source: trunk/src/series.m @ 902

Last change on this file since 902 was 902, checked in by g7moreau, 6 years ago
File size: 155.5 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 2008-2014, LEGI / CNRS UJF G-INP, Joel.Sommeria@legi.grenoble-inp.fr
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=min(RescaleFactor,1);
78end
79Width=Width*RescaleFactor;
80Height=Height*RescaleFactor;
81LeftX=80*RescaleFactor;%position of the left fig side, in pixels (put to the left side, with some margin)
82LowY=round(ScreenSize(4)/2-Height/2); % put at the middle height on the screen
83set(hObject,'Units','points')
84set(hObject,'Position',[LeftX LowY Width Height])% position and size of the GUI at opening
85
86% settings of table MinIndex_j
87set(handles.MinIndex_i,'ColumnFormat',{'numeric'})
88set(handles.MinIndex_i,'ColumnEditable',false)
89set(handles.MinIndex_i,'ColumnName',{'i min'})
90set(handles.MinIndex_i,'Data',[])% initiate Data to double (not cell)
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'})
96set(handles.MinIndex_j,'Data',[])% initiate Data to double (not cell)
97
98% settings of table MaxIndex_i
99set(handles.MaxIndex_i,'ColumnFormat',{'numeric'})
100set(handles.MaxIndex_i,'ColumnEditable',false)
101set(handles.MaxIndex_i,'ColumnName',{'i max'})
102set(handles.MaxIndex_i,'Data',[])% initiate Data to double (not cell)
103
104% settings of table MaxIndex_j
105set(handles.MaxIndex_j,'ColumnFormat',{'numeric'})
106set(handles.MaxIndex_j,'ColumnEditable',false)
107set(handles.MaxIndex_j,'ColumnName',{'j max'})
108set(handles.MaxIndex_j,'Data',[])% initiate Data to double (not cell)
109
110% settings of table PairString
111set(handles.PairString,'ColumnName',{'pairs'})
112set(handles.PairString,'ColumnEditable',false)
113set(handles.PairString,'ColumnFormat',{'char'})
114set(handles.PairString,'Data',{''})
115
116% settings of table MaskTable
117set(handles.MaskTable,'ColumnName',{'mask name'})
118set(handles.PairString,'ColumnEditable',false)
119set(handles.PairString,'ColumnFormat',{'char'})
120set(handles.PairString,'Data',{''})
121
122series_ResizeFcn(hObject, eventdata, handles)%resize table according to series GUI size
123set(hObject,'WindowButtonDownFcn',{'mouse_down'})%allows mouse action with right button (zoom for uicontrol display)
124set(hObject,'DeleteFcn',{@closefcn})%
125
126% check default input data
127if ~exist('Param','var')
128    Param=[]; %default
129end
130
131%% list of builtin functions in the mebu ActionName
132ActionList={'check_data_files';'aver_stat';'time_series';'civ_series';'merge_proj'};% WARNING: fits with nb_builtin_ACTION=4 in ActionName_callback
133NbBuiltinAction=numel(ActionList);
134set(handles.Action,'UserData',NbBuiltinAction)
135[path_series,name,ext]=fileparts(which('series'));% path to the GUI series
136path_series_fct=fullfile(path_series,'series');%path of the functions in subdirectroy 'series'
137[code, message] = system...
138    ('LD_LIBRARY_PATH=$(echo $LD_LIBRARY_PATH | pyp "p.split('':'') |... [s for s in p if ''matlab'' not in s] | '':''.join(p)") python -c "import fluiddyn"');
139if code==0
140    ActionExtList={'.m';'.sh';'.py (in dev.)'};% default choice of extensions (Matlab fct .m or compiled version .sh
141else
142    ActionExtList={'.m';'.sh'};  % python options not installed
143end
144ActionPathList=cell(NbBuiltinAction,1);%initiate the cell matrix of Action fct paths
145ActionPathList(:)={path_series_fct}; %set the default path to series fcts to all list members
146RunModeList={'local';'background'};% default choice of extensions (Matlab fct .m or compiled version .sh)
147[s,w]=system('oarstat');% look for cluster system 'oar'
148if isequal(s,0)
149    RunModeList=[RunModeList;{'cluster_oar'}];
150    set(handles.MonitorCluster,'Visible','on'); % make visible button for access to Monika
151end
152[s,w]=system('qstat --version');% look for cluster system 'sge'
153if isequal(s,0)
154    if regexp(w,'^pbs')
155        RunModeList=[RunModeList;{'cluster_pbs'}];
156    else
157        RunModeList=[RunModeList;{'cluster_sge'}];
158    end
159end
160set(handles.RunMode,'String',RunModeList)
161
162%% list of builtin transform functions in the menu TransformName
163TransformList={'';'sub_field';'phys';'phys_polar'};% WARNING: must fit with the corresponding menu in uvmat and nb_builtin_transform=4 in  TransformName_callback
164NbBuiltinTransform=numel(TransformList);
165path_transform_fct=fullfile(path_series,'transform_field');
166TransformPathList=cell(NbBuiltinTransform,1);%initiate the cell matrix of Action fct paths
167TransformPathList(:)={path_transform_fct}; %set the default path to series fcts to all list members
168
169%% get the user defined functions stored in the personal file uvmat_perso.mat
170dir_perso=prefdir;
171profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
172if exist(profil_perso,'file')
173    h=load (profil_perso);
174    %get the list of previous input files in the upper bar menu Open
175    if isfield(h,'MenuFile')
176        for ifile=1:min(length(h.MenuFile),5)
177            set(handles.(['MenuFile_' num2str(ifile)]),'Label',h.MenuFile{ifile});
178            set(handles.(['MenuFile_' num2str(ifile+5)]),'Label',h.MenuFile{ifile});
179        end
180    end
181    %get the list of previous campaigns in the upper bar menu Open campaign
182    if isfield(h,'MenuCampaign')
183        for ifile=1:min(length(h.MenuCampaign),5)
184            set(handles.(['MenuCampaign_' num2str(ifile)]),'Label',h.MenuCampaign{ifile});
185        end
186    end
187    %get the menu of actions
188%     if isfield(h,'ActionExtListUser') && iscell(h.ActionExtListUser)
189%         ActionExtList=[ActionExtList; h.ActionExtListUser];
190%     end
191    if isfield(h,'ActionListUser') && iscell(h.ActionListUser) && isfield(h,'ActionPathListUser') && iscell(h.ActionPathListUser)
192        ActionList=[ActionList;h.ActionListUser];
193        ActionPathList=[ActionPathList;h.ActionPathListUser(:,1)];
194    end
195    %get the menu of transform fct
196    if isfield(h,'TransformListUser') && iscell(h.TransformListUser) && isfield(h,'TransformPathListUser') && iscell(h.TransformPathListUser)
197        TransformList=[TransformList;h.TransformListUser];
198        TransformPathList=[TransformPathList;h.TransformPathListUser];
199    end
200end
201
202%% selection of the input Action fct
203ActionCheckExist=true(size(ActionList));%initiate the check of the path to the listed action fct
204for ilist=NbBuiltinAction+1:numel(ActionList)%check  the validity of the path of the user defined Action fct
205    ActionCheckExist(ilist)=exist(fullfile(ActionPathList{ilist},[ActionList{ilist} '.m']),'file');
206end
207ActionPathList=ActionPathList(ActionCheckExist,:);% suppress the menu options which are not valid anymore
208ActionList=ActionList(ActionCheckExist);
209set(handles.ActionName,'String',[ActionList;{'more...'}])
210set(handles.ActionName,'UserData',ActionPathList)
211ActionIndex=[];
212if isfield(Param,'ActionName')% copy the selected menu index transferred in Param from uvmat
213    ActionIndex=find(strcmp(Param.ActionName,ActionList),1);
214end
215if isempty(ActionIndex)
216    ActionIndex=1;
217end
218set(handles.ActionName,'Value',ActionIndex)
219set(handles.ActionPath,'String',ActionPathList{ActionIndex})
220set(handles.ActionExt,'Value',1)
221set(handles.ActionExt,'String',ActionExtList)
222
223%% selection of the input transform fct
224TransformCheckExist=true(size(TransformList));
225for ilist=NbBuiltinTransform+1:numel(TransformList)
226    TransformCheckExist(ilist)=exist(fullfile(TransformPathList{ilist},[TransformList{ilist} '.m']),'file');
227end
228TransformPathList=TransformPathList(TransformCheckExist);
229TransformList=TransformList(TransformCheckExist);
230set(handles.TransformName,'String',[TransformList;{'more...'}])
231set(handles.TransformName,'UserData',TransformPathList)
232TransformIndex=[];
233if isfield(Param,'TransformName')% copy the selected menu index transferred in Param from uvmat
234    TransformIndex=find(strcmp(Param.TransformName,TransformList),1);
235end
236if isempty(TransformIndex)
237    TransformIndex=1;
238end
239set(handles.TransformName,'Value',TransformIndex)
240set(handles.TransformPath,'String',TransformPathList{TransformIndex})
241   
242%% fields input initialisation
243if isfield(Param,'list_fields')&& isfield(Param,'index_fields') &&~isempty(Param.list_fields) &&~isempty(Param.index_fields)
244    set(handles.FieldName,'String',Param.list_fields);% list menu fields
245    set(handles.FieldName,'Value',Param.index_fields);% selected string index
246end
247if isfield(Param,'Coordinates')
248    if isfield(Param.Coordinates,'Coord_x')
249        set(handles.Coord_x,'String',Param.Coordinates.Coord_x)
250    end
251    if isfield(Param.Coordinates,'Coord_y')
252        set(handles.Coord_y,'String',Param.Coordinates.Coord_y)
253    end
254    if isfield(Param.Coordinates,'Coord_z')
255        set(handles.Coord_z,'String',Param.Coordinates.Coord_z)
256    end
257end
258% if isfield(Param,'Coord_x_str') && ischar(Param.Coord_x_str)
259%         set(handles.Coord_x,'String',Param.Coord_x_str);% list menu fields
260% end
261% if isfield(Param,'Coord_y_str')&& ischar(Param.Coord_y_str)
262%         set(handles.Coord_y,'String',Param.Coord_y_str);% list menu fields
263% end
264
265%% introduce the input file name(s) if defined from input Param,
266set(handles.series,'UserData',[])% initiate Userdata
267if isfield(Param,'InputFile')
268   
269    %% fill the list of file series
270    InputTable=[{Param.InputFile.RootPath},{Param.InputFile.SubDir},{Param.InputFile.RootFile},{Param.InputFile.NomType},{Param.InputFile.FileExt}];
271    TimeTable=[{Param.InputFile.TimeName},{[]},{[]},{[]},{[]}];
272    if isfield(Param.InputFile,'RootPath_1')
273        InputTable=[InputTable;[{Param.InputFile.RootPath_1},{Param.InputFile.SubDir_1},{Param.InputFile.RootFile_1},{Param.InputFile.NomType_1},{Param.InputFile.FileExt_1}]];
274        TimeTable=[TimeTable; [{Param.InputFile.TimeName_1},{[]},{[]},{[]},{[]}]];
275    end
276    set(handles.InputTable,'Data',InputTable)
277    %% determine the selected reference field indices for pair display
278   
279    [tild,tild,tild,i1,i2,j1,j2]=fileparts_uvmat(Param.InputFile.FileIndex);
280    if isempty(i1)
281        i1=1;
282    end
283    if isempty(i2)
284        i2=i1;
285    end
286    ref_i=floor((i1+i2)/2);% reference image number corresponding to the file
287    % set(handles.num_ref_i,'String',num2str(ref_i));
288    if isempty(j1)
289        j1=1;
290    end
291    if isempty(j2)
292        j2=j1;
293    end
294    ref_j=floor((j1+j2)/2);% reference image number corresponding to the file
295    SeriesData.ref_i=ref_i;
296    SeriesData.ref_j=ref_j;
297    set(handles.series,'UserData',SeriesData)
298    update_rootinfo(handles,Param.HiddenData.i1_series{1},Param.HiddenData.i2_series{1},Param.HiddenData.j1_series{1},Param.HiddenData.j2_series{1},...
299        Param.HiddenData.FileInfo{1},Param.HiddenData.MovieObject{1},1)
300    if isfield(Param,'FileName_1')
301        %         display_file_name(handles,Param,2)
302        update_rootinfo(handles,Param.HiddenData.i1_series{2},Param.HiddenData.i2_series{2},Param.HiddenData.j1_series{2},Param.HiddenData.j2_series{2},...
303            Param.HiddenData.FileInfo{2},Param.HiddenData.MovieObject{2},2)
304    end
305    %% enable field and veltype menus, in accordance with the current action
306    ActionName_Callback([],[], handles)
307   
308    %% set length of waitbar
309    displ_time(handles)
310   
311else
312    set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH button to magenta color to indicate that input refresh is needed
313end
314if isfield(Param,'incr_i')
315    set(handles.num_incr_i,'String',num2str(Param.incr_i))
316else
317    set(handles.num_incr_i,'String','1')
318end
319if isfield(Param,'incr_j')
320    set(handles.num_incr_j,'String',num2str(Param.incr_j))
321else
322    set(handles.num_incr_j,'String','1')
323end
324
325%------------------------------------------------------------------------
326% --- Outputs from this function are returned to the command line.
327function varargout = series_OutputFcn(hObject, eventdata, handles)
328%------------------------------------------------------------------------
329varargout{1} = handles.output;
330
331%------------------------------------------------------------------------
332% --- executed when closing uvmat: delete or desactivate the associated figures if exist
333function closefcn(gcbo,eventdata)
334%------------------------------------------------------------------------
335
336% delete set_object_series if detected
337hh=findobj(allchild(0),'name','view_object_series');
338if ~isempty(hh)
339    delete(hh)
340end
341hh=findobj(allchild(0),'name','edit_object_series');
342if ~isempty(hh)
343    delete(hh)
344end
345
346%delete the bowser if detected
347hh=findobj(allchild(0),'tag','browser');
348if ~isempty(hh)
349    delete(hh)
350end
351
352
353%------------------------------------------------------------------------
354%------------------------------------------------------------------------
355%  II - FUNCTIONS FOR INTRODUCING THE INPUT FILES
356% automatically sets the global properties when the rootfile name is introduced
357% then activate the view-field actionname if selected
358% it is activated either by clicking on the RootPath window or by the
359% browser
360%------------------------------------------------------------------------
361%------------------------------------------------------------------------
362% --- fct activated by the browser under 'Open'
363%------------------------------------------------------------------------ 
364function MenuBrowse_Callback(hObject, eventdata, handles)
365%% look for the previously opened file 'oldfile'
366InputTable=get(handles.InputTable,'Data');
367oldfile=InputTable{1,1};
368if isempty(oldfile)
369    % use a file name stored in prefdir
370    dir_perso=prefdir;
371    profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
372    if exist(profil_perso,'file')
373        h=load (profil_perso);
374        if isfield(h,'RootPath') && ischar(h.RootPath)
375            oldfile=h.RootPath;
376        end
377    end
378end
379%% launch the browser
380fileinput=uigetfile_uvmat('pick an input file in the series',oldfile);
381hh=dir(fileinput);
382if numel(hh)>1
383    msgbox_uvmat('ERROR','invalid input, probably a broken link');
384else
385    if ~isempty(fileinput)
386        display_file_name(handles,fileinput,'one')
387    end
388end
389
390% --------------------------------------------------------------------
391function MenuBrowseAppend_Callback(hObject, eventdata, handles)
392
393%% look for the previously opened file 'oldfile'
394InputTable=get(handles.InputTable,'Data');
395RootPathCell=InputTable(:,1);
396if isempty(RootPathCell{1})% no input file in the table
397     MenuBrowse_Callback(hObject, eventdata, handles)%refresh the input table, not append
398     return
399end
400SubDirCell=InputTable(:,2);
401oldfile=fullfile(RootPathCell{1},SubDirCell{1});
402
403%% use a file name stored in prefdir
404dir_perso=prefdir;
405profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
406if exist(profil_perso,'file')
407    h=load (profil_perso);
408    if isfield(h,'RootPath') && ischar(h.RootPath)
409        oldfile=h.RootPath;
410    end
411end
412
413%% launch the browser
414fileinput=uigetfile_uvmat('pick a file to append in the input table',oldfile);
415hh=dir(fileinput);
416if numel(hh)>1
417    msgbox_uvmat('ERROR','invalid input, probably a broken link');
418else
419    if ~isempty(fileinput)
420        display_file_name(handles,fileinput,'append')
421    end
422end
423
424%------------------------------------------------------------------------
425% --- fct activated by selecting a previous file under the menu Open
426%------------------------------------------------------------------------
427function MenuFile_Callback(hObject, eventdata, handles)
428
429errormsg=display_file_name(handles,get(hObject,'Label'),'one');
430if ~isempty(errormsg)
431    set(hObject,'Label','')
432    MenuFile=[{get(handles.MenuFile_1,'Label')};{get(handles.MenuFile_2,'Label')};...
433        {get(handles.MenuFile_3,'Label')};{get(handles.MenuFile_4,'Label')};{get(handles.MenuFile_5,'Label')}];
434    str_find=strcmp(get(hObject,'Label'),MenuFile);
435    MenuFile(str_find)=[];% suppress the input file to the list
436    for ifile=1:numel(MenuFile)
437        set(handles.(['MenuFile_' num2str(ifile)]),'Label',MenuFile{ifile});
438    end
439end
440
441%------------------------------------------------------------------------
442% --- fct activated by selecting a previous file under the menu Open/append
443%------------------------------------------------------------------------
444function MenuFile_append_Callback(hObject, eventdata, handles)
445
446InputTable=get(handles.InputTable,'Data');
447if isempty(InputTable{1,1})% no input file in the table
448    display_file_name(handles,get(hObject,'Label'),'one') %refresh the input table, not append
449else
450    display_file_name(handles,get(hObject,'Label'),'append')% append the selected file to the current list of InputTable
451end
452
453%------------------------------------------------------------------------
454% --- fct activated by the browser under 'Open campaign/Browse...'
455%------------------------------------------------------------------------
456function MenuBrowseCampaign_Callback(hObject, eventdata, handles)
457
458%% look for the previously opened file 'oldfile'
459InputTable=get(handles.InputTable,'Data');
460RootPathCell=InputTable(:,1);
461SubDirCell=InputTable(:,2);
462oldfile=fullfile(RootPathCell{1},SubDirCell{1});
463if isempty(oldfile)
464    % use a file name stored in prefdir
465    dir_perso=prefdir;
466    profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
467    if exist(profil_perso,'file')
468        h=load (profil_perso);
469        if isfield(h,'RootPath') && ischar(h.RootPath)
470            oldfile=h.RootPath;
471        end
472    end
473end
474%% launch the browser
475fileinput=uigetfile_uvmat('pick an input file in the series',oldfile);
476hh=dir(fileinput);
477if numel(hh)>1
478    msgbox_uvmat('ERROR','invalid input, probably a broken link');
479else
480    if ~isempty(fileinput)
481        display_file_name(handles,fileinput,'one')
482    end
483end
484append='one';
485set(handles.MenuOpenCampaign,'ForegroundColor',[1 1 0])
486drawnow
487browse_campaign(handles,append);
488
489%------------------------------------------------------------------------
490% --- fct activated by the browser under 'Open campaign/Browse...'
491%------------------------------------------------------------------------
492function MenuBrowseCampaignAppend_Callback(hObject, eventdata, handles)
493append='append';
494browse_campaign(handles,append);
495
496%------------------------------------------------------------------------
497function browse_campaign(handles,append);
498
499%% look for the previously opened file 'oldfile'
500
501%
502%
503% InputTable=get(handles.InputTable,'Data');
504% RootPath=InputTable{1,1};
505% CampaignPath=fileparts(fileparts(RootPath));
506% DirFull=uigetfile_uvmat('define this path as the Campaign folder:',CampaignPath,'uigetdir');
507% if ~ischar(DirFull)|| ~exist(DirFull,'dir')
508%     return
509% end
510OutPut=browse_data(oldfile);% open the GUI browse_data to get select a campaign dir, experiment and device
511if ~isfield(OutPut,'Campaign')
512    return
513end
514DirName=fullfile(OutPut.Campaign,OutPut.Experiment{1},OutPut.DataSeries{1});
515ListStruct=dir(DirName); %list files and the dir DataSeries
516% select the first appropriate file in the dir
517FileName='';
518for ilist=1:numel(ListStruct)
519    if ~isequal(ListStruct(ilist).isdir,1)%look for files, not dir
520        FileName=ListStruct(ilist).name;
521        FileInfo=get_file_info(fullfile(DirName,FileName));
522        switch FileInfo.FileType
523            case {'image','multimage','civx','civdata','netcdf'}
524                break
525        end
526    end
527end
528if isempty(FileName)
529    msgbox_uvmat('ERROR',['no appropriate input file in the DataSeries folder ' fullfile(DirName)])
530    return
531end
532
533%% update the list of campaigns in the menubar
534MenuCampaign=[{get(handles.MenuCampaign_1,'Label')};{get(handles.MenuCampaign_2,'Label')};...
