source: trunk/src/series.m @ 1104

Last change on this file since 1104 was 1104, checked in by sommeria, 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 2008-2021, 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
170if isequal(s,0)
171    RunModeList=[RunModeList;{'cluster'}];
172    set(handles.MonitorCluster,'Visible','on'); % make visible button for access to Monika
173    set(handles.num_CPUTime,'Visible','on'); % make visible button for CPU time estimate for one ref index
174    set(handles.num_CPUTime,'String','')% default CPU time undefined
175    set(handles.CPUTime_txt,'Visible','on'); % make visible button for CPU time title
176end
177set(handles.RunMode,'String',RunModeList)% display the menu of available run modes, local, background or cluster manager
178
179%% list of builtin transform functions in the menu TransformName
180TransformList={'';'sub_field';'phys';'phys_polar'}; % WARNING: must fit with the corresponding menu in uvmat and nb_builtin_transform=4 in  TransformName_callback
181NbBuiltinTransform=numel(TransformList);
182path_transform_fct=fullfile(path_series,'transform_field');
183TransformPathList=cell(NbBuiltinTransform,1); % initiate the cell matrix of Action fct paths
184TransformPathList(:)={path_transform_fct}; % set the default path to series fcts to all list members
185SeriesData.TransformPath=path_transform_fct;% store the standard path for trqnsform functions (needed for compilation)
186
187%% get the user defined functions stored in the personal file uvmat_perso.mat
188dir_perso=prefdir;
189profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
190if exist(profil_perso,'file')
191    h=load (profil_perso);
192    %get the list of previous input files in the upper bar menu Open
193    if isfield(h,'MenuFile')
194        for ifile=1:min(length(h.MenuFile),5)
195            set(handles.(['MenuFile_' num2str(ifile)]),'Label',h.MenuFile{ifile});
196            set(handles.(['MenuFile_' num2str(ifile+5)]),'Label',h.MenuFile{ifile});
197        end
198    end
199    %get the menu of actions
200    if isfield(h,'ActionListUser') && iscell(h.ActionListUser) && isfield(h,'ActionPathListUser') && iscell(h.ActionPathListUser)
201        ActionList=[ActionList;h.ActionListUser];
202        ActionPathList=[ActionPathList;h.ActionPathListUser(:,1)];
203    end
204    %get the menu of transform fct
205    if isfield(h,'TransformListUser') && iscell(h.TransformListUser) && isfield(h,'TransformPathListUser') && iscell(h.TransformPathListUser)
206        TransformList=[TransformList;h.TransformListUser];
207        TransformPathList=[TransformPathList;h.TransformPathListUser];
208    end
209end
210
211%% selection of the input Action fct
212ActionCheckExist=true(size(ActionList)); % initiate the check of the path to the listed action fct
213for ilist=NbBuiltinAction+1:numel(ActionList)%check  the validity of the path of the user defined Action fct
214    ActionCheckExist(ilist)=exist(fullfile(ActionPathList{ilist},[ActionList{ilist} '.m']),'file');
215end
216ActionPathList=ActionPathList(ActionCheckExist,:); % suppress the menu options which are not valid anymore
217ActionList=ActionList(ActionCheckExist);
218set(handles.ActionName,'String',[ActionList;{'more...'}])
219set(handles.ActionName,'UserData',ActionPathList)
220ActionIndex=[];
221if isfield(Param,'ActionName')% copy the selected menu index transferred in Param from uvmat
222    ActionIndex=find(strcmp(Param.ActionName,ActionList),1);
223end
224if isempty(ActionIndex)
225    ActionIndex=1;
226end
227set(handles.ActionName,'Value',ActionIndex)
228set(handles.ActionPath,'String',ActionPathList{ActionIndex})
229set(handles.ActionExt,'Value',1)
230set(handles.ActionExt,'String',ActionExtList)
231
232%% selection of the input transform fct
233TransformCheckExist=true(size(TransformList));
234for ilist=NbBuiltinTransform+1:numel(TransformList)
235    TransformCheckExist(ilist)=exist(fullfile(TransformPathList{ilist},[TransformList{ilist} '.m']),'file');
236end
237TransformPathList=TransformPathList(TransformCheckExist);
238TransformList=TransformList(TransformCheckExist);
239set(handles.TransformName,'String',[TransformList;{'more...'}])
240set(handles.TransformName,'UserData',TransformPathList)
241TransformIndex=[];
242if isfield(Param,'TransformName')% copy the selected menu index transferred in Param from uvmat
243    TransformIndex=find(strcmp(Param.TransformName,TransformList),1);
244end
245if isempty(TransformIndex)
246    TransformIndex=1;
247end
248set(handles.TransformName,'Value',TransformIndex)
249set(handles.TransformPath,'String',TransformPathList{TransformIndex})
250   
251%% fields input initialisation
252if isfield(Param,'list_fields')&& isfield(Param,'index_fields') &&~isempty(Param.list_fields) &&~isempty(Param.index_fields)
253    set(handles.FieldName,'String',Param.list_fields); % list menu fields
254    set(handles.FieldName,'Value',Param.index_fields); % selected string index
255end
256if isfield(Param,'Coordinates')
257    if isfield(Param.Coordinates,'Coord_x')
258        set(handles.Coord_x,'String',Param.Coordinates.Coord_x)
259    end
260    if isfield(Param.Coordinates,'Coord_y')
261        set(handles.Coord_y,'String',Param.Coordinates.Coord_y)
262    end
263    if isfield(Param.Coordinates,'Coord_z')
264        set(handles.Coord_z,'String',Param.Coordinates.Coord_z)
265    end
266end
267
268%% introduce the input file name(s) if defined from input Param,
269set(handles.series,'UserData',SeriesData)% initiate Userdata
270if isfield(Param,'InputFile')
271   
272    %% fill the list of input file series
273    InputTable=[{Param.InputFile.RootPath},{Param.InputFile.SubDir},{Param.InputFile.RootFile},{Param.InputFile.NomType},{Param.InputFile.FileExt}];
274    if isempty(find(cellfun('isempty',InputTable)==0)) % if there is no input file, do not introduce input info
275        set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH button to magenta color to indicate that input refresh is needed
276        return
277    end
278    TimeTable=[{Param.InputFile.TimeName},{[]},{[]},{[]},{[]}];
279    if isfield(Param.InputFile,'RootPath_1')
280        InputTable=[InputTable;[{Param.InputFile.RootPath_1},{Param.InputFile.SubDir_1},{Param.InputFile.RootFile_1},{Param.InputFile.NomType_1},{Param.InputFile.FileExt_1}]];
281        TimeTable=[TimeTable; [{Param.InputFile.TimeName_1},{[]},{[]},{[]},{[]}]];
282    end
283    set(handles.InputTable,'Data',InputTable)
284   
285    %% define the default path for the output files
286    [InputPath,Device,DeviceExt]=fileparts(InputTable{1,1});
287    [InputPath,Experiment,ExperimentExt]=fileparts(InputPath);
288    set(handles.Device,'String',[Device DeviceExt])
289    set(handles.Experiment,'String',[Experiment ExperimentExt])
290    if ~isempty(regexp(InputTable{1,1},'(^http://)|(^https://)'))
291    set(handles.OutputPathBrowse,'Value',1)% an output folder needs to be specified for OpenDAP data
292    end
293
294    %update the output path if needed
295    if ~(isfield(SeriesData,'InputPath') && strcmp(SeriesData.InputPath,InputPath))
296    if get(handles.OutputPathBrowse,'Value')==1  % fix the output path in manual mode
297        OutputPathOld=get(handles.OutputPath,'String');
298        OutputPath=uigetdir(OutputPathOld,'pick a root folder for output data');
299        set(handles.OutputPath,'String',OutputPath)
300    else %reproduce the input path for output
301        set(handles.OutputPath,'String',InputPath)
302    end
303    end
304   
305    %% determine the selected reference field indices for pair display
306   
307    [tild,tild,tild,i1,i2,j1,j2]=fileparts_uvmat(Param.InputFile.FileIndex);
308    if isempty(i1)
309        i1=1;
310    end
311    if isempty(i2)
312        i2=i1;
313    end
314    ref_i=floor((i1+i2)/2); % reference image number corresponding to the file
315    % set(handles.num_ref_i,'String',num2str(ref_i));
316    if isempty(j1)
317        j1=1;
318    end
319    if isempty(j2)
320        j2=j1;
321    end
322    ref_j=floor((j1+j2)/2); % reference image number corresponding to the file
323    SeriesData.ref_i=ref_i;
324    SeriesData.ref_j=ref_j;
325    set(handles.series,'UserData',SeriesData)
326    update_rootinfo(handles,Param.HiddenData.i1_series{1},Param.HiddenData.i2_series{1},Param.HiddenData.j1_series{1},Param.HiddenData.j2_series{1},...
327        Param.HiddenData.FileInfo{1},Param.HiddenData.MovieObject{1},1)
328    if isfield(Param,'FileName_1')
329        %         display_file_name(handles,Param,2)
330        update_rootinfo(handles,Param.HiddenData.i1_series{2},Param.HiddenData.i2_series{2},Param.HiddenData.j1_series{2},Param.HiddenData.j2_series{2},...
331            Param.HiddenData.FileInfo{2},Param.HiddenData.MovieObject{2},2)
332    end
333    %% enable field and veltype menus, in accordance with the current action
334    ActionName_Callback([],[], handles)
335   
336    %% set length of waitbar
337    displ_time(handles)
338   
339else
340    set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH button to magenta color to indicate that input refresh is needed
341end
342if isfield(Param,'incr_i')
343    set(handles.num_incr_i,'String',num2str(Param.incr_i))
344else
345    set(handles.num_incr_i,'String','1')
346end
347if isfield(Param,'incr_j')
348    set(handles.num_incr_j,'String',num2str(Param.incr_j))
349else
350    set(handles.num_incr_j,'String','1')
351end
352
353%------------------------------------------------------------------------
354% --- Outputs from this function are returned to the command line.
355function varargout = series_OutputFcn(hObject, eventdata, handles)
356%------------------------------------------------------------------------
357varargout{1} = handles.output;
358
359%------------------------------------------------------------------------
360% --- executed when closing uvmat: delete or desactivate the associated figures if exist
361function closefcn(gcbo,eventdata)
362%------------------------------------------------------------------------
363
364% delete set_object_series if detected
365hh=findobj(allchild(0),'name','view_object_series');
366if ~isempty(hh)
367    delete(hh)
368end
369hh=findobj(allchild(0),'name','edit_object_series');
370if ~isempty(hh)
371    delete(hh)
372end
373
374%delete the bowser if detected
375hh=findobj(allchild(0),'tag','browser');
376if ~isempty(hh)
377    delete(hh)
378end
379
380
381%------------------------------------------------------------------------
382%------------------------------------------------------------------------
383%  II - FUNCTIONS FOR INTRODUCING THE INPUT FILES
384% automatically sets the global properties when the rootfile name is introduced
385% then activate the view-field actionname if selected
386% it is activated either by clicking on the RootPath window or by the
387% browser
388%------------------------------------------------------------------------
389%------------------------------------------------------------------------
390% --- fct activated by the browser under 'Open'
391%------------------------------------------------------------------------ 
392function MenuBrowse_Callback(hObject, eventdata, handles)
393%% look for the previously opened file 'oldfile'
394InputTable=get(handles.InputTable,'Data');
395oldfile=InputTable{1,1};
396if isempty(oldfile)
397    % use a file name stored in prefdir
398    dir_perso=prefdir;
399    profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
400    if exist(profil_perso,'file')
401        h=load (profil_perso);
402        if isfield(h,'RootPath') && ischar(h.RootPath)
403            oldfile=h.RootPath;
404        end
405    end
406end
407%% launch the browser
408fileinput=uigetfile_uvmat('pick an input file in the series',oldfile);
409hh=dir(fileinput);
410if numel(hh)>1
411    msgbox_uvmat('ERROR','invalid input, probably a broken link');
412else
413    if ~isempty(fileinput)
414        display_file_name(handles,fileinput,'one')
415    end
416end
417
418% --------------------------------------------------------------------
419function MenuBrowseAppend_Callback(hObject, eventdata, handles)
420
421%% look for the previously opened file 'oldfile'
422InputTable=get(handles.InputTable,'Data');
423RootPathCell=InputTable(:,1);
424if isempty(RootPathCell{1})% no input file in the table
425     MenuBrowse_Callback(hObject, eventdata, handles)%refresh the input table, not append
426     return
427end
428SubDirCell=InputTable(:,2);
429oldfile=fullfile(RootPathCell{1},SubDirCell{1});
430
431%% use a file name stored in prefdir
432dir_perso=prefdir;
433profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
434if exist(profil_perso,'file')
435    h=load (profil_perso);
436    if isfield(h,'RootPath') && ischar(h.RootPath)
437        oldfile=h.RootPath;
438    end
439end
440
441%% launch the browser
442fileinput=uigetfile_uvmat('pick a file to append in the input table',oldfile);
443hh=dir(fileinput);
444if numel(hh)>1
445    msgbox_uvmat('ERROR','invalid input, probably a broken link');
446else
447    if ~isempty(fileinput)
448        display_file_name(handles,fileinput,'append')
449    end
450end
451
452%------------------------------------------------------------------------
453% --- fct activated by selecting a previous file under the menu Open
454%------------------------------------------------------------------------
455function MenuFile_Callback(hObject, eventdata, handles)
456
457errormsg=display_file_name(handles,get(hObject,'Label'),'one');
458if ~isempty(errormsg)
459    set(hObject,'Label','')
460    MenuFile=[{get(handles.MenuFile_1,'Label')};{get(handles.MenuFile_2,'Label')};...
461        {get(handles.MenuFile_3,'Label')};{get(handles.MenuFile_4,'Label')};{get(handles.MenuFile_5,'Label')}];
462    str_find=strcmp(get(hObject,'Label'),MenuFile);
463    MenuFile(str_find)=[]; % suppress the input file to the list
464    for ifile=1:numel(MenuFile)
465        set(handles.(['MenuFile_' num2str(ifile)]),'Label',MenuFile{ifile});
466    end
467end
468
469%------------------------------------------------------------------------
470% --- fct activated by selecting a previous file under the menu Open/append
471%------------------------------------------------------------------------
472function MenuFile_append_Callback(hObject, eventdata, handles)
473
474InputTable=get(handles.InputTable,'Data');
475if isempty(InputTable{1,1})% no input file in the table
476    display_file_name(handles,get(hObject,'Label'),'one') %refresh the input table, not append
477else
478    display_file_name(handles,get(hObject,'Label'),'append')% append the selected file to the current list of InputTable
479end
480
481%------------------------------------------------------------------------
482% --- fct activated by the browser under 'Open campaign/Browse...'
483%------------------------------------------------------------------------
484function MenuBrowseCampaign_Callback(hObject, eventdata, handles)
485
486%% look for the previously opened file 'oldfile'
487InputTable=get(handles.InputTable,'Data');
488if ~isempty(InputTable)
489oldfile=[InputTable{1,1} InputTable{1,2}];
490else
491    % use a file name stored in prefdir
492    dir_perso=prefdir;
493    profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
494    if exist(profil_perso,'file')
495        h=load (profil_perso);
496        if isfield(h,'MenuCampaign') && ~isempty(h.MenuCampaign)&& ischar(h.MenuCampaign{1})
497            oldfile=h.MenuCampaign{1};
498        end
499    end
500end
501InputTable{1,1}='...';
502set(handles.InputTable,'Data',InputTable)
503browse_data(oldfile,'on','on'); % open the GUI browse_data to get select a campaign dir, experiment and device
504% NbLines=numel(OutPut.Experiment)*numel(OutPut.DataSeries);
505% icount=0;
506% for iexp=1:numel(OutPut.Experiment)
507%     for idevice=1:numel(OutPut.DataSeries)
508%         icount=icount+1;
509%         InputTable{icount,1}=fullfile(OutPut.Campaign,OutPut.Experiment{iexp});
510%         InputTable{icount,2}=OutPut.DataSeries{idevice};
511%         if isempty(InputTable{icount,3})
512%             if icount>1
513%             InputTable{icount,3}=InputTable{icount-1,3};
514%             else
515%                 InputTable{icount,3}='';
516%             end
517%         end
518%         if isempty(InputTable{icount,4})
519%             if icount>1
520%             InputTable{icount,4}=InputTable{icount-1,4};
521%             else
522%                 InputTable{icount,4}='';
523%             end
524%         end
525%                 if isempty(InputTable{icount,5})
526%             if icount>1
527%             InputTable{icount,5}=InputTable{icount-1,5};
528%             else
529%                 InputTable{icount,5}='';
530%             end
531%         end
532%     end
533% end
534% if size(InputTable,1)>icount
535%     InputTable(icount+1:size(InputTable,1),:)=[];
536% end
537%REFRESH_Callback(hObject, eventdata, handles)
538
539% --------------------------------------------------------------------
540% function MenuCampaign_Callback(hObject, eventdata, handles)
541% % --------------------------------------------------------------------
542%
543% OutPut=browse_data(get(hObject,'Label'),'on','on'); % open the GUI browse_data to get select a campaign dir, experiment and device
544% if ~isfield(OutPut,'Campaign')
545%     return
546% end
547% NbLines=numel(OutPut.Experiment)*numel(OutPut.DataSeries);
548% icount=0;
549% InputTable=get(handles.InputTable,'Data');
550% for iexp=1:numel(OutPut.Experiment)
551%     for idevice=1:numel(OutPut.DataSeries)
552%         icount=icount+1;
553%         InputTable{icount,1}=fullfile(OutPut.Campaign,OutPut.Experiment{iexp});
554%         InputTable{icount,2}=OutPut.DataSeries{idevice};
555%         if isempty(InputTable{icount,3})
556%             if icount>1
557%                 InputTable{icount,3}=InputTable{icount-1,3};
558%             else
559%                 InputTable{icount,3}='';
560%             end
561%         end
562%         if isempty(InputTable{icount,4})
563%             if icount>1
564%                 InputTable{icount,4}=InputTable{icount-1,4};
565%             else
566%                 InputTable{icount,4}='';
567%             end
568%         end
569%         if isempty(InputTable{icount,5})
570%             if icount>1
571%                 InputTable{icount,5}=InputTable{icount-1,5};
572%             else
573%                 InputTable{icount,5}='';
574%             end
575%         end
576%     end
577% end
578% if size(InputTable,1)>icount
579%     InputTable(icount+1:size(InputTable,1),:)=[];
580% end
581% set(handles.InputTable,'Data',InputTable)
582% REFRESH_Callback(hObject, eventdata, handles)
583
584
585% --- Executes when selected cell(s) is changed in InputTable.
