source: trunk/src/series.m @ 399

Last change on this file since 399 was 399, checked in by sommeria, 9 years ago

implementation of thin plate interpolation (proj on planes with mode 'filter'), rationalisation of variable formats in civ_matlab

File size: 80.0 KB
Line 
1%'series': master function associated to the GUI series.m for analysis field series 
2%------------------------------------------------------------------------
3% function varargout = series(varargin)
4% associated with the GUI series.fig
5%
6%INPUT
7% param: structure with input parameters (link with the GUI uvmat)
8%      .menu_coord_str: string for the transform_fct (menu for coordinate transforms)
9%      .menu_coord_val: value for transform_fct (menu for coordinate transforms)
10%      .FileName: input file name
11%      .FileName_1: second input file name
12%      .list_field: menu of input fields
13%      .index_fields: chosen index
14%      .civ1=0 or 1, .interp1,  ... : input civ field type
15%
16%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
17%  Copyright Joel Sommeria, 2008, LEGI / CNRS-UJF-INPG, sommeria@coriolis-legi.org.
18%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
19%     This file is part of the toolbox UVMAT.
20%
21%     UVMAT is free software; you can redistribute it and/or modify
22%     it under the terms of the GNU General Public License as published by
23%     the Free Software Foundation; either version 2 of the License, or
24%     (at your option) any later version.
25%
26%     UVMAT is distributed in the hope that it will be useful,
27%     but WITHOUT ANY WARRANTY; without even the implied warranty of
28%     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
29%     GNU General Public License (file UVMAT/COPYING.txt) for more details.
30%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
31
32function varargout = series(varargin)
33
34% Begin initialization code - DO NOT EDIT
35gui_Singleton = 1;
36gui_State = struct('gui_Name',       mfilename, ...
37                   'gui_Singleton',  gui_Singleton, ...
38                   'gui_OpeningFcn', @series_OpeningFcn, ...
39                   'gui_OutputFcn',  @series_OutputFcn, ...
40                   'gui_LayoutFcn',  [] , ...
41                   'gui_Callback',   []);
42if nargin && ischar(varargin{1})
43    gui_State.gui_Callback = str2func(varargin{1});
44end
45
46if nargout
47    [varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:});
48else
49    gui_mainfcn(gui_State, varargin{:});
50end
51% End initialization code - DO NOT EDIT
52
53%--------------------------------------------------------------------------
54% --- Executes just before series is made visible.
55%--------------------------------------------------------------------------
56function series_OpeningFcn(hObject, eventdata, handles,param)
57global nb_builtin_ACTION nb_builtin_transform
58% Choose default command line output for series
59handles.output = hObject;
60% Update handles structure
61guidata(hObject, handles);
62%default initial parameters
63drawnow
64set(hObject,'Units','pixels')
65% set(0,'Units','pixels')
66% screensize=get(0,'ScreenSize'); %screen size in pixels
67set(hObject,'WindowButtonDownFcn',{'mouse_down'})%allows mouse action with right button (zoom for uicontrol display)
68%set(hObject,'Position',[150 100 1000 600] );%position and size in pixels (get adjusted to the screen size in case of excess)
69%load the list of previously browsed files in menus Open and Open_1
70dir_perso=prefdir;
71test_profil_perso=0;
72profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
73if exist(profil_perso,'file')
74     h=load (profil_perso);
75     test_profil_perso=1;
76     if isfield(h,'MenuFile_1')
77          set(handles.MenuFile_1,'Label',h.MenuFile_1);
78          set(handles.MenuFile_insert_1,'Label',h.MenuFile_1);
79     end
80     if isfield(h,'MenuFile_1')
81          set(handles.MenuFile_2,'Label',h.MenuFile_2);
82          set(handles.MenuFile_insert_2,'Label',h.MenuFile_2);
83     end
84     if isfield(h,'MenuFile_1')
85          set(handles.MenuFile_3,'Label',h.MenuFile_3);
86          set(handles.MenuFile_insert_3,'Label',h.MenuFile_3);
87     end
88     if isfield(h,'MenuFile_1')
89          set(handles.MenuFile_4,'Label',h.MenuFile_4);
90          set(handles.MenuFile_insert_4,'Label',h.MenuFile_4);
91     end
92     if isfield(h,'MenuFile_1')
93          set(handles.MenuFile_5,'Label',h.MenuFile_5);
94          set(handles.MenuFile_insert_5,'Label',h.MenuFile_5);
95     end
96end
97
98%check default input data
99if ~exist('param','var')
100    param=[]; %default
101end
102
103%% file name and browser initialisation
104if isfield(param,'menu_coord_str')
105    set(handles.transform_fct,'String',param.menu_coord_str)
106end
107if isfield(param,'menu_coord_val')
108    set(handles.transform_fct,'Value',param.menu_coord_val);
109else
110     set(handles.transform_fct,'Value',1);%default
111end
112if isfield(param,'FileName')
113    if isfield(param,'FileName_1')
114        update_rootfile(handles,param.FileName_1,0)
115        update_rootfile(handles,param.FileName,1)
116    else
117        update_rootfile(handles,param.FileName,0)
118    end
119end 
120
121%% fields input initialisation
122if isfield(param,'list_fields')&& isfield(param,'index_fields') &&~isempty(param.list_fields) &&~isempty(param.index_fields)
123    set(handles.FieldMenu,'String',param.list_fields);% list menu fields
124    set(handles.FieldMenu,'Value',param.index_fields);% selected string index
125    FieldCell{1}=param.list_fields{param.index_fields};
126end
127
128%REFRESH_INDICES_Callback(hObject, eventdata, handles)
129%loads the information stored in prefdir to initiate  the list of ACTION functions
130fct_menu={'check_data_files';'aver_stat';'time_series';'merge_proj';'clean_civ_cmx'};
131transform_menu={'';'phys';'px';'phys_polar'};
132nb_builtin_ACTION=numel(fct_menu); %number of functions
133nb_transform=numel(transform_menu);
134[path_series,name,ext]=fileparts(which('series'));
135path_series=fullfile(path_series,'series');%path of the function 'series'
136addpath (path_series) ; %add the path to UVMAT, (useful in case of change of working directory after civ has been s opened in the working directory)
137path_transform=fullfile(path_series,'transform_field');%path to the field transform functions
138for ilist=1:length(fct_menu)
139    fct_path{ilist,1}=path_series;%paths of the fuctions buil-in in 'series.m'
140end
141
142%% TRANSFORM menu: loads the information stored in prefdir to initiate  the list of field transform functions
143menu_str={'';'phys';'px';'phys_polar'};
144nb_builtin_transform=numel(menu_str); %number of functions
145[path_uvmat,name,ext]=fileparts(which('uvmat'));
146addpath(fullfile(path_uvmat,'transform_field'))
147fct_handle{1,1}=[];
148testexist(1)=1;
149for ilist=2:length(menu_str)
150    if exist(menu_str{ilist},'file')
151        fct_handle{ilist,1}=str2func(menu_str{ilist});
152        testexist(ilist)=1;
153    else
154        testexist(ilist)=0;
155    end
156end
157rmpath(fullfile(path_uvmat,'transform_field'))
158
159%% read the list of functions stored in the personal file 'uvmat_perso.mat' in prefdir
160if test_profil_perso
161    if isfield(h,'series_fct') && iscell(h.series_fct)
162         for ilist=1:length(h.series_fct)
163             [path,file]=fileparts(h.series_fct{ilist});
164             fct_path=[fct_path; {path}];%concatene the list of paths
165             fct_menu=[fct_menu; {file}];
166         end
167    end
168    if isfield(h,'transform_fct') && iscell(h.transform_fct)
169        for ilist=1:length(h.transform_fct);
170             [path,file]=fileparts(h.transform_fct{ilist});
171             addpath(path)
172             if exist(file,'file')
173                h_func=str2func(file);
174                testexist=[testexist 1];
175             else
176                h_func=[];
177                testexist=[testexist 0];
178             end
179             fct_handle=[fct_handle; {h_func}];%concatene the list of paths
180             rmpath(path)
181             menu_str=[menu_str; {file}];
182        end
183    end
184end
185fct_menu=[fct_menu;{'more...'}];
186set(handles.ACTION,'String',fct_menu)
187set(handles.ACTION,'UserData',fct_path)% store the list of path in UserData of ACTION
188menu_str=menu_str(find(testexist));
189fct_handle=fct_handle(find(testexist));
190menu_str=[menu_str;{'more...'}];
191set(handles.transform_fct,'String',menu_str)
192set(handles.transform_fct,'UserData',fct_handle)% store the list of path in UserData of ACTION
193
194% display the GUI for the default action 'check_data_files'
195ACTION_Callback(hObject, eventdata, handles)
196
197%--------------------------------------------------------------
198% --- Outputs from this function are returned to the command line.
199%-----------------------------------------------------------------
200function varargout = series_OutputFcn(hObject, eventdata, handles)
201% varargout  cell array for returning output args (see VARARGOUT);
202% hObject    handle to figure
203% eventdata  reserved - to be defined in a future version of MATLAB
204% handles    structure with handles and user data (see GUIDATA)
205% Get default command line output from handles structure
206varargout{1} = handles.output;
207
208% --------------------------------------------------------------------
209function MenuBrowse_Callback(hObject, eventdata, handles)
210InputTable=get(handles.InputTable,'Data');
211RootPathCell=InputTable(:,1);
212SubDirCell=InputTable(:,2);
213RootFileCell=InputTable(:,3);
214%RootPathCell=get(handles.RootPath,'String');
215%SubDirCell=get(handles.SubDir,'String'); 
216%RootFileCell=get(handles.RootFile,'String');
217oldfile=''; %default
218if isempty(RootPathCell)||isequal(RootPathCell,{''})%loads the previously stored file name and set it as default in the file_input box
219     dir_perso=prefdir;
220     profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
221     if exist(profil_perso,'file')
222          h=load (profil_perso);
223         if isfield(h,'filebase')&&ischar(h.filebase)
224                 oldfile=h.filebase;
225         end
226         if isfield(h,'RootPath')&&ischar(h.RootPath)
227                 oldfile=h.RootPath;
228         end
229     end
230 else
231     oldfile=fullfile(RootPathCell{1},SubDirCell{1},RootFileCell{1});
232 end
233[FileName, PathName, filterindex] = uigetfile( ...
234       {'*.xml;*.xls;*.png;*.tif;*.avi;*.AVI;*.nc', ' (*.xml,*.xls, *.png,*.tif, *.avi,*.nc)';
235       '*.xml',  '.xml files '; ...
236        '*.xls',  '.xls files '; ...
237        '*.png','.png image files'; ...
238        '*.tif','.tif image files'; ...
239        '*.avi;*.AVI','.avi movie files'; ...
240        '*.nc','.netcdf files'; ...
241        '*.*',  'All Files (*.*)'}, ...
