source: trunk/src/series.m @ 26

Last change on this file since 26 was 26, checked in by gostiaux, 11 years ago

series native functions removed from series.m

File size: 122.4 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)
57
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
131%set(hObject,'UserData', SeriesData)
132set(hObject,'WindowButtonUpFcn',{@mouse_up_gui,handles})
133NomType_Callback(hObject, eventdata, handles)
134%mode_Callback(hObject, eventdata, handles)
135
136%loads the information stored in prefdir to initiate the browser and the list of functions
137menu_str={'check_files';'aver_stat';'time_series';'merge_proj';'clean_civ_cmx'};
138 
139% menu_str=get(handles.ACTION,'String');%list of functions included in 'series.m'
140
141%remove from the list the last option 'more...'
142[path_series,name,ext]=fileparts(which('series'));
143path_series=fullfile(path_series,'/series');%path of the function 'series'
144
145for ilist=1:length(menu_str)
146    fct_path{ilist,1}=path_series;%paths of the fuctions buil-in in 'series.m'
147end
148dir_perso=prefdir;
149profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
150if exist(profil_perso,'file')
151    h=load (profil_perso);
152    if isfield(h,'series_fct') && iscell(h.series_fct)
153         for ilist=1:length(h.series_fct)
154             [path,file]=fileparts(h.series_fct{ilist});
155             fct_path=[fct_path; {path}];%concatene the list of paths
156             menu_str=[menu_str; {file}];
157         end
158    end
159end
160
161menu_str=[menu_str;{'more...'}];
162set(handles.ACTION,'String',menu_str)
163set(handles.ACTION,'UserData',fct_path)% store the list of path in UserData of ACTION
164
165% display the GUI for the default action 'check_files'
166ACTION_Callback(hObject, eventdata, handles)
167
168%--------------------------------------------------------------
169% --- Outputs from this function are returned to the command line.
170%-----------------------------------------------------------------
171function varargout = series_OutputFcn(hObject, eventdata, handles)
172% varargout  cell array for returning output args (see VARARGOUT);
173% hObject    handle to figure
174% eventdata  reserved - to be defined in a future version of MATLAB
175% handles    structure with handles and user data (see GUIDATA)
176% Get default command line output from handles structure
177varargout{1} = handles.output;
178
179
180% --------------------------------------------------------------------
181function MenuBrowse_Callback(hObject, eventdata, handles)
182
183RootPathCell=get(handles.RootPath,'String');
184SubDirCell=get(handles.SubDir,'String'); 
185RootFileCell=get(handles.RootFile,'String');
186oldfile=''; %default
187if isempty(RootPathCell)|isequal(RootPathCell,{''})%loads the previously stored file name and set it as default in the file_input box
188     dir_perso=prefdir;
189     profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
190     if exist(profil_perso,'file')
191          h=load (profil_perso);
192         if isfield(h,'filebase')&ischar(h.filebase)
193                 oldfile=h.filebase;
194         end
195         if isfield(h,'RootPath')&ischar(h.RootPath)
196                 oldfile=h.RootPath;
197         end
198     end
199 else
200     oldfile=fullfile(RootPathCell{1},SubDirCell{1},RootFileCell{1});
201 end
202[FileName, PathName, filterindex] = uigetfile( ...
203       {'*.xml;*.xls;*.png;*.tif;*.avi;*.AVI;*.nc', ' (*.xml,*.xls, *.png,*.tif, *.avi,*.nc)';
204       '*.xml',  '.xml files '; ...
205        '*.xls',  '.xls files '; ...
206        '*.png','.png image files'; ...
207        '*.tif','.tif image files'; ...
208        '*.avi;*.AVI','.avi movie files'; ...
209        '*.nc','.netcdf files'; ...
210        '*.*',  'All Files (*.*)'}, ...
211        'Pick a file',oldfile);
212fileinput=[PathName FileName];%complete file name
213testblank=findstr(fileinput,' ');%look for blanks
214if ~isempty(testblank)
215    errordlg('forbidden input file name: contain blanks')
216    return
217end
218sizf=size(fileinput);
219if (~ischar(fileinput)|~isequal(sizf(1),1)),return;end
220[path,name,ext]=fileparts(fileinput);
221SeriesData=[];%dfault
222if isequal(ext,'.xml')
223    errordlg('input file type not implemented')%A Faire: ouvrir le fichier pour naviguer
224elseif isequal(ext,'.xls')
225    errordlg('input file type not implemented')%A Faire: ouvrir le fichier pour naviguer
226else
227    update_file(hObject, eventdata, handles,fileinput,0)
228     %update list of recent files in the menubar
229    MenuFile_1=fileinput;
230    MenuFile_2=get(handles.MenuFile_1,'Label');
231    MenuFile_3=get(handles.MenuFile_2,'Label');
232    MenuFile_4=get(handles.MenuFile_3,'Label');
233    MenuFile_5=get(handles.MenuFile_4,'Label');
234    set(handles.MenuFile_1,'Label',MenuFile_1)
235    set(handles.MenuFile_2,'Label',MenuFile_2)
236    set(handles.MenuFile_3,'Label',MenuFile_3)
237    set(handles.MenuFile_4,'Label',MenuFile_4)
238    set(handles.MenuFile_5,'Label',MenuFile_5)
239    set(handles.MenuFile_insert_1,'Label',MenuFile_1)
240    set(handles.MenuFile_insert_2,'Label',MenuFile_2)
241    set(handles.MenuFile_insert_3,'Label',MenuFile_3)
242    set(handles.MenuFile_insert_4,'Label',MenuFile_4)
243    set(handles.MenuFile_insert_5,'Label',MenuFile_5)
244    dir_perso=prefdir;
245    profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
246    if exist(profil_perso,'file')
247        save (profil_perso,'MenuFile_1','MenuFile_2','MenuFile_3','MenuFile_4', 'MenuFile_5','-append'); %store the file names for future opening of uvmat
248    else
249        txt=ver;
250        Release=txt(1).Release;
251        relnumb=str2num(Release(3:4));
252        if relnumb >= 14
253            save (profil_perso,'MenuFile_1','MenuFile_2','MenuFile_3','MenuFile_4', 'MenuFile_5','-V6'); %store the file names for future opening of uvmat
254        else
255            save (profil_perso,'MenuFile_1','MenuFile_2','MenuFile_3','MenuFile_4', 'MenuFile_5'); %store the file names for future opening of uvmat
256        end
257    end
258end
259% set(hseries,'UserData',SeriesData);
260% RootFile_Callback(hObject, eventdata, handles);
261% FileExt_Callback(hObject, eventdata, handles);
262% NomType_Callback(hObject, eventdata, handles)
263% mode_Callback(hObject, eventdata, handles)
264
265
266% --------------------------------------------------------------------
267function MenuFile_1_Callback(hObject, eventdata, handles)
268fileinput=get(handles.MenuFile_1,'Label');
269update_file(hObject, eventdata, handles,fileinput,0)
270
271% --------------------------------------------------------------------
272function MenuFile_2_Callback(hObject, eventdata, handles)
273fileinput=get(handles.MenuFile_2,'Label');
274update_file(hObject, eventdata, handles,fileinput,0)
275
276% --------------------------------------------------------------------
277function MenuFile_3_Callback(hObject, eventdata, handles)
278fileinput=get(handles.MenuFile_3,'Label');
279update_file(hObject, eventdata, handles,fileinput,0)
280
281% --------------------------------------------------------------------
282function MenuFile_4_Callback(hObject, eventdata, handles)
283fileinput=get(handles.MenuFile_4,'Label');
284update_file(hObject, eventdata, handles,fileinput,0)
285
286% --------------------------------------------------------------------
287function MenuFile_5_Callback(hObject, eventdata, handles)
288fileinput=get(handles.MenuFile_5,'Label');
289update_file(hObject, eventdata, handles,fileinput,0)
290
291% --------------------------------------------------------------------
292function MenuBrowse_insert_Callback(hObject, eventdata, handles)
293
294%hseries=get(handles.browse_root,'parent');
295RootPathCell=get(handles.RootPath,'String');
296% SubDirCell=get(handles.SubDir,'String'); 
297RootFileCell=get(handles.RootFile,'String');
298oldfile=''; %default
299if isempty(RootPathCell)|isequal(RootPathCell,{''})%loads the previously stored file name and set it as default in the file_input box
300     dir_perso=prefdir;
301     profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
302     if exist(profil_perso,'file')
303          h=load (profil_perso);
304         if isfield(h,'filebase')&ischar(h.filebase)
305                 oldfile=h.filebase;
306         end
307         if isfield(h,'RootPath')&ischar(h.RootPath)
308                 oldfile=h.RootPath;
309         end
310     end
311 else
312     oldfile=fullfile(RootPathCell{1},RootFileCell{1});
313 end
314[FileName, PathName, filterindex] = uigetfile( ...
315       {'*.xml;*.xls;*.png;*.avi;*.AVI;*.nc', ' (*.xml,*.xls, *.png, *.avi,*.nc)';
316       '*.xml',  '.xml files '; ...
317        '*.xls',  '.xls files '; ...
318        '*.png','.png image files'; ...
319        '*.avi;*.AVI','.avi movie files'; ...
320        '*.nc','.netcdf files'; ...
321        '*.*',  'All Files (*.*)'}, ...
322        'Pick a file',oldfile);
323fileinput=[PathName FileName];%complete file name
324testblank=findstr(fileinput,' ');%look for blanks
325if ~isempty(testblank)
326    errordlg('forbidden input file name: contain blanks')
327    return
328end
329sizf=size(fileinput);
330if (~ischar(fileinput)|~isequal(sizf(1),1)),return;end
331[path,name,ext]=fileparts(fileinput);
332SeriesData=[];%dfault
333if isequal(ext,'.xml')
334    errordlg('input file type not implemented')%A Faire: ouvrir le fichier pour naviguer
335elseif isequal(ext,'.xls')
336    errordlg('input file type not implemented')%A Faire: ouvrir le fichier pour naviguer
337else
338    update_file(hObject, eventdata, handles,fileinput,1)
339    %update list of recent files in the menubar
340    MenuFile_1=fileinput;
341    MenuFile_2=get(handles.MenuFile_1,'Label');
342    MenuFile_3=get(handles.MenuFile_2,'Label');
343    MenuFile_4=get(handles.MenuFile_3,'Label');
344    MenuFile_5=get(handles.MenuFile_4,'Label');
345    set(handles.MenuFile_1,'Label',MenuFile_1)
346    set(handles.MenuFile_2,'Label',MenuFile_2)
347    set(handles.MenuFile_3,'Label',MenuFile_3)
348    set(handles.MenuFile_4,'Label',MenuFile_4)
349    set(handles.MenuFile_5,'Label',MenuFile_5)
350    set(handles.MenuFile_insert_1,'Label',MenuFile_1)
351    set(handles.MenuFile_insert_2,'Label',MenuFile_2)
352    set(handles.MenuFile_insert_3,'Label',MenuFile_3)
353    set(handles.MenuFile_insert_4,'Label',MenuFile_4)
354    set(handles.MenuFile_insert_5,'Label',MenuFile_5)
355    dir_perso=prefdir;
356    profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
357    if exist(profil_perso,'file')
358        save (profil_perso,'MenuFile_1','MenuFile_2','MenuFile_3','MenuFile_4', 'MenuFile_5','-append'); %store the file names for future opening of uvmat
359    else
360        txt=ver;
361        Release=txt(1).Release;
362        relnumb=str2num(Release(3:4));
363        if relnumb >= 14
364            save (profil_perso,'MenuFile_1','MenuFile_2','MenuFile_3','MenuFile_4', 'MenuFile_5','-V6'); %store the file names for future opening of uvmat
365        else
366            save (profil_perso,'MenuFile_1','MenuFile_2','MenuFile_3','MenuFile_4', 'MenuFile_5'); %store the file names for future opening of uvmat
367        end
368    end
369end
370%------------------------------------------------
371
372% --------------------------------------------------------------------
373function MenuFile_insert_1_Callback(hObject, eventdata, handles)
374fileinput=get(handles.MenuFile_insert_1,'Label');
375update_file(hObject, eventdata, handles,fileinput,1)
376
377% --------------------------------------------------------------------
378function MenuFile_insert_2_Callback(hObject, eventdata, handles)
379fileinput=get(handles.MenuFile_insert_2,'Label');
380update_file(hObject, eventdata, handles,fileinput,1)
381
382% --------------------------------------------------------------------
383function MenuFile_insert_3_Callback(hObject, eventdata, handles)
384fileinput=get(handles.MenuFile_insert_3,'Label');
385update_file(hObject, eventdata, handles,fileinput,1)
386
387% --------------------------------------------------------------------
388function MenuFile_insert_4_Callback(hObject, eventdata, handles)
389fileinput=get(handles.MenuFile_insert_4,'Label');
390update_file(hObject, eventdata, handles,fileinput,1)
391
392% --------------------------------------------------------------------
393function MenuFile_insert_5_Callback(hObject, eventdata, handles)
394fileinput=get(handles.MenuFile_insert_5,'Label');
395update_file(hObject, eventdata, handles,fileinput,1)
396
397% --------------------------------------------------------------------
398% refresh the GUI data after introduction of a new file series
399function update_file(hObject, eventdata, handles,fileinput,addtest)
400hseries=get(handles.RootPath,'parent'); 
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(imformats(FileExt(2:end)))
405    imainfo=imfinfo(fileinput);     
406    if length(imainfo) >1 %case of image with multiple frames
407        NomType='*';
408        [RootPath,RootFile]=fileparts(fileinput);
409    end
410end
411NcType='none';%default
412if isequal(FileExt,'.nc')
413   Data=nc2struct(fileinput,[]);
414   if isfield(Data,'absolut_time_T0')
415       NcType='civx'; % test for civx velocity fields
416   end
417end
418
419set(handles.RootPath,'Value',1)
420set(handles.SubDir,'Value',1)
421set(handles.RootFile,'Value',1)
422set(handles.NomType,'Value',1)
423set(handles.FileExt,'Value',1)
424set(handles.nb_field,'Value',1)
425set(handles.nb_field2,'Value',1)
426if addtest
427    SeriesData=get(hseries,'UserData');
428    SeriesData.displ_num=[0 0 0 0;SeriesData.displ_num];
429    SeriesData.CurrentInputFile_1=SeriesData.CurrentInputFile;
430    RootPathCell=[{RootPath}; get(handles.RootPath,'String')] ;
431    SubDirCell=[{SubDir}; get(handles.SubDir,'String')];
432    RootFileCell=[{RootFile}; get(handles.RootFile,'String')];
433    NomTypeCell=[{NomType}; SeriesData.NomType];
434    FileExtCell=[{FileExt}; get(handles.FileExt,'String')];
435    NcTypeCell=[{NcType};SeriesData.NcType];
436    set(handles.NomType,'String',[{};get(handles.NomType,'String')])
437else
438    SeriesData=[];%re-initialisation
439    SeriesData.displ_num=[0 0 0 0];
440    RootPathCell={RootPath};
441    SubDirCell={SubDir};
442    RootFileCell={RootFile};   
443    NomTypeCell={NomType};
444    FileExtCell={FileExt};   
445    NcTypeCell={NcType};
446end
447
448SeriesData.NomType=NomTypeCell;
449SeriesData.NcType=NcTypeCell;
450SeriesData.CurrentInputFile=fileinput;
451set(handles.RootPath,'String',RootPathCell);
452set(handles.SubDir,'String',SubDirCell);
453set(handles.RootFile,'String',RootFileCell);
454set(handles.NomType,'String',NomTypeCell);
455set(handles.FileExt,'String',FileExtCell); 
456
457%determine field indices
458ref_i=1; %default ref_i is a reference frame index used to find existing pairs from PIV
459if ~isempty(str2num(field_count))
460    ref_i=str2num(field_count);
461    if ~isempty(str2num(str2))
462        ref_i=floor((ref_i+str2num(str2))/2);% reference image number corresponding to the file
463        SeriesData.browse_Di=str2num(str2)-str2num(field_count);
464    end
465end
466set(handles.ref_i,'String',num2str(ref_i));
467set(handles.first_i,'String',num2str(ref_i));
468set(handles.last_i,'String',num2str(ref_i));
469ref_j=1; %default  ref_j is a reference frame index used to find existing pairs from PIV
470if ~isempty(str2num(str_a))
471    ref_j=str2num(str_a);
472    if ~isempty(str2num(str_b))
473        ref_j=floor((str2num(str_a)+str2num(str_b))/2);