586function InputTable_CellSelectionCallback(hObject, eventdata, handles)
587iline=[];
588if ~isempty(eventdata.Indices)
589    iline=eventdata.Indices(1);
590end
591set(handles.InputLine,'String',num2str(iline));
592
593%------------------------------------------------------------------------
594% --- 'key_press_fcn:' function activated when a key is pressed on the keyboard
595%------------------------------------------------------------------------
596function InputTable_KeyPressFcn(hObject, eventdata, handles)
597set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH button to magenta color to indicate that input refresh is needed
598set(handles.OutputSubDir,'BackgroundColor',[1 0 1])% set edit box OutputSubDir to magenta color to indicate that refresh may be needed
599xx=double(get(handles.series,'CurrentCharacter')); % get the keyboard character
600if ~isempty(xx)
601    switch xx
602        case 31 %downward arrow
603            InputTable=get(handles.InputTable,'Data');
604            iline=str2double(get(handles.InputLine,'String'));
605            if isequal(iline,size(InputTable,1))% arrow downward
606                InputTable=[InputTable;InputTable(iline,:)]; % create a new line as a copy of the last one
607                set(handles.InputTable,'Data',InputTable);
608            end
609        case 127  %key 'Suppress'
610            ClearLine_Callback(hObject, eventdata, handles)
611    end
612end
613
614%------------------------------------------------------------------------
615% --- Executes on button press in REFRESH.
616function REFRESH_Callback(hObject, eventdata, handles)
617%------------------------------------------------------------------------
618check_input_file_series(handles)
619
620%% enable field and veltype menus, in accordance with the current action
621ActionInput_Callback([],[], handles)
622
623
624function check_input_file_series(handles)
625InputTable=get(handles.InputTable,'Data');
626set(handles.series,'Pointer','watch') % set the mouse pointer to 'watch'
627set(handles.REFRESH,'BackgroundColor',[1 1 0])% set REFRESH  button to yellow color (indicate activation)
628drawnow
629empty_line=false(size(InputTable,1),1);
630for iline=1:size(InputTable,1)
631    empty_line(iline)= isempty(cell2mat(InputTable(iline,1:3)));
632end
633if ~isempty(find(empty_line,1))
634    InputTable(empty_line,:)=[]; % remove empty lines
635    set(handles.InputTable,'Data',InputTable)
636    ListTable={'MinIndex_i','MaxIndex_i','MinIndex_j','MaxIndex_j','PairString','TimeTable'};
637    for ilist=1:numel(ListTable)
638        Table=get(handles.(ListTable{ilist}),'Data');
639        Table(empty_line,:)=[]; % remove empty lines
640        set(handles.(ListTable{ilist}),'Data',Table);
641    end
642    set(handles.series,'UserData',[])%refresh the stored info
643end
644nbview=size(InputTable,1);
645for iview=1:nbview
646    RootPath=fullfile(InputTable{iview,1},InputTable{iview,2});
647    if ~exist(RootPath,'dir')
648        i1_series=[];
649        RootFile='';
650    else %scan the input folder
651        InputTable{iview,3}=regexprep(InputTable{iview,3},'^/','');
652            [RootPath,~,RootFile,i1_series,i2_series,j1_series,j2_series,tild,FileInfo,MovieObject]=...
653                find_file_series(fullfile(InputTable{iview,1},InputTable{iview,2}),[InputTable{iview,3} InputTable{iview,4} InputTable{iview,5}]);
654    end
655    % if no file is found, open a browser
656    if isempty(RootFile)&& isempty(i1_series)
657        fileinput=uigetfile_uvmat(['wrong input at line ' num2str(iview) ':pick a new input file'],RootPath);
658        if isempty(fileinput)
659            set(handles.REFRESH,'BackgroundColor',[1 0 0])% set REFRESH  back to red color
660            return
661        else
662            display_file_name(handles,fileinput,iview)
663        end
664    else
665       update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileInfo,MovieObject,iview)
666    end
667end
668
669%% update MinIndex_i and MaxIndex_i if the input table content has been reduced in line nbre
670MinIndex_i_table=get(handles.MinIndex_i,'Data'); % retrieve the min indices in the table MinIndex
671set(handles.MinIndex_i,'Data',MinIndex_i_table(1:nbview,:));
672MinIndex_j_table=get(handles.MinIndex_j,'Data'); % retrieve the min indices in the table MinIndex
673set(handles.MinIndex_j,'Data',MinIndex_j_table(1:nbview,:));
674MaxIndex_i_table=get(handles.MaxIndex_i,'Data'); % retrieve the min indices in the table MinIndex
675
676set(handles.MaxIndex_i,'Data',MaxIndex_i_table(1:nbview,:));
677MaxIndex_j_table=get(handles.MaxIndex_j,'Data'); % retrieve the min indices in the table MinIndex
678set(handles.MaxIndex_j,'Data',MaxIndex_j_table(1:nbview,:));
679PairString=get(handles.PairString,'Data'); % retrieve the min indices in the table MinIndex
680set(handles.PairString,'Data',PairString(1:nbview,:));
681TimeTable=get(handles.TimeTable,'Data'); % retrieve the min indices in the table MinIndex
682set(handles.TimeTable,'Data',TimeTable(1:nbview,:));
683
684%% set length of waitbar
685displ_time(handles)
686set(handles.REFRESH,'BackgroundColor',[1 0 0])% set REFRESH  button to red color (indicate activation finished)
687set(handles.series,'Pointer','arrow') % set the mouse pointer to 'watch'
688
689
690
691%------------------------------------------------------------------------
692% --- Function called when a new file is opened, either by series_OpeningFcn or by the browser
693%------------------------------------------------------------------------
694% INPUT:
695% handles: handles of elements in the GUI
696% Param: structure of input parameters, including  input file name and path
697% iview: line index in the input table
698%       or 'one': refresh the list
699%         'append': add a new line to the input table
700function errormsg=display_file_name(handles,Param,iview)
701 
702set(handles.REFRESH,'BackgroundColor',[1 1 0])% set REFRESH  button to yellow color (indicate activation)
703drawnow
704errormsg=''; % default
705if ischar(Param)
706    fileinput=Param;
707else% input set when series is opened (called by the GUI uvmat)
708    fileinput=Param.FileName;
709end
710   
711%% get the input root name, indices, file extension and nomenclature NomType
712if isempty(regexp(fileinput,'^http')) && ~exist(fileinput,'file')
713    errormsg=['input file ' fileinput  ' does not exist'];
714    msgbox_uvmat('ERROR',errormsg)
715    set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH  button to magenta color (refresh still needed)
716    return
717end
718
719%% detect root name, nomenclature and indices in the input file name:
720[FilePath,FileName,FileExt]=fileparts(fileinput);
721%%%%%%%%%%%%%%%%%%
722%TODO: case of input by uvmat: do not check agai the input seies %%%%%%%
723%%%%%%%%%%%%%%%%%%%
724% detect the file type, get the movie object if relevant, and look for the corresponding file series:
725% the root name and indices may be corrected by including the first index i1 if a corresponding xml file exists
726[RootPath,SubDir,RootFile,i1_series,i2_series,j1_series,j2_series,NomType,FileInfo,MovieObject,i1,i2,j1,j2]=find_file_series(FilePath,[FileName FileExt]);
727FileType=FileInfo.FileType;
728if isempty(RootFile)&&isempty(i1_series)
729    errormsg='no input file in the series';
730    msgbox_uvmat('ERROR',errormsg)
731    set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH  button to magenta color (end of activation)
732    return
733end
734if strcmp(FileType,'txt')
735    edit(fileinput)
736    set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH  button to  magenta color (end of activation)
737    return
738elseif strcmp(FileType,'xml')
739    editxml(fileinput)
740    set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH  button to magenta  color (end of activation)
741     return
742elseif strcmp(FileType,'figure')
743    open(fileinput)
744    set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH  button to magenta  color (end of activation)
745     return
746end
747
748%% enable other menus and uicontrols
749set(handles.RUN, 'Enable','On')
750set(handles.RUN,'BackgroundColor',[1 0 0])% set RUN button to red
751set(handles.InputTable,'BackgroundColor',[1 1 0]) % set RootPath edit box  to yellow
752drawnow
753
754
755%% fill the list of file series
756InputTable=get(handles.InputTable,'Data');
757SeriesData=get(handles.series,'UserData');
758
759if strcmp(iview,'append') % display the input data as a new line in the table
760    iview=size(InputTable,1)+1; % the next line in InputTable becomes the current line
761elseif strcmp(iview,'one') % refresh the list of  input  file series
762    iview=1; % the first line in InputTable becomes the current line
763    InputTable={'','','','',''};
764    set(handles.TimeTable,'Data',[{''},{[]},{[]},{[]},{[]}])
765    set(handles.MinIndex_i,'Data',[])
766    set(handles.MaxIndex_i,'Data',[])
767    set(handles.MinIndex_j,'Data',[])
768    set(handles.MaxIndex_j,'Data',[])
769    set(handles.PairString,'Data',{''})
770    SeriesData.CheckPair=0; % reset the list of input lines with pairs
771    SeriesData.i1_series={};
772    SeriesData.i2_series={};
773    SeriesData.j1_series={};
774    SeriesData.j2_series={};
775    SeriesData.FileType={};
776    SeriesData.FileInfo={};
777    SeriesData.Time={};
778end
779if isfield(SeriesData,'i1_series')
780    SeriesData.i1_series(iview+1:end)=[];
781    SeriesData.i2_series(iview+1:end)=[];
782    SeriesData.j1_series(iview+1:end)=[];
783    SeriesData.j2_series(iview+1:end)=[];
784    SeriesData.FileType(iview+1:end)=[];
785    SeriesData.FileInfo(iview+1:end)=[];
786    SeriesData.Time(iview+1:end)=[];
787end
788InputTable(iview,:)=[{RootPath},{SubDir},{RootFile},{NomType},{FileExt}];
789if iview >1
790    set(handles.InputLine,'String',num2str(iview))
791end
792set(handles.InputTable,'Data',InputTable)
793
794%% determine the selected reference field indices for pair display
795if isempty(i1)
796    i1=1;
797end
798if isempty(i2)
799    i2=i1;
800end
801ref_i=floor((i1+i2)/2); % reference image number corresponding to the file
802% set(handles.num_ref_i,'String',num2str(ref_i));
803if isempty(j1)
804    j1=1;
805end
806if isempty(j2)
807    j2=j1;
808end
809ref_j=floor((j1+j2)/2); % reference image number corresponding to the file
810SeriesData.ref_i=ref_i;
811SeriesData.ref_j=ref_j;
812
813%% update first and last indices if they do not exist
814Param=read_GUI(handles.series);
815first_j=[];
816if isfield(Param.IndexRange,'first_j'); first_j=Param.IndexRange.first_j; end
817last_j=[];
818if isfield(Param.IndexRange,'last_j'); last_j=Param.IndexRange.last_j; end
819PairString='';
820if isfield(Param.IndexRange,'PairString'); PairString=Param.IndexRange.PairString; end
821[i1,i2,j1,j2] = get_file_index(Param.IndexRange.first_i,first_j,PairString);
822FirstFileName=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},...
823    Param.InputTable{1,5},Param.InputTable{1,4},i1,i2,j1,j2);
824if ~exist(FirstFileName,'file')
825    set(handles.num_first_i,'String',num2str(ref_i))
826    set(handles.num_first_j,'String',num2str(ref_j))
827end
828[i1,i2,j1,j2] = get_file_index(Param.IndexRange.last_i,last_j,PairString);
829LastFileName=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},...
830    Param.InputTable{1,5},Param.InputTable{1,4},i1,i2,j1,j2);
831if ~exist(LastFileName,'file')
832    set(handles.num_last_i,'String',num2str(ref_i))
833    set(handles.num_last_j,'String',num2str(ref_j))
834end
835
836%% update the list of recent files in the menubar and save it for future opening
837MenuFile=[{get(handles.MenuFile_1,'Label')};{get(handles.MenuFile_2,'Label')};...
838    {get(handles.MenuFile_3,'Label')};{get(handles.MenuFile_4,'Label')};{get(handles.MenuFile_5,'Label')}];
839str_find=strcmp(fileinput,MenuFile);
840if isempty(find(str_find,1))
841    MenuFile=[{fileinput};MenuFile]; % insert the current file if not already in the list
842end
843for ifile=1:min(length(MenuFile),5)
844    eval(['set(handles.MenuFile_' num2str(ifile) ',''Label'',MenuFile{ifile});'])
845end
846dir_perso=prefdir;
847profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
848if exist(profil_perso,'file')
849    save (profil_perso,'MenuFile','-append'); % store the file names for future opening of uvmat
850else
851    save (profil_perso,'MenuFile','-V6'); % store the file names for future opening of uvmat
852end
853% save the opened file to initiate future opening
854SeriesData.RefFile{iview}=fileinput; % reference opening file for line iview
855SeriesData.Ref_i1=i1;
856SeriesData.Ref_i2=i2;
857SeriesData.Ref_j1=j1;
858SeriesData.Ref_j2=j2;
859
860%% define the path for the output files
861[InputPath,Device,DeviceExt]=fileparts(InputTable{1,1});
862[InputPath,Experiment,ExperimentExt]=fileparts(InputPath);
863set(handles.Device,'String',[Device DeviceExt])
864set(handles.Experiment,'String',[Experiment ExperimentExt])
865if ~isempty(regexp(InputTable{1,1},'(^http://)|(^https://)'))
866    set(handles.OutputPathBrowse,'Value',1)% an output folder needs to be specified for OpenDAP data
867end
868
869%update the output path if needed
870if ~(isfield(SeriesData,'InputPath') && strcmp(SeriesData.InputPath,InputPath))
871    if get(handles.OutputPathBrowse,'Value')==1  % fix the output path in manual mode
872        OutputPathOld=get(handles.OutputPath,'String');
873        OutputPath=uigetdir(OutputPathOld,'pick a root folder for output data');
874        set(handles.OutputPath,'String',OutputPath)
875    else %reproduce the input path for output
876        set(handles.OutputPath,'String',InputPath)
877    end
878    SeriesData.InputPath=InputPath;
879end
880
881set(handles.series,'UserData',SeriesData)
882
883set(handles.InputTable,'BackgroundColor',[1 1 1])
884
885%% initiate input file series and refresh the current field view:     
886update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileInfo,MovieObject,iview);
887%% enable field and veltype menus, in accordance with the current action
888ActionName_Callback([],[], handles)
889
890%% set length of waitbar
891displ_time(handles)
892
893set(handles.REFRESH,'BackgroundColor',[1 0 0])% set REFRESH  button to red color (end of activation)
894
895%------------------------------------------------------------------------
896% --- Update information about a new field series (indices to scan, timing,
897%     calibration from an xml file
898function update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileInfo,VideoObject,iview)
899%------------------------------------------------------------------------
900InputTable=get(handles.InputTable,'Data');
901
902%% display the min and max indices for the whole file series
903if size(i1_series,2)==2 && min(min(i1_series(:,1,:)))==0
904    MinIndex_j=1; % index j set to 1 by default
905    MaxIndex_j=1;
906    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)
907    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)
908else
909    ref_i=squeeze(max(i1_series(1,:,:),[],2)); % select ref_j index for each ref_i
910    ref_j=squeeze(max(j1_series(1,:,:),[],3)); % select ref_i index for each ref_j
911     MinIndex_i=min(find(ref_i))-1;
912     MaxIndex_i=max(find(ref_i))-1;
913     MaxIndex_j=max(find(ref_j))-1;
914     MinIndex_j=min(find(ref_j))-1;
915    diff_j_max=diff(ref_j);
916    diff_i_max=diff(ref_i);
917    if ~isempty(diff_i_max) && isequal (diff_i_max,diff_i_max(1)*ones(size(diff_i_max)))
918        set(handles.num_incr_i,'String',num2str(diff_i_max(1)))% detect an increment to dispaly by default
919    end
920    if ~isempty(diff_j_max) && isequal (diff_j_max,diff_j_max(1)*ones(size(diff_j_max)))
921        set(handles.num_incr_j,'String',num2str(diff_j_max(1)))
922    end
923end
924if isequal(MinIndex_i,-1)
925    MinIndex_i=0;
926end
927if isequal(MinIndex_j,-1)
928    MinIndex_j=0;
929end
930MinIndex_i_table=get(handles.MinIndex_i,'Data'); % retrieve the min indices in the table MinIndex
931MinIndex_j_table=get(handles.MinIndex_j,'Data'); % retrieve the min indices in the table MinIndex
932MaxIndex_i_table=get(handles.MaxIndex_i,'Data'); % retrieve the min indices in the table MinIndex
933MaxIndex_j_table=get(handles.MaxIndex_j,'Data'); % retrieve the min indices in the table MinIndex
934if ~isempty(MinIndex_i)&&~isempty(MaxIndex_i)
935    MinIndex_i_table(iview,1)=MinIndex_i;
936    MaxIndex_i_table(iview,1)=MaxIndex_i;
937end
938if ~isempty(MinIndex_j)&&~isempty(MaxIndex_j)
939    MinIndex_j_table(iview,1)=MinIndex_j;
940    MaxIndex_j_table(iview,1)=MaxIndex_j;
941end
942set(handles.MinIndex_i,'Data',MinIndex_i_table)%display the min indices in the table MinIndex
943set(handles.MinIndex_j,'Data',MinIndex_j_table)%display the max indices in the table MaxIndex
944set(handles.MaxIndex_i,'Data',MaxIndex_i_table)%display the min indices in the table MinIndex
945set(handles.MaxIndex_j,'Data',MaxIndex_j_table)%display the max indices in the table MaxIndex
946SeriesData=get(handles.series,'UserData');
947
948%% adjust the first and last indices for the selected series, only if requested by the bounds
949% i index, compare input to min index i
950first_i=str2num(get(handles.num_first_i,'String')); % retrieve previous first i
951% ref_i=str2num(get(handles.num_ref_i,'String')); % index i given by the input field
952ref_i=1;
953if isfield(SeriesData,'ref_i')
954    ref_i=SeriesData.ref_i;
955end
956if isempty(first_i)
957    first_i=ref_i; % first_i updated by the input value
958elseif first_i < MinIndex_i
959    first_i=MinIndex_i; % first_i set to the min i index (restricted by oter input lines)
960elseif first_i >MaxIndex_i
961    first_i=MaxIndex_i; % first_i set to the max i index (restricted by oter input lines)
962end
963% j index,  compare input to min index j
