source: trunk/src/series.m @ 622

Last change on this file since 622 was 620, checked in by sommeria, 8 years ago

bugs repaired in series + cleaning.
Introducing of a demo program (test stage)

File size: 114.3 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
69% position and  size of the GUI at opening
70set(0,'Unit','points')
71ScreenSize=get(0,'ScreenSize');%size of the current screen, in points (1/72 inch)
72Width=900;% prefered width of the GUI in points (1/72 inch)
73Height=624;% prefered height of the GUI in points (1/72 inch)
74%adjust to screen size (reduced by a min margin)
75RescaleFactor=min((ScreenSize(3)-80)/Width,(ScreenSize(4)-80)/Height);
76if RescaleFactor>1
77    %RescaleFactor=RescaleFactor/2+1/2; %reduce the rescale factor to provide an increased margin for a big screen
78    RescaleFactor=min(RescaleFactor,1);
79end
80Width=Width*RescaleFactor;
81Height=Height*RescaleFactor;
82LeftX=80*RescaleFactor;%position of the left fig side, in pixels (put to the left side, with some margin)
83LowY=round(ScreenSize(4)/2-Height/2); % put at the middle height on the screen
84set(hObject,'Units','points')
85set(hObject,'Position',[LeftX LowY Width Height])% position and size of the GUI at opening
86
87% settings of table MinIndex_j
88set(handles.MinIndex_i,'ColumnFormat',{'numeric'})
89set(handles.MinIndex_i,'ColumnEditable',false)
90set(handles.MinIndex_i,'ColumnName',{'i min'})
91
92% settings of table MinIndex_j
93set(handles.MinIndex_j,'ColumnFormat',{'numeric'})
94set(handles.MinIndex_j,'ColumnEditable',false)
95set(handles.MinIndex_j,'ColumnName',{'j min'})
96
97% settings of table MaxIndex_i
98set(handles.MaxIndex_i,'ColumnFormat',{'numeric'})
99set(handles.MaxIndex_i,'ColumnEditable',false)
100set(handles.MaxIndex_i,'ColumnName',{'i max'})
101
102% settings of table MaxIndex_j
103set(handles.MaxIndex_j,'ColumnFormat',{'numeric'})
104set(handles.MaxIndex_j,'ColumnEditable',false)
105set(handles.MaxIndex_j,'ColumnName',{'j max'})
106
107% settings of table PairString
108set(handles.PairString,'ColumnName',{'pairs'})
109set(handles.PairString,'ColumnEditable',false)
110set(handles.PairString,'ColumnFormat',{'char'})
111set(handles.PairString,'Data',{''})
112
113series_ResizeFcn(hObject, eventdata, handles)%resize table according to series GUI size
114set(hObject,'WindowButtonDownFcn',{'mouse_down'})%allows mouse action with right button (zoom for uicontrol display)
115
116% check default input data
117if ~exist('Param','var')
118    Param=[]; %default
119end
120
121%% list of builtin functions in the mebu ActionName
122ActionList={'check_data_files';'aver_stat';'time_series';'merge_proj'};% WARNING: fits with nb_builtin_ACTION=4 in ActionName_callback
123NbBuiltinAction=numel(ActionList);
124[path_series,name,ext]=fileparts(which('series'));% path to the GUI series
125path_series_fct=fullfile(path_series,'series');%path of the functions in subdirectroy 'series'
126ActionExtList={'.m';'.sh'};% default choice of extensions (Matlab fct .m or compiled version .sh
127ActionPathList=cell(NbBuiltinAction,numel(ActionExtList));%initiate the cell matrix of Action fct paths
128ActionPathList(:)={path_series_fct}; %set the default path to series fcts to all list members
129RunModeList={'local';'background'};% default choice of extensions (Matlab fct .m or compiled version .sh)
130[s,w]=system('oarstat');% look for cluster system 'oar'
131if isequal(s,0)
132    RunModeList=[RunModeList;{'cluster_oar'}];
133end
134[s,w]=system('qstat');% look for cluster system 'sge'
135if isequal(s,0)
136    RunModeList=[RunModeList;{'cluster_sge'}];
137end
138set(handles.RunMode,'String',RunModeList)
139
140%% list of builtin transform functions in the mebu TransformName
141TransformList={'';'sub_field';'phys';'phys_polar'};% WARNING: must fit with the corresponding menu in uvmat and nb_builtin_transform=4 in  TransformName_callback
142NbBuiltinTransform=numel(TransformList);
143path_transform_fct=fullfile(path_series,'transform_field');
144TransformPathList=cell(NbBuiltinTransform,1);%initiate the cell matrix of Action fct paths
145TransformPathList(:)={path_transform_fct}; %set the default path to series fcts to all list members
146
147%% get the user defined functions stored in the personal file uvmat_perso.mat
148dir_perso=prefdir;
149profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
150if exist(profil_perso,'file')
151    h=load (profil_perso);
152    %get the list of previous input files in the upper bar menu Open
153    if isfield(h,'MenuFile')
154        for ifile=1:min(length(h.MenuFile),5)
155            eval(['set(handles.MenuFile_' num2str(ifile) ',''Label'',h.MenuFile{ifile});'])
156        end
157    end
158    %get the menu of actions
159    if isfield(h,'ActionExtListUser') && iscell(h.ActionExtListUser)
160        ActionExtList=[ActionExtList; h.ActionExtListUser];
161    end
162    if isfield(h,'ActionListUser') && iscell(h.ActionListUser) && isfield(h,'ActionPathListUser') && iscell(h.ActionPathListUser)
163        ActionList=[ActionList;h.ActionListUser];
164        ActionPathList=[ActionPathList;h.ActionPathListUser];
165    end
166    %get the menu of transform fct
167    if isfield(h,'TransformListUser') && iscell(h.TransformListUser) && isfield(h,'TransformPathListUser') && iscell(h.TransformPathListUser)
168        TransformList=[TransformList;h.TransformListUser];
169        TransformPathList=[TransformPathList;h.TransformPathListUser];
170    end
171end
172
173%% selection of the input Action fct
174ActionCheckExist=true(size(ActionList));%initiate the check of the path to the listed action fct
175for ilist=NbBuiltinAction+1:numel(ActionList)%check  the validity of the path of the user defined Action fct
176    ActionCheckExist(ilist)=exist(fullfile(ActionPathList{ilist},[ActionList{ilist} '.m']),'file');
177end
178ActionPathList=ActionPathList(ActionCheckExist,:);% suppress the menu options which are not valid anymore
179ActionList=ActionList(ActionCheckExist);
180set(handles.ActionName,'String',[ActionList;{'more...'}])
181set(handles.ActionName,'UserData',ActionPathList)
182ActionIndex=[];
183if isfield(Param,'ActionName')% copy the selected menu index transferred in Param from uvmat
184    ActionIndex=find(strcmp(Param.ActionName,ActionList),1);
185end
186if isempty(ActionIndex)
187    ActionIndex=1;
188end
189set(handles.ActionName,'Value',ActionIndex)
190set(handles.ActionPath,'String',ActionPathList{ActionIndex})
191set(handles.ActionExt,'Value',1)
192set(handles.ActionExt,'String',ActionExtList)
193
194%% selection of the input transform fct
195TransformCheckExist=true(size(TransformList));
196for ilist=NbBuiltinTransform+1:numel(TransformList)
197    TransformCheckExist(ilist)=exist(fullfile(TransformPathList{ilist},[TransformList{ilist} '.m']),'file');
198end
199TransformPathList=TransformPathList(TransformCheckExist);
200TransformList=TransformList(TransformCheckExist);
201set(handles.TransformName,'String',[TransformList;{'more...'}])
202set(handles.TransformName,'UserData',TransformPathList)
203TransformIndex=[];
204if isfield(Param,'TransformName')% copy the selected menu index transferred in Param from uvmat
205    TransformIndex=find(strcmp(Param.TransformName,TransformList),1);
206end
207if isempty(TransformIndex)
208    TransformIndex=1;
209end
210set(handles.TransformName,'Value',TransformIndex)
211set(handles.TransformPath,'String',TransformPathList{TransformIndex})
212   
213%% fields input initialisation
214if isfield(Param,'list_fields')&& isfield(Param,'index_fields') &&~isempty(Param.list_fields) &&~isempty(Param.index_fields)
215    set(handles.FieldName,'String',Param.list_fields);% list menu fields
216    set(handles.FieldName,'Value',Param.index_fields);% selected string index
217end
218if isfield(Param,'Coord_x_str')&& isfield(Param,'Coord_x_val')
219        set(handles.Coord_x,'String',Param.Coord_x_str);% list menu fields
220    set(handles.Coord_x,'Value',Param.Coord_x_val);% selected string index
221end
222if isfield(Param,'Coord_y_str')&& isfield(Param,'Coord_y_val')
223        set(handles.Coord_y,'String',Param.Coord_y_str);% list menu fields
224    set(handles.Coord_y,'Value',Param.Coord_y_val);% selected string index
225end
226
227%% Adjust the GUI according to the binaries available in PARAM.xml
228% path_uvmat=fileparts(which('uvmat')); %path to civ
229% 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)
230% errormsg=[];%default error message
231% xmlfile='PARAM.xml';
232% if exist(xmlfile,'file')
233%     try
234%         t=xmltree(xmlfile);
235%         sparam=convert(t);
236%     catch ME
237%         errormsg={' Unable to read the file PARAM.xml defining the  binaries:';ME.message};
238%     end
239% else
240%     errormsg=[xmlfile ' not found: path to binaries undefined'];
241% end
242% if ~isempty(errormsg)
243%     msgbox_uvmat('WARNING',errormsg);
244% end
245% test_batch=0;%default: ,no batch mode available
246% if isfield(sparam,'BatchParam') && isfield(sparam.BatchParam,'BatchMode')
247%     test_batch=strcmp(sparam.BatchParam.BatchMode,'sge'); %sge is currently the only implemented batch mod
248% end
249% RUNVal=get(handles.RunMode,'Value');
250% if test_batch==0
251%    if RUNVal>2
252%        set(handles.RunMode,'Value',1)
253%    end
254%    set(handles.RunMode,'String',{'local';'background'})
255% else
256%     set(handles.RunMode,'String',{'local';'background';'cluster'})
257% end
258
259%% introduce the input file name(s) if defined from input Param
260if isfield(Param,'FileName')
261    InputTable={'','','','',''}; % refresh the file input table
262    set(handles.InputTable,'Data',InputTable)
263    if isfield(Param,'FileName_1')
264        display_file_name(handles,Param.FileName,'one')%refresh the input table
265        display_file_name(handles,Param.FileName_1,1)
266    else
267        display_file_name(handles,Param.FileName,'one')%refresh the input table
268    end
269end 
270if isfield(Param,'incr_i')
271    set(handles.num_incr_i,'String',num2str(Param.incr_i))
272end
273if isfield(Param,'incr_j')
274    set(handles.num_incr_j,'String',num2str(Param.incr_j))
275end
276
277
278%------------------------------------------------------------------------
279% --- Outputs from this function are returned to the command line.
280function varargout = series_OutputFcn(hObject, eventdata, handles)
281%------------------------------------------------------------------------
282% varargout  cell array for returning output args (see VARARGOUT);
283% hObject    handle to figure
284% eventdata  reserved - to be defined in a future version of MATLAB
285% handles    structure with handles and user data (see GUIDATA)
286% Get default command line output from handles structure
287varargout{1} = handles.output;
288
289%------------------------------------------------------------------------
290%------------------------------------------------------------------------
291%  II - FUNCTIONS FOR INTRODUCING THE INPUT FILES
292% automatically sets the global properties when the rootfile name is introduced
293% then activate the view-field actionname if selected
294% it is activated either by clicking on the RootPath window or by the
295% browser
296%------------------------------------------------------------------------
297%------------------------------------------------------------------------
298function MenuBrowse_Callback(hObject, eventdata, handles)
299%------------------------------------------------------------------------   
300%get the previous input file in the Input Table
301oldfile=''; %default
302SeriesData=get(handles.series,'UserData');
303if isfield(SeriesData,'RefFile')
304    oldfile=SeriesData.RefFile{1};
305end
306if ~exist(oldfile,'file')
307    dir_perso=prefdir;
308    profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
309    if exist(profil_perso,'file')
310         h=load (profil_perso);
311        if isfield(h,'RootPath')&&ischar(h.RootPath)
312            oldfile=h.RootPath;
313        end
314    end
315end
316fileinput=uigetfile_uvmat('pick a file to refresh the input table',oldfile);
317if ~isempty(fileinput)
318     display_file_name(handles,fileinput,'one')
319end
320
321
322% --------------------------------------------------------------------
323function MenuFile_1_Callback(hObject, eventdata, handles)
324fileinput=get(handles.MenuFile_1,'Label');
325display_file_name(handles,fileinput,'one')
326
327% --------------------------------------------------------------------
328function MenuFile_2_Callback(hObject, eventdata, handles)
329fileinput=get(handles.MenuFile_2,'Label');
330display_file_name(handles,fileinput,'one')
331
332% --------------------------------------------------------------------
333function MenuFile_3_Callback(hObject, eventdata, handles)
334fileinput=get(handles.MenuFile_3,'Label');
335display_file_name( handles,fileinput,'one')
336
337% --------------------------------------------------------------------
338function MenuFile_4_Callback(hObject, eventdata, handles)
339fileinput=get(handles.MenuFile_4,'Label');
340display_file_name(handles,fileinput,'one')
341
342% --------------------------------------------------------------------
343function MenuFile_5_Callback(hObject, eventdata, handles)
344fileinput=get(handles.MenuFile_5,'Label');
345display_file_name(handles,fileinput,'one')
346
347% --------------------------------------------------------------------
348function MenuBrowse_insert_Callback(hObject, eventdata, handles)
349InputTable=get(handles.InputTable,'Data');
350RootPathCell=InputTable(:,1);
351SubDirCell=InputTable(:,3);
352RootFileCell=InputTable(:,2);
353oldfile=''; %default
354if isempty(RootPathCell)||isequal(RootPathCell,{''})%loads the previously stored file name and set it as default in the file_input box
355     dir_perso=prefdir;
356     profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
357     if exist(profil_perso,'file')
358          h=load (profil_perso);
359         if isfield(h,'filebase')&ischar(h.filebase)
360                 oldfile=h.filebase;
361         end
362         if isfield(h,'RootPath')&ischar(h.RootPath)
363                 oldfile=h.RootPath;
364         end
365     end
366 else
367     oldfile=fullfile(RootPathCell{1},RootFileCell{1});
368 end
369[FileName, PathName, filterindex] = uigetfile( ...
370       {'*.xml;*.xls;*.png;*.avi;*.AVI;*.nc', ' (*.xml,*.xls, *.png, *.avi,*.nc)';
371       '*.xml',  '.xml files '; ...
372        '*.xls',  '.xls files '; ...
373        '*.png','.png image files'; ...
374        '*.avi;*.AVI','.avi movie files'; ...
375        '*.nc','.netcdf files'; ...
376        '*.*',  'All Files (*.*)'}, ...
377        'Pick a file',oldfile);
378fileinput=[PathName FileName];%complete file name
379sizf=size(fileinput);
380if (~ischar(fileinput)|~isequal(sizf(1),1)),return;end
381[path,name,ext]=fileparts(fileinput);
382if isequal(ext,'.xml')
383    msgbox_uvmat('ERROR','input file type not implemented')%A Faire: ouvrir le fichier pour naviguer
384elseif isequal(ext,'.xls')
385    msgbox_uvmat('ERROR','input file type not implemented')%A Faire: ouvrir le fichier pour naviguer
386else
387    display_file_name(handles,fileinput,'append')
388end
389
390% --------------------------------------------------------------------
391function MenuFile_insert_1_Callback(hObject, eventdata, handles)
392% --------------------------------------------------------------------   
393fileinput=get(handles.MenuFile_insert_1,'Label');
394display_file_name(handles,fileinput,'append')
395
396% --------------------------------------------------------------------
397function MenuFile_insert_2_Callback(hObject, eventdata, handles)
398% --------------------------------------------------------------------   
399fileinput=get(handles.MenuFile_insert_2,'Label');
400display_file_name(handles,fileinput,'append')
401
402% --------------------------------------------------------------------
403function MenuFile_insert_3_Callback(hObject, eventdata, handles)
404% --------------------------------------------------------------------   
405fileinput=get(handles.MenuFile_insert_3,'Label');
406display_file_name( handles,fileinput,'append')
407
408% --------------------------------------------------------------------
409function MenuFile_insert_4_Callback(hObject, eventdata, handles)
410% --------------------------------------------------------------------   
411fileinput=get(handles.MenuFile_insert_4,'Label');
412display_file_name( handles,fileinput,'append')
413
414% --------------------------------------------------------------------
415function MenuFile_insert_5_Callback(hObject, eventdata, handles)
416% --------------------------------------------------------------------   
417fileinput=get(handles.MenuFile_insert_5,'Label');
418display_file_name(handles,fileinput,'append')
419
420%------------------------------------------------------------------------
421% --- Executes when entered data in editable cell(s) in InputTable.