474        SeriesData.browse_Dj=str2num(str_b)-str2num(str_a);
475    end         
476end
477set(handles.ref_j,'String',num2str(ref_j));
478set(handles.first_j,'String',num2str(ref_j))
479set(handles.last_j,'String',num2str(ref_j));
480%set(hseries,'UserData',SeriesData);
481
482%enable other menus and uicontrols
483set(handles.MenuOpen_insert,'Enable','on')
484set(handles.MenuFile_insert_1,'Enable','on')
485set(handles.MenuFile_insert_2,'Enable','on')
486set(handles.MenuFile_insert_3,'Enable','on')
487set(handles.MenuFile_insert_4,'Enable','on')
488set(handles.MenuFile_insert_5,'Enable','on')
489set(handles.RUN, 'Enable','On')
490set(handles.RUN,'BackgroundColor',[1 0 0])% set RUN button to red
491set(handles.RootPath,'BackgroundColor',[1 1 0]) % set RootPath edit box  to yellow
492drawnow
493
494% hseries=get(handles.RootFile,'parent');
495% SeriesData=get(hseries,'UserData');%read information set by the browser
496% ext_ima_read=[];
497% field_count=1;%default
498% pxcmx=1;
499% pxcmy=1;
500TimeUnit=''; %default
501% CoordUnit='';%default
502time=[];%default
503GeometryCalib=[];%default
504nb_field=[];%default
505nb_field2=[];%default
506% Heading=[];
507% [PD,Device]=fileparts(RootPathCell{1});
508SeriesData.PathCampaign=get(handles.PathCampaign,'String');
509
510% read timing and total frame number from the current file (movie files) !! may be overrid by xml file
511%icell=length(RootPathCell);
512FileBase=fullfile(RootPath,RootFile);
513
514% nb_field{icell,1}='?';%default
515% nb_field2{icell,1}='?';%default
516testima=0; %test for image input
517if isequal(lower(FileExt),'.avi') %.avi file
518    testima=1;
519    info=aviinfo([FileBase FileExt]);
520    time=[0:1/info.FramesPerSecond:(info.NumFrames-1)/info.FramesPerSecond]';
521    nb_field=info.NumFrames;
522    nb_field2=1;
523elseif ~isempty(imformats(FileExt(2:end)))
524    testima=1;
525    if isequal(NomType,'*')% multi-frame image
526        imainfo=imfinfo([FileBase FileExt]);     
527        if length(imainfo) >1 %case of image with multiple frames
528            nb_field=length(imainfo);
529            nb_field2=1;
530        end
531    end
532elseif isequal(FileExt,'.vol')
533     testima=1;
534end
535
536% enable field and veltype menus
537testfield=isequal(get(handles.FieldMenu,'enable'),'on');
538testfield_1=isequal(get(handles.FieldMenu_1,'enable'),'on');
539testveltype=isequal(get(handles.VelTypeMenu,'enable'),'on');
540testveltype_1=isequal(get(handles.VelTypeMenu_1,'enable'),'on');
541testtransform=isequal(get(handles.CoordType,'Enable'),'on');
542testnc=0;
543testnc_1=0;
544testcivx=0;
545testcivx_1=0;
546if length(FileExtCell)==1 || length(FileExtCell)>2
547    for iview=1:length(FileExtCell)
548        if isequal(FileExtCell{iview},'.nc')
549            testnc=1;
550        end
551        if isequal(NcTypeCell{iview},'civx')
552            testcivx=1;
553        end
554    end
555elseif length(FileExtCell)==2
556    testnc=isequal(FileExtCell{1},'.nc');
557    testnc_1=isequal(FileExtCell{2},'.nc');
558    testcivx=isequal(NcTypeCell{1},'civx');
559    testcivx_1=isequal(NcTypeCell{2},'civx');
560end
561if testfield && testnc
562    view_FieldMenu(handles,'on')
563    if testcivx
564        menustr=get(handles.FieldMenu,'String');
565        if isequal(menustr,{'get_field...'})
566            set(handles.FieldMenu,'String',{'get_field...';'velocity';'vort';'div';'more...'})
567        end
568    else
569        set(handles.FieldMenu,'Value',1)
570        set(handles.FieldMenu,'String',{'get_field...'})
571    end
572else
573    view_FieldMenu(handles,'off')
574end
575if testfield_1 && testnc_1
576    view_FieldMenu_1(handles,'on')
577    if testcivx_1
578        menustr=get(handles.FieldMenu_1,'String');
579        if isequal(menustr,{'get_field...'})
580            set(handles.FieldMenu_1,'String',{'get_field...';'velocity';'vort';'div';'more...'})
581        end
582    else
583        set(handles.FieldMenu_1,'Value',1)
584        set(handles.FieldMenu_1,'String',{'get_field...'})
585    end
586else
587    view_FieldMenu_1(handles,'off')
588end
589if testveltype && testcivx
590    set(handles.VelTypeMenu,'Visible','on')
591    set(handles.VelType_text,'Visible','on');
592else
593    set(handles.VelTypeMenu,'Visible','off')
594    set(handles.VelType_text,'Visible','off');
595end
596if testveltype_1 && testcivx_1
597    set(handles.VelTypeMenu_1,'Visible','on')
598    set(handles.VelType_text_1,'Visible','on');
599else
600    set(handles.VelTypeMenu_1,'Visible','off')
601    set(handles.VelType_text_1,'Visible','off');
602end
603if testtransform && (testcivx || testima)
604     view_TRANSFORM(handles,'on')
605else
606    view_TRANSFORM(handles,'off')
607end
608if ~isequal(FileExt,'.nc') && ~isequal(FileExt,'.cdf') && ~testima
609    msgbox_uvmat('ERROR',['invalid input file extension ' FileExt])
610    return
611end 
612
613%%%%%%%%   read image documentation file  if found%%%%%%%%%%%%%%%%%%%%%%%%%%%
614      %look for the file existence
615ext_imadoc='';
616if isequal(FileExt,'.xml')||isequal(FileExt,'.civ')
617    ext_imadoc=FileExt;
618elseif exist([FileBase '.xml'],'file')
619    ext_imadoc='.xml';
620elseif exist([FileBase '.civ'],'file')
621    ext_imadoc='.civ';
622end
623      %read the ImaDoc file
624% mode=''; %default
625% testheading=0; 
626XmlData=[];
627NbSlice_calib={};
628if isequal(ext_imadoc,'.xml')
629        [XmlData,warntext]=imadoc2struct([FileBase '.xml']);
630        if isfield(XmlData,'Heading') && isfield(XmlData.Heading,'ImageName')
631            [PP,FF,ext_ima_read]=fileparts(XmlData.Heading.ImageName);
632        end
633        if isfield(XmlData,'Time')
634            time=XmlData.Time;
635        end
636        if isfield(XmlData,'Camera')
637            if isfield(XmlData.Camera,'NbSlice')&& ~isempty(XmlData.Camera.NbSlice)
638                NbSlice_calib{iview}=XmlData.Camera.NbSlice;% Nbre of slices for Zindex in phys transform
639                if ~isequal(NbSlice_calib{iview},NbSlice_calib{1})
640                    msgbox_uvmat('WARNING','inconsistent number of Z indices for the two field series');
641                end
642            end
643            if isfield(XmlData.Camera,'TimeUnit')&& ~isempty(XmlData.Camera.TimeUnit)
644                TimeUnit=XmlData.Camera.TimeUnit;
645            end
646        end
647        if ~isempty(warntext)
648            msgbox_uvmat('WARNING',warntext)
649        end 
650elseif isequal(ext_imadoc,'.civ')
651    [error,XmlData.Time,TimeUnit,mode,npx,npy,pxcmx,pxcmy]=read_imatext([FileBase '.civ']);
652    time=XmlData.Time;
653    size(time)
654    GeometryCalib.R=[pxcmx 0 0; 0 pxcmy 0;0 0 0];
655    GeometryCalib.Tx=0;
656    GeometryCalib.Ty=0;
657    GeometryCalib.Tz=1;
658    GeometryCalib.dpx=1;
659    GeometryCalib.dpy=1;
660    GeometryCalib.sx=1;
661    GeometryCalib.Cx=0;
662    GeometryCalib.Cy=0;
663    GeometryCalib.f=1;
664    GeometryCalib.kappa1=0;
665    GeometryCalib.CoordUnit='cm';
666    XmlData.GeometryCalib=GeometryCalib;
667    if error==2, warntext=['no file ' FileBase '.civ'];
668    elseif error==1, warntext='inconsistent number of fields in the .civ file';
669    end 
670%     set(handles.npx,'String',num2str(npx));%fills nbre of pixels x box
671%     set(handles.npy,'String',num2str(npy));%fills nbre of pixels y box
672%     set(handles.pxcm,'String',num2str(pxcmx));%fills scale x (pixel/cm) box
673%     set(handles.pycm,'String',num2str(pxcmy));%fills scale y (pixel/cm) box
674%     set(handles.pxcm,'Visible','on');%fills scale x (pixel/cm) box
675%     set(handles.pycm,'Visible','on');%fills scale y (pixel/cm) box
676%     set(handles.view_xml,'Visible','on')
677%     set(handles.view_xml,'String','view .civ')
678end 
679if addtest
680    SeriesData.Time=[{time} SeriesData.Time];
681else
682   SeriesData.Time={time};
683end
684
685if ~isempty(time)
686    siztime=size(time);
687    nb_field=siztime(1);
688    nb_field2=siztime(2);
689end   
690set(handles.TimeUnit,'String',TimeUnit)
691if isempty(nb_field)
692    nb_field_str='?';
693    nb_field_str2='?';
694else
695    nb_field_str=num2str(nb_field);
696    nb_field_str2=num2str(nb_field2);
697end
698if addtest
699    nb_field_cell=[{nb_field_str} ;get(handles.nb_field,'String')];
700    nb_field2_cell=[{nb_field_str2} ;get(handles.nb_field2,'String')];
701else
702    nb_field_cell={nb_field_str};
703    nb_field2_cell={nb_field_str2};
704end
705set(handles.nb_field,'String',nb_field_cell);
706set(handles.nb_field2,'String',nb_field2_cell);
707set(hseries,'UserData',SeriesData);
708
709%number of slices
710if isfield(XmlData,'GeometryCalib') && isfield(XmlData.GeometryCalib,'SliceCoord')
711       siz=size(XmlData.GeometryCalib.SliceCoord);
712       if siz(1)>1
713           NbSlice=siz(1);
714       else
715           NbSlice=1;
716       end
717       set(handles.NbSlice,'String',num2str(NbSlice))
718end
719
720% set menus of index pairs
721NomType_Callback(hObject, eventdata, handles)
722
723dir_perso=prefdir;
724profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
725% save(profil_perso, 'FileBase'); %store the root name for future opening of uvmat
726if exist(profil_perso,'file')
727    save (profil_perso,'RootPath','SubDir','RootFile','NomType', '-append'); %store the root name for future opening of uvmat
728else
729    txt=ver;
730    Release=txt(1).Release;
731    relnumb=str2num(Release(3:4));
732    if relnumb >= 14
733        save (profil_perso,'RootPath','SubDir','RootFile','NomType','-V6') %store the root name for future opening of uvmat
734    else
735        save(profil_perso,'RootPath','SubDir','RootFile','NomType')
736    end         
737end
738set(handles.RootPath,'BackgroundColor',[1 1 1])
739set(handles.PathCampaign,'String',SeriesData.PathCampaign)
740last_j_Callback(hObject, eventdata, handles)
741last_i_Callback(hObject, eventdata, handles)
742
743%------------------------------------------------------------
744function RootPath_Callback(hObject, eventdata, handles)
745Val=get(handles.RootPath,'Value');
746synchronise_view(handles,Val)
747NomType_Callback(hObject, eventdata, handles)
748%------------------------------------------------------------
749
750function synchronise_view(handles,Val)
751set(handles.RootPath,'Value',Val)
752set(handles.SubDir,'Value',Val)
753set(handles.RootFile,'Value',Val)
754set(handles.NomType,'Value',Val)
755set(handles.FileExt,'Value',Val)
756set(handles.nb_field,'Value',Val)
757set(handles.nb_field2,'Value',Val)
758set(handles.time_first,'Value',Val)
759set(handles.time_last,'Value',Val)
760
761
762%---------------------------------------------------------
763% Executes on carriage return on the subdir civ1 edit window
764%--------------------------------------------------------
765function SubDir_Callback(hObject, eventdata, handles)
766
767Val=get(handles.SubDir,'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 RootFile_Callback(hObject, eventdata, handles)
775Val=get(handles.RootFile,'Value');
776synchronise_view(handles,Val)
777NomType_Callback(hObject, eventdata, handles)
778
779%--------------------------------------------------------------
780%function activated when a new filebase (image series) is introduced
781%------------------------------------------------------------
782function FileExt_Callback(hObject, eventdata, handles)
783Val=get(handles.FileExt,'Value');
784synchronise_view(handles,Val)
785
786%--------------------------------------------------------------
787%function activated when a new filebase (image series) is introduced
788%------------------------------------------------------------
789function nb_field_Callback(hObject, eventdata, handles)
790Val=get(handles.nb_field,'Value');
791synchronise_view(handles,Val)
792
793%--------------------------------------------------------------
794%function activated when a new filebase (image series) is introduced
795%------------------------------------------------------------
796function nb_field2_Callback(hObject, eventdata, handles)
797Val=get(handles.nb_field2,'Value');
798synchronise_view(handles,Val)
799
800%--------------------------------------------------------------
801%function activated when a new filebase (image series) is introduced
802%------------------------------------------------------------
803function time_first_Callback(hObject, eventdata, handles)
804Val=get(handles.time_first,'Value');
805synchronise_view(handles,Val)
806
807%--------------------------------------------------------------
808%function activated when a new filebase (image series) is introduced
809%------------------------------------------------------------
810function time_last_Callback(hObject, eventdata, handles)
811Val=get(handles.time_last,'Value');
812synchronise_view(handles,Val)
813
814%--------------------------------------------------------------
815%function activated by NomType
816%------------------------------------------------------------
817NomType_Callback(hObject, eventdata, handles)
818
819function NomType_Callback(hObject, eventdata, handles)
820hseries=get(handles.ProjObject,'Parent');
821SeriesData=get(hseries,'UserData');
822if isfield(SeriesData,'NomType')
823    NomTypeCell=SeriesData.NomType;
824else
825    NomTypeCell={};
826end
827nbfield2_cell=get(handles.nb_field2,'String');
828val=get(handles.nb_field2,'Value');
829if iscell(nbfield2_cell)
830    nbfield2=str2num(nbfield2_cell{val});
831else
832    nbfield2=str2num(nbfield2_cell);
833end
834nbfield_cell=get(handles.nb_field,'String');
835if iscell(nbfield_cell)
836    nbfield=str2num(nbfield_cell{val});
837else
838   nbfield=str2num(nbfield_cell);
839end
840
841set(handles.mode,'Visible','off') % do not show index pairs by default
842set(handles.list_pair_civ,'Visible','off')
843set(handles.ref_i,'Visible','off')
844set(handles.ref_i_text,'Visible','off')
845testpair=0;
846state_j='off';
847%set the menus of image pairs and default selection for series
848%list pairs if relevant
849Val=get(handles.NomType,'Value');
850synchronise_view(handles,Val)
851if ~isempty(NomTypeCell)
852    NomType=NomTypeCell{Val};
853    switch NomType 
854            case {'_i1-i2_j', '_i1-i2'}
855                set(handles.mode,'String',{'series(Di)'})
856                set(handles.mode,'Value',1);
857                set(handles.mode,'Visible','on')
858                testpair=1;
859            case {'#_ab'}
860                set(handles.mode,'String',{'bursts'})
861                set(handles.mode,'Value',1);
862                testpair=1;
863            case '_i_j1-j2'
864                set(handles.mode,'String',{'bursts';'series(Dj)'})%multiple choice
865                if ~isempty(nbfield) && ~isempty(nbfield2) && ((nbfield2>10) || (nbfield==1))
866                    set(handles.mode,'Value',2);
867                else
868                    set(handles.mode,'Value',1);% advice 'bursts' for small bursts
869                end
870                set(handles.mode,'Visible','on')
871                testpair=1;
872    end
873    switch NomType   
874            case {'_i_j','_i_j1-j2','_i1-i2_j','#_ab'},% two navigation indices
875                state_j='on';
876    end
877end   
878if testpair
879    mode_Callback(hObject, eventdata, handles) 
880else
881    set(handles.NomType,'String',NomTypeCell)
882end
883set(handles.first_j,'Visible',state_j)
884set(handles.incr_j,'Visible',state_j)
885set(handles.last_j,'Visible',state_j)
886set(handles.nb_field2,'Visible',state_j)
887
888%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%????????????
889% --- Executes on button press in mode.
