source: trunk/src/series.m @ 1085

Last change on this file since 1085 was 1085, checked in by sommeria, 4 months ago

aver_spectral added andsmall bug repairs

File size: 173.9 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
17%=======================================================================
18% Copyright 2008-2020, LEGI UMR 5519 / CNRS UGA G-INP, Grenoble, France
19%   http://www.legi.grenoble-inp.fr
20%   Joel.Sommeria - Joel.Sommeria (A) legi.cnrs.fr
21%
22%     This file is part of the toolbox UVMAT.
23%
24%     UVMAT is free software; you can redistribute it and/or modify
25%     it under the terms of the GNU General Public License as published
26%     by the Free Software Foundation; either version 2 of the license,
27%     or (at your option) any later version.
28%
29%     UVMAT is distributed in the hope that it will be useful,
30%     but WITHOUT ANY WARRANTY; without even the implied warranty of
31%     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
32%     GNU General Public License (see LICENSE.txt) for more details.
33%=======================================================================
34
35%------------------------------------------------------------------------
36%------------------------------------------------------------------------
37%  I - MAIN FUNCTION series
38%------------------------------------------------------------------------
39%------------------------------------------------------------------------
40function varargout = series(varargin)
41
42% Begin initialization code - DO NOT EDIT
43gui_Singleton = 1;
44gui_State = struct('gui_Name',       mfilename, ...
45                   'gui_Singleton',  gui_Singleton, ...
46                   'gui_OpeningFcn', @series_OpeningFcn, ...
47                   'gui_OutputFcn',  @series_OutputFcn, ...
48                   'gui_LayoutFcn',  [] , ...
49                   'gui_Callback',   []);
50if nargin && ischar(varargin{1})
51    gui_State.gui_Callback = str2func(varargin{1});
52end
53
54if nargout
55    [varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:});
56else
57    gui_mainfcn(gui_State, varargin{:});
58end
59% End initialization code - DO NOT EDIT
60
61%--------------------------------------------------------------------------
62% --- Executes just before series is made visible.
63%--------------------------------------------------------------------------
64function series_OpeningFcn(hObject, eventdata, handles,Param)
65
66% Choose default command line output for series
67handles.output = hObject;
68% Update handles structure
69guidata(hObject, handles);
70
71%% initial settings
72% position and  size of the GUI at opening
73set(0,'Unit','points')
74ScreenSize=get(0,'ScreenSize'); % size of the current screen, in points (1/72 inch)
75Width=900; % prefered width of the GUI in points (1/72 inch)
76Height=624; % prefered height of the GUI in points (1/72 inch)
77%adjust to screen size (reduced by a min margin)
78RescaleFactor=min((ScreenSize(3)-80)/Width,(ScreenSize(4)-80)/Height);
79if RescaleFactor>1
80    RescaleFactor=min(RescaleFactor,1);
81end
82Width=Width*RescaleFactor;
83Height=Height*RescaleFactor;
84LeftX=80*RescaleFactor; % position of the left fig side, in pixels (put to the left side, with some margin)
85LowY=round(ScreenSize(4)/2-Height/2); % put at the middle height on the screen
86set(hObject,'Units','points')
87set(hObject,'Position',[LeftX LowY Width Height])% position and size of the GUI at opening
88
89% settings of table MinIndex_j
90set(handles.MinIndex_i,'ColumnFormat',{'numeric'})
91set(handles.MinIndex_i,'ColumnEditable',false)
92set(handles.MinIndex_i,'ColumnName',{'i min'})
93set(handles.MinIndex_i,'Data',[])% initiate Data to double (not cell)
94
95% settings of table MinIndex_j
96set(handles.MinIndex_j,'ColumnFormat',{'numeric'})
97set(handles.MinIndex_j,'ColumnEditable',false)
98set(handles.MinIndex_j,'ColumnName',{'j min'})
99set(handles.MinIndex_j,'Data',[])% initiate Data to double (not cell)
100
101% settings of table MaxIndex_i
102set(handles.MaxIndex_i,'ColumnFormat',{'numeric'})
103set(handles.MaxIndex_i,'ColumnEditable',false)
104set(handles.MaxIndex_i,'ColumnName',{'i max'})
105set(handles.MaxIndex_i,'Data',[])% initiate Data to double (not cell)
106
107% settings of table MaxIndex_j
108set(handles.MaxIndex_j,'ColumnFormat',{'numeric'})
109set(handles.MaxIndex_j,'ColumnEditable',false)
110set(handles.MaxIndex_j,'ColumnName',{'j max'})
111set(handles.MaxIndex_j,'Data',[])% initiate Data to double (not cell)
112
113% settings of table PairString
114set(handles.PairString,'ColumnName',{'pairs'})
115set(handles.PairString,'ColumnEditable',false)
116set(handles.PairString,'ColumnFormat',{'char'})
117set(handles.PairString,'Data',{''})
118
119% settings of table MaskTable
120set(handles.MaskTable,'ColumnName',{'mask name'})
121set(handles.PairString,'ColumnEditable',false)
122set(handles.PairString,'ColumnFormat',{'char'})
123set(handles.PairString,'Data',{''})
124
125series_ResizeFcn(hObject, eventdata, handles)%resize table according to series GUI size
126set(hObject,'WindowButtonDownFcn',{'mouse_down'})%allows mouse action with right button (zoom for uicontrol display)
127set(hObject,'DeleteFcn',{@closefcn})%
128
129% check default input data
130if ~exist('Param','var')
131    Param=[]; % default
132end
133
134%% Read the parameter file series.xml, or created from series.xml.default if it does not exist
135SeriesData=[];
136[path_series,name,ext]=fileparts(which('series'));% path to the GUI series
137xmlfile=fullfile(path_series,'series.xml');
138if ~exist(xmlfile,'file')
139    [success,message]=copyfile(fullfile(path_series,'series.xml.default'),xmlfile);
140end
141if exist(xmlfile,'file')
142    SeriesData.SeriesParam=xml2struct(xmlfile);
143    if ~(isfield(SeriesData.SeriesParam,'ClusterParam')&& isfield(SeriesData.SeriesParam.ClusterParam,'LaunchCmdFcn'))
144        [success,message]=copyfile(xmlfile,fullfile(path_series,'series_old.xml'));% update the file series.xml inot correctly documented
145        delete(xmlfile);
146        [success,message]=copyfile(fullfile(path_series,'series.xml.default'),xmlfile);
147    end 
148    SeriesData.SeriesParam=xml2struct(xmlfile);
149end
150
151%% list of builtin functions in the menu ActionName
152ActionList={'check_data_files';'aver_stat';'time_series';'civ_series';'merge_proj'}; % WARNING: fits with nb_builtin_ACTION=4 in ActionName_callback
153NbBuiltinAction=numel(ActionList);
154set(handles.Action,'UserData',NbBuiltinAction)
155path_series_fct=fullfile(path_series,'series');%path of the functions in subdirectroy 'series'
156[path_series,name,ext]=fileparts(which('series')); % path to the GUI series
157path_series_fct=fullfile(path_series,'series'); % path of the functions in subdirectroy 'series'
158command = ['LD_LIBRARY_PATH=$(echo $LD_LIBRARY_PATH | pyp "l = x.split('':''); l = [s for s in l if ''matlab'' not in s]; print('':''.join(l))") ' ...
159            'python -c "import fluidimage"'];
160[code, ~] = system(command);
161if code==0
162    ActionExtList={'.m';'.sh';'.py (in dev.)'}; % default choice of extensions (Matlab fct .m or compiled version .sh
163else
164    ActionExtList={'.m';'.sh'};  % python options not installed
165end
166ActionPathList=cell(NbBuiltinAction,1); % initiate the cell matrix of Action fct paths
167ActionPathList(:)={path_series_fct}; % set the default path to series fcts to all list members
168RunModeList={'local';'background'}; % default choice of extensions (Matlab fct .m or compiled version .sh)
169[s,w]=system(SeriesData.SeriesParam.ClusterParam.ExistenceTest); % look for cluster system presence
170% [s,w]=system('oarstat'); % look for cluster system 'oar'
171if isequal(s,0)
172    RunModeList=[RunModeList;{'cluster'}];
173    set(handles.MonitorCluster,'Visible','on'); % make visible button for access to Monika
174    set(handles.num_CPUTime,'Visible','on'); % make visible button for CPU time estimate for one ref index
175    set(handles.num_CPUTime,'String','1')% defqult CPU time estimate 1 minute
176    set(handles.CPUTime_txt,'Visible','on'); % make visible button for CPU time title
177end
178% [s,w]=system('qstat -help'); % look for cluster system 'sge'
179% if isequal(s,0)
180%     if regexp(w,'^pbs')
181%         RunModeList=[RunModeList;{'cluster_pbs'}];
182%     elseif regexp(w,'^SGE')
183%         RunModeList=[RunModeList;{'cluster_sge'}];
184%     else
185%         RunModeList=[RunModeList;{'cluster_qstat_unknown'}];
186%     end
187% end
188set(handles.RunMode,'String',RunModeList)% display the menu of available run modes, local, background or cluster manager
189
190%% list of builtin transform functions in the menu TransformName
191TransformList={'';'sub_field';'phys';'phys_polar'}; % WARNING: must fit with the corresponding menu in uvmat and nb_builtin_transform=4 in  TransformName_callback
192NbBuiltinTransform=numel(TransformList);
193path_transform_fct=fullfile(path_series,'transform_field');
194TransformPathList=cell(NbBuiltinTransform,1); % initiate the cell matrix of Action fct paths
195TransformPathList(:)={path_transform_fct}; % set the default path to series fcts to all list members
196SeriesData.TransformPath=path_transform_fct;% store the standard path for trqnsform functions (needed for compilation)
197
198%% get the user defined functions stored in the personal file uvmat_perso.mat
199dir_perso=prefdir;
200profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
201if exist(profil_perso,'file')
202    h=load (profil_perso);
203    %get the list of previous input files in the upper bar menu Open
204    if isfield(h,'MenuFile')
205        for ifile=1:min(length(h.MenuFile),5)
206            set(handles.(['MenuFile_' num2str(ifile)]),'Label',h.MenuFile{ifile});
207            set(handles.(['MenuFile_' num2str(ifile+5)]),'Label',h.MenuFile{ifile});
208        end
209    end
210    %get the list of previous campaigns in the upper bar menu Open campaign
211%     if isfield(h,'MenuCampaign')
212%         for ifile=1:min(length(h.MenuCampaign),5)
213%             set(handles.(['MenuCampaign_' num2str(ifile)]),'Label',h.MenuCampaign{ifile});
214%         end
215%     end
216    %get the menu of actions
217    if isfield(h,'ActionListUser') && iscell(h.ActionListUser) && isfield(h,'ActionPathListUser') && iscell(h.ActionPathListUser)
218        ActionList=[ActionList;h.ActionListUser];
219        ActionPathList=[ActionPathList;h.ActionPathListUser(:,1)];
220    end
221    %get the menu of transform fct
222    if isfield(h,'TransformListUser') && iscell(h.TransformListUser) && isfield(h,'TransformPathListUser') && iscell(h.TransformPathListUser)
223        TransformList=[TransformList;h.TransformListUser];
224        TransformPathList=[TransformPathList;h.TransformPathListUser];
225    end
226end
227
228%% selection of the input Action fct
229ActionCheckExist=true(size(ActionList)); % initiate the check of the path to the listed action fct
230for ilist=NbBuiltinAction+1:numel(ActionList)%check  the validity of the path of the user defined Action fct
231    ActionCheckExist(ilist)=exist(fullfile(ActionPathList{ilist},[ActionList{ilist} '.m']),'file');
232end
233ActionPathList=ActionPathList(ActionCheckExist,:); % suppress the menu options which are not valid anymore
234ActionList=ActionList(ActionCheckExist);
235set(handles.ActionName,'String',[ActionList;{'more...'}])
236set(handles.ActionName,'UserData',ActionPathList)
237ActionIndex=[];
238if isfield(Param,'ActionName')% copy the selected menu index transferred in Param from uvmat
239    ActionIndex=find(strcmp(Param.ActionName,ActionList),1);
240end
241if isempty(ActionIndex)
242    ActionIndex=1;
243end
244set(handles.ActionName,'Value',ActionIndex)
245set(handles.ActionPath,'String',ActionPathList{ActionIndex})
246set(handles.ActionExt,'Value',1)
247set(handles.ActionExt,'String',ActionExtList)
248
249%% selection of the input transform fct
250TransformCheckExist=true(size(TransformList));
251for ilist=NbBuiltinTransform+1:numel(TransformList)
252    TransformCheckExist(ilist)=exist(fullfile(TransformPathList{ilist},[TransformList{ilist} '.m']),'file');
253end
254TransformPathList=TransformPathList(TransformCheckExist);
255TransformList=TransformList(TransformCheckExist);
256set(handles.TransformName,'String',[TransformList;{'more...'}])
257set(handles.TransformName,'UserData',TransformPathList)
258TransformIndex=[];
259if isfield(Param,'TransformName')% copy the selected menu index transferred in Param from uvmat
260    TransformIndex=find(strcmp(Param.TransformName,TransformList),1);
261end
262if isempty(TransformIndex)
263    TransformIndex=1;
264end
265set(handles.TransformName,'Value',TransformIndex)
266set(handles.TransformPath,'String',TransformPathList{TransformIndex})
267   
268%% fields input initialisation
269if isfield(Param,'list_fields')&& isfield(Param,'index_fields') &&~isempty(Param.list_fields) &&~isempty(Param.index_fields)
270    set(handles.FieldName,'String',Param.list_fields); % list menu fields
271    set(handles.FieldName,'Value',Param.index_fields); % selected string index
272end
273if isfield(Param,'Coordinates')
274    if isfield(Param.Coordinates,'Coord_x')
275        set(handles.Coord_x,'String',Param.Coordinates.Coord_x)
276    end
277    if isfield(Param.Coordinates,'Coord_y')
278        set(handles.Coord_y,'String',Param.Coordinates.Coord_y)
279    end
280    if isfield(Param.Coordinates,'Coord_z')
281        set(handles.Coord_z,'String',Param.Coordinates.Coord_z)
282    end
283end
284
285%% introduce the input file name(s) if defined from input Param,
286set(handles.series,'UserData',SeriesData)% initiate Userdata
287if isfield(Param,'InputFile')
288   
289    %% fill the list of file series
290    InputTable=[{Param.InputFile.RootPath},{Param.InputFile.SubDir},{Param.InputFile.RootFile},{Param.InputFile.NomType},{Param.InputFile.FileExt}];
291    if isempty(find(cellfun('isempty',InputTable)==0)); % if there is no input file, do not introduce input info
292        set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH button to magenta color to indicate that input refresh is needed
293        return
294    end
295    TimeTable=[{Param.InputFile.TimeName},{[]},{[]},{[]},{[]}];
296    if isfield(Param.InputFile,'RootPath_1')
297        InputTable=[InputTable;[{Param.InputFile.RootPath_1},{Param.InputFile.SubDir_1},{Param.InputFile.RootFile_1},{Param.InputFile.NomType_1},{Param.InputFile.FileExt_1}]];
298        TimeTable=[TimeTable; [{Param.InputFile.TimeName_1},{[]},{[]},{[]},{[]}]];
299    end
300    set(handles.InputTable,'Data',InputTable)
301    %% determine the selected reference field indices for pair display
302   
303    [tild,tild,tild,i1,i2,j1,j2]=fileparts_uvmat(Param.InputFile.FileIndex);
304    if isempty(i1)
305        i1=1;
306    end
307    if isempty(i2)
308        i2=i1;
309    end
310    ref_i=floor((i1+i2)/2); % reference image number corresponding to the file
311    % set(handles.num_ref_i,'String',num2str(ref_i));
312    if isempty(j1)
313        j1=1;
314    end
315    if isempty(j2)
316        j2=j1;
317    end
318    ref_j=floor((j1+j2)/2); % reference image number corresponding to the file
319    SeriesData.ref_i=ref_i;
320    SeriesData.ref_j=ref_j;
321    set(handles.series,'UserData',SeriesData)
322    update_rootinfo(handles,Param.HiddenData.i1_series{1},Param.HiddenData.i2_series{1},Param.HiddenData.j1_series{1},Param.HiddenData.j2_series{1},...
323        Param.HiddenData.FileInfo{1},Param.HiddenData.MovieObject{1},1)
324    if isfield(Param,'FileName_1')
325        %         display_file_name(handles,Param,2)
326        update_rootinfo(handles,Param.HiddenData.i1_series{2},Param.HiddenData.i2_series{2},Param.HiddenData.j1_series{2},Param.HiddenData.j2_series{2},...
327            Param.HiddenData.FileInfo{2},Param.HiddenData.MovieObject{2},2)
328    end
329    %% enable field and veltype menus, in accordance with the current action
330    ActionName_Callback([],[], handles)
331   
332    %% set length of waitbar
333    displ_time(handles)
334   
335else
336    set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH button to magenta color to indicate that input refresh is needed
337end
338if isfield(Param,'incr_i')
339    set(handles.num_incr_i,'String',num2str(Param.incr_i))
340else
341    set(handles.num_incr_i,'String','1')
342end
343if isfield(Param,'incr_j')
344    set(handles.num_incr_j,'String',num2str(Param.incr_j))
345else
346    set(handles.num_incr_j,'String','1')
347end
348
349%------------------------------------------------------------------------
350% --- Outputs from this function are returned to the command line.
351function varargout = series_OutputFcn(hObject, eventdata, handles)
352%------------------------------------------------------------------------
353varargout{1} = handles.output;
354
355%------------------------------------------------------------------------
356% --- executed when closing uvmat: delete or desactivate the associated figures if exist
357function closefcn(gcbo,eventdata)
358%------------------------------------------------------------------------
359
360% delete set_object_series if detected
361hh=findobj(allchild(0),'name','view_object_series');
362if ~isempty(hh)
363    delete(hh)
364end
365hh=findobj(allchild(0),'name','edit_object_series');
366if ~isempty(hh)
367    delete(hh)
368end
369
370%delete the bowser if detected
371hh=findobj(allchild(0),'tag','browser');
372if ~isempty(hh)
373    delete(hh)
374end
375
376
377%------------------------------------------------------------------------
378%------------------------------------------------------------------------
379%  II - FUNCTIONS FOR INTRODUCING THE INPUT FILES
380% automatically sets the global properties when the rootfile name is introduced
381% then activate the view-field actionname if selected
382% it is activated either by clicking on the RootPath window or by the
383% browser
384%------------------------------------------------------------------------
385%------------------------------------------------------------------------
386% --- fct activated by the browser under 'Open'
387%------------------------------------------------------------------------ 
388function MenuBrowse_Callback(hObject, eventdata, handles)
389%% look for the previously opened file 'oldfile'
390InputTable=get(handles.InputTable,'Data');
391oldfile=InputTable{1,1};
392if isempty(oldfile)
393    % use a file name stored in prefdir
394    dir_perso=prefdir;
395    profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
396    if exist(profil_perso,'file')
397        h=load (profil_perso);
398        if isfield(h,'RootPath') && ischar(h.RootPath)
399            oldfile=h.RootPath;
400        end
401    end
402end
403%% launch the browser
404fileinput=uigetfile_uvmat('pick an input file in the series',oldfile);
405hh=dir(fileinput);
406if numel(hh)>1
407    msgbox_uvmat('ERROR','invalid input, probably a broken link');
408else
409    if ~isempty(fileinput)
410        display_file_name(handles,fileinput,'one')
411    end
412end
413
414% --------------------------------------------------------------------
415function MenuBrowseAppend_Callback(hObject, eventdata, handles)
416
417%% look for the previously opened file 'oldfile'
418InputTable=get(handles.InputTable,'Data');
419RootPathCell=InputTable(:,1);
420if isempty(RootPathCell{1})% no input file in the table
421     MenuBrowse_Callback(hObject, eventdata, handles)%refresh the input table, not append
422     return
423end
424SubDirCell=InputTable(:,2);
425oldfile=fullfile(RootPathCell{1},SubDirCell{1});
426
427%% use a file name stored in prefdir
428dir_perso=prefdir;
429profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
430if exist(profil_perso,'file')
431    h=load (profil_perso);
432    if isfield(h,'RootPath') && ischar(h.RootPath)
433        oldfile=h.RootPath;
434    end
435end
436
437%% launch the browser
438fileinput=uigetfile_uvmat('pick a file to append in the input table',oldfile);
439hh=dir(fileinput);
440if numel(hh)>1
441    msgbox_uvmat('ERROR','invalid input, probably a broken link');
442else
443    if ~isempty(fileinput)
444        display_file_name(handles,fileinput,'append')
445    end
446end
447
448%------------------------------------------------------------------------
449% --- fct activated by selecting a previous file under the menu Open
450%------------------------------------------------------------------------
451function MenuFile_Callback(hObject, eventdata, handles)
452
453errormsg=display_file_name(handles,get(hObject,'Label'),'one');
454if ~isempty(errormsg)
455    set(hObject,'Label','')
456    MenuFile=[{get(handles.MenuFile_1,'Label')};{get(handles.MenuFile_2,'Label')};...
457        {get(handles.MenuFile_3,'Label')};{get(handles.MenuFile_4,'Label')};{get(handles.MenuFile_5,'Label')}];
458    str_find=strcmp(get(hObject,'Label'),MenuFile);
459    MenuFile(str_find)=[]; % suppress the input file to the list
460    for ifile=1:numel(MenuFile)
461        set(handles.(['MenuFile_' num2str(ifile)]),'Label',MenuFile{ifile});
462    end
463end
464
465%------------------------------------------------------------------------
466% --- fct activated by selecting a previous file under the menu Open/append
467%------------------------------------------------------------------------
468function MenuFile_append_Callback(hObject, eventdata, handles)
469
470InputTable=get(handles.InputTable,'Data');
471if isempty(InputTable{1,1})% no input file in the table
472    display_file_name(handles,get(hObject,'Label'),'one') %refresh the input table, not append
473else
474    display_file_name(handles,get(hObject,'Label'),'append')% append the selected file to the current list of InputTable
475end
476
477%------------------------------------------------------------------------
478% --- fct activated by the browser under 'Open campaign/Browse...'