422function InputTable_CellEditCallback(hObject, eventdata, handles)
423%------------------------------------------------------------------------
424set(handles.REFRESH,'Visible','on')
425set(handles.REFRESH_title,'Visible','on')
426iview=eventdata.Indices(1);
427view_set=get(handles.REFRESH,'UserData');
428if isempty(find(view_set==iview))
429    set(handles.REFRESH,'UserData',[view_set iview])
430end
431%% enable other menus and uicontrols
432set(handles.MenuOpen_insert,'Enable','on')
433set(handles.MenuFile_insert_1,'Enable','on')
434set(handles.MenuFile_insert_2,'Enable','on')
435set(handles.MenuFile_insert_3,'Enable','on')
436set(handles.MenuFile_insert_4,'Enable','on')
437set(handles.MenuFile_insert_5,'Enable','on')
438set(handles.RUN, 'Enable','On')
439set(handles.RUN,'BackgroundColor',[1 0 0])% set RUN button to red
440
441%------------------------------------------------------------------------
442% --- Executes on button press in REFRESH.
443function REFRESH_Callback(hObject, eventdata, handles)
444%------------------------------------------------------------------------
445InputTable=get(handles.InputTable,'Data');
446view_set=get(handles.REFRESH,'UserData');% list of lines to refresh
447set(handles.REFRESH,'BackgroundColor',[1 1 0])% set REFRESH  button to yellow color (indicate activation)
448drawnow
449for iview=view_set
450    RootPath=fullfile(InputTable{iview,1},InputTable{iview,2});
451    if ~exist(RootPath,'dir')
452        i1_series=[];
453        RootPath=fileparts(RootPath); %will try the upped forldr
454    else
455        [RootPath,SubDir,RootFile,i1_series,i2_series,j1_series,j2_series,tild,FileType,FileInfo,MovieObject]=...
456            find_file_series(fullfile(InputTable{iview,1},InputTable{iview,2}),[InputTable{iview,3} InputTable{iview,4} InputTable{iview,5}]);
457    end
458    if isempty(i1_series)
459        fileinput=uigetfile_uvmat(['wrong input at line ' num2str(iview) ':pick a new input file'],RootPath);
460        if isempty(fileinput)
461            set(handles.REFRESH,'BackgroundColor',[1 0 0])% set REFRESH  back to red color
462            return
463        else
464            display_file_name(handles,fileinput,iview)
465        end
466    else
467       update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileType,FileInfo,MovieObject,iview)
468    end
469end
470set(handles.REFRESH,'Visible','off')
471set(handles.REFRESH_title,'Visible','off')
472set(handles.REFRESH,'UserData',[])
473
474%------------------------------------------------------------------------
475% --- Function called when a new file is opened, either by series_OpeningFcn or by the browser
476function display_file_name(handles,fileinput,iview)
477%------------------------------------------------------------------------ 
478%
479% INPUT:
480% handles: handles of elements in the GUI
481% fileinput: input file name, including path
482% iview: line index in the input table
483%       or 'one': refresh the list
484%       'append': add a new line to the list
485
486%% get the input root name, indices, file extension and nomenclature NomType
487if ~exist(fileinput,'file')
488    msgbox_uvmat('ERROR',['input file ' fileinput  ' does not exist'])
489    return
490end
491
492%% enable other menus and uicontrols
493set(handles.MenuOpen_insert,'Enable','on')
494set(handles.MenuFile_insert_1,'Enable','on')
495set(handles.MenuFile_insert_2,'Enable','on')
496set(handles.MenuFile_insert_3,'Enable','on')
497set(handles.MenuFile_insert_4,'Enable','on')
498set(handles.MenuFile_insert_5,'Enable','on')
499set(handles.RUN, 'Enable','On')
500set(handles.RUN,'BackgroundColor',[1 0 0])% set RUN button to red
501set(handles.InputTable,'BackgroundColor',[1 1 0]) % set RootPath edit box  to yellow
502drawnow
503
504%% detect root name, nomenclature and indices in the input file name:
505[FilePath,FileName,FileExt]=fileparts(fileinput);
506% detect the file type, get the movie object if relevant, and look for the corresponding file series:
507% the root name and indices may be corrected by including the first index i1 if a corresponding xml file exists
508[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]);
509if isempty(RootFile)&&isempty(i1_series)
510    errormsg='no input file in the series';
511    return
512end
513
514%% fill the list of file series
515InputTable=get(handles.InputTable,'Data');
516SeriesData=get(handles.series,'UserData');
517if strcmp(iview,'append') % display the input data as a new line in the table
518    iview=size(InputTable,1);% the next line in InputTable becomes the current line
519    InputTable(iview+1,:)={'','','','',''};
520    InputTable(iview,:)=[{RootPath},{SubDir},{RootFile},{NomType},{FileExt}];
521elseif strcmp(iview,'one') % refresh the list of  input  file series
522    iview=1; %the first line in InputTable becomes the current line
523    InputTable=[{'','','','',''};{'','','','',''}];
524    InputTable(iview,:)=[{RootPath},{SubDir},{RootFile},{NomType},{FileExt}];
525    set(handles.TimeTable,'Data',[{[]},{[]},{[]},{[]}])
526    set(handles.MinIndex_i,'Data',[{[]}])
527    set(handles.MaxIndex_i,'Data',[{[]}])
528    set(handles.MinIndex_j,'Data',[{[]}])
529    set(handles.MaxIndex_j,'Data',[{[]}])
530    set(handles.ListView,'Value',1)
531    set(handles.ListView,'String',{'1'})
532    set(handles.PairString,'Data',{''})
533    SeriesData.i1_series={};
534    SeriesData.i2_series={};
535    SeriesData.j1_series={};
536    SeriesData.j2_series={};
537    SeriesData.FileType={};
538    SeriesData.FileInfo={};
539    SeriesData.Time={};
540end
541nbview=size(InputTable,1)-1;% rmq: the last line is set blank to allow manual addition of a line
542set(handles.ListView,'String',mat2cell((1:nbview)',ones(nbview,1)))
543set(handles.ListView,'Value',iview)
544set(handles.InputTable,'Data',InputTable)
545
546%% determine the selected reference field indices for pair display
547if isempty(i1)
548    i1=1;
549end
550if isempty(i2)
551    i2=i1;
552end
553ref_i=floor((i1+i2)/2);% reference image number corresponding to the file
554set(handles.num_ref_i,'String',num2str(ref_i));
555% set(handles.num_ref_i,'UserData',[i1 i2])%store the indices for future opening
556if isempty(j1)
557    j1=1;
558end
559if isempty(j2)
560    j2=j1;
561end
562ref_j=floor((j1+j2)/2);% reference image number corresponding to the file
563set(handles.num_ref_j,'String',num2str(ref_j));
564% set(handles.num_ref_j,'UserData',[j1 j2]);%store the indices for future opening
565
566%% update the list of recent files in the menubar and save it for future opening
567MenuFile=[{get(handles.MenuFile_1,'Label')};{get(handles.MenuFile_2,'Label')};...
568    {get(handles.MenuFile_3,'Label')};{get(handles.MenuFile_4,'Label')};{get(handles.MenuFile_5,'Label')}];
569str_find=strcmp(fileinput,MenuFile);
570if isempty(find(str_find,1))
571    MenuFile=[{fileinput};MenuFile];%insert the current file if not already in the list
572end
573for ifile=1:min(length(MenuFile),5)
574    eval(['set(handles.MenuFile_' num2str(ifile) ',''Label'',MenuFile{ifile});'])
575    eval(['set(handles.MenuFile_insert_' num2str(ifile) ',''Label'',MenuFile{ifile});'])
576end
577dir_perso=prefdir;
578profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
579if exist(profil_perso,'file')
580    save (profil_perso,'MenuFile','-append'); %store the file names for future opening of uvmat
581else
582    save (profil_perso,'MenuFile','-V6'); %store the file names for future opening of uvmat
583end
584% save the opened file to initiate future opening
585SeriesData.RefFile{iview}=fileinput;% reference opening file for line iview
586SeriesData.Ref_i1=i1;
587SeriesData.Ref_i2=i2;
588SeriesData.Ref_j1=j1;
589SeriesData.Ref_j2=j2;
590set(handles.series,'UserData',SeriesData)
591
592set(handles.InputTable,'BackgroundColor',[1 1 1])
593
594%% initiate input file series and refresh the current field view:     
595update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileType,FileInfo,MovieObject,iview);
596
597%------------------------------------------------------------------------
598% --- Update information about a new field series (indices to scan, timing,
599%     calibration from an xml file
600function update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileType,FileInfo,VideoObject,iview)
601%------------------------------------------------------------------------
602InputTable=get(handles.InputTable,'Data');
603
604%% display the min and max indices for the whole file series
605if size(i1_series,2)==2 && min(min(i1_series(:,1,:)))==0
606    MinIndex_j=1;% index j set to 1 by default
607    MaxIndex_j=1;
608    MinIndex_i=find(i1_series(:,2,:), 1 )-1;
609    MaxIndex_i=find(i1_series(:,2,:), 1, 'last' )-1;
610else
611    pair_max=squeeze(max(i1_series,[],1)); %max on pair index
612    j_max=max(pair_max,[],1);
613    MaxIndex_i=find(j_max, 1, 'last' )-1;% max ref index i
614    MinIndex_i=find(j_max, 1 )-1;% min ref index i
615    diff_i_max=diff(j_max);
616    if ~isempty(diff_i_max) && isequal (diff_i_max,diff_i_max(1)*ones(size(diff_i_max)))
617        set(handles.num_incr_i,'String',num2str(diff_i_max(1)))% detect an increment to dispaly by default
618    end
619    i_max=max(pair_max,[],2);
620    MaxIndex_j=max(find(i_max))-1;% max ref index i
621    MinIndex_j=min(find(i_max))-1;% min ref index i
622    diff_j_max=diff(i_max);
623    if isequal (diff_j_max,diff_j_max(1)*ones(size(diff_j_max)))
624        set(handles.num_incr_j,'String',num2str(diff_j_max(1)))
625    end
626end
627if isequal(MinIndex_i,-1)
628    MinIndex_i=0;
629end
630if isequal(MinIndex_j,-1)
631    MinIndex_j=0;
632end
633MinIndex_i_cell=get(handles.MinIndex_i,'Data');%retrieve the min indices in the table MinIndex
634MinIndex_j_cell=get(handles.MinIndex_j,'Data');%retrieve the min indices in the table MinIndex
635MaxIndex_i_cell=get(handles.MaxIndex_i,'Data');%retrieve the min indices in the table MinIndex
636MaxIndex_j_cell=get(handles.MaxIndex_j,'Data');%retrieve the min indices in the table MinIndex
637MinIndex_i_cell{iview,1}=MinIndex_i;
638MinIndex_j_cell{iview,1}=MinIndex_j;
639MaxIndex_i_cell{iview,1}=MaxIndex_i;
640MaxIndex_j_cell{iview,1}=MaxIndex_j;
641set(handles.MinIndex_i,'Data',MinIndex_i_cell)%display the min indices in the table MinIndex
642set(handles.MinIndex_j,'Data',MinIndex_j_cell)%display the max indices in the table MaxIndex
643set(handles.MaxIndex_i,'Data',MaxIndex_i_cell)%display the min indices in the table MinIndex
644set(handles.MaxIndex_j,'Data',MaxIndex_j_cell)%display the max indices in the table MaxIndex
645
646%% adjust the first and last indices for the selected series, only if requested by the bounds
647% i index, compare input to min index i
648first_i=str2num(get(handles.num_first_i,'String'));%retrieve previous first i
649ref_i=str2num(get(handles.num_ref_i,'String'));%index i given by the input field
650if isempty(first_i)
651    first_i=ref_i;% first_i updated by the input value
652elseif first_i < MinIndex_i
653    first_i=MinIndex_i; % first_i set to the min i index (restricted by oter input lines)
654elseif first_i >MaxIndex_i
655    first_i=MaxIndex_i;% first_i set to the max i index (restricted by oter input lines)
656end
657% j index,  compare input to min index j
658first_j=str2num(get(handles.num_first_j,'String'));
659ref_j=str2num(get(handles.num_ref_j,'String'));%index j given by the input field
660if isempty(first_j)
661    first_j=ref_j;% first_j updated by the input value
662elseif first_j<MinIndex_j
663    first_j=MinIndex_j; % first_j set to the min j index (restricted by oter input lines)
664elseif first_j >MaxIndex_j
665    first_j=MaxIndex_j; % first_j set to the max j index (restricted by oter input lines)
666end
667% i index, compare input to max index i
668last_i=str2num(get(handles.num_last_i,'String'));
669if isempty(last_i)
670    last_i=ref_i;
671elseif last_i > MaxIndex_i
672    last_i=MaxIndex_i;
673elseif last_i<first_i
674    last_i=first_i;
675end
676% j index, compare input to max index j
677last_j=str2num(get(handles.num_last_j,'String'));
678if isempty(last_j)
679    last_j=ref_j;
680elseif last_j>MaxIndex_j
681    last_j=MaxIndex_j;
682elseif last_j<first_j
683    last_j=first_j;
684end
685set(handles.num_first_i,'String',num2str(first_i));
686set(handles.num_first_j,'String',num2str(first_j));
687set(handles.num_last_i,'String',num2str(last_i));
688set(handles.num_last_j,'String',num2str(last_j));
689
690%% number of slices set by default
691NbSlice=1;%default
692% read  value set by the first series for the append mode (iwiew >1)
693if iview>1 && strcmp(get(handles.num_NbSlice,'Visible'),'on')
694    NbSlice=str2num(get(handles.num_NbSlice,'String'));
695end
696
697%% default time unit
698TimeUnit='';
699% read  value set by the first series for the append mode (iwiew >1)
700if iview>1
701    TimeUnit=get(handles.TimeUnit,'String');
702end
703TimeSource='';
704Time=[];%default
705
706%%  read image documentation file if found
707XmlData=[];
708check_calib=0;
709XmlFileName=find_imadoc(InputTable{iview,1},InputTable{iview,2},InputTable{iview,3},InputTable{iview,5});
710if ~isempty(XmlFileName)
711    [XmlData,errormsg]=imadoc2struct(XmlFileName);
712    if ~isempty(errormsg)
713         msgbox_uvmat('WARNING',['error in reading ' XmlFileName ': ' errormsg]);
714    end
715    % read time if available
716    if isfield(XmlData,'Time')
717        Time=XmlData.Time;
718        TimeSource='xml';
719    end
720    if isfield(XmlData,'Camera')
721        if isfield(XmlData.Camera,'NbSlice')&& ~isempty(XmlData.Camera.NbSlice)
722            if iview>1 && ~isempty(NbSlice) && ~strcmp(NbSlice,XmlData.Camera.NbSlice)
723                msgbox_uvmat('WARNING','inconsistent number of slices with the first field series');
724            end
725            NbSlice=XmlData.Camera.NbSlice;% Nbre of slices from camera
726        end
727        if isfield(XmlData.Camera,'TimeUnit')&& ~isempty(XmlData.Camera.TimeUnit)
728            if iview>1 && ~isempty(TimeUnit) && ~strcmp(TimeUnit,XmlData.Camera.TimeUnit)
729                msgbox_uvmat('WARNING','inconsistent time unit with the first field series');
730            end
731            TimeUnit=XmlData.Camera.TimeUnit;
732        end
733    end
734    % number of slices
735    if isfield(XmlData,'GeometryCalib')
736        check_calib=1;
737        if isfield(XmlData.GeometryCalib,'SliceCoord')
738            siz=size(XmlData.GeometryCalib.SliceCoord);
739            if siz(1)>1
740                if iview>1 && ~isempty(NbSlice) && ~strcmp(NbSlice,siz(1))
741                    msgbox_uvmat('WARNING','inconsistent number of Z indices with the first field series');
742                end
743                NbSlice=siz(1);
744            end
745        end
746    end
747    set(handles.num_NbSlice,'String',num2str(NbSlice))
748end
749