535    {get(handles.MenuCampaign_3,'Label')};{get(handles.MenuCampaign_4,'Label')};{get(handles.MenuCampaign_5,'Label')}];
536check_dir=isempty(find(strcmp(DirName,MenuCampaign)));
537if check_dir %insert the new campaign in the list if it is not found
538    MenuCampaign(end)=[]; %suppress the last item
539    MenuCampaign=[{DirName};MenuCampaign];%insert the new campaign
540    for ilist=1:numel(MenuCampaign)
541        set(handles.(['MenuCampaign_' num2str(ilist)]),'Label',MenuCampaign{ilist})
542    end
543    % save the list for future opening:
544    dir_perso=prefdir;
545    profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
546    if exist(profil_perso,'file')
547        save (profil_perso,'MenuCampaign','-append'); %store the file names for future opening of uvmat
548    else
549        save (profil_perso,'MenuCampaign','-V6'); %store the file names for future opening of uvmat
550    end
551end
552
553%% display the selected field and related information
554if get(handles.CheckAppend,'Value')
555    display_file_name(handles,fullfile(DirName,FileName),'append')
556else
557    display_file_name(handles,fullfile(DirName,FileName),'one')
558end
559set(handles.MenuOpenCampaign,'ForegroundColor',[0 0 0])
560
561% --------------------------------------------------------------------
562function MenuCampaign_Callback(hObject, eventdata, handles)
563% --------------------------------------------------------------------
564set(handles.MenuOpenCampaign,'ForegroundColor',[1 1 0])
565OutPut=browse_data(get(hObject,'Label'));% open the GUI browse_data to get select a campaign dir, experiment and device
566if ~isfield(OutPut,'Campaign')
567    return
568end
569DirName=fullfile(OutPut.Campaign,OutPut.Experiment{1},OutPut.DataSeries{1});
570hdir=dir(DirName); %list files and dirs
571for ilist=1:numel(hdir)
572    if ~isequal(hdir(ilist).isdir,1)%look for files, not dir
573        FileName=hdir(ilist).name;
574        FileInfo=get_file_info(fullfile(DirName,FileName));
575        switch FileInfo.FileType
576            case {'image','multimage','civx','civdata','netcdf'}
577            break
578        end
579    end
580end
581if get(handles.CheckAppend,'Value')
582    display_file_name(handles,fullfile(DirName,FileName),'append')
583else
584    display_file_name(handles,fullfile(DirName,FileName),'one')
585end
586set(handles.MenuOpenCampaign,'ForegroundColor',[0 0 0])
587
588
589% --- Executes when selected cell(s) is changed in InputTable.
590function InputTable_CellSelectionCallback(hObject, eventdata, handles)
591iline=[];
592if ~isempty(eventdata.Indices)
593    iline=eventdata.Indices(1);
594end
595set(handles.InputLine,'String',num2str(iline));
596% set(handles.InputTable,'UserData',iline);
597
598%------------------------------------------------------------------------
599% --- 'key_press_fcn:' function activated when a key is pressed on the keyboard
600%------------------------------------------------------------------------
601function InputTable_KeyPressFcn(hObject, eventdata, handles)
602set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH button to magenta color to indicate that input refresh is needed
603set(handles.OutputSubDir,'BackgroundColor',[1 0 1])% set edit box OutputSubDir to magenta color to indicate that refresh may be needed
604xx=double(get(handles.series,'CurrentCharacter')); %get the keyboard character
605if ~isempty(xx)
606    switch xx
607        case 31 %downward arrow
608            InputTable=get(handles.InputTable,'Data');
609            iline=str2double(get(handles.InputLine,'String'));
610            if isequal(iline,size(InputTable,1))% arrow downward
611                InputTable=[InputTable;InputTable(iline,:)];% create a new line as a copy of the last one
612                set(handles.InputTable,'Data',InputTable);
613            end
614        case 127  %key 'Suppress'
615            ClearLine_Callback(hObject, eventdata, handles)
616    end
617end
618
619%------------------------------------------------------------------------
620% --- Executes on button press in REFRESH.
621function REFRESH_Callback(hObject, eventdata, handles)
622%------------------------------------------------------------------------
623InputTable=get(handles.InputTable,'Data');
624set(handles.series,'Pointer','watch') % set the mouse pointer to 'watch'
625set(handles.REFRESH,'BackgroundColor',[1 1 0])% set REFRESH  button to yellow color (indicate activation)
626drawnow
627empty_line=false(size(InputTable,1),1);
628for iline=1:size(InputTable,1)
629    empty_line(iline)= isempty(cell2mat(InputTable(iline,1:3)));
630end
631if ~isempty(find(empty_line));
632    InputTable(empty_line,:)=[];%remove empty lines
633    set(handles.InputTable,'Data',InputTable)
634    ListTable={'MinIndex_i','MaxIndex_i','MinIndex_j','MaxIndex_j','PairString','TimeTable'};
635    for ilist=1:numel(ListTable)
636        Table=get(handles.(ListTable{ilist}),'Data');
637        Table(empty_line,:)=[];%remove empty lines
638        set(handles.(ListTable{ilist}),'Data',Table);
639    end
640    set(handles.series,'UserData',[])%refresh the stored info
641end
642nbview=size(InputTable,1);
643for iview=1:nbview
644    RootPath=fullfile(InputTable{iview,1},InputTable{iview,2});
645    if ~exist(RootPath,'dir')
646        i1_series=[];
647        RootFile='';
648    else %scan the input folder
649        [RootPath,SubDir,RootFile,i1_series,i2_series,j1_series,j2_series,tild,FileInfo,MovieObject]=...
650            find_file_series(fullfile(InputTable{iview,1},InputTable{iview,2}),[InputTable{iview,3} InputTable{iview,4} InputTable{iview,5}]);
651    end
652    % if no file is found, open a browser
653    if isempty(RootFile)&& isempty(i1_series)
654        fileinput=uigetfile_uvmat(['wrong input at line ' num2str(iview) ':pick a new input file'],RootPath);
655        if isempty(fileinput)
656            set(handles.REFRESH,'BackgroundColor',[1 0 0])% set REFRESH  back to red color
657            return
658        else
659            display_file_name(handles,fileinput,iview)
660        end
661    else
662       update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileInfo,MovieObject,iview)
663    end
664end
665
666%% update MinIndex_i and MaxIndex_i if the input table content has been reduced in line nbre
667MinIndex_i_table=get(handles.MinIndex_i,'Data');%retrieve the min indices in the table MinIndex
668set(handles.MinIndex_i,'Data',MinIndex_i_table(1:nbview,:));
669MinIndex_j_table=get(handles.MinIndex_j,'Data');%retrieve the min indices in the table MinIndex
670set(handles.MinIndex_j,'Data',MinIndex_j_table(1:nbview,:));
671MaxIndex_i_table=get(handles.MaxIndex_i,'Data');%retrieve the min indices in the table MinIndex
672set(handles.MaxIndex_i,'Data',MaxIndex_i_table(1:nbview,:));
673MaxIndex_j_table=get(handles.MaxIndex_j,'Data');%retrieve the min indices in the table MinIndex
674set(handles.MaxIndex_j,'Data',MaxIndex_j_table(1:nbview,:));
675PairString=get(handles.PairString,'Data');%retrieve the min indices in the table MinIndex
676set(handles.PairString,'Data',PairString(1:nbview,:));
677TimeTable=get(handles.TimeTable,'Data');%retrieve the min indices in the table MinIndex
678set(handles.TimeTable,'Data',TimeTable(1:nbview,:));
679
680%% enable field and veltype menus, in accordance with the current action
681ActionName_Callback([],[], handles)
682
683%% set length of waitbar
684displ_time(handles)
685
686set(handles.REFRESH,'BackgroundColor',[1 0 0])% set REFRESH  button to red color (indicate activation finished)
687set(handles.series,'Pointer','arrow') % set the mouse pointer to 'watch'
688
689%------------------------------------------------------------------------
690% --- Function called when a new file is opened, either by series_OpeningFcn or by the browser
691%------------------------------------------------------------------------
692% INPUT:
693% handles: handles of elements in the GUI
694% Param: structure of input parameters, including  input file name and path
695% iview: line index in the input table
696%       or 'one': refresh the list
697%         'append': add a new line to the input table
698function errormsg=display_file_name(handles,Param,iview)
699 
700set(handles.REFRESH,'BackgroundColor',[1 1 0])% set REFRESH  button to yellow color (indicate activation)
701drawnow
702errormsg='';%default
703if ischar(Param)
704    fileinput=Param;
705else% input set when series is opened (called by the GUI uvmat)
706    fileinput=Param.FileName;
707end
708   
709%% get the input root name, indices, file extension and nomenclature NomType
710if ~exist(fileinput,'file')
711    errormsg=['input file ' fileinput  ' does not exist'];
712    msgbox_uvmat('ERROR',errormsg)
713    set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH  button to magenta color (refresh still needed)
714    return
715end
716
717%% detect root name, nomenclature and indices in the input file name:
718[FilePath,FileName,FileExt]=fileparts(fileinput);
719%%%%%%%%%%%%%%%%%%
720%TODO: case of input by uvmat: do not check agai the input seies %%%%%%%
721%%%%%%%%%%%%%%%%%%%
722% detect the file type, get the movie object if relevant, and look for the corresponding file series:
723% the root name and indices may be corrected by including the first index i1 if a corresponding xml file exists
724[RootPath,SubDir,RootFile,i1_series,i2_series,j1_series,j2_series,NomType,FileInfo,MovieObject,i1,i2,j1,j2]=find_file_series(FilePath,[FileName FileExt]);
725FileType=FileInfo.FileType;
726if isempty(RootFile)&&isempty(i1_series)
727    errormsg='no input file in the series';
728    msgbox_uvmat('ERROR',errormsg)
729    set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH  button to magenta color (end of activation)
730    return
731end
732if strcmp(FileType,'txt')
733    edit(fileinput)
734    set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH  button to  magenta color (end of activation)
735    return
736elseif strcmp(FileType,'xml')
737    editxml(fileinput)
738    set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH  button to magenta  color (end of activation)
739     return
740elseif strcmp(FileType,'figure')
741    open(fileinput)
742    set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH  button to magenta  color (end of activation)
743     return
744end
745
746%% enable other menus and uicontrols
747set(handles.MenuOpenCampaign,'Enable','on')
748set(handles.MenuCampaign_1,'Enable','on')
749set(handles.MenuCampaign_2,'Enable','on')
750set(handles.MenuCampaign_3,'Enable','on')
751set(handles.MenuCampaign_4,'Enable','on')
752set(handles.MenuCampaign_5,'Enable','on')
753set(handles.RUN, 'Enable','On')
754set(handles.RUN,'BackgroundColor',[1 0 0])% set RUN button to red
755set(handles.InputTable,'BackgroundColor',[1 1 0]) % set RootPath edit box  to yellow
756drawnow
757
758
759%% fill the list of file series
760InputTable=get(handles.InputTable,'Data');
761SeriesData=get(handles.series,'UserData');
762if strcmp(iview,'append') % display the input data as a new line in the table
763    iview=size(InputTable,1)+1;% the next line in InputTable becomes the current line
764%     InputTable(iview,:)=[{RootPath},{SubDir},{RootFile},{NomType},{FileExt}];
765elseif strcmp(iview,'one') % refresh the list of  input  file series
766    iview=1; %the first line in InputTable becomes the current line
767    InputTable={'','','','',''};
768%     InputTable(iview,:)=[{RootPath},{SubDir},{RootFile},{NomType},{FileExt}];
769    set(handles.TimeTable,'Data',[{''},{[]},{[]},{[]},{[]}])
770    set(handles.MinIndex_i,'Data',[])
771    set(handles.MaxIndex_i,'Data',[])
772    set(handles.MinIndex_j,'Data',[])
773    set(handles.MaxIndex_j,'Data',[])
774    set(handles.PairString,'Data',{''})
775    SeriesData.CheckPair=0;%reset the list of input lines with pairs
776    SeriesData.i1_series={};
777    SeriesData.i2_series={};
778    SeriesData.j1_series={};
779    SeriesData.j2_series={};
780    SeriesData.FileType={};
781    SeriesData.FileInfo={};
782    SeriesData.Time={};
783end
784if isfield(SeriesData,'i1_series')
785    SeriesData.i1_series(iview+1:end)=[];
786    SeriesData.i2_series(iview+1:end)=[];
787    SeriesData.j1_series(iview+1:end)=[];
788    SeriesData.j2_series(iview+1:end)=[];
789    SeriesData.FileType(iview+1:end)=[];
790    SeriesData.FileInfo(iview+1:end)=[];
791    SeriesData.Time(iview+1:end)=[];
792end
793InputTable(iview,:)=[{RootPath},{SubDir},{RootFile},{NomType},{FileExt}];
794if iview >1
795    set(handles.InputLine,'String',num2str(iview))
796end
797set(handles.InputTable,'Data',InputTable)
798
799%% determine the selected reference field indices for pair display
800if isempty(i1)
801    i1=1;
802end
803if isempty(i2)
804    i2=i1;
805end
806ref_i=floor((i1+i2)/2);% reference image number corresponding to the file
807% set(handles.num_ref_i,'String',num2str(ref_i));
808if isempty(j1)
809    j1=1;
810end
811if isempty(j2)
812    j2=j1;
813end
814ref_j=floor((j1+j2)/2);% reference image number corresponding to the file
815SeriesData.ref_i=ref_i;
816SeriesData.ref_j=ref_j;
817
818%% update first and last indices if they do not exist
819Param=read_GUI(handles.series);
820first_j=[];
821if isfield(Param.IndexRange,'first_j'); first_j=Param.IndexRange.first_j; end
822last_j=[];
823if isfield(Param.IndexRange,'last_j'); last_j=Param.IndexRange.last_j; end
824PairString='';
825if isfield(Param.IndexRange,'PairString'); PairString=Param.IndexRange.PairString; end
826[i1,i2,j1,j2] = get_file_index(Param.IndexRange.first_i,first_j,PairString);
827FirstFileName=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},...
828    Param.InputTable{1,5},Param.InputTable{1,4},i1,i2,j1,j2);
829if ~exist(FirstFileName,'file')
830    set(handles.num_first_i,'String',num2str(ref_i))
831    set(handles.num_first_j,'String',num2str(ref_j))
832end
833[i1,i2,j1,j2] = get_file_index(Param.IndexRange.last_i,last_j,PairString);
834LastFileName=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},...
835    Param.InputTable{1,5},Param.InputTable{1,4},i1,i2,j1,j2);
836if ~exist(LastFileName,'file')
837    set(handles.num_last_i,'String',num2str(ref_i))
838    set(handles.num_last_j,'String',num2str(ref_j))
839end
840
841%% update the list of recent files in the menubar and save it for future opening
842MenuFile=[{get(handles.MenuFile_1,'Label')};{get(handles.MenuFile_2,'Label')};...
843    {get(handles.MenuFile_3,'Label')};{get(handles.MenuFile_4,'Label')};{get(handles.MenuFile_5,'Label')}];
844str_find=strcmp(fileinput,MenuFile);
845if isempty(find(str_find,1))
846    MenuFile=[{fileinput};MenuFile];%insert the current file if not already in the list
847end
848for ifile=1:min(length(MenuFile),5)
849    eval(['set(handles.MenuFile_' num2str(ifile) ',''Label'',MenuFile{ifile});'])
850end
851dir_perso=prefdir;
852profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
853if exist(profil_perso,'file')
854    save (profil_perso,'MenuFile','-append'); %store the file names for future opening of uvmat
855else
856    save (profil_perso,'MenuFile','-V6'); %store the file names for future opening of uvmat
857end
858% save the opened file to initiate future opening
859SeriesData.RefFile{iview}=fileinput;% reference opening file for line iview
860SeriesData.Ref_i1=i1;
861SeriesData.Ref_i2=i2;
862SeriesData.Ref_j1=j1;
863SeriesData.Ref_j2=j2;
864set(handles.series,'UserData',SeriesData)
865
866set(handles.InputTable,'BackgroundColor',[1 1 1])
867
868%% initiate input file series and refresh the current field view:     
869update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileInfo,MovieObject,iview);
870%% enable field and veltype menus, in accordance with the current action
871ActionName_Callback([],[], handles)
872
873%% set length of waitbar
874displ_time(handles)
875
876set(handles.REFRESH,'BackgroundColor',[1 0 0])% set REFRESH  button to red color (end of activation)
877
878%------------------------------------------------------------------------
879% --- Update information about a new field series (indices to scan, timing,
880%     calibration from an xml file
881function update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileInfo,VideoObject,iview)
882%------------------------------------------------------------------------
883InputTable=get(handles.InputTable,'Data');
884
885%% display the min and max indices for the whole file series
886if size(i1_series,2)==2 && min(min(i1_series(:,1,:)))==0
887    MinIndex_j=1;% index j set to 1 by default
888    MaxIndex_j=1;
889    MinIndex_i=find(i1_series(1,2,:), 1 )-1;% min ref index i detected in the series (corresponding to the first non-zero value of i1_series, except for zero index)
890    MaxIndex_i=find(i1_series(1,2,:),1,'last' )-1;%max ref index i detected in the series (corresponding to the last non-zero value of i1_series)
891else
892    ref_i=squeeze(max(i1_series(1,:,:),[],2));% select ref_j index for each ref_i
893    ref_j=squeeze(max(j1_series(1,:,:),[],3));% select ref_i index for each ref_j
894     MinIndex_i=min(find(ref_i))-1;
895     MaxIndex_i=max(find(ref_i))-1;
896     MaxIndex_j=max(find(ref_j))-1;
897     MinIndex_j=min(find(ref_j))-1;
898    diff_j_max=diff(ref_j);
899    diff_i_max=diff(ref_i);
900    if ~isempty(diff_i_max) && isequal (diff_i_max,diff_i_max(1)*ones(size(diff_i_max)))
901        set(handles.num_incr_i,'String',num2str(diff_i_max(1)))% detect an increment to dispaly by default
902    end
903    if ~isempty(diff_j_max) && isequal (diff_j_max,diff_j_max(1)*ones(size(diff_j_max)))
904        set(handles.num_incr_j,'String',num2str(diff_j_max(1)))
905    end
906end
907if isequal(MinIndex_i,-1)
908    MinIndex_i=0;
909end
910if isequal(MinIndex_j,-1)
911    MinIndex_j=0;
912end
913MinIndex_i_table=get(handles.MinIndex_i,'Data');%retrieve the min indices in the table MinIndex
914MinIndex_j_table=get(handles.MinIndex_j,'Data');%retrieve the min indices in the table MinIndex
915MaxIndex_i_table=get(handles.MaxIndex_i,'Data');%retrieve the min indices in the table MinIndex
916MaxIndex_j_table=get(handles.MaxIndex_j,'Data');%retrieve the min indices in the table MinIndex
917if ~isempty(MinIndex_i)&&~isempty(MaxIndex_i)
918    MinIndex_i_table(iview,1)=MinIndex_i;
919    MaxIndex_i_table(iview,1)=MaxIndex_i;
920end
921if ~isempty(MinIndex_j)&&~isempty(MaxIndex_j)
922    MinIndex_j_table(iview,1)=MinIndex_j;
923    MaxIndex_j_table(iview,1)=MaxIndex_j;
924end
925set(handles.MinIndex_i,'Data',MinIndex_i_table)%display the min indices in the table MinIndex
926set(handles.MinIndex_j,'Data',MinIndex_j_table)%display the max indices in the table MaxIndex
927set(handles.MaxIndex_i,'Data',MaxIndex_i_table)%display the min indices in the table MinIndex
928set(handles.MaxIndex_j,'Data',MaxIndex_j_table)%display the max indices in the table MaxIndex
929SeriesData=get(handles.series,'UserData');
930
931%% adjust the first and last indices for the selected series, only if requested by the bounds
932% i index, compare input to min index i
933first_i=str2num(get(handles.num_first_i,'String'));%retrieve previous first i
934% ref_i=str2num(get(handles.num_ref_i,'String'));%index i given by the input field
935ref_i=1;
936if isfield(SeriesData,'ref_i')
937ref_i=SeriesData.ref_i;
938end
939if isempty(first_i)
940    first_i=ref_i;% first_i updated by the input value
941elseif first_i < MinIndex_i
942    first_i=MinIndex_i; % first_i set to the min i index (restricted by oter input lines)
943elseif first_i >MaxIndex_i
944    first_i=MaxIndex_i;% first_i set to the max i index (restricted by oter input lines)
945end
946% j index,  compare input to min index j
947first_j=str2num(get(handles.num_first_j,'String'));
948ref_j=1;
949if isfield(SeriesData,'ref_j')
950ref_j=SeriesData.ref_j;
951end
952if isempty(first_j)
953    first_j=ref_j;% first_j updated by the input value
954elseif first_j<MinIndex_j
955    first_j=MinIndex_j; % first_j set to the min j index (restricted by oter input lines)
956elseif first_j >MaxIndex_j
957    first_j=MaxIndex_j; % first_j set to the max j index (restricted by oter input lines)
958end
959% i index, compare input to max index i
960last_i=str2num(get(handles.num_last_i,'String'));
961if isempty(last_i)
962    last_i=ref_i;
963elseif last_i > MaxIndex_i
964    last_i=MaxIndex_i;