479%------------------------------------------------------------------------
480function MenuBrowseCampaign_Callback(hObject, eventdata, handles)
481
482%% look for the previously opened file 'oldfile'
483InputTable=get(handles.InputTable,'Data');
484if ~isempty(InputTable)
485oldfile=[InputTable{1,1} InputTable{1,2}];
486else
487    % use a file name stored in prefdir
488    dir_perso=prefdir;
489    profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
490    if exist(profil_perso,'file')
491        h=load (profil_perso);
492        if isfield(h,'MenuCampaign') && ~isempty(h.MenuCampaign)&& ischar(h.MenuCampaign{1})
493            oldfile=h.MenuCampaign{1};
494        end
495    end
496end
497InputTable{1,1}='...';
498set(handles.InputTable,'Data',InputTable)
499browse_data(oldfile,'on','on'); % open the GUI browse_data to get select a campaign dir, experiment and device
500% NbLines=numel(OutPut.Experiment)*numel(OutPut.DataSeries);
501% icount=0;
502% for iexp=1:numel(OutPut.Experiment)
503%     for idevice=1:numel(OutPut.DataSeries)
504%         icount=icount+1;
505%         InputTable{icount,1}=fullfile(OutPut.Campaign,OutPut.Experiment{iexp});
506%         InputTable{icount,2}=OutPut.DataSeries{idevice};
507%         if isempty(InputTable{icount,3})
508%             if icount>1
509%             InputTable{icount,3}=InputTable{icount-1,3};
510%             else
511%                 InputTable{icount,3}='';
512%             end
513%         end
514%         if isempty(InputTable{icount,4})
515%             if icount>1
516%             InputTable{icount,4}=InputTable{icount-1,4};
517%             else
518%                 InputTable{icount,4}='';
519%             end
520%         end
521%                 if isempty(InputTable{icount,5})
522%             if icount>1
523%             InputTable{icount,5}=InputTable{icount-1,5};
524%             else
525%                 InputTable{icount,5}='';
526%             end
527%         end
528%     end
529% end
530% if size(InputTable,1)>icount
531%     InputTable(icount+1:size(InputTable,1),:)=[];
532% end
533%REFRESH_Callback(hObject, eventdata, handles)
534
535% --------------------------------------------------------------------
536% function MenuCampaign_Callback(hObject, eventdata, handles)
537% % --------------------------------------------------------------------
538%
539% OutPut=browse_data(get(hObject,'Label'),'on','on'); % open the GUI browse_data to get select a campaign dir, experiment and device
540% if ~isfield(OutPut,'Campaign')
541%     return
542% end
543% NbLines=numel(OutPut.Experiment)*numel(OutPut.DataSeries);
544% icount=0;
545% InputTable=get(handles.InputTable,'Data');
546% for iexp=1:numel(OutPut.Experiment)
547%     for idevice=1:numel(OutPut.DataSeries)
548%         icount=icount+1;
549%         InputTable{icount,1}=fullfile(OutPut.Campaign,OutPut.Experiment{iexp});
550%         InputTable{icount,2}=OutPut.DataSeries{idevice};
551%         if isempty(InputTable{icount,3})
552%             if icount>1
553%                 InputTable{icount,3}=InputTable{icount-1,3};
554%             else
555%                 InputTable{icount,3}='';
556%             end
557%         end
558%         if isempty(InputTable{icount,4})
559%             if icount>1
560%                 InputTable{icount,4}=InputTable{icount-1,4};
561%             else
562%                 InputTable{icount,4}='';
563%             end
564%         end
565%         if isempty(InputTable{icount,5})
566%             if icount>1
567%                 InputTable{icount,5}=InputTable{icount-1,5};
568%             else
569%                 InputTable{icount,5}='';
570%             end
571%         end
572%     end
573% end
574% if size(InputTable,1)>icount
575%     InputTable(icount+1:size(InputTable,1),:)=[];
576% end
577% set(handles.InputTable,'Data',InputTable)
578% REFRESH_Callback(hObject, eventdata, handles)
579
580
581% --- Executes when selected cell(s) is changed in InputTable.
582function InputTable_CellSelectionCallback(hObject, eventdata, handles)
583iline=[];
584if ~isempty(eventdata.Indices)
585    iline=eventdata.Indices(1);
586end
587set(handles.InputLine,'String',num2str(iline));
588
589%------------------------------------------------------------------------
590% --- 'key_press_fcn:' function activated when a key is pressed on the keyboard
591%------------------------------------------------------------------------
592function InputTable_KeyPressFcn(hObject, eventdata, handles)
593set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH button to magenta color to indicate that input refresh is needed
594set(handles.OutputSubDir,'BackgroundColor',[1 0 1])% set edit box OutputSubDir to magenta color to indicate that refresh may be needed
595xx=double(get(handles.series,'CurrentCharacter')); % get the keyboard character
596if ~isempty(xx)
597    switch xx
598        case 31 %downward arrow
599            InputTable=get(handles.InputTable,'Data');
600            iline=str2double(get(handles.InputLine,'String'));
601            if isequal(iline,size(InputTable,1))% arrow downward
602                InputTable=[InputTable;InputTable(iline,:)]; % create a new line as a copy of the last one
603                set(handles.InputTable,'Data',InputTable);
604            end
605        case 127  %key 'Suppress'
606            ClearLine_Callback(hObject, eventdata, handles)
607    end
608end
609
610%------------------------------------------------------------------------
611% --- Executes on button press in REFRESH.
612function REFRESH_Callback(hObject, eventdata, handles)
613%------------------------------------------------------------------------
614check_input_file_series(handles)
615
616%% enable field and veltype menus, in accordance with the current action
617ActionInput_Callback([],[], handles)
618
619
620function check_input_file_series(handles)
621InputTable=get(handles.InputTable,'Data');
622set(handles.series,'Pointer','watch') % set the mouse pointer to 'watch'
623set(handles.REFRESH,'BackgroundColor',[1 1 0])% set REFRESH  button to yellow color (indicate activation)
624drawnow
625empty_line=false(size(InputTable,1),1);
626for iline=1:size(InputTable,1)
627    empty_line(iline)= isempty(cell2mat(InputTable(iline,1:3)));
628end
629if ~isempty(find(empty_line));
630    InputTable(empty_line,:)=[]; % remove empty lines
631    set(handles.InputTable,'Data',InputTable)
632    ListTable={'MinIndex_i','MaxIndex_i','MinIndex_j','MaxIndex_j','PairString','TimeTable'};
633    for ilist=1:numel(ListTable)
634        Table=get(handles.(ListTable{ilist}),'Data');
635        Table(empty_line,:)=[]; % remove empty lines
636        set(handles.(ListTable{ilist}),'Data',Table);
637    end
638    set(handles.series,'UserData',[])%refresh the stored info
639end
640nbview=size(InputTable,1);
641for iview=1:nbview
642    RootPath=fullfile(InputTable{iview,1},InputTable{iview,2});
643    if ~exist(RootPath,'dir')
644        i1_series=[];
645        RootFile='';
646    else %scan the input folder
647        InputTable{iview,3}=regexprep(InputTable{iview,3},'^/','');
648            [RootPath,~,RootFile,i1_series,i2_series,j1_series,j2_series,tild,FileInfo,MovieObject]=...
649                find_file_series(fullfile(InputTable{iview,1},InputTable{iview,2}),[InputTable{iview,3} InputTable{iview,4} InputTable{iview,5}]);
650    end
651    % if no file is found, open a browser
652    if isempty(RootFile)&& isempty(i1_series)
653        fileinput=uigetfile_uvmat(['wrong input at line ' num2str(iview) ':pick a new input file'],RootPath);
654        if isempty(fileinput)
655            set(handles.REFRESH,'BackgroundColor',[1 0 0])% set REFRESH  back to red color
656            return
657        else
658            display_file_name(handles,fileinput,iview)
659        end
660    else
661       update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileInfo,MovieObject,iview)
662    end
663end
664
665%% update MinIndex_i and MaxIndex_i if the input table content has been reduced in line nbre
666MinIndex_i_table=get(handles.MinIndex_i,'Data'); % retrieve the min indices in the table MinIndex
667set(handles.MinIndex_i,'Data',MinIndex_i_table(1:nbview,:));
668MinIndex_j_table=get(handles.MinIndex_j,'Data'); % retrieve the min indices in the table MinIndex
669set(handles.MinIndex_j,'Data',MinIndex_j_table(1:nbview,:));
670MaxIndex_i_table=get(handles.MaxIndex_i,'Data'); % retrieve the min indices in the table MinIndex
671
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%% set length of waitbar
681displ_time(handles)
682set(handles.REFRESH,'BackgroundColor',[1 0 0])% set REFRESH  button to red color (indicate activation finished)
683set(handles.series,'Pointer','arrow') % set the mouse pointer to 'watch'
684
685
686
687%------------------------------------------------------------------------
688% --- Function called when a new file is opened, either by series_OpeningFcn or by the browser
689%------------------------------------------------------------------------
690% INPUT:
691% handles: handles of elements in the GUI
692% Param: structure of input parameters, including  input file name and path
693% iview: line index in the input table
694%       or 'one': refresh the list
695%         'append': add a new line to the input table
696function errormsg=display_file_name(handles,Param,iview)
697 
698set(handles.REFRESH,'BackgroundColor',[1 1 0])% set REFRESH  button to yellow color (indicate activation)
699drawnow
700errormsg=''; % default
701if ischar(Param)
702    fileinput=Param;
703else% input set when series is opened (called by the GUI uvmat)
704    fileinput=Param.FileName;
705end
706   
707%% get the input root name, indices, file extension and nomenclature NomType
708if ~exist(fileinput,'file')
709    errormsg=['input file ' fileinput  ' does not exist'];
710    msgbox_uvmat('ERROR',errormsg)
711    set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH  button to magenta color (refresh still needed)
712    return
713end
714
715%% detect root name, nomenclature and indices in the input file name:
716[FilePath,FileName,FileExt]=fileparts(fileinput);
717%%%%%%%%%%%%%%%%%%
718%TODO: case of input by uvmat: do not check agai the input seies %%%%%%%
719%%%%%%%%%%%%%%%%%%%
720% detect the file type, get the movie object if relevant, and look for the corresponding file series:
721% the root name and indices may be corrected by including the first index i1 if a corresponding xml file exists
722[RootPath,SubDir,RootFile,i1_series,i2_series,j1_series,j2_series,NomType,FileInfo,MovieObject,i1,i2,j1,j2]=find_file_series(FilePath,[FileName FileExt]);
723FileType=FileInfo.FileType;
724if isempty(RootFile)&&isempty(i1_series)
725    errormsg='no input file in the series';
726    msgbox_uvmat('ERROR',errormsg)
727    set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH  button to magenta color (end of activation)
728    return
729end
730if strcmp(FileType,'txt')
731    edit(fileinput)
732    set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH  button to  magenta color (end of activation)
733    return
734elseif strcmp(FileType,'xml')
735    editxml(fileinput)
736    set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH  button to magenta  color (end of activation)
737     return
738elseif strcmp(FileType,'figure')
739    open(fileinput)
740    set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH  button to magenta  color (end of activation)
741     return
742end
743
744%% enable other menus and uicontrols
745% set(handles.MenuOpenCampaign,'Enable','on')
746% set(handles.MenuCampaign_1,'Enable','on')
747% set(handles.MenuCampaign_2,'Enable','on')
748% set(handles.MenuCampaign_3,'Enable','on')
749% set(handles.MenuCampaign_4,'Enable','on')
750% set(handles.MenuCampaign_5,'Enable','on')
751set(handles.RUN, 'Enable','On')
752set(handles.RUN,'BackgroundColor',[1 0 0])% set RUN button to red
753set(handles.InputTable,'BackgroundColor',[1 1 0]) % set RootPath edit box  to yellow
754drawnow
755
756
757%% fill the list of file series
758InputTable=get(handles.InputTable,'Data');
759SeriesData=get(handles.series,'UserData');
760if strcmp(iview,'append') % display the input data as a new line in the table
761    iview=size(InputTable,1)+1; % the next line in InputTable becomes the current line
762%     InputTable(iview,:)=[{RootPath},{SubDir},{RootFile},{NomType},{FileExt}];
763elseif strcmp(iview,'one') % refresh the list of  input  file series
764    iview=1; % the first line in InputTable becomes the current line
765    InputTable={'','','','',''};
766%     InputTable(iview,:)=[{RootPath},{SubDir},{RootFile},{NomType},{FileExt}];
767    set(handles.TimeTable,'Data',[{''},{[]},{[]},{[]},{[]}])
768    set(handles.MinIndex_i,'Data',[])
769    set(handles.MaxIndex_i,'Data',[])
770    set(handles.MinIndex_j,'Data',[])
771    set(handles.MaxIndex_j,'Data',[])
772    set(handles.PairString,'Data',{''})
773    SeriesData.CheckPair=0; % reset the list of input lines with pairs
774    SeriesData.i1_series={};
775    SeriesData.i2_series={};
776    SeriesData.j1_series={};
777    SeriesData.j2_series={};
778    SeriesData.FileType={};
779    SeriesData.FileInfo={};
780    SeriesData.Time={};
781end
782if isfield(SeriesData,'i1_series')
783    SeriesData.i1_series(iview+1:end)=[];
784    SeriesData.i2_series(iview+1:end)=[];
785    SeriesData.j1_series(iview+1:end)=[];
786    SeriesData.j2_series(iview+1:end)=[];
787    SeriesData.FileType(iview+1:end)=[];
788    SeriesData.FileInfo(iview+1:end)=[];
789    SeriesData.Time(iview+1:end)=[];
790end
791InputTable(iview,:)=[{RootPath},{SubDir},{RootFile},{NomType},{FileExt}];
792if iview >1
793    set(handles.InputLine,'String',num2str(iview))
794end
795set(handles.InputTable,'Data',InputTable)
796
797%% determine the selected reference field indices for pair display
798if isempty(i1)
799    i1=1;
800end
801if isempty(i2)
802    i2=i1;
803end
804ref_i=floor((i1+i2)/2); % reference image number corresponding to the file
805% set(handles.num_ref_i,'String',num2str(ref_i));
806if isempty(j1)
807    j1=1;
808end
809if isempty(j2)
810    j2=j1;
811end
812ref_j=floor((j1+j2)/2); % reference image number corresponding to the file
813SeriesData.ref_i=ref_i;
814SeriesData.ref_j=ref_j;
815
816%% update first and last indices if they do not exist
817Param=read_GUI(handles.series);
818first_j=[];
819if isfield(Param.IndexRange,'first_j'); first_j=Param.IndexRange.first_j; end
820last_j=[];
821if isfield(Param.IndexRange,'last_j'); last_j=Param.IndexRange.last_j; end
822PairString='';
823if isfield(Param.IndexRange,'PairString'); PairString=Param.IndexRange.PairString; end
824[i1,i2,j1,j2] = get_file_index(Param.IndexRange.first_i,first_j,PairString);
825FirstFileName=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},...
826    Param.InputTable{1,5},Param.InputTable{1,4},i1,i2,j1,j2);
827if ~exist(FirstFileName,'file')
828    set(handles.num_first_i,'String',num2str(ref_i))
829    set(handles.num_first_j,'String',num2str(ref_j))
830end
831[i1,i2,j1,j2] = get_file_index(Param.IndexRange.last_i,last_j,PairString);
832LastFileName=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},...
833    Param.InputTable{1,5},Param.InputTable{1,4},i1,i2,j1,j2);
834if ~exist(LastFileName,'file')
835    set(handles.num_last_i,'String',num2str(ref_i))
836    set(handles.num_last_j,'String',num2str(ref_j))
837end
838
839%% update the list of recent files in the menubar and save it for future opening
840MenuFile=[{get(handles.MenuFile_1,'Label')};{get(handles.MenuFile_2,'Label')};...
841    {get(handles.MenuFile_3,'Label')};{get(handles.MenuFile_4,'Label')};{get(handles.MenuFile_5,'Label')}];
842str_find=strcmp(fileinput,MenuFile);
843if isempty(find(str_find,1))
844    MenuFile=[{fileinput};MenuFile]; % insert the current file if not already in the list
845end
846for ifile=1:min(length(MenuFile),5)
847    eval(['set(handles.MenuFile_' num2str(ifile) ',''Label'',MenuFile{ifile});'])
848end
849dir_perso=prefdir;
850profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
851if exist(profil_perso,'file')
852    save (profil_perso,'MenuFile','-append'); % store the file names for future opening of uvmat
853else
854    save (profil_perso,'MenuFile','-V6'); % store the file names for future opening of uvmat
855end
856% save the opened file to initiate future opening
857SeriesData.RefFile{iview}=fileinput; % reference opening file for line iview
858SeriesData.Ref_i1=i1;
859SeriesData.Ref_i2=i2;
860SeriesData.Ref_j1=j1;
861SeriesData.Ref_j2=j2;
862set(handles.series,'UserData',SeriesData)
863
864set(handles.InputTable,'BackgroundColor',[1 1 1])
865
866%% initiate input file series and refresh the current field view:     
867update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileInfo,MovieObject,iview);
868%% enable field and veltype menus, in accordance with the current action
869ActionName_Callback([],[], handles)
870
871%% set length of waitbar
872displ_time(handles)
873
874set(handles.REFRESH,'BackgroundColor',[1 0 0])% set REFRESH  button to red color (end of activation)
875
876%------------------------------------------------------------------------
877% --- Update information about a new field series (indices to scan, timing,
878%     calibration from an xml file
879function update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileInfo,VideoObject,iview)
880%------------------------------------------------------------------------
881InputTable=get(handles.InputTable,'Data');
882
883%% display the min and max indices for the whole file series
884if size(i1_series,2)==2 && min(min(i1_series(:,1,:)))==0
885    MinIndex_j=1; % index j set to 1 by default
886    MaxIndex_j=1;
887    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)
888    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)
889else
890    ref_i=squeeze(max(i1_series(1,:,:),[],2)); % select ref_j index for each ref_i
891    ref_j=squeeze(max(j1_series(1,:,:),[],3)); % select ref_i index for each ref_j
892     MinIndex_i=min(find(ref_i))-1;
893     MaxIndex_i=max(find(ref_i))-1;
894     MaxIndex_j=max(find(ref_j))-1;
895     MinIndex_j=min(find(ref_j))-1;
896    diff_j_max=diff(ref_j);
897    diff_i_max=diff(ref_i);
898    if ~isempty(diff_i_max) && isequal (diff_i_max,diff_i_max(1)*ones(size(diff_i_max)))
899        set(handles.num_incr_i,'String',num2str(diff_i_max(1)))% detect an increment to dispaly by default
900    end
901    if ~isempty(diff_j_max) && isequal (diff_j_max,diff_j_max(1)*ones(size(diff_j_max)))
902        set(handles.num_incr_j,'String',num2str(diff_j_max(1)))
903    end
904end
905if isequal(MinIndex_i,-1)
906    MinIndex_i=0;
907end
908if isequal(MinIndex_j,-1)
909    MinIndex_j=0;
910end
911MinIndex_i_table=get(handles.MinIndex_i,'Data'); % retrieve the min indices in the table MinIndex
912MinIndex_j_table=get(handles.MinIndex_j,'Data'); % retrieve the min indices in the table MinIndex
913MaxIndex_i_table=get(handles.MaxIndex_i,'Data'); % retrieve the min indices in the table MinIndex
914MaxIndex_j_table=get(handles.MaxIndex_j,'Data'); % retrieve the min indices in the table MinIndex
915if ~isempty(MinIndex_i)&&~isempty(MaxIndex_i)
916    MinIndex_i_table(iview,1)=MinIndex_i;
917    MaxIndex_i_table(iview,1)=MaxIndex_i;
918end
919if ~isempty(MinIndex_j)&&~isempty(MaxIndex_j)
920    MinIndex_j_table(iview,1)=MinIndex_j;
921    MaxIndex_j_table(iview,1)=MaxIndex_j;
922end
923set(handles.MinIndex_i,'Data',MinIndex_i_table)%display the min indices in the table MinIndex
924set(handles.MinIndex_j,'Data',MinIndex_j_table)%display the max indices in the table MaxIndex
925set(handles.MaxIndex_i,'Data',MaxIndex_i_table)%display the min indices in the table MinIndex
926set(handles.MaxIndex_j,'Data',MaxIndex_j_table)%display the max indices in the table MaxIndex
927SeriesData=get(handles.series,'UserData');
928
929%% adjust the first and last indices for the selected series, only if requested by the bounds
930% i index, compare input to min index i
931first_i=str2num(get(handles.num_first_i,'String')); % retrieve previous first i
932% ref_i=str2num(get(handles.num_ref_i,'String')); % index i given by the input field
933ref_i=1;
934if isfield(SeriesData,'ref_i')
935    ref_i=SeriesData.ref_i;
936end
937if isempty(first_i)
938    first_i=ref_i; % first_i updated by the input value
939elseif first_i < MinIndex_i
940    first_i=MinIndex_i; % first_i set to the min i index (restricted by oter input lines)
941elseif first_i >MaxIndex_i
942    first_i=MaxIndex_i; % first_i set to the max i index (restricted by oter input lines)
943end
944% j index,  compare input to min index j
945first_j=str2num(get(handles.num_first_j,'String'));
946ref_j=1;
947if isfield(SeriesData,'ref_j')
948    ref_j=SeriesData.ref_j;
949end
950if isempty(first_j)
951    first_j=ref_j; % first_j updated by the input value
952elseif first_j<MinIndex_j
953    first_j=MinIndex_j; % first_j set to the min j index (restricted by oter input lines)
954elseif first_j >MaxIndex_j
955    first_j=MaxIndex_j; % first_j set to the max j index (restricted by oter input lines)
956end
957% i index, compare input to max index i
958last_i=str2num(get(handles.num_last_i,'String'));
959if isempty(last_i)
960    last_i=ref_i;
961elseif last_i > MaxIndex_i
962    last_i=MaxIndex_i;
963elseif last_i<first_i
964    last_i=first_i;
965end
966% j index, compare input to max index j
967last_j=str2num(get(handles.num_last_j,'String'));
968if isempty(last_j)
969    last_j=ref_j;
970elseif last_j>MaxIndex_j
971    last_j=MaxIndex_j;
972elseif last_j<first_j
973    last_j=first_j;
974end
975set(handles.num_first_i,'String',num2str(first_i));
976set(handles.num_first_j,'String',num2str(first_j));
977set(handles.num_last_i,'String',num2str(last_i));
978set(handles.num_last_j,'String',num2str(last_j));
979
980%% number of slices set by default
981NbSlice=[]; % default
982% read  value set by the first series for the append mode (iwiew >1)
983if iview>1 && strcmp(get(handles.num_NbSlice,'Visible'),'on')
984    NbSlice=str2double(get(handles.num_NbSlice,'String'));
985end
986
987%% default time settings
988TimeUnit='';
989% read  value set by the first series for the append mode (iwiew >1)
990if iview>1
991    TimeUnit=get(handles.TimeUnit,'String');
992end
993TimeName='';
994Time=[]; % default
995TimeMin=[];
996TimeFirst=[];
997TimeLast=[];
998TimeMax=[];
999
1000%%  read image documentation file if found
1001XmlData=[];
1002check_calib=0;
1003XmlFileName=find_imadoc(InputTable{iview,1},InputTable{iview,2},InputTable{iview,3},InputTable{iview,5});
1004if ~isempty(XmlFileName)
1005    [XmlData,errormsg]=imadoc2struct(XmlFileName);
1006    if ~isempty(errormsg)
1007        msgbox_uvmat('WARNING',['error in reading ' XmlFileName ': ' errormsg]);
1008    end
1009    % read time if available
1010    if isfield(XmlData,'Time')
