source: trunk/src/series.m @ 612

Last change on this file since 612 was 612, checked in by sommeria, 8 years ago

a few bugs repaired

File size: 112.7 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 TransformName (menu for coordinate transforms)
9%      .menu_coord_val: value for TransformName (menu for coordinate transforms)
10%      .FileName: input file name
11%      .FileName_1: second input file name
12%      .list_field: menu of input fields
13%      .index_fields: chosen index
14%      .civ1=0 or 1, .interp1,  ... : input civ field type
15%
16%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
17%  Copyright Joel Sommeria, 2008, LEGI / CNRS-UJF-INPG, sommeria@coriolis-legi.org.
18%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
19%     This file is part of the toolbox UVMAT.
20%
21%     UVMAT is free software; you can redistribute it and/or modify
22%     it under the terms of the GNU General Public License as published by
23%     the Free Software Foundation; either version 2 of the License, or
24%     (at your option) any later version.
25%
26%     UVMAT is distributed in the hope that it will be useful,
27%     but WITHOUT ANY WARRANTY; without even the implied warranty of
28%     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
29%     GNU General Public License (file UVMAT/COPYING.txt) for more details.
30%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
31
32%------------------------------------------------------------------------
33%------------------------------------------------------------------------
34%  I - MAIN FUNCTION series
35%------------------------------------------------------------------------
36%------------------------------------------------------------------------
37function varargout = series(varargin)
38
39% Begin initialization code - DO NOT EDIT
40gui_Singleton = 1;
41gui_State = struct('gui_Name',       mfilename, ...
42                   'gui_Singleton',  gui_Singleton, ...
43                   'gui_OpeningFcn', @series_OpeningFcn, ...
44                   'gui_OutputFcn',  @series_OutputFcn, ...
45                   'gui_LayoutFcn',  [] , ...
46                   'gui_Callback',   []);
47if nargin && ischar(varargin{1})
48    gui_State.gui_Callback = str2func(varargin{1});
49end
50
51if nargout
52    [varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:});
53else
54    gui_mainfcn(gui_State, varargin{:});
55end
56% End initialization code - DO NOT EDIT
57
58%--------------------------------------------------------------------------
59% --- Executes just before series is made visible.
60%--------------------------------------------------------------------------
61function series_OpeningFcn(hObject, eventdata, handles,Param)
62
63% Choose default command line output for series
64handles.output = hObject;
65% Update handles structure
66guidata(hObject, handles);
67
68%% initial settings
69set(0,'Unit','points')
70ScreenSize=get(0,'ScreenSize');%size of the current screen
71Width=900;% prefered width of the GUI in points (1/72 inch)
72Height=624;
73%adjust to screen size (reduced by a min margin)
74RescaleFactor=min((ScreenSize(3)-80)/Width,(ScreenSize(4)-80)/Height);
75if RescaleFactor>1
76    %RescaleFactor=RescaleFactor/2+1/2; %reduce the rescale factor to provide an increased margin for a big screen
77    RescaleFactor=min(RescaleFactor,1);
78end
79Width=Width*RescaleFactor;
80Height=Height*RescaleFactor;
81LeftX=80*RescaleFactor;%position of the left fig side, in pixels (put to the left side, with some margin)
82LowY=round(ScreenSize(4)/2-Height/2); % put at the middle height on the screen
83set(hObject,'Units','points')
84set(hObject,'Position',[LeftX LowY Width Height])
85set(handles.PairString,'ColumnName',{'pairs'})
86set(handles.PairString,'ColumnEditable',false)
87set(handles.PairString,'ColumnFormat',{'char'})
88set(handles.PairString,'Data',{''})
89series_ResizeFcn(hObject, eventdata, handles)%resize table according to series GUI size
90set(hObject,'WindowButtonDownFcn',{'mouse_down'})%allows mouse action with right button (zoom for uicontrol display)
91% check default input data
92if ~exist('Param','var')
93    Param=[]; %default
94end
95
96%% list of builtin functions in the mebu ActionName
97ActionList={'check_data_files';'aver_stat';'time_series';'merge_proj'};% WARNING: fits with nb_builtin_ACTION=4 in ActionName_callback
98NbBuiltinAction=numel(ActionList);
99[path_series,name,ext]=fileparts(which('series'));% path to the GUI series
100path_series_fct=fullfile(path_series,'series');%path of the functions in subdirectroy 'series'
101ActionExtList={'.m';'.sh'};% default choice of extensions (Matlab fct .m or compiled version .sh
102ActionPathList=cell(NbBuiltinAction,numel(ActionExtList));%initiate the cell matrix of Action fct paths
103ActionPathList(:)={path_series_fct}; %set the default path to series fcts to all list members
104RunModeList={'local';'background'};% default choice of extensions (Matlab fct .m or compiled version .sh)
105[s,w]=system('oarstat');% look for cluster system 'oar'
106if isequal(s,0)
107    RunModeList=[RunModeList;{'cluster_oar'}];
108end
109[s,w]=system('qstat');% look for cluster system 'sge'
110if isequal(s,0)
111    RunModeList=[RunModeList;{'cluster_sge'}];
112end
113set(handles.RunMode,'String',RunModeList)
114
115%% list of builtin transform functions in the mebu TransformName
116TransformList={'';'sub_field';'phys';'phys_polar'};% WARNING: must fit with the corresponding menu in uvmat and nb_builtin_transform=4 in  TransformName_callback
117NbBuiltinTransform=numel(TransformList);
118path_transform_fct=fullfile(path_series,'transform_field');
119TransformPathList=cell(NbBuiltinTransform,1);%initiate the cell matrix of Action fct paths
120TransformPathList(:)={path_transform_fct}; %set the default path to series fcts to all list members
121
122%% get the user defined functions stored in the personal file uvmat_perso.mat
123dir_perso=prefdir;
124profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
125if exist(profil_perso,'file')
126    h=load (profil_perso);
127    %get the list of previous input files in the upper bar menu Open
128    if isfield(h,'MenuFile')
129        for ifile=1:min(length(h.MenuFile),5)
130            eval(['set(handles.MenuFile_' num2str(ifile) ',''Label'',h.MenuFile{ifile});'])
131        end
132    end
133    %get the menu of actions
134    if isfield(h,'ActionExtListUser') && iscell(h.ActionExtListUser)
135        ActionExtList=[ActionExtList; h.ActionExtListUser];
136    end
137    if isfield(h,'ActionListUser') && iscell(h.ActionListUser) && isfield(h,'ActionPathListUser') && iscell(h.ActionPathListUser)
138        ActionList=[ActionList;h.ActionListUser];
139        ActionPathList=[ActionPathList;h.ActionPathListUser];
140    end
141    %get the menu of transform fct
142    if isfield(h,'TransformListUser') && iscell(h.TransformListUser) && isfield(h,'TransformPathListUser') && iscell(h.TransformPathListUser)
143        TransformList=[TransformList;h.TransformListUser];
144        TransformPathList=[TransformPathList;h.TransformPathListUser];
145    end
146end
147
148%% selection of the input Action fct
149ActionCheckExist=true(size(ActionList));%initiate the check of the path to the listed action fct
150for ilist=NbBuiltinAction+1:numel(ActionList)%check  the validity of the path of the user defined Action fct
151    ActionCheckExist(ilist)=exist(fullfile(ActionPathList{ilist},[ActionList{ilist} '.m']),'file');
152end
153ActionPathList=ActionPathList(ActionCheckExist,:);% suppress the menu options which are not valid anymore
154ActionList=ActionList(ActionCheckExist);
155set(handles.ActionName,'String',[ActionList;{'more...'}])
156set(handles.ActionName,'UserData',ActionPathList)
157ActionIndex=[];
158if isfield(Param,'ActionName')% copy the selected menu index transferred in Param from uvmat
159    ActionIndex=find(strcmp(Param.ActionName,ActionList),1);
160end
161if isempty(ActionIndex)
162    ActionIndex=1;
163end
164set(handles.ActionName,'Value',ActionIndex)
165set(handles.ActionPath,'String',ActionPathList{ActionIndex})
166set(handles.ActionExt,'Value',1)
167set(handles.ActionExt,'String',ActionExtList)
168
169%% selection of the input transform fct
170TransformCheckExist=true(size(TransformList));
171for ilist=NbBuiltinTransform+1:numel(TransformList)
172    TransformCheckExist(ilist)=exist(fullfile(TransformPathList{ilist},[TransformList{ilist} '.m']),'file');
173end
174TransformPathList=TransformPathList(TransformCheckExist);
175TransformList=TransformList(TransformCheckExist);
176set(handles.TransformName,'String',[TransformList;{'more...'}])
177set(handles.TransformName,'UserData',TransformPathList)
178TransformIndex=[];
179if isfield(Param,'TransformName')% copy the selected menu index transferred in Param from uvmat
180    TransformIndex=find(strcmp(Param.TransformName,TransformList),1);
181end
182if isempty(TransformIndex)
183    TransformIndex=1;
184end
185set(handles.TransformName,'Value',TransformIndex)
186set(handles.TransformPath,'String',TransformPathList{TransformIndex})
187   
188%% fields input initialisation
189if isfield(Param,'list_fields')&& isfield(Param,'index_fields') &&~isempty(Param.list_fields) &&~isempty(Param.index_fields)
190    set(handles.FieldName,'String',Param.list_fields);% list menu fields
191    set(handles.FieldName,'Value',Param.index_fields);% selected string index
192end
193if isfield(Param,'Coord_x_str')&& isfield(Param,'Coord_x_val')
194        set(handles.Coord_x,'String',Param.Coord_x_str);% list menu fields
195    set(handles.Coord_x,'Value',Param.Coord_x_val);% selected string index
196end
197if isfield(Param,'Coord_y_str')&& isfield(Param,'Coord_y_val')
198        set(handles.Coord_y,'String',Param.Coord_y_str);% list menu fields
199    set(handles.Coord_y,'Value',Param.Coord_y_val);% selected string index
200end
201
202%% Adjust the GUI according to the binaries available in PARAM.xml
203% path_uvmat=fileparts(which('uvmat')); %path to civ
204% addpath (path_uvmat) ; %add the path to civ, (useful in case of change of working directory after civ has been s opened in the working directory)
205% errormsg=[];%default error message
206% xmlfile='PARAM.xml';
207% if exist(xmlfile,'file')
208%     try
209%         t=xmltree(xmlfile);
210%         sparam=convert(t);
211%     catch ME
212%         errormsg={' Unable to read the file PARAM.xml defining the  binaries:';ME.message};
213%     end
214% else
215%     errormsg=[xmlfile ' not found: path to binaries undefined'];
216% end
217% if ~isempty(errormsg)
218%     msgbox_uvmat('WARNING',errormsg);
219% end
220% test_batch=0;%default: ,no batch mode available
221% if isfield(sparam,'BatchParam') && isfield(sparam.BatchParam,'BatchMode')
222%     test_batch=strcmp(sparam.BatchParam.BatchMode,'sge'); %sge is currently the only implemented batch mod
223% end
224% RUNVal=get(handles.RunMode,'Value');
225% if test_batch==0
226%    if RUNVal>2
227%        set(handles.RunMode,'Value',1)
228%    end
229%    set(handles.RunMode,'String',{'local';'background'})
230% else
231%     set(handles.RunMode,'String',{'local';'background';'cluster'})
232% end
233
234%% introduce the input file name(s) if defined from input Param
235if isfield(Param,'FileName')
236    InputTable={'','','','',''}; % refresh the file input table
237    set(handles.InputTable,'Data',InputTable)
238    if isfield(Param,'FileName_1')
239        display_file_name(handles,Param.FileName_1,0)
240        display_file_name(handles,Param.FileName,1)
241    else
242        display_file_name(handles,Param.FileName,0)
243    end
244end 
245if isfield(Param,'incr_i')
246    set(handles.num_incr_i,'String',num2str(Param.incr_i))
247end
248if isfield(Param,'incr_j')
249    set(handles.num_incr_j,'String',num2str(Param.incr_j))
250end
251
252
253%------------------------------------------------------------------------
254% --- Outputs from this function are returned to the command line.
255function varargout = series_OutputFcn(hObject, eventdata, handles)
256%------------------------------------------------------------------------
257% varargout  cell array for returning output args (see VARARGOUT);
258% hObject    handle to figure
259% eventdata  reserved - to be defined in a future version of MATLAB
260% handles    structure with handles and user data (see GUIDATA)
261% Get default command line output from handles structure
262varargout{1} = handles.output;
263
264%------------------------------------------------------------------------
265%------------------------------------------------------------------------
266%  II - FUNCTIONS FOR INTRODUCING THE INPUT FILES
267% automatically sets the global properties when the rootfile name is introduced
268% then activate the view-field actionname if selected
269% it is activated either by clicking on the RootPath window or by the
270% browser
271%------------------------------------------------------------------------
272%------------------------------------------------------------------------
273function MenuBrowse_Callback(hObject, eventdata, handles)
274%------------------------------------------------------------------------   
275%get the previous input file in the Input Table
276oldfile=''; %default
277SeriesData=get(handles.series,'UserData');
278if isfield(SeriesData,'RefFile')
279    oldfile=SeriesData.RefFile{1};
280end
281if ~exist(oldfile,'file')
282    dir_perso=prefdir;
283    profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
284    if exist(profil_perso,'file')
285         h=load (profil_perso);
286        if isfield(h,'RootPath')&&ischar(h.RootPath)
287            oldfile=h.RootPath;
288        end
289    end
290end
291fileinput=uigetfile_uvmat('file browser',oldfile);
292if ~isempty(fileinput)
293     display_file_name(handles,fileinput,0)
294end
295%
296% [FileName, PathName] = uigetfile( ...
297%        {'*.xml;*.xls;*.png;*.tif;*.avi;*.AVI;*.nc', ' (*.xml,*.xls, *.png,*.tif, *.avi,*.nc)';
298%        '*.xml',  '.xml files '; ...
299%         '*.xls',  '.xls files '; ...
300%         '*.png','.png image files'; ...
301%         '*.tif','.tif image files'; ...
302%         '*.avi;*.AVI','.avi movie files'; ...
303%         '*.nc','.netcdf files'; ...
304%         '*.*',  'All Files (*.*)'}, ...
305%         'Pick a file',oldfile);
306% fileinput=[PathName FileName];%complete file name
307% [path,name,ext]=fileparts(fileinput);
308% if isequal(ext,'.xml')
309%     [Param,Heading]=xml2struct(fileinput);
310%     if ~strcmp(Heading,'Series')
311%         msg_box_uvmat('ERROR','xml file heading is not <Series>')
312%     else
313%         fill_GUI(Param,handles.series);%fill the GUI with the parameters retrieved from the xml file
314%         if isfield(Param,'CheckObject')&& Param.CheckObject
315%             set_object(Param.ProjObject)
316%         end
317%         set(handles.REFRESH,'UserData',1:size(Param.InputTable,1))
318%         REFRESH_Callback([],[], handles)
319%         return
320%     end
321% elseif isequal(ext,'.xls')
322%     msg_box_uvmat('ERROR','input file type not implemented')%A Faire: ouvrir le fichier pour naviguer
323% else
324%     display_file_name(handles,fileinput,0)
325% end
326
327% --------------------------------------------------------------------
328function MenuFile_1_Callback(hObject, eventdata, handles)
329fileinput=get(handles.MenuFile_1,'Label');
330display_file_name(handles,fileinput,0)
331
332% --------------------------------------------------------------------
333function MenuFile_2_Callback(hObject, eventdata, handles)
334fileinput=get(handles.MenuFile_2,'Label');
335display_file_name(handles,fileinput,0)
336
337% --------------------------------------------------------------------
338function MenuFile_3_Callback(hObject, eventdata, handles)
339fileinput=get(handles.MenuFile_3,'Label');
340display_file_name( handles,fileinput,0)
341
342% --------------------------------------------------------------------
343function MenuFile_4_Callback(hObject, eventdata, handles)
344fileinput=get(handles.MenuFile_4,'Label');
345display_file_name(handles,fileinput,0)
346
347% --------------------------------------------------------------------
348function MenuFile_5_Callback(hObject, eventdata, handles)
349fileinput=get(handles.MenuFile_5,'Label');
350display_file_name(handles,fileinput,0)
351
352% --------------------------------------------------------------------
353function MenuBrowse_insert_Callback(hObject, eventdata, handles)
354InputTable=get(handles.InputTable,'Data');
355RootPathCell=InputTable(:,1);
356SubDirCell=InputTable(:,3);
357RootFileCell=InputTable(:,2);
358oldfile=''; %default
359if isempty(RootPathCell)||isequal(RootPathCell,{''})%loads the previously stored file name and set it as default in the file_input box
360     dir_perso=prefdir;
361     profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
362     if exist(profil_perso,'file')
363          h=load (profil_perso);
364         if isfield(h,'filebase')&ischar(h.filebase)
365                 oldfile=h.filebase;
366         end
367         if isfield(h,'RootPath')&ischar(h.RootPath)
368                 oldfile=h.RootPath;
369         end
370     end
371 else
372     oldfile=fullfile(RootPathCell{1},RootFileCell{1});
373 end
374[FileName, PathName, filterindex] = uigetfile( ...
