source: trunk/src/series.m @ 360

Last change on this file since 360 was 360, checked in by sommeria, 9 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
Line 
1%'series': master function associated to the GUI series.m for analysis field series 
2%------------------------------------------------------------------------
3% function varargout = series(varargin)
4% associated with the GUI series.fig
5%
6%INPUT
7% param: structure with input parameters (link with the GUI uvmat)
8%      .menu_coord_str: string for the transform_fct (menu for coordinate transforms)
9%      .menu_coord_val: value for transform_fct (menu for coordinate transforms)
10%      .FileName: input file name
11%      .FileName_1: second input file name
12%      .list_field: menu of input fields
13%      .index_fields: chosen index
14%      .civ1=0 or 1, .interp1,  ... : input civ field type
15%
16%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
17%  Copyright Joel Sommeria, 2008, LEGI / CNRS-UJF-INPG, sommeria@coriolis-legi.org.
18%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
19%     This file is part of the toolbox UVMAT.
20%
21%     UVMAT is free software; you can redistribute it and/or modify
22%     it under the terms of the GNU General Public License as published by
23%     the Free Software Foundation; either version 2 of the License, or
24%     (at your option) any later version.
25%
26%     UVMAT is distributed in the hope that it will be useful,
27%     but WITHOUT ANY WARRANTY; without even the implied warranty of
28%     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
29%     GNU General Public License (file UVMAT/COPYING.txt) for more details.
30%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
31
32function varargout = series(varargin)
33
34% Begin initialization code - DO NOT EDIT
35gui_Singleton = 1;
36gui_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',   []);
42if nargin && ischar(varargin{1})
43    gui_State.gui_Callback = str2func(varargin{1});
44end
45
46if nargout
47    [varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:});
48else
49    gui_mainfcn(gui_State, varargin{:});
50end
51% End initialization code - DO NOT EDIT
52
53%--------------------------------------------------------------------------
54% --- Executes just before series is made visible.
55%--------------------------------------------------------------------------
56function series_OpeningFcn(hObject, eventdata, handles,param)
57global nb_builtin_ACTION nb_builtin_transform
58% Choose default command line output for series
59handles.output = hObject;
60% Update handles structure
61guidata(hObject, handles);
62%default initial parameters
63drawnow
64set(hObject,'Units','pixels')
65% set(0,'Units','pixels')
66% screensize=get(0,'ScreenSize'); %screen size in pixels
67set(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
70dir_perso=prefdir;
71test_profil_perso=0;
72profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
73if 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
96end
97
98%check default input data
99if ~exist('param','var')
100    param=[]; %default
101end
102
103%file name and browser initialisation
104if isfield(param,'menu_coord_str')
105    set(handles.transform_fct,'String',param.menu_coord_str)
106end
107if isfield(param,'menu_coord_val')
108    set(handles.transform_fct,'Value',param.menu_coord_val);
109else
110     set(handles.transform_fct,'Value',1);%default
111end
112
113if 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
120end 
121
122%fields input initialisation
123if 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};
127end
128% NomType_Callback(hObject, eventdata, handles)
129REFRESH_INDICES_Callback(hObject, eventdata, handles)
130%loads the information stored in prefdir to initiate  the list of ACTION functions
131fct_menu={'check_data_files';'aver_stat';'time_series';'merge_proj';'clean_civ_cmx'};
132transform_menu={'';'phys';'px';'phys_polar'};
133nb_builtin_ACTION=numel(fct_menu); %number of functions
134nb_transform=numel(transform_menu);
135[path_series,name,ext]=fileparts(which('series'));
136path_series=fullfile(path_series,'series');%path of the function 'series'
137addpath (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)
138path_transform=fullfile(path_series,'transform_field');%path to the field transform functions
139for ilist=1:length(fct_menu)
140    fct_path{ilist,1}=path_series;%paths of the fuctions buil-in in 'series.m'
141end
142
143%TRANSFORM menu: loads the information stored in prefdir to initiate  the list of field transform functions
144menu_str={'';'phys';'px';'phys_polar'};
145nb_builtin_transform=numel(menu_str); %number of functions
146[path_uvmat,name,ext]=fileparts(which('uvmat'));
147addpath(fullfile(path_uvmat,'transform_field'))
148fct_handle{1,1}=[];
149testexist(1)=1;
150for 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
157end
158rmpath(fullfile(path_uvmat,'transform_field'))
159
160% read the list of functions stored in the personal file 'uvmat_perso.mat' in prefdir
161if 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
185end
186fct_menu=[fct_menu;{'more...'}];
187set(handles.ACTION,'String',fct_menu)
188set(handles.ACTION,'UserData',fct_path)% store the list of path in UserData of ACTION
189
190menu_str=menu_str(find(testexist));
191fct_handle=fct_handle(find(testexist));
192menu_str=[menu_str;{'more...'}];
193set(handles.transform_fct,'String',menu_str)
194set(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'
197ACTION_Callback(hObject, eventdata, handles)
198
199%--------------------------------------------------------------
200% --- Outputs from this function are returned to the command line.
