source: trunk/src/series.m @ 1071

Last change on this file since 1071 was 1071, checked in by g7moreau, 3 years ago
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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,'i1_series')
1455    errormsg='The input field series needs to be refreshed: press REFRESH';
1456    return
1457end
1458if isfield(Param,'InputFields')&& isfield(Param.InputFields,'FieldName')&& isequal(Param.InputFields.FieldName,'get_field...')
1459    errormsg='input field name(s) not defined, select get_field...';
1460    return
1461end
1462
1463%% select the Action mode, 'local', 'background' or 'cluster' (if available)
1464RunMode='local'; % default (needed for first opening of the GUI series)
1465if isfield(Param.Action,'RunMode')
1466    RunMode=Param.Action.RunMode;
1467    Param.Action=rmfield(Param.Action,'RunMode'); % remove from the recorded xml file to avoid interference during ImportConfig
1468    Param.RunMode=RunMode; % keep track of the mode
1469end
1470ActionExt='.m'; % default
1471if isfield(Param.Action,'ActionExt')
1472    ActionExt=Param.Action.ActionExt; % '.m', '.sh' (compiled)  or '.py' (Python)
1473    Param.Action=rmfield(Param.Action,'ActionExt'); % remove from the recorded xml file to avoid interference during ImportConfig
1474end
1475ActionName=Param.Action.ActionName;
1476ActionPath=Param.Action.ActionPath;
1477path_series=fileparts(which('series'));
1478
1479%% create the Action fct handle if RunMode option = 'local'
1480if strcmp(RunMode,'local')
1481    if ~isequal(ActionPath,path_series)
1482        eval(['spath=which(''' ActionName ''');']) %spath = current path of the selected function ACTION
1483        if ~exist(ActionPath,'dir')
1484            errormsg=['The prescribed function path ' ActionPath ' does not exist'];
1485            return
1486        end
1487        if ~isequal(spath,ActionPath)
1488            addpath(ActionPath)% add the prescribed path if not the current one
1489        end
1490    end
1491    eval(['h_fun=@' ActionName ';'])%create a function handle for ACTION
1492    if ~isequal(ActionPath,path_series)
1493        rmpath(ActionPath)% add the prescribed path if not the current one
1494    end
1495end
1496
1497%% Get  parameters from series.xml
1498errormsg=''; % default error message
1499ActionFullName=fullfile(get(handles.ActionPath,'String'),ActionName);
1500
1501%% If a compiled version has been selected (ext .sh) check wether it needs to be recompiled
1502if strcmp(ActionExt,'.sh')
1503    TransformPath='';
1504    if isfield(SeriesData,'TransformPath')
1505        TransformPath=SeriesData.TransformPath;
1506        if isfield(SeriesData,'TransformList')
1507            TransformList=get(handles.TransformName,'String');
1508            TransformIndex=get(handles.TransformName,'Value');
1509            TransformName=TransformList{TransformIndex};
1510            if ~ismember(TransformName,SeriesData.TransformList)
1511                TransformPath='';
1512            end
1513        end
1514    end
1515    if ~isempty(TransformPath)&&...
1516          ~strcmp(TransformPath,get(handles.TransformPath,'String'))% if the transform is not in paths set for compilation
1517        msgbox_uvmat('ERROR', 'compilation not available for this transform function, select .m')
1518        return
1519    end
1520    set(handles.series,'Pointer','watch') % set the mouse pointer to 'watch'
1521    set(handles.ActionExt,'BackgroundColor',[1 1 0])
1522    [mcrmajor, mcrminor] = mcrversion;   
1523    MCRROOT = ['MCRROOT',int2str(mcrmajor),int2str(mcrminor)];
1524    RunTime = getenv('MCRROOT'); % Just variable MCRROOT with no version in it's name
1525    if strcmp(RunTime,'')
1526        RunTime = getenv(MCRROOT); % Use specialize MCRROOT with version
1527    end
1528    ActionNameVersion=[ActionName '_' MCRROOT];
1529    ActionFullName=fullfile(get(handles.ActionPath,'String'),[ActionNameVersion '.sh']);
1530    % compile the .m file if the .sh file does not exist yet
1531    if ~exist(ActionFullName,'file')
1532        answer=msgbox_uvmat('INPUT_Y-N','compiled version has not been created: compile now?');
1533        if strcmp(answer,'Yes')
1534            set(handles.ActionExt,'BackgroundColor',[1 1 0])
1535            path_uvmat=fileparts(which('series'));
1536            currentdir=pwd;
1537            cd(get(handles.ActionPath,'String'))% go to the directory of Action
1538            addpath(path_uvmat)% add the path to uvmat to run the fct 'compile'
1539            compile(ActionName,TransformPath)
1540            cd(currentdir)
1541        else
1542            errormsg='Action launch interrupted';
1543            return
1544        end       
1545    else
1546        sh_file_info=dir(fullfile(get(handles.ActionPath,'String'),[ActionNameVersion '.sh']));
1547        m_file_info=dir(fullfile(get(handles.ActionPath,'String'),[ActionName '.m']));
1548        if isfield(m_file_info,'datenum') && m_file_info.datenum>sh_file_info.datenum
1549            set(handles.ActionExt,'BackgroundColor',[1 1 0])
1550            drawnow
1551            answer=msgbox_uvmat('INPUT_Y-N',[ActionNameVersion '.sh needs to be updated: recompile now?']);
1552            if strcmp(answer,'Yes')
1553                path_uvmat=fileparts(which('series'));
1554                currentdir=pwd;
1555                cd(get(handles.ActionPath,'String'))% go to the directory of Action
1556                addpath(path_uvmat)% add the path to uvmat to run the fct 'compile'
1557                addpath(fullfile(path_uvmat,'transform_field'))% add the path to transform functions to run the fct 'compile'
1558                compile(ActionName,TransformPath)
1559                cd(currentdir)
1560            end
1561        end
1562    end
1563
1564    set(handles.ActionExt,'BackgroundColor',[1 1 1])
1565     set(handles.series,'Pointer','arrow') % set the mouse pointer to 'watch
1566end
1567
1568%% set nbre of cluster cores and processes:
1569% NbCore is the number of computer processors used
1570% NbProcess is the number of independent processes in which the required calculation is split.
1571switch RunMode
1572    case {'local','background'}
1573        NbCore=1; % no need to split the calculation
1574    case 'cluster'
1575        %proposed number of cores to reserve in the cluster
1576        NbCoreAdvised=SeriesData.SeriesParam.ClusterParam.NbCoreAdvised;
1577        NbCoreMax=SeriesData.SeriesParam.ClusterParam.NbCoreMax;
1578        if NbCoreMax~=1
1579            if strcmp(ActionExt,'.m')% case of Matlab function (uncompiled)
1580                warning_string=', preferably use .sh option to save Matlab licences';
1581            else
1582                warning_string=')';
1583            end
1584            answer=msgbox_uvmat('INPUT_TXT',['Number of cores (max ' num2str(NbCoreMax) ', ' warning_string],num2str(NbCoreAdvised));
1585            if isempty(answer)
1586                errormsg='Action launch interrupted by user';
1587                return
1588            end
1589            NbCore=str2double(answer);
1590            if NbCore > NbCoreMax
1591                NbCore=NbCoreMax;
1592            end
1593        else
1594            NbCore=1;
1595        end
1596end
1597if ~isfield(Param.IndexRange,'NbSlice')
1598    Param.IndexRange.NbSlice=[];
1599end
1600
1601%% Look for processing on multiple experiments set by the GUI browse_data
1602NbExp=1;% initiate the number of experiments set by the GUI browse_data, =1 otherwise
1603if get(handles.Replicate,'Value')
1604    set(handles.Replicate,'BackgroundColor',[1 1 0])%paint Relicate button in yellow
1605    hh=findobj(allchild(0),'Tag','browse_data');
1606    BrowseData=guidata(hh);
1607    SourceDir=get(BrowseData.SourceDir,'String');
1608    ListExp=get(BrowseData.ListExperiments,'String');
1609    ExpIndices=get(BrowseData.ListExperiments,'Value');
1610    ListExp=ListExp(ExpIndices);
1611    ListDevices=get(BrowseData.ListDevices,'String');
1612    DeviceIndices=get(BrowseData.ListDevices,'Value');
1613    ListDevices=ListDevices(DeviceIndices);
1614    ListDataSeries=get(BrowseData.DataSeries,'String');
1615    DataSeriesIndices=get(BrowseData.DataSeries,'Value');
1616    ListDataSeries=ListDataSeries(DataSeriesIndices);
1617    NbExp=0; % counter of the number of experiments set by the GUI browse_data
1618    for iexp=1:numel(ListExp)
1619        if ~isempty(regexp(ListExp{iexp},'^\+/'))% if it is a folder
1620            if strcmp(get(BrowseData.DataSeries,'enable'),'off');%case of a multiple input line for series
1621                NbExp=NbExp+1;
1622                ExpIndex{NbExp}=iexp;
1623                for idevice=1:numel(ListDevices)
1624                    lpath= fullfile(SourceDir,regexprep(ListExp{iexp},'^\+/',''),...
1625                        regexprep(ListDevices{idevice},'^\+/',''));
1626                    ldir=regexprep(ListDataSeries{idevice},'^\+/','');
1627                    ListPath{idevice,NbExp}=lpath;
1628                    ListSubdir{idevice,NbExp}=ldir;
1629                end
1630            else
1631                for idevice=1:numel(ListDevices)
1632                    if ~isempty(regexp(ListDevices{idevice},'^\+/'))% if it is a folder
1633                        for isubdir=1:numel(ListDataSeries)
1634                            if ~isempty(regexp(ListDataSeries{isubdir},'^\+/'))% if it is a folder
1635                                lpath= fullfile(SourceDir,regexprep(ListExp{iexp},'^\+/',''),...
1636                                    regexprep(ListDevices{idevice},'^\+/',''));
1637                                ldir= regexprep(ListDataSeries{isubdir},'^\+/','');
1638                                if exist(fullfile(lpath,ldir),'dir')
1639                                    NbExp=NbExp+1;
1640                                    ExpIndex{NbExp}=iexp;
1641                                    ListPath{NbExp}=lpath;
1642                                    ListSubdir{NbExp}=ldir;
1643                                end
1644                            end
1645                        end
1646                    end
1647                end
1648            end
1649        end
1650    end
1651    answer=msgbox_uvmat('INPUT_Y-N-Cancel',['replicate the processing on ' num2str(NbExp) ' data series']);
1652    if strcmp(answer,'Cancel')||strcmp(answer,'No')
1653        return
1654    end
1655end
1656%      set(handles.OutputSubDir,'String',SubDir)
1657%      Param.OutputSubDir=SubDir;
1658%%%%%%%%%%%%%%%%%%% LOOP ON EXPERIMENTS POSSIBLY SET BY THE GUI browse_data, NbExp=1 otherwise %%%%%%%%%
1659for iexp=1:NbExp
1660    if get(handles.Replicate,'Value')
1661        if ~strcmp(get(handles.RUN,'BusyAction'),'queue')% allow for STOP action
1662            disp('program stopped by user')
1663            return
1664        end
1665        set(BrowseData.ListExperiments,'Value',ExpIndex{iexp})
1666        Param.InputTable(:,1)=ListPath(:,iexp);
1667        Param.InputTable(:,2)=ListSubdir(:,iexp);
1668        OutputSubDir=unique(ListSubdir(:,iexp));
1669        Param.OutputSubDir=OutputSubDir{1};
1670        if numel(OutputSubDir)>1% case
1671            for iout=2:numel(OutputSubDir)
1672                Param.OutputSubDir=[Param.OutputSubDir '-' OutputSubDir{iout}];
1673            end               
1674        end       
1675    end
1676    [xx,ExpName]=fileparts(Param.InputTable{1,1});
1677    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
1678    Param.IndexRange.last_i=str2num(get(handles.num_last_i,'String'));
1679   
1680    %% create the output data directory if needed, after chcking its existence
1681    OutputDir='';
1682    answer='';
1683    if isfield(Param,'OutputSubDir')% possibly update the output dir if it already exists
1684        SubDirOut=[Param.OutputSubDir Param.OutputDirExt];
1685        SubDirOutNew=SubDirOut;
1686        detect=exist(fullfile(Param.InputTable{1,1},SubDirOutNew),'dir'); % test if  the dir  already exist
1687        check_create=1; % need to create the result directory by default
1688        CheckOverwrite=1;
1689        if isfield(Param,'CheckOverwrite')
1690            CheckOverwrite=Param.CheckOverwrite;
1691        end
1692        while detect
1693            if CheckOverwrite
1694                comment=', possibly overwrite previous data';
1695            else
1696                comment=', will complement existing result files (no overwriting)';
1697            end
1698            answer=msgbox_uvmat('INPUT_Y-N-Cancel',['use existing ouput directory: ' fullfile(Param.InputTable{1,1},SubDirOutNew) comment]);
1699            if strcmp(answer,'Cancel')
1700                break
1701            elseif strcmp(answer,'Yes')
1702                detect=0;
1703                check_create=0;
1704            else
1705                r=regexp(SubDirOutNew,'(?<root>.*\D)(?<num1>\d+)$','names'); % detect whether name ends by a number
1706                if isempty(r)
1707                    r(1).root=[SubDirOutNew '_'];
1708                    r(1).num1='0';
1709                end
1710                SubDirOutNew=[r(1).root num2str(str2num(r(1).num1)+1)]; % increment the index by 1 or put 1
1711                detect=exist(fullfile(Param.InputTable{1,1},SubDirOutNew),'dir'); % test if  the dir  already exists
1712                check_create=1;
1713            end
1714        end
1715        if strcmp(answer,'Cancel')
1716            continue
1717        end
1718        Param.OutputDirExt=regexprep(SubDirOutNew,['^' Param.OutputSubDir],'');
1719        Param.OutputRootFile=Param.InputTable{1,3}; % the first sorted RootFile taken for output
1720        OutputDir=fullfile(Param.InputTable{1,1},[Param.OutputSubDir Param.OutputDirExt]); % full name (with path) of output directory
1721        if check_create    % create output directory if it does not exist
1722            [tild,msg1]=mkdir(OutputDir);
1723            if ~strcmp(msg1,'')
1724                errormsg=['cannot create ' OutputDir ': ' msg1]; % error message for directory creation
1725                return
1726            end
1727        end
1728       
1729    elseif isfield(Param,'ActionInput')&&isfield(Param.ActionInput,'LogPath')% custom definition of the output dir
1730        OutputDir=Param.ActionInput.LogPath;
1731    end
1732   
1733    set(handles.OutputSubDir,'String',Param.OutputSubDir)
1734    set(handles.OutputDirExt,'String',Param.OutputDirExt)
1735    drawnow
1736    if get(handles.Replicate,'Value')
1737        set(handles.InputTable,'Data',Param.InputTable)
1738        check_input_file_series(handles)
1739    end
1740    DirXml=fullfile(OutputDir,'0_XML');
1741    if ~exist(DirXml,'dir')
1742        [~,msg1]=mkdir(DirXml);
1743        if ~strcmp(msg1,'')
1744            errormsg=['cannot create ' DirXml ': ' msg1]; % error message for directory creation
1745            return
1746        end
1747        [success,msg] = fileattrib(DirXml,'+w','g','s'); % allow writing access for the group of users, recursively in the folder
1748        if success==0
1749            msgbox_uvmat('WARNING',{['unable to set group write access to ' DirXml ':']; msg}); % error message for directory creation
1750        end
1751    end
1752    OutputNomType=nomtype2pair(Param.InputTable{1,4}); % nomenclature for output files
1753   
1754    %% get the set of reference input field indices
1755    first_i=1; % first i index to process
1756    last_i=1; % last i index to process
1757    incr_i=1; % increment step in i index
1758    first_j=1; % first j index to process
1759    last_j=1; % last j index to process
1760    incr_j=1; % increment step in j index
1761    if isfield(Param.IndexRange,'first_i')
1762        first_i=Param.IndexRange.first_i;
1763        incr_i=Param.IndexRange.incr_i;
1764        last_i=Param.IndexRange.last_i;
1765    end
1766    if isfield(Param.IndexRange,'incr_j')
1767        first_j=Param.IndexRange.first_j;
1768        last_j=Param.IndexRange.last_j;
1769        incr_j=Param.IndexRange.incr_j;
1770    end
1771    if last_i < first_i || last_j < first_j
1772        errormsg= 'series/Run_Callback:last field index must be larger or equal to the first one';
1773        return
1774    end
1775    %incr_i must be defined, =1 by default, if NbSlice is active
1776    if isempty(incr_i)&& ~isempty(Param.IndexRange.NbSlice)
1777        incr_i=1;
1778        set(handles.num_incr_i,'String','1')
1779    end
1780    % case of no increment i defined: processing is done on the available files found in i1_series
1781    if isempty(incr_i)
1782        if isempty(incr_j)
1783            [ref_j,ref_i]=find(squeeze(SeriesData.i1_series{1}(1,:,:)));
1784            ref_j=ref_j(ref_j>=first_j & ref_j<=last_j);
1785            ref_i=ref_i(ref_i>=first_i & ref_i<=last_i);
1786            ref_j=ref_j-1;
1787            ref_i=ref_i-1;
1788        else
1789            ref_j=first_j:incr_j:last_j;
1790            [tild,ref_i]=find(squeeze(SeriesData.i1_series{1}(1,:,:)));
1791            ref_i=ref_i-1;
1792            ref_i=ref_i(ref_i>=first_i & ref_i<=last_i);
1793        end
1794        % increment i is defined: processing is done on first_i:incr_i:last_i;
1795    else
1796        ref_i=first_i:incr_i:last_i;
1797        if isempty(incr_j)% automatic finding of the existing j indices
1798            [ref_j,tild]=find(squeeze(SeriesData.i1_series{1}(1,:,:)));
1799            ref_j=ref_j-1;
1800            ref_j=ref_j(ref_j>=first_j & ref_j<=last_j);
1801        else
1802            ref_j=first_j:incr_j:last_j;
1803        end
1804    end
1805    CPUTime=1; % job time estimated at 1 min per iteration (on index i and j) by default
1806    if isfield(Param.Action, 'CPUTime') && ~isempty(Param.Action.CPUTime)
1807        CPUTime=Param.Action.CPUTime; % Note: CpUTime for one iteration ref_i has to be multiplied by the number of j indices nbfield_j
1808    end
1809    nbfield_j=numel(ref_j); % number of j indices
1810    BlockLength=numel(ref_i); % by default, job involves the full set of i field indices
1811    NbProcess=1;
1812    switch RunMode
1813        case 'cluster'
1814            JobNumberMax=SeriesData.SeriesParam.ClusterParam.JobNumberMax;
1815            JobCPUTimeAdvised=SeriesData.SeriesParam.ClusterParam.JobCPUTimeAdvised;
1816            if isempty(Param.IndexRange.NbSlice)% if NbSlice is not defined
1817                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.