965elseif last_i<first_i
966    last_i=first_i;
967end
968% j index, compare input to max index j
969last_j=str2num(get(handles.num_last_j,'String'));
970if isempty(last_j)
971    last_j=ref_j;
972elseif last_j>MaxIndex_j
973    last_j=MaxIndex_j;
974elseif last_j<first_j
975    last_j=first_j;
976end
977set(handles.num_first_i,'String',num2str(first_i));
978set(handles.num_first_j,'String',num2str(first_j));
979set(handles.num_last_i,'String',num2str(last_i));
980set(handles.num_last_j,'String',num2str(last_j));
981
982%% number of slices set by default
983NbSlice=1;%default
984% read  value set by the first series for the append mode (iwiew >1)
985if iview>1 && strcmp(get(handles.num_NbSlice,'Visible'),'on')
986    NbSlice=str2num(get(handles.num_NbSlice,'String'));
987end
988
989%% default time settings
990TimeUnit='';
991% read  value set by the first series for the append mode (iwiew >1)
992if iview>1
993    TimeUnit=get(handles.TimeUnit,'String');
994end
995TimeName='';
996Time=[];%default
997TimeMin=[];
998TimeFirst=[];
999TimeLast=[];
1000TimeMax=[];
1001
1002%%  read image documentation file if found
1003XmlData=[];
1004check_calib=0;
1005XmlFileName=find_imadoc(InputTable{iview,1},InputTable{iview,2},InputTable{iview,3},InputTable{iview,5});
1006if ~isempty(XmlFileName)
1007    [XmlData,errormsg]=imadoc2struct(XmlFileName);
1008    if ~isempty(errormsg)
1009         msgbox_uvmat('WARNING',['error in reading ' XmlFileName ': ' errormsg]);
1010    end
1011    % read time if available
1012    if isfield(XmlData,'Time')
1013         Time=XmlData.Time;
1014        TimeName='xml';
1015    end
1016    if isfield(XmlData,'Camera')
1017        if isfield(XmlData.Camera,'NbSlice')&& ~isempty(XmlData.Camera.NbSlice)
1018            if iview>1 && ~isempty(NbSlice) && ~strcmp(NbSlice,XmlData.Camera.NbSlice)
1019                msgbox_uvmat('WARNING','inconsistent number of slices with the first field series');
1020            end
1021            NbSlice=XmlData.Camera.NbSlice;% Nbre of slices from camera
1022        end
1023        if isfield(XmlData.Camera,'TimeUnit')&& ~isempty(XmlData.Camera.TimeUnit)
1024            if iview>1 && ~isempty(TimeUnit) && ~strcmp(TimeUnit,XmlData.Camera.TimeUnit)
1025                msgbox_uvmat('WARNING','inconsistent time unit with the first field series');
1026            end
1027            TimeUnit=XmlData.Camera.TimeUnit;
1028        end
1029    end
1030    % number of slices
1031    if isfield(XmlData,'GeometryCalib')
1032        check_calib=1;
1033        if isfield(XmlData.GeometryCalib,'SliceCoord')
1034            siz=size(XmlData.GeometryCalib.SliceCoord);
1035            if siz(1)>1
1036                if iview>1 && ~isempty(NbSlice) && ~strcmp(NbSlice,siz(1))
1037                    msgbox_uvmat('WARNING','inconsistent number of Z indices with the first field series');
1038                end
1039                NbSlice=siz(1);
1040            end
1041        end
1042    end
1043    set(handles.num_NbSlice,'String',num2str(NbSlice))
1044end
1045
1046%% read timing  from the current file (prioritary)
1047if ~isempty(VideoObject)% case of movies
1048    imainfo=get(VideoObject);
1049    if isempty(j1_series); %frame index along i
1050        Time=zeros(imainfo.NumberOfFrames+1,2);
1051        Time(:,2)=(0:1/imainfo.FrameRate:(imainfo.NumberOfFrames)/imainfo.FrameRate)';
1052    else
1053        Time=[0;ones(size(i1_series,3)-1,1)]*(0:1/imainfo.FrameRate:(imainfo.NumberOfFrames)/imainfo.FrameRate);
1054    end
1055    TimeName='video';
1056end
1057
1058
1059%% determine the min and max times: case of Netcdf files will be treated later in FieldName_Callback
1060if ~isempty(TimeName)
1061    TimeMin=Time(MinIndex_i+1,MinIndex_j+1);
1062    if size(Time)>=[first_i+1 first_j+1]
1063        TimeFirst=Time(first_i+1,first_j+1);
1064    end
1065    if size(Time)>=[last_i+1 last_j+1]
1066        TimeLast=Time(last_i+1,last_j+1);
1067    end
1068    if size(Time)>=[MaxIndex_i+1 MaxIndex_j+1];
1069        TimeMax=Time(MaxIndex_i+1,MaxIndex_j+1);
1070    end
1071end
1072
1073%% update the time table
1074TimeTable=get(handles.TimeTable,'Data');
1075TimeTable{iview,1}=TimeName;
1076TimeTable{iview,2}=TimeMin;
1077TimeTable{iview,3}=TimeFirst;
1078TimeTable{iview,4}=TimeLast;
1079TimeTable{iview,5}=TimeMax;
1080set(handles.TimeTable,'Data',TimeTable)
1081
1082%% update the series info in 'UserData'
1083SeriesData.i1_series{iview}=i1_series;
1084SeriesData.i2_series{iview}=i2_series;
1085SeriesData.j1_series{iview}=j1_series;
1086SeriesData.j2_series{iview}=j2_series;
1087SeriesData.FileType{iview}=FileInfo.FileType;
1088SeriesData.FileInfo{iview}=FileInfo;
1089SeriesData.Time{iview}=Time;
1090% if ~isempty(TimeName)
1091%     SeriesData.TimeSource=TimeSource;
1092% end
1093if check_calib
1094    SeriesData.GeometryCalib{iview}=XmlData.GeometryCalib;
1095end
1096set(handles.series,'UserData',SeriesData)
1097
1098%% update pair menus
1099hset_pair=findobj(allchild(0),'Tag','set_pairs');
1100if ~isempty(hset_pair), delete(hset_pair); end % delete the GUI set_pair if opened
1101CheckPair= ~isempty(i2_series)||~isempty(j2_series); % check whether index pairs need to be defined
1102PairString=get(handles.PairString,'Data');
1103if CheckPair% if pairs need to be display for line iview
1104    [ModeMenu,ModeValue]=update_mode(i1_series,i2_series,j2_series);
1105    Menu=update_listpair(i1_series,i2_series,j1_series,j2_series,ModeMenu{ModeValue},Time,TimeUnit,ref_i,ref_j,TimeName,InputTable(iview,:),FileInfo);
1106    PairString{iview,1}=Menu{1};
1107else
1108    PairString{iview,1}='';%no pair for #iview
1109end
1110set(handles.PairString,'Data',PairString)
1111if isempty(find(cellfun('isempty',get(handles.PairString,'Data'))==0, 1))% if all lines of pairs are empty
1112    set(handles.PairString,'Visible','off')
1113    set(handles.SetPairs,'Visible','off')
1114else
1115    set(handles.PairString,'Visible','on')
1116    set(handles.SetPairs,'Visible','on')
1117end
1118
1119
1120%% display the set of existing files as an image
1121set(handles.FileStatus,'Units','pixels')
1122Position=get(handles.FileStatus,'Position');
1123set(handles.FileStatus,'Units','normalized')
1124%xI=0.5:Position(3)-0.5;
1125nbview=numel(SeriesData.i1_series);
1126j_max=cell(1,nbview);
1127MaxIndex_i=ones(1,nbview);%default
1128MinIndex_i=ones(1,nbview);%default
1129for iline=1:nbview
1130    pair_max=squeeze(max(SeriesData.i1_series{iline},[],1)); %max on pair index
1131    j_max{iline}=max(pair_max,[],1);%max on j index
1132    if ~isempty(j_max{iline})
1133    MaxIndex_i(iline)=max(find(j_max{iline}))-1;% max ref index i
1134    MinIndex_i(iline)=min(find(j_max{iline}))-1;% min ref index i
1135    end
1136end
1137MinIndex_i=min(MinIndex_i);
1138MaxIndex_i=max(MaxIndex_i);
1139range_index=MaxIndex_i-MinIndex_i+1;
1140range_y=max(1,floor(Position(4)/nbview));
1141npx=floor(Position(3));
1142file_indices=MinIndex_i+floor(((0.5:npx-0.5)/npx)*range_index)+1;
1143CData=zeros(nbview*range_y,npx);% initiate the image representing the existing files
1144for iline=1:nbview
1145    ind_y=1+(iline-1)*range_y:iline*range_y;
1146    LineData=zeros(size(file_indices));
1147    file_select=file_indices(file_indices<=numel(j_max{iline}));
1148    ind_select=find(file_indices<=numel(j_max{iline}));
1149    LineData(ind_select)=j_max{iline}(file_select)~=0;
1150    CData(ind_y,:)=ones(size(ind_y'))*LineData;
1151end
1152CData=cat(3,zeros(size(CData)),CData,zeros(size(CData)));%make color images r=0,g,b=0
1153set(handles.FileStatus,'CData',CData);
1154
1155%-----------------------------------------------------------guide -------------
1156%------------------------------------------------------------------------
1157%  III - FUNCTIONS ASSOCIATED TO THE FRAME IndexRange
1158%------------------------------------------------------------------------
1159
1160
1161% ---- determine the menu to put in mode and advice a default choice
1162%------------------------------------------------------------------------
1163function [ModeMenu,ModeValue]=update_mode(i1_series,i2_series,j2_series)
1164%------------------------------------------------------------------------   
1165ModeMenu={''};
1166if isempty(j2_series)% no j pair
1167    ModeValue=1;
1168    if ~isempty(i2_series)
1169        ModeMenu={'series(Di)'}; % pair menu with only option Di
1170    end
1171else %existence of j pairs
1172    pair_max=squeeze(max(i1_series,[],1)); %max on pair index
1173    j_max=max(pair_max,[],1);
1174    MaxIndex_i=find(j_max, 1, 'last' )-1;% max ref index i
1175    MinIndex_i=find(j_max, 1 )-1;% min ref index i
1176    i_max=max(pair_max,[],2);
1177    MaxIndex_j=find(i_max, 1, 'last' )-1;% max ref index i
1178    MinIndex_j=find(i_max, 1 )-1;% min ref index i
1179    if MaxIndex_j==MinIndex_j
1180        ModeValue=1;
1181        ModeMenu={'bursts'};
1182    elseif MaxIndex_i==MinIndex_i
1183        ModeValue=1;
1184        ModeMenu={'series(Dj)'};
1185    else
1186        ModeMenu={'bursts';'series(Dj)'};
1187        if (MaxIndex_j-MinIndex_j)>10
1188            ModeValue=2;%set mode to series(Dj) if more than 10 j values
1189        else
1190            ModeValue=1;
1191        end
1192    end
1193end
1194
1195
1196%------------------------------------------------------------------------
1197function displ_pair=update_listpair(i1_series,i2_series,j1_series,j2_series,mode,time,TimeUnit,ref_i,ref_j,TimeName,InputTable,FileInfo)
1198%------------------------------------------------------------------------
1199displ_pair={};
1200if isempty(TimeUnit)
1201    dtunit='e-03';
1202else
1203    dtunit=['m' TimeUnit];
1204end
1205switch mode
1206    case 'series(Di)'
1207        diff_i=i2_series-i1_series;
1208        min_diff=min(diff_i(diff_i>0));
1209        max_diff=max(diff_i(diff_i>0));
1210        for ipair=min_diff:max_diff
1211            if numel(diff_i(diff_i==ipair))>0
1212                pair_string=['Di= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2)) ];
1213                if ~isempty(time)
1214                    if ref_i<=floor(ipair/2)
1215                        ref_i=floor(ipair/2)+1;% shift ref_i to get the first pair
1216                    end
1217                    Dt=time(ref_i+ceil(ipair/2),ref_j)-time(ref_i-floor(ipair/2),ref_j);
1218                    pair_string=[pair_string ', Dt=' num2str(Dt) ' ' dtunit];
1219                end
1220                displ_pair=[displ_pair;{pair_string}];
1221            end
1222        end
1223        if ~isempty(displ_pair)
1224            displ_pair=[displ_pair;{'Di=*|*'}];
1225        end
1226    case 'series(Dj)'
1227        if isempty(j2_series)
1228            msgbox_uvmat('ERROR','no j1-j2 pair available')
1229            return
1230        end
1231        diff_j=j2_series-j1_series;
1232        min_diff=min(diff_j(diff_j>0));
1233        max_diff=max(diff_j(diff_j>0));
1234        for ipair=min_diff:max_diff
1235            if numel(diff_j(diff_j==ipair))>0
1236                pair_string=['Dj= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2)) ];
1237                if ~isempty(time)
1238                    if ref_j<=floor(ipair/2)
1239                        ref_j=floor(ipair/2)+1;% shift ref_i to get the first pair
1240                    end
1241                    Dt=time(ref_i,ref_j+ceil(ipair/2))-time(ref_i,ref_j-floor(ipair/2));
1242                    pair_string=[pair_string ', Dt=' num2str(Dt) ' ' dtunit];
1243                end
1244                displ_pair=[displ_pair;{pair_string}];
1245            end
1246        end
1247        if ~isempty(displ_pair)
1248            displ_pair=[displ_pair;{'Dj=*|*'}];
1249        end
1250    case 'bursts'
1251        if isempty(j2_series)
1252            msgbox_uvmat('ERROR','no j1-j2 pair available')
1253            return
1254        end
1255        %diff_j=j2_series-j1_series;
1256        min_j1=min(j1_series(j1_series>0));
1257        max_j1=max(j1_series(j1_series>0));
1258        min_j2=min(j2_series(j2_series>0));
1259        max_j2=max(j2_series(j2_series>0));
1260        for pair1=min_j1:min(max_j1,min_j1+20)
1261            for pair2=min_j2:min(max_j2,min_j2+20)
1262                if numel(j1_series(j1_series==pair1))>0 && numel(j2_series(j2_series==pair2))>0
1263                    pair_string=['j= ' num2str(pair1) '-' num2str(pair2)];
1264                    [TimeValue,DtValue]=get_time(ref_i,[],pair_string,InputTable,FileInfo,TimeName,'Dt');
1265                    %Dt=time(ref_i,pair2+1)-time(ref_i,pair1+1);
1266                    pair_string=[pair_string ', Dt=' num2str(DtValue) ' ' dtunit];
1267                    displ_pair=[displ_pair;{pair_string}];
1268                end
1269            end
1270        end
1271        if ~isempty(displ_pair)
1272            displ_pair=[displ_pair;{'j=*-*'}];
1273        end
1274end
1275
1276%------------------------------------------------------------------------
1277function num_first_i_Callback(hObject, eventdata, handles)
1278%------------------------------------------------------------------------
1279num_last_i_Callback(hObject, eventdata, handles)
1280
1281%------------------------------------------------------------------------
1282function num_last_i_Callback(hObject, eventdata, handles)
1283%------------------------------------------------------------------------
1284SeriesData=get(handles.series,'UserData');
1285if ~isfield(SeriesData,'Time')
1286    SeriesData.Time{1}=[];
1287end
1288displ_time(handles);
1289
1290%------------------------------------------------------------------------
1291function num_first_j_Callback(hObject, eventdata, handles)
1292%------------------------------------------------------------------------
1293 num_last_j_Callback(hObject, eventdata, handles)
1294
1295%------------------------------------------------------------------------
1296function num_last_j_Callback(hObject, eventdata, handles)
1297%------------------------------------------------------------------------
1298% first_j=str2num(get(handles.num_first_j,'String'));
1299% last_j=str2num(get(handles.num_last_j,'String'));
1300% ref_j=ceil((first_j+last_j)/2);
1301% set(handles.num_ref_j,'String', num2str(ref_j))
1302% num_ref_j_Callback(hObject, eventdata, handles)
1303SeriesData=get(handles.series,'UserData');
1304if ~isfield(SeriesData,'Time')
1305    SeriesData.Time{1}=[];
1306end
1307displ_time(handles);
1308
1309%------------------------------------------------------------------------
1310% ---- find the times corresponding to the first and last indices of a series
1311function displ_time(handles)
1312%------------------------------------------------------------------------
1313SeriesData=get(handles.series,'UserData');%
1314if ~isfield(SeriesData,'Time')
1315    return
1316end
1317PairString=get(handles.PairString,'Data');
1318ref_i_1=str2num(get(handles.num_first_i,'String'));%first reference index
1319ref_i_2=str2num(get(handles.num_last_i,'String'));%last reference index
1320ref_j_1=[];ref_j_2=[];
1321if strcmp(get(handles.num_first_j,'Visible'),'on')
1322ref_j_1=str2num(get(handles.num_first_j,'String'));
1323ref_j_2=str2num(get(handles.num_last_j,'String'));
1324end
1325[i1_1,i2_1,j1_1,j2_1] = get_file_index(ref_i_1,ref_j_1,PairString);
1326[i1_2,i2_2,j1_2,j2_2] = get_file_index(ref_i_2,ref_j_2,PairString);
1327TimeTable=get(handles.TimeTable,'Data');
1328%%%%%%
1329%TODO: read time in netcdf file, see ActionName_Callback
1330%%%%%%%
1331%Pairs=get(handles.PairString,'Data');
1332for iview=1:size(TimeTable,1)
1333    if size(SeriesData.Time,1)<iview
1334        break
1335    end
1336    TimeTable{iview,3}=[];
1337    TimeTable{iview,4}=[];
1338    if size(SeriesData.Time{iview},1)>=i2_2+1 && (isempty(ref_j_1)||size(SeriesData.Time{iview},2)>=j2_2+1)
1339        if isempty(ref_j_1)
1340            time_first=(SeriesData.Time{iview}(i1_1+1,2)+SeriesData.Time{iview}(i2_1+1,2))/2;
1341            time_last=(SeriesData.Time{iview}(i1_2+1,2)+SeriesData.Time{iview}(i2_2+1,2))/2;
1342        else
1343            time_first=(SeriesData.Time{iview}(i1_1+1,j1_1+1)+SeriesData.Time{iview}(i2_1+1,j2_1+1))/2;
1344            time_last=(SeriesData.Time{iview}(i1_2+1,j1_2+1)+SeriesData.Time{iview}(i2_2+1,j2_1+1))/2;
1345        end
1346        TimeTable{iview,3}=time_first; %TODO: take into account pairs
1347        TimeTable{iview,4}=time_last; %TODO: take into account pairs
1348    end
1349end
1350set(handles.TimeTable,'Data',TimeTable)
1351
1352%% set the waitbar position with respect to the min and max in the series
1353MinIndex_i=min(get(handles.MinIndex_i,'Data'));
1354MaxIndex_i=max(get(handles.MaxIndex_i,'Data'));
1355pos_first=(ref_i_1-MinIndex_i)/(MaxIndex_i-MinIndex_i+1);
1356pos_last=(ref_i_2-MinIndex_i+1)/(MaxIndex_i-MinIndex_i+1);
1357if isempty(pos_first), pos_first=0; end
1358if isempty(pos_last), pos_last=1; end
1359Position=get(handles.Waitbar,'Position');% position of the waitbar:= [ x,y, width, height]
1360Position_status=get(handles.FileStatus,'Position');
1361Position(1)=Position_status(1)+Position_status(3)*pos_first;
1362Position(3)=max(Position_status(3)*(pos_last-pos_first),0.001);% width must remain positive
1363set(handles.Waitbar,'Position',Position)
1364update_waitbar(handles.Waitbar,0)
1365
1366%------------------------------------------------------------------------
1367% --- Executes when selected cell(s) is changed in PairString.
1368function PairString_CellSelectionCallback(hObject, eventdata, handles)
1369%------------------------------------------------------------------------   
1370if numel(eventdata.Indices)>=1
1371    PairString=get(hObject,'Data');
1372    if ~isempty(PairString{eventdata.Indices(1)})
1373        SetPairs_Callback(hObject, eventdata.Indices(1), handles)
1374    end
1375end
1376
1377%-------------------------------------
1378function enable_i(handles,state)
1379set(handles.i_txt,'Visible',state)
1380set(handles.num_first_i,'Visible',state)
1381set(handles.num_last_i,'Visible',state)
1382set(handles.num_incr_i,'Visible',state)
1383
1384%-----------------------------------
1385function enable_j(handles,state)
1386set(handles.j_txt,'Visible',state)
1387set(handles.num_first_j,'Visible',state)
1388set(handles.num_last_j,'Visible',state)
1389set(handles.num_incr_j,'Visible',state)
1390set(handles.MinIndex_j,'Visible',state)
1391set(handles.MaxIndex_j,'Visible',state)
1392
1393
1394%%%%%%%%%%%%%%%%%%%%
1395%%  MAIN ActionName FUNCTIONS
1396%%%%%%%%%%%%%%%%%%%%
1397%------------------------------------------------------------------------
1398% --- Executes on button press in RUN.
1399%------------------------------------------------------------------------
1400function RUN_Callback(hObject, eventdata, handles)
1401
1402%% settings of the button RUN
1403set(handles.RUN,'BusyAction','queue');% activation of STOP button will set BusyAction to 'cancel'
1404set(handles.RUN, 'Enable','Off')% avoid further RUN action until the current one is finished
1405set(handles.RUN,'BackgroundColor',[1 1 0])%show activation of RUN by yellow color
1406drawnow
1407set(handles.status,'Value',0)% desable status display if relevant
1408status_Callback([], eventdata, handles)
1409
1410%% launch action
1411errormsg=launch_action(handles);
1412if ~isempty(errormsg)
1413     msgbox_uvmat('ERROR',errormsg)
1414end
1415
1416%% reset the GUI series
1417update_waitbar(handles.Waitbar,1); % put the waitbar to end position to indicate launching is finished
1418set(handles.RUN, 'Enable','On')
1419set(handles.RUN,'BackgroundColor',[1 0 0])
1420set(handles.RUN, 'Value',0)
1421
1422%------------------------------------------------------------------------
1423% --- called by RUN_Callback
1424%------------------------------------------------------------------------
1425function errormsg=launch_action(handles)
1426errormsg='';%default
1427
1428%% read the data on the GUI series
1429Param=read_GUI_series(handles);%displayed parameters
1430SeriesData=get(handles.series,'UserData');%hidden parameters
1431if isfield(SeriesData,'TransformInput')
1432    Param.TransformInput=SeriesData.TransformInput;
1433end
1434if ~isfield(SeriesData,'i1_series')
1435    errormsg='The input field series needs to be refreshed: press REFRESH';
1436    return
1437end
1438if isfield(Param,'InputFields')&& isequal(Param.InputFields.FieldName,'get_field...')