201%-----------------------------------------------------------------
202function 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
208varargout{1} = handles.output;
209
210
211% --------------------------------------------------------------------
212function MenuBrowse_Callback(hObject, eventdata, handles)
213InputTable=get(handles.InputTable,'Data');
214RootPathCell=InputTable(:,1);
215SubDirCell=InputTable(:,2);
216RootFileCell=InputTable(:,3);
217%RootPathCell=get(handles.RootPath,'String');
218%SubDirCell=get(handles.SubDir,'String'); 
219%RootFileCell=get(handles.RootFile,'String');
220oldfile=''; %default
221if 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);
246fileinput=[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
252sizf=size(fileinput);
253if (~ischar(fileinput)|~isequal(sizf(1),1)),return;end
254[path,name,ext]=fileparts(fileinput);
255SeriesData=[];%dfault
256if isequal(ext,'.xml')
257    warndlg_uvmat('ERROR','input file type not implemented')%A Faire: ouvrir le fichier pour naviguer
258elseif isequal(ext,'.xls')
259    warndlg_uvmat('ERROR','input file type not implemented')%A Faire: ouvrir le fichier pour naviguer
260else
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
292end
293
294
295% --------------------------------------------------------------------
296function MenuFile_1_Callback(hObject, eventdata, handles)
297fileinput=get(handles.MenuFile_1,'Label');
298update_rootfile(handles,fileinput,0)
299
300% --------------------------------------------------------------------
301function MenuFile_2_Callback(hObject, eventdata, handles)
302fileinput=get(handles.MenuFile_2,'Label');
303update_rootfile(handles,fileinput,0)
304
305% --------------------------------------------------------------------
306function MenuFile_3_Callback(hObject, eventdata, handles)
307fileinput=get(handles.MenuFile_3,'Label');
308update_rootfile( handles,fileinput,0)
309
310% --------------------------------------------------------------------
311function MenuFile_4_Callback(hObject, eventdata, handles)
312fileinput=get(handles.MenuFile_4,'Label');
313update_rootfile(handles,fileinput,0)
314
315% --------------------------------------------------------------------
316function MenuFile_5_Callback(hObject, eventdata, handles)
317fileinput=get(handles.MenuFile_5,'Label');
318update_rootfile(handles,fileinput,0)
319
320% --------------------------------------------------------------------
321function MenuBrowse_insert_Callback(hObject, eventdata, handles)
322InputTable=get(handles.InputTable,'Data');
323RootPathCell=InputTable(:,1);
324SubDirCell=InputTable(:,3);
325RootFileCell=InputTable(:,2);
326% RootPathCell=get(handles.RootPath,'String');
327% RootFileCell=get(handles.RootFile,'String');
328oldfile=''; %default
329if 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);
353fileinput=[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
359sizf=size(fileinput);
360if (~ischar(fileinput)|~isequal(sizf(1),1)),return;end
361[path,name,ext]=fileparts(fileinput);
362SeriesData=[];%dfault
363if isequal(ext,'.xml')
364    msgbox_uvmat('ERROR','input file type not implemented')%A Faire: ouvrir le fichier pour naviguer
365elseif isequal(ext,'.xls')
366    msgbox_uvmat('ERROR','input file type not implemented')%A Faire: ouvrir le fichier pour naviguer
367else
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
399end
400%------------------------------------------------
401
402% --------------------------------------------------------------------
403function MenuFile_insert_1_Callback(hObject, eventdata, handles)
404fileinput=get(handles.MenuFile_insert_1,'Label');
405update_rootfile(handles,fileinput,1)
406
407% --------------------------------------------------------------------
408function MenuFile_insert_2_Callback(hObject, eventdata, handles)
409fileinput=get(handles.MenuFile_insert_2,'Label');
410update_rootfile(handles,fileinput,1)
411
412% --------------------------------------------------------------------
413function MenuFile_insert_3_Callback(hObject, eventdata, handles)
414fileinput=get(handles.MenuFile_insert_3,'Label');
415update_rootfile( handles,fileinput,1)
416
417% --------------------------------------------------------------------
418function MenuFile_insert_4_Callback(hObject, eventdata, handles)
419fileinput=get(handles.MenuFile_insert_4,'Label');
420update_rootfile( handles,fileinput,1)
421
422% --------------------------------------------------------------------
423function MenuFile_insert_5_Callback(hObject, eventdata, handles)
424fileinput=get(handles.MenuFile_insert_5,'Label');
425update_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')
433function update_rootfile(handles,fileinput,addtest)
434%------------------------------------------------------------------------ 
435
436%% enable other menus and uicontrols
437set(handles.MenuOpen_insert,'Enable','on')
438set(handles.MenuFile_insert_1,'Enable','on')
439set(handles.MenuFile_insert_2,'Enable','on')
440set(handles.MenuFile_insert_3,'Enable','on')
441set(handles.MenuFile_insert_4,'Enable','on')
442set(handles.MenuFile_insert_5,'Enable','on')
443set(handles.RUN, 'Enable','On')
444set(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
446set(handles.InputTable,'BackgroundColor',[1 1 0]) % set RootPath edit box  to yellow
447drawnow
448
449%% get the input root name, indices, file extension and nomenclature NomType
450if ~exist(fileinput,'file')
451    msgbox_uvmat('ERROR',['input file ' fileinput  ' does not exist'])
452    return
453end
454[RootPath,SubDir,RootFile,i1,i2,j1,j2,FileExt,NomType]=fileparts_uvmat(fileinput);
455
456%% determine reference field indices
457ref_i=1; %default ref_i is a reference frame index used to find existing pairs from PIV
458if ~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
