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source: trunk/src/series.m @ 244

Last change on this file since 244 was 244, checked in by sommeria, 13 years ago
various bug repair, improved display of msgbox_uvmat
File size: 93.1 KB

Line
1	%'series': master function associated to the GUI series.m for analysis field series
2	%------------------------------------------------------------------------
3	% function varargout = series(varargin)
4	% associated with the GUI series.fig
5	%
6	%INPUT
7	% param: structure with input parameters (link with the GUI uvmat)
8	% .menu_coord_str: string for the transform_fct (menu for coordinate transforms)
9	% .menu_coord_val: value for transform_fct (menu for coordinate transforms)
10	% .FileName: input file name
11	% .FileName_1: second input file name
12	% .list_field: menu of input fields
13	% .index_fields: chosen index
14	% .civ1=0 or 1, .interp1, ... : input civ field type
15	%
16	%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
17	% Copyright Joel Sommeria, 2008, LEGI / CNRS-UJF-INPG, sommeria@coriolis-legi.org.
18	%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
19	% This file is part of the toolbox UVMAT.
20	%
21	% UVMAT is free software; you can redistribute it and/or modify
22	% it under the terms of the GNU General Public License as published by
23	% the Free Software Foundation; either version 2 of the License, or
24	% (at your option) any later version.
25	%
26	% UVMAT is distributed in the hope that it will be useful,
27	% but WITHOUT ANY WARRANTY; without even the implied warranty of
28	% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
29	% GNU General Public License (file UVMAT/COPYING.txt) for more details.
30	%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
31
32	function varargout = series(varargin)
33
34	% Begin initialization code - DO NOT EDIT
35	gui_Singleton = 1;
36	gui_State = struct('gui_Name', mfilename, ...
37	'gui_Singleton', gui_Singleton, ...
38	'gui_OpeningFcn', @series_OpeningFcn, ...
39	'gui_OutputFcn', @series_OutputFcn, ...
40	'gui_LayoutFcn', [] , ...
41	'gui_Callback', []);
42	if nargin && ischar(varargin{1})
43	gui_State.gui_Callback = str2func(varargin{1});
44	end
45
46	if nargout
47	[varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:});
48	else
49	gui_mainfcn(gui_State, varargin{:});
50	end
51	% End initialization code - DO NOT EDIT
52
53	%--------------------------------------------------------------------------
54	% --- Executes just before series is made visible.
55	%--------------------------------------------------------------------------
56	function series_OpeningFcn(hObject, eventdata, handles,param)
57	global nb_builtin_ACTION nb_builtin_transform
58	% Choose default command line output for series
59	handles.output = hObject;
60	% Update handles structure
61	guidata(hObject, handles);
62	%default initial parameters
63	drawnow
64	set(hObject,'Units','pixels')
65	% set(0,'Units','pixels')
66	% screensize=get(0,'ScreenSize'); %screen size in pixels
67	set(hObject,'Position',[150 100 1000 600] );%position and size in pixels (get adjusted to the screen size in case of excess)
68	%load the list of previously browsed files in menus Open and Open_1
69	dir_perso=prefdir;
70	test_profil_perso=0;
71	profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
72	if exist(profil_perso,'file')
73	h=load (profil_perso);
74	test_profil_perso=1;
75	if isfield(h,'MenuFile_1')
76	set(handles.MenuFile_1,'Label',h.MenuFile_1);
77	set(handles.MenuFile_insert_1,'Label',h.MenuFile_1);
78	end
79	if isfield(h,'MenuFile_1')
80	set(handles.MenuFile_2,'Label',h.MenuFile_2);
81	set(handles.MenuFile_insert_2,'Label',h.MenuFile_2);
82	end
83	if isfield(h,'MenuFile_1')
84	set(handles.MenuFile_3,'Label',h.MenuFile_3);
85	set(handles.MenuFile_insert_3,'Label',h.MenuFile_3);
86	end
87	if isfield(h,'MenuFile_1')
88	set(handles.MenuFile_4,'Label',h.MenuFile_4);
89	set(handles.MenuFile_insert_4,'Label',h.MenuFile_4);
90	end
91	if isfield(h,'MenuFile_1')
92	set(handles.MenuFile_5,'Label',h.MenuFile_5);
93	set(handles.MenuFile_insert_5,'Label',h.MenuFile_5);
94	end
95	end
96
97	%check default input data
98	if ~exist('param','var')
99	param=[]; %default
100	end
101
102	%file name and browser initialisation
103	if isfield(param,'menu_coord_str')
104	set(handles.transform_fct,'String',param.menu_coord_str)
105	end
106	if isfield(param,'menu_coord_val')
107	set(handles.transform_fct,'Value',param.menu_coord_val);
108	else
109	set(handles.transform_fct,'Value',1);%default
110	end
111
112	if isfield(param,'FileName')
113	if isfield(param,'FileName_1')
114	update_file(hObject, eventdata, handles,param.FileName_1,0)
115	update_file(hObject, eventdata, handles,param.FileName,1)
116	else
117	update_file(hObject, eventdata, handles,param.FileName,0)
118	end
119	end
120
121	%fields input initialisation
122	if isfield(param,'list_fields')&& isfield(param,'index_fields') &&~isempty(param.list_fields) &&~isempty(param.index_fields)
123	set(handles.FieldMenu,'String',param.list_fields);% list menu fields
124	set(handles.FieldMenu,'Value',param.index_fields);% selected string index
125	FieldCell{1}=param.list_fields{param.index_fields};
126	end
127	% if isfield(param,'velTypeMenu')&&isfield(param,'velTypeIndex')
128	% set(handles.VelTypeMenu,'Value',param.VelTypeIndex)
129	% set(handles.VelTypeMenu,'String',param.VelTypeMenu)
130	% end
131	set(hObject,'WindowButtonUpFcn',{@mouse_up_gui,handles})
132	NomType_Callback(hObject, eventdata, handles)
133
134	%loads the information stored in prefdir to initiate the list of ACTION functions
135	fct_menu={'check_files';'aver_stat';'time_series';'merge_proj';'clean_civ_cmx'};
136	transform_menu={'';'phys';'px';'phys_polar'};
137	nb_builtin_ACTION=numel(fct_menu); %number of functions
138	nb_transform=numel(transform_menu);
139	[path_series,name,ext]=fileparts(which('series'));
140	path_series=fullfile(path_series,'series');%path of the function 'series'
141	path_transform=fullfile(path_series,'transform_field');%path of the field transform functions
142	for ilist=1:length(fct_menu)
143	fct_path{ilist,1}=path_series;%paths of the fuctions buil-in in 'series.m'
144	end
145
146	%TRANSFORM menu: loads the information stored in prefdir to initiate the list of field transform functions
147	menu_str={'';'phys';'px';'phys_polar'};
148	nb_builtin_transform=numel(menu_str); %number of functions
149	[path_uvmat,name,ext]=fileparts(which('uvmat'));
150	addpath(fullfile(path_uvmat,'transform_field'))
151	fct_handle{1,1}=[];
152	testexist(1)=1;
153	for ilist=2:length(menu_str)
154	if exist(menu_str{ilist},'file')
155	fct_handle{ilist,1}=str2func(menu_str{ilist});
156	testexist(ilist)=1;
157	else
158	testexist(ilist)=0;
159	end
160	end
161	rmpath(fullfile(path_uvmat,'transform_field'))
162
163	% read the list of functions stored in the personal file 'uvmat_perso.mat' in prefdir
164	if test_profil_perso
165	if isfield(h,'series_fct') && iscell(h.series_fct)
166	for ilist=1:length(h.series_fct)
167	[path,file]=fileparts(h.series_fct{ilist});
168	fct_path=[fct_path; {path}];%concatene the list of paths
169	fct_menu=[fct_menu; {file}];
170	end
171	end
172	if isfield(h,'transform_fct') && iscell(h.transform_fct)
173	for ilist=1:length(h.transform_fct);
174	[path,file]=fileparts(h.transform_fct{ilist});
175	addpath(path)
176	if exist(file,'file')
177	h_func=str2func(file);
178	testexist=[testexist 1];
179	else
180	h_func=[];
181	testexist=[testexist 0];
182	end
183	fct_handle=[fct_handle; {h_func}];%concatene the list of paths
184	rmpath(path)
185	menu_str=[menu_str; {file}];
186	end
187	end
188	end
189	fct_menu=[fct_menu;{'more...'}];
190	set(handles.ACTION,'String',fct_menu)
191	set(handles.ACTION,'UserData',fct_path)% store the list of path in UserData of ACTION
192
193	menu_str=menu_str(find(testexist));
194	fct_handle=fct_handle(find(testexist));
195	menu_str=[menu_str;{'more...'}];
196	set(handles.transform_fct,'String',menu_str)
197	set(handles.transform_fct,'UserData',fct_handle)% store the list of path in UserData of ACTION
198
199	% display the GUI for the default action 'check_files'
200	ACTION_Callback(hObject, eventdata, handles)
201
202	%--------------------------------------------------------------
203	% --- Outputs from this function are returned to the command line.
204	%-----------------------------------------------------------------
205	function varargout = series_OutputFcn(hObject, eventdata, handles)
206	% varargout cell array for returning output args (see VARARGOUT);
207	% hObject handle to figure
208	% eventdata reserved - to be defined in a future version of MATLAB
209	% handles structure with handles and user data (see GUIDATA)
210	% Get default command line output from handles structure
211	varargout{1} = handles.output;
212
213
214	% --------------------------------------------------------------------
215	function MenuBrowse_Callback(hObject, eventdata, handles)
216
217	RootPathCell=get(handles.RootPath,'String');
218	SubDirCell=get(handles.SubDir,'String');
219	RootFileCell=get(handles.RootFile,'String');
220	oldfile=''; %default
221	if isempty(RootPathCell)\|isequal(RootPathCell,{''})%loads the previously stored file name and set it as default in the file_input box
222	dir_perso=prefdir;
223	profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
224	if exist(profil_perso,'file')
225	h=load (profil_perso);
226	if isfield(h,'filebase')&ischar(h.filebase)
227	oldfile=h.filebase;
228	end
229	if isfield(h,'RootPath')&ischar(h.RootPath)
230	oldfile=h.RootPath;
231	end
232	end
233	else
234	oldfile=fullfile(RootPathCell{1},SubDirCell{1},RootFileCell{1});
235	end
236	[FileName, PathName, filterindex] = uigetfile( ...
237	{'.xml;.xls;.png;.tif;.avi;.AVI;.nc', ' (.xml,.xls, .png,.tif, .avi,*.nc)';
238	'*.xml', '.xml files '; ...
239	'*.xls', '.xls files '; ...
240	'*.png','.png image files'; ...
241	'*.tif','.tif image files'; ...
242	'.avi;.AVI','.avi movie files'; ...
243	'*.nc','.netcdf files'; ...
244	'.', 'All Files (.)'}, ...
245	'Pick a file',oldfile);
246	fileinput=[PathName FileName];%complete file name
247	%testblank=findstr(fileinput,' ');%look for blanks
248	% if ~isempty(testblank)
249	% errordlg('forbidden input file name: contain blanks')
250	% return
251	% end
252	sizf=size(fileinput);
253	if (~ischar(fileinput)\|~isequal(sizf(1),1)),return;end
254	[path,name,ext]=fileparts(fileinput);
255	SeriesData=[];%dfault
256	if isequal(ext,'.xml')
257	warndlg_uvmat('ERROR','input file type not implemented')%A Faire: ouvrir le fichier pour naviguer
258	elseif isequal(ext,'.xls')
259	warndlg_uvmat('ERROR','input file type not implemented')%A Faire: ouvrir le fichier pour naviguer
260	else
261	update_file(hObject, eventdata, handles,fileinput,0)
262	%update list of recent files in the menubar
263	MenuFile_1=fileinput;
264	MenuFile_2=get(handles.MenuFile_1,'Label');
265	MenuFile_3=get(handles.MenuFile_2,'Label');
266	MenuFile_4=get(handles.MenuFile_3,'Label');
267	MenuFile_5=get(handles.MenuFile_4,'Label');
268	set(handles.MenuFile_1,'Label',MenuFile_1)
269	set(handles.MenuFile_2,'Label',MenuFile_2)
270	set(handles.MenuFile_3,'Label',MenuFile_3)
271	set(handles.MenuFile_4,'Label',MenuFile_4)
272	set(handles.MenuFile_5,'Label',MenuFile_5)
273	set(handles.MenuFile_insert_1,'Label',MenuFile_1)
274	set(handles.MenuFile_insert_2,'Label',MenuFile_2)
275	set(handles.MenuFile_insert_3,'Label',MenuFile_3)
276	set(handles.MenuFile_insert_4,'Label',MenuFile_4)
277	set(handles.MenuFile_insert_5,'Label',MenuFile_5)
278	dir_perso=prefdir;
279	profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
280	if exist(profil_perso,'file')
281	save (profil_perso,'MenuFile_1','MenuFile_2','MenuFile_3','MenuFile_4', 'MenuFile_5','-append'); %store the file names for future opening of uvmat
282	else
283	txt=ver('MATLAB');
284	Release=txt.Release;
285	relnumb=str2num(Release(3:4));
286	if relnumb >= 14
287	save (profil_perso,'MenuFile_1','MenuFile_2','MenuFile_3','MenuFile_4', 'MenuFile_5','-V6'); %store the file names for future opening of uvmat
288	else
289	save (profil_perso,'MenuFile_1','MenuFile_2','MenuFile_3','MenuFile_4', 'MenuFile_5'); %store the file names for future opening of uvmat
290	end
291	end
292	end
293
294
295	% --------------------------------------------------------------------
296	function MenuFile_1_Callback(hObject, eventdata, handles)
297	fileinput=get(handles.MenuFile_1,'Label');
298	update_file(hObject, eventdata, handles,fileinput,0)
299
300	% --------------------------------------------------------------------
301	function MenuFile_2_Callback(hObject, eventdata, handles)
302	fileinput=get(handles.MenuFile_2,'Label');
303	update_file(hObject, eventdata, handles,fileinput,0)
304
305	% --------------------------------------------------------------------
306	function MenuFile_3_Callback(hObject, eventdata, handles)
307	fileinput=get(handles.MenuFile_3,'Label');
308	update_file(hObject, eventdata, handles,fileinput,0)
309
310	% --------------------------------------------------------------------
311	function MenuFile_4_Callback(hObject, eventdata, handles)
312	fileinput=get(handles.MenuFile_4,'Label');
313	update_file(hObject, eventdata, handles,fileinput,0)
314
315	% --------------------------------------------------------------------
316	function MenuFile_5_Callback(hObject, eventdata, handles)
317	fileinput=get(handles.MenuFile_5,'Label');
318	update_file(hObject, eventdata, handles,fileinput,0)
319
320	% --------------------------------------------------------------------
321	function MenuBrowse_insert_Callback(hObject, eventdata, handles)
322
323	RootPathCell=get(handles.RootPath,'String');
324	RootFileCell=get(handles.RootFile,'String');
325	oldfile=''; %default
326	if isempty(RootPathCell)\|\|isequal(RootPathCell,{''})%loads the previously stored file name and set it as default in the file_input box
327	dir_perso=prefdir;
328	profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
329	if exist(profil_perso,'file')
330	h=load (profil_perso);
331	if isfield(h,'filebase')&ischar(h.filebase)
332	oldfile=h.filebase;
333	end
334	if isfield(h,'RootPath')&ischar(h.RootPath)
335	oldfile=h.RootPath;
336	end
337	end
338	else
339	oldfile=fullfile(RootPathCell{1},RootFileCell{1});
340	end
341	[FileName, PathName, filterindex] = uigetfile( ...