375       {'*.xml;*.xls;*.png;*.avi;*.AVI;*.nc', ' (*.xml,*.xls, *.png, *.avi,*.nc)';
376       '*.xml',  '.xml files '; ...
377        '*.xls',  '.xls files '; ...
378        '*.png','.png image files'; ...
379        '*.avi;*.AVI','.avi movie files'; ...
380        '*.nc','.netcdf files'; ...
381        '*.*',  'All Files (*.*)'}, ...
382        'Pick a file',oldfile);
383fileinput=[PathName FileName];%complete file name
384sizf=size(fileinput);
385if (~ischar(fileinput)|~isequal(sizf(1),1)),return;end
386[path,name,ext]=fileparts(fileinput);
387if isequal(ext,'.xml')
388    msgbox_uvmat('ERROR','input file type not implemented')%A Faire: ouvrir le fichier pour naviguer
389elseif isequal(ext,'.xls')
390    msgbox_uvmat('ERROR','input file type not implemented')%A Faire: ouvrir le fichier pour naviguer
391else
392    display_file_name(handles,fileinput,'append')
393end
394
395% --------------------------------------------------------------------
396function MenuFile_insert_1_Callback(hObject, eventdata, handles)
397% --------------------------------------------------------------------   
398fileinput=get(handles.MenuFile_insert_1,'Label');
399display_file_name(handles,fileinput,'append')
400
401% --------------------------------------------------------------------
402function MenuFile_insert_2_Callback(hObject, eventdata, handles)
403% --------------------------------------------------------------------   
404fileinput=get(handles.MenuFile_insert_2,'Label');
405display_file_name(handles,fileinput,'append')
406
407% --------------------------------------------------------------------
408function MenuFile_insert_3_Callback(hObject, eventdata, handles)
409% --------------------------------------------------------------------   
410fileinput=get(handles.MenuFile_insert_3,'Label');
411display_file_name( handles,fileinput,'append')
412
413% --------------------------------------------------------------------
414function MenuFile_insert_4_Callback(hObject, eventdata, handles)
415% --------------------------------------------------------------------   
416fileinput=get(handles.MenuFile_insert_4,'Label');
417display_file_name( handles,fileinput,'append')
418
419% --------------------------------------------------------------------
420function MenuFile_insert_5_Callback(hObject, eventdata, handles)
421% --------------------------------------------------------------------   
422fileinput=get(handles.MenuFile_insert_5,'Label');
423display_file_name(handles,fileinput,'append')
424
425%------------------------------------------------------------------------
426% --- Executes when entered data in editable cell(s) in InputTable.
427function InputTable_CellEditCallback(hObject, eventdata, handles)
428%------------------------------------------------------------------------
429set(handles.REFRESH,'Visible','on')
430set(handles.REFRESH_title,'Visible','on')
431iview=eventdata.Indices(1);
432view_set=get(handles.REFRESH,'UserData');
433if isempty(find(view_set==iview))
434    set(handles.REFRESH,'UserData',[view_set iview])
435end
436%% enable other menus and uicontrols
437set(handles.MenuOpen_insert,'Enable','on')
438set(handles.MenuFile_insert_1,'Enable','on')
439set(handles.MenuFile_insert_2,'Enable','on')
440set(handles.MenuFile_insert_3,'Enable','on')
441set(handles.MenuFile_insert_4,'Enable','on')
442set(handles.MenuFile_insert_5,'Enable','on')
443set(handles.RUN, 'Enable','On')
444set(handles.RUN,'BackgroundColor',[1 0 0])% set RUN button to red
445
446%------------------------------------------------------------------------
447% --- Executes on button press in REFRESH.
448function REFRESH_Callback(hObject, eventdata, handles)
449%------------------------------------------------------------------------
450InputTable=get(handles.InputTable,'Data');
451view_set=get(handles.REFRESH,'UserData');
452set(handles.REFRESH,'BackgroundColor',[1 1 0])% set REFRESH  button to yellow color (indicate activation)
453drawnow
454for iview=view_set
455    RootPath=fullfile(InputTable{iview,1},InputTable{iview,2});
456    if ~exist(RootPath,'dir')
457        i1_series=[];
458        RootPath=fileparts(RootPath); %will try the upped forldr
459    else
460        [RootPath,SubDir,RootFile,i1_series,i2_series,j1_series,j2_series,tild,FileType,FileInfo,MovieObject]=...
461            find_file_series(fullfile(InputTable{iview,1},InputTable{iview,2}),[InputTable{iview,3} InputTable{iview,4} InputTable{iview,5}]);
462    end
463    if isempty(i1_series)
464        [FileName, PathName] = uigetfile( ...
465            {'*.xml;*.xls;*.png;*.tif;*.avi;*.AVI;*.nc', ' (*.xml,*.xls, *.png,*.tif, *.avi,*.nc)';
466            '*.xml',  '.xml files '; ...
467            '*.xls',  '.xls files '; ...
468            '*.png','.png image files'; ...
469            '*.tif','.tif image files'; ...
470            '*.avi;*.AVI','.avi movie files'; ...
471            '*.nc','.netcdf files'; ...
472            '*.*',  'All Files (*.*)'}, ...
473            ['unvalid entry at line ' num2str(iview) ', pick a new input file'],RootPath);
474        fileinput=[PathName FileName];%complete file name
475        if isempty(fileinput) %abandon if the operation has been cancelled: no input from browser
476            set(handles.REFRESH,'BackgroundColor',[1 0 0])% set REFRESH  back to red color
477            return;
478        end
479        [path,name,ext]=fileparts(fileinput);
480        display_file_name(handles,fileinput,iview)
481    else
482        update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileType,FileInfo,MovieObject,iview)
483    end
484end
485set(handles.REFRESH,'Visible','off')
486set(handles.REFRESH_title,'Visible','off')
487set(handles.REFRESH,'UserData',[])
488
489%------------------------------------------------------------------------
490% --- Function called when a new file is opened, either by series_OpeningFcn or by the browser
491function display_file_name(handles,fileinput,iview)
492%------------------------------------------------------------------------ 
493%
494% INPUT:
495% handles: handles of elements in the GUI
496% fileinput: input file name, including path
497% iview: line index in the input table
498
499%% get the input root name, indices, file extension and nomenclature NomType
500if ~exist(fileinput,'file')
501    msgbox_uvmat('ERROR',['input file ' fileinput  ' does not exist'])
502    return
503end
504
505%% enable other menus and uicontrols
506set(handles.MenuOpen_insert,'Enable','on')
507set(handles.MenuFile_insert_1,'Enable','on')
508set(handles.MenuFile_insert_2,'Enable','on')
509set(handles.MenuFile_insert_3,'Enable','on')
510set(handles.MenuFile_insert_4,'Enable','on')
511set(handles.MenuFile_insert_5,'Enable','on')
512set(handles.RUN, 'Enable','On')
513set(handles.RUN,'BackgroundColor',[1 0 0])% set RUN button to red
514set(handles.InputTable,'BackgroundColor',[1 1 0]) % set RootPath edit box  to yellow
515drawnow
516
517%% detect root name, nomenclature and indices in the input file name:
518[FilePath,FileName,FileExt]=fileparts(fileinput);
519% detect the file type, get the movie object if relevant, and look for the corresponding file series:
520% the root name and indices may be corrected by including the first index i1 if a corresponding xml file exists
521[RootPath,SubDir,RootFile,i1_series,i2_series,j1_series,j2_series,NomType,FileType,FileInfo,MovieObject,i1,i2,j1,j2]=find_file_series(FilePath,[FileName FileExt]);
522if isempty(RootFile)&&isempty(i1_series)
523    errormsg='no input file in the series';
524    return
525end
526
527%% fill the list of file series
528InputTable=get(handles.InputTable,'Data');
529if strcmp(iview,'append') % display the input data as a new line in the table
530     iview=size(InputTable,1);
531     InputTable(iview+1,:)={'','','','',''};
532     InputTable(iview,:)=[{RootPath},{SubDir},{RootFile},{NomType},{FileExt}];
533elseif iview==0 % or re-initialise the list of  input  file series
534    iview=1;
535    InputTable=[{'','','','',''};{'','','','',''}];
536     InputTable(iview,:)=[{RootPath},{SubDir},{RootFile},{NomType},{FileExt}];
537    set(handles.TimeTable,'Data',[{[]},{[]},{[]},{[]}])
538    set(handles.MinIndex,'Data',[{[]},{[]}])
539    set(handles.MaxIndex,'Data',[{[]},{[]}])
540    set(handles.ListView,'Value',1)
541    set(handles.ListView,'String',{'1'})
542end
543nbview=size(InputTable,1);
544set(handles.ListView,'String',mat2cell((1:nbview)',ones(nbview,1)))
545set(handles.ListView,'Value',iview)
546set(handles.InputTable,'Data',InputTable)
547
548%% determine the selected reference field indices for pair display
549if isempty(i1)
550    i1=1;
551end
552if isempty(i2)
553    i2=i1;
554end
555ref_i=floor((i1+i2)/2);% reference image number corresponding to the file
556set(handles.num_ref_i,'String',num2str(ref_i));
557% set(handles.num_ref_i,'UserData',[i1 i2])%store the indices for future opening
558if isempty(j1)
559    j1=1;
560end
561if isempty(j2)
562    j2=j1;
563end
564ref_j=floor((j1+j2)/2);% reference image number corresponding to the file
565set(handles.num_ref_j,'String',num2str(ref_j));
566% set(handles.num_ref_j,'UserData',[j1 j2]);%store the indices for future opening
567
568%% update the list of recent files in the menubar and save it for future opening
569MenuFile=[{get(handles.MenuFile_1,'Label')};{get(handles.MenuFile_2,'Label')};...
570    {get(handles.MenuFile_3,'Label')};{get(handles.MenuFile_4,'Label')};{get(handles.MenuFile_5,'Label')}];
571str_find=strcmp(fileinput,MenuFile);
572if isempty(find(str_find,1))
573    MenuFile=[{fileinput};MenuFile];%insert the current file if not already in the list
574end
575for ifile=1:min(length(MenuFile),5)
576    eval(['set(handles.MenuFile_' num2str(ifile) ',''Label'',MenuFile{ifile});'])
577    eval(['set(handles.MenuFile_insert_' num2str(ifile) ',''Label'',MenuFile{ifile});'])
578end
579dir_perso=prefdir;
580profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
581if exist(profil_perso,'file')
582    save (profil_perso,'MenuFile','-append'); %store the file names for future opening of uvmat
583else
584    save (profil_perso,'MenuFile','-V6'); %store the file names for future opening of uvmat
585end
586% save the opened file to initiate future opening
587SeriesData=get(handles.series,'UserData');
588SeriesData.RefFile{iview}=fileinput;
589set(handles.series,'UserData',SeriesData)
590
591set(handles.InputTable,'BackgroundColor',[1 1 1])
592
593%% initiate input file series and refresh the current field view:     
594update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileType,FileInfo,MovieObject,iview);
595
596%------------------------------------------------------------------------
597% --- Update information about a new field series (indices to scan, timing,
598%     calibration from an xml file
599function update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileType,FileInfo,VideoObject,iview)
600%------------------------------------------------------------------------
601%% update the output dir
602InputTable=get(handles.InputTable,'Data');
603SubDir=sort(InputTable(1:end-1,2)); %set of subdirectories sorted in alphabetical order
604SubDirOut=SubDir{1};
605if numel(SubDir)>1
606    for ilist=2:numel(SubDir)
607        SubDirOut=[SubDirOut '-' SubDir{ilist}];
608    end
609end
610set(handles.OutputSubDir,'String',SubDirOut)
611
612%% display the min and max indices for the file series
613if size(i1_series,2)==2 && min(min(i1_series(:,1,:)))==0
614    MinIndex_j=1;% index j set to 1 by default
615    MaxIndex_j=1;
616    MinIndex_i=find(i1_series(:,2,:), 1 )-1;
617    MaxIndex_i=find(i1_series(:,2,:), 1, 'last' )-1;
618else
619    pair_max=squeeze(max(i1_series,[],1)); %max on pair index
620    j_max=max(pair_max,[],1);
621    MaxIndex_i=find(j_max, 1, 'last' )-1;% max ref index i
622    MinIndex_i=find(j_max, 1 )-1;% min ref index i
623    diff_i_max=diff(j_max);
624    if ~isempty(diff_i_max) && isequal (diff_i_max,diff_i_max(1)*ones(size(diff_i_max)))
625        set(handles.num_incr_i,'String',num2str(diff_i_max(1)))% detect an increment to dispaly by default
626    end
627    i_max=max(pair_max,[],2);
628    MaxIndex_j=max(find(i_max))-1;% max ref index i
629    MinIndex_j=min(find(i_max))-1;% min ref index i
630    diff_j_max=diff(i_max);
631    if isequal (diff_j_max,diff_j_max(1)*ones(size(diff_j_max)))
632        set(handles.num_incr_j,'String',num2str(diff_j_max(1)))
633    end
634end
635MinIndex=get(handles.MinIndex,'Data');%retrieve the min indices in the table MinIndex
636MaxIndex=get(handles.MaxIndex,'Data');%retrieve the max indices in the table MaxIndex
637if isequal(MinIndex_i,-1)
638    MinIndex_i=0;
639end
640if isequal(MinIndex_j,-1)
641    MinIndex_j=0;
642end
643MinIndex{iview,1}=MinIndex_i;
644MinIndex{iview,2}=MinIndex_j;
645MaxIndex{iview,1}=MaxIndex_i;
646MaxIndex{iview,2}=MaxIndex_j;
647
648set(handles.MinIndex,'Data',MinIndex)%display the min indices in the table MinIndex
649set(handles.MaxIndex,'Data',MaxIndex)%display the max indices in the table MaxIndex
650
651%% adjust the first and last indices, only if requested by the bounds
652% i index, compare input to min index i
653first_i=str2num(get(handles.num_first_i,'String'));%retrieve previous first i
654ref_i=str2num(get(handles.num_ref_i,'String'));%index i given by the input field
655if isempty(first_i)
656    first_i=ref_i;% first_i updated by the input value
657elseif first_i < MinIndex_i
658    first_i=MinIndex_i; % first_i set to the min i index (restricted by oter input lines)
659elseif first_i >MaxIndex_i
660    first_i=MaxIndex_i;% first_i set to the max i index (restricted by oter input lines)
661end
662% j index,  compare input to min index j
663first_j=str2num(get(handles.num_first_j,'String'));
664ref_j=str2num(get(handles.num_ref_j,'String'));%index j given by the input field
665if isempty(first_j)
666    first_j=ref_j;% first_j updated by the input value
667elseif first_j<MinIndex_j
668    first_j=MinIndex_j; % first_j set to the min j index (restricted by oter input lines)
669elseif first_j >MaxIndex_j
670    first_j=MaxIndex_j; % first_j set to the max j index (restricted by oter input lines)
671end
672% i index, compare input to max index i
673last_i=str2num(get(handles.num_last_i,'String'));
674if isempty(last_i)
675    last_i=ref_i;
676elseif last_i > MaxIndex_i
677    last_i=MaxIndex_i;
678elseif last_i<first_i
679    last_i=first_i;
680end
681% j index, compare input to max index j
682last_j=str2num(get(handles.num_last_j,'String'));
683if isempty(last_j)
684    last_j=ref_j;
685elseif last_j>MaxIndex_j
686    last_j=MaxIndex_j;
687elseif last_j<first_j
688    last_j=first_j;
689end
690set(handles.num_first_i,'String',num2str(first_i));
691set(handles.num_first_j,'String',num2str(first_j));
692set(handles.num_last_i,'String',num2str(last_i));
693set(handles.num_last_j,'String',num2str(last_j));
694
695%% read timing and total frame number from the current file (movie files) may be overrid by xml file
696InputTable=get(handles.InputTable,'Data');
697FileBase=fullfile(InputTable{iview,1},InputTable{iview,3});
698time=[];%default
