source: trunk/src/civ.m @ 263

Last change on this file since 263 was 263, checked in by sommeria, 12 years ago

stereo option repaired

File size: 202.5 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,xx,yy,compare]=...
1511    set_civ_filenames(handles,ref_i,ref_j,box_test)
1512
1513set(handles.civ,'UserData',filecell);%store for futur use of status callback
1514if isempty(filecell)% (error message displayed in fct set_civ_filenames)
1515    return
1516end
1517nbfield=numel(num1_civ1);
1518nbslice=numel(num_a_civ1);
1519
1520%% choose the batch or run mode
1521path_UVMAT=fileparts(which('uvmat')); %path to the source directory of uvmat
1522xmlfile='PARAM.xml';
1523if exist(xmlfile,'file')% search parameter xml file in the whole matlab path
1524    t=xmltree(xmlfile);
1525    s=convert(t);
1526end
1527test_interp=0;
1528if batch
1529    if isfield(s,'BatchParam')
1530        sparam=s.BatchParam;
1531        if isfield(sparam,'BatchMode')
1532            batch_mode=sparam.BatchMode;
1533            if ~ismember(batch_mode,{'sge','oar'})
1534                errormsg=['batch mode ' batch_mode ' not supported by UVMAT'];
1535                return
1536            end
1537        end
1538    else
1539        errormsg='no batch civ binaries defined in PARAM.xml';
1540        return
1541    end
1542   
1543    switch batch_mode
1544        case 'sge'
1545            % choice of batch priority:
1546            ind_answer=2;
1547            [s,w]=unix('qstat -q civ.q|grep job_| wc -l'); %check the waiting list (command unix)
1548            if isequal(s,0)
1549                w(end)=[];
1550                str_displ={[w ' jobs in the waiting list'];...
1551                    '***********************';...
1552                    'JOBS PRIORITY POLICY';...
1553                    '- urgent = less than 100 images pairs';...
1554                    '- normal = during the experiments';...
1555                    '- low = post processing';...
1556                    '***********************';...
1557                    'Select a priority:'};
1558                ' ';...
1559                    str={'urgent';'normal';'low'};
1560                [ind_answer,v] = listdlg('PromptString',str_displ,...
1561                    'SelectionMode','single',...
1562                    'ListString',str,'ListSize',[200 100],'Name','job priority','InitialValue',3);
1563                if isequal(v,0) % to handle Cancel button and figure close,
1564                    errormsg='job cancelled';
1565                    return % a better way should be create
1566                end
1567            else
1568                msgbox_uvmat('ERROR','sge batch system not available')
1569                return
1570            end
1571    end
1572else % run
1573    if isfield(s,'RunParam')
1574        sparam=s.RunParam;
1575    else
1576        msgbox_uvmat('ERROR','no run civ binaries defined in PARAM.xml')
1577        return
1578    end
1579end
1580
1581%% choose the civ program
1582ProgList=get(handles.CivMode,'String');
1583index=get(handles.CivMode,'Value');
1584% CivX=isequal(ProgList{index},'CivX');
1585% CivAll=isequal(ProgList{index},'CivAll');
1586% CivUvmat=isequal(ProgList{index},'CivUvmat');
1587CivMode=ProgList{index};
1588%CivMode=isequal(get(handles.CivMode,'Value'),2); % Boolean for new civ programs
1589
1590switch CivMode
1591    case 'CivAll'
1592        if isfield(sparam,'CivBin')
1593            CivBin=sparam.CivBin;
1594            if ~exist(CivBin,'file') || isempty(which(CivBin))% if path defined as relative to uvmat
1595                sparam.CivBin=fullfile(path_UVMAT,CivBin);
1596                if ~exist(sparam.CivBin,'file')
1597                    msgbox_uvmat('ERROR',['CIVx binary ' CivBin ' defined in PARAM.xm does not exist'])
1598                    return
1599                end
1600            end
1601        end
1602    case 'CivX'
1603        if isfield(sparam,'Civ1Bin')
1604            Civ1Bin=sparam.Civ1Bin;
1605            if ~exist(Civ1Bin,'file')&&~isempty(which(Civ1Bin))% if path defined as relative to uvmat
1606                sparam.Civ1Bin=fullfile(path_UVMAT,Civ1Bin);
1607                if ~exist(sparam.Civ1Bin,'file')
1608                    msgbox_uvmat('ERROR',['civ1 binary ' Civ1Bin ' defined in PARAM.xm does not exist'])
1609                    return
1610                end
1611            end
1612        end
1613        if isfield(sparam,'Civ2Bin')
1614            Civ2Bin=sparam.Civ2Bin;
1615            if ~exist(Civ2Bin,'file')&&~isempty(which(Civ2Bin))% if path defined as relative to uvmat
1616                sparam.Civ2Bin=fullfile(path_UVMAT,Civ2Bin);
1617                if ~exist(sparam.Civ2Bin,'file')
1618                    msgbox_uvmat('ERROR',['civ2 binary ' Civ2Bin ' defined in PARAM.xm does not exist'])
1619                    return
1620                end
1621            end
1622        end
1623        if  isfield(sparam,'PatchBin')
1624            if ~exist(sparam.PatchBin,'file')&&~isempty(which(sparam.PatchBin))% if path defined as relative to uvmat
1625                sparam.PatchBin=fullfile(path_UVMAT,sparam.PatchBin);
1626            end
1627        end
1628        if isfield(sparam,'FixBin')
1629            if ~exist(sparam.FixBin,'file')&&~isempty(which(sparam.FixBin))% if path defined as relative to uvmat
1630                sparam.FixBin=fullfile(path_UVMAT,sparam.FixBin);
1631            end
1632        end
1633    case 'Matlab'
1634        if batch
1635            %% vérifier Mtlab installé sur le cluster
1636        end         
1637end
1638
1639
1640
1641%% get civ1 parameters:
1642display('files OK, processing...')
1643if box_test(1)==1
1644    par_civ1=read_param_civ1(handles,filecell.ima1.civ1{1,1});
1645end
1646
1647%% get fix1 parameters TODO : par_fix1=read_param_fix1(handles);
1648if box_test(2)==1
1649    flagindex1(1)=get(handles.vec_Fmin2, 'Value');
1650    flagindex1(2)=get(handles.vec_F3, 'Value');
1651    flagindex1(3)=get(handles.vec_F2, 'Value');
1652    thresh_vecC1=str2double(get(handles.thresh_vecC,'String'));%threshold on image correlation vec_C
1653    thresh_vel1=str2double(get(handles.thresh_vel,'String'));%threshold on velocity modulus
1654    test_mask=get(handles.get_mask_fix1,'Value');
1655    nbslice_mask=get(handles.mask_fix1,'UserData'); % get the number of slices (= number of masks)
1656    %%%%%%%%%%%%%COMPLETER LE PROGRAMME FIX
1657    %     inf_sup=get(handles.inf_sup1,'Value');80
1658    %     fileref=get(handles.ref_fix1,'String');
1659    %     refpath=get(handles.ref_fix1,'UserData');
1660    %     fileref=fullfile(refpath,fileref);
1661    menu=get(handles.field_ref1,'String');
1662    index=get(handles.field_ref1,'Value');
1663    if isempty(menu)
1664        fieldchoice='';
1665    else
1666        fieldchoice=menu{index};
1667        msgbox_uvmat('WARNING','reference field is not used presently with batch, use RUN option')
1668    end
1669end
1670
1671%% get patch1 parameters
1672if box_test(3)==1
1673    rho_patch1=str2double(get(handles.rho_patch1,'String'));
1674    if isnan(rho_patch1)
1675        rho_patch1='1000';
1676        set(handles.rho_patch1,'String','1')
1677    else
1678        rho_patch1=num2str(1000*rho_patch1);
1679    end
1680    nx_patch1=get(handles.nx_patch1,'String');
1681    ny_patch1=get(handles.ny_patch1,'String');
1682    if isnan(str2double(nx_patch1))
1683        nx_patch1='50' ;%default
1684        set(handles.nx_patch1,'String','50');
1685    end
1686    if isnan(str2double(ny_patch1))
1687        ny_patch1='50' ;%default
1688        set(handles.ny_patch1,'String','50');
1689    end
1690    subdomain_patch1=get(handles.subdomain_patch1,'String');
1691    thresh_patch1=get(handles.thresh_patch1,'String');
1692end
1693
1694%% get civ2 parameters:
1695if box_test(4)==1
1696    par_civ2=read_param_civ2(handles,cell2mat(filecell.ima1.civ2(1,1)));
1697end
1698
1699%% get fix2 parameters
1700if box_test(5)==1
1701    flagindex2(1)=get(handles.vec_Fmin2_2, 'Value');
1702    flagindex2(2)=get(handles.vec_F3_2, 'Value');
1703    flagindex2(3)=get(handles.vec_F4, 'Value');
1704    thresh_vec2C=str2double(get(handles.thresh_vec2C,'String'));%threshold on image correlation vec_C
1705    thresh_vel2=str2double(get(handles.thresh_vel2,'String'));%threshold on velocity modulus
1706    test_mask=get(handles.get_mask_fix2,'Value');
1707    nbslice_mask=get(handles.mask_fix2,'UserData'); % get the number of slices (= number of masks)
1708    %%%%%%%%%%%%%COMPLETER LE PROGRAMME FIX AVEC REF FILE ET OPTION inf_sup=2
1709    %     inf_sup=get(handles.inf_sup2,'Value');
1710    %     ref=get(handles.ref_fix2,'UserData');
1711   
1712    %%%%%%%%%%%%%%%%%%%
1713end
1714
1715%% get patch2 parameters
1716if box_test(6)==1
1717    rho_patch2=str2double(get(handles.rho_patch2,'String'));
1718    if isnan(rho_patch2)
1719        rho_patch2='1000';
1720        set(handles.rho_patch2,'String','1')
1721    else
1722        rho_patch2=num2str(1000*rho_patch2);
1723    end
1724    nx_patch2=get(handles.nx_patch2,'String');
1725    ny_patch2=get(handles.ny_patch2,'String');
1726    if isnan(str2double(nx_patch2))
1727        nx_patch2='50' ;%default
1728        set(handles.nx_patch2,'String','50');
1729    end
1730    if isnan(str2double(ny_patch2))
1731        ny_patch2='50' ;%default
1732        set(handles.ny_patch2,'String','50');
1733    end
1734    subdomain_patch2=get(handles.subdomain_patch2,'String');
1735    thresh_patch2=get(handles.thresh_patch2,'String');
1736end
1737
1738%% MAIN LOOP
1739time=get(handles.RootName,'UserData'); %get the set of times
1740super_cmd=[];
1741
1742for ifile=1:nbfield
1743    for j=1:nbslice
1744        % initiate system command
1745        i_cmd=0;
1746        switch CivMode
1747            case 'CivX'
1748                cmd='';
1749                if isunix % check: necessaire aussi en RUN?
1750                    cmd='#!/bin/bash \n';
1751                    cmd=[cmd '#$ -cwd \n'];
1752                    cmd=[cmd 'hostname && date \n'];
1753                    cmd=[cmd 'umask 002 \n'];%allow writting access to created files for user group
1754                end
1755            case 'CivAll'
1756                %         if CivAll
1757                CivAllxml=xmltree;% xml contents,  all parameters
1758                CivAllCmd='';
1759                CivAllxml=set(CivAllxml,1,'name','CivDoc');
1760        end
1761        [Rootbat,Filebat]=fileparts(filecell.nc.civ1{ifile,j});%output netcdf file (without extension)
1762        flname=fullfile(Rootbat,Filebat);
1763        if batch
1764            filename_bat=fullfile(Rootbat,['job_' Filebat]);
1765        else
1766            filename_bat=flname;
1767        end
1768        filename_bat=[filename_bat '.bat'];
1769       
1770        %CIV1
1771        if box_test(1)==1
1772            par_civ1.filename_ima_a=filecell.ima1.civ1{ifile,j};
1773            par_civ1.filename_ima_b=filecell.ima2.civ1{ifile,j};
1774            par_civ1.Dt=num2str(time(num2_civ1(ifile),num_b_civ1(j))-time(num1_civ1(ifile),num_a_civ1(j)));
1775            par_civ1.T0=num2str((time(num2_civ1(ifile),num_b_civ1(j))+time(num1_civ1(ifile),num_a_civ1(j)))/2);
1776            par_civ1.term_a=num2stra(num_a_civ1(j),nom_type_nc);%UTILITE?
1777            par_civ1.term_b=num2stra(num_b_civ1(j),nom_type_nc);%
1778            test_mask=get(handles.get_mask_civ1,'Value');
1779            if test_mask==0
1780                par_civ1.maskname='noFile use default';
1781                par_civ1.maskflag='n';
1782            else
1783                maskdispl=get(handles.mask_civ1,'String');
1784                if exist(maskdispl,'file')
1785                    par_civ1.maskname=maskdispl;
1786                    par_civ1.maskflag='y';
1787                else
1788                    maskbase=[filecell.filebase '_' maskdispl]; %
1789                    nbslice_mask=str2double(maskdispl(1:end-4)); %
1790                    num1_mask=mod(num1_civ1(ifile)-1,nbslice_mask)+1;
1791                    par_civ1.maskname=name_generator(maskbase,num1_mask,1,'.png','_i');
1792                    if exist(par_civ1.maskname,'file')
1793                        par_civ1.maskflag='y';
1794                    else
1795                        par_civ1.maskname='noFile use default';
1796                        par_civ1.maskflag='n';
1797                    end
1798                end
1799            end
1800            test_grid=get(handles.browse_gridciv1,'Value');
1801            if test_grid
1802                par_civ1.gridflag='y';
1803                gridname=get(handles.grid_civ1,'String');
1804                if isequal(gridname(end-3:end),'grid')
1805                    nbslice_grid=str2double(gridname(1:end-4)); %
1806                    if ~isnan(nbslice_grid)
1807                        num1_grid=mod(num1_civ1(ifile)-1,nbslice_grid)+1;
1808                        par_civ1.gridname=[filecell.filebase '_' name_generator(gridname,num1_grid,1,'.grid','_i')];
1809                        if ~exist(par_civ1.gridname,'file')
1810                            msgbox_uvmat('ERROR','grid file absent for civ1')
1811                        end
1812                    elseif exist(gridname,'file')
1813                        par_civ1.gridname=gridname;
1814                    else
1815                        msgbox_uvmat('ERROR','grid file absent for civ1')
1816                    end
1817                end
1818            else
1819                par_civ1.gridname='noFile use default';
1820                par_civ1.gridflag='n';
1821            end
1822           
1823            i_cmd=i_cmd+1;
1824            switch CivMode
1825                case 'CivX'
1826                    civ1_exe=CIV1_CMD(fullfile(Rootbat,Filebat),'',par_civ1,handles,sparam);%create the parameter file .civ1.cmx and set the execution string civ1_exe
1827                    cmd=[cmd civ1_exe '\n'];
1828                case 'CivAll'
1829                    CivAllCmd=[CivAllCmd ' civ1 '];
1830                    str=CIV1_CMD_Unified(fullfile(Rootbat,Filebat),'',par_civ1);
1831                    fieldnames=fields(str);
1832                    [CivAllxml,uid_civ1]=add(CivAllxml,1,'element','civ1');
1833                    for ilist=1:length(fieldnames)
1834                        val=eval(['str.' fieldnames{ilist}]);
1835                        if ischar(val)
1836                            [CivAllxml,uid_t]=add(CivAllxml,uid_civ1,'element',fieldnames{ilist});
1837                            [CivAllxml,uid_t2]=add(CivAllxml,uid_t,'chardata',val);
1838                        end
1839                    end
1840            end
1841        end
1842       
1843        % FIX1
1844        if box_test(2)==1
1845            test_mask=get(handles.get_mask_fix1,'Value');
1846            if test_mask==0
1847                maskname='';
1848            else
1849                maskdispl=get(handles.mask_fix1,'String');
1850                nbslice_mask=str2double(maskdispl(1:end-4)); %
1851                num1_mask=mod(num1_civ1(ifile)-1,nbslice_mask)+1;
1852                maskbase=[filecell.filebase '_' maskdispl];
1853                maskname=name_generator(maskbase,num1_mask,1,'.png','_i');
1854            end
1855            switch CivMode
1856                %             if CivX
1857                case 'CivX'
1858                    if isunix %unix system
1859                        cmd_FIX=[sparam.FixBin ' -f ' filecell.nc.civ1{ifile,j} ' -fi1 ' num2str(flagindex1(1)) ...
1860                            ' -fi2 ' num2str(flagindex1(2)) ' -fi3 ' num2str(flagindex1(3)) ...
1861                            ' -threshC ' num2str(thresh_vecC1) ' -threshV ' num2str(thresh_vel1) ' -maskName ' maskname];
1862                    else %windows system
1863                        cmd_FIX=['"' sparam.FixBin '" -f "' filecell.nc.civ1{ifile,j} '" -fi1 ' num2str(flagindex1(1)) ...
1864                            ' -fi2 ' num2str(flagindex1(2)) ' -fi3 ' num2str(flagindex1(3)) ...
1865                            ' -threshC ' num2str(thresh_vecC1) ' -threshV ' num2str(thresh_vel1) ' -maskName "' maskname '"'];
1866                        cmd_FIX=regexprep(cmd_FIX,'\\','\\\\');
1867                    end
1868                    cmd=[cmd cmd_FIX '\n'];
1869                case 'CivAll'
1870                    fix1.inputFileName=filecell.nc.civ1{ifile,j} ;
1871                    fix1.fi1=num2str(flagindex1(1));
1872                    fix1.fi2=num2str(flagindex1(2));
1873                    fix1.fi3=num2str(flagindex1(3));
1874                    fix1.threshC=num2str(thresh_vecC1);
1875                    fix1.threshV=num2str(thresh_vel1);
1876                    fieldnames=fields(fix1);
1877                    [CivAllxml,uid_fix1]=add(CivAllxml,1,'element','fix1');
1878                    for ilist=1:length(fieldnames)
1879                        val=eval(['fix1.' fieldnames{ilist}]);
1880                        if ischar(val)
1881                            [CivAllxml,uid_t]=add(CivAllxml,uid_fix1,'element',fieldnames{ilist});
1882                            [CivAllxml,uid_t2]=add(CivAllxml,uid_t,'chardata',val);
1883                        end
1884                    end
1885                    CivAllCmd=[CivAllCmd ' fix1 '];
1886            end
1887        end
1888       
1889        %PATCH1
1890        if box_test(3)==1
1891            switch CivMode
1892                case 'CivX'
1893                    cmd_PATCH=PATCH_CMD(filecell.nc.civ1{ifile,j},nx_patch1,ny_patch1,rho_patch1,subdomain_patch1,thresh_patch1,test_interp,sparam.PatchBin);
1894                    cmd=[cmd cmd_PATCH '\n'];
1895                case 'CivAll'
1896                    patch1.inputFileName=filecell.nc.civ1{ifile,j} ;
1897                    patch1.nopt=subdomain_patch1;
1898                    patch1.maxdiff=thresh_patch1;
1899                    patch1.ro=rho_patch1;
1900                    test_grid=get(handles.get_gridpatch1,'Value');
1901                    if test_grid
1902                        patch1.gridflag='y';
1903                        gridname=get(handles.grid_patch1,'String');
1904                        if isequal(gridname(end-3:end),'grid')
1905                            nbslice_grid=str2double(gridname(1:end-4)); %
1906                            if ~isnan(nbslice_grid)
1907                                num1_grid=mod(num1_civ1(ifile)-1,nbslice_grid)+1;
1908                                patch1.gridPatch=[filecell.filebase '_' name_generator(gridname,num1_grid,1,'.grid','_i')];
1909                                if ~exist(patch1.gridPatch,'file')
1910                                    msgbox_uvmat('ERROR','grid file absent for patch1')
1911                                end
1912                            elseif exist(gridname,'file')
1913                                patch1.gridPatch=gridname;
1914                            else
1915                                msgbox_uvmat('ERROR','grid file absent for patch1')
1916                            end
1917                        end
1918                    else
1919                        patch1.gridPatch='none';
1920                        patch1.gridflag='n';
1921                        patch1.m=nx_patch1;
1922                        patch1.n=ny_patch1;
1923                    end
1924                    patch1.convectFlow='n';
1925                    fieldnames=fields(patch1);
1926                    [CivAllxml,uid_patch1]=add(CivAllxml,1,'element','patch1');
1927                    for ilist=1:length(fieldnames)
1928                        val=eval(['patch1.' fieldnames{ilist}]);
1929                        if ischar(val)
1930                            [CivAllxml,uid_t]=add(CivAllxml,uid_patch1,'element',fieldnames{ilist});
1931                            [CivAllxml,uid_t2]=add(CivAllxml,uid_t,'chardata',val);
1932                        end
1933                    end
1934                    CivAllCmd=[CivAllCmd ' patch1 '];
1935            end
1936        end
1937        if box_test(4)==1 || box_test(5)==1 || box_test(6)==1
1938            filename_cmx=filecell.nc.civ2{ifile,j};%output netcdf file
1939            filename_cmx(end-1:end+1)='cmx';%name of cmx file
1940        end
1941        if box_test(4)==1
1942            par_civ2.filename_ima_a=filecell.ima1.civ2{ifile,j};
1943            par_civ2.filename_ima_b=filecell.ima2.civ2{ifile,j};
1944            [Rootbat,Filebat]=fileparts(filecell.nc.civ2{ifile,j});%output netcdf file (without extention)
1945            par_civ2.Dt=num2str(time(num2_civ2(ifile),num_b_civ2(j))-time(num1_civ2(ifile),num_a_civ2(j)));
1946            par_civ2.T0=num2str((time(num2_civ1(ifile),num_b_civ2(j))+time(num1_civ2(ifile),num_a_civ2(j)))/2);
1947            par_civ2.term_a=num2stra(num_a_civ2(j),nom_type_nc);
1948            par_civ2.term_b=num2stra(num_b_civ2(j),nom_type_nc);
1949            par_civ2.filename_nc1=filecell.nc.civ1{ifile,j};
1950            par_civ2.filename_nc1(end-2:end)=[]; % remove '.nc'
1951            test_mask=get(handles.get_mask_civ2,'Value');
1952            if test_mask==0
1953                par_civ2.maskname='noFile use default';
1954                par_civ2.maskflag='n';
1955            else
1956                maskdispl=get(handles.mask_civ2,'String');
1957                if exist(maskdispl,'file')
1958                    par_civ2.maskname=maskdispl;
1959                    par_civ2.maskflag='y';
1960                else
1961                    maskbase=[filecell.filebase '_' maskdispl]; %
1962                    nbslice_mask=str2double(maskdispl(1:end-4)); %
1963                    num1_mask=mod(num1_civ2(ifile)-1,nbslice_mask)+1;
1964                    par_civ2.maskname=name_generator(maskbase,num1_mask,1,'.png','_i');
1965                    if exist(par_civ2.maskname,'file')
1966                        par_civ2.maskflag='y';
1967                    else
1968                        par_civ2.maskname='noFile use default';
1969                        par_civ2.maskflag='n';
1970                    end
1971                end
1972            end
1973            gridname=get(handles.grid_civ2,'String');
1974            if numel(gridname)>=4 && isequal(gridname(end-3:end),'grid')
1975                nbslice_grid=str2double(gridname(1:end-4)); %
1976                if ~isnan(nbslice_grid)
1977                    par_civ2.gridflag='y';
1978                    num1_grid=mod(num1_civ2(ifile)-1,nbslice_grid)+1;
1979                    par_civ2.gridname=[filecell.filebase '_' name_generator(gridname,num1_grid,1,'.grid','_i')];
1980                    if exist(par_civ2.gridname,'file')
1981                        par_civ2.gridflag='y';
1982                    else
1983                        par_civ2.gridname='noFile use default';
1984                        par_civ2.gridflag='n';
1985                    end
1986                elseif exist(gridname,'file')
1987                    par_civ2.gridflag='y';
1988                else
1989                    par_civ2.gridname='noFile use default';
1990                    par_civ2.gridflag='n';
1991                end
1992            end
1993            i_cmd=i_cmd+1;
1994            flname=fullfile(Rootbat,Filebat);
1995            switch CivMode
1996                case 'CivX'
1997                    cmd_CIV2=CIV2_CMD(flname,[],par_civ2,sparam);%creates the cmx file [fullfile(Rootbat,Filebat) '.civ2.cmx]
1998                    cmd=[cmd cmd_CIV2 '\n'];
1999                case 'CivAll'
2000                    CivAllCmd=[CivAllCmd ' civ2 '];
2001                    str=CIV2_CMD_Unified(flname,'',par_civ2);
2002                    fieldnames=fields(str);
2003                    [CivAllxml,uid_civ2]=add(CivAllxml,1,'element','civ2');
2004                    for ilist=1:length(fieldnames)
2005                        val=eval(['str.' fieldnames{ilist}]);
2006                        if ischar(val)
2007                            [CivAllxml,uid_t]=add(CivAllxml,uid_civ2,'element',fieldnames{ilist});
2008                            [CivAllxml,uid_t2]=add(CivAllxml,uid_t,'chardata',val);
2009                        end
2010                    end
2011            end
2012        end
2013       
2014        % FIX2
2015        if box_test(5)==1
2016            test_mask=get(handles.get_mask_fix2,'Value');
2017            if test_mask==0
2018                maskname=''; %no mask used
2019            else
2020                maskdispl=get(handles.mask_fix2,'String');
2021                maskbase=[filecell.filebase '_' maskdispl]; %
2022                nbslice_mask=str2double(maskdispl(1:end-4)); %
2023                num1_mask=mod(num1_civ2(ifile)-1,nbslice_mask)+1;
2024                maskname =name_generator(maskbase,num1_mask,1,'.png','_i');
2025            end
2026            switch CivMode
2027                case 'CivX'
2028                    if isunix
2029                        cmd_FIX=[sparam.FixBin ' -f ' filecell.nc.civ2{ifile,j} ' -fi1 ' num2str(flagindex2(1)) ...