1818                BlockLength=max(BlockLength,ceil(numel(ref_i)*NbExp/JobNumberMax)); % possibly increase the BlockLength to have less than MaxJobNumber jobs
1819                NbProcess=ceil(numel(ref_i)/BlockLength) ; % nbre of processes sent to oar
1820            else
1821                NbProcess=Param.IndexRange.NbSlice; % the parameter NbSlice sets the nbre of run processes
1822            end
1823            NbCore=min(NbCore,NbProcess); % reduces the number of cores if it exceeds the number of processes
1824        otherwise
1825            if ~isempty(Param.IndexRange.NbSlice)
1826                NbProcess=Param.IndexRange.NbSlice; % the parameter NbSlice sets the nbre of run processes
1827            end
1828    end
1829   
1830    %% record nbre of output files and starting time for computation for status
1831    StatusData=get(handles.status,'UserData');
1832    if isfield(StatusData,'OutputFileMode')
1833        switch StatusData.OutputFileMode
1834            case 'NbInput'
1835                StatusData.NbOutputFile=numel(ref_i)*nbfield_j;
1836            case 'NbInput_i'
1837                StatusData.NbOutputFile=numel(ref_i);
1838            case 'NbSlice'
1839                StatusData.NbOutputFile=str2num(get(handles.num_NbSlice,'String'));
1840        end
1841    end
1842    StatusData.TimeStart=now;
1843    set(handles.status,'UserData',StatusData)
1844   
1845    %% case of a function in Python
1846    if strcmp(ActionExt, '.py (in dev.)')
1847        fprintf([
1848            '\n' ...
1849            '!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n' ...
1850            'The option .py is used. It is still in development.\n' ...
1851            'To try it, first install pyper and the most recent version of fluidimage\n' ...
1852            '(see https://bitbucket.org/fluiddyn/fluidimage).\n' ...
1853            'Warning: there is no direct correspondance between UVMAT and fluidimage parameters\n' ...
1854            '!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n'])
1855        RunMode = 'python';
1856    end
1857   
1858   
1859    %% direct processing on the current Matlab session or creation of command files
1860    filexml=cell(1,NbProcess); % initialisation of the names of the files containing the processing parameters
1861    extxml=cell(1,NbProcess); % initialisation of the set of labels used for the files documenting each process
1862    for iprocess=1:NbProcess
1863        extxml{iprocess}='.xml';
1864    end
1865    for iprocess=1:NbProcess
1866        if ~strcmp(get(handles.RUN,'BusyAction'),'queue')% allow for STOP action
1867            disp('program stopped by user')
1868            return
1869        end
1870        if isempty(Param.IndexRange.NbSlice)
1871            Param.IndexRange.first_i=first_i+(iprocess-1)*BlockLength*incr_i;
1872            if Param.IndexRange.first_i>last_i
1873                NbProcess=iprocess-1; % leave the loop, we are at the end of the calculation
1874                break
1875            end
1876            Param.IndexRange.last_i=min(last_i,first_i+(iprocess)*BlockLength*incr_i-1);
1877        else %multislices (then incr_i is not empty)
1878            Param.IndexRange.first_i= first_i+iprocess-1;
1879            Param.IndexRange.incr_i=incr_i*Param.IndexRange.NbSlice;
1880        end
1881        for ilist=1:size(Param.InputTable,1)
1882            Param.InputTable{ilist,1}=regexprep(Param.InputTable{ilist,1},'\','/'); % correct path name for PCWIN system
1883        end
1884       
1885        if isfield(Param,'OutputSubDir')
1886            t=struct2xml(Param);
1887            t=set(t,1,'name','Series');
1888            extxml{iprocess}=fullfile_uvmat('','',Param.InputTable{1,3},'.xml',OutputNomType,...
1889                Param.IndexRange.first_i,Param.IndexRange.last_i,first_j,last_j);
1890            filexml{iprocess}=fullfile(OutputDir,'0_XML',extxml{iprocess});
1891            try
1892                save(t, filexml{iprocess}); % save the xml file containing the processing parameters
1893            catch ME
1894                if ~strcmp (RunMode,'local')
1895                    errormsg=['error writting ' filexml{iprocess} ': ' ME.message];
1896                    return
1897                end
1898            end
1899        end
1900        if strcmp (RunMode,'local')
1901            switch ActionExt
1902                case '.m'
1903                    h_fun(Param); % direct launching
1904                   
1905                case '.sh'
1906                    switch computer
1907                        case {'PCWIN','PCWIN64'} %Windows system
1908                            filexml=regexprep(filexml,'\\','\\\\'); % add '\' so that '\' are left as characters
1909                            system([ActionFullName ' ' RunTime ' ' filexml{iprocess}]); % TODO: adapt to DOS system
1910                        case {'GLNX86','GLNXA64','MACI64'}%Linux  system
1911                            system([ActionFullName ' ' RunTime ' ' filexml{iprocess}]);
1912                    end
1913            end
1914        end
1915    end
1916   
1917    if ~strcmp (RunMode,'local') && ~strcmp(RunMode,'python')
1918        %% processing on a different session of the same computer (background) or cluster, create executable files
1919        batch_file_list=cell(NbProcess,1); % initiate the list of executable files
1920        DirExe=fullfile(OutputDir,'0_EXE'); % directory name for executable files
1921        switch computer
1922            case {'PCWIN','PCWIN64'} %Windows system
1923                ExeExt='.bat';
1924            case {'GLNX86','GLNXA64','MACI64'}%Linux  system
1925                ExeExt='.sh';
1926        end
1927        %create subdirectory for executable files
1928        if ~exist(DirExe,'dir')
1929            [tild,msg1]=mkdir(DirExe);
1930            if ~strcmp(msg1,'')
1931                errormsg=['cannot create ' DirExe ': ' msg1]; % error message for directory creation
1932                return
1933            end
1934            [success,msg] = fileattrib(DirExe,'+w','g','s'); % allow writing access for the group of users, recursively in the folder
1935            if success==0
1936                msgbox_uvmat('WARNING',{['unable to set group write access to ' DirExe ':']; msg}); % error message for directory creation
1937            end
1938        end
1939        %create subdirectory for log files
1940        DirLog=fullfile(OutputDir,'0_LOG');
1941        if ~exist(DirLog,'dir')
1942            [tild,msg1]=mkdir(DirLog);
1943            if ~strcmp(msg1,'')
1944                errormsg=['cannot create ' DirLog ': ' msg1]; % error message for directory creation
1945                return
1946            end
1947            [success,msg] = fileattrib(DirLog,'+w','g','s'); % allow writing access for the group of users, recursively in the folder
1948            if success==0
1949                msgbox_uvmat('WARNING',{['unable to set group write access to ' DirLog ':']; msg}); % error message for directory creation
1950            end
1951        end
1952       
1953        %create the executable file
1954        file_exe_global=fullfile_uvmat('','',Param.InputTable{1,3},ExeExt,OutputNomType,...
1955            first_i,last_i,first_j,last_j);
1956        file_exe_global=fullfile(OutputDir,'0_EXE',file_exe_global);
1957        filelog_global=fullfile_uvmat('','',Param.InputTable{1,3},'.log',OutputNomType,...
1958            first_i,last_i,first_j,last_j);
1959        filelog_global=fullfile(OutputDir,'0_LOG',filelog_global);
1960       
1961        for iprocess=1:NbProcess
1962            %create the executable file
1963            batch_file_list{iprocess}=fullfile(OutputDir,'0_EXE',regexprep(extxml{iprocess},'.xml$',ExeExt));
1964           
1965            % set the log file name
1966            filelog{iprocess}=fullfile(OutputDir,'0_LOG',regexprep(extxml{iprocess},'.xml$','.log'));
1967        end
1968    end
1969   
1970    %% launch the executable files for background or cluster processing
1971   
1972    switch RunMode
1973       
1974        case 'background'
1975            [fid,message]=fopen(file_exe_global,'w');
1976            if isequal(fid,-1)
1977                errormsg=['creation of ' file_exe_global ':' message];
1978                return
1979            end
1980            switch ActionExt
1981                case '.m'% Matlab function
1982                    switch computer
1983                        case {'GLNX86','GLNXA64','MACI64'}
1984                            matlab_ver = ver('MATLAB');
1985                            matlab_version = matlab_ver.Version;
1986                            cmd=[...
1987                                '#!/bin/bash\n'...
1988                                'source /etc/profile\n'...
1989                                'module load matlab/' matlab_version '\n'...% CHOICE OF MATLAB VERSION
1990                                'time_start=$(date +%%s)\n'...
1991                                'matlab -nodisplay -nosplash -nojvm -logfile ''' filelog_global ''' <<END_MATLAB\n'...
1992                                'addpath(''' path_series ''');\n'...
1993                                'addpath(''' Param.Action.ActionPath ''');\n'];
1994                            for iprocess=1:NbProcess
1995                                cmd=[cmd '' Param.Action.ActionName  '(''' filexml{iprocess} ''');\n'];
1996                            end
1997                            cmd=[cmd  'exit\n' 'END_MATLAB\n'...
1998                                'time_end=$(date +%%s)\n'...
1999                                'echo "global time = " $(($time_end - $time_start)) >> ''' filelog_global '''\n'];
2000                            fprintf(fid,cmd); % fill the executable file with the  char string cmd
2001                            fclose(fid); % close the executable filefilelog_global
2002                            system(['chmod +x ' file_exe_global]); % set the file to executable
2003                        case {'PCWIN','PCWIN64'}
2004                            cmd=['matlab -automation -logfile ' regexprep(filelog{iprocess},'\\','\\\\')...
2005                                ' -r "addpath(''' regexprep(path_series,'\\','\\\\') ''');'...
2006                                'addpath(''' regexprep(Param.Action.ActionPath,'\\','\\\\') ''');'];
2007                            for iprocess=1:NbProcess
2008                                cmd=[cmd '' Param.Action.ActionName  '( ''' regexprep(filexml{iprocess},'\\','\\\\') ''');']
2009                            end
2010                            cmd=[cmd ';exit"'];
2011                            fprintf(fid,cmd); % fill the executable file with the  char string cmd
2012                            fclose(fid); % close the executable file
2013                    end
2014                    system([file_exe_global ' &'])% directly execute the command file
2015                case '.sh' % compiled Matlab function
2016                    for iprocess=1:NbProcess
2017                        switch computer
2018                            case {'GLNX86','GLNXA64','MACI64'}
2019                                [fid,message]=fopen(batch_file_list{iprocess},'w'); % create the executable file
2020                                if isequal(fid,-1)
2021                                    errormsg=['creation of .bat file: ' message];
2022                                    return
2023                                end
2024                                cmd=['#!/bin/bash \n '...
2025                                    '#$ -cwd \n '...
2026                                    'hostname && date \n '...
2027                                    'umask 002 \n'...
2028                                    ActionFullName ' ' RunTime ' ' filexml{iprocess}]; % allow writting access to created files for user group
2029                                fprintf(fid,cmd); % fill the executable file with the  char string cmd
2030                                fclose(fid); % close the executable file
2031                                system(['chmod +x ' batch_file_list{iprocess}]); % set the file to executable
2032                                system([batch_file_list{iprocess} ' &'])% directly execute the command file
2033                            case {'PCWIN','PCWIN64'}
2034                                msgbox_uvmat('ERROR','option for compiled Matlab functions not implemented for Windows system')
2035                                return
2036                        end
2037                    end
2038                    msgbox_uvmat('CONFIRMATION',[ActionFullName ' launched in background for ' ExpName ': press STATUS to see results'])
2039            end
2040           
2041        case 'cluster' % option 'oar-parexec' used
2042            %create subdirectory for oar commands
2043            for iprocess=1:NbProcess
2044                [fid,message]=fopen(batch_file_list{iprocess},'w'); % create the executable file
2045                if isequal(fid,-1)
2046                    errormsg=['creation of .bat file: ' message];
2047                    return
2048                end
2049                if  strcmp(ActionExt,'.sh')
2050                    cmd=['#!/bin/bash \n '...
2051                        '#$ -cwd \n '...