1011        Time=XmlData.Time;
1012        TimeName='xml';
1013    end
1014    if isfield(XmlData,'Camera')
1015        if isfield(XmlData.Camera,'TimeUnit')&& ~isempty(XmlData.Camera.TimeUnit)
1016            if iview>1 && ~isempty(TimeUnit) && ~strcmp(TimeUnit,XmlData.Camera.TimeUnit)
1017                msgbox_uvmat('WARNING','inconsistent time unit with the first field series');
1018            end
1019            TimeUnit=XmlData.Camera.TimeUnit;
1020        end
1021    end
1022    % number of slices
1023    if isfield(XmlData,'TranslationMotor')&& isfield(XmlData.TranslationMotor,'NbSlice')
1024        NbSlice_motor=XmlData.TranslationMotor.NbSlice;
1025        if ~isempty(NbSlice) && ~isequal(NbSlice_motor,NbSlice)
1026                msgbox_uvmat('WARNING','inconsistent Z numbers of Z indices');
1027        else
1028            NbSlice=NbSlice_motor;
1029        end
1030    end
1031   
1032%     if isfield(XmlData,'GeometryCalib')
1033%         check_calib=1;
1034%         if isfield(XmlData.GeometryCalib,'SliceCoord')
1035%             siz=size(XmlData.GeometryCalib.SliceCoord);
1036%             if ~isempty(NbSlice)&& ~isequal(size(1),NbSlice)
1037%                 msgbox_uvmat('WARNING','inconsistent numbers of Z indices between motor and calibration');
1038%             else
1039%                 NbSlice=siz(1);
1040%             end
1041%         end
1042%     end
1043end
1044if ~isempty(NbSlice)
1045set(handles.num_NbSlice,'String',num2str(NbSlice))
1046set(handles.num_NbSlice,'Visible','on')
1047end
1048
1049%% read timing  from the current file (prioritary)
1050if ~isempty(VideoObject)% case of movies
1051    imainfo=get(VideoObject);
1052    if isempty(j1_series); % frame index along i
1053        Time=zeros(imainfo.NumberOfFrames+1,2);
1054        Time(:,2)=(0:1/imainfo.FrameRate:(imainfo.NumberOfFrames)/imainfo.FrameRate)';
1055    else
1056        Time=[0;ones(size(i1_series,3)-1,1)]*(0:1/imainfo.FrameRate:(imainfo.NumberOfFrames)/imainfo.FrameRate);
1057    end
1058    TimeName='video';
1059end
1060
1061
1062%% determine the min and max times: case of Netcdf files will be treated later in FieldName_Callback
1063if ~isempty(TimeName)
1064    TimeMin=Time(MinIndex_i+1,MinIndex_j+1);
1065    if size(Time)>=[first_i+1 first_j+1]
1066        TimeFirst=Time(first_i+1,first_j+1);
1067    end
1068    if size(Time)>=[last_i+1 last_j+1]
1069        TimeLast=Time(last_i+1,last_j+1);
1070    end
1071    if size(Time)>=[MaxIndex_i+1 MaxIndex_j+1];
1072        TimeMax=Time(MaxIndex_i+1,MaxIndex_j+1);
1073    end
1074end
1075
1076%% update the time table
1077TimeTable=get(handles.TimeTable,'Data');
1078TimeTable{iview,1}=TimeName;
1079TimeTable{iview,2}=TimeMin;
1080TimeTable{iview,3}=TimeFirst;
1081TimeTable{iview,4}=TimeLast;
1082TimeTable{iview,5}=TimeMax;
1083set(handles.TimeTable,'Data',TimeTable)
1084
1085%% update the series info in 'UserData'
1086SeriesData.i1_series{iview}=i1_series;
1087SeriesData.i2_series{iview}=i2_series;
1088SeriesData.j1_series{iview}=j1_series;
1089SeriesData.j2_series{iview}=j2_series;
1090SeriesData.FileType{iview}=FileInfo.FileType;
1091SeriesData.FileInfo{iview}=FileInfo;
1092SeriesData.Time{iview}=Time;
1093
1094SeriesData.TimeName=TimeName;
1095
1096if check_calib
1097    SeriesData.GeometryCalib{iview}=XmlData.GeometryCalib;
1098end
1099set(handles.series,'UserData',SeriesData)
1100
1101%% update pair menus
1102hset_pair=findobj(allchild(0),'Tag','set_pairs');
1103if ~isempty(hset_pair), delete(hset_pair); end % delete the GUI set_pair if opened
1104CheckPair= ~isempty(i2_series)||~isempty(j2_series); % check whether index pairs need to be defined
1105PairString=get(handles.PairString,'Data');
1106if CheckPair% if pairs need to be display for line iview
1107    [ModeMenu,ModeValue]=update_mode(i1_series,i2_series,j2_series);
1108    Menu=update_listpair(i1_series,i2_series,j1_series,j2_series,ModeMenu{ModeValue},Time,TimeUnit,ref_i,ref_j,TimeName,InputTable(iview,:),FileInfo);
1109    PairString{iview,1}=Menu{1};
1110else
1111    PairString{iview,1}=''; % no pair for #iview
1112end
1113set(handles.PairString,'Data',PairString)
1114if isempty(find(cellfun('isempty',get(handles.PairString,'Data'))==0, 1))% if all lines of pairs are empty
1115    set(handles.PairString,'Visible','off')
1116    set(handles.SetPairs,'Visible','off')
1117else
1118    set(handles.PairString,'Visible','on')
1119    set(handles.SetPairs,'Visible','on')
1120end
1121
1122
1123%% display the set of existing files as an image
1124set(handles.FileStatus,'Units','pixels')
1125Position=get(handles.FileStatus,'Position');
1126set(handles.FileStatus,'Units','normalized')
1127%xI=0.5:Position(3)-0.5;
1128nbview=numel(SeriesData.i1_series);
1129j_max=cell(1,nbview);
1130MaxIndex_i=ones(1,nbview); % default
1131MinIndex_i=ones(1,nbview); % default
1132for iline=1:nbview
1133    pair_max=squeeze(max(SeriesData.i1_series{iline},[],1)); % max on pair index
1134    j_max{iline}=max(pair_max,[],1); % max on j index
1135    if ~isempty(j_max{iline})
1136    MaxIndex_i(iline)=max(find(j_max{iline}))-1; % max ref index i
1137    MinIndex_i(iline)=min(find(j_max{iline}))-1; % min ref index i
1138    end
1139end
1140MinIndex_i=min(MinIndex_i);
1141MaxIndex_i=max(MaxIndex_i);
1142range_index=MaxIndex_i-MinIndex_i+1;
1143range_y=max(1,floor(Position(4)/nbview));
1144npx=floor(Position(3));
1145file_indices=MinIndex_i+floor(((0.5:npx-0.5)/npx)*range_index)+1;
1146CData=zeros(nbview*range_y,npx); % initiate the image representing the existing files
1147for iline=1:nbview
1148    ind_y=1+(iline-1)*range_y:iline*range_y;
1149    LineData=zeros(size(file_indices));
1150    file_select=file_indices(file_indices<=numel(j_max{iline}));
1151    ind_select=find(file_indices<=numel(j_max{iline}));
1152    LineData(ind_select)=j_max{iline}(file_select)~=0;
1153    CData(ind_y,:)=ones(size(ind_y'))*LineData;
1154end
1155CData=cat(3,zeros(size(CData)),CData,zeros(size(CData))); % make color images r=0,g,b=0
1156set(handles.FileStatus,'CData',CData);
1157
1158%-----------------------------------------------------------guide -------------
1159%------------------------------------------------------------------------
1160%  III - FUNCTIONS ASSOCIATED TO THE FRAME IndexRange
1161%------------------------------------------------------------------------
1162
1163
1164% ---- determine the menu to put in mode and advice a default choice
1165%------------------------------------------------------------------------
1166function [ModeMenu,ModeValue]=update_mode(i1_series,i2_series,j2_series)
1167%------------------------------------------------------------------------   
1168ModeMenu={''};
1169if isempty(j2_series)% no j pair
1170    ModeValue=1;
1171    if ~isempty(i2_series)
1172        ModeMenu={'series(Di)'}; % pair menu with only option Di
1173    end
1174else %existence of j pairs
1175    pair_max=squeeze(max(i1_series,[],1)); % max on pair index
1176    j_max=max(pair_max,[],1);
1177    MaxIndex_i=find(j_max, 1, 'last' )-1; % max ref index i
1178    MinIndex_i=find(j_max, 1 )-1; % min ref index i
1179    i_max=max(pair_max,[],2);
1180    MaxIndex_j=find(i_max, 1, 'last' )-1; % max ref index i
1181    MinIndex_j=find(i_max, 1 )-1; % min ref index i
1182    if MaxIndex_j==MinIndex_j
1183        ModeValue=1;
1184        ModeMenu={'bursts'};
1185    elseif MaxIndex_i==MinIndex_i
1186        ModeValue=1;
1187        ModeMenu={'series(Dj)'};
1188    else
1189        ModeMenu={'bursts';'series(Dj)'};
1190        if (MaxIndex_j-MinIndex_j)>10
1191            ModeValue=2; % set mode to series(Dj) if more than 10 j values
1192        else
1193            ModeValue=1;
1194        end
1195    end
1196end
1197
1198
1199%------------------------------------------------------------------------
1200function displ_pair=update_listpair(i1_series,i2_series,j1_series,j2_series,mode,time,TimeUnit,ref_i,ref_j,TimeName,InputTable,FileInfo)
1201%------------------------------------------------------------------------
1202displ_pair={};
1203if isempty(TimeUnit)
1204    dtunit='e-03';
1205else
1206    dtunit=['m' TimeUnit];
1207end
1208switch mode
1209    case 'series(Di)'
1210        diff_i=i2_series-i1_series;
1211        min_diff=min(diff_i(diff_i>0));
1212        max_diff=max(diff_i(diff_i>0));
1213        for ipair=min_diff:max_diff
1214            if numel(diff_i(diff_i==ipair))>0
1215                pair_string=['Di= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2)) ];
1216                if ~isempty(time)
1217                    if ref_i<=floor(ipair/2)
1218                        ref_i=floor(ipair/2)+1; % shift ref_i to get the first pair
1219                    end
1220                    Dt=time(ref_i+ceil(ipair/2),ref_j)-time(ref_i-floor(ipair/2),ref_j);
1221                    pair_string=[pair_string ', Dt=' num2str(Dt) ' ' dtunit];
1222                end
1223                displ_pair=[displ_pair;{pair_string}];
1224            end
1225        end
1226        if ~isempty(displ_pair)
1227            displ_pair=[displ_pair;{'Di=*|*'}];
1228        end
1229    case 'series(Dj)'
1230        if isempty(j2_series)
1231            msgbox_uvmat('ERROR','no j1-j2 pair available')
1232            return
1233        end
1234        diff_j=j2_series-j1_series;
1235        min_diff=min(diff_j(diff_j>0));
1236        max_diff=max(diff_j(diff_j>0));
1237        for ipair=min_diff:max_diff
1238            if numel(diff_j(diff_j==ipair))>0
1239                pair_string=['Dj= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2)) ];
1240                if ~isempty(time)
1241                    if ref_j<=floor(ipair/2)
1242                        ref_j=floor(ipair/2)+1; % shift ref_i to get the first pair
1243                    end
1244                    Dt=time(ref_i,ref_j+ceil(ipair/2))-time(ref_i,ref_j-floor(ipair/2));
1245                    pair_string=[pair_string ', Dt=' num2str(Dt) ' ' dtunit];
1246                end
1247                displ_pair=[displ_pair;{pair_string}];
1248            end
1249        end
1250        if ~isempty(displ_pair)
1251            displ_pair=[displ_pair;{'Dj=*|*'}];
1252        end
1253    case 'bursts'
1254        if isempty(j2_series)
1255            msgbox_uvmat('ERROR','no j1-j2 pair available')
1256            return
1257        end
1258        %diff_j=j2_series-j1_series;
1259        min_j1=min(j1_series(j1_series>0));
1260        max_j1=max(j1_series(j1_series>0));
1261        min_j2=min(j2_series(j2_series>0));
1262        max_j2=max(j2_series(j2_series>0));
1263        for pair1=min_j1:min(max_j1,min_j1+20)
1264            for pair2=min_j2:min(max_j2,min_j2+20)
1265                if numel(j1_series(j1_series==pair1))>0 && numel(j2_series(j2_series==pair2))>0
1266                    pair_string=['j= ' num2str(pair1) '-' num2str(pair2)];
1267                    [TimeValue,DtValue]=get_time(ref_i,[],pair_string,InputTable,FileInfo,TimeName,'Dt');
1268                    %Dt=time(ref_i,pair2+1)-time(ref_i,pair1+1);
1269                    pair_string=[pair_string ', Dt=' num2str(DtValue) ' ' dtunit];
1270                    displ_pair=[displ_pair;{pair_string}];
1271                end
1272            end
1273        end
1274        if ~isempty(displ_pair)
1275            displ_pair=[displ_pair;{'j=*-*'}];
1276        end
1277end
1278
1279%------------------------------------------------------------------------
1280function num_first_i_Callback(hObject, eventdata, handles)
1281%------------------------------------------------------------------------
1282num_last_i_Callback(hObject, eventdata, handles)
1283
1284%------------------------------------------------------------------------
1285function num_last_i_Callback(hObject, eventdata, handles)
1286%------------------------------------------------------------------------
1287SeriesData=get(handles.series,'UserData');
1288if ~isfield(SeriesData,'Time')
1289    SeriesData.Time{1}=[];
1290end
1291displ_time(handles);
1292
1293%------------------------------------------------------------------------
1294function num_first_j_Callback(hObject, eventdata, handles)
1295%------------------------------------------------------------------------
1296 num_last_j_Callback(hObject, eventdata, handles)
1297
1298%------------------------------------------------------------------------
1299function num_last_j_Callback(hObject, eventdata, handles)
1300%------------------------------------------------------------------------
1301% first_j=str2num(get(handles.num_first_j,'String'));
1302% last_j=str2num(get(handles.num_last_j,'String'));
1303% ref_j=ceil((first_j+last_j)/2);
1304% set(handles.num_ref_j,'String', num2str(ref_j))
1305% num_ref_j_Callback(hObject, eventdata, handles)
1306SeriesData=get(handles.series,'UserData');
1307if ~isfield(SeriesData,'Time')
1308    SeriesData.Time{1}=[];
1309end
1310displ_time(handles);
1311
1312%------------------------------------------------------------------------
1313% ---- find the times corresponding to the first and last indices of a series
1314function displ_time(handles)
1315%------------------------------------------------------------------------
1316SeriesData=get(handles.series,'UserData'); %
1317if ~isfield(SeriesData,'Time')
1318    return
1319end
1320PairString=get(handles.PairString,'Data');
1321ref_i_1=str2num(get(handles.num_first_i,'String')); % first reference index
1322ref_i_2=str2num(get(handles.num_last_i,'String')); % last reference index
1323ref_j_1=[];ref_j_2=[];
1324if strcmp(get(handles.num_first_j,'Visible'),'on')
1325ref_j_1=str2num(get(handles.num_first_j,'String'));
1326ref_j_2=str2num(get(handles.num_last_j,'String'));
1327end
1328[i1_1,i2_1,j1_1,j2_1] = get_file_index(ref_i_1,ref_j_1,PairString);
1329[i1_2,i2_2,j1_2,j2_2] = get_file_index(ref_i_2,ref_j_2,PairString);
1330TimeTable=get(handles.TimeTable,'Data');
1331%%%%%%
1332%TODO: read time in netcdf file, see ActionName_Callback
1333%%%%%%%
1334%Pairs=get(handles.PairString,'Data');
1335for iview=1:size(TimeTable,1)
1336    if size(SeriesData.Time,1)<iview
1337        break
1338    end
1339    TimeTable{iview,3}=[];
1340    TimeTable{iview,4}=[];
1341    if size(SeriesData.Time{iview},1)>=i2_2+1 && (isempty(ref_j_1)||size(SeriesData.Time{iview},2)>=j2_2+1)
1342        if isempty(ref_j_1)
1343            time_first=(SeriesData.Time{iview}(i1_1+1,2)+SeriesData.Time{iview}(i2_1+1,2))/2;
1344            time_last=(SeriesData.Time{iview}(i1_2+1,2)+SeriesData.Time{iview}(i2_2+1,2))/2;
1345        else
1346            time_first=(SeriesData.Time{iview}(i1_1+1,j1_1+1)+SeriesData.Time{iview}(i2_1+1,j2_1+1))/2;
1347            time_last=(SeriesData.Time{iview}(i1_2+1,j1_2+1)+SeriesData.Time{iview}(i2_2+1,j2_1+1))/2;
1348        end
1349        TimeTable{iview,3}=time_first; % TODO: take into account pairs
1350        TimeTable{iview,4}=time_last; % TODO: take into account pairs
1351    end
1352end
1353set(handles.TimeTable,'Data',TimeTable)
1354
1355%% set the waitbar position with respect to the min and max in the series
1356MinIndex_i=min(get(handles.MinIndex_i,'Data'));
1357MaxIndex_i=max(get(handles.MaxIndex_i,'Data'));
1358pos_first=(ref_i_1-MinIndex_i)/(MaxIndex_i-MinIndex_i+1);
1359pos_last=(ref_i_2-MinIndex_i+1)/(MaxIndex_i-MinIndex_i+1);
1360if isempty(pos_first), pos_first=0; end
1361if isempty(pos_last), pos_last=1; end
1362Position=get(handles.Waitbar,'Position'); % position of the waitbar:= [ x,y, width, height]
1363Position_status=get(handles.FileStatus,'Position');
1364Position(1)=Position_status(1)+Position_status(3)*pos_first;
1365Position(3)=max(Position_status(3)*(pos_last-pos_first),0.001); % width must remain positive
1366set(handles.Waitbar,'Position',Position)
1367update_waitbar(handles.Waitbar,0)
1368
1369%------------------------------------------------------------------------
1370% --- Executes when selected cell(s) is changed in PairString.
1371function PairString_CellSelectionCallback(hObject, eventdata, handles)
1372%------------------------------------------------------------------------   
1373if numel(eventdata.Indices)>=1
1374    PairString=get(hObject,'Data');
1375    if ~isempty(PairString{eventdata.Indices(1)})
1376        SetPairs_Callback(hObject, eventdata.Indices(1), handles)
1377    end
1378end
1379
1380%-------------------------------------
1381function enable_i(handles,state)
1382set(handles.i_txt,'Visible',state)
1383set(handles.num_first_i,'Visible',state)
1384set(handles.num_last_i,'Visible',state)
1385set(handles.num_incr_i,'Visible',state)
1386
1387%-----------------------------------
1388function enable_j(handles,state)
1389set(handles.j_txt,'Visible',state)
1390set(handles.num_first_j,'Visible',state)
1391set(handles.num_last_j,'Visible',state)
1392set(handles.num_incr_j,'Visible',state)
1393set(handles.MinIndex_j,'Visible',state)
1394set(handles.MaxIndex_j,'Visible',state)
1395
1396
1397%%%%%%%%%%%%%%%%%%%%
1398%%  MAIN ActionName FUNCTIONS
1399%%%%%%%%%%%%%%%%%%%%
1400%------------------------------------------------------------------------
1401% --- Executes on button press in RUN.
1402%------------------------------------------------------------------------
1403function RUN_Callback(hObject, eventdata, handles)
1404
1405%% settings of the button RUN
1406if ~isequal(get(handles.ActionInput,'BackgroundColor'),[1 0 0])
1407    msgbox_uvmat('ERROR','first activate the button ActionInput')
1408    return
1409end
1410set(handles.RUN,'BusyAction','queue'); % activation of STOP button will set BusyAction to 'cancel'
1411set(handles.RUN, 'Enable','Off')% avoid further RUN action until the current one is finished
1412set(handles.RUN,'BackgroundColor',[1 1 0])%show activation of RUN by yellow color
1413drawnow
1414set(handles.status,'Value',0)% desable status display if relevant
1415status_Callback([], eventdata, handles)
1416
1417%% launch action
1418errormsg=launch_action(handles);
1419if ~isempty(errormsg)
1420     msgbox_uvmat('ERROR',errormsg)
1421end
1422
1423%% reset the GUI series
1424update_waitbar(handles.Waitbar,1); % put the waitbar to end position to indicate launching is finished
1425set(handles.RUN, 'Enable','On')
1426set(handles.RUN,'BackgroundColor',[1 0 0])
1427set(handles.RUN, 'Value',0)
1428
1429%------------------------------------------------------------------------
1430% --- called by RUN_Callback
1431%------------------------------------------------------------------------
1432% The calculations are launched in three different ways:
1433% RunMode='local': calculation on the local Matlab session, will prevent other actions during that time.
1434% RunMode='background': calculation on the local computer, but in a new Matlab session (with no graphic output).
1435% RunMode='cluster': calculations dispatched in a cluster, using a managing system, 'oar, 'sge, or 'sgb'.
1436% In the latter case, the calculation is split in 'packets' of i index (all j indices are contained in a single packet).
1437% This splitting is possible only if the different calculations in the series are independent. Otherwise the action
1438% function imposes a number of processes NbSlice in input, for instance NbSlice=1 for a time series.
1439% If NbSlice is not imposed, the splitting in packets (jobs) is determined
1440% so that a job is optimum length AdvisedJobCPUTime), and the total job number in any case smaller
1441% than MaxJobNumber (these parameters are defined in the file series.xml in
1442% accordance with the management strategy for the cluster). The jobs are
1443% dispatched in parallel into NbCore processors by the cluster managing system.
1444
1445function errormsg=launch_action(handles)
1446errormsg=''; % default
1447
1448%% read the data on the GUI series
1449Param=read_GUI_series(handles); % displayed parameters
1450SeriesData=get(handles.series,'UserData'); % hidden parameters
1451if isfield(SeriesData,'TransformInput')
1452    Param.TransformInput=SeriesData.TransformInput;
1453end
1454if isfield(SeriesData,'ProjObject')
1455    Param.ProjObject=SeriesData.ProjObject;
1456end
1457if ~isfield(SeriesData,'i1_series')
1458    errormsg='The input field series needs to be refreshed: press REFRESH';
1459    return
1460end
1461if isfield(Param,'InputFields')&& isfield(Param.InputFields,'FieldName')&& isequal(Param.InputFields.FieldName,'add_field...')
1462    errormsg='input field name(s) not defined, select add_field...';
1463    return
1464end
1465
1466%% select the Action mode, 'local', 'background' or 'cluster' (if available)
1467RunMode='local'; % default (needed for first opening of the GUI series)
1468if isfield(Param.Action,'RunMode')
1469    RunMode=Param.Action.RunMode;
1470    Param.Action=rmfield(Param.Action,'RunMode'); % remove from the recorded xml file to avoid interference during ImportConfig
1471    Param.RunMode=RunMode; % keep track of the mode
1472end
1473ActionExt='.m'; % default
1474if isfield(Param.Action,'ActionExt')
1475    ActionExt=Param.Action.ActionExt; % '.m', '.sh' (compiled)  or '.py' (Python)
1476    Param.Action=rmfield(Param.Action,'ActionExt'); % remove from the recorded xml file to avoid interference during ImportConfig
1477end
1478ActionName=Param.Action.ActionName;
1479ActionPath=Param.Action.ActionPath;
1480path_series=fileparts(which('series'));
1481
1482%% create the Action fct handle if RunMode option = 'local'
1483if strcmp(RunMode,'local')
1484    if ~isequal(ActionPath,path_series)
1485        eval(['spath=which(''' ActionName ''');']) %spath = current path of the selected function ACTION
1486        if ~exist(ActionPath,'dir')
1487            errormsg=['The prescribed function path ' ActionPath ' does not exist'];
1488            return
1489        end
1490        if ~isequal(spath,ActionPath)
1491            addpath(ActionPath)% add the prescribed path if not the current one
1492        end
1493    end
1494    eval(['h_fun=@' ActionName ';'])%create a function handle for ACTION
1495    if ~isequal(ActionPath,path_series)
1496        rmpath(ActionPath)% add the prescribed path if not the current one
1497    end
1498end
1499
1500%% Get  parameters from series.xml
1501errormsg=''; % default error message
1502ActionFullName=fullfile(get(handles.ActionPath,'String'),ActionName);
1503
1504%% If a compiled version has been selected (ext .sh) check wether it needs to be recompiled
1505if strcmp(ActionExt,'.sh')
1506    TransformPath='';
1507    if isfield(SeriesData,'TransformPath')
1508        TransformPath=SeriesData.TransformPath;
1509        if isfield(SeriesData,'TransformList')
1510            TransformList=get(handles.TransformName,'String');
1511            TransformIndex=get(handles.TransformName,'Value');
1512            TransformName=TransformList{TransformIndex};
1513            if ~ismember(TransformName,SeriesData.TransformList)
1514                TransformPath='';
1515            end
1516        end
1517    end
1518    if ~isempty(TransformPath)&&...