699TimeSource='';
700% case of movies
701if strcmp(InputTable{iview,4},'*')
702    if ~isempty(VideoObject)
703        imainfo=get(VideoObject);
704        time=zeros(imainfo.NumberOfFrames+1,2);
705        time(:,2)=(0:1/imainfo.FrameRate:(imainfo.NumberOfFrames)/imainfo.FrameRate)';
706        TimeSource='video';
707       % set(han:dles.Dt_txt,'String',['Dt=' num2str(1000/imainfo.FrameRate) 'ms']);%display the elementary time interval in millisec
708        ColorType='truecolor';
709    elseif ~isempty(imformats(regexprep(InputTable{iview,5},'^.',''))) || isequal(InputTable{iview,5},'.vol')%&& isequal(NomType,'*')% multi-frame image
710        if ~isempty(InputTable{iview,2})
711            imainfo=imfinfo(fullfile(InputTable{iview,1},InputTable{iview,2},[InputTable{iview,3} InputTable{iview,5}]));
712        else
713            imainfo=imfinfo([FileBase InputTable{iview,5}]);
714        end
715        ColorType=imainfo.ColorType;%='truecolor' for color images
716        if length(imainfo) >1 %case of image with multiple frames
717            nbfield=length(imainfo);
718            nbfield_j=1;
719        end
720    end
721end
722
723%%  read image documentation file  if found
724XmlData=[];
725NbSlice_calib={};
726XmlFileName=find_imadoc(InputTable{iview,1},InputTable{iview,2},InputTable{iview,3},InputTable{iview,5});
727TimeUnit='';
728if ~isempty(XmlFileName)
729        [XmlData,warntext]=imadoc2struct(XmlFileName);
730        if isfield(XmlData,'Heading') && isfield(XmlData.Heading,'ImageName') && ischar(XmlData.Heading.ImageName)
731            [PP,FF,ext_ima_read]=fileparts(XmlData.Heading.ImageName);
732        end
733        if isfield(XmlData,'Time')
734            time=XmlData.Time;
735            TimeSource='xml';
736        end
737        if isfield(XmlData,'Camera')
738            if isfield(XmlData.Camera,'NbSlice')&& ~isempty(XmlData.Camera.NbSlice)
739                NbSlice_calib{iview}=XmlData.Camera.NbSlice;% Nbre of slices for Zindex in phys transform
740                if ~isequal(NbSlice_calib{iview},NbSlice_calib{1})
741                    msgbox_uvmat('WARNING','inconsistent number of Z indices for the two field series');
742                end
743            end
744            if isfield(XmlData.Camera,'TimeUnit')&& ~isempty(XmlData.Camera.TimeUnit)
745                TimeUnit=XmlData.Camera.TimeUnit;
746            end
747        end
748        if ~isempty(warntext)
749            msgbox_uvmat('WARNING',warntext)
750        end 
751end
752
753%% update time table
754if ~isempty(time)
755    TimeTable=get(handles.TimeTable,'Data');
756    first_i=str2num(get(handles.num_first_i,'String'));
757    last_i=str2num(get(handles.num_last_i,'String'));
758    first_j=str2num(get(handles.num_first_j,'String'));
759    last_j=str2num(get(handles.num_last_j,'String'));
760    MinIndexTable=get(handles.MinIndex,'Data');
761    MinIndex_i=MinIndexTable{iview,1};
762    MinIndex_j=MinIndexTable{iview,2};
763    MaxIndexTable=get(handles.MaxIndex,'Data');
764    MaxIndex_i=MaxIndexTable{iview,1};
765    MaxIndex_j=MaxIndexTable{iview,2};
766%     if isempty(MinIndex_j)% only i index
767%         TimeTable{iview,1}=time(MinIndex_i+1,2);
768%         TimeTable{iview,2}=time(first_i+1,2);
769%         TimeTable{iview,3}=time(last_i+1,2);
770%         TimeTable{iview,4}=time(MaxIndex_i+1,2);
771    if ~isempty(time)
772        TimeTable{iview,1}=time(MinIndex_i+1,MinIndex_j+1);
773        if size(time)>=[first_i+1 first_j+1]
774        TimeTable{iview,2}=time(first_i+1,first_j+1);
775        end
776        if size(time)>=[last_i+1 last_j+1]
777            TimeTable{iview,3}=time(last_i+1,last_j+1);
778        end
779        if size(time)>=[MaxIndex_i+1 MaxIndex_j+1];
780            TimeTable{iview,4}=time(MaxIndex_i+1,MaxIndex_j+1);
781        end
782    end
783    set(handles.TimeTable,'Data',TimeTable)
784end
785
786%% number of slices
787NbSlice=1;%default
788check_calib=0;
789if isfield(XmlData,'GeometryCalib')
790    check_calib=1;
791    if isfield(XmlData.GeometryCalib,'SliceCoord')
792    siz=size(XmlData.GeometryCalib.SliceCoord);
793    if siz(1)>1
794        NbSlice=siz(1);
795    end
796    end
797end
798set(handles.num_NbSlice,'String',num2str(NbSlice))
799   
800%% update pair menus
801set(handles.Pairs,'Visible','on')
802set(handles.PairString,'Visible','on')
803ListView=get(handles.ListView,'String');
804ListView{iview}=num2str(iview);
805set(handles.ListView,'String',ListView);
806set(handles.ListView,'Value',iview)
807update_mode(handles,i1_series,i2_series,j1_series,j2_series,time)
808
809%% update the series info in 'UserData'
810SeriesData=get(handles.series,'UserData');
811SeriesData.i1_series{iview}=i1_series;
812SeriesData.i2_series{iview}=i2_series;
813SeriesData.j1_series{iview}=j1_series;
814SeriesData.j2_series{iview}=j2_series;
815SeriesData.FileType{iview}=FileType;
816SeriesData.FileInfo{iview}=FileInfo;
817SeriesData.Time{iview}=time;
818if ~isempty(TimeSource)
819    SeriesData.TimeSource=TimeSource;
820end
821if ~isempty(TimeUnit)
822    SeriesData.TimeUnit=TimeUnit;
823end
824if check_calib
825SeriesData.GeometryCalib{iview}=XmlData.GeometryCalib;
826end
827set(handles.series,'UserData',SeriesData)
828
829%% enable j index visibilitycellfun(@isempty,regexp(PairString,'^j'))
830% state='off';
831check_jindex=~cellfun(@isempty,SeriesData.j1_series); %look for non empty j indices
832if isempty(find(check_jindex))
833    enable_j(handles,'off') % no j index needed
834else
835    PairString=get(handles.PairString,'Data');
836    if isempty(find(cellfun(@isempty,regexp(PairString,'^j'))))% if all pair string begins by j (burst)
837        enable_j(handles,'off') % no j index needed
838    else
839        enable_j(handles,'on')
840    end
841end
842
843%% display the set of existing files as an image
844set(handles.FileStatus,'Units','pixels')
845Position=get(handles.FileStatus,'Position');
846set(handles.FileStatus,'Units','normalized')
847xI=0.5:Position(3)-0.5;
848nbview=numel(SeriesData.i1_series);
849pair_max=cell(1,nbview);
850for iview=1:nbview
851    pair_max{iview}=squeeze(max(SeriesData.i1_series{iview},[],1)); %max on pair index
852    if (strcmp(get(handles.num_first_j,'Visible'),'off')&& size(pair_max{iview},2)~=1)
853        pair_max{iview}=squeeze(max(pair_max{iview},[],1)); % consider only the i index
854    end
855    index_min(iview)=find(pair_max{iview}>0, 1 );
856    index_max(iview)=find(pair_max{iview}>0, 1, 'last' );
857end
858index_min=min(index_min);
859index_max=max(index_max);
860range_index=index_max-index_min+1;
861scale_y=Position(4)/nbview;
862scale_x=Position(3)/range_index;
863x=(0.5:range_index-0.5)*Position(3)/range_index;
864% y=(0.5:nbview-0.5)*Position(4)/nbview;
865range_y=max(1,floor(Position(4)/nbview));
866CData=zeros(nbview*range_y,floor(Position(3)));
867for iview=1:nbview
868    ind_y=1+(iview-1)*range_y:iview*range_y;
869    LineData=zeros(1,range_index);
870    x_index=find(pair_max{iview}>0)-index_min+1;
871    LineData(x_index)=1;
872    if numel(x)>1
873    LineData=interp1(x,LineData,xI,'nearest');
874    CData(ind_y,:)=ones(size(ind_y'))*LineData;
875    end
876end
877CData=cat(3,zeros(size(CData)),CData,zeros(size(CData)));
878set(handles.FileStatus,'CData',CData);
879
880
881%% enable field and veltype menus, in accordance with the current action
882ActionName_Callback([],[], handles)
883
884%% check for pair display
885check_pairs=0;
886for iview=1:numel(SeriesData.i2_series)
887    if ~isempty(SeriesData.i2_series{iview})||~isempty(SeriesData.j2_series{iview})
888        check_pairs=1;
889    end
890end
891if check_pairs
892    set(handles.Pairs,'Visible','on')
893    set(handles.PairString,'Visible','on')
894else
895    set(handles.Pairs,'Visible','off')
896    set(handles.PairString,'Visible','off')
897end
898
899%% set length of waitbar
900displ_time(handles)
901
902
903%% set default options in menu 'Fields'
904switch FileType
905    case {'civx','civdata'}
906        [FieldList,ColorList]=set_field_list('U','V','C');
907        set(handles.FieldName,'String',[{'image'};FieldList;{'get_field...'}]);%standard menu for civx data
908        set(handles.FieldName,'Value',2) % set menu to 'velocity
909        set(handles.Coord_x,'Value',1);
910        set(handles.Coord_x,'String',{'X'});
911        set(handles.Coord_y,'Value',1);
912        set(handles.Coord_y,'String',{'Y'});
913    case 'netcdf'
914        set(handles.FieldName,'Value',1)
915        set(handles.FieldName,'String',{'get_field...'})
916        if isempty(i2_series)
917            i2=[];
918        else
919            i2=i2_series(1,ref_j+1,ref_i+1);
920        end
921        if isempty(j1_series)
922            j1=[];j2=[];
923        else
924            j1=j1_series(1,ref_j+1,ref_i+1);
925            if isempty(j2_series)
926                j2=[];
927            else
928                j2=j2_series(1,ref_j+1,ref_i+1);
929            end
930        end
931        FileName=fullfile_uvmat(InputTable{iview,1},InputTable{iview,2},InputTable{iview,3},InputTable{iview,5},InputTable{iview,4},i1_series(1,ref_j+1,ref_i+1),i2,j1,j2);
932%         hget_field=get_field(FileName);
933%         hhget_field=guidata(hget_field);
934%         get_field('RUN_Callback',hhget_field.RUN,[],hhget_field);
935    otherwise
936        set(handles.FieldName,'Value',1) % set menu to 'image'
937        set(handles.FieldName,'String',{'image'})
938        set(handles.Coord_x,'Value',1);
939        set(handles.Coord_x,'String',{'AX'});
940        set(handles.Coord_y,'Value',1);
941        set(handles.Coord_y,'String',{'AY'});
942end
943
944%------------------------------------------------------------------------
945function num_first_i_Callback(hObject, eventdata, handles)
946%------------------------------------------------------------------------
947num_last_i_Callback(hObject, eventdata, handles)
948
949%------------------------------------------------------------------------
950function num_last_i_Callback(hObject, eventdata, handles)
951%------------------------------------------------------------------------
952SeriesData=get(handles.series,'UserData');
953if ~isfield(SeriesData,'Time')
954    SeriesData.Time{1}=[];
955end
956displ_time(handles);
957
958%------------------------------------------------------------------------
959function num_first_j_Callback(hObject, eventdata, handles)
960%------------------------------------------------------------------------
961 num_last_j_Callback(hObject, eventdata, handles)
962
963%------------------------------------------------------------------------
964function num_last_j_Callback(hObject, eventdata, handles)
965%------------------------------------------------------------------------
966first_j=str2num(get(handles.num_first_j,'String'));
967last_j=str2num(get(handles.num_last_j,'String'));
968ref_j=ceil((first_j+last_j)/2);
969set(handles.num_ref_j,'String', num2str(ref_j))
970num_ref_j_Callback(hObject, eventdata, handles)
971SeriesData=get(handles.series,'UserData');
972if ~isfield(SeriesData,'Time')
973    SeriesData.Time{1}=[];
974end
975displ_time(handles);
976
977
978%------------------------------------------------------------------------
979% ---- find the times corresponding to the first and last indices of a series
980function displ_time(handles)
981%------------------------------------------------------------------------
982SeriesData=get(handles.series,'UserData');%
983ref_i=[str2num(get(handles.num_first_i,'String')) str2num(get(handles.num_last_i,'String'))];
984ref_j=[str2num(get(handles.num_first_j,'String')) str2num(get(handles.num_last_j,'String'))];
985TimeTable=get(handles.TimeTable,'Data');
986Pairs=get(handles.PairString,'Data');
987for iview=1:size(TimeTable,1)
988    if size(SeriesData.Time,1)<iview
989        break
990    end
991    i1=ref_i;
992    j1=ref_j;
993    i2=ref_i;
994    j2=ref_j;
995    % case of pairs
996    if ~isempty(Pairs{iview,1})
997        r=regexp(Pairs{iview,1},'(?<mode>(Di=)|(Dj=)) -*(?<num1>\d+)\|(?<num2>\d+)','names');
998        if isempty(r)
999            r=regexp(Pairs{iview,1},'(?<num1>\d+)(?<mode>-)(?<num2>\d+)','names');
1000        end
1001        switch r.mode
1002            case 'Di='  %  case 'series(Di)')
1003                i1=ref_i-str2num(r.num1);
1004                i2=ref_i+str2num(r.num2);
1005            case 'Dj='  %  case 'series(Dj)'
1006                j1=ref_j-str2num(r.num1);
1007                j2=ref_j+str2num(r.num2);
1008            case '-'  % case 'bursts'
1009                j1=str2num(r.num1)*ones(size(ref_i));
1010                j2=str2num(r.num2)*ones(size(ref_i));
1011        end
1012    end
1013    TimeTable{iview,2}=[];
1014    TimeTable{iview,3}=[];
1015    if size(SeriesData.Time{iview},1)>=i2(2)&&size(SeriesData.Time{iview},1)>=j2(2)
1016        if isempty(ref_j)
1017            time_first=(SeriesData.Time{iview}(i1(1)+1)+SeriesData.Time{iview}(i2(1)+1))/2;
1018            time_last=(SeriesData.Time{iview}(i1(2)+1)+SeriesData.Time{iview}(i2(2))+1)/2;
1019        else
1020            time_first=(SeriesData.Time{iview}(i1(1)+1,j1(1)+1)+SeriesData.Time{iview}(i2(1)+1,j2(1)+1))/2;
1021            time_last=(SeriesData.Time{iview}(i1(2)+1,j1(2)+1)+SeriesData.Time{iview}(i2(2)+1,j2(2)+1))/2;
1022        end
1023        TimeTable{iview,2}=time_first; %TODO: take into account pairs
1024        TimeTable{iview,3}=time_last; %TODO: take into account pairs
1025    end
1026end
1027set(handles.TimeTable,'Data',TimeTable)
1028
1029%% set the waitbar position with respect to the min and max in the series
1030for iview=1:numel(SeriesData.i1_series)
1031    pair_max{iview}=squeeze(max(SeriesData.i1_series{iview},[],1)); %max on pair index
1032    if (strcmp(get(handles.num_first_j,'Visible'),'off')&& size(pair_max{iview},2)~=1)
1033        pair_max{iview}=squeeze(max(pair_max{iview},[],1)); % consider only the i index
1034    end
1035    pair_max{iview}=reshape(pair_max{iview},1,[]);
1036    index_min(iview)=find(pair_max{iview}>0, 1 );
1037    index_max(iview)=find(pair_max{iview}>0, 1, 'last' );
1038end
1039[index_min,iview_min]=min(index_min);
1040[index_max,iview_max]=min(index_max);
1041if size(SeriesData.i1_series{iview_min},2)==1% movie
1042    index_first=ref_i(1);
1043    index_last=ref_i(2);
1044else
1045    index_first=(ref_i(1)-1)*(size(SeriesData.i1_series{iview_min},1))+ref_j(1)+1;
1046    index_last=(ref_i(2)-1)*(size(SeriesData.i1_series{iview_max},1))+ref_j(2)+1;
1047end
1048range=index_max-index_min+1;
1049coeff_min=(index_first-index_min)/range;
1050coeff_max=(index_last-index_min+1)/range;
1051Position=get(handles.Waitbar,'Position');% position of the waitbar:= [ x,y, width, height]
1052Position_status=get(handles.FileStatus,'Position');
1053Position(1)=coeff_min*Position_status(3)+Position_status(1);
1054Position(3)=Position_status(3)*(coeff_max-coeff_min);
1055set(handles.Waitbar,'Position',Position)
1056update_waitbar(handles.Waitbar,0)
1057
1058%------------------------------------------------------------------------
1059% --- Executes when selected cell(s) is changed in PairString.