342	{'.xml;.xls;.png;.avi;.AVI;.nc', ' (.xml,.xls, .png, .avi,*.nc)';
343	'*.xml', '.xml files '; ...
344	'*.xls', '.xls files '; ...
345	'*.png','.png image files'; ...
346	'.avi;.AVI','.avi movie files'; ...
347	'*.nc','.netcdf files'; ...
348	'.', 'All Files (.)'}, ...
349	'Pick a file',oldfile);
350	fileinput=[PathName FileName];%complete file name
351	% testblank=findstr(fileinput,' ');%look for blanks
352	% if ~isempty(testblank)
353	% errordlg('forbidden input file name: contain blanks')
354	% return
355	% end
356	sizf=size(fileinput);
357	if (~ischar(fileinput)\|~isequal(sizf(1),1)),return;end
358	[path,name,ext]=fileparts(fileinput);
359	SeriesData=[];%dfault
360	if isequal(ext,'.xml')
361	msgbox_uvmat('ERROR','input file type not implemented')%A Faire: ouvrir le fichier pour naviguer
362	elseif isequal(ext,'.xls')
363	msgbox_uvmat('ERROR','input file type not implemented')%A Faire: ouvrir le fichier pour naviguer
364	else
365	update_file(hObject, eventdata, handles,fileinput,1)
366	%update list of recent files in the menubar
367	MenuFile_1=fileinput;
368	MenuFile_2=get(handles.MenuFile_1,'Label');
369	MenuFile_3=get(handles.MenuFile_2,'Label');
370	MenuFile_4=get(handles.MenuFile_3,'Label');
371	MenuFile_5=get(handles.MenuFile_4,'Label');
372	set(handles.MenuFile_1,'Label',MenuFile_1)
373	set(handles.MenuFile_2,'Label',MenuFile_2)
374	set(handles.MenuFile_3,'Label',MenuFile_3)
375	set(handles.MenuFile_4,'Label',MenuFile_4)
376	set(handles.MenuFile_5,'Label',MenuFile_5)
377	set(handles.MenuFile_insert_1,'Label',MenuFile_1)
378	set(handles.MenuFile_insert_2,'Label',MenuFile_2)
379	set(handles.MenuFile_insert_3,'Label',MenuFile_3)
380	set(handles.MenuFile_insert_4,'Label',MenuFile_4)
381	set(handles.MenuFile_insert_5,'Label',MenuFile_5)
382	dir_perso=prefdir;
383	profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
384	if exist(profil_perso,'file')
385	save (profil_perso,'MenuFile_1','MenuFile_2','MenuFile_3','MenuFile_4', 'MenuFile_5','-append'); %store the file names for future opening of uvmat
386	else
387	txt=ver('MATLAB');
388	Release=txt.Release;
389	relnumb=str2num(Release(3:4));
390	if relnumb >= 14
391	save (profil_perso,'MenuFile_1','MenuFile_2','MenuFile_3','MenuFile_4', 'MenuFile_5','-V6'); %store the file names for future opening of uvmat
392	else
393	save (profil_perso,'MenuFile_1','MenuFile_2','MenuFile_3','MenuFile_4', 'MenuFile_5'); %store the file names for future opening of uvmat
394	end
395	end
396	end
397	%------------------------------------------------
398
399	% --------------------------------------------------------------------
400	function MenuFile_insert_1_Callback(hObject, eventdata, handles)
401	fileinput=get(handles.MenuFile_insert_1,'Label');
402	update_file(hObject, eventdata, handles,fileinput,1)
403
404	% --------------------------------------------------------------------
405	function MenuFile_insert_2_Callback(hObject, eventdata, handles)
406	fileinput=get(handles.MenuFile_insert_2,'Label');
407	update_file(hObject, eventdata, handles,fileinput,1)
408
409	% --------------------------------------------------------------------
410	function MenuFile_insert_3_Callback(hObject, eventdata, handles)
411	fileinput=get(handles.MenuFile_insert_3,'Label');
412	update_file(hObject, eventdata, handles,fileinput,1)
413
414	% --------------------------------------------------------------------
415	function MenuFile_insert_4_Callback(hObject, eventdata, handles)
416	fileinput=get(handles.MenuFile_insert_4,'Label');
417	update_file(hObject, eventdata, handles,fileinput,1)
418
419	% --------------------------------------------------------------------
420	function MenuFile_insert_5_Callback(hObject, eventdata, handles)
421	fileinput=get(handles.MenuFile_insert_5,'Label');
422	update_file(hObject, eventdata, handles,fileinput,1)
423
424	%------------------------------------------------------------------------
425	% --- refresh the GUI data after introduction of a new file series
426	function update_file(hObject, eventdata, handles,fileinput,addtest)
427	%------------------------------------------------------------------------
428	if ~exist(fileinput,'file')
429	msgbox_uvmat('ERROR',['input file ' fileinput ' does not exist'])
430	return
431	end
432
433	% refresh input root name, indices, file extension and nomenclature
434	[RootPath,RootFile,field_count,str2,str_a,str_b,FileExt,NomType,SubDir]=name2display(fileinput);
435
436	%check for movie image files
437	if ~isempty(FileExt)
438	if ~isempty(imformats(FileExt(2:end)))
439	imainfo=imfinfo(fileinput);
440	if length(imainfo) >1 %case of image with multiple frames
441	NomType='*';
442	[RootPath,RootFile]=fileparts(fileinput);
443	end
444	end
445	end
446	NcType='none';%default
447	if isequal(FileExt,'.nc')
448	Data=nc2struct(fileinput,[]);
449	if isfield(Data,'absolut_time_T0')
450	NcType='civx'; % test for civx velocity fields
451	end
452	end
453
454	set(handles.RootPath,'Value',1)
455	set(handles.SubDir,'Value',1)
456	set(handles.RootFile,'Value',1)
457	set(handles.NomType,'Value',1)
458	set(handles.FileExt,'Value',1)
459	set(handles.nb_field,'Value',1)
460	set(handles.nb_field2,'Value',1)
461	if addtest
462	SeriesData=get(handles.figure1,'UserData');
463	SeriesData.displ_num=[0 0 0 0;SeriesData.displ_num];
464	SeriesData.CurrentInputFile_1=SeriesData.CurrentInputFile;
465	RootPathCell=[{RootPath}; get(handles.RootPath,'String')] ;
466	SubDirCell=[{SubDir}; get(handles.SubDir,'String')];
467	RootFileCell=[{RootFile}; get(handles.RootFile,'String')];
468	NomTypeCell=[{NomType}; SeriesData.NomType];
469	FileExtCell=[{FileExt}; get(handles.FileExt,'String')];
470	NcTypeCell=[{NcType};SeriesData.NcType];
471	set(handles.NomType,'String',[{};get(handles.NomType,'String')])
472	else
473	SeriesData=[];%re-initialisation
474	SeriesData.displ_num=[0 0 0 0];
475	RootPathCell={RootPath};
476	SubDirCell={SubDir};
477	RootFileCell={RootFile};
478	NomTypeCell={NomType};
479	FileExtCell={FileExt};
480	NcTypeCell={NcType};
481	end
482
483	SeriesData.NomType=NomTypeCell;
484	SeriesData.NcType=NcTypeCell;
485	SeriesData.CurrentInputFile=fileinput;
486	set(handles.RootPath,'String',RootPathCell);
487	set(handles.SubDir,'String',SubDirCell);
488	set(handles.RootFile,'String',RootFileCell);
489	set(handles.NomType,'String',NomTypeCell);
490	set(handles.FileExt,'String',FileExtCell);
491
492	%determine field indices
493	ref_i=1; %default ref_i is a reference frame index used to find existing pairs from PIV
494	if ~isempty(str2num(field_count))
495	ref_i=str2num(field_count);
496	if ~isempty(str2num(str2))
497	ref_i=floor((ref_i+str2num(str2))/2);% reference image number corresponding to the file
498	SeriesData.browse_Di=str2num(str2)-str2num(field_count);
499	end
500	end
501	set(handles.ref_i,'String',num2str(ref_i));
502	set(handles.first_i,'String',num2str(ref_i));
503	set(handles.last_i,'String',num2str(ref_i));
504	ref_j=1; %default ref_j is a reference frame index used to find existing pairs from PIV
505	if ~isempty(str2num(str_a))
506	ref_j=str2num(str_a);
507	if ~isempty(str2num(str_b))
508	ref_j=floor((str2num(str_a)+str2num(str_b))/2);
509	SeriesData.browse_Dj=str2num(str_b)-str2num(str_a);
510	end
511	end
512	set(handles.ref_j,'String',num2str(ref_j));
513	set(handles.first_j,'String',num2str(ref_j))
514	set(handles.last_j,'String',num2str(ref_j));
515
516	%enable other menus and uicontrols
517	set(handles.MenuOpen_insert,'Enable','on')
518	set(handles.MenuFile_insert_1,'Enable','on')
519	set(handles.MenuFile_insert_2,'Enable','on')
520	set(handles.MenuFile_insert_3,'Enable','on')
521	set(handles.MenuFile_insert_4,'Enable','on')
522	set(handles.MenuFile_insert_5,'Enable','on')
523	set(handles.RUN, 'Enable','On')
524	set(handles.RUN,'BackgroundColor',[1 0 0])% set RUN button to red
525	set(handles.RootPath,'BackgroundColor',[1 1 0]) % set RootPath edit box to yellow
526	drawnow
527
528	TimeUnit=''; %default
529	time=[];%default
530	GeometryCalib=[];%default
531	nb_field=NaN;%default
532	nb_field2=NaN;%default
533	SeriesData.PathCampaign=get(handles.PathCampaign,'String');
534
535	% read timing and total frame number from the current file (movie files) !! may be overrid by xml file
536	FileBase=fullfile(RootPath,RootFile);
537
538	testima=0; %test for image input
539	if isequal(lower(FileExt),'.avi') %.avi file
540	testima=1;
541	info=aviinfo([FileBase FileExt]);
542	time=(0:1/info.FramesPerSecond:(info.NumFrames-1)/info.FramesPerSecond)';
543	nb_field=info.NumFrames;
544	nb_field2=1;
545	elseif ~isempty(imformats(FileExt(2:end)))
546	testima=1;
547	if isequal(NomType,'*')% multi-frame image
548	imainfo=imfinfo([FileBase FileExt]);
549	if length(imainfo) >1 %case of image with multiple frames
550	nb_field=length(imainfo);
551	nb_field2=1;
552	end
553	end
554	elseif isequal(FileExt,'.vol')
555	testima=1;
556	end
557
558	% enable field and veltype menus
559	testfield=isequal(get(handles.FieldMenu,'enable'),'on');
560	testfield_1=isequal(get(handles.FieldMenu_1,'enable'),'on');
561	testveltype=isequal(get(handles.VelTypeMenu,'enable'),'on');
562	testveltype_1=isequal(get(handles.VelTypeMenu_1,'enable'),'on');
563	testtransform=isequal(get(handles.transform_fct,'Enable'),'on');
564	testnc=0;
565	testnc_1=0;
566	testcivx=0;
567	testcivx_1=0;
568	if length(FileExtCell)==1 \|\| length(FileExtCell)>2
569	for iview=1:length(FileExtCell)
570	if isequal(FileExtCell{iview},'.nc')
571	testnc=1;
572	end
573	if isequal(NcTypeCell{iview},'civx')
574	testcivx=1;
575	end
576	end
577	elseif length(FileExtCell)==2
578	testnc=isequal(FileExtCell{1},'.nc');
579	testnc_1=isequal(FileExtCell{2},'.nc');
580	testcivx=isequal(NcTypeCell{1},'civx');
581	testcivx_1=isequal(NcTypeCell{2},'civx');
582	end
583	if testfield && testnc
584	view_FieldMenu(handles,'on')
585	if testcivx
586	menustr=get(handles.FieldMenu,'String');
587	if isequal(menustr,{'get_field...'})
588	set(handles.FieldMenu,'String',{'get_field...';'velocity';'vort';'div';'more...'})
589	end
590	else
591	set(handles.FieldMenu,'Value',1)
592	set(handles.FieldMenu,'String',{'get_field...'})
593	end
594	else
595	view_FieldMenu(handles,'off')
596	end
597	if testfield_1 && testnc_1
598	view_FieldMenu_1(handles,'on')
599	if testcivx_1
600	menustr=get(handles.FieldMenu_1,'String');
601	if isequal(menustr,{'get_field...'})
602	set(handles.FieldMenu_1,'String',{'get_field...';'velocity';'vort';'div';'more...'})
603	end
604	else
605	set(handles.FieldMenu_1,'Value',1)
606	set(handles.FieldMenu_1,'String',{'get_field...'})
607	end
608	else
609	view_FieldMenu_1(handles,'off')
