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source: trunk/src/series.m @ 363

Last change on this file since 363 was 360, checked in by sommeria, 13 years ago
civ: bugs corrected. Iintroduction of an xm file for parameters read using the new fct fill_GUI (to test and improve) cleaning in uvmat. Possibility of using blank increment added (go to the next available file) fullfile_uvmat: case of two equal indices in a pair, bug repair. find_fileseries: improved speed.
File size: 97.6 KB

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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,'WindowButtonDownFcn',{'mouse_down'})%allows mouse action with right button (zoom for uicontrol display)
68	%set(hObject,'Position',[150 100 1000 600] );%position and size in pixels (get adjusted to the screen size in case of excess)
69	%load the list of previously browsed files in menus Open and Open_1
70	dir_perso=prefdir;
71	test_profil_perso=0;
72	profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
73	if exist(profil_perso,'file')
74	h=load (profil_perso);
75	test_profil_perso=1;
76	if isfield(h,'MenuFile_1')
77	set(handles.MenuFile_1,'Label',h.MenuFile_1);
78	set(handles.MenuFile_insert_1,'Label',h.MenuFile_1);
79	end
80	if isfield(h,'MenuFile_1')
81	set(handles.MenuFile_2,'Label',h.MenuFile_2);
82	set(handles.MenuFile_insert_2,'Label',h.MenuFile_2);
83	end
84	if isfield(h,'MenuFile_1')
85	set(handles.MenuFile_3,'Label',h.MenuFile_3);
86	set(handles.MenuFile_insert_3,'Label',h.MenuFile_3);
87	end
88	if isfield(h,'MenuFile_1')
89	set(handles.MenuFile_4,'Label',h.MenuFile_4);
90	set(handles.MenuFile_insert_4,'Label',h.MenuFile_4);
91	end
92	if isfield(h,'MenuFile_1')
93	set(handles.MenuFile_5,'Label',h.MenuFile_5);
94	set(handles.MenuFile_insert_5,'Label',h.MenuFile_5);
95	end
96	end
97
98	%check default input data
99	if ~exist('param','var')
100	param=[]; %default
101	end
102
103	%file name and browser initialisation
104	if isfield(param,'menu_coord_str')
105	set(handles.transform_fct,'String',param.menu_coord_str)
106	end
107	if isfield(param,'menu_coord_val')
108	set(handles.transform_fct,'Value',param.menu_coord_val);
109	else
110	set(handles.transform_fct,'Value',1);%default
111	end
112
113	if isfield(param,'FileName')
114	if isfield(param,'FileName_1')
115	update_rootfile(handles,param.FileName_1,0)
116	update_rootfile(handles,param.FileName,1)
117	else
118	update_rootfile(handles,param.FileName,0)
119	end
120	end
121
122	%fields input initialisation
123	if isfield(param,'list_fields')&& isfield(param,'index_fields') &&~isempty(param.list_fields) &&~isempty(param.index_fields)
124	set(handles.FieldMenu,'String',param.list_fields);% list menu fields
125	set(handles.FieldMenu,'Value',param.index_fields);% selected string index
126	FieldCell{1}=param.list_fields{param.index_fields};
127	end
128	% NomType_Callback(hObject, eventdata, handles)
129	REFRESH_INDICES_Callback(hObject, eventdata, handles)
130	%loads the information stored in prefdir to initiate the list of ACTION functions
131	fct_menu={'check_data_files';'aver_stat';'time_series';'merge_proj';'clean_civ_cmx'};
132	transform_menu={'';'phys';'px';'phys_polar'};
133	nb_builtin_ACTION=numel(fct_menu); %number of functions
134	nb_transform=numel(transform_menu);
135	[path_series,name,ext]=fileparts(which('series'));
136	path_series=fullfile(path_series,'series');%path of the function 'series'
137	addpath (path_series) ; %add the path to UVMAT, (useful in case of change of working directory after civ has been s opened in the working directory)
138	path_transform=fullfile(path_series,'transform_field');%path to the field transform functions
139	for ilist=1:length(fct_menu)
140	fct_path{ilist,1}=path_series;%paths of the fuctions buil-in in 'series.m'
141	end
142
143	%TRANSFORM menu: loads the information stored in prefdir to initiate the list of field transform functions
144	menu_str={'';'phys';'px';'phys_polar'};
145	nb_builtin_transform=numel(menu_str); %number of functions
146	[path_uvmat,name,ext]=fileparts(which('uvmat'));
147	addpath(fullfile(path_uvmat,'transform_field'))
148	fct_handle{1,1}=[];
149	testexist(1)=1;
150	for ilist=2:length(menu_str)
151	if exist(menu_str{ilist},'file')
152	fct_handle{ilist,1}=str2func(menu_str{ilist});
153	testexist(ilist)=1;
154	else
155	testexist(ilist)=0;
156	end
157	end
158	rmpath(fullfile(path_uvmat,'transform_field'))
159
160	% read the list of functions stored in the personal file 'uvmat_perso.mat' in prefdir
161	if test_profil_perso
162	if isfield(h,'series_fct') && iscell(h.series_fct)
163	for ilist=1:length(h.series_fct)
164	[path,file]=fileparts(h.series_fct{ilist});
165	fct_path=[fct_path; {path}];%concatene the list of paths
166	fct_menu=[fct_menu; {file}];
167	end
168	end
169	if isfield(h,'transform_fct') && iscell(h.transform_fct)
170	for ilist=1:length(h.transform_fct);
171	[path,file]=fileparts(h.transform_fct{ilist});
172	addpath(path)
173	if exist(file,'file')
174	h_func=str2func(file);
175	testexist=[testexist 1];
176	else
177	h_func=[];
178	testexist=[testexist 0];
179	end
180	fct_handle=[fct_handle; {h_func}];%concatene the list of paths
181	rmpath(path)
182	menu_str=[menu_str; {file}];
183	end
184	end
185	end
186	fct_menu=[fct_menu;{'more...'}];
187	set(handles.ACTION,'String',fct_menu)
188	set(handles.ACTION,'UserData',fct_path)% store the list of path in UserData of ACTION
189
190	menu_str=menu_str(find(testexist));
191	fct_handle=fct_handle(find(testexist));
192	menu_str=[menu_str;{'more...'}];
193	set(handles.transform_fct,'String',menu_str)
194	set(handles.transform_fct,'UserData',fct_handle)% store the list of path in UserData of ACTION
195
196	% display the GUI for the default action 'check_data_files'
197	ACTION_Callback(hObject, eventdata, handles)
198
199	%--------------------------------------------------------------
200	% --- Outputs from this function are returned to the command line.
201	%-----------------------------------------------------------------
202	function varargout = series_OutputFcn(hObject, eventdata, handles)
203	% varargout cell array for returning output args (see VARARGOUT);
204	% hObject handle to figure
205	% eventdata reserved - to be defined in a future version of MATLAB
206	% handles structure with handles and user data (see GUIDATA)
207	% Get default command line output from handles structure
208	varargout{1} = handles.output;
209
210
211	% --------------------------------------------------------------------
212	function MenuBrowse_Callback(hObject, eventdata, handles)
213	InputTable=get(handles.InputTable,'Data');
214	RootPathCell=InputTable(:,1);
215	SubDirCell=InputTable(:,2);
216	RootFileCell=InputTable(:,3);
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_rootfile(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_rootfile(handles,fileinput,0)
299
300	% --------------------------------------------------------------------
301	function MenuFile_2_Callback(hObject, eventdata, handles)
302	fileinput=get(handles.MenuFile_2,'Label');
303	update_rootfile(handles,fileinput,0)
304
305	% --------------------------------------------------------------------
306	function MenuFile_3_Callback(hObject, eventdata, handles)
307	fileinput=get(handles.MenuFile_3,'Label');
308	update_rootfile( handles,fileinput,0)
309
310	% --------------------------------------------------------------------
311	function MenuFile_4_Callback(hObject, eventdata, handles)
312	fileinput=get(handles.MenuFile_4,'Label');
313	update_rootfile(handles,fileinput,0)
314
315	% --------------------------------------------------------------------
316	function MenuFile_5_Callback(hObject, eventdata, handles)
317	fileinput=get(handles.MenuFile_5,'Label');
318	update_rootfile(handles,fileinput,0)
319
320	% --------------------------------------------------------------------
321	function MenuBrowse_insert_Callback(hObject, eventdata, handles)
322	InputTable=get(handles.InputTable,'Data');
323	RootPathCell=InputTable(:,1);
324	SubDirCell=InputTable(:,3);
325	RootFileCell=InputTable(:,2);
326	% RootPathCell=get(handles.RootPath,'String');
327	% RootFileCell=get(handles.RootFile,'String');
328	oldfile=''; %default
329	if isempty(RootPathCell)\|\|isequal(RootPathCell,{''})%loads the previously stored file name and set it as default in the file_input box
330	dir_perso=prefdir;
331	profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
332	if exist(profil_perso,'file')
333	h=load (profil_perso);
334	if isfield(h,'filebase')&ischar(h.filebase)
335	oldfile=h.filebase;
336	end
337	if isfield(h,'RootPath')&ischar(h.RootPath)
338	oldfile=h.RootPath;
339	end
340	end
341	else
342	oldfile=fullfile(RootPathCell{1},RootFileCell{1});
343	end
344	[FileName, PathName, filterindex] = uigetfile( ...
345	{'.xml;.xls;.png;.avi;.AVI;.nc', ' (.xml,.xls, .png, .avi,*.nc)';
346	'*.xml', '.xml files '; ...
347	'*.xls', '.xls files '; ...
348	'*.png','.png image files'; ...
349	'.avi;.AVI','.avi movie files'; ...
350	'*.nc','.netcdf files'; ...
351	'.', 'All Files (.)'}, ...
352	'Pick a file',oldfile);
353	fileinput=[PathName FileName];%complete file name
354	% testblank=findstr(fileinput,' ');%look for blanks
355	% if ~isempty(testblank)
356	% errordlg('forbidden input file name: contain blanks')
357	% return
358	% end
359	sizf=size(fileinput);
360	if (~ischar(fileinput)\|~isequal(sizf(1),1)),return;end
361	[path,name,ext]=fileparts(fileinput);
362	SeriesData=[];%dfault
363	if isequal(ext,'.xml')
364	msgbox_uvmat('ERROR','input file type not implemented')%A Faire: ouvrir le fichier pour naviguer
365	elseif isequal(ext,'.xls')
366	msgbox_uvmat('ERROR','input file type not implemented')%A Faire: ouvrir le fichier pour naviguer
367	else
368	update_rootfile(handles,fileinput,1)
369	%update list of recent files in the menubar
370	MenuFile_1=fileinput;
371	MenuFile_2=get(handles.MenuFile_1,'Label');
372	MenuFile_3=get(handles.MenuFile_2,'Label');
373	MenuFile_4=get(handles.MenuFile_3,'Label');
374	MenuFile_5=get(handles.MenuFile_4,'Label');
375	set(handles.MenuFile_1,'Label',MenuFile_1)
376	set(handles.MenuFile_2,'Label',MenuFile_2)
377	set(handles.MenuFile_3,'Label',MenuFile_3)
378	set(handles.MenuFile_4,'Label',MenuFile_4)
379	set(handles.MenuFile_5,'Label',MenuFile_5)
380	set(handles.MenuFile_insert_1,'Label',MenuFile_1)
381	set(handles.MenuFile_insert_2,'Label',MenuFile_2)
382	set(handles.MenuFile_insert_3,'Label',MenuFile_3)
383	set(handles.MenuFile_insert_4,'Label',MenuFile_4)
384	set(handles.MenuFile_insert_5,'Label',MenuFile_5)
385	dir_perso=prefdir;
386	profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
387	if exist(profil_perso,'file')
388	save (profil_perso,'MenuFile_1','MenuFile_2','MenuFile_3','MenuFile_4', 'MenuFile_5','-append'); %store the file names for future opening of uvmat
389	else
390	txt=ver('MATLAB');
391	Release=txt.Release;
392	relnumb=str2num(Release(3:4));
393	if relnumb >= 14
394	save (profil_perso,'MenuFile_1','MenuFile_2','MenuFile_3','MenuFile_4', 'MenuFile_5','-V6'); %store the file names for future opening of uvmat
395	else
396	save (profil_perso,'MenuFile_1','MenuFile_2','MenuFile_3','MenuFile_4', 'MenuFile_5'); %store the file names for future opening of uvmat
397	end
398	end
399	end
400	%------------------------------------------------
401
402	% --------------------------------------------------------------------
403	function MenuFile_insert_1_Callback(hObject, eventdata, handles)
404	fileinput=get(handles.MenuFile_insert_1,'Label');
405	update_rootfile(handles,fileinput,1)
406
407	% --------------------------------------------------------------------
408	function MenuFile_insert_2_Callback(hObject, eventdata, handles)
409	fileinput=get(handles.MenuFile_insert_2,'Label');
410	update_rootfile(handles,fileinput,1)
411
412	% --------------------------------------------------------------------
413	function MenuFile_insert_3_Callback(hObject, eventdata, handles)
414	fileinput=get(handles.MenuFile_insert_3,'Label');
415	update_rootfile( handles,fileinput,1)
416
417	% --------------------------------------------------------------------
418	function MenuFile_insert_4_Callback(hObject, eventdata, handles)
419	fileinput=get(handles.MenuFile_insert_4,'Label');
420	update_rootfile( handles,fileinput,1)
421
422	% --------------------------------------------------------------------
423	function MenuFile_insert_5_Callback(hObject, eventdata, handles)
424	fileinput=get(handles.MenuFile_insert_5,'Label');
425	update_rootfile(handles,fileinput,1)
426
427	%------------------------------------------------------------------------
428	% --- refresh the GUI data after introduction of a new file series
429	% INPUT:
430	% handles:
431	% fileinput: name of the input file
432	% addtest: =0 to refresh the list of file series, =1 to append a new series to the list (from the menu bar option 'Open_insert')
433	function update_rootfile(handles,fileinput,addtest)
434	%------------------------------------------------------------------------
435
436	%% enable other menus and uicontrols
437	set(handles.MenuOpen_insert,'Enable','on')
438	set(handles.MenuFile_insert_1,'Enable','on')
439	set(handles.MenuFile_insert_2,'Enable','on')