1060function PairString_CellSelectionCallback(hObject, eventdata, handles)
1061%------------------------------------------------------------------------   
1062set(handles.ListView,'Value',eventdata.Indices(1))% detect the selected raw index
1063ListView_Callback ([],[],handles) % update the list of available pairs
1064
1065%------------------------------------------------------------------------
1066%------------------------------------------------------------------------
1067%  III - FUNCTIONS ASSOCIATED TO THE FRAME SET PAIRS
1068%------------------------------------------------------------------------
1069%------------------------------------------------------------------------
1070% --- Executes on selection change in ListView.
1071function ListView_Callback(hObject, eventdata, handles)
1072%------------------------------------------------------------------------   
1073SeriesData=get(handles.series,'UserData');
1074i2_series=[];
1075j2_series=[];
1076iview=get(handles.ListView,'Value');
1077if ~isempty(SeriesData.i2_series{iview})
1078    i2_series=SeriesData.i2_series{iview};
1079end
1080if ~isempty(SeriesData.j2_series{iview})
1081    j2_series=SeriesData.j2_series{iview};
1082end
1083update_mode(handles,SeriesData.i1_series{iview},SeriesData.i2_series{iview},...
1084    SeriesData.j1_series{iview},SeriesData.j2_series{iview},SeriesData.Time{iview})
1085
1086%------------------------------------------------------------------------
1087% --- Executes on button press in mode.
1088function mode_Callback(hObject, eventdata, handles)
1089%------------------------------------------------------------------------       
1090SeriesData=get(handles.series,'UserData');
1091iview=get(handles.ListView,'Value');
1092mode_list=get(handles.mode,'String');
1093mode=mode_list{get(handles.mode,'Value')};
1094if isequal(mode,'bursts')
1095    enable_i(handles,'On')
1096    enable_j(handles,'Off') %do not display j index scanning in burst mode (j is fixed by the burst choice)
1097else
1098    enable_i(handles,'On')
1099    enable_j(handles,'Off')
1100end
1101fill_ListPair(handles,SeriesData.i1_series{iview},SeriesData.i2_series{iview},...
1102    SeriesData.j1_series{iview},SeriesData.j2_series{iview},SeriesData.Time{iview})
1103ListPairs_Callback([],[],handles)
1104
1105%-------------------------------------------------------------
1106% --- Executes on selection in ListPairs.
1107function ListPairs_Callback(hObject,eventdata,handles)
1108%------------------------------------------------------------
1109list_pair=get(handles.ListPairs,'String');%get the menu of image pairs
1110if isempty(list_pair)
1111    string='';
1112else
1113    string=list_pair{get(handles.ListPairs,'Value')};
1114    string=regexprep(string,',.*','');%removes time indication (after ',')
1115end
1116PairString=get(handles.PairString,'Data');
1117iview=get(handles.ListView,'Value');
1118PairString{iview,1}=string;
1119% report the selected pair string to the table PairString
1120set(handles.PairString,'Data',PairString)
1121
1122%------------------------------------------------------------------------
1123function num_ref_i_Callback(hObject, eventdata, handles)
1124%------------------------------------------------------------------------
1125mode_list=get(handles.mode,'String');
1126mode=mode_list{get(handles.mode,'Value')};
1127SeriesData=get(handles.series,'UserData');
1128iview=get(handles.ListView,'Value');
1129fill_ListPair(handles,SeriesData.i1_series{iview},SeriesData.i2_series{iview},...
1130    SeriesData.j1_series{iview},SeriesData.j2_series{iview},SeriesData.Time{iview});% update the menu of pairs depending on the available netcdf files
1131ListPairs_Callback([],[],handles)
1132
1133%------------------------------------------------------------------------
1134function num_ref_j_Callback(hObject, eventdata, handles)
1135%------------------------------------------------------------------------
1136num_ref_i_Callback(hObject, eventdata, handles)
1137
1138%------------------------------------------------------------------------
1139function update_mode(handles,i1_series,i2_series,j1_series,j2_series,time)
1140%------------------------------------------------------------------------   
1141% check_burst=0;
1142if isempty(j2_series)% no j pair
1143    if isempty(i2_series)
1144        set(handles.mode,'Value',1)
1145        set(handles.mode,'String',{''})% no pair menu to display
1146    else   
1147        set(handles.mode,'Value',1)
1148        set(handles.mode,'String',{'series(Di)'}) % pair menu with only option Di
1149    end
1150else %existence of j pairs
1151    pair_max=squeeze(max(i1_series,[],1)); %max on pair index
1152    j_max=max(pair_max,[],1);
1153    MaxIndex_i=max(find(j_max))-1;% max ref index i
1154    MinIndex_i=min(find(j_max))-1;% min ref index i
1155    i_max=max(pair_max,[],2);
1156    MaxIndex_j=max(find(i_max))-1;% max ref index i
1157    MinIndex_j=min(find(i_max))-1;% min ref index i
1158    if MaxIndex_j==MinIndex_j
1159        set(handles.mode,'Value',1);
1160        set(handles.mode,'String',{'bursts'})
1161%         check_burst=1;
1162    elseif MaxIndex_i==MinIndex_i
1163        set(handles.mode,'Value',1);
1164        set(handles.mode,'String',{'series(Dj)'})
1165    else
1166        set(handles.mode,'String',{'bursts';'series(Dj)'})
1167        if (MaxIndex_j-MinIndex_j)>10
1168            set(handles.mode,'Value',2);%set mode to series(Dj) if more than 10 j values
1169        else
1170            set(handles.mode,'Value',1);
1171%             check_burst=1;
1172        end
1173    end
1174end
1175% if check_burst
1176%     enable_i(handles,'On')
1177%     enable_j(handles,'Off') %do not display j index scanning in burst mode (j is fixed by the burst choice)
1178% else
1179%     enable_i(handles,'On')
1180%     if isempty(j1_series)
1181%          enable_j(handles,'Off')
1182%     else
1183%         enable_j(handles,'On')
1184%     end
1185% end
1186fill_ListPair(handles,i1_series,i2_series,j1_series,j2_series,time)
1187ListPairs_Callback([],[],handles)
1188
1189%--------------------------------------------------------------
1190% determine the menu for civ1 pairstring depending on existing netcdf files
1191% with the reference indices num_ref_i and num_ref_j
1192%----------------------------------------------------------------
1193function fill_ListPair(handles,i1_series,i2_series,j1_series,j2_series,time)
1194
1195mode_list=get(handles.mode,'String');
1196mode=mode_list{get(handles.mode,'Value')};
1197ref_i=str2num(get(handles.num_ref_i,'String'));
1198if isempty(ref_i)
1199    ref_i=1;
1200end
1201if strcmp(get(handles.num_ref_j,'Visible'),'on')
1202    ref_j=str2num(get(handles.num_ref_j,'String'));
1203    if isempty(ref_j)
1204        ref_j=1;
1205    end
1206else
1207    ref_j=1;
1208end
1209TimeUnit=get(handles.TimeUnit,'String');
1210if length(TimeUnit)>=1
1211    dtunit=['m' TimeUnit];
1212else
1213    dtunit='e-03';
1214end
1215
1216displ_pair={};
1217if strcmp(mode,'series(Di)')
1218    if isempty(i2_series)
1219        msgbox_uvmat('ERROR','no i1-i2 pair available')
1220        return
1221    end
1222    diff_i=i2_series-i1_series;
1223    min_diff=min(diff_i(diff_i>0));
1224    max_diff=max(diff_i(diff_i>0));
1225    for ipair=min_diff:max_diff
1226        if numel(diff_i(diff_i==ipair))>0
1227            pair_string=['Di= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2)) ];
1228            if ~isempty(time)
1229                if ref_i<=floor(ipair/2)
1230                    ref_i=floor(ipair/2)+1;% shift ref_i to get the first pair
1231                end
1232                Dt=time(ref_i+ceil(ipair/2),ref_j)-time(ref_i-floor(ipair/2),ref_j);
1233                pair_string=[pair_string ', Dt=' num2str(Dt) ' ' dtunit];
1234            end
1235            displ_pair=[displ_pair;{pair_string}];
1236        end
1237    end
1238    if ~isempty(displ_pair)
1239        displ_pair=[displ_pair;{'Di=*|*'}];
1240    end
1241elseif strcmp(mode,'series(Dj)')
1242    if isempty(j2_series)
1243        msgbox_uvmat('ERROR','no j1-j2 pair available')
1244        return
1245    end
1246    diff_j=j2_series-j1_series;
1247    min_diff=min(diff_j(diff_j>0));
1248    max_diff=max(diff_j(diff_j>0));
1249    for ipair=min_diff:max_diff
1250        if numel(diff_j(diff_j==ipair))>0
1251            pair_string=['Dj= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2)) ];
1252            if ~isempty(time)
1253                if ref_j<=floor(ipair/2)
1254                    ref_j=floor(ipair/2)+1;% shift ref_i to get the first pair
1255                end
1256                Dt=time(ref_i,ref_j+ceil(ipair/2))-time(ref_i,ref_j-floor(ipair/2));
1257                pair_string=[pair_string ', Dt=' num2str(Dt) ' ' dtunit];
1258            end
1259            displ_pair=[displ_pair;{pair_string}];
1260        end
1261    end
1262    if ~isempty(displ_pair)
1263        displ_pair=[displ_pair;{'Dj=*|*'}];
1264    end
1265elseif strcmp(mode,'bursts')
1266    if isempty(j2_series)
1267        msgbox_uvmat('ERROR','no j1-j2 pair available')
1268        return
1269    end
1270    diff_j=j2_series-j1_series;
1271    min_j1=min(j1_series(j1_series>0));
1272    max_j1=max(j1_series(j1_series>0));
1273    min_j2=min(j2_series(j2_series>0));
1274    max_j2=max(j2_series(j2_series>0));
1275    for pair1=min_j1:min(max_j1,min_j1+20)
1276        for pair2=min_j2:min(max_j2,min_j2+20)
1277        if numel(j1_series(j1_series==pair1))>0 && numel(j2_series(j2_series==pair2))>0
1278            displ_pair=[displ_pair;{['j= ' num2str(pair1) '-' num2str(pair2)]}];
1279        end
1280        end
1281    end
1282    if ~isempty(displ_pair)
1283        displ_pair=[displ_pair;{'j=*-*'}];
1284    end
1285end
1286set(handles.num_ref_i,'String',num2str(ref_i)) % update ref_i and ref_j
1287set(handles.num_ref_j,'String',num2str(ref_j))
1288
1289%% display list of pairstring
1290displ_pair_list=get(handles.ListPairs,'String');
1291NewVal=[];
1292if ~isempty(displ_pair_list)
1293Val=get(handles.ListPairs,'Value');
1294NewVal=find(strcmp(displ_pair_list{Val},displ_pair),1);% look at the previous display in the new menu displ_pï¿œir
1295end
1296if ~isempty(NewVal)
1297    set(handles.ListPairs,'Value',NewVal)
1298else
1299    set(handles.ListPairs,'Value',1)
1300end
1301set(handles.ListPairs,'String',displ_pair)
1302
1303%-------------------------------------
1304function enable_i(handles,state)
1305set(handles.i_txt,'Visible',state)
1306set(handles.num_first_i,'Visible',state)
1307set(handles.num_last_i,'Visible',state)
1308set(handles.num_incr_i,'Visible',state)
1309% set(handles.num_MaxIndex_i,'Visible',state)
1310set(handles.num_ref_i,'Visible',state)
1311set(handles.ref_i_text,'Visible',state)
1312
1313%-----------------------------------
1314function enable_j(handles,state)
1315set(handles.j_txt,'Visible',state)
1316set(handles.num_first_j,'Visible',state)
1317set(handles.num_last_j,'Visible',state)
1318set(handles.num_incr_j,'Visible',state)
1319set(handles.num_ref_j,'Visible',state)
1320set(handles.ref_j_text,'Visible',state)
1321% if strcmp(state,'off')
1322%     set(handles.MinIndex,'ColumnName',{'imax'})
1323% set(handles.MinIndex,'ColumnEditable',logical(0))
1324% else
1325%         set(handles.MinIndex,'ColumnName',{'imax','jmax'})
1326% end
1327
1328
1329%%%%%%%%%%%%%%%%%%%%
1330%%  MAIN ActionName FUNCTIONS
1331%%%%%%%%%%%%%%%%%%%%
1332%------------------------------------------------------------------------
1333% --- Executes on button press in RUN.