610	end
611	if testveltype && testcivx
612	set(handles.VelTypeMenu,'Visible','on')
613	set(handles.VelType_text,'Visible','on');
614	else
615	set(handles.VelTypeMenu,'Visible','off')
616	set(handles.VelType_text,'Visible','off');
617	end
618	if testveltype_1 && testcivx_1
619	set(handles.VelTypeMenu_1,'Visible','on')
620	set(handles.VelType_text_1,'Visible','on');
621	else
622	set(handles.VelTypeMenu_1,'Visible','off')
623	set(handles.VelType_text_1,'Visible','off');
624	end
625	if testtransform && (testcivx \|\| testima)
626	view_TRANSFORM(handles,'on')
627	else
628	view_TRANSFORM(handles,'off')
629	end
630	if ~isequal(FileExt,'.nc') && ~isequal(FileExt,'.cdf') && ~testima
631	msgbox_uvmat('ERROR',['invalid input file extension ' FileExt])
632	return
633	end
634
635	%%%%%%%% read image documentation file if found%%%%%%%%%%%%%%%%%%%%%%%%%%%
636	%look for the file existence
637	ext_imadoc='';
638	if isequal(FileExt,'.xml')\|\|isequal(FileExt,'.civ')
639	ext_imadoc=FileExt;
640	elseif exist([FileBase '.xml'],'file')
641	ext_imadoc='.xml';
642	elseif exist([FileBase '.civ'],'file')
643	ext_imadoc='.civ';
644	end
645	%read the ImaDoc file
646	XmlData=[];
647	NbSlice_calib={};
648	if isequal(ext_imadoc,'.xml')
649	[XmlData,warntext]=imadoc2struct([FileBase '.xml']);
650	if isfield(XmlData,'Heading') && isfield(XmlData.Heading,'ImageName') && ischar(XmlData.Heading.ImageName)
651	[PP,FF,ext_ima_read]=fileparts(XmlData.Heading.ImageName);
652	end
653	if isfield(XmlData,'Time')
654	time=XmlData.Time;
655	end
656	if isfield(XmlData,'Camera')
657	if isfield(XmlData.Camera,'NbSlice')&& ~isempty(XmlData.Camera.NbSlice)
658	NbSlice_calib{iview}=XmlData.Camera.NbSlice;% Nbre of slices for Zindex in phys transform
659	if ~isequal(NbSlice_calib{iview},NbSlice_calib{1})
660	msgbox_uvmat('WARNING','inconsistent number of Z indices for the two field series');
661	end
662	end
663	if isfield(XmlData.Camera,'TimeUnit')&& ~isempty(XmlData.Camera.TimeUnit)
664	TimeUnit=XmlData.Camera.TimeUnit;
665	end
666	end
667	if ~isempty(warntext)
668	msgbox_uvmat('WARNING',warntext)
669	end
670	elseif isequal(ext_imadoc,'.civ')
671	[error,XmlData.Time,TimeUnit,mode,npx,npy,pxcmx,pxcmy]=read_imatext([FileBase '.civ']);
672	time=XmlData.Time;
673	if error==2, warntext=['no file ' FileBase '.civ'];
674	elseif error==1, warntext='inconsistent number of fields in the .civ file';
675	end
676	end
677	if addtest
678	SeriesData.Time=[{time} SeriesData.Time];
679	else
680	SeriesData.Time={time};
681	end
682
683
684	% if ~isempty(time)
685	% siztime=size(time);
686	% nb_field=siztime(1);
687	% nb_field2=siztime(2);
688	% end
689	set(handles.TimeUnit,'String',TimeUnit)
690	%look for max indices
691	if ~strcmp(NomType,'*')
692	[num_i1,num_i2,num_j1,num_j2]=find_indexseries(fileinput);
693	nb_field=max(floor((max(num_i1)+max(num_i2))/2));
694	nb_field2=max(floor((max(num_j1)+max(num_j2))/2));
695	end
696	if isnan(nb_field)
697	nb_field_str='?';
698	nb_field_str2='?';
699	else
700	nb_field_str=num2str(nb_field);
701	nb_field_str2=num2str(nb_field2);
702	end
703	if addtest
704	nb_field_cell=[{nb_field_str} ;get(handles.nb_field,'String')];
705	nb_field2_cell=[{nb_field_str2} ;get(handles.nb_field2,'String')];
706	else
707	nb_field_cell={nb_field_str};
708	nb_field2_cell={nb_field_str2};
709	end
710	set(handles.nb_field,'String',nb_field_cell);
711	set(handles.nb_field2,'String',nb_field2_cell);
712	set(handles.figure1,'UserData',SeriesData);
713
714	%number of slices
715	if isfield(XmlData,'GeometryCalib') && isfield(XmlData.GeometryCalib,'SliceCoord')
716	siz=size(XmlData.GeometryCalib.SliceCoord);
717	if siz(1)>1
718	NbSlice=siz(1);
719	else
720	NbSlice=1;
721	end
722	set(handles.NbSlice,'String',num2str(NbSlice))
723	end
724
725	% set menus of index pairs
726	NomType_Callback(hObject, eventdata, handles)
727
728	%store the root name for future opening of uvmat
729	dir_perso=prefdir;
730	profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
731	if exist(profil_perso,'file')
732	save (profil_perso,'RootPath','SubDir','RootFile','NomType', '-append'); %store the root name for future opening of uvmat
733	else
734	txt=ver('MATLAB');
735	Release=txt.Release;
736	relnumb=str2num(Release(3:4));
737	if relnumb >= 14
738	save (profil_perso,'RootPath','SubDir','RootFile','NomType','-V6') %store the root name for future opening of uvmat
739	else
740	save(profil_perso,'RootPath','SubDir','RootFile','NomType')
741	end
742	end
743	set(handles.RootPath,'BackgroundColor',[1 1 1])
744	set(handles.PathCampaign,'String',SeriesData.PathCampaign)
745	last_j_Callback(hObject, eventdata, handles)
746	last_i_Callback(hObject, eventdata, handles)
747
748	%------------------------------------------------------------
749	function RootPath_Callback(hObject, eventdata, handles)
750	Val=get(handles.RootPath,'Value');
751	synchronise_view(handles,Val)
752	NomType_Callback(hObject, eventdata, handles)
753	%------------------------------------------------------------
754
755	function synchronise_view(handles,Val)
756	set(handles.RootPath,'Value',Val)
757	set(handles.SubDir,'Value',Val)
758	set(handles.RootFile,'Value',Val)
759	set(handles.NomType,'Value',Val)
760	set(handles.FileExt,'Value',Val)
761	set(handles.nb_field,'Value',Val)
762	set(handles.nb_field2,'Value',Val)
763	set(handles.time_first,'Value',Val)
764	set(handles.time_last,'Value',Val)
765
766
767	%---------------------------------------------------------
768	% Executes on carriage return on the subdir civ1 edit window
769	%--------------------------------------------------------
770	function SubDir_Callback(hObject, eventdata, handles)
771
772	Val=get(handles.SubDir,'Value');
773	synchronise_view(handles,Val)
774	NomType_Callback(hObject, eventdata, handles)
775
776	%--------------------------------------------------------------
777	%function activated when a new filebase (image series) is introduced
778	%------------------------------------------------------------
779	function RootFile_Callback(hObject, eventdata, handles)
780	Val=get(handles.RootFile,'Value');
781	synchronise_view(handles,Val)
782	NomType_Callback(hObject, eventdata, handles)
783
784	%--------------------------------------------------------------
785	%function activated when a new filebase (image series) is introduced
786	%------------------------------------------------------------
787	function FileExt_Callback(hObject, eventdata, handles)
788	Val=get(handles.FileExt,'Value');
789	synchronise_view(handles,Val)
790
791	%--------------------------------------------------------------
792	%function activated when a new filebase (image series) is introduced
793	%------------------------------------------------------------
794	function nb_field_Callback(hObject, eventdata, handles)
795	Val=get(handles.nb_field,'Value');
796	synchronise_view(handles,Val)
797
798	%--------------------------------------------------------------
799	%function activated when a new filebase (image series) is introduced
800	%------------------------------------------------------------
801	function nb_field2_Callback(hObject, eventdata, handles)
802	Val=get(handles.nb_field2,'Value');
803	synchronise_view(handles,Val)
804
805	%--------------------------------------------------------------
806	%function activated when a new filebase (image series) is introduced
807	%------------------------------------------------------------
808	function time_first_Callback(hObject, eventdata, handles)
809	Val=get(handles.time_first,'Value');
810	synchronise_view(handles,Val)
811
812	%--------------------------------------------------------------
813	%function activated when a new filebase (image series) is introduced
814	%------------------------------------------------------------
815	function time_last_Callback(hObject, eventdata, handles)
816	Val=get(handles.time_last,'Value');
817	synchronise_view(handles,Val)
818
819	%--------------------------------------------------------------
820	%function activated by NomType
821	%------------------------------------------------------------
822	NomType_Callback(hObject, eventdata, handles)
823
824	%------------------------------------------------------------------------
825	function NomType_Callback(hObject, eventdata, handles)
826	%------------------------------------------------------------------------
827	hseries=get(handles.ProjObject,'Parent');
828	SeriesData=get(hseries,'UserData');
829	if isfield(SeriesData,'NomType')
830	NomTypeCell=SeriesData.NomType;
831	else
832	NomTypeCell={};
833	end
834	nbfield2_cell=get(handles.nb_field2,'String');
835	val=get(handles.nb_field2,'Value');
836	if iscell(nbfield2_cell)
837	nbfield2=str2num(nbfield2_cell{val});
838	else
839	nbfield2=str2num(nbfield2_cell);
840	end
841	nbfield_cell=get(handles.nb_field,'String');
842	if iscell(nbfield_cell)
843	nbfield=str2num(nbfield_cell{val});
844	else
845	nbfield=str2num(nbfield_cell);
846	end
847
848	set(handles.mode,'Visible','off') % do not show index pairs by default
849	set(handles.list_pair_civ,'Visible','off')
850	set(handles.ref_i,'Visible','off')
851	set(handles.ref_i_text,'Visible','off')
852	testpair=0;
853	state_j='off';
854	%set the menus of image pairs and default selection for series
855	%list pairs if relevant
856	Val=get(handles.NomType,'Value');
857	synchronise_view(handles,Val)
858	if ~isempty(NomTypeCell)
859	NomType=NomTypeCell{Val};
860	switch NomType
861	case {'_i1-i2_j', '_i1-i2'}
862	set(handles.mode,'String',{'series(Di)'})
863	set(handles.mode,'Value',1);
864	set(handles.mode,'Visible','on')
865	testpair=1;
866	case {'#_ab'}
867	set(handles.mode,'String',{'bursts'})
868	set(handles.mode,'Value',1);
869	testpair=1;
870	case '_i_j1-j2'
871	set(handles.mode,'String',{'bursts';'series(Dj)'})%multiple choice
872	if ~isempty(nbfield) && ~isempty(nbfield2) && ((nbfield2>10) \|\| (nbfield==1))
873	set(handles.mode,'Value',2);
874	else
875	set(handles.mode,'Value',1);% advice 'bursts' for small bursts
876	end
877	set(handles.mode,'Visible','on')
878	testpair=1;
879	end
880	switch NomType
881	case {'_1_1','_i_j1-j2','_i1-i2_j','1_ab','01_ab'},% two navigation indices
882	state_j='on';
883	end
884	end
885	if testpair
886	mode_Callback(hObject, eventdata, handles)
887	else
888	set(handles.NomType,'String',NomTypeCell)
889	set(handles.first_j,'Visible',state_j)
890	set(handles.incr_j,'Visible',state_j)
891	set(handles.last_j,'Visible',state_j)
892	set(handles.nb_field2,'Visible',state_j)
893	end
894
895
896	%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%????????????
897	% --- Executes on button press in mode.