2030                            ' -fi2 ' num2str(flagindex2(2)) ' -fi3 ' num2str(flagindex2(3)) ...
2031                            ' -threshC ' num2str(thresh_vec2C) ' -threshV ' num2str(thresh_vel2) ' -maskName ' maskname];
2032                    else
2033                        cmd_FIX=['"' sparam.FixBin '" -f "' filecell.nc.civ2{ifile,j} '" -fi1 ' num2str(flagindex2(1)) ...
2034                            ' -fi2 ' num2str(flagindex2(2)) ' -fi3 ' num2str(flagindex2(3)) ...
2035                            ' -threshC ' num2str(thresh_vec2C) ' -threshV ' num2str(thresh_vel2) ' -maskName "' maskname '"'];
2036                        cmd_FIX=regexprep(cmd_FIX,'\\','\\\\');
2037                    end
2038                    cmd=[cmd cmd_FIX '\n'];
2039                case 'CivAll'
2040                    fix2.inputFileName=filecell.nc.civ2{ifile,j} ;
2041                    fix2.fi1=num2str(flagindex2(1));
2042                    fix2.fi2=num2str(flagindex2(2));
2043                    fix2.fi3=num2str(flagindex2(3));
2044                    fix2.threshC=num2str(thresh_vec2C);
2045                    fix2.threshV=num2str(thresh_vel2);
2046                    fieldnames=fields(fix2);
2047                    [CivAllxml,uid_fix2]=add(CivAllxml,1,'element','fix2');
2048                    for ilist=1:length(fieldnames)
2049                        val=eval(['fix2.' fieldnames{ilist}]);
2050                        if ischar(val)
2051                            [CivAllxml,uid_t]=add(CivAllxml,uid_fix2,'element',fieldnames{ilist});
2052                            [CivAllxml,uid_t2]=add(CivAllxml,uid_t,'chardata',val);
2053                        end
2054                    end
2055                    CivAllCmd=[CivAllCmd ' fix2 '];
2056            end
2057        end
2058       
2059        %PATCH2
2060        if box_test(6)==1
2061            switch CivMode
2062                case 'CivX'
2063                    cmd_PATCH=PATCH_CMD(filecell.nc.civ2{ifile,j},nx_patch2,ny_patch2,rho_patch2,subdomain_patch2,thresh_patch2,test_interp,sparam.PatchBin);
2064                    cmd=[cmd cmd_PATCH '\n'];
2065                case 'CivAll'
2066                    patch2.inputFileName=filecell.nc.civ1{ifile,j} ;
2067                    patch2.nopt=subdomain_patch2;
2068                    patch2.maxdiff=thresh_patch2;
2069                    patch2.ro=rho_patch2;
2070                    test_grid=get(handles.get_gridpatch2,'Value');
2071                    if test_grid
2072                        patch2.gridflag='y';
2073                        gridname=get(handles.grid_patch2,'String');
2074                        if isequal(gridname(end-3:end),'grid')
2075                            nbslice_grid=str2double(gridname(1:end-4)); %
2076                            if ~isnan(nbslice_grid)
2077                                num1_grid=mod(num1_civ2(ifile)-1,nbslice_grid)+1;
2078                                patch2.gridPatch=[filecell.filebase '_' name_generator(gridname,num1_grid,1,'.grid','_i')];
2079                                if ~exist(patch2.gridPatch,'file')
2080                                    msgbox_uvmat('ERROR','grid file absent for patch2')
2081                                end
2082                            elseif exist(gridname,'file')
2083                                patch2.gridPatch=gridname;
2084                            else
2085                                msgbox_uvmat('ERROR','grid file absent for patch2')
2086                            end
2087                        end
2088                    else
2089                        patch2.gridPatch='none';
2090                        patch2.gridflag='n';
2091                        patch2.m=nx_patch2;
2092                        patch2.n=ny_patch2;
2093                    end
2094                    patch2.convectFlow='n';
2095                    fieldnames=fields(patch2);
2096                    [CivAllxml,uid_patch2]=add(CivAllxml,1,'element','patch2');
2097                    for ilist=1:length(fieldnames)
2098                        val=eval(['patch2.' fieldnames{ilist}]);
2099                        if ischar(val)
2100                            [CivAllxml,uid_t]=add(CivAllxml,uid_patch2,'element',fieldnames{ilist});
2101                            [CivAllxml,uid_t2]=add(CivAllxml,uid_t,'chardata',val);
2102                        end
2103                    end
2104                    CivAllCmd=[CivAllCmd ' patch2 '];
2105            end
2106        end
2107 
2108        switch CivMode
2109            case {'CivX','CivAll'}
2110                if isequal(CivMode,'CivAll')
2111                    save(CivAllxml,[flname '.xml']);
2112                    cmd=[cmd sparam.CivBin ' -f ' flname '.xml '  CivAllCmd ' >' flname '.log' '\n'];
2113                end
2114                % create the .bat file:
2115                [fid,message]=fopen(filename_bat,'w');
2116                if isequal(fid,-1)
2117                    msgbox_uvmat('ERROR', ['creation of .bat file: ' message])
2118                    return
2119                end
2120                fprintf(fid,cmd);
2121                fclose(fid);
2122                if batch
2123                    switch batch_mode
2124                        case 'sge'
2125                            pvalue=num2str((1-ind_answer)*500);
2126                            display(['!qsub -p ' pvalue ' -q civ.q -e ' flname '.errors -o ' flname '.log' ' ' filename_bat]);
2127                            eval(  ['!qsub -p ' pvalue ' -q civ.q -e ' flname '.errors -o ' flname '.log' ' ' filename_bat]);
2128                        case 'oar'
2129                            eval(  ['!chmod +x ' filename_bat]);
2130                            eval(  ['!oarsub -n CIVX -l /core=1,walltime=00:10:00  ' filename_bat]);
2131                    end
2132                else
2133                    %% to lauch the jobs locally :
2134                    if(isunix)
2135                        cmd_str=['. ' filename_bat];
2136                    else %case of Windows
2137                        cmd_str=['@call "' regexprep(filename_bat,'\\','\\\\') '"'];
2138                    end
2139                    super_cmd=[super_cmd cmd_str '\n'];
2140                    disp(cmd_str);
2141                end
2142            case 'Matlab'
2143                drawnow
2144                if box_test(1)==1
2145                    Param.Civ1=par_civ1;
2146                end
2147                if box_test(2)==1
2148                    fix1.WarnFlags=[];
2149                    if get(handles.vec_Fmin2,'Value')
2150                        fix1.WarnFlags=[fix1.WarnFlags -2];
2151                    end
2152                    if get(handles.vec_F3,'Value')
2153                        fix1.WarnFlags=[fix1.WarnFlags 3];
2154                    end
2155                    fix1.LowerBoundCorr=thresh_vecC1;
2156                    if get(handles.inf_sup1,'Value')
2157                        fix1.UppperBoundVel=thresh_vel1;
2158                    else
2159                        fix1.LowerBoundVel=thresh_vel1;
2160                    end
2161                    if get(handles.get_mask_fix1,'Value')
2162                        fix1.MaskName=maskname;
2163                    end
2164                    Param.Fix1=fix1;
2165                end
2166                if box_test(3)==1
2167                    if strcmp(compare,'stereo PIV')
2168                        filebase_A=filecell.filebase;
2169                        [pp,ff]=fileparts(filebase_A);
2170                        filebase_B=fullfile(pp,get(handles.RootName_1,'String'));
2171                        RUN_STLIN(filecell.ncA.civ1{ifile,j},filecell.nc.civ1{ifile,j},'civ1',filecell.st{ifile,j},...
2172                            str2num(nx_patch1),str2num(ny_patch1),str2num(thresh_patch1),[filebase_A '.xml'],[filebase_B '.xml'])
2173                    else
2174                        Param.Patch1.Rho=rho_patch1;
2175                        Param.Patch1.Threshold=thresh_patch1;
2176                        Param.Patch1.SubDomain=subdomain_patch1;
2177                    end
2178                end
2179                if box_test(4)==1
2180                    Param.Civ2=par_civ2;
2181                end
2182                if box_test(5)==1
2183                    fix2.WarnFlags=[];
2184                    if get(handles.vec_Fmin2_2,'Value')
2185                        fix2.WarnFlags=[fix2.WarnFlags -2];
2186                    end
2187                    if get(handles.vec_F4,'Value')
2188                        fix2.WarnFlags=[fix2.WarnFlags 4];
2189                    end
2190                    if get(handles.vec_F3_2,'Value')
2191                        fix2.WarnFlags=[fix2.WarnFlags 3];
2192                    end
2193                    fix2.LowerBoundCorr=thresh_vec2C;
2194                    if get(handles.inf_sup2,'Value')
2195                        fix2.UppperBoundVel=thresh_vel2;
2196                    else
2197                        fix2.LowerBoundVel=thresh_vel2;
2198                    end
2199                    if get(handles.get_mask_fix2,'Value')
2200                        fix2.MaskName=maskname;
2201                    end
2202                    Param.Fix2=fix2;
2203                end
2204                if box_test(6)==1
2205                    if strcmp(compare,'stereo PIV')
2206                        filebase_A=filecell.filebase;
2207                        [pp,ff]=fileparts(filebase_A);
2208                        filebase_B=fullfile(pp,get(handles.RootName_1,'String'));
2209                        RUN_STLIN(filecell.ncA.civ2{ifile,j},filecell.nc.civ2{ifile,j},'civ2',filecell.st{ifile,j},...
2210                            str2num(nx_patch2),str2num(ny_patch2),str2num(thresh_patch2),[filebase_A '.xml'],[filebase_B '.xml'])
2211                    end
2212                end
2213                if ~strcmp(compare,'stereo PIV')
2214                    [Data,erromsg]=civ_uvmat(Param,filecell.nc.civ1{ifile,j});
2215                    if isempty(errormsg)
2216                        display([filecell.nc.civ1{ifile,j} ' written'])
2217                    else
2218                        msgbox_uvmat('ERROR',errormsg)
2219                    end
2220                end
2221        end
2222    end
2223end
2224
2225if ~batch && ~isequal(CivMode,'Matlab')
2226    [Rootbat,Filebat,extbat]=fileparts(filename_bat);
2227    filename_superbat=fullfile(Rootbat,'job_list.bat');
2228    fid=fopen(filename_superbat,'w');
2229    if fid==-1
2230        msgbox_uvmat('ERROR',['cannot create the command file ' filename_superbat])
2231        return
2232    end
2233    fprintf(fid,super_cmd');
2234    fclose(fid);
2235    if(isunix)
2236        system(['chmod +x ' filename_superbat])
2237    end
2238    system([filename_superbat ' &'])% execute main commmand
2239end
2240
2241%% save interface state
2242if isfield(filecell,'nc')
2243    if isfield(filecell.nc,'civ2')
2244        fileresu=filecell.nc.civ2{1,1};
2245    else
2246        fileresu=filecell.nc.civ1{1,1};
2247    end
2248end
2249[RootPath,RootFile,field_count,str2,str_a,str_b,ext,nom_type,subdir]=name2display(fileresu);
2250namedoc=fullfile(RootPath,subdir,RootFile);
2251detect=1;
2252while detect==1
2253    namefigfull=[namedoc '.fig'];
2254    hh=dir(namefigfull);
2255    if ~isempty(hh)
2256        detect=1;
2257        namedoc=[namedoc '.0'];
2258    else
2259        detect=0;
2260    end
2261end
2262saveas(gcbf,namefigfull);%save the interface with name namefigfull (A CHANGER EN FICHIER  .xml)
2263
2264%------------------------------------------------------------------------
2265% --- determine the list of reference indices of processing file
2266function [ref_i,ref_j,errormsg]=find_ref_indices(handles)
2267%------------------------------------------------------------------------
2268errormsg=''; %default error message
2269first_i=str2double(get(handles.first_i,'String'));%first index i
2270last_i=str2double(get(handles.last_i,'String'));%last index i
2271incr_i=str2double(get(handles.incr_i,'String'));% increment
2272if isequal(get(handles.first_j,'Visible'),'on')
2273    first_j=str2double(get(handles.first_j,'String'));%first index j
2274    last_j=str2double(get(handles.last_j,'String'));%last index j
2275    incr_j=str2double(get(handles.incr_j,'String'));% increment
2276else
2277    first_j=1;
2278    last_j=1;
2279    incr_j=1;
2280end
2281ref_i=first_i:incr_i:last_i;% list of i indices (reference values for each pair)
2282ref_j=first_j:incr_j:last_j;% list of j indices (reference values for each pair)
2283if isnan(first_i)||isnan(first_j)
2284    errormsg='first field number not defined';
2285elseif isnan(last_i)||isnan(last_j)
2286    errormsg='last field number not defined';
2287elseif isnan(incr_i)||isnan(incr_j)
2288    errormsg='increment in field number not defined';
2289elseif last_i < first_i || last_j < first_j
2290    errormsg='last field number must be larger than the first one';
2291end
2292
2293%------------------------------------------------------------------------
2294% --- determine the list of filenames and indices needed for launch_job
2295function [filecell,num1_civ1,num2_civ1,num_a_civ1,num_b_civ1,num1_civ2,num2_civ2,num_a_civ2,num_b_civ2,nom_type_nc,file_ref_fix1,file_ref_fix2,compare]=...
2296    set_civ_filenames(handles,ref_i,ref_j,box_test)
2297%------------------------------------------------------------------------
2298filecell=[];%default
2299
2300%% get the root names nomenclature and numbers
2301filebase=get(handles.RootName,'String');
2302
2303if isempty(filebase)||isequal(filebase,'')
2304    msgbox_uvmat('ERROR','no input files')
2305    return
2306end
2307
2308%filebase=regexprep(filebase,'\.fsnet','fsnet');% temporary fix for cluster Coriolis
2309filecell.filebase=filebase;
2310
2311browse=get(handles.browse_root,'UserData');
2312compare_list=get(handles.compare,'String');
2313val=get(handles.compare,'Value');
2314compare=compare_list{val};
2315if strcmp(compare,'displacement')
2316    mode='displacement';
2317else
2318    mode_list=get(handles.mode,'String');
2319    mode_value=get(handles.mode,'Value');
2320    mode=mode_list{mode_value};
2321end
2322%time=get(handles.RootName,'UserData'); %get the set of times
2323ext_ima=get(handles.ImaExt,'String');
2324nom_type_nc=browse.nom_type_nc;
2325if isfield(browse,'nom_type_ima')
2326    nom_type_ima2=browse.nom_type_ima;
2327end
2328if isempty(nom_type_ima2),nom_type_ima2='1';end; %default
2329if isempty(nom_type_nc),nom_type_nc='_i1-i2';end; %default
2330[num1_civ1,num2_civ1,num_a_civ1,num_b_civ1,num1_civ2,num2_civ2,num_a_civ2,num_b_civ2]=...
