source: trunk/src/series.m @ 29

Last change on this file since 29 was 29, checked in by sommeria, 11 years ago

read_imadoc suppressed (obsolete, replaced by imadoc2struct)
update_imadoc: bug repaired: existing xml file was erased
various cleaning (deals with non existing input file for series and uvmat)

File size: 90.9 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 CoordType (menu for coordinate transforms)
9%      .menu_coord_val: value for CoordType (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
58% Choose default command line output for series
59handles.output = hObject;
60% Update handles structure
61guidata(hObject, handles);
62%default initial parameters
63
64%load the list of previously browsed files in menus Open and Open_1
65dir_perso=prefdir;
66profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
67if exist(profil_perso,'file')
68     h=load (profil_perso);
69     if isfield(h,'MenuFile_1')
70          set(handles.MenuFile_1,'Label',h.MenuFile_1);
71          set(handles.MenuFile_insert_1,'Label',h.MenuFile_1);
72     end
73     if isfield(h,'MenuFile_1')
74          set(handles.MenuFile_2,'Label',h.MenuFile_2);
75          set(handles.MenuFile_insert_2,'Label',h.MenuFile_2);
76     end
77     if isfield(h,'MenuFile_1')
78          set(handles.MenuFile_3,'Label',h.MenuFile_3);
79          set(handles.MenuFile_insert_3,'Label',h.MenuFile_3);
80     end
81     if isfield(h,'MenuFile_1')
82          set(handles.MenuFile_4,'Label',h.MenuFile_4);
83          set(handles.MenuFile_insert_4,'Label',h.MenuFile_4);
84     end
85     if isfield(h,'MenuFile_1')
86          set(handles.MenuFile_5,'Label',h.MenuFile_5);
87          set(handles.MenuFile_insert_5,'Label',h.MenuFile_5);
88     end
89end
90
91%check default input data
92if ~exist('param','var')
93    param=[]; %default
94end
95
96%file name and browser initialisation
97if isfield(param,'menu_coord_str')
98    set(handles.CoordType,'String',param.menu_coord_str)
99end
100if isfield(param,'menu_coord_val')
101    set(handles.CoordType,'Value',param.menu_coord_val);
102else
103     set(handles.CoordType,'Value',1);%default
104end
105
106if isfield(param,'FileName')
107    if isfield(param,'FileName_1')
108        update_file(hObject, eventdata, handles,param.FileName_1,0)
109        update_file(hObject, eventdata, handles,param.FileName,1)
110    else
111        update_file(hObject, eventdata, handles,param.FileName,0)
112    end
113end 
114
115%fields input initialisation
116if isfield(param,'list_fields')&& isfield(param,'index_fields') &&~isempty(param.list_fields) &&~isempty(param.index_fields)
117    set(handles.FieldMenu,'String',param.list_fields);% list menu fields
118    set(handles.FieldMenu,'Value',param.index_fields);% selected string index
119    FieldCell{1}=param.list_fields{param.index_fields};
120end
121if isfield(param,'civ1')&& islogical(param.civ1) && isfield(param,'civ2')&& islogical(param.civ2)&...
122        isfield(param,'interp1')&& islogical(param.interp1)&&isfield(param,'interp2')&& islogical(param.interp2)&...
123        isfield(param,'filter1')&& islogical(param.filter1)&&isfield(param,'filter2')&& islogical(param.filter2)
124    set(handles.civ1,'Value',param.civ1);
125    set(handles.civ2,'Value',param.civ1);
126    set(handles.interp1,'Value',param.interp1);
127    set(handles.interp2,'Value',param.interp2);
128    set(handles.filter1,'Value',param.filter1);
129    set(handles.filter2,'Value',param.filter2);
130end
131set(hObject,'WindowButtonUpFcn',{@mouse_up_gui,handles})
132NomType_Callback(hObject, eventdata, handles)
133
134%loads the information stored in prefdir to initiate the browser and the list of functions
135menu_str={'check_files';'aver_stat';'time_series';'merge_proj';'clean_civ_cmx'};
136nb_builtin=numel(menu_str); %number of functions
137 
138%remove from the list the last option 'more...'
139[path_series,name,ext]=fileparts(which('series'));
140path_series=fullfile(path_series,'/series');%path of the function 'series'
141
142for ilist=1:length(menu_str)
143    fct_path{ilist,1}=path_series;%paths of the fuctions buil-in in 'series.m'
144end
145dir_perso=prefdir;
146profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
147if exist(profil_perso,'file')
148    h=load (profil_perso);
149    if isfield(h,'series_fct') && iscell(h.series_fct)
150         for ilist=1:length(h.series_fct)
151             [path,file]=fileparts(h.series_fct{ilist});
152             fct_path=[fct_path; {path}];%concatene the list of paths
153             menu_str=[menu_str; {file}];
154         end
155    end
156end
157
158menu_str=[menu_str;{'more...'}];
159set(handles.ACTION,'String',menu_str)
160set(handles.ACTION,'UserData',fct_path)% store the list of path in UserData of ACTION
161
162% display the GUI for the default action 'check_files'
163ACTION_Callback(hObject, eventdata, handles)
164
165%--------------------------------------------------------------
166% --- Outputs from this function are returned to the command line.
167%-----------------------------------------------------------------
168function varargout = series_OutputFcn(hObject, eventdata, handles)
169% varargout  cell array for returning output args (see VARARGOUT);
170% hObject    handle to figure
171% eventdata  reserved - to be defined in a future version of MATLAB
172% handles    structure with handles and user data (see GUIDATA)
173% Get default command line output from handles structure
174varargout{1} = handles.output;
175
176
177% --------------------------------------------------------------------
178function MenuBrowse_Callback(hObject, eventdata, handles)
179
180RootPathCell=get(handles.RootPath,'String');
181SubDirCell=get(handles.SubDir,'String'); 
182RootFileCell=get(handles.RootFile,'String');
183oldfile=''; %default
184if isempty(RootPathCell)|isequal(RootPathCell,{''})%loads the previously stored file name and set it as default in the file_input box
185     dir_perso=prefdir;
186     profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
187     if exist(profil_perso,'file')
188          h=load (profil_perso);
189         if isfield(h,'filebase')&ischar(h.filebase)
190                 oldfile=h.filebase;
191         end
192         if isfield(h,'RootPath')&ischar(h.RootPath)
193                 oldfile=h.RootPath;
194         end
195     end
196 else
197     oldfile=fullfile(RootPathCell{1},SubDirCell{1},RootFileCell{1});
198 end
199[FileName, PathName, filterindex] = uigetfile( ...
200       {'*.xml;*.xls;*.png;*.tif;*.avi;*.AVI;*.nc', ' (*.xml,*.xls, *.png,*.tif, *.avi,*.nc)';
201       '*.xml',  '.xml files '; ...
202        '*.xls',  '.xls files '; ...
203        '*.png','.png image files'; ...
204        '*.tif','.tif image files'; ...
205        '*.avi;*.AVI','.avi movie files'; ...
206        '*.nc','.netcdf files'; ...
207        '*.*',  'All Files (*.*)'}, ...
208        'Pick a file',oldfile);
209fileinput=[PathName FileName];%complete file name
210testblank=findstr(fileinput,' ');%look for blanks
211if ~isempty(testblank)
212    errordlg('forbidden input file name: contain blanks')
213    return
214end
215sizf=size(fileinput);
216if (~ischar(fileinput)|~isequal(sizf(1),1)),return;end
217[path,name,ext]=fileparts(fileinput);
218SeriesData=[];%dfault
219if isequal(ext,'.xml')
220    errordlg('input file type not implemented')%A Faire: ouvrir le fichier pour naviguer
221elseif isequal(ext,'.xls')
222    errordlg('input file type not implemented')%A Faire: ouvrir le fichier pour naviguer
223else
224    update_file(hObject, eventdata, handles,fileinput,0)
225     %update list of recent files in the menubar
226    MenuFile_1=fileinput;
227    MenuFile_2=get(handles.MenuFile_1,'Label');
228    MenuFile_3=get(handles.MenuFile_2,'Label');
229    MenuFile_4=get(handles.MenuFile_3,'Label');
230    MenuFile_5=get(handles.MenuFile_4,'Label');
231    set(handles.MenuFile_1,'Label',MenuFile_1)
232    set(handles.MenuFile_2,'Label',MenuFile_2)
233    set(handles.MenuFile_3,'Label',MenuFile_3)
234    set(handles.MenuFile_4,'Label',MenuFile_4)
235    set(handles.MenuFile_5,'Label',MenuFile_5)
236    set(handles.MenuFile_insert_1,'Label',MenuFile_1)
237    set(handles.MenuFile_insert_2,'Label',MenuFile_2)
238    set(handles.MenuFile_insert_3,'Label',MenuFile_3)
239    set(handles.MenuFile_insert_4,'Label',MenuFile_4)
240    set(handles.MenuFile_insert_5,'Label',MenuFile_5)
241    dir_perso=prefdir;
242    profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
243    if exist(profil_perso,'file')
244        save (profil_perso,'MenuFile_1','MenuFile_2','MenuFile_3','MenuFile_4', 'MenuFile_5','-append'); %store the file names for future opening of uvmat
245    else
246        txt=ver;
247        Release=txt(1).Release;
248        relnumb=str2num(Release(3:4));
249        if relnumb >= 14
250            save (profil_perso,'MenuFile_1','MenuFile_2','MenuFile_3','MenuFile_4', 'MenuFile_5','-V6'); %store the file names for future opening of uvmat
251        else
252            save (profil_perso,'MenuFile_1','MenuFile_2','MenuFile_3','MenuFile_4', 'MenuFile_5'); %store the file names for future opening of uvmat
253        end
254    end
255end
256% set(hseries,'UserData',SeriesData);
257% RootFile_Callback(hObject, eventdata, handles);
258% FileExt_Callback(hObject, eventdata, handles);
259% NomType_Callback(hObject, eventdata, handles)
260% mode_Callback(hObject, eventdata, handles)
261
262
263% --------------------------------------------------------------------
264function MenuFile_1_Callback(hObject, eventdata, handles)
265fileinput=get(handles.MenuFile_1,'Label');
266update_file(hObject, eventdata, handles,fileinput,0)
267
268% --------------------------------------------------------------------
269function MenuFile_2_Callback(hObject, eventdata, handles)
270fileinput=get(handles.MenuFile_2,'Label');
271update_file(hObject, eventdata, handles,fileinput,0)
272
273% --------------------------------------------------------------------
274function MenuFile_3_Callback(hObject, eventdata, handles)
275fileinput=get(handles.MenuFile_3,'Label');
276update_file(hObject, eventdata, handles,fileinput,0)
277
278% --------------------------------------------------------------------
279function MenuFile_4_Callback(hObject, eventdata, handles)
280fileinput=get(handles.MenuFile_4,'Label');
281update_file(hObject, eventdata, handles,fileinput,0)
282
283% --------------------------------------------------------------------
284function MenuFile_5_Callback(hObject, eventdata, handles)
285fileinput=get(handles.MenuFile_5,'Label');
286update_file(hObject, eventdata, handles,fileinput,0)
287
288% --------------------------------------------------------------------
289function MenuBrowse_insert_Callback(hObject, eventdata, handles)
290
291RootPathCell=get(handles.RootPath,'String');
292RootFileCell=get(handles.RootFile,'String');
293oldfile=''; %default
294if isempty(RootPathCell)|isequal(RootPathCell,{''})%loads the previously stored file name and set it as default in the file_input box
295     dir_perso=prefdir;
296     profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
297     if exist(profil_perso,'file')
298          h=load (profil_perso);
299         if isfield(h,'filebase')&ischar(h.filebase)
300                 oldfile=h.filebase;
301         end
302         if isfield(h,'RootPath')&ischar(h.RootPath)
303                 oldfile=h.RootPath;
304         end
305     end
306 else
307     oldfile=fullfile(RootPathCell{1},RootFileCell{1});
308 end
309[FileName, PathName, filterindex] = uigetfile( ...
310       {'*.xml;*.xls;*.png;*.avi;*.AVI;*.nc', ' (*.xml,*.xls, *.png, *.avi,*.nc)';
311       '*.xml',  '.xml files '; ...
312        '*.xls',  '.xls files '; ...
313        '*.png','.png image files'; ...
314        '*.avi;*.AVI','.avi movie files'; ...
315        '*.nc','.netcdf files'; ...
316        '*.*',  'All Files (*.*)'}, ...