898	%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
899	function mode_Callback(hObject, eventdata, handles)
900	%hseries=get(handles.mode,'parent');
901	hseries=handles.figure1;
902	SeriesData=get(hseries,'UserData');
903	mode_list=get(handles.mode,'String');
904	mode_value=get(handles.mode,'Value');
905	mode=mode_list{mode_value};
906	NomType=[];
907	test_find_pair=0;
908	if isfield(SeriesData,'NomType')
909	NomTypeCell=SeriesData.NomType;
910	Val=get(handles.NomType,'Value');
911	NomType=NomTypeCell{Val};
912	test_find_pair=isequal(NomType,'_i_j1-j2')\|\| isequal(NomType,'_i1-i2_j')\|\| isequal(NomType,'_i1-i2')\|\| isequal(NomType,'#_ab');
913	end
914	time=[];
915	if isfield(SeriesData,'Time')
916	time=SeriesData.Time{1}; %get the set of times
917	end
918	siztime=size(time);
919	nbfield=siztime(1);
920	nbfield2=siztime(2);
921	indchosen=1; %%first pair selected by default
922	if isequal(mode,'bursts')
923	enable_i(handles,'On')
924	enable_j(handles,'Off') %do not display j index scanning in burst mode (j is fixed by the burst choice)
925	elseif isequal(NomType,'_i_j1-j2')\|\| isequal(NomType,'_i1-i2_j')
926	enable_i(handles,'On')
927	enable_j(handles,'On') % allow both i and j index scanning
928	else
929	enable_i(handles,'On')
930	enable_j(handles,'Off')
931	end
932	set(handles.list_pair_civ,'Value',indchosen);%set the default choice of image pairs for civ1
933	set(hseries,'UserData',SeriesData)
934
935	%list pairs if relevant
936	if test_find_pair
937	find_netcpair_civ(hObject, eventdata, handles,Val)
938	end
939
940	%-------------------------------------
941	function enable_i(handles,state)
942	set(handles.i_txt,'Visible',state)
943	set(handles.first_i,'Visible',state)
944	set(handles.last_i,'Visible',state)
945	set(handles.incr_i,'Visible',state)
946	set(handles.nb_field,'Visible',state)
947	set(handles.ref_i,'Visible',state)
948	set(handles.ref_i_text,'Visible',state)
949
950	%-----------------------------------
951	function enable_j(handles,state)
952	set(handles.j_txt,'Visible',state)
953	set(handles.first_j,'Visible',state)
954	set(handles.last_j,'Visible',state)
955	set(handles.incr_j,'Visible',state)
956	set(handles.nb_field2,'Visible',state)
957	set(handles.ref_j,'Visible',state)
958	set(handles.ref_j_text,'Visible',state)
959
960	%-----------------------------------
961	function view_FieldMenu(handles,state)
962	set(handles.FieldMenu,'Visible',state)
963	set(handles.Field_text,'Visible',state)
964	set(handles.Field_frame,'Visible',state)
965
966	%-----------------------------------
967	function view_FieldMenu_1(handles,state)
968	set(handles.FieldMenu_1,'Visible',state)
969	set(handles.Field_text_1,'Visible',state)
970
971	%-----------------------------------
972	function view_TRANSFORM(handles,state)
973	set(handles.TRANSFORM_frame,'Visible',state)
974	set(handles.transform_fct,'Visible',state);
975	set(handles.TRANSFORM_title,'Visible',state)
976
977	%--------------------------------------------------------------
978	% determine the menu for civ1 pairs depending on existing netcdf files
979	% with the reference indices ref_i and ref_j
980	%----------------------------------------------------------------
981	function find_netcpair_civ(hObject, eventdata, handles,Val)
982	%hseries=get(handles.list_pair_civ,'parent');
983	SeriesData=get(handles.figure1,'UserData');
984	% NomTypeCell=get(handles.NomType,'String');
985	NomTypeCell=SeriesData.NomType;
986	NomType=NomTypeCell{Val};
987	set(handles.list_pair_civ,'Visible','on')
988	%nomenclature types
989	RootPathCell=get(handles.RootPath,'String');
990	filepath=RootPathCell{Val};
991	RootFileCell=get(handles.RootFile,'String');
992	filename=RootFileCell{Val};
993	filebase=fullfile(filepath,filename);
994	SubDirCell=get(handles.SubDir,'String');
995	subdir=SubDirCell{Val};
996	if ~exist(fullfile(filepath,subdir),'dir')
997	msgbox_uvmat('ERROR',['no civ file available: subdirectory ' subdir ' does not exist'])
998	set(handles.list_pair_civ,'String',{''});
999	return
1000	end
1001	mode_list=get(handles.mode,'String');
1002	mode_value=get(handles.mode,'Value');
1003	mode=mode_list{mode_value};
1004
1005	%reads image numbers from the interface
1006	ref_i=str2num(get(handles.ref_i,'String'));
1007	ref_j=str2num(get(handles.ref_j,'String'));
1008	ref_time=0;
1009	nbfield=50;
1010	nbfield2=50;%default max number of pairs
1011
1012	%look for existing processed pairs involving the field at the middle of the series if civ1 will not
1013	% be performed, while the result is needed for next steps.
1014	displ_pair={''};
1015	displ_num=[];
1016	ind_exist=0;
1017	TimeUnit=get(handles.TimeUnit,'String');
1018	if length(TimeUnit)>=1
1019	dtunit=['m' TimeUnit];
1020	else
1021	dtunit='e-03';
1022	end
1023	if strcmp(mode,'series(Di)')
1024	for index=1:min(nbfield-1,50)
1025	filename=name_generator(filebase,ref_i-floor(index/2),ref_j,'.nc',NomType,1,ref_i+ceil(index/2),ref_j,subdir);
1026	select=(exist(filename,'file')==2);
1027	if select==1
1028	ind_exist=ind_exist+1;
1029	displ_num(1,ind_exist)=0;
1030	displ_num(2,ind_exist)=0;
1031	displ_num(3,ind_exist)=-floor(index/2);
1032	displ_num(4,ind_exist)=ceil(index/2);
1033	%[cte_detect,vdt,cte_read]=read_netcdf(filename,{'dt','dt2','absolut_time_T0','absolute_time_TO_2'});
1034	[Cte,var_detect,ichoice]=nc2struct(filename,{});
1035	if isfield(Cte,'dt2')
1036	dt=Cte.dt2;
1037	elseif isfield(Cte,'dt')
1038	dt=Cte.dt;
1039	end
1040	if isfield(Cte,'absolut_time_TO_2')
1041	ref_time(ind_exist)=Cte.absolut_time_TO_2;%civ2 data used in priority
1042	elseif isfield(Cte,'absolut_time_TO')
1043	ref_time(ind_exist)=Cte.absolut_time_TO;%civ2 data used in priorit
1044	elseif isfield(Cte,'Time')
1045	ref_time(ind_exist)=Cte.Time;
1046	end
1047	displ_pair{ind_exist}=['Di= ' num2str(-floor(index/2)) '\|' num2str(ceil(index/2)) ' :dt= ' num2str(dt*1000) dtunit];
1048	end
1049	end
1050	set(handles.list_pair_civ,'String',[displ_pair';{'Di=\|'}]);
1051	elseif isequal(mode,'series(Dj)')% series on the j index
1052	for index=1:min(nbfield2-1,50)
1053	filename=name_generator(filebase,ref_i,ref_j-floor(index/2),'.nc',NomType,1,ref_i,ref_j+ceil(index/2),subdir);
1054	select=(exist(filename,'file')==2);
1055	if select==1
1056	ind_exist=ind_exist+1;
1057	displ_num(1,ind_exist)=-floor(index/2);
1058	displ_num(2,ind_exist)=ceil(index/2);
1059	displ_num(3,ind_exist)=0;
1060	displ_num(4,ind_exist)=0;
1061	[Cte,var_detect,ichoice]=nc2struct(filename,{});
1062	if isfield(Cte,'dt2')
1063	dt=Cte.dt2;
1064	elseif isfield(Cte,'dt')
1065	dt=Cte.dt;
1066	end
1067	if isfield(Cte,'absolut_time_TO_2')
1068	ref_time(ind_exist)=Cte.absolut_time_TO_2;%civ2 data used in priority
1069	elseif isfield(Cte,'absolut_time_TO')
1070	ref_time(ind_exist)=Cte.absolut_time_TO;%civ2 data used in priorit
1071	elseif isfield(Cte,'Time')
1072	ref_time(ind_exist)=Cte.Time;
1073	end
1074	% if cte_detect(2)==1;
1075	% dt=cte_read(2);
1076	% ref_time(ind_exist)=cte_read(4);%civ2 data used in priority
1077	% else
1078	% dt=cte_read(1);
1079	% ref_time(ind_exist)=cte_read(3);
1080	% end
1081	displ_pair{ind_exist}=['Dj= ' num2str(-floor(index/2)) '\|' num2str(ceil(index/2)) ' :dt= ' num2str(dt*1000) dtunit];
1082	end
1083	end
1084	set(handles.list_pair_civ,'String',[displ_pair';{'Dj=\|'}]);
1085	elseif isequal(mode,'bursts') %case of bursts
1086	for numod_a=1:nbfield2-1 %nbfield2 always >=2 for 'bursts' mode
1087	for numod_b=(numod_a+1):nbfield2
1088	[filename]=name_generator(filebase,ref_i,numod_a,'.nc',NomType,1,ref_i,numod_b,subdir);
1089	select=(exist(filename,'file')==2);
1090	if select==1
1091	ind_exist=ind_exist+1;
1092	numlist_a(ind_exist)=numod_a;
1093	numlist_b(ind_exist)=numod_b;
1094	Attr=nc2struct(filename,[]);
1095	isfield(Attr,'absolut_time_T0_2')
1096	if isfield(Attr,'dt2')
1097	dt(ind_exist)=Attr.dt2;
1098	ref_time(ind_exist)=Attr.absolut_time_T0_2;
1099	elseif isfield(Attr,'dt')& isfield(Attr,'absolut_time_T0')
1100	dt(ind_exist)=Attr.dt;
1101	ref_time(ind_exist)=Attr.absolut_time_T0;
1102	else
1103	dt(ind_exist)=NaN;%no information on dt
1104	end
1105	%determine nom_type_ima for pair display (used in num2stra.m)
1106	switch NomType
1107	case {'#ab'}
1108	nom_type_ima='#a';
1109	case {'#AB'}
1110	nom_type_ima='#A';
1111	otherwise
1112	nom_type_ima='_i_j';
1113	end
1114	displ_pair{ind_exist}=['j= ' num2stra(numod_a,nom_type_ima,2) '-' num2stra(numod_b,nom_type_ima,2) ...
1115	' :dt= ' num2str(dt(ind_exist)*1000)];
1116	end
1117	end
1118	set(handles.list_pair_civ,'String',[displ_pair';{'j=-'}]);
1119	end
1120	if exist('dt','var') & ~isempty(dt)
1121	[dtsort,indsort]=sort(dt);
1122	displ_num(1,:)=numlist_a(indsort);
1123	displ_num(2,:)=numlist_b(indsort);
1124	displ_num(3,:)=0;
1125	displ_num(4,:)=0;
1126	displ_pair=displ_pair(indsort);
1127	ref_time=ref_time(indsort);
1128	end
1129	end
1130	if ind_exist==0
1131	if isequal(mode,'series(Dj)') \| isequal(mode,'st_series(Dj)')
1132	msgbox_uvmat('ERROR',['no .nc file available for the selected reference index j=' num2str(ref_j) ' and subdirectory ' subdir])
1133	else
1134	msgbox_uvmat('ERROR',['no .nc file available for the selected reference index i=' num2str(ref_i) ' and subdirectory ' subdir])
1135	end
1136	if isequal(mode,'bursts') %case of bursts
1137	set(handles.list_pair_civ,'String',{'j=-'});
1138	elseif isequal(mode,'series(Di)') %case of bursts
1139	set(handles.list_pair_civ,'String',{'Di=\|'});
1140	elseif isequal(mode,'series(Dj)') %case of bursts
1141	set(handles.list_pair_civ,'String',{'Dj=\|'});
1142	end
1143	end
1144
1145	val=get(handles.list_pair_civ,'Value');
1146	if val > length(displ_pair)
1147	set(handles.list_pair_civ,'Value',1);% first pair proposed by default in the menu
1148	val=1;
1149	end
1150	iview=get(handles.NomType,'Value');
1151	SeriesData.displ_num(iview,:)=(displ_num(:,val))';
1152	SeriesData.ref_time=ref_time;
1153	set(handles.figure1,'UserData',SeriesData)
1154	list_pair_civ_Callback(hObject, eventdata, handles)
1155
1156	%-------------------------------------------------------------
1157	% --- Executes on selection in list_pair_civ.
1158	function list_pair_civ_Callback(hObject, eventdata, handles)
1159	%------------------------------------------------------------
1160
1161	%update first_i and last_i according to the chosen image pairs
1162	testupdate=0;
1163	Val=get(handles.RootPath,'Value');
1164	IndexCell=get(handles.NomType,'String');
1165	%hseries=get(handles.list_pair_civ,'parent');
1166	SeriesData=get(handles.figure1,'UserData');
1167	NomType=SeriesData.NomType{Val};
1168	list_pair=get(handles.list_pair_civ,'String');%get the menu of image pairs
1169	index_pair=get(handles.list_pair_civ,'Value');
1170	str_pair=list_pair{index_pair};
1171	ind_equ=strfind(str_pair,'=');%find '='
1172	ind_sep=strfind(str_pair,'\|');%find pair separator '\|'
1173	ind_com=strfind(str_pair,':');%find ':'
1174	test_bursts=0;
1175	if isempty(ind_sep)
1176	ind_sep=strfind(str_pair,'-');%find pair separator if it is not '\|'
1177	test_bursts=1;% we are in the case of bursts
1178	end
1179	displ_num=[0 0 0 0]; %default
1180	if ~isempty(ind_sep)&& ~strcmp(str_pair(ind_sep-1),'*')% if there is a pair separator ('\|' or '-')
1181	num1_str=str_pair(ind_equ(1)+1:ind_sep-1);
1182	num2_str=str_pair(ind_sep+1:ind_com-1);
1183	num1=str2double(num1_str);
1184	num2=str2double(num2_str);
1185	if isequal(num1_str(1),' ')
1186	num1_str(1)=[];
1187	end
1188	if isequal(num2_str(end),' ')
1189	num2_str(end)=[];
1190	end
1191	switch NomType
1192	case {'_i1-i2_j'}
1193	if isequal(num1_str(1),'0')
1194	IndexCell{Val}=['_(i-(i+' num2_str ')_j'];
1195	else
1196	IndexCell{Val}=['_(i' num1_str ')-(i+' num2_str ')_j'];
1197	end
1198	displ_num(3)=num1;
1199	displ_num(4)=num2;
1200	case {'_i1-i2'}
1201	if isequal(num1_str(1),'0')
1202	IndexCell{Val}=['_(i' num1_str ')-(i+' num2_str ')'];
1203	else
1204	IndexCell{Val}=['_(i' num1_str ')-(i+' num2_str ')'];
1205	end
1206	displ_num(3)=num1;
1207	displ_num(4)=num2;
1208	case '_i_j1-j2'
1209	if test_bursts
1210	IndexCell{Val}=['_i_' num1_str '-' num2_str ];
1211	else
1212	if isequal(num1_str(1),'0')
1213	IndexCell{Val}=['_i_j-(j+' num2_str ')'];
1214	else
1215	IndexCell{Val}=['_i_(j' num1_str ')-(j+' num2_str ')'];
1216	end
1217	end
1218	displ_num(1)=num1;
1219	displ_num(2)=num2;
1220	case {'#_ab'} %TO COMPLETE
1221	IndexCell{Val}=['_i_' num1_str '-' num2_str ];
1222
1223	end
1224	end
1225	set(handles.NomType,'String',IndexCell)
1226	SeriesData.displ_num(Val,:)=displ_num;
1227	set(handles.figure1,'UserData',SeriesData)
1228	% set(handles.NomType,'Value',Val)
1229
1230	if ~isequal(str_pair,'Dj=\|')&~isequal(str_pair,'Di=\|')
1231	mode_list=get(handles.mode,'String');
1232	mode_value=get(handles.mode,'Value');
1233	mode=mode_list{mode_value};
1234	if isequal(mode,'series(Di)')
1235	first_i=str2num(get(handles.first_i,'String'));
1236	last_i=str2num(get(handles.last_i,'String'));
1237	incr_i=str2num(get(handles.incr_i,'String'));
1238	num1=first_i:incr_i:last_i;
1239	lastfieldCell=get(handles.nb_field,'String');
1240	lastfield=str2num(lastfieldCell{1});
1241	if ~isempty(lastfield)
1242	ind=find((num1-floor(index_pair/2)ones(size(num1))>0)& (num1+ceil(index_pair/2)ones(size(num1))<=lastfield));
1243	num1=num1(ind);
1244	end
1245	if ~isempty(num1)
1246	set(handles.first_i,'String',num2str(num1(1)));
1247	set(handles.last_i,'String',num2str(num1(end)));
1248	end
1249	testupdate=1;
1250	elseif isequal(mode,'series(Dj)')
1251	first_j=str2num(get(handles.first_j,'String'));
1252	last_j=str2num(get(handles.last_j,'String'));
1253	incr_j=str2num(get(handles.incr_j,'String'));
1254	num_j=first_j:incr_j:last_j;
1255	lastfieldCell=get(handles.nb_field2,'String');
1256	if ~isempty(lastfieldCell)
1257	lastfield2=lastfieldCell{1};
1258	ind=find((num_j-floor(index_pair/2)*ones(size(num_j))>0)& ...