2331    find_pair_indices(handles,ref_i,ref_j,mode);
2332%determine the new filebase for 'displacement' mode (comparison of two series)
2333filebase_B=filebase;% root name of the second field series for stereo
2334if strcmp(compare,'displacement') || strcmp(compare,'stereo PIV')
2335%     test_disp=1;
2336    nom_type_ima1=browse.nom_type_ima_1; %nomenclature type of the second file series
2337    [Path2,Name2]=fileparts(filebase_B);
2338    Path1=Path2;
2339    Name1=get(handles.RootName_1,'String');% root name of the first field series for stereo
2340    filebase_A=fullfile(Path1,Name1);
2341    if length(Name1)>6
2342        Name1=Name1(end-5:end);
2343    end
2344    if length(Name2)>6
2345        Name2=Name2(end-5:end);
2346    end
2347    filebase_AB=fullfile(Path2,[Name2 '-' Name1]);
2348else
2349%     test_disp=0;
2350    filebase_A=filebase;
2351    nom_type_ima1=nom_type_ima2;
2352    filebase_AB=filebase;
2353end
2354if strcmp(compare,'displacement')
2355    filebase_ima1=filebase_A;
2356    filebase_ima2=filebase_B;
2357    filebase_nc=filebase_AB; %root name for the result of civ2
2358else
2359    filebase_ima1=filebase_B;
2360    filebase_ima2=filebase_B;
2361    filebase_nc=filebase_B;
2362end
2363
2364%determine reference files for fix:
2365file_ref_fix1={};%default
2366file_ref_fix2={};
2367nbfield=length(num1_civ1);
2368nbslice=length(num_a_civ1);
2369if box_test(2)==1% fix1 performed
2370    ref=get(handles.ref_fix1,'UserData');%read data on the ref file stored by get_ref_fix1_Callback
2371    if ~isempty(ref)
2372        first_i=str2double(get(handles.first_i,'String'));
2373        last_i=str2double(get(handles.last_i,'String'));
2374        incr_i=str2double(get(handles.incr_i,'String'));
2375        first_j=str2double(get(handles.first_j,'String'));
2376        last_j=str2double(get(handles.last_j,'String'));
2377        incr_j=str2double(get(handles.incr_j,'String'));
2378        num_i_ref=first_i:incr_i:last_i;
2379        num_j_ref=first_j:incr_j:last_j;
2380        if isequal(mode,'displacement')
2381            num_i1=num_i_ref;
2382            num_i2=num_i_ref;
2383            num_j1=num_j_ref;
2384            num_j2=num_j_ref;
2385        elseif isequal(mode,'pair j1-j2')% isequal(mode,'st_pair j1-j2')
2386            num_i1=num_i_ref;
2387            num_i2=num_i1;
2388            num_j1=ref.num_a*ones(size(num_i_ref));
2389            num_j2=ref.num_b*ones(size(num_i_ref));
2390        elseif isequal(mode,'series(Di)') % isequal(mode,'st_series(Di)')
2391            delta1=floor((ref.num2-ref.num1)/2);
2392            delta2=ceil((ref.num2-ref.num1)/2);
2393            num_i1=num_i_ref-delta1*ones(size(num_i_ref));
2394            num_i2=num_i_ref+delta2*ones(size(num_i_ref));
2395            if isempty(ref.num_a)
2396                ref.num_a=1;
2397            end
2398            num_j1=ref.num_a*ones(size(num_i1));
2399            num_j2=num_j1;
2400        elseif isequal(mode,'series(Dj)')%| isequal(mode,'st_series(Dj)')
2401            delta1=floor((ref.num_b-ref.num_a)/2);
2402            delta2=ceil((ref.num_b-ref.num_a)/2);
2403            num_i1=ref.num1*ones(size(num_i_ref));
2404            num_i2=num_i1;
2405            num_j1=num_j_ref-delta1*ones(size(num_j_ref));
2406            num_j2=num_j_ref+delta2*ones(size(num_j_ref));
2407        end
2408        for ifile=1:nbfield
2409            for j=1:nbslice
2410                file_ref=name_generator(ref.filebase,num_i1(ifile),num_j1(j),'.nc',ref.nom_type,1,num_i2(ifile),num_j2(j),ref.subdir);%
2411                file_ref_fix1(ifile,j)={file_ref};
2412                if ~exist(file_ref,'file')
2413                    msgbox_uvmat('ERROR',['reference file ' file_ref ' not found for fix1'])
2414                    filecell=[];
2415                    return
2416                end
2417            end
2418        end
2419    end
2420end
2421
2422%determine reference files for fix2:
2423if box_test(5)==1% fix2 performed
2424    ref=get(handles.ref_fix2,'UserData');
2425    if ~isempty(ref)
2426        first_i=str2double(get(handles.first_i,'String'));
2427        last_i=str2double(get(handles.last_i,'String'));
2428        incr_i=str2double(get(handles.incr_i,'String'));
2429        first_j=str2double(get(handles.first_j,'String'));
2430        last_j=str2double(get(handles.last_j,'String'));
2431        incr_j=str2double(get(handles.incr_j,'String'));
2432        num_i_ref=first_i:incr_i:last_i;
2433        num_j_ref=first_j:incr_j:last_j;
2434        if isequal(mode,'displacement')
2435            num_i1=num_i_ref;
2436            num_i2=num_i_ref;
2437            num_j1=num_j_ref;
2438            num_j2=num_j_ref;
2439        elseif isequal(mode,'pair j1-j2')
2440            num_i1=num_i_ref;
2441            num_i2=num_i1;
2442            num_j1=ref.num_a;
2443            num_j2=ref.num_b;
2444        elseif isequal(mode,'series(Di)')
2445            delta1=floor((ref.num2-ref.num1)/2);
2446            delta2=ceil((ref.num2-ref.num1)/2);
2447            num_i1=num_i_ref-delta1*ones(size(num_i_ref));
2448            num_i2=num_i_ref+delta2*ones(size(num_i_ref));
2449            num_j1=ref.num_a*ones(size(num_i1));
2450            num_j2=num_j1;
2451        elseif isequal(mode,'series(Dj)')
2452            delta1=floor((ref.num_b-ref.num_a)/2);
2453            delta2=ceil((ref.num_b-ref.num_a)/2);
2454            num_i1=ref.num1*ones(size(num_i_ref));
2455            num_i2=num_i1;
2456            num_j1=num_j_ref-delta1*ones(size(num_j_ref));
2457            num_j2=num_j_ref+delta2*ones(size(num_j_ref));
2458        end
2459        for ifile=1:nbfield
2460            for j=1:nbslice
2461                file_ref=name_generator(ref.filebase,num_i1(ifile),num_j1(j),'.nc',ref.nom_type,1,num_i2(ifile),num_j2(j),ref.subdir);%
2462                file_ref_fix2(ifile,j)={file_ref};
2463                if ~exist(file_ref,'file')
2464                    msgbox_uvmat('ERROR',['reference file ' file_ref ' not found for fix2'])
2465                    filecell={};
2466                    return
2467                end
2468            end
2469        end
2470    end
2471end
2472
2473%check dir
2474subdir_civ1=get(handles.subdir_civ1,'String');%subdirectory subdir_civ1 for the netcdf output data
2475subdir_civ2=get(handles.subdir_civ2,'String');
2476if isequal(subdir_civ1,''),subdir_civ1='CIV'; end% put default subdir
2477if isequal(subdir_civ2,''),subdir_civ2=subdir_civ1; end% put default subdir
2478currentdir=pwd;%store the current working directory
2479[Path_ima,Name]=fileparts(filebase);%Path of the image files (.civ)
2480if ~exist(Path_ima,'dir')
2481    msgbox_uvmat('ERROR',['path to images ' Path_ima ' not found'])
2482    filecell={};
2483    return
2484end
2485[xx,message]=fileattrib(Path_ima);
2486if ~isempty(message) && ~isequal(message.UserWrite,1)
2487    msgbox_uvmat('ERROR',['No writting access to ' Path_ima])
2488    filecell={};
2489    cd(currentdir);
2490    return
2491end
2492
2493%check the existence of the netcdf and image files involved
2494% %%%%%%%%%%%%  case CIV1 activated   %%%%%%%%%%%%%
2495if box_test(1)==1;
2496    detect=1;
2497    vers=0;
2498    subdir_civ1_new=subdir_civ1;
2499    while detect==1 %create a new subdir if the netcdf files already exist
2500        for ifile=1:nbfield
2501            for j=1:nbslice
2502                filename=name_generator(filebase_nc,num1_civ1(ifile),num_a_civ1(j),'.nc',nom_type_nc,1,num2_civ1(ifile),num_b_civ1(j),subdir_civ1_new);
2503                detect=exist(filename,'file')==2;
2504                if detect% if a netcdf file already exists
2505                    indstr=regexp(subdir_civ1_new,'\D');
2506                    if indstr(end)<length(subdir_civ1_new) %subdir_civ1 ends by a number
2507                        vers=str2double(subdir_civ1_new(indstr(end)+1:end))+1;
2508                        subdir_civ1_new=[subdir_civ1_new(1:indstr(end)) num2str(vers)];
2509                    else
2510                        vers=vers+1;
2511                        subdir_civ1_new=[subdir_civ1_new(1:indstr(end)) '_' num2str(vers)];       
2512                    end
2513                    subdir_civ2=subdir_civ1_new;
2514                    break
2515                end
2516                filecell.nc.civ1(ifile,j)={filename};
2517            end
2518            if detect% if a netcdf file already exists
2519                break
2520            end
2521        end
2522 
2523        %create the new subdir_civ1
2524        if ~exist(fullfile(Path_ima,subdir_civ1_new),'dir')
2525%             cd(Path_ima);         
2526            [xx,msg1]=mkdir(fullfile(Path_ima,subdir_civ1_new));
2527
2528            if ~strcmp(msg1,'')
2529                msgbox_uvmat('ERROR',['cannot create ' subdir_civ1_new ': ' msg1])%error message for directory creation
2530                filecell={};
2531                return
2532            elseif isunix         
2533                [xx,msg2] = fileattrib(subdir_civ1_new,'+w','g'); %yield writing access (+w) to user group (g)
2534                if ~strcmp(msg2,'')
2535                    msgbox_uvmat('ERROR',['pb of permission for  ' subdir_civ1_new ': ' msg2])%error message for directory creation
2536                    filecell={};
2537                    return
2538                end
2539            end
2540%             cd(currentdir);
2541        end
2542        if strcmp(compare,'stereo PIV')&&(strcmp(mode,'pair j1-j2')||strcmp(mode,'series(Dj)')||strcmp(mode,'series(Di)'))%check second nc series
2543            for ifile=1:nbfield
2544                for j=1:nbslice
2545                    filename=name_generator(filebase_A,num1_civ1(ifile),num_a_civ1(j),'.nc',nom_type_nc,1,num2_civ1(ifile),num_b_civ1(j),subdir_civ1_new);%
2546                    detect=exist(filename,'file')==2;
2547                    if detect% if a netcdf file already exists
2548                       indstr=regexp(subdir_civ1_new,'\D');
2549                       if indstr(end)<length(subdir_civ1_new) %subdir_civ1 ends by a number
2550                           vers=str2double(subdir_civ1_new(indstr(end)+1:end))+1;
2551                           subdir_civ1_new=[subdir_civ1_new(1:indstr(end)) num2str(vers)];
2552                       else
2553                           vers=vers+1;
2554                           subdir_civ1_new=[subdir_civ1_new '_' num2str(vers)];
2555                       end
2556                       subdir_civ2=subdir_civ1;
2557                       break
2558                    end
2559                    filecell.ncA.civ1(ifile,j)={filename};
2560                end
2561                if detect% if a netcdf file already exists
2562                    break
2563                end
2564            end
2565            %create the new subdir_civ1
2566            if ~exist(fullfile(Path_ima,subdir_civ1_new),'dir')
2567%                    cd(Path_ima);         
2568                [xx,msg1]=mkdir(fullfile(Path_ima,subdir_civ1_new));
2569%                             cd(currentdir);
2570                if ~strcmp(msg1,'')
2571                    msgbox_uvmat('ERROR',['cannot create ' subdir_civ1_new ': ' msg1])
2572%                     cd(currentdir)
2573                    filecell={};
2574                    return
2575                else
2576                    [xx,msg2] = fileattrib(subdir_civ1_new,'+w','g'); %yield writing access (+w) to user group (g)
2577                    if ~strcmp(msg2,'')
2578                        msgbox_uvmat('ERROR',['pb of permission for ' subdir_civ1_new ': ' msg2])%error message for directory creation
2579%                         cd(currentdir)
2580                        filecell={};
2581                        return
2582                    end
2583                end
2584            end
2585        end
2586    end
2587    subdir_civ1=subdir_civ1_new;
2588    % get image names
2589    for ifile=1:nbfield
2590        for j=1:nbslice
2591            filename=name_generator(filebase_ima1, num1_civ1(ifile),num_a_civ1(j),ext_ima,nom_type_ima1);
2592            idetect(j)=exist(filename,'file')==2;
2593            filecell.ima1.civ1(ifile,j)={filename}; %first image
2594            filename=name_generator(filebase_ima2, num2_civ1(ifile),num_b_civ1(j),ext_ima,nom_type_ima2);
2595            idetect_1(j)=exist(filename,'file')==2;
2596            filecell.ima2.civ1(ifile,j)={filename};%second image
2597        end
2598        [idetectmin,indexj]=min(idetect);
2599        if idetectmin==0,
2600            msgbox_uvmat('ERROR',[filecell.ima1.civ1{ifile,indexj} ' not found'])
2601            filecell={};
2602            cd(currentdir)
2603            return
2604        end
2605        [idetectmin,indexj]=min(idetect_1);
2606        if idetectmin==0,
2607            msgbox_uvmat('ERROR',[filecell.ima2.civ1{ifile,indexj} ' not found'])
2608            filecell={};
2609            cd(currentdir)
2610            return
2611        end
2612    end
2613    if strcmp(compare,'stereo PIV') && (strcmp(mode,'pair j1-j2') || strcmp(mode,'series(Dj)') || strcmp(mode,'series(Di)'))
2614        for ifile=1:nbfield
2615            for j=1:nbslice
2616                filename=name_generator(filebase_A, num1_civ1(ifile),num_a_civ1(j),ext_ima,nom_type_ima1);
2617                idetect(j)=exist(filename,'file')==2;
2618                filecell.imaA1.civ1(ifile,j)={filename} ;%first image
2619                filename=name_generator(filebase_A, num2_civ1(ifile),num_b_civ1(j),ext_ima,nom_type_ima2);
2620                idetect_1(j)=exist(filename,'file')==2;
2621                filecell.imaA2.civ1(ifile,j)={filename};%second image
2622            end
2623            [idetectmin,indexj]=min(idetect);
2624            if idetectmin==0,
2625                msgbox_uvmat('ERROR',[filecell.imaA1.civ1{ifile,indexj} ' not found'])
2626                filecell={};
2627                cd(currentdir)
2628                return
2629            end
2630            [idetectmin,indexj]=min(idetect_1);
2631            if idetectmin==0,
2632                msgbox_uvmat('ERROR',[filecell.imaA2.civ1{ifile,indexj} ' not found'])
2633                filecell={};
2634                cd(currentdir)
2635                return
2636            end
2637        end
2638    end
2639   
2640    %%%%%%%%%%%%%  fix1 or patch1 activated but no civ1   %%%%%%%%%%%%%
2641elseif (box_test(2)==1 || box_test(3)==1);
2642    for ifile=1:nbfield
2643        for j=1:nbslice
2644            filename=name_generator(filebase_nc,num1_civ1(ifile),num_a_civ1(j),'.nc',...
2645                nom_type_nc,1,num2_civ1(ifile),num_b_civ1(j),subdir_civ1);%
2646            detect=exist(filename,'file')==2;
2647            if detect==0
2648                msgbox_uvmat('ERROR',[filename ' not found'])
2649                filecell={};
2650                cd(currentdir)
2651                return
2652            end
2653            filecell.nc.civ1(ifile,j)={filename};
2654        end
2655    end
2656    if strcmp(compare,'stereo PIV')
2657        for ifile=1:nbfield
2658            for j=1:nbslice
2659                filename=name_generator(filebase_A,num1_civ1(ifile),num_a_civ1(j),'.nc',nom_type_nc,1,num2_civ1(ifile),num_b_civ1(j),subdir_civ1);%
2660                filecell.ncA.civ1(ifile,j)={filename};
2661                if ~exist(filename,'file')
2662                    msgbox_uvmat('ERROR',['input file ' filename ' not found'])
2663                    set(handles.RUN, 'Enable','On')
2664                    set(handles.RUN,'BackgroundColor',[1 0 0])
2665                    filecell={};
2666                    cd(currentdir)
2667                    return
2668                end
2669            end
2670        end
2671    end
2672end
2673
2674%%%%%%%%%%%%%  if civ2 performed with pairs different than civ1  %%%%%%%%%%%%%
2675testdiff=0;
2676if (box_test(4)==1)&&...
2677        ((get(handles.list_pair_civ1,'Value')~=get(handles.list_pair_civ2,'Value'))||~strcmp(subdir_civ2,subdir_civ1))
2678    testdiff=1;
2679    detect=1;
2680    vers=0;
2681    subdir_civ2_new=subdir_civ2;
2682    while detect==1 %create a new subdir if the netcdf files already exist
2683        for ifile=1:nbfield
2684            for j=1:nbslice
2685                filename=name_generator(filebase_nc,num1_civ2(ifile),num_a_civ2(j),'.nc',nom_type_nc,1,num2_civ2(ifile),num_b_civ2(j),subdir_civ2_new);%
2686                detect=exist(filename,'file')==2;
2687                if detect% if a netcdf file already exists
2688                    indstr=regexp(subdir_civ2,'\D');
2689                    if indstr(end)<length(subdir_civ2) %subdir_civ1 ends by a number
2690                        vers=str2double(subdir_civ2(indstr(end)+1:end))+1;
2691                        subdir_civ2_new=[subdir_civ2(1:indstr(end)) num2str(vers)];
2692                    else
2693                        vers=vers+1;
2694                        subdir_civ2_new=[subdir_civ1 '_' num2str(vers)];
2695                    end
2696                    break
2697                end
2698                filecell.nc.civ2(ifile,j)={filename};
2699            end
2700            if detect% if a netcdf file already exists
2701                break
2702            end
2703        end
2704        %create the new subdir_civ2_new
2705        if ~exist(fullfile(Path_ima,subdir_civ2_new),'dir')
2706            [xx,m2]=mkdir(fullfile(Path_ima,subdir_civ2_new));
2707            [xx,msg2] = fileattrib(subdir_civ2_new,'+w','g'); %yield writing access (+w) to user group (g)
2708            if ~isequal(m2,'')
2709                msgbox_uvmat('ERROR',['cannot create ' subdir_civ2_new ': ' m2])
2710                filecell={};
2711                cd(currentdir)
2712                return
2713            end
2714        end
2715        if strcmp(compare,'stereo PIV')%check second nc series
2716            for ifile=1:nbfield
2717                for j=1:nbslice
2718                    filename=name_generator(filebase_A,num1_civ2(ifile),num_a_civ2(j),'.nc',...
2719                        nom_type_nc,1,num2_civ2(ifile),num_b_civ1(j),subdir_civ2_new);%
2720                    detect=exist(filename,'file')==2;
2721                    if detect% if a netcdf file already exists
2722                        indstr=regexp(subdir_civ2,'\D');
2723                        if indstr(end)<length(subdir_civ2) %subdir_civ1 ends by a number
2724                           vers=str2double(subdir_civ2(indstr(end)+1:end))+1;
2725                           subdir_civ2_new=[subdir_civ2(1:indstr(end)) num2str(vers)];
2726                        else
2727                           vers=vers+1;
2728                           subdir_civ2_new=[subdir_civ1 '_' num2str(vers)];
2729                        end
2730                        break
2731                    end
2732                    filecell.ncA.civ2(ifile,j)={filename};
2733                end
2734                if detect% if a netcdf file already exists
2735                    break
2736                end
2737            end
2738            subdir_civ2=subdir_civ2_new;
2739            %create the new subdir_civ1
2740            if ~exist(fullfile(Path_ima,subdir_civ2_new),'dir')
2741                [xx,m2]=mkdir(subdir_civ2_new);
2742                 [xx,msg2] = fileattrib(subdir_civ2_new,'+w','g'); %yield writing access (+w) to user group (g)
2743                if ~isequal(m2,'')
2744                    msgbox_uvmat('ERROR', ['cannot create ' subdir_civ2_new ': ' m2])%error message for directory creation
2745                    cd(currentdir)
2746                    filecell={};
2747                    return
2748                end
2749            end
2750        end
2751    end
2752    subdir_civ2=subdir_civ2_new;
2753end
2754cd(currentdir);%come back to the current working directory
2755
2756%%%%%%%%%%%%%  if civ2 results are obtained or used  %%%%%%%%%%%%%
2757if box_test(4)==1 || box_test(5)==1 || box_test(6)==1 %civ2
2758    %check source netcdf file of civ1 estimates
2759    if box_test(1)==0; %no civ1 performed
2760        for ifile=1:nbfield
2761            for j=1:nbslice
2762                filename=name_generator(filebase_nc,num1_civ1(ifile),num_a_civ1(j),'.nc',...
2763                    nom_type_nc,1,num2_civ1(ifile),num_b_civ1(j),subdir_civ1);%
2764                filecell.nc.civ1(ifile,j)={filename};% name of the civ1 file
2765                if ~exist(filename,'file')
2766                    msgbox_uvmat('ERROR',['input file ' filename ' not found'])
2767                    filecell={};
2768                    return
2769                end
2770                if ~testdiff % civ2 or patch2 are written in the same file as civ1
2771                    if box_test(4)==0 ; %check the existence of civ2 if it is not calculated
2772                        Data=nc2struct(filename,'ListGlobalAttribute','CivStage','civ2');
2773                        if ~isempty(Data.CivStage) && Data.CivStage<4 %test for civ files
2774                            msgbox_uvmat('ERROR',['no civ2 data in ' filename])
2775                            filecell=[];
2776                            return
2777                        elseif isempty(Data.civ2)||isequal(Data.civ2,0)
2778                            msgbox_uvmat('ERROR',['no civ2 data in ' filename])
2779                            filecell=[];
2780                            return
2781                        end
2782                    elseif box_test(3)==0; %check the existence of patch if it is not calculated
2783                        Data=nc2struct(filename,'ListGlobalAttribute','CivStage','patch')
2784                        if ~isempty(Data.CivStage)
2785                            if Data.CivStage<3 %test for civ files
2786                                msgbox_uvmat('ERROR',['no patch data in ' filename])
2787                                filecell=[];
2788                                return
2789                            end
2790                        elseif isempty(Data.patch)||isequal(Data.patch,0)
2791                            msgbox_uvmat('ERROR',['no patch data in ' filename])
2792                            filecell=[];
2793                            return
2794                        end
2795                    end
2796                end
2797            end
2798        end
2799        if strcmp(compare,'stereo PIV')
2800            for ifile=1:nbfield
2801                for j=1:nbslice
2802                    filename=name_generator(filebase_A,num1_civ2(ifile),num_a_civ2(j),'.nc',...
2803                        nom_type_nc,1,num2_civ2(ifile),num_b_civ2(j),subdir_civ2);%
2804                    filecell.ncA.civ2(ifile,j)={filename};
2805                    if ~exist(filename,'file')
2806                        msgbox_uvmat('ERROR',['input file ' filename ' not found'])
2807                        set(handles.RUN, 'Enable','On')
2808                        set(handles.RUN,'BackgroundColor',[1 0 0])
2809                        return
2810                    end
2811                end
2812            end
2813        end
2814    end
2815   
2816    detect=1;
2817    %     while detect==1%creates a new subdir if the netcdf files already contain civ2 data
2818    for ifile=1:nbfield
2819        for j=1:nbslice
2820            filename=name_generator(filebase_nc,num1_civ2(ifile),num_a_civ2(j),'.nc',...