890%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
891function mode_Callback(hObject, eventdata, handles)
892hseries=get(handles.mode,'parent');
893SeriesData=get(hseries,'UserData');
894mode_list=get(handles.mode,'String');
895mode_value=get(handles.mode,'Value');
896mode=mode_list{mode_value};
897NomType=[];
898test_find_pair=0;
899if isfield(SeriesData,'NomType')
900    NomTypeCell=SeriesData.NomType;
901    Val=get(handles.NomType,'Value');
902    NomType=NomTypeCell{Val};
903    test_find_pair=isequal(NomType,'_i_j1-j2')|| isequal(NomType,'_i1-i2_j')|| isequal(NomType,'_i1-i2')|| isequal(NomType,'#_ab');
904end
905% displ_num=[];%default
906% first_i=str2num(get(handles.first_i,'String'));
907% last_i=str2num(get(handles.last_i,'String'));
908time=[];
909if isfield(SeriesData,'Time')
910time=SeriesData.Time{1}; %get the set of times
911end
912siztime=size(time);
913nbfield=siztime(1);
914nbfield2=siztime(2);
915indchosen=1;  %%first pair selected by default
916if isequal(mode,'bursts')
917    enable_i(handles,'On')
918    enable_j(handles,'Off')   
919elseif  isequal(NomType,'_i_j1-j2')|| isequal(NomType,'_i1-i2_j')
920    enable_i(handles,'On')
921    enable_j(handles,'On')
922else
923    enable_i(handles,'On')
924    enable_j(handles,'Off')
925end   
926   
927   
928% elseif isequal(mode,'series(Dj)')       
929%     enable_j(handles,'On')     
930%     if nbfield==1
931%         enable_i(handles,'Off')
932%     else
933%         enable_i(handles,'On')
934%     end
935% elseif isequal(mode,'series(Di)')
936%     if nbfield2 > 1
937%          enable_j(handles,'On')
938%     else
939%          enable_j(handles,'Off')
940%     end
941% end 
942set(handles.list_pair_civ,'Value',indchosen);%set the default choice of image pairs for civ1
943% SetSeries.displ_num=displ_num;
944set(hseries,'UserData',SeriesData)
945
946%list pairs if relevant
947if test_find_pair
948     find_netcpair_civ(hObject, eventdata, handles,Val)
949end
950
951%-------------------------------------
952function enable_i(handles,state)
953set(handles.i_txt,'Visible',state)
954set(handles.first_i,'Visible',state)
955set(handles.last_i,'Visible',state)
956set(handles.incr_i,'Visible',state)
957set(handles.nb_field,'Visible',state)
958set(handles.ref_i,'Visible',state)
959set(handles.ref_i_text,'Visible',state)
960
961%-----------------------------------
962function enable_j(handles,state)
963set(handles.j_txt,'Visible',state)
964set(handles.first_j,'Visible',state)
965set(handles.last_j,'Visible',state)
966set(handles.incr_j,'Visible',state)
967set(handles.nb_field2,'Visible',state)
968set(handles.ref_j,'Visible',state)
969set(handles.ref_j_text,'Visible',state)
970
971%-----------------------------------
972function view_FieldMenu(handles,state)
973set(handles.FieldMenu,'Visible',state)
974set(handles.Field_text,'Visible',state)
975set(handles.Field_frame,'Visible',state)
976
977%-----------------------------------
978function view_FieldMenu_1(handles,state)
979set(handles.FieldMenu_1,'Visible',state)
980set(handles.Field_text_1,'Visible',state)
981
982%-----------------------------------
983function view_TRANSFORM(handles,state)
984set(handles.TRANSFORM_frame,'Visible',state)
985set(handles.CoordType,'Visible',state);
986set(handles.TRANSFORM_title,'Visible',state)
987
988%--------------------------------------------------------------
989% determine the menu for civ1 pairs depending on existing netcdf file at the middle of
990% the field series set by first_i, incr, last_i
991%----------------------------------------------------------------
992function find_netcpair_civ(hObject, eventdata, handles,Val)
993hseries=get(handles.list_pair_civ,'parent');
994SeriesData=get(hseries,'UserData');
995% NomTypeCell=get(handles.NomType,'String');
996NomTypeCell=SeriesData.NomType;
997NomType=NomTypeCell{Val};
998  set(handles.list_pair_civ,'Visible','on')
999%nomenclature types
1000RootPathCell=get(handles.RootPath,'String');
1001filepath=RootPathCell{Val};
1002RootFileCell=get(handles.RootFile,'String');
1003filename=RootFileCell{Val};
1004filebase=fullfile(filepath,filename);
1005SubDirCell=get(handles.SubDir,'String');
1006subdir=SubDirCell{Val};
1007if ~exist(fullfile(filepath,subdir),'dir')
1008         msgbox_uvmat('ERROR',['no civ file available: subdirectory ' subdir ' does not exist'])
1009         set(handles.list_pair_civ,'String',{''});
1010         return
1011end
1012mode_list=get(handles.mode,'String');
1013mode_value=get(handles.mode,'Value');
1014mode=mode_list{mode_value};
1015
1016%reads image numbers from the interface
1017ref_i=str2num(get(handles.ref_i,'String'));
1018ref_j=str2num(get(handles.ref_j,'String'));
1019% time=[];
1020% ref_time=[];
1021 ref_time=0;
1022if isfield(SeriesData,'Time')&~isempty(SeriesData.Time{Val})&~isequal(SeriesData.Time{Val},0)
1023    time=SeriesData.Time{Val}; %get the set of times
1024    siztime=size(time);
1025    nbfield=siztime(1);
1026    nbfield2=siztime(2);
1027%     test_imadoc=1;
1028else
1029%     test_imadoc=0;%no image documentation file
1030    nbfield=50;
1031    nbfield2=50;%default max number of pairs
1032end
1033%look for existing processed pairs involving the field at the middle of the series if civ1 will not
1034% be performed, while the result is needed for next steps.
1035displ_pair={''};
1036displ_num=[];
1037ind_exist=0;
1038TimeUnit=get(handles.TimeUnit,'String');
1039if length(TimeUnit)>=1
1040    dtunit=['m' TimeUnit];
1041else
1042    dtunit='e-03';
1043end
1044if isequal(mode,'series(Di)')
1045     for index=1:min(nbfield-1,50)
1046         filename=name_generator(filebase,ref_i-floor(index/2),ref_j,'.nc',NomType,1,ref_i+ceil(index/2),ref_j,subdir);
1047         select=(exist(filename,'file')==2);
1048         if select==1
1049               ind_exist=ind_exist+1;
1050                displ_num(1,ind_exist)=0;
1051                displ_num(2,ind_exist)=0;
1052                displ_num(3,ind_exist)=-floor(index/2);
1053                displ_num(4,ind_exist)=ceil(index/2);
1054                %[cte_detect,vdt,cte_read]=read_netcdf(filename,{'dt','dt2','absolut_time_T0','absolute_time_TO_2'});
1055                [Cte,var_detect,ichoice]=nc2struct(filename,{});
1056                if isfield(Cte,'dt2')
1057                    dt=Cte.dt2;
1058                elseif isfield(Cte,'dt')
1059                    dt=Cte.dt;
1060                end
1061                if isfield(Cte,'absolut_time_TO_2')
1062                    ref_time(ind_exist)=Cte.absolut_time_TO_2;%civ2 data used in priority
1063                elseif isfield(Cte,'absolut_time_TO')
1064                    ref_time(ind_exist)=Cte.absolut_time_TO;%civ2 data used in priorit
1065                elseif isfield(Cte,'Time')
1066                    ref_time(ind_exist)=Cte.Time;
1067                end
1068                displ_pair{ind_exist}=['Di= ' num2str(-floor(index/2)) '|' num2str(ceil(index/2)) ' :dt= ' num2str(dt*1000) dtunit];
1069         end
1070     end
1071     set(handles.list_pair_civ,'String',[displ_pair';{'Di=*|*'}]);   
1072elseif isequal(mode,'series(Dj)')% series on the j index
1073       for index=1:min(nbfield2-1,50)
1074           filename=name_generator(filebase,ref_i,ref_j-floor(index/2),'.nc',NomType,1,ref_i,ref_j+ceil(index/2),subdir);
1075           select=(exist(filename,'file')==2);
1076           if select==1
1077               ind_exist=ind_exist+1;
1078                displ_num(1,ind_exist)=-floor(index/2);
1079                displ_num(2,ind_exist)=ceil(index/2);
1080                displ_num(3,ind_exist)=0;
1081                displ_num(4,ind_exist)=0;
1082                %[cte_detect,vdt,cte_read]=read_netcdf(filename,{'dt','dt2','absolut_time_T0','absolute_time_TO_2'});
1083                [Cte,var_detect,ichoice]=nc2struct(nc,{});
1084                if isfield(Cte,'dt2')
1085                    dt=Cte.dt2;
1086                elseif isfield(Cte,'dt')
1087                    dt=Cte.dt;
1088                end
1089                if isfield(Cte,'absolut_time_TO_2')
1090                    ref_time(ind_exist)=Cte.absolut_time_TO_2;%civ2 data used in priority
1091                elseif isfield(Cte,'absolut_time_TO')
1092                    ref_time(ind_exist)=Cte.absolut_time_TO;%civ2 data used in priorit
1093                elseif isfield(Cte,'Time')
1094                    ref_time(ind_exist)=Cte.Time;
1095                end
1096%                 if cte_detect(2)==1;
1097%                     dt=cte_read(2);
1098%                     ref_time(ind_exist)=cte_read(4);%civ2 data used in priority
1099%                 else
1100%                     dt=cte_read(1);
1101%                     ref_time(ind_exist)=cte_read(3);
1102%                 end
1103                displ_pair{ind_exist}=['Dj= ' num2str(-floor(index/2)) '|' num2str(ceil(index/2)) ' :dt= ' num2str(dt*1000) dtunit];
1104           end
1105       end
1106       set(handles.list_pair_civ,'String',[displ_pair';{'Dj=*|*'}]);
1107elseif isequal(mode,'bursts') %case of bursts
1108    for numod_a=1:nbfield2-1 %nbfield2 always >=2 for 'bursts' mode
1109        for numod_b=(numod_a+1):nbfield2
1110            [filename]=name_generator(filebase,ref_i,numod_a,'.nc',NomType,1,ref_i,numod_b,subdir);
1111            select=(exist(filename,'file')==2);
1112            if select==1
1113                ind_exist=ind_exist+1;
1114                numlist_a(ind_exist)=numod_a;
1115                numlist_b(ind_exist)=numod_b;
1116                Attr=nc2struct(filename,[]);
1117                isfield(Attr,'absolut_time_T0_2')
1118                if isfield(Attr,'dt2')
1119                   dt(ind_exist)=Attr.dt2;
1120                   ref_time(ind_exist)=Attr.absolut_time_T0_2;
1121                elseif isfield(Attr,'dt')& isfield(Attr,'absolut_time_T0')
1122                   dt(ind_exist)=Attr.dt;
1123                   ref_time(ind_exist)=Attr.absolut_time_T0;
1124                else
1125                   dt(ind_exist)=NaN;%no information on dt
1126                end
1127                %determine nom_type_ima for pair display (used in num2stra.m)
1128                switch NomType
1129                    case {'#ab'}
1130                        nom_type_ima='#a';
1131                    case {'#AB'}
1132                        nom_type_ima='#A';
1133                    otherwise
1134                         nom_type_ima='_i_j';
1135                end
1136               displ_pair{ind_exist}=['j= ' num2stra(numod_a,nom_type_ima,2) '-' num2stra(numod_b,nom_type_ima,2) ...
1137                        ' :dt= ' num2str(dt(ind_exist)*1000)];
1138            end
1139         end
1140         set(handles.list_pair_civ,'String',[displ_pair';{'j=*-*'}]);
1141     end
1142     if exist('dt','var') & ~isempty(dt)
1143         [dtsort,indsort]=sort(dt);
1144         displ_num(1,:)=numlist_a(indsort);
1145         displ_num(2,:)=numlist_b(indsort);
1146         displ_num(3,:)=0;
1147         displ_num(4,:)=0;
1148         displ_pair=displ_pair(indsort);
1149         ref_time=ref_time(indsort);
1150     end
1151end
1152if ind_exist==0
1153         if  isequal(mode,'series(Dj)') | isequal(mode,'st_series(Dj)')
1154            msgbox_uvmat('ERROR',['no .nc file available for the selected reference index j=' num2str(ref_j) ' and subdirectory ' subdir])
1155        else
1156            msgbox_uvmat('ERROR',['no .nc file available for the selected reference index i=' num2str(ref_i) ' and subdirectory ' subdir])
1157        end
1158        if isequal(mode,'bursts') %case of bursts
1159            set(handles.list_pair_civ,'String',{'j=*-*'});
1160        elseif isequal(mode,'series(Di)') %case of bursts
1161            set(handles.list_pair_civ,'String',{'Di=*|*'});
1162        elseif isequal(mode,'series(Dj)') %case of bursts
1163            set(handles.list_pair_civ,'String',{'Dj=*|*'});
1164        end
1165end
1166
1167val=get(handles.list_pair_civ,'Value');
1168if val > length(displ_pair)
1169    set(handles.list_pair_civ,'Value',1);% first pair proposed by default in the menu
1170    val=1;
1171end
1172iview=get(handles.NomType,'Value');
1173SeriesData.displ_num(iview,:)=(displ_num(:,val))';
1174SeriesData.ref_time=ref_time;
1175set(hseries,'UserData',SeriesData)
1176list_pair_civ_Callback(hObject, eventdata, handles)
1177
1178%-------------------------------------------------------------
1179% --- Executes on selection in list_pair_civ.
1180function list_pair_civ_Callback(hObject, eventdata, handles)
1181%------------------------------------------------------------
1182
1183%update first_i and last_i according to the chosen image pairs
1184testupdate=0;
1185Val=get(handles.RootPath,'Value');
1186IndexCell=get(handles.NomType,'String');
1187hseries=get(handles.list_pair_civ,'parent');
1188SeriesData=get(hseries,'UserData');
1189NomType=SeriesData.NomType{Val};
1190list_pair=get(handles.list_pair_civ,'String');%get the menu of image pairs
1191index_pair=get(handles.list_pair_civ,'Value');
1192str_pair=list_pair{index_pair};
1193ind_equ=strfind(str_pair,'=');%find '='
1194ind_sep=strfind(str_pair,'|');%find pair separator '|'
1195ind_com=strfind(str_pair,':');%find ':'
1196test_bursts=0;
1197if isempty(ind_sep)
1198    ind_sep=strfind(str_pair,'-');%find pair separator if it is not '|'
1199    test_bursts=1;% we are in the case of bursts
1200end
1201displ_num=[0 0 0 0]; %default
1202if ~isempty(ind_sep)&& ~strcmp(str_pair(ind_sep-1),'*')% if there is a pair separator ('|' or '-')
1203    num1_str=str_pair(ind_equ(1)+1:ind_sep-1);
1204    num2_str=str_pair(ind_sep+1:ind_com-1);
1205    num1=str2double(num1_str);
1206    num2=str2double(num2_str);
1207    if isequal(num1_str(1),' ')
1208        num1_str(1)=[];
1209    end   
1210    if isequal(num2_str(end),' ')
1211        num2_str(end)=[];
1212    end
1213    switch NomType
1214       case {'_i1-i2_j'}
1215           if isequal(num1_str(1),'0')
1216               IndexCell{Val}=['_(i-(i+' num2_str ')_j'];
1217           else
1218               IndexCell{Val}=['_(i' num1_str ')-(i+' num2_str ')_j'];
1219           end
1220           displ_num(3)=num1;
1221           displ_num(4)=num2;
1222       case {'_i1-i2'}
1223           if isequal(num1_str(1),'0')
1224               IndexCell{Val}=['_(i' num1_str ')-(i+' num2_str ')'];
1225           else
1226               IndexCell{Val}=['_(i' num1_str ')-(i+' num2_str ')'];
1227           end
1228           displ_num(3)=num1;
1229           displ_num(4)=num2;
1230       case '_i_j1-j2'
1231          if test_bursts
1232              IndexCell{Val}=['_i_' num1_str '-' num2_str ];
1233          else
1234              if isequal(num1_str(1),'0')
1235                 IndexCell{Val}=['_i_j-(j+' num2_str ')'];
1236              else
1237                 IndexCell{Val}=['_i_(j' num1_str ')-(j+' num2_str ')'];
1238              end
1239          end
1240          displ_num(1)=num1;
1241          displ_num(2)=num2;
1242       case {'#_ab'} %TO COMPLETE
1243           IndexCell{Val}=['_i_' num1_str '-' num2_str ];
1244
1245    end
1246end
1247set(handles.NomType,'String',IndexCell)
1248SeriesData.displ_num(Val,:)=displ_num;
1249set(hseries,'UserData',SeriesData)
1250% set(handles.NomType,'Value',Val)
1251
1252if ~isequal(str_pair,'Dj=*|*')&~isequal(str_pair,'Di=*|*')
1253        mode_list=get(handles.mode,'String');
1254    mode_value=get(handles.mode,'Value');
1255    mode=mode_list{mode_value};
1256        if isequal(mode,'series(Di)')
1257        first_i=str2num(get(handles.first_i,'String'));
1258        last_i=str2num(get(handles.last_i,'String'));
1259        incr_i=str2num(get(handles.incr_i,'String'));
1260        num1=first_i:incr_i:last_i;
1261        lastfieldCell=get(handles.nb_field,'String');
1262        lastfield=str2num(lastfieldCell{1});
1263        if ~isempty(lastfield)
1264            ind=find((num1-floor(index_pair/2)*ones(size(num1))>0)& (num1+ceil(index_pair/2)*ones(size(num1))<=lastfield));
1265            num1=num1(ind);       
1266        end
1267        set(handles.first_i,'String',num2str(num1(1)));
1268        set(handles.last_i,'String',num2str(num1(end)));
1269        testupdate=1;
1270        elseif isequal(mode,'series(Dj)')
1271        first_j=str2num(get(handles.first_j,'String'));
1272        last_j=str2num(get(handles.last_j,'String'));
1273        incr_j=str2num(get(handles.incr_j,'String'));
1274        num_j=first_j:incr_j:last_j;
1275        lastfieldCell=get(handles.nb_field2,'String');
1276        if ~isempty(lastfieldCell)
1277            lastfield2=lastfieldCell{1};
1278            ind=find((num_j-floor(index_pair/2)*ones(size(num_j))>0)& ...