242        'Pick a file',oldfile);
243fileinput=[PathName FileName];%complete file name
244%testblank=findstr(fileinput,' ');%look for blanks
245% if ~isempty(testblank)
246%     errordlg('forbidden input file name: contain blanks')
247%     return
248% end
249sizf=size(fileinput);
250if (~ischar(fileinput)|~isequal(sizf(1),1)),return;end
251[path,name,ext]=fileparts(fileinput);
252SeriesData=[];%dfault
253if isequal(ext,'.xml')
254    warndlg_uvmat('ERROR','input file type not implemented')%A Faire: ouvrir le fichier pour naviguer
255elseif isequal(ext,'.xls')
256    warndlg_uvmat('ERROR','input file type not implemented')%A Faire: ouvrir le fichier pour naviguer
257else
258    update_rootfile(handles,fileinput,0)
259     %update list of recent files in the menubar
260    MenuFile_1=fileinput;
261    MenuFile_2=get(handles.MenuFile_1,'Label');
262    MenuFile_3=get(handles.MenuFile_2,'Label');
263    MenuFile_4=get(handles.MenuFile_3,'Label');
264    MenuFile_5=get(handles.MenuFile_4,'Label');
265    set(handles.MenuFile_1,'Label',MenuFile_1)
266    set(handles.MenuFile_2,'Label',MenuFile_2)
267    set(handles.MenuFile_3,'Label',MenuFile_3)
268    set(handles.MenuFile_4,'Label',MenuFile_4)
269    set(handles.MenuFile_5,'Label',MenuFile_5)
270    set(handles.MenuFile_insert_1,'Label',MenuFile_1)
271    set(handles.MenuFile_insert_2,'Label',MenuFile_2)
272    set(handles.MenuFile_insert_3,'Label',MenuFile_3)
273    set(handles.MenuFile_insert_4,'Label',MenuFile_4)
274    set(handles.MenuFile_insert_5,'Label',MenuFile_5)
275    dir_perso=prefdir;
276    profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
277    if exist(profil_perso,'file')
278        save (profil_perso,'MenuFile_1','MenuFile_2','MenuFile_3','MenuFile_4', 'MenuFile_5','-append'); %store the file names for future opening of uvmat
279    else
280    txt=ver('MATLAB');
281    Release=txt.Release;
282        relnumb=str2num(Release(3:4));
283        if relnumb >= 14
284            save (profil_perso,'MenuFile_1','MenuFile_2','MenuFile_3','MenuFile_4', 'MenuFile_5','-V6'); %store the file names for future opening of uvmat
285        else
286            save (profil_perso,'MenuFile_1','MenuFile_2','MenuFile_3','MenuFile_4', 'MenuFile_5'); %store the file names for future opening of uvmat
287        end
288    end
289end
290
291
292% --------------------------------------------------------------------
293function MenuFile_1_Callback(hObject, eventdata, handles)
294fileinput=get(handles.MenuFile_1,'Label');
295update_rootfile(handles,fileinput,0)
296
297% --------------------------------------------------------------------
298function MenuFile_2_Callback(hObject, eventdata, handles)
299fileinput=get(handles.MenuFile_2,'Label');
300update_rootfile(handles,fileinput,0)
301
302% --------------------------------------------------------------------
303function MenuFile_3_Callback(hObject, eventdata, handles)
304fileinput=get(handles.MenuFile_3,'Label');
305update_rootfile( handles,fileinput,0)
306
307% --------------------------------------------------------------------
308function MenuFile_4_Callback(hObject, eventdata, handles)
309fileinput=get(handles.MenuFile_4,'Label');
310update_rootfile(handles,fileinput,0)
311
312% --------------------------------------------------------------------
313function MenuFile_5_Callback(hObject, eventdata, handles)
314fileinput=get(handles.MenuFile_5,'Label');
315update_rootfile(handles,fileinput,0)
316
317% --------------------------------------------------------------------
318function MenuBrowse_insert_Callback(hObject, eventdata, handles)
319InputTable=get(handles.InputTable,'Data');
320RootPathCell=InputTable(:,1);
321SubDirCell=InputTable(:,3);
322RootFileCell=InputTable(:,2);
323% RootPathCell=get(handles.RootPath,'String');
324% RootFileCell=get(handles.RootFile,'String');
325oldfile=''; %default
326if isempty(RootPathCell)||isequal(RootPathCell,{''})%loads the previously stored file name and set it as default in the file_input box
327     dir_perso=prefdir;
328     profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
329     if exist(profil_perso,'file')
330          h=load (profil_perso);
331         if isfield(h,'filebase')&ischar(h.filebase)
332                 oldfile=h.filebase;
333         end
334         if isfield(h,'RootPath')&ischar(h.RootPath)
335                 oldfile=h.RootPath;
336         end
337     end
338 else
339     oldfile=fullfile(RootPathCell{1},RootFileCell{1});
340 end
341[FileName, PathName, filterindex] = uigetfile( ...
342       {'*.xml;*.xls;*.png;*.avi;*.AVI;*.nc', ' (*.xml,*.xls, *.png, *.avi,*.nc)';
343       '*.xml',  '.xml files '; ...
344        '*.xls',  '.xls files '; ...
345        '*.png','.png image files'; ...
346        '*.avi;*.AVI','.avi movie files'; ...
347        '*.nc','.netcdf files'; ...
348        '*.*',  'All Files (*.*)'}, ...
349        'Pick a file',oldfile);
350fileinput=[PathName FileName];%complete file name
351% testblank=findstr(fileinput,' ');%look for blanks
352% if ~isempty(testblank)
353%     errordlg('forbidden input file name: contain blanks')
354%     return
355% end
356sizf=size(fileinput);
357if (~ischar(fileinput)|~isequal(sizf(1),1)),return;end
358[path,name,ext]=fileparts(fileinput);
359SeriesData=[];%dfault
360if isequal(ext,'.xml')
361    msgbox_uvmat('ERROR','input file type not implemented')%A Faire: ouvrir le fichier pour naviguer
362elseif isequal(ext,'.xls')
363    msgbox_uvmat('ERROR','input file type not implemented')%A Faire: ouvrir le fichier pour naviguer
364else
365    update_rootfile(handles,fileinput,1)
366    %update list of recent files in the menubar
367    MenuFile_1=fileinput;
368    MenuFile_2=get(handles.MenuFile_1,'Label');
369    MenuFile_3=get(handles.MenuFile_2,'Label');
370    MenuFile_4=get(handles.MenuFile_3,'Label');
371    MenuFile_5=get(handles.MenuFile_4,'Label');
372    set(handles.MenuFile_1,'Label',MenuFile_1)
373    set(handles.MenuFile_2,'Label',MenuFile_2)
374    set(handles.MenuFile_3,'Label',MenuFile_3)
375    set(handles.MenuFile_4,'Label',MenuFile_4)
376    set(handles.MenuFile_5,'Label',MenuFile_5)
377    set(handles.MenuFile_insert_1,'Label',MenuFile_1)
378    set(handles.MenuFile_insert_2,'Label',MenuFile_2)
379    set(handles.MenuFile_insert_3,'Label',MenuFile_3)
380    set(handles.MenuFile_insert_4,'Label',MenuFile_4)
381    set(handles.MenuFile_insert_5,'Label',MenuFile_5)
382    dir_perso=prefdir;
383    profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
384    if exist(profil_perso,'file')
385        save (profil_perso,'MenuFile_1','MenuFile_2','MenuFile_3','MenuFile_4', 'MenuFile_5','-append'); %store the file names for future opening of uvmat
386    else
387    txt=ver('MATLAB');
388    Release=txt.Release;
389        relnumb=str2num(Release(3:4));
390        if relnumb >= 14
391            save (profil_perso,'MenuFile_1','MenuFile_2','MenuFile_3','MenuFile_4', 'MenuFile_5','-V6'); %store the file names for future opening of uvmat
392        else
393            save (profil_perso,'MenuFile_1','MenuFile_2','MenuFile_3','MenuFile_4', 'MenuFile_5'); %store the file names for future opening of uvmat
394        end
395    end
396end
397%------------------------------------------------
398
399% --------------------------------------------------------------------
400function MenuFile_insert_1_Callback(hObject, eventdata, handles)
401fileinput=get(handles.MenuFile_insert_1,'Label');
402update_rootfile(handles,fileinput,1)
403
404% --------------------------------------------------------------------
405function MenuFile_insert_2_Callback(hObject, eventdata, handles)
406fileinput=get(handles.MenuFile_insert_2,'Label');
407update_rootfile(handles,fileinput,1)
408
409% --------------------------------------------------------------------
410function MenuFile_insert_3_Callback(hObject, eventdata, handles)
411fileinput=get(handles.MenuFile_insert_3,'Label');
412update_rootfile( handles,fileinput,1)
413
414% --------------------------------------------------------------------
415function MenuFile_insert_4_Callback(hObject, eventdata, handles)
416fileinput=get(handles.MenuFile_insert_4,'Label');
417update_rootfile( handles,fileinput,1)
418
419% --------------------------------------------------------------------
420function MenuFile_insert_5_Callback(hObject, eventdata, handles)
421fileinput=get(handles.MenuFile_insert_5,'Label');
422update_rootfile(handles,fileinput,1)
423
424%------------------------------------------------------------------------
425% ---  refresh the GUI data after introduction of a new file series
426% INPUT:
427% handles:
428% fileinput: name of the input file
429% addtest: =0 to refresh the list of file series, =1 to append a new series to the list (from the menu bar option 'Open_insert')
430function update_rootfile(handles,fileinput,addtest)
431%------------------------------------------------------------------------ 
432
433%% enable other menus and uicontrols
434set(handles.MenuOpen_insert,'Enable','on')
435set(handles.MenuFile_insert_1,'Enable','on')
436set(handles.MenuFile_insert_2,'Enable','on')
437set(handles.MenuFile_insert_3,'Enable','on')
438set(handles.MenuFile_insert_4,'Enable','on')
439set(handles.MenuFile_insert_5,'Enable','on')
440set(handles.RUN, 'Enable','On')
441set(handles.RUN,'BackgroundColor',[1 0 0])% set RUN button to red
442% set(handles.RootPath,'BackgroundColor',[1 1 0]) % set RootPath edit box  to yellow
443set(handles.InputTable,'BackgroundColor',[1 1 0]) % set RootPath edit box  to yellow
444drawnow
445
446%% get the input root name, indices, file extension and nomenclature NomType
447if ~exist(fileinput,'file')
448    msgbox_uvmat('ERROR',['input file ' fileinput  ' does not exist'])
449    return
450end
451[RootPath,SubDir,RootFile,i1,i2,j1,j2,FileExt,NomType]=fileparts_uvmat(fileinput);
452
453%% fill the list of file series
454InputTable=get(handles.InputTable,'Data');
455if addtest % display the input data as a new line in the table
456     val=size(InputTable,1)+1;
457     InputTable(val,:)=[{RootPath},{SubDir},{RootFile},{NomType},{FileExt}];
458    check_lines=get(handles.REFRESH_INDICES,'UserData');
459else % or re-initialise the list of  input  file series
460    val=1;
461    InputTable=[{RootPath},{SubDir},{RootFile},{NomType},{FileExt}];
462    set(handles.TimeTable,'Data',[{[]},{[]},{[]},{[]}])
463    set(handles.MinIndex,'Data',[{[]},{[]}])
464    set(handles.MaxIndex,'Data',[{[]},{[]}])
465end
466set(handles.InputTable,'Data',InputTable)
467check_lines(val)=1; %select the edited line for refresh
468set(handles.REFRESH_INDICES,'UserData',check_lines);
469
470%% refresh menus with info from the new series
471REFRESH_INDICES_Callback([],[], handles)
472
473%% determine the selected reference field indices for pair dispaly
474ref_i=1; %default ref_i is a reference frame index used to find existing pairs from PIV
475if ~isempty(i1)
476    ref_i=i1;
477    if ~isempty(i2)
478        ref_i=floor((ref_i+i2)/2);% reference image number corresponding to the file
479    end
480end
481set(handles.ref_i,'String',num2str(ref_i));
482ref_j=1; %default  ref_j is a reference frame index used to find existing pairs from PIV
483if ~isempty(j1)
484    ref_j=j1;
485    if ~isempty(j2)
486        ref_j=floor((j1+j2)/2);
487    end         
488end
489set(handles.ref_j,'String',num2str(ref_j));
490ref_i_Callback([],[], handles)
491ref_j_Callback([],[], handles)
492
493%% update the first and last reference indices if empty
494first_i=str2num(get(handles.num_first_i,'String'));
495if isempty(first_i)
496set(handles.num_first_i,'String',num2str(ref_i));
497set(handles.num_last_i,'String',num2str(ref_i));
498set(handles.num_first_j,'String',num2str(ref_j))
499set(handles.num_last_j,'String',num2str(ref_j));
500end
501
502%% store the root name for future opening of uvmat
503dir_perso=prefdir;
504profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
505if exist(profil_perso,'file')
506    save (profil_perso,'RootPath','SubDir','RootFile','NomType', '-append'); %store the root name for future opening of uvmat
507else
508    txt=ver('MATLAB');
509    Release=txt.Release;
510    relnumb=str2num(Release(3:4));
511    if relnumb >= 14
512        save (profil_perso,'RootPath','SubDir','RootFile','NomType','-V6') %store the root name for future opening of uvmat
513    else
514        save(profil_perso,'RootPath','SubDir','RootFile','NomType')
515    end         
516end
517set(handles.InputTable,'BackgroundColor',[1 1 1])
518% set(handles.PathCampaign,'String',SeriesData.PathCampaign)
519%num_last_j_Callback([], [], handles)% TODO:update
520%num_last_i_Callback([], [], handles)
521
522
523% --- Executes when entered data in editable cell(s) in InputTable.