464end
465set(handles.ref_i,'String',num2str(ref_i));
466set(handles.num_first_i,'String',num2str(ref_i));
467set(handles.num_last_i,'String',num2str(ref_i));
468ref_j=1; %default  ref_j is a reference frame index used to find existing pairs from PIV
469if ~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         
475end
476set(handles.ref_j,'String',num2str(ref_j));
477set(handles.num_first_j,'String',num2str(ref_j))
478set(handles.num_last_j,'String',num2str(ref_j));
479TimeUnit=''; %default
480time=[];%default
481
482% read timing and total frame number from the current file (movie files) !! may be overrid by xml file
483FileBase=fullfile(RootPath,RootFile);
484
485testima=0; %test for image input
486if isequal(lower(FileExt),'.avi') %.avi file
487    testima=1;
488elseif ~isempty(imformats(FileExt(2:end)))
489    testima=1;
490elseif isequal(FileExt,'.vol')
491     testima=1;
492end
493
494%% fill the list of file series
495
496% insert the current file series at the head of the list
497InputTable=get(handles.InputTable,'Data');
498if 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');
502else % 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',[{[]},{[]}])
508end
509set(handles.InputTable,'Data',InputTable)
510check_lines(val)=1; %select the edited line for refresh
511set(handles.REFRESH_INDICES,'UserData',check_lines);
512REFRESH_INDICES_Callback([],[], handles)
513
514%store the root name for future opening of uvmat
515dir_perso=prefdir;
516profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
517if exist(profil_perso,'file')
518    save (profil_perso,'RootPath','SubDir','RootFile','NomType', '-append'); %store the root name for future opening of uvmat
519else
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         
528end
529set(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.
612function 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)
621eventdata
622check_lines=get(handles.REFRESH_INDICES,'UserData');
623check_lines(eventdata.Indices(1))=1; %select the edited line for refresh
624set(handles.REFRESH_INDICES,'UserData',check_lines);
625set(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%-------------------------------------
674function enable_i(handles,state)
675set(handles.i_txt,'Visible',state)
676set(handles.num_first_i,'Visible',state)
677set(handles.num_last_i,'Visible',state)
678set(handles.num_incr_i,'Visible',state)
679% set(handles.num_MaxIndex_i,'Visible',state)
680set(handles.ref_i,'Visible',state)
681set(handles.ref_i_text,'Visible',state)
682
683%-----------------------------------
684function enable_j(handles,state)
685set(handles.j_txt,'Visible',state)
686% set(handles.num_MinIndex_j,'Visible',state)
687set(handles.num_first_j,'Visible',state)
688set(handles.num_last_j,'Visible',state)
689set(handles.num_incr_j,'Visible',state)
690% set(handles.num_MaxIndex_j,'Visible',state)
691set(handles.ref_j,'Visible',state)
692set(handles.ref_j_text,'Visible',state)
693
694%-----------------------------------
695function view_FieldMenu(handles,state)
696% set(handles.FieldMenu,'Visible',state)
697% set(handles.Field_text,'Visible',state)
698set(handles.InputFields,'Visible',state)
699
700%-----------------------------------
701function view_FieldMenu_1(handles,state)
702set(handles.FieldMenu_1,'Visible',state)
703set(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%----------------------------------------------------------------
715function find_netcpair_civ(handles)
716SeriesData=get(handles.series,'UserData');
717% NomTypeCell=get(handles.NomType,'String');
718% NomTypeCell=SeriesData.NomType;
719% NomType=NomTypeCell{Val};
720
721set(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
735mode_list=get(handles.mode,'String');
736mode_value=get(handles.mode,'Value');
737mode=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;
750TimeUnit=get(handles.TimeUnit,'String');
751if length(TimeUnit)>=1
752    dtunit=['m' TimeUnit];
753else
754    dtunit='e-03';
755end
756
757%% NEW
758for Val=1:numel(SeriesData.i1_series)
759   
760i1_series=SeriesData.i1_series{Val};
761i2_series=SeriesData.i2_series{Val};
762j1_series=SeriesData.j1_series{Val};
763j2_series=SeriesData.j2_series{Val};
764displ_pair={};
765if 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
781elseif 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
797elseif 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
817end
818end
819%% display list of pairs
820displ_pair_list=get(handles.list_pair_civ,'String');
821NewVal=[];
822if ~isempty(displ_pair_list)
823Val=get(handles.list_pair_civ,'Value');
824NewVal=find(strcmp(displ_pair_list{Val},displ_pair),1);% look at the previous display in the new menu displ_pâir
825end
826if ~isempty(NewVal)
827    set(handles.list_pair_civ,'Value',NewVal)
828else
829    set(handles.list_pair_civ,'Value',1)
830end
831set(handles.list_pair_civ,'String',displ_pair)
832displ_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
935if isempty(displ_pair)
936    msgbox_uvmat('ERROR',['no file available for the selected subdirectory ' subdir])
937end
938return
939%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%END FUNCTION
940
941
942if 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
955end
956return
957%TO update
958val=get(handles.list_pair_civ,'Value');
959if val > length(displ_pair)
960    set(handles.list_pair_civ,'Value',1);% first pair proposed by default in the menu
961    val=1;
962end
963iview=get(handles.NomType,'Value');
964SeriesData.displ_num(iview,:)=(displ_num(:,val))';
965SeriesData.ref_time=ref_time;
966set(handles.series,'UserData',SeriesData)
967list_pair_civ_Callback([],[],handles)
968
969%-------------------------------------------------------------
970% --- Executes on selection in list_pair_civ.
