082par.dy=get(handles.dy_civ2,'String');
4083if isnan(str2double(par.dx))
4084    if isempty(get(handles.grid_civ2,'String'));
4085        par.dx='0'; %just read by civ program, not used
4086    else
4087        par.dx='20';%default
4088        set(handles.dx_civ2,'String','20');
4089    end
4090end
4091if isnan(str2double(par.dy))
4092    if isempty(get(handles.grid_civ2,'String'));
4093        par.dy='0';%just read by civ program, not used
4094    else
4095        par.dy='20';%default
4096        set(handles.dy_civ2,'String','20');
4097    end
4098end
4099par.pxcmx='1';
4100par.pxcmy='1';
4101A=imread(file_ima);%read the first image to get the size
4102sizim=size(A);
4103par.npx=num2str(sizim(2));
4104par.npy=num2str(sizim(1));
4105%time=get(handles.RootName,'UserData'); %get the set of times
4106par.gridname=get(handles.grid_civ2,'String');
4107par.gridflag='y';
4108if strcmp(par.gridname,'')|| isempty(par.gridname)
4109    par.gridname='nogrid';
4110    par.gridflag='n';
4111end
4112
4113%------------------------------------------------------------------------
4114% --- CIV1  CIV1  CIV1 CIV1
4115function cmd_CIV1=CIV1_CMD(filename,namelog,par,handles,sparam)
4116%------------------------------------------------------------------------
4117%pixels per cm and matrix of the image times, read from the .civ file by uvmat
4118
4119%changes : filename_cmx -> filename ( no extension )
4120% input namelog not used
4121if isequal(par.Dt,'0')
4122    par.Dt='1' ;%case of 'displacement' mode
4123end
4124par.filename_ima_a=regexprep(par.filename_ima_a,'.png','');
4125par.filename_ima_b=regexprep(par.filename_ima_b,'.png','');
4126fid=fopen([filename '.civ1.cmx'],'w');
4127fprintf(fid,['##############   CMX file' '\n' ]);
4128fprintf(fid,   ['FirstImage ' regexprep(par.filename_ima_a,'\\','\\\\') '\n' ]);% for windows compatibility
4129fprintf(fid,   ['LastImage  ' regexprep(par.filename_ima_b,'\\','\\\\') '\n' ]);% for windows compatibility
4130fprintf(fid,  ['XX' '\n' ]);
4131fprintf(fid,  ['Mask ' par.maskflag '\n' ]);
4132fprintf(fid,  ['MaskName ' regexprep(par.maskname,'\\','\\\\') '\n' ]);
4133fprintf(fid,   ['ImageSize ' par.npx ' ' par.npy '\n' ]);   %VERIFIER CAS GENERAL ?
4134fprintf(fid,   ['CorrelationBoxesSize ' par.ibx ' ' par.iby '\n' ]);
4135fprintf(fid,   ['SearchBoxeSize ' par.isx ' ' par.isy '\n' ]);
4136fprintf(fid,   ['RO ' par.rho '\n' ]);
4137fprintf(fid,   ['GridSpacing ' par.dx ' ' par.dy '\n' ]);
4138fprintf(fid,   ['XX 1.0' '\n' ]);
4139fprintf(fid,   ['Dt_TO ' par.Dt ' ' par.T0 '\n' ]);
4140fprintf(fid,  ['PixCmXY ' par.pxcmx ' ' par.pxcmy '\n' ]);
4141fprintf(fid,  ['XX 1' '\n' ]);
4142fprintf(fid,   ['ShiftXY ' par.shiftx ' '  par.shifty '\n' ]);
4143fprintf(fid,  ['Grid ' par.gridflag '\n' ]);
4144fprintf(fid,   ['GridName ' regexprep(par.gridname,'\\','\\\\') '\n' ]);
4145fprintf(fid,   ['XX 85' '\n' ]);
4146fprintf(fid,   ['XX 1.0' '\n' ]);
4147fprintf(fid,   ['XX 1.0' '\n' ]);
4148fprintf(fid,   ['Hart 1' '\n' ]);
4149fprintf(fid,  [ 'DecimalShift 0' '\n' ]);
4150fprintf(fid,   ['Deformation 0' '\n' ]);
4151fprintf(fid,  ['CorrelationMin 0' '\n' ]);
4152fprintf(fid,   ['IntensityMin 0' '\n' ]);
4153fprintf(fid,  ['SeuilImage n' '\n' ]);
4154fprintf(fid,   ['SeuilImageValues 0 4096' '\n' ]);
4155fprintf(fid,   ['ImageToUse ' par.term_a ' ' par.term_b '\n' ]); % VERIFIER ?