750%% read timing and total frame number from the current file (movie files) if not already set by the xml file (prioritary)
751InputTable=get(handles.InputTable,'Data');
752% FileBase=fullfile(InputTable{iview,1},InputTable{iview,3});
753
754% case of movies
755% if strcmp(InputTable{iview,4},'*')
756if isempty(Time)
757    if ~isempty(VideoObject)
758        imainfo=get(VideoObject);
759        if isempty(j1_series); %frame index along i
760            Time=zeros(imainfo.NumberOfFrames+1,2);
761            Time(:,2)=(0:1/imainfo.FrameRate:(imainfo.NumberOfFrames)/imainfo.FrameRate)';
762        else
763            Time=[0;ones(size(i1_series,3)-1,1)]*(0:1/imainfo.FrameRate:(imainfo.NumberOfFrames)/imainfo.FrameRate);
764        end
765        TimeSource='video';
766        % set(han:dles.Dt_txt,'String',['Dt=' num2str(1000/imainfo.FrameRate) 'ms']);%display the elementary time interval in millisec
767        %     ColorType='truecolor';
768%     elseif ~isempty(imformats(regexprep(InputTable{iview,5},'^.',''))) || isequal(InputTable{iview,5},'.vol')%&& isequal(NomType,'*')% multi-frame image
769%         if ~isempty(InputTable{iview,2})
770%             imainfo=imfinfo(fullfile(InputTable{iview,1},InputTable{iview,2},[InputTable{iview,3} InputTable{iview,5}]));
771%         else
772%             imainfo=imfinfo([FileBase InputTable{iview,5}]);
773%         end
774%         %     ColorType=imainfo.ColorType;%='truecolor' for color images
775% %         if length(imainfo) >1 %case of image with multiple frames
776% %             nbfield=length(imainfo);
777% %             nbfield_j=1;
778% %         end
779    end
780end
781
782%% update time table
783if ~isempty(Time)
784    TimeTable=get(handles.TimeTable,'Data');
785    %     first_i=str2num(get(handles.num_first_i,'String'));
786    %     last_i=str2num(get(handles.num_last_i,'String'));
787    %     first_j=str2num(get(handles.num_first_j,'String'));
788    %     last_j=str2num(get(handles.num_last_j,'String'));
789    %     MinIndex_i=get(handles.MinIndex_i,'Data');
790    %     MinIndex_j=get(handles.MinIndex_j,'Data');
791    %     MaxIndex_i=get(handles.MaxIndex_i,'Data');
792    %     MaxIndex_j=get(handles.MaxIndex_j,'Data');
793    TimeTable{iview,1}=Time(MinIndex_i+1,MinIndex_j+1);
794    if size(Time)>=[first_i+1 first_j+1]
795        TimeTable{iview,2}=Time(first_i+1,first_j+1);
796    end
797    if size(Time)>=[last_i+1 last_j+1]
798        TimeTable{iview,3}=Time(last_i+1,last_j+1);
799    end
800    if size(Time)>=[MaxIndex_i+1 MaxIndex_j+1];
801        TimeTable{iview,4}=Time(MaxIndex_i+1,MaxIndex_j+1);
802    end
803    set(handles.TimeTable,'Data',TimeTable)
804end
805   
806
807%% update the series info in 'UserData'
808SeriesData=get(handles.series,'UserData');
809SeriesData.i1_series{iview}=i1_series;
810SeriesData.i2_series{iview}=i2_series;
811SeriesData.j1_series{iview}=j1_series;
812SeriesData.j2_series{iview}=j2_series;
813SeriesData.FileType{iview}=FileType;
814SeriesData.FileInfo{iview}=FileInfo;
815SeriesData.Time{iview}=Time;
816if ~isempty(TimeSource)
817    SeriesData.TimeSource=TimeSource;
818end
819% if ~isempty(TimeUnit)
820%     SeriesData.TimeUnit=TimeUnit;
821% end
822if check_calib
823    SeriesData.GeometryCalib{iview}=XmlData.GeometryCalib;
824end
825set(handles.series,'UserData',SeriesData)
826
827%% update pair menus
828ListView=get(handles.ListView,'String');
829ListView{iview}=num2str(iview);
830set(handles.ListView,'String',ListView);
831set(handles.ListView,'Value',iview)
832update_mode(handles,i1_series,i2_series,j1_series,j2_series,Time)
833
834%% enable j index visibilitycellfun(@isempty,regexp(PairString,'^j'))
835check_jindex=~cellfun(@isempty,SeriesData.j1_series); %look for non empty j indices
836if isempty(find(check_jindex))
837    enable_j(handles,'off') % no j index needed
838else
839    PairString=get(handles.PairString,'Data');
840    % ~cellfun(@isempty,regexp(PairString,'^j'): gives 1 when the pair string begins by 'j' (burst case)
841    % cellfun(@isempty,PairString): gives 1 when the pair string is empty
842    if isempty(find(~cellfun(@isempty,regexp(PairString,'^j'))&cellfun(@isempty,PairString)))% if all pair string begins by j (burst) or empty
843        enable_j(handles,'off') % no j index needed
844    else
845        enable_j(handles,'on')
846    end
847end
848
849%% display the set of existing files as an image
850set(handles.FileStatus,'Units','pixels')
851Position=get(handles.FileStatus,'Position');
852set(handles.FileStatus,'Units','normalized')
853xI=0.5:Position(3)-0.5;
854nbview=numel(SeriesData.i1_series);
855pair_max=cell(1,nbview);
856for iview=1:nbview
857    pair_max{iview}=squeeze(max(SeriesData.i1_series{iview},[],1)); %max on pair index
858    if (strcmp(get(handles.num_first_j,'Visible'),'off')&& size(pair_max{iview},2)~=1)
859        pair_max{iview}=squeeze(max(pair_max{iview},[],1)); % consider only the i index
860    end
861    index_min(iview)=find(pair_max{iview}>0, 1 );
862    index_max(iview)=find(pair_max{iview}>0, 1, 'last' );
863end
864index_min=min(index_min);
865index_max=max(index_max);
866range_index=index_max-index_min+1;
867scale_y=Position(4)/nbview;
868scale_x=Position(3)/range_index;
869x=(0.5:range_index-0.5)*Position(3)/range_index;
870% y=(0.5:nbview-0.5)*Position(4)/nbview;
871range_y=max(1,floor(Position(4)/nbview));
872CData=zeros(nbview*range_y,floor(Position(3)));
873for iview=1:nbview
874    ind_y=1+(iview-1)*range_y:iview*range_y;
875    LineData=zeros(1,range_index);
876    x_index=find(pair_max{iview}>0)-index_min+1;
877    LineData(x_index)=1;
878    if numel(x)>1
879    LineData=interp1(x,LineData,xI,'nearest');
880    CData(ind_y,:)=ones(size(ind_y'))*LineData;
881    end
882end
883CData=cat(3,zeros(size(CData)),CData,zeros(size(CData)));
884set(handles.FileStatus,'CData',CData);
885
886
887%% enable field and veltype menus, in accordance with the current action
888ActionName_Callback([],[], handles)
889
890%% check for pair display
891check_pairs=0;
892for iview=1:numel(SeriesData.i2_series)
893    if ~isempty(SeriesData.i2_series{iview})||~isempty(SeriesData.j2_series{iview})
894        check_pairs=1;
895    end
896end
897if check_pairs
898    set(handles.Pairs,'Visible','on')
899    set(handles.PairString,'Visible','on')
900else
901    set(handles.Pairs,'Visible','off')
902    set(handles.PairString,'Visible','off')
903end
904
905%% set length of waitbar
906displ_time(handles)
907
908
909%% set default options in menu 'Fields'
910switch FileType
911    case {'civx','civdata'}
912        [FieldList,ColorList]=set_field_list('U','V','C');
913        set(handles.FieldName,'String',[{'image'};FieldList;{'get_field...'}]);%standard menu for civx data
914        set(handles.FieldName,'Value',2) % set menu to 'velocity
915        set(handles.Coord_x,'Value',1);
916        set(handles.Coord_x,'String',{'X'});
917        set(handles.Coord_y,'Value',1);
918        set(handles.Coord_y,'String',{'Y'});
919    case 'netcdf'
920        set(handles.FieldName,'Value',1)
921        set(handles.FieldName,'String',{'get_field...'})
922        if isempty(i2_series)
923            i2=[];
924        else
925            i2=i2_series(1,ref_j+1,ref_i+1);
926        end
927        if isempty(j1_series)
928            j1=[];j2=[];
929        else
930            j1=j1_series(1,ref_j+1,ref_i+1);
931            if isempty(j2_series)
932                j2=[];
933            else
934                j2=j2_series(1,ref_j+1,ref_i+1);
935            end
936        end
937        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);
938%         hget_field=get_field(FileName);
939%         hhget_field=guidata(hget_field);
940%         get_field('RUN_Callback',hhget_field.RUN,[],hhget_field);
941    otherwise
942        set(handles.FieldName,'Value',1) % set menu to 'image'
943        set(handles.FieldName,'String',{'image'})
944        set(handles.Coord_x,'Value',1);
945        set(handles.Coord_x,'String',{'AX'});
946        set(handles.Coord_y,'Value',1);
947        set(handles.Coord_y,'String',{'AY'});
948end
949
950%------------------------------------------------------------------------
951function num_first_i_Callback(hObject, eventdata, handles)
952%------------------------------------------------------------------------
953num_last_i_Callback(hObject, eventdata, handles)
954
955%------------------------------------------------------------------------
956function num_last_i_Callback(hObject, eventdata, handles)
957%------------------------------------------------------------------------
958SeriesData=get(handles.series,'UserData');
959if ~isfield(SeriesData,'Time')
960    SeriesData.Time{1}=[];
961end
962displ_time(handles);
963
964%------------------------------------------------------------------------
965function num_first_j_Callback(hObject, eventdata, handles)
966%------------------------------------------------------------------------
967 num_last_j_Callback(hObject, eventdata, handles)
968
969%------------------------------------------------------------------------
970function num_last_j_Callback(hObject, eventdata, handles)
971%------------------------------------------------------------------------
972first_j=str2num(get(handles.num_first_j,'String'));
973last_j=str2num(get(handles.num_last_j,'String'));
974ref_j=ceil((first_j+last_j)/2);
975set(handles.num_ref_j,'String', num2str(ref_j))
976num_ref_j_Callback(hObject, eventdata, handles)
977SeriesData=get(handles.series,'UserData');
978if ~isfield(SeriesData,'Time')
979    SeriesData.Time{1}=[];
980end
981displ_time(handles);
982
983
984%------------------------------------------------------------------------
985% ---- find the times corresponding to the first and last indices of a series
986function displ_time(handles)
987%------------------------------------------------------------------------
988SeriesData=get(handles.series,'UserData');%
989ref_i=[str2num(get(handles.num_first_i,'String')) str2num(get(handles.num_last_i,'String'))];
990ref_j=[str2num(get(handles.num_first_j,'String')) str2num(get(handles.num_last_j,'String'))];
991TimeTable=get(handles.TimeTable,'Data');
992Pairs=get(handles.PairString,'Data');
993for iview=1:size(TimeTable,1)
994    if size(SeriesData.Time,1)<iview
995        break
996    end
997    i1=ref_i;
998    j1=ref_j;
999    i2=ref_i;
1000    j2=ref_j;
1001    % case of pairs
1002    if ~isempty(Pairs{iview,1})
1003        r=regexp(Pairs{iview,1},'(?<mode>(Di=)|(Dj=)) -*(?<num1>\d+)\|(?<num2>\d+)','names');
1004        if isempty(r)
1005            r=regexp(Pairs{iview,1},'(?<num1>\d+)(?<mode>-)(?<num2>\d+)','names');
1006        end
1007        switch r.mode
1008            case 'Di='  %  case 'series(Di)')
1009                i1=ref_i-str2num(r.num1);
1010                i2=ref_i+str2num(r.num2);
1011            case 'Dj='  %  case 'series(Dj)'
1012                j1=ref_j-str2num(r.num1);
1013                j2=ref_j+str2num(r.num2);
1014            case '-'  % case 'bursts'
1015                j1=str2num(r.num1)*ones(size(ref_i));
1016                j2=str2num(r.num2)*ones(size(ref_i));
1017        end
1018    end
1019    TimeTable{iview,2}=[];
1020    TimeTable{iview,3}=[];
1021    if size(SeriesData.Time{iview},1)>=i2(2)+1&&size(SeriesData.Time{iview},2)>=j2(2)+1
1022        if isempty(ref_j)
1023            time_first=(SeriesData.Time{iview}(i1(1)+1)+SeriesData.Time{iview}(i2(1)+1))/2;
1024            time_last=(SeriesData.Time{iview}(i1(2)+1)+SeriesData.Time{iview}(i2(2))+1)/2;
1025        else
1026            time_first=(SeriesData.Time{iview}(i1(1)+1,j1(1)+1)+SeriesData.Time{iview}(i2(1)+1,j2(1)+1))/2;
1027            time_last=(SeriesData.Time{iview}(i1(2)+1,j1(2)+1)+SeriesData.Time{iview}(i2(2)+1,j2(2)+1))/2;
1028        end
1029        TimeTable{iview,2}=time_first; %TODO: take into account pairs
1030        TimeTable{iview,3}=time_last; %TODO: take into account pairs
1031    end
1032end
1033set(handles.TimeTable,'Data',TimeTable)
1034
1035%% set the waitbar position with respect to the min and max in the series
1036for iview=1:numel(SeriesData.i1_series)
1037    pair_max{iview}=squeeze(max(SeriesData.i1_series{iview},[],1)); %max on pair index
1038    if (strcmp(get(handles.num_first_j,'Visible'),'off')&& size(pair_max{iview},2)~=1)
1039        pair_max{iview}=squeeze(max(pair_max{iview},[],1)); % consider only the i index
1040    end
1041    pair_max{iview}=reshape(pair_max{iview},1,[]);
1042    index_min(iview)=find(pair_max{iview}>0, 1 );
1043    index_max(iview)=find(pair_max{iview}>0, 1, 'last' );
1044end
1045[index_min,iview_min]=min(index_min);
1046[index_max,iview_max]=min(index_max);
1047if size(SeriesData.i1_series{iview_min},2)==1% movie
1048    index_first=ref_i(1);
1049    index_last=ref_i(2);
1050else
1051    index_first=(ref_i(1)-1)*(size(SeriesData.i1_series{iview_min},1))+ref_j(1)+1;
1052    index_last=(ref_i(2)-1)*(size(SeriesData.i1_series{iview_max},1))+ref_j(2)+1;
1053end
1054range=index_max-index_min+1;
1055coeff_min=(index_first-index_min)/range;
1056coeff_max=(index_last-index_min+1)/range;
1057Position=get(handles.Waitbar,'Position');% position of the waitbar:= [ x,y, width, height]
1058Position_status=get(handles.FileStatus,'Position');
1059Position(1)=coeff_min*Position_status(3)+Position_status(1);
1060Position(3)=Position_status(3)*(coeff_max-coeff_min);
1061set(handles.Waitbar,'Position',Position)
1062update_waitbar(handles.Waitbar,0)
1063
1064%------------------------------------------------------------------------
1065% --- Executes when selected cell(s) is changed in PairString.
1066function PairString_CellSelectionCallback(hObject, eventdata, handles)
1067%------------------------------------------------------------------------   
1068set(handles.ListView,'Value',eventdata.Indices(1))% detect the selected raw index
1069ListView_Callback ([],[],handles) % update the list of available pairs
1070
1071%------------------------------------------------------------------------
1072%------------------------------------------------------------------------
1073%  III - FUNCTIONS ASSOCIATED TO THE FRAME SET PAIRS
1074%------------------------------------------------------------------------
1075%------------------------------------------------------------------------
1076% --- Executes on selection change in ListView.
1077function ListView_Callback(hObject, eventdata, handles)
1078%------------------------------------------------------------------------   
1079SeriesData=get(handles.series,'UserData');
1080i2_series=[];
1081j2_series=[];
1082iview=get(handles.ListView,'Value');
1083if ~isempty(SeriesData.i2_series{iview})
1084    i2_series=SeriesData.i2_series{iview};
1085end
1086if ~isempty(SeriesData.j2_series{iview})
1087    j2_series=SeriesData.j2_series{iview};
1088end
1089update_mode(handles,SeriesData.i1_series{iview},SeriesData.i2_series{iview},...