1519          ~strcmp(TransformPath,get(handles.TransformPath,'String'))% if the transform is not in paths set for compilation
1520        msgbox_uvmat('ERROR', 'compilation not available for this transform function, select .m')
1521        return
1522    end
1523    set(handles.series,'Pointer','watch') % set the mouse pointer to 'watch'
1524    set(handles.ActionExt,'BackgroundColor',[1 1 0])
1525    [mcrmajor, mcrminor] = mcrversion;   
1526    MCRROOT = ['MCRROOT',int2str(mcrmajor),int2str(mcrminor)];
1527    RunTime = getenv('MCRROOT'); % Just variable MCRROOT with no version in it's name
1528    if strcmp(RunTime,'')
1529        RunTime = getenv(MCRROOT); % Use specialize MCRROOT with version
1530    end
1531    ActionNameVersion=[ActionName '_' MCRROOT];
1532    ActionFullName=fullfile(get(handles.ActionPath,'String'),[ActionNameVersion '.sh']);
1533    % compile the .m file if the .sh file does not exist yet
1534    if ~exist(ActionFullName,'file')
1535        answer=msgbox_uvmat('INPUT_Y-N','compiled version has not been created: compile now?');
1536        if strcmp(answer,'Yes')
1537            set(handles.ActionExt,'BackgroundColor',[1 1 0])
1538            path_uvmat=fileparts(which('series'));
1539            currentdir=pwd;
1540            cd(get(handles.ActionPath,'String'))% go to the directory of Action
1541            addpath(path_uvmat)% add the path to uvmat to run the fct 'compile'
1542            compile(ActionName,TransformPath)
1543            cd(currentdir)
1544        else
1545            errormsg='Action launch interrupted';
1546            return
1547        end       
1548    else
1549        sh_file_info=dir(fullfile(get(handles.ActionPath,'String'),[ActionNameVersion '.sh']));
1550        m_file_info=dir(fullfile(get(handles.ActionPath,'String'),[ActionName '.m']));
1551        if isfield(m_file_info,'datenum') && m_file_info.datenum>sh_file_info.datenum
1552            set(handles.ActionExt,'BackgroundColor',[1 1 0])
1553            drawnow
1554            answer=msgbox_uvmat('INPUT_Y-N',[ActionNameVersion '.sh needs to be updated: recompile now?']);
1555            if strcmp(answer,'Yes')
1556                path_uvmat=fileparts(which('series'));
1557                currentdir=pwd;
1558                cd(get(handles.ActionPath,'String'))% go to the directory of Action
1559                addpath(path_uvmat)% add the path to uvmat to run the fct 'compile'
1560                addpath(fullfile(path_uvmat,'transform_field'))% add the path to transform functions to run the fct 'compile'
1561                compile(ActionName,TransformPath)
1562                cd(currentdir)
1563            end
1564        end
1565    end
1566
1567    set(handles.ActionExt,'BackgroundColor',[1 1 1])
1568     set(handles.series,'Pointer','arrow') % set the mouse pointer to 'watch
1569end
1570
1571%% set nbre of cluster cores and processes:
1572% NbCore is the number of computer processors used
1573% NbProcess is the number of independent processes in which the required calculation is split.
1574switch RunMode
1575    case {'local','background'}
1576        NbCore=1; % no need to split the calculation
1577    case 'cluster'
1578        %proposed number of cores to reserve in the cluster
1579        NbCoreAdvised=SeriesData.SeriesParam.ClusterParam.NbCoreAdvised;
1580        NbCoreMax=SeriesData.SeriesParam.ClusterParam.NbCoreMax;
1581        if NbCoreMax~=1
1582            if strcmp(ActionExt,'.m')% case of Matlab function (uncompiled)
1583                warning_string=', preferably use .sh option to save Matlab licences';
1584            else
1585                warning_string=')';
1586            end
1587            answer=msgbox_uvmat('INPUT_TXT',['Number of cores (max ' num2str(NbCoreMax) ', ' warning_string],num2str(NbCoreAdvised));
1588            if isempty(answer)
1589                errormsg='Action launch interrupted by user';
1590                return
1591            end
1592            NbCore=str2double(answer);
1593            if NbCore > NbCoreMax
1594                NbCore=NbCoreMax;
1595            end
1596        else
1597            NbCore=1;
1598        end
1599end
1600if ~isfield(Param.IndexRange,'NbSlice')
1601    Param.IndexRange.NbSlice=[];
1602end
1603
1604%% Look for processing on multiple experiments set by the GUI browse_data
1605NbExp=1;% initiate the number of experiments set by the GUI browse_data, =1 otherwise
1606if get(handles.Replicate,'Value')
1607    hh=findobj(allchild(0),'Tag','browse_data');
1608    if isempty(hh)
1609        set(handles.Replicate,'Value',0)
1610    else
1611        set(handles.Replicate,'BackgroundColor',[1 1 0])%paint Relicate button in yellow
1612        BrowseData=guidata(hh);
1613        SourceDir=get(BrowseData.SourceDir,'String');
1614        ListExp=get(BrowseData.ListExperiments,'String');
1615        ExpIndices=get(BrowseData.ListExperiments,'Value');
1616        ListExp=ListExp(ExpIndices);
1617        ListDevices=get(BrowseData.ListDevices,'String');
1618        DeviceIndices=get(BrowseData.ListDevices,'Value');
1619        ListDevices=ListDevices(DeviceIndices);
1620        ListDataSeries=get(BrowseData.DataSeries,'String');
1621        DataSeriesIndices=get(BrowseData.DataSeries,'Value');
1622        ListDataSeries=ListDataSeries(DataSeriesIndices);
1623        NbExp=0; % counter of the number of experiments set by the GUI browse_data
1624        for iexp=1:numel(ListExp)
1625            if ~isempty(regexp(ListExp{iexp},'^\+/'))% if it is a folder
1626                if strcmp(get(BrowseData.DataSeries,'enable'),'off');%case of a multiple input line for series
1627                    NbExp=NbExp+1;
1628                    ExpIndex{NbExp}=iexp;
1629                    for idevice=1:numel(ListDevices)
1630                        lpath= fullfile(SourceDir,regexprep(ListExp{iexp},'^\+/',''),...
1631                            regexprep(ListDevices{idevice},'^\+/',''));
1632                        ldir=regexprep(ListDataSeries{idevice},'^\+/','');
1633                        ListPath{idevice,NbExp}=lpath;
1634                        ListSubdir{idevice,NbExp}=ldir;
1635                    end
1636                else
1637                    for idevice=1:numel(ListDevices)
1638                        if ~isempty(regexp(ListDevices{idevice},'^\+/'))% if it is a folder
1639                            for isubdir=1:numel(ListDataSeries)
1640                                if ~isempty(regexp(ListDataSeries{isubdir},'^\+/'))% if it is a folder
1641                                    lpath= fullfile(SourceDir,regexprep(ListExp{iexp},'^\+/',''),...
1642                                        regexprep(ListDevices{idevice},'^\+/',''));
1643                                    ldir= regexprep(ListDataSeries{isubdir},'^\+/','');
1644                                    if exist(fullfile(lpath,ldir),'dir')
1645                                        NbExp=NbExp+1;
1646                                        ExpIndex{NbExp}=iexp;
1647                                        ListPath{NbExp}=lpath;
1648                                        ListSubdir{NbExp}=ldir;
1649                                    end
1650                                end
1651                            end
1652                        end
1653                    end
1654                end
1655            end
1656        end
1657        answer=msgbox_uvmat('INPUT_Y-N-Cancel',['replicate the processing on ' num2str(NbExp) ' data series']);
1658        if strcmp(answer,'Cancel')||strcmp(answer,'No')
1659            return
1660        end
1661    end
1662end
1663%      set(handles.OutputSubDir,'String',SubDir)
1664%      Param.OutputSubDir=SubDir;
1665%%%%%%%%%%%%%%%%%%% LOOP ON EXPERIMENTS POSSIBLY SET BY THE GUI browse_data, NbExp=1 otherwise %%%%%%%%%
1666for iexp=1:NbExp
1667    if get(handles.Replicate,'Value')
1668        if ~strcmp(get(handles.RUN,'BusyAction'),'queue')% allow for STOP action
1669            disp('program stopped by user')
1670            return
1671        end
1672        set(BrowseData.ListExperiments,'Value',ExpIndex{iexp})
1673        Param.InputTable(:,1)=ListPath(:,iexp);
1674        Param.InputTable(:,2)=ListSubdir(:,iexp);
1675        OutputSubDir=unique(ListSubdir(:,iexp));
1676        Param.OutputSubDir=OutputSubDir{1};
1677        if numel(OutputSubDir)>1% case
1678            for iout=2:numel(OutputSubDir)
1679                Param.OutputSubDir=[Param.OutputSubDir '-' OutputSubDir{iout}];
1680            end               
1681        end       
1682    end
1683    [xx,ExpName]=fileparts(Param.InputTable{1,1});
1684    Param.IndexRange.first_i=str2num(get(handles.num_first_i,'String'));%reset the firrst_i and last_i for multiple experiments, modified by the splitting into NbProcess
1685    Param.IndexRange.last_i=str2num(get(handles.num_last_i,'String'));
1686   
1687    %% create the output data directory if needed, after checking its existence
1688    OutputDir='';
1689    answer='';
1690    if isfield(Param,'OutputSubDir')% possibly update the output dir if it already exists
1691        SubDirOut=[Param.OutputSubDir Param.OutputDirExt];
1692        SubDirOutNew=SubDirOut;
1693        detect=exist(fullfile(Param.InputTable{1,1},SubDirOutNew),'dir'); % test if  the dir  already exist
1694        check_create=1; % need to create the result directory by default
1695        CheckOverwrite=1;
1696        if isfield(Param,'CheckOverwrite')
1697            CheckOverwrite=Param.CheckOverwrite;
1698        end
1699        while detect
1700            if CheckOverwrite
1701                comment=', possibly overwrite previous data';
1702            else
1703                comment=', will complement existing result files (no overwriting)';
1704            end
1705            answer=msgbox_uvmat('INPUT_Y-N-Cancel',['use existing ouput directory: ' fullfile(Param.InputTable{1,1},SubDirOutNew) comment]);
1706            if strcmp(answer,'Cancel')
1707                break
1708            elseif strcmp(answer,'Yes')
1709                detect=0;
1710                check_create=0;
1711            else
1712                r=regexp(SubDirOutNew,'(?<root>.*\D)(?<num1>\d+)$','names'); % detect whether name ends by a number
1713                if isempty(r)
1714                    r(1).root=[SubDirOutNew '_'];
1715                    r(1).num1='0';
1716                end
1717                SubDirOutNew=[r(1).root num2str(str2num(r(1).num1)+1)]; % increment the index by 1 or put 1
1718                detect=exist(fullfile(Param.InputTable{1,1},SubDirOutNew),'dir'); % test if  the dir  already exists
1719                check_create=1;
1720            end
1721        end
1722        if strcmp(answer,'Cancel')
1723            continue
1724        end
1725        Param.OutputDirExt=regexprep(SubDirOutNew,['^' Param.OutputSubDir],'');
1726        Param.OutputRootFile=Param.InputTable{1,3}; % the first sorted RootFile taken for output
1727        OutputDir=fullfile(Param.InputTable{1,1},[Param.OutputSubDir Param.OutputDirExt]); % full name (with path) of output directory
1728        if check_create    % create output directory if it does not exist
1729            [tild,msg1]=mkdir(OutputDir);
1730            if ~strcmp(msg1,'')
1731                errormsg=['cannot create ' OutputDir ': ' msg1]; % error message for directory creation
1732                return
1733            end
1734        end
1735       
1736    elseif isfield(Param,'ActionInput')&&isfield(Param.ActionInput,'LogPath')% custom definition of the output dir
1737        OutputDir=Param.ActionInput.LogPath;
1738    end
1739   
1740    set(handles.OutputSubDir,'String',Param.OutputSubDir)
1741    set(handles.OutputDirExt,'String',Param.OutputDirExt)
1742    drawnow
1743    if get(handles.Replicate,'Value')
1744        set(handles.InputTable,'Data',Param.InputTable)
1745        check_input_file_series(handles)
1746    end
1747    DirXml=fullfile(OutputDir,'0_XML');
1748    if ~exist(DirXml,'dir')
1749        [~,msg1]=mkdir(DirXml);
1750        if ~strcmp(msg1,'')
1751            errormsg=['cannot create ' DirXml ': ' msg1]; % error message for directory creation
1752            return
1753        end
1754        [success,msg] = fileattrib(DirXml,'+w','g','s'); % allow writing access for the group of users, recursively in the folder
1755        if success==0
1756            msgbox_uvmat('WARNING',{['unable to set group write access to ' DirXml ':']; msg}); % error message for directory creation
1757        end
1758    end
1759    OutputNomType=nomtype2pair(Param.InputTable{1,4}); % nomenclature for output files
1760   
1761    %% get the set of reference input field indices
1762    first_i=1; % first i index to process
1763    last_i=1; % last i index to process
1764    incr_i=1; % increment step in i index
1765    first_j=1; % first j index to process
1766    last_j=1; % last j index to process
1767    incr_j=1; % increment step in j index
1768    if isfield(Param.IndexRange,'first_i')
1769        first_i=Param.IndexRange.first_i;
1770        incr_i=Param.IndexRange.incr_i;
1771        last_i=Param.IndexRange.last_i;
1772    end
1773    if isfield(Param.IndexRange,'incr_j')
1774        first_j=Param.IndexRange.first_j;
1775        last_j=Param.IndexRange.last_j;
1776        incr_j=Param.IndexRange.incr_j;
1777    end
1778    if last_i < first_i || last_j < first_j
1779        errormsg= 'series/Run_Callback:last field index must be larger or equal to the first one';
1780        return
1781    end
1782    %incr_i must be defined, =1 by default, if NbSlice is active
1783    if isempty(incr_i)&& ~isempty(Param.IndexRange.NbSlice)
1784        incr_i=1;
1785        set(handles.num_incr_i,'String','1')
1786    end
1787    % case of no increment i defined: processing is done on the available files found in i1_series
1788    if isempty(incr_i)
1789        if isempty(incr_j)
1790            [ref_j,ref_i]=find(squeeze(SeriesData.i1_series{1}(1,:,:)));
1791            ref_j=ref_j(ref_j>=first_j & ref_j<=last_j);
1792            ref_i=ref_i(ref_i>=first_i & ref_i<=last_i);
1793            ref_j=ref_j-1;
1794            ref_i=ref_i-1;
1795        else
1796            ref_j=first_j:incr_j:last_j;
1797            [tild,ref_i]=find(squeeze(SeriesData.i1_series{1}(1,:,:)));
1798            ref_i=ref_i-1;
1799            ref_i=ref_i(ref_i>=first_i & ref_i<=last_i);
1800        end
1801        % increment i is defined: processing is done on first_i:incr_i:last_i;
1802    else
1803        ref_i=first_i:incr_i:last_i;
1804        if isempty(incr_j)% automatic finding of the existing j indices
1805            [ref_j,tild]=find(squeeze(SeriesData.i1_series{1}(1,:,:)));
1806            ref_j=ref_j-1;
1807            ref_j=ref_j(ref_j>=first_j & ref_j<=last_j);
1808        else
1809            ref_j=first_j:incr_j:last_j;
1810        end
1811    end
1812    CPUTime=1; % job time estimated at 1 min per iteration (on index i and j) by default
1813    if isfield(Param.Action, 'CPUTime') && ~isempty(Param.Action.CPUTime)
1814        CPUTime=Param.Action.CPUTime; % Note: CpUTime for one iteration ref_i has to be multiplied by the number of j indices nbfield_j
1815    end
1816    nbfield_j=numel(ref_j); % number of j indices
1817    BlockLength=numel(ref_i); % by default, job involves the full set of i field indices
1818    NbProcess=1;
1819    switch RunMode
1820        case 'cluster'
1821            JobNumberMax=SeriesData.SeriesParam.ClusterParam.JobNumberMax;
1822            JobCPUTimeAdvised=SeriesData.SeriesParam.ClusterParam.JobCPUTimeAdvised;
1823            if isempty(Param.IndexRange.NbSlice)% if NbSlice is not defined
1824                BlockLength= ceil(JobCPUTimeAdvised/(CPUTime*nbfield_j)); % iterations are grouped in sets with length BlockLength  such that the typical CPU time of a job is JobCPUTimeAdvised.
1825                BlockLength=max(BlockLength,ceil(numel(ref_i)*NbExp/JobNumberMax)); % possibly increase the BlockLength to have less than MaxJobNumber jobs
1826                NbProcess=ceil(numel(ref_i)/BlockLength) ; % nbre of processes sent to oar
1827            else
1828                NbProcess=Param.IndexRange.NbSlice; % the parameter NbSlice sets the nbre of run processes
1829            end
1830            NbCore=min(NbCore,NbProcess); % reduces the number of cores if it exceeds the number of processes
1831        otherwise
1832            if ~isempty(Param.IndexRange.NbSlice)
1833                NbProcess=Param.IndexRange.NbSlice; % the parameter NbSlice sets the nbre of run processes
1834            end
1835    end
1836   
1837    %% record nbre of output files and starting time for computation for status
1838    StatusData=get(handles.status,'UserData');
1839    if isfield(StatusData,'OutputFileMode')
1840        switch StatusData.OutputFileMode
1841            case 'NbInput'
1842                StatusData.NbOutputFile=numel(ref_i)*nbfield_j;
1843            case 'NbInput_i'
1844                StatusData.NbOutputFile=numel(ref_i);
1845            case 'NbSlice'
1846                StatusData.NbOutputFile=str2num(get(handles.num_NbSlice,'String'));
1847        end
1848    end
1849    StatusData.TimeStart=now;
1850    set(handles.status,'UserData',StatusData)
1851   
1852    %% case of a function in Python
1853    if strcmp(ActionExt, '.py (in dev.)')
1854        fprintf([
1855            '\n' ...
1856            '!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n' ...
1857            'The option .py is used. It is still in development.\n' ...
1858            'To try it, first install pyper and the most recent version of fluidimage\n' ...
1859            '(see https://bitbucket.org/fluiddyn/fluidimage).\n' ...
1860            'Warning: there is no direct correspondance between UVMAT and fluidimage parameters\n' ...
1861            '!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n'])
1862        RunMode = 'python';
1863    end
1864   
1865   
1866    %% direct processing on the current Matlab session or creation of command files
1867    filexml=cell(1,NbProcess); % initialisation of the names of the files containing the processing parameters
1868    extxml=cell(1,NbProcess); % initialisation of the set of labels used for the files documenting each process
1869    for iprocess=1:NbProcess
1870        extxml{iprocess}='.xml';
1871    end
1872    for iprocess=1:NbProcess
1873        if ~strcmp(get(handles.RUN,'BusyAction'),'queue')% allow for STOP action
1874            disp('program stopped by user')
1875            return
1876        end
1877        if isempty(Param.IndexRange.NbSlice)
1878            Param.IndexRange.first_i=first_i+(iprocess-1)*BlockLength*incr_i;
1879            if Param.IndexRange.first_i>last_i
1880                NbProcess=iprocess-1; % leave the loop, we are at the end of the calculation
1881                break
1882            end
1883            Param.IndexRange.last_i=min(last_i,first_i+(iprocess)*BlockLength*incr_i-1);
1884        else %multislices (then incr_i is not empty)
1885            Param.IndexRange.first_i= first_i+iprocess-1;
1886            Param.IndexRange.incr_i=incr_i*Param.IndexRange.NbSlice;
1887        end
1888        for ilist=1:size(Param.InputTable,1)
1889            Param.InputTable{ilist,1}=regexprep(Param.InputTable{ilist,1},'\','/'); % correct path name for PCWIN system
1890        end
1891       
1892        if isfield(Param,'OutputSubDir')
1893            t=struct2xml(Param);
1894            t=set(t,1,'name','Series');
1895            extxml{iprocess}=fullfile_uvmat('','',Param.InputTable{1,3},'.xml',OutputNomType,...
1896                Param.IndexRange.first_i,Param.IndexRange.last_i,first_j,last_j);
1897            filexml{iprocess}=fullfile(OutputDir,'0_XML',extxml{iprocess});
1898            try
1899                save(t, filexml{iprocess}); % save the xml file containing the processing parameters
1900            catch ME
1901                if ~strcmp (RunMode,'local')
1902                    errormsg=['error writting ' filexml{iprocess} ': ' ME.message];
1903                    return
1904                end
1905            end
1906        end
1907        if strcmp (RunMode,'local')
1908            switch ActionExt
1909                case '.m'
1910                    h_fun(Param); % direct launching
1911                   
1912                case '.sh'
1913                    switch computer
1914                        case {'PCWIN','PCWIN64'} %Windows system
1915                            filexml=regexprep(filexml,'\\','\\\\'); % add '\' so that '\' are left as characters
1916                            system([ActionFullName ' ' RunTime ' ' filexml{iprocess}]); % TODO: adapt to DOS system
1917                        case {'GLNX86','GLNXA64','MACI64'}%Linux  system
1918                            system([ActionFullName ' ' RunTime ' ' filexml{iprocess}]);
1919                    end
1920            end
1921        end
1922    end
1923   
1924    if ~strcmp (RunMode,'local') && ~strcmp(RunMode,'python')
1925        %% processing on a different session of the same computer (background) or cluster, create executable files
1926        batch_file_list=cell(NbProcess,1); % initiate the list of executable files
1927        DirExe=fullfile(OutputDir,'0_EXE'); % directory name for executable files
1928        switch computer
1929            case {'PCWIN','PCWIN64'} %Windows system
1930                ExeExt='.bat';
1931            case {'GLNX86','GLNXA64','MACI64'}%Linux  system
1932                ExeExt='.sh';
1933        end
1934        %create subdirectory for executable files
1935        if ~exist(DirExe,'dir')
1936            [tild,msg1]=mkdir(DirExe);
1937            if ~strcmp(msg1,'')
1938                errormsg=['cannot create ' DirExe ': ' msg1]; % error message for directory creation
1939                return
1940            end
1941            [success,msg] = fileattrib(DirExe,'+w','g','s'); % allow writing access for the group of users, recursively in the folder
1942            if success==0
1943                msgbox_uvmat('WARNING',{['unable to set group write access to ' DirExe ':']; msg}); % error message for directory creation
1944            end
1945        end
1946        %create subdirectory for log files
1947        DirLog=fullfile(OutputDir,'0_LOG');
1948        if ~exist(DirLog,'dir')
1949            [tild,msg1]=mkdir(DirLog);
1950            if ~strcmp(msg1,'')
1951                errormsg=['cannot create ' DirLog ': ' msg1]; % error message for directory creation
1952                return
1953            end
1954            [success,msg] = fileattrib(DirLog,'+w','g','s'); % allow writing access for the group of users, recursively in the folder
1955            if success==0
1956                msgbox_uvmat('WARNING',{['unable to set group write access to ' DirLog ':']; msg}); % error message for directory creation
1957            end
1958        end
1959       
1960        %create the executable file
1961        file_exe_global=fullfile_uvmat('','',Param.InputTable{1,3},ExeExt,OutputNomType,...
1962            first_i,last_i,first_j,last_j);
1963        file_exe_global=fullfile(OutputDir,'0_EXE',file_exe_global);
1964        filelog_global=fullfile_uvmat('','',Param.InputTable{1,3},'.log',OutputNomType,...
1965            first_i,last_i,first_j,last_j);
1966        filelog_global=fullfile(OutputDir,'0_LOG',filelog_global);
1967       
1968        for iprocess=1:NbProcess
1969            %create the executable file
1970            batch_file_list{iprocess}=fullfile(OutputDir,'0_EXE',regexprep(extxml{iprocess},'.xml$',ExeExt));
1971           
1972            % set the log file name
1973            filelog{iprocess}=fullfile(OutputDir,'0_LOG',regexprep(extxml{iprocess},'.xml$','.log'));
1974        end
1975    end
1976   
1977    %% launch the executable files for background or cluster processing
1978   
1979    switch RunMode
1980       
1981        case 'background'
1982            [fid,message]=fopen(file_exe_global,'w');
1983            if isequal(fid,-1)
1984                errormsg=['creation of ' file_exe_global ':' message];
1985                return
1986            end
1987            switch ActionExt
1988                case '.m'% Matlab function
1989                    switch computer
1990                        case {'GLNX86','GLNXA64','MACI64'}
1991                            matlab_ver = ver('MATLAB');
1992                            matlab_version = matlab_ver.Version;
1993                            cmd=[...
1994                                '#!/bin/bash\n'...
1995                                'source /etc/profile\n'...
1996                                'module load matlab/' matlab_version '\n'...% CHOICE OF MATLAB VERSION
1997                                'time_start=$(date +%%s)\n'...
1998                                'matlab -nodisplay -nosplash -nojvm -logfile ''' filelog_global ''' <<END_MATLAB\n'...
1999                                'addpath(''' path_series ''');\n'...
2000                                'addpath(''' Param.Action.ActionPath ''');\n'];
2001                            for iprocess=1:NbProcess
2002                                cmd=[cmd '' Param.Action.ActionName  '(''' filexml{iprocess} ''');\n'];
2003                            end
2004                            cmd=[cmd  'exit\n' 'END_MATLAB\n'...
2005                                'time_end=$(date +%%s)\n'...