4156fprintf(fid,   ['ImageUsedBefore null null' '\n' ]);
4157fclose(fid);
4158
4159% cmd_CIV1=[sparam.Civ1Bin ' -f ' filename '.cmx >' filename '.log' ]; % redirect standard output to the log file
4160% cmd_CIV1=regexprep(cmd_CIV1,'\\','\\\\');
4161% namelog=regexprep(namelog,'\\','\\\\');
4162if(isunix)
4163    cmd_CIV1=['cp -f ' filename '.civ1.cmx ' filename '.cmx\n'];
4164    cmd_CIV1=[cmd_CIV1 sparam.Civ1Bin ' -f ' filename '.cmx >' filename '.log' ]; % redirect standard output to the log file, the result file is named [filename '.nc'] by CIVx
4165    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
4166   % cmd_CIV1=[cmd_CIV1 '\n' 'mv ' filename '.cmx' ' ' filename '.civ1.cmx' '\n'];%rename .cmx as .civ1.cmx
4167else %Windows system
4168                    flname=regexprep(flname,'\\','\\\\');
4169%                     cmd=[cmd 'copy /Y "' flname '.civ1.cmx" "' flname '.cmx"\n'];
4170    filename=regexprep(filename,'\\','\\\\');
4171    cmd_CIV1=['copy /Y "' filename '.civ1.cmx" "' filename '.cmx"\n'];% copy the .civ1.cmx parameter file to .cmx
4172    cmd_CIV1=['"' sparam.Civ1Bin '" -f "' filename '.cmx" >"' filename '.log"' ]; % redirect standard output to the log file
4173    cmd_CIV1=regexprep(cmd_CIV1,'\\','\\\\');
4174    namelog=regexprep(namelog,'\\','\\\\');
4175    cmd_CIV1=[cmd_CIV1 '\n' 'copy /Y "' filename '.log' '" "' filename '.civ1.log"']; %preserve the log file as .civ1.log
4176  %  cmd_CIV1=[cmd_CIV1 '\n' 'copy /Y "' filename '.cmx' '" "' filename '.civ1.cmx"'];
4177end
4178
4179%------------------------------------------------------------------------
4180% --- CIV1  Unified
4181function xml_civ1_parameters=CIV1_CMD_Unified(filename,namelog,par)
4182%------------------------------------------------------------------------
4183%pixels per cm and matrix of the image times, read from the .civ file by uvmat
4184%global CivBin%name of the executable for civ1 calculation
4185
4186civ1.image1=par.filename_ima_a;
4187civ1.image2=par.filename_ima_b;
4188civ1.imageSize_X=par.npx;
4189civ1.imageSize_Y=par.npy;
4190civ1.outputFileName=[filename '.nc'];
4191civ1.correlationBoxesSize_X=par.ibx;
4192civ1.correlationBoxesSize_Y=par.iby;
4193civ1.searchBoxesSize_X=par.isx;
4194civ1.searchBoxesSize_Y=par.isy;
4195civ1.globalShift_X=par.shiftx;
4196civ1.globalShift_Y=par.shifty;
4197civ1.ro=par.rho;
4198civ1.hart='y';
4199if isequal(par.gridflag,'y')
4200    civ1.grid=par.gridname;
4201else
4202    civ1.grid='n';
4203    civ1.gridSpacing_X=par.dx;
4204    civ1.gridSpacing_Y=par.dy;
4205end
4206if isequal(par.maskflag,'y')
4207    civ1.mask=par.maskname;
4208end
4209civ1.dt=par.Dt;
4210civ1.unit='pixel';
4211civ1.absolut_time_T0=par.T0;
4212civ1.pixcmx=par.pxcmx;
4213civ1.pixcmy=par.pxcmy;
4214civ1.convectFlow='n';
4215
4216xml_civ1_parameters=civ1;
4217
4218%------------------------------------------------------------------------
4219% --- CIV2  Unified
4220function civ2=CIV2_CMD_Unified(filename,namelog,par)
4221%------------------------------------------------------------------------
4222%pixels per cm and matrix of the image times, read from the .civ file by uvmat
4223%global CivBin%name of the executable for civ1 calculation
4224
4225civ2.image1=par.filename_ima_a;
4226civ2.image2=par.filename_ima_b;
4227civ2.imageSize_X=par.npx;
4228civ2.imageSize_Y=par.npy;
4229civ2.inputFileName=[par.filename_nc1 '.nc'];
4230civ2.outputFileName=[filename '.nc'];
4231civ2.correlationBoxesSize_X=par.ibx;
4232civ2.correlationBoxesSize_Y=par.iby;
4233civ2.ro=par.rho;
4234%civ2.decimalShift=par.decimal;
4235%civ2.deformation=par.deformation;
4236if isequal(par.decimal,'1')
4237    civ2.decimalShift='y';
4238else
4239    civ2.decimalShift='n';
4240end
4241if isequal(par.deformation,'1')
4242    civ2.deformation='y';
4243else
4244    civ2.deformation='n';
4245end
4246if isequal(par.gridflag,'y')
4247    civ2.grid=par.gridname;
4248else
4249    civ2.grid='n';
4250    civ2.gridSpacing_X=par.dx;
4251    civ2.gridSpacing_Y=par.dy;
4252end
4253civ2.gridSpacing_X='10';
4254civ2.gridSpacing_Y='10';%NOTE: faut mettre gridSpacing pourque ca tourne, meme si c'est la grille qui est utilisee
4255if isequal(par.maskflag,'y')
4256    civ2.mask=par.maskname;
4257else
4258    civ2.mask='n';
4259end
4260civ2.dt=par.Dt;
4261civ2.unit='pixel';
4262civ2.absolut_time_T0=par.T0;
4263civ2.pixcmx=par.pxcmx;
4264civ2.pixcmy=par.pxcmy;
4265civ2.convectFlow='n';
4266civ2.pixcmx=par.pxcmx;
4267civ2.pixcmy=par.pxcmy;
4268civ2.convectFlow='n';
4269
4270%------------------------------------------------------------------------
4271% --- CIV2  CIV2  CIV2 CIV2
4272function cmd_CIV2=CIV2_CMD(filename,namelog,par,sparam)
4273%------------------------------------------------------------------------
4274%pixels per cm and matrix of the image times, read from the .civ file by uvmat
4275% global civ2Bin sge%name of the executable for civ1 calculation
4276if isequal(par.Dt,'0')
4277    par.Dt='1' ;%case of 'displacement' mode
4278end
4279par.filename_ima_a=regexprep(par.filename_ima_a,'.png','');
4280par.filename_ima_b=regexprep(par.filename_ima_b,'.png','');% bug : .png appears two times ?
4281[fid,errormsg]=fopen([filename '.civ2.cmx'],'w');
4282if isequal(fid,-1)
4283    msgbox_uvmat('ERROR',errormsg)
4284    cmd_CIV2='';
4285    return
4286end
4287fprintf(fid,['##############   CMX file' '\n' ]);
4288fprintf(fid,   ['FirstImage ' regexprep(par.filename_ima_a,'\\','\\\\') '\n' ]);% for windows compatibility
4289fprintf(fid,   ['LastImage  ' regexprep(par.filename_ima_b,'\\','\\\\') '\n' ]);% for windows compatibility
4290fprintf(fid,  ['XX' '\n' ]);
4291fprintf(fid, ['Mask ' par.maskflag '\n' ]);
4292fprintf(fid, ['MaskName ' regexprep(par.maskname,'\\','\\\\') '\n' ]);% for windows compatibility
4293fprintf(fid, ['ImageSize ' par.npx ' ' par.npy '\n' ]);   %VERIFIER CAS GENERAL ?