1334function RUN_Callback(hObject, eventdata, handles)
1335%------------------------------------------------------------------------
1336
1337set(handles.RUN,'BusyAction','queue');
1338set(0,'CurrentFigure',handles.series)
1339set(handles.RUN, 'Enable','Off')
1340set(handles.RUN,'BackgroundColor',[0.831 0.816 0.784])
1341drawnow
1342
1343%% read the input parameters and set the output dir and nomenclature
1344[Series,OutputDir,errormsg]=prepare_jobs(handles);% get parameters form the GUI series
1345if ~isempty(errormsg)
1346    if ~strcmp(errormsg,'Cancel')
1347    msgbox_uvmat('ERROR',errormsg)
1348    end
1349    STOP_Callback([],[], handles)
1350    return
1351end
1352OutputNomType=nomtype2pair(Series.InputTable{1,4});% nomenclature for output files
1353DirXml=fullfile(OutputDir,'0_XML');
1354if ~exist(DirXml,'dir')
1355    [tild,msg1]=mkdir(DirXml);
1356    if ~strcmp(msg1,'')
1357        msgbox_uvmat('ERROR',['cannot create ' DirXml ': ' msg1]);%error message for directory creation
1358        return
1359    end
1360end
1361
1362%% select the Action modes
1363RunMode='local';%default
1364if isfield(Series.Action,'RunMode')
1365RunMode=Series.Action.RunMode;
1366end
1367ActionExt='.m';%default
1368if isfield(Series.Action,'ActionExt')
1369    ActionExt=Series.Action.ActionExt;% '.m' or '.sh' (compiled)
1370end
1371ActionName=Series.Action.ActionName;
1372ActionPath=Series.Action.ActionPath;
1373path_series=fileparts(which('series'));
1374
1375%% create the Action fct handle if RunMode option = 'local'
1376if strcmp(RunMode,'local')
1377    if ~isequal(ActionPath,path_series)
1378        eval(['spath=which(''' ActionName ''');']) %spath = current path of the selected function ACTION
1379        if ~exist(ActionPath,'dir')
1380            msgbox_uvmat('ERROR',['The prescribed function path ' ActionPath ' does not exist']);
1381            return
1382        end
1383        if ~isequal(spath,ActionPath)
1384            addpath(ActionPath)% add the prescribed path if not the current one
1385        end
1386    end
1387    eval(['h_fun=@' ActionName ';'])%create a function handle for ACTION
1388    if ~isequal(ActionPath,path_series)
1389        rmpath(ActionPath)% add the prescribed path if not the current one
1390    end
1391end
1392
1393%% Get RunTime code from the file PARAM.xml (needed to run compiled functions)
1394errormsg='';%default error message
1395xmlfile=fullfile(path_series,'PARAM.xml');
1396test_batch=0;%default: ,no batch mode available
1397if ~exist(xmlfile,'file')
1398    [success,message]=copyfile(fullfile(path_series,'PARAM.xml.default'),xmlfile);
1399end
1400RunTime='';
1401if strcmp(ActionExt,'.sh')
1402    if exist(xmlfile,'file')
1403        s=xml2struct(xmlfile);
1404        if strcmp(RunMode,'cluster_oar') && isfield(s,'BatchParam')
1405            if isfield(s.BatchParam,'RunTime')
1406                RunTime=s.BatchParam.RunTime;
1407            end
1408            if isfield(s.BatchParam,'NbCore')
1409                NbCore=s.BatchParam.NbCore;
1410            end
1411        elseif (strcmp(RunMode,'background')||strcmp(RunMode,'local')) && isfield(s,'RunParam')
1412            if isfield(s.RunParam,'RunTime')
1413                RunTime=s.RunParam.RunTime;
1414            end
1415            if isfield(s.RunParam,'NbCore')
1416                NbCore=s.RunParam.NbCore;
1417            end
1418        end
1419    end
1420    if isempty(RunTime) && strcmp(RunMode,'cluster_oar')
1421        msgbox_uvmat('ERROR','RunTime name not found in PARAM.xml, compiled version .sh cannot run on cluster')
1422        return
1423    end
1424%     Series.RunTime=RunTime;
1425end
1426
1427%% set nbre of cluster cores and processes
1428switch RunMode
1429    case {'local','background'}
1430        NbCore=1;% no need to split the calculation
1431    case 'cluster_oar'
1432        if strcmp(Series.Action.ActionExt,'.m')% case of Matlab function (uncompiled)
1433            NbCore=1;% one core used only (limitation of Matlab licences)
1434            msgbox_uvmat('WARNING','Number of cores =1: select the compiled version civ_matlab.sh for multi-core processing');
1435            extra_oar='';
1436        else
1437            answer=inputdlg({'Number of cores (max 36)','extra oar options'},'oarsub parameter',1,{'12',''});
1438            NbCore=str2double(answer{1});
1439            extra_oar=answer{2};
1440        end
1441end
1442if ~isfield(Series.IndexRange,'NbSlice')
1443    Series.IndexRange.NbSlice=[];
1444end
1445if isempty(Series.IndexRange.NbSlice)
1446    NbProcess=NbCore;% choose one process per core
1447else
1448    NbProcess=Series.IndexRange.NbSlice;% the nbre of run processes is equal to the number of slices
1449    NbCore=min(NbCore,NbProcess);% at least one process per core
1450end
1451       
1452
1453%% read index ranges
1454[first_i,incr_i,last_i,first_j,incr_j,last_j,errormsg]=get_index_range(Series.IndexRange);
1455if ~isempty(errormsg)
1456    msgbox_uvmat('ERROR',['series/Run_Callback/get_index_range' errormsg])
1457    set(handles.RUN, 'Enable','On'),
1458    set(handles.RUN,'BackgroundColor',[1 0 0])
1459    return
1460else
1461    BlockLength=ceil(numel(first_i:incr_i:last_i)/NbProcess);
1462end
1463nbfield_j=numel(first_j:incr_j:last_j);
1464
1465%% record nbre of output files and starting time for computation for status
1466StatusData=get(handles.status,'UserData');
1467if isfield(StatusData,'OutputFileMode')
1468    switch StatusData.OutputFileMode
1469        case 'NbInput'
1470            StatusData.NbOutputFile=numel(first_i:incr_i:last_i)*numel(first_j:incr_j:last_j);
1471        case 'NbInput_i'
1472            StatusData.NbOutputFile=numel(first_i:incr_i:last_i);
1473        case 'NbSlice'   
1474            StatusData.NbOutputFile=str2num(get(handles.num_NbSlice,'String'));
1475    end
1476end
1477StatusData.TimeStart=now;
1478set(handles.status,'UserData',StatusData)
1479
1480%% direct processing on the current Matlab session
1481if strcmp (RunMode,'local')
1482    Series.RUNHandle=handles.RUN;
1483    Series.WaitbarHandle=handles.Waitbar;
1484    for iprocess=1:NbProcess
1485        if isempty(Series.IndexRange.NbSlice)
1486            Series.IndexRange.first_i=first_i+(iprocess-1)*BlockLength*incr_i;
1487            if Series.IndexRange.first_i>last_i
1488                break
1489            end
1490            Series.IndexRange.last_i=min(first_i+(iprocess)*BlockLength*incr_i-1,last_i);
1491        else
1492            Series.IndexRange.first_i= first_i+incr_i*(iprocess-1);
1493            Series.IndexRange.incr_i=incr_i*Series.IndexRange.NbSlice;
1494        end
1495        t=struct2xml(Series);
1496        t=set(t,1,'name','Series');
1497        filexml=fullfile_uvmat(DirXml,'',Series.InputTable{1,3},'.xml',OutputNomType,...
1498            Series.IndexRange.first_i,Series.IndexRange.last_i,first_j,last_j);
1499        save(t,filexml);
1500        switch ActionExt
1501            case '.m'
1502                h_fun(Series);
1503            case '.sh'
1504                switch computer
1505                    case {'PCWIN','PCWIN64'} %Windows system
1506                        filexml=regexprep(filexml,'\\','\\\\');% add '\' so that '\' are left as characters
1507                        system([fullfile(ActionPath,[ActionName '.sh']) ' ' RunTime ' ' filexml]);% TODO: adapt to DOS system
1508                    case {'GLNX86','GLNXA64','MACI64'}%Linux  system
1509                        system([fullfile(ActionPath,[ActionName '.sh']) ' ' RunTime ' ' filexml]);
1510                end
1511        end
1512    end
1513elseif strcmp(get(handles.OutputDirExt,'Visible'),'off')
1514    msgbox_uvmat('ERROR',['no output file for Action ' ActionName ', use run mode = local']);% a output dir is needed for background option
1515    return
1516else
1517    %% processing on a different session of the same computer (background) or cluster, create executable files
1518    batch_file_list=cell(NbProcess,1);% initiate the list of executable files
1519    DirBat=fullfile(OutputDir,'0_BAT');
1520    %create subdirectory for executable files
1521    if ~exist(DirBat,'dir')
1522        [tild,msg1]=mkdir(DirBat);
1523        if ~strcmp(msg1,'')
1524            msgbox_uvmat('ERROR',['cannot create ' DirBat ': ' msg1]);%error message for directory creation
1525            return
1526        end
1527    end
1528    %create subdirectory for log files
1529    DirLog=fullfile(OutputDir,'0_LOG');
1530    if ~exist(DirLog,'dir')
1531        [tild,msg1]=mkdir(DirLog);
1532        if ~strcmp(msg1,'')
1533            msgbox_uvmat('ERROR',['cannot create ' DirLog ': ' msg1]);%error message for directory creation
1534            return
1535        end
1536    end
1537    for iprocess=1:NbProcess
1538        if isempty(Series.IndexRange.NbSlice)% process by blocks of i index
1539            Series.IndexRange.first_i=first_i+(iprocess-1)*BlockLength*incr_i;
1540            if Series.IndexRange.first_i>last_i
1541                NbProcess=iprocess-1;
1542                break% leave the loop, we are at the end of the calculation
1543            end
1544            Series.IndexRange.last_i=min(last_i,first_i+(iprocess)*BlockLength*incr_i-1);
1545        else% process by slices of i index if NbSlice is defined, computation in a single process if NbSlice =1
1546            Series.IndexRange.first_i= first_i+iprocess-1;
1547            Series.IndexRange.incr_i=incr_i*Series.IndexRange.NbSlice;
1548        end
1549       
1550        % create, fill and save the xml parameter file
1551        t=struct2xml(Series);
1552        t=set(t,1,'name','Series');
1553        filexml=fullfile_uvmat(DirXml,'',Series.InputTable{1,3},'.xml',OutputNomType,...
1554            Series.IndexRange.first_i,Series.IndexRange.last_i,first_j,last_j);
1555        save(t,filexml);% save the parameter file
1556       
1557        %create the executable file
1558%         filebat=fullfile_uvmat(DirBat,'',Series.InputTable{1,3},'.bat',OutputNomType,...
1559%             Series.IndexRange.first_i,Series.IndexRange.last_i,first_j,last_j);
1560         filebat=fullfile_uvmat(DirBat,'',Series.InputTable{1,3},'.sh',OutputNomType,...
1561           Series.IndexRange.first_i,Series.IndexRange.last_i,first_j,last_j);
1562        batch_file_list{iprocess}=filebat;
1563        [fid,message]=fopen(filebat,'w');% create the executable file
1564        if isequal(fid,-1)
1565            msgbox_uvmat('ERROR', ['creation of .bat file: ' message]);
1566            return
1567        end
1568       
1569        % set the log file name
1570        filelog=fullfile_uvmat(DirLog,'',Series.InputTable{1,3},'.log',OutputNomType,...
1571            Series.IndexRange.first_i,Series.IndexRange.last_i,first_j,last_j);
1572       
1573        % fill and save the executable file
1574        switch ActionExt
1575            case '.m'% Matlab function
1576                switch computer
1577                    case {'GLNX86','GLNXA64','MACI64'}
1578                        cmd=[...
1579                            '#!/bin/bash \n'...
1580                            '. /etc/sysprofile \n'...
1581                            'matlab -nodisplay -nosplash -nojvm -logfile ''' filelog ''' <<END_MATLAB \n'...
1582                            'addpath(''' path_series '''); \n'...
1583                            'addpath(''' Series.Action.ActionPath '''); \n'...
1584                            '' Series.Action.ActionName  '( ''' filexml '''); \n'...
1585                            'exit \n'...
1586                            'END_MATLAB \n'];
1587                        fprintf(fid,cmd);%fill the executable file with the  char string cmd
1588                        fclose(fid);% close the executable file
1589                        system(['chmod +x ' filebat]);% set the file to executable
1590                    case {'PCWIN','PCWIN64'}
1591                        text_matlabscript=['matlab -automation -logfile ' regexprep(filelog,'\\','\\\\')...
1592                            ' -r "addpath(''' regexprep(path_series,'\\','\\\\') ''');'...
1593                            'addpath(''' regexprep(Series.Action.ActionPath,'\\','\\\\') ''');'...
1594                            '' Series.Action.ActionName  '( ''' regexprep(filexml,'\\','\\\\') ''');exit"'];
1595                        fprintf(fid,text_matlabscript);%fill the executable file with the  char string cmd
1596                        fclose(fid);% close the executable file
1597                end
1598            case '.sh' % compiled Matlab function
1599                switch computer
1600                    case {'GLNX86','GLNXA64','MACI64'}
1601                        cmd=['#!/bin/bash \n '...
1602                            '#$ -cwd \n '...
1603                            'hostname && date \n '...
1604                            'umask 002 \n'...
1605                            fullfile(ActionPath,[ActionName '.sh']) ' ' RunTime ' ' filexml];%allow writting access to created files for user group
1606                        fprintf(fid,cmd);%fill the executable file with the  char string cmd
1607                        fclose(fid);% close the executable file
1608                        system(['chmod +x ' filebat]);% set the file to executable
1609                       
1610                    case {'PCWIN','PCWIN64'}    %       TODO: adapt to Windows system
1611                        %                                 cmd=['matlab -automation -logfile ' regexprep(filelog,'\\','\\\\')...
1612                        %                                     ' -r "addpath(''' regexprep(path_series,'\\','\\\\') ''');'...
1613                        %                                     'addpath(''' regexprep(Series.Action.ActionPath,'\\','\\\\') ''');'...
1614                        %                                     '' Series.Action.ActionName  '( ''' regexprep(filexml,'\\','\\\\') ''');exit"'];
1615                        fprintf(fid,cmd);
1616                        fclose(fid);
1617                        %                               dos([filebat ' &']);
1618                end
1619        end
1620    end
1621end
1622
1623%% launch the executable files for background or cluster processing
1624switch RunMode
1625    case 'background'
1626        for iprocess=1:NbProcess
1627            system([batch_file_list{iprocess} ' &'])% directly execute the command file for each process
1628        end
1629    case 'cluster_oar' % option 'oar-parexec' used
1630        %create subdirectory for oar command and log files
1631        DirOAR=fullfile(OutputDir,'0_OAR');
1632        if ~exist(DirOAR,'dir')
1633            [tild,msg1]=mkdir(DirOAR);
1634            if ~strcmp(msg1,'')
1635                msgbox_uvmat('ERROR',['cannot create ' DirOAR ': ' msg1]);%error message for directory creation
1636                return
1637            end
1638        end
1639        max_walltime=3600*12; % 12h max total calculation
1640        walltime_onejob=600;%seconds, max estimated time for asingle file index value
1641        filename_joblist=fullfile(DirOAR,'job_list.txt');%create name of the global executable file
1642        fid=fopen(filename_joblist,'w');
1643        for p=1:length(batch_file_list)
1644            fprintf(fid,[batch_file_list{p} '\n']);% list of exe files
1645        end
1646        fclose(fid);
1647        system(['chmod +x ' filename_joblist]);% set the file to executable
1648        oar_command=['oarsub -n CIVX '...
1649            '-t idempotent --checkpoint ' num2str(walltime_onejob+60) ' '...
1650            '-l /core=' num2str(NbCore) ','...
1651            'walltime=' datestr(min(1.05*walltime_onejob/86400*max(NbProcess*BlockLength*nbfield_j,NbCore)/NbCore,max_walltime/86400),13) ' '...
1652            '-E ' regexprep(filename_joblist,'\.txt\>','.stderr') ' '...
1653            '-O ' regexprep(filename_joblist,'\.txt\>','.stdout') ' '...
1654            extra_oar ' '...
1655            '"oar-parexec -s -f ' filename_joblist ' '...
1656            '-l ' filename_joblist '.log"\n'];
1657        filename_oarcommand=fullfile(DirOAR,'oar_command');
1658        fid=fopen(filename_oarcommand,'w');
1659        fprintf(fid,oar_command);
1660        fclose(fid);
1661        fprintf(oar_command);% display in command line
1662        %system(['chmod +x ' oar_command]);% set the file to executable
1663        system(oar_command);     
1664end
1665
1666%% reset the GUI series
1667update_waitbar(handles.Waitbar,1); % put the waitbar to end position to indicate launching is finished
1668set(handles.RUN, 'Enable','On')
1669set(handles.RUN,'BackgroundColor',[1 0 0])
1670set(handles.RUN, 'Value',0)
1671
1672%------------------------------------------------------------------------
1673function STOP_Callback(hObject, eventdata, handles)
1674%------------------------------------------------------------------------
1675set(handles.RUN, 'BusyAction','cancel')
1676set(handles.RUN,'BackgroundColor',[1 0 0])
1677set(handles.RUN,'enable','on')
1678set(handles.RUN, 'Value',0)
1679
1680% %------------------------------------------------------------------------
1681% % --- Executes on button press in BIN.
1682% function BIN_Callback(hObject, eventdata, handles)
1683% %------------------------------------------------------------------------
1684%     cmd=['#!/bin/bash \n '...
1685%         '#$ -cwd \n '...
1686%         'hostname && date \n '...
1687%         'umask 002 \n'...
1688%         Param.xml.CivmBin ' ' Param.xml.RunTime ' ' filename_xml ' ' OutputFile '.nc'];
1689%     
1690%------------------------------------------------------------------------
1691% --- Main launch command, called by RUN and BATCH
1692
1693function [Series,OutputDir,errormsg]=prepare_jobs(handles)
1694%INPUT:
1695% handles: handles of graphic objects on the GUI series
1696
1697%------------------------------------------------------------------------
1698OutputDir='';
1699errormsg='';
1700
1701%% Read parameters from series
1702Series=read_GUI(handles.series);
1703
1704%% get_field GUI
1705% if isfield(Series,'InputFields')&&isfield(Series.InputFields,'Field')
1706%     if strcmp(Series.InputFields.Field,'get_field...')