2821                nom_type_nc,1,num2_civ2(ifile),num_b_civ2(j),subdir_civ2);
2822            detect=exist(filename,'file')==2;
2823            filecell.nc.civ2(ifile,j)={filename};
2824        end
2825    end
2826    %get first image names for civ2
2827    if box_test(1)==1 & isequal(num1_civ1,num1_civ2) & isequal(num_a_civ1,num_a_civ2)
2828        filecell.ima1.civ2=filecell.ima1.civ1;
2829    elseif box_test(4)==1
2830        for ifile=1:nbfield
2831            for j=1:nbslice
2832                filename=name_generator(filebase_ima1, num1_civ2(ifile),num_a_civ2(j),ext_ima,nom_type_ima1);
2833                idetect_2(j)=exist(filename,'file')==2;
2834                filecell.ima1.civ2(ifile,j)={filename};%first image
2835            end
2836            [idetectmin,indexj]=min(idetect_2);
2837            if idetectmin==0,
2838                msgbox_uvmat('ERROR',['input image ' filecell.ima1.civ2{ifile,indexj} ' not found'])
2839                filecell=[];
2840                return
2841            end
2842        end
2843    end
2844   
2845    %get second image names for civ2
2846    if box_test(1)==1 & isequal(num2_civ1,num2_civ2) & isequal(num_b_civ1,num_b_civ2)
2847        filecell.ima2.civ2=filecell.ima2.civ1;
2848    elseif box_test(4)==1
2849        for ifile=1:nbfield
2850            for j=1:nbslice
2851                filename=name_generator(filebase_ima2, num2_civ2(ifile),num_b_civ2(j),ext_ima,nom_type_ima2);
2852                idetect_3(j)=exist(filename,'file')==2;
2853                filecell.ima2.civ2(ifile,j)={filename};%first image
2854            end
2855            [idetectmin,indexj]=min(idetect_3);
2856            if idetectmin==0,
2857                msgbox_uvmat('ERROR',['input image ' filecell.ima2.civ2{ifile,indexj} ' not found'])
2858                filecell=[];
2859                return
2860            end
2861        end
2862    end
2863end
2864if (box_test(5)==1 || box_test(6)==1 ) && box_test(4)==0  % need to read an existing netcdf civ2 file
2865    if ~testdiff
2866        filecell.nc.civ2=filecell.nc.civ1;% file already checked
2867    else     % check the civ2 files
2868        for ifile=1:nbfield
2869            for j=1:nbslice
2870                filename=name_generator(filebase_nc,num1_civ2(ifile),num_a_civ2(j),'.nc',...
2871                    nom_type_nc,1,num2_civ2(ifile),num_b_civ2(j),subdir_civ2);%
2872                filecell.nc.civ2(ifile,j)={filename};
2873                if ~exist(filename,'file')
2874                    msgbox_uvmat('ERROR',['input file ' filename ' not found'])
2875                    filecell=[];
2876                    return
2877                else
2878                    Data=nc2struct(filename,'ListGlobalAttribute','CivStage','civ2');
2879                    if ~isempty(Data.CivStage) && Data.CivStage<4 %test for civ files
2880                            msgbox_uvmat('ERROR',['no civ2 data in ' filename])
2881                            filecell=[];
2882                            return
2883                    elseif isempty(Data.civ2)||isequal(Data.civ2,0)
2884                        msgbox_uvmat('ERROR',['no civ2 data in ' filename])
2885                        filecell=[];
2886                        return
2887                    end
2888                end
2889            end
2890        end
2891    end
2892end
2893
2894%%%%%%%%%%%%%  if stereo fields are calculated by PATCH %%%%%%%%%%%%%
2895if strcmp(compare,'stereo PIV')
2896    if  box_test(3)==1 && isequal(get(handles.test_stereo1,'Value'),1)
2897        for ifile=1:nbfield
2898            for j=1:nbslice
2899                filename=name_generator(filebase_AB,num1_civ1(ifile),num_a_civ1(j),'.nc',...
2900                    nom_type_nc,1,num2_civ1(ifile),num_b_civ1(j),subdir_civ1);%
2901                filecell.st(ifile,j)={filename};
2902            end
2903        end
2904    end
2905    if  box_test(6)==1 && isequal(get(handles.test_stereo2,'Value'),1)
2906        for ifile=1:nbfield
2907            for j=1:nbslice
2908                filename=name_generator(filebase_AB,num1_civ2(ifile),num_a_civ2(j),'.nc',...
2909                    nom_type_nc,1,num2_civ2(ifile),num_b_civ2(j),subdir_civ2);%
2910                filecell.st(ifile,j)={filename};
2911            end
2912        end
2913    end
2914end
2915set(handles.subdir_civ1,'String',subdir_civ1);%update the edit box
2916set(handles.subdir_civ2,'String',subdir_civ2);%update the edit box
2917browse.nom_type_nc=nom_type_nc;
2918set(handles.browse_root,'UserData',browse); %update the nomenclature type for uvmat
2919
2920
2921%COPY IMAGES TO THE FORMAT .png IF NEEDED
2922if isequal(nom_type_ima1,'*')%case of movie files
2923    nom_type_imanew1='_i';
2924else
2925    nom_type_imanew1=nom_type_ima1;
2926end
2927if isequal(nom_type_ima2,'*')%case of movie files
2928    nom_type_imanew2='_i';
2929else
2930    nom_type_imanew2=nom_type_ima2;
2931end
2932if ~isequal(ext_ima,'.png')
2933    %%type of image file
2934    type_ima1='none';%default
2935    movieobject1=[];%default
2936    if strcmpi(ext_ima,'.avi')
2937        hhh=which('mmreader');
2938        if ~isequal(hhh,'')&& mmreader.isPlatformSupported()% if the mmreader function is found (recent version of matlab)
2939            type_ima1='movie';
2940            movieobject1=mmreader([filebase_ima2 ext_ima]);
2941        else
2942            type_ima1='avi';
2943        end
2944    elseif ischar(ext_ima) && ~isempty(ext_ima(2:end))
2945        form=imformats(ext_ima(2:end));
2946        if ~isempty(form)% if the extension corresponds to an image format recognized by Matlab
2947            if isequal(nom_type_ima1,'*');
2948                type_ima1='multimage';%image series in a single image file
2949            else
2950                type_ima1='image';
2951            end
2952        end
2953    end
2954    type_ima2='none';%default
2955    movieobject2=[];
2956    if strcmpi(ext_ima,'.avi')
2957        hhh=which('mmreader');
2958        if ~isequal(hhh,'')&& mmreader.isPlatformSupported()% if the mmreader function is found (recent version of matlab)
2959            type_ima2='movie';
2960            movieobject2=mmreader([filebase_ima2 ext_ima]);
2961        else
2962            type_ima2='avi';
2963        end
2964    elseif ischar(ext_ima) && ~isempty(ext_ima(2:end))
2965        form=imformats(ext_ima(2:end));
2966        if ~isempty(form)% if the extension corresponds to an image format recognized by Matlab
2967            if isequal(nom_type_ima1,'*');
2968                type_ima2='multimage';%image series in a single image file
2969            else
2970                type_ima2='image';
2971            end
2972        end
2973    end
2974    %npxy=get(handles.ImaExt,'UserData');
2975    % %     if numel(npxy)<2
2976    %
2977    %         filename=name_generator(filebase_ima1,num1_civ1(1),num_a_civ1(1),ImaExt,nom_type_ima1);
2978    %         A=imread(filename);
2979    %         npxy=size(A);
2980    % %     end
2981    %     npy=npxy(1);
2982    %     npx=npxy(2);
2983    if box_test(1)==1 %if civ1 is performed
2984        h = waitbar(0,'copy images to the .png format for civ1');% display a wait bar
2985        for ifile=1:nbfield
2986            waitbar(ifile/nbfield);
2987            for j=1:nbslice
2988                filename=name_generator(filebase_ima1,num1_civ1(ifile),num_a_civ1(j),'.png',nom_type_imanew1);
2989                if ~exist(filename,'file')
2990                    A=read_image(filecell.ima1.civ1{ifile,j},type_ima1,num1_civ1(ifile),movieobject1);
2991                    imwrite(A,filename,'BitDepth',16);
2992                end
2993                filecell.ima1.civ1(ifile,j)={filename};
2994                filename=name_generator(filebase_ima2, num2_civ1(ifile),num_b_civ1(j),'.png',nom_type_imanew2);
2995                if ~exist(filename,'file')
2996                    A=read_image(filecell.ima2.civ1{ifile,j},type_ima2,num2_civ1(ifile),movieobject2);
2997                    imwrite(A,filename,'BitDepth',16);
2998                end
2999                filecell.ima2.civ1(ifile,j)={filename};
3000            end
3001        end
3002        close(h)
3003    end
3004    if box_test(4)==1 %if civ2 is performed
3005        h = waitbar(0,'copy images to the .png format for civ2');% display a wait bar
3006        for ifile=1:nbfield
3007            waitbar(ifile/nbfield);
3008            for j=1:nbslice
3009                filename=name_generator(filebase_ima1,num1_civ2(ifile),num_a_civ2(j),'.png',nom_type_imanew1);
3010                if ~exist(filename,'file')
3011                    A=read_image(cell2mat(filecell.ima1.civ2(ifile,j)),type_ima2,num1_civ2(ifile));
3012                    imwrite(A,filename,'BitDepth',16);
3013                end
3014                filecell.ima1.civ2(ifile,j)={filename};
3015                filename=name_generator(filebase_ima2, num2_civ2(ifile),num_b_civ2(j),'.png',nom_type_imanew2);
3016                if ~exist(filename,'file')
3017                    A=read_image(cell2mat(filecell.ima2.civ2(ifile,j)),type_ima2,num2_civ2(ifile));
3018                    imwrite(A,filename,'BitDepth',16);
3019                end
3020                filecell.ima2.civ2(ifile,j)={filename};
3021            end
3022        end
3023        close(h);
3024    end
3025end
3026
3027%------------------------------------------------------------------------
3028% --- determine the list of index pairs of processing file
3029function [num1_civ1,num2_civ1,num_a_civ1,num_b_civ1,num1_civ2,num2_civ2,num_a_civ2,num_b_civ2]=...
3030    find_pair_indices(handles,ref_i,ref_j,mode)
3031%------------------------------------------------------------------------
3032
3033list_civ1=get(handles.list_pair_civ1,'String');
3034index_civ1=get(handles.list_pair_civ1,'Value');
3035str_civ1=list_civ1{index_civ1};%string defining the image pairs for civ1
3036if isempty(str_civ1)||isequal(str_civ1,'')
3037    msgbox_uvmat('ERROR','no image pair selected for civ1')
3038    return
3039end
3040list_civ2=get(handles.list_pair_civ2,'String');
3041index_civ2=get(handles.list_pair_civ2,'Value');
3042if index_civ2>length(list_civ2)
3043    list_civ2=list_civ1;
3044    index_civ2=index_civ1;
3045end
3046str_civ2=list_civ2{index_civ2};%string defining the image pairs for civ2
3047
3048if isequal (mode,'series(Di)')
3049    lastfield=str2double(get(handles.nb_field,'String'));
3050    num1_civ1=ref_i-floor(index_civ1/2)*ones(size(ref_i));% set of first image numbers
3051    num2_civ1=ref_i+ceil(index_civ1/2)*ones(size(ref_i));
3052    num_a_civ1=ref_j;
3053    num_b_civ1=ref_j;
3054    num1_civ2=ref_i-floor(index_civ2/2)*ones(size(ref_i));
3055    num2_civ2=ref_i+ceil(index_civ2/2)*ones(size(ref_i));
3056    num_a_civ2=ref_j;
3057    num_b_civ2=ref_j;   
3058   
3059    % adjust the first and last field number
3060    lastfield=str2double(get(handles.nb_field,'String'));
3061    if isnan(lastfield)
3062        indsel=find((num1_civ1 >= 1)&(num1_civ2 >= 1));
3063    else
3064        indsel=find((num2_civ1 <= lastfield)&(num2_civ2 <= lastfield)&(num1_civ1 >= 1)&(num1_civ2 >= 1));
3065    end
3066    if length(indsel)>=1
3067        firstind=indsel(1);
3068        lastind=indsel(end);
3069        set(handles.first_i,'String',num2str(ref_i(firstind)))%update the display of first and last fields
3070        set(handles.last_i,'String',num2str(ref_i(lastind)))
3071        ref_i=ref_i(indsel);
3072        num1_civ1=num1_civ1(indsel);
3073        num1_civ2=num1_civ2(indsel);
3074        num2_civ1=num2_civ1(indsel);
3075        num2_civ2=num2_civ2(indsel);
3076    end
3077elseif isequal (mode,'series(Dj)')
3078    lastfield_j=str2double(get(handles.nb_field2,'String'));
3079    num1_civ1=ref_i;% set of first image numbers
3080    num2_civ1=ref_i;
3081    num_a_civ1=ref_j-floor(index_civ1/2)*ones(size(ref_j));
3082    num_b_civ1=ref_j+ceil(index_civ1/2)*ones(size(ref_j));
3083    num1_civ2=ref_i;
3084    num2_civ2=ref_i;
3085    num_a_civ2=ref_j-floor(index_civ2/2)*ones(size(ref_j));
3086    num_b_civ2=ref_j+ceil(index_civ2/2)*ones(size(ref_j));
3087    % adjust the first and last field number
3088    if isnan(lastfield_j)
3089        indsel=find((num_a_civ1 >= 1)&(num_a_civ2 >= 1));
3090    else
3091        indsel=find((num_b_civ1 <= lastfield_j)&(num_b_civ2 <= lastfield_j)&(num_a_civ1 >= 1)&(num_a_civ2 >= 1));
3092    end
3093    if length(indsel)>=1
3094        firstind=indsel(1);
3095        lastind=indsel(end);
3096        set(handles.first_j,'String',num2str(ref_j(firstind)))%update the display of first and last fields
3097        set(handles.last_j,'String',num2str(ref_j(lastind)))
3098        ref_j=ref_j(indsel);
3099        num_a_civ1=num_a_civ1(indsel);
3100        num_b_civ1=num_b_civ1(indsel);
3101        num_a_civ2=num_a_civ2(indsel);
3102        num_b_civ2=num_b_civ2(indsel);
3103    end
3104elseif isequal(mode,'pair j1-j2') %case of bursts (png_old or png_2D)
3105    displ_num=get(handles.list_pair_civ1,'UserData');
3106    num1_civ1=ref_i;
3107    num2_civ1=ref_i;
3108    num_a_civ1=displ_num(1,index_civ1);
3109    num_b_civ1=displ_num(2,index_civ1);
3110    num1_civ2=ref_i;
3111    num2_civ2=ref_i;
3112    num_a_civ2=displ_num(1,index_civ2);
3113    num_b_civ2=displ_num(2,index_civ2);
3114elseif isequal(mode,'displacement')
3115    num1_civ1=ref_i;
3116    num2_civ1=ref_i;
3117    num_a_civ1=ref_j;
3118    num_b_civ1=ref_j;
3119    num1_civ2=ref_i;
3120    num2_civ2=ref_i;
3121    num_a_civ2=ref_j;
3122    num_b_civ2=ref_j;
3123end
3124
3125
3126%------------------------------------------------------------------------
3127% --- PATCH
3128function cmd_PATCH=PATCH_CMD(filename_nc,nx_patch,ny_patch,rho_patch,subdomain_patch,thresh_value,test_interp,PatchBin)
3129%------------------------------------------------------------------------
3130namelog=[filename_nc(1:end-3) '_patch.log'];
3131if test_interp==0
3132    if isunix
3133    cmd_PATCH=[PatchBin ' -f ' filename_nc ' -m ' nx_patch  ' -n ' ny_patch ' -ro ' rho_patch ' -nopt ' subdomain_patch ...
3134        '  > ' namelog ' 2>&1']; % redirect standard output to the log file
3135    else
3136      cmd_PATCH=['"' PatchBin '" -f "' filename_nc '" -m ' nx_patch  ' -n ' ny_patch ' -ro ' rho_patch ' -nopt ' subdomain_patch ...
3137        '  > "' namelog '" 2>&1']; % redirect standard output to the log file
3138    end
3139else %nouveau programme patch
3140    cmd_PATCH=[PatchBin ' -f ' filename_nc ' -m ' nx_patch  ' -n ' ny_patch ' -ro ' rho_patch ...
3141        ' -max ' thresh_value ' -nopt ' subdomain_patch  '  > ' namelog ' 2>&1']; % redirect standard output to the log file
3142end
3143cmd_PATCH=regexprep(cmd_PATCH,'\\','\\\\');
3144%------------------------------------------------------------------------
3145% --- STEREO Interp
3146function cmd=RUN_STINTERP(stinterpBin,filename_A_nc,filename_B_nc,filename_nc,nx_patch,ny_patch,rho_patch,subdomain_patch,thresh_value,xmlA,xmlB)
3147%------------------------------------------------------------------------
3148namelog=[filename_nc(1:end-3) '_stinterp.log'];
3149cmd=[stinterpBin ' -f1 ' filename_A_nc  ' -f2 ' filename_B_nc ' -f  ' filename_nc ...
3150    ' -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
3151
3152%------------------------------------------------------------------------
3153% --- Executes on button press in CIV1.
3154function CIV1_Callback(hObject, eventdata, handles)
3155%------------------------------------------------------------------------
3156val=get(handles.CIV1,'Value');
3157if isequal(val,1)
3158    enable_civ1(handles,'on')
3159    enable_pair1(handles,'on')
3160else
3161    enable_civ1(handles,'off')
3162end
3163find_netcpair_civ1(hObject, eventdata, handles);
3164
3165%------------------------------------------------------------------------
3166% --- Executes on button press in FIX1.
3167function FIX1_Callback(hObject, eventdata, handles)
3168%------------------------------------------------------------------------
3169enable_fix1(handles,get(handles.FIX1,'Value'))
3170
3171%------------------------------------------------------------------------
3172% --- Executes on button press in PATCH1.
3173function PATCH1_Callback(hObject, eventdata, handles)
3174%------------------------------------------------------------------------
3175if get(handles.PATCH1,'Value')==1
3176    enable_patch1(handles)
3177else
3178    desable_patch1(handles)
3179end
3180
3181%------------------------------------------------------------------------
3182% --- Executes on button press in CIV2.
3183function CIV2_Callback(hObject, eventdata, handles)
3184%------------------------------------------------------------------------
3185state=get(handles.CIV2,'Value');
3186enable_civ2(handles,state)
3187if state
3188    find_netcpair_civ2(hObject, eventdata, handles)
3189    enable_pair1(handles,'on')
3190end
3191
3192%------------------------------------------------------------------------
3193% --- Executes on button press in FIX2.
3194function FIX2_Callback(hObject, eventdata, handles)
3195%------------------------------------------------------------------------
3196if get(handles.FIX2,'Value')==1
3197    enable_fix2(handles)
3198    if get(handles.CIV2,'Value')==0
3199        find_netcpair_civ2(hObject, eventdata, handles) % select the available netcdf files
3200    end
3201else
3202    desable_fix2(handles)
3203end
3204
3205%------------------------------------------------------------------------
3206% --- Executes on button press in PATCH2.