1090    SeriesData.j1_series{iview},SeriesData.j2_series{iview},SeriesData.Time{iview})
1091
1092%------------------------------------------------------------------------
1093% --- Executes on button press in mode.
1094function mode_Callback(hObject, eventdata, handles)
1095%------------------------------------------------------------------------       
1096SeriesData=get(handles.series,'UserData');
1097iview=get(handles.ListView,'Value');
1098mode_list=get(handles.mode,'String');
1099mode=mode_list{get(handles.mode,'Value')};
1100if isequal(mode,'bursts')
1101    enable_i(handles,'On')
1102    enable_j(handles,'Off') %do not display j index scanning in burst mode (j is fixed by the burst choice)
1103else
1104    enable_i(handles,'On')
1105    enable_j(handles,'Off')
1106end
1107fill_ListPair(handles,SeriesData.i1_series{iview},SeriesData.i2_series{iview},...
1108    SeriesData.j1_series{iview},SeriesData.j2_series{iview},SeriesData.Time{iview})
1109ListPairs_Callback([],[],handles)
1110
1111%-------------------------------------------------------------
1112% --- Executes on selection in ListPairs.
1113function ListPairs_Callback(hObject,eventdata,handles)
1114%------------------------------------------------------------
1115list_pair=get(handles.ListPairs,'String');%get the menu of image pairs
1116if isempty(list_pair)
1117    string='';
1118else
1119    string=list_pair{get(handles.ListPairs,'Value')};
1120    string=regexprep(string,',.*','');%removes time indication (after ',')
1121end
1122PairString=get(handles.PairString,'Data');
1123iview=get(handles.ListView,'Value');
1124PairString{iview,1}=string;
1125% report the selected pair string to the table PairString
1126set(handles.PairString,'Data',PairString)
1127
1128%------------------------------------------------------------------------
1129function num_ref_i_Callback(hObject, eventdata, handles)
1130%------------------------------------------------------------------------
1131mode_list=get(handles.mode,'String');
1132mode=mode_list{get(handles.mode,'Value')};
1133SeriesData=get(handles.series,'UserData');
1134iview=get(handles.ListView,'Value');
1135fill_ListPair(handles,SeriesData.i1_series{iview},SeriesData.i2_series{iview},...
1136    SeriesData.j1_series{iview},SeriesData.j2_series{iview},SeriesData.Time{iview});% update the menu of pairs depending on the available netcdf files
1137ListPairs_Callback([],[],handles)
1138
1139%------------------------------------------------------------------------
1140function num_ref_j_Callback(hObject, eventdata, handles)
1141%------------------------------------------------------------------------
1142num_ref_i_Callback(hObject, eventdata, handles)
1143
1144%------------------------------------------------------------------------
1145function update_mode(handles,i1_series,i2_series,j1_series,j2_series,time)
1146%------------------------------------------------------------------------   
1147% check_burst=0;
1148if isempty(j2_series)% no j pair
1149    if isempty(i2_series)
1150        set(handles.mode,'Value',1)
1151        set(handles.mode,'String',{''})% no pair menu to display
1152    else   
1153        set(handles.mode,'Value',1)
1154        set(handles.mode,'String',{'series(Di)'}) % pair menu with only option Di
1155    end
1156else %existence of j pairs
1157    pair_max=squeeze(max(i1_series,[],1)); %max on pair index
1158    j_max=max(pair_max,[],1);
1159    MaxIndex_i=max(find(j_max))-1;% max ref index i
1160    MinIndex_i=min(find(j_max))-1;% min ref index i
1161    i_max=max(pair_max,[],2);
1162    MaxIndex_j=max(find(i_max))-1;% max ref index i
1163    MinIndex_j=min(find(i_max))-1;% min ref index i
1164    if MaxIndex_j==MinIndex_j
1165        set(handles.mode,'Value',1);
1166        set(handles.mode,'String',{'bursts'})
1167%         check_burst=1;
1168    elseif MaxIndex_i==MinIndex_i
1169        set(handles.mode,'Value',1);
1170        set(handles.mode,'String',{'series(Dj)'})
1171    else
1172        set(handles.mode,'String',{'bursts';'series(Dj)'})
1173        if (MaxIndex_j-MinIndex_j)>10
1174            set(handles.mode,'Value',2);%set mode to series(Dj) if more than 10 j values
1175        else
1176            set(handles.mode,'Value',1);
1177%             check_burst=1;
1178        end
1179    end
1180end
1181fill_ListPair(handles,i1_series,i2_series,j1_series,j2_series,time)
1182ListPairs_Callback([],[],handles)
1183
1184%--------------------------------------------------------------
1185% determine the menu for pairstring depending on existing netcdf files
1186% with the reference indices num_ref_i and num_ref_j
1187%----------------------------------------------------------------
1188function fill_ListPair(handles,i1_series,i2_series,j1_series,j2_series,time)
1189
1190mode_list=get(handles.mode,'String');
1191mode=mode_list{get(handles.mode,'Value')};
1192ref_i=str2num(get(handles.num_ref_i,'String'));
1193if isempty(ref_i)
1194    ref_i=1;
1195end
1196if strcmp(get(handles.num_ref_j,'Visible'),'on')
1197    ref_j=str2num(get(handles.num_ref_j,'String'));
1198    if isempty(ref_j)
1199        ref_j=1;
1200    end
1201else
1202    ref_j=1;
1203end
1204TimeUnit=get(handles.TimeUnit,'String');
1205if length(TimeUnit)>=1
1206    dtunit=['m' TimeUnit];
1207else
1208    dtunit='e-03';
1209end
1210
1211displ_pair={};
1212if strcmp(mode,'series(Di)')
1213    if isempty(i2_series)
1214        msgbox_uvmat('ERROR','no i1-i2 pair available')
1215        return
1216    end
1217    diff_i=i2_series-i1_series;
1218    min_diff=min(diff_i(diff_i>0));
1219    max_diff=max(diff_i(diff_i>0));
1220    for ipair=min_diff:max_diff
1221        if numel(diff_i(diff_i==ipair))>0
1222            pair_string=['Di= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2)) ];
1223            if ~isempty(time)
1224                if ref_i<=floor(ipair/2)
1225                    ref_i=floor(ipair/2)+1;% shift ref_i to get the first pair
1226                end
1227                Dt=time(ref_i+ceil(ipair/2),ref_j)-time(ref_i-floor(ipair/2),ref_j);
1228                pair_string=[pair_string ', Dt=' num2str(Dt) ' ' dtunit];
1229            end
1230            displ_pair=[displ_pair;{pair_string}];
1231        end
1232    end
1233    if ~isempty(displ_pair)
1234        displ_pair=[displ_pair;{'Di=*|*'}];
1235    end
1236elseif strcmp(mode,'series(Dj)')
1237    if isempty(j2_series)
1238        msgbox_uvmat('ERROR','no j1-j2 pair available')
1239        return
1240    end
1241    diff_j=j2_series-j1_series;
1242    min_diff=min(diff_j(diff_j>0));
1243    max_diff=max(diff_j(diff_j>0));
1244    for ipair=min_diff:max_diff
1245        if numel(diff_j(diff_j==ipair))>0
1246            pair_string=['Dj= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2)) ];
1247            if ~isempty(time)
1248                if ref_j<=floor(ipair/2)
1249                    ref_j=floor(ipair/2)+1;% shift ref_i to get the first pair
1250                end
1251                Dt=time(ref_i,ref_j+ceil(ipair/2))-time(ref_i,ref_j-floor(ipair/2));
1252                pair_string=[pair_string ', Dt=' num2str(Dt) ' ' dtunit];
1253            end
1254            displ_pair=[displ_pair;{pair_string}];
1255        end
1256    end
1257    if ~isempty(displ_pair)
1258        displ_pair=[displ_pair;{'Dj=*|*'}];
1259    end
1260elseif strcmp(mode,'bursts')
1261    if isempty(j2_series)
1262        msgbox_uvmat('ERROR','no j1-j2 pair available')
1263        return
1264    end
1265    diff_j=j2_series-j1_series;
1266    min_j1=min(j1_series(j1_series>0));
1267    max_j1=max(j1_series(j1_series>0));
1268    min_j2=min(j2_series(j2_series>0));
1269    max_j2=max(j2_series(j2_series>0));
1270    for pair1=min_j1:min(max_j1,min_j1+20)
1271        for pair2=min_j2:min(max_j2,min_j2+20)
1272        if numel(j1_series(j1_series==pair1))>0 && numel(j2_series(j2_series==pair2))>0
1273            displ_pair=[displ_pair;{['j= ' num2str(pair1) '-' num2str(pair2)]}];
1274        end
1275        end
1276    end
1277    if ~isempty(displ_pair)
1278        displ_pair=[displ_pair;{'j=*-*'}];
1279    end
1280end
1281set(handles.num_ref_i,'String',num2str(ref_i)) % update ref_i and ref_j
1282set(handles.num_ref_j,'String',num2str(ref_j))
1283
1284%% display list of pairstring
1285displ_pair_list=get(handles.ListPairs,'String');
1286NewVal=[];
1287if ~isempty(displ_pair_list)
1288Val=get(handles.ListPairs,'Value');
1289NewVal=find(strcmp(displ_pair_list{Val},displ_pair),1);% look at the previous display in the new menu displ_pï¿œir
1290end
1291if ~isempty(NewVal)
1292    set(handles.ListPairs,'Value',NewVal)
1293else
1294    set(handles.ListPairs,'Value',1)
1295end
1296set(handles.ListPairs,'String',displ_pair)
1297
1298%-------------------------------------
1299function enable_i(handles,state)
1300set(handles.i_txt,'Visible',state)
1301set(handles.num_first_i,'Visible',state)
1302set(handles.num_last_i,'Visible',state)
1303set(handles.num_incr_i,'Visible',state)
1304set(handles.num_ref_i,'Visible',state)
1305set(handles.ref_i_text,'Visible',state)
1306
1307%-----------------------------------
1308function enable_j(handles,state)
1309set(handles.j_txt,'Visible',state)
1310set(handles.num_first_j,'Visible',state)
1311set(handles.num_last_j,'Visible',state)
1312set(handles.num_incr_j,'Visible',state)
1313set(handles.num_ref_j,'Visible',state)
1314set(handles.ref_j_text,'Visible',state)
1315set(handles.MinIndex_j,'Visible',state)
1316set(handles.MaxIndex_j,'Visible',state)
1317
1318
1319%%%%%%%%%%%%%%%%%%%%
1320%%  MAIN ActionName FUNCTIONS
1321%%%%%%%%%%%%%%%%%%%%
1322%------------------------------------------------------------------------
1323% --- Executes on button press in RUN.
1324function RUN_Callback(hObject, eventdata, handles)
1325%------------------------------------------------------------------------
1326
1327set(handles.RUN,'BusyAction','queue');
1328set(0,'CurrentFigure',handles.series)
1329set(handles.RUN, 'Enable','Off')
1330set(handles.RUN,'BackgroundColor',[0.831 0.816 0.784])
1331drawnow
1332
1333%% read the input parameters and set the output dir and nomenclature
1334[Series,OutputDir,errormsg]=prepare_jobs(handles);% get parameters form the GUI series
1335if ~isempty(errormsg)
1336    if ~strcmp(errormsg,'Cancel')
1337    msgbox_uvmat('ERROR',errormsg)
1338    end
1339    STOP_Callback([],[], handles)
1340    return
1341end
1342OutputNomType=nomtype2pair(Series.InputTable{1,4});% nomenclature for output files
1343DirXml=fullfile(OutputDir,'0_XML');
1344if ~exist(DirXml,'dir')
1345    [tild,msg1]=mkdir(DirXml);
1346    if ~strcmp(msg1,'')
1347        msgbox_uvmat('ERROR',['cannot create ' DirXml ': ' msg1]);%error message for directory creation
1348        return
1349    end
1350end
1351
1352%% select the Action modes
1353RunMode='local';%default
1354if isfield(Series.Action,'RunMode')
1355RunMode=Series.Action.RunMode;
1356end
1357ActionExt='.m';%default
1358if isfield(Series.Action,'ActionExt')
1359    ActionExt=Series.Action.ActionExt;% '.m' or '.sh' (compiled)
1360end
1361ActionName=Series.Action.ActionName;
1362ActionPath=Series.Action.ActionPath;
1363path_series=fileparts(which('series'));
1364
1365%% create the Action fct handle if RunMode option = 'local'
1366if strcmp(RunMode,'local')
1367    if ~isequal(ActionPath,path_series)
1368        eval(['spath=which(''' ActionName ''');']) %spath = current path of the selected function ACTION
1369        if ~exist(ActionPath,'dir')
1370            msgbox_uvmat('ERROR',['The prescribed function path ' ActionPath ' does not exist']);
1371            return
1372        end
1373        if ~isequal(spath,ActionPath)
1374            addpath(ActionPath)% add the prescribed path if not the current one
1375        end
1376    end
1377    eval(['h_fun=@' ActionName ';'])%create a function handle for ACTION
1378    if ~isequal(ActionPath,path_series)
1379        rmpath(ActionPath)% add the prescribed path if not the current one
1380    end
1381end
1382
1383%% Get RunTime code from the file PARAM.xml (needed to run compiled functions)
1384errormsg='';%default error message
1385xmlfile=fullfile(path_series,'PARAM.xml');
1386test_batch=0;%default: ,no batch mode available
1387if ~exist(xmlfile,'file')
1388    [success,message]=copyfile(fullfile(path_series,'PARAM.xml.default'),xmlfile);
1389end
1390RunTime='';
1391if strcmp(ActionExt,'.sh')
1392    if exist(xmlfile,'file')
1393        s=xml2struct(xmlfile);
1394        if strcmp(RunMode,'cluster_oar') && isfield(s,'BatchParam')
1395            if isfield(s.BatchParam,'RunTime')
1396                RunTime=s.BatchParam.RunTime;
1397            end
1398            if isfield(s.BatchParam,'NbCore')
1399                NbCore=s.BatchParam.NbCore;
1400            end
1401        elseif (strcmp(RunMode,'background')||strcmp(RunMode,'local')) && isfield(s,'RunParam')
1402            if isfield(s.RunParam,'RunTime')
1403                RunTime=s.RunParam.RunTime;
1404            end
1405            if isfield(s.RunParam,'NbCore')
1406                NbCore=s.RunParam.NbCore;
1407            end
1408        end
1409    end
1410    if isempty(RunTime) && strcmp(RunMode,'cluster_oar')
1411        msgbox_uvmat('ERROR','RunTime name not found in PARAM.xml, compiled version .sh cannot run on cluster')
1412        return
1413    end
1414%     Series.RunTime=RunTime;
1415end
1416
1417%% set nbre of cluster cores and processes
1418switch RunMode
1419    case {'local','background'}
1420        NbCore=1;% no need to split the calculation
1421    case 'cluster_oar'
1422        if strcmp(Series.Action.ActionExt,'.m')% case of Matlab function (uncompiled)
1423            NbCore=1;% one core used only (limitation of Matlab licences)
1424            msgbox_uvmat('WARNING','Number of cores =1: select the compiled version civ_matlab.sh for multi-core processing');
1425            extra_oar='';
1426        else
1427            answer=inputdlg({'Number of cores (max 36)','extra oar options'},'oarsub parameter',1,{'12',''});
1428            NbCore=str2double(answer{1});
1429            extra_oar=answer{2};
1430        end
1431end
1432if ~isfield(Series.IndexRange,'NbSlice')
1433    Series.IndexRange.NbSlice=[];
1434end
1435if isempty(Series.IndexRange.NbSlice)
1436    NbProcess=NbCore;% choose one process per core
1437else
1438    NbProcess=Series.IndexRange.NbSlice;% the nbre of run processes is equal to the number of slices
1439    NbCore=min(NbCore,NbProcess);% at least one process per core
1440end
1441       
1442
1443%% read index ranges
1444[first_i,incr_i,last_i,first_j,incr_j,last_j,errormsg]=get_index_range(Series.IndexRange);
1445if ~isempty(errormsg)
1446    msgbox_uvmat('ERROR',['series/Run_Callback/get_index_range' errormsg])
1447    set(handles.RUN, 'Enable','On'),
1448    set(handles.RUN,'BackgroundColor',[1 0 0])
1449    return
1450else
1451    BlockLength=ceil(numel(first_i:incr_i:last_i)/NbProcess);
1452end
1453nbfield_j=numel(first_j:incr_j:last_j);
1454
1455%% record nbre of output files and starting time for computation for status
1456StatusData=get(handles.status,'UserData');
1457if isfield(StatusData,'OutputFileMode')
1458    switch StatusData.OutputFileMode
1459        case 'NbInput'
1460            StatusData.NbOutputFile=numel(first_i:incr_i:last_i)*numel(first_j:incr_j:last_j);
1461        case 'NbInput_i'
1462            StatusData.NbOutputFile=numel(first_i:incr_i:last_i);
1463        case 'NbSlice'   
1464            StatusData.NbOutputFile=str2num(get(handles.num_NbSlice,'String'));
1465    end
1466end
1467StatusData.TimeStart=now;
1468set(handles.status,'UserData',StatusData)
1469
1470%% direct processing on the current Matlab session
1471if strcmp (RunMode,'local')
1472    Series.RUNHandle=handles.RUN;
1473    Series.WaitbarHandle=handles.Waitbar;
1474    for iprocess=1:NbProcess
1475        if isempty(Series.IndexRange.NbSlice)
1476            Series.IndexRange.first_i=first_i+(iprocess-1)*BlockLength*incr_i;
1477            if Series.IndexRange.first_i>last_i
1478                break
1479            end
1480            Series.IndexRange.last_i=min(first_i+(iprocess)*BlockLength*incr_i-1,last_i);
1481        else
1482            Series.IndexRange.first_i= first_i+incr_i*(iprocess-1);
1483            Series.IndexRange.incr_i=incr_i*Series.IndexRange.NbSlice;
1484        end
1485        t=struct2xml(Series);
1486        t=set(t,1,'name','Series');
1487        filexml=fullfile_uvmat(DirXml,'',Series.InputTable{1,3},'.xml',OutputNomType,...