1707%         hget_field=findobj(allchild(0),'name','get_field');
1708%         Series.GetField=read_GUI(hget_field);
1709%     end
1710% end
1711
1712%% create the output data directory
1713%determine the root file corresponding to the first sub dir
1714if get(handles.RUN,'value') && isfield(Series,'OutputSubDir')
1715    SubDirOut=[get(handles.OutputSubDir,'String') Series.OutputDirExt];
1716    SubDirOutNew=SubDirOut;
1717    SeriesData=get(handles.series,'UserData');
1718    if size(Series.InputTable,1)>1 && isfield(SeriesData,'AllowInputSort') && SeriesData.AllowInputSort
1719        [tild,iview]=sort(Series.InputTable(:,2)); %subdirectories sorted in alphabetical order
1720        Series.InputTable=Series.InputTable(iview,:);
1721    end
1722    detect=exist(fullfile(Series.InputTable{1,1},SubDirOutNew),'dir');% test if  the dir  already exist
1723    check_create=1; %need to create the result directory by default
1724    while detect
1725        answer=msgbox_uvmat('INPUT_Y-N',['use existing ouput directory: ' fullfile(Series.InputTable{1,1},SubDirOutNew) ', possibly delete previous data']);
1726        if strcmp(answer,'Cancel')
1727            errormsg='Cancel';
1728            return
1729        elseif strcmp(answer,'Yes')
1730            detect=0;
1731            check_create=0;
1732        else
1733            r=regexp(SubDirOutNew,'(?<root>.*\D)(?<num1>\d+)$','names');%detect whether name ends by a number
1734            if isempty(r)
1735                r(1).root=[SubDirOutNew '_'];
1736                r(1).num1='0';
1737            end
1738            SubDirOutNew=[r(1).root num2str(str2num(r(1).num1)+1)];%increment the index by 1 or put 1
1739            detect=exist(fullfile(Series.InputTable{1,1},SubDirOutNew),'dir');% test if  the dir  already exists   
1740            check_create=1;
1741        end
1742    end
1743    Series.OutputDirExt=regexprep(SubDirOutNew,Series.OutputSubDir,'');
1744    Series.OutputRootFile=Series.InputTable{1,3};% the first sorted RootFile taken for output
1745    set(handles.OutputDirExt,'String',Series.OutputDirExt)
1746    OutputDir=fullfile(Series.InputTable{1,1},[Series.OutputSubDir Series.OutputDirExt]);% full name (with path) of output directory
1747    if check_create    % create output directory if it does not exist
1748        [tild,msg1]=mkdir(OutputDir);
1749        if ~strcmp(msg1,'')
1750            errormsg=['cannot create ' OutputDir ': ' msg1];%error message for directory creation
1751            return
1752        end
1753    end
1754   % RootOut=fullfile(OutputDir,Series.InputTable{1,3});% name of the parameter xml file set in this directory
1755end
1756
1757%% removes unused information on Series
1758if isfield(Series,'Pairs')
1759    Series=rmfield(Series,'Pairs'); %info Pairs not needed for output
1760end
1761Series.IndexRange=rmfield(Series.IndexRange,'TimeTable');
1762% Series.IndexRange=rmfield(Series.IndexRange,'MinIndex');
1763% Series.IndexRange=rmfield(Series.IndexRange,'MaxIndex');
1764empty_line=false(size(Series.InputTable,1),1);
1765for iline=1:size(Series.InputTable,1)
1766    empty_line(iline)=isequal(Series.InputTable(iline,1:3),{'','',''});
1767end
1768Series.InputTable(empty_line,:)=[];
1769
1770%------------------------------------------------------------------------
1771% --- Executes on selection change in ActionName.
1772function ActionName_Callback(hObject, eventdata, handles)
1773%------------------------------------------------------------------------
1774%% stop any ongoing series processing
1775if isequal(get(handles.RUN,'Value'),1)
1776    answer= msgbox_uvmat('INPUT_Y-N','stop current Action process?');
1777    if strcmp(answer,'Yes')
1778        STOP_Callback(hObject, eventdata, handles)
1779    else
1780        return
1781    end
1782end
1783set(handles.ActionName,'BackgroundColor',[1 1 0])
1784drawnow
1785
1786%% get Action name and path
1787nb_builtin_ACTION=4; %nbre of functions initially proposed in the menu ActionName (as defined in the Opening fct of series)
1788ActionList=get(handles.ActionName,'String');% list menu fields
1789ActionIndex=get(handles.ActionName,'Value');
1790if ~isequal(ActionIndex,1)
1791    InputTable=get(handles.InputTable,'Data');
1792    if isempty(InputTable{1,4})
1793        msgbox_uvmat('ERROR','no input file available: use Open in the menu bar')
1794        return
1795    end
1796end
1797ActionName= ActionList{get(handles.ActionName,'Value')}; % selected function name
1798ActionPathList=get(handles.ActionName,'UserData');%list of recorded paths to functions of the list ActionName
1799
1800%% add a new function to the menu if 'more...' has been selected in the menu ActionName
1801if isequal(ActionName,'more...')
1802    [FileName, PathName] = uigetfile( ...
1803        {'*.m', ' (*.m)';
1804        '*.m',  '.m files '; ...
1805        '*.*', 'All Files (*.*)'}, ...
1806        'Pick a series processing function ',get(handles.ActionPath,'String'));
1807    if length(FileName)<2
1808        return
1809    end
1810    [ActionPath,ActionName,ActionExt]=fileparts(FileName);
1811   
1812    % insert the choice in the menu ActionName
1813    ActionIndex=find(strcmp(ActionName,ActionList),1);% look for the selected function in the menu Action
1814    if isempty(ActionIndex)%the input string does not exist in the menu
1815        ActionIndex= length(ActionList);
1816        ActionList=[ActionList(1:end-1);{ActionName};ActionList(end)];% the selected function is appended in the menu, before the last item 'more...'
1817        set(handles.ActionName,'String',ActionList)
1818    end
1819   
1820    % record the file extension and extend the path list if it is a new extension
1821    ActionExtList=get(handles.ActionExt,'String');
1822    ActionExtIndex=find(strcmp(ActionExt,ActionExtList), 1);
1823    if isempty(ActionExtIndex)
1824        set(handles.ActionExt,'String',[ActionExtList;{ActionExt}])
1825        ActionExtIndex=numel(ActionExtList)+1;
1826        ActionPathNew=cell(size(ActionPathList,1),1);%new column of ActionPath
1827        ActionPathList=[ActionPathList ActionPathNew];
1828    end
1829    set(handles.ActionName,'UserData',ActionPathList);
1830
1831    % remove old Action options in the menu (keeping a menu length <nb_builtin_ACTION+5)
1832    if length(ActionList)>nb_builtin_ACTION+5; %nb_builtin=nbre of functions always remaining in the initial menu
1833        nbremove=length(ActionList)-nb_builtin_ACTION-5;
1834        ActionList(nb_builtin_ACTION+1:end-5)=[];
1835        ActionPathList(nb_builtin_ACTION+1:end-4,:)=[];
1836        ActionIndex=ActionIndex-nbremove;
1837    end
1838   
1839    % record action menu, choice and path
1840    set(handles.ActionName,'Value',ActionIndex)
1841    set(handles.ActionName,'String',ActionList)
1842    set(handles.ActionExt,'Value',ActionExtIndex)
1843    ActionPathList{ActionIndex,ActionExtIndex}=PathName;
1844       
1845    %record the user defined menu additions in personal file profil_perso
1846    dir_perso=prefdir;
1847    profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
1848    if nb_builtin_ACTION+1<=numel(ActionList)-1
1849        ActionListUser=ActionList(nb_builtin_ACTION+1:numel(ActionList)-1);
1850        ActionPathListUser=ActionPathList(nb_builtin_ACTION+1:numel(ActionList)-1,:);
1851        ActionExtListUser={};
1852        if numel(ActionExtList)>2
1853            ActionExtListUser=ActionExtList(3:end);
1854        end
1855        if exist(profil_perso,'file')
1856            save(profil_perso,'ActionListUser','ActionPathListUser','ActionExtListUser','-append')
1857        else
1858            save(profil_perso,'ActionListUser','ActionPathListUser','ActionExtListUser','-V6')
1859        end
1860    end
1861end
1862
1863%% check the current ActionPath to the selected function
1864ActionPath=ActionPathList{ActionIndex};%current recorded path
1865set(handles.ActionPath,'String',ActionPath); %show the path to the senlected function
1866
1867%% reinitialise the waitbar
1868update_waitbar(handles.Waitbar,0)
1869
1870%% default setting for the visibility of the GUI elements
1871% set(handles.FieldTransform,'Visible','off')
1872% set(handles.CheckObject,'Visible','off');
1873% set(handles.ProjObject,'Visible','off');
1874% set(handles.CheckMask,'Visible','off')
1875% set(handles.Mask,'Visible','off')
1876
1877%% create the function handle for Action
1878path_series=which('series');
1879if ~isequal(ActionPath,path_series)
1880    eval(['spath=which(''' ActionName ''');']) %spath = current path of the selected function ACTION
1881    if ~exist(ActionPath,'dir')
1882        errormsg=['The prescribed function path ' ActionPath ' does not exist'];
1883        return
1884    end
1885    if ~isequal(spath,ActionPath)
1886        addpath(ActionPath)% add the prescribed path if not the current one
1887    end
1888end
1889eval(['h_fun=@' ActionName ';'])%create a function handle for ACTION
1890if ~isequal(ActionPath,path_series)
1891        rmpath(ActionPath)% add the prescribed path if not the current one   
1892end
1893
1894%% Activate the Action fct
1895[Series,tild,errormsg]=prepare_jobs(handles);% read the parameters from the GUI series
1896if ~isempty(errormsg)
1897    if ~strcmp(errormsg,'Cancel')
1898    msgbox_uvmat('ERROR',errormsg)
1899    end
1900    return
1901end
1902ParamOut=h_fun(Series);
1903
1904%% Put the first line of the selected Action fct as tooltip help
1905try
1906    [fid,errormsg] =fopen([ActionName '.m']);
1907    InputText=textscan(fid,'%s',1,'delimiter','\n');
1908    fclose(fid);
1909    set(handles.ActionName,'ToolTipString',InputText{1}{1})% put the first line of the selected function as tooltip help
1910end
1911
1912%% Detect the types of input files
1913SeriesData=get(handles.series,'UserData');
1914nb_civ=0;nb_netcdf=0;
1915if ~isempty(SeriesData)
1916    nb_civ=numel(find(strcmp('civx',SeriesData.FileType)|strcmp('civdata',SeriesData.FileType)));
1917    nb_netcdf=numel(find(strcmp('netcdf',SeriesData.FileType)));
1918end
1919
1920%% Check whether alphabetical sorting of input Subdir is alowed by the Action fct  (for multiples series entries)
1921SeriesData.AllowInputSort=0;%default
1922if isfield(ParamOut,'AllowInputSort')&&isequal(ParamOut.AllowInputSort,'on')
1923    SeriesData.AllowInputSort=1;
1924end
1925
1926%% Impose the whole input file index range if requested
1927if isfield(ParamOut,'WholeIndexRange')&&isequal(ParamOut.WholeIndexRange,'on')
1928    MinIndex=get(handles.MinIndex,'Data');
1929    MaxIndex=get(handles.MaxIndex,'Data');
1930    if ~isempty(MinIndex)
1931        set(handles.num_first_i,'String',num2str(MinIndex{1}))
1932        set(handles.num_last_i,'String',num2str(MaxIndex{1}))
1933        set(handles.num_incr_i,'String','1')
1934        if size(MinIndex,2)>=2
1935            set(handles.num_first_j,'String',num2str(MinIndex{1,2}))
1936            set(handles.num_last_j,'String',num2str(MaxIndex{1,2}))
1937            set(handles.num_incr_j,'String','1')
1938        end
1939    end
1940else
1941% check index ranges
1942first_i=1;last_i=1;first_j=1;last_j=1;
1943if isfield(Series.IndexRange,'first_i')
1944    first_i=Series.IndexRange.first_i;
1945    incr_i=Series.IndexRange.incr_i;
1946    last_i=Series.IndexRange.last_i;
1947end
1948if isfield(Series.IndexRange,'first_j')
1949    first_j=Series.IndexRange.first_j;
1950     incr_j=Series.IndexRange.incr_j;
1951    last_j=Series.IndexRange.last_j;
1952end
1953if last_i < first_i || last_j < first_j , msgbox_uvmat('ERROR','last field number must be larger than the first one'),...
1954    set(handles.RUN, 'Enable','On'), set(handles.RUN,'BackgroundColor',[1 0 0]),return,end;
1955end
1956
1957%% NbSlice visibility
1958NbSliceVisible='off';%default
1959if isfield(ParamOut,'NbSlice') && isequal(ParamOut.NbSlice,'on')
1960    NbSliceVisible='on';
1961    set(handles.num_NbProcess,'String',get(handles.num_NbSlice,'String'))% the nbre of processes is imposed as the nbre of slices
1962else
1963    set(handles.num_NbProcess,'String','')% free nbre of processes
1964end
1965set(handles.num_NbSlice,'Visible',NbSliceVisible)
1966set(handles.NbSlice_title,'Visible',NbSliceVisible)
1967
1968%% Visibility of VelType and VelType_1 menus
1969VelTypeVisible='off';  %hidden by default
1970VelType_1Visible='off';
1971InputFieldsVisible='off';%visibility of the frame Fields
1972if isfield(ParamOut,'VelType')
1973    if strcmp( ParamOut.VelType,'one')||strcmp( ParamOut.VelType,'two')
1974        if nb_civ>=1
1975            VelTypeVisible='on';
1976            InputFieldsVisible='on';
1977        end
1978    end
1979    if strcmp( ParamOut.VelType,'two')
1980        if nb_civ>=2
1981            VelType_1Visible='on';
1982        end
1983    end
1984end
1985set(handles.VelType,'Visible',VelTypeVisible)
1986set(handles.VelType_text,'Visible',VelTypeVisible);
1987set(handles.VelType_1,'Visible',VelType_1Visible)
1988set(handles.VelType_text_1,'Visible',VelType_1Visible);
1989
1990%% Visibility of FieldName and FieldName_1 menus
1991FieldNameVisible='off';  %hidden by default
1992FieldName_1Visible='off';  %hidden by default
1993if isfield(ParamOut,'FieldName')
1994    if strcmp( ParamOut.FieldName,'one')||strcmp( ParamOut.FieldName,'two')
1995        if (nb_civ+nb_netcdf)>=1
1996            InputFieldsVisible='on';
1997            FieldNameVisible='on';
1998        end
1999    end
2000    if strcmp( ParamOut.FieldName,'two')
2001        if (nb_civ+nb_netcdf)>=1
2002            FieldName_1Visible='on';
2003        end
2004    end
2005end
2006set(handles.InputFields,'Visible',InputFieldsVisible)
2007set(handles.FieldName,'Visible',FieldNameVisible) % test for MenuBorser
2008set(handles.FieldName_1,'Visible',FieldName_1Visible)
2009
2010%% Visibility of FieldTransform menu
2011FieldTransformVisible='off';  %hidden by default
2012if isfield(ParamOut,'FieldTransform')
2013    FieldTransformVisible=ParamOut.FieldTransform; 
2014    TransformName_Callback([],[], handles)
2015end
2016set(handles.FieldTransform,'Visible',FieldTransformVisible)
2017if isfield(ParamOut,'TransformPath')
2018    set(handles.ActionExt,'UserData',ParamOut.TransformPath)
2019else
2020    set(handles.ActionExt,'UserData',[])
2021end
2022
2023%% Visibility of projection object
2024ProjObjectVisible='off';  %hidden by default
2025if isfield(ParamOut,'ProjObject')
2026    ProjObjectVisible=ParamOut.ProjObject;
2027end
2028set(handles.CheckObject,'Visible',ProjObjectVisible)
2029if ~get(handles.CheckObject,'Value')
2030    ProjObjectVisible='off';
2031end
2032set(handles.ProjObject,'Visible',ProjObjectVisible)
2033set(handles.DeleteObject,'Visible',ProjObjectVisible)
2034set(handles.ViewObject,'Visible',ProjObjectVisible)
2035
2036
2037%% Visibility of mask input
2038MaskVisible='off';  %hidden by default
2039if isfield(ParamOut,'Mask')
2040    MaskVisible=ParamOut.Mask;
2041end
2042set(handles.Mask,'Visible',MaskVisible)
2043set(handles.CheckMask,'Visible',MaskVisible);
2044
2045%% definition of the directory containing the output files
2046OutputDirVisible='off';
2047if isfield(ParamOut,'OutputDirExt')&&~isempty(ParamOut.OutputDirExt)
2048    set(handles.OutputDirExt,'String',ParamOut.OutputDirExt)
2049    OutputDirVisible='on';
2050end
2051set(handles.OutputDirExt,'Visible',OutputDirVisible)
2052set(handles.OutputSubDir,'Visible',OutputDirVisible)
2053set(handles.OutputDir_title,'Visible',OutputDirVisible)
2054set(handles.RunMode,'Visible',OutputDirVisible)
2055set(handles.ActionExt,'Visible',OutputDirVisible)
2056set(handles.RunMode_title,'Visible',OutputDirVisible)
2057set(handles.ActionExt_title,'Visible',OutputDirVisible)
2058
2059%% Expected nbre of output files
2060if isfield(ParamOut,'OutputFileMode')
2061StatusData.OutputFileMode=ParamOut.OutputFileMode;
2062set(handles.status,'UserData',StatusData)
2063end
2064
2065%% definition of an additional parameter set, determined by an ancillary GUI
2066if isfield(ParamOut,'ActionInput')
2067    set(handles.ActionInput,'Visible','on')
2068    set(handles.ActionInput_title,'Visible','on')
2069    set(handles.ActionInputView,'Visible','on')
2070    set(handles.ActionInputView,'Value',0)
2071    set(handles.ActionInput,'String',ActionName)
2072    ParamOut.ActionInput.Program=ActionName; % record the program in ActionInput
2073    SeriesData.ActionInput=ParamOut.ActionInput;
2074else
2075    set(handles.ActionInput,'Visible','off')
2076    set(handles.ActionInput_title,'Visible','off')
2077    set(handles.ActionInputView,'Visible','off')
2078    if isfield(SeriesData,'ActionInput')
2079    SeriesData=rmfield(SeriesData,'ActionInput');
2080    end
2081end   
2082set(handles.series,'UserData',SeriesData)
2083set(handles.ActionName,'BackgroundColor',[1 1 1])
2084
2085%------------------------------------------------------------------------
2086% --- Executes on button press in ActionInputView.