2006                                'echo "global time = " $(($time_end - $time_start)) >> ''' filelog_global '''\n'];
2007                            fprintf(fid,cmd); % fill the executable file with the  char string cmd
2008                            fclose(fid); % close the executable filefilelog_global
2009                            system(['chmod +x ' file_exe_global]); % set the file to executable
2010                        case {'PCWIN','PCWIN64'}
2011                            cmd=['matlab -automation -logfile ' regexprep(filelog{iprocess},'\\','\\\\')...
2012                                ' -r "addpath(''' regexprep(path_series,'\\','\\\\') ''');'...
2013                                'addpath(''' regexprep(Param.Action.ActionPath,'\\','\\\\') ''');'];
2014                            for iprocess=1:NbProcess
2015                                cmd=[cmd '' Param.Action.ActionName  '( ''' regexprep(filexml{iprocess},'\\','\\\\') ''');']
2016                            end
2017                            cmd=[cmd ';exit"'];
2018                            fprintf(fid,cmd); % fill the executable file with the  char string cmd
2019                            fclose(fid); % close the executable file
2020                    end
2021                    system([file_exe_global ' &'])% directly execute the command file
2022                case '.sh' % compiled Matlab function
2023                    for iprocess=1:NbProcess
2024                        switch computer
2025                            case {'GLNX86','GLNXA64','MACI64'}
2026                                [fid,message]=fopen(batch_file_list{iprocess},'w'); % create the executable file
2027                                if isequal(fid,-1)
2028                                    errormsg=['creation of .bat file: ' message];
2029                                    return
2030                                end
2031                                cmd=['#!/bin/bash \n '...
2032                                    '#$ -cwd \n '...
2033                                    'hostname && date \n '...
2034                                    'umask 002 \n'...
2035                                    ActionFullName ' ' RunTime ' ' filexml{iprocess}]; % allow writting access to created files for user group
2036                                fprintf(fid,cmd); % fill the executable file with the  char string cmd
2037                                fclose(fid); % close the executable file
2038                                system(['chmod +x ' batch_file_list{iprocess}]); % set the file to executable
2039                                system([batch_file_list{iprocess} ' &'])% directly execute the command file
2040                            case {'PCWIN','PCWIN64'}
2041                                msgbox_uvmat('ERROR','option for compiled Matlab functions not implemented for Windows system')
2042                                return
2043                        end
2044                    end
2045                    msgbox_uvmat('CONFIRMATION',[ActionFullName ' launched in background for ' ExpName ': press STATUS to see results'])
2046            end
2047           
2048        case 'cluster' % option 'oar-parexec' used
2049            %create subdirectory for oar commands
2050            for iprocess=1:NbProcess
2051                [fid,message]=fopen(batch_file_list{iprocess},'w'); % create the executable file
2052                if isequal(fid,-1)
2053                    errormsg=['creation of .bat file: ' message];
2054                    return
2055                end
2056                if  strcmp(ActionExt,'.sh')
2057                    cmd=['#!/bin/bash \n '...
2058                        '#$ -cwd \n '...
2059                        'hostname && date \n '...
2060                        'umask 002 \n'...
2061                        ActionFullName ' ' RunTime ' ' filexml{iprocess}]; % allow writting access to created files for user group
2062                else
2063                    matlab_ver = ver('MATLAB');
2064                    matlab_version = matlab_ver.Version;
2065                    cmd=[...
2066                        '#!/bin/bash\n'...
2067                        'source /etc/profile\n'...
2068                        'module load matlab/' matlab_version '\n'...% CHOICE OF MATLAB VERSION
2069                        'matlab -nodisplay -nosplash -nojvm -singleCompThread -logfile ''' filelog{iprocess} ''' <<END_MATLAB\n'...
2070                        'addpath(''' path_series ''');\n'...
2071                        'addpath(''' Param.Action.ActionPath ''');\n'...
2072                        '' Param.Action.ActionName  '(''' filexml{iprocess} ''');\n'...
2073                        'exit\n'...
2074                        'END_MATLAB\n'];
2075                end
2076                fprintf(fid,cmd); % fill the executable file with the  char string cmd
2077                fclose(fid); % close the executable file
2078                system(['chmod +x ' batch_file_list{iprocess}]); % set the file to executable
2079            end
2080            DIR_CLUSTER=fullfile(OutputDir,'0_CLUSTER');
2081            if exist(DIR_CLUSTER,'dir')% delete the content of the dir 0_LOG to allow new input
2082                curdir=pwd;
2083                cd(DIR_CLUSTER)
2084                delete('*')
2085                cd(curdir)
2086            else
2087                [tild,msg1]=mkdir(DIR_CLUSTER);
2088                if ~strcmp(msg1,'')
2089                    errormsg=['cannot create ' DIR_CLUSTER ': ' msg1]; % error message for directory creation
2090                    return
2091                end
2092            end
2093            % create file containing the list of jobs
2094            ListProcess=fullfile(DIR_CLUSTER,'job_list.txt'); % name of the file containing the list of executables
2095            [fid,errormsg]=fopen(ListProcess,'w'); % open it for writting
2096            if isempty(errormsg)
2097            for iprocess=1:length(batch_file_list)
2098                fprintf(fid,[batch_file_list{iprocess} '\n']); % write list of exe files
2099            end
2100            fclose(fid);
2101            system(['chmod +x ' ListProcess]); % set the file to executable
2102            else
2103                errormsg=['error for writting the executable file:' errormsg];
2104            end       
2105            CPUTimeProcess=CPUTime*BlockLength*nbfield_j; % estimated CPU time for one individual process (in minutes)
2106            LaunchCmdFcn=SeriesData.SeriesParam.ClusterParam.LaunchCmdFcn;
2107            oar_command=feval(LaunchCmdFcn,ListProcess,ActionFullName,DirLog,NbProcess, NbCore,CPUTimeProcess)
2108            [status,result]=system(oar_command)% execute system command and show the result (ID number of the launched job) on the Matlab command window
2109            filename_oarcommand=fullfile(DIR_CLUSTER,'0_cluster_command'); % keep track of the command in file '0-OAR/0_cluster_command'
2110            fid=fopen(filename_oarcommand,'w');
2111            fprintf(fid,oar_command); % store the command
2112            fprintf(fid,result); % store the result (job ID number)
2113            fclose(fid);
2114            if status==0
2115                msgbox_uvmat('CONFIRMATION',[ActionFullName ' launched for ' ExpName ' as ' num2str(NbProcess) ' processes in cluster: press STATUS to see results'])
2116            else
2117                msgbox_uvmat('ERROR',result)
2118            end
2119            %     case 'cluster_pbs' % for LMFA Kepler machine:  trqnsferred to fct
2120           
2121            %         %create subdirectory for pbs command and log files
2122            %         DirPBS=fullfile(OutputDir,'0_PBS'); % todo : common name OAR/PBS
2123            %         if exist(DirPBS,'dir')% delete the content of the dir 0_LOG to allow new input
2124            %             curdir=pwd;
2125            %             cd(DirPBS)
2126            %             delete('*')
2127            %             cd(curdir)
2128            %         else
2129            %             [tild,msg1]=mkdir(DirPBS);
2130            %             if ~strcmp(msg1,'')
2131            %                 errormsg=['cannot create ' DirPBS ': ' msg1]; % error message for directory creation
2132            %                 return
2133            %             end
2134            %         end
2135            %         max_walltime=3600*20; % 20h max total calculation (cannot exceed 24 h)
2136            %         walltime_onejob=1800; % seconds, max estimated time for asingle file index value
2137            %         ListProcess=fullfile(DirPBS,'job_list.txt'); % create name of the global executable file
2138            %         fid=fopen(ListProcess,'w');
2139            %         for iprocess=1:length(batch_file_list)
2140            %             fprintf(fid,[batch_file_list{iprocess} '\n']); % list of exe files
2141            %         end
2142            %         fclose(fid);
2143            %         system(['chmod +x ' ListProcess]); % set the file to executable
2144            %         pbs_command=['qsub -n CIVX '...
2145            %             '-t idempotent --checkpoint ' num2str(walltime_onejob+60) ' '...
2146            %             '-l /core=' num2str(NbCore) ','...
2147            %             'walltime=' datestr(min(1.05*walltime_onejob/86400*max(NbProcess*BlockLength*nbfield_j,NbCore)/NbCore,max_walltime/86400),13) ' '...
2148            %             '-E ' regexprep(ListProcess,'\.txt\>','.stderr') ' '...
2149            %             '-O ' regexprep(ListProcess,'\.txt\>','.log') ' '...
2150            %             extra_qstat ' '...
2151            %             '"oar-parexec -s -f ' ListProcess ' '...
2152            %             '-l ' ListProcess '.log"'];
2153            %         filename_oarcommand=fullfile(DirPBS,'pbs_command');
2154            %         fid=fopen(filename_oarcommand,'w');
2155            %         fprintf(fid,pbs_command);
2156            %         fclose(fid);
2157            %         fprintf(pbs_command); % display in command line
2158            %         %system(pbs_command);
2159            %         msgbox_uvmat('CONFIRMATION',[ActionFullName ' command ready to be launched in cluster'])
2160           
2161        case 'cluster_sge' % for PSMN % TODO: use the standard 'cluster' config with an external fct
2162            % Au PSMN, on ne cr??e pas 1 job avec plusieurs c??urs, mais N jobs de 1 c??urs
2163            % o?? N < 1000.
2164            %create subdirectory for pbs command and log files
2165           
2166            DirSGE=fullfile(OutputDir,'0_SGE');
2167            if exist(DirSGE,'dir')% delete the content of the dir 0_LOG to allow new input
2168                curdir=pwd;
2169                cd(DirSGE)
2170                delete('*')
2171                cd(curdir)
2172            else
2173                [tild,msg1]=mkdir(DirSGE);
2174                if ~strcmp(msg1,'')
2175                    errormsg=['cannot create ' DirSGE ': ' msg1]; % error message for directory creation
2176                    return
2177                end
2178            end
2179            maxImgsPerJob = ceil(length(batch_file_list)/NbCore);
2180            disp(['Max number of jobs: ' num2str(NbCore)])
2181            disp(['Images per job: ' num2str(maxImgsPerJob)])
2182           
2183            iprocess = 1;
2184            imgsInJob = [];
2185            currJobIndex = 1;
2186            done = 0;
2187            while(~done)
2188                if(iprocess <= length(batch_file_list))
2189                    imgsInJob = [imgsInJob, iprocess];
2190                end
2191                if((numel(imgsInJob) >= maxImgsPerJob) || (iprocess == length(batch_file_list)))
2192                    cmd=['#!/bin/sh \n'...
2193                        '#$ -cwd \n'...
2194                        'hostname && date\n']
2195                    for ii=1:numel(imgsInJob)
2196                        cmd=[cmd ActionFullName ' /softs/matlab ' filexml{imgsInJob(ii)} '\n'];
2197                    end
2198                    [fid, message] = fopen([DirSGE '/job' num2str(currJobIndex) '.sh'], 'w');
2199                    fprintf(fid, cmd);
2200                    fclose(fid);
2201                    system(['chmod +x ' DirSGE '/job' num2str(currJobIndex) '.sh'])
2202                    sge_command=['qsub -N civ_' num2str(currJobIndex) ' '...
2203                        '-q ' qstat_Queue ' '...
2204                        '-e ' fullfile([DirSGE '/job' num2str(currJobIndex) '.out']) ' '...
2205                        '-o ' fullfile([DirSGE '/job' num2str(currJobIndex) '.out']) ' '...
2206                        fullfile([DirSGE '/job' num2str(currJobIndex) '.sh'])];
2207                    fprintf(sge_command); % display in command line
2208                    [status, result] = system(sge_command);
2209                    fprintf(result);
2210                    currJobIndex = currJobIndex + 1;
2211                    imgsInJob = [];
2212                end
2213                if(iprocess == length(batch_file_list))
2214                    done = 1;
2215                end
2216                iprocess = iprocess + 1;
2217            end
2218            msgbox_uvmat('CONFIRMATION',[num2str(currJobIndex-1) ' jobs launched on queue ' qstat_Queue '.'])
2219        case 'python'
2220            command = ['LD_LIBRARY_PATH=$(echo $LD_LIBRARY_PATH | pyp "l = x.split('':''); l = [s for s in l if ''matlab'' not in s]; print('':''.join(l))") ' ...
2221                'python -m fluidimage.run_from_xml ' filexml{iprocess}];
2222            fprintf(['command:\n' command '\n\n'])
2223            system(command, '-echo');
2224    end
2225    if exist(OutputDir,'dir')
2226        [SUCCESS,MESSAGE,MESSAGEID] = fileattrib (OutputDir);
2227        if MESSAGE.GroupWrite~=1
2228            [success,msg] = fileattrib(OutputDir,'+w','g','s'); % allow writing access for the group of users, recursively in the folder
2229            if success==0
2230                msgbox_uvmat('WARNING',{['unable to set group write access to ' OutputDir ':']; msg}); % error message for directory creation
2231            end
2232        end
2233    end
2234end
2235set(handles.Replicate,'BackgroundColor',[0 1 0])
2236
2237%------------------------------------------------------------------------
2238function STOP_Callback(hObject, eventdata, handles)
2239%------------------------------------------------------------------------
2240set(handles.RUN, 'BusyAction','cancel')
2241set(handles.RUN,'BackgroundColor',[1 0 0])
2242set(handles.RUN,'enable','on')
2243set(handles.RUN, 'Value',0)
2244
2245%------------------------------------------------------------------------
2246% --- read parameters from the GUI series
2247%------------------------------------------------------------------------
2248function Param=read_GUI_series(handles)
2249
2250%% read raw parameters from the GUI series
2251Param=read_GUI(handles.series);
2252
2253%% clean the output structure by removing unused information
2254if isfield(Param,'Pairs')
2255    Param=rmfield(Param,'Pairs'); % info Pairs not needed for output
2256end
2257if isfield(Param,'InputLine')
2258    Param=rmfield(Param,'InputLine');
2259end
2260if isfield(Param,'EditObject')
2261    Param=rmfield(Param,'EditObject');
2262end
2263Param.IndexRange.TimeSource=Param.IndexRange.TimeTable{end,1};
2264Param.IndexRange=rmfield(Param.IndexRange,'TimeTable');
2265empty_line=false(size(Param.InputTable,1),1);
2266for iline=1:size(Param.InputTable,1)
2267    empty_line(iline)=isempty(cell2mat(Param.InputTable(iline,1:3)));
2268end
2269Param.InputTable(empty_line,:)=[];
2270
2271%------------------------------------------------------------------------
2272% --- Executes on selection change in ActionName.
2273function ActionName_Callback(hObject, ActionPath, handles)
2274%------------------------------------------------------------------------
2275
2276%% stop any ongoing series processing
2277if isequal(get(handles.RUN,'Value'),1)
2278    answer= msgbox_uvmat('INPUT_Y-N','stop current Action process?');
2279    if strcmp(answer,'Yes')
2280        STOP_Callback(hObject, [], handles)
2281    else
2282        return
2283    end
2284end
2285set(handles.ActionName,'BackgroundColor',[1 1 0])
2286huigetfile=findobj(allchild(0),'tag','status_display');
2287if ~isempty(huigetfile)
2288    delete(huigetfile)
2289end
2290drawnow
2291
2292%% get Action name and path
2293NbBuiltinAction=get(handles.Action,'UserData'); % nbre of functions initially proposed in the menu ActionName (as defined in the Opening fct of series)
2294ActionList=get(handles.ActionName,'String'); % list menu fields
2295ActionIndex=get(handles.ActionName,'Value');
2296if ~isequal(ActionIndex,1)% if we are not just opening series
2297    InputTable=get(handles.InputTable,'Data');
2298    if isempty(InputTable{1,4})
2299        msgbox_uvmat('ERROR','no input file available: use Open in the menu bar')
2300        return
2301    end
2302end
2303ActionName= ActionList{get(handles.ActionName,'Value')}; % selected function name
2304ActionPathList=get(handles.ActionName,'UserData'); % list of recorded paths to functions of the list ActionName
2305
2306%% add a new function to the menu if 'more...' has been selected in the menu ActionName
2307if isequal(ActionName,'more...')
2308    if ~ischar(ActionPath)
2309        ActionPath=get(handles.ActionPath,'String');
2310    end
2311    [FileName, PathName] = uigetfile( ...
2312        {'*.m', ' (*.m)';
2313        '*.m',  '.m files '; ...
2314        '*.*', 'All Files (*.*)'}, ...
2315        'Pick a series processing function ',ActionPath);
2316    if length(FileName)<2
2317        return
2318    end
2319    [tild,ActionName,ActionExt]=fileparts(FileName);
2320   
2321    % insert the choice in the menu ActionName
2322    ActionIndex=find(strcmp(ActionName,ActionList),1); % look for the selected function in the menu Action
2323    PathName=regexprep(PathName,'/$','');
2324    if ~isempty(ActionIndex) && ~strcmp(ActionPathList{ActionIndex},PathName)%compare the path to the existing fct
2325        ActionIndex=[]; % the selected path is different than the recorded one
2326    end
2327    if isempty(ActionIndex)%the qselected fct (with selected path) does not exist in the menu
2328        ActionIndex= length(ActionList);
2329        ActionList=[ActionList(1:end-1);{ActionName};ActionList(end)]; % the selected function is appended in the menu, before the last item 'more...'
2330         ActionPathList=[ActionPathList; PathName];
2331    end
2332   
2333    % record the file extension and extend the path list if it is a new extension
2334    ActionExtList=get(handles.ActionExt,'String');
2335    ActionExtIndex=find(strcmp(ActionExt,ActionExtList), 1);
2336    if isempty(ActionExtIndex)
2337        set(handles.ActionExt,'String',[ActionExtList;{ActionExt}])
2338    end
2339
2340    % remove old Action options in the menu (keeping a menu length <nb_builtin_ACTION+5)
2341    if length(ActionList)>NbBuiltinAction+5; % nb_builtin_ACTION=nbre of functions always remaining in the initial menu
2342        nbremove=length(ActionList)-NbBuiltinAction-5;
2343        ActionList(NbBuiltinAction+1:end-5)=[];
2344        ActionPathList(NbBuiltinAction+1:end-4,:)=[];
2345        ActionIndex=ActionIndex-nbremove;
2346    end
2347   
2348    % record action menu, choice and path
2349    set(handles.ActionName,'Value',ActionIndex)
2350    set(handles.ActionName,'String',ActionList)
2351       set(handles.ActionName,'UserData',ActionPathList);
2352    set(handles.ActionExt,'Value',ActionExtIndex)
2353       
2354    %record the user defined menu additions in personal file profil_perso
2355    dir_perso=prefdir;
2356    profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
2357    if NbBuiltinAction+1<=numel(ActionList)-1
2358        ActionListUser=ActionList(NbBuiltinAction+1:numel(ActionList)-1);
2359        ActionPathListUser=ActionPathList(NbBuiltinAction+1:numel(ActionList)-1);
2360        ActionExtListUser={};
2361        if numel(ActionExtList)>2
2362            ActionExtListUser=ActionExtList(3:end);
2363        end
2364        if exist(profil_perso,'file')
2365            save(profil_perso,'ActionListUser','ActionPathListUser','ActionExtListUser','-append')
2366        else
2367            save(profil_perso,'ActionListUser','ActionPathListUser','ActionExtListUser','-V6')
2368        end
2369    end
2370end
2371
2372%% check the current ActionPath to the selected function
2373ActionPath=ActionPathList{ActionIndex}; % current recorded path
2374set(handles.ActionPath,'String',ActionPath); % show the path to the senlected function
2375
2376%% reinitialise the waitbar
2377update_waitbar(handles.Waitbar,0)
2378
2379%% Put the first line of the selected Action fct as tooltip help
2380try
2381    [fid,errormsg] =fopen([ActionName '.m']);
2382    InputText=textscan(fid,'%s',1,'delimiter','\n');
2383    fclose(fid);
2384    set(handles.ActionName,'ToolTipString',InputText{1}{1})% put the first line of the selected function as tooltip help
2385end
2386set(handles.ActionName,'BackgroundColor',[1 1 1])
2387set(handles.ActionInput,'BackgroundColor',[1 0 1])% set ActionInput button to magenta color to indicate that input refr
2388
2389
2390% --- Executes on button press in ActionInput.
2391function ActionInput_Callback(hObject, eventdata, handles)
2392
2393set(handles.ActionInput,'BackgroundColor',[1 1 0])
2394SeriesData=get(handles.series,'UserData'); % info on the input file series
2395
2396%% create the function handle for Action
2397ActionPath=get(handles.ActionPath,'String');
2398ActionList=get(handles.ActionName,'String');
2399ActionName= ActionList{get(handles.ActionName,'Value')}; % selected function name
2400if ~exist(ActionPath,'dir')
2401    ActionName_Callback(handles.ActionName, ActionPath, handles)% update the function
2402    return
2403end
2404current_dir=pwd; % current working dir
2405cd(ActionPath)
2406h_fun=str2func(ActionName);
2407cd(current_dir)
2408
2409%% Activate the Action fct to adapt the configuration of the GUI series and bring specific parameters in SeriesData
2410Param=read_GUI_series(handles); % read the parameters from the GUI series
2411Param.Action.RUN=0;
2412Param.SeriesData=SeriesData;
2413ParamOut=h_fun(Param); % run the selected Action function to get the relevant input
2414
2415
2416%% Visibility of VelType and VelType_1 menus asked by ActionName
2417VelTypeRequest=1; % VelType requested by default
2418VelTypeRequest_1=1; % VelType requested by default
2419if isfield(ParamOut,'VelType')
2420    VelTypeRequest=ismember(ParamOut.VelType,{'on','one','two'});
2421    VelTypeRequest_1=strcmp( ParamOut.VelType,'two');
2422end
2423FieldNameRequest=0;  %hidden by default
2424FieldNameRequest_1=0;  %hidden by default
2425if isfield(ParamOut,'FieldName')
2426    FieldNameRequest=ismember(ParamOut.FieldName,{'on','one','two'});
2427    FieldNameRequest_1=strcmp( ParamOut.FieldName,'two');
2428end
2429
2430%% Detect the types of input files and set menus and default options in 'VelType'
2431iview_civ=find(strcmp('civx',SeriesData.FileType)|strcmp('civdata',SeriesData.FileType));
2432iview_netcdf=find(strcmp('netcdf',SeriesData.FileType)|strcmp('civx',SeriesData.FileType)|strcmp('civdata',SeriesData.FileType)); % all nc files, icluding civ
2433FieldList=get(handles.FieldName,'String'); % previous list as default
2434if ~iscell(FieldList),FieldList={FieldList};end
2435FieldList_1=get(handles.FieldName_1,'String'); % previous list as default
2436if ~iscell(FieldList_1),FieldList_1={FieldList_1};end
2437CheckList_1=1; % indicate whether FieldName_1 has been updated
2438handles_coord=[handles.Coord_x handles.Coord_y handles.Coord_z handles.Coord_x_title handles.Coord_y_title handles.Coord_z_title];
2439if VelTypeRequest && numel(iview_civ)>=1
2440    menu=set_veltype_display(SeriesData.FileInfo{iview_civ(1)}.CivStage,SeriesData.FileType{iview_civ(1)});
2441    set(handles.VelType,'Value',1)% set first choice by default
2442    set(handles.VelType,'String',[{'*'};menu])
2443    set(handles.VelType,'Visible','on')
2444    set(handles.VelType_title,'Visible','on')
2445    FieldList=set_field_list('U','V'); % standard menu for civx data
2446    if max(get(handles.FieldName,'Value'))>numel(FieldList)
2447    set(handles.FieldName,'Value',1); % velocity vector choice by default
2448    end
2449    if  VelTypeRequest_1 && numel(iview_civ)>=2
2450        menu=set_veltype_display(SeriesData.FileInfo{iview_civ(2)}.CivStage,SeriesData.FileType{iview_civ(2)});
2451        set(handles.VelType_1,'Value',1)% set first choice by default
2452        set(handles.VelType_1,'String',[{'*'};menu])
2453        set(handles.VelType_1,'Visible','on')
2454        set(handles.VelType_title_1,'Visible','on')
2455        FieldList_1=[set_field_list('U','V');{'C'};{'add_field...'}]; % standard menu for civx data
2456        CheckList_1=1;
2457        set(handles.FieldName_1,'Value',1); % velocity vector choice by default
2458    else
2459        set(handles.VelType_1,'Visible','off')
2460        set(handles.VelType_title_1,'Visible','off')
2461    end
2462else
2463    set(handles.VelType,'Visible','off')
2464    set(handles.VelType_title,'Visible','off')
2465end
2466
2467%% Detect the types of input files and set menus and default options in 'FieldName'
2468if (FieldNameRequest || VelTypeRequest) && numel(iview_netcdf)>=1
2469    set(handles.InputFields,'Visible','on')% set the frame InputFields visible
2470    if FieldNameRequest && isfield(SeriesData.FileInfo{iview_netcdf(1)},'ListVarName')
2471        set(handles.FieldName,'Visible','on')
2472        set(handles.Field_text,'Visible','on')
2473        ListVarName=SeriesData.FileInfo{iview_netcdf(1)}.ListVarName;
2474        ind_var=get(handles.FieldName,'Value'); % indices of previously selected variables
2475        for ilist=1:numel(ind_var)
2476            if isempty(find(strcmp(FieldList{ind_var(ilist)},ListVarName)))
2477                FieldList={}; % previous choice not consistent with new input field
2478                set(handles.FieldName,'Value',1)
2479                break
2480            end
2481        end
2482        if ~isempty(FieldList)
2483            if isempty(find(strcmp(get(handles.Coord_x,'String'),ListVarName)))||...