964first_j=str2num(get(handles.num_first_j,'String'));
965ref_j=1;
966if isfield(SeriesData,'ref_j')
967    ref_j=SeriesData.ref_j;
968end
969if isempty(first_j)
970    first_j=ref_j; % first_j updated by the input value
971elseif first_j<MinIndex_j
972    first_j=MinIndex_j; % first_j set to the min j index (restricted by oter input lines)
973elseif first_j >MaxIndex_j
974    first_j=MaxIndex_j; % first_j set to the max j index (restricted by oter input lines)
975end
976% i index, compare input to max index i
977last_i=str2num(get(handles.num_last_i,'String'));
978if isempty(last_i)
979    last_i=ref_i;
980elseif last_i > MaxIndex_i
981    last_i=MaxIndex_i;
982elseif last_i<first_i
983    last_i=first_i;
984end
985% j index, compare input to max index j
986last_j=str2num(get(handles.num_last_j,'String'));
987if isempty(last_j)
988    last_j=ref_j;
989elseif last_j>MaxIndex_j
990    last_j=MaxIndex_j;
991elseif last_j<first_j
992    last_j=first_j;
993end
994set(handles.num_first_i,'String',num2str(first_i));
995set(handles.num_first_j,'String',num2str(first_j));
996set(handles.num_last_i,'String',num2str(last_i));
997set(handles.num_last_j,'String',num2str(last_j));
998
999%% number of slices set by default
1000NbSlice=[]; % default
1001% read  value set by the first series for the append mode (iwiew >1)
1002if iview>1 && strcmp(get(handles.num_NbSlice,'Visible'),'on')
1003    NbSlice=str2double(get(handles.num_NbSlice,'String'));
1004end
1005
1006%% default time settings
1007TimeUnit='';
1008% read  value set by the first series for the append mode (iwiew >1)
1009if iview>1
1010    TimeUnit=get(handles.TimeUnit,'String');
1011end
1012TimeName='';
1013Time=[]; % default
1014TimeMin=[];
1015TimeFirst=[];
1016TimeLast=[];
1017TimeMax=[];
1018
1019%%  read image documentation file if found
1020XmlData=[];
1021check_calib=0;
1022XmlFileName=find_imadoc(InputTable{iview,1},InputTable{iview,2},InputTable{iview,3},InputTable{iview,5});
1023if ~isempty(XmlFileName)
1024    [XmlData,errormsg]=imadoc2struct(XmlFileName);
1025    if ~isempty(errormsg)
1026        msgbox_uvmat('WARNING',['error in reading ' XmlFileName ': ' errormsg]);
1027    end
1028    % read time if available
1029    if isfield(XmlData,'Time')
1030        Time=XmlData.Time;
1031        TimeName='xml';
1032    end
1033    if isfield(XmlData,'Camera')
1034        if isfield(XmlData.Camera,'TimeUnit')&& ~isempty(XmlData.Camera.TimeUnit)
1035            if iview>1 && ~isempty(TimeUnit) && ~strcmp(TimeUnit,XmlData.Camera.TimeUnit)
1036                msgbox_uvmat('WARNING','inconsistent time unit with the first field series');
1037            end
1038            TimeUnit=XmlData.Camera.TimeUnit;
1039        end
1040    end
1041    % number of slices
1042    if isfield(XmlData,'TranslationMotor')&& isfield(XmlData.TranslationMotor,'NbSlice')
1043        NbSlice_motor=XmlData.TranslationMotor.NbSlice;
1044        if ~isempty(NbSlice) && ~isequal(NbSlice_motor,NbSlice)
1045                msgbox_uvmat('WARNING','inconsistent Z numbers of Z indices');
1046        else
1047            NbSlice=NbSlice_motor;
1048        end
1049    end
1050end
1051if ~isempty(NbSlice)
1052set(handles.num_NbSlice,'String',num2str(NbSlice))
1053set(handles.num_NbSlice,'Visible','on')
1054end
1055
1056%% read timing  from the current file (prioritary)
1057if ~isempty(VideoObject)% case of movies
1058    imainfo=get(VideoObject);
1059    if isempty(j1_series) % frame index along i
1060        Time=zeros(imainfo.NumberOfFrames+1,2);
1061        Time(:,2)=(0:1/imainfo.FrameRate:(imainfo.NumberOfFrames)/imainfo.FrameRate)';
1062    else
1063        Time=[0;ones(size(i1_series,3)-1,1)]*(0:1/imainfo.FrameRate:(imainfo.NumberOfFrames)/imainfo.FrameRate);
1064    end
1065    TimeName='video';
1066end
1067
1068
1069%% determine the min and max times: case of Netcdf files will be treated later in FieldName_Callback
1070if ~isempty(TimeName)
1071    TimeMin=Time(MinIndex_i+1,MinIndex_j+1);
1072    if size(Time)>=[first_i+1 first_j+1]
1073        TimeFirst=Time(first_i+1,first_j+1);
1074    end
1075    if size(Time)>=[last_i+1 last_j+1]
1076        TimeLast=Time(last_i+1,last_j+1);
1077    end
1078    if size(Time)>=[MaxIndex_i+1 MaxIndex_j+1]
1079        TimeMax=Time(MaxIndex_i+1,MaxIndex_j+1);
1080    end
1081end
1082
1083%% update the time table
1084TimeTable=get(handles.TimeTable,'Data');
1085TimeTable{iview,1}=TimeName;
1086TimeTable{iview,2}=TimeMin;
1087TimeTable{iview,3}=TimeFirst;
1088TimeTable{iview,4}=TimeLast;
1089TimeTable{iview,5}=TimeMax;
1090set(handles.TimeTable,'Data',TimeTable)
1091
1092%% update the series info in 'UserData'
1093SeriesData.i1_series{iview}=i1_series;
1094SeriesData.i2_series{iview}=i2_series;
1095SeriesData.j1_series{iview}=j1_series;
1096SeriesData.j2_series{iview}=j2_series;
1097SeriesData.FileType{iview}=FileInfo.FileType;
1098SeriesData.FileInfo{iview}=FileInfo;
1099SeriesData.Time{iview}=Time;
1100
1101SeriesData.TimeName=TimeName;
1102
1103if check_calib
1104    SeriesData.GeometryCalib{iview}=XmlData.GeometryCalib;
1105end
1106set(handles.series,'UserData',SeriesData)
1107
1108%% update pair menus
1109hset_pair=findobj(allchild(0),'Tag','set_pairs');
1110if ~isempty(hset_pair), delete(hset_pair); end % delete the GUI set_pair if opened
1111CheckPair= ~isempty(i2_series)||~isempty(j2_series); % check whether index pairs need to be defined
1112PairString=get(handles.PairString,'Data');
1113if CheckPair% if pairs need to be display for line iview
1114    [ModeMenu,ModeValue]=update_mode(i1_series,i2_series,j2_series);
1115    Menu=update_listpair(i1_series,i2_series,j1_series,j2_series,ModeMenu{ModeValue},Time,TimeUnit,ref_i,ref_j,TimeName,InputTable(iview,:),FileInfo);
1116    PairString{iview,1}=Menu{1};
1117else
1118    PairString{iview,1}=''; % no pair for #iview
1119end
1120set(handles.PairString,'Data',PairString)
1121if isempty(find(cellfun('isempty',get(handles.PairString,'Data'))==0, 1))% if all lines of pairs are empty
1122    set(handles.PairString,'Visible','off')
1123    set(handles.SetPairs,'Visible','off')
1124else
1125    set(handles.PairString,'Visible','on')
1126    set(handles.SetPairs,'Visible','on')
1127end
1128
1129
1130%% display the set of existing files as an image
1131set(handles.FileStatus,'Units','pixels')
1132Position=get(handles.FileStatus,'Position');
1133set(handles.FileStatus,'Units','normalized')
1134%xI=0.5:Position(3)-0.5;
1135nbview=numel(SeriesData.i1_series);
1136j_max=cell(1,nbview);
1137MaxIndex_i=ones(1,nbview); % default
1138MinIndex_i=ones(1,nbview); % default
1139for iline=1:nbview
1140    pair_max=squeeze(max(SeriesData.i1_series{iline},[],1)); % max on pair index
1141    j_max{iline}=max(pair_max,[],1); % max on j index
1142    if ~isempty(j_max{iline})
1143    MaxIndex_i(iline)=find(j_max{iline}, 1, 'last' )-1; % max ref index i
1144    MinIndex_i(iline)=find(j_max{iline}, 1 )-1; % min ref index i
1145    end
1146end
1147MinIndex_i=min(MinIndex_i);
1148MaxIndex_i=max(MaxIndex_i);
1149range_index=MaxIndex_i-MinIndex_i+1;
1150range_y=max(1,floor(Position(4)/nbview));
1151npx=floor(Position(3));
1152file_indices=MinIndex_i+floor(((0.5:npx-0.5)/npx)*range_index)+1;
1153CData=zeros(nbview*range_y,npx); % initiate the image representing the existing files
1154for iline=1:nbview
1155    ind_y=1+(iline-1)*range_y:iline*range_y;
1156    LineData=zeros(size(file_indices));
1157    file_select=file_indices(file_indices<=numel(j_max{iline}));
1158    ind_select=file_indices<=numel(j_max{iline});
1159    LineData(ind_select)=j_max{iline}(file_select)~=0;
1160    CData(ind_y,:)=ones(size(ind_y'))*LineData;
1161end
1162CData=cat(3,zeros(size(CData)),CData,zeros(size(CData))); % make color images r=0,g,b=0
1163set(handles.FileStatus,'CData',CData);
1164
1165%-----------------------------------------------------------guide -------------
1166%------------------------------------------------------------------------
1167%  III - FUNCTIONS ASSOCIATED TO THE FRAME IndexRange
1168%------------------------------------------------------------------------
1169
1170
1171% ---- determine the menu to put in mode and advice a default choice
1172%------------------------------------------------------------------------
1173function [ModeMenu,ModeValue]=update_mode(i1_series,i2_series,j2_series)
1174%------------------------------------------------------------------------   
1175ModeMenu={''};
1176if isempty(j2_series)% no j pair
1177    ModeValue=1;
1178    if ~isempty(i2_series)
1179        ModeMenu={'series(Di)'}; % pair menu with only option Di
1180    end
1181else %existence of j pairs
1182    pair_max=squeeze(max(i1_series,[],1)); % max on pair index
1183    j_max=max(pair_max,[],1);
1184    MaxIndex_i=find(j_max, 1, 'last' )-1; % max ref index i
1185    MinIndex_i=find(j_max, 1 )-1; % min ref index i
1186    i_max=max(pair_max,[],2);
1187    MaxIndex_j=find(i_max, 1, 'last' )-1; % max ref index i
1188    MinIndex_j=find(i_max, 1 )-1; % min ref index i
1189    if MaxIndex_j==MinIndex_j
1190        ModeValue=1;
1191        ModeMenu={'bursts'};
1192    elseif MaxIndex_i==MinIndex_i
1193        ModeValue=1;
1194        ModeMenu={'series(Dj)'};
1195    else
1196        ModeMenu={'bursts';'series(Dj)'};
1197        if (MaxIndex_j-MinIndex_j)>10
1198            ModeValue=2; % set mode to series(Dj) if more than 10 j values
1199        else
1200            ModeValue=1;
1201        end
1202    end
1203end
1204
1205
1206%------------------------------------------------------------------------
1207%fill the menu of possible pairs as input
1208function displ_pair=update_listpair(i1_series,i2_series,j1_series,j2_series,mode,time,TimeUnit,ref_i,ref_j,TimeName,InputTable,FileInfo)
1209%------------------------------------------------------------------------
1210displ_pair={};
1211if isempty(TimeUnit)
1212    dtunit='e-03';
1213else
1214    dtunit=['m' TimeUnit];
1215end
1216switch mode
1217    case 'series(Di)'
1218        diff_i=i2_series-i1_series;
1219        min_diff=min(diff_i(diff_i>0));
1220        max_diff=max(diff_i(diff_i>0));
1221        for ipair=min_diff:max_diff
1222            if ~isempty(find(diff_i==ipair,1))% if the considered difference exists as input
1223                pair_string=['Di= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2)) ];
1224                if size(time,1)>=ref_i+ceil(ipair/2)
1225                    if ref_i<=floor(ipair/2)
1226                        ref_i=floor(ipair/2)+1; % shift ref_i to get the first pair
1227                    end
1228                    Dt=time(ref_i+ceil(ipair/2),ref_j)-time(ref_i-floor(ipair/2),ref_j);
1229                    pair_string=[pair_string ', Dt=' num2str(Dt) ' ' dtunit];
1230                end
1231                displ_pair=[displ_pair;{pair_string}];
1232            end
1233        end
1234        if ~isempty(displ_pair)
1235            displ_pair=[displ_pair;{'Di=*|*'}];
1236        end
1237    case 'series(Dj)'
1238        if isempty(j2_series)
1239            msgbox_uvmat('ERROR','no j1-j2 pair available')
1240            return
1241        end
1242        diff_j=j2_series-j1_series;
1243        min_diff=min(diff_j(diff_j>0));
1244        max_diff=max(diff_j(diff_j>0));
1245        for ipair=min_diff:max_diff
1246            if numel(diff_j(diff_j==ipair))>0
1247                pair_string=['Dj= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2)) ];
1248                if ~isempty(time)
1249                    if ref_j<=floor(ipair/2)
1250                        ref_j=floor(ipair/2)+1; % shift ref_i to get the first pair
1251                    end
1252                    Dt=time(ref_i,ref_j+ceil(ipair/2))-time(ref_i,ref_j-floor(ipair/2));
1253                    pair_string=[pair_string ', Dt=' num2str(Dt) ' ' dtunit];
1254                end
1255                displ_pair=[displ_pair;{pair_string}];
1256            end
1257        end
1258        if ~isempty(displ_pair)
1259            displ_pair=[displ_pair;{'Dj=*|*'}];
1260        end
1261    case 'bursts'
1262        if isempty(j2_series)
1263            msgbox_uvmat('ERROR','no j1-j2 pair available')
1264            return
1265        end
1266        %diff_j=j2_series-j1_series;
1267        min_j1=min(j1_series(j1_series>0));
1268        max_j1=max(j1_series(j1_series>0));
1269        min_j2=min(j2_series(j2_series>0));
1270        max_j2=max(j2_series(j2_series>0));
1271        for pair1=min_j1:min(max_j1,min_j1+20)
1272            for pair2=min_j2:min(max_j2,min_j2+20)
1273                if numel(j1_series(j1_series==pair1))>0 && numel(j2_series(j2_series==pair2))>0
1274                    pair_string=['j= ' num2str(pair1) '-' num2str(pair2)];
1275                    [TimeValue,DtValue]=get_time(ref_i,[],pair_string,InputTable,FileInfo,TimeName,'Dt');
1276                    %Dt=time(ref_i,pair2+1)-time(ref_i,pair1+1);
1277                    pair_string=[pair_string ', Dt=' num2str(DtValue) ' ' dtunit];
1278                    displ_pair=[displ_pair;{pair_string}];
1279                end
1280            end
1281        end
1282        if ~isempty(displ_pair)
1283            displ_pair=[displ_pair;{'j=*-*'}];
1284        end
1285end
1286
1287%------------------------------------------------------------------------
1288function num_first_i_Callback(hObject, eventdata, handles)
1289%------------------------------------------------------------------------
1290num_last_i_Callback(hObject, eventdata, handles)
1291
1292%------------------------------------------------------------------------
1293function num_last_i_Callback(hObject, eventdata, handles)
1294%------------------------------------------------------------------------
1295SeriesData=get(handles.series,'UserData');
1296if ~isfield(SeriesData,'Time')
1297    SeriesData.Time{1}=[];
1298end
1299displ_time(handles);
1300
1301%------------------------------------------------------------------------
1302function num_first_j_Callback(hObject, eventdata, handles)
1303%------------------------------------------------------------------------
1304 num_last_j_Callback(hObject, eventdata, handles)
1305
1306%------------------------------------------------------------------------
1307function num_last_j_Callback(hObject, eventdata, handles)
1308%------------------------------------------------------------------------
1309% first_j=str2num(get(handles.num_first_j,'String'));
1310% last_j=str2num(get(handles.num_last_j,'String'));
1311% ref_j=ceil((first_j+last_j)/2);
1312% set(handles.num_ref_j,'String', num2str(ref_j))
1313% num_ref_j_Callback(hObject, eventdata, handles)
1314SeriesData=get(handles.series,'UserData');
1315if ~isfield(SeriesData,'Time')
1316    SeriesData.Time{1}=[];
1317end
1318displ_time(handles);
1319
1320%------------------------------------------------------------------------
1321% ---- find the times corresponding to the first and last indices of a series
1322function displ_time(handles)
1323%------------------------------------------------------------------------
1324SeriesData=get(handles.series,'UserData'); %
1325if ~isfield(SeriesData,'Time')
1326    return
1327end
1328PairString=get(handles.PairString,'Data');
1329ref_i_1=str2num(get(handles.num_first_i,'String')); % first reference index
1330ref_i_2=str2num(get(handles.num_last_i,'String')); % last reference index
1331ref_j_1=[];ref_j_2=[];
1332if strcmp(get(handles.num_first_j,'Visible'),'on')
1333ref_j_1=str2num(get(handles.num_first_j,'String'));
1334ref_j_2=str2num(get(handles.num_last_j,'String'));
1335end
1336[i1_1,i2_1,j1_1,j2_1] = get_file_index(ref_i_1,ref_j_1,PairString);
1337[i1_2,i2_2,j1_2,j2_2] = get_file_index(ref_i_2,ref_j_2,PairString);
1338TimeTable=get(handles.TimeTable,'Data');
1339%%%%%%
1340%TODO: read time in netcdf file, see ActionName_Callback
1341%%%%%%%
1342%Pairs=get(handles.PairString,'Data');
1343for iview=1:size(TimeTable,1)
1344    if size(SeriesData.Time,1)<iview
1345        break
1346    end
1347    TimeTable{iview,3}=[];
1348    TimeTable{iview,4}=[];
1349    if size(SeriesData.Time{iview},1)>=i2_2+1 && (isempty(ref_j_1)||size(SeriesData.Time{iview},2)>=j2_2+1)
1350        if isempty(ref_j_1)
1351            time_first=(SeriesData.Time{iview}(i1_1+1,2)+SeriesData.Time{iview}(i2_1+1,2))/2;
1352            time_last=(SeriesData.Time{iview}(i1_2+1,2)+SeriesData.Time{iview}(i2_2+1,2))/2;
1353        else
1354            time_first=(SeriesData.Time{iview}(i1_1+1,j1_1+1)+SeriesData.Time{iview}(i2_1+1,j2_1+1))/2;
1355            time_last=(SeriesData.Time{iview}(i1_2+1,j1_2+1)+SeriesData.Time{iview}(i2_2+1,j2_1+1))/2;
1356        end
1357        TimeTable{iview,3}=time_first; % TODO: take into account pairs
1358        TimeTable{iview,4}=time_last; % TODO: take into account pairs
1359    end
1360end
1361set(handles.TimeTable,'Data',TimeTable)
1362
1363%% set the waitbar position with respect to the min and max in the series
1364MinIndex_i=min(get(handles.MinIndex_i,'Data'));
1365MaxIndex_i=max(get(handles.MaxIndex_i,'Data'));
1366pos_first=(ref_i_1-MinIndex_i)/(MaxIndex_i-MinIndex_i+1);
1367pos_last=(ref_i_2-MinIndex_i+1)/(MaxIndex_i-MinIndex_i+1);
1368if isempty(pos_first), pos_first=0; end
1369if isempty(pos_last), pos_last=1; end
1370Position=get(handles.Waitbar,'Position'); % position of the waitbar:= [ x,y, width, height]
1371Position_status=get(handles.FileStatus,'Position');
1372Position(1)=Position_status(1)+Position_status(3)*pos_first;
1373Position(3)=max(Position_status(3)*(pos_last-pos_first),0.001); % width must remain positive
1374set(handles.Waitbar,'Position',Position)
1375update_waitbar(handles.Waitbar,0)
1376
1377%------------------------------------------------------------------------
1378% --- Executes when selected cell(s) is changed in PairString.