971function list_pair_civ_Callback(hObject,eventdata,handles)
972%------------------------------------------------------------
973return
974%%%%%%%%
975%update num_first_i and num_last_i according to the chosen image pairs
976testupdate=0;
977Val=get(handles.RootPath,'Value');
978IndexCell=get(handles.NomType,'String');
979SeriesData=get(handles.series,'UserData');
980NomType=SeriesData.NomType{Val};
981list_pair=get(handles.list_pair_civ,'String');%get the menu of image pairs
982index_pair=get(handles.list_pair_civ,'Value');
983str_pair=list_pair{index_pair};
984ind_equ=strfind(str_pair,'=');%find '='
985ind_sep=strfind(str_pair,'|');%find pair separator '|'
986ind_com=strfind(str_pair,':');%find ':'
987test_bursts=0;
988if 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
991end
992displ_num=[0 0 0 0]; %default
993if ~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
1037end
1038set(handles.NomType,'String',IndexCell)
1039SeriesData.displ_num(Val,:)=displ_num;
1040set(handles.series,'UserData',SeriesData)
1041% set(handles.NomType,'Value',Val)
1042
1043if ~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
1083end
1084
1085%------------------------------------------------------------------------
1086% --- Executes on button press in RUN.
1087function RUN_Callback(hObject, eventdata, handles)
1088%------------------------------------------------------------------------
1089%% Read parameters from series
1090Series=read_GUI(handles.series)%TODO: extend to all input param
1091Series.hseries=handles.series; % handles to the series GUI
1092
1093%% read root name and field type
1094set(handles.RUN,'BusyAction','queue');
1095set(0,'CurrentFigure',handles.series)
1096if isequal(get(handles.GetObject,'Visible'),'on') && isequal(get(handles.GetObject,'Value'),1)
1097    Series.GetObject=1;
1098    GetObject_Callback(hObject, eventdata, handles)
1099else
1100    Series.GetObject=0;
1101end
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;
1111if 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;
1115end
1116if 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;
1120end
1121
1122%% read input file parameters and set menus
1123Series.PathProject=get(handles.PathCampaign,'String');
1124% InputTable=get(handles.InputTable,'Data');
1125RootPath=Series.InputTable(:,1);
1126SubDir=Series.InputTable(:,2);
1127RootFile=Series.InputTable(:,3);
1128NomType=Series.InputTable(:,4);
1129FileExt=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
1153menu_coord_state=get(handles.transform_fct,'Visible');
1154Series.CoordType='';%default
1155if 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
1160end
1161
1162%reinitiate waitbar position
1163Series.WaitbarPos=get(handles.waitbar_frame,'Position');%TO SUPPRESS
1164waitbarpos=Series.WaitbarPos;
1165waitbarpos(4)=0.005;%reinitialize waitbar to zero height
1166waitbarpos(2)=Series.WaitbarPos(2)+Series.WaitbarPos(4)-0.005;
1167% set(handles.waitbar,'Position',waitbarpos)
1168
1169if isfield(Series.IndexRange,'NbSlice')
1170Series.NbSlice=Series.IndexRange.NbSlice;
1171end
1172if 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;
1174num_i=first_i:incr_i:last_i;
1175num_j=first_j:incr_j:last_j;
1176% nbfield_cell=get(handles.num_MaxIndex_i,'String');
1177nbfield=cell2mat(Series.IndexRange.MaxIndex);
1178nb=min(nbfield,1);
1179nbfield=nb(1);
1180nbfield2=nb(2);
1181
1182%get complementary information from the 'series' interface
1183list_action=get(handles.ACTION,'String');% list menu action
1184index_action=get(handles.ACTION,'Value');% selected string index
1185action= list_action{index_action}; % selected string
1186mode_list=get(handles.mode,'String');
1187index_mode=get(handles.mode,'Value');
1188mode=mode_list{index_mode};
1189ind_shift=0;%default
1190
1191%determine the list of input file names
1192nbmissing=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
1253path_series=which('series');
1254list_path=get(handles.ACTION,'UserData');
1255index=get(handles.ACTION,'Value');
1256fct_path=list_path{index}; %path stored for the function ACTION
1257if ~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
1266end