1439    errormsg='input field name(s) not defined, select get_field...';
1440    return
1441end
1442
1443%% select the Action mode, 'local', 'background' or 'cluster' (if available)
1444RunMode='local';%default (needed for first opening of the GUI series)
1445if isfield(Param.Action,'RunMode')
1446    RunMode=Param.Action.RunMode;
1447    Param.Action=rmfield(Param.Action,'RunMode');%remove from the recorded xml file to avoid interference during ImportConfig
1448end
1449ActionExt='.m';%default
1450if isfield(Param.Action,'ActionExt')
1451    ActionExt=Param.Action.ActionExt;% '.m', '.sh' (compiled)  or '.py' (Python)
1452    Param.Action=rmfield(Param.Action,'ActionExt');%remove from the recorded xml file to avoid interference during ImportConfig
1453end
1454ActionName=Param.Action.ActionName;
1455ActionPath=Param.Action.ActionPath;
1456path_series=fileparts(which('series'));
1457
1458%% create the Action fct handle if RunMode option = 'local'
1459if strcmp(RunMode,'local')
1460    if ~isequal(ActionPath,path_series)
1461        eval(['spath=which(''' ActionName ''');']) %spath = current path of the selected function ACTION
1462        if ~exist(ActionPath,'dir')
1463            errormsg=['The prescribed function path ' ActionPath ' does not exist'];
1464            return
1465        end
1466        if ~isequal(spath,ActionPath)
1467            addpath(ActionPath)% add the prescribed path if not the current one
1468        end
1469    end
1470    eval(['h_fun=@' ActionName ';'])%create a function handle for ACTION
1471    if ~isequal(ActionPath,path_series)
1472        rmpath(ActionPath)% add the prescribed path if not the current one
1473    end
1474end
1475
1476%% Get RunTime code from the file PARAM.xml (needed to run compiled functions)
1477errormsg='';%default error message
1478xmlfile=fullfile(path_series,'PARAM.xml');
1479test_batch=0;%default: ,no batch mode available
1480if ~exist(xmlfile,'file')
1481    [success,message]=copyfile(fullfile(path_series,'PARAM.xml.default'),xmlfile);
1482end
1483% RunTime='';
1484if strcmp(ActionExt,'.sh')
1485    if exist(xmlfile,'file')
1486        s=xml2struct(xmlfile);
1487        if strcmp(RunMode,'cluster_oar') && isfield(s,'BatchParam')
1488%             if isfield(s.BatchParam,'RunTime')
1489%                 RunTime=s.BatchParam.RunTime;
1490%             end
1491            if isfield(s.BatchParam,'NbCore')
1492                NbCore=s.BatchParam.NbCore;
1493            end
1494        elseif (strcmp(RunMode,'background')||strcmp(RunMode,'local')) && isfield(s,'RunParam')
1495%             if isfield(s.RunParam,'RunTime')
1496%                 RunTime=s.RunParam.RunTime;
1497%             end
1498            if isfield(s.RunParam,'NbCore')
1499                NbCore=s.RunParam.NbCore;
1500            end
1501        end
1502    end
1503%     if isempty(RunTime) && strcmp(RunMode,'cluster_oar')
1504%        errormsg='RunTime name not found in PARAM.xml, compiled version .sh cannot run on cluster';
1505%         return
1506%     end
1507end
1508
1509%% If a compiled version has been selected (ext .sh) check weather it needs to be recompiled
1510if strcmp(ActionExt,'.sh')
1511    TransformPath='';
1512    if ~isempty(get(handles.ActionExt,'UserData'))
1513        TransformPath=get(handles.ActionExt,'UserData');
1514    end
1515    set(handles.series,'Pointer','watch') % set the mouse pointer to 'watch'
1516    set(handles.ActionExt,'BackgroundColor',[1 1 0])
1517    hver=ver('MATLAB');
1518    MCRROOT=['MCRROOT' regexprep(hver.Version,'\.','')];%suppress the dot in version number
1519    RunTime = getenv(MCRROOT);
1520    ActionNameVersion=[ActionName '_' MCRROOT];
1521    ActionFullName=fullfile(get(handles.ActionPath,'String'),[ActionNameVersion '.sh']);
1522    if ~exist(ActionFullName,'file')
1523        answer=msgbox_uvmat('INPUT_Y-N','compiled version has not been created: compile now?');
1524        if strcmp(answer,'Yes')
1525            set(handles.ActionExt,'BackgroundColor',[1 1 0])
1526            path_uvmat=fileparts(which('series'));
1527            currentdir=pwd;
1528            cd(get(handles.ActionPath,'String'))% go to the directory of Action
1529            addpath(path_uvmat)% add the path to uvmat to run the fct 'compile'
1530            compile(ActionName,TransformPath)
1531            cd(currentdir)
1532        else
1533            errormsg='Action launch interrupted';
1534            return
1535        end       
1536    else
1537        sh_file_info=dir(fullfile(get(handles.ActionPath,'String'),[ActionNameVersion '.sh']));
1538        m_file_info=dir(fullfile(get(handles.ActionPath,'String'),[ActionName '.m']));
1539        if isfield(m_file_info,'datenum') && m_file_info.datenum>sh_file_info.datenum
1540            set(handles.ActionExt,'BackgroundColor',[1 1 0])
1541            drawnow
1542            answer=msgbox_uvmat('INPUT_Y-N',[ActionNameVersion '.sh needs to be updated: recompile now?']);
1543            if strcmp(answer,'Yes')
1544                path_uvmat=fileparts(which('series'));
1545                currentdir=pwd;
1546                cd(get(handles.ActionPath,'String'))% go to the directory of Action
1547                addpath(path_uvmat)% add the path to uvmat to run the fct 'compile'
1548                addpath(fullfile(path_uvmat,'transform_field'))% add the path to uvmat to run the fct 'compile'
1549                compile(ActionName,TransformPath)
1550                cd(currentdir)
1551            end
1552        end
1553    end
1554    set(handles.ActionExt,'BackgroundColor',[1 1 1])
1555     set(handles.series,'Pointer','arrow') % set the mouse pointer to 'watch
1556end
1557
1558%% set nbre of cluster cores and processes:
1559% NbCore is the number of computer processors used
1560% NbProcess is the number of independent processes in which the required calculation is split
1561switch RunMode
1562    case {'local','background'}
1563        NbCore=1;% no need to split the calculation
1564    case 'cluster_oar'
1565        if strcmp(ActionExt,'.m')% case of Matlab function (uncompiled)
1566            NbCore=1;% one core used only (limitation of Matlab licences)
1567            answer=msgbox_uvmat('INPUT_Y-N','Number of cores =1: select the compiled version .sh for multi-core processing. Proceed with the .m version?');
1568            if ~strcmp(answer,'Yes')
1569                errormsg='Action launch interrupted by user';
1570                return
1571            end
1572            extra_oar='';
1573        else
1574            answer=inputdlg({'Number of cores (max 36)','extra oar options'},'oarsub parameter',1,{'12',''});
1575            if isempty(answer)
1576                                errormsg='Action launch interrupted by user';
1577                return
1578            end
1579            NbCore=str2double(answer{1});
1580            extra_oar=answer{2};
1581        end
1582    case 'cluster_pbs'
1583        if strcmp(ActionExt,'.m')% case of Matlab function (uncompiled)
1584            NbCore=1;% one core used only (limitation of Matlab licences)
1585            answer=msgbox_uvmat('INPUT_Y-N','Number of cores =1: select the compiled version .sh for multi-core processing. Proceed with the .m version?');
1586            if ~strcmp(answer,'Yes')
1587                errormsg='Action launch interrupted';
1588                return
1589            end
1590            extra_oar='';
1591        else
1592            answer=inputdlg({'Number of cores (max 36)','extra oar options'},'oarsub parameter',1,{'12',''});
1593            NbCore=str2double(answer{1});
1594            %extra_oar=answer{2};%TODO : fix this for LMFA cluster. Maybe
1595            %extrs_oar and extra_pbs are not the best names
1596        end
1597end
1598if ~isfield(Param.IndexRange,'NbSlice')
1599    Param.IndexRange.NbSlice=[];
1600end
1601
1602%% create the output data directory if needed
1603OutputDir='';
1604if isfield(Param,'OutputSubDir')
1605    SubDirOut=[get(handles.OutputSubDir,'String') Param.OutputDirExt];
1606    SubDirOutNew=SubDirOut;
1607    detect=exist(fullfile(Param.InputTable{1,1},SubDirOutNew),'dir');% test if  the dir  already exist
1608    check_create=1; %need to create the result directory by default
1609    while detect
1610        answer=msgbox_uvmat('INPUT_Y-N-Cancel',['use existing ouput directory: ' fullfile(Param.InputTable{1,1},SubDirOutNew) ', possibly delete previous data']);
1611        if strcmp(answer,'Cancel')
1612            return
1613        elseif strcmp(answer,'Yes')
1614            detect=0;
1615            check_create=0;
1616        else
1617            r=regexp(SubDirOutNew,'(?<root>.*\D)(?<num1>\d+)$','names');%detect whether name ends by a number
1618            if isempty(r)
1619                r(1).root=[SubDirOutNew '_'];
1620                r(1).num1='0';
1621            end
1622            SubDirOutNew=[r(1).root num2str(str2num(r(1).num1)+1)];%increment the index by 1 or put 1
1623            detect=exist(fullfile(Param.InputTable{1,1},SubDirOutNew),'dir');% test if  the dir  already exists
1624            check_create=1;
1625        end
1626    end
1627    Param.OutputDirExt=regexprep(SubDirOutNew,Param.OutputSubDir,'');
1628    Param.OutputRootFile=Param.InputTable{1,3};% the first sorted RootFile taken for output
1629    set(handles.OutputDirExt,'String',Param.OutputDirExt)
1630    OutputDir=fullfile(Param.InputTable{1,1},[Param.OutputSubDir Param.OutputDirExt]);% full name (with path) of output directory
1631    if check_create    % create output directory if it does not exist
1632        [tild,msg1]=mkdir(OutputDir);
1633        if ~strcmp(msg1,'')
1634            errormsg=['cannot create ' OutputDir ': ' msg1];%error message for directory creation
1635            return
1636        end
1637        [success,msg] = fileattrib(OutputDir,'+w','g','s');% allow writing access for the group of users, recursively in the folder 
1638        if success==0
1639            msgbox_uvmat('WARNING',{['unable to set group write access to ' OutputDir ':']; msg1});%error message for directory creation
1640        end
1641    end
1642   
1643elseif isfield(Param,'ActionInput')&&isfield(Param.ActionInput,'LogPath')% custom definition of the output dir
1644    OutputDir=Param.ActionInput.LogPath;   
1645end
1646DirXml=fullfile(OutputDir,'0_XML');
1647if ~exist(DirXml,'dir')
1648    [tild,msg1]=mkdir(DirXml);
1649    if ~strcmp(msg1,'')
1650        errormsg=['cannot create ' DirXml ': ' msg1];%error message for directory creation
1651        return
1652    end
1653    [success,msg] = fileattrib(DirXml,'+w','g','s');% allow writing access for the group of users, recursively in the folder
1654    if success==0
1655        msgbox_uvmat('WARNING',{['unable to set group write access to ' DirXml ':']; msg});%error message for directory creation
1656    end
1657end
1658OutputNomType=nomtype2pair(Param.InputTable{1,4});% nomenclature for output files
1659
1660%% get the set of reference input field indices
1661first_i=1;% first i index to process
1662last_i=1;% last i index to process
1663incr_i=1;% increment step in i index
1664first_j=1;% first j index to process
1665last_j=1;% last j index to process
1666incr_j=1;% increment step in j index
1667if isfield(Param.IndexRange,'first_i')
1668    first_i=Param.IndexRange.first_i;
1669    incr_i=Param.IndexRange.incr_i;
1670    last_i=Param.IndexRange.last_i;
1671end
1672if isfield(Param.IndexRange,'first_j')
1673    first_j=Param.IndexRange.first_j;
1674    last_j=Param.IndexRange.last_j;
1675    incr_j=Param.IndexRange.incr_j;
1676end
1677if last_i < first_i || last_j < first_j
1678    errormsg= 'series/Run_Callback:last field index must be larger or equal to the first one';
1679    return
1680end
1681%incr_i must be defined, =1 by default, if NbSlice is active
1682if isempty(incr_i)&& ~isempty(Param.IndexRange.NbSlice)
1683    incr_i=1;
1684    set(handles.num_incr_i,'String','1')
1685end
1686% case of no increment i defined: processing is done on the available files found in i1_series
1687if isempty(incr_i)
1688    if isempty(incr_j)
1689        [ref_j,ref_i]=find(squeeze(SeriesData.i1_series{1}(1,:,:)));
1690        ref_j=ref_j(ref_j>=first_j & ref_j<=last_j);
1691        ref_i=ref_i(ref_i>=first_i & ref_i<=last_i);
1692        ref_j=ref_j-1;
1693        ref_i=ref_i-1;
1694    else
1695        ref_j=first_j:incr_j:last_j;
1696        [tild,ref_i]=find(squeeze(SeriesData.i1_series{1}(1,:,:)));
1697        ref_i=ref_i-1;
1698        ref_i=ref_i(ref_i>=first_i & ref_i<=last_i);
1699    end
1700% increment i is defined: processing is done on first_i:incr_i:last_i;
1701else
1702    ref_i=first_i:incr_i:last_i;
1703    if isempty(incr_j)
1704        [ref_j,tild]=find(squeeze(SeriesData.i1_series{1}(1,:,:)));
1705        ref_j=ref_j-1;
1706        ref_j=ref_j(ref_j>=first_j & ref_j<=last_j);
1707    else
1708        ref_j=first_j:incr_j:last_j;
1709    end
1710end
1711
1712if isempty(Param.IndexRange.NbSlice)
1713    NbProcess=NbCore;% choose one process per core if NbSlice is not imposed
1714    switch RunMode
1715        case 'cluster_oar'
1716            NbProcess=numel(ref_i); % split big list witdh oar-parexec (Gabriel Moreau)
1717    end
1718else
1719    NbProcess=Param.IndexRange.NbSlice;% the parameter NbSlice sets the nbre of run processes
1720    NbCore=min(NbCore,NbProcess);% reduces the number of cores if it exceeds the number of processes
1721end
1722BlockLength=ceil(numel(ref_i)/NbProcess);% nbre of input fields in each process
1723nbfield_j=numel(ref_j); % number of j indices
1724
1725%% record nbre of output files and starting time for computation for status
1726StatusData=get(handles.status,'UserData');
1727if isfield(StatusData,'OutputFileMode')
1728    switch StatusData.OutputFileMode
1729        case 'NbInput'
1730            StatusData.NbOutputFile=numel(ref_i)*nbfield_j;
1731        case 'NbInput_i'
1732            StatusData.NbOutputFile=numel(ref_i);
1733        case 'NbSlice'   
1734            StatusData.NbOutputFile=str2num(get(handles.num_NbSlice,'String'));
1735    end
1736end
1737StatusData.TimeStart=now;
1738set(handles.status,'UserData',StatusData)
1739
1740%% case of a function in Python
1741if strcmp(ActionExt, '.py (in dev.)')
1742    fprintf([
1743        '\n' ...
1744        '!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n' ...
1745        'The option .py is used. It is still in development.\n' ...
1746        'Do not use it unless you really know what you do!\n' ...
1747        'To try it, first install Pyp and the most recent version of FluidDyn.\n' ...
1748        '!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n'])
1749    RunMode = 'python';
1750    t = struct2xml(Param);
1751    t = set(t, 1, 'name', 'Series');
1752    filexml = fullfile_uvmat(DirXml, '', Param.InputTable{1,3}, '.xml', OutputNomType,...
1753         Param.IndexRange.first_i, Param.IndexRange.last_i, first_j, last_j);
1754    save(t, filexml);
1755end
1756
1757
1758%% direct processing on the current Matlab session
1759if strcmp (RunMode,'local')
1760    for iprocess=1:NbProcess
1761        if isempty(Param.IndexRange.NbSlice)
1762            %Param.IndexRange.first_i=first_i+(iprocess-1)*BlockLength*incr_i;
1763            Param.IndexRange.first_i=ref_i(1+(iprocess-1)*BlockLength);
1764            if Param.IndexRange.first_i>last_i
1765                break
1766            end
1767            Param.IndexRange.last_i=min(ref_i(iprocess*BlockLength),last_i);
1768            %Param.IndexRange.last_i=min(first_i+(iprocess)*BlockLength*incr_i-1,last_i);
1769        else %multislices (then incr_i is not empty)
1770            Param.IndexRange.first_i= first_i+incr_i*(iprocess-1);
1771            Param.IndexRange.incr_i=incr_i*Param.IndexRange.NbSlice;
1772        end
1773        if isfield(Param,'OutputSubDir')
1774            t=struct2xml(Param);
1775            t=set(t,1,'name','Series');
1776            filexml=fullfile_uvmat(DirXml,'',Param.InputTable{1,3},'.xml',OutputNomType,...
1777                Param.IndexRange.first_i,Param.IndexRange.last_i,first_j,last_j);
1778            save(t,filexml);
1779        end
1780        switch ActionExt
1781            case '.m'
1782                h_fun(Param);
1783            case '.sh'
1784                switch computer
1785                    case {'PCWIN','PCWIN64'} %Windows system
1786                        filexml=regexprep(filexml,'\\','\\\\');% add '\' so that '\' are left as characters
1787                        system([fullfile(ActionPath,[ActionName '.sh']) ' ' RunTime ' ' filexml]);% TODO: adapt to DOS system
1788                    case {'GLNX86','GLNXA64','MACI64'}%Linux  system
1789                        system([fullfile(ActionPath,[ActionName '.sh']) ' ' RunTime ' ' filexml]);
1790                end
1791        end
1792    end
1793elseif ~strcmp(RunMode,'python')
1794    %% processing on a different session of the same computer (background) or cluster, create executable files
1795    batch_file_list=cell(NbProcess,1);% initiate the list of executable files
1796    DirBat=fullfile(OutputDir,'0_EXE');
1797    switch computer
1798        case {'PCWIN','PCWIN64'} %Windows system
1799            ExeExt='.bat';
1800        case {'GLNX86','GLNXA64','MACI64'}%Linux  system
1801           ExeExt='.sh';
1802    end
1803    %create subdirectory for executable files
1804    if ~exist(DirBat,'dir')
1805        [tild,msg1]=mkdir(DirBat);
1806        if ~strcmp(msg1,'')
1807            errormsg=['cannot create ' DirBat ': ' msg1];%error message for directory creation
1808            return
1809        end
1810    end
1811    %create subdirectory for log files
1812    DirLog=fullfile(OutputDir,'0_LOG');
1813    if ~exist(DirLog,'dir')
1814        [tild,msg1]=mkdir(DirLog);
1815        if ~strcmp(msg1,'')
1816            errormsg=['cannot create ' DirLog ': ' msg1];%error message for directory creation
1817            return
1818        end
1819    end
1820    for iprocess=1:NbProcess
1821        if isempty(Param.IndexRange.NbSlice)% process by blocks of i index
1822            Param.IndexRange.first_i=first_i+(iprocess-1)*BlockLength*incr_i;
1823            if Param.IndexRange.first_i>last_i
1824                NbProcess=iprocess-1;
1825                break% leave the loop, we are at the end of the calculation
1826            end
1827            Param.IndexRange.last_i=min(last_i,first_i+(iprocess)*BlockLength*incr_i-1);
1828        else% process by slices of i index if NbSlice is defined, computation in a single process if NbSlice =1
1829            Param.IndexRange.first_i= first_i+iprocess-1;
1830            Param.IndexRange.incr_i=incr_i*Param.IndexRange.NbSlice;
1831        end
1832        for ilist=1:size(Param.InputTable,1)
1833        Param.InputTable{ilist,1}=regexprep(Param.InputTable{ilist,1},'\','/');%correct path name for PCWIN system
1834        end
1835        % create, fill and save the xml parameter file
1836        t=struct2xml(Param);
1837        t=set(t,1,'name','Series');
1838        filexml=fullfile_uvmat(DirXml,'',Param.InputTable{1,3},'.xml',OutputNomType,...
1839            Param.IndexRange.first_i,Param.IndexRange.last_i,first_j,last_j);
1840        save(t,filexml);% save the parameter file
1841       
1842        %create the executable file
1843         filebat=fullfile_uvmat(DirBat,'',Param.InputTable{1,3},ExeExt,OutputNomType,...
1844           Param.IndexRange.first_i,Param.IndexRange.last_i,first_j,last_j);
1845        batch_file_list{iprocess}=filebat;
1846        [fid,message]=fopen(filebat,'w');% create the executable file
1847        if isequal(fid,-1)
1848            errormsg=['creation of .bat file: ' message];
1849            return
1850        end
1851       
1852        % set the log file name
1853        filelog=fullfile_uvmat(DirLog,'',Param.InputTable{1,3},'.log',OutputNomType,...
1854            Param.IndexRange.first_i,Param.IndexRange.last_i,first_j,last_j);
1855       
1856        % fill and save the executable file
1857        switch ActionExt
1858            case '.m'% Matlab function
1859                switch computer
1860                    case {'GLNX86','GLNXA64','MACI64'}
1861                        cmd=[...
1862                            '#!/bin/bash \n'...
1863                            '. /etc/sysprofile \n'...
1864                            'matlab -nodisplay -nosplash -nojvm -logfile ''' filelog ''' <<END_MATLAB \n'...
1865                            'addpath(''' path_series '''); \n'...
1866                            'addpath(''' Param.Action.ActionPath '''); \n'...
1867                            '' Param.Action.ActionName  '( ''' filexml '''); \n'...
1868                            'exit \n'...