1379function PairString_CellSelectionCallback(hObject, eventdata, handles)
1380%------------------------------------------------------------------------   
1381if numel(eventdata.Indices)>=1
1382    PairString=get(hObject,'Data');
1383    if ~isempty(PairString{eventdata.Indices(1)})
1384        SetPairs_Callback(hObject, eventdata.Indices(1), handles)
1385    end
1386end
1387
1388%-------------------------------------
1389function enable_i(handles,state)
1390set(handles.i_txt,'Visible',state)
1391set(handles.num_first_i,'Visible',state)
1392set(handles.num_last_i,'Visible',state)
1393set(handles.num_incr_i,'Visible',state)
1394
1395%-----------------------------------
1396function enable_j(handles,state)
1397set(handles.j_txt,'Visible',state)
1398set(handles.num_first_j,'Visible',state)
1399set(handles.num_last_j,'Visible',state)
1400set(handles.num_incr_j,'Visible',state)
1401set(handles.MinIndex_j,'Visible',state)
1402set(handles.MaxIndex_j,'Visible',state)
1403
1404
1405%%%%%%%%%%%%%%%%%%%%
1406%%  MAIN ActionName FUNCTIONS
1407%%%%%%%%%%%%%%%%%%%%
1408%------------------------------------------------------------------------
1409% --- Executes on button press in RUN.
1410%------------------------------------------------------------------------
1411function RUN_Callback(hObject, eventdata, handles)
1412
1413%% settings of the button RUN
1414if ~isequal(get(handles.ActionInput,'BackgroundColor'),[1 0 0])
1415    msgbox_uvmat('ERROR','first activate the button ActionInput')
1416    return
1417end
1418set(handles.RUN,'BusyAction','queue'); % activation of STOP button will set BusyAction to 'cancel'
1419set(handles.RUN, 'Enable','Off')% avoid further RUN action until the current one is finished
1420set(handles.RUN,'BackgroundColor',[1 1 0])%show activation of RUN by yellow color
1421drawnow
1422set(handles.status,'Value',0)% desable status display if relevant
1423status_Callback([], eventdata, handles)
1424
1425%% launch action
1426errormsg=launch_action(handles);
1427if ~isempty(errormsg)
1428     msgbox_uvmat('ERROR',errormsg)
1429end
1430
1431%% reset the GUI series
1432update_waitbar(handles.Waitbar,1); % put the waitbar to end position to indicate launching is finished
1433set(handles.RUN, 'Enable','On')
1434set(handles.RUN,'BackgroundColor',[1 0 0])
1435set(handles.RUN, 'Value',0)
1436
1437%------------------------------------------------------------------------
1438% --- called by RUN_Callback
1439%------------------------------------------------------------------------
1440% The calculations are launched in three different ways:
1441% RunMode='local': calculation on the local Matlab session, will prevent other actions during that time.
1442% RunMode='background': calculation on the local computer, but in a new Matlab session (with no graphic output).
1443% RunMode='cluster': calculations dispatched in a cluster, using a managing system, 'oar, 'sge, or 'sgb'.
1444% In the latter case, the calculation is split in 'packets' of i index (all j indices are contained in a single packet).
1445% This splitting is possible only if the different calculations in the series are independent. Otherwise the action
1446% function imposes a number of processes NbSlice in input, for instance NbSlice=1 for a time series.
1447% If NbSlice is not imposed, the splitting in packets (jobs) is determined
1448% so that a job is optimum length AdvisedJobCPUTime), and the total job number in any case smaller
1449% than MaxJobNumber (these parameters are defined in the file series.xml in
1450% accordance with the management strategy for the cluster). The jobs are
1451% dispatched in parallel into NbCore processors by the cluster managing system.
1452
1453function errormsg=launch_action(handles)
1454errormsg=''; % default
1455
1456%% read the data on the GUI series
1457Param=read_GUI_series(handles); % displayed parameters
1458SeriesData=get(handles.series,'UserData'); % hidden parameters
1459if isfield(SeriesData,'TransformInput')
1460    Param.TransformInput=SeriesData.TransformInput;
1461end
1462if isfield(SeriesData,'ProjObject')
1463    Param.ProjObject=SeriesData.ProjObject;
1464end
1465if ~isfield(SeriesData,'i1_series')
1466    errormsg='The input field series needs to be refreshed: press REFRESH';
1467    return
1468end
1469if isfield(Param,'InputFields')&& isfield(Param.InputFields,'FieldName')&& isequal(Param.InputFields.FieldName,'add_field...')
1470    errormsg='input field name(s) not defined, select add_field...';
1471    return
1472end
1473
1474%% select the Action mode, 'local', 'background' or 'cluster' (if available)
1475RunMode='local'; % default (needed for first opening of the GUI series)
1476if isfield(Param.Action,'RunMode')
1477    RunMode=Param.Action.RunMode;
1478    Param.Action=rmfield(Param.Action,'RunMode'); % remove from the recorded xml file to avoid interference during ImportConfig
1479    Param.RunMode=RunMode; % keep track of the mode
1480end
1481ActionExt='.m'; % default
1482if isfield(Param.Action,'ActionExt')
1483    ActionExt=Param.Action.ActionExt; % '.m', '.sh' (compiled)  or '.py' (Python)
1484    Param.Action=rmfield(Param.Action,'ActionExt'); % remove from the recorded xml file to avoid interference during ImportConfig
1485end
1486ActionName=Param.Action.ActionName;
1487ActionPath=Param.Action.ActionPath;
1488path_series=fileparts(which('series'));
1489
1490%% create the Action fct handle if RunMode option = 'local'
1491if strcmp(RunMode,'local')
1492    if ~isequal(ActionPath,path_series)
1493        eval(['spath=which(''' ActionName ''');']) %spath = current path of the selected function ACTION
1494        if ~exist(ActionPath,'dir')
1495            errormsg=['The prescribed function path ' ActionPath ' does not exist'];
1496            return
1497        end
1498        if ~isequal(spath,ActionPath)
1499            addpath(ActionPath)% add the prescribed path if not the current one
1500        end
1501    end
1502    eval(['h_fun=@' ActionName ';'])%create a function handle for ACTION
1503    if ~isequal(ActionPath,path_series)
1504        rmpath(ActionPath)% add the prescribed path if not the current one
1505    end
1506end
1507
1508%% Get  parameters from series.xml
1509errormsg=''; % default error message
1510ActionFullName=fullfile(get(handles.ActionPath,'String'),ActionName);
1511
1512%% If a compiled version has been selected (ext .sh) check wether it needs to be recompiled
1513if strcmp(ActionExt,'.sh')
1514    TransformPath='';
1515    if isfield(SeriesData,'TransformPath')
1516        TransformPath=SeriesData.TransformPath;
1517        if isfield(SeriesData,'TransformList')
1518            TransformList=get(handles.TransformName,'String');
1519            TransformIndex=get(handles.TransformName,'Value');
1520            TransformName=TransformList{TransformIndex};
1521            if ~ismember(TransformName,SeriesData.TransformList)
1522                TransformPath='';
1523            end
1524        end
1525    end
1526    if ~isempty(TransformPath)&&...
1527          ~strcmp(TransformPath,get(handles.TransformPath,'String'))% if the transform is not in paths set for compilation
1528        msgbox_uvmat('ERROR', 'compilation not available for this transform function, select .m')
1529        return
1530    end
1531    set(handles.series,'Pointer','watch') % set the mouse pointer to 'watch'
1532    set(handles.ActionExt,'BackgroundColor',[1 1 0])
1533    [mcrmajor, mcrminor] = mcrversion;   
1534    MCRROOT = ['MCRROOT',int2str(mcrmajor),int2str(mcrminor)];
1535    RunTime = getenv('MCRROOT'); % Just variable MCRROOT with no version in it's name
1536    if strcmp(RunTime,'')
1537        RunTime = getenv(MCRROOT); % Use specialize MCRROOT with version
1538    end
1539    ActionNameVersion=[ActionName '_' MCRROOT];
1540    ActionFullName=fullfile(get(handles.ActionPath,'String'),[ActionNameVersion '.sh']);
1541    % compile the .m file if the .sh file does not exist yet
1542    if ~exist(ActionFullName,'file')
1543        answer=msgbox_uvmat('INPUT_Y-N','compiled version has not been created: compile now?');
1544        if strcmp(answer,'Yes')
1545            set(handles.ActionExt,'BackgroundColor',[1 1 0])
1546            path_uvmat=fileparts(which('series'));
1547            currentdir=pwd;
1548            cd(get(handles.ActionPath,'String'))% go to the directory of Action
1549            addpath(path_uvmat)% add the path to uvmat to run the fct 'compile'
1550            compile(ActionName,TransformPath)
1551            cd(currentdir)
1552        else
1553            errormsg='Action launch interrupted';
1554            return
1555        end       
1556    else
1557        sh_file_info=dir(fullfile(get(handles.ActionPath,'String'),[ActionNameVersion '.sh']));
1558        m_file_info=dir(fullfile(get(handles.ActionPath,'String'),[ActionName '.m']));
1559        if isfield(m_file_info,'datenum') && m_file_info.datenum>sh_file_info.datenum
1560            set(handles.ActionExt,'BackgroundColor',[1 1 0])
1561            drawnow
1562            answer=msgbox_uvmat('INPUT_Y-N',[ActionNameVersion '.sh needs to be updated: recompile now?']);
1563            if strcmp(answer,'Yes')
1564                path_uvmat=fileparts(which('series'));
1565                currentdir=pwd;
1566                cd(get(handles.ActionPath,'String'))% go to the directory of Action
1567                addpath(path_uvmat)% add the path to uvmat to run the fct 'compile'
1568                addpath(fullfile(path_uvmat,'transform_field'))% add the path to transform functions to run the fct 'compile'
1569                compile(ActionName,TransformPath)
1570                cd(currentdir)
1571            end
1572        end
1573    end
1574
1575    set(handles.ActionExt,'BackgroundColor',[1 1 1])
1576     set(handles.series,'Pointer','arrow') % set the mouse pointer to 'watch
1577end
1578
1579%% set nbre of cluster cores and processes:
1580% NbCore is the number of computer processors used
1581% NbProcess is the number of independent processes in which the required calculation is split.
1582switch RunMode
1583    case {'local','background'}
1584        NbCore=1; % no need to split the calculation
1585    case 'cluster'
1586        %proposed number of cores to reserve in the cluster
1587        NbCoreAdvised=SeriesData.SeriesParam.ClusterParam.NbCoreAdvised;
1588        NbCoreMax=SeriesData.SeriesParam.ClusterParam.NbCoreMax;
1589        if NbCoreMax~=1
1590            if strcmp(ActionExt,'.m')% case of Matlab function (uncompiled)
1591                warning_string=', preferably use .sh option to save Matlab licences';
1592            else
1593                warning_string=')';
1594            end
1595            answer=msgbox_uvmat('INPUT_TXT',['Number of cores (max ' num2str(NbCoreMax) ', ' warning_string],num2str(NbCoreAdvised));
1596            if isempty(answer)
1597                errormsg='Action launch interrupted by user';
1598                return
1599            end
1600            NbCore=str2double(answer);
1601            if NbCore > NbCoreMax
1602                NbCore=NbCoreMax;
1603            end
1604        else
1605            NbCore=1;
1606        end
1607end
1608if ~isfield(Param.IndexRange,'NbSlice')
1609    Param.IndexRange.NbSlice=[];
1610end
1611OutputPath=get(handles.OutputPath,'String');
1612
1613%% Look for processing on multiple experiments set by the GUI browse_data
1614NbExp=1;% initiate the number of experiments set by the GUI browse_data, =1 otherwise
1615if get(handles.Replicate,'Value')
1616    hh=findobj(allchild(0),'Tag','browse_data');
1617    if isempty(hh)
1618        set(handles.Replicate,'Value',0)
1619    else
1620        set(handles.Replicate,'BackgroundColor',[1 1 0])%paint Relicate button in yellow
1621        BrowseData=guidata(hh);
1622        SourceDir=get(BrowseData.SourceDir,'String');
1623        ListExp=get(BrowseData.ListExperiments,'String');
1624        ExpIndices=get(BrowseData.ListExperiments,'Value');
1625        ListExp=ListExp(ExpIndices);
1626        ListDevices=get(BrowseData.ListDevices,'String');
1627        DeviceIndices=get(BrowseData.ListDevices,'Value');
1628        ListDevices=ListDevices(DeviceIndices);
1629        ListDataSeries=get(BrowseData.DataSeries,'String');
1630        DataSeriesIndices=get(BrowseData.DataSeries,'Value');
1631        ListDataSeries=ListDataSeries(DataSeriesIndices);
1632        NbExp=0; % counter of the number of experiments set by the GUI browse_data
1633        for iexp=1:numel(ListExp)
1634            if ~isempty(regexp(ListExp{iexp},'^\+/'))% if it is a folder
1635               %if strcmp(get(BrowseData.DataSeries,'enable'),'off') %case of a multiple input line for series
1636%                     NbExp=NbExp+1;
1637%                     ExpIndex{NbExp}=iexp;
1638%                     for idevice=1:numel(ListDevices)
1639%                         lpath= fullfile(SourceDir,regexprep(ListExp{iexp},'^\+/',''),...
1640%                             regexprep(ListDevices{idevice},'^\+/',''));
1641%                         lpathout=fullfile(OutputPath,regexprep(ListExp{iexp},'^\+/',''),...
1642%                             regexprep(ListDevices{idevice},'^\+/',''));
1643%                         ldir=regexprep(ListDataSeries{idevice},'^\+/','');
1644%                         ListPath{idevice,NbExp}=lpath;
1645%                         ListPathOut{idevice,NbExp}=lpathout;
1646%                         ListSubdir{idevice,NbExp}=ldir;
1647%                     end
1648                %else
1649                    for idevice=1:numel(ListDevices)
1650                        if ~isempty(regexp(ListDevices{idevice},'^\+/'))% if it is a folder
1651                            for isubdir=1:numel(ListDataSeries)
1652                                if ~isempty(regexp(ListDataSeries{isubdir},'^\+/'))% if it is a folder
1653                                    lpath= fullfile(SourceDir,regexprep(ListExp{iexp},'^\+/',''),...
1654                                        regexprep(ListDevices{idevice},'^\+/',''));
1655                                    lpathout= fullfile(OutputPath,regexprep(ListExp{iexp},'^\+/',''),...