1488            Series.IndexRange.first_i,Series.IndexRange.last_i,first_j,last_j);
1489        save(t,filexml);
1490        switch ActionExt
1491            case '.m'
1492                h_fun(Series);
1493            case '.sh'
1494                switch computer
1495                    case {'PCWIN','PCWIN64'} %Windows system
1496                        filexml=regexprep(filexml,'\\','\\\\');% add '\' so that '\' are left as characters
1497                        system([fullfile(ActionPath,[ActionName '.sh']) ' ' RunTime ' ' filexml]);% TODO: adapt to DOS system
1498                    case {'GLNX86','GLNXA64','MACI64'}%Linux  system
1499                        system([fullfile(ActionPath,[ActionName '.sh']) ' ' RunTime ' ' filexml]);
1500                end
1501        end
1502    end
1503elseif strcmp(get(handles.OutputDirExt,'Visible'),'off')
1504    msgbox_uvmat('ERROR',['no output file for Action ' ActionName ', use run mode = local']);% a output dir is needed for background option
1505    return
1506else
1507    %% processing on a different session of the same computer (background) or cluster, create executable files
1508    batch_file_list=cell(NbProcess,1);% initiate the list of executable files
1509    DirBat=fullfile(OutputDir,'0_BAT');
1510    %create subdirectory for executable files
1511    if ~exist(DirBat,'dir')
1512        [tild,msg1]=mkdir(DirBat);
1513        if ~strcmp(msg1,'')
1514            msgbox_uvmat('ERROR',['cannot create ' DirBat ': ' msg1]);%error message for directory creation
1515            return
1516        end
1517    end
1518    %create subdirectory for log files
1519    DirLog=fullfile(OutputDir,'0_LOG');
1520    if ~exist(DirLog,'dir')
1521        [tild,msg1]=mkdir(DirLog);
1522        if ~strcmp(msg1,'')
1523            msgbox_uvmat('ERROR',['cannot create ' DirLog ': ' msg1]);%error message for directory creation
1524            return
1525        end
1526    end
1527    for iprocess=1:NbProcess
1528        if isempty(Series.IndexRange.NbSlice)% process by blocks of i index
1529            Series.IndexRange.first_i=first_i+(iprocess-1)*BlockLength*incr_i;
1530            if Series.IndexRange.first_i>last_i
1531                NbProcess=iprocess-1;
1532                break% leave the loop, we are at the end of the calculation
1533            end
1534            Series.IndexRange.last_i=min(last_i,first_i+(iprocess)*BlockLength*incr_i-1);
1535        else% process by slices of i index if NbSlice is defined, computation in a single process if NbSlice =1
1536            Series.IndexRange.first_i= first_i+iprocess-1;
1537            Series.IndexRange.incr_i=incr_i*Series.IndexRange.NbSlice;
1538        end
1539       
1540        % create, fill and save the xml parameter file
1541        t=struct2xml(Series);
1542        t=set(t,1,'name','Series');
1543        filexml=fullfile_uvmat(DirXml,'',Series.InputTable{1,3},'.xml',OutputNomType,...
1544            Series.IndexRange.first_i,Series.IndexRange.last_i,first_j,last_j);
1545        save(t,filexml);% save the parameter file
1546       
1547        %create the executable file
1548%         filebat=fullfile_uvmat(DirBat,'',Series.InputTable{1,3},'.bat',OutputNomType,...
1549%             Series.IndexRange.first_i,Series.IndexRange.last_i,first_j,last_j);
1550         filebat=fullfile_uvmat(DirBat,'',Series.InputTable{1,3},'.sh',OutputNomType,...
1551           Series.IndexRange.first_i,Series.IndexRange.last_i,first_j,last_j);
1552        batch_file_list{iprocess}=filebat;
1553        [fid,message]=fopen(filebat,'w');% create the executable file
1554        if isequal(fid,-1)
1555            msgbox_uvmat('ERROR', ['creation of .bat file: ' message]);
1556            return
1557        end
1558       
1559        % set the log file name
1560        filelog=fullfile_uvmat(DirLog,'',Series.InputTable{1,3},'.log',OutputNomType,...
1561            Series.IndexRange.first_i,Series.IndexRange.last_i,first_j,last_j);
1562       
1563        % fill and save the executable file
1564        switch ActionExt
1565            case '.m'% Matlab function
1566                switch computer
1567                    case {'GLNX86','GLNXA64','MACI64'}
1568                        cmd=[...
1569                            '#!/bin/bash \n'...
1570                            '. /etc/sysprofile \n'...
1571                            'matlab -nodisplay -nosplash -nojvm -logfile ''' filelog ''' <<END_MATLAB \n'...
1572                            'addpath(''' path_series '''); \n'...
1573                            'addpath(''' Series.Action.ActionPath '''); \n'...
1574                            '' Series.Action.ActionName  '( ''' filexml '''); \n'...
1575                            'exit \n'...
1576                            'END_MATLAB \n'];
1577                        fprintf(fid,cmd);%fill the executable file with the  char string cmd
1578                        fclose(fid);% close the executable file
1579                        system(['chmod +x ' filebat]);% set the file to executable
1580                    case {'PCWIN','PCWIN64'}
1581                        text_matlabscript=['matlab -automation -logfile ' regexprep(filelog,'\\','\\\\')...
1582                            ' -r "addpath(''' regexprep(path_series,'\\','\\\\') ''');'...
1583                            'addpath(''' regexprep(Series.Action.ActionPath,'\\','\\\\') ''');'...
1584                            '' Series.Action.ActionName  '( ''' regexprep(filexml,'\\','\\\\') ''');exit"'];
1585                        fprintf(fid,text_matlabscript);%fill the executable file with the  char string cmd
1586                        fclose(fid);% close the executable file
1587                end
1588            case '.sh' % compiled Matlab function
1589                switch computer
1590                    case {'GLNX86','GLNXA64','MACI64'}
1591                        cmd=['#!/bin/bash \n '...
1592                            '#$ -cwd \n '...
1593                            'hostname && date \n '...
1594                            'umask 002 \n'...
1595                            fullfile(ActionPath,[ActionName '.sh']) ' ' RunTime ' ' filexml];%allow writting access to created files for user group
1596                        fprintf(fid,cmd);%fill the executable file with the  char string cmd
1597                        fclose(fid);% close the executable file
1598                        system(['chmod +x ' filebat]);% set the file to executable
1599                       
1600                    case {'PCWIN','PCWIN64'}    %       TODO: adapt to Windows system
1601                        %                                 cmd=['matlab -automation -logfile ' regexprep(filelog,'\\','\\\\')...
1602                        %                                     ' -r "addpath(''' regexprep(path_series,'\\','\\\\') ''');'...
1603                        %                                     'addpath(''' regexprep(Series.Action.ActionPath,'\\','\\\\') ''');'...
1604                        %                                     '' Series.Action.ActionName  '( ''' regexprep(filexml,'\\','\\\\') ''');exit"'];
1605                        fprintf(fid,cmd);
1606                        fclose(fid);
1607                        %                               dos([filebat ' &']);
1608                end
1609        end
1610    end
1611end
1612
1613%% launch the executable files for background or cluster processing
1614switch RunMode
1615    case 'background'
1616        for iprocess=1:NbProcess
1617            system([batch_file_list{iprocess} ' &'])% directly execute the command file for each process
1618        end
1619    case 'cluster_oar' % option 'oar-parexec' used
1620        %create subdirectory for oar command and log files
1621        DirOAR=fullfile(OutputDir,'0_OAR');
1622        if ~exist(DirOAR,'dir')
1623            [tild,msg1]=mkdir(DirOAR);
1624            if ~strcmp(msg1,'')
1625                msgbox_uvmat('ERROR',['cannot create ' DirOAR ': ' msg1]);%error message for directory creation
1626                return
1627            end
1628        end
1629        max_walltime=3600*12; % 12h max total calculation
1630        walltime_onejob=600;%seconds, max estimated time for asingle file index value
1631        filename_joblist=fullfile(DirOAR,'job_list.txt');%create name of the global executable file
1632        fid=fopen(filename_joblist,'w');
1633        for p=1:length(batch_file_list)
1634            fprintf(fid,[batch_file_list{p} '\n']);% list of exe files
1635        end
1636        fclose(fid);
1637        system(['chmod +x ' filename_joblist]);% set the file to executable
1638        oar_command=['oarsub -n CIVX '...
1639            '-t idempotent --checkpoint ' num2str(walltime_onejob+60) ' '...
1640            '-l /core=' num2str(NbCore) ','...
1641            'walltime=' datestr(min(1.05*walltime_onejob/86400*max(NbProcess*BlockLength*nbfield_j,NbCore)/NbCore,max_walltime/86400),13) ' '...
1642            '-E ' regexprep(filename_joblist,'\.txt\>','.stderr') ' '...
1643            '-O ' regexprep(filename_joblist,'\.txt\>','.stdout') ' '...
1644            extra_oar ' '...
1645            '"oar-parexec -s -f ' filename_joblist ' '...
1646            '-l ' filename_joblist '.log"\n'];
1647        filename_oarcommand=fullfile(DirOAR,'oar_command');
1648        fid=fopen(filename_oarcommand,'w');
1649        fprintf(fid,oar_command);
1650        fclose(fid);
1651        fprintf(oar_command);% display in command line
1652        %system(['chmod +x ' oar_command]);% set the file to executable
1653        system(oar_command);     
1654end
1655
1656%% reset the GUI series
1657update_waitbar(handles.Waitbar,1); % put the waitbar to end position to indicate launching is finished
1658set(handles.RUN, 'Enable','On')
1659set(handles.RUN,'BackgroundColor',[1 0 0])
1660set(handles.RUN, 'Value',0)
1661
1662%------------------------------------------------------------------------
1663function STOP_Callback(hObject, eventdata, handles)
1664%------------------------------------------------------------------------
1665set(handles.RUN, 'BusyAction','cancel')
1666set(handles.RUN,'BackgroundColor',[1 0 0])
1667set(handles.RUN,'enable','on')
1668set(handles.RUN, 'Value',0)
1669
1670% %------------------------------------------------------------------------
1671% % --- Executes on button press in BIN.
1672% function BIN_Callback(hObject, eventdata, handles)
1673% %------------------------------------------------------------------------
1674%     cmd=['#!/bin/bash \n '...
1675%         '#$ -cwd \n '...
1676%         'hostname && date \n '...
1677%         'umask 002 \n'...
1678%         Param.xml.CivmBin ' ' Param.xml.RunTime ' ' filename_xml ' ' OutputFile '.nc'];
1679%     
1680%------------------------------------------------------------------------
1681% --- Main launch command, called by RUN and BATCH
1682
1683function [Series,OutputDir,errormsg]=prepare_jobs(handles)
1684%INPUT:
1685% handles: handles of graphic objects on the GUI series
1686
1687%------------------------------------------------------------------------
1688OutputDir='';
1689errormsg='';
1690
1691%% Read parameters from series
1692Series=read_GUI(handles.series);
1693
1694%% get_field GUI
1695% if isfield(Series,'InputFields')&&isfield(Series.InputFields,'Field')
1696%     if strcmp(Series.InputFields.Field,'get_field...')
1697%         hget_field=findobj(allchild(0),'name','get_field');
1698%         Series.GetField=read_GUI(hget_field);
1699%     end
1700% end
1701
1702%% create the output data directory
1703%determine the root file corresponding to the first sub dir
1704if get(handles.RUN,'value') && isfield(Series,'OutputSubDir')
1705    SubDirOut=[get(handles.OutputSubDir,'String') Series.OutputDirExt];
1706    SubDirOutNew=SubDirOut;
1707    SeriesData=get(handles.series,'UserData');
1708%     if size(Series.InputTable,1)>1 && isfield(SeriesData,'AllowInputSort') && SeriesData.AllowInputSort
1709%         [tild,iview]=sort(Series.InputTable(:,2)); %subdirectories sorted in alphabetical order
1710%         Series.InputTable=Series.InputTable(iview,:);
1711%     end
1712    detect=exist(fullfile(Series.InputTable{1,1},SubDirOutNew),'dir');% test if  the dir  already exist
1713    check_create=1; %need to create the result directory by default
1714    while detect
1715        answer=msgbox_uvmat('INPUT_Y-N',['use existing ouput directory: ' fullfile(Series.InputTable{1,1},SubDirOutNew) ', possibly delete previous data']);
1716        if strcmp(answer,'Cancel')
1717            errormsg='Cancel';
1718            return
1719        elseif strcmp(answer,'Yes')
1720            detect=0;
1721            check_create=0;
1722        else
1723            r=regexp(SubDirOutNew,'(?<root>.*\D)(?<num1>\d+)$','names');%detect whether name ends by a number
1724            if isempty(r)
1725                r(1).root=[SubDirOutNew '_'];
1726                r(1).num1='0';
1727            end
1728            SubDirOutNew=[r(1).root num2str(str2num(r(1).num1)+1)];%increment the index by 1 or put 1
1729            detect=exist(fullfile(Series.InputTable{1,1},SubDirOutNew),'dir');% test if  the dir  already exists   
1730            check_create=1;
1731        end
1732    end
1733    Series.OutputDirExt=regexprep(SubDirOutNew,Series.OutputSubDir,'');
1734    Series.OutputRootFile=Series.InputTable{1,3};% the first sorted RootFile taken for output
1735    set(handles.OutputDirExt,'String',Series.OutputDirExt)
1736    OutputDir=fullfile(Series.InputTable{1,1},[Series.OutputSubDir Series.OutputDirExt]);% full name (with path) of output directory
1737    if check_create    % create output directory if it does not exist
1738        [tild,msg1]=mkdir(OutputDir);
1739        if ~strcmp(msg1,'')
1740            errormsg=['cannot create ' OutputDir ': ' msg1];%error message for directory creation
1741            return
1742        end
1743    end
1744   % RootOut=fullfile(OutputDir,Series.InputTable{1,3});% name of the parameter xml file set in this directory
1745end
1746
1747%% removes unused information on Series
1748if isfield(Series,'Pairs')
1749    Series=rmfield(Series,'Pairs'); %info Pairs not needed for output
1750end
1751Series.IndexRange=rmfield(Series.IndexRange,'TimeTable');
1752% Series.IndexRange=rmfield(Series.IndexRange,'MinIndex_j');
1753% Series.IndexRange=rmfield(Series.IndexRange,'MaxIndex_i');
1754empty_line=false(size(Series.InputTable,1),1);
1755for iline=1:size(Series.InputTable,1)
1756    empty_line(iline)=isequal(Series.InputTable(iline,1:3),{'','',''});
1757end
1758Series.InputTable(empty_line,:)=[];
1759
1760%------------------------------------------------------------------------
1761% --- Executes on selection change in ActionName.