524function InputTable_CellEditCallback(hObject, eventdata, handles)
525% hObject    handle to InputTable (see GCBO)
526% eventdata  structure with the following fields (see UITABLE)
527%       Indices: row and column indices of the cell(s) edited
528%       PreviousData: previous data for the cell(s) edited
529%       EditData: string(s) entered by the user
530%       NewData: EditData or its converted form set on the Data property. Empty if Data was not changed
531%       Error: error string when failed to convert EditData to appropriate value for Data
532% handles    structure with handles and user data (see GUIDATA)
533check_lines=get(handles.REFRESH_INDICES,'UserData');
534check_lines(eventdata.Indices(1))=1; %select the edited line for refresh
535set(handles.REFRESH_INDICES,'UserData',check_lines);
536set(handles.REFRESH_INDICES,'Visible','on')
537
538
539%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%????????????
540% --- Executes on button press in mode.
541%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
542function mode_Callback(hObject, eventdata, handles)
543       
544SeriesData=get(handles.series,'UserData');
545mode_list=get(handles.mode,'String');
546mode_value=get(handles.mode,'Value');
547mode=mode_list{mode_value};
548time=[];
549if isfield(SeriesData,'Time')
550    time=SeriesData.Time{1}; %get the set of times
551end
552if isequal(mode,'bursts')
553    enable_i(handles,'On')
554    enable_j(handles,'Off') %do not display j index scanning in burst mode (j is fixed by the burst choice)
555else
556    enable_i(handles,'On')
557    enable_j(handles,'Off')
558end
559find_netcpair_civ(handles)
560
561%-------------------------------------
562function enable_i(handles,state)
563set(handles.i_txt,'Visible',state)
564set(handles.num_first_i,'Visible',state)
565set(handles.num_last_i,'Visible',state)
566set(handles.num_incr_i,'Visible',state)
567% set(handles.num_MaxIndex_i,'Visible',state)
568set(handles.ref_i,'Visible',state)
569set(handles.ref_i_text,'Visible',state)
570
571%-----------------------------------
572function enable_j(handles,state)
573set(handles.j_txt,'Visible',state)
574% set(handles.num_MinIndex_j,'Visible',state)
575set(handles.num_first_j,'Visible',state)
576set(handles.num_last_j,'Visible',state)
577set(handles.num_incr_j,'Visible',state)
578% set(handles.num_MaxIndex_j,'Visible',state)
579set(handles.ref_j,'Visible',state)
580set(handles.ref_j_text,'Visible',state)
581
582%-----------------------------------
583function view_FieldMenu(handles,state)
584% set(handles.FieldMenu,'Visible',state)
585% set(handles.Field_text,'Visible',state)
586set(handles.InputFields,'Visible',state)
587
588%-----------------------------------
589function view_FieldMenu_1(handles,state)
590set(handles.FieldMenu_1,'Visible',state)
591set(handles.Field_text_1,'Visible',state)
592
593% %-----------------------------------
594% function view_TRANSFORM(handles,state)
595% set(handles.TRANSFORM_frame,'Visible',state)
596% set(handles.transform_fct,'Visible',state);
597% set(handles.TRANSFORM_title,'Visible',state)
598
599%--------------------------------------------------------------
600% determine the menu for civ1 pairs depending on existing netcdf files
601% with the reference indices ref_i and ref_j
602%----------------------------------------------------------------
603function find_netcpair_civ(handles)
604SeriesData=get(handles.series,'UserData');
605set(handles.Pairs,'Visible','on')% makes the panel "Pairs' visible
606mode_list=get(handles.mode,'String');
607mode_value=get(handles.mode,'Value');
608mode=mode_list{mode_value};
609
610%reads image numbers from the interface
611% ref_i=str2num(get(handles.ref_i,'String'));
612% ref_j=str2num(get(handles.ref_j,'String'));
613% ref_time=0;
614% nbfield=50;
615% nbfield2=50;%default max number of pairs
616
617%look for existing processed pairs involving the field at the middle of the series if civ1 will not
618% be performed, while the result is needed for next steps.
619
620% ind_exist=0;
621TimeUnit=get(handles.TimeUnit,'String');
622if length(TimeUnit)>=1
623    dtunit=['m' TimeUnit];
624else
625    dtunit='e-03';
626end
627
628%% NEW
629for Val=1:numel(SeriesData.i1_series)
630   
631i1_series=SeriesData.i1_series{Val};
632i2_series=SeriesData.i2_series{Val};
633j1_series=SeriesData.j1_series{Val};
634j2_series=SeriesData.j2_series{Val};
635displ_pair={};
636if strcmp(mode,'series(Di)')
637    if isempty(i2_series)
638        msgbox_uvmat('ERROR','no i1-i2 pair available')
639        return
640    end
641    diff_i=i2_series-i1_series;
642    min_diff=min(diff_i(diff_i>0));
643    max_diff=max(diff_i(diff_i>0));
644    for ipair=min_diff:max_diff
645        if numel(diff_i(diff_i==ipair))>0
646            displ_pair=[displ_pair;{['Di= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2)) ]}];
647        end
648    end
649    if ~isempty(displ_pair)
650        displ_pair=[displ_pair;{'Di=*|*'}];
651    end
652elseif strcmp(mode,'series(Dj)')
653    if isempty(j2_series)
654        msgbox_uvmat('ERROR','no j1-j2 pair available')
655        return
656    end
657    diff_j=j2_series-j1_series;
658    min_diff=min(diff_j(diff_j>0));
659    max_diff=max(diff_j(diff_j>0));
660    for ipair=min_diff:max_diff
661        if numel(diff_j(diff_j==ipair))>0
662            displ_pair=[displ_pair;{['Dj= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2)) ]}];
663        end
664    end
665    if ~isempty(displ_pair)
666        displ_pair=[displ_pair;{'Dj=*|*'}];
667    end
668elseif strcmp(mode,'bursts')
669    if isempty(j2_series)
670        msgbox_uvmat('ERROR','no j1-j2 pair available')
671        return
672    end
673    diff_j=j2_series-j1_series;
674    min_j1=min(j1_series(j1_series>0));
675    max_j1=max(j1_series(j1_series>0));
676    min_j2=min(j2_series(j2_series>0));
677    max_j2=max(j2_series(j2_series>0));
678    for pair1=min_j1:min(max_j1,min_j1+20)
679        for pair2=min_j2:min(max_j2,min_j2+20)
680        if numel(j1_series(j1_series==pair1))>0 && numel(j2_series(j2_series==pair2))>0
681            displ_pair=[displ_pair;{['j= ' num2str(pair1) '-' num2str(pair2)]}];
682        end
683        end
684    end
685    if ~isempty(displ_pair)
686        displ_pair=[displ_pair;{'j=*-*'}];
687    end
688end
689end
690%% display list of pairs
691displ_pair_list=get(handles.list_pair_civ,'String');
692NewVal=[];
693if ~isempty(displ_pair_list)
694Val=get(handles.list_pair_civ,'Value');
695NewVal=find(strcmp(displ_pair_list{Val},displ_pair),1);% look at the previous display in the new menu displ_pâir
696end
697if ~isempty(NewVal)
698    set(handles.list_pair_civ,'Value',NewVal)
699else
700    set(handles.list_pair_civ,'Value',1)
701end
702set(handles.list_pair_civ,'String',displ_pair)
703if isempty(displ_pair)
704    msgbox_uvmat('ERROR',['no file available for the selected subdirectory ' subdir])
705end
706return
707%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%END FUNCTION
708
709
710if ind_exist==0
711         if  isequal(mode,'series(Dj)') | isequal(mode,'st_series(Dj)')
712            msgbox_uvmat('ERROR',['no .nc file available for the selected reference index j=' num2str(ref_j) ' and subdirectory ' subdir])
713        else
714            msgbox_uvmat('ERROR',['no .nc file available for the selected reference index i=' num2str(ref_i) ' and subdirectory ' subdir])
715        end
716        if isequal(mode,'bursts') %case of bursts
717            set(handles.list_pair_civ,'String',{'j=*-*'});
718        elseif isequal(mode,'series(Di)') %case of bursts
719            set(handles.list_pair_civ,'String',{'Di=*|*'});
720        elseif isequal(mode,'series(Dj)') %case of bursts
721            set(handles.list_pair_civ,'String',{'Dj=*|*'});
722        end
723end
724return
725%TO update
726val=get(handles.list_pair_civ,'Value');
727if val > length(displ_pair)
728    set(handles.list_pair_civ,'Value',1);% first pair proposed by default in the menu
729    val=1;
730end
731iview=get(handles.NomType,'Value');
732SeriesData.displ_num(iview,:)=(displ_num(:,val))';
733SeriesData.ref_time=ref_time;
734set(handles.series,'UserData',SeriesData)
735list_pair_civ_Callback([],[],handles)
736
737%-------------------------------------------------------------
738% --- Executes on selection in list_pair_civ.