2052                        'hostname && date \n '...
2053                        'umask 002 \n'...
2054                        ActionFullName ' ' RunTime ' ' filexml{iprocess}]; % allow writting access to created files for user group
2055                else
2056                    matlab_ver = ver('MATLAB');
2057                    matlab_version = matlab_ver.Version;
2058                    cmd=[...
2059                        '#!/bin/bash\n'...
2060                        'source /etc/profile\n'...
2061                        'module load matlab/' matlab_version '\n'...% CHOICE OF MATLAB VERSION
2062                        'matlab -nodisplay -nosplash -nojvm -singleCompThread -logfile ''' filelog{iprocess} ''' <<END_MATLAB\n'...
2063                        'addpath(''' path_series ''');\n'...
2064                        'addpath(''' Param.Action.ActionPath ''');\n'...
2065                        '' Param.Action.ActionName  '(''' filexml{iprocess} ''');\n'...
2066                        'exit\n'...
2067                        'END_MATLAB\n'];
2068                end
2069                fprintf(fid,cmd); % fill the executable file with the  char string cmd
2070                fclose(fid); % close the executable file
2071                system(['chmod +x ' batch_file_list{iprocess}]); % set the file to executable
2072            end
2073            DIR_CLUSTER=fullfile(OutputDir,'0_CLUSTER');
2074            if exist(DIR_CLUSTER,'dir')% delete the content of the dir 0_LOG to allow new input
2075                curdir=pwd;
2076                cd(DIR_CLUSTER)
2077                delete('*')
2078                cd(curdir)
2079            else
2080                [tild,msg1]=mkdir(DIR_CLUSTER);
2081                if ~strcmp(msg1,'')
2082                    errormsg=['cannot create ' DIR_CLUSTER ': ' msg1]; % error message for directory creation
2083                    return
2084                end
2085            end
2086            % create file containing the list of jobs
2087            ListProcess=fullfile(DIR_CLUSTER,'job_list.txt'); % name of the file containing the list of executables
2088            fid=fopen(ListProcess,'w'); % open it for writting
2089            for iprocess=1:length(batch_file_list)
2090                fprintf(fid,[batch_file_list{iprocess} '\n']); % write list of exe files
2091            end
2092            fclose(fid);
2093            system(['chmod +x ' ListProcess]); % set the file to executable
2094           
2095            CPUTimeProcess=CPUTime*BlockLength*nbfield_j; % estimated CPU time for one individual process (in minutes)
2096            LaunchCmdFcn=SeriesData.SeriesParam.ClusterParam.LaunchCmdFcn;
2097            oar_command=feval(LaunchCmdFcn,ListProcess,ActionFullName,DirLog,NbProcess, NbCore,CPUTimeProcess)
2098            [status,result]=system(oar_command)% execute system command and show the result (ID number of the launched job) on the Matlab command window
2099            filename_oarcommand=fullfile(DIR_CLUSTER,'0_cluster_command'); % keep track of the command in file '0-OAR/0_cluster_command'
2100            fid=fopen(filename_oarcommand,'w');
2101            fprintf(fid,oar_command); % store the command
2102            fprintf(fid,result); % store the result (job ID number)
2103            fclose(fid);
2104            if status==0
2105                msgbox_uvmat('CONFIRMATION',[ActionFullName ' launched for ' ExpName ' as ' num2str(NbProcess) ' processes in cluster: press STATUS to see results'])
2106            else
2107                msgbox_uvmat('ERROR',result)
2108            end
2109            %     case 'cluster_pbs' % for LMFA Kepler machine:  trqnsferred to fct
2110           
2111            %         %create subdirectory for pbs command and log files
2112            %         DirPBS=fullfile(OutputDir,'0_PBS'); % todo : common name OAR/PBS
2113            %         if exist(DirPBS,'dir')% delete the content of the dir 0_LOG to allow new input
2114            %             curdir=pwd;
2115            %             cd(DirPBS)
2116            %             delete('*')
2117            %             cd(curdir)
2118            %         else
2119            %             [tild,msg1]=mkdir(DirPBS);
2120            %             if ~strcmp(msg1,'')
2121            %                 errormsg=['cannot create ' DirPBS ': ' msg1]; % error message for directory creation
2122            %                 return
2123            %             end
2124            %         end
2125            %         max_walltime=3600*20; % 20h max total calculation (cannot exceed 24 h)
2126            %         walltime_onejob=1800; % seconds, max estimated time for asingle file index value
2127            %         ListProcess=fullfile(DirPBS,'job_list.txt'); % create name of the global executable file
2128            %         fid=fopen(ListProcess,'w');
2129            %         for iprocess=1:length(batch_file_list)
2130            %             fprintf(fid,[batch_file_list{iprocess} '\n']); % list of exe files
2131            %         end
2132            %         fclose(fid);
2133            %         system(['chmod +x ' ListProcess]); % set the file to executable
2134            %         pbs_command=['qsub -n CIVX '...
2135            %             '-t idempotent --checkpoint ' num2str(walltime_onejob+60) ' '...
2136            %             '-l /core=' num2str(NbCore) ','...
2137            %             'walltime=' datestr(min(1.05*walltime_onejob/86400*max(NbProcess*BlockLength*nbfield_j,NbCore)/NbCore,max_walltime/86400),13) ' '...
2138            %             '-E ' regexprep(ListProcess,'\.txt\>','.stderr') ' '...
2139            %             '-O ' regexprep(ListProcess,'\.txt\>','.log') ' '...
2140            %             extra_qstat ' '...
2141            %             '"oar-parexec -s -f ' ListProcess ' '...
2142            %             '-l ' ListProcess '.log"'];
2143            %         filename_oarcommand=fullfile(DirPBS,'pbs_command');
2144            %         fid=fopen(filename_oarcommand,'w');
2145            %         fprintf(fid,pbs_command);
2146            %         fclose(fid);
2147            %         fprintf(pbs_command); % display in command line
2148            %         %system(pbs_command);
2149            %         msgbox_uvmat('CONFIRMATION',[ActionFullName ' command ready to be launched in cluster'])
2150           
2151        case 'cluster_sge' % for PSMN % TODO: use the standard 'cluster' config with an external fct
2152            % Au PSMN, on ne cr??e pas 1 job avec plusieurs c??urs, mais N jobs de 1 c??urs
2153            % o?? N < 1000.
2154            %create subdirectory for pbs command and log files
2155           
2156            DirSGE=fullfile(OutputDir,'0_SGE');
2157            if exist(DirSGE,'dir')% delete the content of the dir 0_LOG to allow new input
2158                curdir=pwd;
2159                cd(DirSGE)
2160                delete('*')
2161                cd(curdir)
2162            else
2163                [tild,msg1]=mkdir(DirSGE);
2164                if ~strcmp(msg1,'')
2165                    errormsg=['cannot create ' DirSGE ': ' msg1]; % error message for directory creation
2166                    return
2167                end
2168            end
2169            maxImgsPerJob = ceil(length(batch_file_list)/NbCore);
2170            disp(['Max number of jobs: ' num2str(NbCore)])
2171            disp(['Images per job: ' num2str(maxImgsPerJob)])
2172           
2173            iprocess = 1;
2174            imgsInJob = [];
2175            currJobIndex = 1;
2176            done = 0;
2177            while(~done)
2178                if(iprocess <= length(batch_file_list))
2179                    imgsInJob = [imgsInJob, iprocess];
2180                end
2181                if((numel(imgsInJob) >= maxImgsPerJob) || (iprocess == length(batch_file_list)))
2182                    cmd=['#!/bin/sh \n'...
2183                        '#$ -cwd \n'...
2184                        'hostname && date\n']
2185                    for ii=1:numel(imgsInJob)
2186                        cmd=[cmd ActionFullName ' /softs/matlab ' filexml{imgsInJob(ii)} '\n'];
2187                    end
2188                    [fid, message] = fopen([DirSGE '/job' num2str(currJobIndex) '.sh'], 'w');
2189                    fprintf(fid, cmd);
2190                    fclose(fid);
2191                    system(['chmod +x ' DirSGE '/job' num2str(currJobIndex) '.sh'])
2192                    sge_command=['qsub -N civ_' num2str(currJobIndex) ' '...
2193                        '-q ' qstat_Queue ' '...
2194                        '-e ' fullfile([DirSGE '/job' num2str(currJobIndex) '.out']) ' '...
2195                        '-o ' fullfile([DirSGE '/job' num2str(currJobIndex) '.out']) ' '...
2196                        fullfile([DirSGE '/job' num2str(currJobIndex) '.sh'])];
2197                    fprintf(sge_command); % display in command line
2198                    [status, result] = system(sge_command);
2199                    fprintf(result);
2200                    currJobIndex = currJobIndex + 1;
2201                    imgsInJob = [];
2202                end
2203                if(iprocess == length(batch_file_list))
2204                    done = 1;
2205                end
2206                iprocess = iprocess + 1;
2207            end
2208            msgbox_uvmat('CONFIRMATION',[num2str(currJobIndex-1) ' jobs launched on queue ' qstat_Queue '.'])
2209        case 'python'
2210            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))") ' ...
2211                'python -m fluidimage.run_from_xml ' filexml{iprocess}];
2212            fprintf(['command:\n' command '\n\n'])
2213            system(command, '-echo');
2214    end
2215    if exist(OutputDir,'dir')
2216        [SUCCESS,MESSAGE,MESSAGEID] = fileattrib (OutputDir);
2217        if MESSAGE.GroupWrite~=1
2218            [success,msg] = fileattrib(OutputDir,'+w','g','s'); % allow writing access for the group of users, recursively in the folder
2219            if success==0
2220                msgbox_uvmat('WARNING',{['unable to set group write access to ' OutputDir ':']; msg}); % error message for directory creation
2221            end
2222        end
2223    end
2224end
2225set(handles.Replicate,'BackgroundColor',[0 1 0])
2226
2227%------------------------------------------------------------------------
2228function STOP_Callback(hObject, eventdata, handles)
2229%------------------------------------------------------------------------
2230set(handles.RUN, 'BusyAction','cancel')
2231set(handles.RUN,'BackgroundColor',[1 0 0])
2232set(handles.RUN,'enable','on')
2233set(handles.RUN, 'Value',0)
2234
2235%------------------------------------------------------------------------
2236% --- read parameters from the GUI series
2237%------------------------------------------------------------------------
2238function Param=read_GUI_series(handles)
2239
2240%% read raw parameters from the GUI series
2241Param=read_GUI(handles.series);
2242
2243%% clean the output structure by removing unused information
2244if isfield(Param,'Pairs')
2245    Param=rmfield(Param,'Pairs'); % info Pairs not needed for output
2246end
2247if isfield(Param,'InputLine')
2248    Param=rmfield(Param,'InputLine');
2249end
2250if isfield(Param,'EditObject')
2251    Param=rmfield(Param,'EditObject');
2252end
2253Param.IndexRange.TimeSource=Param.IndexRange.TimeTable{end,1};
2254Param.IndexRange=rmfield(Param.IndexRange,'TimeTable');
2255empty_line=false(size(Param.InputTable,1),1);
2256for iline=1:size(Param.InputTable,1)
2257    empty_line(iline)=isempty(cell2mat(Param.InputTable(iline,1:3)));
2258end
2259Param.InputTable(empty_line,:)=[];
2260
2261%------------------------------------------------------------------------
2262% --- Executes on selection change in ActionName.
2263function ActionName_Callback(hObject, ActionPath, handles)
2264%------------------------------------------------------------------------
2265
2266%% stop any ongoing series processing
2267if isequal(get(handles.RUN,'Value'),1)
2268    answer= msgbox_uvmat('INPUT_Y-N','stop current Action process?');
2269    if strcmp(answer,'Yes')
2270        STOP_Callback(hObject, [], handles)
2271    else
2272        return
2273    end
2274end
2275set(handles.ActionName,'BackgroundColor',[1 1 0])
2276huigetfile=findobj(allchild(0),'tag','status_display');
2277if ~isempty(huigetfile)
2278    delete(huigetfile)
2279end
2280drawnow
2281
2282%% get Action name and path
2283NbBuiltinAction=get(handles.Action,'UserData'); % nbre of functions initially proposed in the menu ActionName (as defined in the Opening fct of series)
2284ActionList=get(handles.ActionName,'String'); % list menu fields
2285ActionIndex=get(handles.ActionName,'Value');
2286if ~isequal(ActionIndex,1)% if we are not just opening series
2287    InputTable=get(handles.InputTable,'Data');
2288    if isempty(InputTable{1,4})
2289        msgbox_uvmat('ERROR','no input file available: use Open in the menu bar')
2290        return
2291    end
2292end
2293ActionName= ActionList{get(handles.ActionName,'Value')}; % selected function name
2294ActionPathList=get(handles.ActionName,'UserData'); % list of recorded paths to functions of the list ActionName
2295
2296%% add a new function to the menu if 'more...' has been selected in the menu ActionName
2297if isequal(ActionName,'more...')
2298    if ~ischar(ActionPath)
2299        ActionPath=get(handles.ActionPath,'String');
2300    end
2301    [FileName, PathName] = uigetfile( ...
2302        {'*.m', ' (*.m)';
2303        '*.m',  '.m files '; ...
2304        '*.*', 'All Files (*.*)'}, ...
2305        'Pick a series processing function ',ActionPath);
2306    if length(FileName)<2
2307        return
2308    end
2309    [tild,ActionName,ActionExt]=fileparts(FileName);
2310   
2311    % insert the choice in the menu ActionName
2312    ActionIndex=find(strcmp(ActionName,ActionList),1); % look for the selected function in the menu Action
2313    PathName=regexprep(PathName,'/$','');
2314    if ~isempty(ActionIndex) && ~strcmp(ActionPathList{ActionIndex},PathName)%compare the path to the existing fct
2315        ActionIndex=[]; % the selected path is different than the recorded one
2316    end
2317    if isempty(ActionIndex)%the qselected fct (with selected path) does not exist in the menu
2318        ActionIndex= length(ActionList);
2319        ActionList=[ActionList(1:end-1);{ActionName};ActionList(end)]; % the selected function is appended in the menu, before the last item 'more...'