1762function ActionName_Callback(hObject, eventdata, handles)
1763%------------------------------------------------------------------------
1764%% stop any ongoing series processing
1765if isequal(get(handles.RUN,'Value'),1)
1766    answer= msgbox_uvmat('INPUT_Y-N','stop current Action process?');
1767    if strcmp(answer,'Yes')
1768        STOP_Callback(hObject, eventdata, handles)
1769    else
1770        return
1771    end
1772end
1773set(handles.ActionName,'BackgroundColor',[1 1 0])
1774drawnow
1775
1776%% get Action name and path
1777nb_builtin_ACTION=4; %nbre of functions initially proposed in the menu ActionName (as defined in the Opening fct of series)
1778ActionList=get(handles.ActionName,'String');% list menu fields
1779ActionIndex=get(handles.ActionName,'Value');
1780if ~isequal(ActionIndex,1)% if we are not just opening series
1781    InputTable=get(handles.InputTable,'Data');
1782    if isempty(InputTable{1,4})
1783        msgbox_uvmat('ERROR','no input file available: use Open in the menu bar')
1784        return
1785    end
1786end
1787ActionName= ActionList{get(handles.ActionName,'Value')}; % selected function name
1788ActionPathList=get(handles.ActionName,'UserData');%list of recorded paths to functions of the list ActionName
1789
1790%% add a new function to the menu if 'more...' has been selected in the menu ActionName
1791if isequal(ActionName,'more...')
1792    [FileName, PathName] = uigetfile( ...
1793        {'*.m', ' (*.m)';
1794        '*.m',  '.m files '; ...
1795        '*.*', 'All Files (*.*)'}, ...
1796        'Pick a series processing function ',get(handles.ActionPath,'String'));
1797    if length(FileName)<2
1798        return
1799    end
1800    [ActionPath,ActionName,ActionExt]=fileparts(FileName);
1801   
1802    % insert the choice in the menu ActionName
1803    ActionIndex=find(strcmp(ActionName,ActionList),1);% look for the selected function in the menu Action
1804    if isempty(ActionIndex)%the input string does not exist in the menu
1805        ActionIndex= length(ActionList);
1806        ActionList=[ActionList(1:end-1);{ActionName};ActionList(end)];% the selected function is appended in the menu, before the last item 'more...'
1807        set(handles.ActionName,'String',ActionList)
1808    end
1809   
1810    % record the file extension and extend the path list if it is a new extension
1811    ActionExtList=get(handles.ActionExt,'String');
1812    ActionExtIndex=find(strcmp(ActionExt,ActionExtList), 1);
1813    if isempty(ActionExtIndex)
1814        set(handles.ActionExt,'String',[ActionExtList;{ActionExt}])
1815        ActionExtIndex=numel(ActionExtList)+1;
1816        ActionPathNew=cell(size(ActionPathList,1),1);%new column of ActionPath
1817        ActionPathList=[ActionPathList ActionPathNew];
1818    end
1819    set(handles.ActionName,'UserData',ActionPathList);
1820
1821    % remove old Action options in the menu (keeping a menu length <nb_builtin_ACTION+5)
1822    if length(ActionList)>nb_builtin_ACTION+5; %nb_builtin=nbre of functions always remaining in the initial menu
1823        nbremove=length(ActionList)-nb_builtin_ACTION-5;
1824        ActionList(nb_builtin_ACTION+1:end-5)=[];
1825        ActionPathList(nb_builtin_ACTION+1:end-4,:)=[];
1826        ActionIndex=ActionIndex-nbremove;
1827    end
1828   
1829    % record action menu, choice and path
1830    set(handles.ActionName,'Value',ActionIndex)
1831    set(handles.ActionName,'String',ActionList)
1832    set(handles.ActionExt,'Value',ActionExtIndex)
1833    ActionPathList{ActionIndex,ActionExtIndex}=PathName;
1834       
1835    %record the user defined menu additions in personal file profil_perso
1836    dir_perso=prefdir;
1837    profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
1838    if nb_builtin_ACTION+1<=numel(ActionList)-1
1839        ActionListUser=ActionList(nb_builtin_ACTION+1:numel(ActionList)-1);
1840        ActionPathListUser=ActionPathList(nb_builtin_ACTION+1:numel(ActionList)-1,:);
1841        ActionExtListUser={};
1842        if numel(ActionExtList)>2
1843            ActionExtListUser=ActionExtList(3:end);
1844        end
1845        if exist(profil_perso,'file')
1846            save(profil_perso,'ActionListUser','ActionPathListUser','ActionExtListUser','-append')
1847        else
1848            save(profil_perso,'ActionListUser','ActionPathListUser','ActionExtListUser','-V6')
1849        end
1850    end
1851end
1852
1853%% check the current ActionPath to the selected function
1854ActionPath=ActionPathList{ActionIndex};%current recorded path
1855set(handles.ActionPath,'String',ActionPath); %show the path to the senlected function
1856
1857%% reinitialise the waitbar
1858update_waitbar(handles.Waitbar,0)
1859
1860%% default setting for the visibility of the GUI elements
1861% set(handles.FieldTransform,'Visible','off')
1862% set(handles.CheckObject,'Visible','off');
1863% set(handles.ProjObject,'Visible','off');
1864% set(handles.CheckMask,'Visible','off')
1865% set(handles.Mask,'Visible','off')
1866
1867%% create the function handle for Action
1868path_series=which('series');
1869if ~isequal(ActionPath,path_series)
1870    eval(['spath=which(''' ActionName ''');']) %spath = current path of the selected function ACTION
1871    if ~exist(ActionPath,'dir')
1872        errormsg=['The prescribed function path ' ActionPath ' does not exist'];
1873        return
1874    end
1875    if ~isequal(spath,ActionPath)
1876        addpath(ActionPath)% add the prescribed path if not the current one
1877    end
1878end
1879eval(['h_fun=@' ActionName ';'])%create a function handle for ACTION
1880if ~isequal(ActionPath,path_series)
1881        rmpath(ActionPath)% add the prescribed path if not the current one   
1882end
1883
1884%% Activate the Action fct
1885[Series,tild,errormsg]=prepare_jobs(handles);% read the parameters from the GUI series
1886if ~isempty(errormsg)
1887    if ~strcmp(errormsg,'Cancel')
1888    msgbox_uvmat('ERROR',errormsg)
1889    end
1890    return
1891end
1892ParamOut=h_fun(Series);
1893
1894%% Put the first line of the selected Action fct as tooltip help
1895try
1896    [fid,errormsg] =fopen([ActionName '.m']);
1897    InputText=textscan(fid,'%s',1,'delimiter','\n');
1898    fclose(fid);
1899    set(handles.ActionName,'ToolTipString',InputText{1}{1})% put the first line of the selected function as tooltip help
1900end
1901
1902%% Detect the types of input files
1903SeriesData=get(handles.series,'UserData');
1904nb_civ=0;nb_netcdf=0;
1905if ~isempty(SeriesData)
1906    nb_civ=numel(find(strcmp('civx',SeriesData.FileType)|strcmp('civdata',SeriesData.FileType)));
1907    nb_netcdf=numel(find(strcmp('netcdf',SeriesData.FileType)));
1908end
1909
1910%% Check whether alphabetical sorting of input Subdir is alowed by the Action fct  (for multiples series entries)
1911if isfield(ParamOut,'AllowInputSort')&&isequal(ParamOut.AllowInputSort,'on')&& size(Series.InputTable,1)>1
1912    [tild,iview]=sort(InputTable(:,2)); %subdirectories sorted in alphabetical order
1913    set(handles.InputTable,'Data',InputTable(iview,:));
1914    MinIndex_i=get(handles.MinIndex_i,'Data');
1915    MinIndex_j=get(handles.MinIndex_j,'Data');
1916    MaxIndex_i=get(handles.MaxIndex_i,'Data');
1917    MaxIndex_j=get(handles.MaxIndex_j,'Data');
1918    set(handles.MinIndex_i,'Data',MinIndex_i(iview,:));
1919    set(handles.MinIndex_j,'Data',MinIndex_j(iview,:));
1920    set(handles.MaxIndex_i,'Data',MaxIndex_i(iview,:));
1921    set(handles.MaxIndex_j,'Data',MaxIndex_j(iview,:));
1922    TimeTable=get(handles.TimeTable,'Data');
1923    set(handles.TimeTable,'Data',TimeTable(iview,:));
1924    PairString=get(handles.PairString,'Data');
1925    set(handles.PairString,'Data',PairString(iview,:));
1926end
1927
1928%% Impose the whole input file index range if requested
1929if isfield(ParamOut,'WholeIndexRange')&&isequal(ParamOut.WholeIndexRange,'on')
1930    MinIndex_i=get(handles.MinIndex_i,'Data');
1931    MinIndex_j=get(handles.MinIndex_j,'Data');
1932    MaxIndex_i=get(handles.MaxIndex_i,'Data');
1933    MaxIndex_j=get(handles.MaxIndex_j,'Data');
1934    set(handles.num_first_i,'String',num2str(MinIndex_i{1}))% set first as the min index (for the first line)
1935    set(handles.num_last_i,'String',num2str(MaxIndex_i{1}))% set last as the max index (for the first line)
1936    set(handles.num_incr_i,'String','1')
1937    set(handles.num_first_j,'String',num2str(MinIndex_j{1}))% set first as the min index (for the first line)
1938    set(handles.num_last_j,'String',num2str(MaxIndex_j{1}))% set last as the max index (for the first line)
1939    set(handles.num_incr_j,'String','1')
1940else  % check index ranges
1941    first_i=1;last_i=1;first_j=1;last_j=1;
1942    if isfield(Series.IndexRange,'first_i')
1943        first_i=Series.IndexRange.first_i;
1944       % incr_i=Series.IndexRange.incr_i;
1945        last_i=Series.IndexRange.last_i;
1946    end
1947    if isfield(Series.IndexRange,'first_j')
1948        first_j=Series.IndexRange.first_j;
1949       % incr_j=Series.IndexRange.incr_j;
1950        last_j=Series.IndexRange.last_j;
1951    end
1952    if last_i < first_i || last_j < first_j , msgbox_uvmat('ERROR','last field number must be larger than the first one'),...
1953            set(handles.RUN, 'Enable','On'), set(handles.RUN,'BackgroundColor',[1 0 0]),return,end;
1954end
1955
1956%% NbSlice visibility
1957NbSliceVisible='off';%default
1958if isfield(ParamOut,'NbSlice') && isequal(ParamOut.NbSlice,'on')
1959    NbSliceVisible='on';
1960    set(handles.num_NbProcess,'String',get(handles.num_NbSlice,'String'))% the nbre of processes is imposed as the nbre of slices
1961else
1962    set(handles.num_NbProcess,'String','')% free nbre of processes
1963end
1964set(handles.num_NbSlice,'Visible',NbSliceVisible)
1965set(handles.NbSlice_title,'Visible',NbSliceVisible)
1966
1967%% Visibility of VelType and VelType_1 menus
1968VelTypeVisible='off';  %hidden by default
1969VelType_1Visible='off';
1970InputFieldsVisible='off';%visibility of the frame Fields
1971if isfield(ParamOut,'VelType')
1972    if strcmp( ParamOut.VelType,'one')||strcmp( ParamOut.VelType,'two')
1973        if nb_civ>=1
1974            VelTypeVisible='on';
1975            InputFieldsVisible='on';
1976        end
1977    end
1978    if strcmp( ParamOut.VelType,'two')
1979        if nb_civ>=2
1980            VelType_1Visible='on';
1981        end
1982    end
1983end
1984set(handles.VelType,'Visible',VelTypeVisible)
1985set(handles.VelType_text,'Visible',VelTypeVisible);
1986set(handles.VelType_1,'Visible',VelType_1Visible)
1987set(handles.VelType_text_1,'Visible',VelType_1Visible);
1988
1989%% Visibility of FieldName and FieldName_1 menus
1990FieldNameVisible='off';  %hidden by default
1991FieldName_1Visible='off';  %hidden by default
1992if isfield(ParamOut,'FieldName')
1993    if strcmp( ParamOut.FieldName,'one')||strcmp( ParamOut.FieldName,'two')
1994        if (nb_civ+nb_netcdf)>=1
1995            InputFieldsVisible='on';
1996            FieldNameVisible='on';
1997        end
1998    end
1999    if strcmp( ParamOut.FieldName,'two')
2000        if (nb_civ+nb_netcdf)>=1
2001            FieldName_1Visible='on';
2002        end
2003    end
2004end
2005set(handles.InputFields,'Visible',InputFieldsVisible)
2006set(handles.FieldName,'Visible',FieldNameVisible) % test for MenuBorser
2007set(handles.FieldName_1,'Visible',FieldName_1Visible)
2008
2009%% Visibility of FieldTransform menu
2010FieldTransformVisible='off';  %hidden by default
2011if isfield(ParamOut,'FieldTransform')
2012    FieldTransformVisible=ParamOut.FieldTransform; 
2013    TransformName_Callback([],[], handles)
2014end
2015set(handles.FieldTransform,'Visible',FieldTransformVisible)
2016if isfield(ParamOut,'TransformPath')
2017    set(handles.ActionExt,'UserData',ParamOut.TransformPath)
2018else
2019    set(handles.ActionExt,'UserData',[])
2020end
2021
2022%% Visibility of projection object
2023ProjObjectVisible='off';  %hidden by default
2024if isfield(ParamOut,'ProjObject')
2025    ProjObjectVisible=ParamOut.ProjObject;
2026end
2027set(handles.CheckObject,'Visible',ProjObjectVisible)
2028if ~get(handles.CheckObject,'Value')
2029    ProjObjectVisible='off';
2030end
2031set(handles.ProjObject,'Visible',ProjObjectVisible)
2032set(handles.DeleteObject,'Visible',ProjObjectVisible)
2033set(handles.ViewObject,'Visible',ProjObjectVisible)
2034
2035
2036%% Visibility of mask input
2037MaskVisible='off';  %hidden by default
2038if isfield(ParamOut,'Mask')
2039    MaskVisible=ParamOut.Mask;
2040end
2041set(handles.Mask,'Visible',MaskVisible)
2042set(handles.CheckMask,'Visible',MaskVisible);
2043
2044%% definition of the directory containing the output files
2045OutputDirVisible='off';
2046if isfield(ParamOut,'OutputDirExt')&&~isempty(ParamOut.OutputDirExt)
2047    set(handles.OutputDirExt,'String',ParamOut.OutputDirExt)
2048    OutputDirVisible='on';
2049    SubDir=InputTable(1:end-1,2); %set of subdirectories sorted in alphabetical order
2050    SubDirOut=SubDir{1};
2051    if numel(SubDir)>1
2052        for ilist=2:numel(SubDir)
2053            SubDirOut=[SubDirOut '-' SubDir{ilist}];
2054        end
2055    end
2056    set(handles.OutputSubDir,'String',SubDirOut)
2057end
2058set(handles.OutputDirExt,'Visible',OutputDirVisible)
2059set(handles.OutputSubDir,'Visible',OutputDirVisible)
2060set(handles.OutputDir_title,'Visible',OutputDirVisible)
2061set(handles.RunMode,'Visible',OutputDirVisible)
2062set(handles.ActionExt,'Visible',OutputDirVisible)
2063set(handles.RunMode_title,'Visible',OutputDirVisible)
2064set(handles.ActionExt_title,'Visible',OutputDirVisible)
2065
2066
2067%% Expected nbre of output files
2068if isfield(ParamOut,'OutputFileMode')
2069StatusData.OutputFileMode=ParamOut.OutputFileMode;
2070set(handles.status,'UserData',StatusData)
2071end
2072
2073%% definition of an additional parameter set, determined by an ancillary GUI
2074if isfield(ParamOut,'ActionInput')
2075    set(handles.ActionInput,'Visible','on')
2076    set(handles.ActionInput_title,'Visible','on')
2077    set(handles.ActionInputView,'Visible','on')
2078    set(handles.ActionInputView,'Value',0)
2079    set(handles.ActionInput,'String',ActionName)
2080    ParamOut.ActionInput.Program=ActionName; % record the program in ActionInput
2081    SeriesData.ActionInput=ParamOut.ActionInput;
2082else
2083    set(handles.ActionInput,'Visible','off')
2084    set(handles.ActionInput_title,'Visible','off')
2085    set(handles.ActionInputView,'Visible','off')
2086    if isfield(SeriesData,'ActionInput')
2087    SeriesData=rmfield(SeriesData,'ActionInput');
2088    end
2089end   
2090set(handles.series,'UserData',SeriesData)
2091set(handles.ActionName,'BackgroundColor',[1 1 1])
2092
2093%------------------------------------------------------------------------
2094% --- Executes on button press in ActionInputView.