317        'Pick a file',oldfile);
318fileinput=[PathName FileName];%complete file name
319testblank=findstr(fileinput,' ');%look for blanks
320if ~isempty(testblank)
321    errordlg('forbidden input file name: contain blanks')
322    return
323end
324sizf=size(fileinput);
325if (~ischar(fileinput)|~isequal(sizf(1),1)),return;end
326[path,name,ext]=fileparts(fileinput);
327SeriesData=[];%dfault
328if isequal(ext,'.xml')
329    errordlg('input file type not implemented')%A Faire: ouvrir le fichier pour naviguer
330elseif isequal(ext,'.xls')
331    errordlg('input file type not implemented')%A Faire: ouvrir le fichier pour naviguer
332else
333    update_file(hObject, eventdata, handles,fileinput,1)
334    %update list of recent files in the menubar
335    MenuFile_1=fileinput;
336    MenuFile_2=get(handles.MenuFile_1,'Label');
337    MenuFile_3=get(handles.MenuFile_2,'Label');
338    MenuFile_4=get(handles.MenuFile_3,'Label');
339    MenuFile_5=get(handles.MenuFile_4,'Label');
340    set(handles.MenuFile_1,'Label',MenuFile_1)
341    set(handles.MenuFile_2,'Label',MenuFile_2)
342    set(handles.MenuFile_3,'Label',MenuFile_3)
343    set(handles.MenuFile_4,'Label',MenuFile_4)
344    set(handles.MenuFile_5,'Label',MenuFile_5)
345    set(handles.MenuFile_insert_1,'Label',MenuFile_1)
346    set(handles.MenuFile_insert_2,'Label',MenuFile_2)
347    set(handles.MenuFile_insert_3,'Label',MenuFile_3)
348    set(handles.MenuFile_insert_4,'Label',MenuFile_4)
349    set(handles.MenuFile_insert_5,'Label',MenuFile_5)
350    dir_perso=prefdir;
351    profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
352    if exist(profil_perso,'file')
353        save (profil_perso,'MenuFile_1','MenuFile_2','MenuFile_3','MenuFile_4', 'MenuFile_5','-append'); %store the file names for future opening of uvmat
354    else
355        txt=ver;
356        Release=txt(1).Release;
357        relnumb=str2num(Release(3:4));
358        if relnumb >= 14
359            save (profil_perso,'MenuFile_1','MenuFile_2','MenuFile_3','MenuFile_4', 'MenuFile_5','-V6'); %store the file names for future opening of uvmat
360        else
361            save (profil_perso,'MenuFile_1','MenuFile_2','MenuFile_3','MenuFile_4', 'MenuFile_5'); %store the file names for future opening of uvmat
362        end
363    end
364end
365%------------------------------------------------
366
367% --------------------------------------------------------------------
368function MenuFile_insert_1_Callback(hObject, eventdata, handles)
369fileinput=get(handles.MenuFile_insert_1,'Label');
370update_file(hObject, eventdata, handles,fileinput,1)
371
372% --------------------------------------------------------------------
373function MenuFile_insert_2_Callback(hObject, eventdata, handles)
374fileinput=get(handles.MenuFile_insert_2,'Label');
375update_file(hObject, eventdata, handles,fileinput,1)
376
377% --------------------------------------------------------------------
378function MenuFile_insert_3_Callback(hObject, eventdata, handles)
379fileinput=get(handles.MenuFile_insert_3,'Label');
380update_file(hObject, eventdata, handles,fileinput,1)
381
382% --------------------------------------------------------------------
383function MenuFile_insert_4_Callback(hObject, eventdata, handles)
384fileinput=get(handles.MenuFile_insert_4,'Label');
385update_file(hObject, eventdata, handles,fileinput,1)
386
387% --------------------------------------------------------------------
388function MenuFile_insert_5_Callback(hObject, eventdata, handles)
389fileinput=get(handles.MenuFile_insert_5,'Label');
390update_file(hObject, eventdata, handles,fileinput,1)
391
392% --------------------------------------------------------------------
393% refresh the GUI data after introduction of a new file series
394function update_file(hObject, eventdata, handles,fileinput,addtest)
395%hseries=get(handles.RootPath,'parent'); 
396if ~exist(fileinput,'file')
397    msgbox_uvmat('ERROR',['input file ' fileinput  ' does not exist'])
398    return
399end
400hseries=handles.figure1;
401% refresh input root name, indices, file extension and nomenclature
402[RootPath,RootFile,field_count,str2,str_a,str_b,FileExt,NomType,SubDir]=name2display(fileinput);
403%check for movie image files
404if ~isempty(FileExt)
405if ~isempty(imformats(FileExt(2:end)))
406    imainfo=imfinfo(fileinput);     
407    if length(imainfo) >1 %case of image with multiple frames
408        NomType='*';
409        [RootPath,RootFile]=fileparts(fileinput);
410    end
411end
412end
413NcType='none';%default
414if isequal(FileExt,'.nc')
415   Data=nc2struct(fileinput,[]);
416   if isfield(Data,'absolut_time_T0')
417       NcType='civx'; % test for civx velocity fields
418   end
419end
420
421set(handles.RootPath,'Value',1)
422set(handles.SubDir,'Value',1)
423set(handles.RootFile,'Value',1)
424set(handles.NomType,'Value',1)
425set(handles.FileExt,'Value',1)
426set(handles.nb_field,'Value',1)
427set(handles.nb_field2,'Value',1)
428if addtest
429    SeriesData=get(hseries,'UserData');
430    SeriesData.displ_num=[0 0 0 0;SeriesData.displ_num];
431    SeriesData.CurrentInputFile_1=SeriesData.CurrentInputFile;
432    RootPathCell=[{RootPath}; get(handles.RootPath,'String')] ;
433    SubDirCell=[{SubDir}; get(handles.SubDir,'String')];
434    RootFileCell=[{RootFile}; get(handles.RootFile,'String')];
435    NomTypeCell=[{NomType}; SeriesData.NomType];
436    FileExtCell=[{FileExt}; get(handles.FileExt,'String')];
437    NcTypeCell=[{NcType};SeriesData.NcType];
438    set(handles.NomType,'String',[{};get(handles.NomType,'String')])
439else
440    SeriesData=[];%re-initialisation
441    SeriesData.displ_num=[0 0 0 0];
442    RootPathCell={RootPath};
443    SubDirCell={SubDir};
444    RootFileCell={RootFile};   
445    NomTypeCell={NomType};
446    FileExtCell={FileExt};   
447    NcTypeCell={NcType};
448end
449
450SeriesData.NomType=NomTypeCell;
451SeriesData.NcType=NcTypeCell;
452SeriesData.CurrentInputFile=fileinput;
453set(handles.RootPath,'String',RootPathCell);
454set(handles.SubDir,'String',SubDirCell);
455set(handles.RootFile,'String',RootFileCell);
456set(handles.NomType,'String',NomTypeCell);
457set(handles.FileExt,'String',FileExtCell); 
458
459%determine field indices
460ref_i=1; %default ref_i is a reference frame index used to find existing pairs from PIV
461if ~isempty(str2num(field_count))
462    ref_i=str2num(field_count);
463    if ~isempty(str2num(str2))
464        ref_i=floor((ref_i+str2num(str2))/2);% reference image number corresponding to the file
465        SeriesData.browse_Di=str2num(str2)-str2num(field_count);
466    end
467end
468set(handles.ref_i,'String',num2str(ref_i));
469set(handles.first_i,'String',num2str(ref_i));
470set(handles.last_i,'String',num2str(ref_i));
471ref_j=1; %default  ref_j is a reference frame index used to find existing pairs from PIV
472if ~isempty(str2num(str_a))
473    ref_j=str2num(str_a);
474    if ~isempty(str2num(str_b))
475        ref_j=floor((str2num(str_a)+str2num(str_b))/2);
476        SeriesData.browse_Dj=str2num(str_b)-str2num(str_a);
477    end         
478end
479set(handles.ref_j,'String',num2str(ref_j));
480set(handles.first_j,'String',num2str(ref_j))
481set(handles.last_j,'String',num2str(ref_j));
482%set(hseries,'UserData',SeriesData);
483
484%enable other menus and uicontrols
485set(handles.MenuOpen_insert,'Enable','on')
486set(handles.MenuFile_insert_1,'Enable','on')
487set(handles.MenuFile_insert_2,'Enable','on')
488set(handles.MenuFile_insert_3,'Enable','on')
489set(handles.MenuFile_insert_4,'Enable','on')
490set(handles.MenuFile_insert_5,'Enable','on')
491set(handles.RUN, 'Enable','On')
492set(handles.RUN,'BackgroundColor',[1 0 0])% set RUN button to red
493set(handles.RootPath,'BackgroundColor',[1 1 0]) % set RootPath edit box  to yellow
494drawnow
495
496TimeUnit=''; %default
497time=[];%default
498GeometryCalib=[];%default
499nb_field=[];%default
500nb_field2=[];%default
501SeriesData.PathCampaign=get(handles.PathCampaign,'String');
502
503% read timing and total frame number from the current file (movie files) !! may be overrid by xml file
504FileBase=fullfile(RootPath,RootFile);
505
506% nb_field{icell,1}='?';%default
507% nb_field2{icell,1}='?';%default
508testima=0; %test for image input
509if isequal(lower(FileExt),'.avi') %.avi file
510    testima=1;
511    info=aviinfo([FileBase FileExt]);
512    time=[0:1/info.FramesPerSecond:(info.NumFrames-1)/info.FramesPerSecond]';
513    nb_field=info.NumFrames;
514    nb_field2=1;
515elseif ~isempty(imformats(FileExt(2:end)))
516    testima=1;
517    if isequal(NomType,'*')% multi-frame image
518        imainfo=imfinfo([FileBase FileExt]);     
519        if length(imainfo) >1 %case of image with multiple frames
520            nb_field=length(imainfo);
521            nb_field2=1;
522        end
523    end
524elseif isequal(FileExt,'.vol')
525     testima=1;
526end
527
528% enable field and veltype menus
529testfield=isequal(get(handles.FieldMenu,'enable'),'on');
530testfield_1=isequal(get(handles.FieldMenu_1,'enable'),'on');
531testveltype=isequal(get(handles.VelTypeMenu,'enable'),'on');
532testveltype_1=isequal(get(handles.VelTypeMenu_1,'enable'),'on');
533testtransform=isequal(get(handles.CoordType,'Enable'),'on');
534testnc=0;
535testnc_1=0;
536testcivx=0;
537testcivx_1=0;
538if length(FileExtCell)==1 || length(FileExtCell)>2
539    for iview=1:length(FileExtCell)
540        if isequal(FileExtCell{iview},'.nc')
541            testnc=1;
542        end
543        if isequal(NcTypeCell{iview},'civx')
544            testcivx=1;
545        end
546    end
547elseif length(FileExtCell)==2
548    testnc=isequal(FileExtCell{1},'.nc');
549    testnc_1=isequal(FileExtCell{2},'.nc');
550    testcivx=isequal(NcTypeCell{1},'civx');
551    testcivx_1=isequal(NcTypeCell{2},'civx');
552end
553if testfield && testnc
554    view_FieldMenu(handles,'on')
555    if testcivx
556        menustr=get(handles.FieldMenu,'String');
557        if isequal(menustr,{'get_field...'})
558            set(handles.FieldMenu,'String',{'get_field...';'velocity';'vort';'div';'more...'})
559        end
560    else
561        set(handles.FieldMenu,'Value',1)
562        set(handles.FieldMenu,'String',{'get_field...'})
563    end
564else
565    view_FieldMenu(handles,'off')
566end
567if testfield_1 && testnc_1
568    view_FieldMenu_1(handles,'on')
569    if testcivx_1
570        menustr=get(handles.FieldMenu_1,'String');
571        if isequal(menustr,{'get_field...'})
572            set(handles.FieldMenu_1,'String',{'get_field...';'velocity';'vort';'div';'more...'})
573        end
574    else
575        set(handles.FieldMenu_1,'Value',1)
576        set(handles.FieldMenu_1,'String',{'get_field...'})
577    end
578else
579    view_FieldMenu_1(handles,'off')
580end
581if testveltype && testcivx
582    set(handles.VelTypeMenu,'Visible','on')
583    set(handles.VelType_text,'Visible','on');
584else
585    set(handles.VelTypeMenu,'Visible','off')
586    set(handles.VelType_text,'Visible','off');
587end
588if testveltype_1 && testcivx_1
589    set(handles.VelTypeMenu_1,'Visible','on')
590    set(handles.VelType_text_1,'Visible','on');
591else
592    set(handles.VelTypeMenu_1,'Visible','off')
593    set(handles.VelType_text_1,'Visible','off');
594end
595if testtransform && (testcivx || testima)
596     view_TRANSFORM(handles,'on')
597else
598    view_TRANSFORM(handles,'off')
599end
600if ~isequal(FileExt,'.nc') && ~isequal(FileExt,'.cdf') && ~testima
601    msgbox_uvmat('ERROR',['invalid input file extension ' FileExt])
602    return
603end 
604
605%%%%%%%%   read image documentation file  if found%%%%%%%%%%%%%%%%%%%%%%%%%%%
606      %look for the file existence
607ext_imadoc='';
608if isequal(FileExt,'.xml')||isequal(FileExt,'.civ')
609    ext_imadoc=FileExt;
610elseif exist([FileBase '.xml'],'file')
611    ext_imadoc='.xml';
612elseif exist([FileBase '.civ'],'file')
613    ext_imadoc='.civ';
614end
615      %read the ImaDoc file
616% mode=''; %default
617% testheading=0; 
618XmlData=[];
619NbSlice_calib={};
620if isequal(ext_imadoc,'.xml')
621        [XmlData,warntext]=imadoc2struct([FileBase '.xml']);
622        if isfield(XmlData,'Heading') && isfield(XmlData.Heading,'ImageName')
623            [PP,FF,ext_ima_read]=fileparts(XmlData.Heading.ImageName);
624        end
625        if isfield(XmlData,'Time')
626            time=XmlData.Time;
627        end
628        if isfield(XmlData,'Camera')
629            if isfield(XmlData.Camera,'NbSlice')&& ~isempty(XmlData.Camera.NbSlice)
630                NbSlice_calib{iview}=XmlData.Camera.NbSlice;% Nbre of slices for Zindex in phys transform
631                if ~isequal(NbSlice_calib{iview},NbSlice_calib{1})
632                    msgbox_uvmat('WARNING','inconsistent number of Z indices for the two field series');
633                end
634            end
635            if isfield(XmlData.Camera,'TimeUnit')&& ~isempty(XmlData.Camera.TimeUnit)
636                TimeUnit=XmlData.Camera.TimeUnit;
637            end
638        end
639        if ~isempty(warntext)
640            msgbox_uvmat('WARNING',warntext)
641        end 
642elseif isequal(ext_imadoc,'.civ')
643    [error,XmlData.Time,TimeUnit,mode,npx,npy,pxcmx,pxcmy]=read_imatext([FileBase '.civ']);
644    time=XmlData.Time;
645    size(time)
646    GeometryCalib.R=[pxcmx 0 0; 0 pxcmy 0;0 0 0];
647    GeometryCalib.Tx=0;
648    GeometryCalib.Ty=0;
649    GeometryCalib.Tz=1;
650    GeometryCalib.dpx=1;
651    GeometryCalib.dpy=1;
652    GeometryCalib.sx=1;
653    GeometryCalib.Cx=0;
654    GeometryCalib.Cy=0;
655    GeometryCalib.f=1;
656    GeometryCalib.kappa1=0;
657    GeometryCalib.CoordUnit='cm';
658    XmlData.GeometryCalib=GeometryCalib;
659    if error==2, warntext=['no file ' FileBase '.civ'];
660    elseif error==1, warntext='inconsistent number of fields in the .civ file';
661    end 
662%     set(handles.npx,'String',num2str(npx));%fills nbre of pixels x box