1869                            'END_MATLAB \n'];
1870                        fprintf(fid,cmd);%fill the executable file with the  char string cmd
1871                        fclose(fid);% close the executable file
1872                        system(['chmod +x ' filebat]);% set the file to executable
1873                    case {'PCWIN','PCWIN64'}
1874                        text_matlabscript=['matlab -automation -logfile ' regexprep(filelog,'\\','\\\\')...
1875                            ' -r "addpath(''' regexprep(path_series,'\\','\\\\') ''');'...
1876                            'addpath(''' regexprep(Param.Action.ActionPath,'\\','\\\\') ''');'...
1877                            '' Param.Action.ActionName  '( ''' regexprep(filexml,'\\','\\\\') ''');exit"'];
1878                        fprintf(fid,text_matlabscript);%fill the executable file with the  char string cmd
1879                        fclose(fid);% close the executable file
1880                end
1881            case '.sh' % compiled Matlab function
1882                switch computer
1883                    case {'GLNX86','GLNXA64','MACI64'}
1884                        cmd=['#!/bin/bash \n '...
1885                            '#$ -cwd \n '...
1886                            'hostname && date \n '...
1887                            'umask 002 \n'...
1888                            fullfile(ActionPath,[ActionName '.sh']) ' ' RunTime ' ' filexml];%allow writting access to created files for user group
1889                        fprintf(fid,cmd);%fill the executable file with the  char string cmd
1890                        fclose(fid);% close the executable file
1891                        system(['chmod +x ' filebat]);% set the file to executable
1892                       
1893                    case {'PCWIN','PCWIN64'}   
1894                        fprintf(fid,cmd);
1895                        fclose(fid);
1896                end
1897        end
1898    end
1899end
1900
1901%% launch the executable files for background or cluster processing
1902switch RunMode
1903    case 'background'
1904        for iprocess=1:NbProcess
1905            system([batch_file_list{iprocess} ' &'])% directly execute the command file for each process
1906        end
1907        msgbox_uvmat('CONFIRMATION',[ActionName ' launched in background: press STATUS to see results'])
1908    case 'cluster_oar' % option 'oar-parexec' used
1909        %create subdirectory for oar command and log files
1910        DirOAR=fullfile(OutputDir,'0_OAR');
1911        if exist(DirOAR,'dir')% delete the content of the dir 0_OAR to allow new input
1912            curdir=pwd;
1913            cd(DirOAR)
1914            delete('*')
1915            cd(curdir)
1916        else
1917            [tild,msg1]=mkdir(DirOAR);
1918            if ~strcmp(msg1,'')
1919                errormsg=['cannot create ' DirOAR ': ' msg1];%error message for directory creation
1920                return
1921            end
1922        end
1923        max_walltime=3600*20; % 20h max total calculation (cannot exceed 24 h)
1924        walltime_onejob=1800; % seconds, max estimated time for asingle file index value
1925        filename_joblist=fullfile(DirOAR,'job_list.txt');%create name of the global executable file
1926        fid=fopen(filename_joblist,'w');
1927        for p=1:length(batch_file_list)
1928            fprintf(fid,[batch_file_list{p} '\n']);% list of exe files
1929        end
1930        fclose(fid);
1931        system(['chmod +x ' filename_joblist]);% set the file to executable
1932        oar_command=['oarsub -n CIVX '...
1933            '-t idempotent --checkpoint ' num2str(walltime_onejob+60) ' '...
1934            '-l /core=' num2str(NbCore) ','...
1935            'walltime=' datestr(min(1.05*walltime_onejob/86400*max(NbProcess*BlockLength*nbfield_j,NbCore)/NbCore,max_walltime/86400),13) ' '...
1936            '-E ' regexprep(filename_joblist,'\.txt\>','.stderr') ' '...
1937            '-O ' regexprep(filename_joblist,'\.txt\>','.stdout') ' '...
1938            extra_oar ' '...
1939            '"oar-parexec -f ' filename_joblist ' '...
1940            '-l ' filename_joblist '.log"\n'];
1941        filename_oarcommand=fullfile(DirOAR,'oar_command');
1942        fid=fopen(filename_oarcommand,'w');
1943        fprintf(fid,oar_command);
1944        fclose(fid);
1945        fprintf(oar_command);% display in command line
1946        system(oar_command); 
1947        msgbox_uvmat('CONFIRMATION',[ActionName ' launched in cluster: press STATUS to see results'])
1948    case 'cluster_pbs' % for LMFA Kepler machine
1949        %create subdirectory for pbs command and log files
1950        DirPBS=fullfile(OutputDir,'0_PBS'); %todo : common name OAR/PBS
1951        if exist(DirPBS,'dir')% delete the content of the dir 0_OAR to allow new input
1952            curdir=pwd;
1953            cd(DirPBS)
1954            delete('*')
1955            cd(curdir)
1956        else
1957            [tild,msg1]=mkdir(DirPBS);
1958            if ~strcmp(msg1,'')
1959                errormsg=['cannot create ' DirPBS ': ' msg1];%error message for directory creation
1960                return
1961            end
1962        end
1963        max_walltime=3600*20; % 20h max total calculation (cannot exceed 24 h)
1964        walltime_onejob=1800; % seconds, max estimated time for asingle file index value
1965        filename_joblist=fullfile(DirPBS,'job_list.txt');%create name of the global executable file
1966        fid=fopen(filename_joblist,'w');
1967        for p=1:length(batch_file_list)
1968            fprintf(fid,[batch_file_list{p} '\n']);% list of exe files
1969        end
1970        fclose(fid);
1971        system(['chmod +x ' filename_joblist]);% set the file to executable
1972        pbs_command=['qstat -n CIVX '...
1973            '-t idempotent --checkpoint ' num2str(walltime_onejob+60) ' '...
1974            '-l /core=' num2str(NbCore) ','...
1975            'walltime=' datestr(min(1.05*walltime_onejob/86400*max(NbProcess*BlockLength*nbfield_j,NbCore)/NbCore,max_walltime/86400),13) ' '...
1976            '-E ' regexprep(filename_joblist,'\.txt\>','.stderr') ' '...
1977            '-O ' regexprep(filename_joblist,'\.txt\>','.stdout') ' '...
1978            extra_oar ' '...
1979            '"oar-parexec -s -f ' filename_joblist ' '...
1980            '-l ' filename_joblist '.log"\n'];
1981        filename_oarcommand=fullfile(DirPBS,'pbs_command');
1982        fid=fopen(filename_oarcommand,'w');
1983        fprintf(fid,pbs_command);
1984        fclose(fid);
1985        fprintf(pbs_command);% display in command line
1986        %system(pbs_command); 
1987        msgbox_uvmat('CONFIRMATION',[ActionName ' command ready to be launched in cluster'])       
1988    case 'python'
1989        command = [
1990            'LD_LIBRARY_PATH=$(echo $LD_LIBRARY_PATH | pyp "p.split('':'') | [s for s in p if ''matlab'' not in s] | '':''.join(p)") ' ...
1991            'python -m fluiddyn.postproc.uvmat ' filexml];
1992        % fprintf(['command:\n' command '\n\n'])
1993        system(command, '-echo');
1994end
1995
1996%------------------------------------------------------------------------
1997function STOP_Callback(hObject, eventdata, handles)
1998%------------------------------------------------------------------------
1999set(handles.RUN, 'BusyAction','cancel')
2000set(handles.RUN,'BackgroundColor',[1 0 0])
2001set(handles.RUN,'enable','on')
2002set(handles.RUN, 'Value',0)
2003
2004
2005%------------------------------------------------------------------------
2006% --- read parameters from the GUI series
2007%------------------------------------------------------------------------
2008function Param=read_GUI_series(handles)
2009
2010%% read raw parameters from the GUI series
2011Param=read_GUI(handles.series);
2012
2013%% clean the output structure by removing unused information
2014if isfield(Param,'Pairs')
2015    Param=rmfield(Param,'Pairs'); %info Pairs not needed for output
2016end
2017if isfield(Param,'InputLine')
2018    Param=rmfield(Param,'InputLine');
2019end
2020if isfield(Param,'EditObject')
2021    Param=rmfield(Param,'EditObject');
2022end
2023Param.IndexRange.TimeSource=Param.IndexRange.TimeTable{end,1};
2024Param.IndexRange=rmfield(Param.IndexRange,'TimeTable');
2025empty_line=false(size(Param.InputTable,1),1);
2026for iline=1:size(Param.InputTable,1)
2027    empty_line(iline)=isempty(cell2mat(Param.InputTable(iline,1:3)));
2028end
2029Param.InputTable(empty_line,:)=[];
2030
2031%------------------------------------------------------------------------
2032% --- Executes on selection change in ActionName.
2033function ActionName_Callback(hObject, eventdata, handles)
2034%------------------------------------------------------------------------
2035
2036%% stop any ongoing series processing
2037if isequal(get(handles.RUN,'Value'),1)
2038    answer= msgbox_uvmat('INPUT_Y-N','stop current Action process?');
2039    if strcmp(answer,'Yes')
2040        STOP_Callback(hObject, eventdata, handles)
2041    else
2042        return
2043    end
2044end
2045set(handles.ActionName,'BackgroundColor',[1 1 0])
2046huigetfile=findobj(allchild(0),'tag','status_display');
2047if ~isempty(huigetfile)
2048    delete(huigetfile)
2049end
2050drawnow
2051
2052%% get Action name and path
2053NbBuiltinAction=get(handles.Action,'UserData'); %nbre of functions initially proposed in the menu ActionName (as defined in the Opening fct of series)
2054ActionList=get(handles.ActionName,'String');% list menu fields
2055ActionIndex=get(handles.ActionName,'Value');
2056if ~isequal(ActionIndex,1)% if we are not just opening series
2057    InputTable=get(handles.InputTable,'Data');
2058    if isempty(InputTable{1,4})
2059        msgbox_uvmat('ERROR','no input file available: use Open in the menu bar')
2060        return
2061    end
2062end
2063ActionName= ActionList{get(handles.ActionName,'Value')}; % selected function name
2064ActionPathList=get(handles.ActionName,'UserData');%list of recorded paths to functions of the list ActionName
2065
2066%% add a new function to the menu if 'more...' has been selected in the menu ActionName
2067if isequal(ActionName,'more...')
2068    [FileName, PathName] = uigetfile( ...
2069        {'*.m', ' (*.m)';
2070        '*.m',  '.m files '; ...
2071        '*.*', 'All Files (*.*)'}, ...
2072        'Pick a series processing function ',get(handles.ActionPath,'String'));
2073    if length(FileName)<2
2074        return
2075    end
2076    [tild,ActionName,ActionExt]=fileparts(FileName);
2077   
2078    % insert the choice in the menu ActionName
2079    ActionIndex=find(strcmp(ActionName,ActionList),1);% look for the selected function in the menu Action
2080    PathName=regexprep(PathName,'/$','');
2081    if ~isempty(ActionIndex) && ~strcmp(ActionPathList{ActionIndex},PathName)%compare the path to the existing fct
2082        ActionIndex=[]; % the selected path is different than the recorded one
2083    end
2084    if isempty(ActionIndex)%the qselected fct (with selected path) does not exist in the menu
2085        ActionIndex= length(ActionList);
2086        ActionList=[ActionList(1:end-1);{ActionName};ActionList(end)];% the selected function is appended in the menu, before the last item 'more...'
2087         ActionPathList=[ActionPathList; PathName];
2088    end
2089   
2090    % record the file extension and extend the path list if it is a new extension
2091    ActionExtList=get(handles.ActionExt,'String');
2092    ActionExtIndex=find(strcmp(ActionExt,ActionExtList), 1);
2093    if isempty(ActionExtIndex)
2094        set(handles.ActionExt,'String',[ActionExtList;{ActionExt}])
2095    end
2096
2097    % remove old Action options in the menu (keeping a menu length <nb_builtin_ACTION+5)
2098    if length(ActionList)>NbBuiltinAction+5; %nb_builtin_ACTION=nbre of functions always remaining in the initial menu
2099        nbremove=length(ActionList)-NbBuiltinAction-5;
2100        ActionList(NbBuiltinAction+1:end-5)=[];
2101        ActionPathList(NbBuiltinAction+1:end-4,:)=[];
2102        ActionIndex=ActionIndex-nbremove;
2103    end
2104   
2105    % record action menu, choice and path
2106    set(handles.ActionName,'Value',ActionIndex)
2107    set(handles.ActionName,'String',ActionList)
2108       set(handles.ActionName,'UserData',ActionPathList);
2109    set(handles.ActionExt,'Value',ActionExtIndex)
2110       
2111    %record the user defined menu additions in personal file profil_perso
2112    dir_perso=prefdir;
2113    profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
2114    if NbBuiltinAction+1<=numel(ActionList)-1
2115        ActionListUser=ActionList(NbBuiltinAction+1:numel(ActionList)-1);
2116        ActionPathListUser=ActionPathList(NbBuiltinAction+1:numel(ActionList)-1);
2117        ActionExtListUser={};
2118        if numel(ActionExtList)>2
2119            ActionExtListUser=ActionExtList(3:end);
2120        end
2121        if exist(profil_perso,'file')
2122            save(profil_perso,'ActionListUser','ActionPathListUser','ActionExtListUser','-append')
2123        else
2124            save(profil_perso,'ActionListUser','ActionPathListUser','ActionExtListUser','-V6')
2125        end
2126    end
2127end
2128
2129%% check the current ActionPath to the selected function
2130ActionPath=ActionPathList{ActionIndex};%current recorded path
2131set(handles.ActionPath,'String',ActionPath); %show the path to the senlected function
2132
2133%% reinitialise the waitbar
2134update_waitbar(handles.Waitbar,0)
2135
2136%% create the function handle for Action
2137if ~exist(ActionPath,'dir')
2138    msgbox_uvmat('ERROR',['The prescribed function path ' ActionPath ' does not exist']);
2139    return
2140end
2141current_dir=pwd;%current working dir
2142cd(ActionPath)
2143h_fun=str2func(ActionName);
2144cd(current_dir)
2145
2146%
2147% checkaddpath=0;
2148% path_series=which('series');
2149% %eval(['spath=which(''' ActionName ''');']) %spath = current path of the selected function ACTION
2150% spath=fileparts(which(ActionName)); %spath = current path of the selected function ACTION
2151% if ~exist(ActionPath,'dir')
2152%     msgbox_uvmat('ERROR',['The prescribed function path ' ActionPath ' does not exist']);
2153%     return
2154% end
2155% if ~strcmp(spath,ActionPath)
2156%     if strcmp(pwd,spath)
2157%         msgbox_uvmat('ERROR',[ 'a function called ' ActionName ' on your working space oversets the selected one']);
2158%         return
2159%     else
2160%         addpath(ActionPath)% add the prescribed path if not the current one
2161%         checkaddpath=1;
2162%     end
2163% end
2164% eval(['h_fun=@' ActionName ';'])%create a function handle for ACTION
2165% if checkaddpath && ~isequal(ActionPath,path_series)
2166%     rmpath(ActionPath)% add the prescribed path if not the current one
2167% end
2168
2169%% Activate the Action fct to adapt the configuration of the GUI series and bring specific parameters in SeriesData
2170Param=read_GUI_series(handles);% read the parameters from the GUI series
2171ParamOut=h_fun(Param);%run the selected Action function to get the relevant input
2172
2173%% Put the first line of the selected Action fct as tooltip help
2174try
2175    [fid,errormsg] =fopen([ActionName '.m']);
2176    InputText=textscan(fid,'%s',1,'delimiter','\n');
2177    fclose(fid);
2178    set(handles.ActionName,'ToolTipString',InputText{1}{1})% put the first line of the selected function as tooltip help
2179end
2180
2181
2182%% Visibility of VelType and VelType_1 menus asked by ActionName
2183VelTypeRequest=1;%VelType requested by default
2184VelTypeRequest_1=1;%VelType requested by default
2185if isfield(ParamOut,'VelType')
2186    VelTypeRequest=ismember(ParamOut.VelType,{'on','one','two'});
2187    VelTypeRequest_1=strcmp( ParamOut.VelType,'two');
2188end
2189FieldNameRequest=0;  %hidden by default
2190FieldNameRequest_1=0;  %hidden by default
2191if isfield(ParamOut,'FieldName')
2192    FieldNameRequest=ismember(ParamOut.FieldName,{'on','one','two'});
2193    FieldNameRequest_1=strcmp( ParamOut.FieldName,'two');
2194end
2195
2196%% Detect the types of input files and set menus and default options in 'VelType'
2197SeriesData=get(handles.series,'UserData');% info on the input file series
2198iview_civ=find(strcmp('civx',SeriesData.FileType)|strcmp('civdata',SeriesData.FileType));
2199iview_netcdf=find(strcmp('netcdf',SeriesData.FileType)|strcmp('civx',SeriesData.FileType)|strcmp('civdata',SeriesData.FileType));% all nc files, icluding civ
2200FieldList=get(handles.FieldName,'String');% previous list as default
2201if ~iscell(FieldList),FieldList={FieldList};end
2202FieldList_1=get(handles.FieldName_1,'String');% previous list as default
2203if ~iscell(FieldList_1),FieldList_1={FieldList_1};end
2204%CheckList=0;% indicate whether FieldName has been updated
2205CheckList_1=1;% indicate whether FieldName_1 has been updated
2206handles_coord=[handles.Coord_x handles.Coord_y handles.Coord_z handles.Coord_x_title handles.Coord_y_title handles.Coord_z_title];
2207if VelTypeRequest && numel(iview_civ)>=1
2208    menu=set_veltype_display(SeriesData.FileInfo{iview_civ(1)}.CivStage,SeriesData.FileType{iview_civ(1)});
2209    set(handles.VelType,'Value',1)% set first choice by default
2210    set(handles.VelType,'String',[{'*'};menu])
2211    set(handles.VelType,'Visible','on')
2212    set(handles.VelType_title,'Visible','on')
2213    FieldList=[set_field_list('U','V');{'C'};{'get_field...'}];%standard menu for civx data
2214    %CheckList=1;
2215    set(handles.FieldName,'Value',1); %velocity vector choice by default
2216    if  VelTypeRequest_1 && numel(iview_civ)>=2
2217        menu=set_veltype_display(SeriesData.FileInfo{iview_civ(2)}.CivStage,SeriesData.FileType{iview_civ(2)});
2218        set(handles.VelType_1,'Value',1)% set first choice by default
2219        set(handles.VelType_1,'String',[{'*'};menu])
2220        set(handles.VelType_1,'Visible','on')
2221        set(handles.VelType_title_1,'Visible','on')
2222        FieldList_1=[set_field_list('U','V');{'C'};{'get_field...'}];%standard menu for civx data
2223        CheckList_1=1;
2224        set(handles.FieldName_1,'Value',1); %velocity vector choice by default
2225    else
2226        set(handles.VelType_1,'Visible','off')
2227        set(handles.VelType_title_1,'Visible','off')
2228    end
2229else
2230    set(handles.VelType,'Visible','off')
2231    set(handles.VelType_title,'Visible','off')
2232end   
2233
2234%% Detect the types of input files and set menus and default options in 'FieldName'
2235if FieldNameRequest && numel(iview_netcdf)>=1
2236    set(handles.InputFields,'Visible','on')
2237    %if CheckList==0        % not civ input made
2238        if isfield(SeriesData.FileInfo{iview_netcdf(1)},'ListVarName')
2239        ListVarName=SeriesData.FileInfo{iview_netcdf(1)}.ListVarName;
2240        ind_var=get(handles.FieldName,'Value');%indices of previously selected variables
2241        for ilist=1:numel(ind_var)
2242            if isempty(find(strcmp(FieldList{ind_var(ilist)},ListVarName)))
2243                FieldList={};% previous choice not consistent with new input field
2244                set(handles.FieldName,'Value',1)
2245                break
2246            end
2247        end
2248        if ~isempty(FieldList)
2249            if isempty(find(strcmp(get(handles.Coord_x,'String'),ListVarName)))||...
2250                    isempty(find(strcmp(get(handles.Coord_y,'String'),ListVarName)))
2251                FieldList={};
2252                set(handles.Coord_x,'String','')
2253                set(handles.Coord_y,'String','')
2254            end
2255            Coord_z=get(handles.Coord_z,'String');
2256            if ~isempty(Coord_z) && isempty(find(strcmp(Coord_z,ListVarName)))
2257                FieldList={};
2258                set(handles.Coord_z,'String','')
2259            end
2260        end
2261        set(handles_coord,'Visible','on')
2262        FieldList=[FieldList;{'get_field...'}];
2263        if FieldNameRequest_1 && numel(iview_netcdf)>=2
2264            set(handles.FieldName_1,'Visible','on')
2265            if CheckList_1==0        % not civ input made
2266                ListVarName=SeriesData.FileInfo{iview_netcdf(2)}.ListVarName;
2267                ind_var=get(handles.FieldName,'Value');%indices of previously selected variables
2268                for ilist=1:numel(ind_var)
2269                    if isempty(find(strcmp(FieldList{ind_var(ilist)},ListVarName)))
2270                        FieldList_1={};% previous choice not consistent with new input field
2271                        set(handles.FieldName_1,'Value',1)
2272                        break
2273                    end
2274                end
2275                warn_coord=0;
2276                if isempty(find(strcmp(get(handles.Coord_x,'String'),ListVarName)))||...