739function list_pair_civ_Callback(hObject,eventdata,handles)
740%------------------------------------------------------------
741return
742%%%%%%%%
743%update num_first_i and num_last_i according to the chosen image pairs
744testupdate=0;
745Val=get(handles.RootPath,'Value');
746IndexCell=get(handles.NomType,'String');
747SeriesData=get(handles.series,'UserData');
748NomType=SeriesData.NomType{Val};
749list_pair=get(handles.list_pair_civ,'String');%get the menu of image pairs
750index_pair=get(handles.list_pair_civ,'Value');
751str_pair=list_pair{index_pair};
752ind_equ=strfind(str_pair,'=');%find '='
753ind_sep=strfind(str_pair,'|');%find pair separator '|'
754ind_com=strfind(str_pair,':');%find ':'
755test_bursts=0;
756if isempty(ind_sep)
757    ind_sep=strfind(str_pair,'-');%find pair separator if it is not '|'
758    test_bursts=1;% we are in the case of bursts
759end
760displ_num=[0 0 0 0]; %default
761if ~isempty(ind_sep)&& ~strcmp(str_pair(ind_sep-1),'*')% if there is a pair separator ('|' or '-')
762    num1_str=str_pair(ind_equ(1)+1:ind_sep-1);
763    num2_str=str_pair(ind_sep+1:ind_com-1);
764    num1=str2double(num1_str);
765    num2=str2double(num2_str);
766    if isequal(num1_str(1),' ')
767        num1_str(1)=[];
768    end   
769    if isequal(num2_str(end),' ')
770        num2_str(end)=[];
771    end
772    switch NomType
773       case {'_1-2_1'}
774           if isequal(num1_str(1),'0')
775               IndexCell{Val}=['_(i-(i+' num2_str ')_j'];
776           else
777               IndexCell{Val}=['_(i' num1_str ')-(i+' num2_str ')_j'];
778           end
779           displ_num(3)=num1;
780           displ_num(4)=num2;
781       case {'_1-2'}
782           if isequal(num1_str(1),'0')
783               IndexCell{Val}=['_(i' num1_str ')-(i+' num2_str ')'];
784           else
785               IndexCell{Val}=['_(i' num1_str ')-(i+' num2_str ')'];
786           end
787           displ_num(3)=num1;
788           displ_num(4)=num2;
789       case '_1_1-2'
790          if test_bursts
791              IndexCell{Val}=['_i_' num1_str '-' num2_str ];
792          else
793              if isequal(num1_str(1),'0')
794                 IndexCell{Val}=['_i_j-(j+' num2_str ')'];
795              else
796                 IndexCell{Val}=['_i_(j' num1_str ')-(j+' num2_str ')'];
797              end
798          end
799          displ_num(1)=num1;
800          displ_num(2)=num2;
801       case {'#_ab'} %TO COMPLETE
802           IndexCell{Val}=['_i_' num1_str '-' num2_str ];
803
804    end
805end
806set(handles.NomType,'String',IndexCell)
807SeriesData.displ_num(Val,:)=displ_num;
808set(handles.series,'UserData',SeriesData)
809% set(handles.NomType,'Value',Val)
810
811if ~isequal(str_pair,'Dj=*|*')&~isequal(str_pair,'Di=*|*')
812        mode_list=get(handles.mode,'String');
813    mode_value=get(handles.mode,'Value');
814    mode=mode_list{mode_value};
815        if isequal(mode,'series(Di)')
816        first_i=str2num(get(handles.num_first_i,'String'));
817        last_i=str2num(get(handles.num_last_i,'String'));
818        incr_i=str2num(get(handles.num_incr_i,'String'));
819        num1=first_i:incr_i:last_i;
820        lastfieldCell=get(handles.num_MaxIndex_i,'String');
821        lastfield=str2num(lastfieldCell{1});
822        if ~isempty(lastfield)
823            ind=find((num1-floor(index_pair/2)*ones(size(num1))>0)& (num1+ceil(index_pair/2)*ones(size(num1))<=lastfield));
824            num1=num1(ind);       
825        end
826        if ~isempty(num1)
827            set(handles.num_first_i,'String',num2str(num1(1)));
828            set(handles.num_last_i,'String',num2str(num1(end)));
829        end
830        testupdate=1;
831        elseif isequal(mode,'series(Dj)')
832        first_j=str2num(get(handles.num_first_j,'String'));
833        last_j=str2num(get(handles.num_last_j,'String'));
834        incr_j=str2num(get(handles.num_incr_j,'String'));
835        num_j=first_j:incr_j:last_j;
836        lastfieldCell=get(handles.num_MaxIndex_j,'String');
837        if ~isempty(lastfieldCell)
838            lastfield2=lastfieldCell{1};
839            ind=find((num_j-floor(index_pair/2)*ones(size(num_j))>0)& ...
840                 (num_j+ceil(index_pair/2)*ones(size(num_j))<=lastfield2));
841        end
842        testupdate=1;
843        end
844       
845        %update the first and last times of the series
846        if testupdate && isfield(SeriesData,'Time')
847        if ~isempty(SeriesData.Time{1})
848            displ_time(handles);
849        end
850        end
851end
852
853%------------------------------------------------------------------------
854% --- Executes on button press in RUN.
855function RUN_Callback(hObject, eventdata, handles)
856%------------------------------------------------------------------------
857%% Read parameters from series
858Series=read_GUI(handles.series);%TODO: extend to all input param
859Series.hseries=handles.series; % handles to the series GUI
860
861%% read root name and field type
862set(handles.RUN,'BusyAction','queue');
863set(0,'CurrentFigure',handles.series)
864if isequal(get(handles.GetObject,'Visible'),'on') && isequal(get(handles.GetObject,'Value'),1)
865    Series.GetObject=1;
866    GetObject_Callback(hObject, eventdata, handles)
867else
868    Series.GetObject=0;
869end
870% SeriesData=get(handles.series,'UserData');
871
872% Series.hseries=handles.series; % handles to the series GUI
873   first_i=1;
874   last_i=1;
875   incr_i=1;
876       first_j=1;
877    last_j=1;
878    incr_j=1;
879if isfield(Series.IndexRange,'first_i')
880    first_i=Series.IndexRange.first_i;
881    incr_i=Series.IndexRange.incr_i;
882    last_i=Series.IndexRange.last_i;
883end
884if isfield(Series.IndexRange,'first_j')
885    first_j=Series.IndexRange.first_j;
886    incr_j=Series.IndexRange.incr_j;
887    last_j=Series.IndexRange.last_j;
888end
889
890%% read input file parameters and set menus
891Series.PathProject=get(handles.PathCampaign,'String');
892% InputTable=get(handles.InputTable,'Data');
893% RootPath=Series.InputTable(:,1);
894% SubDir=Series.InputTable(:,2);
895% RootFile=Series.InputTable(:,3);
896% NomType=Series.InputTable(:,4);
897% FileExt=Series.InputTable(:,5);
898% if isempty(SeriesData)
899%     msgbox_uvmat('ERROR','no input file series')
900%     return
901% end
902% NomType=SeriesData.NomType;
903% if length(RootPath)==1 %string character input for user fct
904%     Series.RootPath=RootPath{1};
905%     Series.RootFile=RootFile{1};
906%     Series.SubDir=SubDir{1};
907%     Series.FileExt=FileExt{1};
908%     Series.NomType=NomType{1};
909% else %cell input for user fct
910%     Series.RootPath=RootPath;
911%     Series.RootFile=RootFile;
912%     Series.SubDir=SubDir;
913%     Series.FileExt=FileExt;
914%     Series.NomType=NomType;
915% end
916% if isequal(get(handles.FieldMenu,'Visible'),'on')
917%     FieldMenu=get(handles.FieldMenu,'String');
918%     FieldValue=get(handles.FieldMenu,'Value');
919%     Series.Field=FieldMenu(FieldValue);
920% end
921menu_coord_state=get(handles.transform_fct,'Visible');
922Series.CoordType='';%default
923if isequal(menu_coord_state,'on')
924%     menu_coord=get(handles.transform_fct,'String');
925    menu_index=get(handles.transform_fct,'Value');
926    transform_list=get(handles.transform_fct,'UserData');
927    Series.FieldTransform.fct_handle=transform_list{menu_index};% transform function handles
928end
929
930%reinitiate waitbar position
931Series.WaitbarPos=get(handles.waitbar_frame,'Position');%TO SUPPRESS
932waitbarpos=Series.WaitbarPos;
933waitbarpos(4)=0.005;%reinitialize waitbar to zero height
934waitbarpos(2)=Series.WaitbarPos(2)+Series.WaitbarPos(4)-0.005;
935% set(handles.waitbar,'Position',waitbarpos)
936
937if isfield(Series.IndexRange,'NbSlice')
938Series.NbSlice=Series.IndexRange.NbSlice;
939end
940if last_i < first_i | last_j < first_j , msgbox_uvmat('ERROR','last field number must be larger than the first one'),...
941    set(handles.RUN, 'Enable','On'), set(handles.RUN,'BackgroundColor',[1 0 0]),return,end;
942num_i=first_i:incr_i:last_i;
943num_j=first_j:incr_j:last_j;
944% nbfield_cell=get(handles.num_MaxIndex_i,'String');
945nbfield=cell2mat(Series.IndexRange.MaxIndex);
946nb=min(nbfield,1);
947% nbfield=nb(1);
948% nbfield2=nb(2);
949
950%get complementary information from the 'series' interface
951list_action=get(handles.ACTION,'String');% list menu action
952index_action=get(handles.ACTION,'Value');% selected string index
953action= list_action{index_action}; % selected string
954mode_list=get(handles.mode,'String');
955index_mode=get(handles.mode,'Value');
956mode=mode_list{index_mode};
957ind_shift=0;%default
958
959
960%% defining the ACTION function handle
961path_series=which('series');
962list_path=get(handles.ACTION,'UserData');
963index=get(handles.ACTION,'Value');
964fct_path=list_path{index}; %path stored for the function ACTION
965if ~isequal(fct_path,path_series)
966    eval(['spath=which(''' action ''');']) %spath = current path of the selected function ACTION
967    if ~exist(fct_path,'dir')
968        msgbox_uvmat('ERROR',['The prescibed function path ' fct_path ' does not exist'])
969        return
970    end
971    if ~isequal(spath,fct_path)
972        addpath(fct_path)% add the prescribed path if not the current one
973    end
974end
975eval(['h_fun=@' action ';'])%create a function handle for ACTION
976if ~isequal(fct_path,path_series)
977        rmpath(fct_path)% add the prescribed path if not the current one   
978end
979
980%% RUN ACTION
981Series.Action=action;%name of the processing programme
982set(handles.RUN,'BackgroundColor',[0.831 0.816 0.784])
983h_fun(Series);
984% if length(RootPath)>1
985%     h_fun(i1_series_cell,i2_series_cell,j1_series_cell,j2_series_cell,Series);
986% else
987%     h_fun(i1_series,i2_series,j1_series,j2_series,Series);
988% end
989set(handles.RUN,'BackgroundColor',[1 0 0])
990
991% %save the current interface setting as figure namefig, append .0 to the name if it already exists
992% detect=1;
993% while detect==1
994%     namefigfull=[namedoc '.fig'];
995%     hh=dir(namefigfull);
996%     if ~isempty(hh)
997%         detect=1;
998%         namedoc=[namedoc '.0'];
999%     else
1000%         detect=0;
1001%     end
1002% end
1003% saveas(gcbf,namefigfull);%save the interface with name namefigfull (A CHANGER EN FICHIER  .xml)
1004
1005%------------------------------------------------------------------------
1006function STOP_Callback(hObject, eventdata, handles)
1007%------------------------------------------------------------------------
1008set(handles.RUN, 'BusyAction','cancel')
1009set(handles.RUN,'BackgroundColor',[1 0 0])
1010
1011
1012%------------------------------------------------------------------------
1013function num_first_i_Callback(hObject, eventdata, handles)
1014%------------------------------------------------------------------------
1015num_last_i_Callback(hObject, eventdata, handles)
1016
1017%------------------------------------------------------------------------
1018function num_last_i_Callback(hObject, eventdata, handles)
1019%------------------------------------------------------------------------
1020SeriesData=get(handles.series,'UserData');
1021if ~isfield(SeriesData,'Time')
1022    SeriesData.Time{1}=[];
1023end
1024displ_time(handles);
1025
1026%------------------------------------------------------------------------
1027function num_first_j_Callback(hObject, eventdata, handles)
1028%------------------------------------------------------------------------
1029 num_last_j_Callback(hObject, eventdata, handles)
1030
1031%------------------------------------------------------------------------
1032function num_last_j_Callback(hObject, eventdata, handles)
1033%------------------------------------------------------------------------
1034first_j=str2num(get(handles.num_first_j,'String'));
1035last_j=str2num(get(handles.num_last_j,'String'));
1036ref_j=ceil((first_j+last_j)/2);
1037set(handles.ref_j,'String', num2str(ref_j))
1038ref_j_Callback(hObject, eventdata, handles)
1039SeriesData=get(handles.series,'UserData');
1040if ~isfield(SeriesData,'Time')
1041    SeriesData.Time{1}=[];
1042end
1043displ_time(handles);
1044
1045
1046%------------------------------------------------------------------------
1047function ref_i_Callback(hObject, eventdata, handles)
1048%------------------------------------------------------------------------
1049mode_list=get(handles.mode,'String');
1050mode_value=get(handles.mode,'Value');
1051mode=mode_list{mode_value};
1052SeriesData=get(handles.series,'UserData');
1053% if ~isempty(SeriesData)
1054if ~isempty(SeriesData.i2_series)||~isempty(SeriesData.j2_series)
1055    if isequal(mode,'series(Di)')
1056        find_netcpair_civ(handles);% update the menu of pairs depending on the available netcdf files
1057    end
1058end
1059% end
1060
1061%------------------------------------------------------------------------
1062function ref_j_Callback(hObject, eventdata, handles)
1063%------------------------------------------------------------------------
1064mode_list=get(handles.mode,'String');
1065mode_value=get(handles.mode,'Value');
1066mode=mode_list{mode_value};
1067SeriesData=get(handles.series,'UserData');
1068if ~isempty(SeriesData)
1069if ~isempty(SeriesData.i2_series)||~isempty(SeriesData.j2_series)
1070    if isequal(mode,'series(Di)')
1071        find_netcpair_civ(handles);% update the menu of pairs depending on the available netcdf files
1072    end
1073end
1074end
1075% NomTypeCell=SeriesData.NomType;
1076% if ~isempty(NomTypeCell)
1077%     Val=get(handles.NomType,'Value');
1078%     NomType=NomTypeCell{Val};
1079%     if isequal(NomType,'_1_1-2')|| isequal(NomType,'_1-2_1')|| isequal(NomType,'_1-2')
1080%         if isequal(mode,'series(Dj)')
1081%             find_netcpair_civ(handles,Val);% update the menu of pairs depending on the available netcdf files
1082%         end
1083%     end
1084% end
1085
1086%------------------------------------------------------------------------
1087% --- Executes on selection change in ACTION.