2320         ActionPathList=[ActionPathList; PathName];
2321    end
2322   
2323    % record the file extension and extend the path list if it is a new extension
2324    ActionExtList=get(handles.ActionExt,'String');
2325    ActionExtIndex=find(strcmp(ActionExt,ActionExtList), 1);
2326    if isempty(ActionExtIndex)
2327        set(handles.ActionExt,'String',[ActionExtList;{ActionExt}])
2328    end
2329
2330    % remove old Action options in the menu (keeping a menu length <nb_builtin_ACTION+5)
2331    if length(ActionList)>NbBuiltinAction+5; % nb_builtin_ACTION=nbre of functions always remaining in the initial menu
2332        nbremove=length(ActionList)-NbBuiltinAction-5;
2333        ActionList(NbBuiltinAction+1:end-5)=[];
2334        ActionPathList(NbBuiltinAction+1:end-4,:)=[];
2335        ActionIndex=ActionIndex-nbremove;
2336    end
2337   
2338    % record action menu, choice and path
2339    set(handles.ActionName,'Value',ActionIndex)
2340    set(handles.ActionName,'String',ActionList)
2341       set(handles.ActionName,'UserData',ActionPathList);
2342    set(handles.ActionExt,'Value',ActionExtIndex)
2343       
2344    %record the user defined menu additions in personal file profil_perso
2345    dir_perso=prefdir;
2346    profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
2347    if NbBuiltinAction+1<=numel(ActionList)-1
2348        ActionListUser=ActionList(NbBuiltinAction+1:numel(ActionList)-1);
2349        ActionPathListUser=ActionPathList(NbBuiltinAction+1:numel(ActionList)-1);
2350        ActionExtListUser={};
2351        if numel(ActionExtList)>2
2352            ActionExtListUser=ActionExtList(3:end);
2353        end
2354        if exist(profil_perso,'file')
2355            save(profil_perso,'ActionListUser','ActionPathListUser','ActionExtListUser','-append')
2356        else
2357            save(profil_perso,'ActionListUser','ActionPathListUser','ActionExtListUser','-V6')
2358        end
2359    end
2360end
2361
2362%% check the current ActionPath to the selected function
2363ActionPath=ActionPathList{ActionIndex}; % current recorded path
2364set(handles.ActionPath,'String',ActionPath); % show the path to the senlected function
2365
2366%% reinitialise the waitbar
2367update_waitbar(handles.Waitbar,0)
2368
2369%% Put the first line of the selected Action fct as tooltip help
2370try
2371    [fid,errormsg] =fopen([ActionName '.m']);
2372    InputText=textscan(fid,'%s',1,'delimiter','\n');
2373    fclose(fid);
2374    set(handles.ActionName,'ToolTipString',InputText{1}{1})% put the first line of the selected function as tooltip help
2375end
2376set(handles.ActionName,'BackgroundColor',[1 1 1])
2377set(handles.ActionInput,'BackgroundColor',[1 0 1])% set ActionInput button to magenta color to indicate that input refr
2378
2379
2380% --- Executes on button press in ActionInput.
2381function ActionInput_Callback(hObject, eventdata, handles)
2382
2383set(handles.ActionInput,'BackgroundColor',[1 1 0])
2384SeriesData=get(handles.series,'UserData'); % info on the input file series
2385
2386%% create the function handle for Action
2387ActionPath=get(handles.ActionPath,'String');
2388ActionList=get(handles.ActionName,'String');
2389ActionName= ActionList{get(handles.ActionName,'Value')}; % selected function name
2390if ~exist(ActionPath,'dir')
2391    ActionName_Callback(handles.ActionName, ActionPath, handles)% update the function
2392    return
2393end
2394current_dir=pwd; % current working dir
2395cd(ActionPath)
2396h_fun=str2func(ActionName);
2397cd(current_dir)
2398
2399%% Activate the Action fct to adapt the configuration of the GUI series and bring specific parameters in SeriesData
2400Param=read_GUI_series(handles); % read the parameters from the GUI series
2401Param.Action.RUN=0;
2402Param.SeriesData=SeriesData;
2403ParamOut=h_fun(Param); % run the selected Action function to get the relevant input
2404
2405
2406%% Visibility of VelType and VelType_1 menus asked by ActionName
2407VelTypeRequest=1; % VelType requested by default
2408VelTypeRequest_1=1; % VelType requested by default
2409if isfield(ParamOut,'VelType')
2410    VelTypeRequest=ismember(ParamOut.VelType,{'on','one','two'});
2411    VelTypeRequest_1=strcmp( ParamOut.VelType,'two');
2412end
2413FieldNameRequest=0;  %hidden by default
2414FieldNameRequest_1=0;  %hidden by default
2415if isfield(ParamOut,'FieldName')
2416    FieldNameRequest=ismember(ParamOut.FieldName,{'on','one','two'});
2417    FieldNameRequest_1=strcmp( ParamOut.FieldName,'two');
2418end
2419
2420%% Detect the types of input files and set menus and default options in 'VelType'
2421iview_civ=find(strcmp('civx',SeriesData.FileType)|strcmp('civdata',SeriesData.FileType));
2422iview_netcdf=find(strcmp('netcdf',SeriesData.FileType)|strcmp('civx',SeriesData.FileType)|strcmp('civdata',SeriesData.FileType)); % all nc files, icluding civ
2423FieldList=get(handles.FieldName,'String'); % previous list as default
2424if ~iscell(FieldList),FieldList={FieldList};end
2425FieldList_1=get(handles.FieldName_1,'String'); % previous list as default
2426if ~iscell(FieldList_1),FieldList_1={FieldList_1};end
2427CheckList_1=1; % indicate whether FieldName_1 has been updated
2428handles_coord=[handles.Coord_x handles.Coord_y handles.Coord_z handles.Coord_x_title handles.Coord_y_title handles.Coord_z_title];
2429if VelTypeRequest && numel(iview_civ)>=1
2430    menu=set_veltype_display(SeriesData.FileInfo{iview_civ(1)}.CivStage,SeriesData.FileType{iview_civ(1)});
2431    set(handles.VelType,'Value',1)% set first choice by default
2432    set(handles.VelType,'String',[{'*'};menu])
2433    set(handles.VelType,'Visible','on')
2434    set(handles.VelType_title,'Visible','on')
2435    FieldList=set_field_list('U','V'); % standard menu for civx data
2436    if max(get(handles.FieldName,'Value'))>numel(FieldList)
2437    set(handles.FieldName,'Value',1); % velocity vector choice by default
2438    end
2439    if  VelTypeRequest_1 && numel(iview_civ)>=2
2440        menu=set_veltype_display(SeriesData.FileInfo{iview_civ(2)}.CivStage,SeriesData.FileType{iview_civ(2)});
2441        set(handles.VelType_1,'Value',1)% set first choice by default
2442        set(handles.VelType_1,'String',[{'*'};menu])
2443        set(handles.VelType_1,'Visible','on')
2444        set(handles.VelType_title_1,'Visible','on')
2445        FieldList_1=[set_field_list('U','V');{'C'};{'get_field...'}]; % standard menu for civx data
2446        CheckList_1=1;
2447        set(handles.FieldName_1,'Value',1); % velocity vector choice by default
2448    else
2449        set(handles.VelType_1,'Visible','off')
2450        set(handles.VelType_title_1,'Visible','off')
2451    end
2452else
2453    set(handles.VelType,'Visible','off')
2454    set(handles.VelType_title,'Visible','off')
2455end
2456
2457%% Detect the types of input files and set menus and default options in 'FieldName'
2458if (FieldNameRequest || VelTypeRequest) && numel(iview_netcdf)>=1
2459    set(handles.InputFields,'Visible','on')% set the frame InputFields visible
2460    if FieldNameRequest && isfield(SeriesData.FileInfo{iview_netcdf(1)},'ListVarName')
2461        set(handles.FieldName,'Visible','on')
2462        ListVarName=SeriesData.FileInfo{iview_netcdf(1)}.ListVarName;
2463        ind_var=get(handles.FieldName,'Value'); % indices of previously selected variables
2464        for ilist=1:numel(ind_var)
2465            if isempty(find(strcmp(FieldList{ind_var(ilist)},ListVarName)))
2466                FieldList={}; % previous choice not consistent with new input field
2467                set(handles.FieldName,'Value',1)
2468                break
2469            end
2470        end
2471        if ~isempty(FieldList)
2472            if isempty(find(strcmp(get(handles.Coord_x,'String'),ListVarName)))||...
2473                    isempty(find(strcmp(get(handles.Coord_y,'String'),ListVarName)))
2474                FieldList={};
2475                set(handles.Coord_x,'String','')
2476                set(handles.Coord_y,'String','')
2477            end
2478            Coord_z=get(handles.Coord_z,'String');
2479            if ~isempty(Coord_z) && isempty(find(strcmp(Coord_z,ListVarName)))
2480                FieldList={};
2481                set(handles.Coord_z,'String','')
2482            end
2483        end
2484    else
2485        set(handles.FieldName,'Visible','off')
2486    end
2487   
2488    set(handles_coord,'Visible','on')
2489    if isempty(find(strcmp('get_field...',FieldList)))
2490    FieldList=[FieldList;{'get_field...'}];%add 'get_field...' to the menu FieldName if it is not already
2491    end
2492    if FieldNameRequest_1 && numel(iview_netcdf)>=2
2493        set(handles.FieldName_1,'Visible','on')
2494        if CheckList_1==0        % not civ input made
2495            ListVarName=SeriesData.FileInfo{iview_netcdf(2)}.ListVarName;
2496            ind_var=get(handles.FieldName,'Value'); % indices of previously selected variables
2497            for ilist=1:numel(ind_var)
2498                if isempty(find(strcmp(FieldList{ind_var(ilist)},ListVarName)))
2499                    FieldList_1={}; % previous choice not consistent with new input field
2500                    set(handles.FieldName_1,'Value',1)
2501                    break
2502                end
2503            end
2504            warn_coord=0;
2505            if isempty(find(strcmp(get(handles.Coord_x,'String'),ListVarName)))||...
2506                    isempty(find(strcmp(get(handles.Coord_y,'String'),ListVarName)))
2507                warn_coord=1;
2508            end
2509            if ~isempty(Coord_z) && isempty(find(strcmp(Coord_z,ListVarName)))
2510                FieldList_1={};
2511                warn_coord=1;
2512            end
2513            if warn_coord
2514                msgbox_uvmat('WARNING','coordinate names do not exist in the second netcdf input file')
2515            end
2516           
2517            set(handles.FieldName_1,'Visible','on')
2518            set(handles.FieldName_1,'Value',1)
2519            set(handles.FieldName_1,'String',FieldList_1)
2520        end
2521    else
2522        set(handles.FieldName_1,'Visible','off')
2523    end
2524    if isempty(FieldList)
2525        set(handles.FieldName,'Visible','off')
2526    else
2527        set(handles.FieldName,'Visible','on')
2528        set(handles.FieldName,'String',FieldList)
2529    end
2530else
2531    set(handles.InputFields,'Visible','off')
2532end
2533
2534%% Introduce visibility of file overwrite option
2535if isfield(ParamOut,'CheckOverwriteVisible')&& strcmp(ParamOut.CheckOverwriteVisible,'on')
2536    set(handles.CheckOverwrite,'Visible','on')
2537else
2538    set(handles.CheckOverwrite,'Visible','off')
2539end
2540
2541%% Check whether alphabetical sorting of input Subdir is allowed by the Action fct  (for multiples series entries)
2542if isfield(ParamOut,'AllowInputSort')&&isequal(ParamOut.AllowInputSort,'on')&& size(Param.InputTable,1)>1
2543    [tild,iview]=sort(Param.InputTable(:,2)); % subdirectories sorted in alphabetical order
2544    set(handles.InputTable,'Data',Param.InputTable(iview,:));
2545    MinIndex_i=get(handles.MinIndex_i,'Data');
2546    MinIndex_j=get(handles.MinIndex_j,'Data');
2547    MaxIndex_i=get(handles.MaxIndex_i,'Data');
2548    MaxIndex_j=get(handles.MaxIndex_j,'Data');
2549    set(handles.MinIndex_i,'Data',MinIndex_i(iview,:));
2550    set(handles.MinIndex_j,'Data',MinIndex_j(iview,:));
2551    set(handles.MaxIndex_i,'Data',MaxIndex_i(iview,:));
2552    set(handles.MaxIndex_j,'Data',MaxIndex_j(iview,:));;
2553    TimeTable=get(handles.TimeTable,'Data');
2554    if size(TimeTable,1)<size(Param.InputTable,1)%if the time table is not complete, copy the missing lines from the previous ones
2555        for iline=size(TimeTable,1)+1:size(Param.InputTable,1)
2556            TimeTable(iline,:)=TimeTable(iline-1,:);
2557        end
2558    end
2559    set(handles.TimeTable,'Data',TimeTable(iview,:));% sort the time tables
2560    PairString=get(handles.PairString,'Data');
2561    set(handles.PairString,'Data',PairString(iview,:));
2562end
2563
2564%% Impose the whole input file index range if requested
2565if isfield(ParamOut,'WholeIndexRange')&&isequal(ParamOut.WholeIndexRange,'on')
2566    MinIndex_i=get(handles.MinIndex_i,'Data');
2567    MinIndex_j=get(handles.MinIndex_j,'Data');
2568    MaxIndex_i=get(handles.MaxIndex_i,'Data');
2569    MaxIndex_j=get(handles.MaxIndex_j,'Data');
2570    set(handles.num_first_i,'String',num2str(MinIndex_i(1)))% set first as the min index (for the first line)
2571    set(handles.num_last_i,'String',num2str(MaxIndex_i(1)))% set last as the max index (for the first line)
2572    set(handles.num_incr_i,'String','1')
2573    set(handles.num_first_j,'String',num2str(MinIndex_j(1)))% set first as the min index (for the first line)
2574    set(handles.num_last_j,'String',num2str(MaxIndex_j(1)))% set last as the max index (for the first line)
2575    set(handles.num_incr_j,'String','1')
2576else  % check index ranges
2577    first_i=1;last_i=1;first_j=1;last_j=1;
2578    if isfield(Param.IndexRange,'first_i')
2579        first_i=Param.IndexRange.first_i;
2580        last_i=Param.IndexRange.last_i;
2581    end
2582    if isfield(Param.IndexRange,'first_j')
2583        first_j=Param.IndexRange.first_j;
2584        last_j=Param.IndexRange.last_j;
2585    end
2586    if last_i < first_i || last_j < first_j , msgbox_uvmat('ERROR','last field number must be larger than the first one'),...