663%     set(handles.npy,'String',num2str(npy));%fills nbre of pixels y box
664%     set(handles.pxcm,'String',num2str(pxcmx));%fills scale x (pixel/cm) box
665%     set(handles.pycm,'String',num2str(pxcmy));%fills scale y (pixel/cm) box
666%     set(handles.pxcm,'Visible','on');%fills scale x (pixel/cm) box
667%     set(handles.pycm,'Visible','on');%fills scale y (pixel/cm) box
668%     set(handles.view_xml,'Visible','on')
669%     set(handles.view_xml,'String','view .civ')
670end 
671if addtest
672    SeriesData.Time=[{time} SeriesData.Time];
673else
674   SeriesData.Time={time};
675end
676
677if ~isempty(time)
678    siztime=size(time);
679    nb_field=siztime(1);
680    nb_field2=siztime(2);
681end   
682set(handles.TimeUnit,'String',TimeUnit)
683if isempty(nb_field)
684    nb_field_str='?';
685    nb_field_str2='?';
686else
687    nb_field_str=num2str(nb_field);
688    nb_field_str2=num2str(nb_field2);
689end
690if addtest
691    nb_field_cell=[{nb_field_str} ;get(handles.nb_field,'String')];
692    nb_field2_cell=[{nb_field_str2} ;get(handles.nb_field2,'String')];
693else
694    nb_field_cell={nb_field_str};
695    nb_field2_cell={nb_field_str2};
696end
697set(handles.nb_field,'String',nb_field_cell);
698set(handles.nb_field2,'String',nb_field2_cell);
699set(hseries,'UserData',SeriesData);
700
701%number of slices
702if isfield(XmlData,'GeometryCalib') && isfield(XmlData.GeometryCalib,'SliceCoord')
703       siz=size(XmlData.GeometryCalib.SliceCoord);
704       if siz(1)>1
705           NbSlice=siz(1);
706       else
707           NbSlice=1;
708       end
709       set(handles.NbSlice,'String',num2str(NbSlice))
710end
711
712% set menus of index pairs
713NomType_Callback(hObject, eventdata, handles)
714
715dir_perso=prefdir;
716profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
717% save(profil_perso, 'FileBase'); %store the root name for future opening of uvmat
718if exist(profil_perso,'file')
719    save (profil_perso,'RootPath','SubDir','RootFile','NomType', '-append'); %store the root name for future opening of uvmat
720else
721    txt=ver;
722    Release=txt(1).Release;
723    relnumb=str2num(Release(3:4));
724    if relnumb >= 14
725        save (profil_perso,'RootPath','SubDir','RootFile','NomType','-V6') %store the root name for future opening of uvmat
726    else
727        save(profil_perso,'RootPath','SubDir','RootFile','NomType')
728    end         
729end
730set(handles.RootPath,'BackgroundColor',[1 1 1])
731set(handles.PathCampaign,'String',SeriesData.PathCampaign)
732last_j_Callback(hObject, eventdata, handles)
733last_i_Callback(hObject, eventdata, handles)
734
735%------------------------------------------------------------
736function RootPath_Callback(hObject, eventdata, handles)
737Val=get(handles.RootPath,'Value');
738synchronise_view(handles,Val)
739NomType_Callback(hObject, eventdata, handles)
740%------------------------------------------------------------
741
742function synchronise_view(handles,Val)
743set(handles.RootPath,'Value',Val)
744set(handles.SubDir,'Value',Val)
745set(handles.RootFile,'Value',Val)
746set(handles.NomType,'Value',Val)
747set(handles.FileExt,'Value',Val)
748set(handles.nb_field,'Value',Val)
749set(handles.nb_field2,'Value',Val)
750set(handles.time_first,'Value',Val)
751set(handles.time_last,'Value',Val)
752
753
754%---------------------------------------------------------
755% Executes on carriage return on the subdir civ1 edit window
756%--------------------------------------------------------
757function SubDir_Callback(hObject, eventdata, handles)
758
759Val=get(handles.SubDir,'Value');
760synchronise_view(handles,Val)
761NomType_Callback(hObject, eventdata, handles)
762
763%--------------------------------------------------------------
764%function activated when a new filebase (image series) is introduced
765%------------------------------------------------------------
766function RootFile_Callback(hObject, eventdata, handles)
767Val=get(handles.RootFile,'Value');
768synchronise_view(handles,Val)
769NomType_Callback(hObject, eventdata, handles)
770
771%--------------------------------------------------------------
772%function activated when a new filebase (image series) is introduced
773%------------------------------------------------------------
774function FileExt_Callback(hObject, eventdata, handles)
775Val=get(handles.FileExt,'Value');
776synchronise_view(handles,Val)
777
778%--------------------------------------------------------------
779%function activated when a new filebase (image series) is introduced
780%------------------------------------------------------------
781function nb_field_Callback(hObject, eventdata, handles)
782Val=get(handles.nb_field,'Value');
783synchronise_view(handles,Val)
784
785%--------------------------------------------------------------
786%function activated when a new filebase (image series) is introduced
787%------------------------------------------------------------
788function nb_field2_Callback(hObject, eventdata, handles)
789Val=get(handles.nb_field2,'Value');
790synchronise_view(handles,Val)
791
792%--------------------------------------------------------------
793%function activated when a new filebase (image series) is introduced
794%------------------------------------------------------------
795function time_first_Callback(hObject, eventdata, handles)
796Val=get(handles.time_first,'Value');
797synchronise_view(handles,Val)
798
799%--------------------------------------------------------------
800%function activated when a new filebase (image series) is introduced
801%------------------------------------------------------------
802function time_last_Callback(hObject, eventdata, handles)
803Val=get(handles.time_last,'Value');
804synchronise_view(handles,Val)
805
806%--------------------------------------------------------------
807%function activated by NomType
808%------------------------------------------------------------
809NomType_Callback(hObject, eventdata, handles)
810
811function NomType_Callback(hObject, eventdata, handles)
812hseries=get(handles.ProjObject,'Parent');
813SeriesData=get(hseries,'UserData');
814if isfield(SeriesData,'NomType')
815    NomTypeCell=SeriesData.NomType;
816else
817    NomTypeCell={};
818end
819nbfield2_cell=get(handles.nb_field2,'String');
820val=get(handles.nb_field2,'Value');
821if iscell(nbfield2_cell)
822    nbfield2=str2num(nbfield2_cell{val});
823else
824    nbfield2=str2num(nbfield2_cell);
825end
826nbfield_cell=get(handles.nb_field,'String');
827if iscell(nbfield_cell)
828    nbfield=str2num(nbfield_cell{val});
829else
830   nbfield=str2num(nbfield_cell);
831end
832
833set(handles.mode,'Visible','off') % do not show index pairs by default
834set(handles.list_pair_civ,'Visible','off')
835set(handles.ref_i,'Visible','off')
836set(handles.ref_i_text,'Visible','off')
837testpair=0;
838state_j='off';
839%set the menus of image pairs and default selection for series
840%list pairs if relevant
841Val=get(handles.NomType,'Value');
842synchronise_view(handles,Val)
843if ~isempty(NomTypeCell)
844    NomType=NomTypeCell{Val};
845    switch NomType 
846            case {'_i1-i2_j', '_i1-i2'}
847                set(handles.mode,'String',{'series(Di)'})
848                set(handles.mode,'Value',1);
849                set(handles.mode,'Visible','on')
850                testpair=1;
851            case {'#_ab'}
852                set(handles.mode,'String',{'bursts'})
853                set(handles.mode,'Value',1);
854                testpair=1;
855            case '_i_j1-j2'
856                set(handles.mode,'String',{'bursts';'series(Dj)'})%multiple choice
857                if ~isempty(nbfield) && ~isempty(nbfield2) && ((nbfield2>10) || (nbfield==1))
858                    set(handles.mode,'Value',2);
859                else
860                    set(handles.mode,'Value',1);% advice 'bursts' for small bursts
861                end
862                set(handles.mode,'Visible','on')
863                testpair=1;
864    end
865    switch NomType   
866            case {'_i_j','_i_j1-j2','_i1-i2_j','#_ab'},% two navigation indices
867                state_j='on';
868    end
869end   
870if testpair
871    mode_Callback(hObject, eventdata, handles) 
872else
873    set(handles.NomType,'String',NomTypeCell)
874end
875set(handles.first_j,'Visible',state_j)
876set(handles.incr_j,'Visible',state_j)
877set(handles.last_j,'Visible',state_j)
878set(handles.nb_field2,'Visible',state_j)
879
880%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%????????????
881% --- Executes on button press in mode.
882%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
883function mode_Callback(hObject, eventdata, handles)
884%hseries=get(handles.mode,'parent');
885hseries=handles.figure1;
886SeriesData=get(hseries,'UserData');
887mode_list=get(handles.mode,'String');
888mode_value=get(handles.mode,'Value');
889mode=mode_list{mode_value};
890NomType=[];
891test_find_pair=0;
892if isfield(SeriesData,'NomType')
893    NomTypeCell=SeriesData.NomType;
894    Val=get(handles.NomType,'Value');
895    NomType=NomTypeCell{Val};
896    test_find_pair=isequal(NomType,'_i_j1-j2')|| isequal(NomType,'_i1-i2_j')|| isequal(NomType,'_i1-i2')|| isequal(NomType,'#_ab');
897end
898% displ_num=[];%default
899% first_i=str2num(get(handles.first_i,'String'));
900% last_i=str2num(get(handles.last_i,'String'));
901time=[];
902if isfield(SeriesData,'Time')
903time=SeriesData.Time{1}; %get the set of times
904end
905siztime=size(time);
906nbfield=siztime(1);
907nbfield2=siztime(2);
908indchosen=1;  %%first pair selected by default
909if isequal(mode,'bursts')
910    enable_i(handles,'On')
911    enable_j(handles,'Off')   
912elseif  isequal(NomType,'_i_j1-j2')|| isequal(NomType,'_i1-i2_j')
913    enable_i(handles,'On')
914    enable_j(handles,'On')
915else
916    enable_i(handles,'On')
917    enable_j(handles,'Off')
918end   
919   
920   
921% elseif isequal(mode,'series(Dj)')       
922%     enable_j(handles,'On')     
923%     if nbfield==1
924%         enable_i(handles,'Off')
925%     else
926%         enable_i(handles,'On')
927%     end
928% elseif isequal(mode,'series(Di)')
929%     if nbfield2 > 1
930%          enable_j(handles,'On')
931%     else
932%          enable_j(handles,'Off')
933%     end
934% end 
935set(handles.list_pair_civ,'Value',indchosen);%set the default choice of image pairs for civ1
936% SetSeries.displ_num=displ_num;
937set(hseries,'UserData',SeriesData)
938
939%list pairs if relevant
940if test_find_pair
941     find_netcpair_civ(hObject, eventdata, handles,Val)
942end
943
944%-------------------------------------
945function enable_i(handles,state)
946set(handles.i_txt,'Visible',state)
947set(handles.first_i,'Visible',state)
948set(handles.last_i,'Visible',state)
949set(handles.incr_i,'Visible',state)
950set(handles.nb_field,'Visible',state)
951set(handles.ref_i,'Visible',state)
952set(handles.ref_i_text,'Visible',state)
953
954%-----------------------------------
955function enable_j(handles,state)
956set(handles.j_txt,'Visible',state)
957set(handles.first_j,'Visible',state)
958set(handles.last_j,'Visible',state)
959set(handles.incr_j,'Visible',state)
960set(handles.nb_field2,'Visible',state)
961set(handles.ref_j,'Visible',state)
962set(handles.ref_j_text,'Visible',state)
963
964%-----------------------------------
965function view_FieldMenu(handles,state)
966set(handles.FieldMenu,'Visible',state)
967set(handles.Field_text,'Visible',state)
968set(handles.Field_frame,'Visible',state)
969
970%-----------------------------------
971function view_FieldMenu_1(handles,state)
972set(handles.FieldMenu_1,'Visible',state)
973set(handles.Field_text_1,'Visible',state)
974
975%-----------------------------------
976function view_TRANSFORM(handles,state)
977set(handles.TRANSFORM_frame,'Visible',state)
978set(handles.CoordType,'Visible',state);
979set(handles.TRANSFORM_title,'Visible',state)
980
981%--------------------------------------------------------------
982% determine the menu for civ1 pairs depending on existing netcdf file at the middle of
983% the field series set by first_i, incr, last_i
984%----------------------------------------------------------------
985function find_netcpair_civ(hObject, eventdata, handles,Val)
986%hseries=get(handles.list_pair_civ,'parent');
987SeriesData=get(handles.figure1,'UserData');
988% NomTypeCell=get(handles.NomType,'String');
989NomTypeCell=SeriesData.NomType;
990NomType=NomTypeCell{Val};
991  set(handles.list_pair_civ,'Visible','on')
992%nomenclature types
993RootPathCell=get(handles.RootPath,'String');
994filepath=RootPathCell{Val};
995RootFileCell=get(handles.RootFile,'String');
996filename=RootFileCell{Val};
997filebase=fullfile(filepath,filename);
998SubDirCell=get(handles.SubDir,'String');
999subdir=SubDirCell{Val};
1000if ~exist(fullfile(filepath,subdir),'dir')
1001         msgbox_uvmat('ERROR',['no civ file available: subdirectory ' subdir ' does not exist'])
1002         set(handles.list_pair_civ,'String',{''});
1003         return
1004end
1005mode_list=get(handles.mode,'String');
1006mode_value=get(handles.mode,'Value');
1007mode=mode_list{mode_value};
1008
1009%reads image numbers from the interface
1010ref_i=str2num(get(handles.ref_i,'String'));
1011ref_j=str2num(get(handles.ref_j,'String'));
1012% time=[];
1013% ref_time=[];
1014 ref_time=0;
1015if isfield(SeriesData,'Time')&~isempty(SeriesData.Time{Val})&~isequal(SeriesData.Time{Val},0)
1016    time=SeriesData.Time{Val}; %get the set of times
1017    siztime=size(time);
1018    nbfield=siztime(1);
1019    nbfield2=siztime(2);
1020%     test_imadoc=1;
1021else
1022%     test_imadoc=0;%no image documentation file
1023    nbfield=50;
1024    nbfield2=50;%default max number of pairs
1025end
1026%look for existing processed pairs involving the field at the middle of the series if civ1 will not
1027% be performed, while the result is needed for next steps.