1656                                        regexprep(ListDevices{idevice},'^\+/',''));
1657                                    ldir= regexprep(ListDataSeries{isubdir},'^\+/','');
1658                                    if exist(fullfile(lpath,ldir),'dir')
1659                                        NbExp=NbExp+1;
1660                                        ExpIndex(NbExp)=ExpIndices(iexp);
1661                                        DeviceIndex(NbExp)=DeviceIndices(idevice);
1662                                        ListPath{NbExp}=lpath;
1663                                        ListPathOut{NbExp}=lpathout;
1664                                        ListDeviceOut{NbExp}=regexprep(ListDevices{idevice},'^\+/','');
1665                                        ListExpOut{NbExp}=regexprep(ListExp{iexp},'^\+/','');
1666                                        ListSubdir{NbExp}=ldir;
1667                                    end
1668                                end
1669                            end
1670                        end
1671                    end
1672%                 end
1673            end
1674        end
1675        answer=msgbox_uvmat('INPUT_Y-N-Cancel',['replicate the processing on ' num2str(NbExp) ' data series']);
1676        if strcmp(answer,'Cancel')||strcmp(answer,'No')
1677            return
1678        end
1679    end
1680end
1681
1682%%%%%%%%%%%%%%%%%%% LOOP ON EXPERIMENTS POSSIBLY SET BY THE GUI browse_data, NbExp=1 otherwise %%%%%%%%%
1683
1684for iexp=1:NbExp
1685    if get(handles.Replicate,'Value')
1686        if ~strcmp(get(handles.RUN,'BusyAction'),'queue')% allow for STOP action
1687            disp('program stopped by user')
1688            return
1689        end
1690        set(BrowseData.ListExperiments,'Value',ExpIndex(iexp))
1691        set(BrowseData.ListDevices,'Value',DeviceIndex(iexp))
1692        Param.InputTable(:,1)=ListPath(:,iexp);
1693        Param.InputTable(:,2)=ListSubdir(:,iexp);
1694        OutputSubDir=unique(ListSubdir(:,iexp));
1695        Param.OutputSubDir=OutputSubDir{1};
1696        if numel(OutputSubDir)>1% case
1697            for iout=2:numel(OutputSubDir)
1698                Param.OutputSubDir=[Param.OutputSubDir '-' OutputSubDir{iout}];
1699            end               
1700        end       
1701    end
1702    [xx,ExpName]=fileparts(Param.InputTable{1,1});
1703    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
1704    Param.IndexRange.last_i=str2num(get(handles.num_last_i,'String'));
1705   
1706    %% create the output data directory if needed, after checking its existence
1707    OutputDir='';
1708    answer='';
1709    if isfield(Param,'OutputSubDir')% possibly update the output dir if it already exists
1710        PathOut=get(handles.OutputPath,'String');
1711        if ~exist(PathOut,'dir') % test if  the dir  already exist
1712            PathOut=uigetdir(PathOut,'pick the output root path');
1713            set(handles.OutputPath,'String',PathOut);
1714        end
1715        %PathExpOut=fullfile(PathOut,get(handles.Experiment,'String'));
1716        PathExpOut=fileparts(ListPath{iexp});
1717        if ~exist(PathExpOut,'dir')
1718            [tild,msg1]=mkdir(PathExpOut);
1719            if ~strcmp(msg1,'')
1720                errormsg=['cannot create ' PathExpOut ': ' msg1]; % error message for directory creation
1721                return
1722            end
1723        end
1724        %PathExpDeviceOut=fullfile(PathExpOut,get(handles.Device,'String'));
1725        PathExpDeviceOut=ListPath{iexp};
1726        if ~exist(PathExpDeviceOut,'dir')
1727            [tild,msg1]=mkdir(PathExpDeviceOut);
1728            if ~strcmp(msg1,'')
1729                errormsg=['cannot create ' PathExpDeviceOut ': ' msg1]; % error message for directory creation
1730                return
1731            end
1732        end
1733        SubDirOut=[Param.OutputSubDir Param.OutputDirExt];
1734        SubDirOutNew=SubDirOut;
1735        detect=exist(fullfile(PathExpDeviceOut,SubDirOutNew),'dir'); % test if  the dir  already exist
1736        check_create=1; % need to create the result directory by default
1737        CheckOverwrite=1;
1738        if isfield(Param,'CheckOverwrite')
1739            CheckOverwrite=Param.CheckOverwrite;% will overwrite previous data if it is equal to 1
1740        end
1741        while detect
1742            if CheckOverwrite
1743                comment=', possibly overwrite previous data';
1744            else
1745                comment=', will complement existing result files (no overwriting)';
1746            end
1747            answer=msgbox_uvmat('INPUT_Y-N-Cancel',['use existing ouput directory: ' fullfile(PathExpDeviceOut,SubDirOutNew) comment]);
1748            if strcmp(answer,'Cancel')
1749                break
1750            elseif strcmp(answer,'Yes')
1751                detect=0;
1752                check_create=0;
1753            else
1754                r=regexp(SubDirOutNew,'(?<root>.*\D)(?<num1>\d+)$','names'); % detect whether name ends by a number
1755                if isempty(r)
1756                    r(1).root=[SubDirOutNew '_'];
1757                    r(1).num1='0';
1758                end
1759                SubDirOutNew=[r(1).root num2str(str2num(r(1).num1)+1)]; % increment the index by 1 or put 1
1760                detect=exist(fullfile(PathExpDeviceOut,SubDirOutNew),'dir'); % test if  the dir  already exists
1761                check_create=1;
1762            end
1763        end
1764        if strcmp(answer,'Cancel')
1765            continue
1766        end
1767        Param.OutputDirExt=regexprep(SubDirOutNew,['^' Param.OutputSubDir],'');
1768        Param.OutputRootFile=Param.InputTable{1,3}; % the first sorted RootFile taken for output
1769        OutputDir=fullfile(PathExpDeviceOut,[Param.OutputSubDir Param.OutputDirExt]); % full name (with path) of output directory
1770        if check_create    % create output directory if it does not exist
1771            [tild,msg1]=mkdir(OutputDir);
1772            if ~strcmp(msg1,'')
1773                errormsg=['cannot create ' OutputDir ': ' msg1]; % error message for directory creation
1774                return
1775            end
1776        end
1777       
1778    elseif isfield(Param,'ActionInput')&&isfield(Param.ActionInput,'LogPath')% custom definition of the output dir
1779        OutputDir=Param.ActionInput.LogPath;
1780    end
1781    if isfield(Param,'OutputSubDir')
1782    set(handles.OutputSubDir,'String',Param.OutputSubDir)
1783    set(handles.OutputDirExt,'String',Param.OutputDirExt)
1784    drawnow
1785    end
1786    if get(handles.Replicate,'Value')
1787        set(handles.InputTable,'Data',Param.InputTable)
1788        set(handles.OutputPath,'String',OutputPath)
1789         set(handles.Experiment,'String',ListExpOut{iexp})
1790        set(handles.Device,'String',ListDeviceOut{iexp})
1791        Param.Experiment=ListExpOut{iexp};
1792        Param.Device=ListDeviceOut{iexp};
1793        check_input_file_series(handles)     
1794    end
1795    DirXml=fullfile(OutputDir,'0_XML');
1796    if ~exist(DirXml,'dir')
1797        [~,msg1]=mkdir(DirXml);
1798        if ~strcmp(msg1,'')
1799            errormsg=['cannot create ' DirXml ': ' msg1]; % error message for directory creation
1800            return
1801        end
1802        [success,msg] = fileattrib(DirXml,'+w','g','s'); % allow writing access for the group of users, recursively in the folder
1803        if success==0
1804            msgbox_uvmat('WARNING',{['unable to set group write access to ' DirXml ':']; msg}); % error message for directory creation
1805        end
1806    end
1807    OutputNomType=nomtype2pair(Param.InputTable{1,4}); % nomenclature for output files
1808   
1809    %% get the set of reference input field indices
1810    first_i=1; % first i index to process
1811    last_i=1; % last i index to process
1812    incr_i=1; % increment step in i index
1813    first_j=1; % first j index to process
1814    last_j=1; % last j index to process
1815    incr_j=1; % increment step in j index
1816    if isfield(Param.IndexRange,'first_i')
1817        first_i=Param.IndexRange.first_i;
1818        incr_i=Param.IndexRange.incr_i;
1819        last_i=Param.IndexRange.last_i;
1820    end
1821    if isfield(Param.IndexRange,'incr_j')
1822        first_j=Param.IndexRange.first_j;
1823        last_j=Param.IndexRange.last_j;
1824        incr_j=Param.IndexRange.incr_j;
1825    end
1826    if last_i < first_i || last_j < first_j
1827        errormsg= 'series/Run_Callback:last field index must be larger or equal to the first one';
1828        return
1829    end
1830    %incr_i must be defined, =1 by default, if NbSlice is active
1831    if isempty(incr_i)&& ~isempty(Param.IndexRange.NbSlice)
1832        incr_i=1;
1833        set(handles.num_incr_i,'String','1')
1834    end
1835    % case of no increment i defined: processing is done on the available files found in i1_series
1836    if isempty(incr_i)
1837        if isempty(incr_j)
1838            [ref_j,ref_i]=find(squeeze(SeriesData.i1_series{1}(1,:,:)));
1839            ref_j=ref_j(ref_j>=first_j & ref_j<=last_j);
1840            ref_i=ref_i(ref_i>=first_i & ref_i<=last_i);
1841            ref_j=ref_j-1;
1842            ref_i=ref_i-1;
1843        else
1844            ref_j=first_j:incr_j:last_j;
1845            [tild,ref_i]=find(squeeze(SeriesData.i1_series{1}(1,:,:)));
1846            ref_i=ref_i-1;
1847            ref_i=ref_i(ref_i>=first_i & ref_i<=last_i);
1848        end
1849        % increment i is defined: processing is done on first_i:incr_i:last_i;
1850    else
1851        ref_i=first_i:incr_i:last_i;
1852        if isempty(incr_j)% automatic finding of the existing j indices
1853            [ref_j,tild]=find(squeeze(SeriesData.i1_series{1}(1,:,:)));
1854            ref_j=ref_j-1;
1855            ref_j=ref_j(ref_j>=first_j & ref_j<=last_j);
1856        else
1857            ref_j=first_j:incr_j:last_j;
1858        end
1859    end
1860    nbfield_j=numel(ref_j); % number of j indices
1861    BlockLength=numel(ref_i); % by default, job involves the full set of i field indices
1862    NbProcess=1;
1863    switch RunMode
1864        case 'cluster'
1865            if (isfield(Param.Action, 'CPUTime') && ~isempty(Param.Action.CPUTime))
1866                CPUTime=Param.Action.CPUTime; % Note: CpUTime for one iteration ref_i has to be multiplied by the number of j indices nbfield_j
1867            else
1868                answer=msgbox_uvmat('INPUT_TXT','estimate the CPU time(in minutes) for each value of index i:' ,'');
1869                CPUTime=str2num(answer);
1870                set(handles.num_CPUTime,'String',answer)
1871                Param.Action.CPUTime=CPUTime;
1872            end
1873            JobNumberMax=SeriesData.SeriesParam.ClusterParam.JobNumberMax;
1874            JobCPUTimeAdvised=SeriesData.SeriesParam.ClusterParam.JobCPUTimeAdvised;
1875            if isempty(Param.IndexRange.NbSlice)% if NbSlice is not defined
1876                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.
1877                BlockLength=max(BlockLength,ceil(numel(ref_i)*NbExp/JobNumberMax)); % possibly increase the BlockLength to have less than MaxJobNumber jobs
1878                NbProcess=ceil(numel(ref_i)/BlockLength) ; % nbre of processes sent to oar
1879            else
1880                NbProcess=Param.IndexRange.NbSlice; % the parameter NbSlice sets the nbre of run processes
1881            end
1882            NbCore=min(NbCore,NbProcess); % reduces the number of cores if it exceeds the number of processes
1883        otherwise
1884            if ~isempty(Param.IndexRange.NbSlice)
1885                NbProcess=Param.IndexRange.NbSlice; % the parameter NbSlice sets the nbre of run processes
1886            end
1887    end
1888   
1889    %% record nbre of output files and starting time for computation for status
1890    StatusData=get(handles.status,'UserData');
1891    if isfield(StatusData,'OutputFileMode')
1892        switch StatusData.OutputFileMode
1893            case 'NbInput'
1894                StatusData.NbOutputFile=numel(ref_i)*nbfield_j;
1895            case 'NbInput_i'
1896                StatusData.NbOutputFile=numel(ref_i);
1897            case 'NbSlice'
1898                StatusData.NbOutputFile=str2num(get(handles.num_NbSlice,'String'));
1899        end
1900    end
1901    StatusData.TimeStart=now;
1902    set(handles.status,'UserData',StatusData)
1903   
1904    %% case of a function in Python
1905    if strcmp(ActionExt, '.py (in dev.)')
1906        fprintf([
1907            '\n' ...
1908            '!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n' ...
1909            'The option .py is used. It is still in development.\n' ...
1910            'To try it, first install pyper and the most recent version of fluidimage\n' ...
1911            '(see https://bitbucket.org/fluiddyn/fluidimage).\n' ...
1912            'Warning: there is no direct correspondance between UVMAT and fluidimage parameters\n' ...
1913            '!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n'])
1914        RunMode = 'python';
1915    end
1916   
1917   
1918    %% direct processing on the current Matlab session or creation of command files
1919    filexml=cell(1,NbProcess); % initialisation of the names of the files containing the processing parameters
1920    extxml=cell(1,NbProcess); % initialisation of the set of labels used for the files documenting each process
1921    for iprocess=1:NbProcess
1922        extxml{iprocess}='.xml';
1923    end
1924    for iprocess=1:NbProcess
1925        if ~strcmp(get(handles.RUN,'BusyAction'),'queue')% allow for STOP action
1926            disp('program stopped by user')
1927            return
1928        end
1929        Param.IndexRange.incr_slice=incr_i;
1930        if isempty(Param.IndexRange.NbSlice)
1931            Param.IndexRange.first_i=first_i+(iprocess-1)*BlockLength*incr_i;
1932            if Param.IndexRange.first_i>last_i
1933                NbProcess=iprocess-1; % leave the loop, we are at the end of the calculation
1934                break
1935            end
1936            Param.IndexRange.last_i=min(last_i,first_i+(iprocess)*BlockLength*incr_i-1);
1937        else %multislices (then incr_i is not empty)
1938            Param.IndexRange.first_i= first_i+iprocess-1;
1939            Param.IndexRange.incr_slice=incr_i*Param.IndexRange.NbSlice;
1940        end
1941        for ilist=1:size(Param.InputTable,1)
1942            Param.InputTable{ilist,1}=regexprep(Param.InputTable{ilist,1},'\','/'); % correct path name for PCWIN system
1943        end
1944       
1945        if isfield(Param,'OutputSubDir')
1946            t=struct2xml(Param);
1947            t=set(t,1,'name','Series');
1948            extxml{iprocess}=fullfile_uvmat('','',Param.InputTable{1,3},'.xml',OutputNomType,...
1949                Param.IndexRange.first_i,Param.IndexRange.last_i,first_j,last_j);
1950            filexml{iprocess}=fullfile(OutputDir,'0_XML',extxml{iprocess});
1951            try
1952                save(t, filexml{iprocess}); % save the xml file containing the processing parameters
1953            catch ME
1954                if ~strcmp (RunMode,'local')
1955                    errormsg=['error writting ' filexml{iprocess} ': ' ME.message];
1956                    return
1957                end
1958            end
1959        end
1960        if strcmp (RunMode,'local')
1961            switch ActionExt
1962                case '.m'
1963                    h_fun(Param); % direct launching
1964                   
1965                case '.sh'
1966                    switch computer
1967                        case {'PCWIN','PCWIN64'} %Windows system
1968                            filexml=regexprep(filexml,'\\','\\\\'); % add '\' so that '\' are left as characters
1969                            system([ActionFullName ' ' RunTime ' ' filexml{iprocess}]); % TODO: adapt to DOS system
1970                        case {'GLNX86','GLNXA64','MACI64'}%Linux  system
1971                            system([ActionFullName ' ' RunTime ' ' filexml{iprocess}]);
1972                    end
1973            end
1974        end
1975    end
1976   
1977    if ~strcmp (RunMode,'local') && ~strcmp(RunMode,'python')
1978        %% processing on a different session of the same computer (background) or cluster, create executable files
1979        batch_file_list=cell(NbProcess,1); % initiate the list of executable files
1980        DirExe=fullfile(OutputDir,'0_EXE'); % directory name for executable files
1981        switch computer
1982            case {'PCWIN','PCWIN64'} %Windows system
1983                ExeExt='.bat';
1984            case {'GLNX86','GLNXA64','MACI64'}%Linux  system
1985                ExeExt='.sh';
1986        end
1987        %create subdirectory for executable files
1988        if ~exist(DirExe,'dir')
1989            [tild,msg1]=mkdir(DirExe);
1990            if ~strcmp(msg1,'')
1991                errormsg=['cannot create ' DirExe ': ' msg1]; % error message for directory creation
1992                return
1993            end
1994            [success,msg] = fileattrib(DirExe,'+w','g','s'); % allow writing access for the group of users, recursively in the folder
1995            if success==0
1996                msgbox_uvmat('WARNING',{['unable to set group write access to ' DirExe ':']; msg}); % error message for directory creation
1997            end
1998        end
1999        %create subdirectory for log files
2000        DirLog=fullfile(OutputDir,'0_LOG');
2001        if ~exist(DirLog,'dir')
2002            [tild,msg1]=mkdir(DirLog);
2003            if ~strcmp(msg1,'')
2004                errormsg=['cannot create ' DirLog ': ' msg1]; % error message for directory creation
2005                return
2006            end
2007            [success,msg] = fileattrib(DirLog,'+w','g','s'); % allow writing access for the group of users, recursively in the folder
2008            if success==0
2009                msgbox_uvmat('WARNING',{['unable to set group write access to ' DirLog ':']; msg}); % error message for directory creation
2010            end
2011        end
2012       
2013        %create the executable file
2014        file_exe_global=fullfile_uvmat('','',Param.InputTable{1,3},ExeExt,OutputNomType,...
2015            first_i,last_i,first_j,last_j);
2016        file_exe_global=fullfile(OutputDir,'0_EXE',file_exe_global);
2017        filelog_global=fullfile_uvmat('','',Param.InputTable{1,3},'.log',OutputNomType,...
2018            first_i,last_i,first_j,last_j);
2019        filelog_global=fullfile(OutputDir,'0_LOG',filelog_global);
2020       
2021        for iprocess=1:NbProcess
2022            %create the executable file
2023            batch_file_list{iprocess}=fullfile(OutputDir,'0_EXE',regexprep(extxml{iprocess},'.xml$',ExeExt));
2024           
2025            % set the log file name
2026            filelog{iprocess}=fullfile(OutputDir,'0_LOG',regexprep(extxml{iprocess},'.xml$','.log'));
2027        end
2028    end
2029   
2030    %% launch the executable files for background or cluster processing
2031   
2032    switch RunMode
2033       
2034        case 'background'
2035            [fid,message]=fopen(file_exe_global,'w');
2036            if isequal(fid,-1)
2037                errormsg=['creation of ' file_exe_global ':' message];
2038                return
2039            end
2040            switch ActionExt
2041                case '.m'% Matlab function
2042                    switch computer
2043                        case {'GLNX86','GLNXA64','MACI64'}
2044                            matlab_ver = ver('MATLAB');
2045                            matlab_version = matlab_ver.Version;
2046                            cmd=[...
2047                                '#!/bin/bash\n'...
2048                                'source /etc/profile\n'...
2049                                'module load matlab/' matlab_version '\n'...% CHOICE OF MATLAB VERSION
2050                                'time_start=$(date +%%s)\n'...
2051                                'matlab -nodisplay -nosplash -nojvm -logfile ''' filelog_global ''' <<END_MATLAB\n'...
2052                                'addpath(''' path_series ''');\n'...
2053                                'addpath(''' Param.Action.ActionPath ''');\n'];
2054                            for iprocess=1:NbProcess
2055                                cmd=[cmd '' Param.Action.ActionName  '(''' filexml{iprocess} ''');\n'];
2056                            end
2057                            cmd=[cmd  'exit\n' 'END_MATLAB\n'...
2058                                'time_end=$(date +%%s)\n'...
2059                                'echo "global time = " $(($time_end - $time_start)) >> ''' filelog_global '''\n'];
2060                            fprintf(fid,cmd); % fill the executable file with the  char string cmd
2061                            fclose(fid); % close the executable filefilelog_global
2062                            system(['chmod +x ' file_exe_global]); % set the file to executable
2063                        case {'PCWIN','PCWIN64'}
2064                            cmd=['matlab -automation -logfile ' regexprep(filelog{iprocess},'\\','\\\\')...
2065                                ' -r "addpath(''' regexprep(path_series,'\\','\\\\') ''');'...
2066                                'addpath(''' regexprep(Param.Action.ActionPath,'\\','\\\\') ''');'];
2067                            for iprocess=1:NbProcess
2068                                cmd=[cmd '' Param.Action.ActionName  '( ''' regexprep(filexml{iprocess},'\\','\\\\') ''');']
2069                            end
2070                            cmd=[cmd ';exit"'];
2071                            fprintf(fid,cmd); % fill the executable file with the  char string cmd
2072                            fclose(fid); % close the executable file
2073                    end
2074                    system([file_exe_global ' &'])% directly execute the command file
2075                case '.sh' % compiled Matlab function
2076                    for iprocess=1:NbProcess
2077                        switch computer
2078                            case {'GLNX86','GLNXA64','MACI64'}
2079                                [fid,message]=fopen(batch_file_list{iprocess},'w'); % create the executable file
2080                                if isequal(fid,-1)
2081                                    errormsg=['creation of .bat file: ' message];
2082                                    return
2083                                end
2084                                cmd=['#!/bin/bash \n '...
2085                                    '#$ -cwd \n '...
2086                                    'hostname && date \n '...
2087                                    'umask 002 \n'...