2087function ActionInputView_Callback(hObject, eventdata, handles)
2088%------------------------------------------------------------------------
2089if get(handles.ActionInputView,'Value')
2090ActionName_Callback(hObject, eventdata, handles)
2091end
2092
2093%------------------------------------------------------------------------
2094% --- Executes on selection change in FieldName.
2095function FieldName_Callback(hObject, eventdata, handles)
2096%------------------------------------------------------------------------
2097field_str=get(handles.FieldName,'String');
2098field_index=get(handles.FieldName,'Value');
2099field=field_str{field_index(1)};
2100if isequal(field,'get_field...')
2101    hget_field=findobj(allchild(0),'name','get_field');
2102    if ~isempty(hget_field)
2103        delete(hget_field)%delete opened versions of get_field
2104    end
2105    Series=read_GUI(handles.series);
2106    Series.InputTable=Series.InputTable(1,:);
2107    filecell=get_file_series(Series);
2108    if exist(filecell{1,1},'file')
2109        GetFieldData=get_field(filecell{1,1});
2110        FieldList={};
2111        XName=GetFieldData.XVarName;
2112        if GetFieldData.CheckVector
2113            UName=GetFieldData.PanelVectors.vector_x;
2114            VName=GetFieldData.PanelVectors.vector_y;
2115            XName=GetFieldData.XVarName;
2116            YName=GetFieldData.YVarName;
2117            CName=GetFieldData.PanelVectors.vec_color;
2118            [FieldList,VecColorList]=set_field_list(UName,VName,CName);
2119        elseif GetFieldData.CheckScalar
2120            AName=GetFieldData.PanelScalar.scalar;
2121            XName=GetFieldData.XVarName;
2122            YName=GetFieldData.YVarName;
2123            FieldList={AName};
2124        elseif GetFieldData.CheckPlot1D;
2125            YName=GetFieldData.CheckPlot1D.ordinate;
2126        end
2127        set(handles.Coord_x,'String',{XName})
2128        set(handles.Coord_y,'String',{YName})
2129        set(handles.FieldName,'Value',1)
2130        set(handles.FieldName,'String',[FieldList; {'get_field...'}]);
2131        %         set(handles.ColorScalar,'Value',1)
2132        %         set(handles.ColorScalar,'String',VecColorList);
2133        %         UvData.FileType{1}='netcdf';
2134        %         set(handles.uvmat,'UserData',UvData)
2135    end
2136    % elseif isequal(field,'more...')
2137    %     str=calc_field;
2138    %     [ind_answer,v] = listdlg('PromptString','Select a file:',...
2139    %                 'SelectionMode','single',...
2140    %                 'ListString',str);
2141    %        % edit the choice in the fields and actionname menu
2142    %      scalar=cell2mat(str(ind_answer));
2143    %      update_menu(handles.FieldName,scalar)
2144end
2145
2146%------------------------------------------------------------------------
2147% --- Executes on selection change in FieldName_1.
2148function FieldName_1_Callback(hObject, eventdata, handles)
2149%------------------------------------------------------------------------
2150field_str=get(handles.FieldName_1,'String');
2151field_index=get(handles.FieldName_1,'Value');
2152field=field_str{field_index};
2153if isequal(field,'get_field...')   
2154     hget_field=findobj(allchild(0),'name','get_field_1');
2155     if ~isempty(hget_field)
2156         delete(hget_field)
2157     end
2158     SeriesData=get(handles.series,'UserData');
2159     filename=SeriesData.CurrentInputFile_1;
2160     if exist(filename,'file')
2161        hget_field=get_field(filename);
2162        set(hget_field,'name','get_field_1')
2163     end
2164% elseif isequal(field,'more...')
2165%     str=calc_field;
2166%     [ind_answer,v] = listdlg('PromptString','Select a file:',...
2167%                 'SelectionMode','single',...
2168%                 'ListString',str);
2169%        % edit the choice in the fields and actionname menu
2170%      scalar=cell2mat(str(ind_answer));
2171%      update_menu(handles.FieldName_1,scalar)
2172end   
2173
2174
2175%%%%%%%%%%%%%
2176function [ind_remove]=find_pairs(dirpair,ind_i,last_i)
2177indsel=ind_i;
2178indiff=diff(ind_i); %test index increment to detect multiplets (several pairs with the same index ind_i) and holes in the series
2179indiff=[1 indiff last_i-ind_i(end)+1];%for testing gaps with the imposed bounds
2180if ~isempty(indiff)
2181    indiff2=diff(indiff);
2182    indiffp=[indiff2 1];
2183    indiffm=[1 indiff2];
2184    ind_multi_m=find((indiff==0)&(indiffm<0))-1;%indices of first members of multiplets
2185    ind_multi_p=find((indiff==0)&(indiffp>0));%indices of last members of multiplets
2186    %for each multiplet, select the most recent file
2187    ind_remove=[];
2188    for i=1:length(ind_multi_m)
2189        ind_pairs=ind_multi_m(i):ind_multi_p(i);
2190        for imulti=1:length(ind_pairs)
2191            datepair(imulti)=datenum(dirpair(ind_pairs(imulti)).date);%dates of creation
2192        end
2193        [datenew,indsort2]=sort(datepair); %sort the multiplet by creation date
2194        ind_s=indsort2(1:end-1);%
2195        ind_remove=[ind_remove ind_pairs(ind_s)];%remove these indices, leave the last one
2196    end
2197end
2198
2199%------------------------------------------------------------------------
2200% --- determine the list of index pairstring of processing file
2201function [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)
2202%------------------------------------------------------------------------
2203num_i1=num_i;% set of first image numbers by default
2204num_i2=num_i;
2205num_j1=num_j;
2206num_j2=num_j;
2207num_i_out=num_i;
2208num_j_out=num_j;
2209% if isequal (NomType,'_1-2_1') || isequal (NomType,'_1-2')
2210if isequal(mode,'series(Di)')
2211    num_i1_line=num_i+ind_shift(3);% set of first image numbers
2212    num_i2_line=num_i+ind_shift(4);
2213    % adjust the first and last field number
2214        indsel=find(num_i1_line >= 1);
2215    num_i_out=num_i(indsel);
2216    num_i1_line=num_i1_line(indsel);
2217    num_i2_line=num_i2_line(indsel);
2218    num_j1=meshgrid(num_j,ones(size(num_i1_line)));
2219    num_j2=meshgrid(num_j,ones(size(num_i1_line)));
2220    [xx,num_i1]=meshgrid(num_j,num_i1_line);
2221    [xx,num_i2]=meshgrid(num_j,num_i2_line);
2222elseif isequal (mode,'series(Dj)')||isequal (mode,'bursts')
2223    if isequal(mode,'bursts') %case of bursts (png_old or png_2D)
2224        num_j1=ind_shift(1)*ones(size(num_i));
2225        num_j2=ind_shift(2)*ones(size(num_i));
2226    else
2227        num_j1_col=num_j+ind_shift(1);% set of first image numbers
2228        num_j2_col=num_j+ind_shift(2);
2229        % adjust the first field number
2230        indsel=find((num_j1_col >= 1));   
2231        num_j_out=num_j(indsel);
2232        num_j1_col=num_j1_col(indsel);
2233        num_j2_col=num_j2_col(indsel);
2234        [num_i1,num_j1]=meshgrid(num_i,num_j1_col);
2235        [num_i2,num_j2]=meshgrid(num_i,num_j2_col);
2236    end   
2237end
2238
2239%------------------------------------------------------------------------
2240% --- Executes on button press in CheckObject.
2241function CheckObject_Callback(hObject, eventdata, handles)
2242%------------------------------------------------------------------------
2243hset_object=findobj(allchild(0),'tag','set_object');%find the set_object interface handle
2244value=get(handles.CheckObject,'Value');
2245if value
2246    SeriesData=get(handles.series,'UserData');
2247    if ~(isfield(SeriesData,'ProjObject')&&~isempty(SeriesData.ProjObject))
2248        if ishandle(hset_object)
2249            uistack(hset_object,'top')% show the GUI set_object if opened
2250        else
2251            %get the object file
2252            InputTable=get(handles.InputTable,'Data');
2253            defaultname=InputTable{1,1};
2254            if isempty(defaultname)
2255                defaultname={''};
2256            end
2257            [FileName, PathName] = uigetfile( ...
2258                {'*.xml;*.mat', ' (*.xml,*.mat)';
2259                '*.xml',  '.xml files '; ...
2260                '*.mat',  '.mat matlab files '}, ...
2261                'Pick an xml object file (or use uvmat to create it)',defaultname);
2262            fileinput=[PathName FileName];%complete file name
2263            sizf=size(fileinput);
2264            if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end
2265            %read the file
2266            data=xml2struct(fileinput);
2267            if ~isfield(data,'Type')
2268                msgbox_uvmat('ERROR',[fileinput ' is not an object xml file'])
2269                return
2270            end
2271            if ~isfield(data,'ProjMode')
2272                data.ProjMode='none';
2273            end
2274            hset_object=set_object(data);% call the set_object interface
2275        end
2276        ProjObject=read_GUI(hset_object);
2277        set(handles.ProjObject,'String',ProjObject.Name);%display the object name
2278        SeriesData=get(handles.series,'UserData');
2279        SeriesData.ProjObject=ProjObject;
2280        set(handles.series,'UserData',SeriesData);
2281    end
2282    set(handles.DeleteObject,'Visible','on');
2283    set(handles.ViewObject,'Visible','on');
2284    set(handles.ProjObject,'Visible','on');
2285else
2286    set(handles.DeleteObject,'Visible','off');
2287    set(handles.ViewObject,'Visible','off');
2288    if ~ishandle(hset_object)
2289    set(handles.ViewObject,'Value',0);
2290    end
2291    set(handles.ProjObject,'Visible','off');
2292end
2293%set(handles.series,'UserData',SeriesData)
2294
2295%--------------------------------------------------------------
2296function CheckMask_Callback(hObject, eventdata, handles)
2297value=get(handles.CheckMask,'Value');
2298if value
2299    msgbox_uvmat('ERROR','not implemented yet')
2300end
2301%--------------------------------------------------------------
2302
2303%-------------------------------------------------------------------
2304%'uv_ncbrowser': interactively calls the netcdf file browser 'get_field.m'
2305function ncbrowser_uvmat(hObject, eventdata)
2306%-------------------------------------------------------------------
2307     bla=get(gcbo,'String');
2308     ind=get(gcbo,'Value');
2309     filename=cell2mat(bla(ind));
2310      blank=find(filename==' ');
2311      filename=filename(1:blank-1);
2312     get_field(filename)
2313
2314% ------------------------------------------------------------------
2315function MenuHelp_Callback(hObject, eventdata, handles)
2316%-------------------------------------------------------------------
2317path_to_uvmat=which ('uvmat');% check the path of uvmat
2318pathelp=fileparts(path_to_uvmat);
2319helpfile=fullfile(pathelp,'uvmat_doc','uvmat_doc.html');
2320if isempty(dir(helpfile)), msgbox_uvmat('ERROR','Please put the help file uvmat_doc.html in the sub-directory /uvmat_doc of the UVMAT package')
2321else
2322    addpath (fullfile(pathelp,'uvmat_doc'))
2323    web([helpfile '#series'])
2324end
2325
2326%-------------------------------------------------------------------
2327% --- Executes on selection change in TransformName.
2328function TransformName_Callback(hObject, eventdata, handles)
2329%----------------------------------------------------------------------
2330TransformList=get(handles.TransformName,'String');
2331TransformIndex=get(handles.TransformName,'Value');
2332TransformName=TransformList{TransformIndex};
2333TransformPathList=get(handles.TransformName,'UserData');
2334nb_builtin_transform=4;
2335% ff=functions(list_transform{end});
2336if isequal(TransformName,'more...');
2337%     coord_fct='';
2338%     prompt = {'Enter the name of the transform function'};
2339%     dlg_title = 'user defined transform';
2340%     num_lines= 1;
2341    [FileName, PathName] = uigetfile( ...
2342       {'*.m', ' (*.m)';
2343        '*.m',  '.m files '; ...
2344        '*.*', 'All Files (*.*)'}, ...
2345        'Pick a transform function',get(handles.TransformPath,'String'));
2346    if isequal(FileName,0)
2347        return     %browser closed without choice
2348    end
2349    if isequal(PathName(end),'/')||isequal(PathName(end),'\')
2350        PathName(end)=[];
2351    end
2352    [TransformPath,TransformName,TransformExt]=fileparts(FileName);% removes extension .m
2353    if ~strcmp(TransformExt,'.m')
2354        msgbox_uvmat('ERROR','a Matlab function .m must be introduced');
2355        return
2356    end
2357     % insert the choice in the menu
2358    TransformIndex=find(strcmp(TransformName,TransformList),1);% look for the selected function in the menu Action
2359    if isempty(TransformIndex)%the input string does not exist in the menu
2360        TransformIndex= length(TransformList);
2361        TransformList=[TransformList(1:end-1);{TransformnName};TransformList(end)];% the selected function is appended in the menu, before the last item 'more...'
2362        set(handles.TransformName,'String',TransformList)
2363        TransformPathList=[TransformPathList;{TransformPath}];
2364    end
2365   % save the new menu in the personal file 'uvmat_perso.mat'
2366   dir_perso=prefdir;%personal Matalb directory
2367   profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
2368   if exist(profil_perso,'file')
2369       for ilist=nb_builtin_transform+1:numel(TransformPathList)
2370           TransformListUser{ilist-nb_builtin_transform}=TransformList{ilist};
2371           TransformPathListUser{ilist-nb_builtin_transform}=TransformPathList{ilist};
2372       end
2373       save (profil_perso,'TransformPathListUser','TransformListUser','-append'); %store the root name for future opening of uvmat
2374   end
2375end
2376
2377%display the current function path
2378set(handles.TransformPath,'String',TransformPathList{TransformIndex}); %show the path to the senlected function
2379set(handles.TransformName,'UserData',TransformPathList);
2380
2381
2382% --------------------------------------------------------------------
2383function MenuExportConfig_Callback(hObject, eventdata, handles)
2384global Series
2385[Series,errormsg]=prepare_jobs(handles);
2386
2387evalin('base','global Series')%make CurData global in the workspace
2388display('current series config :')
2389evalin('base','Series') %display CurData in the workspace
2390commandwindow; %brings the Matlab command window to the front
2391
2392
2393% --------------------------------------------------------------------
2394function MenuImportConfig_Callback(hObject, eventdata, handles)
2395% --------------------------------------------------------------------
2396InputTable=get(handles.InputTable,'Data');
2397[FileName, PathName] = uigetfile( ...
2398       {'*.xml', ' (*.xml)';
2399       '*.xml',  '.xml files '; ...
2400        '*.*',  'All Files (*.*)'}, ...
2401        'Pick a file',InputTable{1,1});
2402filexml=[PathName FileName];%complete file name
2403if isempty(filexml),return;end %abandon if no file is introduced by the browser
2404Param=xml2struct(filexml);
2405fill_GUI(Param,handles.series)
2406
2407% --- Executes on selection change in RunMode.
2408function RunMode_Callback(hObject, eventdata, handles)
2409
2410% --- Executes on selection change in Coord_x.
2411function Coord_x_Callback(hObject, eventdata, handles)
2412
2413
2414% --- Executes on selection change in Coord_y.
2415function Coord_y_Callback(hObject, eventdata, handles)
2416
2417
2418
2419% --- Executes when series is resized.