2484                    isempty(find(strcmp(get(handles.Coord_y,'String'),ListVarName)))
2485                FieldList={};
2486                set(handles.Coord_x,'String','')
2487                set(handles.Coord_y,'String','')
2488            end
2489            Coord_z=get(handles.Coord_z,'String');
2490            if ~isempty(Coord_z) && isempty(find(strcmp(Coord_z,ListVarName)))
2491                FieldList={};
2492                set(handles.Coord_z,'String','')
2493            end
2494        end
2495    else
2496        set(handles.FieldName,'Visible','off')
2497        set(handles.Field_text,'Visible','off')
2498    end
2499   
2500    set(handles_coord,'Visible','on')
2501    if isempty(find(strcmp('add_field...',FieldList)))
2502    FieldList=[FieldList;{'add_field...'}];%add 'add_field...' to the menu FieldName if it is not already
2503    end
2504    if FieldNameRequest_1 && numel(iview_netcdf)>=2
2505        set(handles.FieldName_1,'Visible','on')
2506        if CheckList_1==0        % not civ input made
2507            ListVarName=SeriesData.FileInfo{iview_netcdf(2)}.ListVarName;
2508            ind_var=get(handles.FieldName,'Value'); % indices of previously selected variables
2509            for ilist=1:numel(ind_var)
2510                if isempty(find(strcmp(FieldList{ind_var(ilist)},ListVarName)))
2511                    FieldList_1={}; % previous choice not consistent with new input field
2512                    set(handles.FieldName_1,'Value',1)
2513                    break
2514                end
2515            end
2516            warn_coord=0;
2517            if isempty(find(strcmp(get(handles.Coord_x,'String'),ListVarName)))||...
2518                    isempty(find(strcmp(get(handles.Coord_y,'String'),ListVarName)))
2519                warn_coord=1;
2520            end
2521            if ~isempty(Coord_z) && isempty(find(strcmp(Coord_z,ListVarName)))
2522                FieldList_1={};
2523                warn_coord=1;
2524            end
2525            if warn_coord
2526                msgbox_uvmat('WARNING','coordinate names do not exist in the second netcdf input file')
2527            end
2528           
2529            set(handles.FieldName_1,'Visible','on')
2530            set(handles.FieldName_1,'Value',1)
2531            set(handles.FieldName_1,'String',FieldList_1)
2532        end
2533    else
2534        set(handles.FieldName_1,'Visible','off')
2535    end
2536    if isempty(FieldList)
2537        set(handles.Field_text,'Visible','off')
2538        set(handles.FieldName,'Visible','off')
2539    else
2540        set(handles.Field_text,'Visible','on')
2541        set(handles.FieldName,'Visible','on')
2542        set(handles.FieldName,'String',FieldList)
2543    end
2544else
2545    set(handles.InputFields,'Visible','off')
2546end
2547
2548%% Introduce visibility of file overwrite option
2549if isfield(ParamOut,'CheckOverwriteVisible')&& strcmp(ParamOut.CheckOverwriteVisible,'on')
2550    set(handles.CheckOverwrite,'Visible','on')
2551else
2552    set(handles.CheckOverwrite,'Visible','off')
2553end
2554
2555%% Check whether alphabetical sorting of input Subdir is allowed by the Action fct  (for multiples series entries)
2556if isfield(ParamOut,'AllowInputSort')&&isequal(ParamOut.AllowInputSort,'on')&& size(Param.InputTable,1)>1
2557    [tild,iview]=sort(Param.InputTable(:,2)); % subdirectories sorted in alphabetical order
2558    set(handles.InputTable,'Data',Param.InputTable(iview,:));
2559    MinIndex_i=get(handles.MinIndex_i,'Data');
2560    MinIndex_j=get(handles.MinIndex_j,'Data');
2561    MaxIndex_i=get(handles.MaxIndex_i,'Data');
2562    MaxIndex_j=get(handles.MaxIndex_j,'Data');
2563    set(handles.MinIndex_i,'Data',MinIndex_i(iview,:));
2564    set(handles.MinIndex_j,'Data',MinIndex_j(iview,:));
2565    set(handles.MaxIndex_i,'Data',MaxIndex_i(iview,:));
2566    set(handles.MaxIndex_j,'Data',MaxIndex_j(iview,:));;
2567    TimeTable=get(handles.TimeTable,'Data');
2568    if size(TimeTable,1)<size(Param.InputTable,1)%if the time table is not complete, copy the missing lines from the previous ones
2569        for iline=size(TimeTable,1)+1:size(Param.InputTable,1)
2570            TimeTable(iline,:)=TimeTable(iline-1,:);
2571        end
2572    end
2573    set(handles.TimeTable,'Data',TimeTable(iview,:));% sort the time tables
2574    PairString=get(handles.PairString,'Data');
2575    set(handles.PairString,'Data',PairString(iview,:));
2576end
2577
2578%% Impose the whole input file index range if requested
2579if isfield(ParamOut,'WholeIndexRange')&&isequal(ParamOut.WholeIndexRange,'on')
2580    MinIndex_i=get(handles.MinIndex_i,'Data');
2581    MinIndex_j=get(handles.MinIndex_j,'Data');
2582    MaxIndex_i=get(handles.MaxIndex_i,'Data');
2583    MaxIndex_j=get(handles.MaxIndex_j,'Data');
2584    set(handles.num_first_i,'String',num2str(MinIndex_i(1)))% set first as the min index (for the first line)
2585    set(handles.num_last_i,'String',num2str(MaxIndex_i(1)))% set last as the max index (for the first line)
2586    set(handles.num_incr_i,'String','1')
2587    set(handles.num_first_j,'String',num2str(MinIndex_j(1)))% set first as the min index (for the first line)
2588    set(handles.num_last_j,'String',num2str(MaxIndex_j(1)))% set last as the max index (for the first line)
2589    set(handles.num_incr_j,'String','1')
2590else  % check index ranges
2591    first_i=1;last_i=1;first_j=1;last_j=1;
2592    if isfield(Param.IndexRange,'first_i')
2593        first_i=Param.IndexRange.first_i;
2594        last_i=Param.IndexRange.last_i;
2595    end
2596    if isfield(Param.IndexRange,'first_j')
2597        first_j=Param.IndexRange.first_j;
2598        last_j=Param.IndexRange.last_j;
2599    end
2600    if last_i < first_i || last_j < first_j , msgbox_uvmat('ERROR','last field number must be larger than the first one'),...
2601            set(handles.RUN, 'Enable','On'), set(handles.RUN,'BackgroundColor',[1 0 0]),return,end;
2602end
2603
2604%% enable or desable j index visibility
2605status_j='on'; % default
2606if isempty(find(~cellfun(@isempty,SeriesData.j1_series), 1)); % case of empty j indices
2607    status_j='off'; % no j index needed
2608elseif strcmp(get(handles.PairString,'Visible'),'on')
2609    check_burst=cellfun(@isempty,regexp(get(handles.PairString,'Data'),'^j')); % =0 for burst case, 1 otherwise
2610    if isempty(find(check_burst, 1))% if all pair string begins by j (burst)
2611        status_j='off'; % no j index needed for bust case
2612    end
2613end
2614enable_j(handles,status_j) % no j index needed
2615if isfield(ParamOut,'j_index_1')&& isfield(ParamOut,'j_index_2')%strcmp(ParamOut.Desable_j_index,'on')
2616    %status_j='off';
2617    set(handles.num_first_j,'String',num2str(ParamOut.j_index_1))
2618    set(handles.num_last_j,'String',num2str(ParamOut.j_index_2))
2619    set(handles.num_first_j,'enable','off')
2620    set(handles.num_last_j,'enable','off')
2621    set(handles.num_incr_j,'visible','off')
2622else
2623    set(handles.num_first_j,'enable','on')
2624    set(handles.num_last_j,'enable','on')
2625    set(handles.num_incr_j,'visible',status_j)
2626end
2627
2628%% NbSlice visibility
2629if isfield(ParamOut,'NbSlice') && (strcmp(ParamOut.NbSlice,'on')||isnumeric(ParamOut.NbSlice))
2630    set(handles.num_NbSlice,'Visible','on')
2631    set(handles.NbSlice_title,'Visible','on')
2632else
2633    set(handles.num_NbSlice,'Visible','off')
2634    set(handles.NbSlice_title,'Visible','off')
2635end
2636if isfield(ParamOut,'NbSlice') && isnumeric(ParamOut.NbSlice)
2637    set(handles.num_NbSlice,'String',num2str(ParamOut.NbSlice))
2638    set(handles.num_NbSlice,'Enable','off'); % NbSlice set by the activation of the Action function
2639else
2640    set(handles.num_NbSlice,'Enable','on'); % NbSlice can be modified on the GUI series
2641end
2642
2643%% Visibility of FieldTransform menu
2644FieldTransformVisible='off';  %hidden by default
2645if isfield(ParamOut,'FieldTransform')
2646    if ~strcmp(ParamOut.FieldTransform,'off')
2647    FieldTransformVisible='on'; 
2648    end
2649    if iscell(ParamOut.FieldTransform)
2650        SeriesData.TransformList=ParamOut.FieldTransform;
2651    end
2652    TransformName_Callback([],[], handles)
2653end
2654set(handles.FieldTransform,'Visible',FieldTransformVisible)
2655if isfield(ParamOut,'TransformPath');% record the path of transform function requested for compilation
2656    set(handles.TransformPath,'UserData',ParamOut.TransformPath)
2657else
2658    set(handles.TransformPath,'UserData',[])
2659end
2660
2661%% Visibility of projection object
2662ProjObjectVisible='off';  %hidden by default
2663if isfield(ParamOut,'ProjObject')
2664    ProjObjectVisible=ParamOut.ProjObject;
2665end
2666set(handles.CheckObject,'Visible',ProjObjectVisible)
2667if ~get(handles.CheckObject,'Value')
2668    ProjObjectVisible='off';
2669end
2670set(handles.ProjObjectName,'Visible',ProjObjectVisible)
2671set(handles.DeleteObject,'Visible',ProjObjectVisible)
2672set(handles.ViewObject,'Visible',ProjObjectVisible)
2673set(handles.EditObject,'Visible',ProjObjectVisible)
2674
2675%% Visibility of mask input
2676MaskVisible='off';  %hidden by default
2677if isfield(ParamOut,'Mask')
2678    MaskVisible=ParamOut.Mask;
2679end
2680set(handles.CheckMask,'Visible',MaskVisible);
2681%% Setting of expected iteration time
2682if isfield(ParamOut,'CPUTime')
2683    set(handles.num_CPUTime,'String',num2str(ParamOut.CPUTime));
2684end
2685
2686%% definition of the directory containing the output files
2687if  ~(isfield(SeriesData,'ActionName') && strcmp(ActionName,SeriesData.ActionName))
2688    OutputDirExt='.series'; % default
2689    if isfield(ParamOut,'OutputDirExt')&&~isempty(ParamOut.OutputDirExt)
2690        OutputDirExt=ParamOut.OutputDirExt;
2691    end
2692    set(handles.OutputDirExt,'String',OutputDirExt)
2693end
2694OutputDirVisible='off';
2695OutputSubDirMode='auto'; % default
2696SubDirOut='';
2697if isfield(ParamOut,'OutputSubDirMode')
2698    OutputSubDirMode=ParamOut.OutputSubDirMode;
2699end
2700InputTable=get(handles.InputTable,'Data');
2701switch OutputSubDirMode
2702    case 'auto'; % default
2703        OutputDirVisible='on';
2704        SubDir=InputTable(1:end,2); % set of subdirectories
2705        SubDirOut=SubDir{1};
2706        if numel(SubDir)>1
2707            for ilist=2:numel(SubDir)
2708                SubDirOut=[SubDirOut '-' regexprep(SubDir{ilist},'^/','')];
2709            end
2710        end
2711    case 'one'
2712        OutputDirVisible='on';
2713        SubDirOut=InputTable{1,2}; % use the first subdir name (+OutputDirExt) as output  subdirectory
2714    case 'two'
2715        OutputDirVisible='on';   
2716        SubDir=InputTable(1:2,2); % set of subdirectories
2717        SubDirOut=SubDir{1};
2718        if numel(SubDir)>1
2719                SubDirOut=[SubDirOut '-' regexprep(SubDir{2},'^/','')];
2720        end
2721    case 'last'
2722        OutputDirVisible='on';
2723        SubDirOut=InputTable{end,2}; % use the last subdir name (+OutputDirExt) as output  subdirectory
2724end
2725set(handles.OutputSubDir,'String',SubDirOut)
2726set(handles.OutputSubDir,'BackgroundColor',[1 1 1])% set edit box to white color to indicate refreshment
2727set(handles.OutputDirExt,'Visible',OutputDirVisible)
2728set(handles.OutputSubDir,'Visible',OutputDirVisible)
2729%set(handles.CheckOverwrite,'Visible',OutputDirVisible)
2730set(handles.OutputDir_title,'Visible',OutputDirVisible)
2731SeriesData.ActionName=ActionName; % record ActionName for next use
2732
2733
2734%% visibility of the run mode (local or background or cluster)
2735if strcmp(OutputSubDirMode,'none')
2736    RunModeVisible='off'; % only local mode available if no output file is produced
2737else
2738    RunModeVisible='on';
2739end
2740set(handles.RunMode,'Visible',RunModeVisible)
2741set(handles.ActionExt,'Visible',RunModeVisible)
2742set(handles.RunMode_title,'Visible',RunModeVisible)
2743set(handles.ActionExt_title,'Visible',RunModeVisible)
2744
2745
2746%% Expected nbre of output files
2747if isfield(ParamOut,'OutputFileMode')
2748    StatusData.OutputFileMode=ParamOut.OutputFileMode;
2749    set(handles.status,'UserData',StatusData)
2750end
2751
2752%% definition of an additional parameter set, determined by an ancillary GUI
2753if isfield(ParamOut,'ActionInput')
2754%     set(handles.ActionInput,'Visible','on')
2755    ParamOut.ActionInput.Program=ActionName; % record the program in ActionInput
2756    SeriesData.ActionInput=ParamOut.ActionInput;
2757else
2758%     set(handles.ActionInput,'Visible','off')
2759    if isfield(SeriesData,'ActionInput')
2760        SeriesData=rmfield(SeriesData,'ActionInput');
2761    end
2762end
2763set(handles.series,'UserData',SeriesData)
2764set(handles.ActionInput,'BackgroundColor',[1 0 0])
2765
2766
2767%------------------------------------------------------------------------
2768% --- Executes on button press in RefreshField.
2769function RefreshField_Callback(hObject, eventdata, handles)
2770%------------------------------------------------------------------------
2771set(handles.FieldName,'String',{'add_field...'});
2772set(handles.FieldName,'Value',1);
2773FieldName_Callback(hObject, eventdata, handles)
2774
2775
2776%------------------------------------------------------------------------
2777% --- Executes on selection change in FieldName.
2778function FieldName_Callback(hObject, eventdata, handles)
2779%------------------------------------------------------------------------
2780FieldListInit=get(handles.FieldName,'String');
2781field_index=get(handles.FieldName,'Value');
2782field=FieldListInit{field_index(1)};
2783if isequal(field,'add_field...')
2784    FieldListInit(field_index(1))=[];
2785    SeriesData=get(handles.series,'UserData');
2786    % input line for which the field choice is relevant
2787    iview=find(ismember(SeriesData.FileType,{'netcdf','civx','civdata'})); % all nc files, icluding civ
2788    hget_field=findobj(allchild(0),'name','get_field');
2789    if ~isempty(hget_field)
2790        delete(hget_field)%delete opened versions of get_field
2791    end
2792    Param=read_GUI(handles.series);
2793    InputTable=Param.InputTable(iview,:);
2794    % check the existence of the first file in the series
2795    first_j=[];last_j=[];MinIndex_j=1;MaxIndex_j=1; % default setting for index j
2796    if isfield(Param.IndexRange,'first_j') % if index j is used     
2797        first_j=Param.IndexRange.first_j;
2798        last_j=Param.IndexRange.last_j;
2799        MinIndex_j=Param.IndexRange.MinIndex_j(iview);
2800        MaxIndex_j=Param.IndexRange.MaxIndex_j(iview);
2801    end
2802    PairString='';
2803    if isfield(Param.IndexRange,'PairString'); PairString=Param.IndexRange.PairString{iview}; end
2804    [i1,i2,j1,j2] = get_file_index(Param.IndexRange.first_i,first_j,PairString);
2805    LineIndex=iview(1);
2806    if numel(iview)>1     
2807        answer=msgbox_uvmat('INPUT_TXT',['select the line of the input table:' num2str(iview)] ,num2str(iview(1)));
2808        LineIndex=str2num(answer);
2809    end
2810    FirstFileName=fullfile_uvmat(InputTable{LineIndex,1},InputTable{LineIndex,2},InputTable{LineIndex,3},...
2811        InputTable{LineIndex,5},InputTable{LineIndex,4},i1,i2,j1,j2);
2812    if exist(FirstFileName,'file')
2813        ParamIn.Title='get_field: pick input variables and coordinates for series processing';
2814        ParamIn.SeriesInput=1;
2815        GetFieldData=get_field(FirstFileName,ParamIn);
2816        FieldList={};
2817        if isfield(GetFieldData,'FieldOption')% if a field has been selected
2818        switch GetFieldData.FieldOption
2819            case 'vectors'
2820                UName=GetFieldData.PanelVectors.vector_x;
2821                VName=GetFieldData.PanelVectors.vector_y;
2822                YName={GetFieldData.Coordinates.Coord_y};
2823                FieldList={['vec(' UName ',' VName ')'];...
2824                    ['norm(' UName ',' VName ')'];...
2825                    UName;VName};
2826                set(handles.VelType,'Visible','off')
2827            case {'scalar'}
2828                FieldList=GetFieldData.PanelScalar.scalar;
2829                YName={GetFieldData.Coordinates.Coord_y};
2830                if ischar(FieldList)
2831                    FieldList={FieldList};
2832                end
2833                set(handles.VelType,'Visible','off')
2834            case 'civdata...'
2835                FieldList=[set_field_list('U','V') ;{'C'}];
2836                set(handles.FieldName,'Value',1) % set menu to 'velocity
2837                XName='X';
2838                YName='y';
2839                set(handles.VelType,'Visible','on')
2840        end
2841        set(handles.FieldName,'Value',1)
2842        set(handles.FieldName,'String',[FieldListInit; FieldList; {'add_field...'}]);
2843        if ~strcmp(GetFieldData.FieldOption,'civdata...')
2844           if ~isempty(regexp(FieldList{1},'^vec'))
2845                set(handles.FieldName,'Value',1)
2846           else
2847                set(handles.FieldName,'Value',1:numel(FieldList))%select all input fields by default
2848           end
2849            XName=GetFieldData.Coordinates.Coord_x;
2850            YName=GetFieldData.Coordinates.Coord_y;
2851            TimeNameStr=GetFieldData.Time.SwitchVarIndexTime;
2852            % get the time info                     
2853            TimeTable=get(handles.TimeTable,'Data');
2854            switch TimeNameStr
2855                case 'file index'
2856                    TimeName='';
2857                case 'attribute'
2858                    TimeName=['att:' GetFieldData.Time.TimeName];
2859                    % update the time table
2860                    TimeTable{LineIndex,2}=get_time(Param.IndexRange.MinIndex_i(LineIndex),MinIndex_j,PairString,InputTable,SeriesData.FileInfo{LineIndex},GetFieldData.Time.TimeName);  % Min time     
2861                    TimeTable{LineIndex,3}=get_time(Param.IndexRange.first_i,first_j,PairString,InputTable,SeriesData.FileInfo{LineIndex},GetFieldData.Time.TimeName);  % first time             
2862                    TimeTable{LineIndex,4}=get_time(Param.IndexRange.last_i,last_j,PairString,InputTable,SeriesData.FileInfo{LineIndex},GetFieldData.Time.TimeName);  % last time                     
2863                    TimeTable{LineIndex,5}=get_time(Param.IndexRange.MaxIndex_i(LineIndex),MaxIndex_j,PairString,InputTable,SeriesData.FileInfo{LineIndex},GetFieldData.Time.TimeName);  % Max time
2864                case 'variable'
2865                    set(handles.TimeName,'String',['var:' GetFieldData.Time.TimeName])
2866                    set(handles.NomType,'String','*')
2867                    set(handles.RootFile,'String',[get(handles.RootFile,'String') get(handles.FileIndex,'String')])% A VERIFIER !!!!!!
2868                    set(handles.FileIndex,'String','')
2869                    ParamIn.TimeVarName=GetFieldData.Time.TimeName;
2870                case 'matrix_index'
2871                    TimeName=['dim:' GetFieldData.Time.TimeName];
2872                    set(handles.NomType,'String','*')
2873                    set(handles.RootFile,'String',[get(handles.RootFile,'String') get(handles.FileIndex,'String')])
2874                    set(handles.FileIndex,'String','')
2875                    ParamIn.TimeDimName=GetFieldData.Time.TimeName;
2876            end
2877            TimeTable{LineIndex,1}=TimeName;
2878            set(handles.TimeTable,'Data',TimeTable);
2879        end
2880        set(handles.Coord_x,'String',XName)
2881        set(handles.Coord_y,'String',YName)
2882        set(handles.Coord_x,'Visible','on')
2883        set(handles.Coord_y,'Visible','on')
2884        end
2885    else
2886        msgbox_uvmat('ERROR',[FirstFileName ' does not exist'])
2887    end
2888end
2889
2890
2891function [TimeValue,DtValue]=get_time(ref_i,ref_j,PairString,InputTable,FileInfo,TimeName,DtName)
2892[i1,i2,j1,j2] = get_file_index(ref_i,ref_j,PairString);
2893FileName=fullfile_uvmat(InputTable{1},InputTable{2},InputTable{3},InputTable{5},InputTable{4},i1,i2,j1,j2);
2894Data=nc2struct(FileName,[]);
2895TimeValue=[];
2896DtValue=[];
2897if isequal(FileInfo.FileType,'civdata')
2898    if ismember(TimeName,{'civ1','filter1'})
2899        if isfield(Data,'Civ1_Time')
2900        TimeValue=Data.Civ1_Time;
2901        end
2902        if isfield(Data,'Civ1_Dt')
2903        DtValue=Data.Civ1_Dt;
2904        end
2905    else
2906        if isfield(Data,'Civ2_Time')
2907        TimeValue=Data.Civ2_Time;
2908        end
2909        if isfield(Data,'Civ2_Dt')
2910        DtValue=Data.Civ2_Dt;
2911        end
2912    end
2913else
2914    if ~isempty(TimeName)&& isfield(Data,TimeName)
2915        TimeValue=Data.(TimeName);
2916    end
2917    if exist('DtName','var') && isfield(Data,DtName)
2918        DtValue=Data.(DtName);
2919    end
2920end
2921
2922%------------------------------------------------------------------------
2923% --- Executes on selection change in FieldName_1.