1279                 (num_j+ceil(index_pair/2)*ones(size(num_j))<=lastfield2));
1280        end
1281        testupdate=1;
1282        end
1283       
1284        %update the first and last times of the series
1285        if testupdate & isfield(SeriesData,'Time')
1286        if ~isempty(SeriesData.Time{1})
1287            displ_time(handles,SeriesData.Time{1});
1288        end
1289        end
1290end
1291%---------------------------------------------------
1292% --- Executes on button press in RUN.
1293%------------------------------------------------------
1294function RUN_Callback(hObject, eventdata, handles)
1295
1296%read root name and field type
1297set(handles.RUN,'BusyAction','queue');
1298hseries=get(handles.RUN,'parent');
1299set(0,'CurrentFigure',hseries)
1300if isequal(get(handles.GetObject,'Value'),1)
1301    Series.GetObject=1;
1302    GetObject_Callback(hObject, eventdata, handles)
1303else
1304    Series.GetObject=0;
1305end
1306SeriesData=get(hseries,'UserData');
1307if isfield(SeriesData,'sethandles')
1308    if iscell(SeriesData.sethandles)
1309        Series.sethandles=SeriesData.sethandles{1};
1310    else
1311        Series.sethandles=SeriesData.sethandles;%retrieve the handles of the set_object interface (to define projection objects)
1312    end
1313end
1314
1315%reinitiate waitbar position
1316Series.WaitbarPos=get(handles.waitbar_frame,'Position');%TO SUPPRESS
1317waitbarpos=Series.WaitbarPos;
1318waitbarpos(4)=0.005;%reinitialize waitbar to zero height
1319waitbarpos(2)=Series.WaitbarPos(2)+Series.WaitbarPos(4)-0.005;
1320set(handles.waitbar,'Position',waitbarpos)
1321
1322% read input file parameters and set menus
1323Series.PathProject=get(handles.PathCampaign,'String');
1324RootPath=get(handles.RootPath,'String');% path of the root name of the first field series
1325RootFile=get(handles.RootFile,'String');% root name of the first field series
1326SubDir=get(handles.SubDir,'String');% subdirectory for netcdf files
1327FileExt=get(handles.FileExt,'String');%file extension
1328if isempty(SeriesData)
1329    msgbox_uvmat('ERROR','no input file series')
1330    return
1331end
1332NomType=SeriesData.NomType;
1333if length(RootPath)==1 %string character input for user fct
1334    Series.RootPath=RootPath{1};
1335    Series.RootFile=RootFile{1};
1336    Series.SubDir=SubDir{1};
1337    Series.FileExt=FileExt{1};
1338    Series.NomType=NomType{1};
1339else %cell input for user fct
1340    Series.RootPath=RootPath;
1341    Series.RootFile=RootFile;
1342    Series.SubDir=SubDir;
1343    Series.FileExt=FileExt;
1344    Series.NomType=NomType;
1345end
1346if isequal(get(handles.FieldMenu,'Visible'),'on')
1347    FieldMenu=get(handles.FieldMenu,'String');
1348    FieldValue=get(handles.FieldMenu,'Value');
1349    Series.Field=FieldMenu(FieldValue);
1350end
1351menu_coord_state=get(handles.CoordType,'Visible');
1352Series.CoordType='';%default
1353if isequal(menu_coord_state,'on')
1354    menu_coord=get(handles.CoordType,'String');
1355    menu_index=get(handles.CoordType,'Value');
1356    Series.CoordType=menu_coord{menu_index};
1357end
1358Series.hseries=get(hObject,'Parent');
1359if isequal(get(handles.ParamVal,'Visible'),'on')
1360    ParamKey=get(handles.ParamKey,'String');
1361    if ischar(ParamKey)
1362        ParamKey{1}=ParamKey;
1363    end
1364    ParamString=get(handles.ParamVal,'String');
1365    if ischar(ParamString)
1366        for ilist=1:size(ParamString,1)
1367            ParamVal{ilist}=ParamString(ilist,:);
1368        end
1369    else
1370        ParamVal=ParamString;
1371    end   
1372end
1373
1374%read the set of field numbers
1375first_i=str2num(get(handles.first_i,'String'));
1376last_i=str2num(get(handles.last_i,'String'));
1377incr_i=str2num(get(handles.incr_i,'String'));
1378first_j=str2num(get(handles.first_j,'String'));
1379last_j=str2num(get(handles.last_j,'String'));
1380incr_j=str2num(get(handles.incr_j,'String'));
1381if ~isequal(get(handles.first_i,'Visible'),'on')
1382   first_i=1;
1383   last_i=1;
1384   incr_i=1;
1385end
1386if ~isequal(get(handles.first_j,'Visible'),'on')
1387    first_j=1;
1388    last_j=1;
1389    incr_j=1;
1390end
1391Series.NbSlice=str2num(get(handles.NbSlice,'String'));
1392if isequal(first_i,[])|isequal(first_j,[]), msgbox_uvmat('ERROR','first field number not defined'),...
1393    set(handles.RUN, 'Enable','On'), set(handles.RUN,'BackgroundColor',[1 0 0]),return,end;
1394if isequal(last_i,[])| isequal(last_j,[]),msgbox_uvmat('ERROR','last field number not defined'),...
1395    set(handles.RUN, 'Enable','On'), set(handles.RUN,'BackgroundColor',[1 0 0]),return,end;
1396if isequal(incr_i,[])| isequal(incr_j,[]),msgbox_uvmat('ERROR','increment in field number not defined'),...
1397    set(handles.RUN, 'Enable','On'), set(handles.RUN,'BackgroundColor',[1 0 0]),return,end;
1398if last_i < first_i | last_j < first_j , msgbox_uvmat('ERROR','last field number must be larger than the first one'),...
1399    set(handles.RUN, 'Enable','On'), set(handles.RUN,'BackgroundColor',[1 0 0]),return,end;
1400num_i=[first_i:incr_i:last_i];
1401num_j=[first_j:incr_j:last_j];
1402nbfield_cell=get(handles.nb_field,'String');
1403nbfield=[]; %default
1404for iview=1:length(nbfield_cell)
1405    nb=str2num(nbfield_cell{iview});
1406    if ~isempty(nb)
1407        nbfield=[nbfield nb];
1408    end
1409end
1410nbfield=min(nbfield);
1411nbfield2_cell=get(handles.nb_field2,'String');
1412nbfield2=[]; %default
1413for iview=1:length(nbfield2_cell)
1414    nb=str2num(nbfield2_cell{iview});
1415    if ~isempty(nb)
1416        nbfield2=[nbfield2 nb];
1417    end
1418end
1419nbfield2=min(nbfield2);
1420
1421%get complementary information from the 'series' interface
1422list_action=get(handles.ACTION,'String');% list menu action
1423index_action=get(handles.ACTION,'Value');% selected string index
1424action= list_action{index_action}; % selected string
1425mode_list=get(handles.mode,'String');
1426index_mode=get(handles.mode,'Value');
1427mode=mode_list{index_mode};
1428ind_shift=0;%default
1429
1430%determine the list of input file names
1431nbmissing=0;
1432for iview=1:length(RootPath)
1433    %case of pairs (.nc files)
1434   
1435    if isequal(NomType{iview},'_i_j1-j2')| isequal(NomType{iview},'_i1-i2_j')| isequal(NomType{iview},'_i1-i2')| isequal(NomType{iview},'#_ab')
1436        ind_shift=SeriesData.displ_num(iview,:);
1437        if isequal(ind_shift,[0 0 0 0]) % undefined pairs
1438            if isequal(NomType{iview},'#_ab')
1439                mode='#_ab';
1440            end
1441            [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);
1442        else   
1443            [num_i1,num_i2,num_j1,num_j2,num_i,num_j]=find_file_indices(num_i,num_j,ind_shift,NomType{iview},mode);
1444            if isempty(num_i)
1445                msgbox_uvmat('ERROR','ERROR: empty set of input files chosen')
1446                return
1447            end
1448            if num_i(1)>first_i
1449               set(handles.first_i,'String',num2str(num_i(1)))%update the display of first field
1450               last_i_Callback(hObject, eventdata, handles)
1451            end
1452            if num_i(end)<last_i
1453               set(handles.last_i,'String',num2str(num_i(end)))%update the display of last field
1454               last_i_Callback(hObject, eventdata, handles)
1455            end
1456            if num_j(1)>first_j
1457               set(handles.first_j,'String',num2str(num_j(1)))%update the display of first field
1458               last_j_Callback(hObject, eventdata, handles)
1459            end
1460            if num_j(end)<last_j
1461               set(handles.last_j,'String',num2str(num_j(end)))%update the display of last field
1462               last_j_Callback(hObject, eventdata, handles)
1463            end
1464        end
1465    else%case of images
1466        [num_i1,num_j1]=meshgrid(num_i,num_j);
1467        num_i2=num_i1;
1468        num_j2=num_j1;
1469    end
1470    if length(RootPath)>1
1471        num_i1_cell{iview}=num_i1;
1472        num_i2_cell{iview}=num_i2;
1473        num_j1_cell{iview}=num_j1;
1474        num_j2_cell{iview}=num_j2;
1475    end
1476end
1477
1478% RUN RUN'
1479path_series=which('series');
1480list_path=get(handles.ACTION,'UserData');
1481index=get(handles.ACTION,'Value');
1482fct_path=list_path{index}; %path stored for the function ACTION
1483if ~isequal(fct_path,path_series)
1484    eval(['spath=which(''' action ''');']) %spath = current path of the selected function ACTION
1485    if ~isequal(spath,fct_path)& exist(fct_path,'dir')
1486        addpath(fct_path)% add the prescribed path if not the current one
1487    end
1488end
1489% fct_path
1490        eval(['h_fun=@' action])
1491if ~isequal(fct_path,path_series)
1492        rmpath(fct_path)% add the prescribed path if not the current one   
1493end
1494
1495Series.Action=action;%name of the processing programme
1496set(handles.RUN,'BackgroundColor',[0.831 0.816 0.784])
1497drawnow
1498if length(RootPath)>1
1499%    feval(action,num_i1_cell,num_i2_cell,num_j1_cell,num_j2_cell,Series);
1500    h_fun(num_i1_cell,num_i2_cell,num_j1_cell,num_j2_cell,Series);
1501else
1502    h_fun(num_i1,num_i2,num_j1,num_j2,Series);
1503%     feval(action,num_i1,num_i2,num_j1,num_j2,Series);
1504end
1505set(handles.RUN,'BackgroundColor',[1 0 0])
1506
1507% %save the current interface setting as figure namefig, append .0 to the name if it already exists
1508% detect=1;
1509% while detect==1
1510%     namefigfull=[namedoc '.fig'];
1511%     hh=dir(namefigfull);
1512%     if ~isempty(hh)
1513%         detect=1;
1514%         namedoc=[namedoc '.0'];
1515%     else
1516%         detect=0;
1517%     end
1518% end
1519% saveas(gcbf,namefigfull);%save the interface with name namefigfull (A CHANGER EN FICHIER  .xml)
1520
1521%----------------------------------------------------
1522function STOP_Callback(hObject, eventdata, handles)
1523set(handles.RUN, 'BusyAction','cancel')
1524set(handles.RUN,'BackgroundColor',[1 0 0])
1525
1526%----------------------------------------------
1527
1528%----------------------------------------------------
1529function first_i_Callback(hObject, eventdata, handles)
1530last_i_Callback(hObject, eventdata, handles)
1531
1532%----------------------------------------------
1533function last_i_Callback(hObject, eventdata, handles)
1534    hseries=get(handles.last_i,'parent');
1535first_i=str2num(get(handles.first_i,'String'));
1536last_i=str2num(get(handles.last_i,'String'));
1537ref_i=ceil((first_i+last_i)/2);
1538set(handles.ref_i,'String', num2str(ref_i))
1539ref_i_Callback(hObject, eventdata, handles)
1540SeriesData=get(hseries,'UserData');
1541if ~isfield(SeriesData,'Time')
1542    SeriesData.Time{1}=[];
1543end
1544displ_time(handles,SeriesData.Time{1});
1545
1546%-------------------------------------------------------
1547function first_j_Callback(hObject, eventdata, handles)
1548 last_j_Callback(hObject, eventdata, handles)
1549
1550%-------------------------------------------------------
1551function last_j_Callback(hObject, eventdata, handles)
1552    hseries=get(handles.last_i,'parent');
1553first_j=str2num(get(handles.first_j,'String'));
1554last_j=str2num(get(handles.last_j,'String'));
1555ref_j=ceil((first_j+last_j)/2);
1556set(handles.ref_j,'String', num2str(ref_j))
1557
1558ref_j_Callback(hObject, eventdata, handles)
1559SeriesData=get(hseries,'UserData');
1560if ~isfield(SeriesData,'Time')
1561    SeriesData.Time{1}=[];
1562end
1563displ_time(handles,SeriesData.Time{1});
1564
1565
1566
1567
1568%-------------------------------------------------------
1569function ref_i_Callback(hObject, eventdata, handles)
1570mode_list=get(handles.mode,'String');
1571mode_value=get(handles.mode,'Value');
1572mode=mode_list{mode_value};
1573hseries=get(handles.ref_i,'parent');
1574SeriesData=get(hseries,'UserData');
1575%NomTypeCell=get(handles.NomType,'String');
1576NomTypeCell=SeriesData.NomType;
1577if ~isempty(NomTypeCell)
1578Val=get(handles.NomType,'Value');
1579NomType=NomTypeCell{Val};
1580% for ilist=1:length(NomType)
1581    if isequal(NomType,'_i_j1-j2')|| isequal(NomType,'_i1-i2_j')|| isequal(NomType,'_i1-i2')
1582        if isequal(mode,'series(Di)')
1583            find_netcpair_civ(hObject, eventdata, handles,Val);% update the menu of pairs depending on the available netcdf files
1584%             break
1585        end
1586    end
1587end
1588
1589%----------------------------------------------------
1590function ref_j_Callback(hObject, eventdata, handles)
1591mode_list=get(handles.mode,'String');
1592mode_value=get(handles.mode,'Value');
1593mode=mode_list{mode_value};
1594hseries=get(handles.ref_i,'parent');
1595SeriesData=get(hseries,'UserData');
1596%NomTypeCell=get(handles.NomType,'String');
1597NomTypeCell=SeriesData.NomType;
1598if ~isempty(NomTypeCell)
1599Val=get(handles.NomType,'Value');
1600NomType=NomTypeCell{Val};
1601% NomType=get(handles.NomType,'String');
1602    if isequal(NomType,'_i_j1-j2')|| isequal(NomType,'_i1-i2_j')|| isequal(NomType,'_i1-i2')
1603        if isequal(mode,'series(Dj)')
1604            find_netcpair_civ(hObject, eventdata, handles,Val);% update the menu of pairs depending on the available netcdf files
1605%             break
1606        end
1607    end
1608end
1609
1610%----------------------------------------------------
1611% --- Executes on selection change in ACTION.
1612function ACTION_Callback(hObject, eventdata, handles)
1613list_ACTION=get(handles.ACTION,'String');% list menu fields
1614index_ACTION=get(handles.ACTION,'Value');% selected string index
1615ACTION= list_ACTION{index_ACTION}; % selected function name
1616path_series=which('series');%path to series.m
1617list_path=get(handles.ACTION,'UserData');%list of recorded paths to functions of the list ACTION
1618nb_builtin=0;
1619for ilist=1:length(list_path)
1620    if isequal(list_path{ilist},path_series)
1621        nb_builtin=nb_builtin+1;
1622    else
1623        break
1624    end
1625end
1626if nb_builtin==0% the path of series has been changed, reinitialize
1627%     series_OpeningFcn(hObject, eventdata, handles)
1628    return
1629end
1630
1631% add a new function to the menu
1632if isequal(ACTION,'more...')
1633    pathfct=fileparts(path_series);
1634    browse_name=fullfile(path_series,'series');%go to UVMAT/SERIES_FCT by default
1635    if length(list_path)>nb_builtin
1636        browse_name=list_path{end};% initialize browser with  the path of the last introduced function
1637     end
1638    [FileName, PathName, filterindex] = uigetfile( ...
1639       {'*.m', ' (*.m)';
1640        '*.m',  '.m files '; ...
1641        '*.*', 'All Files (*.*)'}, ...