440	set(handles.MenuFile_insert_3,'Enable','on')
441	set(handles.MenuFile_insert_4,'Enable','on')
442	set(handles.MenuFile_insert_5,'Enable','on')
443	set(handles.RUN, 'Enable','On')
444	set(handles.RUN,'BackgroundColor',[1 0 0])% set RUN button to red
445	% set(handles.RootPath,'BackgroundColor',[1 1 0]) % set RootPath edit box to yellow
446	set(handles.InputTable,'BackgroundColor',[1 1 0]) % set RootPath edit box to yellow
447	drawnow
448
449	%% get the input root name, indices, file extension and nomenclature NomType
450	if ~exist(fileinput,'file')
451	msgbox_uvmat('ERROR',['input file ' fileinput ' does not exist'])
452	return
453	end
454	[RootPath,SubDir,RootFile,i1,i2,j1,j2,FileExt,NomType]=fileparts_uvmat(fileinput);
455
456	%% determine reference field indices
457	ref_i=1; %default ref_i is a reference frame index used to find existing pairs from PIV
458	if ~isempty(i1)
459	ref_i=i1;
460	if ~isempty(i2)
461	ref_i=floor((ref_i+i2)/2);% reference image number corresponding to the file
462	% SeriesData.browse_Di=i2-i1;
463	end
464	end
465	set(handles.ref_i,'String',num2str(ref_i));
466	set(handles.num_first_i,'String',num2str(ref_i));
467	set(handles.num_last_i,'String',num2str(ref_i));
468	ref_j=1; %default ref_j is a reference frame index used to find existing pairs from PIV
469	if ~isempty(j1)
470	ref_j=j1;
471	if ~isempty(j2)
472	ref_j=floor((j1+j2)/2);
473	% SeriesData.browse_Dj=j2-j1;
474	end
475	end
476	set(handles.ref_j,'String',num2str(ref_j));
477	set(handles.num_first_j,'String',num2str(ref_j))
478	set(handles.num_last_j,'String',num2str(ref_j));
479	TimeUnit=''; %default
480	time=[];%default
481
482	% read timing and total frame number from the current file (movie files) !! may be overrid by xml file
483	FileBase=fullfile(RootPath,RootFile);
484
485	testima=0; %test for image input
486	if isequal(lower(FileExt),'.avi') %.avi file
487	testima=1;
488	elseif ~isempty(imformats(FileExt(2:end)))
489	testima=1;
490	elseif isequal(FileExt,'.vol')
491	testima=1;
492	end
493
494	%% fill the list of file series
495
496	% insert the current file series at the head of the list
497	InputTable=get(handles.InputTable,'Data');
498	if addtest %insert the new data at the first line of the table
499	val=size(InputTable,1)+1;
500	InputTable(val,:)=[{RootPath},{SubDir},{RootFile},{NomType},{FileExt}];
501	check_lines=get(handles.REFRESH_INDICES,'UserData');
502	else % or re-initialise the list of input file series
503	val=1;
504	InputTable=[{RootPath},{SubDir},{RootFile},{NomType},{FileExt}]
505	set(handles.TimeTable,'Data',[{[]},{[]},{[]},{[]}])
506	set(handles.MinIndex,'Data',[{[]},{[]}])
507	set(handles.MaxIndex,'Data',[{[]},{[]}])
508	end
509	set(handles.InputTable,'Data',InputTable)
510	check_lines(val)=1; %select the edited line for refresh
511	set(handles.REFRESH_INDICES,'UserData',check_lines);
512	REFRESH_INDICES_Callback([],[], handles)
513
514	%store the root name for future opening of uvmat
515	dir_perso=prefdir;
516	profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
517	if exist(profil_perso,'file')
518	save (profil_perso,'RootPath','SubDir','RootFile','NomType', '-append'); %store the root name for future opening of uvmat
519	else
520	txt=ver('MATLAB');
521	Release=txt.Release;
522	relnumb=str2num(Release(3:4));
523	if relnumb >= 14
524	save (profil_perso,'RootPath','SubDir','RootFile','NomType','-V6') %store the root name for future opening of uvmat
525	else
526	save(profil_perso,'RootPath','SubDir','RootFile','NomType')
527	end
528	end
529	set(handles.InputTable,'BackgroundColor',[1 1 1])
530	% set(handles.PathCampaign,'String',SeriesData.PathCampaign)
531	%num_last_j_Callback([], [], handles)% TODO:update
532	%num_last_i_Callback([], [], handles)
533
534	% %------------------------------------------------------------------------
535	% function RootPath_Callback(hObject, eventdata, handles)
536	% %------------------------------------------------------------------------
537	% Val=get(handles.RootPath,'Value');
538	% synchronise_view(handles,Val)
539	% NomType_Callback(hObject, eventdata, handles)
540
541	% %------------------------------------------------------------------------
542	% function synchronise_view(handles,Val)
543	% %------------------------------------------------------------------------
544	% set(handles.RootPath,'Value',Val)
545	% set(handles.SubDir,'Value',Val)
546	% set(handles.RootFile,'Value',Val)
547	% set(handles.NomType,'Value',Val)
548	% set(handles.FileExt,'Value',Val)
549	% set(handles.num_MaxIndex_i,'Value',Val)
550	% set(handles.num_MaxIndex_j,'Value',Val)
551	% % set(handles.time_first,'Value',Val)
552	% % set(handles.time_last,'Value',Val)
553
554
555	% %------------------------------------------------------------------------
556	% % Executes on carriage return on the subdir civ1 edit window
557	% function SubDir_Callback(hObject, eventdata, handles)
558	% %------------------------------------------------------------------------
559	% Val=get(handles.SubDir,'Value');
560	% synchronise_view(handles,Val)
561	% NomType_Callback(hObject, eventdata, handles)
562
563	% %------------------------------------------------------------------------
564	% % --- function activated when a new filebase (image series) is introduced
565	% function RootFile_Callback(hObject, eventdata, handles)
566	% %------------------------------------------------------------------------
567	% Val=get(handles.RootFile,'Value');
568	% synchronise_view(handles,Val)
569	% NomType_Callback(hObject, eventdata, handles)
570
571	%--------------------------------------------------------------
572	% %function activated when a new filebase (image series) is introduced
573	% %------------------------------------------------------------
574	% function FileExt_Callback(hObject, eventdata, handles)
575	% Val=get(handles.FileExt,'Value');
576	% synchronise_view(handles,Val)
577
578	% %--------------------------------------------------------------
579	% %function activated when a new filebase (image series) is introduced
580	% %------------------------------------------------------------
581	% function num_MaxIndex_i_Callback(hObject, eventdata, handles)
582	% Val=get(handles.num_MaxIndex_i,'Value');
583	% synchronise_view(handles,Val)
584
585	% %--------------------------------------------------------------
586	% %function activated when a new filebase (image series) is introduced
587	% %------------------------------------------------------------
588	% function num_MaxIndex_j_Callback(hObject, eventdata, handles)
589	% Val=get(handles.num_MaxIndex_j,'Value');
590	% synchronise_view(handles,Val)
591	%
592	% %--------------------------------------------------------------
593	% %function activated when a new filebase (image series) is introduced
594	% %------------------------------------------------------------
595	% function time_first_Callback(hObject, eventdata, handles)
596	% Val=get(handles.time_first,'Value');
597	% synchronise_view(handles,Val)
598	%
599	% %--------------------------------------------------------------
600	% %function activated when a new filebase (image series) is introduced
601	% %------------------------------------------------------------
602	% function time_last_Callback(hObject, eventdata, handles)
603	% Val=get(handles.time_last,'Value');
604	% synchronise_view(handles,Val)
605	% NomType_Callback(hObject, eventdata, handles)
606
607	% %------------------------------------------------------------------------
608	% function NomType_Callback(hObject, eventdata, handles)
609	% %------------------------------------------------------------------------
610
611	% --- Executes when entered data in editable cell(s) in InputTable.
612	function InputTable_CellEditCallback(hObject, eventdata, handles)
613	% hObject handle to InputTable (see GCBO)
614	% eventdata structure with the following fields (see UITABLE)
615	% Indices: row and column indices of the cell(s) edited
616	% PreviousData: previous data for the cell(s) edited
617	% EditData: string(s) entered by the user
618	% NewData: EditData or its converted form set on the Data property. Empty if Data was not changed
619	% Error: error string when failed to convert EditData to appropriate value for Data
620	% handles structure with handles and user data (see GUIDATA)
621	eventdata
622	check_lines=get(handles.REFRESH_INDICES,'UserData');
623	check_lines(eventdata.Indices(1))=1; %select the edited line for refresh
624	set(handles.REFRESH_INDICES,'UserData',check_lines);
625	set(handles.REFRESH_INDICES,'Visible','on')
626
627
628	%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%????????????
629	% --- Executes on button press in mode.
630	%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
631	function mode_Callback(hObject, eventdata, handles)
632
633	SeriesData=get(handles.series,'UserData');
634	mode_list=get(handles.mode,'String');
635	mode_value=get(handles.mode,'Value');
636	mode=mode_list{mode_value};
637	% NomType=[];
638	% test_find_pair=0;
639	% if isfield(SeriesData,'NomType')
640	% NomTypeCell=SeriesData.NomType;
641	% Val=get(handles.NomType,'Value');
642	% NomType=NomTypeCell{Val};
643	% check_pairs=0;
644	% for
645	% check_pairs=~isempty(SeriesData.i2_series{Val})\|\|~isempty(SeriesData.j2_series{Val});
646
647	time=[];
648	if isfield(SeriesData,'Time')
649	time=SeriesData.Time{1}; %get the set of times
650	end
651	% siztime=size(time);
652	% nbfield=siztime(1);
653	% nbfield2=siztime(2);
654	% indchosen=1; %%first pair selected by default
655	if isequal(mode,'bursts')
656	enable_i(handles,'On')
657	enable_j(handles,'Off') %do not display j index scanning in burst mode (j is fixed by the burst choice)
658	% elseif ~isempty(SeriesData.j2_series{Val})
659	% enable_i(handles,'On')
660	% enable_j(handles,'On') % allow both i and j index scanning
661	else
662	enable_i(handles,'On')
663	enable_j(handles,'Off')
664	end
665	% set(handles.list_pair_civ,'Value',indchosen);%set the default choice of image pairs for civ1
666	% set(handles.series,'UserData',SeriesData)
667
668	%list pairs if relevant
669	% if check_pairs
670	find_netcpair_civ(handles)
671	% end
672
673	%-------------------------------------
674	function enable_i(handles,state)
675	set(handles.i_txt,'Visible',state)
676	set(handles.num_first_i,'Visible',state)
677	set(handles.num_last_i,'Visible',state)
678	set(handles.num_incr_i,'Visible',state)
679	% set(handles.num_MaxIndex_i,'Visible',state)
680	set(handles.ref_i,'Visible',state)
681	set(handles.ref_i_text,'Visible',state)
682
683	%-----------------------------------
684	function enable_j(handles,state)
685	set(handles.j_txt,'Visible',state)
686	% set(handles.num_MinIndex_j,'Visible',state)
687	set(handles.num_first_j,'Visible',state)
688	set(handles.num_last_j,'Visible',state)
689	set(handles.num_incr_j,'Visible',state)
690	% set(handles.num_MaxIndex_j,'Visible',state)
691	set(handles.ref_j,'Visible',state)
692	set(handles.ref_j_text,'Visible',state)
693
694	%-----------------------------------
695	function view_FieldMenu(handles,state)
696	% set(handles.FieldMenu,'Visible',state)
697	% set(handles.Field_text,'Visible',state)
698	set(handles.InputFields,'Visible',state)
699
700	%-----------------------------------
701	function view_FieldMenu_1(handles,state)
702	set(handles.FieldMenu_1,'Visible',state)
703	set(handles.Field_text_1,'Visible',state)
704
705	% %-----------------------------------
706	% function view_TRANSFORM(handles,state)
707	% set(handles.TRANSFORM_frame,'Visible',state)
708	% set(handles.transform_fct,'Visible',state);
709	% set(handles.TRANSFORM_title,'Visible',state)
710
711	%--------------------------------------------------------------
712	% determine the menu for civ1 pairs depending on existing netcdf files
713	% with the reference indices ref_i and ref_j
714	%----------------------------------------------------------------
715	function find_netcpair_civ(handles)
716	SeriesData=get(handles.series,'UserData');
717	% NomTypeCell=get(handles.NomType,'String');
718	% NomTypeCell=SeriesData.NomType;
719	% NomType=NomTypeCell{Val};
720
721	set(handles.Pairs,'Visible','on')% makes the panel "Pairs' visible
722	%nomenclature types
723	% RootPathCell=get(handles.RootPath,'String');
724	% filepath=RootPathCell{Val};
725	% RootFileCell=get(handles.RootFile,'String');
726	% filename=RootFileCell{Val};
727	% filebase=fullfile(filepath,filename);
728	% SubDirCell=get(handles.SubDir,'String');
729	% subdir=SubDirCell{Val};
730	% if ~exist(fullfile(filepath,subdir),'dir')
731	% msgbox_uvmat('ERROR',['no civ file available: subdirectory ' subdir ' does not exist'])
732	% set(handles.list_pair_civ,'String',{''});
733	% return
734	% end
735	mode_list=get(handles.mode,'String');
736	mode_value=get(handles.mode,'Value');
737	mode=mode_list{mode_value};
738
739	%reads image numbers from the interface
740	% ref_i=str2num(get(handles.ref_i,'String'));
741	% ref_j=str2num(get(handles.ref_j,'String'));
742	% ref_time=0;
743	% nbfield=50;
744	% nbfield2=50;%default max number of pairs
745
746	%look for existing processed pairs involving the field at the middle of the series if civ1 will not
747	% be performed, while the result is needed for next steps.