1259	(num_j+ceil(index_pair/2)*ones(size(num_j))<=lastfield2));
1260	end
1261	testupdate=1;
1262	end
1263
1264	%update the first and last times of the series
1265	if testupdate && isfield(SeriesData,'Time')
1266	if ~isempty(SeriesData.Time{1})
1267	displ_time(handles,SeriesData.Time{1});
1268	end
1269	end
1270	end
1271
1272	%------------------------------------------------------------------------
1273	% --- Executes on button press in RUN.
1274	function RUN_Callback(hObject, eventdata, handles)
1275	%------------------------------------------------------------------------
1276	%read root name and field type
1277	set(handles.RUN,'BusyAction','queue');
1278	%hseries=get(handles.RUN,'parent');
1279	set(0,'CurrentFigure',handles.figure1)
1280	if isequal(get(handles.GetObject,'Visible'),'on') && isequal(get(handles.GetObject,'Value'),1)
1281	Series.GetObject=1;
1282	GetObject_Callback(hObject, eventdata, handles)
1283	else
1284	Series.GetObject=0;
1285	end
1286	SeriesData=get(handles.figure1,'UserData');
1287
1288	%reinitiate waitbar position
1289	Series.WaitbarPos=get(handles.waitbar_frame,'Position');%TO SUPPRESS
1290	waitbarpos=Series.WaitbarPos;
1291	waitbarpos(4)=0.005;%reinitialize waitbar to zero height
1292	waitbarpos(2)=Series.WaitbarPos(2)+Series.WaitbarPos(4)-0.005;
1293	set(handles.waitbar,'Position',waitbarpos)
1294
1295	% read input file parameters and set menus
1296	Series.PathProject=get(handles.PathCampaign,'String');
1297	RootPath=get(handles.RootPath,'String');% path of the root name of the first field series
1298	RootFile=get(handles.RootFile,'String');% root name of the first field series
1299	SubDir=get(handles.SubDir,'String');% subdirectory for netcdf files
1300	FileExt=get(handles.FileExt,'String');%file extension
1301	if isempty(SeriesData)
1302	msgbox_uvmat('ERROR','no input file series')
1303	return
1304	end
1305	NomType=SeriesData.NomType;
1306	if length(RootPath)==1 %string character input for user fct
1307	Series.RootPath=RootPath{1};
1308	Series.RootFile=RootFile{1};
1309	Series.SubDir=SubDir{1};
1310	Series.FileExt=FileExt{1};
1311	Series.NomType=NomType{1};
1312	else %cell input for user fct
1313	Series.RootPath=RootPath;
1314	Series.RootFile=RootFile;
1315	Series.SubDir=SubDir;
1316	Series.FileExt=FileExt;
1317	Series.NomType=NomType;
1318	end
1319	if isequal(get(handles.FieldMenu,'Visible'),'on')
1320	FieldMenu=get(handles.FieldMenu,'String');
1321	FieldValue=get(handles.FieldMenu,'Value');
1322	Series.Field=FieldMenu(FieldValue);
1323	end
1324	menu_coord_state=get(handles.transform_fct,'Visible');
1325	Series.CoordType='';%default
1326	if isequal(menu_coord_state,'on')
1327	% menu_coord=get(handles.transform_fct,'String');
1328	menu_index=get(handles.transform_fct,'Value');
1329	transform_list=get(handles.transform_fct,'UserData');
1330	Series.transform_fct=transform_list{menu_index};% transform function handles
1331	end
1332	Series.hseries=handles.figure1; % handles to the series GUI
1333
1334	%read the set of field numbers
1335	first_i=str2num(get(handles.first_i,'String'));
1336	last_i=str2num(get(handles.last_i,'String'));
1337	incr_i=str2num(get(handles.incr_i,'String'));
1338	first_j=str2num(get(handles.first_j,'String'));
1339	last_j=str2num(get(handles.last_j,'String'));
1340	incr_j=str2num(get(handles.incr_j,'String'));
1341	if ~isequal(get(handles.first_i,'Visible'),'on')
1342	first_i=1;
1343	last_i=1;
1344	incr_i=1;
1345	end
1346	if ~isequal(get(handles.first_j,'Visible'),'on')
1347	first_j=1;
1348	last_j=1;
1349	incr_j=1;
1350	end
1351	Series.NbSlice=str2num(get(handles.NbSlice,'String'));
1352	if isequal(first_i,[])\|isequal(first_j,[]), msgbox_uvmat('ERROR','first field number not defined'),...
1353	set(handles.RUN, 'Enable','On'), set(handles.RUN,'BackgroundColor',[1 0 0]),return,end;
1354	if isequal(last_i,[])\| isequal(last_j,[]),msgbox_uvmat('ERROR','last field number not defined'),...
1355	set(handles.RUN, 'Enable','On'), set(handles.RUN,'BackgroundColor',[1 0 0]),return,end;
1356	if isequal(incr_i,[])\| isequal(incr_j,[]),msgbox_uvmat('ERROR','increment in field number not defined'),...
1357	set(handles.RUN, 'Enable','On'), set(handles.RUN,'BackgroundColor',[1 0 0]),return,end;
1358	if last_i < first_i \| last_j < first_j , msgbox_uvmat('ERROR','last field number must be larger than the first one'),...
1359	set(handles.RUN, 'Enable','On'), set(handles.RUN,'BackgroundColor',[1 0 0]),return,end;
1360	num_i=first_i:incr_i:last_i;
1361	num_j=first_j:incr_j:last_j;
1362	nbfield_cell=get(handles.nb_field,'String');
1363	nbfield=[]; %default
1364	for iview=1:length(nbfield_cell)
1365	nb=str2num(nbfield_cell{iview});
1366	if ~isempty(nb)
1367	nbfield=[nbfield nb];
1368	end
1369	end
1370	nbfield=min(nbfield);
1371	nbfield2_cell=get(handles.nb_field2,'String');
1372	nbfield2=[]; %default
1373	for iview=1:length(nbfield2_cell)
1374	nb=str2num(nbfield2_cell{iview});
1375	if ~isempty(nb)
1376	nbfield2=[nbfield2 nb];
1377	end
1378	end
1379	nbfield2=min(nbfield2);
1380
1381	%get complementary information from the 'series' interface
1382	list_action=get(handles.ACTION,'String');% list menu action
1383	index_action=get(handles.ACTION,'Value');% selected string index
1384	action= list_action{index_action}; % selected string
1385	mode_list=get(handles.mode,'String');
1386	index_mode=get(handles.mode,'Value');
1387	mode=mode_list{index_mode};
1388	ind_shift=0;%default
1389
1390	%determine the list of input file names
1391	nbmissing=0;
1392	for iview=1:length(RootPath)
1393	%case of pairs (.nc files)
1394
1395	if isequal(NomType{iview},'_i_j1-j2')\|\| isequal(NomType{iview},'_i1-i2_j')\|\| isequal(NomType{iview},'_i1-i2')\|\| isequal(NomType{iview},'#_ab')
1396	ind_shift=SeriesData.displ_num(iview,:);
1397	if isequal(ind_shift,[0 0 0 0]) % undefined pairs
1398	if isequal(NomType{iview},'#_ab')
1399	mode='#_ab';
1400	end
1401	[num_i1,num_i2,num_j1,num_j2,nbmissing]=netseries_generator(fullfile(RootPath{iview},RootFile{iview}),SubDir{iview},mode,first_i,incr_i,last_i,first_j,incr_j,last_j);
1402	else
1403	[num_i1,num_i2,num_j1,num_j2,num_i,num_j]=find_file_indices(num_i,num_j,ind_shift,NomType{iview},mode);
1404	if isempty(num_i)
1405	msgbox_uvmat('ERROR','ERROR: empty set of input files chosen')
1406	return
1407	end
1408	if num_i(1)>first_i
1409	set(handles.first_i,'String',num2str(num_i(1)))%update the display of first field
1410	last_i_Callback(hObject, eventdata, handles)
1411	end
1412	if num_i(end)<last_i
1413	set(handles.last_i,'String',num2str(num_i(end)))%update the display of last field
1414	last_i_Callback(hObject, eventdata, handles)
1415	end
1416	if num_j(1)>first_j
1417	set(handles.first_j,'String',num2str(num_j(1)))%update the display of first field
1418	last_j_Callback(hObject, eventdata, handles)
1419	end
1420	if num_j(end)<last_j
1421	set(handles.last_j,'String',num2str(num_j(end)))%update the display of last field
1422	last_j_Callback(hObject, eventdata, handles)
1423	end
1424	end
1425	else%case of images
1426	[num_i1,num_j1]=meshgrid(num_i,num_j);
1427	num_i2=num_i1;
1428	num_j2=num_j1;
1429	end
1430	if length(RootPath)>1
1431	num_i1_cell{iview}=num_i1;
1432	num_i2_cell{iview}=num_i2;
1433	num_j1_cell{iview}=num_j1;
1434	num_j2_cell{iview}=num_j2;
1435	end
1436	end
1437
1438	% defining the ACTION function handle
1439	path_series=which('series');
1440	list_path=get(handles.ACTION,'UserData');
1441	index=get(handles.ACTION,'Value');
1442	fct_path=list_path{index}; %path stored for the function ACTION
1443	if ~isequal(fct_path,path_series)
1444	eval(['spath=which(''' action ''');']) %spath = current path of the selected function ACTION
1445	if ~exist(fct_path,'dir')
1446	msgbox_uvmat('ERROR',['The prescibed function path ' fct_path ' does not exist'])
1447	return
1448	end
1449	if ~isequal(spath,fct_path)
1450	addpath(fct_path)% add the prescribed path if not the current one
1451	end
1452	end
1453	eval(['h_fun=@' action ';'])%create a function handle for ACTION
1454	if ~isequal(fct_path,path_series)
1455	rmpath(fct_path)% add the prescribed path if not the current one
1456	end
1457
1458	% RUN ACTION
1459	Series.Action=action;%name of the processing programme
1460	set(handles.RUN,'BackgroundColor',[0.831 0.816 0.784])
1461
1462	if length(RootPath)>1
1463	h_fun(num_i1_cell,num_i2_cell,num_j1_cell,num_j2_cell,Series);
1464	else
1465	h_fun(num_i1,num_i2,num_j1,num_j2,Series);
1466	end
1467	set(handles.RUN,'BackgroundColor',[1 0 0])
1468
1469	% %save the current interface setting as figure namefig, append .0 to the name if it already exists
1470	% detect=1;
1471	% while detect==1
1472	% namefigfull=[namedoc '.fig'];
1473	% hh=dir(namefigfull);
1474	% if ~isempty(hh)
1475	% detect=1;
1476	% namedoc=[namedoc '.0'];
1477	% else
1478	% detect=0;
1479	% end
1480	% end
1481	% saveas(gcbf,namefigfull);%save the interface with name namefigfull (A CHANGER EN FICHIER .xml)
1482
1483	%------------------------------------------------------------------------
1484	function STOP_Callback(hObject, eventdata, handles)
1485	%------------------------------------------------------------------------
1486	set(handles.RUN, 'BusyAction','cancel')
1487	set(handles.RUN,'BackgroundColor',[1 0 0])
1488
1489
1490	%------------------------------------------------------------------------
1491	function first_i_Callback(hObject, eventdata, handles)
1492	%------------------------------------------------------------------------
1493	last_i_Callback(hObject, eventdata, handles)
1494
1495	%------------------------------------------------------------------------
1496	function last_i_Callback(hObject, eventdata, handles)
1497	%------------------------------------------------------------------------
1498	% hseries=get(handles.last_i,'parent');
1499	% first_i=str2num(get(handles.first_i,'String'));
1500	% last_i=str2num(get(handles.last_i,'String'));
1501	% ref_i=ceil((first_i+last_i)/2);
1502	% set(handles.ref_i,'String', num2str(ref_i))
1503	% ref_i_Callback(hObject, eventdata, handles)
1504	SeriesData=get(handles.figure1,'UserData');
1505	if ~isfield(SeriesData,'Time')
1506	SeriesData.Time{1}=[];
1507	end
1508	displ_time(handles,SeriesData.Time{1});
1509
1510	%------------------------------------------------------------------------
1511	function first_j_Callback(hObject, eventdata, handles)
1512	%------------------------------------------------------------------------
1513	last_j_Callback(hObject, eventdata, handles)
1514
1515	%------------------------------------------------------------------------
1516	function last_j_Callback(hObject, eventdata, handles)
1517	%------------------------------------------------------------------------
1518	first_j=str2num(get(handles.first_j,'String'));
1519	last_j=str2num(get(handles.last_j,'String'));
1520	ref_j=ceil((first_j+last_j)/2);
1521	set(handles.ref_j,'String', num2str(ref_j))
1522	ref_j_Callback(hObject, eventdata, handles)
1523	SeriesData=get(handles.figure1,'UserData');
1524	if ~isfield(SeriesData,'Time')
1525	SeriesData.Time{1}=[];
1526	end
1527	displ_time(handles,SeriesData.Time{1});
1528
1529
1530	%------------------------------------------------------------------------
1531	function ref_i_Callback(hObject, eventdata, handles)
1532	%------------------------------------------------------------------------
1533	mode_list=get(handles.mode,'String');
1534	mode_value=get(handles.mode,'Value');
1535	mode=mode_list{mode_value};
1536	%hseries=get(handles.ref_i,'parent');
1537	SeriesData=get(handles.figure1,'UserData');
1538	%NomTypeCell=get(handles.NomType,'String');
1539	NomTypeCell=SeriesData.NomType;
1540	if ~isempty(NomTypeCell)
1541	Val=get(handles.NomType,'Value');
1542	NomType=NomTypeCell{Val};
1543	% for ilist=1:length(NomType)
1544	if isequal(NomType,'_i_j1-j2')\|\| isequal(NomType,'_i1-i2_j')\|\| isequal(NomType,'_i1-i2')
1545	if isequal(mode,'series(Di)')
1546	find_netcpair_civ(hObject, eventdata, handles,Val);% update the menu of pairs depending on the available netcdf files
1547	% break
1548	end
1549	end
1550	end
1551
1552	%------------------------------------------------------------------------
1553	function ref_j_Callback(hObject, eventdata, handles)
1554	%------------------------------------------------------------------------
1555	mode_list=get(handles.mode,'String');
1556	mode_value=get(handles.mode,'Value');
1557	mode=mode_list{mode_value};
1558	%hseries=get(handles.ref_i,'parent');
1559	SeriesData=get(handles.figure1,'UserData');
1560	NomTypeCell=SeriesData.NomType;
1561	if ~isempty(NomTypeCell)
1562	Val=get(handles.NomType,'Value');
1563	NomType=NomTypeCell{Val};
1564	if isequal(NomType,'_i_j1-j2')\|\| isequal(NomType,'_i1-i2_j')\|\| isequal(NomType,'_i1-i2')
1565	if isequal(mode,'series(Dj)')
1566	find_netcpair_civ(hObject, eventdata, handles,Val);% update the menu of pairs depending on the available netcdf files
1567	end
1568	end
1569	end
1570
1571	%------------------------------------------------------------------------
1572	% --- Executes on selection change in ACTION.