3207function PATCH2_Callback(hObject, eventdata, handles)
3208%------------------------------------------------------------------------
3209if get(handles.PATCH2,'Value')==1
3210    enable_patch2(handles)
3211    if get(handles.CIV2,'Value')==0
3212        find_netcpair_civ2(hObject, eventdata, handles) % select the available netcdf files
3213    end
3214else
3215    desable_patch2(handles)
3216end
3217
3218%------------------------------------------------------------------------
3219function first_i_Callback(hObject, eventdata, handles)
3220%------------------------------------------------------------------------
3221% last_i_Callback(hObject, eventdata, handles)
3222first_i=str2double(get(handles.first_i,'String'));
3223% last_i=str2num(get(handles.last_i,'String'));
3224% ref_i=ceil((first_i+last_i)/2);
3225set(handles.ref_i,'String', num2str(first_i))% reference index for pair dt = first index
3226set(handles.ref_i_civ2,'String', num2str(first_i))% reference index for pair dt = first index
3227ref_i_Callback(hObject, eventdata, handles)%refresh dispaly of dt for pairs (in case of non constant dt)
3228
3229%------------------------------------------------------------------------
3230function first_j_Callback(hObject, eventdata, handles)
3231%------------------------------------------------------------------------
3232first_j=str2num(get(handles.first_j,'String'));
3233set(handles.ref_j,'String', num2str(first_j))% reference index for pair dt = first index
3234ref_j_Callback(hObject, eventdata, handles)%refresh dispaly of dt for pairs (in case of non constant dt)
3235
3236%------------------------------------------------------------------------
3237% --- Executes on button press in calcul_search: determine the search range isx,isy
3238function calcul_search_Callback(hObject, eventdata, handles)
3239%------------------------------------------------------------------------
3240%determine pair numbers
3241list_pair=get(handles.list_pair_civ1,'String');%get the menu of image pairs
3242index=get(handles.list_pair_civ1,'Value');
3243displ_num=get(handles.list_pair_civ1,'UserData');
3244time=get(handles.RootName,'UserData'); %get the set of times
3245pxcm_xy=get(handles.calcul_search,'UserData');
3246pxcmx=pxcm_xy(1);
3247pxcmy=pxcm_xy(2);
3248mode_list=get(handles.mode,'String');
3249mode_value=get(handles.mode,'Value');
3250mode=mode_list{mode_value};
3251if isequal (mode, 'series(Di)' )
3252    ref_i=str2double(get(handles.ref_i,'String'));
3253    num1=ref_i-floor(index/2);%  first image numbers
3254    num2=ref_i+ceil(index/2);
3255    num_a=1;
3256    num_b=1;
3257elseif isequal (mode, 'series(Dj)')
3258    num1=1;
3259    num2=1;
3260    ref_j=str2double(get(handles.ref_j,'String'));
3261    num_a=ref_j-floor(index/2);%  first image numbers
3262    num_b=ref_j+ceil(index/2);
3263elseif isequal(mode,'pair j1-j2') %case of bursts (png_old or png_2D)
3264    ref_i=str2double(get(handles.ref_i,'String'));
3265    num1=ref_i;
3266    num2=ref_i;
3267    num_a=displ_num(1,index);
3268    num_b=displ_num(2,index);
3269end
3270dt=time(num2,num_b)-time(num1,num_a);
3271ibx=str2double(get(handles.ibx,'String'));
3272iby=str2double(get(handles.iby,'String'));
3273umin=dt*pxcmx*str2double(get(handles.umin,'String'));
3274umax=dt*pxcmx*str2double(get(handles.umax,'String'));
3275vmin=dt*pxcmy*str2double(get(handles.vmin,'String'));
3276vmax=dt*pxcmy*str2double(get(handles.vmax,'String'));
3277shiftx=round((umin+umax)/2);
3278shifty=round((vmin+vmax)/2);
3279isx=(umax+2-shiftx)*2+ibx;
3280isx=2*ceil(isx/2)+1;
3281isy=(vmax+2-shifty)*2+iby;
3282isy=2*ceil(isy/2)+1;
3283set(handles.shiftx,'String',num2str(shiftx));
3284set(handles.shifty,'String',num2str(shifty));
3285set(handles.isx,'String',num2str(isx));
3286set(handles.isy,'String',num2str(isy));
3287
3288%------------------------------------------------------------------------
3289% --- Executes on carriage return on the subdir civ1 edit window
3290function subdir_civ1_Callback(hObject, eventdata, handles)
3291%------------------------------------------------------------------------
3292subdir=get(handles.subdir_civ1,'String');
3293set(handles.subdir_civ2,'String',subdir);
3294if get(handles.CIV1,'Value')==0
3295    find_netcpair_civ1(hObject, eventdata, handles); %update the list of available pairs from netcdf files in the new directory
3296end
3297
3298%------------------------------------------------------------------------
3299% --- Executes on carriage return on the subdir civ1 edit window
3300function subdir_civ2_Callback(hObject, eventdata, handles)
3301%------------------------------------------------------------------------
3302%update the list of available pairs from netcdf files in the new directory
3303if get(handles.CIV2,'Value')==0 & get(handles.CIV1,'Value')==0 & get(handles.FIX1,'Value')==0 & get(handles.PATCH1,'Value')==0
3304    find_netcpair_civ2(hObject, eventdata, handles);
3305end
3306
3307%------------------------------------------------------------------------
3308% --- Executes on button press in get_mask_civ1: select box for mask option
3309function get_mask_civ1_Callback(hObject, eventdata, handles)
3310%------------------------------------------------------------------------
3311maskval=get(handles.get_mask_civ1,'Value')
3312if isequal(maskval,0)
3313    set(handles.mask_civ1,'String','')
3314else
3315    mask_displ='no mask'; %default
3316    filebase=get(handles.RootName,'String');
3317    [ nbslice_mask, flag_mask]=get_mask(filebase,handles);
3318    if isequal(flag_mask,1)
3319        mask_displ=[num2str(nbslice_mask) 'mask'];
3320    elseif get(handles.compare,'Value')>1 & ~isequal(mask_displ,'no mask')% look for the second mask series
3321        common_path=fileparts(filebase);
3322        filebase_a=fullfile(common_path,get(handles.RootName_1,'String'));
3323        [nbslice_a, flag_mask_a]=get_mask(filebase_a,handles);
3324        if isequal(flag_mask_a,0) || ~isequal(nbslice_a,nbslice_mask)
3325            mask_displ='no mask';
3326        end
3327    end
3328    if isequal(mask_displ,'no mask')
3329        [FileName, PathName, filterindex] = uigetfile( ...
3330            {'*.png', ' (*.png)';
3331            '*.png',  '.png files '; ...
3332            '*.*', 'All Files (*.*)'}, ...
3333            'Pick a mask file *.png',filebase);
3334        mask_displ=fullfile(PathName,FileName);
3335        if ~exist(mask_displ,'file')
3336            mask_displ='no mask';
3337        end
3338    end
3339    if isequal(mask_displ,'no mask')
3340        set(handles.get_mask_civ1,'Value',0)
3341        set(handles.get_mask_fix1,'Value',0)
3342        set(handles.get_mask_civ2,'Value',0)
3343        set(handles.get_mask_fix2,'Value',0)
3344    else
3345        set(handles.get_mask_fix1,'Value',1)
3346        set(handles.get_mask_fix2,'Value',1)
3347    end
3348    set(handles.mask_civ1,'String',mask_displ)
3349    set(handles.mask_fix1,'String',mask_displ)
3350    set(handles.mask_civ2,'String',mask_displ)
3351    set(handles.mask_fix2,'String',mask_displ)
3352end
3353set(handles.get_mask_civ2,'Value',maskval)%update the civ2 mask with the same option as civ1
3354
3355%------------------------------------------------------------------------
3356% --- Executes on button press in get_mask_fix1.
3357function get_mask_fix1_Callback(hObject, eventdata, handles)
3358%------------------------------------------------------------------------
3359maskval=get(handles.get_mask_fix1,'Value');
3360if isequal(maskval,0)
3361    set(handles.mask_fix1,'String','')
3362else
3363    mask_displ='no mask'; %default
3364    filebase=get(handles.RootName,'String');
3365    [nbslice, flag_mask]=get_mask(filebase,handles);
3366    if isequal(flag_mask,1)
3367        mask_displ=[num2str(nbslice) 'mask'];
3368    elseif get(handles.compare,'Value')>1 & ~isequal(mask_displ,'no mask')% look for the second mask series
3369        filebase_a=get(handles.RootName_1,'String');
3370        [nbslice_a, flag_mask_a]=get_mask(filebase_a,handles);
3371        if isequal(flag_mask_a,0) || ~isequal(nbslice_a,nbslice)
3372            mask_displ='no mask';
3373        end
3374    end
3375    if isequal(mask_displ,'no mask')
3376        [FileName, PathName, filterindex] = uigetfile( ...
3377            {'*.png', ' (*.png)';
3378            '*.png',  '.png files '; ...
3379            '*.*', 'All Files (*.*)'}, ...
3380            'Pick a mask file *.png',filebase);
3381        mask_displ=fullfile(PathName,FileName);
3382        if ~exist(mask_displ,'file')
3383            mask_displ='no mask';
3384        end
3385    end
3386    if isequal(mask_displ,'no mask')
3387        set(handles.get_mask_fix1,'Value',0)
3388        set(handles.get_mask_civ2,'Value',0)
3389        set(handles.get_mask_fix2,'Value',0)
3390    else
3391        %set(handles.get_mask_civ2,'Value',1)
3392        set(handles.get_mask_fix2,'Value',1)
3393    end
3394    set(handles.mask_fix1,'String',mask_displ)
3395    set(handles.mask_civ2,'String',mask_displ)
3396    set(handles.mask_fix2,'String',mask_displ)
3397end
3398
3399%------------------------------------------------------------------------
3400% --- Executes on button press in get_mask_civ2: select box for mask option
3401function get_mask_civ2_Callback(hObject, eventdata, handles)
3402%------------------------------------------------------------------------
3403maskval=get(handles.get_mask_civ2,'Value');
3404if isequal(maskval,0)
3405    set(handles.mask_civ2,'String','')
3406else
3407    mask_displ='no mask'; %default
3408    filebase=get(handles.RootName,'String');
3409    [nbslice, flag_mask]=get_mask(filebase,handles);
3410    if isequal(flag_mask,1)
3411        mask_displ=[num2str(nbslice) 'mask'];
3412    elseif get(handles.compare,'Value')>1 & ~isequal(mask_displ,'no mask')% look for the second mask series
3413        filebase_a=get(handles.RootName_1,'String');
3414        [nbslice_a, flag_mask_a]=get_mask(filebase_a,handles);
3415        if isequal(flag_mask_a,0) || ~isequal(nbslice_a,nbslice)
3416            mask_displ='no mask';
3417        end
3418    end
3419    if isequal(mask_displ,'no mask')
3420        [FileName, PathName, filterindex] = uigetfile( ...
3421            {'*.png', ' (*.png)';
3422            '*.png',  '.png files '; ...
3423            '*.*', 'All Files (*.*)'}, ...
3424            'Pick a mask file *.png',filebase);
3425        mask_displ=fullfile(PathName,FileName);
3426        if ~exist(mask_displ,'file')
3427            mask_displ='no mask';
3428        end
3429    end
3430    if isequal(mask_displ,'no mask')
3431        set(handles.get_mask_civ2,'Value',0)
3432        set(handles.get_mask_fix2,'Value',0)
3433    else
3434        set(handles.get_mask_fix2,'Value',1)
3435    end
3436    set(handles.mask_civ2,'String',mask_displ)
3437    set(handles.mask_fix2,'String',mask_displ)
3438end
3439
3440%------------------------------------------------------------------------
3441% --- Executes on button press in get_mask_fix2.
3442function get_mask_fix2_Callback(hObject, eventdata, handles)
3443%------------------------------------------------------------------------
3444maskval=get(handles.get_mask_fix2,'Value');
3445if isequal(maskval,0)
3446    set(handles.mask_fix2,'String','')
3447else
3448    mask_displ='no mask'; %default
3449    filebase=get(handles.RootName,'String');
3450    [nbslice, flag_mask]=get_mask(filebase,handles);
3451    if isequal(flag_mask,1)
3452        mask_displ=[num2str(nbslice) 'mask'];
3453    elseif get(handles.compare,'Value')>1 & ~isequal(mask_displ,'no mask')% look for the second mask series
3454        filebase_a=get(handles.RootName_1,'String');
3455        [nbslice_a, flag_mask_a]=get_mask(filebase_a,handles);
3456        if isequal(flag_mask_a,0) || ~isequal(nbslice_a,nbslice)
3457            mask_displ='no mask';
3458        end
3459    end
3460    if isequal(mask_displ,'no mask')
3461        [FileName, PathName, filterindex] = uigetfile( ...
3462            {'*.png', ' (*.png)';
3463            '*.png',  '.png files '; ...
3464            '*.*', 'All Files (*.*)'}, ...
3465            'Pick a mask file *.png',filebase);
3466        mask_displ=fullfile(PathName,FileName);
3467        if ~exist(mask_displ,'file')
3468            mask_displ='no mask';
3469        end
3470    end
3471    if isequal(mask_displ,'no mask')
3472        set(handles.get_mask_fix2,'Value',0)
3473    end
3474    set(handles.mask_fix2,'String',mask_displ)
3475end
3476
3477%------------------------------------------------------------------------
3478% --- function called to look for mask files
3479function [nbslice, flag_mask]=get_mask(filebase,handles)
3480%------------------------------------------------------------------------
3481%detect mask files, images with appropriate file base
3482%[filebase '_' xx 'mask'], xx=nbslice
3483%flag_mask=1 indicates detection
3484
3485flag_mask=0;%default
3486nbslice=1;
3487
3488% subdir=get(handles.subdir_civ1,'String');
3489[Path,Name]=fileparts(filebase);
3490if ~isdir(Path)
3491    msgbox_uvmat('ERROR','no path for input files')
3492    return
3493end
3494currentdir=pwd;
3495cd(Path);%move in the dir of the root name filebase
3496maskfiles=dir([Name '_*mask_*.png']);%look for mask files
3497cd(currentdir);%come back to the current working directory
3498if ~isempty(maskfiles)
3499    %     msgbox_uvmat('ERROR','no mask available, to create it use Tools/Make mask in the upper menu bar of uvmat')
3500    % else
3501    flag_mask=1;
3502    maskname=maskfiles(1).name;% take the first mask file in the list
3503    [Path2,Name,ext]=fileparts(maskname);
3504    Namedouble=double(Name);
3505    val=(48>Namedouble)|(Namedouble>57);% select the non-numerical characters
3506    ind_mask=findstr('mask',Name);
3507    i=ind_mask-1;
3508    while val(i)==0 && i>0
3509        i=i-1;
3510    end
3511    nbslice=str2double(Name(i+1:ind_mask-1));
3512    if ~isnan(nbslice) && Name(i)=='_'
3513        flag_mask=1;
3514    else
3515        msgbox_uvmat('ERROR',['bad mask file ' Name ext ' found in ' Path2])
3516        return
3517        nbslice=1;
3518    end
3519end
3520
3521%------------------------------------------------------------------------
3522% --- function called to look for grid files
3523function [nbslice, flag_mask]=get_grid(filebase,handles)
3524%------------------------------------------------------------------------
3525flag_mask=0;%default
3526nbslice=1;
3527[Path,Name]=fileparts(filebase);
3528currentdir=pwd;
3529cd(Path);%move in the dir of the root name filebase
3530maskfiles=dir([Name '_*grid_*.grid']);%look for mask files
3531cd(currentdir);%come back to the current working directory
3532if ~isempty(maskfiles)
3533    flag_mask=1;
3534    maskname=maskfiles(1).name;% take the first mask file in the list
3535    [Path2,Name,ext]=fileparts(maskname);
3536    Namedouble=double(Name);
3537    val=(48>Namedouble)|(Namedouble>57);% select the non-numerical characters
3538    ind_mask=findstr('grid',Name);
3539    i=ind_mask-1;
3540    while val(i)==0 && i>0
3541        i=i-1;
3542    end
3543    nbslice=str2double(Name(i+1:ind_mask-1));
3544    if ~isnan(nbslice) && Name(i)=='_'
3545        flag_mask=1;
3546    else
3547        msgbox_uvmat('ERROR',['bad grid file ' Name ext ' found in ' Path2])
3548        return
3549        nbslice=1;
3550    end
3551end
3552
3553%------------------------------------------------------------------------
3554% --- transform numbers to letters
3555function str=num2stra(num,nom_type)
3556%------------------------------------------------------------------------
3557if isempty(nom_type)
3558    str='';
3559elseif strcmp(nom_type(end),'a')
3560    str=char(96+num);
3561elseif strcmp(nom_type(end),'A')
3562    str=char(96+num);
3563elseif isempty(nom_type(2:end))%a single index
3564    str='';
3565else
3566    str=num2str(num);
3567end
3568
3569%------------------------------------------------------------------------
3570% --- Executes on button press in list_subdir_civ1.
3571function list_subdir_civ1_Callback(hObject, eventdata, handles)
3572%------------------------------------------------------------------------
3573list_subdir_civ1=get(handles.list_subdir_civ1,'String');
3574val=get(handles.list_subdir_civ1,'Value');
3575if val>1
3576    subdir=list_subdir_civ1{val};
3577    set(handles.subdir_civ1,'String',subdir);
3578    set(handles.list_subdir_civ1,'Value',1);
3579end
3580
3581%------------------------------------------------------------------------
3582% --- Executes on button press in list_subdir_civ2.
3583function list_subdir_civ2_Callback(hObject, eventdata, handles)
3584%------------------------------------------------------------------------
3585list_subdir_civ2=get(handles.list_subdir_civ2,'String');
3586val=get(handles.list_subdir_civ2,'Value');
3587if val>1
3588    subdir=list_subdir_civ2{val};
3589    set(handles.subdir_civ2,'String',subdir);
3590    set(handles.list_subdir_civ2,'Value',1);
3591end
3592
3593%------------------------------------------------------------------------
3594% --- Executes on button press in browse_gridciv1.
3595function browse_gridciv1_Callback(hObject, eventdata, handles)
3596%------------------------------------------------------------------------
3597value=get(handles.browse_gridciv1,'Value');
3598testgrid=0;
3599if value
3600    filebase=get(handles.RootName,'String');
3601    [nbslice, flag_grid]=get_grid(filebase,handles);
3602    if isequal(flag_grid,1)
3603        filegrid=[num2str(nbslice) 'grid'];
3604        testgrid=1;
3605    else
3606        [FileName, PathName, filterindex] = uigetfile( ...
3607            {'*.grid', ' (*.grid)';
3608            '*.grid',  '.grid files '; ...
3609            '*.*', 'All Files (*.*)'}, ...
3610            'Pick a file',filebase);
3611        filegrid=fullfile(PathName,FileName);
3612        if ~(isempty(FileName)||isempty(PathName)||isequal(FileName,0)||~exist(filegrid,'file'))
3613            testgrid=1;
3614        end
3615    end
3616end
3617if testgrid
3618    set(handles.browse_gridciv2,'Value',1)
3619    set(handles.get_gridpatch1,'Value',1)
3620    set(handles.get_gridpatch2,'Value',1)
3621    set(handles.dx_civ1,'Visible','off');
3622    set(handles.dy_civ1,'Visible','off');
3623    set(handles.dx_civ2,'Visible','off');
3624    set(handles.dy_civ2,'Visible','off');
3625    set(handles.grid_civ1,'String',filegrid)
3626    set(handles.grid_patch1,'String',filegrid)
3627    set(handles.grid_civ2,'String',filegrid)
3628    set(handles.grid_patch2,'String',filegrid)
3629else
3630    set(handles.browse_gridciv1,'Value',0);
3631    set(handles.browse_gridciv2,'Value',0);
3632    set(handles.get_gridpatch1,'Value',0)
3633    set(handles.get_gridpatch2,'Value',0)
3634    set(handles.dx_civ1,'Visible','on');
3635    set(handles.dy_civ1,'Visible','on');
3636    set(handles.dx_civ2,'Visible','on');
3637    set(handles.dy_civ2,'Visible','on');
3638    set(handles.grid_civ1,'String','')
3639    set(handles.grid_patch1,'String','')
3640    set(handles.grid_civ2,'String','')
3641    set(handles.grid_patch2,'String','')
3642end
3643
3644%------------------------------------------------------------------------
3645% --- Executes on button press in browse_gridciv1.
3646function browse_gridciv2_Callback(hObject, eventdata, handles)
3647%------------------------------------------------------------------------
3648value=get(handles.browse_gridciv2,'Value');
3649if value
3650    filebase=get(handles.RootName,'String');
3651    [nbslice, flag_grid]=get_grid(filebase,handles);
3652    if isequal(flag_grid,1)
3653        mask_displ=[num2str(nbslice) 'grid'];
3654        set(handles.grid_civ2,'String',mask_displ)
3655        set(handles.dx_civ2,'Visible','off');
3656        set(handles.dy_civ2,'Visible','off');
3657    else
3658        [FileName, PathName, filterindex] = uigetfile( ...
3659            {'*.grid', ' (*.grid)';
3660            '*.grid',  '.grid files '; ...
3661            '*.*', 'All Files (*.*)'}, ...
3662            'Pick a file',filebase);
3663        filegrid=fullfile(PathName,FileName);
3664        if isempty(FileName)||isempty(PathName)||isequal(FileName,0)||~exist(filegrid,'file')
3665            set(handles.browse_gridciv2,'Value',0);
3666            set(handles.grid_civ2,'string','');
3667            set(handles.dx_civ2,'Visible','on');
3668            set(handles.dy_civ2,'Visible','on');
3669            set(handles.grid_civ2,'string','');
3670        else
3671            set(handles.grid_civ2,'string',filegrid);
3672            set(handles.dx_civ2,'Visible','off');
3673            set(handles.dy_civ2,'Visible','off');
3674            set(handles.grid_civ2,'string',filegrid);
3675        end
3676    end
3677else
3678    set(handles.grid_civ2,'string','');
3679    set(handles.dx_civ2,'Visible','on');
3680    set(handles.dy_civ2,'Visible','on');
3681    set(handles.grid_civ2,'string','');
3682end
3683
3684% % --- Executes on button press in browse_gridciv2.
3685% function browse_gridciv2_Callback(hObject, eventdata, handles)
3686%
3687% filebase=get(handles.RootName,'String');
3688% [FileName, PathName, filterindex] = uigetfile( ...
3689%        {'*.grid', ' (*.grid)';
3690%         '*.grid',  '.grid files '; ...
3691%         '*.*', 'All Files (*.*)'}, ...
3692%         'Pick a file',filebase);
3693% filegrid=fullfile(PathName,FileName);
3694% set(handles.grid_civ2,'string',filegrid);
3695% set(handles.dx_civ2,'String',' ');
3696% set(handles.dy_civ2,'String',' ');
3697% % set(handles.grid_patch2,'string',filegrid);
3698
3699% --- Executes on button press in get_gridpatch1.
3700function get_gridpatch1_Callback(hObject, eventdata, handles)
3701% hObject    handle to get_gridpatch1 (see GCBO)
3702% eventdata  reserved - to be defined in a future version of MATLAB
3703% handles    structure with handles and user data (see GUIDATA)
3704
3705filebase=get(handles.RootName,'String');
3706[FileName, PathName, filterindex] = uigetfile( ...
3707    {'*.grid', ' (*.grid)';
3708    '*.grid',  '.grid files '; ...
3709    '*.*', 'All Files (*.*)'}, ...
3710    'Pick a file',filebase);
3711filegrid=fullfile(PathName,FileName);
3712set(handles.grid_patch1,'string',filegrid);
3713% set(handles.grid_patch2,'string',filegrid
3714
3715%------------------------------------------------------------------------
3716% --- Executes on button press in get_gridpatch2.