2420function series_ResizeFcn(hObject, eventdata, handles)
2421%% input table
2422set(handles.InputTable,'Unit','pixel')
2423Pos=get(handles.InputTable,'Position');
2424set(handles.InputTable,'Unit','normalized')
2425ColumnWidth=round([0.5 0.14 0.14 0.14 0.08]*(Pos(3)-52));
2426ColumnWidth=num2cell(ColumnWidth);
2427set(handles.InputTable,'ColumnWidth',ColumnWidth)
2428
2429%% MinIndex and MaxIndex
2430set(handles.MinIndex,'Unit','pixel')
2431Pos=get(handles.MinIndex,'Position');
2432set(handles.MinIndex,'Unit','normalized')
2433ColumnWidth=get(handles.MinIndex,'ColumnWidth');
2434if numel(ColumnWidth)==2
2435    ColumnWidth=num2cell(floor([0.5 0.5]*(Pos(3)-20)));
2436else
2437    ColumnWidth={Pos(3)-5};
2438end   
2439set(handles.MinIndex,'ColumnWidth',ColumnWidth)
2440set(handles.MaxIndex,'ColumnWidth',ColumnWidth)
2441
2442%% TimeTable
2443set(handles.TimeTable,'Unit','pixel')
2444Pos=get(handles.TimeTable,'Position');
2445set(handles.TimeTable,'Unit','normalized')
2446ColumnWidth=get(handles.TimeTable,'ColumnWidth');
2447ColumnWidth=num2cell(floor([0.25 0.25 0.25 0.25]*(Pos(3)-20)));
2448set(handles.TimeTable,'ColumnWidth',ColumnWidth)
2449
2450
2451%% PairString
2452set(handles.PairString,'Unit','pixel')
2453Pos=get(handles.PairString,'Position');
2454set(handles.PairString,'Unit','normalized')
2455set(handles.PairString,'ColumnWidth',{Pos(3)-5})
2456
2457
2458% --- Executes on button press in status.
2459function status_Callback(hObject, eventdata, handles)
2460
2461if get(handles.status,'Value')
2462    set(handles.status,'BackgroundColor',[1 1 0])
2463    drawnow
2464    %StatusData.time_ref=get(handles.RUN,'UserData');% get the time of launch
2465    Param=read_GUI(handles.series);
2466    RootPath=Param.InputTable{1,1};
2467    if ~isfield(Param,'OutputSubDir')   
2468        msgbox_uvmat('ERROR','no directory defined for output files')
2469        return
2470    end
2471    OutputSubDir=[Param.OutputSubDir Param.OutputDirExt];% subdirectory for output files
2472    OutputDir=fullfile(RootPath,OutputSubDir);
2473    uigetfile_uvmat('status_display',OutputDir)
2474   
2475%     hfig=findobj(allchild(0),'name','series_status');
2476%     if isempty(hfig)
2477%         ScreenSize=get(0,'ScreenSize');
2478%         hfig=figure('DeleteFcn',@stop_status,'Position',[ScreenSize(3)-600 ScreenSize(4)-640 560 600]);
2479%         set(hfig,'MenuBar','none')% suppress the menu bar
2480%         set(hfig,'NumberTitle','off')%suppress the fig number in the title
2481%         set(hfig,'name','series_status')
2482%         set(hfig,'tag','series_status')
2483%         uicontrol('Style','listbox','Units','normalized', 'Position',[0.05 0.09 0.9 0.71], 'Callback', @view_file,'tag','list','UserData',OutputDir);
2484%         uicontrol('Style','edit','Units','normalized', 'Position', [0.05 0.87 0.9 0.1],'tag','titlebox','Max',2,'String',OutputDir);
2485%         uicontrol('Style','frame','Units','normalized', 'Position', [0.05 0.81 0.9 0.05]);
2486%         uicontrol('Style','pushbutton','Units','normalized', 'Position', [0.7 0.01 0.2 0.07],'String','Close','FontWeight','bold','FontUnits','points','FontSize',11,'Callback',@stop_status);
2487%         uicontrol('Style','pushbutton','Units','normalized', 'Position', [0.1 0.01 0.2 0.07],'String','Refresh','FontWeight','bold','FontUnits','points','FontSize',11,'Callback',@refresh_GUI);
2488%         %set(hrefresh,'UserData',StatusData)
2489%         BarPosition=[0.05 0.81 0.01 0.05];
2490%         uicontrol('Style','frame','Units','normalized', 'Position',BarPosition ,'BackgroundColor',[1 0 0],'tag','waitbar');
2491%         drawnow
2492%     end
2493%     refresh_GUI(hfig)
2494else
2495    %% delete current display fig if selection is off
2496    set(handles.status,'BackgroundColor',[0 1 0])
2497    hfig=findobj(allchild(0),'name','series_status');
2498    if ~isempty(hfig)
2499        delete(hfig)
2500    end
2501    return
2502end
2503
2504
2505%------------------------------------------------------------------------   
2506% launched by selecting a file on the list
2507function view_file(hObject, eventdata)
2508%------------------------------------------------------------------------
2509list=get(hObject,'String');
2510index=get(hObject,'Value');
2511rootroot=get(hObject,'UserData');
2512selectname=list{index};
2513ind_dot=regexp(selectname,'\.\.\.');
2514if ~isempty(ind_dot)
2515    selectname=selectname(1:ind_dot-1);
2516end
2517FullSelectName=fullfile(rootroot,selectname);
2518if exist(FullSelectName,'dir')% a directory has been selected
2519    ListFiles=dir(FullSelectName);
2520    ListDisplay=cell(numel(ListFiles),1);
2521    for ilist=2:numel(ListDisplay)% suppress the first line '.'
2522        ListDisplay{ilist-1}=ListFiles(ilist).name;
2523    end
2524    set(hObject,'Value',1)
2525    set(hObject,'String',ListDisplay)
2526    if strcmp(selectname,'..')
2527        FullSelectName=fileparts(fileparts(FullSelectName));
2528    end
2529    set(hObject,'UserData',FullSelectName)
2530    hfig=get(hObject,'parent');
2531    htitlebox=findobj(hfig,'tag','titlebox');   
2532    set(htitlebox,'String',FullSelectName)
2533elseif exist(FullSelectName,'file')%visualise the vel field if it exists
2534    FileType=get_file_type(FullSelectName);
2535    if strcmp(FileType,'txt')
2536        edit(FullSelectName)
2537    elseif strcmp(FileType,'xml')
2538        editxml(FullSelectName)
2539    else
2540        uvmat(FullSelectName)
2541    end
2542    set(gcbo,'Value',1)
2543end
2544
2545
2546%------------------------------------------------------------------------   
2547% launched by refreshing the status figure
2548function refresh_GUI(hfig)
2549%------------------------------------------------------------------------
2550htitlebox=findobj(hfig,'tag','titlebox');
2551hlist=findobj(hfig,'tag','list');
2552hseries=findobj(allchild(0),'tag','series');
2553hstatus=findobj(hseries,'tag','status');
2554StatusData=get(hstatus,'UserData');
2555OutputDir=get(htitlebox,'String');
2556if ischar(OutputDir),OutputDir={OutputDir};end
2557ListFiles=dir(OutputDir{1});
2558if numel(ListFiles)<1
2559    return
2560end
2561ListFiles(1)=[];%removes the first line ='.'
2562ListDisplay=cell(numel(ListFiles),1);
2563testrecent=0;
2564datnum=zeros(numel(ListDisplay),1);
2565for ilist=1:numel(ListDisplay)
2566    ListDisplay{ilist}=ListFiles(ilist).name;
2567      if ~ListFiles(ilist).isdir && isfield(ListFiles(ilist),'datenum')
2568            datnum(ilist)=ListFiles(ilist).datenum;%only available in recent matlab versions
2569            testrecent=1;
2570       end
2571end
2572set(hlist,'String',ListDisplay)
2573
2574%% Look at date of creation
2575ListDisplay=ListDisplay(datnum~=0);
2576datnum=datnum(datnum~=0);%keep the non zero values corresponding to existing files
2577NbOutputFile=[];
2578if isempty(datnum)
2579    if testrecent
2580        message='no civ result created yet';
2581    else
2582        message='';
2583    end
2584else
2585    [first,indfirst]=min(datnum);
2586    [last,indlast]=max(datnum);
2587    NbOutputFile_str='?';
2588    NbOutputFile=[];
2589    if isfield(StatusData,'NbOutputFile')
2590        NbOutputFile=StatusData.NbOutputFile;
2591        NbOutputFile_str=num2str(NbOutputFile);
2592    end
2593    message={[num2str(numel(datnum)) ' file(s) done over ' NbOutputFile_str] ;['oldest modification:  ' ListDisplay{indfirst} ' : ' datestr(first)];...
2594        ['latest modification:  ' ListDisplay{indlast} ' : ' datestr(last)]};
2595end
2596set(htitlebox,'String', [OutputDir{1};message])
2597
2598%% update the waitbar
2599hwaitbar=findobj(hfig,'tag','waitbar');
2600if ~isempty(NbOutputFile)
2601    BarPosition=get(hwaitbar,'Position');
2602    BarPosition(3)=0.9*numel(datnum)/NbOutputFile;
2603    set(hwaitbar,'Position',BarPosition)
2604end
2605%TODO: adjust waitbar
2606
2607% civ_files=get(hfig,'UserData');
2608
2609% [filepath,filename,ext]=fileparts(civ_files{1});
2610% [tild,SubDir,extdir]=fileparts(filepath);
2611% SubDir=[SubDir extdir];
2612% option_civ=StatusData.option_civ;
2613% nbfiles=numel(civ_files);
2614% testrecent=0;
2615% count=0;
2616% datnum=zeros(1,nbfiles);
2617% filefound=cell(1,nbfiles);
2618% for ifile=1:nbfiles
2619%     detect=exist(civ_files{ifile},'file'); % check the existence of the file
2620%     option=0;
2621%     if detect==0
2622%         option_str='not created';
2623%     else
2624%         datfile=dir(civ_files{ifile});
2625%         if isfield(datfile,'datenum')
2626%             datnum(ifile)=datfile.datenum;%only available in recent matlab versions
2627%             testrecent=1;
2628%         end
2629%         filefound(ifile)={datfile.name};
2630%         
2631%         % check the content  netcdf file
2632%         Data=nc2struct(civ_files{ifile},'ListGlobalAttribute','CivStage','patch2','fix2','civ2','patch','fix');
2633%         option_list={'civ1','fix1','patch1','civ2','fix2','patch2'};
2634%         if ~isempty(Data.CivStage)
2635%             option=Data.CivStage;%case of Matlab civ
2636%         else
2637%             if ~isempty(Data.patch2) && isequal(Data.patch2,1)
2638%                 option=6;
2639%             elseif ~isempty(Data.fix2) && isequal(Data.fix2,1)
2640%                 option=5;
2641%             elseif ~isempty(Data.civ2) && isequal(Data.civ2,1);
2642%                 option=4;
2643%             elseif ~isempty(Data.patch) && isequal(Data.patch,1);
2644%                 option=3;
2645%             elseif ~isempty(Data.fix) && isequal(Data.fix,1);
2646%                 option=2;
2647%             else
2648%                 option=1;
2649%             end
2650%         end
2651%         option_str=option_list{option};
2652%         if datnum(ifile)<StatusData.time_ref
2653%             option_str=[option_str '  --OLD--'];
2654%         end
2655%     end
2656%     if option >= option_civ
2657%         count=count+1;
2658%     end
2659%     [filepath,filename,ext]=fileparts(civ_files{ifile});
2660%     Tabchar{ifile,1}=[fullfile(SubDir,filename) ext  '...' option_str];
2661% end
2662% datnum=datnum(datnum~=0);%keep the non zero values corresponding to existing files
2663% if isempty(datnum)
2664%     if testrecent
2665%         message='no civ result created yet';
2666%     else
2667%         message='';
2668%     end
2669% else
2670%     datnum=datnum(datnum~=0);%keep the non zero values corresponding to existing files
2671%     [first,ind]=min(datnum);
2672%     [last,indlast]=max(datnum);
2673%     message={[num2str(count) ' file(s) done over ' num2str(nbfiles)] ;['oldest modification:  ' cell2mat(filefound(ind)) ' : ' datestr(first)];...
2674%         ['latest modification:  ' cell2mat(filefound(indlast)) ' : ' datestr(last)]};
2675% end
2676% hlist=findobj(hfig,'tag','list');
2677% htitlebox=findobj(hfig,'tag','titlebox');
2678% hwaitbar=findobj(hfig,'tag','waitbar');
2679% set(hlist,'String',Tabchar)
2680% set(htitlebox,'String', message)
2681%
2682%------------------------------------------------------------------------   
2683% launched by deleting the status figure
2684function stop_status(hObject, eventdata)
2685%------------------------------------------------------------------------
2686hciv=findobj(allchild(0),'tag','series');
2687hhciv=guidata(hciv);
2688set(hhciv.status,'value',0) %reset the status uicontrol in the GUI civ
2689set(hhciv.status,'BackgroundColor',[0 1 0])
2690delete(gcbf)
2691
2692% --- Executes on selection change in ActionExt.
2693function ActionExt_Callback(hObject, eventdata, handles)
2694ActionExtList=get(handles.ActionExt,'String');
2695ActionExt=ActionExtList{get(handles.ActionExt,'Value')};
2696ActionList=get(handles.ActionName,'String');
2697ActionName=ActionList{get(handles.ActionName,'Value')};
2698TransformPath='';
2699if ~isempty(get(handles.ActionExt,'UserData'))
2700    TransformPath=get(handles.ActionExt,'UserData');
2701end
2702if strcmp(ActionExt,'.sh')
2703    set(handles.ActionExt,'BackgroundColor',[1 1 0])
2704    ActionFullName=fullfile(get(handles.ActionPath,'String'),[ActionName '.sh']);
2705    if ~exist(ActionFullName,'file')
2706        answer=msgbox_uvmat('INPUT_Y-N','compiled version has not been created: compile now?');
2707        if strcmp(answer,'Yes')
2708            set(handles.ActionExt,'BackgroundColor',[1 1 0])
2709            path_uvmat=fileparts(which('series'));
2710            currentdir=pwd;
2711            cd(get(handles.ActionPath,'String'))% go to the directory of Action
2712            %  addpath(get(handles.TransformPath,'String'))
2713            addpath(path_uvmat)% add the path to uvmat to run the fct 'compile'
2714           % addpath(fullfile(path_uvmat,'transform_field'))% add the path to uvmat to run the fct 'compile'
2715            compile(ActionName,TransformPath)
2716            cd(currentdir)
2717        end
2718       
2719    else
2720        sh_file_info=dir(fullfile(get(handles.ActionPath,'String'),[ActionName '.sh']));
2721        m_file_info=dir(fullfile(get(handles.ActionPath,'String'),[ActionName '.m']));
2722        if isfield(m_file_info,'datenum') && m_file_info.datenum>sh_file_info.datenum
2723            set(handles.ActionExt,'BackgroundColor',[1 1 0])
2724            drawnow
2725            answer=msgbox_uvmat('INPUT_Y-N',[ActionName '.sh needs to be updated: recompile now?']);
2726            if strcmp(answer,'Yes')
2727                path_uvmat=fileparts(which('series'));
2728                currentdir=pwd;
2729                cd(get(handles.ActionPath,'String'))% go to the directory of Action
2730                %  addpath(get(handles.TransformPath,'String'))
2731                addpath(path_uvmat)% add the path to uvmat to run the fct 'compile'
2732                addpath(fullfile(path_uvmat,'transform_field'))% add the path to uvmat to run the fct 'compile'
2733                compile(ActionName,TransformPath)
2734                cd(currentdir)
2735            end
2736        end
2737    end
2738    set(handles.ActionExt,'BackgroundColor',[1 1 1])
2739end
2740
2741
2742function ActionInput_Callback(hObject, eventdata, handles)
2743
2744
2745% --- Executes on button press in DeleteObject.
2746function DeleteObject_Callback(hObject, eventdata, handles)
2747if get(handles.DeleteObject,'Value')
2748        SeriesData=get(handles.series,'UserData');
2749    SeriesData.ProjObject=[];
2750    set(handles.series,'UserData',SeriesData)
2751    set(handles.ProjObject,'String','')
2752    set(handles.CheckObject,'Value',0)
2753    set(handles.DeleteObject,'Visible','off')
2754    set(handles.ViewObject,'Visible','off')
2755    set(handles.DeleteObject,'Value',0)
2756end
2757
2758% --- Executes on button press in ViewObject.
2759function ViewObject_Callback(hObject, eventdata, handles)
2760if get(handles.ViewObject,'Value')
2761        UserData=get(handles.series,'UserData');
2762    set_object(UserData.ProjObject)
2763else
2764    hset_object=findobj(allchild(0),'Tag','set_object');
2765    if ~isempty(hset_object)
2766        delete(hset_object)
2767    end
2768end
2769
2770
2771function num_NbProcess_Callback(hObject, eventdata, handles)
2772
2773
2774function num_NbSlice_Callback(hObject, eventdata, handles)
2775NbSlice=str2num(get(handles.num_NbSlice,'String'));
2776set(handles.num_NbProcess,'String',num2str(NbSlice))
Note: See TracBrowser for help on using the repository browser.