2277                        isempty(find(strcmp(get(handles.Coord_y,'String'),ListVarName)))
2278                    warn_coord=1;
2279                end
2280                if ~isempty(Coord_z) && isempty(find(strcmp(Coord_z,ListVarName)))
2281                    FieldList_1={};
2282                    warn_coord=1;
2283                end
2284                if warn_coord
2285                    msgbox_uvmat('WARNING','coordiante names do not exist in the second netcdf input file')
2286                end
2287                set(handles.FieldName,'String',[FieldList;{'get_field...'}])
2288                set(handles.FieldName_1,'Visible','on')
2289                set(handles.FieldName_1,'Value',1)
2290                set(handles.FieldName_1,'String',FieldList_1)
2291            end
2292        else
2293            set(handles.FieldName_1,'Visible','off')
2294        end
2295        end
2296%     else
2297%         set(handles_coord,'Visible','off')% no coord display for civ data
2298%     end
2299    set(handles.FieldName,'String',FieldList)
2300else
2301    set(handles.InputFields,'Visible','off')
2302end
2303
2304
2305%% Check whether alphabetical sorting of input Subdir is allowed by the Action fct  (for multiples series entries)
2306if isfield(ParamOut,'AllowInputSort')&&isequal(ParamOut.AllowInputSort,'on')&& size(Param.InputTable,1)>1
2307    [tild,iview]=sort(InputTable(:,2)); %subdirectories sorted in alphabetical order
2308    set(handles.InputTable,'Data',InputTable(iview,:));
2309    MinIndex_i=get(handles.MinIndex_i,'Data');
2310    MinIndex_j=get(handles.MinIndex_j,'Data');
2311    MaxIndex_i=get(handles.MaxIndex_i,'Data');
2312    MaxIndex_j=get(handles.MaxIndex_j,'Data');
2313    set(handles.MinIndex_i,'Data',MinIndex_i(iview,:));
2314    set(handles.MinIndex_j,'Data',MinIndex_j(iview,:));
2315    set(handles.MaxIndex_i,'Data',MaxIndex_i(iview,:));
2316    set(handles.MaxIndex_j,'Data',MaxIndex_j(iview,:));
2317    TimeTable=get(handles.TimeTable,'Data');
2318    set(handles.TimeTable,'Data',TimeTable(iview,:));
2319    PairString=get(handles.PairString,'Data');
2320    set(handles.PairString,'Data',PairString(iview,:));
2321end
2322
2323%% Impose the whole input file index range if requested
2324if isfield(ParamOut,'WholeIndexRange')&&isequal(ParamOut.WholeIndexRange,'on')
2325    MinIndex_i=get(handles.MinIndex_i,'Data');
2326    MinIndex_j=get(handles.MinIndex_j,'Data');
2327    MaxIndex_i=get(handles.MaxIndex_i,'Data');
2328    MaxIndex_j=get(handles.MaxIndex_j,'Data');
2329    set(handles.num_first_i,'String',num2str(MinIndex_i(1)))% set first as the min index (for the first line)
2330    set(handles.num_last_i,'String',num2str(MaxIndex_i(1)))% set last as the max index (for the first line)
2331    set(handles.num_incr_i,'String','1')
2332    set(handles.num_first_j,'String',num2str(MinIndex_j(1)))% set first as the min index (for the first line)
2333    set(handles.num_last_j,'String',num2str(MaxIndex_j(1)))% set last as the max index (for the first line)
2334    set(handles.num_incr_j,'String','1')
2335else  % check index ranges
2336    first_i=1;last_i=1;first_j=1;last_j=1;
2337    if isfield(Param.IndexRange,'first_i')
2338        first_i=Param.IndexRange.first_i;
2339        last_i=Param.IndexRange.last_i;
2340    end
2341    if isfield(Param.IndexRange,'first_j')
2342        first_j=Param.IndexRange.first_j;
2343        last_j=Param.IndexRange.last_j;
2344    end
2345    if last_i < first_i || last_j < first_j , msgbox_uvmat('ERROR','last field number must be larger than the first one'),...
2346            set(handles.RUN, 'Enable','On'), set(handles.RUN,'BackgroundColor',[1 0 0]),return,end;
2347end
2348
2349%% enable or desable j index visibility
2350status_j='on';%default
2351if isfield(ParamOut,'Desable_j_index')&&isequal(ParamOut.Desable_j_index,'on')
2352    status_j='off';
2353end
2354if isempty(find(~cellfun(@isempty,SeriesData.j1_series), 1)); % case of empty j indices
2355    status_j='off'; % no j index needed
2356elseif strcmp(get(handles.PairString,'Visible'),'on')
2357    check_burst=cellfun(@isempty,regexp(get(handles.PairString,'Data'),'^j'));%=0 for burst case, 1 otherwise
2358    if isempty(find(check_burst, 1))% if all pair string begins by j (burst)
2359        status_j='off'; % no j index needed for bust case
2360    end
2361end
2362enable_j(handles,status_j) % no j index needed
2363
2364
2365%% NbSlice visibility
2366%NbSliceVisible='off';%default
2367if isfield(ParamOut,'NbSlice') && (strcmp(ParamOut.NbSlice,'on')||isnumeric(ParamOut.NbSlice))
2368    set(handles.num_NbSlice,'Visible','on')
2369    set(handles.NbSlice_title,'Visible','on')
2370else
2371    set(handles.num_NbSlice,'Visible','off')
2372    set(handles.NbSlice_title,'Visible','off')
2373    %     set(handles.num_NbProcess,'String',get(handles.num_NbSlice,'String'))% the nbre of processes is imposed as the nbre of slices
2374    % else
2375    %     set(handles.num_NbProcess,'String','')% free nbre of processes
2376end
2377if isnumeric(ParamOut.NbSlice)
2378    set(handles.num_NbSlice,'String',num2str(ParamOut.NbSlice))
2379    set(handles.num_NbSlice,'Enable','off'); % NbSlice set by the activation of the Action function
2380else
2381    set(handles.num_NbSlice,'Enable','on'); % NbSlice can be modified on the GUI series
2382end
2383% set(handles.num_NbSlice,'Visible',NbSliceVisible)
2384% set(handles.NbSlice_title,'Visible',NbSliceVisible)
2385
2386
2387
2388%% Visibility of FieldTransform menu
2389FieldTransformVisible='off';  %hidden by default
2390if isfield(ParamOut,'FieldTransform')
2391    FieldTransformVisible=ParamOut.FieldTransform; 
2392    TransformName_Callback([],[], handles)
2393end
2394set(handles.FieldTransform,'Visible',FieldTransformVisible)
2395if isfield(ParamOut,'TransformPath')
2396    set(handles.ActionExt,'UserData',ParamOut.TransformPath)
2397else
2398    set(handles.ActionExt,'UserData',[])
2399end
2400
2401%% Visibility of projection object
2402ProjObjectVisible='off';  %hidden by default
2403if isfield(ParamOut,'ProjObject')
2404    ProjObjectVisible=ParamOut.ProjObject;
2405end
2406set(handles.CheckObject,'Visible',ProjObjectVisible)
2407if ~get(handles.CheckObject,'Value')
2408    ProjObjectVisible='off';
2409end
2410set(handles.ProjObject,'Visible',ProjObjectVisible)
2411set(handles.DeleteObject,'Visible',ProjObjectVisible)
2412set(handles.ViewObject,'Visible',ProjObjectVisible)
2413set(handles.EditObject,'Visible',ProjObjectVisible)
2414
2415%% Visibility of mask input
2416MaskVisible='off';  %hidden by default
2417if isfield(ParamOut,'Mask')
2418    MaskVisible=ParamOut.Mask;
2419end
2420set(handles.CheckMask,'Visible',MaskVisible);
2421
2422%% definition of the directory containing the output files
2423if  ~(isfield(SeriesData,'ActionName') && strcmp(ActionName,SeriesData.ActionName))
2424    OutputDirExt='.series'; %default
2425    if isfield(ParamOut,'OutputDirExt')&&~isempty(ParamOut.OutputDirExt)
2426        OutputDirExt=ParamOut.OutputDirExt;
2427    end
2428    set(handles.OutputDirExt,'String',OutputDirExt)
2429end
2430OutputDirVisible='off';
2431OutputSubDirMode='auto';%default
2432SubDirOut='';
2433if isfield(ParamOut,'OutputSubDirMode')
2434    OutputSubDirMode=ParamOut.OutputSubDirMode;
2435end
2436switch OutputSubDirMode
2437    case 'auto';%default
2438        OutputDirVisible='on';
2439        SubDir=InputTable(1:end,2); %set of subdirectories
2440        SubDirOut=SubDir{1};
2441        if numel(SubDir)>1
2442            for ilist=2:numel(SubDir)
2443                SubDirOut=[SubDirOut '-' regexprep(SubDir{ilist},'^/','')];
2444            end
2445        end
2446    case 'one'
2447        OutputDirVisible='on';
2448        SubDirOut=InputTable{1,2}; %use the first subdir name (+OutputDirExt) as output  subdirectory
2449    case 'two'
2450        OutputDirVisible='on';   
2451        SubDir=InputTable(1:2,2); %set of subdirectories
2452        SubDirOut=SubDir{1};
2453        if numel(SubDir)>1
2454                SubDirOut=[SubDirOut '-' regexprep(SubDir{2},'^/','')];
2455        end
2456    case 'last'
2457        OutputDirVisible='on';
2458        SubDirOut=InputTable{end,2}; %use the last subdir name (+OutputDirExt) as output  subdirectory
2459end
2460set(handles.OutputSubDir,'String',SubDirOut)
2461set(handles.OutputSubDir,'BackgroundColor',[1 1 1])% set edit box to white color to indicate refreshment
2462set(handles.OutputDirExt,'Visible',OutputDirVisible)
2463set(handles.OutputSubDir,'Visible',OutputDirVisible)
2464set(handles.OutputDir_title,'Visible',OutputDirVisible)
2465SeriesData.ActionName=ActionName;%record ActionName for next use
2466
2467
2468%% visibility of the run mode (local or background or cluster)
2469if strcmp(OutputSubDirMode,'none')
2470    RunModeVisible='off';% only local mode available if no output file is produced
2471else
2472    RunModeVisible='on';
2473end
2474set(handles.RunMode,'Visible',RunModeVisible)
2475set(handles.ActionExt,'Visible',RunModeVisible)
2476set(handles.RunMode_title,'Visible',RunModeVisible)
2477set(handles.ActionExt_title,'Visible',RunModeVisible)
2478
2479
2480%% Expected nbre of output files
2481if isfield(ParamOut,'OutputFileMode')
2482    StatusData.OutputFileMode=ParamOut.OutputFileMode;
2483    set(handles.status,'UserData',StatusData)
2484end
2485
2486%% definition of an additional parameter set, determined by an ancillary GUI
2487if isfield(ParamOut,'ActionInput')
2488    set(handles.ActionInput,'Visible','on')
2489    ParamOut.ActionInput.Program=ActionName; % record the program in ActionInput
2490    SeriesData.ActionInput=ParamOut.ActionInput;
2491else
2492    set(handles.ActionInput,'Visible','off')
2493    if isfield(SeriesData,'ActionInput')
2494        SeriesData=rmfield(SeriesData,'ActionInput');
2495    end
2496end
2497set(handles.series,'UserData',SeriesData)
2498set(handles.ActionName,'BackgroundColor',[1 1 1])
2499
2500%------------------------------------------------------------------------
2501% --- Executes on selection change in FieldName.
2502function FieldName_Callback(hObject, eventdata, handles)
2503%------------------------------------------------------------------------
2504field_str=get(handles.FieldName,'String');
2505field_index=get(handles.FieldName,'Value');
2506field=field_str{field_index(1)};
2507if isequal(field,'get_field...')
2508    SeriesData=get(handles.series,'UserData');
2509    % input line for which the field choice is relevant
2510    iview=find(ismember(SeriesData.FileType,{'netcdf','civx','civdata'}));% all nc files, icluding civ
2511    hget_field=findobj(allchild(0),'name','get_field');
2512    if ~isempty(hget_field)
2513        delete(hget_field)%delete opened versions of get_field
2514    end
2515    Param=read_GUI(handles.series);
2516    InputTable=Param.InputTable(iview,:);
2517    % check the existence of the first file in the series
2518    first_j=[];last_j=[];MinIndex_j=1;MaxIndex_j=1;%default setting for index j
2519    if isfield(Param.IndexRange,'first_j');% if index j is used     
2520        first_j=Param.IndexRange.first_j;
2521        last_j=Param.IndexRange.last_j;
2522        MinIndex_j=Param.IndexRange.MinIndex_j(iview);
2523        MaxIndex_j=Param.IndexRange.MaxIndex_j(iview);
2524    end
2525    PairString='';
2526    if isfield(Param.IndexRange,'PairString'); PairString=Param.IndexRange.PairString{iview}; end
2527    [i1,i2,j1,j2] = get_file_index(Param.IndexRange.first_i,first_j,PairString);
2528    LineIndex=iview(1);
2529    if numel(iview)>1     
2530        answer=msgbox_uvmat('INPUT_TXT',['select the line of the input table:' num2str(iview)] ,num2str(iview(1)));
2531        LineIndex=str2num(answer);
2532%         InputLine=str2num(get(handles.InputLine,'String'));
2533%         if ismember(InputLine,iview)
2534%             LineIndex=InputLine;
2535%         end
2536    end
2537    FirstFileName=fullfile_uvmat(InputTable{LineIndex,1},InputTable{LineIndex,2},InputTable{LineIndex,3},...
2538        InputTable{LineIndex,5},InputTable{LineIndex,4},i1,i2,j1,j2);
2539    if exist(FirstFileName,'file')
2540        ParamIn.Title='get_field: pick input variables and coordinates for series processing';
2541        ParamIn.SeriesInput=1;
2542        GetFieldData=get_field(FirstFileName,ParamIn);
2543        FieldList={};
2544        if isfield(GetFieldData,'FieldOption')% if a field has been selected
2545        switch GetFieldData.FieldOption
2546            case 'vectors'
2547                UName=GetFieldData.PanelVectors.vector_x;
2548                VName=GetFieldData.PanelVectors.vector_y;
2549                YName={GetFieldData.Coordinates.Coord_y};
2550                FieldList={['vec(' UName ',' VName ')'];...
2551                    ['norm(' UName ',' VName ')'];...
2552                    UName;VName};
2553            case {'scalar'}
2554                FieldList=GetFieldData.PanelScalar.scalar;
2555                YName={GetFieldData.Coordinates.Coord_y};
2556                if ischar(FieldList)
2557                    FieldList={FieldList};
2558                end
2559            case 'civdata...'
2560                FieldList=[set_field_list('U','V') ;{'C'}];
2561                set(handles.FieldName,'Value',1) % set menu to 'velocity
2562                XName='X';
2563                YName='y';
2564        end
2565        set(handles.FieldName,'Value',1)
2566        set(handles.FieldName,'String',[FieldList; {'get_field...'}]);
2567        if ~strcmp(GetFieldData.FieldOption,'civdata...')
2568           if ~isempty(regexp(FieldList{1},'^vec'))
2569                set(handles.FieldName,'Value',1)
2570           else
2571                set(handles.FieldName,'Value',1:numel(FieldList))%select all input fields by default
2572           end
2573            XName=GetFieldData.Coordinates.Coord_x;
2574            YName=GetFieldData.Coordinates.Coord_y;
2575            TimeNameStr=GetFieldData.Time.SwitchVarIndexTime;
2576            % get the time info                     
2577            TimeTable=get(handles.TimeTable,'Data');
2578            switch TimeNameStr
2579                case 'file index'
2580                    TimeName='';
2581                case 'attribute'
2582                    TimeName=['att:' GetFieldData.Time.TimeName];
2583                    % update the time table
2584                    TimeTable{LineIndex,2}=get_time(Param.IndexRange.MinIndex_i(LineIndex),MinIndex_j,PairString,InputTable,SeriesData.FileInfo{LineIndex},GetFieldData.Time.TimeName);  % Min time     
2585                    TimeTable{LineIndex,3}=get_time(Param.IndexRange.first_i,first_j,PairString,InputTable,SeriesData.FileInfo{LineIndex},GetFieldData.Time.TimeName);  % first time             
2586                    TimeTable{LineIndex,4}=get_time(Param.IndexRange.last_i,last_j,PairString,InputTable,SeriesData.FileInfo{LineIndex},GetFieldData.Time.TimeName);  % last time                     
2587                    TimeTable{LineIndex,5}=get_time(Param.IndexRange.MaxIndex_i(LineIndex),MaxIndex_j,PairString,InputTable,SeriesData.FileInfo{LineIndex},GetFieldData.Time.TimeName);  % Max time
2588                case 'variable'
2589                    set(handles.TimeName,'String',['var:' GetFieldData.Time.TimeName])
2590                    set(handles.NomType,'String','*')
2591                    set(handles.RootFile,'String',[get(handles.RootFile,'String') get(handles.FileIndex,'String')])% A VERIFIER !!!!!!
2592                    set(handles.FileIndex,'String','')
2593                    ParamIn.TimeVarName=GetFieldData.Time.TimeName;
2594                case 'matrix_index'
2595                    TimeName=['dim:' GetFieldData.Time.TimeName];
2596                    set(handles.NomType,'String','*')
2597                    set(handles.RootFile,'String',[get(handles.RootFile,'String') get(handles.FileIndex,'String')])
2598                    set(handles.FileIndex,'String','')
2599                    ParamIn.TimeDimName=GetFieldData.Time.TimeName;
2600            end
2601            TimeTable{LineIndex,1}=TimeName;
2602            set(handles.TimeTable,'Data',TimeTable);
2603        end
2604        set(handles.Coord_x,'String',XName)
2605        set(handles.Coord_y,'String',YName)
2606        set(handles.Coord_x,'Visible','on')
2607        set(handles.Coord_y,'Visible','on')
2608        end
2609    else
2610        msgbox_uvmat('ERROR',[FirstFileName ' does not exist'])
2611    end
2612end
2613
2614function [TimeValue,DtValue]=get_time(ref_i,ref_j,PairString,InputTable,FileInfo,TimeName,DtName)
2615[i1,i2,j1,j2] = get_file_index(ref_i,ref_j,PairString);
2616FileName=fullfile_uvmat(InputTable{1},InputTable{2},InputTable{3},InputTable{5},InputTable{4},i1,i2,j1,j2);
2617Data=nc2struct(FileName,[]);
2618TimeValue=[];
2619DtValue=[];
2620if isequal(FileInfo.FileType,'civdata')
2621    if ismember(TimeName,{'civ1','filter1'})
2622        TimeValue=Data.Civ1_Time;
2623        DtValue=Data.Civ1_Dt;
2624    else
2625        TimeValue=Data.Civ2_Time;
2626        DtValue=Data.Civ2_Dt;
2627    end
2628else
2629    if ~isempty(TimeName)&& isfield(Data,TimeName)
2630        TimeValue=Data.(TimeName);
2631    end
2632    if exist('DtName','var') && isfield(Data,DtName)
2633        DtValue=Data.(DtName);
2634    end
2635end
2636
2637%------------------------------------------------------------------------
2638% --- Executes on selection change in FieldName_1.
2639function FieldName_1_Callback(hObject, eventdata, handles)
2640%------------------------------------------------------------------------
2641field_str=get(handles.FieldName_1,'String');
2642field_index=get(handles.FieldName_1,'Value');
2643field=field_str{field_index(1)};
2644if isequal(field,'get_field...')
2645    hget_field=findobj(allchild(0),'name','get_field');
2646    if ~isempty(hget_field)
2647        delete(hget_field)%delete opened versions of get_field
2648    end
2649    Param=read_GUI(handles.series);
2650    Param.InputTable=Param.InputTable(1,:);
2651    % check the existence of the first file in the series
2652    first_j=[];
2653    if isfield(Param.IndexRange,'first_j'); first_j=Param.IndexRange.first_j; end
2654    if isfield(Param.IndexRange,'last_j'); last_j=Param.IndexRange.last_j; end
2655    PairString='';
2656    if isfield(Param.IndexRange,'PairString'); PairString=Param.IndexRange.PairString; end
2657    [i1,i2,j1,j2] = get_file_index(Param.IndexRange.first_i,first_j,PairString);
2658    FirstFileName=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},...
2659        Param.InputTable{1,5},Param.InputTable{1,4},i1,i2,j1,j2);
2660    if exist(FirstFileName,'file')
2661        ParamIn.SeriesInput=1;
2662        GetFieldData=get_field(FirstFileName,ParamIn);
2663        FieldList={};
2664        switch GetFieldData.FieldOption
2665            case 'vectors'
2666                UName=GetFieldData.PanelVectors.vector_x;
2667                VName=GetFieldData.PanelVectors.vector_y;
2668                FieldList={['vec(' UName ',' VName ')'];...
2669                    ['norm(' UName ',' VName ')'];...
2670                    UName;VName};
2671            case {'scalar','pick variables'}
2672                FieldList=GetFieldData.PanelScalar.scalar;
2673                if ischar(FieldList)
2674                    FieldList={FieldList};
2675                end
2676            case '1D plot'
2677
2678            case 'civdata...'
2679                FieldList=set_field_list('U','V','C');
2680                set(handles.FieldName,'Value',2) % set menu to 'velocity
2681        end
2682        if ~strcmp(GetFieldData.FieldOption,'civdata...')
2683            TimeNameStr=GetFieldData.Time.SwitchVarIndexTime;
2684            switch TimeNameStr
2685                case 'file index'
2686                    set(handles.TimeName,'String','');
2687                case 'attribute'
2688                    set(handles.TimeName,'String',['att:' GetFieldData.Time.TimeName]);
2689                case 'variable'
2690                    set(handles.TimeName,'String',['var:' GetFieldData.Time.TimeName])
2691                    set(handles.NomType,'String','*')
2692                    set(handles.RootFile,'String',[get(handles.RootFile,'String') get(handles.FileIndex,'String')])% A VERIFIER !!!!!!