1642        'Pick a file',browse_name);
1643    if length(FileName)<2
1644        return
1645    end
1646   
1647   
1648   
1649    ext_fct=FileName(end-1:end);% to be replaced by fileparts
1650    if ~isequal(ext_fct,'.m')
1651        msgbox_uvmat('ERROR','a Matlab function .m must be introduced');
1652        return
1653    end
1654    ACTION=FileName(1:end-2);% ACTION choice updated by the selected item
1655   
1656    addpath(PathName)
1657    eval(['h_function=@' ACTION]);
1658    if ~isequal(path_series,PathName)
1659    rmpath(PathName)
1660    end
1661    functions(h_function)
1662   
1663   % insert the choice in the action menu
1664   menu_str=update_menu(handles.ACTION,ACTION);%new action menu in which the new item has been appended if needed
1665   index_ACTION=get(handles.ACTION,'Value');% currently selected index in the list
1666   list_path{index_ACTION}=PathName;
1667   if length(menu_str)>nb_builtin+5;
1668       nbremove=length(menu_str)-nb_builtin-5;
1669       menu_str(nb_builtin+1:end-5)=[];
1670       list_path(nb_builtin+1:end-4)=[];
1671       index_ACTION=index_ACTION-nbremove;
1672       set(handles.ACTION,'Value',index_ACTION)
1673       set(handles.ACTION,'String',menu_str)
1674   end
1675   list_path{index_ACTION}=PathName;
1676   set(handles.ACTION,'UserData',list_path);
1677   set(handles.path,'enable','inactive')% indicate that the current path is accessible (not 'off')
1678   
1679   %record the current menu in personal file profil_perso
1680   dir_perso=prefdir;
1681   profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
1682   for ilist=nb_builtin+1:length(menu_str)-1
1683       series_fct{ilist-nb_builtin}=fullfile(list_path{ilist},[menu_str{ilist} '.m']);
1684   end
1685   if exist(profil_perso,'file')
1686        save(profil_perso,'series_fct','-append')
1687   else
1688        txt=ver;
1689        Release=txt(1).Release;
1690        relnumb=str2num(Release(3:4));
1691        if relnumb >= 14
1692            save(profil_perso,'series_fct','-V6')
1693        else
1694            save(profil_perso, 'series_fct')
1695        end
1696   end
1697end
1698
1699%check the current path to the selected function
1700PathName=list_path{index_ACTION};%current recorded path
1701if ~isequal(path_series,PathName)
1702    CurrentPath=fileparts(which(ACTION));
1703    if ~isequal(CurrentPath,PathName)&&~isequal(CurrentPath,fullfile(PathName,'private'))
1704        addpath(PathName)
1705        errormsg=check_functions;
1706        msgbox_uvmat('CONFIRMATION',[['path ' PathName ' added to the current Matlab pathes'];errormsg])
1707    end
1708end
1709set(handles.path,'String',PathName); %show the path to the senlected function
1710
1711%default setting for the visibility of the GUI elements
1712%set( handles.Field,'Visible','off')%default
1713set(handles.RootPath,'UserData','many')
1714set(handles.SubDir,'Visible','on')
1715set(handles.RootFile,'Visible','on')
1716set(handles.NomType,'Visible','on')
1717set(handles.FileExt,'Visible','on')
1718set(handles.NbSlice,'Visible','off')
1719set(handles.NbSlice_title,'Visible','off')
1720set(handles.VelTypeMenu,'Visible','off');
1721set(handles.VelType_text,'Visible','off');
1722set(handles.VelTypeMenu_1,'Visible','off');
1723set(handles.VelType_text_1,'Visible','off');
1724view_FieldMenu(handles,'off')
1725view_FieldMenu_1(handles,'off')
1726view_TRANSFORM(handles,'off')
1727set(handles.ProjObject_frame,'Visible','off');
1728set(handles.GetMask,'Visible','off')
1729set(handles.Mask,'Visible','off')
1730set(handles.GetObject,'Visible','off');
1731set(handles.ProjObject,'Visible','off');
1732set(handles.OutputDir,'Visible','off');
1733set(handles.PARAMETERS_frame,'Visible','off');
1734set(handles.PARAMETERS_title,'Visible','off');
1735set(handles.ParamKey,'Visible','off')
1736set(handles.ParamVal,'Visible','off')
1737ParamKey={};
1738set(handles.FieldMenu,'Enable','off')
1739set(handles.VelTypeMenu,'Enable','off')
1740set(handles.FieldMenu_1,'Enable','off')
1741set(handles.VelTypeMenu_1,'Enable','off')
1742set(handles.CoordType,'Enable','off')
1743%set the displayed GUI item needed for input parameters
1744%list_input=feval(ACTION);% input list asked by the selected function
1745varargout=feval(ACTION);% input list asked by the selected function
1746Param_list={};
1747% RootPath=get(handles.RootPath,'String');
1748% RootFile=get(handles.RootFile,'String');
1749
1750%nb_series=length(RootFile);
1751FileExt=get(handles.FileExt,'String');
1752nb_series=length(FileExt);
1753testima_series=1; %test for a list of images only
1754testima=1;
1755testima_1=1;
1756testciv_series=1;
1757for iview=1:nb_series
1758    ext=FileExt{iview};
1759    if length(ext)<2
1760        ext='.none';
1761    end
1762    testimaview=~isempty(imformats(ext(2:end))) || isequal(lower(ext),'.avi');
1763    if ~testimaview
1764        if iview==1
1765            testima=0;
1766        end
1767        if iview==2
1768            testima_1=0;
1769        end
1770        testima_series=0;
1771    end
1772end
1773for ilist=1:length(varargout)-1
1774    switch varargout{ilist}
1775                       %RootFile always visible
1776         case 'RootPath'   %visible by default
1777            value=lower(varargout{ilist+1});
1778            if isequal(value,'one')||isequal(value,'two')||isequal(value,'many')
1779                set(handles.RootFile,'UserData',value)% for use in menu Open_insert
1780            end
1781        case 'SubDir' %visible by default
1782            if isequal(lower(varargout{ilist+1}),'off')
1783                set(handles.SubDir,'Visible','off')
1784            end
1785        case 'RootFile'   %visible by default
1786            value=lower(varargout{ilist+1});
1787            if isequal(value,'off')
1788                set(handles.RootFile,'Visible','off')
1789            elseif isequal(value,'one')||isequal(value,'two')||isequal(value,'many')
1790                set(handles.RootFile,'Visible','on')
1791                set(handles.RootFile,'UserData',value)% for use in menu Open_insert
1792            end
1793        case 'NomType'   %visible by default
1794            if isequal(lower(varargout{ilist+1}),'off')
1795                set(handles.NomType,'Visible','off')
1796            end
1797        case 'FileExt'   %visible by default
1798            if isequal(lower(varargout{ilist+1}),'off')
1799                set(handles.FileExt,'Visible','off')
1800            end
1801        case 'NbSlice'   %hidden by default
1802            if isequal(lower(varargout{ilist+1}),'on')
1803                set(handles.NbSlice,'Visible','on')
1804                set(handles.NbSlice_title,'Visible','on')
1805            end
1806        case 'VelTypeMenu'   %hidden by default
1807            if isequal(lower(varargout{ilist+1}),'one') || isequal(lower(varargout{ilist+1}),'two')
1808                set(handles.VelTypeMenu,'Enable','on')
1809                if nb_series >=1 && ~testima_series
1810                    set(handles.VelTypeMenu,'Visible','on')
1811                    set(handles.VelType_text,'Visible','on');
1812                    set(handles.Field_frame,'Visible','on')
1813                end
1814            end
1815            if isequal(lower(varargout{ilist+1}),'two')
1816                set(handles.VelTypeMenu_1,'Enable','on')
1817                if nb_series >=2 && ~testima_series
1818                    set(handles.VelTypeMenu_1,'Visible','on')
1819                    set(handles.VelType_text_1,'Visible','on');
1820                end
1821            end
1822        case 'FieldMenu'   %hidden by default
1823            if isequal(lower(varargout{ilist+1}),'one')||isequal(lower(varargout{ilist+1}),'two')
1824                set(handles.FieldMenu,'Enable','on') % test for MenuBorser
1825                if nb_series >=1 && ~testima_series
1826                    view_FieldMenu(handles,'on')
1827                end
1828            end
1829            if isequal(lower(varargout{ilist+1}),'two')
1830                set(handles.FieldMenu_1,'Enable','on')
1831                if nb_series >=2 && ~testima_1
1832                    view_FieldMenu_1(handles,'on')
1833                end
1834            end
1835        case 'CoordType'   %hidden by default
1836            if isequal(lower(varargout{ilist+1}),'on')
1837                set(handles.CoordType,'Enable','on')
1838                view_TRANSFORM(handles,'on')
1839            end
1840        case 'GetObject'   %hidden by default
1841            if isequal(lower(varargout{ilist+1}),'on')   
1842                set(handles.ProjObject_frame,'Visible','on')
1843                set(handles.GetObject,'Visible','on');
1844            end
1845        case 'Mask'   %hidden by default
1846            if isequal(lower(varargout{ilist+1}),'on')   
1847                set(handles.ProjObject_frame,'Visible','on')
1848                set(handles.GetMask,'Visible','on');
1849            end
1850        case 'PARAMETER' 
1851            set(handles.PARAMETERS_frame,'Visible','on')
1852            set(handles.PARAMETERS_title,'Visible','on')
1853            set(handles.ParamKey,'Visible','on')
1854            %set(handles.ParamVal,'Visible','on')
1855            Param_str=varargout{ilist+1};
1856            Param_list=[Param_list; {Param_str}];         
1857    end
1858end
1859if ~isempty(Param_list)
1860    set(handles.ParamKey,'String',Param_list)
1861    set(handles.ParamVal,'Visible','on')
1862end
1863
1864%-------------------------------------------------------------------
1865% --- Executes on selection change in FieldMenu.
1866%-------------------------------------------------------------------
1867function FieldMenu_Callback(hObject, eventdata, handles)
1868
1869field_str=get(handles.FieldMenu,'String');
1870field_index=get(handles.FieldMenu,'Value');
1871field=field_str{field_index(1)};
1872if isequal(field,'get_field...')   
1873     hget_field=findobj(allchild(0),'name','get_field');
1874     if ~isempty(hget_field)
1875         delete(hget_field)%delete opened versions of get_field
1876     end
1877     hseries=get(handles.FieldMenu,'parent');
1878     SeriesData=get(hseries,'UserData');
1879     filename=SeriesData.CurrentInputFile;
1880     if exist(filename,'file')
1881        get_field(filename)
1882     end
1883elseif isequal(field,'more...')
1884    str=calc_field;
1885    [ind_answer,v] = listdlg('PromptString','Select a file:',...
1886                'SelectionMode','single',...
1887                'ListString',str);
1888       % edit the choice in the fields and action menu
1889     scalar=cell2mat(str(ind_answer));
1890     update_menu(handles.FieldMenu,scalar)
1891end
1892
1893%------------------------------------------------------
1894% --- Executes on selection change in FieldMenu_1.
1895%-----------------------------------------------------
1896function FieldMenu_1_Callback(hObject, eventdata, handles)
1897field_str=get(handles.FieldMenu_1,'String');
1898field_index=get(handles.FieldMenu_1,'Value');
1899field=field_str{field_index};
1900if isequal(field,'get_field...')   
1901     hget_field=findobj(allchild(0),'name','get_field_1');
1902     if ~isempty(hget_field)
1903         delete(hget_field)
1904     end
1905     hseries=get(handles.FieldMenu,'parent');
1906     SeriesData=get(hseries,'UserData');
1907     filename=SeriesData.CurrentInputFile_1;
1908     if exist(filename,'file')
1909        hget_field=get_field(filename);
1910        set(hget_field,'name','get_field_1')
1911     end
1912elseif isequal(field,'more...')
1913    str=calc_field;
1914    [ind_answer,v] = listdlg('PromptString','Select a file:',...
1915                'SelectionMode','single',...
1916                'ListString',str);
1917       % edit the choice in the fields and action menu
1918     scalar=cell2mat(str(ind_answer));
1919     update_menu(handles.FieldMenu_1,scalar)
1920end   
1921% %----------------------------------------------------------------------
1922% % --makes a time averaged velocity field
1923% %----------------------------------------------------------------------
1924% function aver_vel(num_i1,num_i2,num_j1,num_j2,Series)
1925%                           %handles of the GUI series
1926%   
1927% hseries=guidata(Series.hseries);%handles of the GUI series
1928% WaitbarPos=get(hseries.waitbar_frame,'Position');
1929% Field_list=get(hseries.FieldMenu,'String');
1930% val=get(hseries.FieldMenu,'Value');
1931% FieldName=Field_list{val(1)};
1932% set(hseries.FieldMenu,'Value',val(1))% select only one input field
1933% if isequal(FieldName,'get_field...')
1934%     hget_field=findobj(allchild(0),'Name','get_field');%find the get_field... GUI
1935% end
1936% %root input file and type
1937% RootPath=get(hseries.RootPath,'String');
1938% SubDir=get(hseries.SubDir,'String');
1939% RootFile=get(hseries.RootFile,'String');
1940% %NomType=get(hseries.NomType,'String');
1941% NomType=Series.NomType;
1942% FileExt=get(hseries.FileExt,'String');
1943% ext=FileExt{1};     
1944% VelType_str=get(hseries.VelTypeMenu,'String');
1945% VelType_val=get(hseries.VelTypeMenu,'Value');
1946% VelType{1}=VelType_str{VelType_val};
1947%
1948% time=0; %default
1949% % number of slices
1950% NbSlice=str2num(get(hseries.NbSlice,'String'));
1951% if isempty(NbSlice)
1952%     NbSlice=1;
1953% end
1954% NbSlice_name=num2str(NbSlice);
1955% filebase=fullfile(RootPath{1},RootFile{1});
1956% Calib=[];
1957% if exist([filebase '.xml'],'file')
1958%     %[error,Heading,nom_type_read,ext_ima_read,time_imadoc,TimeUnit,mode,NbSlice,npx,npy,Calib]=read_imadoc([filebase '.xml']);
1959%     [XmlData,warntext]=imadoc2struct([filebase '.xml']);
1960% end
1961% if NbSlice==1
1962%    filebase_mean=[filebase '_mean']; %root name for the result
1963% else
1964%    filebase_mean=[filebase '_' NbSlice_name 'mean']; %root name for the results
1965%    answeryes=questdlg({['will make average in ' num2str(NbSlice) ' slices'];['results stored as files ' filebase_mean ' ...']});
1966%     if ~isequal(answeryes,'Yes')
1967%     return
1968%     end
1969% end
1970% siz=size(num_i1);
1971% nbfield2=siz(1); %nb of consecutive fields at each level(burst)
1972% lengthtot=siz(1)*siz(2);
1973% nbfield=floor(lengthtot/(nbfield2*NbSlice));%total number of i indexes (adjusted to an integer number of slices)
1974% nbfield_slice=nbfield*nbfield2;% number of fields per slice
1975% %projection object
1976% GridX=[];
1977% GridY=[];
1978% if isfield(Series,'sethandles')
1979%         Series.ProjObject=read_set_object(Series.sethandles);
1980%         if isfield(Series.ProjObject,'Style')
1981%             answeryes=questdlg({['statistics on field series projected on ' Series.ProjObject.Style]});
1982%             if ~isequal(answeryes,'Yes')
1983%                 return
1984%             end
1985%         end
1986% end
1987%
1988% %LOOP ON SLICES
1989% for i_slice=1:NbSlice
1990%     %select the series of image indices at the level islice
1991%     for ifield=1:nbfield
1992%         indselect(:,ifield)=((ifield-1)*NbSlice+(i_slice-1))*nbfield2+[1:nbfield2]';%selected indices on the list of files of a slice
1993%     end 
1994%     %name of result file
1995%     [filemean,idetect]=...
1996%                name_generator(filebase_mean,num_i1(i_slice),num_j1(1),Series.FileExt{1},'_i1-i2_j1-j2',1,num_i2(i_slice+nbfield_slice*NbSlice-1),num_j2(end),Series.SubDir{1});
1997%
1998%     % field=get(handles.civ1,'UserData');%read current selected field type (civ1,civ2...)
1999%     itime=0;
2000%      dt=[];
2001%      %LOOP ON FIELDS IN  A SLICE
2002%      test_interpolate=0;%default
2003%     for index=1:nbfield*nbfield2
2004%             ifile=indselect(index);
2005%         stopstate=get(hseries.RUN,'BusyAction');
2006%         if isequal(stopstate,'queue')% enable STOP command
2007%             update_waitbar(hseries.waitbar,WaitbarPos,ifile/(nbfield*nbfield2))
2008%             %name of the current file
2009%             [filename,idetect]=name_generator(filebase,num_i1(ifile),num_j1(ifile),Series.FileExt{1},Series.NomType{1},1,num_i2(ifile),num_j2(ifile),Series.SubDir{1});
2010%             %read input file
2011%             itime=itime+1;
2012%             if isequal(FieldName,'get_field...')