2088                                    ActionFullName ' ' RunTime ' ' filexml{iprocess}]; % allow writting access to created files for user group
2089                                fprintf(fid,cmd); % fill the executable file with the  char string cmd
2090                                fclose(fid); % close the executable file
2091                                system(['chmod +x ' batch_file_list{iprocess}]); % set the file to executable
2092                                system([batch_file_list{iprocess} ' &'])% directly execute the command file
2093                            case {'PCWIN','PCWIN64'}
2094                                msgbox_uvmat('ERROR','option for compiled Matlab functions not implemented for Windows system')
2095                                return
2096                        end
2097                    end
2098                    msgbox_uvmat('CONFIRMATION',[ActionFullName ' launched in background for ' ExpName ': press STATUS to see results'])
2099            end
2100           
2101        case 'cluster' % option 'oar-parexec' used
2102            %create subdirectory for oar commands
2103            for iprocess=1:NbProcess
2104                [fid,message]=fopen(batch_file_list{iprocess},'w'); % create the executable file
2105                if isequal(fid,-1)
2106                    errormsg=['creation of .bat file: ' message];
2107                    return
2108                end
2109                if  strcmp(ActionExt,'.sh')
2110                    cmd=['#!/bin/bash \n '...
2111                        '#$ -cwd \n '...
2112                        'hostname && date \n '...
2113                        'umask 002 \n'...
2114                        ActionFullName ' ' RunTime ' ' filexml{iprocess}]; % allow writting access to created files for user group
2115                else
2116                    matlab_ver = ver('MATLAB');
2117                    matlab_version = matlab_ver.Version;
2118                    cmd=[...
2119                        '#!/bin/bash\n'...
2120                        'source /etc/profile\n'...
2121                        'module load matlab/' matlab_version '\n'...% CHOICE OF MATLAB VERSION
2122                        'matlab -nodisplay -nosplash -nojvm -singleCompThread -logfile ''' filelog{iprocess} ''' <<END_MATLAB\n'...
2123                        'addpath(''' path_series ''');\n'...
2124                        'addpath(''' Param.Action.ActionPath ''');\n'...
2125                        '' Param.Action.ActionName  '(''' filexml{iprocess} ''');\n'...
2126                        'exit\n'...
2127                        'END_MATLAB\n'];
2128                end
2129                fprintf(fid,cmd); % fill the executable file with the  char string cmd
2130                fclose(fid); % close the executable file
2131                system(['chmod +x ' batch_file_list{iprocess}]); % set the file to executable
2132            end
2133            DIR_CLUSTER=fullfile(OutputDir,'0_CLUSTER');
2134            if exist(DIR_CLUSTER,'dir')% delete the content of the dir 0_LOG to allow new input
2135                curdir=pwd;
2136                cd(DIR_CLUSTER)
2137                delete('*')
2138                cd(curdir)
2139            else
2140                [tild,msg1]=mkdir(DIR_CLUSTER);
2141                if ~strcmp(msg1,'')
2142                    errormsg=['cannot create ' DIR_CLUSTER ': ' msg1]; % error message for directory creation
2143                    return
2144                end
2145            end
2146            % create file containing the list of jobs
2147            ListProcess=fullfile(DIR_CLUSTER,'job_list.txt'); % name of the file containing the list of executables
2148            [fid,errormsg]=fopen(ListProcess,'w'); % open it for writting
2149            if isempty(errormsg)
2150            for iprocess=1:length(batch_file_list)
2151                fprintf(fid,[batch_file_list{iprocess} '\n']); % write list of exe files
2152            end
2153            fclose(fid);
2154            system(['chmod +x ' ListProcess]); % set the file to executable
2155            else
2156                errormsg=['error for writting the executable file:' errormsg];
2157            end       
2158            CPUTimeProcess=CPUTime*BlockLength*nbfield_j; % estimated CPU time for one individual process (in minutes)
2159            LaunchCmdFcn=SeriesData.SeriesParam.ClusterParam.LaunchCmdFcn;
2160            oar_command=feval(LaunchCmdFcn,ListProcess,ActionFullName,DirLog,NbProcess, NbCore,CPUTimeProcess)
2161            [status,result]=system(oar_command)% execute system command and show the result (ID number of the launched job) on the Matlab command window
2162            filename_oarcommand=fullfile(DIR_CLUSTER,'0_cluster_command'); % keep track of the command in file '0-OAR/0_cluster_command'
2163            [fid,errormsg]=fopen(filename_oarcommand,'w');
2164            if ~isempty(errormsg)
2165                msgbox_uvmat('ERROR',['cannot create ' filename_oarcommand ': ' errormsg])
2166                return
2167            end
2168            fprintf(fid,oar_command); % store the command
2169            fprintf(fid,result); % store the result (job ID number)
2170            fclose(fid);
2171            if status==0
2172                msgbox_uvmat('CONFIRMATION',[ActionFullName ' launched for ' ExpName ' as ' num2str(NbProcess) ' processes in cluster: press STATUS to see results'])
2173            else
2174                msgbox_uvmat('ERROR',result)
2175            end
2176            %     case 'cluster_pbs' % for LMFA Kepler machine:  trqnsferred to fct
2177           
2178            %         %create subdirectory for pbs command and log files
2179            %         DirPBS=fullfile(OutputDir,'0_PBS'); % todo : common name OAR/PBS
2180            %         if exist(DirPBS,'dir')% delete the content of the dir 0_LOG to allow new input
2181            %             curdir=pwd;
2182            %             cd(DirPBS)
2183            %             delete('*')
2184            %             cd(curdir)
2185            %         else
2186            %             [tild,msg1]=mkdir(DirPBS);
2187            %             if ~strcmp(msg1,'')
2188            %                 errormsg=['cannot create ' DirPBS ': ' msg1]; % error message for directory creation
2189            %                 return
2190            %             end
2191            %         end
2192            %         max_walltime=3600*20; % 20h max total calculation (cannot exceed 24 h)
2193            %         walltime_onejob=1800; % seconds, max estimated time for asingle file index value
2194            %         ListProcess=fullfile(DirPBS,'job_list.txt'); % create name of the global executable file
2195            %         fid=fopen(ListProcess,'w');
2196            %         for iprocess=1:length(batch_file_list)
2197            %             fprintf(fid,[batch_file_list{iprocess} '\n']); % list of exe files
2198            %         end
2199            %         fclose(fid);
2200            %         system(['chmod +x ' ListProcess]); % set the file to executable
2201            %         pbs_command=['qsub -n CIVX '...
2202            %             '-t idempotent --checkpoint ' num2str(walltime_onejob+60) ' '...
2203            %             '-l /core=' num2str(NbCore) ','...
2204            %             'walltime=' datestr(min(1.05*walltime_onejob/86400*max(NbProcess*BlockLength*nbfield_j,NbCore)/NbCore,max_walltime/86400),13) ' '...
2205            %             '-E ' regexprep(ListProcess,'\.txt\>','.stderr') ' '...
2206            %             '-O ' regexprep(ListProcess,'\.txt\>','.log') ' '...
2207            %             extra_qstat ' '...
2208            %             '"oar-parexec -s -f ' ListProcess ' '...
2209            %             '-l ' ListProcess '.log"'];
2210            %         filename_oarcommand=fullfile(DirPBS,'pbs_command');
2211            %         fid=fopen(filename_oarcommand,'w');
2212            %         fprintf(fid,pbs_command);
2213            %         fclose(fid);
2214            %         fprintf(pbs_command); % display in command line
2215            %         %system(pbs_command);
2216            %         msgbox_uvmat('CONFIRMATION',[ActionFullName ' command ready to be launched in cluster'])
2217           
2218        case 'cluster_sge' % for PSMN % TODO: use the standard 'cluster' config with an external fct
2219            % Au PSMN, on ne cr??e pas 1 job avec plusieurs c??urs, mais N jobs de 1 c??urs
2220            % o?? N < 1000.
2221            %create subdirectory for pbs command and log files
2222           
2223            DirSGE=fullfile(OutputDir,'0_SGE');
2224            if exist(DirSGE,'dir')% delete the content of the dir 0_LOG to allow new input
2225                curdir=pwd;
2226                cd(DirSGE)
2227                delete('*')
2228                cd(curdir)
2229            else
2230                [tild,msg1]=mkdir(DirSGE);
2231                if ~strcmp(msg1,'')
2232                    errormsg=['cannot create ' DirSGE ': ' msg1]; % error message for directory creation
2233                    return
2234                end
2235            end
2236            maxImgsPerJob = ceil(length(batch_file_list)/NbCore);
2237            disp(['Max number of jobs: ' num2str(NbCore)])
2238            disp(['Images per job: ' num2str(maxImgsPerJob)])
2239           
2240            iprocess = 1;
2241            imgsInJob = [];
2242            currJobIndex = 1;
2243            done = 0;
2244            while(~done)
2245                if(iprocess <= length(batch_file_list))
2246                    imgsInJob = [imgsInJob, iprocess];
2247                end
2248                if((numel(imgsInJob) >= maxImgsPerJob) || (iprocess == length(batch_file_list)))
2249                    cmd=['#!/bin/sh \n'...
2250                        '#$ -cwd \n'...
2251                        'hostname && date\n']
2252                    for ii=1:numel(imgsInJob)
2253                        cmd=[cmd ActionFullName ' /softs/matlab ' filexml{imgsInJob(ii)} '\n'];
2254                    end
2255                    [fid, message] = fopen([DirSGE '/job' num2str(currJobIndex) '.sh'], 'w');
2256                    fprintf(fid, cmd);
2257                    fclose(fid);
2258                    system(['chmod +x ' DirSGE '/job' num2str(currJobIndex) '.sh'])
2259                    sge_command=['qsub -N civ_' num2str(currJobIndex) ' '...
2260                        '-q ' qstat_Queue ' '...
2261                        '-e ' fullfile([DirSGE '/job' num2str(currJobIndex) '.out']) ' '...
2262                        '-o ' fullfile([DirSGE '/job' num2str(currJobIndex) '.out']) ' '...
2263                        fullfile([DirSGE '/job' num2str(currJobIndex) '.sh'])];
2264                    fprintf(sge_command); % display in command line
2265                    [status, result] = system(sge_command);
2266                    fprintf(result);
2267                    currJobIndex = currJobIndex + 1;
2268                    imgsInJob = [];
2269                end
2270                if(iprocess == length(batch_file_list))
2271                    done = 1;
2272                end
2273                iprocess = iprocess + 1;
2274            end
2275            msgbox_uvmat('CONFIRMATION',[num2str(currJobIndex-1) ' jobs launched on queue ' qstat_Queue '.'])
2276        case 'python'
2277            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))") ' ...
2278                'python -m fluidimage.run_from_xml ' filexml{iprocess}];
2279            fprintf(['command:\n' command '\n\n'])
2280            system(command, '-echo');
2281    end
2282    if exist(OutputDir,'dir')
2283        [SUCCESS,MESSAGE,MESSAGEID] = fileattrib (OutputDir);
2284        if MESSAGE.GroupWrite~=1
2285            [success,msg] = fileattrib(OutputDir,'+w','g','s'); % allow writing access for the group of users, recursively in the folder
2286            if success==0
2287                msgbox_uvmat('WARNING',{['unable to set group write access to ' OutputDir ':']; msg}); % error message for directory creation
2288            end
2289        end
2290    end
2291end
2292set(handles.Replicate,'BackgroundColor',[0 1 0])
2293
2294%------------------------------------------------------------------------
2295function STOP_Callback(hObject, eventdata, handles)
2296%------------------------------------------------------------------------
2297set(handles.RUN, 'BusyAction','cancel')
2298set(handles.RUN,'BackgroundColor',[1 0 0])
2299set(handles.RUN,'enable','on')
2300set(handles.RUN, 'Value',0)
2301
2302%------------------------------------------------------------------------
2303% --- read parameters from the GUI series
2304%------------------------------------------------------------------------
2305function Param=read_GUI_series(handles)
2306
2307%% read raw parameters from the GUI series
2308Param=read_GUI(handles.series);
2309
2310%% clean the output structure by removing unused information
2311if isfield(Param,'Pairs')
2312    Param=rmfield(Param,'Pairs'); % info Pairs not needed for output
2313end
2314if isfield(Param,'InputLine')
2315    Param=rmfield(Param,'InputLine');
2316end
2317if isfield(Param,'EditObject')
2318    Param=rmfield(Param,'EditObject');
2319end
2320Param.IndexRange.TimeSource=Param.IndexRange.TimeTable{end,1};
2321Param.IndexRange=rmfield(Param.IndexRange,'TimeTable');
2322empty_line=false(size(Param.InputTable,1),1);
2323for iline=1:size(Param.InputTable,1)
2324    empty_line(iline)=isempty(cell2mat(Param.InputTable(iline,1:3)));
2325end
2326Param.InputTable(empty_line,:)=[];
2327
2328%------------------------------------------------------------------------
2329% --- Executes on selection change in ActionName.
2330function ActionName_Callback(hObject, ActionPath, handles)
2331%------------------------------------------------------------------------
2332
2333%% stop any ongoing series processing
2334if isequal(get(handles.RUN,'Value'),1)
2335    answer= msgbox_uvmat('INPUT_Y-N','stop current Action process?');
2336    if strcmp(answer,'Yes')
2337        STOP_Callback(hObject, [], handles)
2338    else
2339        return
2340    end
2341end
2342set(handles.ActionName,'BackgroundColor',[1 1 0])
2343huigetfile=findobj(allchild(0),'tag','status_display');
2344if ~isempty(huigetfile)
2345    delete(huigetfile)
2346end
2347drawnow
2348
2349%% get Action name and path
2350NbBuiltinAction=get(handles.Action,'UserData'); % nbre of functions initially proposed in the menu ActionName (as defined in the Opening fct of series)
2351ActionList=get(handles.ActionName,'String'); % list menu fields
2352ActionIndex=get(handles.ActionName,'Value');
2353if ~isequal(ActionIndex,1)% if we are not just opening series
2354    InputTable=get(handles.InputTable,'Data');
2355    if isempty(InputTable{1,4})
2356        msgbox_uvmat('ERROR','no input file available: use Open in the menu bar')
2357        return
2358    end
2359end
2360ActionName= ActionList{get(handles.ActionName,'Value')}; % selected function name
2361ActionPathList=get(handles.ActionName,'UserData'); % list of recorded paths to functions of the list ActionName
2362
2363%% add a new function to the menu if 'more...' has been selected in the menu ActionName
2364if isequal(ActionName,'more...')
2365    if ~ischar(ActionPath)
2366        ActionPath=get(handles.ActionPath,'String');
2367    end
2368    [FileName, PathName] = uigetfile( ...
2369        {'*.m', ' (*.m)';
2370        '*.m',  '.m files '; ...
2371        '*.*', 'All Files (*.*)'}, ...
2372        'Pick a series processing function ',ActionPath);
2373    if length(FileName)<2
2374        return
2375    end
2376    [tild,ActionName,ActionExt]=fileparts(FileName);
2377   
2378    % insert the choice in the menu ActionName
2379    ActionIndex=find(strcmp(ActionName,ActionList),1); % look for the selected function in the menu Action
2380    PathName=regexprep(PathName,'/$','');
2381    if ~isempty(ActionIndex) && ~strcmp(ActionPathList{ActionIndex},PathName)%compare the path to the existing fct
2382        ActionIndex=[]; % the selected path is different than the recorded one
2383    end
2384    if isempty(ActionIndex)%the qselected fct (with selected path) does not exist in the menu
2385        ActionIndex= length(ActionList);
2386        ActionList=[ActionList(1:end-1);{ActionName};ActionList(end)]; % the selected function is appended in the menu, before the last item 'more...'
2387         ActionPathList=[ActionPathList; PathName];
2388    end
2389   
2390    % record the file extension and extend the path list if it is a new extension
2391    ActionExtList=get(handles.ActionExt,'String');
2392    ActionExtIndex=find(strcmp(ActionExt,ActionExtList), 1);
2393    if isempty(ActionExtIndex)
2394        set(handles.ActionExt,'String',[ActionExtList;{ActionExt}])
2395    end
2396
2397    % remove old Action options in the menu (keeping a menu length <nb_builtin_ACTION+5)
2398    if length(ActionList)>NbBuiltinAction+5; % nb_builtin_ACTION=nbre of functions always remaining in the initial menu
2399        nbremove=length(ActionList)-NbBuiltinAction-5;
2400        ActionList(NbBuiltinAction+1:end-5)=[];
2401        ActionPathList(NbBuiltinAction+1:end-4,:)=[];
2402        ActionIndex=ActionIndex-nbremove;
2403    end
2404   
2405    % record action menu, choice and path
2406    set(handles.ActionName,'Value',ActionIndex)
2407    set(handles.ActionName,'String',ActionList)
2408       set(handles.ActionName,'UserData',ActionPathList);
2409    set(handles.ActionExt,'Value',ActionExtIndex)
2410       
2411    %record the user defined menu additions in personal file profil_perso
2412    dir_perso=prefdir;
2413    profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
2414    if NbBuiltinAction+1<=numel(ActionList)-1
2415        ActionListUser=ActionList(NbBuiltinAction+1:numel(ActionList)-1);
2416        ActionPathListUser=ActionPathList(NbBuiltinAction+1:numel(ActionList)-1);
2417        ActionExtListUser={};
2418        if numel(ActionExtList)>2
2419            ActionExtListUser=ActionExtList(3:end);
2420        end
2421        if exist(profil_perso,'file')
2422            save(profil_perso,'ActionListUser','ActionPathListUser','ActionExtListUser','-append')
2423        else
2424            save(profil_perso,'ActionListUser','ActionPathListUser','ActionExtListUser','-V6')
2425        end
2426    end
2427end
2428
2429%% check the current ActionPath to the selected function
2430ActionPath=ActionPathList{ActionIndex}; % current recorded path
2431set(handles.ActionPath,'String',ActionPath); % show the path to the senlected function
2432
2433%% reinitialise the waitbar
2434update_waitbar(handles.Waitbar,0)
2435
2436%% Put the first line of the selected Action fct as tooltip help
2437try
2438    [fid,errormsg] =fopen([ActionName '.m']);
2439    InputText=textscan(fid,'%s',1,'delimiter','\n');
2440    fclose(fid);
2441    set(handles.ActionName,'ToolTipString',InputText{1}{1})% put the first line of the selected function as tooltip help
2442end
2443set(handles.ActionName,'BackgroundColor',[1 1 1])
2444set(handles.ActionInput,'BackgroundColor',[1 0 1])% set ActionInput button to magenta color to indicate that input refr
2445set(handles.num_CPUTime,'String','')
2446
2447% --- Executes on button press in ActionInput.