1028displ_pair={''};
1029displ_num=[];
1030ind_exist=0;
1031TimeUnit=get(handles.TimeUnit,'String');
1032if length(TimeUnit)>=1
1033    dtunit=['m' TimeUnit];
1034else
1035    dtunit='e-03';
1036end
1037if isequal(mode,'series(Di)')
1038     for index=1:min(nbfield-1,50)
1039         filename=name_generator(filebase,ref_i-floor(index/2),ref_j,'.nc',NomType,1,ref_i+ceil(index/2),ref_j,subdir);
1040         select=(exist(filename,'file')==2);
1041         if select==1
1042               ind_exist=ind_exist+1;
1043                displ_num(1,ind_exist)=0;
1044                displ_num(2,ind_exist)=0;
1045                displ_num(3,ind_exist)=-floor(index/2);
1046                displ_num(4,ind_exist)=ceil(index/2);
1047                %[cte_detect,vdt,cte_read]=read_netcdf(filename,{'dt','dt2','absolut_time_T0','absolute_time_TO_2'});
1048                [Cte,var_detect,ichoice]=nc2struct(filename,{});
1049                if isfield(Cte,'dt2')
1050                    dt=Cte.dt2;
1051                elseif isfield(Cte,'dt')
1052                    dt=Cte.dt;
1053                end
1054                if isfield(Cte,'absolut_time_TO_2')
1055                    ref_time(ind_exist)=Cte.absolut_time_TO_2;%civ2 data used in priority
1056                elseif isfield(Cte,'absolut_time_TO')
1057                    ref_time(ind_exist)=Cte.absolut_time_TO;%civ2 data used in priorit
1058                elseif isfield(Cte,'Time')
1059                    ref_time(ind_exist)=Cte.Time;
1060                end
1061                displ_pair{ind_exist}=['Di= ' num2str(-floor(index/2)) '|' num2str(ceil(index/2)) ' :dt= ' num2str(dt*1000) dtunit];
1062         end
1063     end
1064     set(handles.list_pair_civ,'String',[displ_pair';{'Di=*|*'}]);   
1065elseif isequal(mode,'series(Dj)')% series on the j index
1066       for index=1:min(nbfield2-1,50)
1067           filename=name_generator(filebase,ref_i,ref_j-floor(index/2),'.nc',NomType,1,ref_i,ref_j+ceil(index/2),subdir);
1068           select=(exist(filename,'file')==2);
1069           if select==1
1070               ind_exist=ind_exist+1;
1071                displ_num(1,ind_exist)=-floor(index/2);
1072                displ_num(2,ind_exist)=ceil(index/2);
1073                displ_num(3,ind_exist)=0;
1074                displ_num(4,ind_exist)=0;
1075                %[cte_detect,vdt,cte_read]=read_netcdf(filename,{'dt','dt2','absolut_time_T0','absolute_time_TO_2'});
1076                [Cte,var_detect,ichoice]=nc2struct(nc,{});
1077                if isfield(Cte,'dt2')
1078                    dt=Cte.dt2;
1079                elseif isfield(Cte,'dt')
1080                    dt=Cte.dt;
1081                end
1082                if isfield(Cte,'absolut_time_TO_2')
1083                    ref_time(ind_exist)=Cte.absolut_time_TO_2;%civ2 data used in priority
1084                elseif isfield(Cte,'absolut_time_TO')
1085                    ref_time(ind_exist)=Cte.absolut_time_TO;%civ2 data used in priorit
1086                elseif isfield(Cte,'Time')
1087                    ref_time(ind_exist)=Cte.Time;
1088                end
1089%                 if cte_detect(2)==1;
1090%                     dt=cte_read(2);
1091%                     ref_time(ind_exist)=cte_read(4);%civ2 data used in priority
1092%                 else
1093%                     dt=cte_read(1);
1094%                     ref_time(ind_exist)=cte_read(3);
1095%                 end
1096                displ_pair{ind_exist}=['Dj= ' num2str(-floor(index/2)) '|' num2str(ceil(index/2)) ' :dt= ' num2str(dt*1000) dtunit];
1097           end
1098       end
1099       set(handles.list_pair_civ,'String',[displ_pair';{'Dj=*|*'}]);
1100elseif isequal(mode,'bursts') %case of bursts
1101    for numod_a=1:nbfield2-1 %nbfield2 always >=2 for 'bursts' mode
1102        for numod_b=(numod_a+1):nbfield2
1103            [filename]=name_generator(filebase,ref_i,numod_a,'.nc',NomType,1,ref_i,numod_b,subdir);
1104            select=(exist(filename,'file')==2);
1105            if select==1
1106                ind_exist=ind_exist+1;
1107                numlist_a(ind_exist)=numod_a;
1108                numlist_b(ind_exist)=numod_b;
1109                Attr=nc2struct(filename,[]);
1110                isfield(Attr,'absolut_time_T0_2')
1111                if isfield(Attr,'dt2')
1112                   dt(ind_exist)=Attr.dt2;
1113                   ref_time(ind_exist)=Attr.absolut_time_T0_2;
1114                elseif isfield(Attr,'dt')& isfield(Attr,'absolut_time_T0')
1115                   dt(ind_exist)=Attr.dt;
1116                   ref_time(ind_exist)=Attr.absolut_time_T0;
1117                else
1118                   dt(ind_exist)=NaN;%no information on dt
1119                end
1120                %determine nom_type_ima for pair display (used in num2stra.m)
1121                switch NomType
1122                    case {'#ab'}
1123                        nom_type_ima='#a';
1124                    case {'#AB'}
1125                        nom_type_ima='#A';
1126                    otherwise
1127                         nom_type_ima='_i_j';
1128                end
1129               displ_pair{ind_exist}=['j= ' num2stra(numod_a,nom_type_ima,2) '-' num2stra(numod_b,nom_type_ima,2) ...
1130                        ' :dt= ' num2str(dt(ind_exist)*1000)];
1131            end
1132         end
1133         set(handles.list_pair_civ,'String',[displ_pair';{'j=*-*'}]);
1134     end
1135     if exist('dt','var') & ~isempty(dt)
1136         [dtsort,indsort]=sort(dt);
1137         displ_num(1,:)=numlist_a(indsort);
1138         displ_num(2,:)=numlist_b(indsort);
1139         displ_num(3,:)=0;
1140         displ_num(4,:)=0;
1141         displ_pair=displ_pair(indsort);
1142         ref_time=ref_time(indsort);
1143     end
1144end
1145if ind_exist==0
1146         if  isequal(mode,'series(Dj)') | isequal(mode,'st_series(Dj)')
1147            msgbox_uvmat('ERROR',['no .nc file available for the selected reference index j=' num2str(ref_j) ' and subdirectory ' subdir])
1148        else
1149            msgbox_uvmat('ERROR',['no .nc file available for the selected reference index i=' num2str(ref_i) ' and subdirectory ' subdir])
1150        end
1151        if isequal(mode,'bursts') %case of bursts
1152            set(handles.list_pair_civ,'String',{'j=*-*'});
1153        elseif isequal(mode,'series(Di)') %case of bursts
1154            set(handles.list_pair_civ,'String',{'Di=*|*'});
1155        elseif isequal(mode,'series(Dj)') %case of bursts
1156            set(handles.list_pair_civ,'String',{'Dj=*|*'});
1157        end
1158end
1159
1160val=get(handles.list_pair_civ,'Value');
1161if val > length(displ_pair)
1162    set(handles.list_pair_civ,'Value',1);% first pair proposed by default in the menu
1163    val=1;
1164end
1165iview=get(handles.NomType,'Value');
1166SeriesData.displ_num(iview,:)=(displ_num(:,val))';
1167SeriesData.ref_time=ref_time;
1168set(handles.figure1,'UserData',SeriesData)
1169list_pair_civ_Callback(hObject, eventdata, handles)
1170
1171%-------------------------------------------------------------
1172% --- Executes on selection in list_pair_civ.
1173function list_pair_civ_Callback(hObject, eventdata, handles)
1174%------------------------------------------------------------
1175
1176%update first_i and last_i according to the chosen image pairs
1177testupdate=0;
1178Val=get(handles.RootPath,'Value');
1179IndexCell=get(handles.NomType,'String');
1180%hseries=get(handles.list_pair_civ,'parent');
1181SeriesData=get(handles.figure1,'UserData');
1182NomType=SeriesData.NomType{Val};
1183list_pair=get(handles.list_pair_civ,'String');%get the menu of image pairs
1184index_pair=get(handles.list_pair_civ,'Value');
1185str_pair=list_pair{index_pair};
1186ind_equ=strfind(str_pair,'=');%find '='
1187ind_sep=strfind(str_pair,'|');%find pair separator '|'
1188ind_com=strfind(str_pair,':');%find ':'
1189test_bursts=0;
1190if isempty(ind_sep)
1191    ind_sep=strfind(str_pair,'-');%find pair separator if it is not '|'
1192    test_bursts=1;% we are in the case of bursts
1193end
1194displ_num=[0 0 0 0]; %default
1195if ~isempty(ind_sep)&& ~strcmp(str_pair(ind_sep-1),'*')% if there is a pair separator ('|' or '-')
1196    num1_str=str_pair(ind_equ(1)+1:ind_sep-1);
1197    num2_str=str_pair(ind_sep+1:ind_com-1);
1198    num1=str2double(num1_str);
1199    num2=str2double(num2_str);
1200    if isequal(num1_str(1),' ')
1201        num1_str(1)=[];
1202    end   
1203    if isequal(num2_str(end),' ')
1204        num2_str(end)=[];
1205    end
1206    switch NomType
1207       case {'_i1-i2_j'}
1208           if isequal(num1_str(1),'0')
1209               IndexCell{Val}=['_(i-(i+' num2_str ')_j'];
1210           else
1211               IndexCell{Val}=['_(i' num1_str ')-(i+' num2_str ')_j'];
1212           end
1213           displ_num(3)=num1;
1214           displ_num(4)=num2;
1215       case {'_i1-i2'}
1216           if isequal(num1_str(1),'0')
1217               IndexCell{Val}=['_(i' num1_str ')-(i+' num2_str ')'];
1218           else
1219               IndexCell{Val}=['_(i' num1_str ')-(i+' num2_str ')'];
1220           end
1221           displ_num(3)=num1;
1222           displ_num(4)=num2;
1223       case '_i_j1-j2'
1224          if test_bursts
1225              IndexCell{Val}=['_i_' num1_str '-' num2_str ];
1226          else
1227              if isequal(num1_str(1),'0')
1228                 IndexCell{Val}=['_i_j-(j+' num2_str ')'];
1229              else
1230                 IndexCell{Val}=['_i_(j' num1_str ')-(j+' num2_str ')'];
1231              end
1232          end
1233          displ_num(1)=num1;
1234          displ_num(2)=num2;
1235       case {'#_ab'} %TO COMPLETE
1236           IndexCell{Val}=['_i_' num1_str '-' num2_str ];
1237
1238    end
1239end
1240set(handles.NomType,'String',IndexCell)
1241SeriesData.displ_num(Val,:)=displ_num;
1242set(handles.figure1,'UserData',SeriesData)
1243% set(handles.NomType,'Value',Val)
1244
1245if ~isequal(str_pair,'Dj=*|*')&~isequal(str_pair,'Di=*|*')
1246        mode_list=get(handles.mode,'String');
1247    mode_value=get(handles.mode,'Value');
1248    mode=mode_list{mode_value};
1249        if isequal(mode,'series(Di)')
1250        first_i=str2num(get(handles.first_i,'String'));
1251        last_i=str2num(get(handles.last_i,'String'));
1252        incr_i=str2num(get(handles.incr_i,'String'));
1253        num1=first_i:incr_i:last_i;
1254        lastfieldCell=get(handles.nb_field,'String');
1255        lastfield=str2num(lastfieldCell{1});
1256        if ~isempty(lastfield)
1257            ind=find((num1-floor(index_pair/2)*ones(size(num1))>0)& (num1+ceil(index_pair/2)*ones(size(num1))<=lastfield));
1258            num1=num1(ind);       
1259        end
1260        set(handles.first_i,'String',num2str(num1(1)));
1261        set(handles.last_i,'String',num2str(num1(end)));
1262        testupdate=1;
1263        elseif isequal(mode,'series(Dj)')
1264        first_j=str2num(get(handles.first_j,'String'));
1265        last_j=str2num(get(handles.last_j,'String'));
1266        incr_j=str2num(get(handles.incr_j,'String'));
1267        num_j=first_j:incr_j:last_j;
1268        lastfieldCell=get(handles.nb_field2,'String');
1269        if ~isempty(lastfieldCell)
1270            lastfield2=lastfieldCell{1};
1271            ind=find((num_j-floor(index_pair/2)*ones(size(num_j))>0)& ...