2013%                 hhget_field=guidata(hget_field);%handles of GUI elements in get_field
2014%                 hObject=0;
2015%                 eventdata=0;
2016%                 SubField=get_field('read_var_names',hObject,eventdata,hhget_field); %read the names of the variables to plot in the get_field GUI
2017%                 [Data,var_detect]=nc2struct(filename,SubField.ListVarName); %read input data   
2018%                 time(itime)=itime;
2019%                 dt=1;
2020%                 Calib_read=[];
2021%             else
2022%                 [nb_coord,nb_dim,Civ,CivStage,timeread,Data,VelTypeOut,Calib_read]=read_ncfield(filename,VelType{1});%reading the first file
2023%                  time(itime)=timeread;
2024%                 if isequal(Civ,1)
2025%                     Data.CoordType='px';%test for pixel coordinates
2026%                     if isequal(itime,1)
2027%                         dt=Data.dt;
2028%                     elseif ~isequal(Data.dt,dt)
2029%                         warndlg_uvmat('series with non constant dt, need phys coordinates','ERROR')
2030%                         return
2031%                     end
2032%                 end
2033%             end
2034%             %increment the detected fields, skip the others
2035%             if idetect==0
2036%                 warndlg_uvmat(['input file ' filename ' not found'],'ERROR')
2037%                 %A FAIRE STOCKER LE RESULT ACTUEL S'IL EXISTE
2038%             end
2039% %             itime=itime+1;
2040% %             time(itime)=timeread;
2041%       
2042%             %coordinate transform
2043%             if isempty(Calib)
2044%                 Calib=Calib_read;%use Calib from xml file in priority, then Calib from the current file
2045%             end
2046%             if ~isequal(Series.CoordType,'')
2047%                 Data=feval(Series.CoordType,Data,Calib);
2048%             end
2049%             %projection on object if defined
2050%             if isfield(Series,'ProjObject');
2051%                 Data=proj_field(Data,Series.ProjObject);
2052%                 if isequal(itime,1)%use the positions on the first field for the whole series, ou utiliser grille
2053%                     if isfield(Data,'Txt')%display error message
2054%                         warndlg(Data.Txt,'ERROR')
2055%                         return
2056%                     end
2057%                 end
2058%             else%remove false vectors and interpolate on the positions of the first field
2059%                 Data=document_field(Data);
2060%                 Data.Style='plane';
2061%             end
2062%     %%%%%%%%% initiate the average at the first iteration: check list and structure of variables
2063%             if ifile==i_slice%first field in the slice
2064%                 testfalse=0;
2065%                 ListIndex={};
2066%                 testnewcell=1;
2067%                 %group the variables (fields of 'Data') in cells of variables with the same dimensions
2068%                 [DimVarIndex,CellVarIndex]=find_field_indices(Data);
2069%                 VarIndex=CellVarIndex{1}; % ONLY THE FIRST VAR GROUP IS AVERAGED
2070%                 DimIndex=Data.VarDimIndex{VarIndex(1)};%indices of the dimensions of the first variable (common to all variables in the cell)         
2071%                 MeanData=Data;%transfer heading
2072%                 MeanData.Time=[time(1) time(end)];
2073%                 MeanData.Action=Series.Action;%name of the processing programme
2074%                 MeanData.ListDimName=Data.ListDimName(DimIndex);%name of dimension
2075%                 MeanData.DimValue=Data.DimValue(DimIndex);%values of dimension (nbre of vectors)
2076%                 MeanData.ListVarName=Data.ListVarName;
2077%                 MeanData.VarDimIndex=Data.VarDimIndex;
2078%                 MeanData.ListVarAttribute={'Role'};%list of variable attribute names A FAIRE: transferer les autres attributs
2079%                 testsum=ones(size(VarIndex));
2080%                 indexfalse=0;
2081%                 CoordName={};
2082%                 indexremove=[];
2083%                 if isfield(Data,'Role') % look for coordinate and flag variables   
2084%                     for ivar=1:length(VarIndex)
2085%                         VarName=Data.ListVarName{VarIndex(ivar)};
2086%                         var_role=Data.Role{VarIndex(ivar)};%'role' of the variable
2087%                         MeanData.Role{ivar}=var_role;
2088%                         if isequal(var_role,'falseflag')
2089%                             indexfalse=ivar; %test for false flag
2090%                             indexremove=ivar;
2091%                             FFName=VarName;
2092%                             testsum(ivar)=0;
2093%                             eval(['MeanData=rmfield(MeanData,''' VarName ''');']);%remove variable                     
2094%                         end
2095%                         if isequal(var_role,'warnflag')                       
2096%                             testsum(ivar)=0; %do not sum warn flag
2097%                             eval(['MeanData=rmfield(MeanData,''' VarName ''');']);%remove variable
2098%                             indexremove=[indexremove ivar];
2099%                         end                 
2100%                         if isequal(var_role,'coord_x')| isequal(var_role,'coord_y')|isequal(var_role,'coord_z')
2101%                             eval(['MeanData.' VarName '=Data.' VarName ';']);
2102%                             testsum(ivar)=0;
2103%                             eval(['CoordName=[CoordName ''' VarName '''];']);
2104%                         end
2105%                         if testsum(ivar)~=0
2106%                            eval(['MeanData.' VarName '=zeros(size(Data.' VarName '));']);%initialise sum
2107%                         end
2108%                     end
2109%                 end
2110%                 findsum=find(testsum);
2111%                 VarIndexSum=VarIndex(findsum);%indices of variables to sum (not coordinates nor flags)
2112%                 if length(CoordName)==0
2113%                     if isempty(DimVarIndex)|isequal(DimVarIndex,0)% no coordinate variable for structured coordinates, prepare histograms
2114%                          for ilist=1:length(VarIndexSum)
2115%                             VarName=Data.ListVarName{VarIndexSum(ilist)};
2116%                             eval(['MeanData=rmfield(MeanData,''' VarName ''');']);%remove variable
2117%                             indexremove=[indexremove ilist];
2118%                             eval(['[MeanData.' VarName 'hist,MeanData.' VarName 'val]=hist(Data.' VarName ',100);']);%make histo
2119%                             eval(['sizhist=size(MeanData.' VarName 'hist);'])
2120%                             if sizhist(1)==1
2121%                                 eval(['MeanData.' VarName 'hist=MeanData.' VarName 'hist'';'])
2122%                             end
2123%                             eval(['maxval=max(MeanData.' VarName 'val);']);
2124%                             eval(['minval=min(MeanData.' VarName 'val);']);
2125%                             dC(ilist)=(maxval-minval)/100;%size of the histogram bin   
2126%                          end
2127%                     else
2128% %                         icoord=0;
2129% %                         for ilist=1:length(DimVarIndex) 
2130% %                             VarDim=Data.ListVarName{DimVarIndex(ilist)};
2131% %                             icoord=icoord+1;
2132% %                             % eval(['Coord{' num2str(icord) '}=[' CoordName ''' VarName ''']']);
2133% %                              %eval(['Data.' CoordName{icoord} '=Data.' CoordName{icoord} '(indsel);']);
2134% %                         end
2135%                     end
2136%                 end
2137%                 if ~isempty(indexremove)
2138%                     MeanData.ListVarName(VarIndex(indexremove))=[];
2139%                     MeanData.VarDimIndex(VarIndex(indexremove))=[];
2140%                     if isfield(MeanData,'Role')%generaliser aus autres attributs
2141%                         MeanData.Role(VarIndex(indexremove))=[];
2142%                     end
2143%                 end
2144%                % END OF INITIALISATION
2145%
2146%             end
2147%       
2148%          % A FAIRE: regular grid if coord_x undefined
2149%             if indexfalse~=0 %suppress false data
2150%                  eval(['testexist=isfield(Data,''' FFName ''');'])
2151%                 if testexist
2152%                     eval(['indsel=find(Data.' FFName '==0);']);
2153%                     for icoord=1:length(CoordName)
2154%                         eval(['Data.' CoordName{icoord} '=Data.' CoordName{icoord} '(indsel);']);
2155%                     end
2156%                 end
2157%             end
2158%             for ilist=1:length(VarIndexSum)
2159%                 VarName=Data.ListVarName{VarIndexSum(ilist)};
2160%                 if indexfalse~=0 & testexist
2161%                     eval(['Data.' VarName '=Data.' VarName '(indsel);']);
2162%                 end
2163%                 if length(CoordName)==0%no variable use dfor unstructured coordinates
2164%                     if isempty(DimVarIndex)|isequal(DimVarIndex,0)% no coordinate variable for structured coordinates
2165% %                         %update histogram with the current field #ifile
2166%                         str_left=['[MeanData.' VarName 'val,MeanData.' VarName 'hist]='];
2167%                         str_right=['hist_update(MeanData.' VarName 'val,MeanData.' VarName 'hist,Data.' VarName ',dC(ilist));'];
2168%                         eval([str_left str_right]);%update global histo
2169%                     else
2170%                        %INTERPOLER
2171%                             
2172%                         eval(['MeanData.' VarName '=MeanData.' VarName '+Data.' VarName ';']);%increment sum%CAS x,y change
2173%                     end
2174%                 else   
2175%                     if length(CoordName)==2
2176%                         eval(['test_interp= ~isequal(Data.' CoordName{1} ',MeanData.' CoordName{1} ...
2177%                             ')|~isequal(Data.' CoordName{2} ',MeanData.' CoordName{2} ');'])
2178%                         if test_interp
2179%                             eval(['Data.' VarName '=griddata_uvmat(Data.' CoordName{1} ',Data.' CoordName{2}...
2180%                                 ',Data.' VarName ',MeanData.' CoordName{1} ',MeanData.' CoordName{2} ');']);
2181%                             test_interpolate=1;
2182%                         end
2183%                     end
2184%                     eval(['MeanData.' VarName '=MeanData.' VarName '+Data.' VarName ';']);%increment sum
2185%                 end
2186%             end
2187%         end
2188%     end
2189%     if length(CoordName)~=0 | ~isequal(DimVarIndex,0)% no coordinate variable for structured coordinates
2190%         for ilist=1:length(VarIndexSum) 
2191%             VarName=Data.ListVarName{VarIndexSum(ilist)};
2192%             eval(['MeanData.' VarName '=MeanData.' VarName '/itime;']);%normalize sum by the number of fields
2193%         end
2194%     else
2195%         MeanData.NbDim=1;
2196%         MeanData.ListDimName={};
2197%         MeanData.DimValue=[];
2198%         for ilist=1:length(VarIndexSum) 
2199%             VarName=Data.ListVarName{VarIndexSum(ilist)};
2200%             MeanData.ListVarName=[MeanData.ListVarName {[VarName 'val']} {[VarName 'hist']}];
2201%             MeanData.VarDimIndex=[MeanData.VarDimIndex {[ilist]} {[ilist]}];
2202%             MeanData.ListDimName=[MeanData.ListDimName {[VarName 'val']}];
2203%             eval(['MeanData.DimValue=[MeanData.DimValue length(MeanData.' VarName 'val)];']);
2204%         end   
2205%     end
2206%     figure
2207%     haxes=axes;
2208%     plot_field(MeanData,haxes)%plot the resulting average
2209%     % change variable names for consitency with civ1 data (need to generalize these programs)
2210%     if length(MeanData.ListVarName) >= 4 & isequal(MeanData.ListVarName(1:4), {'X'  'Y'  'U'  'V'})
2211%        MeanData.ListGlobalAttribute={'nb_coord','nb_dim','dt','absolut_time_T0','pixcmx','pixcmy','hart','civ','fix'};
2212%        MeanData.nb_coord=2;
2213%        MeanData.nb_dim=2;
2214%        MeanData.dt=1;
2215%        MeanData.absolut_time_T0=0;
2216%        MeanData.pixcmx=1; %pix per cm (1 by default)
2217%        MeanData.pixcmy=1; %pix per cm (1 by default)
2218%        MeanData.hart=0;
2219%        if isequal(Data.CoordType,'px')
2220%          MeanData.civ=1;
2221%       else
2222%          MeanData.civ=0;
2223%        end
2224%       MeanData.fix=0;
2225%         MeanData.ListVarName(1:4)={'vec_X'  'vec_Y'  'vec_U'  'vec_V'};
2226%         MeanData.vec_X=MeanData.X;
2227%         MeanData.vec_Y=MeanData.Y;
2228%         MeanData.vec_U=MeanData.U;
2229%         MeanData.vec_V=MeanData.V;
2230%     end
2231%     error=struct2nc(filemean,MeanData); %save result file
2232%     if isequal(error,0)
2233%         if test_interpolate
2234%             'fields interpolated to the positions of the first one'
2235%         end
2236%         [filemean ' written']
2237%     else
2238%         warndlg_uvmat(error,'ERROR')
2239%     end
2240% end
2241
2242%----------------------------------------------------------------------
2243% --project fields on a projection object (e. g. a regular grid), possibly
2244% merge several fields
2245%----------------------------------------------------------------------
2246%INPUT:
2247%num_i1: series of first indices i (given from the series interface as first_i:incr_i:last_i, mode and list_pair_civ)
2248%num_i2: series of second indices i (given from the series interface as first_i:incr_i:last_i, mode and list_pair_civ)
2249%num_j1: series of first indices j (given from the series interface as first_j:incr_j:last_j, mode and list_pair_civ )
2250%num_j2: series of second indices j (given from the series interface as first_j:incr_j:last_j, mode and list_pair_civ)
2251%OTHER INPUTS given by the structure Series
2252function GUI_input=merge_proj(num_i1,num_i2,num_j1,num_j2,Series);
2253
2254%requests for the visibility of input windows in the GUI series  (activated directly by the selection in the menu ACTION)
2255if ~exist('num_i1','var')
2256    GUI_input={'RootPath';'two';...%nbre of possible input series (options 'on'/'two'/'many', default:'one')
2257        'SubDir';'on';... % subdirectory of derived files (PIV fields), ('on' by default)
2258        'RootFile';'on';... %root input file name ('on' by default)
2259        'FileExt';'on';... %input file extension ('on' by default)
2260        'NomType';'on';...%type of file indexing ('on' by default)
2261        'NbSlice';'on'; ...%nbre of slices ('off' by default)
2262        'VelTypeMenu';'one';...% menu for selecting the velocity type (civ1,..) options 'off'/'one'/'two', 'off' by default)
2263        'FieldMenu';'one';...% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default)
2264        'CoordType';'on';...%can use a transform function 'off' by default
2265        'GetObject';'on';...%can use projection object ,'off' by default
2266        %'GetMask';'on'...%can use mask option   ,'off' by default
2267        %'PARAMETER'; options: name of the user defined parameter',repeat a line for each parameter
2268               ''};
2269    return %exit the function
2270end
2271
2272%-------------------------------------------------
2273hseries=guidata(Series.hseries);%handles of the GUI series
2274WaitbarPos=get(hseries.waitbar_frame,'Position'); %positiopn of waitbar frame
2275%-------------------------------------------------
2276
2277%numbers of view fields (nbre of inputs in RootPath)
2278testcell=iscell(Series.RootFile);
2279if ~testcell
2280    Series.RootPath={Series.RootPath};
2281    Series.RootFile={Series.RootFile};
2282    Series.SubDir={Series.SubDir};
2283    Series.FileExt={Series.FileExt};
2284    Series.NomType={Series.NomType};
2285    num_i1={num_i1};
2286    num_i2={num_i2};
2287    num_j1={num_j1};
2288    num_j2={num_j2};
2289end
2290nbview=length(Series.RootFile);%number of views (file series to merge)
2291nbfield=size(num_i1{1},1)*size(num_i1{1},2);%number of fields in the time series
2292transform=Series.CoordType; %  field transform function
2293hhh=which('mmreader');
2294for iview=1:nbview
2295    test_movie(iview)=0;
2296    if ~isequal(hhh,'')&& mmreader.isPlatformSupported()
2297        if isequal(lower(FileExt{iview}),'.avi')
2298            MovieObject{iview}=mmreader(fullfile(RootPath{iview},[RootFile{iview} FileExt{iview}]));
2299            test_movie(iview)=1;
2300        end
2301    end
2302end
2303
2304%Calibration data and timing: read the ImaDoc files
2305mode=''; %default
2306timecell={};
2307itime=0;
2308NbSlice_calib={}; %test for z index
2309for iview=1:nbview%Loop on views
2310    XmlData{iview}=[];%default
2311    filebase{iview}=fullfile(Series.RootPath{iview},Series.RootFile{iview});
2312    if exist([filebase{iview} '.xml'],'file')
2313        [XmlData{iview},error]=imadoc2struct([filebase{iview} '.xml']);
2314        if isfield(XmlData{iview},'Time')
2315            itime=itime+1;
2316            timecell{itime}=XmlData{iview}.Time;
2317        end
2318        if isfield(XmlData{iview},'GeometryCalib') && isfield(XmlData{iview}.GeometryCalib,'SliceCoord')
2319            NbSlice_calib{iview}=size(XmlData{iview}.GeometryCalib.SliceCoord,1);
2320            if ~isequal(NbSlice_calib{iview},NbSlice_calib{1})
2321                msgbox_uvmat('WARNING','inconsistent number of Z indices for the two field series');
2322            end
2323        end   
2324    elseif exist([filebase{iview} '.civ'],'file')
2325        [error,time,TimeUnit,mode,npx,npy,pxcmx,pxcmy]=read_imatext([filebase{iview} '.civ']);
2326        itime=itime+1;
2327        timecell{itime}=time;
2328        XmlData{iview}.Time=time;
2329        GeometryCalib.R=[pxcmx 0 0; 0 pxcmy 0;0 0 0];
2330        GeometryCalib.Tx=0;
2331        GeometryCalib.Ty=0;
2332        GeometryCalib.Tz=1;
2333        GeometryCalib.dpx=1;
2334        GeometryCalib.dpy=1;
2335        GeometryCalib.sx=1;
2336        GeometryCalib.Cx=0;
2337        GeometryCalib.Cy=0;
2338        GeometryCalib.f=1;
2339        GeometryCalib.kappa1=0;
2340        GeometryCalib.CoordUnit='cm';
2341        XmlData{iview}.GeometryCalib=GeometryCalib;
2342        if error==1
2343            msgbox_uvmat('WARNING','inconsistent number of fields in the .civ file');
2344        end
2345    end
2346end
2347
2348%check coincidence in time
2349multitime=0;
2350if length(timecell)==0
2351    time=[];
2352elseif length(timecell)==1
2353    time=timecell{1};
2354elseif length(timecell)>1
2355    multitime=1;
2356    for icell=1:length(timecell)
2357        if ~isequal(size(timecell{icell}),size(timecell{1}))
2358            msgbox_uvmat('WARNING','inconsistent time array dimensions in ImaDoc fields, the time for the first series is used')
2359            time=timecell{1};
2360            multitime=0;
2361            break
2362        end
2363    end
2364end
2365if multitime
2366    for icell=1:length(timecell)
2367        time(icell,:,:)=timecell{icell};
2368    end
2369    diff_time=max(max(diff(time)));
2370    if diff_time>0
2371        msgbox_uvmat('WARNING',['times of series differ by more than ' num2str(diff_time)])
2372    end   
2373end
2374if size(time,2) < num_i2{1}(end) || size(time,3) < num_j2{1}(end)% ime array absent or too short in ImaDoc xml file'
2375    time=[];
2376end
2377
2378% Field and velocity type (the same for all views)
2379Field_str=get(hseries.FieldMenu,'String');
2380val=get(hseries.FieldMenu,'Value');
2381FieldName=Field_str(val);%the same set of fields for all views
2382VelType_str=get(hseries.VelTypeMenu,'String');
2383VelType_val=get(hseries.VelTypeMenu,'Value');
2384VelType=VelType_str{VelType_val}; %the same for all views
2385if isequal(FieldName,'get_field...')