2587            set(handles.RUN, 'Enable','On'), set(handles.RUN,'BackgroundColor',[1 0 0]),return,end;
2588end
2589
2590%% enable or desable j index visibility
2591status_j='on'; % default
2592if isempty(find(~cellfun(@isempty,SeriesData.j1_series), 1)); % case of empty j indices
2593    status_j='off'; % no j index needed
2594elseif strcmp(get(handles.PairString,'Visible'),'on')
2595    check_burst=cellfun(@isempty,regexp(get(handles.PairString,'Data'),'^j')); % =0 for burst case, 1 otherwise
2596    if isempty(find(check_burst, 1))% if all pair string begins by j (burst)
2597        status_j='off'; % no j index needed for bust case
2598    end
2599end
2600enable_j(handles,status_j) % no j index needed
2601if isfield(ParamOut,'j_index_1')&& isfield(ParamOut,'j_index_2')%strcmp(ParamOut.Desable_j_index,'on')
2602    %status_j='off';
2603    set(handles.num_first_j,'String',num2str(ParamOut.j_index_1))
2604    set(handles.num_last_j,'String',num2str(ParamOut.j_index_2))
2605    set(handles.num_first_j,'enable','off')
2606    set(handles.num_last_j,'enable','off')
2607    set(handles.num_incr_j,'visible','off')
2608else
2609    set(handles.num_first_j,'enable','on')
2610    set(handles.num_last_j,'enable','on')
2611    set(handles.num_incr_j,'visible',status_j)
2612end
2613
2614%% NbSlice visibility
2615if isfield(ParamOut,'NbSlice') && (strcmp(ParamOut.NbSlice,'on')||isnumeric(ParamOut.NbSlice))
2616    set(handles.num_NbSlice,'Visible','on')
2617    set(handles.NbSlice_title,'Visible','on')
2618else
2619    set(handles.num_NbSlice,'Visible','off')
2620    set(handles.NbSlice_title,'Visible','off')
2621end
2622if isfield(ParamOut,'NbSlice') && isnumeric(ParamOut.NbSlice)
2623    set(handles.num_NbSlice,'String',num2str(ParamOut.NbSlice))
2624    set(handles.num_NbSlice,'Enable','off'); % NbSlice set by the activation of the Action function
2625else
2626    set(handles.num_NbSlice,'Enable','on'); % NbSlice can be modified on the GUI series
2627end
2628
2629%% Visibility of FieldTransform menu
2630FieldTransformVisible='off';  %hidden by default
2631if isfield(ParamOut,'FieldTransform')
2632    if ~strcmp(ParamOut.FieldTransform,'off')
2633    FieldTransformVisible='on'; 
2634    end
2635    if iscell(ParamOut.FieldTransform)
2636        SeriesData.TransformList=ParamOut.FieldTransform;
2637    end
2638    TransformName_Callback([],[], handles)
2639end
2640set(handles.FieldTransform,'Visible',FieldTransformVisible)
2641if isfield(ParamOut,'TransformPath');% record the path of transform function requested for compilation
2642    set(handles.TransformPath,'UserData',ParamOut.TransformPath)
2643else
2644    set(handles.TransformPath,'UserData',[])
2645end
2646
2647%% Visibility of projection object
2648ProjObjectVisible='off';  %hidden by default
2649if isfield(ParamOut,'ProjObject')
2650    ProjObjectVisible=ParamOut.ProjObject;
2651end
2652set(handles.CheckObject,'Visible',ProjObjectVisible)
2653if ~get(handles.CheckObject,'Value')
2654    ProjObjectVisible='off';
2655end
2656set(handles.ProjObject,'Visible',ProjObjectVisible)
2657set(handles.DeleteObject,'Visible',ProjObjectVisible)
2658set(handles.ViewObject,'Visible',ProjObjectVisible)
2659set(handles.EditObject,'Visible',ProjObjectVisible)
2660
2661%% Visibility of mask input
2662MaskVisible='off';  %hidden by default
2663if isfield(ParamOut,'Mask')
2664    MaskVisible=ParamOut.Mask;
2665end
2666set(handles.CheckMask,'Visible',MaskVisible);
2667%% Setting of expected iteration time
2668if isfield(ParamOut,'CPUTime')
2669    set(handles.num_CPUTime,'String',num2str(ParamOut.CPUTime));
2670end
2671
2672%% definition of the directory containing the output files
2673if  ~(isfield(SeriesData,'ActionName') && strcmp(ActionName,SeriesData.ActionName))
2674    OutputDirExt='.series'; % default
2675    if isfield(ParamOut,'OutputDirExt')&&~isempty(ParamOut.OutputDirExt)
2676        OutputDirExt=ParamOut.OutputDirExt;
2677    end
2678    set(handles.OutputDirExt,'String',OutputDirExt)
2679end
2680OutputDirVisible='off';
2681OutputSubDirMode='auto'; % default
2682SubDirOut='';
2683if isfield(ParamOut,'OutputSubDirMode')
2684    OutputSubDirMode=ParamOut.OutputSubDirMode;
2685end
2686InputTable=get(handles.InputTable,'Data');
2687switch OutputSubDirMode
2688    case 'auto'; % default
2689        OutputDirVisible='on';
2690        SubDir=InputTable(1:end,2); % set of subdirectories
2691        SubDirOut=SubDir{1};
2692        if numel(SubDir)>1
2693            for ilist=2:numel(SubDir)
2694                SubDirOut=[SubDirOut '-' regexprep(SubDir{ilist},'^/','')];
2695            end
2696        end
2697    case 'one'
2698        OutputDirVisible='on';
2699        SubDirOut=InputTable{1,2}; % use the first subdir name (+OutputDirExt) as output  subdirectory
2700    case 'two'
2701        OutputDirVisible='on';   
2702        SubDir=InputTable(1:2,2); % set of subdirectories
2703        SubDirOut=SubDir{1};
2704        if numel(SubDir)>1
2705                SubDirOut=[SubDirOut '-' regexprep(SubDir{2},'^/','')];
2706        end
2707    case 'last'
2708        OutputDirVisible='on';
2709        SubDirOut=InputTable{end,2}; % use the last subdir name (+OutputDirExt) as output  subdirectory
2710end
2711set(handles.OutputSubDir,'String',SubDirOut)
2712set(handles.OutputSubDir,'BackgroundColor',[1 1 1])% set edit box to white color to indicate refreshment
2713set(handles.OutputDirExt,'Visible',OutputDirVisible)
2714set(handles.OutputSubDir,'Visible',OutputDirVisible)
2715%set(handles.CheckOverwrite,'Visible',OutputDirVisible)
2716set(handles.OutputDir_title,'Visible',OutputDirVisible)
2717SeriesData.ActionName=ActionName; % record ActionName for next use
2718
2719
2720%% visibility of the run mode (local or background or cluster)
2721if strcmp(OutputSubDirMode,'none')
2722    RunModeVisible='off'; % only local mode available if no output file is produced
2723else
2724    RunModeVisible='on';
2725end
2726set(handles.RunMode,'Visible',RunModeVisible)
2727set(handles.ActionExt,'Visible',RunModeVisible)
2728set(handles.RunMode_title,'Visible',RunModeVisible)
2729set(handles.ActionExt_title,'Visible',RunModeVisible)
2730
2731
2732%% Expected nbre of output files
2733if isfield(ParamOut,'OutputFileMode')
2734    StatusData.OutputFileMode=ParamOut.OutputFileMode;
2735    set(handles.status,'UserData',StatusData)
2736end
2737
2738%% definition of an additional parameter set, determined by an ancillary GUI
2739if isfield(ParamOut,'ActionInput')
2740%     set(handles.ActionInput,'Visible','on')
2741    ParamOut.ActionInput.Program=ActionName; % record the program in ActionInput
2742    SeriesData.ActionInput=ParamOut.ActionInput;
2743else
2744%     set(handles.ActionInput,'Visible','off')
2745    if isfield(SeriesData,'ActionInput')
2746        SeriesData=rmfield(SeriesData,'ActionInput');
2747    end
2748end
2749set(handles.series,'UserData',SeriesData)
2750set(handles.ActionInput,'BackgroundColor',[1 0 0])
2751
2752%------------------------------------------------------------------------
2753% --- Executes on selection change in FieldName.
2754function FieldName_Callback(hObject, eventdata, handles)
2755%------------------------------------------------------------------------
2756field_str=get(handles.FieldName,'String');
2757field_index=get(handles.FieldName,'Value');
2758field=field_str{field_index(1)};
2759if isequal(field,'get_field...')
2760    SeriesData=get(handles.series,'UserData');
2761    % input line for which the field choice is relevant
2762    iview=find(ismember(SeriesData.FileType,{'netcdf','civx','civdata'})); % all nc files, icluding civ
2763    hget_field=findobj(allchild(0),'name','get_field');
2764    if ~isempty(hget_field)
2765        delete(hget_field)%delete opened versions of get_field
2766    end
2767    Param=read_GUI(handles.series);
2768    InputTable=Param.InputTable(iview,:);
2769    % check the existence of the first file in the series
2770    first_j=[];last_j=[];MinIndex_j=1;MaxIndex_j=1; % default setting for index j
2771    if isfield(Param.IndexRange,'first_j'); % if index j is used     
2772        first_j=Param.IndexRange.first_j;
2773        last_j=Param.IndexRange.last_j;
2774        MinIndex_j=Param.IndexRange.MinIndex_j(iview);
2775        MaxIndex_j=Param.IndexRange.MaxIndex_j(iview);
2776    end
2777    PairString='';
2778    if isfield(Param.IndexRange,'PairString'); PairString=Param.IndexRange.PairString{iview}; end
2779    [i1,i2,j1,j2] = get_file_index(Param.IndexRange.first_i,first_j,PairString);
2780    LineIndex=iview(1);
2781    if numel(iview)>1     
2782        answer=msgbox_uvmat('INPUT_TXT',['select the line of the input table:' num2str(iview)] ,num2str(iview(1)));
2783        LineIndex=str2num(answer);
2784%         InputLine=str2num(get(handles.InputLine,'String'));
2785%         if ismember(InputLine,iview)
2786%             LineIndex=InputLine;
2787%         end
2788    end
2789    FirstFileName=fullfile_uvmat(InputTable{LineIndex,1},InputTable{LineIndex,2},InputTable{LineIndex,3},...
2790        InputTable{LineIndex,5},InputTable{LineIndex,4},i1,i2,j1,j2);
2791    if exist(FirstFileName,'file')
2792        ParamIn.Title='get_field: pick input variables and coordinates for series processing';
2793        ParamIn.SeriesInput=1;
2794        GetFieldData=get_field(FirstFileName,ParamIn);
2795        FieldList={};
2796        if isfield(GetFieldData,'FieldOption')% if a field has been selected
2797        switch GetFieldData.FieldOption
2798            case 'vectors'
2799                UName=GetFieldData.PanelVectors.vector_x;
2800                VName=GetFieldData.PanelVectors.vector_y;
2801                YName={GetFieldData.Coordinates.Coord_y};
2802                FieldList={['vec(' UName ',' VName ')'];...
2803                    ['norm(' UName ',' VName ')'];...
2804                    UName;VName};
2805                set(handles.VelType,'Visible','off')
2806            case {'scalar'}
2807                FieldList=GetFieldData.PanelScalar.scalar;
2808                YName={GetFieldData.Coordinates.Coord_y};
2809                if ischar(FieldList)
2810                    FieldList={FieldList};
2811                end
2812                set(handles.VelType,'Visible','off')
2813            case 'civdata...'
2814                FieldList=[set_field_list('U','V') ;{'C'}];
2815                set(handles.FieldName,'Value',1) % set menu to 'velocity
2816                XName='X';
2817                YName='y';
2818                set(handles.VelType,'Visible','on')
2819        end
2820        set(handles.FieldName,'Value',1)
2821        set(handles.FieldName,'String',[FieldList; {'get_field...'}]);
2822        if ~strcmp(GetFieldData.FieldOption,'civdata...')
2823           if ~isempty(regexp(FieldList{1},'^vec'))
2824                set(handles.FieldName,'Value',1)
2825           else
2826                set(handles.FieldName,'Value',1:numel(FieldList))%select all input fields by default
2827           end
2828            XName=GetFieldData.Coordinates.Coord_x;
2829            YName=GetFieldData.Coordinates.Coord_y;
2830            TimeNameStr=GetFieldData.Time.SwitchVarIndexTime;
2831            % get the time info                     
2832            TimeTable=get(handles.TimeTable,'Data');
2833            switch TimeNameStr
2834                case 'file index'
2835                    TimeName='';
2836                case 'attribute'
2837                    TimeName=['att:' GetFieldData.Time.TimeName];
2838                    % update the time table
2839                    TimeTable{LineIndex,2}=get_time(Param.IndexRange.MinIndex_i(LineIndex),MinIndex_j,PairString,InputTable,SeriesData.FileInfo{LineIndex},GetFieldData.Time.TimeName);  % Min time     
2840                    TimeTable{LineIndex,3}=get_time(Param.IndexRange.first_i,first_j,PairString,InputTable,SeriesData.FileInfo{LineIndex},GetFieldData.Time.TimeName);  % first time             
2841                    TimeTable{LineIndex,4}=get_time(Param.IndexRange.last_i,last_j,PairString,InputTable,SeriesData.FileInfo{LineIndex},GetFieldData.Time.TimeName);  % last time                     
2842                    TimeTable{LineIndex,5}=get_time(Param.IndexRange.MaxIndex_i(LineIndex),MaxIndex_j,PairString,InputTable,SeriesData.FileInfo{LineIndex},GetFieldData.Time.TimeName);  % Max time
2843                case 'variable'
2844                    set(handles.TimeName,'String',['var:' GetFieldData.Time.TimeName])
2845                    set(handles.NomType,'String','*')
2846                    set(handles.RootFile,'String',[get(handles.RootFile,'String') get(handles.FileIndex,'String')])% A VERIFIER !!!!!!
2847                    set(handles.FileIndex,'String','')
2848                    ParamIn.TimeVarName=GetFieldData.Time.TimeName;
2849                case 'matrix_index'
2850                    TimeName=['dim:' GetFieldData.Time.TimeName];
2851                    set(handles.NomType,'String','*')
2852                    set(handles.RootFile,'String',[get(handles.RootFile,'String') get(handles.FileIndex,'String')])
2853                    set(handles.FileIndex,'String','')
2854                    ParamIn.TimeDimName=GetFieldData.Time.TimeName;
2855            end
2856            TimeTable{LineIndex,1}=TimeName;
2857            set(handles.TimeTable,'Data',TimeTable);
2858        end
2859        set(handles.Coord_x,'String',XName)
2860        set(handles.Coord_y,'String',YName)
2861        set(handles.Coord_x,'Visible','on')
2862        set(handles.Coord_y,'Visible','on')
2863        end
2864    else
2865        msgbox_uvmat('ERROR',[FirstFileName ' does not exist'])
2866    end
2867end
2868
2869
2870function [TimeValue,DtValue]=get_time(ref_i,ref_j,PairString,InputTable,FileInfo,TimeName,DtName)
2871[i1,i2,j1,j2] = get_file_index(ref_i,ref_j,PairString);
2872FileName=fullfile_uvmat(InputTable{1},InputTable{2},InputTable{3},InputTable{5},InputTable{4},i1,i2,j1,j2);
2873Data=nc2struct(FileName,[]);
2874TimeValue=[];
2875DtValue=[];
2876if isequal(FileInfo.FileType,'civdata')
2877    if ismember(TimeName,{'civ1','filter1'})
2878        if isfield(Data,'Civ1_Time')
2879        TimeValue=Data.Civ1_Time;
2880        end
2881        if isfield(Data,'Civ1_Dt')
2882        DtValue=Data.Civ1_Dt;
2883        end
2884    else
2885        if isfield(Data,'Civ2_Time')
2886        TimeValue=Data.Civ2_Time;
2887        end
2888        if isfield(Data,'Civ2_Dt')
2889        DtValue=Data.Civ2_Dt;
2890        end
2891    end
2892else
2893    if ~isempty(TimeName)&& isfield(Data,TimeName)
2894        TimeValue=Data.(TimeName);
2895    end
2896    if exist('DtName','var') && isfield(Data,DtName)
2897        DtValue=Data.(DtName);
2898    end
2899end
2900
2901%------------------------------------------------------------------------
2902% --- Executes on selection change in FieldName_1.
2903function FieldName_1_Callback(hObject, eventdata, handles)
2904%------------------------------------------------------------------------
2905field_str=get(handles.FieldName_1,'String');
2906field_index=get(handles.FieldName_1,'Value');
2907field=field_str{field_index(1)};
2908if isequal(field,'get_field...')
2909    hget_field=findobj(allchild(0),'name','get_field');
2910    if ~isempty(hget_field)
2911        delete(hget_field)%delete opened versions of get_field
2912    end
2913    Param=read_GUI(handles.series);
2914    Param.InputTable=Param.InputTable(1,:);
2915    % check the existence of the first file in the series
2916    first_j=[];
2917    if isfield(Param.IndexRange,'first_j'); first_j=Param.IndexRange.first_j; end
2918    if isfield(Param.IndexRange,'last_j'); last_j=Param.IndexRange.last_j; end
2919    PairString='';
2920    if isfield(Param.IndexRange,'PairString'); PairString=Param.IndexRange.PairString; end
2921    [i1,i2,j1,j2] = get_file_index(Param.IndexRange.first_i,first_j,PairString);
2922    FirstFileName=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},...
2923        Param.InputTable{1,5},Param.InputTable{1,4},i1,i2,j1,j2);
2924    if exist(FirstFileName,'file')
2925        ParamIn.SeriesInput=1;
2926        GetFieldData=get_field(FirstFileName,ParamIn);
2927        FieldList={};
2928        switch GetFieldData.FieldOption
2929            case 'vectors'
2930                UName=GetFieldData.PanelVectors.vector_x;
2931                VName=GetFieldData.PanelVectors.vector_y;
2932                FieldList={['vec(' UName ',' VName ')'];...
2933                    ['norm(' UName ',' VName ')'];...