2693                    set(handles.FileIndex,'String','')
2694                    ParamIn.TimeVarName=GetFieldData.Time.TimeName;
2695                case 'matrix_index'
2696                    set(handles.TimeName,'String',['dim:' GetFieldData.Time.TimeName]);
2697                    set(handles.NomType,'String','*')
2698                    set(handles.RootFile,'String',[get(handles.RootFile,'String') get(handles.FileIndex,'String')])
2699                    set(handles.FileIndex,'String','')
2700                    ParamIn.TimeDimName=GetFieldData.Time.TimeName;
2701            end
2702        end
2703        set(handles.FieldName_1,'Value',1)
2704        set(handles.FieldName_1,'String',[FieldList; {'get_field...'}]);
2705    end
2706end   
2707
2708
2709%%%%%%%%%%%%%
2710function [ind_remove]=find_pairs(dirpair,ind_i,last_i)
2711indsel=ind_i;
2712indiff=diff(ind_i); %test index increment to detect multiplets (several pairs with the same index ind_i) and holes in the series
2713indiff=[1 indiff last_i-ind_i(end)+1];%for testing gaps with the imposed bounds
2714if ~isempty(indiff)
2715    indiff2=diff(indiff);
2716    indiffp=[indiff2 1];
2717    indiffm=[1 indiff2];
2718    ind_multi_m=find((indiff==0)&(indiffm<0))-1;%indices of first members of multiplets
2719    ind_multi_p=find((indiff==0)&(indiffp>0));%indices of last members of multiplets
2720    %for each multiplet, select the most recent file
2721    ind_remove=[];
2722    for i=1:length(ind_multi_m)
2723        ind_pairs=ind_multi_m(i):ind_multi_p(i);
2724        for imulti=1:length(ind_pairs)
2725            datepair(imulti)=datenum(dirpair(ind_pairs(imulti)).date);%dates of creation
2726        end
2727        [datenew,indsort2]=sort(datepair); %sort the multiplet by creation date
2728        ind_s=indsort2(1:end-1);%
2729        ind_remove=[ind_remove ind_pairs(ind_s)];%remove these indices, leave the last one
2730    end
2731end
2732
2733%------------------------------------------------------------------------
2734% --- determine the list of index pairstring of processing file
2735function [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)
2736%------------------------------------------------------------------------
2737num_i1=num_i;% set of first image numbers by default
2738num_i2=num_i;
2739num_j1=num_j;
2740num_j2=num_j;
2741num_i_out=num_i;
2742num_j_out=num_j;
2743% if isequal (NomType,'_1-2_1') || isequal (NomType,'_1-2')
2744if isequal(mode,'series(Di)')
2745    num_i1_line=num_i+ind_shift(3);% set of first image numbers
2746    num_i2_line=num_i+ind_shift(4);
2747    % adjust the first and last field number
2748        indsel=find(num_i1_line >= 1);
2749    num_i_out=num_i(indsel);
2750    num_i1_line=num_i1_line(indsel);
2751    num_i2_line=num_i2_line(indsel);
2752    num_j1=meshgrid(num_j,ones(size(num_i1_line)));
2753    num_j2=meshgrid(num_j,ones(size(num_i1_line)));
2754    [xx,num_i1]=meshgrid(num_j,num_i1_line);
2755    [xx,num_i2]=meshgrid(num_j,num_i2_line);
2756elseif isequal (mode,'series(Dj)')||isequal (mode,'bursts')
2757    if isequal(mode,'bursts') %case of bursts (png_old or png_2D)
2758        num_j1=ind_shift(1)*ones(size(num_i));
2759        num_j2=ind_shift(2)*ones(size(num_i));
2760    else
2761        num_j1_col=num_j+ind_shift(1);% set of first image numbers
2762        num_j2_col=num_j+ind_shift(2);
2763        % adjust the first field number
2764        indsel=find((num_j1_col >= 1));   
2765        num_j_out=num_j(indsel);
2766        num_j1_col=num_j1_col(indsel);
2767        num_j2_col=num_j2_col(indsel);
2768        [num_i1,num_j1]=meshgrid(num_i,num_j1_col);
2769        [num_i2,num_j2]=meshgrid(num_i,num_j2_col);
2770    end   
2771end
2772
2773%------------------------------------------------------------------------
2774% --- Executes on button press in CheckObject.
2775function CheckObject_Callback(hObject, eventdata, handles)
2776%------------------------------------------------------------------------
2777hset_object=findobj(allchild(0),'tag','set_object');%find the set_object interface handle
2778if get(handles.CheckObject,'Value')
2779    SeriesData=get(handles.series,'UserData');
2780    if isfield(SeriesData,'ProjObject') && ~isempty(SeriesData.ProjObject)
2781        set(handles.ViewObject,'Value',1)
2782        ViewObject_Callback(hObject, eventdata, handles)
2783    else
2784        if ishandle(hset_object)
2785            uistack(hset_object,'top')% show the GUI set_object if opened
2786        else
2787            %get the object file
2788            InputTable=get(handles.InputTable,'Data');
2789            defaultname=InputTable{1,1};
2790            if isempty(defaultname)
2791                defaultname={''};
2792            end
2793            fileinput=uigetfile_uvmat('pick a xml object file (or use uvmat to create it)',defaultname,'.xml');
2794            if isempty(fileinput)% exit if no object file is selected
2795                set(handles.CheckObject,'Value',0)
2796                return
2797            end
2798            %read the file
2799            data=xml2struct(fileinput);
2800            if ~isfield(data,'Type')
2801                msgbox_uvmat('ERROR',[fileinput ' is not an object xml file'])
2802                set(handles.CheckObject,'Value',0)
2803                return
2804            end
2805            if ~isfield(data,'ProjMode')
2806                data.ProjMode='none';
2807            end
2808            hset_object=set_object(data);% call the set_object interface
2809            set(hset_object,'Name','set_object_series')% name to distinguish from set_object used with uvmat
2810        end
2811        ProjObject=read_GUI(hset_object);
2812        set(handles.ProjObject,'String',ProjObject.Name);%display the object name
2813        SeriesData=get(handles.series,'UserData');
2814        SeriesData.ProjObject=ProjObject;
2815        set(handles.series,'UserData',SeriesData);
2816    end
2817    set(handles.EditObject,'Visible','on');
2818    set(handles.DeleteObject,'Visible','on');
2819    set(handles.ViewObject,'Visible','on');
2820    set(handles.ProjObject,'Visible','on');
2821else
2822    set(handles.EditObject,'Visible','off');
2823    set(handles.DeleteObject,'Visible','off');
2824    set(handles.ViewObject,'Visible','off');
2825    if ~ishandle(hset_object)
2826        set(handles.ViewObject,'Value',0);
2827    end
2828    set(handles.ProjObject,'Visible','off');
2829end
2830
2831%------------------------------------------------------------------------
2832% --- Executes on button press in ViewObject.
2833%------------------------------------------------------------------------
2834function ViewObject_Callback(hObject, eventdata, handles)
2835
2836UserData=get(handles.series,'UserData');
2837hset_object=findobj(allchild(0),'Tag','set_object');
2838if ~isempty(hset_object)
2839    delete(hset_object)% refresh set_object if already opened
2840end
2841hset_object=set_object(UserData.ProjObject);
2842set(hset_object,'Name','view_object_series')
2843
2844
2845%------------------------------------------------------------------------
2846% --- Executes on button press in EditObject.
2847function EditObject_Callback(hObject, eventdata, handles)
2848%------------------------------------------------------------------------
2849if get(handles.EditObject,'Value')
2850    set(handles.ViewObject,'Value',0)
2851        UserData=get(handles.series,'UserData');
2852    hset_object=set_object(UserData.ProjObject);
2853    set(hset_object,'Name','edit_object_series')
2854    set(get(hset_object,'Children'),'Enable','on')
2855else
2856    hset_object=findobj(allchild(0),'Tag','set_object');
2857    if ~isempty(hset_object)
2858        set(get(hset_object,'Children'),'Enable','off')
2859    end
2860end
2861
2862%------------------------------------------------------------------------
2863% --- Executes on button press in DeleteObject.
2864function DeleteObject_Callback(hObject, eventdata, handles)
2865%------------------------------------------------------------------------
2866SeriesData=get(handles.series,'UserData');
2867SeriesData.ProjObject=[];
2868set(handles.series,'UserData',SeriesData)
2869set(handles.ProjObject,'String','')
2870set(handles.ProjObject,'Visible','off')
2871set(handles.CheckObject,'Value',0)
2872set(handles.ViewObject,'Visible','off')
2873set(handles.EditObject,'Visible','off')
2874hset_object=findobj(allchild(0),'name','set_object_series');
2875if ~isempty(hset_object)
2876    delete(hset_object)
2877end
2878set(handles.DeleteObject,'Visible','off')
2879
2880%------------------------------------------------------------------------
2881% --- Executed when CheckMask is activated
2882%------------------------------------------------------------------------
2883function CheckMask_Callback(hObject, eventdata, handles)
2884
2885if get(handles.CheckMask,'Value')
2886    InputTable=get(handles.InputTable,'Data');
2887    nbview=size(InputTable,1);
2888    MaskTable=cell(nbview,1);%default
2889    ListMask=cell(nbview,1);%default
2890    MaskData=get(handles.MaskTable,'Data');
2891    MaskData(size(MaskData,1):nbview,1)=cell(size(MaskData,1):nbview,1);%complement if undefined lines
2892    for iview=1:nbview
2893        ListMask{iview,1}=num2str(iview);
2894        RootPath=InputTable{iview,1};
2895        if ~isempty(RootPath)
2896            if isempty(MaskData{iview})
2897                SubDir=InputTable{iview,2};
2898                MaskPath=fullfile(RootPath,[regexprep(SubDir,'\..*','') '.mask']);%take the root part of SubDir, before the first dot '.'
2899                if exist(MaskPath,'dir')
2900                    ListStruct=dir(MaskPath);%look for a mask file
2901                    ListCells=struct2cell(ListStruct);% transform dir struct to a cell arrray
2902                    check_dir=cell2mat(ListCells(4,:));% =1 for directories, =0 for files
2903                    ListFiles=ListCells(1,:);%list of file and dri names
2904                    ListFiles=ListFiles(~check_dir);%list of file names (excluding dir)
2905                    mdetect=0;
2906                    if ~isempty(ListFiles)
2907                        for ifile=1:numel(ListFiles)
2908                            [tild,tild,MaskFile{ifile},i1_series,i2_series,j1_series,j2_series,MaskNomType,MaskFileType]=find_file_series(MaskPath,ListFiles{ifile},0);
2909                            if strcmp(MaskFileType,'image') && isempty(i2_series) && isempty(j2_series)
2910                                mdetect=1;
2911                                MaskName=ListFiles{ifile};
2912                            end
2913                            if ~strcmp(MaskFile{ifile},MaskFile{1})
2914                                mdetect=0;% cancel detection test in case of multiple masks, use the brower for selection
2915                                break
2916                            end
2917                        end
2918                    end
2919                    if mdetect==1
2920                        MaskName=fullfile(MaskPath,'mask_1.png');
2921                    else
2922                        MaskName=uigetfile_uvmat('select a mask file:',MaskPath,'image');
2923                    end
2924                else
2925                    MaskName=uigetfile_uvmat('select a mask file:',RootPath,'image');
2926                end
2927                MaskTable{iview,1}=MaskName ;
2928                ListMask{iview,1}=num2str(iview);
2929            end
2930        end
2931    end
2932    set(handles.MaskTable,'Data',MaskTable)
2933    set(handles.MaskTable,'Visible','on')
2934    set(handles.MaskBrowse,'Visible','on')
2935    set(handles.ListMask,'Visible','on')
2936    set(handles.ListMask,'String',ListMask)
2937    set(handles.ListMask,'Value',1)
2938else
2939    set(handles.MaskTable,'Visible','off')
2940    set(handles.MaskBrowse,'Visible','off')
2941    set(handles.ListMask,'Visible','off')
2942end
2943
2944%------------------------------------------------------------------------
2945% --- Executes on button press in MaskBrowse.
2946%------------------------------------------------------------------------
2947function MaskBrowse_Callback(hObject, eventdata, handles)
2948
2949InputTable=get(handles.InputTable,'Data');
2950iview=get(handles.ListMask,'Value');
2951RootPath=InputTable{iview,1};
2952MaskName=uigetfile_uvmat('select a mask file:',RootPath,'image');
2953if ~isempty(MaskName)
2954    MaskTable=get(handles.MaskTable,'Data');
2955    MaskTable{iview,1}=MaskName ;
2956    set(handles.MaskTable,'Data',MaskTable)
2957end
2958
2959%------------------------------------------------------------------------
2960% --- Executes when selected cell(s) is changed in MaskTable.
2961%------------------------------------------------------------------------
2962function MaskTable_CellSelectionCallback(hObject, eventdata, handles)
2963
2964if numel(eventdata.Indices)>=1
2965set(handles.ListMask,'Value',eventdata.Indices(1))
2966end
2967
2968%-------------------------------------------------------------------
2969function MenuHelp_Callback(hObject, eventdata, handles)
2970%-------------------------------------------------------------------
2971
2972
2973% path_to_uvmat=which ('uvmat');% check the path of uvmat
2974% pathelp=fileparts(path_to_uvmat);
2975% helpfile=fullfile(pathelp,'uvmat_doc','uvmat_doc.html');
2976% if isempty(dir(helpfile)), msgbox_uvmat('ERROR','Please put the help file uvmat_doc.html in the sub-directory /uvmat_doc of the UVMAT package')
2977% else
2978%     addpath (fullfile(pathelp,'uvmat_doc'))
2979%     web([helpfile '#series'])
2980% end
2981
2982%-------------------------------------------------------------------
2983% --- Executes on selection change in TransformName.
2984function TransformName_Callback(hObject, eventdata, handles)
2985%----------------------------------------------------------------------
2986TransformList=get(handles.TransformName,'String');
2987TransformIndex=get(handles.TransformName,'Value');
2988TransformName=TransformList{TransformIndex};
2989TransformPathList=get(handles.TransformName,'UserData');
2990nb_builtin_transform=4;
2991if isequal(TransformName,'more...');     
2992    FileName=uigetfile_uvmat('Pick a transform function',get(handles.TransformPath,'String'),'.m');
2993    if isempty(FileName)
2994        return     %browser closed without choice
2995    end
2996    [TransformPath,TransformName,TransformExt]=fileparts(FileName);% removes extension .m
2997    if ~strcmp(TransformExt,'.m')
2998        msgbox_uvmat('ERROR','a Matlab function .m must be introduced');
2999        return
3000    end
3001     % insert the choice in the menu
3002    TransformIndex=find(strcmp(TransformName,TransformList),1);% look for the selected function in the menu Action
3003    if isempty(TransformIndex)%the input string does not exist in the menu
3004        TransformIndex= length(TransformList);
3005        TransformList=[TransformList(1:end-1);{TransformName};TransformList(end)];% the selected function is appended in the menu, before the last item 'more...'
3006        set(handles.TransformName,'String',TransformList)
3007        TransformPathList=[TransformPathList;{TransformPath}];
3008    else% the input function already exist, we update its path (possibly new)
3009        TransformPathList{TransformIndex}=TransformPath;%
3010        set(handles.TransformName,'Value',TransformIndex)
3011    end
3012   % save the new menu in the personal file 'uvmat_perso.mat'
3013   dir_perso=prefdir;%personal Matalb directory
3014   profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
3015   if exist(profil_perso,'file')
3016       for ilist=nb_builtin_transform+1:numel(TransformPathList)
3017           TransformListUser{ilist-nb_builtin_transform}=TransformList{ilist};
3018           TransformPathListUser{ilist-nb_builtin_transform}=TransformPathList{ilist};
3019       end
3020       TransformPathListUser=TransformPathListUser';
3021       TransformListUser=TransformListUser';
3022       save (profil_perso,'TransformPathListUser','TransformListUser','-append'); %store the root name for future opening of uvmat
3023   end
3024end
3025
3026%display the current function path
3027set(handles.TransformPath,'String',TransformPathList{TransformIndex}); %show the path to the senlected function
3028set(handles.TransformName,'UserData',TransformPathList);
3029
3030%% create the function handle of the selected fct
3031if ~isempty(TransformName)
3032    if ~exist(TransformPathList{TransformIndex},'dir')
3033        msgbox_uvmat('ERROR',['The prescribed transform function path ' TransformPathList{TransformIndex} ' does not exist']);
3034        return
3035    end
3036    current_dir=pwd;%current working dir
3037    cd(TransformPathList{TransformIndex})
3038    transform_handle=str2func(TransformName);
3039    cd(current_dir)
3040    Field.Action.RUN=0;% indicate that the transform fct is called only to get input param
3041    DataOut=feval(transform_handle,Field,[]);% execute the transform fct to get the required conditions
3042    if isfield(DataOut,'TransformInput')%  used to add transform parameters at selection of the transform fct
3043        SeriesData=get(handles.series,'UserData');
3044        SeriesData.TransformInput=DataOut.TransformInput;
3045        set(handles.series,'UserData',SeriesData)
3046    end
3047end
3048
3049%------------------------------------------------------------------------
3050% --- fct activated by the upper bar menu ExportConfig
3051%------------------------------------------------------------------------
3052function MenuDisplayConfig_Callback(hObject, eventdata, handles)
3053
3054global Param
3055Param=read_GUI_series(handles);
3056evalin('base','global Param')%make CurData global in the workspace
3057display('current series config :')
3058evalin('base','Param') %display CurData in the workspace
3059commandwindow; %brings the Matlab command window to the front
3060
3061%------------------------------------------------------------------------
3062% --- fct activated by the upper bar menu InportConfig: import
3063%     menu settings from an xml file (stored in /0_XML for each run)
3064%------------------------------------------------------------------------
3065function MenuImportConfig_Callback(hObject, eventdata, handles)
3066
3067%% use a browser to choose the xml file containing the processing config
3068InputTable=get(handles.InputTable,'Data');
3069oldfile=InputTable{1,1};%current path in InputTable
3070if isempty(oldfile)
3071    % use a file name stored in prefdir
3072    dir_perso=prefdir;
3073    profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
3074    if exist(profil_perso,'file')
3075        h=load (profil_perso);
3076        if isfield(h,'RootPath') && ischar(h.RootPath)
3077            oldfile=h.RootPath;
3078        end
3079    end
3080end
3081filexml=uigetfile_uvmat('pick a xml parameter file',oldfile,'.xml');% get the xml file containing processing parameters
3082if isempty(filexml), return, end % quit function if an xml file has not been opened
3083
3084%% fill the GUI series with the content of the xml file
3085Param=xml2struct(filexml);% read the input xml file as a Matlab structure
3086
3087% ask to stop current Action if button RUN is in action (another process is already running)
3088if isequal(get(handles.RUN,'Value'),1)
3089    answer= msgbox_uvmat('INPUT_Y-N','stop current Action process?');
3090    if strcmp(answer,'Yes')
3091        STOP_Callback(hObject, eventdata, handles)
3092    else
3093        return
3094    end
3095end
3096Param.Action.RUN=0; %desactivate the input RUN=1
3097
3098fill_GUI(Param,handles.series)% fill the elements of the GUI series with the input parameters
3099SeriesData=get(handles.series,'UserData');
3100if isfield(Param,'InputFields')
3101    ListField=Param.InputFields.FieldName;
3102    if ischar(ListField),ListField={ListField}; end
3103    set(handles.FieldName,'String',[ListField;{'get-field...'}])
3104     set(handles.FieldName,'Value',1:numel(ListField))
3105     set(handles.FieldName,'Visible','on')
3106end       
3107if isfield(Param,'ActionInput')%  introduce  parameters specific to an Action fct, for instance PIV parameters
3108    set(handles.ActionInput,'Visible','on')
3109    set(handles.ActionInput,'Value',0)
3110    Param.ActionInput.ConfigSource=filexml;% record the source of config for future info
3111    SeriesData.ActionInput=Param.ActionInput;
3112end
3113if isfield(Param,'TransformInput')%  introduce  parameters specific to a transform fct
3114    SeriesData.TransformInput=Param.TransformInput;
3115end
3116if isfield(Param,'ProjObject') %introduce projection object if relevant
3117    SeriesData.ProjObject=Param.ProjObject;
3118end
3119set(handles.series,'UserData',SeriesData)
3120if isfield(Param,'CheckObject') && isequal(Param.CheckObject,1)
3121    set(handles.ProjObject,'String',Param.ProjObject.Name)
3122    set(handles.ViewObject,'Visible','on')
3123    set(handles.EditObject,'Visible','on')
3124    set(handles.DeleteObject,'Visible','on')
3125else     
3126    set(handles.ProjObject,'String','')
3127    set(handles.ProjObject,'Visible','off')
3128    set(handles.ViewObject,'Visible','off')
3129    set(handles.EditObject,'Visible','off')
3130    set(handles.DeleteObject,'Visible','off')     
3131end     
3132set(handles.REFRESH,'BackgroundColor',[1 0 1]); %paint REFRESH button in magenta to indicate that it should be activated
3133
3134
3135%------------------------------------------------------------------------
3136% --- Executes when the GUI series is resized.