748
749	% ind_exist=0;
750	TimeUnit=get(handles.TimeUnit,'String');
751	if length(TimeUnit)>=1
752	dtunit=['m' TimeUnit];
753	else
754	dtunit='e-03';
755	end
756
757	%% NEW
758	for Val=1:numel(SeriesData.i1_series)
759
760	i1_series=SeriesData.i1_series{Val};
761	i2_series=SeriesData.i2_series{Val};
762	j1_series=SeriesData.j1_series{Val};
763	j2_series=SeriesData.j2_series{Val};
764	displ_pair={};
765	if strcmp(mode,'series(Di)')
766	if isempty(i2_series)
767	msgbox_uvmat('ERROR','no i1-i2 pair available')
768	return
769	end
770	diff_i=i2_series-i1_series;
771	min_diff=min(diff_i(diff_i>0));
772	max_diff=max(diff_i(diff_i>0));
773	for ipair=min_diff:max_diff
774	if numel(diff_i(diff_i==ipair))>0
775	displ_pair=[displ_pair;{['Di= ' num2str(-floor(ipair/2)) '\|' num2str(ceil(ipair/2)) ]}];
776	end
777	end
778	if ~isempty(displ_pair)
779	displ_pair=[displ_pair;{'Di=\|'}];
780	end
781	elseif strcmp(mode,'series(Dj)')
782	if isempty(j2_series)
783	msgbox_uvmat('ERROR','no j1-j2 pair available')
784	return
785	end
786	diff_j=j2_series-j1_series;
787	min_diff=min(diff_j(diff_j>0));
788	max_diff=max(diff_j(diff_j>0));
789	for ipair=min_diff:max_diff
790	if numel(diff_j(diff_j==ipair))>0
791	displ_pair=[displ_pair;{['Dj= ' num2str(-floor(ipair/2)) '\|' num2str(ceil(ipair/2)) ]}];
792	end
793	end
794	if ~isempty(displ_pair)
795	displ_pair=[displ_pair;{'Dj=\|'}];
796	end
797	elseif strcmp(mode,'bursts')
798	if isempty(j2_series)
799	msgbox_uvmat('ERROR','no j1-j2 pair available')
800	return
801	end
802	diff_j=j2_series-j1_series;
803	min_j1=min(j1_series(j1_series>0));
804	max_j1=max(j1_series(j1_series>0));
805	min_j2=min(j2_series(j2_series>0));
806	max_j2=max(j2_series(j2_series>0));
807	for pair1=min_j1:min(max_j1,min_j1+20)
808	for pair2=min_j2:min(max_j2,min_j2+20)
809	if numel(j1_series(j1_series==pair1))>0 && numel(j2_series(j2_series==pair2))>0
810	displ_pair=[displ_pair;{['j= ' num2str(pair1) '-' num2str(pair2)]}];
811	end
812	end
813	end
814	if ~isempty(displ_pair)
815	displ_pair=[displ_pair;{'j=-'}];
816	end
817	end
818	end
819	%% display list of pairs
820	displ_pair_list=get(handles.list_pair_civ,'String');
821	NewVal=[];
822	if ~isempty(displ_pair_list)
823	Val=get(handles.list_pair_civ,'Value');
824	NewVal=find(strcmp(displ_pair_list{Val},displ_pair),1);% look at the previous display in the new menu displ_pâir
825	end
826	if ~isempty(NewVal)
827	set(handles.list_pair_civ,'Value',NewVal)
828	else
829	set(handles.list_pair_civ,'Value',1)
830	end
831	set(handles.list_pair_civ,'String',displ_pair)
832	displ_pair
833
834	% displ_pair{ind_exist}=['Di= ' num2str(-floor(index/2)) '\|' num2str(ceil(index/2)) ' :dt= ' num2str(dt*1000) dtunit];
835	% if strcmp(mode,'series(Di)')
836	% for index=1:min(nbfield-1,50)
837	% filename=name_generator(filebase,ref_i-floor(index/2),ref_j,'.nc',NomType,1,ref_i+ceil(index/2),ref_j,subdir);
838	% select=(exist(filename,'file')==2);
839	% if select==1
840	% ind_exist=ind_exist+1;
841	% displ_num(1,ind_exist)=0;
842	% displ_num(2,ind_exist)=0;
843	% displ_num(3,ind_exist)=-floor(index/2);
844	% displ_num(4,ind_exist)=ceil(index/2);
845	% %[cte_detect,vdt,cte_read]=read_netcdf(filename,{'dt','dt2','absolut_time_T0','absolute_time_TO_2'});
846	% [Cte,var_detect,ichoice]=nc2struct(filename,{});
847	% if isfield(Cte,'dt2')
848	% dt=Cte.dt2;
849	% elseif isfield(Cte,'dt')
850	% dt=Cte.dt;
851	% end
852	% if isfield(Cte,'absolut_time_TO_2')
853	% ref_time(ind_exist)=Cte.absolut_time_TO_2;%civ2 data used in priority
854	% elseif isfield(Cte,'absolut_time_TO')
855	% ref_time(ind_exist)=Cte.absolut_time_TO;%civ2 data used in priorit
856	% elseif isfield(Cte,'Time')
857	% ref_time(ind_exist)=Cte.Time;
858	% end
859	% displ_pair{ind_exist}=['Di= ' num2str(-floor(index/2)) '\|' num2str(ceil(index/2)) ' :dt= ' num2str(dt*1000) dtunit];
860	% end
861	% end
862	% set(handles.list_pair_civ,'String',[displ_pair';{'Di=\|'}]);
863	% elseif isequal(mode,'series(Dj)')% series on the j index
864	% for index=1:min(nbfield2-1,50)
865	% filename=name_generator(filebase,ref_i,ref_j-floor(index/2),'.nc',NomType,1,ref_i,ref_j+ceil(index/2),subdir);
866	% select=(exist(filename,'file')==2);
867	% if select==1
868	% ind_exist=ind_exist+1;
869	% displ_num(1,ind_exist)=-floor(index/2);
870	% displ_num(2,ind_exist)=ceil(index/2);
871	% displ_num(3,ind_exist)=0;
872	% displ_num(4,ind_exist)=0;
873	% [Cte,var_detect,ichoice]=nc2struct(filename,{});
874	% if isfield(Cte,'dt2')
875	% dt=Cte.dt2;
876	% elseif isfield(Cte,'dt')
877	% dt=Cte.dt;
878	% end
879	% if isfield(Cte,'absolut_time_TO_2')
880	% ref_time(ind_exist)=Cte.absolut_time_TO_2;%civ2 data used in priority
881	% elseif isfield(Cte,'absolut_time_TO')
882	% ref_time(ind_exist)=Cte.absolut_time_TO;%civ2 data used in priorit
883	% elseif isfield(Cte,'Time')
884	% ref_time(ind_exist)=Cte.Time;
885	% end
886	% displ_pair{ind_exist}=['Dj= ' num2str(-floor(index/2)) '\|' num2str(ceil(index/2)) ' :dt= ' num2str(dt*1000) dtunit];
887	% end
888	% end
889	% set(handles.list_pair_civ,'String',[displ_pair';{'Dj=\|'}]);
890	% elseif isequal(mode,'bursts') %case of bursts
891	% for numod_a=1:nbfield2-1 %nbfield2 always >=2 for 'bursts' mode
892	% for numod_b=(numod_a+1):nbfield2
893	% [filename]=name_generator(filebase,ref_i,numod_a,'.nc',NomType,1,ref_i,numod_b,subdir)
894	% select=(exist(filename,'file')==2)
895	% if select==1
896	% ind_exist=ind_exist+1;
897	% numlist_a(ind_exist)=numod_a;
898	% numlist_b(ind_exist)=numod_b;
899	% Attr=nc2struct(filename,[]);
900	% isfield(Attr,'absolut_time_T0_2')
901	% if isfield(Attr,'dt2')
902	% dt(ind_exist)=Attr.dt2;
903	% ref_time(ind_exist)=Attr.absolut_time_T0_2;
904	% elseif isfield(Attr,'dt')& isfield(Attr,'absolut_time_T0')
905	% dt(ind_exist)=Attr.dt;
906	% ref_time(ind_exist)=Attr.absolut_time_T0;
907	% else
908	% dt(ind_exist)=NaN;%no information on dt
909	% end
910	% %determine nom_type_ima for pair display (used in num2stra.m)
911	% switch NomType
912	% case {'#ab'}
913	% nom_type_ima='#a';
914	% case {'#AB'}
915	% nom_type_ima='#A';
916	% otherwise
917	% nom_type_ima='_1_1';
918	% end
919	% displ_pair{ind_exist}=['j= ' num2stra(numod_a,nom_type_ima,2) '-' num2stra(numod_b,nom_type_ima,2) ...
920	% ' :dt= ' num2str(dt(ind_exist)*1000)];
921	% end
922	% end
923	% set(handles.list_pair_civ,'String',[displ_pair';{'j=-'}]);
924	% end
925	% if exist('dt','var') & ~isempty(dt)
926	% [dtsort,indsort]=sort(dt);
927	% displ_num(1,:)=numlist_a(indsort);
928	% displ_num(2,:)=numlist_b(indsort);
929	% displ_num(3,:)=0;
930	% displ_num(4,:)=0;
931	% displ_pair=displ_pair(indsort);
932	% ref_time=ref_time(indsort);
933	% end
934	% end
935	if isempty(displ_pair)
936	msgbox_uvmat('ERROR',['no file available for the selected subdirectory ' subdir])
937	end
938	return
939	%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%END FUNCTION
940
941
942	if ind_exist==0
943	if isequal(mode,'series(Dj)') \| isequal(mode,'st_series(Dj)')
944	msgbox_uvmat('ERROR',['no .nc file available for the selected reference index j=' num2str(ref_j) ' and subdirectory ' subdir])
945	else
946	msgbox_uvmat('ERROR',['no .nc file available for the selected reference index i=' num2str(ref_i) ' and subdirectory ' subdir])
947	end
948	if isequal(mode,'bursts') %case of bursts
949	set(handles.list_pair_civ,'String',{'j=-'});
950	elseif isequal(mode,'series(Di)') %case of bursts
951	set(handles.list_pair_civ,'String',{'Di=\|'});
952	elseif isequal(mode,'series(Dj)') %case of bursts
953	set(handles.list_pair_civ,'String',{'Dj=\|'});
954	end
955	end
956	return
957	%TO update
958	val=get(handles.list_pair_civ,'Value');
959	if val > length(displ_pair)
960	set(handles.list_pair_civ,'Value',1);% first pair proposed by default in the menu
961	val=1;
962	end
963	iview=get(handles.NomType,'Value');
964	SeriesData.displ_num(iview,:)=(displ_num(:,val))';
965	SeriesData.ref_time=ref_time;
966	set(handles.series,'UserData',SeriesData)
967	list_pair_civ_Callback([],[],handles)
968
969	%-------------------------------------------------------------
970	% --- Executes on selection in list_pair_civ.
971	function list_pair_civ_Callback(hObject,eventdata,handles)
972	%------------------------------------------------------------
973	return
974	%%%%%%%%
975	%update num_first_i and num_last_i according to the chosen image pairs
976	testupdate=0;
977	Val=get(handles.RootPath,'Value');
978	IndexCell=get(handles.NomType,'String');
979	SeriesData=get(handles.series,'UserData');
980	NomType=SeriesData.NomType{Val};
981	list_pair=get(handles.list_pair_civ,'String');%get the menu of image pairs
982	index_pair=get(handles.list_pair_civ,'Value');
983	str_pair=list_pair{index_pair};
984	ind_equ=strfind(str_pair,'=');%find '='
985	ind_sep=strfind(str_pair,'\|');%find pair separator '\|'
986	ind_com=strfind(str_pair,':');%find ':'
987	test_bursts=0;
988	if isempty(ind_sep)
989	ind_sep=strfind(str_pair,'-');%find pair separator if it is not '\|'
990	test_bursts=1;% we are in the case of bursts
991	end
992	displ_num=[0 0 0 0]; %default
993	if ~isempty(ind_sep)&& ~strcmp(str_pair(ind_sep-1),'*')% if there is a pair separator ('\|' or '-')
994	num1_str=str_pair(ind_equ(1)+1:ind_sep-1);
995	num2_str=str_pair(ind_sep+1:ind_com-1);
996	num1=str2double(num1_str);
997	num2=str2double(num2_str);
998	if isequal(num1_str(1),' ')
999	num1_str(1)=[];
1000	end
1001	if isequal(num2_str(end),' ')
1002	num2_str(end)=[];
1003	end
1004	switch NomType
1005	case {'_1-2_1'}
1006	if isequal(num1_str(1),'0')
1007	IndexCell{Val}=['_(i-(i+' num2_str ')_j'];
1008	else
1009	IndexCell{Val}=['_(i' num1_str ')-(i+' num2_str ')_j'];
1010	end
1011	displ_num(3)=num1;
1012	displ_num(4)=num2;
1013	case {'_1-2'}
1014	if isequal(num1_str(1),'0')
1015	IndexCell{Val}=['_(i' num1_str ')-(i+' num2_str ')'];
1016	else
1017	IndexCell{Val}=['_(i' num1_str ')-(i+' num2_str ')'];
1018	end
1019	displ_num(3)=num1;
1020	displ_num(4)=num2;
1021	case '_1_1-2'
1022	if test_bursts
1023	IndexCell{Val}=['_i_' num1_str '-' num2_str ];
1024	else
1025	if isequal(num1_str(1),'0')
1026	IndexCell{Val}=['_i_j-(j+' num2_str ')'];
1027	else
1028	IndexCell{Val}=['_i_(j' num1_str ')-(j+' num2_str ')'];
1029	end
1030	end
1031	displ_num(1)=num1;
1032	displ_num(2)=num2;
1033	case {'#_ab'} %TO COMPLETE
1034	IndexCell{Val}=['_i_' num1_str '-' num2_str ];
1035
1036	end
1037	end
1038	set(handles.NomType,'String',IndexCell)
1039	SeriesData.displ_num(Val,:)=displ_num;
1040	set(handles.series,'UserData',SeriesData)
1041	% set(handles.NomType,'Value',Val)
1042
1043	if ~isequal(str_pair,'Dj=\|')&~isequal(str_pair,'Di=\|')
1044	mode_list=get(handles.mode,'String');
1045	mode_value=get(handles.mode,'Value');
1046	mode=mode_list{mode_value};
1047	if isequal(mode,'series(Di)')
1048	first_i=str2num(get(handles.num_first_i,'String'));
1049	last_i=str2num(get(handles.num_last_i,'String'));
1050	incr_i=str2num(get(handles.num_incr_i,'String'));
1051	num1=first_i:incr_i:last_i;
1052	lastfieldCell=get(handles.num_MaxIndex_i,'String');
1053	lastfield=str2num(lastfieldCell{1});
1054	if ~isempty(lastfield)
1055	ind=find((num1-floor(index_pair/2)ones(size(num1))>0)& (num1+ceil(index_pair/2)ones(size(num1))<=lastfield));
1056	num1=num1(ind);
1057	end
1058	if ~isempty(num1)
1059	set(handles.num_first_i,'String',num2str(num1(1)));
1060	set(handles.num_last_i,'String',num2str(num1(end)));
1061	end
1062	testupdate=1;
1063	elseif isequal(mode,'series(Dj)')
1064	first_j=str2num(get(handles.num_first_j,'String'));
1065	last_j=str2num(get(handles.num_last_j,'String'));
1066	incr_j=str2num(get(handles.num_incr_j,'String'));
1067	num_j=first_j:incr_j:last_j;
1068	lastfieldCell=get(handles.num_MaxIndex_j,'String');
1069	if ~isempty(lastfieldCell)
1070	lastfield2=lastfieldCell{1};
1071	ind=find((num_j-floor(index_pair/2)*ones(size(num_j))>0)& ...