4294fprintf(fid, ['CorrelationBoxesSize ' par.ibx ' ' par.iby '\n' ]);
4295fprintf(fid, ['SearchBoxeSize ' par.ibx ' ' par.iby '\n']);
4296fprintf(fid, ['RO ' par.rho '\n']);
4297fprintf(fid, ['GridSpacing ' par.dx ' ' par.dy '\n']);
4298fprintf(fid, ['XX 1.0' '\n' ]);
4299fprintf(fid, ['Dt_TO ' par.Dt ' ' par.T0 '\n' ]);
4300fprintf(fid, ['PixCmXY ' par.pxcmx ' ' par.pxcmy '\n' ]);
4301fprintf(fid, ['XX 1' '\n' ]);
4302fprintf(fid, 'ShiftXY 0 0\n');
4303fprintf(fid, ['Grid ' par.gridflag '\n' ]);
4304fprintf(fid, ['GridName ' regexprep(par.gridname,'\\','\\\\') '\n']);
4305fprintf(fid, ['XX 85' '\n' ]);
4306fprintf(fid, ['XX 1.0' '\n' ]);
4307fprintf(fid, ['XX 1.0' '\n' ]);
4308fprintf(fid, ['Hart 1' '\n' ]);
4309fprintf(fid, ['DecimalShift ' par.decimal '\n']);
4310fprintf(fid, ['Deformation ' par.deformation '\n']);
4311fprintf(fid,  ['CorrelationMin 0' '\n' ]);
4312fprintf(fid,   ['IntensityMin 0' '\n' ]);
4313fprintf(fid,  ['SeuilImage n' '\n' ]);
4314fprintf(fid,   ['SeuilImageValues 0 4096' '\n' ]);
4315fprintf(fid,   ['ImageToUse ' par.term_a ' ' par.term_b '\n' ]); % VERIFIER ?
4316fprintf(fid, ['ImageUsedBefore ' regexprep(par.filename_nc1,'\\','\\\\') '\n']);
4317fclose(fid);
4318
4319if(isunix)
4320    cmd_CIV2=['cp -f ' filename '.civ2.cmx ' filename '.cmx\n'];
4321    cmd_CIV2=[cmd_CIV2 sparam.Civ2Bin ' -f ' filename  '.cmx >' filename '.log' ]; % redirect standard output to the log file, the result file is named [filename '.nc'] by CIVx
4322    cmd_CIV2=[cmd_CIV2 '\n' 'mv ' filename '.log' ' ' filename '.civ2.log' '\n' 'chmod g+w ' filename '.nc'];%preserve the log file as .civ2.log
4323%    cmd_CIV2=[cmd_CIV2 '\n' 'mv ' filename '.cmx' ' ' filename '.civ2.cmx' '\n'];%rename .cmx as .civ2.cmx, the result file is named [filename '.nc'] by CIVx
4324
4325else
4326    filename=regexprep(filename,'\\','\\\\');
4327    cmd_CIV2=['copy /Y "' filename '.civ2.cmx" "' filename '.cmx"\n'];
4328    cmd_CIV2=[cmd_CIV2 '"' sparam.Civ2Bin '" -f "' filename  '.cmx" >"' filename '.log"' ]; % redirect standard output to the log file
4329    cmd_CIV2=regexprep(cmd_CIV2,'\\','\\\\');
4330    cmd_CIV2=[cmd_CIV2 '\n' 'copy /Y "' filename '.log' '" "' filename '.civ2.log"'];
4331 %    cmd_CIV2=[cmd_CIV2 '\n' 'copy /Y "' filename '.cmx' '" "' filename '.civ2.cmx"'];
4332end
4333
4334% %------------------------------------------------------------------------
4335% % --- civ using pivlab
4336% function Data=civ_uvmat(par_civ1)
4337% %------------------------------------------------------------------------
4338% image1=imread(par_civ1.filename_ima_a);
4339% image2=imread(par_civ1.filename_ima_b);
4340% stepx=str2num(par_civ1.dx);
4341% stepy=str2num(par_civ1.dy);
4342% ibx2=ceil(str2num(par_civ1.ibx)/2);
4343% iby2=ceil(str2num(par_civ1.iby)/2);
4344% isx2=ceil(str2num(par_civ1.isx)/2);
4345% isy2=ceil(str2num(par_civ1.isy)/2);
4346% shiftx=str2num(par_civ1.shiftx);
4347% shifty=str2num(par_civ1.shifty);
4348% miniy=max(1+isy2-shifty,1+iby2);
4349% minix=max(1+isx2-shiftx,1+ibx2);
4350% maxiy=min(size(image1,1)-isy2-shifty,size(image1,1)-iby2);
4351% maxix=min(size(image1,2)-isx2-shiftx,size(image1,2)-ibx2);
4352% [GridX,GridY]=meshgrid(minix:stepx:maxix,miniy:stepy:maxiy);
4353% PointCoord(:,1)=reshape(GridX,[],1);
4354% PointCoord(:,2)=reshape(GridY,[],1);
4355% % caluclate velocity data (y and v in indices, reverse to y component)
4356% [xtable ytable utable vtable ctable F] = pivlab (image1,image2,ibx2,iby2,isx2,isy2,shiftx,shifty,PointCoord, 1, []);
4357% Data.ListGlobalAttribute=[{'Conventions','Program','CivStage'} {'Time','Dt'}];
4358% Data.Conventions='uvmat/civdata';
4359% Data.Program='civ_uvmat';
4360% Data.CivStage=1;
4361% % list_param=fieldnames(Param.Civ1);
4362% % for ilist=1:length(list_param)
4363% %     eval(['Data.Civ1_' list_param{ilist} '=Param.Civ1.' list_param{ilist} ';'])
4364% % end
4365% Data.Time=str2double(par_civ1.T0);
4366% Data.Dt=str2double(par_civ1.Dt);
4367% Data.ListVarName={'Civ1_X','Civ1_Y','Civ1_U','Civ1_V','Civ1_C','Civ1_F'};%  cell array containing the names of the fields to record
4368% Data.VarDimName={'nbvec','nbvec','nbvec','nbvec','nbvec','nbvec'};
4369% Data.VarAttribute{1}.Role='coord_x';
4370% Data.VarAttribute{2}.Role='coord_y';
4371% Data.VarAttribute{3}.Role='vector_x';
4372% Data.VarAttribute{4}.Role='vector_y';
4373% Data.VarAttribute{5}.Role='warnflag';
4374% Data.Civ1_X=reshape(xtable,[],1);
4375% Data.Civ1_Y=reshape(size(image1,1)-ytable+1,[],1);
4376% Data.Civ1_U=reshape(utable,[],1);
4377% Data.Civ1_V=reshape(-vtable,[],1);
4378% Data.Civ1_C=reshape(ctable,[],1);
4379% Data.Civ1_F=reshape(F,[],1);
4380
4381%------------------------------------------------------------------------
4382% --- Executes on button press in HELP.