1272                 (num_j+ceil(index_pair/2)*ones(size(num_j))<=lastfield2));
1273        end
1274        testupdate=1;
1275        end
1276       
1277        %update the first and last times of the series
1278        if testupdate & isfield(SeriesData,'Time')
1279        if ~isempty(SeriesData.Time{1})
1280            displ_time(handles,SeriesData.Time{1});
1281        end
1282        end
1283end
1284%---------------------------------------------------
1285% --- Executes on button press in RUN.
1286%------------------------------------------------------
1287function RUN_Callback(hObject, eventdata, handles)
1288
1289%read root name and field type
1290set(handles.RUN,'BusyAction','queue');
1291%hseries=get(handles.RUN,'parent');
1292set(0,'CurrentFigure',handles.figure1)
1293if isequal(get(handles.GetObject,'Value'),1)
1294    Series.GetObject=1;
1295    GetObject_Callback(hObject, eventdata, handles)
1296else
1297    Series.GetObject=0;
1298end
1299SeriesData=get(handles.figure1,'UserData');
1300if isfield(SeriesData,'sethandles')
1301    if iscell(SeriesData.sethandles)
1302        Series.sethandles=SeriesData.sethandles{1};
1303    else
1304        Series.sethandles=SeriesData.sethandles;%retrieve the handles of the set_object interface (to define projection objects)
1305    end
1306end
1307
1308%reinitiate waitbar position
1309Series.WaitbarPos=get(handles.waitbar_frame,'Position');%TO SUPPRESS
1310waitbarpos=Series.WaitbarPos;
1311waitbarpos(4)=0.005;%reinitialize waitbar to zero height
1312waitbarpos(2)=Series.WaitbarPos(2)+Series.WaitbarPos(4)-0.005;
1313set(handles.waitbar,'Position',waitbarpos)
1314
1315% read input file parameters and set menus
1316Series.PathProject=get(handles.PathCampaign,'String');
1317RootPath=get(handles.RootPath,'String');% path of the root name of the first field series
1318RootFile=get(handles.RootFile,'String');% root name of the first field series
1319SubDir=get(handles.SubDir,'String');% subdirectory for netcdf files
1320FileExt=get(handles.FileExt,'String');%file extension
1321if isempty(SeriesData)
1322    msgbox_uvmat('ERROR','no input file series')
1323    return
1324end
1325NomType=SeriesData.NomType;
1326if length(RootPath)==1 %string character input for user fct
1327    Series.RootPath=RootPath{1};
1328    Series.RootFile=RootFile{1};
1329    Series.SubDir=SubDir{1};
1330    Series.FileExt=FileExt{1};
1331    Series.NomType=NomType{1};
1332else %cell input for user fct
1333    Series.RootPath=RootPath;
1334    Series.RootFile=RootFile;
1335    Series.SubDir=SubDir;
1336    Series.FileExt=FileExt;
1337    Series.NomType=NomType;
1338end
1339if isequal(get(handles.FieldMenu,'Visible'),'on')
1340    FieldMenu=get(handles.FieldMenu,'String');
1341    FieldValue=get(handles.FieldMenu,'Value');
1342    Series.Field=FieldMenu(FieldValue);
1343end
1344menu_coord_state=get(handles.CoordType,'Visible');
1345Series.CoordType='';%default
1346if isequal(menu_coord_state,'on')
1347    menu_coord=get(handles.CoordType,'String');
1348    menu_index=get(handles.CoordType,'Value');
1349    Series.CoordType=menu_coord{menu_index};
1350end
1351Series.hseries=get(hObject,'Parent');
1352if isequal(get(handles.ParamVal,'Visible'),'on')
1353    ParamKey=get(handles.ParamKey,'String');
1354    if ischar(ParamKey)
1355        ParamKey{1}=ParamKey;
1356    end
1357    ParamString=get(handles.ParamVal,'String');
1358    if ischar(ParamString)
1359        for ilist=1:size(ParamString,1)
1360            ParamVal{ilist}=ParamString(ilist,:);
1361        end
1362    else
1363        ParamVal=ParamString;
1364    end   
1365end
1366
1367%read the set of field numbers
1368first_i=str2num(get(handles.first_i,'String'));
1369last_i=str2num(get(handles.last_i,'String'));
1370incr_i=str2num(get(handles.incr_i,'String'));
1371first_j=str2num(get(handles.first_j,'String'));
1372last_j=str2num(get(handles.last_j,'String'));
1373incr_j=str2num(get(handles.incr_j,'String'));
1374if ~isequal(get(handles.first_i,'Visible'),'on')
1375   first_i=1;
1376   last_i=1;
1377   incr_i=1;
1378end
1379if ~isequal(get(handles.first_j,'Visible'),'on')
1380    first_j=1;
1381    last_j=1;
1382    incr_j=1;
1383end
1384Series.NbSlice=str2num(get(handles.NbSlice,'String'));
1385if isequal(first_i,[])|isequal(first_j,[]), msgbox_uvmat('ERROR','first field number not defined'),...
1386    set(handles.RUN, 'Enable','On'), set(handles.RUN,'BackgroundColor',[1 0 0]),return,end;
1387if isequal(last_i,[])| isequal(last_j,[]),msgbox_uvmat('ERROR','last field number not defined'),...
1388    set(handles.RUN, 'Enable','On'), set(handles.RUN,'BackgroundColor',[1 0 0]),return,end;
1389if isequal(incr_i,[])| isequal(incr_j,[]),msgbox_uvmat('ERROR','increment in field number not defined'),...
1390    set(handles.RUN, 'Enable','On'), set(handles.RUN,'BackgroundColor',[1 0 0]),return,end;
1391if last_i < first_i | last_j < first_j , msgbox_uvmat('ERROR','last field number must be larger than the first one'),...
1392    set(handles.RUN, 'Enable','On'), set(handles.RUN,'BackgroundColor',[1 0 0]),return,end;
1393num_i=[first_i:incr_i:last_i];
1394num_j=[first_j:incr_j:last_j];
1395nbfield_cell=get(handles.nb_field,'String');
1396nbfield=[]; %default
1397for iview=1:length(nbfield_cell)
1398    nb=str2num(nbfield_cell{iview});
1399    if ~isempty(nb)
1400        nbfield=[nbfield nb];
1401    end
1402end
1403nbfield=min(nbfield);
1404nbfield2_cell=get(handles.nb_field2,'String');
1405nbfield2=[]; %default
1406for iview=1:length(nbfield2_cell)
1407    nb=str2num(nbfield2_cell{iview});
1408    if ~isempty(nb)
1409        nbfield2=[nbfield2 nb];
1410    end
1411end
1412nbfield2=min(nbfield2);
1413
1414%get complementary information from the 'series' interface
1415list_action=get(handles.ACTION,'String');% list menu action
1416index_action=get(handles.ACTION,'Value');% selected string index
1417action= list_action{index_action}; % selected string
1418mode_list=get(handles.mode,'String');
1419index_mode=get(handles.mode,'Value');
1420mode=mode_list{index_mode};
1421ind_shift=0;%default
1422
1423%determine the list of input file names
1424nbmissing=0;
1425for iview=1:length(RootPath)
1426    %case of pairs (.nc files)
1427   
1428    if isequal(NomType{iview},'_i_j1-j2')| isequal(NomType{iview},'_i1-i2_j')| isequal(NomType{iview},'_i1-i2')| isequal(NomType{iview},'#_ab')
1429        ind_shift=SeriesData.displ_num(iview,:);
1430        if isequal(ind_shift,[0 0 0 0]) % undefined pairs
1431            if isequal(NomType{iview},'#_ab')
1432                mode='#_ab';
1433            end
1434            [num_i1,num_i2,num_j1,num_j2,nbmissing]=netseries_generator(fullfile(RootPath{iview},RootFile{iview}),SubDir{iview},mode,first_i,incr_i,last_i,first_j,incr_j,last_j);
1435        else   
1436            [num_i1,num_i2,num_j1,num_j2,num_i,num_j]=find_file_indices(num_i,num_j,ind_shift,NomType{iview},mode);
1437            if isempty(num_i)
1438                msgbox_uvmat('ERROR','ERROR: empty set of input files chosen')
1439                return
1440            end
1441            if num_i(1)>first_i
1442               set(handles.first_i,'String',num2str(num_i(1)))%update the display of first field
1443               last_i_Callback(hObject, eventdata, handles)
1444            end
1445            if num_i(end)<last_i
1446               set(handles.last_i,'String',num2str(num_i(end)))%update the display of last field
1447               last_i_Callback(hObject, eventdata, handles)
1448            end
1449            if num_j(1)>first_j
1450               set(handles.first_j,'String',num2str(num_j(1)))%update the display of first field
1451               last_j_Callback(hObject, eventdata, handles)
1452            end
1453            if num_j(end)<last_j
1454               set(handles.last_j,'String',num2str(num_j(end)))%update the display of last field
1455               last_j_Callback(hObject, eventdata, handles)
1456            end
1457        end
1458    else%case of images
1459        [num_i1,num_j1]=meshgrid(num_i,num_j);
1460        num_i2=num_i1;
1461        num_j2=num_j1;
1462    end
1463    if length(RootPath)>1
1464        num_i1_cell{iview}=num_i1;
1465        num_i2_cell{iview}=num_i2;
1466        num_j1_cell{iview}=num_j1;
1467        num_j2_cell{iview}=num_j2;
1468    end
1469end
1470
1471% RUN RUN'
1472path_series=which('series');
1473list_path=get(handles.ACTION,'UserData');
1474index=get(handles.ACTION,'Value');
1475fct_path=list_path{index}; %path stored for the function ACTION
1476if ~isequal(fct_path,path_series)
1477    eval(['spath=which(''' action ''');']) %spath = current path of the selected function ACTION
1478    if ~isequal(spath,fct_path)& exist(fct_path,'dir')
1479        addpath(fct_path)% add the prescribed path if not the current one
1480    end
1481end
1482% fct_path
1483eval(['h_fun=@' action ';'])
1484if ~isequal(fct_path,path_series)
1485        rmpath(fct_path)% add the prescribed path if not the current one   
1486end
1487
1488Series.Action=action;%name of the processing programme
1489set(handles.RUN,'BackgroundColor',[0.831 0.816 0.784])
1490drawnow
1491if length(RootPath)>1
1492%    feval(action,num_i1_cell,num_i2_cell,num_j1_cell,num_j2_cell,Series);
1493    h_fun(num_i1_cell,num_i2_cell,num_j1_cell,num_j2_cell,Series);
1494else
1495    h_fun(num_i1,num_i2,num_j1,num_j2,Series);
1496%     feval(action,num_i1,num_i2,num_j1,num_j2,Series);
1497end
1498set(handles.RUN,'BackgroundColor',[1 0 0])
1499
1500% %save the current interface setting as figure namefig, append .0 to the name if it already exists
1501% detect=1;
1502% while detect==1
1503%     namefigfull=[namedoc '.fig'];
1504%     hh=dir(namefigfull);
1505%     if ~isempty(hh)
1506%         detect=1;
1507%         namedoc=[namedoc '.0'];
1508%     else
1509%         detect=0;
1510%     end
1511% end
1512% saveas(gcbf,namefigfull);%save the interface with name namefigfull (A CHANGER EN FICHIER  .xml)
1513
1514%----------------------------------------------------
1515function STOP_Callback(hObject, eventdata, handles)
1516set(handles.RUN, 'BusyAction','cancel')
1517set(handles.RUN,'BackgroundColor',[1 0 0])
1518
1519%----------------------------------------------
1520
1521%----------------------------------------------------
1522function first_i_Callback(hObject, eventdata, handles)
1523last_i_Callback(hObject, eventdata, handles)
1524
1525%----------------------------------------------
1526function last_i_Callback(hObject, eventdata, handles)
1527%     hseries=get(handles.last_i,'parent');
1528first_i=str2num(get(handles.first_i,'String'));
1529last_i=str2num(get(handles.last_i,'String'));
1530ref_i=ceil((first_i+last_i)/2);
1531set(handles.ref_i,'String', num2str(ref_i))
1532ref_i_Callback(hObject, eventdata, handles)
1533SeriesData=get(handles.figure1,'UserData');
1534if ~isfield(SeriesData,'Time')
1535    SeriesData.Time{1}=[];
1536end
1537displ_time(handles,SeriesData.Time{1});
1538
1539%-------------------------------------------------------
1540function first_j_Callback(hObject, eventdata, handles)
1541 last_j_Callback(hObject, eventdata, handles)
1542
1543%-------------------------------------------------------
1544function last_j_Callback(hObject, eventdata, handles)
1545   % hseries=get(handles.last_i,'parent');
1546first_j=str2num(get(handles.first_j,'String'));
1547last_j=str2num(get(handles.last_j,'String'));
1548ref_j=ceil((first_j+last_j)/2);
1549set(handles.ref_j,'String', num2str(ref_j))
1550
1551ref_j_Callback(hObject, eventdata, handles)
1552SeriesData=get(handles.figure1,'UserData');
1553if ~isfield(SeriesData,'Time')
1554    SeriesData.Time{1}=[];
1555end
1556displ_time(handles,SeriesData.Time{1});
1557
1558
1559
1560
1561%-------------------------------------------------------
1562function ref_i_Callback(hObject, eventdata, handles)
1563mode_list=get(handles.mode,'String');
1564mode_value=get(handles.mode,'Value');
1565mode=mode_list{mode_value};
1566%hseries=get(handles.ref_i,'parent');
1567SeriesData=get(handles.figure1,'UserData');
1568%NomTypeCell=get(handles.NomType,'String');
1569NomTypeCell=SeriesData.NomType;
1570if ~isempty(NomTypeCell)
1571Val=get(handles.NomType,'Value');
1572NomType=NomTypeCell{Val};
1573% for ilist=1:length(NomType)
1574    if isequal(NomType,'_i_j1-j2')|| isequal(NomType,'_i1-i2_j')|| isequal(NomType,'_i1-i2')
1575        if isequal(mode,'series(Di)')
1576            find_netcpair_civ(hObject, eventdata, handles,Val);% update the menu of pairs depending on the available netcdf files
1577%             break
1578        end
1579    end
1580end
1581
1582%----------------------------------------------------
1583function ref_j_Callback(hObject, eventdata, handles)
1584mode_list=get(handles.mode,'String');
1585mode_value=get(handles.mode,'Value');
1586mode=mode_list{mode_value};
1587%hseries=get(handles.ref_i,'parent');
1588SeriesData=get(handles.figure1,'UserData');
1589NomTypeCell=SeriesData.NomType;
1590if ~isempty(NomTypeCell)
1591    Val=get(handles.NomType,'Value');
1592    NomType=NomTypeCell{Val};
1593    if isequal(NomType,'_i_j1-j2')|| isequal(NomType,'_i1-i2_j')|| isequal(NomType,'_i1-i2')
1594        if isequal(mode,'series(Dj)')
1595            find_netcpair_civ(hObject, eventdata, handles,Val);% update the menu of pairs depending on the available netcdf files
1596        end
1597    end
1598end
1599
1600%----------------------------------------------------
1601% --- Executes on selection change in ACTION.