1072	(num_j+ceil(index_pair/2)*ones(size(num_j))<=lastfield2));
1073	end
1074	testupdate=1;
1075	end
1076
1077	%update the first and last times of the series
1078	if testupdate && isfield(SeriesData,'Time')
1079	if ~isempty(SeriesData.Time{1})
1080	displ_time(handles);
1081	end
1082	end
1083	end
1084
1085	%------------------------------------------------------------------------
1086	% --- Executes on button press in RUN.
1087	function RUN_Callback(hObject, eventdata, handles)
1088	%------------------------------------------------------------------------
1089	%% Read parameters from series
1090	Series=read_GUI(handles.series)%TODO: extend to all input param
1091	Series.hseries=handles.series; % handles to the series GUI
1092
1093	%% read root name and field type
1094	set(handles.RUN,'BusyAction','queue');
1095	set(0,'CurrentFigure',handles.series)
1096	if isequal(get(handles.GetObject,'Visible'),'on') && isequal(get(handles.GetObject,'Value'),1)
1097	Series.GetObject=1;
1098	GetObject_Callback(hObject, eventdata, handles)
1099	else
1100	Series.GetObject=0;
1101	end
1102	% SeriesData=get(handles.series,'UserData');
1103
1104	% Series.hseries=handles.series; % handles to the series GUI
1105	first_i=1;
1106	last_i=1;
1107	incr_i=1;
1108	first_j=1;
1109	last_j=1;
1110	incr_j=1;
1111	if isfield(Series.IndexRange,'first_i')
1112	first_i=Series.IndexRange.first_i;
1113	incr_i=Series.IndexRange.incr_i;
1114	last_i=Series.IndexRange.last_i;
1115	end
1116	if isfield(Series.IndexRange,'first_j')
1117	first_j=Series.IndexRange.first_j;
1118	incr_j=Series.IndexRange.incr_j;
1119	last_j=Series.IndexRange.last_j;
1120	end
1121
1122	%% read input file parameters and set menus
1123	Series.PathProject=get(handles.PathCampaign,'String');
1124	% InputTable=get(handles.InputTable,'Data');
1125	RootPath=Series.InputTable(:,1);
1126	SubDir=Series.InputTable(:,2);
1127	RootFile=Series.InputTable(:,3);
1128	NomType=Series.InputTable(:,4);
1129	FileExt=Series.InputTable(:,5);
1130	% if isempty(SeriesData)
1131	% msgbox_uvmat('ERROR','no input file series')
1132	% return
1133	% end
1134	% NomType=SeriesData.NomType;
1135	% if length(RootPath)==1 %string character input for user fct
1136	% Series.RootPath=RootPath{1};
1137	% Series.RootFile=RootFile{1};
1138	% Series.SubDir=SubDir{1};
1139	% Series.FileExt=FileExt{1};
1140	% Series.NomType=NomType{1};
1141	% else %cell input for user fct
1142	% Series.RootPath=RootPath;
1143	% Series.RootFile=RootFile;
1144	% Series.SubDir=SubDir;
1145	% Series.FileExt=FileExt;
1146	% Series.NomType=NomType;
1147	% end
1148	% if isequal(get(handles.FieldMenu,'Visible'),'on')
1149	% FieldMenu=get(handles.FieldMenu,'String');
1150	% FieldValue=get(handles.FieldMenu,'Value');
1151	% Series.Field=FieldMenu(FieldValue);
1152	% end
1153	menu_coord_state=get(handles.transform_fct,'Visible');
1154	Series.CoordType='';%default
1155	if isequal(menu_coord_state,'on')
1156	% menu_coord=get(handles.transform_fct,'String');
1157	menu_index=get(handles.transform_fct,'Value');
1158	transform_list=get(handles.transform_fct,'UserData');
1159	Series.transform_fct=transform_list{menu_index};% transform function handles
1160	end
1161
1162	%reinitiate waitbar position
1163	Series.WaitbarPos=get(handles.waitbar_frame,'Position');%TO SUPPRESS
1164	waitbarpos=Series.WaitbarPos;
1165	waitbarpos(4)=0.005;%reinitialize waitbar to zero height
1166	waitbarpos(2)=Series.WaitbarPos(2)+Series.WaitbarPos(4)-0.005;
1167	% set(handles.waitbar,'Position',waitbarpos)
1168
1169	if isfield(Series.IndexRange,'NbSlice')
1170	Series.NbSlice=Series.IndexRange.NbSlice;
1171	end
1172	if last_i < first_i \| last_j < first_j , msgbox_uvmat('ERROR','last field number must be larger than the first one'),...
1173	set(handles.RUN, 'Enable','On'), set(handles.RUN,'BackgroundColor',[1 0 0]),return,end;
1174	num_i=first_i:incr_i:last_i;
1175	num_j=first_j:incr_j:last_j;
1176	% nbfield_cell=get(handles.num_MaxIndex_i,'String');
1177	nbfield=cell2mat(Series.IndexRange.MaxIndex);
1178	nb=min(nbfield,1);
1179	nbfield=nb(1);
1180	nbfield2=nb(2);
1181
1182	%get complementary information from the 'series' interface
1183	list_action=get(handles.ACTION,'String');% list menu action
1184	index_action=get(handles.ACTION,'Value');% selected string index
1185	action= list_action{index_action}; % selected string
1186	mode_list=get(handles.mode,'String');
1187	index_mode=get(handles.mode,'Value');
1188	mode=mode_list{index_mode};
1189	ind_shift=0;%default
1190
1191	%determine the list of input file names
1192	nbmissing=0;
1193	% for iview=1:length(RootPath)
1194	% %case of pairs (.nc files)
1195	% fileinput=name_generator(fullfile(RootPath{iview},RootFile{iview}),first_i,first_j,FileExt{iview},NomType{iview},1,first_i+1,first_j+1,SubDir{iview});
1196	% if strcmp(get(handles.Pairs,'Visible'),'on')
1197	% pair_list=get(handles.list_pair_civ,'String');
1198	% val=get(handles.list_pair_civ,'Value');
1199	% pair_string=pair_list{val};
1200	% r=regexp(pair_string,'.\D(?<num1>[\d+\|])(?<delim>[-\|\|])(?<num2>[\d+\|*])','names');
1201	% if ~isempty(r)
1202	% if strcmp(r.num1,'*')%free pairs
1203	% [tild,RootFile,i1_series,i2_series,j1_series,j2_series,tild,tild,Object]=find_file_series(fileinput);% TODO: choice pair when multiple choice
1204	%
1205	% if isempty(i2_series) %j pairs
1206	% ind_sel=i1_series>=i1_series>=first_i & i1_series<=last_i & j1_series>first_j & j2_series<last_j;
1207	% j2_series=j2_series(ind_sel);
1208	% else%i pairs
1209	% if isempty(j1_series) %j pairs
1210	% ind_sel=i1_series>=first_i & i2_series<=last_i ;
1211	% else
1212	% ind_sel=i1_series>=first_i & i2_series<=last_i& j1_series>first_j & j1_series<last_j;
1213	% j1_series=j1_series(ind_sel);
1214	% i2_series=i2_series(ind_sel);
1215	% end
1216	% end
1217	% i1_series=i1_series(ind_sel);
1218	% else
1219	% if strcmp(r.delim,'-')
1220	% ind_shift(1)=str2num(r.num1);
1221	% ind_shift(2)=str2num(r.num2);
1222	% else
1223	% ind_shift(1)=-str2num(r.num1);
1224	% ind_shift(2)=str2num(r.num2);
1225	% end
1226	% [i1_series,i2_series,j1_series,j2_series,nbmissing]=find_file_indices(num_i,num_j,ind_shift,NomType{iview},mode);
1227	% end
1228	% end
1229	% if isempty(i1_series)
1230	% msgbox_uvmat('ERROR','no file in the considered range')
1231	% return
1232	% end
1233	% if isempty(i2_series)
1234	% i2_series=i1_series;
1235	% end
1236	% if isempty(j2_series)
1237	% j2_series=j1_series;
1238	% end
1239	% else%case of images
1240	% [i1_series,j1_series]=meshgrid(num_i,num_j);
1241	% i2_series=i1_series;
1242	% j2_series=j1_series;
1243	% end
1244	% if length(RootPath)>1
1245	% i1_series_cell{iview}=i1_series;
1246	% i2_series_cell{iview}=i2_series;
1247	% j1_series_cell{iview}=j1_series;
1248	% j2_series_cell{iview}=j2_series;
1249	% end
1250	% end
1251
1252	%% defining the ACTION function handle
1253	path_series=which('series');
1254	list_path=get(handles.ACTION,'UserData');
1255	index=get(handles.ACTION,'Value');
1256	fct_path=list_path{index}; %path stored for the function ACTION
1257	if ~isequal(fct_path,path_series)
1258	eval(['spath=which(''' action ''');']) %spath = current path of the selected function ACTION
1259	if ~exist(fct_path,'dir')
1260	msgbox_uvmat('ERROR',['The prescibed function path ' fct_path ' does not exist'])
1261	return
1262	end
1263	if ~isequal(spath,fct_path)
1264	addpath(fct_path)% add the prescribed path if not the current one
1265	end
1266	end
1267	eval(['h_fun=@' action ';'])%create a function handle for ACTION
1268	if ~isequal(fct_path,path_series)
1269	rmpath(fct_path)% add the prescribed path if not the current one
1270	end
1271
1272	%% RUN ACTION
1273	Series.Action=action;%name of the processing programme
1274	Series
1275	set(handles.RUN,'BackgroundColor',[0.831 0.816 0.784])
1276	h_fun(Series);
1277	% if length(RootPath)>1
1278	% h_fun(i1_series_cell,i2_series_cell,j1_series_cell,j2_series_cell,Series);
1279	% else
1280	% h_fun(i1_series,i2_series,j1_series,j2_series,Series);
1281	% end
1282	set(handles.RUN,'BackgroundColor',[1 0 0])
1283
1284	% %save the current interface setting as figure namefig, append .0 to the name if it already exists
1285	% detect=1;
1286	% while detect==1
1287	% namefigfull=[namedoc '.fig'];
1288	% hh=dir(namefigfull);
1289	% if ~isempty(hh)
1290	% detect=1;
1291	% namedoc=[namedoc '.0'];
1292	% else
1293	% detect=0;
1294	% end
1295	% end
1296	% saveas(gcbf,namefigfull);%save the interface with name namefigfull (A CHANGER EN FICHIER .xml)
1297
1298	%------------------------------------------------------------------------
1299	function STOP_Callback(hObject, eventdata, handles)
1300	%------------------------------------------------------------------------
1301	set(handles.RUN, 'BusyAction','cancel')
1302	set(handles.RUN,'BackgroundColor',[1 0 0])
1303
1304
1305	%------------------------------------------------------------------------
1306	function num_first_i_Callback(hObject, eventdata, handles)
1307	%------------------------------------------------------------------------
1308	num_last_i_Callback(hObject, eventdata, handles)
1309
1310	%------------------------------------------------------------------------
1311	function num_last_i_Callback(hObject, eventdata, handles)
1312	%------------------------------------------------------------------------
1313	SeriesData=get(handles.series,'UserData');
1314	if ~isfield(SeriesData,'Time')
1315	SeriesData.Time{1}=[];
1316	end
1317	displ_time(handles);
1318
1319	%------------------------------------------------------------------------
1320	function num_first_j_Callback(hObject, eventdata, handles)
1321	%------------------------------------------------------------------------
1322	num_last_j_Callback(hObject, eventdata, handles)
1323
1324	%------------------------------------------------------------------------
1325	function num_last_j_Callback(hObject, eventdata, handles)
1326	%------------------------------------------------------------------------
1327	first_j=str2num(get(handles.num_first_j,'String'));
1328	last_j=str2num(get(handles.num_last_j,'String'));
1329	ref_j=ceil((first_j+last_j)/2);
1330	set(handles.ref_j,'String', num2str(ref_j))
1331	ref_j_Callback(hObject, eventdata, handles)
1332	SeriesData=get(handles.series,'UserData');
1333	if ~isfield(SeriesData,'Time')
1334	SeriesData.Time{1}=[];
1335	end
1336	displ_time(handles);
1337
1338
1339	%------------------------------------------------------------------------
1340	function ref_i_Callback(hObject, eventdata, handles)
1341	%------------------------------------------------------------------------
1342	mode_list=get(handles.mode,'String');
1343	mode_value=get(handles.mode,'Value');
1344	mode=mode_list{mode_value};
1345	SeriesData=get(handles.series,'UserData');
1346	%NomTypeCell=get(handles.NomType,'String');
1347	NomTypeCell=SeriesData.NomType;
1348	if ~isempty(NomTypeCell)
1349	Val=get(handles.NomType,'Value');
1350	NomType=NomTypeCell{Val};
1351	% for ilist=1:length(NomType)
1352	if isequal(NomType,'_1_1-2')\|\| isequal(NomType,'_1-2_1')\|\| isequal(NomType,'_1-2')
1353	if isequal(mode,'series(Di)')
1354	find_netcpair_civ(handles,Val);% update the menu of pairs depending on the available netcdf files
1355	% break
1356	end
1357	end
1358	end
1359
1360	%------------------------------------------------------------------------
1361	function ref_j_Callback(hObject, eventdata, handles)
1362	%------------------------------------------------------------------------
1363	mode_list=get(handles.mode,'String');
1364	mode_value=get(handles.mode,'Value');
1365	mode=mode_list{mode_value};
1366	SeriesData=get(handles.series,'UserData');
1367	NomTypeCell=SeriesData.NomType;
1368	if ~isempty(NomTypeCell)
1369	Val=get(handles.NomType,'Value');
1370	NomType=NomTypeCell{Val};
1371	if isequal(NomType,'_1_1-2')\|\| isequal(NomType,'_1-2_1')\|\| isequal(NomType,'_1-2')
1372	if isequal(mode,'series(Dj)')
1373	find_netcpair_civ(handles,Val);% update the menu of pairs depending on the available netcdf files
1374	end
1375	end
1376	end
1377
1378	%------------------------------------------------------------------------
1379	% --- Executes on selection change in ACTION.