4383function HELP_Callback(hObject, eventdata, handles)
4384%------------------------------------------------------------------------
4385path_to_uvmat=which ('uvmat');% check the path of uvmat
4386pathelp=fileparts(path_to_uvmat);
4387helpfile=fullfile(pathelp,'uvmat_doc','uvmat_doc.html');
4388if isempty(dir(helpfile)), msgbox_uvmat('ERROR','Please put the help file uvmat_doc.html in the sub-directory /uvmat_doc of the UVMAT package')
4389else
4390    addpath (fullfile(pathelp,'uvmat_doc'))
4391    web([helpfile '#civ'])
4392end
4393
4394%------------------------------------------------------------------------
4395%--read images and convert them to the uint16 format used for PIV
4396function A=read_image(filename,type_ima,num,movieobject)
4397%------------------------------------------------------------------------
4398%num is the view number needed for an avi movie
4399switch type_ima
4400    case 'movie'
4401        A=read(movieobject,num);
4402    case 'avi'
4403        mov=aviread(filename,num);
4404        A=frame2im(mov(1));
4405    case 'multimage'
4406        A=imread(filename,num);
4407    case 'image'
4408        A=imread(filename);
4409end
4410siz=size(A);
4411if length(siz)==3;%color images
4412    A=sum(double(A),3);
4413    A=uint16(A);
4414end
4415
4416%------------------------------------------------------------------------
4417function ref_i_Callback(hObject, eventdata, handles)
4418%------------------------------------------------------------------------
4419mode_list=get(handles.mode,'String');
4420mode_value=get(handles.mode,'Value');
4421mode=mode_list{mode_value};
4422find_netcpair_civ1(hObject, eventdata, handles);% update the menu of pairs depending on the available netcdf files
4423if isequal(mode,'series(Di)') || ...% we do patch2 only
4424        (get(handles.CIV2,'Value')==0 && get(handles.CIV1,'Value')==0 && get(handles.FIX1,'Value')==0 && get(handles.PATCH1,'Value')==0)
4425    find_netcpair_civ2(hObject, eventdata, handles);
4426end
4427
4428%------------------------------------------------------------------------
4429function ref_j_Callback(hObject, eventdata, handles)
4430%------------------------------------------------------------------------
4431mode_list=get(handles.mode,'String');
4432mode_value=get(handles.mode,'Value');
4433mode=mode_list{mode_value};
4434if isequal(get(handles.CIV1,'Value'),0)|| isequal(mode,'series(Dj)')
4435    find_netcpair_civ1(hObject, eventdata, handles);% update the menu of pairs depending on the available netcdf files
4436end
4437if isequal(mode,'series(Dj)') || ...
4438        (get(handles.CIV2,'Value')==0 && get(handles.CIV1,'Value')==0 && get(handles.FIX1,'Value')==0 && get(handles.PATCH1,'Value')==0)
4439    find_netcpair_civ2(hObject, eventdata, handles);
4440end
4441
4442%------------------------------------------------------------------------
4443function ref_i_civ2_Callback(hObject, eventdata, handles)
4444%------------------------------------------------------------------------
4445mode_list=get(handles.mode,'String');
4446mode_value=get(handles.mode,'Value');
4447mode=mode_list{mode_value};
4448find_netcpair_civ2(hObject, eventdata, handles);% update the menu of pairs depending on the available netcdf files
4449
4450%------------------------------------------------------------------------
4451function ref_j_civ2_Callback(hObject, eventdata, handles)
4452%------------------------------------------------------------------------
4453mode_list=get(handles.mode,'String');
4454mode_value=get(handles.mode,'Value');
4455mode=mode_list{mode_value};
4456if  isequal(mode,'series(Dj)')
4457    find_netcpair_civ2(hObject, eventdata, handles);% update the menu of pairs depending on the available netcdf files
4458end
4459
4460%------------------------------------------------------------------------
4461% --- Executes on button press in compare.
4462function compare_Callback(hObject, eventdata, handles)
4463%------------------------------------------------------------------------
4464test=get(handles.compare,'Value');
4465if test==2 || test==3
4466    filebase=get(handles.RootName,'String');
4467    browse=get(handles.browse_root,'Userdata');
4468    browse.nom_type_ima1=browse.nom_type_ima;
4469    set(handles.browse_root,'UserData',browse);
4470    set(handles.sub_txt,'Visible','on')
4471    set(handles.RootName_1,'Visible','On');%mkes the second file input window visible
4472    mode_store=get(handles.mode,'String');%get the present 'mode'
4473    set(handles.compare,'UserData',mode_store);%store the mode display
4474    set(handles.mode,'Visible','off')
4475    if test==2
4476        set(handles.mode,'Visible','off')
4477    else
4478        set(handles.mode,'Visible','on')
4479    end
4480   
4481    %% open an image file with the browser
4482    ind_opening=1;%default
4483    browse.incr_pair=[0 0]; %default
4484    oldfile=get(handles.RootName,'String');
4485     menu={'*.xml;*.civ;*.png;*.jpg;*.tif;*.avi;*.AVI;*.nc;', ' (*.xml,*.civ,*.png,*.jpg ,.tif, *.avi,*.nc)';
4486       '*.xml',  '.xml files '; ...