1602function ACTION_Callback(hObject, eventdata, handles)
1603global nb_builtin
1604list_ACTION=get(handles.ACTION,'String');% list menu fields
1605index_ACTION=get(handles.ACTION,'Value');% selected string index
1606ACTION= list_ACTION{index_ACTION}; % selected function name
1607path_series=which('series');%path to series.m
1608list_path=get(handles.ACTION,'UserData');%list of recorded paths to functions of the list ACTION
1609
1610% add a new function to the menu if the selected item is 'more...'
1611if isequal(ACTION,'more...')
1612    pathfct=fileparts(path_series);
1613%     browse_name=fullfile(path_series,'series');%go to UVMAT/series by default
1614%     if length(list_path)>nb_builtin
1615%         browse_name=list_path{end};% initialize browser with  the path of the last introduced function
1616%      end
1617    [FileName, PathName, filterindex] = uigetfile( ...
1618       {'*.m', ' (*.m)';
1619        '*.m',  '.m files '; ...
1620        '*.*', 'All Files (*.*)'}, ...
1621        'Pick a file',list_path{end});
1622    if length(FileName)<2
1623        return
1624    end
1625    [pp,ACTION,ext_fct]=fileparts(FileName);%(end-1:end);
1626    if ~isequal(ext_fct,'.m')
1627        msgbox_uvmat('ERROR','a Matlab function .m must be introduced');
1628        return
1629    end
1630   
1631   % insert the choice in the action menu
1632   menu_str=update_menu(handles.ACTION,ACTION);%new action menu in which the new item has been appended if needed
1633   index_ACTION=get(handles.ACTION,'Value');% currently selected index in the list
1634   list_path{index_ACTION}=PathName;
1635   if length(menu_str)>nb_builtin+5; %nb_builtin=nbre of functions always remaining in the initial menu
1636       nbremove=length(menu_str)-nb_builtin-5;
1637       menu_str(nb_builtin+1:end-5)=[];
1638       list_path(nb_builtin+1:end-4)=[];
1639       index_ACTION=index_ACTION-nbremove;
1640       set(handles.ACTION,'Value',index_ACTION)
1641       set(handles.ACTION,'String',menu_str)
1642   end
1643   list_path{index_ACTION}=PathName;
1644   set(handles.ACTION,'UserData',list_path);
1645   set(handles.path,'enable','inactive')% indicate that the current path is accessible (not 'off')
1646   
1647   %record the current menu in personal file profil_perso
1648   dir_perso=prefdir;
1649   profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
1650   for ilist=nb_builtin+1:length(menu_str)-1
1651       series_fct{ilist-nb_builtin}=fullfile(list_path{ilist},[menu_str{ilist} '.m']);
1652   end
1653   if exist(profil_perso,'file')
1654        save(profil_perso,'series_fct','-append')
1655   else
1656        txt=ver;
1657        Release=txt(1).Release;
1658        relnumb=str2num(Release(3:4));
1659        if relnumb >= 14
1660            save(profil_perso,'series_fct','-V6')
1661        else
1662            save(profil_perso, 'series_fct')
1663        end
1664   end
1665end
1666
1667%check the current path to the selected function
1668PathName=list_path{index_ACTION};%current recorded path
1669% if ~isequal(path_series,PathName)
1670%     CurrentPath=fileparts(which(ACTION));
1671%     if ~isequal(CurrentPath,PathName)
1672%         addpath(PathName)
1673%         errormsg=check_functions;
1674%         msgbox_uvmat('CONFIRMATION',[['path ' PathName ' added to the current Matlab pathes'];errormsg])
1675%     end
1676% end
1677set(handles.path,'String',PathName); %show the path to the senlected function
1678
1679%default setting for the visibility of the GUI elements
1680%set( handles.Field,'Visible','off')%default
1681set(handles.RootPath,'UserData','many')
1682set(handles.SubDir,'Visible','on')
1683set(handles.RootFile,'Visible','on')
1684set(handles.NomType,'Visible','on')
1685set(handles.FileExt,'Visible','on')
1686set(handles.NbSlice,'Visible','off')
1687set(handles.NbSlice_title,'Visible','off')
1688set(handles.VelTypeMenu,'Visible','off');
1689set(handles.VelType_text,'Visible','off');
1690set(handles.VelTypeMenu_1,'Visible','off');
1691set(handles.VelType_text_1,'Visible','off');
1692view_FieldMenu(handles,'off')
1693view_FieldMenu_1(handles,'off')
1694view_TRANSFORM(handles,'off')
1695set(handles.ProjObject_frame,'Visible','off');
1696set(handles.GetMask,'Visible','off')
1697set(handles.Mask,'Visible','off')
1698set(handles.GetObject,'Visible','off');
1699set(handles.ProjObject,'Visible','off');
1700set(handles.OutputDir,'Visible','off');
1701set(handles.PARAMETERS_frame,'Visible','off');
1702set(handles.PARAMETERS_title,'Visible','off');
1703set(handles.ParamKey,'Visible','off')
1704set(handles.ParamVal,'Visible','off')
1705ParamKey={};
1706set(handles.FieldMenu,'Enable','off')
1707set(handles.VelTypeMenu,'Enable','off')
1708set(handles.FieldMenu_1,'Enable','off')
1709set(handles.VelTypeMenu_1,'Enable','off')
1710set(handles.CoordType,'Enable','off')
1711%set the displayed GUI item needed for input parameters
1712%list_input=feval(ACTION);% input list asked by the selected function
1713if ~isequal(path_series,PathName)
1714    addpath(PathName)
1715end
1716eval(['h_function=@' ACTION ';']);
1717if ~isequal(path_series,PathName)
1718    rmpath(PathName)
1719end
1720
1721varargout=h_function();
1722%varargout=feval(ACTION);% input list asked by the selected function
1723Param_list={};
1724% RootPath=get(handles.RootPath,'String');
1725% RootFile=get(handles.RootFile,'String');
1726
1727%nb_series=length(RootFile);
1728FileExt=get(handles.FileExt,'String');
1729nb_series=length(FileExt);
1730testima_series=1; %test for a list of images only
1731testima=1;
1732testima_1=1;
1733testciv_series=1;
1734for iview=1:nb_series
1735    ext=FileExt{iview};
1736    if length(ext)<2
1737        ext='.none';
1738    end
1739    testimaview=~isempty(imformats(ext(2:end))) || isequal(lower(ext),'.avi');
1740    if ~testimaview
1741        if iview==1
1742            testima=0;
1743        end
1744        if iview==2
1745            testima_1=0;
1746        end
1747        testima_series=0;
1748    end
1749end
1750for ilist=1:length(varargout)-1
1751    switch varargout{ilist}
1752                       %RootFile always visible
1753         case 'RootPath'   %visible by default
1754            value=lower(varargout{ilist+1});
1755            if isequal(value,'one')||isequal(value,'two')||isequal(value,'many')
1756                set(handles.RootFile,'UserData',value)% for use in menu Open_insert
1757            end
1758        case 'SubDir' %visible by default
1759            if isequal(lower(varargout{ilist+1}),'off')
1760                set(handles.SubDir,'Visible','off')
1761            end
1762        case 'RootFile'   %visible by default
1763            value=lower(varargout{ilist+1});
1764            if isequal(value,'off')
1765                set(handles.RootFile,'Visible','off')
1766            elseif isequal(value,'one')||isequal(value,'two')||isequal(value,'many')
1767                set(handles.RootFile,'Visible','on')
1768                set(handles.RootFile,'UserData',value)% for use in menu Open_insert
1769            end
1770        case 'NomType'   %visible by default
1771            if isequal(lower(varargout{ilist+1}),'off')
1772                set(handles.NomType,'Visible','off')
1773            end
1774        case 'FileExt'   %visible by default
1775            if isequal(lower(varargout{ilist+1}),'off')
1776                set(handles.FileExt,'Visible','off')
1777            end
1778        case 'NbSlice'   %hidden by default
1779            if isequal(lower(varargout{ilist+1}),'on')
1780                set(handles.NbSlice,'Visible','on')
1781                set(handles.NbSlice_title,'Visible','on')
1782            end
1783        case 'VelTypeMenu'   %hidden by default
1784            if isequal(lower(varargout{ilist+1}),'one') || isequal(lower(varargout{ilist+1}),'two')
1785                set(handles.VelTypeMenu,'Enable','on')
1786                if nb_series >=1 && ~testima_series
1787                    set(handles.VelTypeMenu,'Visible','on')
1788                    set(handles.VelType_text,'Visible','on');
1789                    set(handles.Field_frame,'Visible','on')
1790                end
1791            end
1792            if isequal(lower(varargout{ilist+1}),'two')
1793                set(handles.VelTypeMenu_1,'Enable','on')
1794                if nb_series >=2 && ~testima_series
1795                    set(handles.VelTypeMenu_1,'Visible','on')
1796                    set(handles.VelType_text_1,'Visible','on');
1797                end
1798            end
1799        case 'FieldMenu'   %hidden by default
1800            if isequal(lower(varargout{ilist+1}),'one')||isequal(lower(varargout{ilist+1}),'two')
1801                set(handles.FieldMenu,'Enable','on') % test for MenuBorser
1802                if nb_series >=1 && ~testima_series
1803                    view_FieldMenu(handles,'on')
1804                end
1805            end
1806            if isequal(lower(varargout{ilist+1}),'two')
1807                set(handles.FieldMenu_1,'Enable','on')
1808                if nb_series >=2 && ~testima_1
1809                    view_FieldMenu_1(handles,'on')
1810                end
1811            end
1812        case 'CoordType'   %hidden by default
1813            if isequal(lower(varargout{ilist+1}),'on')
1814                set(handles.CoordType,'Enable','on')
1815                view_TRANSFORM(handles,'on')
1816            end
1817        case 'GetObject'   %hidden by default
1818            if isequal(lower(varargout{ilist+1}),'on')   
1819                set(handles.ProjObject_frame,'Visible','on')
1820                set(handles.GetObject,'Visible','on');
1821            end
1822        case 'Mask'   %hidden by default
1823            if isequal(lower(varargout{ilist+1}),'on')   
1824                set(handles.ProjObject_frame,'Visible','on')
1825                set(handles.GetMask,'Visible','on');
1826            end
1827        case 'PARAMETER' 
1828            set(handles.PARAMETERS_frame,'Visible','on')
1829            set(handles.PARAMETERS_title,'Visible','on')
1830            set(handles.ParamKey,'Visible','on')
1831            %set(handles.ParamVal,'Visible','on')
1832            Param_str=varargout{ilist+1};
1833            Param_list=[Param_list; {Param_str}];         
1834    end
1835end
1836if ~isempty(Param_list)
1837    set(handles.ParamKey,'String',Param_list)
1838    set(handles.ParamVal,'Visible','on')
1839end
1840
1841%-------------------------------------------------------------------
1842% --- Executes on selection change in FieldMenu.