2924function FieldName_1_Callback(hObject, eventdata, handles)
2925%------------------------------------------------------------------------
2926field_str=get(handles.FieldName_1,'String');
2927field_index=get(handles.FieldName_1,'Value');
2928field=field_str{field_index(1)};
2929if isequal(field,'add_field...')
2930    hget_field=findobj(allchild(0),'name','get_field');
2931    if ~isempty(hget_field)
2932        delete(hget_field)%delete opened versions of get_field
2933    end
2934    Param=read_GUI(handles.series);
2935    Param.InputTable=Param.InputTable(1,:);
2936    % check the existence of the first file in the series
2937    first_j=[];
2938    if isfield(Param.IndexRange,'first_j'); first_j=Param.IndexRange.first_j; end
2939    if isfield(Param.IndexRange,'last_j'); last_j=Param.IndexRange.last_j; end
2940    PairString='';
2941    if isfield(Param.IndexRange,'PairString'); PairString=Param.IndexRange.PairString; end
2942    [i1,i2,j1,j2] = get_file_index(Param.IndexRange.first_i,first_j,PairString);
2943    FirstFileName=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},...
2944        Param.InputTable{1,5},Param.InputTable{1,4},i1,i2,j1,j2);
2945    if exist(FirstFileName,'file')
2946        ParamIn.SeriesInput=1;
2947        GetFieldData=get_field(FirstFileName,ParamIn);
2948        FieldList={};
2949        switch GetFieldData.FieldOption
2950            case 'vectors'
2951                UName=GetFieldData.PanelVectors.vector_x;
2952                VName=GetFieldData.PanelVectors.vector_y;
2953                FieldList={['vec(' UName ',' VName ')'];...
2954                    ['norm(' UName ',' VName ')'];...
2955                    UName;VName};
2956            case {'scalar','pick variables'}
2957                FieldList=GetFieldData.PanelScalar.scalar;
2958                if ischar(FieldList)
2959                    FieldList={FieldList};
2960                end
2961            case '1D plot'
2962
2963            case 'civdata...'
2964                FieldList=set_field_list('U','V','C');
2965                set(handles.FieldName,'Value',2) % set menu to 'velocity
2966        end
2967        if ~strcmp(GetFieldData.FieldOption,'civdata...')
2968            TimeNameStr=GetFieldData.Time.SwitchVarIndexTime;
2969            switch TimeNameStr
2970                case 'file index'
2971                    set(handles.TimeName,'String','');
2972                case 'attribute'
2973                    set(handles.TimeName,'String',['att:' GetFieldData.Time.TimeName]);
2974                case 'variable'
2975                    set(handles.TimeName,'String',['var:' GetFieldData.Time.TimeName])
2976                    set(handles.NomType,'String','*')
2977                    set(handles.RootFile,'String',[get(handles.RootFile,'String') get(handles.FileIndex,'String')])% A VERIFIER !!!!!!
2978                    set(handles.FileIndex,'String','')
2979                    ParamIn.TimeVarName=GetFieldData.Time.TimeName;
2980                case 'matrix_index'
2981                    set(handles.TimeName,'String',['dim:' GetFieldData.Time.TimeName]);
2982                    set(handles.NomType,'String','*')
2983                    set(handles.RootFile,'String',[get(handles.RootFile,'String') get(handles.FileIndex,'String')])
2984                    set(handles.FileIndex,'String','')
2985                    ParamIn.TimeDimName=GetFieldData.Time.TimeName;
2986            end
2987        end
2988        set(handles.FieldName_1,'Value',1)
2989        set(handles.FieldName_1,'String',[FieldList; {'add_field...'}]);
2990    end
2991end   
2992
2993
2994%%%%%%%%%%%%%
2995function [ind_remove]=find_pairs(dirpair,ind_i,last_i)
2996indsel=ind_i;
2997indiff=diff(ind_i); % test index increment to detect multiplets (several pairs with the same index ind_i) and holes in the series
2998indiff=[1 indiff last_i-ind_i(end)+1]; % for testing gaps with the imposed bounds
2999if ~isempty(indiff)
3000    indiff2=diff(indiff);
3001    indiffp=[indiff2 1];
3002    indiffm=[1 indiff2];
3003    ind_multi_m=find((indiff==0)&(indiffm<0))-1; % indices of first members of multiplets
3004    ind_multi_p=find((indiff==0)&(indiffp>0)); % indices of last members of multiplets
3005    %for each multiplet, select the most recent file
3006    ind_remove=[];
3007    for i=1:length(ind_multi_m)
3008        ind_pairs=ind_multi_m(i):ind_multi_p(i);
3009        for imulti=1:length(ind_pairs)
3010            datepair(imulti)=datenum(dirpair(ind_pairs(imulti)).date); % dates of creation
3011        end
3012        [datenew,indsort2]=sort(datepair); % sort the multiplet by creation date
3013        ind_s=indsort2(1:end-1); %
3014        ind_remove=[ind_remove ind_pairs(ind_s)]; % remove these indices, leave the last one
3015    end
3016end
3017
3018%------------------------------------------------------------------------
3019% --- determine the list of index pairstring of processing file
3020function [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)
3021%------------------------------------------------------------------------
3022num_i1=num_i; % set of first image numbers by default
3023num_i2=num_i;
3024num_j1=num_j;
3025num_j2=num_j;
3026num_i_out=num_i;
3027num_j_out=num_j;
3028% if isequal (NomType,'_1-2_1') || isequal (NomType,'_1-2')
3029if isequal(mode,'series(Di)')
3030    num_i1_line=num_i+ind_shift(3); % set of first image numbers
3031    num_i2_line=num_i+ind_shift(4);
3032    % adjust the first and last field number
3033        indsel=find(num_i1_line >= 1);
3034    num_i_out=num_i(indsel);
3035    num_i1_line=num_i1_line(indsel);
3036    num_i2_line=num_i2_line(indsel);
3037    num_j1=meshgrid(num_j,ones(size(num_i1_line)));
3038    num_j2=meshgrid(num_j,ones(size(num_i1_line)));
3039    [xx,num_i1]=meshgrid(num_j,num_i1_line);
3040    [xx,num_i2]=meshgrid(num_j,num_i2_line);
3041elseif isequal (mode,'series(Dj)')||isequal (mode,'bursts')
3042    if isequal(mode,'bursts') %case of bursts (png_old or png_2D)
3043        num_j1=ind_shift(1)*ones(size(num_i));
3044        num_j2=ind_shift(2)*ones(size(num_i));
3045    else
3046        num_j1_col=num_j+ind_shift(1); % set of first image numbers
3047        num_j2_col=num_j+ind_shift(2);
3048        % adjust the first field number
3049        indsel=find((num_j1_col >= 1));   
3050        num_j_out=num_j(indsel);
3051        num_j1_col=num_j1_col(indsel);
3052        num_j2_col=num_j2_col(indsel);
3053        [num_i1,num_j1]=meshgrid(num_i,num_j1_col);
3054        [num_i2,num_j2]=meshgrid(num_i,num_j2_col);
3055    end   
3056end
3057
3058%------------------------------------------------------------------------
3059% --- Executes on button press in CheckObject.
3060function CheckObject_Callback(hObject, eventdata, handles)
3061%------------------------------------------------------------------------
3062hset_object=findobj(allchild(0),'tag','set_object'); % find the set_object interface handle
3063if get(handles.CheckObject,'Value')
3064    SeriesData=get(handles.series,'UserData');
3065    if isfield(SeriesData,'ProjObject') && ~isempty(SeriesData.ProjObject)
3066        set(handles.ViewObject,'Value',1)
3067        ViewObject_Callback(hObject, eventdata, handles)
3068    else
3069        if ishandle(hset_object)
3070            uistack(hset_object,'top')% show the GUI set_object if opened
3071        else
3072            %get the object file
3073            InputTable=get(handles.InputTable,'Data');
3074            defaultname=InputTable{1,1};
3075            if isempty(defaultname)
3076                defaultname={''};
3077            end
3078            fileinput=uigetfile_uvmat('pick a xml object file (or use uvmat to create it)',defaultname,'.xml');
3079            if isempty(fileinput)% exit if no object file is selected
3080                set(handles.CheckObject,'Value',0)
3081                return
3082            end
3083            %read the file
3084            data=xml2struct(fileinput);
3085            if ~isfield(data,'Type')
3086                msgbox_uvmat('ERROR',[fileinput ' is not an object xml file'])
3087                set(handles.CheckObject,'Value',0)
3088                return
3089            end
3090            if ~isfield(data,'ProjMode')
3091                data.ProjMode='none';
3092            end
3093            hset_object=set_object(data); % call the set_object interface
3094            set(hset_object,'Name','set_object_series')% name to distinguish from set_object used with uvmat
3095        end
3096        ProjObject=read_GUI(hset_object);
3097        set(handles.ProjObjectName,'String',ProjObject.Name); % display the object name
3098        SeriesData=get(handles.series,'UserData');
3099        SeriesData.ProjObject=ProjObject;
3100        set(handles.series,'UserData',SeriesData);
3101    end
3102    set(handles.EditObject,'Visible','on');
3103    set(handles.DeleteObject,'Visible','on');
3104    set(handles.ViewObject,'Visible','on');
3105    set(handles.ProjObjectName,'Visible','on');
3106else
3107    set(handles.EditObject,'Visible','off');
3108    set(handles.DeleteObject,'Visible','off');
3109    set(handles.ViewObject,'Visible','off');
3110    if ~ishandle(hset_object)
3111        set(handles.ViewObject,'Value',0);
3112    end
3113    set(handles.ProjObjectName,'Visible','off');
3114end
3115
3116%------------------------------------------------------------------------
3117% --- Executes on button press in ViewObject.
3118%------------------------------------------------------------------------
3119function ViewObject_Callback(hObject, eventdata, handles)
3120
3121UserData=get(handles.series,'UserData');
3122hset_object=findobj(allchild(0),'Tag','set_object');
3123if ~isempty(hset_object)
3124    delete(hset_object)% refresh set_object if already opened
3125end
3126hset_object=set_object(UserData.ProjObject);
3127set(hset_object,'Name','view_object_series')
3128
3129
3130%------------------------------------------------------------------------
3131% --- Executes on button press in EditObject.
3132function EditObject_Callback(hObject, eventdata, handles)
3133%------------------------------------------------------------------------
3134if get(handles.EditObject,'Value')
3135    set(handles.ViewObject,'Value',0)
3136    UserData=get(handles.series,'UserData');
3137    hset_object=set_object(UserData.ProjObject);
3138    set(hset_object,'Name','edit_object_series')
3139    set(get(hset_object,'Children'),'Enable','on')
3140else
3141    hset_object=findobj(allchild(0),'Tag','set_object');
3142    if ~isempty(hset_object)
3143        set(get(hset_object,'Children'),'Enable','off')
3144    end
3145end
3146
3147%------------------------------------------------------------------------
3148% --- Executes on button press in DeleteObject.
3149function DeleteObject_Callback(hObject, eventdata, handles)
3150%------------------------------------------------------------------------
3151SeriesData=get(handles.series,'UserData');
3152SeriesData.ProjObject=[];
3153set(handles.series,'UserData',SeriesData)
3154set(handles.ProjObjectName,'String','')
3155set(handles.ProjObjectName,'Visible','off')
3156set(handles.CheckObject,'Value',0)
3157set(handles.ViewObject,'Visible','off')
3158set(handles.EditObject,'Visible','off')
3159hset_object=findobj(allchild(0),'name','set_object_series');
3160if ~isempty(hset_object)
3161    delete(hset_object)
3162end
3163set(handles.DeleteObject,'Visible','off')
3164
3165%------------------------------------------------------------------------
3166% --- Executed when CheckMask is activated
3167%------------------------------------------------------------------------
3168function CheckMask_Callback(hObject, eventdata, handles)
3169
3170if get(handles.CheckMask,'Value')
3171    InputTable=get(handles.InputTable,'Data');
3172    nbview=size(InputTable,1);
3173    MaskTable=cell(nbview,1); % default
3174    ListMask=cell(nbview,1); % default
3175    MaskData=get(handles.MaskTable,'Data');
3176    MaskData(size(MaskData,1):nbview,1)=cell(size(MaskData,1):nbview,1); % complement if undefined lines
3177    for iview=1:nbview
3178        ListMask{iview,1}=num2str(iview);
3179        RootPath=InputTable{iview,1};
3180        if ~isempty(RootPath)
3181            if isempty(MaskData{iview})
3182                SubDir=InputTable{iview,2};
3183                MaskPath=fullfile(RootPath,[regexprep(SubDir,'\..*','') '.mask']); % take the root part of SubDir, before the first dot '.'
3184                if exist(MaskPath,'dir')
3185                    ListStruct=dir(MaskPath); % look for a mask file
3186                    ListCells=struct2cell(ListStruct); % transform dir struct to a cell arrray
3187                    check_dir=cell2mat(ListCells(4,:)); % =1 for directories, =0 for files
3188                    ListFiles=ListCells(1,:); % list of file and dri names
3189                    ListFiles=ListFiles(~check_dir); % list of file names (excluding dir)
3190                    mdetect=0;
3191                    if ~isempty(ListFiles)
3192                        for ifile=1:numel(ListFiles)
3193                            [tild,tild,MaskFile{ifile},i1_series,i2_series,j1_series,j2_series,MaskNomType,MaskFileType]=find_file_series(MaskPath,ListFiles{ifile},0);
3194                            if strcmp(MaskFileType,'image') && isempty(i2_series) && isempty(j2_series)
3195                                mdetect=1;
3196                                MaskName=ListFiles{ifile};
3197                            end
3198                            if ~strcmp(MaskFile{ifile},MaskFile{1})
3199                                mdetect=0; % cancel detection test in case of multiple masks, use the brower for selection
3200                                break
3201                            end
3202                        end
3203                    end
3204                    if mdetect==1
3205                        MaskName=fullfile(MaskPath,'mask_1.png');
3206                    else
3207                        MaskName=uigetfile_uvmat('select a mask file:',MaskPath,'image');
3208                    end
3209                else
3210                    MaskName=uigetfile_uvmat('select a mask file:',RootPath,'image');
3211                end
3212                MaskTable{iview,1}=MaskName ;
3213                ListMask{iview,1}=num2str(iview);
3214            end
3215        end
3216    end
3217    set(handles.MaskTable,'Data',MaskTable)
3218    set(handles.MaskTable,'Visible','on')
3219    set(handles.MaskBrowse,'Visible','on')
3220    set(handles.ListMask,'Visible','on')
3221    set(handles.ListMask,'String',ListMask)
3222    set(handles.ListMask,'Value',1)
3223else
3224    set(handles.MaskTable,'Visible','off')
3225    set(handles.MaskBrowse,'Visible','off')
3226    set(handles.ListMask,'Visible','off')
3227end
3228
3229%------------------------------------------------------------------------
3230% --- Executes on button press in MaskBrowse.
3231%------------------------------------------------------------------------
3232function MaskBrowse_Callback(hObject, eventdata, handles)
3233
3234InputTable=get(handles.InputTable,'Data');
3235iview=get(handles.ListMask,'Value');
3236RootPath=InputTable{iview,1};
3237MaskName=uigetfile_uvmat('select a mask file:',RootPath,'image');
3238if ~isempty(MaskName)
3239    MaskTable=get(handles.MaskTable,'Data');
3240    MaskTable{iview,1}=MaskName ;
3241    set(handles.MaskTable,'Data',MaskTable)
3242end
3243
3244%------------------------------------------------------------------------
3245% --- Executes when selected cell(s) is changed in MaskTable.
3246%------------------------------------------------------------------------
3247function MaskTable_CellSelectionCallback(hObject, eventdata, handles)
3248
3249if numel(eventdata.Indices)>=1
3250set(handles.ListMask,'Value',eventdata.Indices(1))
3251end
3252
3253%-------------------------------------------------------------------
3254function MenuHelp_Callback(hObject, eventdata, handles)
3255%-------------------------------------------------------------------
3256
3257
3258% path_to_uvmat=which ('uvmat'); % check the path of uvmat
3259% pathelp=fileparts(path_to_uvmat);
3260% helpfile=fullfile(pathelp,'uvmat_doc','uvmat_doc.html');
3261% 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')
3262% else
3263%     addpath (fullfile(pathelp,'uvmat_doc'))
3264%     web([helpfile '#series'])
3265% end
3266
3267%-------------------------------------------------------------------
3268% --- Executes on selection change in TransformName.
3269function TransformName_Callback(hObject, eventdata, handles)
3270%----------------------------------------------------------------------
3271TransformList=get(handles.TransformName,'String');
3272TransformIndex=get(handles.TransformName,'Value');
3273TransformName=TransformList{TransformIndex};
3274TransformPathList=get(handles.TransformName,'UserData');
3275nb_builtin_transform=4;
3276if isequal(TransformName,'more...');     
3277    FileName=uigetfile_uvmat('Pick a transform function',get(handles.TransformPath,'String'),'.m');
3278    if isempty(FileName)
3279        return     %browser closed without choice
3280    end
3281    [TransformPath,TransformName,TransformExt]=fileparts(FileName); % removes extension .m
3282    if ~strcmp(TransformExt,'.m')
3283        msgbox_uvmat('ERROR','a Matlab function .m must be introduced');
3284        return
3285    end
3286     % insert the choice in the menu
3287    TransformIndex=find(strcmp(TransformName,TransformList),1); % look for the selected function in the menu Action
3288    if isempty(TransformIndex)%the input string does not exist in the menu
3289        TransformIndex= length(TransformList);
3290        TransformList=[TransformList(1:end-1);{TransformName};TransformList(end)]; % the selected function is appended in the menu, before the last item 'more...'
3291        set(handles.TransformName,'String',TransformList)
3292        TransformPathList=[TransformPathList;{TransformPath}];
3293    else% the input function already exist, we update its path (possibly new)
3294        TransformPathList{TransformIndex}=TransformPath; %
3295        set(handles.TransformName,'Value',TransformIndex)
3296    end
3297   % save the new menu in the personal file 'uvmat_perso.mat'
3298   dir_perso=prefdir; % personal Matalb directory
3299   profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
3300   if exist(profil_perso,'file')
3301       for ilist=nb_builtin_transform+1:numel(TransformPathList)
3302           TransformListUser{ilist-nb_builtin_transform}=TransformList{ilist};
3303           TransformPathListUser{ilist-nb_builtin_transform}=TransformPathList{ilist};
3304       end
3305       TransformPathListUser=TransformPathListUser';
3306       TransformListUser=TransformListUser';
3307       save (profil_perso,'TransformPathListUser','TransformListUser','-append'); % store the root name for future opening of uvmat
3308   end
3309end
3310
3311%display the current function path
3312set(handles.TransformPath,'String',TransformPathList{TransformIndex}); % show the path to the senlected function
3313set(handles.TransformName,'UserData',TransformPathList);
3314
3315%% create the function handle of the selected fct
3316if ~isempty(TransformName)
3317    if ~exist(TransformPathList{TransformIndex},'dir')
3318        msgbox_uvmat('ERROR',['The prescribed transform function path ' TransformPathList{TransformIndex} ' does not exist']);
3319        return
3320    end
3321    current_dir=pwd; % current working dir
3322    cd(TransformPathList{TransformIndex})
3323    transform_handle=str2func(TransformName);
3324    cd(current_dir)
3325    Field.Action.RUN=0;% indicate that the transform fct is called only to get input param
3326    SeriesData=get(handles.series,'UserData');
3327    ParamIn=[];
3328    if isfield(SeriesData,'TransformInput')
3329        ParamIn.TransformInput=SeriesData.TransformInput;
3330    end
3331    DataOut=feval(transform_handle,Field,ParamIn);% execute the transform fct to get the required conditions
3332    Field.Action.RUN=0; % indicate that the transform fct is called only to get input param
3333    %DataOut=feval(transform_handle,Field,[]); % execute the transform fct to get the required conditions
3334    if isfield(DataOut,'TransformInput')%  used to add transform parameters at selection of the transform fct
3335        SeriesData.TransformInput=DataOut.TransformInput;
3336        set(handles.series,'UserData',SeriesData)
3337    end
3338end
3339
3340%------------------------------------------------------------------------
3341% --- fct activated by the upper bar menu ExportConfig
3342%------------------------------------------------------------------------
3343function MenuDisplayConfig_Callback(hObject, eventdata, handles)
3344
3345global Param
3346Param=read_GUI_series(handles);
3347evalin('base','global Param')%make CurData global in the workspace
3348display('current series config :')
3349evalin('base','Param') %display CurData in the workspace
3350commandwindow; % brings the Matlab command window to the front
3351
3352%------------------------------------------------------------------------
3353% --- fct activated by the upper bar menu InportConfig: import
3354%     menu settings from an xml file (stored in /0_XML for each run)
3355%------------------------------------------------------------------------
3356function MenuImportConfig_Callback(hObject, eventdata, handles)
3357
3358%% use a browser to choose the xml file containing the processing config
3359InputTable=get(handles.InputTable,'Data');
3360oldfile=InputTable{1,1}; % current path in InputTable
3361if isempty(oldfile)
3362    % use a file name stored in prefdir
3363    dir_perso=prefdir;
3364    profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
3365    if exist(profil_perso,'file')
3366        h=load (profil_perso);
3367        if isfield(h,'RootPath') && ischar(h.RootPath)
3368            oldfile=h.RootPath;
3369        end
3370    end
3371end
3372filexml=uigetfile_uvmat('pick a xml parameter file',oldfile,'.xml'); % get the xml file containing processing parameters
3373if isempty(filexml), return, end % quit function if an xml file has not been opened
3374
3375%% fill the GUI series with the content of the xml file
3376Param=xml2struct(filexml); % read the input xml file as a Matlab structure
3377
3378% ask to stop current Action if button RUN is in action (another process is already running)
3379if isequal(get(handles.RUN,'Value'),1)
3380    answer= msgbox_uvmat('INPUT_Y-N','stop current Action process?');
3381    if strcmp(answer,'Yes')
3382        STOP_Callback(hObject, eventdata, handles)
3383    else
3384        return
3385    end
3386end
3387Param.Action.RUN=0; % desactivate the input RUN=1
3388
3389fill_GUI(Param,handles.series)% fill the elements of the GUI series with the input parameters
3390SeriesData=get(handles.series,'UserData');
3391if isfield(Param,'InputFields')
3392    ListField=Param.InputFields.FieldName;
3393    if ischar(ListField),ListField={ListField}; end
3394    set(handles.FieldName,'String',[ListField;{'add_field...'}])
3395     set(handles.FieldName,'Value',1:numel(ListField))
3396     set(handles.FieldName,'Visible','on')
3397end       
3398if isfield(Param,'ActionInput')%  introduce  parameters specific to an Action fct, for instance PIV parameters
3399%     set(handles.ActionInput,'Visible','on')
3400%     set(handles.ActionInput,'Value',0)
3401    Param.ActionInput.ConfigSource=filexml; % record the source of config for future info
3402    SeriesData.ActionInput=Param.ActionInput;
3403end
3404if isfield(Param,'TransformInput')%  introduce  parameters specific to a transform fct
3405    SeriesData.TransformInput=Param.TransformInput;
3406end
3407if isfield(Param,'ProjObject') %introduce projection object if relevant
3408    SeriesData.ProjObject=Param.ProjObject;
3409end
3410set(handles.series,'UserData',SeriesData)
3411if isfield(Param,'CheckObject') && isequal(Param.CheckObject,1)
3412    set(handles.ProjObjectName,'String',Param.ProjObject.Name)
3413    set(handles.ViewObject,'Visible','on')
3414    set(handles.EditObject,'Visible','on')
3415    set(handles.DeleteObject,'Visible','on')
3416else     
3417    set(handles.ProjObjectName,'String','')
3418    set(handles.ProjObjectName,'Visible','off')
3419    set(handles.ViewObject,'Visible','off')
3420    set(handles.EditObject,'Visible','off')
3421    set(handles.DeleteObject,'Visible','off')     
3422end     
3423set(handles.REFRESH,'BackgroundColor',[1 0 1]); % paint REFRESH button in magenta to indicate that it should be activated
3424
3425
3426%------------------------------------------------------------------------
3427% --- Executes when the GUI series is resized.