4487        '*.civ',  '.civ files '; ...
4488        '*.png','.png image files'; ...
4489        '*.jpg',' jpeg image files'; ...
4490        '*.tif','.tif image files'; ...
4491        '*.avi;*.AVI','.avi movie files'; ...
4492        '*.nc','.netcdf files'; ...
4493        '*.*',  'All Files (*.*)'};
4494    [FileName, PathName, filtindex] = uigetfile( menu, 'Pick a file of the second series',oldfile);
4495    fileinput=[PathName FileName];%complete file name
4496    sizf=size(fileinput);
4497    if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end %stop if fileinput not a character string
4498    [path,name,ext]=fileparts(fileinput);
4499    [path1]=fileparts(filebase);
4500%     if isunix
4501%         ['readlink ' path]
4502%         [status,path]=system(['readlink ' path])
4503%         [status,path1]=system(['readlink ' path1])% look for the true path in case of symbolic paths
4504%     end
4505    if ~strcmp(path1,path)
4506        msgbox_uvmat('ERROR','The two  input image series must be in the same directory')
4507        return
4508    end
4509    set(handles.RootName_1,'String',name);
4510    [RootPath,RootFile,field_count,str2,str_a,str_b,xx,nom_type,subdir]=name2display(name);
4511    browse=get(handles.browse_root,'UserData');
4512    browse.nom_type_ima_1=nom_type;
4513    set(handles.browse_root,'UserData',browse)
4514   
4515    %check image extension
4516    if ~strcmp(ext,get(handles.ImaExt,'String'))
4517        msgbox_uvmat('ERROR','The two  input image series must have the same extension name')
4518        return
4519    end
4520   
4521    %% check coincidence of image sizes
4522    ref_i=get(handles.ref_i,'string');
4523    ref_j=get(handles.ref_j,'string');
4524    [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]);
4525    A=imread(filecell.ima1.civ1{1});
4526    A_1=imread(fileinput);
4527    npxy=size(A);
4528    npxy_1=size(A_1);
4529    if ~isequal(size(A),size(A_1))
4530        msgbox_uvmat('ERROR','The two input image series do not have the same size')
4531        return
4532    end
4533else
4534    set(handles.mode,'Visible','on')
4535    set(handles.RootName_1,'Visible','Off');
4536    set(handles.sub_txt,'Visible','off')
4537    set(handles.RootName_1,'String',[]);
4538    mode_store=get(handles.compare,'UserData');
4539    set(handles.mode,'Value',1)
4540    set(handles.mode,'String',mode_store)
4541    set(handles.test_stereo1,'Value',0)
4542    set(handles.test_stereo2,'Value',0)
4543end
4544if test==3 && get(handles.PATCH1,'Value')
4545    set(handles.stereo1,'Visible','on')
4546else
4547    set(handles.stereo1,'Visible','off')
4548end
4549if test==3 && get(handles.PATCH2,'Value')
4550    set(handles.stereo2,'Visible','on')
4551else
4552    set(handles.stereo2,'Visible','off')
4553end
4554mode_Callback(hObject, eventdata, handles)
4555
4556%------------------------------------------------------------------------
4557% --- Executes on button press in get_ref_fix1.
4558function get_ref_fix1_Callback(hObject, eventdata, handles)
4559%------------------------------------------------------------------------
4560filebase=get(handles.RootName,'String');
4561[FileName, PathName, filterindex] = uigetfile( ...
4562    {'*.nc', ' (*.nc)';
4563    '*.nc',  'netcdf files '; ...
4564    '*.*', 'All Files (*.*)'}, ...
4565    'Pick a file',filebase);
4566
4567fileinput=[PathName FileName];
4568sizf=size(fileinput);
4569if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end %stop if fileinput not a character string
4570[Path,File,field_count,str2,str_a,str_b,ref.ext,ref.nom_type,ref.subdir]=name2display(fileinput);
4571ref.filebase=fullfile(Path,File);
4572ref.num_a=stra2num(str_a);
4573ref.num_b=stra2num(str_b);
4574ref.num1=str2double(field_count);
4575ref.num2=str2double(str2);
4576browse=[];%initialisation
4577if ~isequal(ref.ext,'.nc')
4578    msgbox_uvmat('ERROR','the reference file must be in netcdf format (*.nc)')
4579    return
4580end
4581set(handles.ref_fix1,'String',[fullfile(ref.subdir,File) '....nc']);
4582set(handles.ref_fix1,'UserData',ref)
4583menu_field{1}='civ1';
4584Data=nc2struct(fileinput,[]);
4585if isfield(Data,'patch') && isequal(Data.patch,1)
4586    menu_field{2}='filter1';
4587end
4588if isfield(Data,'civ2') && isequal(Data.civ2,1)
4589    menu_field{3}='civ2';
4590end
4591if isfield(Data,'patch2') && isequal(Data.patch2,1)
4592    menu_field{4}='filter2';
4593end
4594set(handles.field_ref1,'String',menu_field);
4595set(handles.field_ref1,'Value',length(menu_field));
4596set(handles.inf_sup1,'Value',2);
4597set(handles.thresh_vel,'String','1');%default threshold
4598set(handles.ref_fix1,'Enable','on')
4599
4600%------------------------------------------------------------------------
4601% --- Executes on button press in get_ref_fix2.
4602function get_ref_fix2_Callback(hObject, eventdata, handles)
4603%------------------------------------------------------------------------
4604if isequal(get(handles.get_ref_fix2,'Value'),1)
4605    filebase=get(handles.RootName,'String');
4606    [FileName, PathName, filterindex] = uigetfile( ...