1843%-------------------------------------------------------------------
1844function FieldMenu_Callback(hObject, eventdata, handles)
1845
1846field_str=get(handles.FieldMenu,'String');
1847field_index=get(handles.FieldMenu,'Value');
1848field=field_str{field_index(1)};
1849if isequal(field,'get_field...')   
1850     hget_field=findobj(allchild(0),'name','get_field');
1851     if ~isempty(hget_field)
1852         delete(hget_field)%delete opened versions of get_field
1853     end
1854     %hseries=get(handles.FieldMenu,'parent');
1855     SeriesData=get(handles.figure1,'UserData');
1856     filename=SeriesData.CurrentInputFile;
1857     if exist(filename,'file')
1858        get_field(filename)
1859     end
1860elseif isequal(field,'more...')
1861    str=calc_field;
1862    [ind_answer,v] = listdlg('PromptString','Select a file:',...
1863                'SelectionMode','single',...
1864                'ListString',str);
1865       % edit the choice in the fields and action menu
1866     scalar=cell2mat(str(ind_answer));
1867     update_menu(handles.FieldMenu,scalar)
1868end
1869
1870%------------------------------------------------------
1871% --- Executes on selection change in FieldMenu_1.
1872%-----------------------------------------------------
1873function FieldMenu_1_Callback(hObject, eventdata, handles)
1874field_str=get(handles.FieldMenu_1,'String');
1875field_index=get(handles.FieldMenu_1,'Value');
1876field=field_str{field_index};
1877if isequal(field,'get_field...')   
1878     hget_field=findobj(allchild(0),'name','get_field_1');
1879     if ~isempty(hget_field)
1880         delete(hget_field)
1881     end
1882     %hseries=get(handles.FieldMenu,'parent');
1883     SeriesData=get(handles.figure1,'UserData');
1884     filename=SeriesData.CurrentInputFile_1;
1885     if exist(filename,'file')
1886        hget_field=get_field(filename);
1887        set(hget_field,'name','get_field_1')
1888     end
1889elseif isequal(field,'more...')
1890    str=calc_field;
1891    [ind_answer,v] = listdlg('PromptString','Select a file:',...
1892                'SelectionMode','single',...
1893                'ListString',str);
1894       % edit the choice in the fields and action menu
1895     scalar=cell2mat(str(ind_answer));
1896     update_menu(handles.FieldMenu_1,scalar)
1897end   
1898
1899
1900% %group the variables (fields of 'FieldData') in cells of variables with the same dimensions
1901% %%%%%%%%%%%%%%%%%%%%%%% Function independante maintenant
1902% %-----------------------------------------------------------------
1903% [CellVarIndex,NbDim,VarTypeCell]=find_field_indices(Data{1});
1904% %LOOP ON GROUPS OF VARIABLES SHARING THE SAME DIMENSIONS
1905% % CellVarIndex=cells of variable index arrays
1906% ivar_new=0; % index of the current variable in the projected field
1907% icoord=0;
1908% for icell=1:length(CellVarIndex)
1909%     if NbDim(icell)==1
1910%         continue
1911%     end
1912%     VarIndex=CellVarIndex{icell};%  indices of the selected variables in the list FieldData.ListVarName
1913%     VarType=VarTypeCell{icell};
1914%     ivar_X=VarType.coord_x;
1915%     ivar_Y=VarType.coord_y;
1916%     ivar_FF=VarType.errorflag;
1917%     if isempty(ivar_X)
1918%         test_grid=1;%test for input data on regular grid (e.g. image)coordinates
1919%     else
1920%         if length(ivar_Y)~=1
1921%                 warndlg_uvmat('y coordinate missing in proj_field.m','ERROR')
1922%                 return
1923%         end
1924%         test_grid=0;
1925%     end
1926% %    DimIndices=Data{1}.VarDimIndex{VarIndex(1)};%indices of the dimensions of the first variable (common to all variables in the cell)
1927%     %case of input fields with unstructured coordinates
1928%     if ~test_grid
1929%         for ivar=VarIndex
1930%             VarName=MergeData.ListVarName{ivar};
1931%             for iview=1:nbview
1932%                 eval(['MergeData.' VarName '=[MergeData.' VarName '; Data{iview}.' VarName ';'])
1933%             end
1934%         end
1935%     %case of fields defined on a structured  grid
1936%     else 
1937% %        DimValue=MergeData.DimValue(DimIndices);%set of dimension values
1938%         testFF=0;
1939%         for iview=2:nbview
1940% %             if ~isequal(DimValue,Data{iview}.DimValue(DimIndices))
1941% %                 MergeData.Txt='ERROR: attempt at merging structured fields with different sizes';
1942% %                 return
1943% %             end
1944%             for ivar=VarIndex
1945%                 VarName=MergeData.ListVarName{ivar};
1946%                 if isfield(MergeData,'VarAttribute')
1947%                     if length(MergeData.VarAttribute)>=ivar && isfield(MergeData.VarAttribute{ivar},'Role') && isequal(MergeData.VarAttribute{ivar}.Role,'errorflag')
1948%                         testFF=1;
1949%                     end
1950%                 end
1951%                 eval(['MergeData.' VarName '=MergeData.' VarName '+ Data{iview}.' VarName ';'])
1952%             end
1953%         end
1954%         if testFF
1955%             nbaver=nbview-MergeData.FF;
1956%             indgood=find(nbaver>0);
1957%             for ivar=VarIndex
1958%                 VarName=MergeData.ListVarName{ivar};
1959%                 eval(['MergeData.' VarName '(indgood)=double(MergeData.' VarName '(indgood))./nbaver(indgood);'])
1960%             end
1961%         else
1962%             for ivar=VarIndex
1963%                 VarName=MergeData.ListVarName{ivar};
1964%                 eval(['MergeData.' VarName '=double(MergeData.' VarName ')./nbview;'])
1965%             end   
1966%         end
1967%     end
1968% end
1969%     
1970
1971%-----------------------------
1972function mouse_up_gui(ggg,eventdata,handles)
1973if isequal(get(ggg,'SelectionType'),'alt')
1974    display('global CurData, UserData of GUI series')
1975    global CurData
1976    CurData=get(ggg,'UserData');
1977    evalin('base','global CurData');%make CurData global in the workspace
1978    evalin('base','CurData'); %display CurData in the workspace
1979    commandwindow
1980   % plot_text(CurData)
1981end
1982
1983
1984
1985% %----------------------------------------------------------------------
1986% % --- display image movie and display time average
1987% %OBSOLETE: A SUPPRIMER
1988% %----------------------------------------------------------------------
1989% function movie_ima(handles,filecell,filecell_1,num1,num_a,field)
1990%
1991% global hfig1 hfig2 hfig3 poscolbar
1992% global A val HIST
1993%
1994% A=[];aviobj=[];
1995% % set(hfig1,'UserData','ima')% set the current field state to 'image'
1996% set(handles.zoom,'Value',1); %put zoom on
1997% nom_type=get(handles.file_input,'UserData');
1998% % field=get(handles.civ1,'UserData');
1999% % fields=field(1).fields;
2000% set(handles.speed,'Visible','On')%show slider to set movie speed
2001% set(handles.mo_speed_txt,'Visible','On')
2002%
2003% if ~isempty(filecell_1)
2004%    file1=get(handles.file1_input,'UserData');
2005%    field1=file1.field;
2006%    scal_type1=field1.fields;
2007%    vel_type1=field1.vel_type;
2008%    filename_1=filecell_1(1);% first file name in the series
2009% else
2010%    filename_1=[];
2011% end
2012% scal_type{1}=field(1).fields;
2013% vel_type{1}=field(1).vel_type;
2014% % display the first field
2015% [A,time,dt,rangx0,rangy0]=view_ima(handles,cell2mat(filecell(1)),filename_1,num1(1),num_a(1));
2016%
2017% % calculate the histogram of the first image
2018% nxy=size(A);
2019% ndim=length(nxy);
2020% if ndim==2 % case of B/W images
2021%     nxy(3)=1;
2022% end
2023% C=reshape(A,nxy(1)*nxy(2),nxy(3));
2024% Amaxmax=double(max(max(max(A))));
2025% Aminmin=double(min(min(min(A))));
2026% if isa(C,'uint8')|isa(C,'uint16')
2027%     C=double(C);
2028%     dC=1;
2029% else
2030%     dC=(Amaxmax-Aminmin)/100;
2031% end
2032% val=[Aminmin:dC:Amaxmax];% define bins for histogram
2033% HIST=hist(C,val);% initiate the global histogram
2034% if ndim==2, HIST=HIST'; end;
2035%
2036% auto_scale=get(handles.auto_scale,'Value');
2037% min_input=str2num(get(handles.min_input,'String'));% select the minimum
2038% max_input=str2num(get(handles.scale_input,'String'));% select the max
2039% zoomstate=get(handles.zoom,'Value');
2040%
2041% if isequal(get(handles.window_input,'String'),'avi'),
2042%     basename=get(handles.file_input,'String');
2043%     prompt = {'file name';'frames per second';'frame resolution ([nbpixels x y])';'axis position relative to the frame'};
2044%     dlg_title = 'select properties of the output avi movie';
2045%     num_lines= 1;
2046%     def     = {[basename '_out.avi'];'5';'[1024 768]';'[0.05 0.07 0.87 0.88]'};
2047%     answer = inputdlg(prompt,dlg_title,num_lines,def);
2048%     aviname=answer{1};
2049%     fps=str2num(answer{2});
2050%     if exist(aviname,'file')==2
2051%         delete(aviname);
2052%     end;
2053%     aviobj=avifile(aviname,'Compression','None','fps',fps);
2054%     
2055%     %display first view for tests
2056%     figure(2);
2057%     hh=get(gcf,'CurrentAxes');
2058%     if isempty(hh),
2059%         hfig1=axes;
2060%     else
2061%         hfig1=hh;
2062%     end;
2063%     if isequal(filecell_1,{})
2064%         filename_1=[];
2065%     else
2066%         filename_1=cell2mat(filecell_1(1));
2067%     end
2068%     poscolbar=[0.93 0.15 0.02 0.7];
2069%     view_ima(handles,cell2mat(filecell(1)),filename_1,num1(1),num_a(1));% show the first field
2070%     nbpix=eval(answer{3});
2071%     set(gcf,'Position',[1 1 nbpix])% resolution XVGA
2072%     set(hfig1,'Position',eval(answer{4}));
2073%     
2074%     msgbox({'adjust figure 2 with its matlab edit menu ' ;...