1380	function ACTION_Callback(hObject, eventdata, handles)
1381	%------------------------------------------------------------------------
1382	global nb_builtin_ACTION
1383	list_ACTION=get(handles.ACTION,'String');% list menu fields
1384	index_ACTION=get(handles.ACTION,'Value');% selected string index
1385	ACTION= list_ACTION{index_ACTION}; % selected function name
1386	path_series=which('series');%path to series.m
1387	list_path=get(handles.ACTION,'UserData');%list of recorded paths to functions of the list ACTION
1388	default_file=fullfile(list_path{end},ACTION);
1389	% add a new function to the menu if the selected item is 'more...'
1390	if isequal(ACTION,'more...')
1391	pathfct=fileparts(path_series);
1392	[FileName, PathName, filterindex] = uigetfile( ...
1393	{'.m', ' (.m)';
1394	'*.m', '.m files '; ...
1395	'.', 'All Files (.)'}, ...
1396	'Pick a file',default_file);
1397	if length(FileName)<2
1398	return
1399	end
1400	[pp,ACTION,ext_fct]=fileparts(FileName);%(end-1:end);
1401	if ~isequal(ext_fct,'.m')
1402	msgbox_uvmat('ERROR','a Matlab function .m must be introduced');
1403	return
1404	end
1405
1406	% insert the choice in the action menu
1407	menu_str=update_menu(handles.ACTION,ACTION);%new action menu in which the new item has been appended if needed
1408	index_ACTION=get(handles.ACTION,'Value');% currently selected index in the list
1409	list_path{index_ACTION}=PathName;
1410	if length(menu_str)>nb_builtin_ACTION+5; %nb_builtin=nbre of functions always remaining in the initial menu
1411	nbremove=length(menu_str)-nb_builtin_ACTION-5;
1412	menu_str(nb_builtin_ACTION+1:end-5)=[];
1413	list_path(nb_builtin_ACTION+1:end-4)=[];
1414	index_ACTION=index_ACTION-nbremove;
1415	set(handles.ACTION,'Value',index_ACTION)
1416	set(handles.ACTION,'String',menu_str)
1417	end
1418	list_path{index_ACTION}=PathName;
1419	set(handles.ACTION,'UserData',list_path);
1420	set(handles.path,'enable','inactive')% indicate that the current path is accessible (not 'off')
1421
1422	%record the current menu in personal file profil_perso
1423	dir_perso=prefdir;
1424	profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
1425	for ilist=nb_builtin_ACTION+1:length(menu_str)-1
1426	series_fct{ilist-nb_builtin_ACTION}=fullfile(list_path{ilist},[menu_str{ilist} '.m']);
1427	end
1428	if nb_builtin_ACTION+1<=length(menu_str)-1
1429	if exist(profil_perso,'file')% && nb_builtin_ACTION+1>=length(menu_str)-1
1430	save(profil_perso,'series_fct','-append')
1431	else
1432	txt=ver('MATLAB');
1433	Release=txt.Release;
1434	relnumb=str2num(Release(3:4));
1435	if relnumb >= 14%recent relaese of Matlab
1436	save(profil_perso,'series_fct','-V6')
1437	else
1438	save(profil_perso, 'series_fct')
1439	end
1440	end
1441	end
1442	end
1443
1444	%check the current path to the selected function
1445	PathName=list_path{index_ACTION};%current recorded path
1446	set(handles.path,'String',PathName); %show the path to the senlected function
1447
1448	%default setting for the visibility of the GUI elements
1449	% set(handles.RootPath,'UserData','many')
1450	% set(handles.SubDir,'Visible','on')
1451	% set(handles.RootFile,'Visible','on')
1452	% set(handles.NomType,'Visible','on')
1453	% set(handles.FileExt,'Visible','on')
1454	set(handles.num_NbSlice,'Visible','off')
1455	set(handles.NbSlice_title,'Visible','off')
1456	set(handles.VelTypeMenu,'Visible','off');
1457	set(handles.VelType_text,'Visible','off');
1458	set(handles.VelTypeMenu_1,'Visible','off');
1459	set(handles.VelType_text_1,'Visible','off');
1460	view_FieldMenu(handles,'off')
1461	view_FieldMenu_1(handles,'off')
1462	set(handles.FieldTransform,'Visible','off')
1463	% view_TRANSFORM(handles,'off')Visible','off')
1464	set(handles.Objects,'Visible','off');
1465	set(handles.GetMask,'Visible','off')
1466	set(handles.Mask,'Visible','off')
1467	% set(handles.GetObject,'Visible','off');
1468	set(handles.OutputDir,'Visible','off');
1469	% set(handles.PARAMETERS_frame,'Visible','off');
1470	% set(handles.PARAMETERS_title,'Visible','off');
1471	set(handles.ParamKey,'Visible','off')
1472	set(handles.ParamVal,'Visible','off')
1473	ParamKey={};
1474	set(handles.FieldMenu,'Enable','off')
1475	set(handles.VelTypeMenu,'Enable','off')
1476	set(handles.FieldMenu_1,'Enable','off')
1477	set(handles.VelTypeMenu_1,'Enable','off')
1478	set(handles.transform_fct,'Enable','off')
1479	%set the displayed GUI item needed for input parameters
1480	if ~isequal(path_series,PathName)
1481	addpath(PathName)
1482	end
1483	eval(['h_function=@' ACTION ';']);
1484	try
1485	[fid,errormsg] =fopen([ACTION '.m']);
1486	InputText=textscan(fid,'%s',1,'delimiter','\n');
1487	fclose(fid)
1488	set(handles.ACTION,'ToolTipString',InputText{1}{1})
1489	end
1490	if ~isequal(path_series,PathName)
1491	rmpath(PathName)
1492	end
1493	varargout=h_function();
1494	Param_list={};
1495
1496	%nb_series=length(RootFile);
1497	% FileExt=get(handles.FileExt,'String');
1498	% nb_series=length(FileExt);
1499	InputFiles=get(handles.InputTable,'Data')
1500	FileExt=InputFiles(:,5);
1501	checkcell=find(cellfun('isempty',FileExt)~=0);
1502	nb_series=0;
1503	if ~isempty(checkcell)
1504	nb_series=checkcell(end);
1505	end
1506	% nb_series=size(InputFiles,1)
1507	testima_series=1; %test for a list of images only
1508	testima=1;
1509	testima_1=1;
1510	testciv_series=1;
1511	for iview=1:nb_series
1512	ext=FileExt{iview};
1513	if length(ext)<2
1514	ext='.none';
1515	end
1516	testimaview=~isempty(imformats(ext(2:end))) \|\| isequal(lower(ext),'.avi');
1517	if ~testimaview
1518	if iview==1
1519	testima=0;
1520	end
1521	if iview==2
1522	testima_1=0;
1523	end
1524	testima_series=0;
1525	end
1526	end
1527	for ilist=1:length(varargout)-1
1528	switch varargout{ilist}
1529	%RootFile always visible
1530	% case 'RootPath' %visible by default
1531	% value=lower(varargout{ilist+1});
1532	% if isequal(value,'one')\|\|isequal(value,'two')\|\|isequal(value,'many')
1533	% set(handles.RootFile,'UserData',value)% for use in menu Open_insert
1534	% end
1535	% case 'SubDir' %visible by default
1536	% if isequal(lower(varargout{ilist+1}),'off')
1537	% set(handles.SubDir,'Visible','off')
1538	% end
1539	% case 'RootFile' %visible by default
1540	% value=lower(varargout{ilist+1});
1541	% if isequal(value,'off')
1542	% set(handles.RootFile,'Visible','off')
1543	% elseif isequal(value,'one')\|\|isequal(value,'two')\|\|isequal(value,'many')
1544	% set(handles.RootFile,'Visible','on')
1545	% set(handles.RootFile,'UserData',value)% for use in menu Open_insert
1546	% end
1547	% case 'NomType' %visible by default
1548	% if isequal(lower(varargout{ilist+1}),'off')
1549	% set(handles.NomType,'Visible','off')
1550	% end
1551	% case 'FileExt' %visible by default
1552	% if isequal(lower(varargout{ilist+1}),'off')
1553	% set(handles.FileExt,'Visible','off')
1554	% end
1555	case 'NbSlice' %hidden by default
1556	if isequal(lower(varargout{ilist+1}),'on')
1557	set(handles.num_NbSlice,'Visible','on')
1558	set(handles.NbSlice_title,'Visible','on')
1559	end
1560	case 'VelTypeMenu' %hidden by default
1561	if isequal(lower(varargout{ilist+1}),'one') \|\| isequal(lower(varargout{ilist+1}),'two')
1562	set(handles.VelTypeMenu,'Enable','on')
1563	if nb_series >=1 && ~testima_series
1564	set(handles.VelTypeMenu,'Visible','on')
1565	set(handles.VelType_text,'Visible','on');
1566	set(handles.Field_frame,'Visible','on')
1567	end
1568	end
1569	if isequal(lower(varargout{ilist+1}),'two')
1570	set(handles.VelTypeMenu_1,'Enable','on')
1571	if nb_series >=2 && ~testima_series
1572	set(handles.VelTypeMenu_1,'Visible','on')
1573	set(handles.VelType_text_1,'Visible','on');
1574	end
1575	end
1576	case 'FieldMenu' %hidden by default
1577	if isequal(lower(varargout{ilist+1}),'one')\|\|isequal(lower(varargout{ilist+1}),'two')
1578	set(handles.FieldMenu,'Enable','on') % test for MenuBorser
1579	if nb_series >=1 && ~testima_series
1580	view_FieldMenu(handles,'on')
1581	end
1582	end
1583	if isequal(lower(varargout{ilist+1}),'two')
1584	set(handles.FieldMenu_1,'Enable','on')
1585	if nb_series >=2 && ~testima_1
1586	view_FieldMenu_1(handles,'on')
1587	end
1588	end
1589	case 'CoordType' %hidden by default
1590	if isequal(lower(varargout{ilist+1}),'on')
1591	set(handles.transform_fct,'Enable','on')
1592	set(handles.FieldTransform,'Visible','on')
1593	% view_TRANSFORM(handles,'on')
1594	end
1595	case 'GetObject' %hidden by default
1596	if isequal(lower(varargout{ilist+1}),'on')
1597	set(handles.Objects,'Visible','on')
1598	% set(handles.GetObject,'Visible','on');
1599	end
1600	case 'Mask' %hidden by default
1601	if isequal(lower(varargout{ilist+1}),'on')
1602	set(handles.Objects,'Visible','on')
1603	% set(handles.GetMask,'Visible','on');
1604	end
1605	case 'PARAMETER'
1606	set(handles.PARAMETERS_frame,'Visible','on')
1607	set(handles.PARAMETERS_title,'Visible','on')
1608	set(handles.ParamKey,'Visible','on')
1609	%set(handles.ParamVal,'Visible','on')
1610	Param_str=varargout{ilist+1};
1611	Param_list=[Param_list; {Param_str}];
1612	end
1613	end
1614	if ~isempty(Param_list)
1615	set(handles.ParamKey,'String',Param_list)
1616	set(handles.ParamVal,'Visible','on')
1617	end
1618
1619	%------------------------------------------------------------------------
1620	% --- Executes on selection change in FieldMenu.
1621	function FieldMenu_Callback(hObject, eventdata, handles)
1622	%------------------------------------------------------------------------
1623	field_str=get(handles.FieldMenu,'String');
1624	field_index=get(handles.FieldMenu,'Value');
1625	field=field_str{field_index(1)};
1626	if isequal(field,'get_field...')