1573	function ACTION_Callback(hObject, eventdata, handles)
1574	%------------------------------------------------------------------------
1575	global nb_builtin_ACTION
1576	list_ACTION=get(handles.ACTION,'String');% list menu fields
1577	index_ACTION=get(handles.ACTION,'Value');% selected string index
1578	ACTION= list_ACTION{index_ACTION}; % selected function name
1579	path_series=which('series');%path to series.m
1580	list_path=get(handles.ACTION,'UserData');%list of recorded paths to functions of the list ACTION
1581	default_file=fullfile(list_path{end},ACTION);
1582	% add a new function to the menu if the selected item is 'more...'
1583	if isequal(ACTION,'more...')
1584	pathfct=fileparts(path_series);
1585	[FileName, PathName, filterindex] = uigetfile( ...
1586	{'.m', ' (.m)';
1587	'*.m', '.m files '; ...
1588	'.', 'All Files (.)'}, ...
1589	'Pick a file',default_file);
1590	if length(FileName)<2
1591	return
1592	end
1593	[pp,ACTION,ext_fct]=fileparts(FileName);%(end-1:end);
1594	if ~isequal(ext_fct,'.m')
1595	msgbox_uvmat('ERROR','a Matlab function .m must be introduced');
1596	return
1597	end
1598
1599	% insert the choice in the action menu
1600	menu_str=update_menu(handles.ACTION,ACTION);%new action menu in which the new item has been appended if needed
1601	index_ACTION=get(handles.ACTION,'Value');% currently selected index in the list
1602	list_path{index_ACTION}=PathName;
1603	if length(menu_str)>nb_builtin_ACTION+5; %nb_builtin=nbre of functions always remaining in the initial menu
1604	nbremove=length(menu_str)-nb_builtin_ACTION-5;
1605	menu_str(nb_builtin_ACTION+1:end-5)=[];
1606	list_path(nb_builtin_ACTION+1:end-4)=[];
1607	index_ACTION=index_ACTION-nbremove;
1608	set(handles.ACTION,'Value',index_ACTION)
1609	set(handles.ACTION,'String',menu_str)
1610	end
1611	list_path{index_ACTION}=PathName;
1612	set(handles.ACTION,'UserData',list_path);
1613	set(handles.path,'enable','inactive')% indicate that the current path is accessible (not 'off')
1614
1615	%record the current menu in personal file profil_perso
1616	dir_perso=prefdir;
1617	profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
1618	for ilist=nb_builtin_ACTION+1:length(menu_str)-1
1619	series_fct{ilist-nb_builtin_ACTION}=fullfile(list_path{ilist},[menu_str{ilist} '.m']);
1620	end
1621	if nb_builtin_ACTION+1<=length(menu_str)-1
1622	if exist(profil_perso,'file')% && nb_builtin_ACTION+1>=length(menu_str)-1
1623	save(profil_perso,'series_fct','-append')
1624	else
1625	txt=ver('MATLAB');
1626	Release=txt.Release;
1627	relnumb=str2num(Release(3:4));
1628	if relnumb >= 14%recent relaese of Matlab
1629	save(profil_perso,'series_fct','-V6')
1630	else
1631	save(profil_perso, 'series_fct')
1632	end
1633	end
1634	end
1635	end
1636
1637	%check the current path to the selected function
1638	PathName=list_path{index_ACTION};%current recorded path
1639	set(handles.path,'String',PathName); %show the path to the senlected function
1640
1641	%default setting for the visibility of the GUI elements
1642	set(handles.RootPath,'UserData','many')
1643	set(handles.SubDir,'Visible','on')
1644	set(handles.RootFile,'Visible','on')
1645	set(handles.NomType,'Visible','on')
1646	set(handles.FileExt,'Visible','on')
1647	set(handles.NbSlice,'Visible','off')
1648	set(handles.NbSlice_title,'Visible','off')
1649	set(handles.VelTypeMenu,'Visible','off');
1650	set(handles.VelType_text,'Visible','off');
1651	set(handles.VelTypeMenu_1,'Visible','off');
1652	set(handles.VelType_text_1,'Visible','off');
1653	view_FieldMenu(handles,'off')
1654	view_FieldMenu_1(handles,'off')
1655	view_TRANSFORM(handles,'off')
1656	set(handles.ProjObject_frame,'Visible','off');
1657	set(handles.GetMask,'Visible','off')
1658	set(handles.Mask,'Visible','off')
1659	set(handles.GetObject,'Visible','off');
1660	set(handles.ProjObject,'Visible','off');
1661	set(handles.OutputDir,'Visible','off');
1662	set(handles.PARAMETERS_frame,'Visible','off');
1663	set(handles.PARAMETERS_title,'Visible','off');
1664	set(handles.ParamKey,'Visible','off')
1665	set(handles.ParamVal,'Visible','off')
1666	ParamKey={};
1667	set(handles.FieldMenu,'Enable','off')
1668	set(handles.VelTypeMenu,'Enable','off')
1669	set(handles.FieldMenu_1,'Enable','off')
1670	set(handles.VelTypeMenu_1,'Enable','off')
1671	set(handles.transform_fct,'Enable','off')
1672	%set the displayed GUI item needed for input parameters
1673	if ~isequal(path_series,PathName)
1674	addpath(PathName)
1675	end
1676	eval(['h_function=@' ACTION ';']);
1677	try
1678	[fid,errormsg] =fopen([ACTION '.m']);
1679	InputText=textscan(fid,'%s',1,'delimiter','\n');
1680	fclose(fid)
1681	set(handles.ACTION,'ToolTipString',InputText{1}{1})
1682	end
1683	if ~isequal(path_series,PathName)
1684	rmpath(PathName)
1685	end
1686	varargout=h_function();
1687	Param_list={};
1688
1689	%nb_series=length(RootFile);
1690	FileExt=get(handles.FileExt,'String');
1691	nb_series=length(FileExt);
1692	testima_series=1; %test for a list of images only
1693	testima=1;
1694	testima_1=1;
1695	testciv_series=1;
1696	for iview=1:nb_series
1697	ext=FileExt{iview};
1698	if length(ext)<2
1699	ext='.none';
1700	end
1701	testimaview=~isempty(imformats(ext(2:end))) \|\| isequal(lower(ext),'.avi');
1702	if ~testimaview
1703	if iview==1
1704	testima=0;
1705	end
1706	if iview==2
1707	testima_1=0;
1708	end
1709	testima_series=0;
1710	end
1711	end
1712	for ilist=1:length(varargout)-1
1713	switch varargout{ilist}
1714	%RootFile always visible
1715	case 'RootPath' %visible by default
1716	value=lower(varargout{ilist+1});
1717	if isequal(value,'one')\|\|isequal(value,'two')\|\|isequal(value,'many')
1718	set(handles.RootFile,'UserData',value)% for use in menu Open_insert
1719	end
1720	case 'SubDir' %visible by default
1721	if isequal(lower(varargout{ilist+1}),'off')
1722	set(handles.SubDir,'Visible','off')
1723	end
1724	case 'RootFile' %visible by default
1725	value=lower(varargout{ilist+1});
1726	if isequal(value,'off')
1727	set(handles.RootFile,'Visible','off')
1728	elseif isequal(value,'one')\|\|isequal(value,'two')\|\|isequal(value,'many')
1729	set(handles.RootFile,'Visible','on')
1730	set(handles.RootFile,'UserData',value)% for use in menu Open_insert
1731	end
1732	case 'NomType' %visible by default
1733	if isequal(lower(varargout{ilist+1}),'off')
1734	set(handles.NomType,'Visible','off')
1735	end
1736	case 'FileExt' %visible by default
1737	if isequal(lower(varargout{ilist+1}),'off')
1738	set(handles.FileExt,'Visible','off')
1739	end
1740	case 'NbSlice' %hidden by default
1741	if isequal(lower(varargout{ilist+1}),'on')
1742	set(handles.NbSlice,'Visible','on')
1743	set(handles.NbSlice_title,'Visible','on')
1744	end
1745	case 'VelTypeMenu' %hidden by default
1746	if isequal(lower(varargout{ilist+1}),'one') \|\| isequal(lower(varargout{ilist+1}),'two')
1747	set(handles.VelTypeMenu,'Enable','on')
1748	if nb_series >=1 && ~testima_series
1749	set(handles.VelTypeMenu,'Visible','on')
1750	set(handles.VelType_text,'Visible','on');
1751	set(handles.Field_frame,'Visible','on')
1752	end
1753	end
1754	if isequal(lower(varargout{ilist+1}),'two')
1755	set(handles.VelTypeMenu_1,'Enable','on')
1756	if nb_series >=2 && ~testima_series
1757	set(handles.VelTypeMenu_1,'Visible','on')
1758	set(handles.VelType_text_1,'Visible','on');
1759	end
1760	end
1761	case 'FieldMenu' %hidden by default
1762	if isequal(lower(varargout{ilist+1}),'one')\|\|isequal(lower(varargout{ilist+1}),'two')
1763	set(handles.FieldMenu,'Enable','on') % test for MenuBorser
1764	if nb_series >=1 && ~testima_series
1765	view_FieldMenu(handles,'on')
1766	end
1767	end
1768	if isequal(lower(varargout{ilist+1}),'two')
1769	set(handles.FieldMenu_1,'Enable','on')
1770	if nb_series >=2 && ~testima_1
1771	view_FieldMenu_1(handles,'on')
1772	end
1773	end
1774	case 'CoordType' %hidden by default
1775	if isequal(lower(varargout{ilist+1}),'on')
1776	set(handles.transform_fct,'Enable','on')
1777	view_TRANSFORM(handles,'on')
1778	end
1779	case 'GetObject' %hidden by default
1780	if isequal(lower(varargout{ilist+1}),'on')
1781	set(handles.ProjObject_frame,'Visible','on')
1782	set(handles.GetObject,'Visible','on');
1783	end
1784	case 'Mask' %hidden by default
1785	if isequal(lower(varargout{ilist+1}),'on')
1786	set(handles.ProjObject_frame,'Visible','on')
1787	set(handles.GetMask,'Visible','on');
1788	end
1789	case 'PARAMETER'
1790	set(handles.PARAMETERS_frame,'Visible','on')
1791	set(handles.PARAMETERS_title,'Visible','on')
1792	set(handles.ParamKey,'Visible','on')
1793	%set(handles.ParamVal,'Visible','on')
1794	Param_str=varargout{ilist+1};
1795	Param_list=[Param_list; {Param_str}];
1796	end
1797	end
1798	if ~isempty(Param_list)
1799	set(handles.ParamKey,'String',Param_list)
1800	set(handles.ParamVal,'Visible','on')
1801	end
1802
1803	%------------------------------------------------------------------------
1804	% --- Executes on selection change in FieldMenu.
1805	function FieldMenu_Callback(hObject, eventdata, handles)
1806	%------------------------------------------------------------------------
1807	field_str=get(handles.FieldMenu,'String');
1808	field_index=get(handles.FieldMenu,'Value');
1809	field=field_str{field_index(1)};
1810	if isequal(field,'get_field...')
1811	hget_field=findobj(allchild(0),'name','get_field');
1812	if ~isempty(hget_field)
1813	delete(hget_field)%delete opened versions of get_field
1814	end
1815	%hseries=get(handles.FieldMenu,'parent');
1816	SeriesData=get(handles.figure1,'UserData');
1817	filename=SeriesData.CurrentInputFile;
1818	if exist(filename,'file')
1819	get_field(filename)
1820	end
1821	elseif isequal(field,'more...')
1822	str=calc_field;
1823	[ind_answer,v] = listdlg('PromptString','Select a file:',...
1824	'SelectionMode','single',...
1825	'ListString',str);
1826	% edit the choice in the fields and action menu
1827	scalar=cell2mat(str(ind_answer));
1828	update_menu(handles.FieldMenu,scalar)
1829	end
1830
1831	%------------------------------------------------------------------------
1832	% --- Executes on selection change in FieldMenu_1.