2095function ActionInputView_Callback(hObject, eventdata, handles)
2096%------------------------------------------------------------------------
2097if get(handles.ActionInputView,'Value')
2098ActionName_Callback(hObject, eventdata, handles)
2099end
2100
2101%------------------------------------------------------------------------
2102% --- Executes on selection change in FieldName.
2103function FieldName_Callback(hObject, eventdata, handles)
2104%------------------------------------------------------------------------
2105field_str=get(handles.FieldName,'String');
2106field_index=get(handles.FieldName,'Value');
2107field=field_str{field_index(1)};
2108if isequal(field,'get_field...')
2109    hget_field=findobj(allchild(0),'name','get_field');
2110    if ~isempty(hget_field)
2111        delete(hget_field)%delete opened versions of get_field
2112    end
2113    Series=read_GUI(handles.series);
2114    Series.InputTable=Series.InputTable(1,:);
2115    filecell=get_file_series(Series);
2116    if exist(filecell{1,1},'file')
2117        GetFieldData=get_field(filecell{1,1});
2118        FieldList={};
2119        XName=GetFieldData.XVarName;
2120        if GetFieldData.CheckVector
2121            UName=GetFieldData.PanelVectors.vector_x;
2122            VName=GetFieldData.PanelVectors.vector_y;
2123            XName=GetFieldData.XVarName;
2124            YName=GetFieldData.YVarName;
2125            CName=GetFieldData.PanelVectors.vec_color;
2126            [FieldList,VecColorList]=set_field_list(UName,VName,CName);
2127        elseif GetFieldData.CheckScalar
2128            AName=GetFieldData.PanelScalar.scalar;
2129            XName=GetFieldData.XVarName;
2130            YName=GetFieldData.YVarName;
2131            FieldList={AName};
2132        elseif GetFieldData.CheckPlot1D;
2133            YName=GetFieldData.CheckPlot1D.ordinate;
2134        end
2135        set(handles.Coord_x,'String',{XName})
2136        set(handles.Coord_y,'String',{YName})
2137        set(handles.FieldName,'Value',1)
2138        set(handles.FieldName,'String',[FieldList; {'get_field...'}]);
2139        %         set(handles.ColorScalar,'Value',1)
2140        %         set(handles.ColorScalar,'String',VecColorList);
2141        %         UvData.FileType{1}='netcdf';
2142        %         set(handles.uvmat,'UserData',UvData)
2143    end
2144    % elseif isequal(field,'more...')
2145    %     str=calc_field;
2146    %     [ind_answer,v] = listdlg('PromptString','Select a file:',...
2147    %                 'SelectionMode','single',...
2148    %                 'ListString',str);
2149    %        % edit the choice in the fields and actionname menu
2150    %      scalar=cell2mat(str(ind_answer));
2151    %      update_menu(handles.FieldName,scalar)
2152end
2153
2154%------------------------------------------------------------------------
2155% --- Executes on selection change in FieldName_1.
2156function FieldName_1_Callback(hObject, eventdata, handles)
2157%------------------------------------------------------------------------
2158field_str=get(handles.FieldName_1,'String');
2159field_index=get(handles.FieldName_1,'Value');
2160field=field_str{field_index};
2161if isequal(field,'get_field...')   
2162     hget_field=findobj(allchild(0),'name','get_field_1');
2163     if ~isempty(hget_field)
2164         delete(hget_field)
2165     end
2166     SeriesData=get(handles.series,'UserData');
2167     filename=SeriesData.CurrentInputFile_1;
2168     if exist(filename,'file')
2169        hget_field=get_field(filename);
2170        set(hget_field,'name','get_field_1')
2171     end
2172% elseif isequal(field,'more...')
2173%     str=calc_field;
2174%     [ind_answer,v] = listdlg('PromptString','Select a file:',...
2175%                 'SelectionMode','single',...
2176%                 'ListString',str);
2177%        % edit the choice in the fields and actionname menu
2178%      scalar=cell2mat(str(ind_answer));
2179%      update_menu(handles.FieldName_1,scalar)
2180end   
2181
2182
2183%%%%%%%%%%%%%
2184function [ind_remove]=find_pairs(dirpair,ind_i,last_i)
2185indsel=ind_i;
2186indiff=diff(ind_i); %test index increment to detect multiplets (several pairs with the same index ind_i) and holes in the series
2187indiff=[1 indiff last_i-ind_i(end)+1];%for testing gaps with the imposed bounds
2188if ~isempty(indiff)
2189    indiff2=diff(indiff);
2190    indiffp=[indiff2 1];
2191    indiffm=[1 indiff2];
2192    ind_multi_m=find((indiff==0)&(indiffm<0))-1;%indices of first members of multiplets
2193    ind_multi_p=find((indiff==0)&(indiffp>0));%indices of last members of multiplets
2194    %for each multiplet, select the most recent file
2195    ind_remove=[];
2196    for i=1:length(ind_multi_m)
2197        ind_pairs=ind_multi_m(i):ind_multi_p(i);
2198        for imulti=1:length(ind_pairs)
2199            datepair(imulti)=datenum(dirpair(ind_pairs(imulti)).date);%dates of creation
2200        end
2201        [datenew,indsort2]=sort(datepair); %sort the multiplet by creation date
2202        ind_s=indsort2(1:end-1);%
2203        ind_remove=[ind_remove ind_pairs(ind_s)];%remove these indices, leave the last one
2204    end
2205end
2206
2207%------------------------------------------------------------------------
2208% --- determine the list of index pairstring of processing file
2209function [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)
2210%------------------------------------------------------------------------
2211num_i1=num_i;% set of first image numbers by default
2212num_i2=num_i;
2213num_j1=num_j;
2214num_j2=num_j;
2215num_i_out=num_i;
2216num_j_out=num_j;
2217% if isequal (NomType,'_1-2_1') || isequal (NomType,'_1-2')
2218if isequal(mode,'series(Di)')
2219    num_i1_line=num_i+ind_shift(3);% set of first image numbers
2220    num_i2_line=num_i+ind_shift(4);
2221    % adjust the first and last field number
2222        indsel=find(num_i1_line >= 1);
2223    num_i_out=num_i(indsel);
2224    num_i1_line=num_i1_line(indsel);
2225    num_i2_line=num_i2_line(indsel);
2226    num_j1=meshgrid(num_j,ones(size(num_i1_line)));
2227    num_j2=meshgrid(num_j,ones(size(num_i1_line)));
2228    [xx,num_i1]=meshgrid(num_j,num_i1_line);
2229    [xx,num_i2]=meshgrid(num_j,num_i2_line);
2230elseif isequal (mode,'series(Dj)')||isequal (mode,'bursts')
2231    if isequal(mode,'bursts') %case of bursts (png_old or png_2D)
2232        num_j1=ind_shift(1)*ones(size(num_i));
2233        num_j2=ind_shift(2)*ones(size(num_i));
2234    else
2235        num_j1_col=num_j+ind_shift(1);% set of first image numbers
2236        num_j2_col=num_j+ind_shift(2);
2237        % adjust the first field number
2238        indsel=find((num_j1_col >= 1));   
2239        num_j_out=num_j(indsel);
2240        num_j1_col=num_j1_col(indsel);
2241        num_j2_col=num_j2_col(indsel);
2242        [num_i1,num_j1]=meshgrid(num_i,num_j1_col);
2243        [num_i2,num_j2]=meshgrid(num_i,num_j2_col);
2244    end   
2245end
2246
2247%------------------------------------------------------------------------
2248% --- Executes on button press in CheckObject.
2249function CheckObject_Callback(hObject, eventdata, handles)
2250%------------------------------------------------------------------------
2251hset_object=findobj(allchild(0),'tag','set_object');%find the set_object interface handle
2252value=get(handles.CheckObject,'Value');
2253if value
2254    SeriesData=get(handles.series,'UserData');
2255    if ~(isfield(SeriesData,'ProjObject')&&~isempty(SeriesData.ProjObject))
2256        if ishandle(hset_object)
2257            uistack(hset_object,'top')% show the GUI set_object if opened
2258        else
2259            %get the object file
2260            InputTable=get(handles.InputTable,'Data');
2261            defaultname=InputTable{1,1};
2262            if isempty(defaultname)
2263                defaultname={''};
2264            end
2265            [FileName, PathName] = uigetfile( ...
2266                {'*.xml;*.mat', ' (*.xml,*.mat)';
2267                '*.xml',  '.xml files '; ...
2268                '*.mat',  '.mat matlab files '}, ...
2269                'Pick an xml object file (or use uvmat to create it)',defaultname);
2270            fileinput=[PathName FileName];%complete file name
2271            sizf=size(fileinput);
2272            if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end
2273            %read the file
2274            data=xml2struct(fileinput);
2275            if ~isfield(data,'Type')
2276                msgbox_uvmat('ERROR',[fileinput ' is not an object xml file'])
2277                return
2278            end
2279            if ~isfield(data,'ProjMode')
2280                data.ProjMode='none';
2281            end
2282            hset_object=set_object(data);% call the set_object interface
2283        end
2284        ProjObject=read_GUI(hset_object);
2285        set(handles.ProjObject,'String',ProjObject.Name);%display the object name
2286        SeriesData=get(handles.series,'UserData');
2287        SeriesData.ProjObject=ProjObject;
2288        set(handles.series,'UserData',SeriesData);
2289    end
2290    set(handles.DeleteObject,'Visible','on');
2291    set(handles.ViewObject,'Visible','on');
2292    set(handles.ProjObject,'Visible','on');
2293else
2294    set(handles.DeleteObject,'Visible','off');
2295    set(handles.ViewObject,'Visible','off');
2296    if ~ishandle(hset_object)
2297    set(handles.ViewObject,'Value',0);
2298    end
2299    set(handles.ProjObject,'Visible','off');
2300end
2301%set(handles.series,'UserData',SeriesData)
2302
2303%--------------------------------------------------------------
2304function CheckMask_Callback(hObject, eventdata, handles)
2305value=get(handles.CheckMask,'Value');
2306if value
2307    msgbox_uvmat('ERROR','not implemented yet')
2308end
2309%--------------------------------------------------------------
2310
2311%-------------------------------------------------------------------
2312%'uv_ncbrowser': interactively calls the netcdf file browser 'get_field.m'
2313function ncbrowser_uvmat(hObject, eventdata)
2314%-------------------------------------------------------------------
2315     bla=get(gcbo,'String');
2316     ind=get(gcbo,'Value');
2317     filename=cell2mat(bla(ind));
2318      blank=find(filename==' ');
2319      filename=filename(1:blank-1);
2320     get_field(filename)
2321
2322% ------------------------------------------------------------------
2323function MenuHelp_Callback(hObject, eventdata, handles)
2324%-------------------------------------------------------------------
2325path_to_uvmat=which ('uvmat');% check the path of uvmat
2326pathelp=fileparts(path_to_uvmat);
2327helpfile=fullfile(pathelp,'uvmat_doc','uvmat_doc.html');
2328if isempty(dir(helpfile)), msgbox_uvmat('ERROR','Please put the help file uvmat_doc.html in the sub-directory /uvmat_doc of the UVMAT package')
2329else
2330    addpath (fullfile(pathelp,'uvmat_doc'))
2331    web([helpfile '#series'])
2332end
2333
2334%-------------------------------------------------------------------
2335% --- Executes on selection change in TransformName.
2336function TransformName_Callback(hObject, eventdata, handles)
2337%----------------------------------------------------------------------
2338TransformList=get(handles.TransformName,'String');
2339TransformIndex=get(handles.TransformName,'Value');
2340TransformName=TransformList{TransformIndex};
2341TransformPathList=get(handles.TransformName,'UserData');
2342nb_builtin_transform=4;
2343% ff=functions(list_transform{end});
2344if isequal(TransformName,'more...');
2345%     coord_fct='';
2346%     prompt = {'Enter the name of the transform function'};
2347%     dlg_title = 'user defined transform';
2348%     num_lines= 1;
2349    [FileName, PathName] = uigetfile( ...
2350       {'*.m', ' (*.m)';
2351        '*.m',  '.m files '; ...
2352        '*.*', 'All Files (*.*)'}, ...
2353        'Pick a transform function',get(handles.TransformPath,'String'));
2354    if isequal(FileName,0)
2355        return     %browser closed without choice
2356    end
2357    if isequal(PathName(end),'/')||isequal(PathName(end),'\')
2358        PathName(end)=[];
2359    end
2360    [TransformPath,TransformName,TransformExt]=fileparts(FileName);% removes extension .m
2361    if ~strcmp(TransformExt,'.m')
2362        msgbox_uvmat('ERROR','a Matlab function .m must be introduced');
2363        return
2364    end
2365     % insert the choice in the menu
2366    TransformIndex=find(strcmp(TransformName,TransformList),1);% look for the selected function in the menu Action
2367    if isempty(TransformIndex)%the input string does not exist in the menu
2368        TransformIndex= length(TransformList);
2369        TransformList=[TransformList(1:end-1);{TransformnName};TransformList(end)];% the selected function is appended in the menu, before the last item 'more...'
2370        set(handles.TransformName,'String',TransformList)
2371        TransformPathList=[TransformPathList;{TransformPath}];
2372    end
2373   % save the new menu in the personal file 'uvmat_perso.mat'
2374   dir_perso=prefdir;%personal Matalb directory
2375   profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
2376   if exist(profil_perso,'file')
2377       for ilist=nb_builtin_transform+1:numel(TransformPathList)
2378           TransformListUser{ilist-nb_builtin_transform}=TransformList{ilist};
2379           TransformPathListUser{ilist-nb_builtin_transform}=TransformPathList{ilist};
2380       end
2381       save (profil_perso,'TransformPathListUser','TransformListUser','-append'); %store the root name for future opening of uvmat
2382   end
2383end
2384
2385%display the current function path
2386set(handles.TransformPath,'String',TransformPathList{TransformIndex}); %show the path to the senlected function
2387set(handles.TransformName,'UserData',TransformPathList);
2388
2389
2390% --------------------------------------------------------------------
2391function MenuExportConfig_Callback(hObject, eventdata, handles)
2392global Series
2393[Series,errormsg]=prepare_jobs(handles);
2394
2395evalin('base','global Series')%make CurData global in the workspace
2396display('current series config :')
2397evalin('base','Series') %display CurData in the workspace
2398commandwindow; %brings the Matlab command window to the front
2399
2400% --------------------------------------------------------------------
2401function MenuImportConfig_Callback(hObject, eventdata, handles)
2402% --------------------------------------------------------------------
2403InputTable=get(handles.InputTable,'Data');
2404[FileName, PathName] = uigetfile( ...
2405       {'*.xml', ' (*.xml)';
2406       '*.xml',  '.xml files '; ...
2407        '*.*',  'All Files (*.*)'}, ...
2408        'Pick a file',InputTable{1,1});
2409filexml=[PathName FileName];%complete file name
2410if isempty(filexml),return;end %abandon if no file is introduced by the browser
2411Param=xml2struct(filexml);
2412fill_GUI(Param,handles.series)
2413
2414% --- Executes on selection change in RunMode.
2415function RunMode_Callback(hObject, eventdata, handles)
2416
2417% --- Executes on selection change in Coord_x.
2418function Coord_x_Callback(hObject, eventdata, handles)
2419
2420% --- Executes on selection change in Coord_y.
2421function Coord_y_Callback(hObject, eventdata, handles)
2422
2423% --------------------------------------------------------------------
2424% --- Executes when series is resized.