1088function ACTION_Callback(hObject, eventdata, handles)
1089%------------------------------------------------------------------------
1090global nb_builtin_ACTION
1091list_ACTION=get(handles.ACTION,'String');% list menu fields
1092index_ACTION=get(handles.ACTION,'Value');% selected string index
1093ACTION= list_ACTION{index_ACTION}; % selected function name
1094path_series=which('series');%path to series.m
1095list_path=get(handles.ACTION,'UserData');%list of recorded paths to functions of the list ACTION
1096default_file=fullfile(list_path{end},ACTION);
1097% add a new function to the menu if the selected item is 'more...'
1098if isequal(ACTION,'more...')
1099    pathfct=fileparts(path_series);
1100    [FileName, PathName, filterindex] = uigetfile( ...
1101       {'*.m', ' (*.m)';
1102        '*.m',  '.m files '; ...
1103        '*.*', 'All Files (*.*)'}, ...
1104        'Pick a file',default_file);
1105    if length(FileName)<2
1106        return
1107    end
1108    [pp,ACTION,ext_fct]=fileparts(FileName);%(end-1:end);
1109    if ~isequal(ext_fct,'.m')
1110        msgbox_uvmat('ERROR','a Matlab function .m must be introduced');
1111        return
1112    end
1113   
1114   % insert the choice in the action menu
1115   menu_str=update_menu(handles.ACTION,ACTION);%new action menu in which the new item has been appended if needed
1116   index_ACTION=get(handles.ACTION,'Value');% currently selected index in the list
1117   list_path{index_ACTION}=PathName;
1118   if length(menu_str)>nb_builtin_ACTION+5; %nb_builtin=nbre of functions always remaining in the initial menu
1119       nbremove=length(menu_str)-nb_builtin_ACTION-5;
1120       menu_str(nb_builtin_ACTION+1:end-5)=[];
1121       list_path(nb_builtin_ACTION+1:end-4)=[];
1122       index_ACTION=index_ACTION-nbremove;
1123       set(handles.ACTION,'Value',index_ACTION)
1124       set(handles.ACTION,'String',menu_str)
1125   end
1126   list_path{index_ACTION}=PathName;
1127   set(handles.ACTION,'UserData',list_path);
1128   set(handles.path,'enable','inactive')% indicate that the current path is accessible (not 'off')
1129   
1130   %record the current menu in personal file profil_perso
1131   dir_perso=prefdir;
1132   profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
1133   for ilist=nb_builtin_ACTION+1:length(menu_str)-1
1134       series_fct{ilist-nb_builtin_ACTION}=fullfile(list_path{ilist},[menu_str{ilist} '.m']);     
1135   end
1136   if nb_builtin_ACTION+1<=length(menu_str)-1
1137       if exist(profil_perso,'file')% && nb_builtin_ACTION+1>=length(menu_str)-1
1138           save(profil_perso,'series_fct','-append')
1139       else
1140           txt=ver('MATLAB');
1141           Release=txt.Release;
1142           relnumb=str2num(Release(3:4));
1143           if relnumb >= 14%recent relaese of Matlab
1144               save(profil_perso,'series_fct','-V6')
1145           else
1146               save(profil_perso, 'series_fct')
1147           end
1148       end
1149   end
1150end
1151
1152%check the current path to the selected function
1153PathName=list_path{index_ACTION};%current recorded path
1154set(handles.path,'String',PathName); %show the path to the senlected function
1155
1156%default setting for the visibility of the GUI elements
1157% set(handles.RootPath,'UserData','many')
1158% set(handles.SubDir,'Visible','on')
1159% set(handles.RootFile,'Visible','on')
1160% set(handles.NomType,'Visible','on')
1161% set(handles.FileExt,'Visible','on')
1162set(handles.num_NbSlice,'Visible','off')
1163set(handles.NbSlice_title,'Visible','off')
1164set(handles.VelTypeMenu,'Visible','off');
1165set(handles.VelType_text,'Visible','off');
1166set(handles.VelTypeMenu_1,'Visible','off');
1167set(handles.VelType_text_1,'Visible','off');
1168view_FieldMenu(handles,'off')
1169view_FieldMenu_1(handles,'off')
1170set(handles.FieldTransform,'Visible','off')
1171% view_TRANSFORM(handles,'off')Visible','off')
1172set(handles.Objects,'Visible','off');
1173set(handles.GetMask,'Visible','off')
1174set(handles.Mask,'Visible','off')
1175% set(handles.GetObject,'Visible','off');
1176set(handles.OutputDir,'Visible','off');
1177% set(handles.PARAMETERS_frame,'Visible','off');
1178% set(handles.PARAMETERS_title,'Visible','off');
1179set(handles.ParamKey,'Visible','off')
1180set(handles.ParamVal,'Visible','off')
1181ParamKey={};
1182set(handles.FieldMenu,'Enable','off')
1183set(handles.VelTypeMenu,'Enable','off')
1184set(handles.FieldMenu_1,'Enable','off')
1185set(handles.VelTypeMenu_1,'Enable','off')
1186set(handles.transform_fct,'Enable','off')
1187%set the displayed GUI item needed for input parameters
1188if ~isequal(path_series,PathName)
1189    addpath(PathName)
1190end
1191eval(['h_function=@' ACTION ';']);
1192try
1193    [fid,errormsg] =fopen([ACTION '.m']);
1194    InputText=textscan(fid,'%s',1,'delimiter','\n');
1195    fclose(fid)
1196    set(handles.ACTION,'ToolTipString',InputText{1}{1})
1197end
1198if ~isequal(path_series,PathName)
1199    rmpath(PathName)
1200end
1201varargout=h_function();
1202Param_list={};
1203
1204%nb_series=length(RootFile);
1205% FileExt=get(handles.FileExt,'String');
1206% nb_series=length(FileExt);
1207InputTable=get(handles.InputTable,'Data');
1208nb_series=size(InputTable,1);
1209% if ~isempty(checkcell)
1210% nb_series=checkcell(end);
1211% end
1212% nb_series=size(InputFiles,1)
1213testima_series=1; %test for a list of images only
1214testima=1;
1215testima_1=1;
1216testciv_series=1;
1217for iview=1:nb_series
1218     ext=InputTable{iview,5};
1219    if length(ext)<2
1220        ext='.none';
1221    end
1222    testimaview=~isempty(imformats(ext(2:end))) || isequal(lower(ext),'.avi');
1223    if ~testimaview
1224        if iview==1
1225            testima=0;
1226        end
1227        if iview==2
1228            testima_1=0;
1229        end
1230        testima_series=0;
1231    end
1232end
1233for ilist=1:length(varargout)-1
1234    switch varargout{ilist}
1235
1236                       %RootFile always visible
1237%          case 'RootPath'   %visible by default
1238%             value=lower(varargout{ilist+1});
1239%             if isequal(value,'one')||isequal(value,'two')||isequal(value,'many')
1240%                 set(handles.RootFile,'UserData',value)% for use in menu Open_insert
1241%             end
1242%         case 'SubDir' %visible by default
1243%             if isequal(lower(varargout{ilist+1}),'off')
1244%                 set(handles.SubDir,'Visible','off')
1245%             end
1246%         case 'RootFile'   %visible by default
1247%             value=lower(varargout{ilist+1});
1248%             if isequal(value,'off')
1249%                 set(handles.RootFile,'Visible','off')
1250%             elseif isequal(value,'one')||isequal(value,'two')||isequal(value,'many')
1251%                 set(handles.RootFile,'Visible','on')
1252%                 set(handles.RootFile,'UserData',value)% for use in menu Open_insert
1253%             end
1254%         case 'NomType'   %visible by default
1255%             if isequal(lower(varargout{ilist+1}),'off')
1256%                 set(handles.NomType,'Visible','off')
1257%             end
1258%         case 'FileExt'   %visible by default
1259%             if isequal(lower(varargout{ilist+1}),'off')
1260%                 set(handles.FileExt,'Visible','off')
1261%             end
1262        case 'NbSlice'   %hidden by default
1263            if isequal(lower(varargout{ilist+1}),'on')
1264                set(handles.num_NbSlice,'Visible','on')
1265                set(handles.NbSlice_title,'Visible','on')
1266            end
1267        case 'VelTypeMenu'   %hidden by default
1268             if isequal(lower(varargout{ilist+1}),'one') || isequal(lower(varargout{ilist+1}),'two')
1269                set(handles.VelTypeMenu,'Enable','on')
1270                if nb_series >=1 && ~testima_series
1271                    set(handles.VelTypeMenu,'Visible','on')
1272                    set(handles.VelType_text,'Visible','on');
1273%                     set(handles.Field_frame,'Visible','on')
1274                end
1275             end
1276            if isequal(lower(varargout{ilist+1}),'two')
1277                set(handles.VelTypeMenu_1,'Enable','on')
1278                if nb_series >=2 && ~testima_series
1279                    set(handles.VelTypeMenu_1,'Visible','on')
1280                    set(handles.VelType_text_1,'Visible','on');
1281                end
1282            end
1283        case 'FieldMenu'   %hidden by default
1284            if isequal(lower(varargout{ilist+1}),'one')||isequal(lower(varargout{ilist+1}),'two')
1285                set(handles.FieldMenu,'Enable','on') % test for MenuBorser
1286                if nb_series >=1 && ~testima_series
1287                    view_FieldMenu(handles,'on')
1288                end
1289            end
1290            if isequal(lower(varargout{ilist+1}),'two')
1291                set(handles.FieldMenu_1,'Enable','on')
1292                if nb_series >=2 && ~testima_1
1293                    view_FieldMenu_1(handles,'on')
1294                end
1295            end
1296        case 'CoordType'   %hidden by default
1297            if isequal(lower(varargout{ilist+1}),'on')
1298                set(handles.transform_fct,'Enable','on')
1299                set(handles.FieldTransform,'Visible','on')
1300%                 view_TRANSFORM(handles,'on')
1301            end
1302        case 'GetObject'   %hidden by default
1303            if isequal(lower(varargout{ilist+1}),'on')   
1304                set(handles.Objects,'Visible','on')
1305%                 set(handles.GetObject,'Visible','on');
1306            end
1307        case 'Mask'   %hidden by default
1308            if isequal(lower(varargout{ilist+1}),'on')   
1309                set(handles.Objects,'Visible','on')
1310%                 set(handles.GetMask,'Visible','on');
1311            end
1312        case 'PARAMETER' 
1313            set(handles.PARAMETERS_frame,'Visible','on')
1314            set(handles.PARAMETERS_title,'Visible','on')
1315            set(handles.ParamKey,'Visible','on')
1316            %set(handles.ParamVal,'Visible','on')
1317            Param_str=varargout{ilist+1};
1318            Param_list=[Param_list; {Param_str}];         
1319    end
1320end
1321if ~isempty(Param_list)
1322    set(handles.ParamKey,'String',Param_list)
1323    set(handles.ParamVal,'Visible','on')
1324end
1325
1326%------------------------------------------------------------------------
1327% --- Executes on selection change in FieldMenu.