1627	hget_field=findobj(allchild(0),'name','get_field');
1628	if ~isempty(hget_field)
1629	delete(hget_field)%delete opened versions of get_field
1630	end
1631	SeriesData=get(handles.series,'UserData');
1632	filename=SeriesData.CurrentInputFile;
1633	if exist(filename,'file')
1634	get_field(filename)
1635	end
1636	elseif isequal(field,'more...')
1637	str=calc_field;
1638	[ind_answer,v] = listdlg('PromptString','Select a file:',...
1639	'SelectionMode','single',...
1640	'ListString',str);
1641	% edit the choice in the fields and action menu
1642	scalar=cell2mat(str(ind_answer));
1643	update_menu(handles.FieldMenu,scalar)
1644	end
1645
1646	%------------------------------------------------------------------------
1647	% --- Executes on selection change in FieldMenu_1.
1648	function FieldMenu_1_Callback(hObject, eventdata, handles)
1649	%------------------------------------------------------------------------
1650	field_str=get(handles.FieldMenu_1,'String');
1651	field_index=get(handles.FieldMenu_1,'Value');
1652	field=field_str{field_index};
1653	if isequal(field,'get_field...')
1654	hget_field=findobj(allchild(0),'name','get_field_1');
1655	if ~isempty(hget_field)
1656	delete(hget_field)
1657	end
1658	SeriesData=get(handles.series,'UserData');
1659	filename=SeriesData.CurrentInputFile_1;
1660	if exist(filename,'file')
1661	hget_field=get_field(filename);
1662	set(hget_field,'name','get_field_1')
1663	end
1664	elseif isequal(field,'more...')
1665	str=calc_field;
1666	[ind_answer,v] = listdlg('PromptString','Select a file:',...
1667	'SelectionMode','single',...
1668	'ListString',str);
1669	% edit the choice in the fields and action menu
1670	scalar=cell2mat(str(ind_answer));
1671	update_menu(handles.FieldMenu_1,scalar)
1672	end
1673
1674
1675	%%%%%%%%%%%%%
1676	function [ind_remove]=find_pairs(dirpair,ind_i,last_i)
1677	indsel=ind_i;
1678	indiff=diff(ind_i); %test index increment to detect multiplets (several pairs with the same index ind_i) and holes in the series
1679	indiff=[1 indiff last_i-ind_i(end)+1];%for testing gaps with the imposed bounds
1680	if ~isempty(indiff)
1681	indiff2=diff(indiff);
1682	indiffp=[indiff2 1];
1683	indiffm=[1 indiff2];
1684	ind_multi_m=find((indiff==0)&(indiffm<0))-1;%indices of first members of multiplets
1685	ind_multi_p=find((indiff==0)&(indiffp>0));%indices of last members of multiplets
1686	%for each multiplet, select the most recent file
1687	ind_remove=[];
1688	for i=1:length(ind_multi_m)
1689	ind_pairs=ind_multi_m(i):ind_multi_p(i);
1690	for imulti=1:length(ind_pairs)
1691	datepair(imulti)=datenum(dirpair(ind_pairs(imulti)).date);%dates of creation
1692	end
1693	[datenew,indsort2]=sort(datepair); %sort the multiplet by creation date
1694	ind_s=indsort2(1:end-1);%
1695	ind_remove=[ind_remove ind_pairs(ind_s)];%remove these indices, leave the last one
1696	end
1697	end
1698
1699	%------------------------------------------------------------------------
1700	% --- determine the list of index pairs of processing file
1701	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)
1702	%------------------------------------------------------------------------
1703	num_i1=num_i;% set of first image numbers by default
1704	num_i2=num_i;
1705	num_j1=num_j;
1706	num_j2=num_j;
1707	num_i_out=num_i;
1708	num_j_out=num_j;
1709	% if isequal (NomType,'_1-2_1') \|\| isequal (NomType,'_1-2')
1710	if isequal(mode,'series(Di)')
1711	num_i1_line=num_i+ind_shift(3);% set of first image numbers
1712	num_i2_line=num_i+ind_shift(4);
1713	% adjust the first and last field number
1714	indsel=find(num_i1_line >= 1);
1715	num_i_out=num_i(indsel);
1716	num_i1_line=num_i1_line(indsel);
1717	num_i2_line=num_i2_line(indsel);
1718	num_j1=meshgrid(num_j,ones(size(num_i1_line)));
1719	num_j2=meshgrid(num_j,ones(size(num_i1_line)));
1720	[xx,num_i1]=meshgrid(num_j,num_i1_line);
1721	[xx,num_i2]=meshgrid(num_j,num_i2_line);
1722	elseif isequal (mode,'series(Dj)')\|\|isequal (mode,'bursts')
1723	if isequal(mode,'bursts') %case of bursts (png_old or png_2D)
1724	num_j1=ind_shift(1)*ones(size(num_i));
1725	num_j2=ind_shift(2)*ones(size(num_i));
1726	else
1727	num_j1_col=num_j+ind_shift(1);% set of first image numbers
1728	num_j2_col=num_j+ind_shift(2);
1729	% adjust the first field number
1730	indsel=find((num_j1_col >= 1));
1731	num_j_out=num_j(indsel);
1732	num_j1_col=num_j1_col(indsel);
1733	num_j2_col=num_j2_col(indsel);
1734	[num_i1,num_j1]=meshgrid(num_i,num_j1_col);
1735	[num_i2,num_j2]=meshgrid(num_i,num_j2_col);
1736	end
1737	end
1738
1739	%------------------------------------------------------------------------
1740	% ---- find the times corresponding to the first and last indices of a series
1741	function displ_time(handles)
1742	%------------------------------------------------------------------------
1743	SeriesData=get(handles.series,'UserData');%
1744	first_i=str2num(get(handles.num_first_i,'String'));
1745	first_j=str2num(get(handles.num_first_j,'String'));
1746	last_i=str2num(get(handles.num_last_i,'String'));
1747	last_j=str2num(get(handles.num_last_j,'String'));
1748	InputTable=get(handles.InputTable,'Data');
1749	NomType=InputTable(:,4);
1750	% NomType=SeriesData.NomType;
1751	mode_list=get(handles.mode,'String');
1752	index_mode=get(handles.mode,'Value');
1753	mode=mode_list{index_mode};
1754
1755	time_first=[];
1756	time_last=[];
1757	if ~isfield(SeriesData,'Time')
1758	SeriesData.Time{1}=[];
1759	end
1760	for iview=1:length(NomType)
1761	time_first_cell{iview}='?';
1762	time_last_cell{iview}='?';%default
1763	time=SeriesData.Time{iview};
1764	if isequal(NomType{iview},'_1-2_1')\|isequal(NomType{iview},'_1_1-2')\|isequal(NomType{iview},'#_ab')\|isequal(NomType{iview},'_1-2')
1765	if isfield(SeriesData,'displ_num')& ~isempty(SeriesData.displ_num)
1766	ind_shift=SeriesData.displ_num(iview,:);
1767	if isequal(mode,'bursts')
1768	first_j=0;
1769	last_j=0;
1770	end
1771	first_i1=first_i +ind_shift(3);
1772	first_i2 =first_i +ind_shift(4);
1773	first_j1 =first_j +ind_shift(1);
1774	first_j2 =first_j +ind_shift(2);
1775	last_i1=last_i +ind_shift(3);
1776	last_i2 =last_i +ind_shift(4);
1777	last_j1 =last_j +ind_shift(1);
1778	last_j2 =last_j +ind_shift(2);
1779	siz=size(SeriesData.Time{1});
1780	if first_i1>=1 && first_j1>=1 && siz(1)>=last_i2 && siz(2)>=last_j2
1781	time_first=(time(first_i1,first_j1)+time(first_i2,first_j2))/2;
1782	time_last=(time(last_i1,last_j1)+time(last_i2,last_j2))/2;
1783	else%read the time in the nc files
1784	RootPath=get(handles.RootPath,'String');
1785	RootFile=get(handles.RootFile,'String');
1786	SubDir=get(handles.SubDir,'String');
1787	%VelType=get(handles.VelType,'String');
1788	VelType_str=get(handles.VelTypeMenu,'String');
1789	VelType_val=get(handles.VelTypeMenu,'Value');
1790	VelType=VelType_str{VelType_val};
1791	filebase=fullfile(RootPath{1},RootFile{1});
1792	[filefirst]=name_generator(filebase,first_i1,first_j1,'.nc',NomType{iview},1,first_i2,first_j2,SubDir{iview});
1793	if exist(filefirst,'file')
1794	Attrib=nc2struct(filefirst,[]);
1795	if isfield(Attrib,'Time')
1796	time_first=Attrib.Time;
1797	else
1798	if isfield(Attrib,'absolut_time_T0')
1799	time_first=Attrib.absolut_time_T0;
1800	end
1801	if isfield(Attrib,'absolut_time_T0_2')&&~(isequal(VelType,'civ1')\|\|isequal(VelType,'interp1')\|\|isequal(VelType,'filter1'))
1802	time_first=Attrib.absolut_time_T0_2;
1803	end
1804	end
1805	end
1806	[filelast]=name_generator(filebase,last_i1,last_j1,'.nc',NomType{iview},1,last_i2,last_j2,SubDir{iview});
1807	if exist(filelast,'file')
1808	Attrib=nc2struct(filelast,[]);
1809	if isfield(Attrib,'Time')
1810	time_last=Attrib.Time;
1811	else
1812	if isfield(Attrib,'absolut_time_T0')
1813	time_last=Attrib.absolut_time_T0;
1814	end
1815	if isfield(Attrib,'absolut_time_T0_2')&&~(isequal(VelType,'civ1')\|\|isequal(VelType,'interp1')\|\|isequal(VelType,'filter1'))
1816	time_last=Attrib.absolut_time_T0_2;
1817	end
1818	end
1819	end
1820	end
1821	end
1822	else
1823	siz=size(time);
1824	if siz(1)>=last_i && siz(2)>=last_j && first_i>=1 && first_j>=1
1825	time_first=times(first_i,first_j);
1826	time_last=times(last_i,last_j);
1827	end
1828	end
1829	time_first_cell{iview}=num2str(time_first,4);
1830	time_last_cell{iview}=num2str(time_last,4);
1831	end
1832	% set(handles.time_first,'Value',1)
1833	% set(handles.time_last,'Value',1)
1834	% set(handles.time_first,'String',time_first_cell);
1835	% set(handles.time_last,'String',time_last_cell);
1836
1837	%------------------------------------------------------------------------
1838	% --- Executes on button press in GetObject.
1839	function GetObject_Callback(hObject, eventdata, handles)
1840	%------------------------------------------------------------------------
1841	SeriesData=get(handles.series,'UserData');
1842	value=get(handles.GetObject,'Value');
1843	if value
1844	set(handles.GetObject,'BackgroundColor',[1 1 0])%put unactivated buttons to yellow
1845	% DataInit.ParentButton=handles.GetObject;
1846	hset_object=findobj(allchild(0),'tag','set_object');%find the set_object interface handle
1847	if ishandle(hset_object)
1848	uistack(hset_object,'top')
1849	%[SeriesData.hset_object,SeriesData.sethandles]=set_object(DataInit); %open the set_object interface
1850	else
1851	%get the object file
1852	defaultname=get(handles.RootPath,'String');
1853	if isempty(defaultname)
1854	defaultname={''};
1855	end
1856	[FileName, PathName, filterindex] = uigetfile( ...
1857	{'.xml;.mat', ' (.xml,.mat)';
1858	'*.xml', '.xml files '; ...
1859	'*.mat', '.mat matlab files '}, ...
1860	'Pick an xml object file (or use uvmat to create it)',defaultname{1});
1861	fileinput=[PathName FileName];%complete file name
1862	testblank=findstr(fileinput,' ');%look for blanks
1863	if ~isempty(testblank)
1864	msgbox_uvmat('ERROR','forbidden input file name: contain blanks')
1865	return
1866	end
1867	sizf=size(fileinput);
1868	if (~ischar(fileinput)\|\|~isequal(sizf(1),1)),return;end
1869	%read the file
1870	t=xmltree(fileinput);
1871	data=convert(t);
1872	if ~isfield(data,'Style')
1873	data.Style='points';
1874	end
1875	if ~isfield(data,'ProjMode')
1876	data.ProjMode='projection';
1877	end
1878	transform_menu=get(handles.transform_fct,'String');
1879	ichoice=get(handles.transform_fct,'Value');
1880	% if isequal(transform_menu{ichoice},'px');
1881	% data.CoordType='px';
1882	% else
1883	% data.CoordType='phys';
1884	% end
1885	data.desable_plot=1;
1886	[SeriesData.hset_object,SeriesData.sethandles]=set_object(data);% call the set_object interface
1887	end
1888	else
1889	set(handles.GetObject,'BackgroundColor',[0.7 0.7 0.7])%put activated buttons to green
1890	% if isfield(SeriesData,'hset_object')&& ishandle(SeriesData.hset_object)
1891	% close(SeriesData.hset_object)
1892	% end
1893	end
1894	set(handles.series,'UserData',SeriesData)
1895
1896	%--------------------------------------------------------------
1897	function GetMask_Callback(hObject, eventdata, handles)
1898	value=get(handles.GetMask,'Value');
1899	if value
1900	msgbox_uvmat('ERROR','not implemented yet')
1901	end
1902	%--------------------------------------------------------------
1903
1904	%-------------------------------------------------------------------
1905	%'uv_ncbrowser': interactively calls the netcdf file browser 'get_field.m'
1906	function ncbrowser_uvmat(hObject, eventdata)
1907	%-------------------------------------------------------------------
1908	bla=get(gcbo,'String');
1909	ind=get(gcbo,'Value');
1910	filename=cell2mat(bla(ind));
1911	blank=find(filename==' ');
1912	filename=filename(1:blank-1);
1913	get_field(filename)
1914
1915	% ------------------------------------------------------------------
1916	function MenuHelp_Callback(hObject, eventdata, handles)
1917	%-------------------------------------------------------------------
1918	path_to_uvmat=which ('uvmat');% check the path of uvmat
1919	pathelp=fileparts(path_to_uvmat);
1920	helpfile=fullfile(pathelp,'uvmat_doc','uvmat_doc.html');
1921	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')
1922	else
1923	addpath (fullfile(pathelp,'uvmat_doc'))
1924	web([helpfile '#series'])
1925	end
1926
1927	%-------------------------------------------------------------------
1928	% --- Executes on selection change in transform_fct.