1833	function FieldMenu_1_Callback(hObject, eventdata, handles)
1834	%------------------------------------------------------------------------
1835	field_str=get(handles.FieldMenu_1,'String');
1836	field_index=get(handles.FieldMenu_1,'Value');
1837	field=field_str{field_index};
1838	if isequal(field,'get_field...')
1839	hget_field=findobj(allchild(0),'name','get_field_1');
1840	if ~isempty(hget_field)
1841	delete(hget_field)
1842	end
1843	%hseries=get(handles.FieldMenu,'parent');
1844	SeriesData=get(handles.figure1,'UserData');
1845	filename=SeriesData.CurrentInputFile_1;
1846	if exist(filename,'file')
1847	hget_field=get_field(filename);
1848	set(hget_field,'name','get_field_1')
1849	end
1850	elseif isequal(field,'more...')
1851	str=calc_field;
1852	[ind_answer,v] = listdlg('PromptString','Select a file:',...
1853	'SelectionMode','single',...
1854	'ListString',str);
1855	% edit the choice in the fields and action menu
1856	scalar=cell2mat(str(ind_answer));
1857	update_menu(handles.FieldMenu_1,scalar)
1858	end
1859
1860	%-----------------------------
1861	function mouse_up_gui(hObject,eventdata,handles)
1862	if isequal(get(hObject,'SelectionType'),'alt')
1863	set(hObject,'Units','pixels')
1864	series_pos=get(hObject,'Position');%position of the GUI series (in pixels)
1865	set(hObject,'Units','normalized')
1866	xy_fig=get(hObject,'CurrentPoint');% current point of the current figure (gcbo)
1867	hchild=get(hObject,'Children');%handles of all objects in the current figure
1868	%% loop on all the objects in the current figure (selected by the last mouse click)
1869
1870	for ichild=1:length(hchild)
1871	obj_pos=get(hchild(ichild),'Position');%position of the object
1872	if numel(obj_pos)>=4 && xy_fig(1) >=obj_pos(1) && xy_fig(2) >= obj_pos(2)&& xy_fig(1) <=obj_pos(1)+obj_pos(3) && xy_fig(2) <= obj_pos(2)+obj_pos(4);
1873	htype=get(hchild(ichild),'Type');%type of object child of the current figure
1874	%if the mouse is over an axis, look at the data
1875	if isequal(htype,'uicontrol') && isequal(get(hchild(ichild),'Visible'),'on')
1876	msg_pos(1:2)=series_pos(1:2)+obj_pos(1:2).*series_pos(3:4);
1877	msgbox_uvmat(['uicontrol: ' get(hchild(ichild),'Tag')],'',get(hchild(ichild),'String'),msg_pos)
1878	break
1879	end
1880	end
1881	end
1882	set(hObject,'Units','pixels')
1883	end
1884
1885	%%%%%%%%%%%%%
1886	function [ind_remove]=find_pairs(dirpair,ind_i,last_i)
1887
1888	indsel=ind_i;
1889	indiff=diff(ind_i); %test index increment to detect multiplets (several pairs with the same index ind_i) and holes in the series
1890	indiff=[1 indiff last_i-ind_i(end)+1];%for testing gaps with the imposed bounds
1891	if ~isempty(indiff)
1892	indiff2=diff(indiff);
1893	indiffp=[indiff2 1];
1894	indiffm=[1 indiff2];
1895	ind_multi_m=find((indiff==0)&(indiffm<0))-1;%indices of first members of multiplets
1896	ind_multi_p=find((indiff==0)&(indiffp>0));%indices of last members of multiplets
1897	%for each multiplet, select the most recent file
1898	ind_remove=[];
1899	for i=1:length(ind_multi_m)
1900	ind_pairs=ind_multi_m(i):ind_multi_p(i);
1901	for imulti=1:length(ind_pairs)
1902	datepair(imulti)=datenum(dirpair(ind_pairs(imulti)).date);%dates of creation
1903	end
1904	[datenew,indsort2]=sort(datepair); %sort the multiplet by creation date
1905	ind_s=indsort2(1:end-1);%
1906	ind_remove=[ind_remove ind_pairs(ind_s)];%remove these indices, leave the last one
1907	end
1908	end
1909
1910	%------------------------------------------------------------------------
1911	% --- determine the list of index pairs of processing file
1912	function [num_i1,num_i2,num_j1,num_j2,num_i_out,num_j_out]=find_file_indices(num_i,num_j,ind_shift,NomType,mode)
1913	%------------------------------------------------------------------------
1914	num_i1=num_i;% set of first image numbers by default
1915	num_i2=num_i;
1916	num_j1=num_j;
1917	num_j2=num_j;
1918	num_i_out=num_i;
1919	num_j_out=num_j;
1920	if isequal (NomType,'_i1-i2_j') \|\| isequal (NomType,'_i1-i2')
1921	num_i1_line=num_i+ind_shift(3);% set of first image numbers
1922	num_i2_line=num_i+ind_shift(4);
1923	% adjust the first and last field number
1924	indsel=find(num_i1_line >= 1);
1925	num_i_out=num_i(indsel);
1926	num_i1_line=num_i1_line(indsel);
1927	num_i2_line=num_i2_line(indsel);
1928	num_j1=meshgrid(num_j,ones(size(num_i1_line)));
1929	num_j2=meshgrid(num_j,ones(size(num_i1_line)));
1930	[xx,num_i1]=meshgrid(num_j,num_i1_line);
1931	[xx,num_i2]=meshgrid(num_j,num_i2_line);
1932	elseif isequal (NomType,'_i_j1-j2') \|\| isequal (NomType,'#_ab')
1933	if isequal(mode,'bursts') %case of bursts (png_old or png_2D)
1934	num_j1=ind_shift(1)*ones(size(num_i));
1935	num_j2=ind_shift(2)*ones(size(num_i));
1936	else
1937	num_j1_col=num_j+ind_shift(1);% set of first image numbers
1938	num_j2_col=num_j+ind_shift(2);
1939	% adjust the first field number
1940	indsel=find((num_j1_col >= 1));
1941	num_j_out=num_j(indsel);
1942	num_j1_col=num_j1_col(indsel);
1943	num_j2_col=num_j2_col(indsel);
1944	[num_i1,num_j1]=meshgrid(num_i,num_j1_col);
1945	[num_i2,num_j2]=meshgrid(num_i,num_j2_col);
1946	end
1947	end
1948
1949	%------------------------------------------------------------------------
1950	% ---- find the times corresponding to the first and last indices of a series
1951	function displ_time(handles,times)
1952	%------------------------------------------------------------------------
1953	hseries=get(handles.last_i,'parent');
1954	SeriesData=get(hseries,'UserData');%
1955	first_i=str2num(get(handles.first_i,'String'));
1956	first_j=str2num(get(handles.first_j,'String'));
1957	last_i=str2num(get(handles.last_i,'String'));
1958	last_j=str2num(get(handles.last_j,'String'));
1959	% index_civ=get(handles.list_pair_civ,'Value');
1960	% NomType=get(handles.NomType,'String');
1961	NomType=SeriesData.NomType;
1962	mode_list=get(handles.mode,'String');
1963	index_mode=get(handles.mode,'Value');
1964	mode=mode_list{index_mode};
1965	% ind_shift=0;%default
1966
1967	time_first=[];
1968	time_last=[];
1969	if ~isfield(SeriesData,'Time')
1970	SeriesData.Time{1}=[];
1971	end
1972	for iview=1:length(NomType)
1973	time_first_cell{iview}='?';
1974	time_last_cell{iview}='?';%default
1975	time=SeriesData.Time{iview};
1976	if isequal(NomType{iview},'_i1-i2_j')\|isequal(NomType{iview},'_i_j1-j2')\|isequal(NomType{iview},'#_ab')\|isequal(NomType{iview},'_i1-i2')
1977	if isfield(SeriesData,'displ_num')& ~isempty(SeriesData.displ_num)
1978	ind_shift=SeriesData.displ_num(iview,:);
1979	if isequal(mode,'bursts')
1980	first_j=0;
1981	last_j=0;
1982	end
1983	first_i1=first_i +ind_shift(3);
1984	first_i2 =first_i +ind_shift(4);
1985	first_j1 =first_j +ind_shift(1);
1986	first_j2 =first_j +ind_shift(2);
1987	last_i1=last_i +ind_shift(3);
1988	last_i2 =last_i +ind_shift(4);
1989	last_j1 =last_j +ind_shift(1);
1990	last_j2 =last_j +ind_shift(2);
1991	siz=size(SeriesData.Time{1});
1992	if first_i1>=1 && first_j1>=1 && siz(1)>=last_i2 && siz(2)>=last_j2
1993	time_first=(time(first_i1,first_j1)+time(first_i2,first_j2))/2;
1994	time_last=(time(last_i1,last_j1)+time(last_i2,last_j2))/2;
1995	else%read the time in the nc files
1996	RootPath=get(handles.RootPath,'String');
1997	RootFile=get(handles.RootFile,'String');
1998	SubDir=get(handles.SubDir,'String');
1999	%VelType=get(handles.VelType,'String');
2000	VelType_str=get(handles.VelTypeMenu,'String');
2001	VelType_val=get(handles.VelTypeMenu,'Value');
2002	VelType=VelType_str{VelType_val};
2003	filebase=fullfile(RootPath{1},RootFile{1});
2004	[filefirst]=name_generator(filebase,first_i1,first_j1,'.nc',NomType{iview},1,first_i2,first_j2,SubDir{iview});
2005	if exist(filefirst,'file')
2006	Attrib=nc2struct(filefirst,[]);
2007	if isfield(Attrib,'Time')
2008	time_first=Attrib.Time;
2009	else
2010	if isfield(Attrib,'absolut_time_T0')
2011	time_first=Attrib.absolut_time_T0;
2012	end
2013	if isfield(Attrib,'absolut_time_T0_2')&&~(isequal(VelType,'civ1')\|\|isequal(VelType,'interp1')\|\|isequal(VelType,'filter1'))
2014	time_first=Attrib.absolut_time_T0_2;
2015	end
2016	end
2017	end
2018	[filelast]=name_generator(filebase,last_i1,last_j1,'.nc',NomType{iview},1,last_i2,last_j2,SubDir{iview});
2019	if exist(filelast,'file')
2020	Attrib=nc2struct(filelast,[]);
2021	if isfield(Attrib,'Time')
2022	time_last=Attrib.Time;
2023	else
2024	if isfield(Attrib,'absolut_time_T0')
2025	time_last=Attrib.absolut_time_T0;
2026	end
2027	if isfield(Attrib,'absolut_time_T0_2')&&~(isequal(VelType,'civ1')\|\|isequal(VelType,'interp1')\|\|isequal(VelType,'filter1'))
2028	time_last=Attrib.absolut_time_T0_2;
2029	end
2030	end
2031	end
2032	end
2033	end
2034	else
2035	siz=size(times);
2036	if siz(1)>=last_i && siz(2)>=last_j && first_i>=1 && first_j>=1
2037	time_first=times(first_i,first_j);
2038	time_last=times(last_i,last_j);
2039	end
2040	end
2041	time_first_cell{iview}=num2str(time_first,4);
2042	time_last_cell{iview}=num2str(time_last,4);
2043	end
2044	set(handles.time_first,'Value',1)
2045	set(handles.time_last,'Value',1)
2046	set(handles.time_first,'String',time_first_cell);
2047	set(handles.time_last,'String',time_last_cell);
2048
2049	%------------------------------------------------------------------------
2050	% --- Executes on button press in GetObject.
2051	function GetObject_Callback(hObject, eventdata, handles)
2052	%------------------------------------------------------------------------
2053	hseries=get(handles.GetObject,'parent');
2054	SeriesData=get(hseries,'UserData');
2055	value=get(handles.GetObject,'Value');
2056	if value
2057	set(handles.GetObject,'BackgroundColor',[1 1 0])%put unactivated buttons to yellow
2058	% DataInit.ParentButton=handles.GetObject;
2059	hset_object=findobj(allchild(0),'tag','set_object');%find the set_object interface handle
2060	if ishandle(hset_object)
2061	uistack(hset_object,'top')
2062	%[SeriesData.hset_object,SeriesData.sethandles]=set_object(DataInit); %open the set_object interface
2063	else
2064	%get the object file
2065	defaultname=get(handles.RootPath,'String');
2066	if isempty(defaultname)
2067	defaultname={''};
2068	end
2069	[FileName, PathName, filterindex] = uigetfile( ...
2070	{'.xml;.mat', ' (.xml,.mat)';
2071	'*.xml', '.xml files '; ...
2072	'*.mat', '.mat matlab files '}, ...