3137%------------------------------------------------------------------------
3138function series_ResizeFcn(hObject, eventdata, handles)
3139
3140%% input table
3141set(handles.InputTable,'Unit','pixel')
3142Pos=get(handles.InputTable,'Position');
3143set(handles.InputTable,'Unit','normalized')
3144ColumnWidth=round([0.5 0.14 0.14 0.14 0.08]*(Pos(3)-52));
3145ColumnWidth=num2cell(ColumnWidth);
3146set(handles.InputTable,'ColumnWidth',ColumnWidth)
3147
3148%% MinIndex_j and MaxIndex_i
3149unit=get(handles.MinIndex_i,'Unit');
3150set(handles.MinIndex_i,'Unit','pixel')
3151Pos=get(handles.MinIndex_i,'Position');
3152set(handles.MinIndex_i,'Unit',unit)
3153set(handles.MinIndex_i,'ColumnWidth',{Pos(3)-18})
3154set(handles.MaxIndex_i,'ColumnWidth',{Pos(3)-18})
3155set(handles.MinIndex_j,'ColumnWidth',{Pos(3)-18})
3156set(handles.MaxIndex_j,'ColumnWidth',{Pos(3)-18})
3157
3158%% TimeTable
3159set(handles.TimeTable,'Unit','pixel')
3160Pos=get(handles.TimeTable,'Position');
3161set(handles.TimeTable,'Unit','normalized')
3162% ColumnWidth=get(handles.TimeTable,'ColumnWidth');
3163ColumnWidth=num2cell(floor([0.2 0.2 0.2 0.2 0.2]*(Pos(3)-20)));
3164set(handles.TimeTable,'ColumnWidth',ColumnWidth)
3165
3166
3167%% PairString
3168set(handles.PairString,'Unit','pixel')
3169Pos=get(handles.PairString,'Position');
3170set(handles.PairString,'Unit','normalized')
3171set(handles.PairString,'ColumnWidth',{Pos(3)-5})
3172
3173%% MaskTable
3174set(handles.MaskTable,'Unit','pixel')
3175Pos=get(handles.MaskTable,'Position');
3176set(handles.MaskTable,'Unit','normalized')
3177set(handles.MaskTable,'ColumnWidth',{Pos(3)-5})
3178
3179%------------------------------------------------------------------------
3180% --- Executes on button press in status.
3181%------------------------------------------------------------------------
3182function status_Callback(hObject, eventdata, handles)
3183
3184if get(handles.status,'Value')
3185    set(handles.status,'BackgroundColor',[1 1 0])
3186    drawnow
3187    Param=read_GUI(handles.series);
3188    RootPath=Param.InputTable{1,1};
3189    if ~isfield(Param,'OutputSubDir')   
3190        msgbox_uvmat('ERROR','no standard sub-directory definition for output files, use a browser to check the output')
3191        set(handles.status,'BackgroundColor',[0 1 0])
3192        return
3193    end
3194    OutputSubDir=[Param.OutputSubDir Param.OutputDirExt];% subdirectory for output files
3195    OutputDir=fullfile(RootPath,OutputSubDir);
3196    if exist(OutputDir,'dir')
3197        uigetfile_uvmat('status_display',OutputDir)
3198    else
3199        msgbox_uvmat('ERROR','output folder not created yet: calculation did not start')
3200        set(handles.status,'BackgroundColor',[0 1 0])
3201    end
3202else
3203    %% delete current display fig if selection is off
3204    set(handles.status,'BackgroundColor',[0 1 0])
3205    hfig=findobj(allchild(0),'name','status_display');
3206    if ~isempty(hfig)
3207        delete(hfig)
3208    end
3209    return
3210end
3211
3212
3213%------------------------------------------------------------------------   
3214% launched by selecting a file on the list
3215%------------------------------------------------------------------------
3216function view_file(hObject, eventdata)
3217
3218list=get(hObject,'String');
3219index=get(hObject,'Value');
3220rootroot=get(hObject,'UserData');
3221selectname=list{index};
3222ind_dot=regexp(selectname,'\.\.\.');
3223if ~isempty(ind_dot)
3224    selectname=selectname(1:ind_dot-1);
3225end
3226FullSelectName=fullfile(rootroot,selectname);
3227if exist(FullSelectName,'dir')% a directory has been selected
3228    ListFiles=dir(FullSelectName);
3229    ListDisplay=cell(numel(ListFiles),1);
3230    for ilist=2:numel(ListDisplay)% suppress the first line '.'
3231        ListDisplay{ilist-1}=ListFiles(ilist).name;
3232    end
3233    set(hObject,'Value',1)
3234    set(hObject,'String',ListDisplay)
3235    if strcmp(selectname,'..')
3236        FullSelectName=fileparts(fileparts(FullSelectName));
3237    end
3238    set(hObject,'UserData',FullSelectName)
3239    hfig=get(hObject,'parent');
3240    htitlebox=findobj(hfig,'tag','titlebox');   
3241    set(htitlebox,'String',FullSelectName)
3242elseif exist(FullSelectName,'file')%visualise the vel field if it exists
3243    FileInfo=get_file_info(FullSelectName);   
3244    if strcmp(FileInfo.FileType,'txt')
3245        edit(FullSelectName)
3246    elseif strcmp(FileInfo.FileType,'xml')
3247        editxml(FullSelectName)
3248    else
3249        uvmat(FullSelectName)
3250    end
3251    set(gcbo,'Value',1)
3252end
3253
3254
3255%------------------------------------------------------------------------   
3256% launched by refreshing the status figure
3257%------------------------------------------------------------------------
3258function refresh_GUI(hfig)
3259
3260htitlebox=findobj(hfig,'tag','titlebox');
3261hlist=findobj(hfig,'tag','list');
3262hseries=findobj(allchild(0),'tag','series');
3263hstatus=findobj(hseries,'tag','status');
3264StatusData=get(hstatus,'UserData');
3265OutputDir=get(htitlebox,'String');
3266if ischar(OutputDir),OutputDir={OutputDir};end
3267ListFiles=dir(OutputDir{1});
3268if numel(ListFiles)<1
3269    return
3270end
3271ListFiles(1)=[];%removes the first line ='.'
3272ListDisplay=cell(numel(ListFiles),1);
3273testrecent=0;
3274datnum=zeros(numel(ListDisplay),1);
3275for ilist=1:numel(ListDisplay)
3276    ListDisplay{ilist}=ListFiles(ilist).name;
3277      if ~ListFiles(ilist).isdir && isfield(ListFiles(ilist),'datenum')
3278            datnum(ilist)=ListFiles(ilist).datenum;%only available in recent matlab versions
3279            testrecent=1;
3280       end
3281end
3282set(hlist,'String',ListDisplay)
3283
3284%% Look at date of creation
3285ListDisplay=ListDisplay(datnum~=0);
3286datnum=datnum(datnum~=0);%keep the non zero values corresponding to existing files
3287NbOutputFile=[];
3288if isempty(datnum)
3289    if testrecent
3290        message='no civ result created yet';
3291    else
3292        message='';
3293    end
3294else
3295    [first,indfirst]=min(datnum);
3296    [last,indlast]=max(datnum);
3297    NbOutputFile_str='?';
3298    NbOutputFile=[];
3299    if isfield(StatusData,'NbOutputFile')
3300        NbOutputFile=StatusData.NbOutputFile;
3301        NbOutputFile_str=num2str(NbOutputFile);
3302    end
3303    message={[num2str(numel(datnum)) ' file(s) done over ' NbOutputFile_str] ;['oldest modification:  ' ListDisplay{indfirst} ' : ' datestr(first)];...
3304        ['latest modification:  ' ListDisplay{indlast} ' : ' datestr(last)]};
3305end
3306set(htitlebox,'String', [OutputDir{1};message])
3307
3308%% update the waitbar
3309hwaitbar=findobj(hfig,'tag','waitbar');
3310if ~isempty(NbOutputFile)
3311    BarPosition=get(hwaitbar,'Position');
3312    BarPosition(3)=0.9*numel(datnum)/NbOutputFile;
3313    set(hwaitbar,'Position',BarPosition)
3314end
3315
3316%------------------------------------------------------------------------
3317% --- Executes on selection change in ActionExt.
3318%------------------------------------------------------------------------
3319function ActionExt_Callback(hObject, eventdata, handles)
3320
3321ActionExtList=get(handles.ActionExt,'String');
3322ActionExt=ActionExtList{get(handles.ActionExt,'Value')};
3323if strcmp(ActionExt,'.py (in dev.)')
3324    set(handles.RunMode,'Value',2)
3325end
3326
3327%function num_NbProcess_Callback(hObject, eventdata, handles)
3328
3329
3330function num_NbSlice_Callback(hObject, eventdata, handles)
3331NbSlice=str2num(get(handles.num_NbSlice,'String'));
3332%set(handles.num_NbProcess,'String',num2str(NbSlice))
3333
3334%------------------------------------------------------------------------
3335% --- set the visibility of relevant velocity type menus:
3336function menu=set_veltype_display(Civ,FileType)
3337%------------------------------------------------------------------------
3338if ~exist('FileType','var')
3339    FileType='civx';
3340end
3341switch FileType
3342    case 'civx'
3343        menu={'civ1';'interp1';'filter1';'civ2';'interp2';'filter2'};
3344        if isequal(Civ,0)
3345            imax=0;
3346        elseif isequal(Civ,1) || isequal(Civ,2)
3347            imax=1;
3348        elseif isequal(Civ,3)
3349            imax=3;
3350        elseif isequal(Civ,4) || isequal(Civ,5)
3351            imax=4;
3352        elseif isequal(Civ,6) %patch2
3353            imax=6;
3354        end
3355    case 'civdata'
3356        menu={'civ1';'filter1';'civ2';'filter2'};
3357        if isequal(Civ,0)
3358            imax=0;
3359        elseif isequal(Civ,1) || isequal(Civ,2)
3360            imax=1;
3361        elseif isequal(Civ,3)
3362            imax=2;
3363        elseif isequal(Civ,4) || isequal(Civ,5)
3364            imax=3;
3365        elseif isequal(Civ,6) %patch2
3366            imax=4;
3367        end
3368end
3369menu=menu(1:imax);
3370
3371
3372% --- Executes on mouse motion over figure - except title and menu.
3373function series_WindowButtonMotionFcn(hObject, eventdata, handles)
3374set(hObject,'Pointer','arrow');
3375
3376
3377% --- Executes on button press in SetPairs.
3378function SetPairs_Callback(hObject, iview, handles)
3379
3380%% delete previous occurrence of 'set_pairs'
3381hfig=findobj(allchild(0),'Tag','set_pairs');
3382if ~isempty(hfig)
3383delete(hfig)
3384end
3385
3386%% create the GUI set_pairs
3387set(0,'Unit','points')
3388ScreenSize=get(0,'ScreenSize');% get the size of the screen, to put the fig on the upper right
3389Width=220;% fig width in points (1/72 inch)
3390Height=min(0.8*ScreenSize(4),300);
3391Left=ScreenSize(3)- Width-40; %right edge close to the right, with margin=40
3392Bottom=ScreenSize(4)-Height-40; %put fig at top right
3393hfig=findobj(allchild(0),'Tag','set_slice');
3394if ~isempty(hfig),delete(hfig), end; %delete existing version of the GUI
3395hfig=figure('name','set_pairs','tag','set_pairs','MenuBar','none','NumberTitle','off','Unit','points','Position',[Left,Bottom,Width,Height]);
3396BackgroundColor=get(hfig,'Color');
3397SeriesData=get(handles.series,'UserData');
3398TimeUnit=get(handles.TimeUnit,'String');
3399PairString=get(handles.PairString,'Data');
3400ListViewLines=find(cellfun('isempty',PairString)==0);%find list of non empty pairs
3401ListViewMenu=cell(numel(ListViewLines),1);
3402for ilist=1:numel(ListViewLines)
3403    ListViewMenu{ilist}=num2str(ListViewLines(ilist));
3404end
3405if isempty(iview)
3406    ListViewValue=numel(ListViewLines);% we work by default on the pair option for the last line which requires pairs
3407    iview=ListViewLines(end);
3408else
3409    ListViewValue=find(ListViewLines==iview);
3410end
3411ref_i=str2num(get(handles.num_first_i,'String'));
3412ref_j=1;%default
3413if strcmp(get(handles.num_first_j,'String'),'Visible')
3414    ref_j=str2num(get(handles.num_first_j,'String'));
3415end
3416[ModeMenu,ModeValue]=update_mode(SeriesData.i1_series{iview},SeriesData.i2_series{iview},SeriesData.j2_series{iview});
3417displ_pair=update_listpair(SeriesData.i1_series{iview},SeriesData.i2_series{iview},SeriesData.j1_series{iview},SeriesData.j2_series{iview},ModeMenu{ModeValue},...
3418                                                     SeriesData.Time{iview},TimeUnit,ref_i,ref_j,SeriesData.FileInfo{iview});
3419% first raw of the GUI
3420uicontrol('Style','text','Units','normalized', 'Position', [0.05 0.88 0.5 0.1],'BackgroundColor',BackgroundColor,...
3421    'String','row to edit #','FontUnits','points','FontSize',12,'FontWeight','bold','ForegroundColor','blue','HorizontalAlignment','right');%title
3422uicontrol('Style','popupmenu','Units','normalized', 'Position', [0.54 0.8 0.3 0.2],'BackgroundColor',[1 1 1],...
3423    'Callback',@(hObject,eventdata)ListView_Callback(hObject,eventdata),'String',ListViewMenu,'Value',ListViewValue,'FontUnits','points','FontSize',12,'FontWeight','bold',...
3424    'Tag','ListView','TooltipString','''ListView'':choice of the file series w for pair display');
3425% second raw of the GUI
3426uicontrol('Style','text','Units','normalized', 'Position', [0.05 0.79 0.7 0.1],'BackgroundColor',BackgroundColor,...
3427    'String','mode of index pairing:','FontUnits','points','FontSize',12,'FontWeight','bold','ForegroundColor','blue','HorizontalAlignment','left');%title
3428uicontrol('Style','popupmenu','Units','normalized', 'Position', [0.05 0.62 0.9 0.2],'BackgroundColor',[1 1 1],...
3429    'Callback',@(hObject,eventdata)Mode_Callback(hObject,eventdata),'String',ModeMenu,'Value',ModeValue,'FontUnits','points','FontSize',12,'FontWeight','bold',...
3430    'Tag','Mode','TooltipString','''Mode'': choice of the image pair mode');
3431% third raw
3432uicontrol('Style','text','Units','normalized', 'Position', [0.05 0.6 0.7 0.1],'BackgroundColor',BackgroundColor,...
3433    'String','pair choice:','FontUnits','points','FontSize',12,'FontWeight','bold','ForegroundColor','blue','HorizontalAlignment','left');%title
3434uicontrol('Style','listbox','Units','normalized', 'Position', [0.05 0.42 0.9 0.2],'BackgroundColor',[1 1 1],...
3435    'Callback',@(hObject,eventdata)ListPair_Callback(hObject,eventdata),'String',displ_pair,'Value',1,'FontUnits','points','FontSize',12,'FontWeight','bold',...
3436    'Tag','ListPair','TooltipString','''ListPair'': menu for selecting the image pair');
3437uicontrol('Style','text','Units','normalized', 'Position', [0.1 0.22 0.8 0.1],'BackgroundColor',BackgroundColor,...
3438    'String','ref_i           ref_j','FontUnits','points','FontSize',12,'FontWeight','bold','ForegroundColor','blue','HorizontalAlignment','center');%title
3439uicontrol('Style','edit','Units','normalized', 'Position', [0.15 0.17 0.3 0.08],'BackgroundColor',[1 1 1],...
3440    'Callback',@(hObject,eventdata)num_ref_i_Callback(hObject,eventdata),'String',num2str(ref_i),'FontUnits','points','FontSize',12,'FontWeight','bold',...
3441    'Tag','num_ref_i','TooltipString','''num_ref_i'': reference field index i used to display dt in ''list_pair_civ''');
3442uicontrol('Style','edit','Units','normalized', 'Position', [0.55 0.17 0.3 0.08],'BackgroundColor',[1 1 1],...
3443    'Callback',@(hObject,eventdata)num_ref_j_Callback(hObject,eventdata),'String',num2str(ref_j),'FontUnits','points','FontSize',12,'FontWeight','bold',...
3444    'Tag','num_ref_j','TooltipString','''num_ref_j'': reference field index i used to display dt in ''list_pair_civ''');
3445uicontrol('Style','pushbutton','Units','normalized', 'Position', [0.01 0.01 0.3 0.12],'BackgroundColor',[0 1 0],...
3446    'Callback',@(hObject,eventdata)OK_Callback(hObject,eventdata),'String','OK','FontUnits','points','FontSize',12,'FontWeight','bold',...
3447    'Tag','OK','TooltipString','''OK'': validate the choice');
3448%  last raw  of the GUI: pushbuttons
3449% uicontrol('Style','pushbutton','Units','normalized', 'Position', [0.35 0.01 0.3 0.15],'BackgroundColor',[0 1 0],'String','OK','Callback',@(hObject,eventdata)OK_Callback(hObject,eventdata),...
3450%     'FontWeight','bold','FontUnits','points','FontSize',12,'TooltipString','''OK'': apply the output to the current field series in uvmat');
3451drawnow
3452
3453%------------------------------------------------------------------------
3454function ListView_Callback(hObject,eventdata)
3455Mode_Callback(hObject,eventdata)
3456
3457%------------------------------------------------------------------------   
3458function Mode_Callback(hObject,eventdata)
3459%% get input info
3460hseries=findobj(allchild(0),'tag','series');%handles of the GUI series
3461hhseries=guidata(hseries);%handles of the elements in the GUI series
3462TimeUnit=get(hhseries.TimeUnit,'String');
3463SeriesData=get(hseries,'UserData');
3464mode_list=get(hObject,'String');
3465mode=mode_list{get(hObject,'Value')};
3466hListView=findobj(get(hObject,'parent'),'Tag','ListView');
3467iview=get(hListView,'Value');
3468i1_series=SeriesData.i1_series{iview};
3469i2_series=SeriesData.i2_series{iview};
3470j1_series=SeriesData.j1_series{iview};
3471j2_series=SeriesData.j2_series{iview};
3472
3473%% enable j index visibility after the new choice
3474status_j='on';%default
3475if isempty(find(~cellfun(@isempty,SeriesData.j1_series), 1)); % case of empty j indices
3476    status_j='off'; % no j index needed
3477elseif strcmp(get(handles.PairString,'Visible'),'on')
3478    check_burst=cellfun(@isempty,regexp(PairString,'^j'));%=0 for burst case, 1 otherwise
3479    if isempty(find(check_burst, 1))% if all pair string begins by j (burst)
3480        status_j='off'; % no j index needed for bust case
3481    end
3482end
3483enable_j(handles,status_j) % no j index needed
3484
3485%% get the reference indices for the time interval Dt
3486href_i=findobj(get(hObject,'parent'),'Tag','ref_i');
3487ref_i=[];ref_j=[];
3488if strcmp(get(href_i,'Visible'),'on')
3489    ref_i=str2num(get(href_i,'String'));
3490end
3491if isempty(ref_i)
3492    ref_i=1;
3493end
3494if isempty(ref_j)
3495    ref_j=1;
3496end
3497
3498%% update the menu ListPair
3499Menu=update_listpair(i1_series,i2_series,j1_series,j2_series,mode,SeriesData.Time{iview},TimeUnit,ref_i,ref_j,FileInfo);
3500hlist_pairs=findobj(get(hObject,'parent'),'Tag','ListPair');
3501set(hlist_pairs,'Value',1)% set the first choice by default in ListPair
3502set(hlist_pairs,'String',Menu)% set the menu in ListPair
3503ListPair_Callback(hlist_pairs,[])% apply the default choice in ListPair
3504
3505%-------------------------------------------------------------
3506% --- Executes on selection in ListPair.
3507function ListPair_Callback(hObject,eventdata)
3508%------------------------------------------------------------
3509list_pair=get(hObject,'String');%get the menu of image pairs
3510if isempty(list_pair)
3511    string='';
3512else
3513    string=list_pair{get(hObject,'Value')};
3514   % string=regexprep(string,',.*','');%removes time indication (after ',')
3515end
3516hseries=findobj(allchild(0),'tag','series');
3517hPairString=findobj(hseries,'tag','PairString');
3518PairString=get(hPairString,'Data');
3519hListView=findobj(get(hObject,'parent'),'Tag','ListView');
3520iview=get(hListView,'Value');
3521PairString{iview,1}=string;
3522% report the selected pair string to the table PairString
3523set(hPairString,'Data',PairString)
3524
3525
3526%------------------------------------------------------------------------
3527function num_ref_i_Callback(hObject, eventdata)
3528%------------------------------------------------------------------------
3529Mode_Callback([],[])
3530
3531%------------------------------------------------------------------------
3532function num_ref_j_Callback(hObject, eventdata)
3533%------------------------------------------------------------------------
3534Mode_Callback([],[])
3535
3536%------------------------------------------------------------------------
3537function OK_Callback(hObject, eventdata)
3538%------------------------------------------------------------------------
3539delete(get(hObject,'parent'))
3540
3541
3542%------------------------------------------------------------------------
3543% --- Executes on button press in ClearLine.
3544%------------------------------------------------------------------------
3545function ClearLine_Callback(hObject, eventdata, handles)
3546InputTable=get(handles.InputTable,'Data');
3547iline=str2double(get(handles.InputLine,'String'));
3548if size(InputTable,1)>1
3549    InputTable(iline,:)=[];% suppress the current line if not the first
3550    set(handles.InputTable,'Data',InputTable);
3551end
3552set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH button to magenta color to indicate that input refr
3553
3554
3555% --- Executes on button press in MonitorCluster.
3556function MonitorCluster_Callback(hObject, eventdata, handles)
3557web('https://www.legi.grenoble-inp.fr/servload/monika')
3558
3559
3560
3561function OutputSubDir_Callback(hObject, eventdata, handles)
3562set(handles.OutputSubDir,'BackgroundColor',[1 1 1])
3563% hObject    handle to OutputSubDir (see GCBO)
3564% eventdata  reserved - to be defined in a future version of MATLAB
3565% handles    structure with handles and user data (see GUIDATA)
3566
3567% Hints: get(hObject,'String') returns contents of OutputSubDir as text
3568%        str2double(get(hObject,'String')) returns contents of OutputSubDir as a double
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