3717function get_gridpatch2_Callback(hObject, eventdata, handles)
3718%------------------------------------------------------------------------
3719
3720%------------------------------------------------------------------------
3721function enable_civ1(handles,state)
3722%------------------------------------------------------------------------
3723if isequal(state,'on')
3724    set(handles.frame_civ1,'BackgroundColor',[1 1 0])
3725    set(handles.frame_para_civ1,'BackgroundColor',[1 1 0])
3726    set(handles.frame_grid_civ1,'BackgroundColor',[1 1 0])
3727else
3728    set(handles.frame_civ1,'BackgroundColor',[0.831 0.816 0.784])
3729    set(handles.frame_para_civ1,'BackgroundColor',[0.831 0.816 0.784])
3730    set(handles.frame_grid_civ1,'BackgroundColor',[0.831 0.816 0.784])
3731end
3732set(handles.ibx,'Visible',state)
3733set(handles.iby,'Visible',state)
3734set(handles.isx,'Visible',state)
3735set(handles.isy,'Visible',state)
3736set(handles.shiftx,'Visible',state)
3737set(handles.shifty,'Visible',state)
3738set(handles.rho,'Visible',state)
3739set(handles.dx_civ1,'Visible',state)
3740set(handles.dy_civ1,'Visible',state)
3741set(handles.calcul_search,'Visible',state)
3742set(handles.u_text,'Visible',state)
3743set(handles.v_text,'Visible',state)
3744set(handles.min,'Visible',state)
3745set(handles.max,'Visible',state)
3746set(handles.umin,'Visible',state)
3747set(handles.umax,'Visible',state)
3748set(handles.vmin,'Visible',state)
3749set(handles.vmax,'Visible',state)
3750set(handles.grid_civ1,'Visible',state)
3751set(handles.mask_civ1,'Visible',state)
3752set(handles.browse_gridciv1,'Visible',state)
3753set(handles.get_mask_civ1,'Visible',state)
3754set(handles.parameters,'Visible',state)
3755set(handles.grid,'Visible',state)
3756set(handles.dx_civ1,'Visible',state)
3757set(handles.dy_civ1,'Visible',state)
3758set(handles.ImaThreshold,'Visible',state)
3759if isequal(state,'off')
3760    set(handles.MinIma,'Visible','off')
3761    set(handles.MaxIma,'Visible','off')
3762    set(handles.ImaThreshold,'Value',0)
3763end
3764set(handles.dx_civ1_title,'Visible',state)
3765set(handles.dy_civ1_title,'Visible',state)
3766set(handles.ImaThreshold_title,'Visible',state)
3767set(handles.ib_title,'Visible',state)
3768set(handles.is_title,'Visible',state)
3769set(handles.shift_title,'Visible',state)
3770set(handles.rho_title,'Visible',state)
3771set(handles.TestCiv1,'Visible',state)
3772%set(handles.CivMode,'Visible',state)
3773
3774%------------------------------------------------------------------------
3775function enable_fix1(handles,state)
3776%------------------------------------------------------------------------
3777if isequal(state,0)
3778    state='off';
3779end
3780if isequal(state,1)
3781    state='on';
3782end
3783if isequal(state,'on')
3784    set(handles.frame_fix1,'BackgroundColor',[1 1 0])
3785else
3786    set(handles.frame_fix1,'BackgroundColor',[0.7 0.7 0.7])
3787end
3788set(handles.REMOVE,'Visible',state)
3789set(handles.vec_Fmin2,'Visible',state)
3790set(handles.vec_F2,'Visible',state)
3791set(handles.vec_F3,'Visible',state)
3792set(handles.thresh_vecC,'Visible',state)
3793set(handles.thresh_vecC_title,'Visible',state)
3794set(handles.thresh_vel,'Visible',state)
3795set(handles.thresh_vel_text,'Visible',state)
3796set(handles.mask_fix1,'Visible',state)
3797set(handles.get_mask_fix1,'Visible',state)
3798set(handles.get_ref_fix1,'Visible',state)
3799set(handles.ref_fix1,'Visible',state)
3800set(handles.inf_sup1,'Visible',state)
3801set(handles.field_ref1,'Visible',state)
3802
3803%------------------------------------------------------------------------
3804function enable_patch1(handles)
3805%------------------------------------------------------------------------
3806set(handles.frame_patch1,'BackgroundColor',[1 1 0])
3807set(handles.rho_patch1,'Visible','on')
3808set(handles.rho_text1,'Visible','on')
3809if get(handles.CivMode,'Value')==2
3810    set(handles.thresh_patch1,'Visible','on')
3811    set(handles.thresh_text1,'Visible','on')
3812end
3813set(handles.subdomain_patch1,'Visible','on')
3814set(handles.subdomain_text1,'Visible','on')
3815set(handles.nx_patch1,'Visible','on')
3816set(handles.ny_patch1,'Visible','on')
3817set(handles.nx_patch1_title,'Visible','on')
3818set(handles.ny_patch1_title,'Visible','on')
3819% if ~isempty(patch_newBin)
3820set(handles.test_interp,'Visible','off');
3821stereo_test=get(handles.compare,'Value');
3822if stereo_test==3
3823    set(handles.test_stereo1,'Visible','on')
3824end
3825% end
3826%set(handles.get_gridpatch1,'Visible','on')
3827%set(handles.grid_patch1,'string','none');
3828%set(handles.grid_patch1,'Visible','on')
3829
3830%------------------------------------------------------------------------
3831function desable_patch1(handles)
3832%------------------------------------------------------------------------
3833set(handles.frame_patch1,'BackgroundColor',[0.831 0.816 0.784])
3834set(handles.rho_patch1,'Visible','off')
3835set(handles.rho_text1,'Visible','off')
3836set(handles.thresh_patch1,'Visible','off')
3837set(handles.thresh_text1,'Visible','off')
3838set(handles.subdomain_patch1,'Visible','off')
3839set(handles.subdomain_text1,'Visible','off')
3840set(handles.nx_patch1,'Visible','off')
3841set(handles.ny_patch1,'Visible','off')
3842set(handles.nx_patch1_title,'Visible','off')
3843set(handles.ny_patch1_title,'Visible','off')
3844set(handles.test_stereo1,'Visible','off')
3845%set(handles.test_interp,'Visible','off')
3846%set(handles.get_gridpatch1,'Visible','off')
3847%set(handles.grid_patch1,'Visible','off')
3848
3849%------------------------------------------------------------------------
3850function enable_civ2(handles,state)
3851%------------------------------------------------------------------------
3852if isequal(state,0)
3853    state='off';
3854end
3855if isequal(state,1)
3856    state='on';
3857end
3858if isequal(state,'on')
3859    set(handles.frame_civ2,'BackgroundColor',[1 1 0])
3860    set(handles.frame_para_civ2,'BackgroundColor',[1 1 0])
3861    set(handles.frame_grid_civ2,'BackgroundColor',[1 1 0])
3862    set(handles.frame_subdirciv2,'BackgroundColor',[1 1 0])
3863else
3864    set(handles.frame_civ2,'BackgroundColor',[0.831 0.816 0.784])
3865    set(handles.frame_para_civ2,'BackgroundColor',[0.831 0.816 0.784])
3866    set(handles.frame_grid_civ2,'BackgroundColor',[0.831 0.816 0.784])
3867    set(handles.frame_subdirciv2,'BackgroundColor',[0.831 0.816 0.784])
3868end
3869set(handles.ibx_civ2,'Visible',state)
3870set(handles.iby_civ2,'Visible',state)
3871set(handles.decimal,'Visible',state)
3872set(handles.deformation,'Visible',state)
3873set(handles.rho_civ2,'Visible',state)
3874set(handles.dx_civ2,'Visible',state)
3875set(handles.dy_civ2,'Visible',state)
3876set(handles.browse_gridciv2,'Visible',state)
3877set(handles.get_mask_civ2,'Visible',state)
3878set(handles.parameters,'Visible',state)
3879set(handles.grid,'Visible',state)
3880set(handles.parameters_text,'Visible',state)
3881set(handles.grid_text,'Visible',state)
3882set(handles.grid_civ2,'Visible',state)
3883set(handles.mask_civ2,'Visible',state)
3884set(handles.dx_civ2_title,'Visible',state)
3885set(handles.dy_civ2_title,'Visible',state)
3886set(handles.ibx_civ2_text,'Visible',state)
3887set(handles.rho_civ2_title,'Visible',state)
3888set(handles.ImaThreshold2,'Visible',state)
3889set(handles.ImaThreshold_title2,'Visible',state)
3890if isequal(state,'off')
3891    set(handles.MinIma2,'Visible','off')
3892    set(handles.MaxIma2,'Visible','off')
3893    set(handles.ImaThreshold2,'Value',0)
3894    if isequal(get(handles.FIX2,'Value'),0) & isequal(get(handles.PATCH2,'Value'),0)
3895        set(handles.list_pair_civ2,'Visible','off')
3896        set(handles.subdir_civ2,'Visible','off')
3897        set(handles.subdir_civ2_text,'Visible','off')
3898        set(handles.dt_unit_civ2,'Visible','off')
3899        set(handles.ref_i_civ2,'Visible','off')
3900        set(handles.i_ref_civ2_title,'Visible','off')
3901        set(handles.j_ref_civ2_title,'Visible','off')
3902        set(handles.ref_j_civ2,'Visible','off')
3903    end
3904else
3905    set(handles.list_pair_civ2,'Visible','on')
3906    set(handles.subdir_civ2,'Visible','on')
3907    set(handles.subdir_civ2_text,'Visible','on')
3908    set(handles.dt_unit_civ2,'Visible','on')
3909    set(handles.ref_i_civ2,'Visible','on')
3910    set(handles.i_ref_civ2_title,'Visible','on')
3911    set(handles.j_ref_civ2_title,'Visible','on')
3912    set(handles.ref_j_civ2,'Visible','on')
3913end
3914set(handles.rho_civ2_title,'Visible',state)
3915
3916%------------------------------------------------------------------------
3917function enable_fix2(handles)
3918%------------------------------------------------------------------------
3919set(handles.frame_fix2,'BackgroundColor',[1 1 0])
3920set(handles.REMOVE2,'Visible','on')
3921set(handles.vec_Fmin2_2,'Visible','on')
3922set(handles.vec_F4,'Visible','on')
3923set(handles.vec_F3_2,'Visible','on')
3924set(handles.thresh_vec2C,'Visible','on')
3925set(handles.thresh_vec2C_text,'Visible','on')
3926set(handles.thresh_vel2,'Visible','on')
3927set(handles.thresh_vel2_text,'Visible','on')
3928set(handles.mask_fix2,'Visible','on')
3929set(handles.get_mask_fix2,'Visible','on')
3930set(handles.list_pair_civ2,'Visible','on')
3931set(handles.subdir_civ2,'Visible','on')
3932set(handles.subdir_civ2_text,'Visible','on')
3933set(handles.get_ref_fix2,'Visible','on')
3934set(handles.ref_fix2,'Visible','on')
3935set(handles.inf_sup2,'Visible','on')
3936set(handles.field_ref2,'Visible','on')
3937
3938%------------------------------------------------------------------------
3939function desable_fix2(handles)
3940%------------------------------------------------------------------------
3941set(handles.frame_fix2,'BackgroundColor',[0.831 0.816 0.784])
3942set(handles.REMOVE2,'Visible','off')
3943set(handles.vec_Fmin2_2,'Visible','off')
3944set(handles.vec_F4,'Visible','off')
3945set(handles.vec_F3_2,'Visible','off')
3946set(handles.thresh_vec2C,'Visible','off')
3947set(handles.thresh_vec2C_text,'Visible','off')
3948set(handles.thresh_vel2,'Visible','off')
3949set(handles.thresh_vel2_text,'Visible','off')
3950set(handles.mask_fix2,'Visible','off')
3951set(handles.get_mask_fix2,'Visible','off')
3952set(handles.get_ref_fix2,'Visible','off')
3953set(handles.ref_fix2,'Visible','off')
3954set(handles.inf_sup2,'Visible','off')
3955set(handles.field_ref2,'Visible','off')
3956if isequal(get(handles.CIV2,'Value'),0) & isequal(get(handles.PATCH2,'Value'),0)
3957    set(handles.list_pair_civ2,'Visible','off')
3958    set(handles.subdir_civ2,'Visible','off')
3959    set(handles.subdir_civ2_text,'Visible','off')
3960end
3961
3962%------------------------------------------------------------------------
3963function enable_patch2(handles)
3964%------------------------------------------------------------------------
3965set(handles.frame_patch2,'BackgroundColor',[1 1 0])
3966set(handles.rho_patch2,'Visible','on')
3967set(handles.rho_text2,'Visible','on')
3968set(handles.thresh_patch2,'Visible','on')
3969set(handles.thresh_text2,'Visible','on')
3970set(handles.subdomain_patch2,'Visible','on')
3971set(handles.subdomain_text2,'Visible','on')
3972set(handles.nx_patch2,'Visible','on')
3973set(handles.ny_patch2,'Visible','on')
3974set(handles.nx_patch2_title,'Visible','on')
3975set(handles.ny_patch2_title,'Visible','on')
3976% set(handles.get_gridpatch2,'Visible','on')
3977% set(handles.grid_patch2,'Visible','on')
3978set(handles.list_pair_civ2,'Visible','on')
3979set(handles.subdir_civ2,'Visible','on')
3980set(handles.subdir_civ2_text,'Visible','on')
3981stereo_test=get(handles.compare,'Value');
3982if stereo_test==3
3983    set(handles.test_stereo2,'Visible','on')
3984end
3985
3986%------------------------------------------------------------------------
3987function desable_patch2(handles)
3988%------------------------------------------------------------------------
3989set(handles.frame_patch2,'BackgroundColor',[0.831 0.816 0.784])
3990set(handles.rho_patch2,'Visible','off')
3991set(handles.rho_text2,'Visible','off')
3992set(handles.thresh_patch2,'Visible','off')
3993set(handles.thresh_text2,'Visible','off')
3994set(handles.subdomain_patch2,'Visible','off')
3995set(handles.subdomain_text2,'Visible','off')
3996set(handles.nx_patch2,'Visible','off')
3997set(handles.ny_patch2,'Visible','off')
3998set(handles.nx_patch2_title,'Visible','off')
3999set(handles.ny_patch2_title,'Visible','off')
4000% set(handles.get_gridpatch2,'Visible','off')
4001% set(handles.grid_patch2,'Visible','off')
4002if isequal(get(handles.CIV2,'Value'),0) & isequal(get(handles.FIX2,'Value'),0)
4003    set(handles.list_pair_civ2,'Visible','off')
4004    set(handles.subdir_civ2,'Visible','off')
4005    set(handles.subdir_civ2_text,'Visible','off')
4006end
4007set(handles.test_stereo2,'Visible','off')
4008%------------------------------------------------------------------------
4009function enable_pair1(handles,state)
4010%------------------------------------------------------------------------
4011set(handles.subdir_civ1,'Visible',state)
4012set(handles.list_subdir_civ1,'Visible',state)
4013set(handles.SUBDIR_CIV1_txt,'Visible',state)
4014set(handles.frame_subdirciv1,'Visible',state)
4015set(handles.list_pair_civ1,'Visible',state)
4016set(handles.PAIR_txt,'Visible',state)
4017%set(handles.dt_unit,'Visible',state)
4018set(handles.PAIR_frame,'Visible',state)
4019
4020%------------------------------------------------------------------------
4021% --- Read the parameters for civ1 on the interface
4022function par=read_param_civ1(handles,file_ima)
4023%------------------------------------------------------------------------
4024ibx_val=str2double(get(handles.ibx,'String'));
4025par.ibx=num2str(ibx_val);
4026iby_val=str2double(get(handles.iby,'String'));
4027par.iby=num2str(iby_val);
4028isx=get(handles.isx,'String');
4029if isnan(str2double(isx)), isx='41'; set(handles.isx,'String','41'), end; %default
4030if str2double(isx)<ibx_val+8,isx=num2str(ibx_val+8); set(handles.isx,'String',num2str(ibx_val+8)); end
4031isy=get(handles.isy,'String');
4032if isnan(str2double(isy)), isy='41'; set(handles.isy,'String','41'), end;%default
4033if str2double(isy)<iby_val+8,isy=num2str(iby_val+8); set(handles.isy,'String',num2str(iby_val+8)); end
4034par.isx=get(handles.isx,'String');
4035par.isy=get(handles.isy,'String');
4036par.shiftx=get(handles.shiftx,'String');
4037par.shifty=get(handles.shifty,'String');
4038if isnan(str2double(par.isx))
4039    par.isx='41';%default
4040    set(handles.isx,'String','41');
4041end
4042if isnan(str2double(par.isy))
4043    par.isy='41'; %default
4044    set(handles.isy,'String','41');
4045end
4046if isnan(str2double(par.shiftx))
4047    par.shiftx='0';%default
4048    set(handles.shiftx,'String','0');
4049end
4050if isnan(str2double(par.shifty))
4051    par.shifty='0'; %default
4052    set(handles.shifty,'String','0');
4053end
4054par.rho=get(handles.rho,'String');
4055if isequal(get(handles.rho,'Style'),'popupmenu')
4056    index=get(handles.rho,'Value');
4057    par.rho=par.rho{index};
4058end
4059par.dx=get(handles.dx_civ1,'String');
4060par.dy=get(handles.dy_civ1,'String');
4061if isnan(str2double(par.dx))
4062    if isempty(get(handles.grid_civ1,'String'));
4063        par.dx='0'; %just read by civ program, not used
4064    else
4065        par.dx='20';%default
4066        set(handles.dx_civ1,'String','20');
4067    end
4068end
4069if isnan(str2double(par.dy))
4070    if isempty(get(handles.grid_civ1,'String'));
4071        par.dy='0';%just read by civ program, not used
4072    else
4073        par.dy='20';%default
4074        set(handles.dy_civ1_title,'String','20');
4075    end
4076end
4077par.pxcmx='1'; %velocities are expressed in pixel dispalcement
4078par.pxcmy='1';
4079if exist('file_ima','var')
4080A=imread(file_ima);%read the first image to get the size
4081sizim=size(A);
4082par.npx=num2str(sizim(2));
4083par.npy=num2str(sizim(1));
4084end
4085%time=get(handles.RootName,'UserData'); %get the set of times
4086par.gridname=get(handles.grid_civ1,'String');
4087par.gridflag='y';
4088if strcmp(par.gridname,'')|| isempty(par.gridname)
4089    par.gridname='nogrid';
4090    par.gridflag='n';
4091end
4092
4093%------------------------------------------------------------------------
4094function par=read_param_civ2(handles,file_ima)
4095%------------------------------------------------------------------------
4096par.ibx=get(handles.ibx_civ2,'String');
4097par.iby=get(handles.iby_civ2,'String');
4098par.rho=get(handles.rho_civ2,'String');
4099par.decimal=int2str(get(handles.decimal,'Value'));
4100par.deformation=int2str(get(handles.deformation,'Value'));
4101par.dx=get(handles.dx_civ2,'String');
4102par.dy=get(handles.dy_civ2,'String');
4103if isnan(str2double(par.dx))
4104    if isempty(get(handles.grid_civ2,'String'));
4105        par.dx='0'; %just read by civ program, not used
4106    else
4107        par.dx='20';%default
4108        set(handles.dx_civ2,'String','20');
4109    end
4110end
4111if isnan(str2double(par.dy))
4112    if isempty(get(handles.grid_civ2,'String'));
4113        par.dy='0';%just read by civ program, not used
4114    else
4115        par.dy='20';%default
4116        set(handles.dy_civ2,'String','20');
4117    end
4118end
4119par.pxcmx='1';
4120par.pxcmy='1';
4121A=imread(file_ima);%read the first image to get the size
4122sizim=size(A);
4123par.npx=num2str(sizim(2));
4124par.npy=num2str(sizim(1));
4125%time=get(handles.RootName,'UserData'); %get the set of times
4126par.gridname=get(handles.grid_civ2,'String');
4127par.gridflag='y';
4128if strcmp(par.gridname,'')|| isempty(par.gridname)
4129    par.gridname='nogrid';
4130    par.gridflag='n';
4131end
4132
4133%------------------------------------------------------------------------
4134% --- CIV1  CIV1  CIV1 CIV1
4135function cmd_CIV1=CIV1_CMD(filename,namelog,par,handles,sparam)
4136%------------------------------------------------------------------------
4137%pixels per cm and matrix of the image times, read from the .civ file by uvmat
4138
4139%changes : filename_cmx -> filename ( no extension )
4140% input namelog not used
4141if isequal(par.Dt,'0')
4142    par.Dt='1' ;%case of 'displacement' mode
4143end
4144par.filename_ima_a=regexprep(par.filename_ima_a,'.png','');
4145par.filename_ima_b=regexprep(par.filename_ima_b,'.png','');
4146fid=fopen([filename '.civ1.cmx'],'w');
4147fprintf(fid,['##############   CMX file' '\n' ]);
4148fprintf(fid,   ['FirstImage ' regexprep(par.filename_ima_a,'\\','\\\\') '\n' ]);% for windows compatibility
4149fprintf(fid,   ['LastImage  ' regexprep(par.filename_ima_b,'\\','\\\\') '\n' ]);% for windows compatibility
4150fprintf(fid,  ['XX' '\n' ]);
4151fprintf(fid,  ['Mask ' par.maskflag '\n' ]);
4152fprintf(fid,  ['MaskName ' regexprep(par.maskname,'\\','\\\\') '\n' ]);
4153fprintf(fid,   ['ImageSize ' par.npx ' ' par.npy '\n' ]);   %VERIFIER CAS GENERAL ?