2934                    UName;VName};
2935            case {'scalar','pick variables'}
2936                FieldList=GetFieldData.PanelScalar.scalar;
2937                if ischar(FieldList)
2938                    FieldList={FieldList};
2939                end
2940            case '1D plot'
2941
2942            case 'civdata...'
2943                FieldList=set_field_list('U','V','C');
2944                set(handles.FieldName,'Value',2) % set menu to 'velocity
2945        end
2946        if ~strcmp(GetFieldData.FieldOption,'civdata...')
2947            TimeNameStr=GetFieldData.Time.SwitchVarIndexTime;
2948            switch TimeNameStr
2949                case 'file index'
2950                    set(handles.TimeName,'String','');
2951                case 'attribute'
2952                    set(handles.TimeName,'String',['att:' GetFieldData.Time.TimeName]);
2953                case 'variable'
2954                    set(handles.TimeName,'String',['var:' GetFieldData.Time.TimeName])
2955                    set(handles.NomType,'String','*')
2956                    set(handles.RootFile,'String',[get(handles.RootFile,'String') get(handles.FileIndex,'String')])% A VERIFIER !!!!!!
2957                    set(handles.FileIndex,'String','')
2958                    ParamIn.TimeVarName=GetFieldData.Time.TimeName;
2959                case 'matrix_index'
2960                    set(handles.TimeName,'String',['dim:' GetFieldData.Time.TimeName]);
2961                    set(handles.NomType,'String','*')
2962                    set(handles.RootFile,'String',[get(handles.RootFile,'String') get(handles.FileIndex,'String')])
2963                    set(handles.FileIndex,'String','')
2964                    ParamIn.TimeDimName=GetFieldData.Time.TimeName;
2965            end
2966        end
2967        set(handles.FieldName_1,'Value',1)
2968        set(handles.FieldName_1,'String',[FieldList; {'get_field...'}]);
2969    end
2970end   
2971
2972
2973%%%%%%%%%%%%%
2974function [ind_remove]=find_pairs(dirpair,ind_i,last_i)
2975indsel=ind_i;
2976indiff=diff(ind_i); % test index increment to detect multiplets (several pairs with the same index ind_i) and holes in the series
2977indiff=[1 indiff last_i-ind_i(end)+1]; % for testing gaps with the imposed bounds
2978if ~isempty(indiff)
2979    indiff2=diff(indiff);
2980    indiffp=[indiff2 1];
2981    indiffm=[1 indiff2];
2982    ind_multi_m=find((indiff==0)&(indiffm<0))-1; % indices of first members of multiplets
2983    ind_multi_p=find((indiff==0)&(indiffp>0)); % indices of last members of multiplets
2984    %for each multiplet, select the most recent file
2985    ind_remove=[];
2986    for i=1:length(ind_multi_m)
2987        ind_pairs=ind_multi_m(i):ind_multi_p(i);
2988        for imulti=1:length(ind_pairs)
2989            datepair(imulti)=datenum(dirpair(ind_pairs(imulti)).date); % dates of creation
2990        end
2991        [datenew,indsort2]=sort(datepair); % sort the multiplet by creation date
2992        ind_s=indsort2(1:end-1); %
2993        ind_remove=[ind_remove ind_pairs(ind_s)]; % remove these indices, leave the last one
2994    end
2995end
2996
2997%------------------------------------------------------------------------
2998% --- determine the list of index pairstring of processing file
2999function [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)
3000%------------------------------------------------------------------------
3001num_i1=num_i; % set of first image numbers by default
3002num_i2=num_i;
3003num_j1=num_j;
3004num_j2=num_j;
3005num_i_out=num_i;
3006num_j_out=num_j;
3007% if isequal (NomType,'_1-2_1') || isequal (NomType,'_1-2')
3008if isequal(mode,'series(Di)')
3009    num_i1_line=num_i+ind_shift(3); % set of first image numbers
3010    num_i2_line=num_i+ind_shift(4);
3011    % adjust the first and last field number
3012        indsel=find(num_i1_line >= 1);
3013    num_i_out=num_i(indsel);
3014    num_i1_line=num_i1_line(indsel);
3015    num_i2_line=num_i2_line(indsel);
3016    num_j1=meshgrid(num_j,ones(size(num_i1_line)));
3017    num_j2=meshgrid(num_j,ones(size(num_i1_line)));
3018    [xx,num_i1]=meshgrid(num_j,num_i1_line);
3019    [xx,num_i2]=meshgrid(num_j,num_i2_line);
3020elseif isequal (mode,'series(Dj)')||isequal (mode,'bursts')
3021    if isequal(mode,'bursts') %case of bursts (png_old or png_2D)
3022        num_j1=ind_shift(1)*ones(size(num_i));
3023        num_j2=ind_shift(2)*ones(size(num_i));
3024    else
3025        num_j1_col=num_j+ind_shift(1); % set of first image numbers
3026        num_j2_col=num_j+ind_shift(2);
3027        % adjust the first field number
3028        indsel=find((num_j1_col >= 1));   
3029        num_j_out=num_j(indsel);
3030        num_j1_col=num_j1_col(indsel);
3031        num_j2_col=num_j2_col(indsel);
3032        [num_i1,num_j1]=meshgrid(num_i,num_j1_col);
3033        [num_i2,num_j2]=meshgrid(num_i,num_j2_col);
3034    end   
3035end
3036
3037%------------------------------------------------------------------------
3038% --- Executes on button press in CheckObject.
3039function CheckObject_Callback(hObject, eventdata, handles)
3040%------------------------------------------------------------------------
3041hset_object=findobj(allchild(0),'tag','set_object'); % find the set_object interface handle
3042if get(handles.CheckObject,'Value')
3043    SeriesData=get(handles.series,'UserData');
3044    if isfield(SeriesData,'ProjObject') && ~isempty(SeriesData.ProjObject)
3045        set(handles.ViewObject,'Value',1)
3046        ViewObject_Callback(hObject, eventdata, handles)
3047    else
3048        if ishandle(hset_object)
3049            uistack(hset_object,'top')% show the GUI set_object if opened
3050        else
3051            %get the object file
3052            InputTable=get(handles.InputTable,'Data');
3053            defaultname=InputTable{1,1};
3054            if isempty(defaultname)
3055                defaultname={''};
3056            end
3057            fileinput=uigetfile_uvmat('pick a xml object file (or use uvmat to create it)',defaultname,'.xml');
3058            if isempty(fileinput)% exit if no object file is selected
3059                set(handles.CheckObject,'Value',0)
3060                return
3061            end
3062            %read the file
3063            data=xml2struct(fileinput);
3064            if ~isfield(data,'Type')
3065                msgbox_uvmat('ERROR',[fileinput ' is not an object xml file'])
3066                set(handles.CheckObject,'Value',0)
3067                return
3068            end
3069            if ~isfield(data,'ProjMode')
3070                data.ProjMode='none';
3071            end
3072            hset_object=set_object(data); % call the set_object interface
3073            set(hset_object,'Name','set_object_series')% name to distinguish from set_object used with uvmat
3074        end
3075        ProjObject=read_GUI(hset_object);
3076        set(handles.ProjObject,'String',ProjObject.Name); % display the object name
3077        SeriesData=get(handles.series,'UserData');
3078        SeriesData.ProjObject=ProjObject;
3079        set(handles.series,'UserData',SeriesData);
3080    end
3081    set(handles.EditObject,'Visible','on');
3082    set(handles.DeleteObject,'Visible','on');
3083    set(handles.ViewObject,'Visible','on');
3084    set(handles.ProjObject,'Visible','on');
3085else
3086    set(handles.EditObject,'Visible','off');
3087    set(handles.DeleteObject,'Visible','off');
3088    set(handles.ViewObject,'Visible','off');
3089    if ~ishandle(hset_object)
3090        set(handles.ViewObject,'Value',0);
3091    end
3092    set(handles.ProjObject,'Visible','off');
3093end
3094
3095%------------------------------------------------------------------------
3096% --- Executes on button press in ViewObject.
3097%------------------------------------------------------------------------
3098function ViewObject_Callback(hObject, eventdata, handles)
3099
3100UserData=get(handles.series,'UserData');
3101hset_object=findobj(allchild(0),'Tag','set_object');
3102if ~isempty(hset_object)
3103    delete(hset_object)% refresh set_object if already opened
3104end
3105hset_object=set_object(UserData.ProjObject);
3106set(hset_object,'Name','view_object_series')
3107
3108
3109%------------------------------------------------------------------------
3110% --- Executes on button press in EditObject.
3111function EditObject_Callback(hObject, eventdata, handles)
3112%------------------------------------------------------------------------
3113if get(handles.EditObject,'Value')
3114    set(handles.ViewObject,'Value',0)
3115    UserData=get(handles.series,'UserData');
3116    hset_object=set_object(UserData.ProjObject);
3117    set(hset_object,'Name','edit_object_series')
3118    set(get(hset_object,'Children'),'Enable','on')
3119else
3120    hset_object=findobj(allchild(0),'Tag','set_object');
3121    if ~isempty(hset_object)
3122        set(get(hset_object,'Children'),'Enable','off')
3123    end
3124end
3125
3126%------------------------------------------------------------------------
3127% --- Executes on button press in DeleteObject.
3128function DeleteObject_Callback(hObject, eventdata, handles)
3129%------------------------------------------------------------------------
3130SeriesData=get(handles.series,'UserData');
3131SeriesData.ProjObject=[];
3132set(handles.series,'UserData',SeriesData)
3133set(handles.ProjObject,'String','')
3134set(handles.ProjObject,'Visible','off')
3135set(handles.CheckObject,'Value',0)
3136set(handles.ViewObject,'Visible','off')
3137set(handles.EditObject,'Visible','off')
3138hset_object=findobj(allchild(0),'name','set_object_series');
3139if ~isempty(hset_object)
3140    delete(hset_object)
3141end
3142set(handles.DeleteObject,'Visible','off')
3143
3144%------------------------------------------------------------------------
3145% --- Executed when CheckMask is activated
3146%------------------------------------------------------------------------
3147function CheckMask_Callback(hObject, eventdata, handles)
3148
3149if get(handles.CheckMask,'Value')
3150    InputTable=get(handles.InputTable,'Data');
3151    nbview=size(InputTable,1);
3152    MaskTable=cell(nbview,1); % default
3153    ListMask=cell(nbview,1); % default
3154    MaskData=get(handles.MaskTable,'Data');
3155    MaskData(size(MaskData,1):nbview,1)=cell(size(MaskData,1):nbview,1); % complement if undefined lines
3156    for iview=1:nbview
3157        ListMask{iview,1}=num2str(iview);
3158        RootPath=InputTable{iview,1};
3159        if ~isempty(RootPath)
3160            if isempty(MaskData{iview})
3161                SubDir=InputTable{iview,2};
3162                MaskPath=fullfile(RootPath,[regexprep(SubDir,'\..*','') '.mask']); % take the root part of SubDir, before the first dot '.'
3163                if exist(MaskPath,'dir')
3164                    ListStruct=dir(MaskPath); % look for a mask file
3165                    ListCells=struct2cell(ListStruct); % transform dir struct to a cell arrray
3166                    check_dir=cell2mat(ListCells(4,:)); % =1 for directories, =0 for files
3167                    ListFiles=ListCells(1,:); % list of file and dri names
3168                    ListFiles=ListFiles(~check_dir); % list of file names (excluding dir)
3169                    mdetect=0;
3170                    if ~isempty(ListFiles)
3171                        for ifile=1:numel(ListFiles)
3172                            [tild,tild,MaskFile{ifile},i1_series,i2_series,j1_series,j2_series,MaskNomType,MaskFileType]=find_file_series(MaskPath,ListFiles{ifile},0);
3173                            if strcmp(MaskFileType,'image') && isempty(i2_series) && isempty(j2_series)
3174                                mdetect=1;
3175                                MaskName=ListFiles{ifile};
3176                            end
3177                            if ~strcmp(MaskFile{ifile},MaskFile{1})
3178                                mdetect=0; % cancel detection test in case of multiple masks, use the brower for selection
3179                                break
3180                            end
3181                        end
3182                    end
3183                    if mdetect==1
3184                        MaskName=fullfile(MaskPath,'mask_1.png');
3185                    else
3186                        MaskName=uigetfile_uvmat('select a mask file:',MaskPath,'image');
3187                    end
3188                else
3189                    MaskName=uigetfile_uvmat('select a mask file:',RootPath,'image');
3190                end
3191                MaskTable{iview,1}=MaskName ;
3192                ListMask{iview,1}=num2str(iview);
3193            end
3194        end
3195    end
3196    set(handles.MaskTable,'Data',MaskTable)
3197    set(handles.MaskTable,'Visible','on')
3198    set(handles.MaskBrowse,'Visible','on')
3199    set(handles.ListMask,'Visible','on')
3200    set(handles.ListMask,'String',ListMask)
3201    set(handles.ListMask,'Value',1)
3202else
3203    set(handles.MaskTable,'Visible','off')
3204    set(handles.MaskBrowse,'Visible','off')
3205    set(handles.ListMask,'Visible','off')
3206end
3207
3208%------------------------------------------------------------------------
3209% --- Executes on button press in MaskBrowse.
3210%------------------------------------------------------------------------
3211function MaskBrowse_Callback(hObject, eventdata, handles)
3212
3213InputTable=get(handles.InputTable,'Data');
3214iview=get(handles.ListMask,'Value');
3215RootPath=InputTable{iview,1};
3216MaskName=uigetfile_uvmat('select a mask file:',RootPath,'image');
3217if ~isempty(MaskName)
3218    MaskTable=get(handles.MaskTable,'Data');
3219    MaskTable{iview,1}=MaskName ;
3220    set(handles.MaskTable,'Data',MaskTable)
3221end
3222
3223%------------------------------------------------------------------------
3224% --- Executes when selected cell(s) is changed in MaskTable.
3225%------------------------------------------------------------------------
3226function MaskTable_CellSelectionCallback(hObject, eventdata, handles)
3227
3228if numel(eventdata.Indices)>=1
3229set(handles.ListMask,'Value',eventdata.Indices(1))
3230end
3231
3232%-------------------------------------------------------------------
3233function MenuHelp_Callback(hObject, eventdata, handles)
3234%-------------------------------------------------------------------
3235
3236
3237% path_to_uvmat=which ('uvmat'); % check the path of uvmat
3238% pathelp=fileparts(path_to_uvmat);
3239% helpfile=fullfile(pathelp,'uvmat_doc','uvmat_doc.html');
3240% 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')
3241% else
3242%     addpath (fullfile(pathelp,'uvmat_doc'))
3243%     web([helpfile '#series'])
3244% end
3245
3246%-------------------------------------------------------------------
3247% --- Executes on selection change in TransformName.