2386    hget_field=findobj(allchild(0),'Name','get_field');%find the get_field... GUI
2387   % hhget_field=guidata(hget_field);%handles of GUI elements in get_field
2388    SubField=get_field('read_get_field',hObject,eventdata,hget_field); %read the names of the variables to plot in the get_field GUI
2389%     if isequal(get(hhget_field.menu_coord,'Visible'),'on')
2390%         list_transform=get(hhget_field.menu_coord,'String');
2391%         val_list=get(hhget_field.menu_coord,'Value');
2392%         transform=list_transform{val_list};
2393%     end
2394end
2395%detect whether all the files are 'images' or 'netcdf'
2396testima=0;
2397testvol=0;
2398testcivx=0;
2399testnc=0;
2400FileExt=get(hseries.FileExt,'String');
2401for iview=1:nbview
2402     ext=FileExt{iview};
2403     form=imformats(ext([2:end]));
2404     if isequal(lower(ext),'.vol')
2405         testvol=testvol+1;
2406     elseif ~isempty(form)||isequal(lower(ext),'.avi')% if the extension corresponds to an image format recognized by Matlab
2407         testima=testima+1;
2408     elseif isequal(ext,'.nc')
2409         testnc=testnc+1;
2410     end
2411end
2412if testvol
2413    msgbox_uvmat('ERROR','volume images not implemented yet')
2414    return
2415end
2416if testnc~=nbview && testima~=nbview && testvol~=nbview
2417    msgbox_uvmat('ERROR','need a set of images or a set of netcdf files with the same fields as input')
2418    return
2419end
2420if ~isequal(FieldName,'get_field...')
2421    testcivx=testnc;
2422end
2423%name of output files and directory:
2424% res_subdir=fullfile(Series.RootPath{1},[Series.SubDir{1} '_STAT']);
2425ProjectDir=fileparts(fileparts(Series.RootPath{1}));% preoject directory (GERK)
2426prompt={['result directory (in' ProjectDir ')']};
2427RootPath=get(hseries.RootPath,'String');
2428SubDir=get(hseries.SubDir,'String');
2429if isequal(length(RootPath),1)
2430    fulldir=RootPath{1};
2431    subdir='GRID';
2432    res_subdir=fullfile(fulldir,subdir);
2433else
2434    def={fullfile(ProjectDir,'0_RESULTS')};
2435    dlgTitle='result directory';
2436    lineNo=1;
2437    answer=msgbox_uvmat('INPUT_TXT',dlgTitle,def);
2438    fulldir=answer{1};
2439    subdir=[];
2440    dirlist=sort(Series.RootFile);
2441    for iview=1:nbview
2442        if ~isempty(subdir)
2443            subdir=[subdir '-'];
2444        end
2445        subdir=[subdir dirlist{iview}];
2446    end 
2447    res_subdir=fullfile(fulldir,subdir);
2448end
2449ext=FileExt{1};
2450if ~exist(fulldir,'dir')
2451    msgbox_uvmat('ERROR',['directory ' fulldir ' needs to be created'])
2452    return
2453end
2454if ~exist(res_subdir,'dir')
2455    dircur=pwd;
2456    cd(fulldir)
2457    error=mkdir(subdir);
2458    cd(dircur)
2459end
2460filebasesub=fullfile(res_subdir,Series.RootFile{1});
2461filebase_merge=fullfile(res_subdir,'merged');%root name for the merged files
2462
2463%projection object
2464if isfield(Series,'sethandles')
2465    if ishandle(Series.sethandles.set_object)
2466        Series.ProjObject=read_set_object(Series.sethandles);
2467        if ~isfield(Series.ProjObject,'Style')
2468            msgbox_uvmat('ERROR','Undefined projection object style')
2469            return
2470        end
2471        if ~isequal(Series.ProjObject.Style,'plane')
2472            msgbox_uvmat('ERROR','The projection object must be a plane')
2473            return
2474        end
2475    end
2476end
2477
2478    %MAIN LOOP
2479for ifile=1:nbfield               
2480    stopstate=get(hseries.RUN,'BusyAction');
2481    if isequal(stopstate,'queue')% enable STOP command from the 'series' interface
2482         update_waitbar(hseries.waitbar,WaitbarPos,ifile/nbfield)
2483         Amerge=0;
2484         
2485         %----------LOOP ON VIEWS----------------------
2486        nbtime=0;
2487        for iview=1:nbview
2488            %name of the current file
2489            filename=name_generator(filebase{iview},num_i1{iview}(ifile),num_j1{iview}(ifile),Series.FileExt{iview},Series.NomType{iview},1,num_i2{iview}(ifile),num_j2{iview}(ifile),SubDir{iview});
2490            if ~exist(filename,'file')
2491                msgbox_uvmat('ERROR',['missing input file' filename])
2492                break
2493            end
2494
2495            %reading the current file
2496            if testima
2497                if test_movie(iview)
2498                    Field{iview}.A=read(MovieObject{iview},num_i1{iview}(ifile));
2499                else
2500                    Field{iview}.A=read_image(filename,Series.NomType{iview},num_i1{iview}(ifile));
2501                end % TODO: introduce ListVarName
2502                npxy=size(Field{iview}.A);
2503                Field{iview}.AX=[0.5 npxy(2)-0.5]; % coordinates of the first and last pixel centers
2504                Field{iview}.AY=[npxy(1)-0.5 0.5];
2505                Field{iview}.CoordType='px';
2506                Field{iview}.AName='image';
2507            else
2508                if testcivx
2509                    [Field{iview},VelTypeOut]=read_civxdata(filename,FieldName,VelType);
2510                else
2511                    [Field{iview},var_detect]=nc2struct(filename,SubField.ListVarName); %read the corresponding input data               
2512                    Field{iview}.VarAttribute=SubField.VarAttribute;
2513                end
2514                if isfield(Field{iview},'Time')
2515                    timeread(iview)=Field{iview}.Time;
2516                    nbtime=nbtime+1;
2517                end
2518            end
2519            % coord transform
2520            % z index
2521            if ~isempty(NbSlice_calib)
2522                Field{iview}.ZIndex=mod(num_i1{iview}(ifile)-1,NbSlice_calib{1})+1;
2523            end
2524            if ~isequal(transform,'')
2525                Field{iview}=feval(Series.CoordType,Field{iview},XmlData{iview});%transform to phys if requested
2526            end
2527            if testcivx
2528                    Field{iview}=calc_field(FieldName,Field{iview});
2529            end
2530
2531            %projection on object (gridded plane)
2532            if isfield(Series,'ProjObject')
2533                Field{iview}=proj_field(Field{iview},Series.ProjObject);
2534            end
2535        end   
2536       
2537         %----------END LOOP ON VIEWS----------------------
2538         
2539        %merge the nbview fields
2540        MergeData=merge_field(Field);
2541        if isfield(MergeData,'Txt')
2542            msgbox_uvmat('ERROR',MergeData.Txt)
2543            return
2544        end
2545       
2546        % generating the name of the merged field
2547        mergename=name_generator(filebase_merge,num_i1{iview}(ifile),num_j1{iview}(ifile),Series.FileExt{iview},Series.NomType{iview},1,num_i2{iview}(ifile),num_j2{iview}(ifile));
2548       
2549        % time:
2550        time_i=0;%default
2551        if isempty(time)% time from ImaDoc prevails
2552            time_i=sum(timeread)/nbtime;
2553        else
2554            time_i=(time(iview,num_i1{iview}(ifile),num_j1{iview}(ifile))+time(iview,num_i2{iview}(ifile),num_j2{iview}(ifile)))/2;
2555        end
2556       
2557        % recording the merged field
2558        if testima    %in case of input images an image is produced   
2559            if isa(MergeData.A,'uint8')
2560                bitdepth=8;
2561            elseif isa(MergeData.A,'uint16')
2562                bitdepth=16;
2563            end
2564            imwrite(MergeData.A,mergename,'BitDepth',bitdepth);
2565            %write xml calibration file
2566            siz=size(MergeData.A);
2567            npy=siz(1);
2568            npx=siz(2);
2569            if isfield(MergeData,'VarAttribute')&&isfield(MergeData.VarAttribute{1},'Coord_2')&&isfield(MergeData.VarAttribute{1},'Coord_1')
2570                Rangx=MergeData.VarAttribute{1}.Coord_2;
2571                Rangy=MergeData.VarAttribute{1}.Coord_1;
2572            elseif isfield(MergeData,'AX')&& isfield(MergeData,'AY')
2573                Rangx=[MergeData.AX(1) MergeData.AX(end)];
2574                Rangy=[MergeData.AY(1) MergeData.AY(end)];
2575            else
2576                Rangx=[0.5 npx-0.5];
2577                Rangy=[npy-0.5 0.5];%default
2578            end
2579            pxcmx=(npx-1)/(Rangx(2)-Rangx(1));
2580            pxcmy=(npy-1)/(Rangy(1)-Rangy(2));
2581            T_x=-pxcmx*Rangx(1)+0.5;
2582            T_y=-pxcmy*Rangy(2)+0.5;
2583            GeometryCal.focal=1;
2584            GeometryCal.R=[pxcmx,0,0;0,pxcmy,0;0,0,1];
2585            GeometryCal.Tx_Ty_Tz=[T_x T_y 1];
2586            ImaDoc.GeometryCalib=GeometryCal;
2587            t=struct2xml(ImaDoc);
2588            t=set(t,1,'name','ImaDoc');
2589            save(t,[filebase_merge '.xml'])     
2590            display([filebase_merge '.xml saved'])
2591        else
2592            MergeData.ListGlobalAttribute={'Project','InputFile_1','InputFile_end','nb_coord','nb_dim','dt','Time','civ'};       
2593            MergeData.nb_coord=2;
2594            MergeData.nb_dim=2;
2595            MergeData.dt=1;
2596            MergeData.Time=time_i;
2597            error=struct2nc(mergename,MergeData); %save result file
2598            if isempty(error)
2599                display(['output file ' mergename ' written'])
2600            else
2601                display(error)
2602            end
2603        end
2604    end
2605end
2606
2607%--------------------------------------------------------------------------   
2608function MergeData=merge_field(Data)
2609% initiate Matlab  structure for physical field
2610if isempty(Data)||~iscell(Data)
2611    MergeData=[];
2612    return
2613end
2614MergeData=Data{1};%default
2615error=0;
2616nbview=length(Data);
2617if nbview==1
2618    return
2619end
2620for iview=1:nbview
2621    if ~isequal(MergeData.ListDimName,Data{iview}.ListDimName)
2622        error=1;
2623    end
2624    if ~isequal(MergeData.ListVarName,Data{iview}.ListVarName)
2625        error=1;
2626    end
2627%      if ~isequal(MergeData.VarDimIndex,Data{iview}.VarDimIndex)
2628%         error=1;
2629%      end
2630end
2631if error
2632    MergeData.Txt='ERROR: attempt at merging fields of incompatible type';
2633    return
2634end
2635%group the variables (fields of 'FieldData') in cells of variables with the same dimensions
2636%-----------------------------------------------------------------
2637[CellVarIndex,NbDim,VarTypeCell]=find_field_indices(Data{1});
2638%LOOP ON GROUPS OF VARIABLES SHARING THE SAME DIMENSIONS
2639% CellVarIndex=cells of variable index arrays
2640ivar_new=0; % index of the current variable in the projected field
2641icoord=0;
2642for icell=1:length(CellVarIndex)
2643    if NbDim(icell)==1
2644        continue
2645    end
2646    VarIndex=CellVarIndex{icell};%  indices of the selected variables in the list FieldData.ListVarName
2647    VarType=VarTypeCell{icell};
2648    ivar_X=VarType.coord_x;
2649    ivar_Y=VarType.coord_y;
2650    ivar_FF=VarType.errorflag;
2651    if isempty(ivar_X)
2652        test_grid=1;%test for input data on regular grid (e.g. image)coordinates
2653    else
2654        if length(ivar_Y)~=1
2655                warndlg_uvmat('y coordinate missing in proj_field.m','ERROR')
2656                return
2657        end
2658        test_grid=0;
2659    end
2660%    DimIndices=Data{1}.VarDimIndex{VarIndex(1)};%indices of the dimensions of the first variable (common to all variables in the cell)
2661    %case of input fields with unstructured coordinates
2662    if ~test_grid
2663        for ivar=VarIndex
2664            VarName=MergeData.ListVarName{ivar};
2665            for iview=1:nbview
2666                eval(['MergeData.' VarName '=[MergeData.' VarName '; Data{iview}.' VarName ';'])
2667            end
2668        end
2669    %case of fields defined on a structured  grid
2670    else 
2671%        DimValue=MergeData.DimValue(DimIndices);%set of dimension values
2672        testFF=0;
2673        for iview=2:nbview
2674%             if ~isequal(DimValue,Data{iview}.DimValue(DimIndices))
2675%                 MergeData.Txt='ERROR: attempt at merging structured fields with different sizes';
2676%                 return
2677%             end
2678            for ivar=VarIndex
2679                VarName=MergeData.ListVarName{ivar};
2680                if isfield(MergeData,'VarAttribute')
2681                    if length(MergeData.VarAttribute)>=ivar && isfield(MergeData.VarAttribute{ivar},'Role') && isequal(MergeData.VarAttribute{ivar}.Role,'errorflag')
2682                        testFF=1;
2683                    end
2684                end
2685                eval(['MergeData.' VarName '=MergeData.' VarName '+ Data{iview}.' VarName ';'])
2686            end
2687        end
2688        if testFF
2689            nbaver=nbview-MergeData.FF;
2690            indgood=find(nbaver>0);
2691            for ivar=VarIndex
2692                VarName=MergeData.ListVarName{ivar};
2693                eval(['MergeData.' VarName '(indgood)=double(MergeData.' VarName '(indgood))./nbaver(indgood);'])
2694            end
2695        else
2696            for ivar=VarIndex
2697                VarName=MergeData.ListVarName{ivar};
2698                eval(['MergeData.' VarName '=double(MergeData.' VarName ')./nbview;'])
2699            end   
2700        end
2701    end
2702end
2703   
2704   
2705
2706
2707%-----------------------------
2708function mouse_up_gui(ggg,eventdata,handles)
2709if isequal(get(ggg,'SelectionType'),'alt')
2710    display('global CurData, UserData of GUI series')
2711    global CurData
2712    CurData=get(ggg,'UserData');
2713    evalin('base','global CurData');%make CurData global in the workspace
2714    evalin('base','CurData'); %display CurData in the workspace
2715    commandwindow
2716   % plot_text(CurData)
2717end
2718
2719
2720
2721% %----------------------------------------------------------------------
2722% % --- display image movie and display time average
2723% %OBSOLETE: A SUPPRIMER
2724% %----------------------------------------------------------------------
2725% function movie_ima(handles,filecell,filecell_1,num1,num_a,field)
2726%
2727% global hfig1 hfig2 hfig3 poscolbar
2728% global A val HIST
2729%
2730% A=[];aviobj=[];
2731% % set(hfig1,'UserData','ima')% set the current field state to 'image'
2732% set(handles.zoom,'Value',1); %put zoom on
2733% nom_type=get(handles.file_input,'UserData');
2734% % field=get(handles.civ1,'UserData');
2735% % fields=field(1).fields;
2736% set(handles.speed,'Visible','On')%show slider to set movie speed
2737% set(handles.mo_speed_txt,'Visible','On')
2738%
2739% if ~isempty(filecell_1)
2740%    file1=get(handles.file1_input,'UserData');
2741%    field1=file1.field;
2742%    scal_type1=field1.fields;
2743%    vel_type1=field1.vel_type;
2744%    filename_1=filecell_1(1);% first file name in the series
2745% else
2746%    filename_1=[];
2747% end
2748% scal_type{1}=field(1).fields;
2749% vel_type{1}=field(1).vel_type;
2750% % display the first field
2751% [A,time,dt,rangx0,rangy0]=view_ima(handles,cell2mat(filecell(1)),filename_1,num1(1),num_a(1));
2752%
2753% % calculate the histogram of the first image
2754% nxy=size(A);
2755% ndim=length(nxy);
2756% if ndim==2 % case of B/W images
2757%     nxy(3)=1;
2758% end
2759% C=reshape(A,nxy(1)*nxy(2),nxy(3));
2760% Amaxmax=double(max(max(max(A))));
2761% Aminmin=double(min(min(min(A))));
2762% if isa(C,'uint8')|isa(C,'uint16')
2763%     C=double(C);
2764%     dC=1;
2765% else
2766%     dC=(Amaxmax-Aminmin)/100;
2767% end
2768% val=[Aminmin:dC:Amaxmax];% define bins for histogram
2769% HIST=hist(C,val);% initiate the global histogram
2770% if ndim==2, HIST=HIST'; end;
2771%
2772% auto_scale=get(handles.auto_scale,'Value');
2773% min_input=str2num(get(handles.min_input,'String'));% select the minimum
2774% max_input=str2num(get(handles.scale_input,'String'));% select the max
2775% zoomstate=get(handles.zoom,'Value');
2776%
2777% if isequal(get(handles.window_input,'String'),'avi'),
2778%     basename=get(handles.file_input,'String');
2779%     prompt = {'file name';'frames per second';'frame resolution ([nbpixels x y])';'axis position relative to the frame'};
2780%     dlg_title = 'select properties of the output avi movie';
2781%     num_lines= 1;
2782%     def     = {[basename '_out.avi'];'5';'[1024 768]';'[0.05 0.07 0.87 0.88]'};
2783%     answer = inputdlg(prompt,dlg_title,num_lines,def);
2784%     aviname=answer{1};
2785%     fps=str2num(answer{2});
2786%     if exist(aviname,'file')==2
2787%         delete(aviname);
2788%     end;
2789%     aviobj=avifile(aviname,'Compression','None','fps',fps);
2790%     
2791%     %display first view for tests
2792%     figure(2);
2793%     hh=get(gcf,'CurrentAxes');
2794%     if isempty(hh),
2795%         hfig1=axes;
2796%     else
2797%         hfig1=hh;
2798%     end;
2799%     if isequal(filecell_1,{})
2800%         filename_1=[];
2801%     else
2802%         filename_1=cell2mat(filecell_1(1));
2803%     end
2804%     poscolbar=[0.93 0.15 0.02 0.7];
2805%     view_ima(handles,cell2mat(filecell(1)),filename_1,num1(1),num_a(1));% show the first field
2806%     nbpix=eval(answer{3});
2807%     set(gcf,'Position',[1 1 nbpix])% resolution XVGA
2808%     set(hfig1,'Position',eval(answer{4}));
2809%     
2810%     msgbox({'adjust figure 2 with its matlab edit menu ' ;...