2425function series_ResizeFcn(hObject, eventdata, handles)
2426% --------------------------------------------------------------------
2427%% input table
2428set(handles.InputTable,'Unit','pixel')
2429Pos=get(handles.InputTable,'Position');
2430set(handles.InputTable,'Unit','normalized')
2431ColumnWidth=round([0.5 0.14 0.14 0.14 0.08]*(Pos(3)-52));
2432ColumnWidth=num2cell(ColumnWidth);
2433set(handles.InputTable,'ColumnWidth',ColumnWidth)
2434
2435%% MinIndex_j and MaxIndex_i
2436unit=get(handles.MinIndex_i,'Unit');
2437set(handles.MinIndex_i,'Unit','pixel')
2438Pos=get(handles.MinIndex_i,'Position');
2439set(handles.MinIndex_i,'Unit',unit)
2440set(handles.MinIndex_i,'ColumnWidth',{Pos(3)-18})
2441set(handles.MaxIndex_i,'ColumnWidth',{Pos(3)-18})
2442set(handles.MinIndex_j,'ColumnWidth',{Pos(3)-18})
2443set(handles.MaxIndex_j,'ColumnWidth',{Pos(3)-18})
2444
2445%% TimeTable
2446set(handles.TimeTable,'Unit','pixel')
2447Pos=get(handles.TimeTable,'Position');
2448set(handles.TimeTable,'Unit','normalized')
2449% ColumnWidth=get(handles.TimeTable,'ColumnWidth');
2450ColumnWidth=num2cell(floor([0.25 0.25 0.25 0.25]*(Pos(3)-20)));
2451set(handles.TimeTable,'ColumnWidth',ColumnWidth)
2452
2453
2454%% PairString
2455set(handles.PairString,'Unit','pixel')
2456Pos=get(handles.PairString,'Position');
2457set(handles.PairString,'Unit','normalized')
2458set(handles.PairString,'ColumnWidth',{Pos(3)-5})
2459
2460
2461% --- Executes on button press in status.
2462function status_Callback(hObject, eventdata, handles)
2463
2464if get(handles.status,'Value')
2465    set(handles.status,'BackgroundColor',[1 1 0])
2466    drawnow
2467    %StatusData.time_ref=get(handles.RUN,'UserData');% get the time of launch
2468    Param=read_GUI(handles.series);
2469    RootPath=Param.InputTable{1,1};
2470    if ~isfield(Param,'OutputSubDir')   
2471        msgbox_uvmat('ERROR','no directory defined for output files')
2472        return
2473    end
2474    OutputSubDir=[Param.OutputSubDir Param.OutputDirExt];% subdirectory for output files
2475    OutputDir=fullfile(RootPath,OutputSubDir);
2476    uigetfile_uvmat('status_display',OutputDir)
2477   
2478%     hfig=findobj(allchild(0),'name','series_status');
2479%     if isempty(hfig)
2480%         ScreenSize=get(0,'ScreenSize');
2481%         hfig=figure('DeleteFcn',@stop_status,'Position',[ScreenSize(3)-600 ScreenSize(4)-640 560 600]);
2482%         set(hfig,'MenuBar','none')% suppress the menu bar
2483%         set(hfig,'NumberTitle','off')%suppress the fig number in the title
2484%         set(hfig,'name','series_status')
2485%         set(hfig,'tag','series_status')
2486%         uicontrol('Style','listbox','Units','normalized', 'Position',[0.05 0.09 0.9 0.71], 'Callback', @view_file,'tag','list','UserData',OutputDir);
2487%         uicontrol('Style','edit','Units','normalized', 'Position', [0.05 0.87 0.9 0.1],'tag','titlebox','Max',2,'String',OutputDir);
2488%         uicontrol('Style','frame','Units','normalized', 'Position', [0.05 0.81 0.9 0.05]);
2489%         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);
2490%         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);
2491%         %set(hrefresh,'UserData',StatusData)
2492%         BarPosition=[0.05 0.81 0.01 0.05];
2493%         uicontrol('Style','frame','Units','normalized', 'Position',BarPosition ,'BackgroundColor',[1 0 0],'tag','waitbar');
2494%         drawnow
2495%     end
2496%     refresh_GUI(hfig)
2497else
2498    %% delete current display fig if selection is off
2499    set(handles.status,'BackgroundColor',[0 1 0])
2500    hfig=findobj(allchild(0),'name','series_status');
2501    if ~isempty(hfig)
2502        delete(hfig)
2503    end
2504    return
2505end
2506
2507
2508%------------------------------------------------------------------------   
2509% launched by selecting a file on the list
2510function view_file(hObject, eventdata)
2511%------------------------------------------------------------------------
2512list=get(hObject,'String');
2513index=get(hObject,'Value');
2514rootroot=get(hObject,'UserData');
2515selectname=list{index};
2516ind_dot=regexp(selectname,'\.\.\.');
2517if ~isempty(ind_dot)
2518    selectname=selectname(1:ind_dot-1);
2519end
2520FullSelectName=fullfile(rootroot,selectname);
2521if exist(FullSelectName,'dir')% a directory has been selected
2522    ListFiles=dir(FullSelectName);
2523    ListDisplay=cell(numel(ListFiles),1);
2524    for ilist=2:numel(ListDisplay)% suppress the first line '.'
2525        ListDisplay{ilist-1}=ListFiles(ilist).name;
2526    end
2527    set(hObject,'Value',1)
2528    set(hObject,'String',ListDisplay)
2529    if strcmp(selectname,'..')
2530        FullSelectName=fileparts(fileparts(FullSelectName));
2531    end
2532    set(hObject,'UserData',FullSelectName)
2533    hfig=get(hObject,'parent');
2534    htitlebox=findobj(hfig,'tag','titlebox');   
2535    set(htitlebox,'String',FullSelectName)
2536elseif exist(FullSelectName,'file')%visualise the vel field if it exists
2537    FileType=get_file_type(FullSelectName);
2538    if strcmp(FileType,'txt')
2539        edit(FullSelectName)
2540    elseif strcmp(FileType,'xml')
2541        editxml(FullSelectName)
2542    else
2543        uvmat(FullSelectName)
2544    end
2545    set(gcbo,'Value',1)
2546end
2547
2548
2549%------------------------------------------------------------------------   
2550% launched by refreshing the status figure
2551function refresh_GUI(hfig)
2552%------------------------------------------------------------------------
2553htitlebox=findobj(hfig,'tag','titlebox');
2554hlist=findobj(hfig,'tag','list');
2555hseries=findobj(allchild(0),'tag','series');
2556hstatus=findobj(hseries,'tag','status');
2557StatusData=get(hstatus,'UserData');
2558OutputDir=get(htitlebox,'String');
2559if ischar(OutputDir),OutputDir={OutputDir};end
2560ListFiles=dir(OutputDir{1});
2561if numel(ListFiles)<1
2562    return
2563end
2564ListFiles(1)=[];%removes the first line ='.'
2565ListDisplay=cell(numel(ListFiles),1);
2566testrecent=0;
2567datnum=zeros(numel(ListDisplay),1);
2568for ilist=1:numel(ListDisplay)
2569    ListDisplay{ilist}=ListFiles(ilist).name;
2570      if ~ListFiles(ilist).isdir && isfield(ListFiles(ilist),'datenum')
2571            datnum(ilist)=ListFiles(ilist).datenum;%only available in recent matlab versions
2572            testrecent=1;
2573       end
2574end
2575set(hlist,'String',ListDisplay)
2576
2577%% Look at date of creation
2578ListDisplay=ListDisplay(datnum~=0);
2579datnum=datnum(datnum~=0);%keep the non zero values corresponding to existing files
2580NbOutputFile=[];
2581if isempty(datnum)
2582    if testrecent
2583        message='no civ result created yet';
2584    else
2585        message='';
2586    end
2587else
2588    [first,indfirst]=min(datnum);
2589    [last,indlast]=max(datnum);
2590    NbOutputFile_str='?';
2591    NbOutputFile=[];
2592    if isfield(StatusData,'NbOutputFile')
2593        NbOutputFile=StatusData.NbOutputFile;
2594        NbOutputFile_str=num2str(NbOutputFile);
2595    end
2596    message={[num2str(numel(datnum)) ' file(s) done over ' NbOutputFile_str] ;['oldest modification:  ' ListDisplay{indfirst} ' : ' datestr(first)];...
2597        ['latest modification:  ' ListDisplay{indlast} ' : ' datestr(last)]};
2598end
2599set(htitlebox,'String', [OutputDir{1};message])
2600
2601%% update the waitbar
2602hwaitbar=findobj(hfig,'tag','waitbar');
2603if ~isempty(NbOutputFile)
2604    BarPosition=get(hwaitbar,'Position');
2605    BarPosition(3)=0.9*numel(datnum)/NbOutputFile;
2606    set(hwaitbar,'Position',BarPosition)
2607end
2608%TODO: adjust waitbar
2609
2610% civ_files=get(hfig,'UserData');
2611
2612% [filepath,filename,ext]=fileparts(civ_files{1});
2613% [tild,SubDir,extdir]=fileparts(filepath);
2614% SubDir=[SubDir extdir];
2615% option_civ=StatusData.option_civ;
2616% nbfiles=numel(civ_files);
2617% testrecent=0;
2618% count=0;
2619% datnum=zeros(1,nbfiles);
2620% filefound=cell(1,nbfiles);
2621% for ifile=1:nbfiles
2622%     detect=exist(civ_files{ifile},'file'); % check the existence of the file
2623%     option=0;
2624%     if detect==0
2625%         option_str='not created';
2626%     else
2627%         datfile=dir(civ_files{ifile});
2628%         if isfield(datfile,'datenum')
2629%             datnum(ifile)=datfile.datenum;%only available in recent matlab versions
2630%             testrecent=1;
2631%         end
2632%         filefound(ifile)={datfile.name};
2633%         
2634%         % check the content  netcdf file
2635%         Data=nc2struct(civ_files{ifile},'ListGlobalAttribute','CivStage','patch2','fix2','civ2','patch','fix');
2636%         option_list={'civ1','fix1','patch1','civ2','fix2','patch2'};
2637%         if ~isempty(Data.CivStage)
2638%             option=Data.CivStage;%case of Matlab civ
2639%         else
2640%             if ~isempty(Data.patch2) && isequal(Data.patch2,1)
2641%                 option=6;
2642%             elseif ~isempty(Data.fix2) && isequal(Data.fix2,1)
2643%                 option=5;
2644%             elseif ~isempty(Data.civ2) && isequal(Data.civ2,1);
2645%                 option=4;
2646%             elseif ~isempty(Data.patch) && isequal(Data.patch,1);
2647%                 option=3;
2648%             elseif ~isempty(Data.fix) && isequal(Data.fix,1);
2649%                 option=2;
2650%             else
2651%                 option=1;
2652%             end
2653%         end
2654%         option_str=option_list{option};
2655%         if datnum(ifile)<StatusData.time_ref
2656%             option_str=[option_str '  --OLD--'];
2657%         end
2658%     end
2659%     if option >= option_civ
2660%         count=count+1;
2661%     end
2662%     [filepath,filename,ext]=fileparts(civ_files{ifile});
2663%     Tabchar{ifile,1}=[fullfile(SubDir,filename) ext  '...' option_str];
2664% end
2665% datnum=datnum(datnum~=0);%keep the non zero values corresponding to existing files
2666% if isempty(datnum)
2667%     if testrecent
2668%         message='no civ result created yet';
2669%     else
2670%         message='';
2671%     end
2672% else
2673%     datnum=datnum(datnum~=0);%keep the non zero values corresponding to existing files
2674%     [first,ind]=min(datnum);
2675%     [last,indlast]=max(datnum);
2676%     message={[num2str(count) ' file(s) done over ' num2str(nbfiles)] ;['oldest modification:  ' cell2mat(filefound(ind)) ' : ' datestr(first)];...
2677%         ['latest modification:  ' cell2mat(filefound(indlast)) ' : ' datestr(last)]};
2678% end
2679% hlist=findobj(hfig,'tag','list');
2680% htitlebox=findobj(hfig,'tag','titlebox');
2681% hwaitbar=findobj(hfig,'tag','waitbar');
2682% set(hlist,'String',Tabchar)
2683% set(htitlebox,'String', message)
2684%
2685%------------------------------------------------------------------------   
2686% launched by deleting the status figure
2687function stop_status(hObject, eventdata)
2688%------------------------------------------------------------------------
2689hciv=findobj(allchild(0),'tag','series');
2690hhciv=guidata(hciv);
2691set(hhciv.status,'value',0) %reset the status uicontrol in the GUI civ
2692set(hhciv.status,'BackgroundColor',[0 1 0])
2693delete(gcbf)
2694
2695% --- Executes on selection change in ActionExt.
2696function ActionExt_Callback(hObject, eventdata, handles)
2697ActionExtList=get(handles.ActionExt,'String');
2698ActionExt=ActionExtList{get(handles.ActionExt,'Value')};
2699ActionList=get(handles.ActionName,'String');
2700ActionName=ActionList{get(handles.ActionName,'Value')};
2701TransformPath='';
2702if ~isempty(get(handles.ActionExt,'UserData'))
2703    TransformPath=get(handles.ActionExt,'UserData');
2704end
2705if strcmp(ActionExt,'.sh')
2706    set(handles.ActionExt,'BackgroundColor',[1 1 0])
2707    ActionFullName=fullfile(get(handles.ActionPath,'String'),[ActionName '.sh']);
2708    if ~exist(ActionFullName,'file')
2709        answer=msgbox_uvmat('INPUT_Y-N','compiled version has not been created: compile now?');
2710        if strcmp(answer,'Yes')
2711            set(handles.ActionExt,'BackgroundColor',[1 1 0])
2712            path_uvmat=fileparts(which('series'));
2713            currentdir=pwd;
2714            cd(get(handles.ActionPath,'String'))% go to the directory of Action
2715            %  addpath(get(handles.TransformPath,'String'))
2716            addpath(path_uvmat)% add the path to uvmat to run the fct 'compile'
2717           % addpath(fullfile(path_uvmat,'transform_field'))% add the path to uvmat to run the fct 'compile'
2718            compile(ActionName,TransformPath)
2719            cd(currentdir)
2720        end
2721       
2722    else
2723        sh_file_info=dir(fullfile(get(handles.ActionPath,'String'),[ActionName '.sh']));
2724        m_file_info=dir(fullfile(get(handles.ActionPath,'String'),[ActionName '.m']));
2725        if isfield(m_file_info,'datenum') && m_file_info.datenum>sh_file_info.datenum
2726            set(handles.ActionExt,'BackgroundColor',[1 1 0])
2727            drawnow
2728            answer=msgbox_uvmat('INPUT_Y-N',[ActionName '.sh needs to be updated: recompile now?']);
2729            if strcmp(answer,'Yes')
2730                path_uvmat=fileparts(which('series'));
2731                currentdir=pwd;
2732                cd(get(handles.ActionPath,'String'))% go to the directory of Action
2733                %  addpath(get(handles.TransformPath,'String'))
2734                addpath(path_uvmat)% add the path to uvmat to run the fct 'compile'
2735                addpath(fullfile(path_uvmat,'transform_field'))% add the path to uvmat to run the fct 'compile'
2736                compile(ActionName,TransformPath)
2737                cd(currentdir)
2738            end
2739        end
2740    end
2741    set(handles.ActionExt,'BackgroundColor',[1 1 1])
2742end
2743
2744
2745function ActionInput_Callback(hObject, eventdata, handles)
2746
2747
2748% --- Executes on button press in DeleteObject.
2749function DeleteObject_Callback(hObject, eventdata, handles)
2750if get(handles.DeleteObject,'Value')
2751        SeriesData=get(handles.series,'UserData');
2752    SeriesData.ProjObject=[];
2753    set(handles.series,'UserData',SeriesData)
2754    set(handles.ProjObject,'String','')
2755    set(handles.CheckObject,'Value',0)
2756    set(handles.DeleteObject,'Visible','off')
2757    set(handles.ViewObject,'Visible','off')
2758    set(handles.DeleteObject,'Value',0)
2759end
2760
2761% --- Executes on button press in ViewObject.
2762function ViewObject_Callback(hObject, eventdata, handles)
2763if get(handles.ViewObject,'Value')
2764        UserData=get(handles.series,'UserData');
2765    set_object(UserData.ProjObject)
2766else
2767    hset_object=findobj(allchild(0),'Tag','set_object');
2768    if ~isempty(hset_object)
2769        delete(hset_object)
2770    end
2771end
2772
2773
2774function num_NbProcess_Callback(hObject, eventdata, handles)
2775
2776
2777function num_NbSlice_Callback(hObject, eventdata, handles)
2778NbSlice=str2num(get(handles.num_NbSlice,'String'));
2779set(handles.num_NbProcess,'String',num2str(NbSlice))
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