1328function FieldMenu_Callback(hObject, eventdata, handles)
1329%------------------------------------------------------------------------
1330field_str=get(handles.FieldMenu,'String');
1331field_index=get(handles.FieldMenu,'Value');
1332field=field_str{field_index(1)};
1333if isequal(field,'get_field...')   
1334     hget_field=findobj(allchild(0),'name','get_field');
1335     if ~isempty(hget_field)
1336         delete(hget_field)%delete opened versions of get_field
1337     end
1338     SeriesData=get(handles.series,'UserData');
1339     filename=SeriesData.CurrentInputFile;
1340     if exist(filename,'file')
1341        get_field(filename)
1342     end
1343elseif isequal(field,'more...')
1344    str=calc_field;
1345    [ind_answer,v] = listdlg('PromptString','Select a file:',...
1346                'SelectionMode','single',...
1347                'ListString',str);
1348       % edit the choice in the fields and action menu
1349     scalar=cell2mat(str(ind_answer));
1350     update_menu(handles.FieldMenu,scalar)
1351end
1352
1353%------------------------------------------------------------------------
1354% --- Executes on selection change in FieldMenu_1.
1355function FieldMenu_1_Callback(hObject, eventdata, handles)
1356%------------------------------------------------------------------------
1357field_str=get(handles.FieldMenu_1,'String');
1358field_index=get(handles.FieldMenu_1,'Value');
1359field=field_str{field_index};
1360if isequal(field,'get_field...')   
1361     hget_field=findobj(allchild(0),'name','get_field_1');
1362     if ~isempty(hget_field)
1363         delete(hget_field)
1364     end
1365     SeriesData=get(handles.series,'UserData');
1366     filename=SeriesData.CurrentInputFile_1;
1367     if exist(filename,'file')
1368        hget_field=get_field(filename);
1369        set(hget_field,'name','get_field_1')
1370     end
1371elseif isequal(field,'more...')
1372    str=calc_field;
1373    [ind_answer,v] = listdlg('PromptString','Select a file:',...
1374                'SelectionMode','single',...
1375                'ListString',str);
1376       % edit the choice in the fields and action menu
1377     scalar=cell2mat(str(ind_answer));
1378     update_menu(handles.FieldMenu_1,scalar)
1379end   
1380
1381
1382%%%%%%%%%%%%%
1383function [ind_remove]=find_pairs(dirpair,ind_i,last_i)
1384indsel=ind_i;
1385indiff=diff(ind_i); %test index increment to detect multiplets (several pairs with the same index ind_i) and holes in the series
1386indiff=[1 indiff last_i-ind_i(end)+1];%for testing gaps with the imposed bounds
1387if ~isempty(indiff)
1388    indiff2=diff(indiff);
1389    indiffp=[indiff2 1];
1390    indiffm=[1 indiff2];
1391    ind_multi_m=find((indiff==0)&(indiffm<0))-1;%indices of first members of multiplets
1392    ind_multi_p=find((indiff==0)&(indiffp>0));%indices of last members of multiplets
1393    %for each multiplet, select the most recent file
1394    ind_remove=[];
1395    for i=1:length(ind_multi_m)
1396        ind_pairs=ind_multi_m(i):ind_multi_p(i);
1397        for imulti=1:length(ind_pairs)
1398            datepair(imulti)=datenum(dirpair(ind_pairs(imulti)).date);%dates of creation
1399        end
1400        [datenew,indsort2]=sort(datepair); %sort the multiplet by creation date
1401        ind_s=indsort2(1:end-1);%
1402        ind_remove=[ind_remove ind_pairs(ind_s)];%remove these indices, leave the last one
1403    end
1404end
1405
1406%------------------------------------------------------------------------
1407% --- determine the list of index pairs of processing file
1408function [num_i1,num_i2,num_j1,num_j2,num_i_out,num_j_out]=find_file_indices(num_i,num_j,ind_shift,NomType,mode)
1409%------------------------------------------------------------------------
1410num_i1=num_i;% set of first image numbers by default
1411num_i2=num_i;
1412num_j1=num_j;
1413num_j2=num_j;
1414num_i_out=num_i;
1415num_j_out=num_j;
1416% if isequal (NomType,'_1-2_1') || isequal (NomType,'_1-2')
1417if isequal(mode,'series(Di)')
1418    num_i1_line=num_i+ind_shift(3);% set of first image numbers
1419    num_i2_line=num_i+ind_shift(4);
1420    % adjust the first and last field number
1421        indsel=find(num_i1_line >= 1);
1422    num_i_out=num_i(indsel);
1423    num_i1_line=num_i1_line(indsel);
1424    num_i2_line=num_i2_line(indsel);
1425    num_j1=meshgrid(num_j,ones(size(num_i1_line)));
1426    num_j2=meshgrid(num_j,ones(size(num_i1_line)));
1427    [xx,num_i1]=meshgrid(num_j,num_i1_line);
1428    [xx,num_i2]=meshgrid(num_j,num_i2_line);
1429elseif isequal (mode,'series(Dj)')||isequal (mode,'bursts')
1430    if isequal(mode,'bursts') %case of bursts (png_old or png_2D)
1431        num_j1=ind_shift(1)*ones(size(num_i));
1432        num_j2=ind_shift(2)*ones(size(num_i));
1433    else
1434        num_j1_col=num_j+ind_shift(1);% set of first image numbers
1435        num_j2_col=num_j+ind_shift(2);
1436        % adjust the first field number
1437        indsel=find((num_j1_col >= 1));   
1438        num_j_out=num_j(indsel);
1439        num_j1_col=num_j1_col(indsel);
1440        num_j2_col=num_j2_col(indsel);
1441        [num_i1,num_j1]=meshgrid(num_i,num_j1_col);
1442        [num_i2,num_j2]=meshgrid(num_i,num_j2_col);
1443    end   
1444end
1445
1446%------------------------------------------------------------------------
1447% ---- find the times corresponding to the first and last indices of a series
1448function displ_time(handles)
1449%------------------------------------------------------------------------
1450SeriesData=get(handles.series,'UserData');%
1451first_i=str2num(get(handles.num_first_i,'String'));
1452first_j=str2num(get(handles.num_first_j,'String'));
1453last_i=str2num(get(handles.num_last_i,'String'));
1454last_j=str2num(get(handles.num_last_j,'String'));
1455InputTable=get(handles.InputTable,'Data');
1456NomType=InputTable(:,4);
1457% NomType=SeriesData.NomType;
1458mode_list=get(handles.mode,'String');
1459index_mode=get(handles.mode,'Value');
1460mode=mode_list{index_mode};
1461
1462time_first=[];
1463time_last=[];
1464if ~isfield(SeriesData,'Time')
1465    SeriesData.Time{1}=[];
1466end
1467for iview=1:length(NomType)
1468    time_first_cell{iview}='?';
1469    time_last_cell{iview}='?';%default
1470    time=SeriesData.Time{iview};
1471    if isequal(NomType{iview},'_1-2_1')|isequal(NomType{iview},'_1_1-2')|isequal(NomType{iview},'#_ab')|isequal(NomType{iview},'_1-2')
1472        if isfield(SeriesData,'displ_num')& ~isempty(SeriesData.displ_num)
1473            ind_shift=SeriesData.displ_num(iview,:);
1474            if isequal(mode,'bursts')
1475                first_j=0;
1476                last_j=0;
1477            end
1478            first_i1=first_i +ind_shift(3);
1479            first_i2 =first_i +ind_shift(4);
1480            first_j1 =first_j +ind_shift(1);
1481            first_j2 =first_j +ind_shift(2);
1482            last_i1=last_i +ind_shift(3);
1483            last_i2 =last_i +ind_shift(4);   
1484            last_j1 =last_j +ind_shift(1);
1485            last_j2 =last_j +ind_shift(2);
1486            siz=size(SeriesData.Time{1});
1487            if first_i1>=1 && first_j1>=1 && siz(1)>=last_i2 && siz(2)>=last_j2
1488                time_first=(time(first_i1,first_j1)+time(first_i2,first_j2))/2;
1489                time_last=(time(last_i1,last_j1)+time(last_i2,last_j2))/2;
1490            else%read the time in the nc files
1491                RootPath=get(handles.RootPath,'String');
1492                RootFile=get(handles.RootFile,'String');
1493                SubDir=get(handles.SubDir,'String');
1494                %VelType=get(handles.VelType,'String');
1495                VelType_str=get(handles.VelTypeMenu,'String');
1496                VelType_val=get(handles.VelTypeMenu,'Value');
1497                VelType=VelType_str{VelType_val};
1498                filebase=fullfile(RootPath{1},RootFile{1});
1499                [filefirst]=name_generator(filebase,first_i1,first_j1,'.nc',NomType{iview},1,first_i2,first_j2,SubDir{iview});
1500                if  exist(filefirst,'file')
1501                    Attrib=nc2struct(filefirst,[]);
1502                    if isfield(Attrib,'Time')
1503                        time_first=Attrib.Time;
1504                    else
1505                        if isfield(Attrib,'absolut_time_T0')
1506                            time_first=Attrib.absolut_time_T0;
1507                        end
1508                        if isfield(Attrib,'absolut_time_T0_2')&&~(isequal(VelType,'civ1')||isequal(VelType,'interp1')||isequal(VelType,'filter1'))
1509                            time_first=Attrib.absolut_time_T0_2;
1510                        end
1511                    end
1512                end
1513                [filelast]=name_generator(filebase,last_i1,last_j1,'.nc',NomType{iview},1,last_i2,last_j2,SubDir{iview});
1514                if exist(filelast,'file')
1515                   Attrib=nc2struct(filelast,[]);
1516                    if isfield(Attrib,'Time')
1517                        time_last=Attrib.Time;
1518                    else
1519                        if isfield(Attrib,'absolut_time_T0')
1520                            time_last=Attrib.absolut_time_T0;
1521                        end
1522                        if isfield(Attrib,'absolut_time_T0_2')&&~(isequal(VelType,'civ1')||isequal(VelType,'interp1')||isequal(VelType,'filter1'))
1523                            time_last=Attrib.absolut_time_T0_2;
1524                        end
1525                    end
1526                end
1527            end
1528        end
1529    else
1530        siz=size(time);
1531        if siz(1)>=last_i && siz(2)>=last_j && first_i>=1 && first_j>=1
1532            time_first=times(first_i,first_j);
1533            time_last=times(last_i,last_j);
1534        end
1535    end
1536    time_first_cell{iview}=num2str(time_first,4);
1537    time_last_cell{iview}=num2str(time_last,4);
1538end
1539% set(handles.time_first,'Value',1)
1540% set(handles.time_last,'Value',1)
1541% set(handles.time_first,'String',time_first_cell);
1542% set(handles.time_last,'String',time_last_cell);
1543
1544%------------------------------------------------------------------------
1545% --- Executes on button press in GetObject.
1546function GetObject_Callback(hObject, eventdata, handles)
1547%------------------------------------------------------------------------
1548SeriesData=get(handles.series,'UserData');
1549value=get(handles.GetObject,'Value');
1550if value
1551     set(handles.GetObject,'BackgroundColor',[1 1 0])%put unactivated buttons to yellow
1552%      DataInit.ParentButton=handles.GetObject;
1553     hset_object=findobj(allchild(0),'tag','set_object');%find the set_object interface handle
1554     if ishandle(hset_object)
1555         uistack(hset_object,'top')
1556        %[SeriesData.hset_object,SeriesData.sethandles]=set_object(DataInit); %open the set_object interface
1557     else
1558         %get the object file
1559         InputTable=get(handles.InputTable,'Data');
1560         defaultname=InputTable{1,1};
1561%          defaultname=get(handles.RootPath,'String');
1562         if isempty(defaultname)
1563            defaultname={''};
1564         end
1565        [FileName, PathName, filterindex] = uigetfile( ...