1929	function transform_fct_Callback(hObject, eventdata, handles)
1930	%-------------------------------------------------------------------
1931	global nb_transform
1932
1933	menu=get(handles.transform_fct,'String');
1934	ind_coord=get(handles.transform_fct,'Value');
1935	coord_option=menu{ind_coord};
1936	list_transform=get(handles.transform_fct,'UserData');
1937	ff=functions(list_transform{end});
1938	if isequal(coord_option,'more...');
1939	coord_fct='';
1940	prompt = {'Enter the name of the transform function'};
1941	dlg_title = 'user defined transform';
1942	num_lines= 1;
1943	[FileName, PathName, filterindex] = uigetfile( ...
1944	{'.m', ' (.m)';
1945	'*.m', '.m files '; ...
1946	'.', 'All Files (.)'}, ...
1947	'Pick a file', ff.file);
1948	if isequal(PathName(end),'/')\|\|isequal(PathName(end),'\')
1949	PathName(end)=[];
1950	end
1951	transform_selected =fullfile(PathName,FileName);
1952	if ~exist(transform_selected,'file')
1953	return
1954	end
1955	[ppp,transform,xt_fct]=fileparts(FileName);% removes extension .m
1956	if ~isequal(ext_fct,'.m')
1957	msgbox_uvmat('ERROR','a Matlab function .m must be introduced');
1958	return
1959	end
1960	menu=update_menu(handles.transform_fct,transform);%add the selected fct to the menu
1961	ind_coord=get(handles.transform_fct,'Value');
1962	addpath(PathName)
1963	list_transform{ind_coord}=str2func(transform);% create the function handle corresponding to the newly seleced function
1964	set(handles.transform_fct,'UserData',list_transform)
1965	rmpath(PathName)
1966	% save the new menu in the personal file 'uvmat_perso.mat'
1967	dir_perso=prefdir;%personal Matalb directory
1968	profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
1969	if exist(profil_perso,'file')
1970	for ilist=nb_transform+1:numel(list_transform)
1971	ff=functions(list_transform{ilist});
1972	transform_fct{ilist-nb_transform}=ff.file;
1973	end
1974	save (profil_perso,'transform_fct','-append'); %store the root name for future opening of uvmat
1975	end
1976	end
1977
1978	%check the current path to the selected function
1979	if ~isempty(list_transform{ind_coord})
1980	func=functions(list_transform{ind_coord});
1981	set(handles.path_transform,'String',fileparts(func.file)); %show the path to the senlected function
1982	else
1983	set(handles.path_transform,'String',''); %show the path to the senlected function
1984	end
1985	%------------------------------------------------------------------------
1986	% --- generates a series of file names with reference numbers between range1 and
1987	% --- range2 with increment incr. The reference number num_ref is the image number at the middle of the
1988	% --- image pair. The set of first numbers num1 of the image pairs is also
1989	% --- given as output
1990	% 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)
1991	% %------------------------------------------------------------------------
1992	% [Path,Name]=fileparts(filebase);
1993	% filebasesub=fullfile(Path,subdir,Name);
1994	% filecell={};%default
1995	% num_i1=[];
1996	% num_i2=[];
1997	% num_j1=[];
1998	% num_j2=[];
1999	% ind0_i=first_i:incr_i:last_i;
2000	% nbcolumn=length(ind0_i);
2001	% ind0_j=first_j:incr_j:last_j;
2002	% nbline=length(ind0_j);
2003	% if isequal(mode,'#_ab')
2004	% dirpair=dir([filebasesub '_.nc']);
2005	% elseif isequal(mode,'bursts')\|\|isequal(mode,'series(Dj)')
2006	% dirpair=dir([filebasesub '__-*.nc']);
2007	% elseif isequal(mode,'series(Di)')
2008	% dirpair=dir([filebasesub '_-_*.nc']);
2009	% else
2010	% msgbox_uvmat('ERROR','option \| not yet implemented')
2011	% return
2012	% end
2013	% if isempty(dirpair)
2014	% msgbox_uvmat('ERROR','no pair detected in the selected range')
2015	% return
2016	% end
2017	%
2018	% if isequal(mode,'bursts')\|\|isequal(mode,'#_ab')
2019	% icount=0;
2020	% for ifile=1:length(dirpair)
2021	% [RootPath,RootFile,str_1,str_2,str_a,str_b,ext,nom_type]=name2display(dirpair(ifile).name);
2022	% num1_r=str2num(str_1);
2023	% if isequal(RootFile,Name) & ~isempty(num1_r)
2024	% num_i1(ifile)=num1_r;
2025	% num_a(ifile)=stra2num(str_a);
2026	% num_b(ifile)=stra2num(str_b);
2027	% end
2028	% end
2029	% test_range= (num_i1 >=first_i)&(num_i1<= last_i);% =1 when both numbers are in the range
2030	% ind_i=((num_i1-first_i)/incr_i)+1;%indices i in the list of prescribed file indices
2031	% select=find(test_range &(floor(ind_i)==ind_i));%selected indices of num_i1 in the file directory
2032	% ind_i=ind_i(select);%set of selected indices ind_i
2033	% [ind_i,indsort]=sort(ind_i);%sorted list of ind_i
2034	% select=select(indsort);
2035	% num_i1=num_i1(select);
2036	% num_a=num_a(select);
2037	% num_b=num_b(select);
2038	% dirpair=dirpair(select);
2039	% [ind_remove]=find_pairs(dirpair,ind_i,nbcolumn);
2040	% ind_i(ind_remove)=[];
2041	% num_a(ind_remove)=[];
2042	% num_b(ind_remove)=[];
2043	% num_j1=zeros(1,nbcolumn);%default
2044	% num_j2=num_j1;
2045	% num_j1(ind_i)=num_a;
2046	% num_j2(ind_i)=num_b;
2047	% num_i1=first_i:incr_i:last_i;
2048	% num_i2=num_i1;
2049	% nbmissing=nbcolumn-length(ind_i);
2050	%
2051	% elseif isequal(mode,'series(Di)')
2052	% %ind0_i=num_first_i:num_incr_i:num_last_i;
2053	% %nbcolumn=length(ind0_i);
2054	% %ind0_j=num_first_j:num_incr_j:num_last_j;
2055	% %nbline=length(ind0_j);
2056	% %dirpair=dir([filebasesub '_-_*.nc']);
2057	% for ifile=1:length(dirpair)
2058	% [RootPath,RootFile,str_1,str_2,str_a,str_b,ext,nom_type]=name2display(dirpair(ifile).name);
2059	% num_i1_r(ifile)=str2num(str_1);
2060	% num_i2_r(ifile)=str2num(str_2);
2061	% num_j(ifile)=str2num(str_a);
2062	% end
2063	% num_i=floor((num_i1_r+num_i2_r)/2); %list of reference indices of the detected files
2064	% 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
2065	% ind_i=((num_i-first_i)/incr_i)+1;%indices i and j in the list of prescribed file indices
2066	% ind_j=((num_j-first_j)/incr_j)+1;
2067	% ind_ij=ind_j+nbline*(ind_i-1);%indices in the reshhaped series of prescribed file indices
2068	% select=find(test_range &(floor(ind_i)==ind_i)&(floor(ind_j)==ind_j));%selected indices in the file directory
2069	% ind_ij=ind_ij(select);%set of selected indices ind_ij
2070	% [ind_ij,indsort]=sort(ind_ij);%sorted list of ind_ij
2071	% select=select(indsort);
2072	% num_i1_r=num_i1_r(select);
2073	% num_i2_r=num_i2_r(select);
2074	% dirpair=dirpair(select);
2075	% [ind_remove]=find_pairs(dirpair,ind_ij,nbcolumn*nbline) ;
2076	% ind_ij(ind_remove)=[];
2077	% num_i1_r(ind_remove)=[];
2078	% num_i2_r(ind_remove)=[];
2079	% num_i1=zeros(1,nbline*nbcolumn);%default
2080	% num_i2=num_i1;
2081	% num_i1(ind_ij)=num_i1_r;
2082	% num_j2(ind_ij)=num_i2_r;
2083	% num_i1=reshape(num_i1,nbline,nbcolumn);
2084	% num_i2=reshape(num_i2,nbline,nbcolumn);
2085	% num_j1=meshgrid(ind0_i,ind0_j);
2086	% num_j2=num_j1;
2087	% nbmissing=nbline*nbcolumn-length(ind_ij);
2088	% elseif isequal(mode,'series(Dj)')
2089	% for ifile=1:length(dirpair)
2090	% [RootPath,RootFile,str_1,str_2,str_a,str_b,ext,nom_type]=name2display(dirpair(ifile).name);
2091	% num_i(ifile)=str2num(str_1);
2092	% num_a(ifile)=str2num(str_a);
2093	% num_b(ifile)=str2num(str_b);
2094	% end
2095	% num_j=floor((num_a+num_b)/2); %list of reference indices of the detected files
2096	% 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
2097	% ind_i=((num_i-first_i)/incr_i)+1;%indices i and j in the list of prescribed file indices
2098	% ind_j=((num_j-first_j)/incr_j)+1;
2099	% ind_ij=ind_j+nbline*(ind_i-1);%indices in the reshhaped series of prescribed file indices
2100	% select=find(test_range &(floor(ind_i)==ind_i)&(floor(ind_j)==ind_j));%selected indices in the file directory
2101	% ind_ij=ind_ij(select);%set of selected indices ind_ij
2102	% [ind_ij,indsort]=sort(ind_ij);%sorted list of ind_ij
2103	% select=select(indsort);
2104	% num_i=num_i(select);
2105	% num_a=num_a(select);
2106	% num_b=num_b(select);
2107	% dirpair=dirpair(select);
2108	% [ind_remove]=find_pairs(dirpair,ind_ij,nbcolumn*nbline) ;
2109	% ind_ij(ind_remove)=[];
2110	% num_a(ind_remove)=[];
2111	% num_b(ind_remove)=[];
2112	% num_j1=zeros(1,nbline*nbcolumn);%default
2113	% num_j2=num_j1;
2114	% num_j1(ind_ij)=num_a;
2115	% num_j2(ind_ij)=num_b;
2116	% num_j1=reshape(num_j1,nbline,nbcolumn);
2117	% num_j2=reshape(num_j2,nbline,nbcolumn);
2118	% num_i1=meshgrid(ind0_i,ind0_j);
2119	% num_i2=num_i1;
2120	% nbmissing=nbline*nbcolumn-length(ind_ij);
2121	% end
2122
2123
2124	% --- Executes on button press in REFRESH_INDICES.