1267eval(['h_fun=@' action ';'])%create a function handle for ACTION
1268if ~isequal(fct_path,path_series)
1269        rmpath(fct_path)% add the prescribed path if not the current one   
1270end
1271
1272%% RUN ACTION
1273Series.Action=action;%name of the processing programme
1274Series
1275set(handles.RUN,'BackgroundColor',[0.831 0.816 0.784])
1276h_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
1282set(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%------------------------------------------------------------------------
1299function STOP_Callback(hObject, eventdata, handles)
1300%------------------------------------------------------------------------
1301set(handles.RUN, 'BusyAction','cancel')
1302set(handles.RUN,'BackgroundColor',[1 0 0])
1303
1304
1305%------------------------------------------------------------------------
1306function num_first_i_Callback(hObject, eventdata, handles)
1307%------------------------------------------------------------------------
1308num_last_i_Callback(hObject, eventdata, handles)
1309
1310%------------------------------------------------------------------------
1311function num_last_i_Callback(hObject, eventdata, handles)
1312%------------------------------------------------------------------------
1313SeriesData=get(handles.series,'UserData');
1314if ~isfield(SeriesData,'Time')
1315    SeriesData.Time{1}=[];
1316end
1317displ_time(handles);
1318
1319%------------------------------------------------------------------------
1320function num_first_j_Callback(hObject, eventdata, handles)
1321%------------------------------------------------------------------------
1322 num_last_j_Callback(hObject, eventdata, handles)
1323
1324%------------------------------------------------------------------------
1325function num_last_j_Callback(hObject, eventdata, handles)
1326%------------------------------------------------------------------------
1327first_j=str2num(get(handles.num_first_j,'String'));
1328last_j=str2num(get(handles.num_last_j,'String'));
1329ref_j=ceil((first_j+last_j)/2);
1330set(handles.ref_j,'String', num2str(ref_j))
1331ref_j_Callback(hObject, eventdata, handles)
1332SeriesData=get(handles.series,'UserData');
1333if ~isfield(SeriesData,'Time')
1334    SeriesData.Time{1}=[];
1335end
1336displ_time(handles);
1337
1338
1339%------------------------------------------------------------------------
1340function ref_i_Callback(hObject, eventdata, handles)
1341%------------------------------------------------------------------------
1342mode_list=get(handles.mode,'String');
1343mode_value=get(handles.mode,'Value');
1344mode=mode_list{mode_value};
1345SeriesData=get(handles.series,'UserData');
1346%NomTypeCell=get(handles.NomType,'String');
1347NomTypeCell=SeriesData.NomType;
1348if ~isempty(NomTypeCell)
1349Val=get(handles.NomType,'Value');
1350NomType=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
1358end
1359
1360%------------------------------------------------------------------------
1361function ref_j_Callback(hObject, eventdata, handles)
1362%------------------------------------------------------------------------
1363mode_list=get(handles.mode,'String');
1364mode_value=get(handles.mode,'Value');
1365mode=mode_list{mode_value};
1366SeriesData=get(handles.series,'UserData');
1367NomTypeCell=SeriesData.NomType;
1368if ~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
1376end
1377
1378%------------------------------------------------------------------------
1379% --- Executes on selection change in ACTION.
1380function ACTION_Callback(hObject, eventdata, handles)
1381%------------------------------------------------------------------------
1382global nb_builtin_ACTION
1383list_ACTION=get(handles.ACTION,'String');% list menu fields
1384index_ACTION=get(handles.ACTION,'Value');% selected string index
1385ACTION= list_ACTION{index_ACTION}; % selected function name
1386path_series=which('series');%path to series.m
1387list_path=get(handles.ACTION,'UserData');%list of recorded paths to functions of the list ACTION
1388default_file=fullfile(list_path{end},ACTION);
1389% add a new function to the menu if the selected item is 'more...'