2448function ActionInput_Callback(hObject, eventdata, handles)
2449
2450set(handles.ActionInput,'BackgroundColor',[1 1 0])
2451SeriesData=get(handles.series,'UserData'); % info on the input file series
2452
2453%% create the function handle for Action
2454ActionPath=get(handles.ActionPath,'String');
2455ActionList=get(handles.ActionName,'String');
2456ActionName= ActionList{get(handles.ActionName,'Value')}; % selected function name
2457if ~exist(ActionPath,'dir')
2458    ActionName_Callback(handles.ActionName, ActionPath, handles)% update the function
2459    return
2460end
2461current_dir=pwd; % current working dir
2462cd(ActionPath)
2463h_fun=str2func(ActionName);
2464cd(current_dir)
2465
2466%% Activate the Action fct to adapt the configuration of the GUI series and bring specific parameters in SeriesData
2467Param=read_GUI_series(handles); % read the parameters from the GUI series
2468Param.Action.RUN=0;
2469Param.SeriesData=SeriesData;
2470ParamOut=h_fun(Param); % run the selected Action function to get the relevant input
2471
2472
2473%% Visibility of VelType and VelType_1 menus asked by ActionName
2474VelTypeRequest=1; % VelType requested by default
2475VelTypeRequest_1=1; % VelType requested by default
2476if isfield(ParamOut,'VelType')
2477    VelTypeRequest=ismember(ParamOut.VelType,{'on','one','two'});
2478    VelTypeRequest_1=strcmp( ParamOut.VelType,'two');
2479end
2480FieldNameRequest=0;  %hidden by default
2481FieldNameRequest_1=0;  %hidden by default
2482if isfield(ParamOut,'FieldName')
2483    FieldNameRequest=ismember(ParamOut.FieldName,{'on','one','two'});
2484    FieldNameRequest_1=strcmp( ParamOut.FieldName,'two');
2485end
2486
2487%% Detect the types of input files and set menus and default options in 'VelType'
2488if ~isfield(SeriesData,'FileType')
2489    SeriesData.FileType={'none'};
2490end
2491iview_civ=find( strcmp('civx',SeriesData.FileType)|strcmp('civdata',SeriesData.FileType));
2492iview_netcdf=find(strcmp('netcdf',SeriesData.FileType)|strcmp('civx',SeriesData.FileType)|strcmp('civdata',SeriesData.FileType)); % all nc files, icluding civ
2493FieldList=get(handles.FieldName,'String'); % previous list as default
2494if ~iscell(FieldList),FieldList={FieldList};end
2495FieldList_1=get(handles.FieldName_1,'String'); % previous list as default
2496if ~iscell(FieldList_1),FieldList_1={FieldList_1};end
2497CheckList_1=1; % indicate whether FieldName_1 has been updated
2498handles_coord=[handles.Coord_x handles.Coord_y handles.Coord_z handles.Coord_x_title handles.Coord_y_title handles.Coord_z_title];
2499if VelTypeRequest && numel(iview_civ)>=1
2500    menu=set_veltype_display(SeriesData.FileInfo{iview_civ(1)}.CivStage,SeriesData.FileType{iview_civ(1)});
2501    set(handles.VelType,'Value',1)% set first choice by default
2502    set(handles.VelType,'String',[{'*'};menu])
2503    set(handles.VelType,'Visible','on')
2504    set(handles.VelType_title,'Visible','on')
2505    FieldList=set_field_list('U','V'); % standard menu for civx data
2506    if max(get(handles.FieldName,'Value'))>numel(FieldList)
2507        set(handles.FieldName,'Value',1); % velocity vector choice by default
2508    end
2509    if  VelTypeRequest_1 && numel(iview_civ)>=2
2510        menu=set_veltype_display(SeriesData.FileInfo{iview_civ(2)}.CivStage,SeriesData.FileType{iview_civ(2)});
2511        set(handles.VelType_1,'Value',1)% set first choice by default
2512        set(handles.VelType_1,'String',[{'*'};menu])
2513        set(handles.VelType_1,'Visible','on')
2514        set(handles.VelType_title_1,'Visible','on')
2515        FieldList_1=[set_field_list('U','V');{'C'};{'add_field...'}]; % standard menu for civx data
2516        CheckList_1=1;
2517        set(handles.FieldName_1,'Value',1); % velocity vector choice by default
2518    else
2519        set(handles.VelType_1,'Visible','off')
2520        set(handles.VelType_title_1,'Visible','off')
2521    end
2522else
2523    set(handles.VelType,'Visible','off')
2524    set(handles.VelType_title,'Visible','off')
2525end
2526
2527%% Detect the types of input files and set menus and default options in 'FieldName'
2528if (FieldNameRequest || VelTypeRequest) && numel(iview_netcdf)>=1
2529    set(handles.InputFields,'Visible','on')% set the frame InputFields visible
2530    if FieldNameRequest && isfield(SeriesData.FileInfo{iview_netcdf(1)},'ListVarName')
2531        set(handles.FieldName,'Visible','on')
2532        set(handles.Field_text,'Visible','on')
2533        ListVarName=SeriesData.FileInfo{iview_netcdf(1)}.ListVarName;
2534        ind_var=get(handles.FieldName,'Value'); % indices of previously selected variables
2535        for ilist=1:numel(ind_var)
2536            if isempty(find(strcmp(FieldList{ind_var(ilist)},ListVarName)))
2537                FieldList={}; % previous choice not consistent with new input field
2538                set(handles.FieldName,'Value',1)
2539                break
2540            end
2541        end
2542        if ~isempty(FieldList)
2543            if isempty(find(strcmp(get(handles.Coord_x,'String'),ListVarName)))||...
2544                    isempty(find(strcmp(get(handles.Coord_y,'String'),ListVarName)))
2545                FieldList={};
2546                set(handles.Coord_x,'String','')
2547                set(handles.Coord_y,'String','')
2548            end
2549            Coord_z=get(handles.Coord_z,'String');
2550            if ~isempty(Coord_z) && isempty(find(strcmp(Coord_z,ListVarName)))
2551                FieldList={};
2552                set(handles.Coord_z,'String','')
2553            end
2554        end
2555    else
2556        set(handles.FieldName,'Visible','off')
2557        set(handles.Field_text,'Visible','off')
2558    end
2559   
2560    set(handles_coord,'Visible','on')
2561    if isempty(find(strcmp('add_field...',FieldList)))
2562        FieldList=[FieldList;{'add_field...'}];%add 'add_field...' to the menu FieldName if it is not already
2563    end
2564    if FieldNameRequest_1 && numel(iview_netcdf)>=2
2565        set(handles.FieldName_1,'Visible','on')
2566        if CheckList_1==0        % not civ input made
2567            ListVarName=SeriesData.FileInfo{iview_netcdf(2)}.ListVarName;
2568            ind_var=get(handles.FieldName,'Value'); % indices of previously selected variables
2569            for ilist=1:numel(ind_var)
2570                if isempty(find(strcmp(FieldList{ind_var(ilist)},ListVarName)))
2571                    FieldList_1={}; % previous choice not consistent with new input field
2572                    set(handles.FieldName_1,'Value',1)
2573                    break
2574                end
2575            end
2576            warn_coord=0;
2577            if isempty(find(strcmp(get(handles.Coord_x,'String'),ListVarName)))||...
2578                    isempty(find(strcmp(get(handles.Coord_y,'String'),ListVarName)))
2579                warn_coord=1;
2580            end
2581            if ~isempty(Coord_z) && isempty(find(strcmp(Coord_z,ListVarName)))
2582                FieldList_1={};
2583                warn_coord=1;
2584            end
2585            if warn_coord
2586                msgbox_uvmat('WARNING','coordinate names do not exist in the second netcdf input file')
2587            end
2588           
2589            set(handles.FieldName_1,'Visible','on')
2590            set(handles.FieldName_1,'Value',1)
2591            set(handles.FieldName_1,'String',FieldList_1)
2592        end
2593    else
2594        set(handles.FieldName_1,'Visible','off')
2595    end
2596    if isempty(FieldList)
2597        set(handles.Field_text,'Visible','off')
2598        set(handles.FieldName,'Visible','off')
2599    else
2600        set(handles.Field_text,'Visible','on')
2601        set(handles.FieldName,'Visible','on')
2602        set(handles.FieldName,'String',FieldList)
2603    end
2604else
2605    set(handles.InputFields,'Visible','off')
2606end
2607
2608%% Introduce visibility of file overwrite option
2609if isfield(ParamOut,'CheckOverwriteVisible')&& strcmp(ParamOut.CheckOverwriteVisible,'on')
2610    set(handles.CheckOverwrite,'Visible','on')
2611else
2612    set(handles.CheckOverwrite,'Visible','off')
2613end
2614
2615%% Check whether alphabetical sorting of input Subdir is allowed by the Action fct  (for multiples series entries)
2616if isfield(ParamOut,'AllowInputSort')&&isequal(ParamOut.AllowInputSort,'on')&& size(Param.InputTable,1)>1
2617    [tild,iview]=sort(Param.InputTable(:,2)); % subdirectories sorted in alphabetical order
2618    set(handles.InputTable,'Data',Param.InputTable(iview,:));
2619    MinIndex_i=get(handles.MinIndex_i,'Data');
2620    MinIndex_j=get(handles.MinIndex_j,'Data');
2621    MaxIndex_i=get(handles.MaxIndex_i,'Data');
2622    MaxIndex_j=get(handles.MaxIndex_j,'Data');
2623    set(handles.MinIndex_i,'Data',MinIndex_i(iview,:));
2624    set(handles.MinIndex_j,'Data',MinIndex_j(iview,:));
2625    set(handles.MaxIndex_i,'Data',MaxIndex_i(iview,:));
2626    set(handles.MaxIndex_j,'Data',MaxIndex_j(iview,:));
2627    TimeTable=get(handles.TimeTable,'Data');
2628    if size(TimeTable,1)<size(Param.InputTable,1)%if the time table is not complete, copy the missing lines from the previous ones
2629        for iline=size(TimeTable,1)+1:size(Param.InputTable,1)
2630            TimeTable(iline,:)=TimeTable(iline-1,:);
2631        end
2632    end
2633    set(handles.TimeTable,'Data',TimeTable(iview,:));% sort the time tables
2634    PairString=get(handles.PairString,'Data');
2635    set(handles.PairString,'Data',PairString(iview,:));
2636end
2637
2638%% Impose the whole input file index range if requested
2639if isfield(ParamOut,'WholeIndexRange')&&isequal(ParamOut.WholeIndexRange,'on')
2640    MinIndex_i=get(handles.MinIndex_i,'Data');
2641    MinIndex_j=get(handles.MinIndex_j,'Data');
2642    MaxIndex_i=get(handles.MaxIndex_i,'Data');
2643    MaxIndex_j=get(handles.MaxIndex_j,'Data');
2644    set(handles.num_first_i,'String',num2str(MinIndex_i(1)))% set first as the min index (for the first line)
2645    set(handles.num_last_i,'String',num2str(MaxIndex_i(1)))% set last as the max index (for the first line)
2646    set(handles.num_incr_i,'String','1')
2647    set(handles.num_first_j,'String',num2str(MinIndex_j(1)))% set first as the min index (for the first line)
2648    set(handles.num_last_j,'String',num2str(MaxIndex_j(1)))% set last as the max index (for the first line)
2649    set(handles.num_incr_j,'String','1')
2650else  % check index ranges
2651    first_i=1;last_i=1;first_j=1;last_j=1;
2652    if isfield(Param.IndexRange,'first_i')
2653        first_i=Param.IndexRange.first_i;
2654        last_i=Param.IndexRange.last_i;
2655    end
2656    if isfield(Param.IndexRange,'first_j')
2657        first_j=Param.IndexRange.first_j;
2658        last_j=Param.IndexRange.last_j;
2659    end
2660    if last_i < first_i || last_j < first_j , msgbox_uvmat('ERROR','last field number must be larger than the first one'),...
2661            set(handles.RUN, 'Enable','On'), set(handles.RUN,'BackgroundColor',[1 0 0]),return,end
2662end
2663
2664%% enable or desable j index visibility
2665status_j='on'; % default
2666if isfield(SeriesData,'j1_series') && isempty(find(~cellfun(@isempty,SeriesData.j1_series), 1)) % case of empty j indices
2667    status_j='off'; % no j index needed
2668elseif strcmp(get(handles.PairString,'Visible'),'on')
2669    check_burst=cellfun(@isempty,regexp(get(handles.PairString,'Data'),'^j')); % =0 for burst case, 1 otherwise
2670    if isempty(find(check_burst, 1))% if all pair string begins by j (burst)
2671        status_j='off'; % no j index needed for bust case
2672    end
2673end
2674enable_j(handles,status_j) % no j index needed
2675if isfield(ParamOut,'j_index_1')&& isfield(ParamOut,'j_index_2')%strcmp(ParamOut.Desable_j_index,'on')
2676    %status_j='off';
2677    set(handles.num_first_j,'String',num2str(ParamOut.j_index_1))
2678    set(handles.num_last_j,'String',num2str(ParamOut.j_index_2))
2679    set(handles.num_first_j,'enable','off')
2680    set(handles.num_last_j,'enable','off')
2681    set(handles.num_incr_j,'visible','off')
2682else
2683    set(handles.num_first_j,'enable','on')
2684    set(handles.num_last_j,'enable','on')
2685    set(handles.num_incr_j,'visible',status_j)
2686end
2687
2688%% NbSlice visibility
2689if isfield(ParamOut,'NbSlice') && (strcmp(ParamOut.NbSlice,'on')||isnumeric(ParamOut.NbSlice))
2690    set(handles.num_NbSlice,'Visible','on')
2691    set(handles.NbSlice_title,'Visible','on')
2692else
2693    set(handles.num_NbSlice,'Visible','off')
2694    set(handles.NbSlice_title,'Visible','off')
2695end
2696if isfield(ParamOut,'NbSlice') && isnumeric(ParamOut.NbSlice)
2697    set(handles.num_NbSlice,'String',num2str(ParamOut.NbSlice))
2698    set(handles.num_NbSlice,'Enable','off'); % NbSlice set by the activation of the Action function
2699else
2700    set(handles.num_NbSlice,'Enable','on'); % NbSlice can be modified on the GUI series
2701end
2702
2703%% Visibility of FieldTransform menu
2704FieldTransformVisible='off';  %hidden by default
2705if isfield(ParamOut,'FieldTransform')
2706    if ~strcmp(ParamOut.FieldTransform,'off')
2707    FieldTransformVisible='on'; 
2708    end
2709    if iscell(ParamOut.FieldTransform)
2710        SeriesData.TransformList=ParamOut.FieldTransform;
2711    end
2712    TransformName_Callback([],[], handles)
2713end
2714set(handles.FieldTransform,'Visible',FieldTransformVisible)
2715if isfield(ParamOut,'TransformPath')% record the path of transform function requested for compilation
2716    set(handles.TransformPath,'UserData',ParamOut.TransformPath)
2717else
2718    set(handles.TransformPath,'UserData',[])
2719end
2720
2721%% Visibility of projection object
2722ProjObjectVisible='off';  %hidden by default
2723if isfield(ParamOut,'ProjObject')
2724    ProjObjectVisible=ParamOut.ProjObject;
2725end
2726set(handles.CheckObject,'Visible',ProjObjectVisible)
2727if ~get(handles.CheckObject,'Value')
2728    ProjObjectVisible='off';
2729end
2730set(handles.ProjObjectName,'Visible',ProjObjectVisible)
2731set(handles.DeleteObject,'Visible',ProjObjectVisible)
2732set(handles.ViewObject,'Visible',ProjObjectVisible)
2733set(handles.EditObject,'Visible',ProjObjectVisible)
2734
2735%% Visibility of mask input
2736MaskVisible='off';  %hidden by default
2737if isfield(ParamOut,'Mask')
2738    MaskVisible=ParamOut.Mask;
2739end
2740set(handles.CheckMask,'Visible',MaskVisible);
2741%% Setting of expected iteration time
2742if isfield(ParamOut,'CPUTime')
2743    set(handles.num_CPUTime,'String',num2str(ParamOut.CPUTime));
2744end
2745
2746%% definition of the path for the output files
2747InputTable=get(handles.InputTable,'Data');
2748[OutputPath,Device,DeviceExt]=fileparts(InputTable{1,1});
2749[OutputPath,Experiment,ExperimentExt]=fileparts(OutputPath);
2750set(handles.Device,'String',[Device DeviceExt])
2751set(handles.Device,'Visible','on')
2752set(handles.Device_title,'Visible','on')
2753set(handles.Experiment,'String',[Experiment ExperimentExt])
2754set(handles.Experiment,'Visible','on')
2755set(handles.Experiment_title,'Visible','on')
2756set(handles.Experiment_title,'Visible','on')
2757set(handles.OutputPath,'Visible','on')
2758set(handles.OutputPathBrowse,'Visible','on')
2759   
2760%% definition of the subdirectory containing the output files
2761
2762if  ~(isfield(SeriesData,'ActionName') && strcmp(ActionName,SeriesData.ActionName))
2763    OutputDirExt='.series'; % default
2764    if isfield(ParamOut,'OutputDirExt')&&~isempty(ParamOut.OutputDirExt)
2765        OutputDirExt=ParamOut.OutputDirExt;
2766    end
2767    set(handles.OutputDirExt,'String',OutputDirExt)
2768end
2769OutputDirVisible='off';
2770OutputSubDirMode='auto'; % default
2771SubDirOut='';
2772if isfield(ParamOut,'OutputSubDirMode')
2773    OutputSubDirMode=ParamOut.OutputSubDirMode;
2774end
2775switch OutputSubDirMode
2776    case 'auto' % default
2777        OutputDirVisible='on';
2778        SubDir=InputTable(1:end,2); % set of subdirectories
2779        SubDirOut=SubDir{1};
2780        if numel(SubDir)>1
2781            for ilist=2:numel(SubDir)
2782                SubDirOut=[SubDirOut '-' regexprep(SubDir{ilist},'^/','')];
2783            end
2784        end
2785    case 'one'
2786        OutputDirVisible='on';
2787        SubDirOut=InputTable{1,2}; % use the first subdir name (+OutputDirExt) as output  subdirectory
2788    case 'two'
2789        OutputDirVisible='on';   
2790        SubDir=InputTable(1:2,2); % set of subdirectories
2791        SubDirOut=SubDir{1};
2792        if numel(SubDir)>1
2793                SubDirOut=[SubDirOut '-' regexprep(SubDir{2},'^/','')];
2794        end
2795    case 'last'
2796        OutputDirVisible='on';
2797        SubDirOut=InputTable{end,2}; % use the last subdir name (+OutputDirExt) as output  subdirectory
2798end
2799set(handles.OutputSubDir,'String',SubDirOut)
2800set(handles.OutputSubDir,'BackgroundColor',[1 1 1])% set edit box to white color to indicate refreshment
2801set(handles.OutputDirExt,'Visible',OutputDirVisible)
2802set(handles.OutputSubDir,'Visible',OutputDirVisible)
2803% set(handles.OutputDir_title,'Visible',OutputDirVisible)
2804SeriesData.ActionName=ActionName; % record ActionName for next use
2805
2806
2807%% visibility of the run mode (local or background or cluster)
2808if strcmp(OutputSubDirMode,'none')
2809    RunModeVisible='off'; % only local mode available if no output file is produced
2810else
2811    RunModeVisible='on';
2812end
2813set(handles.RunMode,'Visible',RunModeVisible)
2814set(handles.ActionExt,'Visible',RunModeVisible)
2815set(handles.RunMode_title,'Visible',RunModeVisible)
2816set(handles.ActionExt_title,'Visible',RunModeVisible)
2817
2818
2819%% Expected nbre of output files
2820if isfield(ParamOut,'OutputFileMode')
2821    StatusData.OutputFileMode=ParamOut.OutputFileMode;
2822    set(handles.status,'UserData',StatusData)
2823end
2824
2825%% definition of an additional parameter set, determined by an ancillary GUI
2826if isfield(ParamOut,'ActionInput')
2827%     set(handles.ActionInput,'Visible','on')
2828    ParamOut.ActionInput.Program=ActionName; % record the program in ActionInput
2829    SeriesData.ActionInput=ParamOut.ActionInput;
2830else
2831%     set(handles.ActionInput,'Visible','off')
2832    if isfield(SeriesData,'ActionInput')
2833        SeriesData=rmfield(SeriesData,'ActionInput');
2834    end
2835end
2836set(handles.series,'UserData',SeriesData)
2837set(handles.ActionInput,'BackgroundColor',[1 0 0])
2838
2839
2840%------------------------------------------------------------------------
2841% --- Executes on button press in RefreshField.