4607        {'*.nc', ' (*.nc)';
4608        '*.nc',  'netcdf files '; ...
4609        '*.*', 'All Files (*.*)'}, ...
4610        'Pick a file',filebase);
4611    fileinput=[PathName FileName];
4612    sizf=size(fileinput);
4613    if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end %stop if fileinput not a character string
4614    [Path,File,field_count,str2,str_a,str_b,ref.ext,ref.nom_type,ref.subdir]=name2display(fileinput);
4615    ref.filebase=fullfile(Path,File);
4616    ref.num_a=stra2num(str_a);
4617    ref.num_b=stra2num(str_b);
4618    ref.num1=str2num(field_count);
4619    ref.num2=str2num(str2);
4620    browse=[];%initialisation
4621    if ~isequal(ref.ext,'.nc')
4622        msgbox_uvmat('ERROR','the reference file must be in netcdf format (*.nc)')
4623        return
4624    end
4625    set(handles.ref_fix2,'String',[fullfile(ref.subdir,File) '....nc']);
4626    set(handles.ref_fix2,'UserData',ref)
4627    menu_field{1}='civ1';
4628    Data=nc2struct(fileinput,[]);
4629    if isfield(Data,'patch') & isequal(Data.patch,1)
4630        menu_field{2}='filter1';
4631    end
4632    if isfield(Data,'civ2') & isequal(Data.civ2,1)
4633        menu_field{3}='civ2';
4634    end
4635    if isfield(Data,'patch2') & isequal(Data.patch2,1)
4636        menu_field{4}='filter2';
4637    end
4638    set(handles.field_ref2,'String',menu_field);
4639    set(handles.field_ref2,'Value',length(menu_field));
4640    set(handles.inf_sup2,'Value',2);
4641    set(handles.thresh_vel2,'String','1');%default threshold
4642    set(handles.ref_fix2,'Enable','on')
4643    set(handles.ref_fix2,'Visible','on')
4644    set(handles.field_ref2,'Visible','on')
4645else
4646    set(handles.ref_fix2,'Visible','off')
4647    set(handles.field_ref2,'Visible','off')
4648end
4649
4650%------------------------------------------------------------------------
4651function ref_fix1_Callback(hObject, eventdata, handles)
4652%------------------------------------------------------------------------
4653set(handles.inf_sup1,'Value',1);
4654set(handles.field_ref1,'Value',1)
4655set(handles.field_ref1,'String',{' '})
4656set(handles.ref_fix1,'UserData',[]);
4657set(handles.ref_fix1,'String','');
4658set(handles.thresh_vel1,'String','0');
4659
4660%------------------------------------------------------------------------
4661function ref_fix2_Callback(hObject, eventdata, handles)
4662%------------------------------------------------------------------------
4663set(handles.inf_sup2,'Value',1);
4664set(handles.field_ref2,'Value',1)
4665set(handles.field_ref2,'String',{' '})
4666set(handles.ref_fix2,'UserData',[]);
4667set(handles.ref_fix2,'String','');
4668set(handles.thresh_vel2,'String','0');
4669
4670%------------------------------------------------------------------------
4671% --- Executes on button press in test_stereo1.
4672function test_stereo1_Callback(hObject, eventdata, handles)
4673%------------------------------------------------------------------------
4674if isequal(get(handles.test_stereo1,'Value'),0)
4675    set(handles.subdomain_patch1,'Visible','on')
4676    set(handles.rho_patch1,'Visible','on')
4677else
4678    set(handles.subdomain_patch1,'Visible','off')
4679    set(handles.rho_patch1,'Visible','off')
4680end
4681
4682%------------------------------------------------------------------------
4683% --- Executes on button press in test_stereo2.
4684function test_stereo2_Callback(hObject, eventdata, handles)
4685%------------------------------------------------------------------------
4686if isequal(get(handles.test_stereo2,'Value'),0)
4687    set(handles.subdomain_patch2,'Visible','on')
4688    set(handles.rho_patch2,'Visible','on')
4689else
4690    set(handles.subdomain_patch2,'Visible','off')
4691    set(handles.rho_patch2,'Visible','off')
4692end
4693
4694%------------------------------------------------------------------------
4695% --- Executes on button press in ImaThreshold.
4696function ImaThreshold_Callback(hObject, eventdata, handles)
4697%------------------------------------------------------------------------
4698if isequal(get(handles.ImaThreshold,'Value'),1)
4699    set(handles.MinIma,'Visible','on')
4700    set(handles.MaxIma,'Visible','on')
4701else
4702    set(handles.MinIma,'Visible','off')
4703    set(handles.MaxIma,'Visible','off')
4704end
4705
4706%------------------------------------------------------------------------
4707% --- Executes on button press in ImaThreshold2.
4708function ImaThreshold2_Callback(hObject, eventdata, handles)
4709%------------------------------------------------------------------------
4710if isequal(get(handles.ImaThreshold2,'Value'),1)
4711    set(handles.MinIma2,'Visible','on')
4712    set(handles.MaxIma2,'Visible','on')
4713else
4714    set(handles.MinIma2,'Visible','off')
4715    set(handles.MaxIma2,'Visible','off')
4716end
4717
4718%------------------------------------------------------------------------
4719% --- Executes on button press in TestCiv1: display image correlation function
4720function TestCiv1_Callback(hObject, eventdata, handles)
4721%------------------------------------------------------------------------
4722set(handles.TestCiv1,'BackgroundColor',[1 1 0])
4723drawnow
4724test_civ1=get(handles.TestCiv1,'Value');
4725if test_civ1
4726    ref_i=str2double(get(handles.ref_i,'String'));
4727    if strcmp(get(handles.ref_j,'Visible'),'on')
4728        ref_j=str2double(get(handles.ref_j,'String'));
4729    else
4730        ref_j=1;%default
4731    end
4732    [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]=...