1390if 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
1442end
1443
1444%check the current path to the selected function
1445PathName=list_path{index_ACTION};%current recorded path
1446set(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')
1454set(handles.num_NbSlice,'Visible','off')
1455set(handles.NbSlice_title,'Visible','off')
1456set(handles.VelTypeMenu,'Visible','off');
1457set(handles.VelType_text,'Visible','off');
1458set(handles.VelTypeMenu_1,'Visible','off');
1459set(handles.VelType_text_1,'Visible','off');
1460view_FieldMenu(handles,'off')
1461view_FieldMenu_1(handles,'off')
1462set(handles.FieldTransform,'Visible','off')
1463% view_TRANSFORM(handles,'off')Visible','off')
1464set(handles.Objects,'Visible','off');
1465set(handles.GetMask,'Visible','off')
1466set(handles.Mask,'Visible','off')
1467% set(handles.GetObject,'Visible','off');
1468set(handles.OutputDir,'Visible','off');
1469% set(handles.PARAMETERS_frame,'Visible','off');
1470% set(handles.PARAMETERS_title,'Visible','off');
1471set(handles.ParamKey,'Visible','off')
1472set(handles.ParamVal,'Visible','off')
1473ParamKey={};
1474set(handles.FieldMenu,'Enable','off')
1475set(handles.VelTypeMenu,'Enable','off')
1476set(handles.FieldMenu_1,'Enable','off')
1477set(handles.VelTypeMenu_1,'Enable','off')
1478set(handles.transform_fct,'Enable','off')
1479%set the displayed GUI item needed for input parameters
1480if ~isequal(path_series,PathName)
1481    addpath(PathName)
1482end
1483eval(['h_function=@' ACTION ';']);
1484try
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})
1489end
1490if ~isequal(path_series,PathName)
1491    rmpath(PathName)
1492end
1493varargout=h_function();
1494Param_list={};
1495
1496%nb_series=length(RootFile);
1497% FileExt=get(handles.FileExt,'String');
1498% nb_series=length(FileExt);
1499InputFiles=get(handles.InputTable,'Data')
1500FileExt=InputFiles(:,5);
1501checkcell=find(cellfun('isempty',FileExt)~=0);
1502nb_series=0;
1503if ~isempty(checkcell)
1504nb_series=checkcell(end);
1505end
1506% nb_series=size(InputFiles,1)
1507testima_series=1; %test for a list of images only
1508testima=1;
1509testima_1=1;
1510testciv_series=1;
1511for 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
1526end
1527for 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
1613end
1614if ~isempty(Param_list)
1615    set(handles.ParamKey,'String',Param_list)
1616    set(handles.ParamVal,'Visible','on')
1617end
1618
1619%------------------------------------------------------------------------
1620% --- Executes on selection change in FieldMenu.
1621function FieldMenu_Callback(hObject, eventdata, handles)
1622%------------------------------------------------------------------------
1623field_str=get(handles.FieldMenu,'String');
1624field_index=get(handles.FieldMenu,'Value');
1625field=field_str{field_index(1)};
1626if 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
1636elseif 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)
1644end
1645
1646%------------------------------------------------------------------------
1647% --- Executes on selection change in FieldMenu_1.
1648function FieldMenu_1_Callback(hObject, eventdata, handles)
1649%------------------------------------------------------------------------
1650field_str=get(handles.FieldMenu_1,'String');
1651field_index=get(handles.FieldMenu_1,'Value');
1652field=field_str{field_index};
1653if 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
1664elseif 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)
1672end   
1673
1674
1675%%%%%%%%%%%%%
1676function [ind_remove]=find_pairs(dirpair,ind_i,last_i)
1677indsel=ind_i;
1678indiff=diff(ind_i); %test index increment to detect multiplets (several pairs with the same index ind_i) and holes in the series
1679indiff=[1 indiff last_i-ind_i(end)+1];%for testing gaps with the imposed bounds
1680if ~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
1697end
1698
1699%------------------------------------------------------------------------
1700% --- determine the list of index pairs of processing file
1701function [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%------------------------------------------------------------------------
1703num_i1=num_i;% set of first image numbers by default
1704num_i2=num_i;
1705num_j1=num_j;
1706num_j2=num_j;
1707num_i_out=num_i;
1708num_j_out=num_j;
1709% if isequal (NomType,'_1-2_1') || isequal (NomType,'_1-2')
1710if 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);
1722elseif 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   
1737end
1738
1739%------------------------------------------------------------------------
1740% ---- find the times corresponding to the first and last indices of a series
1741function displ_time(handles)
1742%------------------------------------------------------------------------
1743SeriesData=get(handles.series,'UserData');%
1744first_i=str2num(get(handles.num_first_i,'String'));
1745first_j=str2num(get(handles.num_first_j,'String'));
1746last_i=str2num(get(handles.num_last_i,'String'));
1747last_j=str2num(get(handles.num_last_j,'String'));
1748InputTable=get(handles.InputTable,'Data');
1749NomType=InputTable(:,4);
1750% NomType=SeriesData.NomType;
1751mode_list=get(handles.mode,'String');
1752index_mode=get(handles.mode,'Value');
1753mode=mode_list{index_mode};
1754
1755time_first=[];
1756time_last=[];
1757if ~isfield(SeriesData,'Time')
1758    SeriesData.Time{1}=[];
1759end
1760for 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);
1831end
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.