4154fprintf(fid,   ['CorrelationBoxesSize ' par.ibx ' ' par.iby '\n' ]);
4155fprintf(fid,   ['SearchBoxeSize ' par.isx ' ' par.isy '\n' ]);
4156fprintf(fid,   ['RO ' par.rho '\n' ]);
4157fprintf(fid,   ['GridSpacing ' par.dx ' ' par.dy '\n' ]);
4158fprintf(fid,   ['XX 1.0' '\n' ]);
4159fprintf(fid,   ['Dt_TO ' par.Dt ' ' par.T0 '\n' ]);
4160fprintf(fid,  ['PixCmXY ' par.pxcmx ' ' par.pxcmy '\n' ]);
4161fprintf(fid,  ['XX 1' '\n' ]);
4162fprintf(fid,   ['ShiftXY ' par.shiftx ' '  par.shifty '\n' ]);
4163fprintf(fid,  ['Grid ' par.gridflag '\n' ]);
4164fprintf(fid,   ['GridName ' regexprep(par.gridname,'\\','\\\\') '\n' ]);
4165fprintf(fid,   ['XX 85' '\n' ]);
4166fprintf(fid,   ['XX 1.0' '\n' ]);
4167fprintf(fid,   ['XX 1.0' '\n' ]);
4168fprintf(fid,   ['Hart 1' '\n' ]);
4169fprintf(fid,  [ 'DecimalShift 0' '\n' ]);
4170fprintf(fid,   ['Deformation 0' '\n' ]);
4171fprintf(fid,  ['CorrelationMin 0' '\n' ]);
4172fprintf(fid,   ['IntensityMin 0' '\n' ]);
4173fprintf(fid,  ['SeuilImage n' '\n' ]);
4174fprintf(fid,   ['SeuilImageValues 0 4096' '\n' ]);
4175fprintf(fid,   ['ImageToUse ' par.term_a ' ' par.term_b '\n' ]); % VERIFIER ?
4176fprintf(fid,   ['ImageUsedBefore null null' '\n' ]);
4177fclose(fid);
4178
4179% cmd_CIV1=[sparam.Civ1Bin ' -f ' filename '.cmx >' filename '.log' ]; % redirect standard output to the log file
4180% cmd_CIV1=regexprep(cmd_CIV1,'\\','\\\\');
4181% namelog=regexprep(namelog,'\\','\\\\');
4182if(isunix)
4183    cmd_CIV1=['cp -f ' filename '.civ1.cmx ' filename '.cmx\n'];
4184    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
4185    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
4186   % cmd_CIV1=[cmd_CIV1 '\n' 'mv ' filename '.cmx' ' ' filename '.civ1.cmx' '\n'];%rename .cmx as .civ1.cmx
4187else %Windows system
4188                    flname=regexprep(flname,'\\','\\\\');
4189%                     cmd=[cmd 'copy /Y "' flname '.civ1.cmx" "' flname '.cmx"\n'];
4190    filename=regexprep(filename,'\\','\\\\');
4191    cmd_CIV1=['copy /Y "' filename '.civ1.cmx" "' filename '.cmx"\n'];% copy the .civ1.cmx parameter file to .cmx
4192    cmd_CIV1=['"' sparam.Civ1Bin '" -f "' filename '.cmx" >"' filename '.log"' ]; % redirect standard output to the log file
4193    cmd_CIV1=regexprep(cmd_CIV1,'\\','\\\\');
4194    namelog=regexprep(namelog,'\\','\\\\');
4195    cmd_CIV1=[cmd_CIV1 '\n' 'copy /Y "' filename '.log' '" "' filename '.civ1.log"']; %preserve the log file as .civ1.log
4196  %  cmd_CIV1=[cmd_CIV1 '\n' 'copy /Y "' filename '.cmx' '" "' filename '.civ1.cmx"'];
4197end
4198
4199%------------------------------------------------------------------------
4200% --- CIV1  Unified
4201function xml_civ1_parameters=CIV1_CMD_Unified(filename,namelog,par)
4202%------------------------------------------------------------------------
4203%pixels per cm and matrix of the image times, read from the .civ file by uvmat
4204%global CivBin%name of the executable for civ1 calculation
4205
4206civ1.image1=par.filename_ima_a;
4207civ1.image2=par.filename_ima_b;
4208civ1.imageSize_X=par.npx;
4209civ1.imageSize_Y=par.npy;
4210civ1.outputFileName=[filename '.nc'];
4211civ1.correlationBoxesSize_X=par.ibx;
4212civ1.correlationBoxesSize_Y=par.iby;
4213civ1.searchBoxesSize_X=par.isx;
4214civ1.searchBoxesSize_Y=par.isy;
4215civ1.globalShift_X=par.shiftx;
4216civ1.globalShift_Y=par.shifty;
4217civ1.ro=par.rho;
4218civ1.hart='y';
4219if isequal(par.gridflag,'y')
4220    civ1.grid=par.gridname;
4221else
4222    civ1.grid='n';
4223    civ1.gridSpacing_X=par.dx;
4224    civ1.gridSpacing_Y=par.dy;
4225end
4226if isequal(par.maskflag,'y')
4227    civ1.mask=par.maskname;
4228end
4229civ1.dt=par.Dt;
4230civ1.unit='pixel';
4231civ1.absolut_time_T0=par.T0;
4232civ1.pixcmx=par.pxcmx;
4233civ1.pixcmy=par.pxcmy;
4234civ1.convectFlow='n';
4235
4236xml_civ1_parameters=civ1;
4237
4238%------------------------------------------------------------------------
4239% --- CIV2  Unified
4240function civ2=CIV2_CMD_Unified(filename,namelog,par)
4241%------------------------------------------------------------------------
4242%pixels per cm and matrix of the image times, read from the .civ file by uvmat
4243%global CivBin%name of the executable for civ1 calculation
4244
4245civ2.image1=par.filename_ima_a;
4246civ2.image2=par.filename_ima_b;
4247civ2.imageSize_X=par.npx;
4248civ2.imageSize_Y=par.npy;
4249civ2.inputFileName=[par.filename_nc1 '.nc'];
4250civ2.outputFileName=[filename '.nc'];
4251civ2.correlationBoxesSize_X=par.ibx;
4252civ2.correlationBoxesSize_Y=par.iby;
4253civ2.ro=par.rho;
4254%civ2.decimalShift=par.decimal;
4255%civ2.deformation=par.deformation;
4256if isequal(par.decimal,'1')
4257    civ2.decimalShift='y';
4258else
4259    civ2.decimalShift='n';
4260end
4261if isequal(par.deformation,'1')
4262    civ2.deformation='y';
4263else
4264    civ2.deformation='n';
4265end
4266if isequal(par.gridflag,'y')
4267    civ2.grid=par.gridname;
4268else
4269    civ2.grid='n';
4270    civ2.gridSpacing_X=par.dx;
4271    civ2.gridSpacing_Y=par.dy;
4272end
4273civ2.gridSpacing_X='10';
4274civ2.gridSpacing_Y='10';%NOTE: faut mettre gridSpacing pourque ca tourne, meme si c'est la grille qui est utilisee
4275if isequal(par.maskflag,'y')
4276    civ2.mask=par.maskname;
4277else
4278    civ2.mask='n';
4279end
4280civ2.dt=par.Dt;
4281civ2.unit='pixel';
4282civ2.absolut_time_T0=par.T0;
4283civ2.pixcmx=par.pxcmx;
4284civ2.pixcmy=par.pxcmy;
4285civ2.convectFlow='n';
4286civ2.pixcmx=par.pxcmx;
4287civ2.pixcmy=par.pxcmy;
4288civ2.convectFlow='n';
4289
4290%------------------------------------------------------------------------
4291% --- CIV2  CIV2  CIV2 CIV2
4292function cmd_CIV2=CIV2_CMD(filename,namelog,par,sparam)
4293%------------------------------------------------------------------------
4294%pixels per cm and matrix of the image times, read from the .civ file by uvmat
4295% global civ2Bin sge%name of the executable for civ1 calculation
4296if isequal(par.Dt,'0')
4297    par.Dt='1' ;%case of 'displacement' mode
4298end
4299par.filename_ima_a=regexprep(par.filename_ima_a,'.png','');
4300par.filename_ima_b=regexprep(par.filename_ima_b,'.png','');% bug : .png appears two times ?
4301[fid,errormsg]=fopen([filename '.civ2.cmx'],'w');
4302if isequal(fid,-1)
4303    msgbox_uvmat('ERROR',errormsg)
4304    cmd_CIV2='';
4305    return
4306end
4307fprintf(fid,['##############   CMX file' '\n' ]);
4308fprintf(fid,   ['FirstImage ' regexprep(par.filename_ima_a,'\\','\\\\') '\n' ]);% for windows compatibility
4309fprintf(fid,   ['LastImage  ' regexprep(par.filename_ima_b,'\\','\\\\') '\n' ]);% for windows compatibility
4310fprintf(fid,  ['XX' '\n' ]);
4311fprintf(fid, ['Mask ' par.maskflag '\n' ]);
4312fprintf(fid, ['MaskName ' regexprep(par.maskname,'\\','\\\\') '\n' ]);% for windows compatibility
4313fprintf(fid, ['ImageSize ' par.npx ' ' par.npy '\n' ]);   %VERIFIER CAS GENERAL ?
4314fprintf(fid, ['CorrelationBoxesSize ' par.ibx ' ' par.iby '\n' ]);
4315fprintf(fid, ['SearchBoxeSize ' par.ibx ' ' par.iby '\n']);
4316fprintf(fid, ['RO ' par.rho '\n']);
4317fprintf(fid, ['GridSpacing ' par.dx ' ' par.dy '\n']);
4318fprintf(fid, ['XX 1.0' '\n' ]);
4319fprintf(fid, ['Dt_TO ' par.Dt ' ' par.T0 '\n' ]);
4320fprintf(fid, ['PixCmXY ' par.pxcmx ' ' par.pxcmy '\n' ]);
4321fprintf(fid, ['XX 1' '\n' ]);
4322fprintf(fid, 'ShiftXY 0 0\n');
4323fprintf(fid, ['Grid ' par.gridflag '\n' ]);
4324fprintf(fid, ['GridName ' regexprep(par.gridname,'\\','\\\\') '\n']);
4325fprintf(fid, ['XX 85' '\n' ]);
4326fprintf(fid, ['XX 1.0' '\n' ]);
4327fprintf(fid, ['XX 1.0' '\n' ]);
4328fprintf(fid, ['Hart 1' '\n' ]);
4329fprintf(fid, ['DecimalShift ' par.decimal '\n']);
4330fprintf(fid, ['Deformation ' par.deformation '\n']);
4331fprintf(fid,  ['CorrelationMin 0' '\n' ]);
4332fprintf(fid,   ['IntensityMin 0' '\n' ]);
4333fprintf(fid,  ['SeuilImage n' '\n' ]);
4334fprintf(fid,   ['SeuilImageValues 0 4096' '\n' ]);
4335fprintf(fid,   ['ImageToUse ' par.term_a ' ' par.term_b '\n' ]); % VERIFIER ?
4336fprintf(fid, ['ImageUsedBefore ' regexprep(par.filename_nc1,'\\','\\\\') '\n']);
4337fclose(fid);
4338
4339if(isunix)
4340    cmd_CIV2=['cp -f ' filename '.civ2.cmx ' filename '.cmx\n'];
4341    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
4342    cmd_CIV2=[cmd_CIV2 '\n' 'mv ' filename '.log' ' ' filename '.civ2.log' '\n' 'chmod g+w ' filename '.nc'];%preserve the log file as .civ2.log
4343%    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
4344
4345else
4346    filename=regexprep(filename,'\\','\\\\');
4347    cmd_CIV2=['copy /Y "' filename '.civ2.cmx" "' filename '.cmx"\n'];
4348    cmd_CIV2=[cmd_CIV2 '"' sparam.Civ2Bin '" -f "' filename  '.cmx" >"' filename '.log"' ]; % redirect standard output to the log file
4349    cmd_CIV2=regexprep(cmd_CIV2,'\\','\\\\');
4350    cmd_CIV2=[cmd_CIV2 '\n' 'copy /Y "' filename '.log' '" "' filename '.civ2.log"'];
4351 %    cmd_CIV2=[cmd_CIV2 '\n' 'copy /Y "' filename '.cmx' '" "' filename '.civ2.cmx"'];
4352end
4353
4354% %------------------------------------------------------------------------
4355% % --- civ using pivlab
4356% function Data=civ_uvmat(par_civ1)
4357% %------------------------------------------------------------------------
4358% image1=imread(par_civ1.filename_ima_a);
4359% image2=imread(par_civ1.filename_ima_b);
4360% stepx=str2num(par_civ1.dx);
4361% stepy=str2num(par_civ1.dy);
4362% ibx2=ceil(str2num(par_civ1.ibx)/2);
4363% iby2=ceil(str2num(par_civ1.iby)/2);
4364% isx2=ceil(str2num(par_civ1.isx)/2);
4365% isy2=ceil(str2num(par_civ1.isy)/2);
4366% shiftx=str2num(par_civ1.shiftx);
4367% shifty=str2num(par_civ1.shifty);
4368% miniy=max(1+isy2-shifty,1+iby2);
4369% minix=max(1+isx2-shiftx,1+ibx2);
4370% maxiy=min(size(image1,1)-isy2-shifty,size(image1,1)-iby2);
4371% maxix=min(size(image1,2)-isx2-shiftx,size(image1,2)-ibx2);
4372% [GridX,GridY]=meshgrid(minix:stepx:maxix,miniy:stepy:maxiy);
4373% PointCoord(:,1)=reshape(GridX,[],1);
4374% PointCoord(:,2)=reshape(GridY,[],1);
4375% % caluclate velocity data (y and v in indices, reverse to y component)
4376% [xtable ytable utable vtable ctable F] = pivlab (image1,image2,ibx2,iby2,isx2,isy2,shiftx,shifty,PointCoord, 1, []);
4377% Data.ListGlobalAttribute=[{'Conventions','Program','CivStage'} {'Time','Dt'}];
4378% Data.Conventions='uvmat/civdata';
4379% Data.Program='civ_uvmat';
4380% Data.CivStage=1;
4381% % list_param=fieldnames(Param.Civ1);
4382% % for ilist=1:length(list_param)
4383% %     eval(['Data.Civ1_' list_param{ilist} '=Param.Civ1.' list_param{ilist} ';'])
4384% % end
4385% Data.Time=str2double(par_civ1.T0);
4386% Data.Dt=str2double(par_civ1.Dt);
4387% Data.ListVarName={'Civ1_X','Civ1_Y','Civ1_U','Civ1_V','Civ1_C','Civ1_F'};%  cell array containing the names of the fields to record
4388% Data.VarDimName={'nbvec','nbvec','nbvec','nbvec','nbvec','nbvec'};
4389% Data.VarAttribute{1}.Role='coord_x';
4390% Data.VarAttribute{2}.Role='coord_y';
4391% Data.VarAttribute{3}.Role='vector_x';
4392% Data.VarAttribute{4}.Role='vector_y';
4393% Data.VarAttribute{5}.Role='warnflag';
4394% Data.Civ1_X=reshape(xtable,[],1);
4395% Data.Civ1_Y=reshape(size(image1,1)-ytable+1,[],1);
4396% Data.Civ1_U=reshape(utable,[],1);
4397% Data.Civ1_V=reshape(-vtable,[],1);
4398% Data.Civ1_C=reshape(ctable,[],1);
4399% Data.Civ1_F=reshape(F,[],1);
4400
4401%------------------------------------------------------------------------
4402% --- Executes on button press in HELP.
4403function HELP_Callback(hObject, eventdata, handles)
4404%------------------------------------------------------------------------
4405path_to_uvmat=which ('uvmat');% check the path of uvmat
4406pathelp=fileparts(path_to_uvmat);
4407helpfile=fullfile(pathelp,'uvmat_doc','uvmat_doc.html');
4408if isempty(dir(helpfile)), msgbox_uvmat('ERROR','Please put the help file uvmat_doc.html in the sub-directory /uvmat_doc of the UVMAT package')
4409else
4410    addpath (fullfile(pathelp,'uvmat_doc'))
4411    web([helpfile '#civ'])
4412end
4413
4414%------------------------------------------------------------------------
4415%--read images and convert them to the uint16 format used for PIV
4416function A=read_image(filename,type_ima,num,movieobject)
4417%------------------------------------------------------------------------
4418%num is the view number needed for an avi movie
4419switch type_ima
4420    case 'movie'
4421        A=read(movieobject,num);
4422    case 'avi'
4423        mov=aviread(filename,num);
4424        A=frame2im(mov(1));
4425    case 'multimage'
4426        A=imread(filename,num);
4427    case 'image'
4428        A=imread(filename);
4429end
4430siz=size(A);
4431if length(siz)==3;%color images
4432    A=sum(double(A),3);
4433    A=uint16(A);
4434end
4435
4436%------------------------------------------------------------------------
4437function ref_i_Callback(hObject, eventdata, handles)
4438%------------------------------------------------------------------------
4439mode_list=get(handles.mode,'String');
4440mode_value=get(handles.mode,'Value');
4441mode=mode_list{mode_value};
4442find_netcpair_civ1(hObject, eventdata, handles);% update the menu of pairs depending on the available netcdf files
4443if isequal(mode,'series(Di)') || ...% we do patch2 only
4444        (get(handles.CIV2,'Value')==0 && get(handles.CIV1,'Value')==0 && get(handles.FIX1,'Value')==0 && get(handles.PATCH1,'Value')==0)
4445    find_netcpair_civ2(hObject, eventdata, handles);
4446end
4447
4448%------------------------------------------------------------------------
4449function ref_j_Callback(hObject, eventdata, handles)
4450%------------------------------------------------------------------------
4451mode_list=get(handles.mode,'String');
4452mode_value=get(handles.mode,'Value');
4453mode=mode_list{mode_value};
4454if isequal(get(handles.CIV1,'Value'),0)|| isequal(mode,'series(Dj)')
4455    find_netcpair_civ1(hObject, eventdata, handles);% update the menu of pairs depending on the available netcdf files
4456end
4457if isequal(mode,'series(Dj)') || ...
4458        (get(handles.CIV2,'Value')==0 && get(handles.CIV1,'Value')==0 && get(handles.FIX1,'Value')==0 && get(handles.PATCH1,'Value')==0)
4459    find_netcpair_civ2(hObject, eventdata, handles);
4460end
4461
4462%------------------------------------------------------------------------
4463function ref_i_civ2_Callback(hObject, eventdata, handles)
4464%------------------------------------------------------------------------
4465mode_list=get(handles.mode,'String');
4466mode_value=get(handles.mode,'Value');
4467mode=mode_list{mode_value};
4468find_netcpair_civ2(hObject, eventdata, handles);% update the menu of pairs depending on the available netcdf files
4469
4470%------------------------------------------------------------------------
4471function ref_j_civ2_Callback(hObject, eventdata, handles)
4472%------------------------------------------------------------------------
4473mode_list=get(handles.mode,'String');
4474mode_value=get(handles.mode,'Value');
4475mode=mode_list{mode_value};
4476if  isequal(mode,'series(Dj)')
4477    find_netcpair_civ2(hObject, eventdata, handles);% update the menu of pairs depending on the available netcdf files
4478end
4479
4480%------------------------------------------------------------------------
4481% --- Executes on button press in compare.
4482function compare_Callback(hObject, eventdata, handles)
4483%------------------------------------------------------------------------
4484test=get(handles.compare,'Value');
4485if test==2 || test==3 % case 'dispalcemen' or 'stereo PIV'
4486    filebase=get(handles.RootName,'String');
4487    browse=get(handles.browse_root,'Userdata');
4488    browse.nom_type_ima1=browse.nom_type_ima;
4489    set(handles.browse_root,'UserData',browse);
4490    set(handles.sub_txt,'Visible','on')
4491    set(handles.RootName_1,'Visible','On');%mkes the second file input window visible
4492    mode_store=get(handles.mode,'String');%get the present 'mode'
4493    set(handles.compare,'UserData',mode_store);%store the mode display
4494    set(handles.mode,'Visible','off')
4495    if test==2
4496        set(handles.mode,'Visible','off')
4497        set(handles.CivMode,'Value',1) % mode 'civX' selected by default
4498    else
4499        set(handles.mode,'Visible','on')
4500        set(handles.CivMode,'Value',3) % mode 'Matlab' selected for stereo
4501    end
4502   
4503    %% open an image file with the browser
4504    ind_opening=1;%default
4505    browse.incr_pair=[0 0]; %default
4506    oldfile=get(handles.RootName,'String');
4507     menu={'*.xml;*.civ;*.png;*.jpg;*.tif;*.avi;*.AVI;*.nc;', ' (*.xml,*.civ,*.png,*.jpg ,.tif, *.avi,*.nc)';
4508       '*.xml',  '.xml files '; ...
4509        '*.civ',  '.civ files '; ...
4510        '*.png','.png image files'; ...
4511        '*.jpg',' jpeg image files'; ...
4512        '*.tif','.tif image files'; ...
4513        '*.avi;*.AVI','.avi movie files'; ...
4514        '*.nc','.netcdf files'; ...