2075%             'then type any keyboard key to get the avi movie as a copy of figure 2 display'})
2076%     pause;
2077%     hh=colorbar;
2078%     poscolbar=get(hh,'Position');
2079% end
2080%
2081% %%%%%%%%%%%%%%%%
2082% %mask and usrdfct
2083% maskname=[]; %default
2084% if isequal(get(handles.mask_test,'Value'),1)
2085%     maskbase=get(handles.mask_test,'UserData');
2086% end
2087% % image or scalar processing programme set by user
2088% % if (get(handles.usr_fct,'Value')==1)
2089% %      usrfct=get(handles.usr_fct,'UserData');
2090% % else
2091% %      usrfct='';
2092% % end
2093% nburst=1; % nburst(1) =nbre of names in filename= nbre of bursts
2094% set(handles.text_display_1,'String',['image movie'])
2095% nbfield=length(filecell);
2096% if nbfield >1
2097% for ifile=2:nbfield
2098%     stopstate=get(handles.run0,'BusyAction');
2099%     if isequal(stopstate,'queue')% enable STOP command
2100%        pausetime=1.02-get(handles.speed,'Value');
2101%          pause(pausetime)
2102%          if isequal(get(handles.mask_test,'Value'),1)
2103%                 maskname=name_generator(maskbase,num1(ifile),1,'.png','png_series');
2104%             end
2105%             if isequal(AName{1},'image')
2106%                 A=read_image(cell2mat(filecell(ifile)),num1(ifile),maskname);% read the first image, num2 is the counter for avi files
2107%             else % read the first field from the netcdf file, imposing the pixel positions in the selected domain
2108%                  [A,time(ifile),dtr,rgx,rgy,vt_out,erread]=read_scalar(filecell{ifile},vel_type,scal_type,rangx0,rangy0,nxy,maskname);
2109%                 if erread==1;
2110%                     errordlg({['no spatial derivative in ' filecell{ifile}]; 'run patch first'}); return
2111%                 elseif erread==2;
2112%                     errordlg(['no field ' vel_type{1} ' in ' filecell{ifile}]); return
2113%                 elseif erread==3;
2114%                     errordlg(['scalar ' scal_type{1} ' not found in' filecell{ifile}]); return
2115%                 elseif erread==4;
2116%                     errordlg(['all points aligned in' filecell{ifile}]); return
2117%                 end
2118%             end
2119%           
2120%             % read the second image
2121%             if ~isempty(filecell_1)
2122%                 if isequal(scal_type{1},'image')
2123%                     A1=read_image(cell2mat(filecell_1(ifile)),num1(ifile),maskname);% read the second image, num2 is the counter for avi files
2124%                     Avalue_1=double(A1(indy,indx,:));
2125%                 else % read the second field from the netcdf file, imposing the pixel positions in the selected domain
2126%                     [Avalue_1,time1(ifile),dtr,rgx,rgy,vt_out,erread]=read_scalar(filecell_1{ifile},{vel_type1},{scal_type1},rangx0,rangy0,npxy,maskname,usrfct);
2127%                     if erread==1;
2128%                         errordlg({['no spatial derivative in ' filecell_1{ifile}]; 'run patch first'}); return
2129%                     elseif erread==2;
2130%                         errordlg(['no field ' vel_type1 ' in ' filecell_1{ifile}]); return
2131%                     elseif erread==3;
2132%                         errordlg(['scalar ' scal_type1 ' not found in' filecell_1{ifile}]); return
2133%                     elseif erread==4;
2134%                         errordlg(['all points aligned in' filecell_1{ifile}]); return
2135%                     end
2136%                 end
2137%                 time(ifile)=(time(ifile)+time1(ifile))/2;
2138%                 Avalue=Avalue-Avalue_1;
2139%             end
2140%         set(handles.abs_time,'String',time);
2141%         set(handles.field_counter,'String',num2str(num1(ifile)));
2142%         set(handles.a_input,'String',num2stra(num_a(ifile),nom_type));
2143%         C=reshape(A,nxy(1)*nxy(2),nxy(3));% reshape in a vector
2144%         [val,HIST]=hist_update(val,HIST,C,dC);
2145%         [h,Amin,Amax]=plot_image(hfig1,rangx0,rangy0,1,scal_type{1},auto_scale,min_input,max_input,poscolbar,A);
2146%         set(handles.min_input,'String',num2str(Amin));% select the minimum
2147%         set(handles.scale_input,'String',num2str(Amax));% select the minimum
2148%          if ~isequal(aviobj,[]),
2149% %              mov=getframe(hfig1);
2150%               mov=getframe(gcf);
2151%              aviobj=addframe(aviobj,mov);end
2152%          if (get(handles.zoom,'Value') == get(handles.zoom,'Max')),zoom on,end
2153%          set(handles.field_counter,'String',num2str(num1(ifile)))
2154% %     end
2155% end
2156% end
2157% end
2158% aviobj=close(aviobj);
2159%
2160% %plot global image histogram
2161%         HIST=HIST/(nbfield*nxy(1)*nxy(2));% normalized by the number of points
2162%         axes(hfig2) %in main window
2163%         if ndim==2
2164%             plot(val,HIST)
2165%         else
2166%             plot(val,HIST(:,1),'r',val,HIST(:,2),'g',val,HIST(:,3),'b')
2167%         end
2168%         residu=1-sum(HIST,1);
2169%         title(['histo, residu ' num2str(residu)])
2170%         grid on
2171%         axes(hfig3)
2172%         cla %clear the second histogram window
2173%         
2174
2175
2176
2177
2178%%%%%%%%%%%%%
2179function [ind_remove]=find_pairs(dirpair,ind_i,last_i)
2180
2181        indsel=ind_i;
2182        indiff=diff(ind_i); %test index increment to detect multiplets (several pairs with the same index ind_i) and holes in the series
2183        indiff=[1 indiff last_i-ind_i(end)+1];%for testing gaps with the imposed bounds
2184        if ~isempty(indiff)
2185            indiff2=diff(indiff);
2186            indiffp=[indiff2 1];
2187            indiffm=[1 indiff2];
2188            ind_multi_m=find((indiff==0)&(indiffm<0))-1;%indices of first members of multiplets
2189            ind_multi_p=find((indiff==0)&(indiffp>0));%indices of last members of multiplets
2190                %for each multiplet, select the most recent file
2191            ind_remove=[];
2192            for i=1:length(ind_multi_m)
2193                ind_pairs=ind_multi_m(i):ind_multi_p(i);
2194                for imulti=1:length(ind_pairs)
2195                    datepair(imulti)=datenum(dirpair(ind_pairs(imulti)).date);%dates of creation
2196                end
2197                [datenew,indsort2]=sort(datepair); %sort the multiplet by creation date
2198                ind_s=indsort2(1:end-1);%
2199                ind_remove=[ind_remove ind_pairs(ind_s)];%remove these indices, leave the last one
2200            end
2201        end
2202
2203%--------------------------------------------------------
2204
2205 
2206%-----------------------------------------------------------
2207% find the times corresponding to the first and last indices of a series
2208%
2209function displ_time(handles,times)
2210hseries=get(handles.last_i,'parent');
2211SeriesData=get(hseries,'UserData');%
2212first_i=str2num(get(handles.first_i,'String'));
2213first_j=str2num(get(handles.first_j,'String'));
2214last_i=str2num(get(handles.last_i,'String'));
2215last_j=str2num(get(handles.last_j,'String'));
2216% index_civ=get(handles.list_pair_civ,'Value');
2217% NomType=get(handles.NomType,'String');
2218NomType=SeriesData.NomType;
2219mode_list=get(handles.mode,'String');
2220index_mode=get(handles.mode,'Value');
2221mode=mode_list{index_mode};
2222% ind_shift=0;%default
2223
2224time_first=[];
2225time_last=[];
2226if ~isfield(SeriesData,'Time')
2227    SeriesData.Time{1}=[];
2228end
2229for iview=1:length(NomType)
2230    time_first_cell{iview}='?';
2231    time_last_cell{iview}='?';%default
2232    time=SeriesData.Time{iview};
2233    if isequal(NomType{iview},'_i1-i2_j')|isequal(NomType{iview},'_i_j1-j2')|isequal(NomType{iview},'#_ab')|isequal(NomType{iview},'_i1-i2')
2234        if isfield(SeriesData,'displ_num')& ~isempty(SeriesData.displ_num)
2235            ind_shift=SeriesData.displ_num(iview,:);
2236            if isequal(mode,'bursts')
2237                first_j=0;
2238                last_j=0;
2239            end
2240            first_i1=first_i +ind_shift(3);
2241            first_i2 =first_i +ind_shift(4);
2242            first_j1 =first_j +ind_shift(1);
2243            first_j2 =first_j +ind_shift(2);
2244            last_i1=last_i +ind_shift(3);
2245            last_i2 =last_i +ind_shift(4);   
2246            last_j1 =last_j +ind_shift(1);
2247            last_j2 =last_j +ind_shift(2);
2248            siz=size(SeriesData.Time{1});
2249            if first_i1>=1 && first_j1>=1 && siz(1)>=last_i2 && siz(2)>=last_j2
2250                time_first=(time(first_i1,first_j1)+time(first_i2,first_j2))/2;
2251                time_last=(time(last_i1,last_j1)+time(last_i2,last_j2))/2;
2252            else%read the time in the nc files
2253                RootPath=get(handles.RootPath,'String');
2254                RootFile=get(handles.RootFile,'String');
2255                SubDir=get(handles.SubDir,'String');
2256                %VelType=get(handles.VelType,'String');
2257                VelType_str=get(handles.VelTypeMenu,'String');
2258                VelType_val=get(handles.VelTypeMenu,'Value');
2259                VelType=VelType_str{VelType_val};
2260                filebase=fullfile(RootPath{1},RootFile{1});
2261                [filefirst]=name_generator(filebase,first_i1,first_j1,'.nc',NomType{iview},1,first_i2,first_j2,SubDir{iview});
2262                if  exist(filefirst,'file')
2263                    Attrib=nc2struct(filefirst,[]);
2264                    if isfield(Attrib,'Time')
2265                        time_first=Attrib.Time;
2266                    else
2267                        if isfield(Attrib,'absolut_time_T0')
2268                            time_first=Attrib.absolut_time_T0;
2269                        end
2270                        if isfield(Attrib,'absolut_time_T0_2')&&~(isequal(VelType,'civ1')||isequal(VelType,'interp1')||isequal(VelType,'filter1'))
2271                            time_first=Attrib.absolut_time_T0_2;
2272                        end
2273                    end
2274                end
2275                [filelast]=name_generator(filebase,last_i1,last_j1,'.nc',NomType{iview},1,last_i2,last_j2,SubDir{iview});
2276                if exist(filelast,'file')
2277                   Attrib=nc2struct(filelast,[]);
2278                    if isfield(Attrib,'Time')
2279                        time_last=Attrib.Time;
2280                    else
2281                        if isfield(Attrib,'absolut_time_T0')
2282                            time_last=Attrib.absolut_time_T0;
2283                        end
2284                        if isfield(Attrib,'absolut_time_T0_2')&&~(isequal(VelType,'civ1')||isequal(VelType,'interp1')||isequal(VelType,'filter1'))
2285                            time_last=Attrib.absolut_time_T0_2;
2286                        end
2287                    end
2288                end
2289            end
2290        end
2291    else
2292        siz=size(times);
2293        if siz(1)>=last_i & siz(2)>=last_j
2294            time_first=times(first_i,first_j);
2295            time_last=times(last_i,last_j);
2296        end
2297    end
2298    time_first_cell{iview}=num2str(time_first,4);
2299    time_last_cell{iview}=num2str(time_last,4);
2300end
2301set(handles.time_first,'Value',1)
2302set(handles.time_last,'Value',1)
2303set(handles.time_first,'String',time_first_cell);
2304set(handles.time_last,'String',time_last_cell);
2305
2306%--------------------------------------------------------------------
2307% --- Executes on selection change in VelTypeMenu.
2308function VelTypeMenu_Callback(hObject, eventdata, handles)
2309% VelTypeList=get(handles.VelTypeMenu,'String');
2310% VelTypeIndex=get(handles.VelTypeMenu,'Value');
2311% VelTypeCell=get(handles.VelType,'String');
2312% VelTypeCell{1}=VelTypeList{VelTypeIndex};
2313% set(handles.VelType,'String',VelTypeCell)
2314
2315
2316%--------------------------------------------------------------------
2317% --- Executes on button press in GetObject.
2318function GetObject_Callback(hObject, eventdata, handles)
2319hseries=get(handles.GetObject,'parent');
2320SeriesData=get(hseries,'UserData');
2321value=get(handles.GetObject,'Value');
2322if value
2323     set(handles.GetObject,'BackgroundColor',[1 1 0])%put unactivated buttons to yellow
2324     DataInit.ParentButton=handles.GetObject;
2325     hset_object=findobj(allchild(0),'Name','set_object');%find the set_object interface handle
2326     if ishandle(hset_object)
2327         [SeriesData.hset_object,SeriesData.sethandles]=set_object(DataInit); %open the set_object interface
2328     else
2329         DataInit.TITLE='POINTS';%default option
2330         [SeriesData.hset_object,SeriesData.sethandles]=set_object(DataInit); %open the set_object interface
2331     end
2332else
2333    set(handles.GetObject,'BackgroundColor',[0 1 0])%put activated buttons to green
2334    if isfield(SeriesData,'hset_object')&& ishandle(SeriesData.hset_object)
2335        close(SeriesData.hset_object)
2336    end
2337end
2338set(hseries,'UserData',SeriesData)
2339
2340%--------------------------------------------------------------
2341function GetMask_Callback(hObject, eventdata, handles)
2342value=get(handles.GetMask,'Value');
2343if value
2344    errordlg('not implemented yet')
2345end
2346%--------------------------------------------------------------
2347
2348%--------------------------------------------------------------------------
2349%'uv_ncbrowser': interactively calls the netcdf file browser 'get_field.m'
2350function ncbrowser_uvmat(hObject, eventdata)
2351     bla=get(gcbo,'String');
2352     ind=get(gcbo,'Value');
2353     filename=cell2mat(bla(ind));
2354      blank=find(filename==' ');
2355      filename=filename(1:blank-1);
2356     get_field(filename)
2357
2358
2359
2360% --------------------------------------------------------------------
2361function MenuHelp_Callback(hObject, eventdata, handles)
2362
2363path_to_uvmat=which ('uvmat');% check the path of uvmat
2364pathelp=fileparts(path_to_uvmat);
2365helpfile=fullfile(pathelp,'UVMAT_DOC','uvmat_doc.html');
2366if isempty(dir(helpfile)), errordlg('Please put the help file uvmat_doc.html in the  directory UVMAT/UVMAT_DOC')
2367else
2368web([helpfile '#series'])   
2369end
2370
2371
2372
2373
2374
2375
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