3428%------------------------------------------------------------------------
3429function series_ResizeFcn(hObject, eventdata, handles)
3430
3431%% input table
3432set(handles.InputTable,'Unit','pixel')
3433Pos=get(handles.InputTable,'Position');
3434set(handles.InputTable,'Unit','normalized')
3435ColumnWidth=round([0.5 0.14 0.14 0.14 0.08]*(Pos(3)-52));
3436ColumnWidth=num2cell(ColumnWidth);
3437set(handles.InputTable,'ColumnWidth',ColumnWidth)
3438
3439%% MinIndex_j and MaxIndex_i
3440unit=get(handles.MinIndex_i,'Unit');
3441set(handles.MinIndex_i,'Unit','pixel')
3442Pos=get(handles.MinIndex_i,'Position');
3443set(handles.MinIndex_i,'Unit',unit)
3444set(handles.MinIndex_i,'ColumnWidth',{Pos(3)-18})
3445set(handles.MaxIndex_i,'ColumnWidth',{Pos(3)-18})
3446set(handles.MinIndex_j,'ColumnWidth',{Pos(3)-18})
3447set(handles.MaxIndex_j,'ColumnWidth',{Pos(3)-18})
3448
3449%% TimeTable
3450set(handles.TimeTable,'Unit','pixel')
3451Pos=get(handles.TimeTable,'Position');
3452set(handles.TimeTable,'Unit','normalized')
3453% ColumnWidth=get(handles.TimeTable,'ColumnWidth');
3454ColumnWidth=num2cell(floor([0.2 0.2 0.2 0.2 0.2]*(Pos(3)-20)));
3455set(handles.TimeTable,'ColumnWidth',ColumnWidth)
3456
3457
3458%% PairString
3459set(handles.PairString,'Unit','pixel')
3460Pos=get(handles.PairString,'Position');
3461set(handles.PairString,'Unit','normalized')
3462set(handles.PairString,'ColumnWidth',{Pos(3)-5})
3463
3464%% MaskTable
3465set(handles.MaskTable,'Unit','pixel')
3466Pos=get(handles.MaskTable,'Position');
3467set(handles.MaskTable,'Unit','normalized')
3468set(handles.MaskTable,'ColumnWidth',{Pos(3)-5})
3469
3470%------------------------------------------------------------------------
3471% --- Executes on button press in status.
3472%------------------------------------------------------------------------
3473function status_Callback(hObject, eventdata, handles)
3474
3475if get(handles.status,'Value')
3476    set(handles.status,'BackgroundColor',[1 1 0])
3477    drawnow
3478    Param=read_GUI(handles.series);
3479    RootPath=Param.InputTable{1,1};
3480    if ~isfield(Param,'OutputSubDir')   
3481        msgbox_uvmat('ERROR','no standard sub-directory definition for output files, use a browser to check the output')
3482        set(handles.status,'BackgroundColor',[0 1 0])
3483        return
3484    end
3485    OutputSubDir=[Param.OutputSubDir Param.OutputDirExt]; % subdirectory for output files
3486    OutputDir=fullfile(RootPath,OutputSubDir);
3487    if exist(OutputDir,'dir')
3488        uigetfile_uvmat('status_display',OutputDir)
3489    else
3490        msgbox_uvmat('ERROR','output folder not created yet: calculation did not start')
3491        set(handles.status,'BackgroundColor',[0 1 0])
3492    end
3493else
3494    %% delete current display fig if selection is off
3495    set(handles.status,'BackgroundColor',[0 1 0])
3496    hfig=findobj(allchild(0),'name','status_display');
3497    if ~isempty(hfig)
3498        delete(hfig)
3499    end
3500    return
3501end
3502
3503
3504%------------------------------------------------------------------------   
3505% launched by selecting a file on the list
3506%------------------------------------------------------------------------
3507function view_file(hObject, eventdata)
3508
3509list=get(hObject,'String');
3510index=get(hObject,'Value');
3511rootroot=get(hObject,'UserData');
3512selectname=list{index};
3513ind_dot=regexp(selectname,'\.\.\.');
3514if ~isempty(ind_dot)
3515    selectname=selectname(1:ind_dot-1);
3516end
3517FullSelectName=fullfile(rootroot,selectname);
3518if exist(FullSelectName,'dir')% a directory has been selected
3519    ListFiles=dir(FullSelectName);
3520    ListDisplay=cell(numel(ListFiles),1);
3521    for ilist=2:numel(ListDisplay)% suppress the first line '.'
3522        ListDisplay{ilist-1}=ListFiles(ilist).name;
3523    end
3524    set(hObject,'Value',1)
3525    set(hObject,'String',ListDisplay)
3526    if strcmp(selectname,'..')
3527        FullSelectName=fileparts(fileparts(FullSelectName));
3528    end
3529    set(hObject,'UserData',FullSelectName)
3530    hfig=get(hObject,'parent');
3531    htitlebox=findobj(hfig,'tag','titlebox');   
3532    set(htitlebox,'String',FullSelectName)
3533elseif exist(FullSelectName,'file')%visualise the vel field if it exists
3534    FileInfo=get_file_info(FullSelectName);   
3535    if strcmp(FileInfo.FileType,'txt')
3536        edit(FullSelectName)
3537    elseif strcmp(FileInfo.FileType,'xml')
3538        editxml(FullSelectName)
3539    else
3540        uvmat(FullSelectName)
3541    end
3542    set(gcbo,'Value',1)
3543end
3544
3545
3546%------------------------------------------------------------------------   
3547% launched by refreshing the status figure
3548%------------------------------------------------------------------------
3549function refresh_GUI(hfig)
3550
3551htitlebox=findobj(hfig,'tag','titlebox');
3552hlist=findobj(hfig,'tag','list');
3553hseries=findobj(allchild(0),'tag','series');
3554hstatus=findobj(hseries,'tag','status');
3555StatusData=get(hstatus,'UserData');
3556OutputDir=get(htitlebox,'String');
3557if ischar(OutputDir),OutputDir={OutputDir};end
3558ListFiles=dir(OutputDir{1});
3559if numel(ListFiles)<1
3560    return
3561end
3562ListFiles(1)=[]; % removes the first line ='.'
3563ListDisplay=cell(numel(ListFiles),1);
3564testrecent=0;
3565datnum=zeros(numel(ListDisplay),1);
3566for ilist=1:numel(ListDisplay)
3567    ListDisplay{ilist}=ListFiles(ilist).name;
3568      if ~ListFiles(ilist).isdir && isfield(ListFiles(ilist),'datenum')
3569            datnum(ilist)=ListFiles(ilist).datenum; % only available in recent matlab versions
3570            testrecent=1;
3571       end
3572end
3573set(hlist,'String',ListDisplay)
3574
3575%% Look at date of creation
3576ListDisplay=ListDisplay(datnum~=0);
3577datnum=datnum(datnum~=0); % keep the non zero values corresponding to existing files
3578NbOutputFile=[];
3579if isempty(datnum)
3580    if testrecent
3581        message='no civ result created yet';
3582    else
3583        message='';
3584    end
3585else
3586    [first,indfirst]=min(datnum);
3587    [last,indlast]=max(datnum);
3588    NbOutputFile_str='?';
3589    NbOutputFile=[];
3590    if isfield(StatusData,'NbOutputFile')
3591        NbOutputFile=StatusData.NbOutputFile;
3592        NbOutputFile_str=num2str(NbOutputFile);
3593    end
3594    message={[num2str(numel(datnum)) ' file(s) done over ' NbOutputFile_str] ;['oldest modification:  ' ListDisplay{indfirst} ' : ' datestr(first)];...
3595        ['latest modification:  ' ListDisplay{indlast} ' : ' datestr(last)]};
3596end
3597set(htitlebox,'String', [OutputDir{1};message])
3598
3599%% update the waitbar
3600hwaitbar=findobj(hfig,'tag','waitbar');
3601if ~isempty(NbOutputFile)
3602    BarPosition=get(hwaitbar,'Position');
3603    BarPosition(3)=0.9*numel(datnum)/NbOutputFile;
3604    set(hwaitbar,'Position',BarPosition)
3605end
3606
3607%------------------------------------------------------------------------
3608% --- Executes on selection change in ActionExt.
3609%------------------------------------------------------------------------
3610function ActionExt_Callback(hObject, eventdata, handles)
3611
3612ActionExtList=get(handles.ActionExt,'String');
3613ActionExt=ActionExtList{get(handles.ActionExt,'Value')};
3614if strcmp(ActionExt,'.py (in dev.)')
3615    set(handles.RunMode,'Value',2)
3616end
3617
3618
3619function num_NbSlice_Callback(hObject, eventdata, handles)
3620NbSlice=str2num(get(handles.num_NbSlice,'String'));
3621
3622%------------------------------------------------------------------------
3623% --- set the visibility of relevant velocity type menus:
3624function menu=set_veltype_display(Civ,FileType)
3625%------------------------------------------------------------------------
3626if ~exist('FileType','var')
3627    FileType='civx';
3628end
3629switch FileType
3630    case 'civx'
3631        menu={'civ1';'interp1';'filter1';'civ2';'interp2';'filter2'};
3632        if isequal(Civ,0)
3633            imax=0;
3634        elseif isequal(Civ,1) || isequal(Civ,2)
3635            imax=1;
3636        elseif isequal(Civ,3)
3637            imax=3;
3638        elseif isequal(Civ,4) || isequal(Civ,5)
3639            imax=4;
3640        elseif isequal(Civ,6) %patch2
3641            imax=6;
3642        end
3643    case 'civdata'
3644        menu={'civ1';'filter1';'civ2';'filter2'};
3645        if isequal(Civ,0)
3646            imax=0;
3647        elseif isequal(Civ,1) || isequal(Civ,2)
3648            imax=1;
3649        elseif isequal(Civ,3)
3650            imax=2;
3651        elseif isequal(Civ,4) || isequal(Civ,5)
3652            imax=3;
3653        else%if isequal(Civ,6) %patch2
3654            imax=4;
3655        end
3656end
3657menu=menu(1:imax);
3658
3659
3660% --- Executes on mouse motion over figure - except title and menu.
3661% function series_WindowButtonMotionFcn(hObject, eventdata, handles)
3662% set(hObject,'Pointer','arrow');
3663
3664
3665% --- Executes on button press in SetPairs.
3666function SetPairs_Callback(hObject, eventdata, handles)
3667
3668%% delete previous occurrence of 'set_pairs'
3669hfig=findobj(allchild(0),'Tag','set_pairs');
3670if ~isempty(hfig)
3671delete(hfig)
3672end
3673
3674%% create the GUI set_pairs
3675set(0,'Unit','points')
3676ScreenSize=get(0,'ScreenSize'); % get the size of the screen, to put the fig on the upper right
3677Width=220; % fig width in points (1/72 inch)
3678Height=min(0.8*ScreenSize(4),300);
3679Left=ScreenSize(3)- Width-40; % right edge close to the right, with margin=40
3680Bottom=ScreenSize(4)-Height-40; % put fig at top right
3681hfig=findobj(allchild(0),'Tag','set_slice');
3682if ~isempty(hfig),delete(hfig), end; % delete existing version of the GUI
3683hfig=figure('name','set_pairs','tag','set_pairs','MenuBar','none','NumberTitle','off','Unit','points','Position',[Left,Bottom,Width,Height]);
3684BackgroundColor=get(hfig,'Color');
3685SeriesData=get(handles.series,'UserData');
3686TimeUnit=get(handles.TimeUnit,'String');
3687PairString=get(handles.PairString,'Data');
3688ListViewLines=find(cellfun('isempty',PairString)==0); % find list of non empty pairs
3689ListViewMenu=cell(numel(ListViewLines),1);
3690%iview=get(handles.PairString,'Value');
3691iview=[];
3692for ilist=1:numel(ListViewLines)
3693    ListViewMenu{ilist}=num2str(ListViewLines(ilist));
3694end
3695if isempty(iview)
3696    ListViewValue=numel(ListViewLines); % we work by default on the pair option for the last line which requires pairs
3697    iview=ListViewLines(end);
3698else
3699    ListViewValue=find(ListViewLines==iview);
3700end
3701ref_i=str2num(get(handles.num_first_i,'String'));
3702ref_j=1; % default
3703if strcmp(get(handles.num_first_j,'String'),'Visible')
3704    ref_j=str2num(get(handles.num_first_j,'String'));
3705end
3706[ModeMenu,ModeValue]=update_mode(SeriesData.i1_series{1},SeriesData.i2_series{1},SeriesData.j2_series{1});
3707InputTable=get(handles.InputTable,'Data');
3708displ_pair=update_listpair(SeriesData.i1_series{1},SeriesData.i2_series{1},SeriesData.j1_series{1},SeriesData.j2_series{1},ModeMenu{ModeValue},...
3709                                                 SeriesData.Time{1},TimeUnit,ref_i,ref_j,SeriesData.TimeName,InputTable,SeriesData.FileInfo{1});
3710for iline=1:size(InputTable,1)
3711    viewcell{iline}=num2str(iline);
3712end
3713viewcell=viewcell';
3714ModeMenu={'bursts';'series(Dj)'};
3715ModeValue=1;                                               
3716                   %i1_series,i2_series,j1_series,j2_series,mode,time,TimeUnit,ref_i,ref_j,TimeName,InputTable,FileInfo                             
3717% first raw of the GUI
3718uicontrol('Style','text','Units','normalized', 'Position', [0.05 0.88 0.5 0.1],'BackgroundColor',BackgroundColor,...
3719    'String','row to edit #','FontUnits','points','FontSize',12,'FontWeight','bold','ForegroundColor','blue','HorizontalAlignment','right'); % title
3720uicontrol('Style','popupmenu','Units','normalized', 'Position', [0.54 0.8 0.3 0.2],'BackgroundColor',[1 1 1],...
3721    'Callback',@(hObject,eventdata)ListView_Callback(hObject,eventdata),'String',viewcell,'Value',1,'FontUnits','points','FontSize',12,'FontWeight','bold',...
3722    'Tag','ListView','TooltipString','''ListView'':choice of the file series w for pair display');
3723% second raw of the GUI
3724uicontrol('Style','text','Units','normalized', 'Position', [0.05 0.79 0.7 0.1],'BackgroundColor',BackgroundColor,...
3725    'String','mode of index pairing:','FontUnits','points','FontSize',12,'FontWeight','bold','ForegroundColor','blue','HorizontalAlignment','left'); % title
3726uicontrol('Style','popupmenu','Units','normalized', 'Position', [0.05 0.62 0.9 0.2],'BackgroundColor',[1 1 1],...
3727    'Callback',@(hObject,eventdata)Mode_Callback(hObject,eventdata),'String',ModeMenu,'Value',ModeValue,'FontUnits','points','FontSize',12,'FontWeight','bold',...
3728    'Tag','Mode','TooltipString','''Mode'': choice of the image pair mode');
3729% third raw
3730uicontrol('Style','text','Units','normalized', 'Position', [0.05 0.6 0.7 0.1],'BackgroundColor',BackgroundColor,...
3731    'String','pair choice:','FontUnits','points','FontSize',12,'FontWeight','bold','ForegroundColor','blue','HorizontalAlignment','left'); % title
3732uicontrol('Style','listbox','Units','normalized', 'Position', [0.05 0.42 0.9 0.2],'BackgroundColor',[1 1 1],...
3733    'Callback',@(hObject,eventdata)ListPair_Callback(hObject,eventdata),'String',displ_pair,'Value',1,'FontUnits','points','FontSize',12,'FontWeight','bold',...
3734    'Tag','ListPair','TooltipString','''ListPair'': menu for selecting the image pair');
3735uicontrol('Style','text','Units','normalized', 'Position', [0.1 0.22 0.8 0.1],'BackgroundColor',BackgroundColor,...
3736    'String','ref_i           ref_j','FontUnits','points','FontSize',12,'FontWeight','bold','ForegroundColor','blue','HorizontalAlignment','center'); % title
3737uicontrol('Style','edit','Units','normalized', 'Position', [0.15 0.17 0.3 0.08],'BackgroundColor',[1 1 1],...
3738    'Callback',@(hObject,eventdata)num_ref_i_Callback(hObject,eventdata),'String',num2str(ref_i),'FontUnits','points','FontSize',12,'FontWeight','bold',...
3739    'Tag','num_ref_i','TooltipString','''num_ref_i'': reference field index i used to display dt in ''list_pair_civ''');
3740uicontrol('Style','edit','Units','normalized', 'Position', [0.55 0.17 0.3 0.08],'BackgroundColor',[1 1 1],...
3741    'Callback',@(hObject,eventdata)num_ref_j_Callback(hObject,eventdata),'String',num2str(ref_j),'FontUnits','points','FontSize',12,'FontWeight','bold',...
3742    'Tag','num_ref_j','TooltipString','''num_ref_j'': reference field index i used to display dt in ''list_pair_civ''');
3743uicontrol('Style','pushbutton','Units','normalized', 'Position', [0.01 0.01 0.3 0.12],'BackgroundColor',[0 1 0],...
3744    'Callback',@(hObject,eventdata)OK_Callback(hObject,eventdata),'String','OK','FontUnits','points','FontSize',12,'FontWeight','bold',...
3745    'Tag','OK','TooltipString','''OK'': validate the choice');
3746%  last raw  of the GUI: pushbuttons
3747% 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),...
3748%     'FontWeight','bold','FontUnits','points','FontSize',12,'TooltipString','''OK'': apply the output to the current field series in uvmat');
3749drawnow
3750
3751%------------------------------------------------------------------------
3752function ListView_Callback(hObject,eventdata)
3753Mode_Callback(hObject,eventdata)
3754
3755%------------------------------------------------------------------------   
3756function Mode_Callback(hObject,eventdata)
3757%% get input info
3758hseries=findobj(allchild(0),'tag','series'); % handles of the GUI series
3759hhseries=guidata(hseries); % handles of the elements in the GUI series
3760TimeUnit=get(hhseries.TimeUnit,'String');
3761SeriesData=get(hseries,'UserData');
3762mode_list=get(hObject,'String');
3763mode=mode_list{get(hObject,'Value')};
3764hListView=findobj(get(hObject,'parent'),'Tag','ListView');
3765iview=get(hListView,'Value');
3766i1_series=SeriesData.i1_series{iview};
3767i2_series=SeriesData.i2_series{iview};
3768j1_series=SeriesData.j1_series{iview};
3769j2_series=SeriesData.j2_series{iview};
3770
3771%% enable j index visibility after the new choice
3772
3773if strcmp(mode,'series(Dj)')
3774   status_j='on'; % default
3775else
3776       status_j='off'; % no j index needed for bust case
3777end
3778enable_j(hhseries,status_j) % no j index needed
3779
3780%% get the reference indices for the time interval Dt
3781href_i=findobj(get(hObject,'parent'),'Tag','ref_i');
3782ref_i=[];ref_j=[];
3783if strcmp(get(href_i,'Visible'),'on')
3784    ref_i=str2num(get(href_i,'String'));
3785end
3786if isempty(ref_i)
3787    ref_i=1;
3788end
3789if isempty(ref_j)
3790    ref_j=1;
3791end
3792
3793%% update the menu ListPair
3794Menu=update_listpair(i1_series,i2_series,j1_series,j2_series,mode,SeriesData.Time{iview},TimeUnit,ref_i,ref_j,SeriesData.FileInfo);
3795hlist_pairs=findobj(get(hObject,'parent'),'Tag','ListPair');
3796set(hlist_pairs,'Value',1)% set the first choice by default in ListPair
3797set(hlist_pairs,'String',Menu)% set the menu in ListPair
3798ListPair_Callback(hlist_pairs,[])% apply the default choice in ListPair
3799
3800%-------------------------------------------------------------
3801% --- Executes on selection in ListPair.
3802function ListPair_Callback(hObject,eventdata)
3803%------------------------------------------------------------
3804list_pair=get(hObject,'String'); % get the menu of image pairs
3805if isempty(list_pair)
3806    string='';
3807else
3808    string=list_pair{get(hObject,'Value')};
3809   % string=regexprep(string,',.*',''); % removes time indication (after ',')
3810end
3811hseries=findobj(allchild(0),'tag','series');
3812hPairString=findobj(hseries,'tag','PairString');
3813PairString=get(hPairString,'Data');
3814hListView=findobj(get(hObject,'parent'),'Tag','ListView');
3815iview=get(hListView,'Value');
3816PairString{iview,1}=string;
3817% report the selected pair string to the table PairString
3818set(hPairString,'Data',PairString)
3819
3820
3821%------------------------------------------------------------------------
3822function num_ref_i_Callback(hObject, eventdata)
3823%------------------------------------------------------------------------
3824Mode_Callback([],[])
3825
3826%------------------------------------------------------------------------
3827function num_ref_j_Callback(hObject, eventdata)
3828%------------------------------------------------------------------------
3829Mode_Callback([],[])
3830
3831%------------------------------------------------------------------------
3832function OK_Callback(hObject, eventdata)
3833%------------------------------------------------------------------------
3834delete(get(hObject,'parent'))
3835
3836
3837%------------------------------------------------------------------------
3838% --- Executes on button press in ClearLine.
3839%------------------------------------------------------------------------
3840function ClearLine_Callback(hObject, eventdata, handles)
3841InputTable=get(handles.InputTable,'Data');
3842iline=str2double(get(handles.InputLine,'String'));
3843if size(InputTable,1)>1
3844    InputTable(iline,:)=[]; % suppress the current line if not the first
3845    set(handles.InputTable,'Data',InputTable);
3846end
3847set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH button to magenta color to indicate that input refr
3848
3849
3850% --- Executes on button press in MonitorCluster.
3851function MonitorCluster_Callback(hObject, eventdata, handles)
3852
3853[rr,ss]=system('oarstat |grep N=UVmat');% check the list of jobs launched with uvmat
3854if isempty(ss)
3855   disp( 'no job presently submitted with uvmat')
3856else
3857    disp('format: R/W=run/wait, time lapsed, R=nbre of cores,W=walltime')
3858    disp(ss)
3859end
3860
3861
3862function OutputSubDir_Callback(hObject, eventdata, handles)
3863set(handles.OutputSubDir,'BackgroundColor',[1 1 1])
3864
3865
3866% --- Executes on button press in CheckOverwrite.
3867function CheckOverwrite_Callback(hObject, eventdata, handles)
3868
3869% --- Executes on button press in TestCPUTime.
3870function TestCPUTime_Callback(hObject, eventdata, handles)
3871% hObject    handle to TestCPUTime (see GCBO)
3872% eventdata  reserved - to be defined in a future version of MATLAB
3873% handles    structure with handles and user data (see GUIDATA)
3874
3875
3876% --- Executes on button press in DiskQuota.
3877function DiskQuota_Callback(hObject, eventdata, handles)
3878SeriesData=get(handles.series,'UserData');
3879system(SeriesData.SeriesParam.DiskQuotaCmd)
3880
3881
3882% --- Executes on button press in Replicate.
3883function Replicate_Callback(hObject, eventdata, handles)
3884if get(handles.Replicate,'Value')
3885    InputTable=get(handles.InputTable,'Data');
3886    for ilist=1:size(InputTable,1)
3887        InputDir{ilist}=fullfile(InputTable{ilist,1},InputTable{ilist,2});
3888    end
3889    browse_data(InputDir)
3890else
3891    hh=findobj(allchild(0),'Tag','browse_data');
3892    if ~isempty(hh)
3893        delete(hh)
3894    end
3895end
3896
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