1839function GetObject_Callback(hObject, eventdata, handles)
1840%------------------------------------------------------------------------
1841SeriesData=get(handles.series,'UserData');
1842value=get(handles.GetObject,'Value');
1843if 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
1888else
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
1893end
1894set(handles.series,'UserData',SeriesData)
1895
1896%--------------------------------------------------------------
1897function GetMask_Callback(hObject, eventdata, handles)
1898value=get(handles.GetMask,'Value');
1899if value
1900    msgbox_uvmat('ERROR','not implemented yet')
1901end
1902%--------------------------------------------------------------
1903
1904%-------------------------------------------------------------------
1905%'uv_ncbrowser': interactively calls the netcdf file browser 'get_field.m'
1906function 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% ------------------------------------------------------------------
1916function MenuHelp_Callback(hObject, eventdata, handles)
1917%-------------------------------------------------------------------
1918path_to_uvmat=which ('uvmat');% check the path of uvmat
1919pathelp=fileparts(path_to_uvmat);
1920helpfile=fullfile(pathelp,'uvmat_doc','uvmat_doc.html');
1921if isempty(dir(helpfile)), msgbox_uvmat('ERROR','Please put the help file uvmat_doc.html in the sub-directory /uvmat_doc of the UVMAT package')
1922else
1923    addpath (fullfile(pathelp,'uvmat_doc'))
1924    web([helpfile '#series'])
1925end
1926
1927%-------------------------------------------------------------------
1928% --- Executes on selection change in transform_fct.
1929function transform_fct_Callback(hObject, eventdata, handles)
1930%-------------------------------------------------------------------
1931global nb_transform
1932
1933menu=get(handles.transform_fct,'String');
1934ind_coord=get(handles.transform_fct,'Value');
1935coord_option=menu{ind_coord};
1936list_transform=get(handles.transform_fct,'UserData');
1937ff=functions(list_transform{end});
1938if 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
1976end
1977
1978%check the current path to the selected function
1979if ~isempty(list_transform{ind_coord})
1980func=functions(list_transform{ind_coord});
1981set(handles.path_transform,'String',fileparts(func.file)); %show the path to the senlected function
1982else
1983   set(handles.path_transform,'String',''); %show the path to the senlected function
1984end
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)
2131set(handles.REFRESH_INDICES,'BackgroundColor',[0.7 0.7 0.7])
2132InputTable=get(handles.InputTable,'Data');
2133check_lines=get(handles.REFRESH_INDICES,'UserData');
2134
2135%% check the indices and FileTypes for each series (limited to the new ones to save time)
2136for 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
2154end
2155set(handles.InputTable,'Data',InputTable)
2156SeriesData=get(handles.series,'UserData');
2157
2158state_j='off';
2159state_Pairs='off';
2160state_InputFields='off';
2161val=get(handles.ListView,'Value');
2162ListViewString={''};
2163if ~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
2180end
2181set(handles.ListView,'Value',val)
2182set(handles.ListView,'String',ListViewString)
2183if strcmp(state_Pairs,'on')
2184    ListView_Callback(hObject,eventdata,handles)
2185end
2186set(handles.Pairs,'Visible',state_InputFields)
2187enable_j(handles,state_j)
2188set(handles.REFRESH_INDICES,'BackgroundColor',[1 0 0])
2189set(handles.REFRESH_INDICES,'visible','off')
2190
2191% update min and max indices for a series
2192function [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
2195errormsg='';
2196[RootPath,RootFile,i1_series,i2_series,j1_series,j2_series,NomType,FileType,Object]=find_file_series(fileinput);
2197if isempty(RootFile)&&isempty(i1_series)
2198    errormsg='no input file in the series';
2199    return
2200end
2201[tild,tild,FileExt]=fileparts(fileinput);
2202
2203MinIndex=get(handles.MinIndex,'Data');
2204MaxIndex=get(handles.MaxIndex,'Data');
2205MinIndex_i=min(i1_series(i1_series>0));
2206if ~isempty(i2_series)
2207    MaxIndex_i=max(i2_series(i2_series>0));
2208else
2209    MaxIndex_i=max(i1_series(i1_series>0));
2210end
2211MinIndex_j=min(j1_series(j1_series>0));
2212if ~isempty(j2_series)
2213    MaxIndex_j=max(j2_series(j2_series>0));
2214else
2215    MaxIndex_j=max(j1_series(j1_series>0));
2216end
2217MinIndex{iview,1}=MinIndex_i;
2218MinIndex{iview,2}=MinIndex_j;
2219MaxIndex{iview,1}=MaxIndex_i;
2220MaxIndex{iview,2}=MaxIndex_j;
2221set(handles.MinIndex,'Data',MinIndex)
2222set(handles.MaxIndex,'Data',MaxIndex)
2223SeriesData=get(handles.series,'UserData');
2224SeriesData.i1_series{iview}=i1_series;
2225SeriesData.i2_series{iview}=i2_series;
2226SeriesData.j1_series{iview}=j1_series;
2227SeriesData.j2_series{iview}=j2_series;
2228SeriesData.FileType{iview}=FileType;