2811%             'then type any keyboard key to get the avi movie as a copy of figure 2 display'})
2812%     pause;
2813%     hh=colorbar;
2814%     poscolbar=get(hh,'Position');
2815% end
2816%
2817% %%%%%%%%%%%%%%%%
2818% %mask and usrdfct
2819% maskname=[]; %default
2820% if isequal(get(handles.mask_test,'Value'),1)
2821%     maskbase=get(handles.mask_test,'UserData');
2822% end
2823% % image or scalar processing programme set by user
2824% % if (get(handles.usr_fct,'Value')==1)
2825% %      usrfct=get(handles.usr_fct,'UserData');
2826% % else
2827% %      usrfct='';
2828% % end
2829% nburst=1; % nburst(1) =nbre of names in filename= nbre of bursts
2830% set(handles.text_display_1,'String',['image movie'])
2831% nbfield=length(filecell);
2832% if nbfield >1
2833% for ifile=2:nbfield
2834%     stopstate=get(handles.run0,'BusyAction');
2835%     if isequal(stopstate,'queue')% enable STOP command
2836%        pausetime=1.02-get(handles.speed,'Value');
2837%          pause(pausetime)
2838%          if isequal(get(handles.mask_test,'Value'),1)
2839%                 maskname=name_generator(maskbase,num1(ifile),1,'.png','png_series');
2840%             end
2841%             if isequal(AName{1},'image')
2842%                 A=read_image(cell2mat(filecell(ifile)),num1(ifile),maskname);% read the first image, num2 is the counter for avi files
2843%             else % read the first field from the netcdf file, imposing the pixel positions in the selected domain
2844%                  [A,time(ifile),dtr,rgx,rgy,vt_out,erread]=read_scalar(filecell{ifile},vel_type,scal_type,rangx0,rangy0,nxy,maskname);
2845%                 if erread==1;
2846%                     errordlg({['no spatial derivative in ' filecell{ifile}]; 'run patch first'}); return
2847%                 elseif erread==2;
2848%                     errordlg(['no field ' vel_type{1} ' in ' filecell{ifile}]); return
2849%                 elseif erread==3;
2850%                     errordlg(['scalar ' scal_type{1} ' not found in' filecell{ifile}]); return
2851%                 elseif erread==4;
2852%                     errordlg(['all points aligned in' filecell{ifile}]); return
2853%                 end
2854%             end
2855%           
2856%             % read the second image
2857%             if ~isempty(filecell_1)
2858%                 if isequal(scal_type{1},'image')
2859%                     A1=read_image(cell2mat(filecell_1(ifile)),num1(ifile),maskname);% read the second image, num2 is the counter for avi files
2860%                     Avalue_1=double(A1(indy,indx,:));
2861%                 else % read the second field from the netcdf file, imposing the pixel positions in the selected domain
2862%                     [Avalue_1,time1(ifile),dtr,rgx,rgy,vt_out,erread]=read_scalar(filecell_1{ifile},{vel_type1},{scal_type1},rangx0,rangy0,npxy,maskname,usrfct);
2863%                     if erread==1;
2864%                         errordlg({['no spatial derivative in ' filecell_1{ifile}]; 'run patch first'}); return
2865%                     elseif erread==2;
2866%                         errordlg(['no field ' vel_type1 ' in ' filecell_1{ifile}]); return
2867%                     elseif erread==3;
2868%                         errordlg(['scalar ' scal_type1 ' not found in' filecell_1{ifile}]); return
2869%                     elseif erread==4;
2870%                         errordlg(['all points aligned in' filecell_1{ifile}]); return
2871%                     end
2872%                 end
2873%                 time(ifile)=(time(ifile)+time1(ifile))/2;
2874%                 Avalue=Avalue-Avalue_1;
2875%             end
2876%         set(handles.abs_time,'String',time);
2877%         set(handles.field_counter,'String',num2str(num1(ifile)));
2878%         set(handles.a_input,'String',num2stra(num_a(ifile),nom_type));
2879%         C=reshape(A,nxy(1)*nxy(2),nxy(3));% reshape in a vector
2880%         [val,HIST]=hist_update(val,HIST,C,dC);
2881%         [h,Amin,Amax]=plot_image(hfig1,rangx0,rangy0,1,scal_type{1},auto_scale,min_input,max_input,poscolbar,A);
2882%         set(handles.min_input,'String',num2str(Amin));% select the minimum
2883%         set(handles.scale_input,'String',num2str(Amax));% select the minimum
2884%          if ~isequal(aviobj,[]),
2885% %              mov=getframe(hfig1);
2886%               mov=getframe(gcf);
2887%              aviobj=addframe(aviobj,mov);end
2888%          if (get(handles.zoom,'Value') == get(handles.zoom,'Max')),zoom on,end
2889%          set(handles.field_counter,'String',num2str(num1(ifile)))
2890% %     end
2891% end
2892% end
2893% end
2894% aviobj=close(aviobj);
2895%
2896% %plot global image histogram
2897%         HIST=HIST/(nbfield*nxy(1)*nxy(2));% normalized by the number of points
2898%         axes(hfig2) %in main window
2899%         if ndim==2
2900%             plot(val,HIST)
2901%         else
2902%             plot(val,HIST(:,1),'r',val,HIST(:,2),'g',val,HIST(:,3),'b')
2903%         end
2904%         residu=1-sum(HIST,1);
2905%         title(['histo, residu ' num2str(residu)])
2906%         grid on
2907%         axes(hfig3)
2908%         cla %clear the second histogram window
2909%         
2910
2911
2912
2913
2914%%%%%%%%%%%%%
2915function [ind_remove]=find_pairs(dirpair,ind_i,last_i)
2916
2917        indsel=ind_i;
2918        indiff=diff(ind_i); %test index increment to detect multiplets (several pairs with the same index ind_i) and holes in the series
2919        indiff=[1 indiff last_i-ind_i(end)+1];%for testing gaps with the imposed bounds
2920        if ~isempty(indiff)
2921            indiff2=diff(indiff);
2922            indiffp=[indiff2 1];
2923            indiffm=[1 indiff2];
2924            ind_multi_m=find((indiff==0)&(indiffm<0))-1;%indices of first members of multiplets
2925            ind_multi_p=find((indiff==0)&(indiffp>0));%indices of last members of multiplets
2926                %for each multiplet, select the most recent file
2927            ind_remove=[];
2928            for i=1:length(ind_multi_m)
2929                ind_pairs=ind_multi_m(i):ind_multi_p(i);
2930                for imulti=1:length(ind_pairs)
2931                    datepair(imulti)=datenum(dirpair(ind_pairs(imulti)).date);%dates of creation
2932                end
2933                [datenew,indsort2]=sort(datepair); %sort the multiplet by creation date
2934                ind_s=indsort2(1:end-1);%
2935                ind_remove=[ind_remove ind_pairs(ind_s)];%remove these indices, leave the last one
2936            end
2937        end
2938
2939%--------------------------------------------------------
2940
2941 
2942%-----------------------------------------------------------
2943% find the times corresponding to the first and last indices of a series
2944%
2945function displ_time(handles,times)
2946hseries=get(handles.last_i,'parent');
2947SeriesData=get(hseries,'UserData');%
2948first_i=str2num(get(handles.first_i,'String'));
2949first_j=str2num(get(handles.first_j,'String'));
2950last_i=str2num(get(handles.last_i,'String'));
2951last_j=str2num(get(handles.last_j,'String'));
2952% index_civ=get(handles.list_pair_civ,'Value');
2953% NomType=get(handles.NomType,'String');
2954NomType=SeriesData.NomType;
2955mode_list=get(handles.mode,'String');
2956index_mode=get(handles.mode,'Value');
2957mode=mode_list{index_mode};
2958% ind_shift=0;%default
2959
2960time_first=[];
2961time_last=[];
2962if ~isfield(SeriesData,'Time')
2963    SeriesData.Time{1}=[];
2964end
2965for iview=1:length(NomType)
2966    time_first_cell{iview}='?';
2967    time_last_cell{iview}='?';%default
2968    time=SeriesData.Time{iview};
2969    if isequal(NomType{iview},'_i1-i2_j')|isequal(NomType{iview},'_i_j1-j2')|isequal(NomType{iview},'#_ab')|isequal(NomType{iview},'_i1-i2')
2970        if isfield(SeriesData,'displ_num')& ~isempty(SeriesData.displ_num)
2971            ind_shift=SeriesData.displ_num(iview,:);
2972            if isequal(mode,'bursts')
2973                first_j=0;
2974                last_j=0;
2975            end
2976            first_i1=first_i +ind_shift(3);
2977            first_i2 =first_i +ind_shift(4);
2978            first_j1 =first_j +ind_shift(1);
2979            first_j2 =first_j +ind_shift(2);
2980            last_i1=last_i +ind_shift(3);
2981            last_i2 =last_i +ind_shift(4);   
2982            last_j1 =last_j +ind_shift(1);
2983            last_j2 =last_j +ind_shift(2);
2984            siz=size(SeriesData.Time{1});
2985            if first_i1>=1 && first_j1>=1 && siz(1)>=last_i2 && siz(2)>=last_j2
2986                time_first=(time(first_i1,first_j1)+time(first_i2,first_j2))/2;
2987                time_last=(time(last_i1,last_j1)+time(last_i2,last_j2))/2;
2988            else%read the time in the nc files
2989                RootPath=get(handles.RootPath,'String');
2990                RootFile=get(handles.RootFile,'String');
2991                SubDir=get(handles.SubDir,'String');
2992                %VelType=get(handles.VelType,'String');
2993                VelType_str=get(handles.VelTypeMenu,'String');
2994                VelType_val=get(handles.VelTypeMenu,'Value');
2995                VelType=VelType_str{VelType_val};
2996                filebase=fullfile(RootPath{1},RootFile{1});
2997                [filefirst]=name_generator(filebase,first_i1,first_j1,'.nc',NomType{iview},1,first_i2,first_j2,SubDir{iview});
2998                if  exist(filefirst,'file')
2999                    Attrib=nc2struct(filefirst,[]);
3000                    if isfield(Attrib,'Time')
3001                        time_first=Attrib.Time;
3002                    else
3003                        if isfield(Attrib,'absolut_time_T0')
3004                            time_first=Attrib.absolut_time_T0;
3005                        end
3006                        if isfield(Attrib,'absolut_time_T0_2')&&~(isequal(VelType,'civ1')||isequal(VelType,'interp1')||isequal(VelType,'filter1'))
3007                            time_first=Attrib.absolut_time_T0_2;
3008                        end
3009                    end
3010                end
3011                [filelast]=name_generator(filebase,last_i1,last_j1,'.nc',NomType{iview},1,last_i2,last_j2,SubDir{iview});
3012                if exist(filelast,'file')
3013                   Attrib=nc2struct(filelast,[]);
3014                    if isfield(Attrib,'Time')
3015                        time_last=Attrib.Time;
3016                    else
3017                        if isfield(Attrib,'absolut_time_T0')
3018                            time_last=Attrib.absolut_time_T0;
3019                        end
3020                        if isfield(Attrib,'absolut_time_T0_2')&&~(isequal(VelType,'civ1')||isequal(VelType,'interp1')||isequal(VelType,'filter1'))
3021                            time_last=Attrib.absolut_time_T0_2;
3022                        end
3023                    end
3024                end
3025            end
3026        end
3027    else
3028        siz=size(times);
3029        if siz(1)>=last_i & siz(2)>=last_j
3030            time_first=times(first_i,first_j);
3031            time_last=times(last_i,last_j);
3032        end
3033    end
3034    time_first_cell{iview}=num2str(time_first,4);
3035    time_last_cell{iview}=num2str(time_last,4);
3036end
3037set(handles.time_first,'Value',1)
3038set(handles.time_last,'Value',1)
3039set(handles.time_first,'String',time_first_cell);
3040set(handles.time_last,'String',time_last_cell);
3041
3042%--------------------------------------------------------------------
3043% --- Executes on selection change in VelTypeMenu.
3044function VelTypeMenu_Callback(hObject, eventdata, handles)
3045% VelTypeList=get(handles.VelTypeMenu,'String');
3046% VelTypeIndex=get(handles.VelTypeMenu,'Value');
3047% VelTypeCell=get(handles.VelType,'String');
3048% VelTypeCell{1}=VelTypeList{VelTypeIndex};
3049% set(handles.VelType,'String',VelTypeCell)
3050
3051
3052%--------------------------------------------------------------------
3053% --- Executes on button press in GetObject.
3054function GetObject_Callback(hObject, eventdata, handles)
3055hseries=get(handles.GetObject,'parent');
3056SeriesData=get(hseries,'UserData');
3057value=get(handles.GetObject,'Value');
3058if value
3059     set(handles.GetObject,'BackgroundColor',[1 1 0])%put unactivated buttons to yellow
3060     DataInit.ParentButton=handles.GetObject;
3061     hset_object=findobj(allchild(0),'Name','set_object');%find the set_object interface handle
3062     if ishandle(hset_object)
3063         [SeriesData.hset_object,SeriesData.sethandles]=set_object(DataInit); %open the set_object interface
3064     else
3065         DataInit.TITLE='POINTS';%default option
3066         [SeriesData.hset_object,SeriesData.sethandles]=set_object(DataInit); %open the set_object interface
3067     end
3068else
3069    set(handles.GetObject,'BackgroundColor',[0 1 0])%put activated buttons to green
3070    if isfield(SeriesData,'hset_object')&& ishandle(SeriesData.hset_object)
3071        close(SeriesData.hset_object)
3072    end
3073end
3074set(hseries,'UserData',SeriesData)
3075
3076%--------------------------------------------------------------
3077function GetMask_Callback(hObject, eventdata, handles)
3078value=get(handles.GetMask,'Value');
3079if value
3080    errordlg('not implemented yet')
3081end
3082%--------------------------------------------------------------
3083
3084%--------------------------------------------------------------------------
3085%'uv_ncbrowser': interactively calls the netcdf file browser 'get_field.m'
3086function ncbrowser_uvmat(hObject, eventdata)
3087     bla=get(gcbo,'String');
3088     ind=get(gcbo,'Value');
3089     filename=cell2mat(bla(ind));
3090      blank=find(filename==' ');
3091      filename=filename(1:blank-1);
3092     get_field(filename)
3093
3094
3095
3096% --------------------------------------------------------------------
3097function MenuHelp_Callback(hObject, eventdata, handles)
3098
3099path_to_uvmat=which ('uvmat');% check the path of uvmat
3100pathelp=fileparts(path_to_uvmat);
3101helpfile=fullfile(pathelp,'UVMAT_DOC','uvmat_doc.html');
3102if isempty(dir(helpfile)), errordlg('Please put the help file uvmat_doc.html in the  directory UVMAT/UVMAT_DOC')
3103else
3104web([helpfile '#series'])   
3105end
3106
3107
3108
3109
3110
3111
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