4515        '*.*',  'All Files (*.*)'};
4516    [FileName, PathName, filtindex] = uigetfile( menu, 'Pick a file of the second series',oldfile);
4517    fileinput=[PathName FileName];%complete file name
4518    sizf=size(fileinput);
4519    if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end %stop if fileinput not a character string
4520    [path,name,ext]=fileparts(fileinput)
4521    [path1]=fileparts(filebase);
4522    if isunix
4523        [status,path]=system(['readlink ' path])
4524        [status,path1]=system(['readlink ' path1])% look for the true path in case of symbolic paths
4525    end
4526    if ~strcmp(path1,path)
4527        msgbox_uvmat('ERROR','The second image series must be in the same directory as the first one')
4528        return
4529     end
4530%     set(handles.RootName_1,'String',name);
4531    [RootPath,RootFile,field_count,str2,str_a,str_b,xx,nom_type,subdir]=name2display(name);
4532    set(handles.RootName_1,'String',RootFile);
4533    browse=get(handles.browse_root,'UserData');
4534    browse.nom_type_ima_1=nom_type;
4535    set(handles.browse_root,'UserData',browse)
4536   
4537    %check image extension
4538    if ~strcmp(ext,get(handles.ImaExt,'String'))
4539        msgbox_uvmat('ERROR','The second image series must have the same extension name as the first one')
4540        return
4541    end
4542   
4543    %% check coincidence of image sizes
4544%     ref_i=get(handles.ref_i,'string');
4545%     ref_j=get(handles.ref_j,'string');
4546%     [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]);
4547%     A=imread(filecell.ima1.civ1{1});
4548%     A_1=imread(fileinput);
4549%     npxy=size(A);
4550%     npxy_1=size(A_1);
4551%     if ~isequal(size(A),size(A_1))
4552%         msgbox_uvmat('ERROR','The two input image series do not have the same size')
4553%         return
4554%     end
4555else
4556    set(handles.mode,'Visible','on')
4557    set(handles.RootName_1,'Visible','Off');
4558    set(handles.sub_txt,'Visible','off')
4559    set(handles.RootName_1,'String',[]);
4560    mode_store=get(handles.compare,'UserData');
4561    set(handles.mode,'Value',1)
4562    set(handles.mode,'String',mode_store)
4563    set(handles.test_stereo1,'Value',0)
4564    set(handles.test_stereo2,'Value',0)
4565    set(handles.CivMode,'Value',1) % mode 'civX' selected by default
4566end
4567if test==3 && get(handles.PATCH1,'Value')
4568    set(handles.test_stereo1,'Visible','on')
4569else
4570    set(handles.test_stereo1,'Visible','off')
4571end
4572if test==3 && get(handles.PATCH2,'Value')
4573    set(handles.test_stereo2,'Visible','on')
4574else
4575    set(handles.test_stereo2,'Visible','off')
4576end
4577mode_Callback(hObject, eventdata, handles)
4578
4579%------------------------------------------------------------------------
4580% --- Executes on button press in get_ref_fix1.
4581function get_ref_fix1_Callback(hObject, eventdata, handles)
4582%------------------------------------------------------------------------
4583filebase=get(handles.RootName,'String');
4584[FileName, PathName, filterindex] = uigetfile( ...
4585    {'*.nc', ' (*.nc)';
4586    '*.nc',  'netcdf files '; ...
4587    '*.*', 'All Files (*.*)'}, ...
4588    'Pick a file',filebase);
4589
4590fileinput=[PathName FileName];
4591sizf=size(fileinput);
4592if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end %stop if fileinput not a character string
4593[Path,File,field_count,str2,str_a,str_b,ref.ext,ref.nom_type,ref.subdir]=name2display(fileinput);
4594ref.filebase=fullfile(Path,File);
4595ref.num_a=stra2num(str_a);
4596ref.num_b=stra2num(str_b);
4597ref.num1=str2double(field_count);
4598ref.num2=str2double(str2);
4599browse=[];%initialisation
4600if ~isequal(ref.ext,'.nc')
4601    msgbox_uvmat('ERROR','the reference file must be in netcdf format (*.nc)')
4602    return
4603end
4604set(handles.ref_fix1,'String',[fullfile(ref.subdir,File) '....nc']);
4605set(handles.ref_fix1,'UserData',ref)
4606menu_field{1}='civ1';
4607Data=nc2struct(fileinput,[]);
4608if isfield(Data,'patch') && isequal(Data.patch,1)
4609    menu_field{2}='filter1';
4610end
4611if isfield(Data,'civ2') && isequal(Data.civ2,1)
4612    menu_field{3}='civ2';
4613end
4614if isfield(Data,'patch2') && isequal(Data.patch2,1)
4615    menu_field{4}='filter2';
4616end
4617set(handles.field_ref1,'String',menu_field);
4618set(handles.field_ref1,'Value',length(menu_field));
4619set(handles.inf_sup1,'Value',2);
4620set(handles.thresh_vel,'String','1');%default threshold
4621set(handles.ref_fix1,'Enable','on')
4622
4623%------------------------------------------------------------------------
4624% --- Executes on button press in get_ref_fix2.
4625function get_ref_fix2_Callback(hObject, eventdata, handles)
4626%------------------------------------------------------------------------
4627if isequal(get(handles.get_ref_fix2,'Value'),1)
4628    filebase=get(handles.RootName,'String');
4629    [FileName, PathName, filterindex] = uigetfile( ...
4630        {'*.nc', ' (*.nc)';
4631        '*.nc',  'netcdf files '; ...
4632        '*.*', 'All Files (*.*)'}, ...
4633        'Pick a file',filebase);
4634    fileinput=[PathName FileName];
4635    sizf=size(fileinput);
4636    if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end %stop if fileinput not a character string
4637    [Path,File,field_count,str2,str_a,str_b,ref.ext,ref.nom_type,ref.subdir]=name2display(fileinput);
4638    ref.filebase=fullfile(Path,File);
4639    ref.num_a=stra2num(str_a);
4640    ref.num_b=stra2num(str_b);
4641    ref.num1=str2num(field_count);
4642    ref.num2=str2num(str2);
4643    browse=[];%initialisation
4644    if ~isequal(ref.ext,'.nc')
4645        msgbox_uvmat('ERROR','the reference file must be in netcdf format (*.nc)')
4646        return
4647    end
4648    set(handles.ref_fix2,'String',[fullfile(ref.subdir,File) '....nc']);
4649    set(handles.ref_fix2,'UserData',ref)
4650    menu_field{1}='civ1';
4651    Data=nc2struct(fileinput,[]);
4652    if isfield(Data,'patch') & isequal(Data.patch,1)
4653        menu_field{2}='filter1';
4654    end
4655    if isfield(Data,'civ2') & isequal(Data.civ2,1)
4656        menu_field{3}='civ2';
4657    end
4658    if isfield(Data,'patch2') & isequal(Data.patch2,1)
4659        menu_field{4}='filter2';
4660    end
4661    set(handles.field_ref2,'String',menu_field);
4662    set(handles.field_ref2,'Value',length(menu_field));
4663    set(handles.inf_sup2,'Value',2);
4664    set(handles.thresh_vel2,'String','1');%default threshold
4665    set(handles.ref_fix2,'Enable','on')
4666    set(handles.ref_fix2,'Visible','on')
4667    set(handles.field_ref2,'Visible','on')
4668else
4669    set(handles.ref_fix2,'Visible','off')
4670    set(handles.field_ref2,'Visible','off')
4671end
4672
4673%------------------------------------------------------------------------
4674function ref_fix1_Callback(hObject, eventdata, handles)
4675%------------------------------------------------------------------------
4676set(handles.inf_sup1,'Value',1);
4677set(handles.field_ref1,'Value',1)
4678set(handles.field_ref1,'String',{' '})
4679set(handles.ref_fix1,'UserData',[]);
4680set(handles.ref_fix1,'String','');
4681set(handles.thresh_vel1,'String','0');
4682
4683%------------------------------------------------------------------------
4684function ref_fix2_Callback(hObject, eventdata, handles)
4685%------------------------------------------------------------------------
4686set(handles.inf_sup2,'Value',1);
4687set(handles.field_ref2,'Value',1)
4688set(handles.field_ref2,'String',{' '})
4689set(handles.ref_fix2,'UserData',[]);
4690set(handles.ref_fix2,'String','');
4691set(handles.thresh_vel2,'String','0');
4692
4693%------------------------------------------------------------------------
4694% --- Executes on button press in test_stereo1.
4695function test_stereo1_Callback(hObject, eventdata, handles)
4696%------------------------------------------------------------------------
4697if isequal(get(handles.test_stereo1,'Value'),0)
4698    set(handles.subdomain_patch1,'Visible','on')
4699    set(handles.rho_patch1,'Visible','on')
4700else
4701    set(handles.subdomain_patch1,'Visible','off')
4702    set(handles.rho_patch1,'Visible','off')
4703end
4704
4705%------------------------------------------------------------------------
4706% --- Executes on button press in test_stereo2.
4707function test_stereo2_Callback(hObject, eventdata, handles)
4708%------------------------------------------------------------------------
4709if isequal(get(handles.test_stereo2,'Value'),0)
4710    set(handles.subdomain_patch2,'Visible','on')
4711    set(handles.rho_patch2,'Visible','on')
4712else
4713    set(handles.subdomain_patch2,'Visible','off')
4714    set(handles.rho_patch2,'Visible','off')
4715end
4716
4717%------------------------------------------------------------------------
4718% --- Executes on button press in ImaThreshold.
4719function ImaThreshold_Callback(hObject, eventdata, handles)
4720%------------------------------------------------------------------------
4721if isequal(get(handles.ImaThreshold,'Value'),1)
4722    set(handles.MinIma,'Visible','on')
4723    set(handles.MaxIma,'Visible','on')
4724else
4725    set(handles.MinIma,'Visible','off')
4726    set(handles.MaxIma,'Visible','off')
4727end
4728
4729%------------------------------------------------------------------------
4730% --- Executes on button press in ImaThreshold2.
4731function ImaThreshold2_Callback(hObject, eventdata, handles)
4732%------------------------------------------------------------------------
4733if isequal(get(handles.ImaThreshold2,'Value'),1)
4734    set(handles.MinIma2,'Visible','on')
4735    set(handles.MaxIma2,'Visible','on')
4736else
4737    set(handles.MinIma2,'Visible','off')
4738    set(handles.MaxIma2,'Visible','off')
4739end
4740
4741%------------------------------------------------------------------------
4742% --- Executes on button press in TestCiv1: display image correlation function
4743function TestCiv1_Callback(hObject, eventdata, handles)
4744%------------------------------------------------------------------------
4745set(handles.TestCiv1,'BackgroundColor',[1 1 0])
4746drawnow
4747test_civ1=get(handles.TestCiv1,'Value');
4748if test_civ1
4749    ref_i=str2double(get(handles.ref_i,'String'));
4750    if strcmp(get(handles.ref_j,'Visible'),'on')
4751        ref_j=str2double(get(handles.ref_j,'String'));
4752    else
4753        ref_j=1;%default
4754    end
4755    [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]=...
4756        set_civ_filenames(handles,ref_i,ref_j,[1 0 0 0 0 0])
4757    Data.ListVarName={'ny','nx','A'};
4758    Data.VarDimName={'ny','nx',{'ny','nx'}};
4759    Data.A=imread(filecell.ima1.civ1{1});
4760    Data.ny=[size(Data.A,1) 1];
4761    Data.nx=[1 size(Data.A,2)];
4762    par_civ1=read_param_civ1(handles,filecell.ima1.civ1{1});
4763    par_civ1.filename_ima_a=filecell.ima1.civ1{1};
4764    par_civ1.filename_ima_b=filecell.ima2.civ1{1};
4765    par_civ1.T0=0;
4766    par_civ1.Dt=1;
4767    Param.Civ1=par_civ1;
4768    Data=civ_uvmat(Param);
4769    Data.ListVarName=[Data.ListVarName {'ny','nx','A'}];
4770    Data.VarDimName=[Data.VarDimName {'ny','nx',{'ny','nx'}}];
4771    Data.A=imread(filecell.ima1.civ1{1});
4772    Data.ny=[size(Data.A,1) 1];
4773    Data.nx=[1 size(Data.A,2)];
4774    hview_field=view_field(Data);
4775    set(0,'CurrentFigure',hview_field)
4776    hhview_field=guihandles(hview_field);
4777    set(hview_field,'CurrentAxes',hhview_field.axes3)
4778    ViewData=get(hview_field,'UserData');
4779    ViewData.CivHandle=handles.civ;% indicate the handle of the civ GUI in view_field
4780    ViewData.axes3.B=imread(filecell.ima2.civ1{1});%store the second image in the UserData of the GUI view_field
4781    ViewData.axes3.X=Data.Civ1_X; %keep the set of points in memeory
4782    ViewData.axes3.Y=Data.Civ1_Y;
4783    set(hview_field,'UserData',ViewData)
4784    corrfig=findobj(allchild(0),'tag','corrfig');% look for a current figure for image correlation display
4785    if isempty(corrfig)
4786        corrfig=figure;
4787        set(corrfig,'tag','corrfig')
4788        set(corrfig,'name','image correlation')
4789        set(corrfig,'DeleteFcn',{@closeview_field})%
4790    end
4791    set(handles.TestCiv1,'BackgroundColor',[1 0 0])
4792else
4793    corrfig=findobj(allchild(0),'tag','corrfig');% look for a current figure for image correlation display
4794    if ~isempty(corrfig)
4795        delete(corrfig)
4796    end
4797    hview_field=findobj(allchild(0),'tag','view_field');% look for view_field   
4798    if ~isempty(hview_field)
4799        delete(hview_field)
4800    end
4801end
4802
4803function closeview_field(gcbo,eventdata)
4804hview_field=findobj(allchild(0),'tag','view_field');% look for view_field   
4805    if ~isempty(hview_field)
4806        delete(hview_field)
4807    end
4808%-------------------------------------------------------------------
4809% --- Executes on button press in status.
4810function status_Callback(hObject, eventdata, handles)
4811%-------------------------------------------------------------------
4812val=get(handles.status,'Value');
4813if val==0
4814    set(handles.status,'BackgroundColor',[0 1 0])
4815    hfig=findobj(allchild(0),'name','civ_status');
4816    if ~isempty(hfig)
4817        delete(hfig)
4818    end
4819    return
4820end
4821set(handles.status,'BackgroundColor',[1 1 0])
4822drawnow
4823listtype={'civ1','fix1','patch1','civ2','fix2','patch2'};
4824box_test(1)=get(handles.CIV1,'Value');
4825box_test(2)=get(handles.FIX1,'Value');
4826box_test(3)=get(handles.PATCH1,'Value');
4827box_test(4)=get(handles.CIV2,'Value');
4828box_test(5)=get(handles.FIX2,'Value');
4829box_test(6)=get(handles.PATCH2,'Value');
4830option_civ=find(box_test,1,'last');%last selected option (non-zero index of box_test)
4831filecell=get(handles.civ,'UserData');%retrieve the list of output files expected for PIV
4832test_new=0;
4833if ~isfield(filecell,'nc')
4834    test_new=1;
4835    [ref_i,ref_j,errormsg]=find_ref_indices(handles);
4836    if ~isempty(errormsg)
4837        msgbox_uvmat('ERROR',errormsg)
4838        return
4839    end
4840    filecell=set_civ_filenames(handles,ref_i,ref_j,box_test);%determine the output file expected from the GUI status
4841end
4842if ~isequal(box_test(4:6),[0 0 0])
4843    civ_files=filecell.nc.civ2;%case of civ2 operations
4844else
4845    civ_files=filecell.nc.civ1;
4846end
4847[root,filename,ext]=fileparts(civ_files{1});
4848[rootroot,subdir,extdir]=fileparts(root);
4849hfig=findobj(allchild(0),'name','civ_status');
4850if isempty(hfig)
4851    hfig=figure('DeleteFcn',@stop_status);
4852    set(hfig,'name','civ_status')
4853    hlist=uicontrol('Style','listbox','Units','normalized', 'Position',[0.05 0.09 0.9 0.71], 'Callback', @open_view_field,'tag','list');
4854    uicontrol('Style','edit','Units','normalized', 'Position', [0.05 0.87 0.9 0.1],'tag','msgbox','Max',2,'String','checking files...');
4855    uicontrol('Style','frame','Units','normalized', 'Position', [0.05 0.81 0.9 0.05]);
4856    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);
4857    BarPosition=[0.05 0.81 0.01 0.05];
4858    hwaitbar=uicontrol('Style','frame','Units','normalized', 'Position',BarPosition ,'BackgroundColor',[1 0 0],'tag','waitbar');
4859    drawnow
4860end
4861% datnum=[];
4862Tabchar={};
4863nbfiles=numel(civ_files);
4864count=0;
4865testrecent=0;
4866while count<nbfiles
4867    count=0;
4868    datnum=zeros(1,nbfiles);
4869    for ifile=1:nbfiles
4870        detect=exist(civ_files{ifile},'file'); % check the existence of the file
4871        option=0;
4872        if detect==0
4873            option_str='not created';
4874        else
4875            datfile=dir(civ_files{ifile});
4876            if isfield(datfile,'datenum')
4877                datnum(ifile)=datfile.datenum;%only available in recent matlab versions
4878                testrecent=1;
4879            end
4880            filefound(ifile)={datfile.name};
4881            lastfield='';
4882            % check the content  netcdf file
4883            Data=nc2struct(civ_files{ifile},'ListGlobalAttribute','patch2','fix2','civ2','patch','fix');
4884            if ~isempty(Data.patch2) && isequal(Data.patch2,1)
4885                option=6;
4886                option_str='patch2';
4887            elseif ~isempty(Data.fix2) && isequal(Data.fix2,1)
4888                option=5;
4889                option_str='fix2';
4890            elseif ~isempty(Data.civ2) && isequal(Data.civ2,1);
4891                option=4;
4892                option_str='civ2';
4893            elseif ~isempty(Data.patch) && isequal(Data.patch,1);
4894                option=3;
4895                option_str='patch1';
4896            elseif ~isempty(Data.fix) && isequal(Data.fix,1);
4897                option=2;
4898                option_str='fix1';
4899            else
4900                option=1;
4901                option_str='civ1';
4902            end
4903        end
4904        if option >= option_civ
4905            count=count+1;
4906        end
4907        [rr,filename,ext]=fileparts(civ_files{ifile});
4908        Tabchar{ifile,1}=[fullfile([subdir extdir],filename) ext  '...' option_str];
4909    end
4910    datnum=datnum(datnum~=0);%keep the non zero values corresponding to existing files
4911    if isempty(datnum)
4912        if testrecent
4913            message='no civ result created yet';
4914        else
4915            message='';
4916        end
4917    else
4918        datnum=datnum(datnum~=0);%keep the non zero values corresponding to existing files
4919        [first,ind]=min(datnum);
4920        [last,indlast]=max(datnum);
4921        if test_new
4922            message='existing file status, no processing launched yet';
4923        else
4924        message={[num2str(count) ' file(s) done over ' num2str(nbfiles)] ;['oldest modification:  ' cell2mat(filefound(ind)) ' : ' datestr(first)];...
4925            ['latest modification:  ' cell2mat(filefound(indlast)) ' : ' datestr(last)]};
4926        end
4927    end
4928    hfig=findobj(allchild(0),'name','civ_status');
4929    if isempty(hfig)% the status list has been deleted
4930        return
4931    else
4932        hlist=findobj(hfig,'tag','list');
4933        hmsgbox=findobj(hfig,'tag','msgbox');
4934        hwaitbar=findobj(hfig,'tag','waitbar');
4935        set(hlist,'String',Tabchar)
4936        set(hmsgbox,'String', message)
4937        if count>0 && ~test_new
4938            BarPosition(3)=0.9*count/nbfiles;
4939            set(hwaitbar,'Position',BarPosition)
4940        end
4941    end
4942    set(hlist,'UserData',rootroot)
4943    pause(10)% wait 10 seconds for next check
4944end
4945
4946   
4947%------------------------------------------------------------------------   
4948% call 'view_field.fig' to display the  field selected in the list of 'status'
4949function open_view_field(hObject, eventdata)
4950%------------------------------------------------------------------------
4951list=get(hObject,'String');
4952index=get(hObject,'Value');
4953rootroot=get(hObject,'UserData');
4954filename=list{index};
4955ind_dot=findstr(filename,'...');
4956filename=filename(1:ind_dot-1);
4957filename=fullfile(rootroot,filename);
4958delete(get(hObject,'parent'))%delete the display figure to stop the check process
4959if exist(filename,'file')%visualise the vel field if it exists
4960    uvmat(filename)
4961    set(gcbo,'Value',1)
4962end
4963
4964%------------------------------------------------------------------------   
4965% launched by pressing OK on the status figure
4966function close_GUI(hObject, eventdata)
4967%------------------------------------------------------------------------
4968    delete(gcbf)
4969   
4970%------------------------------------------------------------------------   
4971% launched by deleting the status figure
4972function stop_status(hObject, eventdata)
4973%------------------------------------------------------------------------
4974hciv=findobj(allchild(0),'tag','civ');
4975hhciv=guidata(hciv);
4976set(hhciv.status,'value',0) %reset the status uicontrol in the GUI civ
4977set(hhciv.status,'BackgroundColor',[0 1 0])
4978
4979%------------------------------------------------------------------------
4980% --- Executes on button press in CivMode.
4981function CivMode_Callback(hObject, eventdata, handles)
4982%------------------------------------------------------------------------
4983Listprog=get(handles.CivMode,'String');
4984index=get(handles.CivMode,'Value');
4985prog=Listprog{index};
4986switch prog
4987    case 'CivX'
4988        set(handles.thresh_patch1,'Visible','off')
4989        set(handles.thresh_text1,'Visible','off')
4990        set(handles.thresh_patch2,'Visible','off')
4991        set(handles.thresh_text2,'Visible','off')
4992        set(handles.rho,'Style','edit')
4993        set(handles.rho,'String','1')
4994        set(handles.BATCH,'Enable','on')
4995    case 'CivAll'
4996        if get(handles.PATCH1,'Value')
4997            set(handles.thresh_patch1,'Visible','on')
4998            set(handles.thresh_text1,'Visible','on')
4999        end
5000        set(handles.rho,'Style','edit')
5001        set(handles.rho,'String','1')
5002        set(handles.BATCH,'Enable','on')
5003    case 'CivUvmat'
5004        if get(handles.PATCH1,'Value')
5005            set(handles.thresh_patch1,'Visible','on')
5006            set(handles.thresh_text1,'Visible','on')
5007        end
5008        if get(handles.PATCH2,'Value')
5009            set(handles.thresh_patch2,'Visible','on')
5010            set(handles.thresh_text2,'Visible','on')
5011        end
5012        set(handles.rho,'Style','popupmenu')
5013        set(handles.rho,'Value',1)
5014        set(handles.rho,'String',{'1';'2'})
5015        set(handles.BATCH,'Enable','off')
5016end
Note: See TracBrowser for help on using the repository browser.