2073	'Pick an xml object file (or use uvmat to create it)',defaultname{1});
2074	fileinput=[PathName FileName];%complete file name
2075	testblank=findstr(fileinput,' ');%look for blanks
2076	if ~isempty(testblank)
2077	msgbox_uvmat('ERROR','forbidden input file name: contain blanks')
2078	return
2079	end
2080	sizf=size(fileinput);
2081	if (~ischar(fileinput)\|\|~isequal(sizf(1),1)),return;end
2082	%read the file
2083	t=xmltree(fileinput);
2084	data=convert(t);
2085	if ~isfield(data,'Style')
2086	data.Style='points';
2087	end
2088	if ~isfield(data,'ProjMode')
2089	data.ProjMode='projection';
2090	end
2091	transform_menu=get(handles.transform_fct,'String');
2092	ichoice=get(handles.transform_fct,'Value');
2093	% if isequal(transform_menu{ichoice},'px');
2094	% data.CoordType='px';
2095	% else
2096	% data.CoordType='phys';
2097	% end
2098	data.desable_plot=1;
2099	[SeriesData.hset_object,SeriesData.sethandles]=set_object(data);% call the set_object interface
2100	end
2101	else
2102	set(handles.GetObject,'BackgroundColor',[0.7 0.7 0.7])%put activated buttons to green
2103	% if isfield(SeriesData,'hset_object')&& ishandle(SeriesData.hset_object)
2104	% close(SeriesData.hset_object)
2105	% end
2106	end
2107	set(hseries,'UserData',SeriesData)
2108
2109	%--------------------------------------------------------------
2110	function GetMask_Callback(hObject, eventdata, handles)
2111	value=get(handles.GetMask,'Value');
2112	if value
2113	msgbox_uvmat('ERROR','not implemented yet')
2114	end
2115	%--------------------------------------------------------------
2116
2117	%-------------------------------------------------------------------
2118	%'uv_ncbrowser': interactively calls the netcdf file browser 'get_field.m'
2119	function ncbrowser_uvmat(hObject, eventdata)
2120	%-------------------------------------------------------------------
2121	bla=get(gcbo,'String');
2122	ind=get(gcbo,'Value');
2123	filename=cell2mat(bla(ind));
2124	blank=find(filename==' ');
2125	filename=filename(1:blank-1);
2126	get_field(filename)
2127
2128	% ------------------------------------------------------------------
2129	function MenuHelp_Callback(hObject, eventdata, handles)
2130	%-------------------------------------------------------------------
2131	path_to_uvmat=which ('uvmat');% check the path of uvmat
2132	pathelp=fileparts(path_to_uvmat);
2133	helpfile=fullfile(pathelp,'uvmat_doc','uvmat_doc.html');
2134	if isempty(dir(helpfile)), msgbox_uvmat('ERROR','Please put the help file uvmat_doc.html in the sub-directory /uvmat_doc of the UVMAT package')
2135	else
2136	addpath (fullfile(pathelp,'uvmat_doc'))
2137	web([helpfile '#series'])
2138	end
2139
2140	%-------------------------------------------------------------------
2141	% --- Executes on selection change in transform_fct.
2142	function transform_fct_Callback(hObject, eventdata, handles)
2143	%-------------------------------------------------------------------
2144	global nb_transform
2145
2146	% huvmat=get(handles.transform_fct,'parent');
2147	menu=get(handles.transform_fct,'String');
2148	ind_coord=get(handles.transform_fct,'Value');
2149	coord_option=menu{ind_coord};
2150	list_transform=get(handles.transform_fct,'UserData');
2151	ff=functions(list_transform{end});
2152	if isequal(coord_option,'more...');
2153	coord_fct='';
2154	prompt = {'Enter the name of the transform function'};
2155	dlg_title = 'user defined transform';
2156	num_lines= 1;
2157	[FileName, PathName, filterindex] = uigetfile( ...
2158	{'.m', ' (.m)';
2159	'*.m', '.m files '; ...
2160	'.', 'All Files (.)'}, ...
2161	'Pick a file', ff.file);
2162	if isequal(PathName(end),'/')\|\|isequal(PathName(end),'\')
2163	PathName(end)=[];
2164	end
2165	transform_selected =fullfile(PathName,FileName);
2166	if ~exist(transform_selected,'file')
2167	return
2168	end
2169	[ppp,transform,xt_fct]=fileparts(FileName);% removes extension .m
2170	if ~isequal(ext_fct,'.m')
2171	msgbox_uvmat('ERROR','a Matlab function .m must be introduced');
2172	return
2173	end
2174	menu=update_menu(handles.transform_fct,transform);%add the selected fct to the menu
2175	ind_coord=get(handles.transform_fct,'Value');
2176	addpath(PathName)
2177	list_transform{ind_coord}=str2func(transform);% create the function handle corresponding to the newly seleced function
2178	set(handles.transform_fct,'UserData',list_transform)
2179	rmpath(PathName)
2180	% save the new menu in the personal file 'uvmat_perso.mat'
2181	dir_perso=prefdir;%personal Matalb directory
2182	profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
2183	if exist(profil_perso,'file')
2184	for ilist=nb_transform+1:numel(list_transform)
2185	ff=functions(list_transform{ilist});
2186	transform_fct{ilist-nb_transform}=ff.file;
2187	end
2188	save (profil_perso,'transform_fct','-append'); %store the root name for future opening of uvmat
2189	end
2190	end
2191
2192	%check the current path to the selected function
2193	func=functions(list_transform{ind_coord});
2194	set(handles.path_transform,'String',fileparts(func.file)); %show the path to the senlected function
2195
2196	%------------------------------------------------------------------------
2197	% --- generates a series of file names with reference numbers between range1 and
2198	% --- range2 with increment incr. The reference number num_ref is the image number at the middle of the
2199	% --- image pair. The set of first numbers num1 of the image pairs is also
2200	% --- given as output
2201	function [num_i1,num_i2,num_j1,num_j2,nbmissing]=netseries_generator(filebase,subdir,mode,first_i,incr_i,last_i,first_j,incr_j,last_j)
2202	%------------------------------------------------------------------------
2203	[Path,Name]=fileparts(filebase);
2204	filebasesub=fullfile(Path,subdir,Name);
2205	filecell={};%default
2206	num_i1=[];
2207	num_i2=[];
2208	num_j1=[];
2209	num_j2=[];
2210	ind0_i=first_i:incr_i:last_i;
2211	nbcolumn=length(ind0_i);
2212	ind0_j=first_j:incr_j:last_j;
2213	nbline=length(ind0_j);
2214	if isequal(mode,'#_ab')
2215	dirpair=dir([filebasesub '_.nc']);
2216	elseif isequal(mode,'bursts')\|\|isequal(mode,'series(Dj)')
2217	dirpair=dir([filebasesub '__-*.nc']);
2218	elseif isequal(mode,'series(Di)')
2219	dirpair=dir([filebasesub '_-_*.nc']);
2220	else
2221	msgbox_uvmat('ERROR','option \| not yet implemented')
2222	return
2223	end
2224	if isempty(dirpair)
2225	msgbox_uvmat('ERROR','no pair detected in the selected range')
2226	return
2227	end
2228
2229	if isequal(mode,'bursts')\|\|isequal(mode,'#_ab')
2230	icount=0;
2231	for ifile=1:length(dirpair)
2232	[RootPath,RootFile,str_1,str_2,str_a,str_b,ext,nom_type]=name2display(dirpair(ifile).name);
2233	num1_r=str2num(str_1);
2234	if isequal(RootFile,Name) & ~isempty(num1_r)
2235	num_i1(ifile)=num1_r;
2236	num_a(ifile)=stra2num(str_a);
2237	num_b(ifile)=stra2num(str_b);
2238	end
2239	end
2240	test_range= (num_i1 >=first_i)&(num_i1<= last_i);% =1 when both numbers are in the range
2241	ind_i=((num_i1-first_i)/incr_i)+1;%indices i in the list of prescribed file indices
2242	select=find(test_range &(floor(ind_i)==ind_i));%selected indices of num_i1 in the file directory
2243	ind_i=ind_i(select);%set of selected indices ind_i
2244	[ind_i,indsort]=sort(ind_i);%sorted list of ind_i
2245	select=select(indsort);
2246	num_i1=num_i1(select);
2247	num_a=num_a(select);
2248	num_b=num_b(select);
2249	dirpair=dirpair(select);
2250	[ind_remove]=find_pairs(dirpair,ind_i,nbcolumn);
2251	ind_i(ind_remove)=[];
2252	num_a(ind_remove)=[];
2253	num_b(ind_remove)=[];
2254	num_j1=zeros(1,nbcolumn);%default
2255	num_j2=num_j1;
2256	num_j1(ind_i)=num_a;
2257	num_j2(ind_i)=num_b;
2258	num_i1=first_i:incr_i:last_i;
2259	num_i2=num_i1;
2260	nbmissing=nbcolumn-length(ind_i);
2261
2262	elseif isequal(mode,'series(Di)')
2263	%ind0_i=first_i:incr_i:last_i;
2264	%nbcolumn=length(ind0_i);
2265	%ind0_j=first_j:incr_j:last_j;
2266	%nbline=length(ind0_j);
2267	%dirpair=dir([filebasesub '_-_*.nc']);
2268	for ifile=1:length(dirpair)
2269	[RootPath,RootFile,str_1,str_2,str_a,str_b,ext,nom_type]=name2display(dirpair(ifile).name);
2270	num_i1_r(ifile)=str2num(str_1);
2271	num_i2_r(ifile)=str2num(str_2);
2272	num_j(ifile)=str2num(str_a);
2273	end
2274	num_i=floor((num_i1_r+num_i2_r)/2); %list of reference indices of the detected files
2275	test_range= (num_i >=first_i)&(num_i<= last_i)&(num_j >=first_j)&(num_j<= last_j);% =1 when both numbers are in the range
2276	ind_i=((num_i-first_i)/incr_i)+1;%indices i and j in the list of prescribed file indices
2277	ind_j=((num_j-first_j)/incr_j)+1;
2278	ind_ij=ind_j+nbline*(ind_i-1);%indices in the reshhaped series of prescribed file indices
2279	select=find(test_range &(floor(ind_i)==ind_i)&(floor(ind_j)==ind_j));%selected indices in the file directory
2280	ind_ij=ind_ij(select);%set of selected indices ind_ij
2281	[ind_ij,indsort]=sort(ind_ij);%sorted list of ind_ij
2282	select=select(indsort);
2283	num_i1_r=num_i1_r(select);
2284	num_i2_r=num_i2_r(select);
2285	dirpair=dirpair(select);
2286	[ind_remove]=find_pairs(dirpair,ind_ij,nbcolumn*nbline) ;
2287	ind_ij(ind_remove)=[];
2288	num_i1_r(ind_remove)=[];
2289	num_i2_r(ind_remove)=[];
2290	num_i1=zeros(1,nbline*nbcolumn);%default
2291	num_i2=num_i1;
2292	num_i1(ind_ij)=num_i1_r;
2293	num_j2(ind_ij)=num_i2_r;
2294	num_i1=reshape(num_i1,nbline,nbcolumn);
2295	num_i2=reshape(num_i2,nbline,nbcolumn);
2296	num_j1=meshgrid(ind0_i,ind0_j);
2297	num_j2=num_j1;
2298	nbmissing=nbline*nbcolumn-length(ind_ij);
2299	elseif isequal(mode,'series(Dj)')
2300	for ifile=1:length(dirpair)
2301	[RootPath,RootFile,str_1,str_2,str_a,str_b,ext,nom_type]=name2display(dirpair(ifile).name);
2302	num_i(ifile)=str2num(str_1);
2303	num_a(ifile)=str2num(str_a);
2304	num_b(ifile)=str2num(str_b);
2305	end
2306	num_j=floor((num_a+num_b)/2); %list of reference indices of the detected files
2307	test_range= (num_i >=first_i)&(num_i<= last_i)&(num_j >=first_j)&(num_j<= last_j);% =1 when both numbers are in the range
2308	ind_i=((num_i-first_i)/incr_i)+1;%indices i and j in the list of prescribed file indices
2309	ind_j=((num_j-first_j)/incr_j)+1;
2310	ind_ij=ind_j+nbline*(ind_i-1);%indices in the reshhaped series of prescribed file indices
2311	select=find(test_range &(floor(ind_i)==ind_i)&(floor(ind_j)==ind_j));%selected indices in the file directory
2312	ind_ij=ind_ij(select);%set of selected indices ind_ij
2313	[ind_ij,indsort]=sort(ind_ij);%sorted list of ind_ij
2314	select=select(indsort);
2315	num_i=num_i(select);
2316	num_a=num_a(select);
2317	num_b=num_b(select);
2318	dirpair=dirpair(select);
2319	[ind_remove]=find_pairs(dirpair,ind_ij,nbcolumn*nbline) ;
2320	ind_ij(ind_remove)=[];
2321	num_a(ind_remove)=[];
2322	num_b(ind_remove)=[];
2323	num_j1=zeros(1,nbline*nbcolumn);%default
2324	num_j2=num_j1;
2325	num_j1(ind_ij)=num_a;
2326	num_j2(ind_ij)=num_b;
2327	num_j1=reshape(num_j1,nbline,nbcolumn);
2328	num_j2=reshape(num_j2,nbline,nbcolumn);
2329	num_i1=meshgrid(ind0_i,ind0_j);
2330	num_i2=num_i1;
2331	nbmissing=nbline*nbcolumn-length(ind_ij);
2332	end
2333
2334	%------------------------------------------------------------------------
2335	% --- generates series of file indices corresponding to a file fileinput
2336	function [num_i1,num_i2,num_j1,num_j2]=find_indexseries(fileinput)
2337	%------------------------------------------------------------------------
2338	num_i1=NaN;%default
2339	num_i2=NaN;%default
2340	num_j1=NaN;%default
2341	num_j2=NaN;%default
2342	% refresh input root name, indices, file extension and nomenclature
2343	[RootPath,RootFile,field_count,str2,str_a,str_b,FileExt,NomType,SubDir]=name2display(fileinput);
2344	if strcmp(SubDir,'')
2345	filebasesub=fullfile(RootPath,RootFile);
2346	else
2347	filebasesub=fullfile(RootPath,SubDir,RootFile);
2348	end
2349	dirpair=[]; %default
2350	switch NomType
2351	case '_1'
2352	dirpair=dir([filebasesub '_*' FileExt]);
2353	case '_1_1'
2354	dirpair=dir([filebasesub '__' FileExt]);
2355	case '_i1-i2'
2356	dirpair=dir([filebasesub '_-' FileExt]);
2357	case '1_ab'
2358	dirpair=dir([filebasesub '_' FileExt]);
2359	case '_i_j1-j2'
2360	dirpair=dir([filebasesub '_-*' FileExt]);
2361	case '_i1-i2_j'
2362	dirpair=dir([filebasesub '-_*' FileExt]);
2363	end
2364	for ifile=1:length(dirpair)
2365	[RootPath,RF,str_1,str_2,str_a,str_b]=name2display(dirpair(ifile).name);
2366	num_i1(ifile)=str2double(str_1);
2367	num_i2(ifile)=str2double(str_2);
2368	if isnan(num_i2(ifile))
2369	num_i2(ifile)=num_i1(ifile);
2370	end
2371	num_j1(ifile)=stra2num(str_a);
2372	if isnan(num_j1(ifile))
2373	num_j1(ifile)=1;
2374	end
2375	num_j2(ifile)=stra2num(str_b);
2376	if isnan(num_j2(ifile))
2377	num_j2(ifile)=num_j1(ifile);
2378	end
2379	end
2380

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