4733        set_civ_filenames(handles,ref_i,ref_j,[1 0 0 0 0 0])
4734    Data.ListVarName={'ny','nx','A'};
4735    Data.VarDimName={'ny','nx',{'ny','nx'}};
4736    Data.A=imread(filecell.ima1.civ1{1});
4737    Data.ny=[size(Data.A,1) 1];
4738    Data.nx=[1 size(Data.A,2)];
4739    par_civ1=read_param_civ1(handles,filecell.ima1.civ1{1});
4740    par_civ1.filename_ima_a=filecell.ima1.civ1{1};
4741    par_civ1.filename_ima_b=filecell.ima2.civ1{1};
4742    par_civ1.T0=0;
4743    par_civ1.Dt=1;
4744    Param.Civ1=par_civ1;
4745    Data=civ_uvmat(Param);
4746    Data.ListVarName=[Data.ListVarName {'ny','nx','A'}];
4747    Data.VarDimName=[Data.VarDimName {'ny','nx',{'ny','nx'}}];
4748    Data.A=imread(filecell.ima1.civ1{1});
4749    Data.ny=[size(Data.A,1) 1];
4750    Data.nx=[1 size(Data.A,2)];
4751    hview_field=view_field(Data);
4752    set(0,'CurrentFigure',hview_field)
4753    hhview_field=guihandles(hview_field);
4754    set(hview_field,'CurrentAxes',hhview_field.axes3)
4755    ViewData=get(hview_field,'UserData');
4756    ViewData.CivHandle=handles.civ;% indicate the handle of the civ GUI in view_field
4757    ViewData.axes3.B=imread(filecell.ima2.civ1{1});%store the second image in the UserData of the GUI view_field
4758    ViewData.axes3.X=Data.Civ1_X; %keep the set of points in memeory
4759    ViewData.axes3.Y=Data.Civ1_Y;
4760    set(hview_field,'UserData',ViewData)
4761    corrfig=findobj(allchild(0),'tag','corrfig');% look for a current figure for image correlation display
4762    if isempty(corrfig)
4763        corrfig=figure;
4764        set(corrfig,'tag','corrfig')
4765        set(corrfig,'name','image correlation')
4766        set(corrfig,'DeleteFcn',{@closeview_field})%
4767    end
4768    set(handles.TestCiv1,'BackgroundColor',[1 0 0])
4769else
4770    corrfig=findobj(allchild(0),'tag','corrfig');% look for a current figure for image correlation display
4771    if ~isempty(corrfig)
4772        delete(corrfig)
4773    end
4774    hview_field=findobj(allchild(0),'tag','view_field');% look for view_field   
4775    if ~isempty(hview_field)
4776        delete(hview_field)
4777    end
4778end
4779
4780function closeview_field(gcbo,eventdata)
4781hview_field=findobj(allchild(0),'tag','view_field');% look for view_field   
4782    if ~isempty(hview_field)
4783        delete(hview_field)
4784    end
4785%-------------------------------------------------------------------
4786% --- Executes on button press in status.
4787function status_Callback(hObject, eventdata, handles)
4788%-------------------------------------------------------------------
4789val=get(handles.status,'Value');
4790if val==0
4791    set(handles.status,'BackgroundColor',[0 1 0])
4792    hfig=findobj(allchild(0),'name','civ_status');
4793    if ~isempty(hfig)
4794        delete(hfig)
4795    end
4796    return
4797end
4798set(handles.status,'BackgroundColor',[1 1 0])
4799drawnow
4800listtype={'civ1','fix1','patch1','civ2','fix2','patch2'};
4801box_test(1)=get(handles.CIV1,'Value');
4802box_test(2)=get(handles.FIX1,'Value');
4803box_test(3)=get(handles.PATCH1,'Value');
4804box_test(4)=get(handles.CIV2,'Value');
4805box_test(5)=get(handles.FIX2,'Value');
4806box_test(6)=get(handles.PATCH2,'Value');
4807option_civ=find(box_test,1,'last');%last selected option (non-zero index of box_test)
4808filecell=get(handles.civ,'UserData');%retrieve the list of output files expected for PIV
4809test_new=0;
4810if ~isfield(filecell,'nc')
4811    test_new=1;
4812    [ref_i,ref_j,errormsg]=find_ref_indices(handles);
4813    if ~isempty(errormsg)
4814        msgbox_uvmat('ERROR',errormsg)
4815        return
4816    end
4817    filecell=set_civ_filenames(handles,ref_i,ref_j,box_test);%determine the output file expected from the GUI status
4818end
4819if ~isequal(box_test(4:6),[0 0 0])
4820    civ_files=filecell.nc.civ2;%case of civ2 operations
4821else
4822    civ_files=filecell.nc.civ1;
4823end
4824[root,filename,ext]=fileparts(civ_files{1});
4825[rootroot,subdir,extdir]=fileparts(root);
4826hfig=findobj(allchild(0),'name','civ_status');
4827if isempty(hfig)
4828    hfig=figure('DeleteFcn',@stop_status);
4829    set(hfig,'name','civ_status')
4830    hlist=uicontrol('Style','listbox','Units','normalized', 'Position',[0.05 0.09 0.9 0.71], 'Callback', @open_view_field,'tag','list');
4831    uicontrol('Style','edit','Units','normalized', 'Position', [0.05 0.87 0.9 0.1],'tag','msgbox','Max',2,'String','checking files...');
4832    uicontrol('Style','frame','Units','normalized', 'Position', [0.05 0.81 0.9 0.05]);
4833    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);
4834    BarPosition=[0.05 0.81 0.01 0.05];
4835    hwaitbar=uicontrol('Style','frame','Units','normalized', 'Position',BarPosition ,'BackgroundColor',[1 0 0],'tag','waitbar');
4836    drawnow
4837end
4838% datnum=[];
4839Tabchar={};
4840nbfiles=numel(civ_files);
4841count=0;
4842testrecent=0;
4843while count<nbfiles
4844    count=0;
4845    datnum=zeros(1,nbfiles);
4846    for ifile=1:nbfiles
4847        detect=exist(civ_files{ifile},'file'); % check the existence of the file
4848        option=0;
4849        if detect==0
4850            option_str='not created';
4851        else
4852            datfile=dir(civ_files{ifile});
4853            if isfield(datfile,'datenum')
4854                datnum(ifile)=datfile.datenum;%only available in recent matlab versions
4855                testrecent=1;
4856            end
4857            filefound(ifile)={datfile.name};
4858            lastfield='';
4859            % check the content  netcdf file
4860            Data=nc2struct(civ_files{ifile},'ListGlobalAttribute','patch2','fix2','civ2','patch','fix');