3248function TransformName_Callback(hObject, eventdata, handles)
3249%----------------------------------------------------------------------
3250TransformList=get(handles.TransformName,'String');
3251TransformIndex=get(handles.TransformName,'Value');
3252TransformName=TransformList{TransformIndex};
3253TransformPathList=get(handles.TransformName,'UserData');
3254nb_builtin_transform=4;
3255if isequal(TransformName,'more...');     
3256    FileName=uigetfile_uvmat('Pick a transform function',get(handles.TransformPath,'String'),'.m');
3257    if isempty(FileName)
3258        return     %browser closed without choice
3259    end
3260    [TransformPath,TransformName,TransformExt]=fileparts(FileName); % removes extension .m
3261    if ~strcmp(TransformExt,'.m')
3262        msgbox_uvmat('ERROR','a Matlab function .m must be introduced');
3263        return
3264    end
3265     % insert the choice in the menu
3266    TransformIndex=find(strcmp(TransformName,TransformList),1); % look for the selected function in the menu Action
3267    if isempty(TransformIndex)%the input string does not exist in the menu
3268        TransformIndex= length(TransformList);
3269        TransformList=[TransformList(1:end-1);{TransformName};TransformList(end)]; % the selected function is appended in the menu, before the last item 'more...'
3270        set(handles.TransformName,'String',TransformList)
3271        TransformPathList=[TransformPathList;{TransformPath}];
3272    else% the input function already exist, we update its path (possibly new)
3273        TransformPathList{TransformIndex}=TransformPath; %
3274        set(handles.TransformName,'Value',TransformIndex)
3275    end
3276   % save the new menu in the personal file 'uvmat_perso.mat'
3277   dir_perso=prefdir; % personal Matalb directory
3278   profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
3279   if exist(profil_perso,'file')
3280       for ilist=nb_builtin_transform+1:numel(TransformPathList)
3281           TransformListUser{ilist-nb_builtin_transform}=TransformList{ilist};
3282           TransformPathListUser{ilist-nb_builtin_transform}=TransformPathList{ilist};
3283       end
3284       TransformPathListUser=TransformPathListUser';
3285       TransformListUser=TransformListUser';
3286       save (profil_perso,'TransformPathListUser','TransformListUser','-append'); % store the root name for future opening of uvmat
3287   end
3288end
3289
3290%display the current function path
3291set(handles.TransformPath,'String',TransformPathList{TransformIndex}); % show the path to the senlected function
3292set(handles.TransformName,'UserData',TransformPathList);
3293
3294%% create the function handle of the selected fct
3295if ~isempty(TransformName)
3296    if ~exist(TransformPathList{TransformIndex},'dir')
3297        msgbox_uvmat('ERROR',['The prescribed transform function path ' TransformPathList{TransformIndex} ' does not exist']);
3298        return
3299    end
3300    current_dir=pwd; % current working dir
3301    cd(TransformPathList{TransformIndex})
3302    transform_handle=str2func(TransformName);
3303    cd(current_dir)
3304    Field.Action.RUN=0;% indicate that the transform fct is called only to get input param
3305    SeriesData=get(handles.series,'UserData');
3306    ParamIn=[];
3307    if isfield(SeriesData,'TransformInput')
3308        ParamIn.TransformInput=SeriesData.TransformInput;
3309    end
3310    DataOut=feval(transform_handle,Field,ParamIn);% execute the transform fct to get the required conditions
3311    Field.Action.RUN=0; % indicate that the transform fct is called only to get input param
3312    DataOut=feval(transform_handle,Field,[]); % execute the transform fct to get the required conditions
3313    if isfield(DataOut,'TransformInput')%  used to add transform parameters at selection of the transform fct
3314        SeriesData.TransformInput=DataOut.TransformInput;
3315        set(handles.series,'UserData',SeriesData)
3316    end
3317end
3318
3319%------------------------------------------------------------------------
3320% --- fct activated by the upper bar menu ExportConfig
3321%------------------------------------------------------------------------
3322function MenuDisplayConfig_Callback(hObject, eventdata, handles)
3323
3324global Param
3325Param=read_GUI_series(handles);
3326evalin('base','global Param')%make CurData global in the workspace
3327display('current series config :')
3328evalin('base','Param') %display CurData in the workspace
3329commandwindow; % brings the Matlab command window to the front
3330
3331%------------------------------------------------------------------------
3332% --- fct activated by the upper bar menu InportConfig: import
3333%     menu settings from an xml file (stored in /0_XML for each run)
3334%------------------------------------------------------------------------
3335function MenuImportConfig_Callback(hObject, eventdata, handles)
3336
3337%% use a browser to choose the xml file containing the processing config
3338InputTable=get(handles.InputTable,'Data');
3339oldfile=InputTable{1,1}; % current path in InputTable
3340if isempty(oldfile)
3341    % use a file name stored in prefdir
3342    dir_perso=prefdir;
3343    profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
3344    if exist(profil_perso,'file')
3345        h=load (profil_perso);
3346        if isfield(h,'RootPath') && ischar(h.RootPath)
3347            oldfile=h.RootPath;
3348        end
3349    end
3350end
3351filexml=uigetfile_uvmat('pick a xml parameter file',oldfile,'.xml'); % get the xml file containing processing parameters
3352if isempty(filexml), return, end % quit function if an xml file has not been opened
3353
3354%% fill the GUI series with the content of the xml file
3355Param=xml2struct(filexml); % read the input xml file as a Matlab structure
3356
3357% ask to stop current Action if button RUN is in action (another process is already running)
3358if isequal(get(handles.RUN,'Value'),1)
3359    answer= msgbox_uvmat('INPUT_Y-N','stop current Action process?');
3360    if strcmp(answer,'Yes')
3361        STOP_Callback(hObject, eventdata, handles)
3362    else
3363        return
3364    end
3365end
3366Param.Action.RUN=0; % desactivate the input RUN=1
3367
3368fill_GUI(Param,handles.series)% fill the elements of the GUI series with the input parameters
3369SeriesData=get(handles.series,'UserData');
3370if isfield(Param,'InputFields')
3371    ListField=Param.InputFields.FieldName;
3372    if ischar(ListField),ListField={ListField}; end
3373    set(handles.FieldName,'String',[ListField;{'get-field...'}])
3374     set(handles.FieldName,'Value',1:numel(ListField))
3375     set(handles.FieldName,'Visible','on')
3376end       
3377if isfield(Param,'ActionInput')%  introduce  parameters specific to an Action fct, for instance PIV parameters
3378%     set(handles.ActionInput,'Visible','on')
3379%     set(handles.ActionInput,'Value',0)
3380    Param.ActionInput.ConfigSource=filexml; % record the source of config for future info
3381    SeriesData.ActionInput=Param.ActionInput;
3382end
3383if isfield(Param,'TransformInput')%  introduce  parameters specific to a transform fct
3384    SeriesData.TransformInput=Param.TransformInput;
3385end
3386if isfield(Param,'ProjObject') %introduce projection object if relevant
3387    SeriesData.ProjObject=Param.ProjObject;
3388end
3389set(handles.series,'UserData',SeriesData)
3390if isfield(Param,'CheckObject') && isequal(Param.CheckObject,1)
3391    set(handles.ProjObject,'String',Param.ProjObject.Name)
3392    set(handles.ViewObject,'Visible','on')
3393    set(handles.EditObject,'Visible','on')
3394    set(handles.DeleteObject,'Visible','on')
3395else     
3396    set(handles.ProjObject,'String','')
3397    set(handles.ProjObject,'Visible','off')
3398    set(handles.ViewObject,'Visible','off')
3399    set(handles.EditObject,'Visible','off')
3400    set(handles.DeleteObject,'Visible','off')     
3401end     
3402set(handles.REFRESH,'BackgroundColor',[1 0 1]); % paint REFRESH button in magenta to indicate that it should be activated
3403
3404
3405%------------------------------------------------------------------------
3406% --- Executes when the GUI series is resized.
3407%------------------------------------------------------------------------
3408function series_ResizeFcn(hObject, eventdata, handles)
3409
3410%% input table
3411set(handles.InputTable,'Unit','pixel')
3412Pos=get(handles.InputTable,'Position');
3413set(handles.InputTable,'Unit','normalized')
3414ColumnWidth=round([0.5 0.14 0.14 0.14 0.08]*(Pos(3)-52));
3415ColumnWidth=num2cell(ColumnWidth);
3416set(handles.InputTable,'ColumnWidth',ColumnWidth)
3417
3418%% MinIndex_j and MaxIndex_i
3419unit=get(handles.MinIndex_i,'Unit');
3420set(handles.MinIndex_i,'Unit','pixel')
3421Pos=get(handles.MinIndex_i,'Position');
3422set(handles.MinIndex_i,'Unit',unit)
3423set(handles.MinIndex_i,'ColumnWidth',{Pos(3)-18})
3424set(handles.MaxIndex_i,'ColumnWidth',{Pos(3)-18})
3425set(handles.MinIndex_j,'ColumnWidth',{Pos(3)-18})
3426set(handles.MaxIndex_j,'ColumnWidth',{Pos(3)-18})
3427
3428%% TimeTable
3429set(handles.TimeTable,'Unit','pixel')
3430Pos=get(handles.TimeTable,'Position');
3431set(handles.TimeTable,'Unit','normalized')
3432% ColumnWidth=get(handles.TimeTable,'ColumnWidth');
3433ColumnWidth=num2cell(floor([0.2 0.2 0.2 0.2 0.2]*(Pos(3)-20)));
3434set(handles.TimeTable,'ColumnWidth',ColumnWidth)
3435
3436
3437%% PairString
3438set(handles.PairString,'Unit','pixel')
3439Pos=get(handles.PairString,'Position');
3440set(handles.PairString,'Unit','normalized')
3441set(handles.PairString,'ColumnWidth',{Pos(3)-5})
3442
3443%% MaskTable
3444set(handles.MaskTable,'Unit','pixel')
3445Pos=get(handles.MaskTable,'Position');
3446set(handles.MaskTable,'Unit','normalized')
3447set(handles.MaskTable,'ColumnWidth',{Pos(3)-5})
3448
3449%------------------------------------------------------------------------
3450% --- Executes on button press in status.
3451%------------------------------------------------------------------------
3452function status_Callback(hObject, eventdata, handles)
3453
3454if get(handles.status,'Value')
3455    set(handles.status,'BackgroundColor',[1 1 0])
3456    drawnow
3457    Param=read_GUI(handles.series);
3458    RootPath=Param.InputTable{1,1};
3459    if ~isfield(Param,'OutputSubDir')   
3460        msgbox_uvmat('ERROR','no standard sub-directory definition for output files, use a browser to check the output')
3461        set(handles.status,'BackgroundColor',[0 1 0])
3462        return
3463    end
3464    OutputSubDir=[Param.OutputSubDir Param.OutputDirExt]; % subdirectory for output files
3465    OutputDir=fullfile(RootPath,OutputSubDir);
3466    if exist(OutputDir,'dir')
3467        uigetfile_uvmat('status_display',OutputDir)
3468    else
3469        msgbox_uvmat('ERROR','output folder not created yet: calculation did not start')
3470        set(handles.status,'BackgroundColor',[0 1 0])
3471    end
3472else
3473    %% delete current display fig if selection is off
3474    set(handles.status,'BackgroundColor',[0 1 0])
3475    hfig=findobj(allchild(0),'name','status_display');
3476    if ~isempty(hfig)
3477        delete(hfig)
3478    end
3479    return
3480end
3481
3482
3483%------------------------------------------------------------------------   
3484% launched by selecting a file on the list
3485%------------------------------------------------------------------------
3486function view_file(hObject, eventdata)
3487
3488list=get(hObject,'String');
3489index=get(hObject,'Value');
3490rootroot=get(hObject,'UserData');
3491selectname=list{index};
3492ind_dot=regexp(selectname,'\.\.\.');
3493if ~isempty(ind_dot)
3494    selectname=selectname(1:ind_dot-1);
3495end
3496FullSelectName=fullfile(rootroot,selectname);
3497if exist(FullSelectName,'dir')% a directory has been selected
3498    ListFiles=dir(FullSelectName);
3499    ListDisplay=cell(numel(ListFiles),1);
3500    for ilist=2:numel(ListDisplay)% suppress the first line '.'
3501        ListDisplay{ilist-1}=ListFiles(ilist).name;
3502    end
3503    set(hObject,'Value',1)
3504    set(hObject,'String',ListDisplay)
3505    if strcmp(selectname,'..')
3506        FullSelectName=fileparts(fileparts(FullSelectName));
3507    end
3508    set(hObject,'UserData',FullSelectName)
3509    hfig=get(hObject,'parent');
3510    htitlebox=findobj(hfig,'tag','titlebox');   
3511    set(htitlebox,'String',FullSelectName)
3512elseif exist(FullSelectName,'file')%visualise the vel field if it exists
3513    FileInfo=get_file_info(FullSelectName);   
3514    if strcmp(FileInfo.FileType,'txt')
3515        edit(FullSelectName)
3516    elseif strcmp(FileInfo.FileType,'xml')
3517        editxml(FullSelectName)
3518    else
3519        uvmat(FullSelectName)
3520    end
3521    set(gcbo,'Value',1)
3522end
3523
3524
3525%------------------------------------------------------------------------   
3526% launched by refreshing the status figure
3527%------------------------------------------------------------------------
3528function refresh_GUI(hfig)
3529
3530htitlebox=findobj(hfig,'tag','titlebox');
3531hlist=findobj(hfig,'tag','list');
3532hseries=findobj(allchild(0),'tag','series');
3533hstatus=findobj(hseries,'tag','status');
3534StatusData=get(hstatus,'UserData');
3535OutputDir=get(htitlebox,'String');
3536if ischar(OutputDir),OutputDir={OutputDir};end
3537ListFiles=dir(OutputDir{1});
3538if numel(ListFiles)<1
3539    return
3540end
3541ListFiles(1)=[]; % removes the first line ='.'
3542ListDisplay=cell(numel(ListFiles),1);
3543testrecent=0;
3544datnum=zeros(numel(ListDisplay),1);
3545for ilist=1:numel(ListDisplay)
3546    ListDisplay{ilist}=ListFiles(ilist).name;
3547      if ~ListFiles(ilist).isdir && isfield(ListFiles(ilist),'datenum')
3548            datnum(ilist)=ListFiles(ilist).datenum; % only available in recent matlab versions
3549            testrecent=1;
3550       end
3551end
3552set(hlist,'String',ListDisplay)
3553
3554%% Look at date of creation
3555ListDisplay=ListDisplay(datnum~=0);
3556datnum=datnum(datnum~=0); % keep the non zero values corresponding to existing files
3557NbOutputFile=[];
3558if isempty(datnum)
3559    if testrecent
3560        message='no civ result created yet';
3561    else
3562        message='';
3563    end
3564else
3565    [first,indfirst]=min(datnum);
3566    [last,indlast]=max(datnum);
3567    NbOutputFile_str='?';
3568    NbOutputFile=[];
3569    if isfield(StatusData,'NbOutputFile')
3570        NbOutputFile=StatusData.NbOutputFile;
3571        NbOutputFile_str=num2str(NbOutputFile);
3572    end
3573    message={[num2str(numel(datnum)) ' file(s) done over ' NbOutputFile_str] ;['oldest modification:  ' ListDisplay{indfirst} ' : ' datestr(first)];...
3574        ['latest modification:  ' ListDisplay{indlast} ' : ' datestr(last)]};
3575end
3576set(htitlebox,'String', [OutputDir{1};message])
3577
3578%% update the waitbar
3579hwaitbar=findobj(hfig,'tag','waitbar');
3580if ~isempty(NbOutputFile)
3581    BarPosition=get(hwaitbar,'Position');
3582    BarPosition(3)=0.9*numel(datnum)/NbOutputFile;
3583    set(hwaitbar,'Position',BarPosition)
3584end
3585
3586%------------------------------------------------------------------------
3587% --- Executes on selection change in ActionExt.