1566       {'*.xml;*.mat', ' (*.xml,*.mat)';
1567       '*.xml',  '.xml files '; ...
1568        '*.mat',  '.mat matlab files '}, ...
1569        'Pick an xml object file (or use uvmat to create it)',defaultname{1});
1570        fileinput=[PathName FileName];%complete file name
1571        testblank=findstr(fileinput,' ');%look for blanks
1572        if ~isempty(testblank)
1573            msgbox_uvmat('ERROR','forbidden input file name: contain blanks')
1574            return
1575        end
1576        sizf=size(fileinput);
1577        if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end
1578        %read the file
1579        t=xmltree(fileinput);
1580        data=convert(t);
1581        if ~isfield(data,'Style')
1582             data.Style='points';
1583        end
1584        if ~isfield(data,'ProjMode')
1585             data.ProjMode='projection';
1586        end
1587        transform_menu=get(handles.transform_fct,'String');
1588        ichoice=get(handles.transform_fct,'Value');
1589%         if isequal(transform_menu{ichoice},'px');
1590%             data.CoordType='px';
1591%         else
1592%             data.CoordType='phys';
1593%         end
1594        data.desable_plot=1;
1595        [SeriesData.hset_object,SeriesData.sethandles]=set_object(data);% call the set_object interface
1596     end
1597else
1598    set(handles.GetObject,'BackgroundColor',[0.7 0.7 0.7])%put activated buttons to green
1599%     if isfield(SeriesData,'hset_object')&& ishandle(SeriesData.hset_object)
1600%         close(SeriesData.hset_object)
1601%     end
1602end
1603set(handles.series,'UserData',SeriesData)
1604
1605%--------------------------------------------------------------
1606function GetMask_Callback(hObject, eventdata, handles)
1607value=get(handles.GetMask,'Value');
1608if value
1609    msgbox_uvmat('ERROR','not implemented yet')
1610end
1611%--------------------------------------------------------------
1612
1613%-------------------------------------------------------------------
1614%'uv_ncbrowser': interactively calls the netcdf file browser 'get_field.m'
1615function ncbrowser_uvmat(hObject, eventdata)
1616%-------------------------------------------------------------------
1617     bla=get(gcbo,'String');
1618     ind=get(gcbo,'Value');
1619     filename=cell2mat(bla(ind));
1620      blank=find(filename==' ');
1621      filename=filename(1:blank-1);
1622     get_field(filename)
1623
1624% ------------------------------------------------------------------
1625function MenuHelp_Callback(hObject, eventdata, handles)
1626%-------------------------------------------------------------------
1627path_to_uvmat=which ('uvmat');% check the path of uvmat
1628pathelp=fileparts(path_to_uvmat);
1629helpfile=fullfile(pathelp,'uvmat_doc','uvmat_doc.html');
1630if isempty(dir(helpfile)), msgbox_uvmat('ERROR','Please put the help file uvmat_doc.html in the sub-directory /uvmat_doc of the UVMAT package')
1631else
1632    addpath (fullfile(pathelp,'uvmat_doc'))
1633    web([helpfile '#series'])
1634end
1635
1636%-------------------------------------------------------------------
1637% --- Executes on selection change in transform_fct.
1638function transform_fct_Callback(hObject, eventdata, handles)
1639%-------------------------------------------------------------------
1640global nb_transform
1641
1642menu=get(handles.transform_fct,'String');
1643ind_coord=get(handles.transform_fct,'Value');
1644coord_option=menu{ind_coord};
1645list_transform=get(handles.transform_fct,'UserData');
1646ff=functions(list_transform{end});
1647if isequal(coord_option,'more...');
1648    coord_fct='';
1649    prompt = {'Enter the name of the transform function'};
1650    dlg_title = 'user defined transform';
1651    num_lines= 1;
1652    [FileName, PathName, filterindex] = uigetfile( ...
1653       {'*.m', ' (*.m)';
1654        '*.m',  '.m files '; ...
1655        '*.*', 'All Files (*.*)'}, ...
1656        'Pick a file', ff.file);
1657    if isequal(PathName(end),'/')||isequal(PathName(end),'\')
1658        PathName(end)=[];
1659    end
1660    transform_selected =fullfile(PathName,FileName);
1661    if ~exist(transform_selected,'file')
1662          return
1663    end
1664    [ppp,transform,xt_fct]=fileparts(FileName);% removes extension .m
1665    if ~isequal(ext_fct,'.m')
1666        msgbox_uvmat('ERROR','a Matlab function .m must be introduced');
1667        return
1668    end
1669   menu=update_menu(handles.transform_fct,transform);%add the selected fct to the menu
1670   ind_coord=get(handles.transform_fct,'Value');
1671   addpath(PathName)
1672   list_transform{ind_coord}=str2func(transform);% create the function handle corresponding to the newly seleced function
1673   set(handles.transform_fct,'UserData',list_transform)
1674   rmpath(PathName)
1675   % save the new menu in the personal file 'uvmat_perso.mat'
1676   dir_perso=prefdir;%personal Matalb directory
1677   profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
1678   if exist(profil_perso,'file')
1679       for ilist=nb_transform+1:numel(list_transform)
1680           ff=functions(list_transform{ilist});
1681           transform_fct{ilist-nb_transform}=ff.file;
1682       end
1683        save (profil_perso,'transform_fct','-append'); %store the root name for future opening of uvmat
1684   end
1685end
1686
1687%check the current path to the selected function
1688if ~isempty(list_transform{ind_coord})
1689func=functions(list_transform{ind_coord});
1690set(handles.path_transform,'String',fileparts(func.file)); %show the path to the senlected function
1691else
1692   set(handles.path_transform,'String',''); %show the path to the senlected function
1693end
1694
1695% --- Executes on button press in REFRESH_INDICES.
1696    function REFRESH_INDICES_Callback(hObject, eventdata, handles)
1697% hObject    handle to REFRESH_INDICES (see GCBO)
1698% eventdata  reserved - to be defined in a future version of MATLAB
1699% handles    structure with handles and user data (see GUIDATA)
1700set(handles.REFRESH_INDICES,'BackgroundColor',[0.7 0.7 0.7])
1701InputTable=get(handles.InputTable,'Data');
1702check_lines=get(handles.REFRESH_INDICES,'UserData');
1703
1704%% check the indices and FileTypes for each series (limited to the new ones to save time)
1705for ind_list=1:length(check_lines)
1706    if  check_lines(ind_list)
1707        InputLine=InputTable(ind_list,:);
1708        detect_idem=strcmp('"',InputLine);% look for '" (repeat of previous data)
1709        detect_idem=detect_idem(detect_idem>0);
1710        if ~isempty (detect_idem)
1711            InputLine(detect_idem)=InputTable(ind_list-1,detect_idem);
1712            set(handles.InputTable,'Data',InputTable)
1713        end
1714        fileinput=fullfile_uvmat(InputLine{1},InputLine{2},InputLine{3},InputLine{5},InputLine{4},1,2,1,2);
1715        %fileinput=name_generator(fullfile(InputLine{1},InputLine{3}),1,1,InputLine{5},InputLine{4},1,2,2,InputLine{2})
1716        %update file series defined by the selected line
1717        [InputTable{ind_list,3},InputTable{(ind_list),4},errormsg]=update_indices(handles,fileinput,ind_list);
1718        if ~isempty(errormsg)
1719                msgbox_uvmat('ERROR',errormsg)
1720                return
1721        end
1722    end
1723end
1724set(handles.InputTable,'Data',InputTable)
1725SeriesData=get(handles.series,'UserData');
1726
1727state_j='off';
1728state_Pairs='off';
1729state_InputFields='off';
1730val=get(handles.ListView,'Value');
1731ListViewString={''};
1732if ~isempty(SeriesData)
1733%     ListViewString={};
1734    for iview=1:size(InputTable,1)
1735        if ~isempty(SeriesData.j1_series{iview})
1736            state_j='on';
1737        end
1738        if ~isempty(SeriesData.i2_series{iview})||~isempty(SeriesData.j2_series{iview})
1739            state_Pairs='on';
1740            ListViewString{iview}=num2str(iview);
1741            if check_lines(iview)
1742                val=iview;%select the last pair if it is a new entry
1743            end
1744        end
1745        if strcmp(SeriesData.FileType{iview},'civx')||strcmp(SeriesData.FileType{iview},'civdata')
1746            state_InputFields='on';
1747        end
1748    end
1749end
1750set(handles.ListView,'Value',val)
1751set(handles.ListView,'String',ListViewString)
1752if strcmp(state_Pairs,'on')
1753    ListView_Callback(hObject,eventdata,handles)
1754end
1755set(handles.Pairs,'Visible',state_Pairs)
1756enable_j(handles,state_j)
1757set(handles.REFRESH_INDICES,'BackgroundColor',[1 0 0])
1758set(handles.REFRESH_INDICES,'visible','off')
1759
1760% -----------------------------------------------------------------------
1761% --- Update min and max indices of a file series by scanning with find_file_series
1762% --- which also changes the root file and NomType in case of movie. Also adjust the string representation of indices (e.g;
1763% --- 1 or 001 by the function find_file_series
1764% --- This function also dispaly the set of availbale files in the series
1765% --- and the menus appropriate to the file type as well as timing possibly set
1766% --- by an xml image documentation file
1767function [RootFile,NomType,errormsg]=update_indices(handles,fileinput,iview)
1768% -----------------------------------------------------------------------
1769%% look for min and max indices existing in the file series and update SeriesData
1770errormsg='';
1771[FilePath,FileName,FileExt]=fileparts(fileinput);
1772% detect the file type, get the movie object if relevant, and look for the corresponding file series:
1773% the root name and indices may be corrected by including the first index i1 if a corresponding xml file exists
1774[RootPath,SubDir,RootFile,i1_series,i2_series,j1_series,j2_series,NomType,FileType,Object,i1,i2,j1,j2]=find_file_series(FilePath,[FileName FileExt]);
1775
1776%
1777% [RootPathSub,FileName,FileExt]=fileparts(fileinput);
1778% [RootFile,i1_series,i2_series,j1_series,j2_series,NomType,FileType,Object]=find_file_series(RootPathSub,[FileName FileExt]);
1779if isempty(RootFile)&&isempty(i1_series)
1780    errormsg='no input file in the series';
1781    return
1782end
1783% [tild,tild,FileExt]=fileparts(fileinput);
1784
1785MinIndex=get(handles.MinIndex,'Data');
1786MaxIndex=get(handles.MaxIndex,'Data');
1787MinIndex_i=min(i1_series(i1_series>0));
1788if ~isempty(i2_series)
1789    MaxIndex_i=max(i2_series(i2_series>0));
1790else
1791    MaxIndex_i=max(i1_series(i1_series>0));
1792end
1793MinIndex_j=min(j1_series(j1_series>0));
1794if ~isempty(j2_series)
1795    MaxIndex_j=max(j2_series(j2_series>0));
1796else
1797    MaxIndex_j=max(j1_series(j1_series>0));