2229
2230%% represents the set of existing files as an image
2231set(handles.waitbar_frame,'Units','pixels')
2232pos=get(handles.waitbar_frame,'Position');
2233xima=0.5:pos(3)-0.5;% pixel positions on the image representing the existing file indices
2234yima=0.5:pos(4)-0.5;
2235[XIma,YIma]=meshgrid(xima,yima);
2236nb_i=size(i1_series,1);
2237nb_j=size(i1_series,2);
2238ind_i=(0.5:nb_i-0.5)*pos(3)/nb_i;
2239ind_j=(0.5:nb_j-0.5)*pos(4)/nb_j;
2240[Ind_i,Ind_j]=meshgrid(ind_i,ind_j);
2241CData=zeros([size(XIma) 3]);
2242file_ima=double((i1_series(:,:,1)>0)');
2243if numel(file_ima)>=2
2244if size(file_ima,1)==1
2245    CLine=interp1(ind_i,file_ima,xima,'nearest');
2246    CData(:,:,2)=ones(size(yima'))*CLine;
2247else
2248    CData(:,:,2)=interp2(Ind_i,Ind_j,file_ima,XIma,YIma,'nearest');
2249end
2250set(handles.waitbar_frame,'CData',CData)
2251end
2252set(handles.waitbar_frame,'Units','normalized')
2253
2254%% enable field and veltype menus
2255testfield=isequal(get(handles.FieldMenu,'enable'),'on');
2256testfield_1=isequal(get(handles.FieldMenu_1,'enable'),'on');
2257testveltype=isequal(get(handles.VelTypeMenu,'enable'),'on');
2258testveltype_1=isequal(get(handles.VelTypeMenu_1,'enable'),'on');
2259testtransform=isequal(get(handles.transform_fct,'Enable'),'on');
2260testnc=0;
2261testnc_1=0;
2262testcivx=0;
2263testcivx_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
2280if 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
2291else
2292    view_FieldMenu(handles,'off')
2293end
2294if 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
2305else
2306    view_FieldMenu_1(handles,'off')
2307end
2308if testveltype && testcivx
2309    set(handles.VelTypeMenu,'Visible','on')
2310    set(handles.VelType_text,'Visible','on');
2311else
2312    set(handles.VelTypeMenu,'Visible','off')
2313    set(handles.VelType_text,'Visible','off');
2314end
2315if testveltype_1 && testcivx_1
2316    set(handles.VelTypeMenu_1,'Visible','on')
2317    set(handles.VelType_text_1,'Visible','on');
2318else
2319    set(handles.VelTypeMenu_1,'Visible','off')
2320    set(handles.VelType_text_1,'Visible','off');
2321end
2322if testtransform && (testcivx || testima)
2323    set(handles.FieldTransform,'Visible','on')
2324%      view_TRANSFORM(handles,'on')
2325else
2326    set(handles.FieldTransform,'Visible','off')
2327%     view_TRANSFORM(handles,'off')
2328end
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%%%%%%%%%%%%%%%%%%%%%%%%%%%
2336ext_imadoc='';
2337FileBase=fullfile(RootPath,RootFile);
2338if isequal(FileExt,'.xml')||isequal(FileExt,'.civ')
2339    ext_imadoc=FileExt;
2340elseif exist([FileBase '.xml'],'file')
2341    ext_imadoc='.xml';
2342elseif exist([FileBase '.civ'],'file')
2343    ext_imadoc='.civ';
2344end
2345%read the ImaDoc file
2346XmlData=[];
2347NbSlice_calib={};
2348if 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 
2370elseif 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 
2376end 
2377
2378
2379%% number of slices
2380if 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))
2388end
2389% set(handles.mode,'Visible','off') % do not show index pairs by default
2390set(handles.Pairs,'Visible','off')
2391% set(handles.ref_i,'Visible','off')
2392% set(handles.ref_i_text,'Visible','off')
2393testpair=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
2405set(handles.series,'UserData',SeriesData)
2406
2407
2408
2409% --- Executes on button press in BATCH.
2410function 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)
2414Series=read_GUI(handles.series);
2415t=struct2xml(Series);
2416save(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
2423path_series=which('series');
2424list_path=get(handles.ACTION,'UserData');
2425index=get(handles.ACTION,'Value');
2426fct_path=list_path{index}; %path stored for the function ACTION
2427if ~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
2436end
2437eval(['h_fun=@' action ';'])%create a function handle for ACTION
2438if ~isequal(fct_path,path_series)
2439        rmpath(fct_path)% add the prescribed path if not the current one   
2440end
2441
2442h_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
2446function txt_Pairs_Callback(hObject, eventdata, handles)
2447
2448%------------------------------------------------------------------------
2449% --- Executes on selection change in ListView.
2450function ListView_Callback(hObject, eventdata, handles)
2451%------------------------------------------------------------------------   
2452ListViewString=get(handles.ListView,'String');
2453if isempty(ListViewString)
2454    ListViewString={''};
2455end
2456ListViewValue=get(handles.ListView,'Value');
2457View=str2double(ListViewString{ListViewValue});
2458if isnan(View)
2459    set(handles.Pairs,'Visible','off')
2460else
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)
2480end
2481
2482   
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