3588%------------------------------------------------------------------------
3589function ActionExt_Callback(hObject, eventdata, handles)
3590
3591ActionExtList=get(handles.ActionExt,'String');
3592ActionExt=ActionExtList{get(handles.ActionExt,'Value')};
3593if strcmp(ActionExt,'.py (in dev.)')
3594    set(handles.RunMode,'Value',2)
3595end
3596
3597
3598function num_NbSlice_Callback(hObject, eventdata, handles)
3599NbSlice=str2num(get(handles.num_NbSlice,'String'));
3600
3601%------------------------------------------------------------------------
3602% --- set the visibility of relevant velocity type menus:
3603function menu=set_veltype_display(Civ,FileType)
3604%------------------------------------------------------------------------
3605if ~exist('FileType','var')
3606    FileType='civx';
3607end
3608switch FileType
3609    case 'civx'
3610        menu={'civ1';'interp1';'filter1';'civ2';'interp2';'filter2'};
3611        if isequal(Civ,0)
3612            imax=0;
3613        elseif isequal(Civ,1) || isequal(Civ,2)
3614            imax=1;
3615        elseif isequal(Civ,3)
3616            imax=3;
3617        elseif isequal(Civ,4) || isequal(Civ,5)
3618            imax=4;
3619        elseif isequal(Civ,6) %patch2
3620            imax=6;
3621        end
3622    case 'civdata'
3623        menu={'civ1';'filter1';'civ2';'filter2'};
3624        if isequal(Civ,0)
3625            imax=0;
3626        elseif isequal(Civ,1) || isequal(Civ,2)
3627            imax=1;
3628        elseif isequal(Civ,3)
3629            imax=2;
3630        elseif isequal(Civ,4) || isequal(Civ,5)
3631            imax=3;
3632        else%if isequal(Civ,6) %patch2
3633            imax=4;
3634        end
3635end
3636menu=menu(1:imax);
3637
3638
3639% --- Executes on mouse motion over figure - except title and menu.
3640% function series_WindowButtonMotionFcn(hObject, eventdata, handles)
3641% set(hObject,'Pointer','arrow');
3642
3643
3644% --- Executes on button press in SetPairs.
3645function SetPairs_Callback(hObject, eventdata, handles)
3646
3647%% delete previous occurrence of 'set_pairs'
3648hfig=findobj(allchild(0),'Tag','set_pairs');
3649if ~isempty(hfig)
3650delete(hfig)
3651end
3652
3653%% create the GUI set_pairs
3654set(0,'Unit','points')
3655ScreenSize=get(0,'ScreenSize'); % get the size of the screen, to put the fig on the upper right
3656Width=220; % fig width in points (1/72 inch)
3657Height=min(0.8*ScreenSize(4),300);
3658Left=ScreenSize(3)- Width-40; % right edge close to the right, with margin=40
3659Bottom=ScreenSize(4)-Height-40; % put fig at top right
3660hfig=findobj(allchild(0),'Tag','set_slice');
3661if ~isempty(hfig),delete(hfig), end; % delete existing version of the GUI
3662hfig=figure('name','set_pairs','tag','set_pairs','MenuBar','none','NumberTitle','off','Unit','points','Position',[Left,Bottom,Width,Height]);
3663BackgroundColor=get(hfig,'Color');
3664SeriesData=get(handles.series,'UserData');
3665TimeUnit=get(handles.TimeUnit,'String');
3666PairString=get(handles.PairString,'Data');
3667ListViewLines=find(cellfun('isempty',PairString)==0); % find list of non empty pairs
3668ListViewMenu=cell(numel(ListViewLines),1);
3669%iview=get(handles.PairString,'Value');
3670iview=[];
3671for ilist=1:numel(ListViewLines)
3672    ListViewMenu{ilist}=num2str(ListViewLines(ilist));
3673end
3674if isempty(iview)
3675    ListViewValue=numel(ListViewLines); % we work by default on the pair option for the last line which requires pairs
3676    iview=ListViewLines(end);
3677else
3678    ListViewValue=find(ListViewLines==iview);
3679end
3680ref_i=str2num(get(handles.num_first_i,'String'));
3681ref_j=1; % default
3682if strcmp(get(handles.num_first_j,'String'),'Visible')
3683    ref_j=str2num(get(handles.num_first_j,'String'));
3684end
3685[ModeMenu,ModeValue]=update_mode(SeriesData.i1_series{1},SeriesData.i2_series{1},SeriesData.j2_series{1});
3686InputTable=get(handles.InputTable,'Data');
3687displ_pair=update_listpair(SeriesData.i1_series{1},SeriesData.i2_series{1},SeriesData.j1_series{1},SeriesData.j2_series{1},ModeMenu{ModeValue},...
3688                                                 SeriesData.Time{1},TimeUnit,ref_i,ref_j,SeriesData.TimeName,InputTable,SeriesData.FileInfo{1});
3689for iline=1:size(InputTable,1)
3690    viewcell{iline}=num2str(iline);
3691end
3692viewcell=viewcell';
3693ModeMenu={'bursts';'series(Dj)'};
3694ModeValue=1;                                               
3695                   %i1_series,i2_series,j1_series,j2_series,mode,time,TimeUnit,ref_i,ref_j,TimeName,InputTable,FileInfo                             
3696% first raw of the GUI
3697uicontrol('Style','text','Units','normalized', 'Position', [0.05 0.88 0.5 0.1],'BackgroundColor',BackgroundColor,...
3698    'String','row to edit #','FontUnits','points','FontSize',12,'FontWeight','bold','ForegroundColor','blue','HorizontalAlignment','right'); % title
3699uicontrol('Style','popupmenu','Units','normalized', 'Position', [0.54 0.8 0.3 0.2],'BackgroundColor',[1 1 1],...
3700    'Callback',@(hObject,eventdata)ListView_Callback(hObject,eventdata),'String',viewcell,'Value',1,'FontUnits','points','FontSize',12,'FontWeight','bold',...
3701    'Tag','ListView','TooltipString','''ListView'':choice of the file series w for pair display');
3702% second raw of the GUI
3703uicontrol('Style','text','Units','normalized', 'Position', [0.05 0.79 0.7 0.1],'BackgroundColor',BackgroundColor,...
3704    'String','mode of index pairing:','FontUnits','points','FontSize',12,'FontWeight','bold','ForegroundColor','blue','HorizontalAlignment','left'); % title
3705uicontrol('Style','popupmenu','Units','normalized', 'Position', [0.05 0.62 0.9 0.2],'BackgroundColor',[1 1 1],...
3706    'Callback',@(hObject,eventdata)Mode_Callback(hObject,eventdata),'String',ModeMenu,'Value',ModeValue,'FontUnits','points','FontSize',12,'FontWeight','bold',...
3707    'Tag','Mode','TooltipString','''Mode'': choice of the image pair mode');
3708% third raw
3709uicontrol('Style','text','Units','normalized', 'Position', [0.05 0.6 0.7 0.1],'BackgroundColor',BackgroundColor,...
3710    'String','pair choice:','FontUnits','points','FontSize',12,'FontWeight','bold','ForegroundColor','blue','HorizontalAlignment','left'); % title
3711uicontrol('Style','listbox','Units','normalized', 'Position', [0.05 0.42 0.9 0.2],'BackgroundColor',[1 1 1],...
3712    'Callback',@(hObject,eventdata)ListPair_Callback(hObject,eventdata),'String',displ_pair,'Value',1,'FontUnits','points','FontSize',12,'FontWeight','bold',...
3713    'Tag','ListPair','TooltipString','''ListPair'': menu for selecting the image pair');
3714uicontrol('Style','text','Units','normalized', 'Position', [0.1 0.22 0.8 0.1],'BackgroundColor',BackgroundColor,...
3715    'String','ref_i           ref_j','FontUnits','points','FontSize',12,'FontWeight','bold','ForegroundColor','blue','HorizontalAlignment','center'); % title
3716uicontrol('Style','edit','Units','normalized', 'Position', [0.15 0.17 0.3 0.08],'BackgroundColor',[1 1 1],...
3717    'Callback',@(hObject,eventdata)num_ref_i_Callback(hObject,eventdata),'String',num2str(ref_i),'FontUnits','points','FontSize',12,'FontWeight','bold',...
3718    'Tag','num_ref_i','TooltipString','''num_ref_i'': reference field index i used to display dt in ''list_pair_civ''');
3719uicontrol('Style','edit','Units','normalized', 'Position', [0.55 0.17 0.3 0.08],'BackgroundColor',[1 1 1],...
3720    'Callback',@(hObject,eventdata)num_ref_j_Callback(hObject,eventdata),'String',num2str(ref_j),'FontUnits','points','FontSize',12,'FontWeight','bold',...
3721    'Tag','num_ref_j','TooltipString','''num_ref_j'': reference field index i used to display dt in ''list_pair_civ''');
3722uicontrol('Style','pushbutton','Units','normalized', 'Position', [0.01 0.01 0.3 0.12],'BackgroundColor',[0 1 0],...
3723    'Callback',@(hObject,eventdata)OK_Callback(hObject,eventdata),'String','OK','FontUnits','points','FontSize',12,'FontWeight','bold',...
3724    'Tag','OK','TooltipString','''OK'': validate the choice');
3725%  last raw  of the GUI: pushbuttons
3726% 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),...
3727%     'FontWeight','bold','FontUnits','points','FontSize',12,'TooltipString','''OK'': apply the output to the current field series in uvmat');
3728drawnow
3729
3730%------------------------------------------------------------------------
3731function ListView_Callback(hObject,eventdata)
3732Mode_Callback(hObject,eventdata)
3733
3734%------------------------------------------------------------------------   
3735function Mode_Callback(hObject,eventdata)
3736%% get input info
3737hseries=findobj(allchild(0),'tag','series'); % handles of the GUI series
3738hhseries=guidata(hseries); % handles of the elements in the GUI series
3739TimeUnit=get(hhseries.TimeUnit,'String');
3740SeriesData=get(hseries,'UserData');
3741mode_list=get(hObject,'String');
3742mode=mode_list{get(hObject,'Value')};
3743hListView=findobj(get(hObject,'parent'),'Tag','ListView');
3744iview=get(hListView,'Value');
3745i1_series=SeriesData.i1_series{iview};
3746i2_series=SeriesData.i2_series{iview};
3747j1_series=SeriesData.j1_series{iview};
3748j2_series=SeriesData.j2_series{iview};
3749
3750%% enable j index visibility after the new choice
3751
3752if strcmp(mode,'series(Dj)')
3753   status_j='on'; % default
3754else
3755       status_j='off'; % no j index needed for bust case
3756end
3757enable_j(hhseries,status_j) % no j index needed
3758
3759%% get the reference indices for the time interval Dt
3760href_i=findobj(get(hObject,'parent'),'Tag','ref_i');
3761ref_i=[];ref_j=[];
3762if strcmp(get(href_i,'Visible'),'on')
3763    ref_i=str2num(get(href_i,'String'));
3764end
3765if isempty(ref_i)
3766    ref_i=1;
3767end
3768if isempty(ref_j)
3769    ref_j=1;
3770end
3771
3772%% update the menu ListPair
3773Menu=update_listpair(i1_series,i2_series,j1_series,j2_series,mode,SeriesData.Time{iview},TimeUnit,ref_i,ref_j,SeriesData.FileInfo);
3774hlist_pairs=findobj(get(hObject,'parent'),'Tag','ListPair');
3775set(hlist_pairs,'Value',1)% set the first choice by default in ListPair
3776set(hlist_pairs,'String',Menu)% set the menu in ListPair
3777ListPair_Callback(hlist_pairs,[])% apply the default choice in ListPair
3778
3779%-------------------------------------------------------------
3780% --- Executes on selection in ListPair.
3781function ListPair_Callback(hObject,eventdata)
3782%------------------------------------------------------------
3783list_pair=get(hObject,'String'); % get the menu of image pairs
3784if isempty(list_pair)
3785    string='';
3786else
3787    string=list_pair{get(hObject,'Value')};
3788   % string=regexprep(string,',.*',''); % removes time indication (after ',')
3789end
3790hseries=findobj(allchild(0),'tag','series');
3791hPairString=findobj(hseries,'tag','PairString');
3792PairString=get(hPairString,'Data');
3793hListView=findobj(get(hObject,'parent'),'Tag','ListView');
3794iview=get(hListView,'Value');
3795PairString{iview,1}=string;
3796% report the selected pair string to the table PairString
3797set(hPairString,'Data',PairString)
3798
3799
3800%------------------------------------------------------------------------
3801function num_ref_i_Callback(hObject, eventdata)
3802%------------------------------------------------------------------------
3803Mode_Callback([],[])
3804
3805%------------------------------------------------------------------------
3806function num_ref_j_Callback(hObject, eventdata)
3807%------------------------------------------------------------------------
3808Mode_Callback([],[])
3809
3810%------------------------------------------------------------------------
3811function OK_Callback(hObject, eventdata)
3812%------------------------------------------------------------------------
3813delete(get(hObject,'parent'))
3814
3815
3816%------------------------------------------------------------------------
3817% --- Executes on button press in ClearLine.
3818%------------------------------------------------------------------------
3819function ClearLine_Callback(hObject, eventdata, handles)
3820InputTable=get(handles.InputTable,'Data');
3821iline=str2double(get(handles.InputLine,'String'));
3822if size(InputTable,1)>1
3823    InputTable(iline,:)=[]; % suppress the current line if not the first
3824    set(handles.InputTable,'Data',InputTable);
3825end
3826set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH button to magenta color to indicate that input refr
3827
3828
3829% --- Executes on button press in MonitorCluster.
3830function MonitorCluster_Callback(hObject, eventdata, handles)
3831
3832[rr,ss]=system('oarstat |grep N=UVmat');% check the list of jobs launched with uvmat
3833if isempty(ss)
3834   disp( 'no job presently submitted with uvmat')
3835else
3836    disp('format: R/W=run/wait, time lapsed, R=nbre of cores,W=walltime')
3837    disp(ss)
3838end
3839
3840
3841function OutputSubDir_Callback(hObject, eventdata, handles)
3842set(handles.OutputSubDir,'BackgroundColor',[1 1 1])
3843
3844
3845% --- Executes on button press in CheckOverwrite.
3846function CheckOverwrite_Callback(hObject, eventdata, handles)
3847
3848% --- Executes on button press in TestCPUTime.
3849function TestCPUTime_Callback(hObject, eventdata, handles)
3850% hObject    handle to TestCPUTime (see GCBO)
3851% eventdata  reserved - to be defined in a future version of MATLAB
3852% handles    structure with handles and user data (see GUIDATA)
3853
3854
3855% --- Executes on button press in DiskQuota.
3856function DiskQuota_Callback(hObject, eventdata, handles)
3857SeriesData=get(handles.series,'UserData');
3858system(SeriesData.SeriesParam.DiskQuotaCmd)
3859
3860
3861
3862% --- Executes on button press in Replicate.
3863function Replicate_Callback(hObject, eventdata, handles)
3864if get(handles.Replicate,'Value')
3865    InputTable=get(handles.InputTable,'Data');
3866    for ilist=1:size(InputTable,1)
3867        InputDir{ilist}=fullfile(InputTable{ilist,1},InputTable{ilist,2});
3868    end
3869    browse_data(InputDir)
3870else
3871    hh=findobj(allchild(0),'Tag','browse_data');
3872    if ~isempty(hh)
3873        delete(hh)
3874    end
3875end
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