1798end
1799MinIndex{iview,1}=MinIndex_i;
1800MinIndex{iview,2}=MinIndex_j;
1801MaxIndex{iview,1}=MaxIndex_i;
1802MaxIndex{iview,2}=MaxIndex_j;
1803set(handles.MinIndex,'Data',MinIndex)
1804set(handles.MaxIndex,'Data',MaxIndex)
1805SeriesData=get(handles.series,'UserData');
1806SeriesData.i1_series{iview}=i1_series;
1807SeriesData.i2_series{iview}=i2_series;
1808SeriesData.j1_series{iview}=j1_series;
1809SeriesData.j2_series{iview}=j2_series;
1810SeriesData.FileType{iview}=FileType;
1811
1812%% display the set of existing files as an image
1813set(handles.waitbar_frame,'Units','pixels')
1814pos=get(handles.waitbar_frame,'Position');
1815xima=0.5:pos(3)-0.5;% pixel positions on the image representing the existing file indices
1816yima=0.5:pos(4)-0.5;
1817[XIma,YIma]=meshgrid(xima,yima);
1818nb_i=size(i1_series,1);
1819nb_j=size(i1_series,2);
1820ind_i=(0.5:nb_i-0.5)*pos(3)/nb_i;
1821ind_j=(0.5:nb_j-0.5)*pos(4)/nb_j;
1822[Ind_i,Ind_j]=meshgrid(ind_i,ind_j);
1823CData=zeros([size(XIma) 3]);
1824file_ima=double((i1_series(:,:,1)>0)');
1825if numel(file_ima)>=2
1826if size(file_ima,1)==1
1827    CLine=interp1(ind_i,file_ima,xima,'nearest');
1828    CData(:,:,2)=ones(size(yima'))*CLine;
1829else
1830    CData(:,:,2)=interp2(Ind_i,Ind_j,file_ima,XIma,YIma,'nearest');
1831end
1832set(handles.waitbar_frame,'CData',CData)
1833end
1834set(handles.waitbar_frame,'Units','normalized')
1835
1836%% enable field and veltype menus
1837testfield=isequal(get(handles.FieldMenu,'enable'),'on');
1838testfield_1=isequal(get(handles.FieldMenu_1,'enable'),'on');
1839testveltype=isequal(get(handles.VelTypeMenu,'enable'),'on');
1840testveltype_1=isequal(get(handles.VelTypeMenu_1,'enable'),'on');
1841testtransform=isequal(get(handles.transform_fct,'Enable'),'on');
1842% testnc=0;
1843% testnc_1=0;
1844% testcivx=0;
1845% testcivx_1=0;
1846% testima=0; %test for image input
1847% if isequal(lower(FileExt),'.avi') %.avi file
1848%     testima=1;
1849% elseif ~isempty(imformats(FileExt(2:end)))
1850%     testima=1;
1851% elseif isequal(FileExt,'.vol')
1852%      testima=1;
1853% end
1854%TODO: update
1855% if length(FileExtCell)==1 || length(FileExtCell)>2
1856%     for iview=1:length(FileExtCell)
1857%         if isequal(FileExtCell{iview},'.nc')
1858%             testnc=1;
1859%         end
1860%         if isequal(FileTypeCell{iview},'civx')
1861%             testcivx=1;
1862%         end
1863%     end
1864% elseif length(FileExtCell)==2
1865%     testnc=isequal(FileExtCell{1},'.nc');
1866%     testnc_1=isequal(FileExtCell{2},'.nc');
1867%     testcivx=isequal(FileTypeCell{1},'civx');
1868%     testcivx_1=isequal(FileTypeCell{2},'civx');
1869% end
1870switch FileType
1871    case {'civx','civdata'}
1872    view_FieldMenu(handles,'on')
1873    menustr=get(handles.FieldMenu,'String');
1874    if isequal(menustr,{'get_field...'})
1875        set(handles.FieldMenu,'String',{'get_field...';'velocity';'vort';'div';'more...'})
1876    end
1877    set(handles.VelTypeMenu,'Visible','on')
1878    set(handles.FieldTransform,'Visible','on')
1879    %      view_TRANSFORM(handles,'on')
1880    %     TODO: second menu
1881    %           view_FieldMenu_1(handles,'on')
1882    %     if testcivx_1
1883    %         menustr=get(handles.FieldMenu_1,'String');
1884    %         if isequal(menustr,{'get_field...'})
1885    %             set(handles.FieldMenu_1,'String',{'get_field...';'velocity';'vort';'div';'more...'})
1886    %         end
1887    %     else
1888    %         set(handles.FieldMenu_1,'Value',1)
1889    %         set(handles.FieldMenu_1,'String',{'get_field...'})
1890    %     set(handles.VelTypeMenu_1,'Visible','on')
1891    %     set(handles.VelType_text_1,'Visible','on');
1892    %     end
1893    %     view_FieldMenu_1(handles,'off')
1894    case 'netcdf'
1895    view_FieldMenu(handles,'on')
1896    set(handles.FieldMenu,'Value',1)
1897    set(handles.FieldMenu,'String',{'get_field...'})
1898    set(handles.FieldTransform,'Visible','off')
1899    %     view_TRANSFORM(handles,'off')
1900    case {'image','multimage','video'}
1901    view_FieldMenu(handles,'off')
1902    view_FieldMenu_1(handles,'off')
1903    set(handles.VelTypeMenu,'Visible','off')
1904    set(handles.VelType_text,'Visible','off');
1905end
1906
1907
1908%TODO:update
1909% if ~isequal(FileExt,'.nc') && ~isequal(FileExt,'.cdf') && ~testima
1910%     msgbox_uvmat('ERROR',['invalid input file extension ' FileExt])
1911%     return
1912% end 
1913
1914%%  read image documentation file  if found%%%%%%%%%%%%%%%%%%%%%%%%%%%
1915ext_imadoc='';
1916FileBase=fullfile(RootPath,RootFile);
1917if isequal(FileExt,'.xml')||isequal(FileExt,'.civ')
1918    ext_imadoc=FileExt;
1919elseif exist([FileBase '.xml'],'file')
1920    ext_imadoc='.xml';
1921elseif exist([FileBase '.civ'],'file')
1922    ext_imadoc='.civ';
1923end
1924%read the ImaDoc file
1925XmlData=[];
1926NbSlice_calib={};
1927if isequal(ext_imadoc,'.xml')
1928        [XmlData,warntext]=imadoc2struct([FileBase '.xml']);
1929        if isfield(XmlData,'Heading') && isfield(XmlData.Heading,'ImageName') && ischar(XmlData.Heading.ImageName)
1930            [PP,FF,ext_ima_read]=fileparts(XmlData.Heading.ImageName);
1931        end
1932        if isfield(XmlData,'Time')
1933            time=XmlData.Time;
1934        end
1935        if isfield(XmlData,'Camera')
1936            if isfield(XmlData.Camera,'NbSlice')&& ~isempty(XmlData.Camera.NbSlice)
1937                NbSlice_calib{iview}=XmlData.Camera.NbSlice;% Nbre of slices for Zindex in phys transform
1938                if ~isequal(NbSlice_calib{iview},NbSlice_calib{1})
1939                    msgbox_uvmat('WARNING','inconsistent number of Z indices for the two field series');
1940                end
1941            end
1942            if isfield(XmlData.Camera,'TimeUnit')&& ~isempty(XmlData.Camera.TimeUnit)
1943                TimeUnit=XmlData.Camera.TimeUnit;
1944            end
1945        end
1946        if ~isempty(warntext)
1947            msgbox_uvmat('WARNING',warntext)
1948        end 
1949elseif isequal(ext_imadoc,'.civ')
1950    [error,XmlData.Time,TimeUnit,mode,npx,npy,pxcmx,pxcmy]=read_imatext([FileBase '.civ']);
1951    time=XmlData.Time;
1952    if error==2, warntext=['no file ' FileBase '.civ'];
1953    elseif error==1, warntext='inconsistent number of fields in the .civ file';
1954    end 
1955end 
1956
1957
1958%% number of slices
1959if isfield(XmlData,'GeometryCalib') && isfield(XmlData.GeometryCalib,'SliceCoord')
1960       siz=size(XmlData.GeometryCalib.SliceCoord);
1961       if siz(1)>1
1962           NbSlice=siz(1);
1963       else
1964           NbSlice=1;
1965       end
1966       set(handles.num_NbSlice,'String',num2str(NbSlice))
1967end
1968% set(handles.mode,'Visible','off') % do not show index pairs by default
1969set(handles.Pairs,'Visible','off')
1970% set(handles.ref_i,'Visible','off')
1971% set(handles.ref_i_text,'Visible','off')
1972testpair=0;
1973%set the menus of image pairs and default selection for series
1974%list pairs if relevant
1975% Val=get(handles.NomType,'Value');
1976% synchronise_view(handles,Val)
1977
1978% if ~isfield(SeriesData,'j1_series')||isempty(SeriesData.j1_series{index})
1979%     state_j='off'; %no need for j index
1980% else
1981%     state_j='on'; %case of j index
1982% end
1983% show index pairs if files exist
1984set(handles.series,'UserData',SeriesData)
1985
1986
1987
1988% --- Executes on button press in BATCH.
1989function BATCH_Callback(hObject, eventdata, handles)
1990% hObject    handle to BATCH (see GCBO)
1991% eventdata  reserved - to be defined in a future version of MATLAB
1992% handles    structure with handles and user data (see GUIDATA)
1993Series=read_GUI(handles.series);
1994t=struct2xml(Series);
1995save(t); %TODO: determine a xml file name
1996
1997% list_action=get(handles.ACTION,'String');% list menu action
1998% index_action=get(handles.ACTION,'Value');% selected string index
1999% action= list_action{index_action}; % selected string
2000
2001%% defining the ACTION function handle
2002path_series=which('series');
2003list_path=get(handles.ACTION,'UserData');
2004index=get(handles.ACTION,'Value');
2005fct_path=list_path{index}; %path stored for the function ACTION
2006if ~isequal(fct_path,path_series)
2007    eval(['spath=which(''' action ''');']) %spath = current path of the selected function ACTION
2008    if ~exist(fct_path,'dir')
2009        msgbox_uvmat('ERROR',['The prescibed function path ' fct_path ' does not exist'])
2010        return
2011    end
2012    if ~isequal(spath,fct_path)
2013        addpath(fct_path)% add the prescribed path if not the current one
2014    end
2015end
2016eval(['h_fun=@' action ';'])%create a function handle for ACTION
2017if ~isequal(fct_path,path_series)
2018        rmpath(fct_path)% add the prescribed path if not the current one   
2019end
2020
2021h_fun('BATCH');% TODO modify the called function to read the xml file as input parameter
2022
2023
2024% --- Executes on selection change in txt_Pairs
2025function txt_Pairs_Callback(hObject, eventdata, handles)
2026
2027%------------------------------------------------------------------------
2028% --- Executes on selection change in ListView.
2029function ListView_Callback(hObject, eventdata, handles)
2030%------------------------------------------------------------------------   
2031ListViewString=get(handles.ListView,'String');
2032if isempty(ListViewString)
2033    ListViewString={''};
2034end
2035ListViewValue=get(handles.ListView,'Value');
2036View=str2double(ListViewString{ListViewValue});
2037if isnan(View)
2038    set(handles.Pairs,'Visible','off')
2039else
2040    set(handles.Pairs,'Visible','on')
2041    SeriesData=get(handles.series,'UserData');
2042    if isfield(SeriesData,'j1_series')&&(~isempty(SeriesData.i2_series{View})||~isempty(SeriesData.j2_series{View}))
2043        if ~isempty(SeriesData.i2_series{View}) %pairs with i View
2044            set(handles.mode,'Value',1)
2045            set(handles.mode,'String',{'series(Di)'})
2046        else  %pairs with j View
2047            nbfield=size(SeriesData.j2_series{View},1);
2048            nbfield2=size(SeriesData.j2_series{View},2);
2049            set(handles.mode,'Value',1)
2050            set(handles.mode,'String',{'bursts';'series(Dj)'})
2051            if nbfield2>10 || nbfield==1
2052                set(handles.mode,'Value',2);
2053            else
2054                set(handles.mode,'Value',1);
2055            end
2056        end
2057    end
2058    mode_Callback([],[], handles)
2059end
2060
2061   
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