4861            if ~isempty(Data.patch2) && isequal(Data.patch2,1)
4862                option=6;
4863                option_str='patch2';
4864            elseif ~isempty(Data.fix2) && isequal(Data.fix2,1)
4865                option=5;
4866                option_str='fix2';
4867            elseif ~isempty(Data.civ2) && isequal(Data.civ2,1);
4868                option=4;
4869                option_str='civ2';
4870            elseif ~isempty(Data.patch) && isequal(Data.patch,1);
4871                option=3;
4872                option_str='patch1';
4873            elseif ~isempty(Data.fix) && isequal(Data.fix,1);
4874                option=2;
4875                option_str='fix1';
4876            else
4877                option=1;
4878                option_str='civ1';
4879            end
4880        end
4881        if option >= option_civ
4882            count=count+1;
4883        end
4884        [rr,filename,ext]=fileparts(civ_files{ifile});
4885        Tabchar{ifile,1}=[fullfile([subdir extdir],filename) ext  '...' option_str];
4886    end
4887    datnum=datnum(datnum~=0);%keep the non zero values corresponding to existing files
4888    if isempty(datnum)
4889        if testrecent
4890            message='no civ result created yet';
4891        else
4892            message='';
4893        end
4894    else
4895        datnum=datnum(datnum~=0);%keep the non zero values corresponding to existing files
4896        [first,ind]=min(datnum);
4897        [last,indlast]=max(datnum);
4898        if test_new
4899            message='existing file status, no processing launched yet';
4900        else
4901        message={[num2str(count) ' file(s) done over ' num2str(nbfiles)] ;['oldest modification:  ' cell2mat(filefound(ind)) ' : ' datestr(first)];...
4902            ['latest modification:  ' cell2mat(filefound(indlast)) ' : ' datestr(last)]};
4903        end
4904    end
4905    hfig=findobj(allchild(0),'name','civ_status');
4906    if isempty(hfig)% the status list has been deleted
4907        return
4908    else
4909        hlist=findobj(hfig,'tag','list');
4910        hmsgbox=findobj(hfig,'tag','msgbox');
4911        hwaitbar=findobj(hfig,'tag','waitbar');
4912        set(hlist,'String',Tabchar)
4913        set(hmsgbox,'String', message)
4914        if count>0 && ~test_new
4915            BarPosition(3)=0.9*count/nbfiles;
4916            set(hwaitbar,'Position',BarPosition)
4917        end
4918    end
4919    set(hlist,'UserData',rootroot)
4920    pause(10)% wait 10 seconds for next check
4921end
4922
4923   
4924%------------------------------------------------------------------------   
4925% call 'view_field.fig' to display the  field selected in the list of 'status'
4926function open_view_field(hObject, eventdata)
4927%------------------------------------------------------------------------
4928list=get(hObject,'String');
4929index=get(hObject,'Value');
4930rootroot=get(hObject,'UserData');
4931filename=list{index};
4932ind_dot=findstr(filename,'...');
4933filename=filename(1:ind_dot-1);
4934filename=fullfile(rootroot,filename);
4935delete(get(hObject,'parent'))%delete the display figure to stop the check process
4936if exist(filename,'file')%visualise the vel field if it exists
4937    uvmat(filename)
4938    set(gcbo,'Value',1)
4939end
4940
4941%------------------------------------------------------------------------   
4942% launched by pressing OK on the status figure
4943function close_GUI(hObject, eventdata)
4944%------------------------------------------------------------------------
4945    delete(gcbf)
4946   
4947%------------------------------------------------------------------------   
4948% launched by deleting the status figure
4949function stop_status(hObject, eventdata)
4950%------------------------------------------------------------------------
4951hciv=findobj(allchild(0),'tag','civ');
4952hhciv=guidata(hciv);
4953set(hhciv.status,'value',0) %reset the status uicontrol in the GUI civ
4954set(hhciv.status,'BackgroundColor',[0 1 0])
4955
4956%------------------------------------------------------------------------
4957% --- Executes on button press in CivMode.
4958function CivMode_Callback(hObject, eventdata, handles)
4959%------------------------------------------------------------------------
4960Listprog=get(handles.CivMode,'String');
4961index=get(handles.CivMode,'Value');
4962prog=Listprog{index};
4963switch prog
4964    case 'CivX'
4965        set(handles.thresh_patch1,'Visible','off')
4966        set(handles.thresh_text1,'Visible','off')
4967        set(handles.thresh_patch2,'Visible','off')
4968        set(handles.thresh_text2,'Visible','off')
4969        set(handles.rho,'Style','edit')
4970        set(handles.rho,'String','1')
4971        set(handles.BATCH,'Enable','on')
4972    case 'CivAll'
4973        if get(handles.PATCH1,'Value')
4974            set(handles.thresh_patch1,'Visible','on')
4975            set(handles.thresh_text1,'Visible','on')
4976        end
4977        set(handles.rho,'Style','edit')
4978        set(handles.rho,'String','1')
4979        set(handles.BATCH,'Enable','on')
4980    case 'CivUvmat'
4981        if get(handles.PATCH1,'Value')
4982            set(handles.thresh_patch1,'Visible','on')
4983            set(handles.thresh_text1,'Visible','on')
4984        end
4985        if get(handles.PATCH2,'Value')
4986            set(handles.thresh_patch2,'Visible','on')
4987            set(handles.thresh_text2,'Visible','on')
4988        end
4989        set(handles.rho,'Style','popupmenu')
4990        set(handles.rho,'Value',1)
4991        set(handles.rho,'String',{'1';'2'})
4992        set(handles.BATCH,'Enable','off')
4993end
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