2125
2126
2127	function REFRESH_INDICES_Callback(hObject, eventdata, handles)
2128	% hObject handle to REFRESH_INDICES (see GCBO)
2129	% eventdata reserved - to be defined in a future version of MATLAB
2130	% handles structure with handles and user data (see GUIDATA)
2131	set(handles.REFRESH_INDICES,'BackgroundColor',[0.7 0.7 0.7])
2132	InputTable=get(handles.InputTable,'Data');
2133	check_lines=get(handles.REFRESH_INDICES,'UserData');
2134
2135	%% check the indices and FileTypes for each series (limited to the new ones to save time)
2136	for ind_list=1:length(check_lines)
2137	if check_lines(ind_list)
2138	InputLine=InputTable(ind_list,:);
2139	detect_idem=strcmp('"',InputLine);% look for '" (repeat of previous data)
2140	detect_idem=detect_idem(detect_idem>0);
2141	if ~isempty (detect_idem)
2142	InputLine(detect_idem)=InputTable(ind_list-1,detect_idem);
2143	set(handles.InputTable,'Data',InputTable)
2144	end
2145	fileinput=fullfile_uvmat(InputLine{1},InputLine{2},InputLine{3},InputLine{5},InputLine{4},1,2,1,2);
2146	%fileinput=name_generator(fullfile(InputLine{1},InputLine{3}),1,1,InputLine{5},InputLine{4},1,2,2,InputLine{2})
2147	%update file series defined by the selected line
2148	[InputTable{ind_list,1},InputTable{ind_list,3},InputTable{(ind_list),4},errormsg]=update_indices(handles,fileinput,ind_list);
2149	if ~isempty(errormsg)
2150	msgbox_uvmat('ERROR',errormsg)
2151	return
2152	end
2153	end
2154	end
2155	set(handles.InputTable,'Data',InputTable)
2156	SeriesData=get(handles.series,'UserData');
2157
2158	state_j='off';
2159	state_Pairs='off';
2160	state_InputFields='off';
2161	val=get(handles.ListView,'Value');
2162	ListViewString={''};
2163	if ~isempty(SeriesData)
2164	% ListViewString={};
2165	for ilist=1:size(InputTable,1)
2166	if ~isempty(SeriesData.j1_series{ilist})
2167	state_j='on';
2168	end
2169	if ~isempty(SeriesData.i2_series{ilist})\|\|~isempty(SeriesData.j2_series{ilist})
2170	state_Pairs='on';
2171	ListViewString{ilist}=num2str(ilist);
2172	if check_lines(ilist)
2173	val=ilist;%select the last pair if it is a new entry
2174	end
2175	end
2176	if strcmp(SeriesData.FileType,'civx')\|\|strcmp(SeriesData.FileType,'civdata')
2177	state_InputFields='on';
2178	end
2179	end
2180	end
2181	set(handles.ListView,'Value',val)
2182	set(handles.ListView,'String',ListViewString)
2183	if strcmp(state_Pairs,'on')
2184	ListView_Callback(hObject,eventdata,handles)
2185	end
2186	set(handles.Pairs,'Visible',state_InputFields)
2187	enable_j(handles,state_j)
2188	set(handles.REFRESH_INDICES,'BackgroundColor',[1 0 0])
2189	set(handles.REFRESH_INDICES,'visible','off')
2190
2191	% update min and max indices for a series
2192	function [RootPath,RootFile,NomType,errormsg]=update_indices(handles,fileinput,iview)
2193
2194	%% look for min and max indices existing in the file series and update SeriesData
2195	errormsg='';
2196	[RootPath,RootFile,i1_series,i2_series,j1_series,j2_series,NomType,FileType,Object]=find_file_series(fileinput);
2197	if isempty(RootFile)&&isempty(i1_series)
2198	errormsg='no input file in the series';
2199	return
2200	end
2201	[tild,tild,FileExt]=fileparts(fileinput);
2202
2203	MinIndex=get(handles.MinIndex,'Data');
2204	MaxIndex=get(handles.MaxIndex,'Data');
2205	MinIndex_i=min(i1_series(i1_series>0));
2206	if ~isempty(i2_series)
2207	MaxIndex_i=max(i2_series(i2_series>0));
2208	else
2209	MaxIndex_i=max(i1_series(i1_series>0));
2210	end
2211	MinIndex_j=min(j1_series(j1_series>0));
2212	if ~isempty(j2_series)
2213	MaxIndex_j=max(j2_series(j2_series>0));
2214	else
2215	MaxIndex_j=max(j1_series(j1_series>0));
2216	end
2217	MinIndex{iview,1}=MinIndex_i;
2218	MinIndex{iview,2}=MinIndex_j;
2219	MaxIndex{iview,1}=MaxIndex_i;
2220	MaxIndex{iview,2}=MaxIndex_j;
2221	set(handles.MinIndex,'Data',MinIndex)
2222	set(handles.MaxIndex,'Data',MaxIndex)
2223	SeriesData=get(handles.series,'UserData');
2224	SeriesData.i1_series{iview}=i1_series;
2225	SeriesData.i2_series{iview}=i2_series;
2226	SeriesData.j1_series{iview}=j1_series;
2227	SeriesData.j2_series{iview}=j2_series;
2228	SeriesData.FileType{iview}=FileType;
2229
2230	%% represents the set of existing files as an image
2231	set(handles.waitbar_frame,'Units','pixels')
2232	pos=get(handles.waitbar_frame,'Position');
2233	xima=0.5:pos(3)-0.5;% pixel positions on the image representing the existing file indices
2234	yima=0.5:pos(4)-0.5;
2235	[XIma,YIma]=meshgrid(xima,yima);
2236	nb_i=size(i1_series,1);
2237	nb_j=size(i1_series,2);
2238	ind_i=(0.5:nb_i-0.5)*pos(3)/nb_i;
2239	ind_j=(0.5:nb_j-0.5)*pos(4)/nb_j;
2240	[Ind_i,Ind_j]=meshgrid(ind_i,ind_j);
2241	CData=zeros([size(XIma) 3]);
2242	file_ima=double((i1_series(:,:,1)>0)');
2243	if numel(file_ima)>=2
2244	if size(file_ima,1)==1
2245	CLine=interp1(ind_i,file_ima,xima,'nearest');
2246	CData(:,:,2)=ones(size(yima'))*CLine;
2247	else
2248	CData(:,:,2)=interp2(Ind_i,Ind_j,file_ima,XIma,YIma,'nearest');
2249	end
2250	set(handles.waitbar_frame,'CData',CData)
2251	end
2252	set(handles.waitbar_frame,'Units','normalized')
2253
2254	%% enable field and veltype menus
2255	testfield=isequal(get(handles.FieldMenu,'enable'),'on');
2256	testfield_1=isequal(get(handles.FieldMenu_1,'enable'),'on');
2257	testveltype=isequal(get(handles.VelTypeMenu,'enable'),'on');
2258	testveltype_1=isequal(get(handles.VelTypeMenu_1,'enable'),'on');
2259	testtransform=isequal(get(handles.transform_fct,'Enable'),'on');
2260	testnc=0;
2261	testnc_1=0;
2262	testcivx=0;
2263	testcivx_1=0;
2264	%TODO: update
2265	% if length(FileExtCell)==1 \|\| length(FileExtCell)>2
2266	% for iview=1:length(FileExtCell)
2267	% if isequal(FileExtCell{iview},'.nc')
2268	% testnc=1;
2269	% end
2270	% if isequal(FileTypeCell{iview},'civx')
2271	% testcivx=1;
2272	% end
2273	% end
2274	% elseif length(FileExtCell)==2
2275	% testnc=isequal(FileExtCell{1},'.nc');
2276	% testnc_1=isequal(FileExtCell{2},'.nc');
2277	% testcivx=isequal(FileTypeCell{1},'civx');
2278	% testcivx_1=isequal(FileTypeCell{2},'civx');
2279	% end
2280	if testfield && testnc
2281	view_FieldMenu(handles,'on')
2282	if testcivx
2283	menustr=get(handles.FieldMenu,'String');
2284	if isequal(menustr,{'get_field...'})
2285	set(handles.FieldMenu,'String',{'get_field...';'velocity';'vort';'div';'more...'})
2286	end
2287	else
2288	set(handles.FieldMenu,'Value',1)
2289	set(handles.FieldMenu,'String',{'get_field...'})
2290	end
2291	else
2292	view_FieldMenu(handles,'off')
2293	end
2294	if testfield_1 && testnc_1
2295	view_FieldMenu_1(handles,'on')
2296	if testcivx_1
2297	menustr=get(handles.FieldMenu_1,'String');
2298	if isequal(menustr,{'get_field...'})
2299	set(handles.FieldMenu_1,'String',{'get_field...';'velocity';'vort';'div';'more...'})
2300	end
2301	else
2302	set(handles.FieldMenu_1,'Value',1)
2303	set(handles.FieldMenu_1,'String',{'get_field...'})
2304	end
2305	else
2306	view_FieldMenu_1(handles,'off')
2307	end
2308	if testveltype && testcivx
2309	set(handles.VelTypeMenu,'Visible','on')
2310	set(handles.VelType_text,'Visible','on');
2311	else
2312	set(handles.VelTypeMenu,'Visible','off')
2313	set(handles.VelType_text,'Visible','off');
2314	end
2315	if testveltype_1 && testcivx_1
2316	set(handles.VelTypeMenu_1,'Visible','on')
2317	set(handles.VelType_text_1,'Visible','on');
2318	else
2319	set(handles.VelTypeMenu_1,'Visible','off')
2320	set(handles.VelType_text_1,'Visible','off');
2321	end
2322	if testtransform && (testcivx \|\| testima)
2323	set(handles.FieldTransform,'Visible','on')
2324	% view_TRANSFORM(handles,'on')
2325	else
2326	set(handles.FieldTransform,'Visible','off')
2327	% view_TRANSFORM(handles,'off')
2328	end
2329	%TODO:update
2330	% if ~isequal(FileExt,'.nc') && ~isequal(FileExt,'.cdf') && ~testima
2331	% msgbox_uvmat('ERROR',['invalid input file extension ' FileExt])
2332	% return
2333	% end
2334
2335	%% read image documentation file if found%%%%%%%%%%%%%%%%%%%%%%%%%%%
2336	ext_imadoc='';
2337	FileBase=fullfile(RootPath,RootFile);
2338	if isequal(FileExt,'.xml')\|\|isequal(FileExt,'.civ')
2339	ext_imadoc=FileExt;
2340	elseif exist([FileBase '.xml'],'file')
2341	ext_imadoc='.xml';
2342	elseif exist([FileBase '.civ'],'file')
2343	ext_imadoc='.civ';
2344	end
2345	%read the ImaDoc file
2346	XmlData=[];
2347	NbSlice_calib={};
2348	if isequal(ext_imadoc,'.xml')
2349	[XmlData,warntext]=imadoc2struct([FileBase '.xml']);
2350	if isfield(XmlData,'Heading') && isfield(XmlData.Heading,'ImageName') && ischar(XmlData.Heading.ImageName)
2351	[PP,FF,ext_ima_read]=fileparts(XmlData.Heading.ImageName);
2352	end
2353	if isfield(XmlData,'Time')
2354	time=XmlData.Time;
2355	end
2356	if isfield(XmlData,'Camera')
2357	if isfield(XmlData.Camera,'NbSlice')&& ~isempty(XmlData.Camera.NbSlice)
2358	NbSlice_calib{iview}=XmlData.Camera.NbSlice;% Nbre of slices for Zindex in phys transform
2359	if ~isequal(NbSlice_calib{iview},NbSlice_calib{1})
2360	msgbox_uvmat('WARNING','inconsistent number of Z indices for the two field series');
2361	end
2362	end
2363	if isfield(XmlData.Camera,'TimeUnit')&& ~isempty(XmlData.Camera.TimeUnit)
2364	TimeUnit=XmlData.Camera.TimeUnit;
2365	end
2366	end
2367	if ~isempty(warntext)
2368	msgbox_uvmat('WARNING',warntext)
2369	end
2370	elseif isequal(ext_imadoc,'.civ')
2371	[error,XmlData.Time,TimeUnit,mode,npx,npy,pxcmx,pxcmy]=read_imatext([FileBase '.civ']);
2372	time=XmlData.Time;
2373	if error==2, warntext=['no file ' FileBase '.civ'];
2374	elseif error==1, warntext='inconsistent number of fields in the .civ file';
2375	end
2376	end
2377
2378
2379	%% number of slices
2380	if isfield(XmlData,'GeometryCalib') && isfield(XmlData.GeometryCalib,'SliceCoord')
2381	siz=size(XmlData.GeometryCalib.SliceCoord);
2382	if siz(1)>1
2383	NbSlice=siz(1);
2384	else
2385	NbSlice=1;
2386	end
2387	set(handles.num_NbSlice,'String',num2str(NbSlice))
2388	end
2389	% set(handles.mode,'Visible','off') % do not show index pairs by default
2390	set(handles.Pairs,'Visible','off')
2391	% set(handles.ref_i,'Visible','off')
2392	% set(handles.ref_i_text,'Visible','off')
2393	testpair=0;
2394	%set the menus of image pairs and default selection for series
2395	%list pairs if relevant
2396	% Val=get(handles.NomType,'Value');
2397	% synchronise_view(handles,Val)
2398
2399	% if ~isfield(SeriesData,'j1_series')\|\|isempty(SeriesData.j1_series{index})
2400	% state_j='off'; %no need for j index
2401	% else
2402	% state_j='on'; %case of j index
2403	% end
2404	% show index pairs if files exist
2405	set(handles.series,'UserData',SeriesData)
2406
2407
2408
2409	% --- Executes on button press in BATCH.
2410	function BATCH_Callback(hObject, eventdata, handles)
2411	% hObject handle to BATCH (see GCBO)
2412	% eventdata reserved - to be defined in a future version of MATLAB
2413	% handles structure with handles and user data (see GUIDATA)
2414	Series=read_GUI(handles.series);
2415	t=struct2xml(Series);
2416	save(t); %TODO: determine a xml file name
2417
2418	% list_action=get(handles.ACTION,'String');% list menu action
2419	% index_action=get(handles.ACTION,'Value');% selected string index
2420	% action= list_action{index_action}; % selected string
2421
2422	%% defining the ACTION function handle
2423	path_series=which('series');
2424	list_path=get(handles.ACTION,'UserData');
2425	index=get(handles.ACTION,'Value');
2426	fct_path=list_path{index}; %path stored for the function ACTION
2427	if ~isequal(fct_path,path_series)
2428	eval(['spath=which(''' action ''');']) %spath = current path of the selected function ACTION
2429	if ~exist(fct_path,'dir')
2430	msgbox_uvmat('ERROR',['The prescibed function path ' fct_path ' does not exist'])
2431	return
2432	end
2433	if ~isequal(spath,fct_path)
2434	addpath(fct_path)% add the prescribed path if not the current one
2435	end
2436	end
2437	eval(['h_fun=@' action ';'])%create a function handle for ACTION
2438	if ~isequal(fct_path,path_series)
2439	rmpath(fct_path)% add the prescribed path if not the current one
2440	end
2441
2442	h_fun('BATCH');% TODO modify the called function to read the xml file as input parameter
2443
2444
2445	% --- Executes on selection change in txt_Pairs
2446	function txt_Pairs_Callback(hObject, eventdata, handles)
2447
2448	%------------------------------------------------------------------------
2449	% --- Executes on selection change in ListView.
2450	function ListView_Callback(hObject, eventdata, handles)
2451	%------------------------------------------------------------------------
2452	ListViewString=get(handles.ListView,'String');
2453	if isempty(ListViewString)
2454	ListViewString={''};
2455	end
2456	ListViewValue=get(handles.ListView,'Value');
2457	View=str2double(ListViewString{ListViewValue});
2458	if isnan(View)
2459	set(handles.Pairs,'Visible','off')
2460	else
2461	set(handles.Pairs,'Visible','on')
2462	SeriesData=get(handles.series,'UserData');
2463	if isfield(SeriesData,'j1_series')&&(~isempty(SeriesData.i2_series{View})\|\|~isempty(SeriesData.j2_series{View}))
2464	if ~isempty(SeriesData.i2_series{View}) %pairs with i View
2465	set(handles.mode,'Value',1)
2466	set(handles.mode,'String',{'series(Di)'})
2467	else %pairs with j View
2468	nbfield=size(SeriesData.j2_series{View},1);
2469	nbfield2=size(SeriesData.j2_series{View},2);
2470	set(handles.mode,'Value',1)
2471	set(handles.mode,'String',{'bursts';'series(Dj)'})
2472	if nbfield2>10 \|\| nbfield==1
2473	set(handles.mode,'Value',2);
2474	else
2475	set(handles.mode,'Value',1);
2476	end
2477	end
2478	end
2479	mode_Callback([],[], handles)
2480	end
2481
2482

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