2842function RefreshField_Callback(hObject, eventdata, handles)
2843%------------------------------------------------------------------------
2844set(handles.FieldName,'String',{'add_field...'});
2845set(handles.FieldName,'Value',1);
2846FieldName_Callback(hObject, eventdata, handles)
2847
2848
2849%------------------------------------------------------------------------
2850% --- Executes on selection change in FieldName.
2851function FieldName_Callback(hObject, eventdata, handles)
2852%------------------------------------------------------------------------
2853FieldListInit=get(handles.FieldName,'String');
2854field_index=get(handles.FieldName,'Value');
2855field=FieldListInit{field_index(1)};
2856if isequal(field,'add_field...')
2857    FieldListInit(field_index(1))=[];
2858    SeriesData=get(handles.series,'UserData');
2859    % input line for which the field choice is relevant
2860    iview=find(ismember(SeriesData.FileType,{'netcdf','civx','civdata'})); % all nc files, icluding civ
2861    hget_field=findobj(allchild(0),'name','get_field');
2862    if ~isempty(hget_field)
2863        delete(hget_field)%delete opened versions of get_field
2864    end
2865    Param=read_GUI(handles.series);
2866    InputTable=Param.InputTable(iview,:);
2867    % check the existence of the first file in the series
2868    first_j=[];last_j=[];MinIndex_j=1;MaxIndex_j=1; % default setting for index j
2869    if isfield(Param.IndexRange,'first_j') % if index j is used     
2870        first_j=Param.IndexRange.first_j;
2871        last_j=Param.IndexRange.last_j;
2872        MinIndex_j=Param.IndexRange.MinIndex_j(iview);
2873        MaxIndex_j=Param.IndexRange.MaxIndex_j(iview);
2874    end
2875    PairString='';
2876    if isfield(Param.IndexRange,'PairString'); PairString=Param.IndexRange.PairString{iview}; end
2877    [i1,i2,j1,j2] = get_file_index(Param.IndexRange.first_i,first_j,PairString);
2878    LineIndex=iview(1);
2879    if numel(iview)>1     
2880        answer=msgbox_uvmat('INPUT_TXT',['select the line of the input table:' num2str(iview)] ,num2str(iview(1)));
2881        LineIndex=str2num(answer);
2882    end
2883    FirstFileName=fullfile_uvmat(InputTable{LineIndex,1},InputTable{LineIndex,2},InputTable{LineIndex,3},...
2884        InputTable{LineIndex,5},InputTable{LineIndex,4},i1,i2,j1,j2);
2885    if exist(FirstFileName,'file') || ~isempty(regexp(InputTable{LineIndex,1},'^http'))
2886        ParamIn.Title='get_field: pick input variables and coordinates for series processing';
2887        ParamIn.SeriesInput=1;
2888        GetFieldData=get_field(FirstFileName,ParamIn);
2889        FieldList={};
2890        if isfield(GetFieldData,'FieldOption')% if a field has been selected
2891        switch GetFieldData.FieldOption
2892            case 'vectors'
2893                UName=GetFieldData.PanelVectors.vector_x;
2894                VName=GetFieldData.PanelVectors.vector_y;
2895                YName={GetFieldData.Coordinates.Coord_y};
2896                FieldList={['vec(' UName ',' VName ')'];...
2897                    ['norm(' UName ',' VName ')'];...
2898                    UName;VName};
2899                set(handles.VelType,'Visible','off')
2900            case {'scalar'}
2901                FieldList=GetFieldData.PanelScalar.scalar;
2902                YName={GetFieldData.Coordinates.Coord_y};
2903                if ischar(FieldList)
2904                    FieldList={FieldList};
2905                end
2906                set(handles.VelType,'Visible','off')
2907            case 'civdata...'
2908                FieldList=[set_field_list('U','V') ;{'C'}];
2909                set(handles.FieldName,'Value',1) % set menu to 'velocity
2910                XName='X';
2911                YName='y';
2912                set(handles.VelType,'Visible','on')
2913        end
2914        set(handles.FieldName,'Value',1)
2915        set(handles.FieldName,'String',[FieldListInit; FieldList; {'add_field...'}]);
2916        if ~strcmp(GetFieldData.FieldOption,'civdata...')
2917           if ~isempty(regexp(FieldList{1},'^vec'))
2918                set(handles.FieldName,'Value',1)
2919           else
2920                set(handles.FieldName,'Value',1:numel(FieldList))%select all input fields by default
2921           end
2922            XName=GetFieldData.Coordinates.Coord_x;
2923            YName=GetFieldData.Coordinates.Coord_y;
2924            TimeNameStr=GetFieldData.Time.SwitchVarIndexTime;
2925            % get the time info                     
2926            TimeTable=get(handles.TimeTable,'Data');
2927            switch TimeNameStr
2928                case 'file index'
2929                    TimeName='';
2930                case 'attribute'
2931                    TimeName=['att:' GetFieldData.Time.TimeName];
2932                    % update the time table
2933                    TimeTable{LineIndex,2}=get_time(Param.IndexRange.MinIndex_i(LineIndex),MinIndex_j,PairString,InputTable,SeriesData.FileInfo{LineIndex},GetFieldData.Time.TimeName);  % Min time     
2934                    TimeTable{LineIndex,3}=get_time(Param.IndexRange.first_i,first_j,PairString,InputTable,SeriesData.FileInfo{LineIndex},GetFieldData.Time.TimeName);  % first time             
2935                    TimeTable{LineIndex,4}=get_time(Param.IndexRange.last_i,last_j,PairString,InputTable,SeriesData.FileInfo{LineIndex},GetFieldData.Time.TimeName);  % last time                     
2936                    TimeTable{LineIndex,5}=get_time(Param.IndexRange.MaxIndex_i(LineIndex),MaxIndex_j,PairString,InputTable,SeriesData.FileInfo{LineIndex},GetFieldData.Time.TimeName);  % Max time
2937                case 'variable'
2938                    set(handles.TimeName,'String',['var:' GetFieldData.Time.TimeName])
2939                    set(handles.NomType,'String','*')
2940                    set(handles.RootFile,'String',[get(handles.RootFile,'String') get(handles.FileIndex,'String')])% A VERIFIER !!!!!!
2941                    set(handles.FileIndex,'String','')
2942                    ParamIn.TimeVarName=GetFieldData.Time.TimeName;
2943                case 'matrix_index'
2944                    TimeName=['dim:' GetFieldData.Time.TimeName];
2945                    set(handles.NomType,'String','*')
2946                    set(handles.RootFile,'String',[get(handles.RootFile,'String') get(handles.FileIndex,'String')])
2947                    set(handles.FileIndex,'String','')
2948                    ParamIn.TimeDimName=GetFieldData.Time.TimeName;
2949            end
2950            TimeTable{LineIndex,1}=TimeName;
2951            set(handles.TimeTable,'Data',TimeTable);
2952        end
2953        set(handles.Coord_x,'String',XName)
2954        set(handles.Coord_y,'String',YName)
2955        set(handles.Coord_x,'Visible','on')
2956        set(handles.Coord_y,'Visible','on')
2957        end
2958    else
2959        msgbox_uvmat('ERROR',[FirstFileName ' does not exist'])
2960    end
2961end
2962
2963
2964function [TimeValue,DtValue]=get_time(ref_i,ref_j,PairString,InputTable,FileInfo,TimeName,DtName)
2965[i1,i2,j1,j2] = get_file_index(ref_i,ref_j,PairString);
2966FileName=fullfile_uvmat(InputTable{1},InputTable{2},InputTable{3},InputTable{5},InputTable{4},i1,i2,j1,j2);
2967Data=nc2struct(FileName,[]);
2968TimeValue=[];
2969DtValue=[];
2970if isequal(FileInfo.FileType,'civdata')
2971    if ismember(TimeName,{'civ1','filter1'})
2972        if isfield(Data,'Civ1_Time')
2973        TimeValue=Data.Civ1_Time;
2974        end
2975        if isfield(Data,'Civ1_Dt')
2976        DtValue=Data.Civ1_Dt;
2977        end
2978    else
2979        if isfield(Data,'Civ2_Time')
2980        TimeValue=Data.Civ2_Time;
2981        end
2982        if isfield(Data,'Civ2_Dt')
2983        DtValue=Data.Civ2_Dt;
2984        end
2985    end
2986else
2987    if ~isempty(TimeName)&& isfield(Data,TimeName)
2988        TimeValue=Data.(TimeName);
2989    end
2990    if exist('DtName','var') && isfield(Data,DtName)
2991        DtValue=Data.(DtName);
2992    end
2993end
2994
2995%------------------------------------------------------------------------
2996% --- Executes on selection change in FieldName_1.
2997function FieldName_1_Callback(hObject, eventdata, handles)
2998%------------------------------------------------------------------------
2999field_str=get(handles.FieldName_1,'String');
3000field_index=get(handles.FieldName_1,'Value');
3001field=field_str{field_index(1)};
3002if isequal(field,'add_field...')
3003    hget_field=findobj(allchild(0),'name','get_field');
3004    if ~isempty(hget_field)
3005        delete(hget_field)%delete opened versions of get_field
3006    end
3007    Param=read_GUI(handles.series);
3008    Param.InputTable=Param.InputTable(1,:);
3009    % check the existence of the first file in the series
3010    first_j=[];
3011    if isfield(Param.IndexRange,'first_j'); first_j=Param.IndexRange.first_j; end
3012    if isfield(Param.IndexRange,'last_j'); last_j=Param.IndexRange.last_j; end
3013    PairString='';
3014    if isfield(Param.IndexRange,'PairString'); PairString=Param.IndexRange.PairString; end
3015    [i1,i2,j1,j2] = get_file_index(Param.IndexRange.first_i,first_j,PairString);
3016    FirstFileName=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},...
3017        Param.InputTable{1,5},Param.InputTable{1,4},i1,i2,j1,j2);
3018    if exist(FirstFileName,'file')
3019        ParamIn.SeriesInput=1;
3020        GetFieldData=get_field(FirstFileName,ParamIn);
3021        FieldList={};
3022        switch GetFieldData.FieldOption
3023            case 'vectors'
3024                UName=GetFieldData.PanelVectors.vector_x;
3025                VName=GetFieldData.PanelVectors.vector_y;
3026                FieldList={['vec(' UName ',' VName ')'];...
3027                    ['norm(' UName ',' VName ')'];...
3028                    UName;VName};
3029            case {'scalar','pick variables'}
3030                FieldList=GetFieldData.PanelScalar.scalar;
3031                if ischar(FieldList)
3032                    FieldList={FieldList};
3033                end
3034            case '1D plot'
3035
3036            case 'civdata...'
3037                FieldList=set_field_list('U','V','C');
3038                set(handles.FieldName,'Value',2) % set menu to 'velocity
3039        end
3040        if ~strcmp(GetFieldData.FieldOption,'civdata...')
3041            TimeNameStr=GetFieldData.Time.SwitchVarIndexTime;
3042            switch TimeNameStr
3043                case 'file index'
3044                    set(handles.TimeName,'String','');
3045                case 'attribute'
3046                    set(handles.TimeName,'String',['att:' GetFieldData.Time.TimeName]);
3047                case 'variable'
3048                    set(handles.TimeName,'String',['var:' GetFieldData.Time.TimeName])
3049                    set(handles.NomType,'String','*')
3050                    set(handles.RootFile,'String',[get(handles.RootFile,'String') get(handles.FileIndex,'String')])% A VERIFIER !!!!!!
3051                    set(handles.FileIndex,'String','')
3052                    ParamIn.TimeVarName=GetFieldData.Time.TimeName;
3053                case 'matrix_index'
3054                    set(handles.TimeName,'String',['dim:' GetFieldData.Time.TimeName]);
3055                    set(handles.NomType,'String','*')
3056                    set(handles.RootFile,'String',[get(handles.RootFile,'String') get(handles.FileIndex,'String')])
3057                    set(handles.FileIndex,'String','')
3058                    ParamIn.TimeDimName=GetFieldData.Time.TimeName;
3059            end
3060        end
3061        set(handles.FieldName_1,'Value',1)
3062        set(handles.FieldName_1,'String',[FieldList; {'add_field...'}]);
3063    end
3064end   
3065
3066
3067%%%%%%%%%%%%%
3068function [ind_remove]=find_pairs(dirpair,ind_i,last_i)
3069indsel=ind_i;
3070indiff=diff(ind_i); % test index increment to detect multiplets (several pairs with the same index ind_i) and holes in the series
3071indiff=[1 indiff last_i-ind_i(end)+1]; % for testing gaps with the imposed bounds
3072if ~isempty(indiff)
3073    indiff2=diff(indiff);
3074    indiffp=[indiff2 1];
3075    indiffm=[1 indiff2];
3076    ind_multi_m=find((indiff==0)&(indiffm<0))-1; % indices of first members of multiplets
3077    ind_multi_p=find((indiff==0)&(indiffp>0)); % indices of last members of multiplets
3078    %for each multiplet, select the most recent file
3079    ind_remove=[];
3080    for i=1:length(ind_multi_m)
3081        ind_pairs=ind_multi_m(i):ind_multi_p(i);
3082        for imulti=1:length(ind_pairs)
3083            datepair(imulti)=datenum(dirpair(ind_pairs(imulti)).date); % dates of creation
3084        end
3085        [datenew,indsort2]=sort(datepair); % sort the multiplet by creation date
3086        ind_s=indsort2(1:end-1); %
3087        ind_remove=[ind_remove ind_pairs(ind_s)]; % remove these indices, leave the last one
3088    end
3089end
3090
3091%------------------------------------------------------------------------
3092% --- determine the list of index pairstring of processing file
3093function [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)
3094%------------------------------------------------------------------------
3095num_i1=num_i; % set of first image numbers by default
3096num_i2=num_i;
3097num_j1=num_j;
3098num_j2=num_j;
3099num_i_out=num_i;
3100num_j_out=num_j;
3101% if isequal (NomType,'_1-2_1') || isequal (NomType,'_1-2')
3102if isequal(mode,'series(Di)')
3103    num_i1_line=num_i+ind_shift(3); % set of first image numbers
3104    num_i2_line=num_i+ind_shift(4);
3105    % adjust the first and last field number
3106        indsel=find(num_i1_line >= 1);
3107    num_i_out=num_i(indsel);
3108    num_i1_line=num_i1_line(indsel);
3109    num_i2_line=num_i2_line(indsel);
3110    num_j1=meshgrid(num_j,ones(size(num_i1_line)));
3111    num_j2=meshgrid(num_j,ones(size(num_i1_line)));
3112    [xx,num_i1]=meshgrid(num_j,num_i1_line);
3113    [xx,num_i2]=meshgrid(num_j,num_i2_line);
3114elseif isequal (mode,'series(Dj)')||isequal (mode,'bursts')
3115    if isequal(mode,'bursts') %case of bursts (png_old or png_2D)
3116        num_j1=ind_shift(1)*ones(size(num_i));
3117        num_j2=ind_shift(2)*ones(size(num_i));
3118    else
3119        num_j1_col=num_j+ind_shift(1); % set of first image numbers
3120        num_j2_col=num_j+ind_shift(2);
3121        % adjust the first field number
3122        indsel=find((num_j1_col >= 1));   
3123        num_j_out=num_j(indsel);
3124        num_j1_col=num_j1_col(indsel);
3125        num_j2_col=num_j2_col(indsel);
3126        [num_i1,num_j1]=meshgrid(num_i,num_j1_col);
3127        [num_i2,num_j2]=meshgrid(num_i,num_j2_col);
3128    end   
3129end
3130
3131%------------------------------------------------------------------------
3132% --- Executes on button press in CheckObject.
3133function CheckObject_Callback(hObject, eventdata, handles)
3134%------------------------------------------------------------------------
3135hset_object=findobj(allchild(0),'tag','set_object'); % find the set_object interface handle
3136if get(handles.CheckObject,'Value')
3137    SeriesData=get(handles.series,'UserData');
3138    if isfield(SeriesData,'ProjObject') && ~isempty(SeriesData.ProjObject)
3139        set(handles.ViewObject,'Value',1)
3140        ViewObject_Callback(hObject, eventdata, handles)
3141    else
3142        if ishandle(hset_object)
3143            uistack(hset_object,'top')% show the GUI set_object if opened
3144        else
3145            %get the object file
3146            InputTable=get(handles.InputTable,'Data');
3147            defaultname=InputTable{1,1};
3148            if isempty(defaultname)
3149                defaultname={''};
3150            end
3151            fileinput=uigetfile_uvmat('pick a xml object file (or use uvmat to create it)',defaultname,'.xml');
3152            if isempty(fileinput)% exit if no object file is selected
3153                set(handles.CheckObject,'Value',0)
3154                return
3155            end
3156            %read the file
3157            data=xml2struct(fileinput);
3158            if ~isfield(data,'Type')
3159                msgbox_uvmat('ERROR',[fileinput ' is not an object xml file'])
3160                set(handles.CheckObject,'Value',0)
3161                return
3162            end
3163            if ~isfield(data,'ProjMode')
3164                data.ProjMode='none';
3165            end
3166            hset_object=set_object(data); % call the set_object interface
3167            set(hset_object,'Name','set_object_series')% name to distinguish from set_object used with uvmat
3168        end
3169        ProjObject=read_GUI(hset_object);
3170        set(handles.ProjObjectName,'String',ProjObject.Name); % display the object name
3171        SeriesData=get(handles.series,'UserData');
3172        SeriesData.ProjObject=ProjObject;
3173        set(handles.series,'UserData',SeriesData);
3174    end
3175    set(handles.EditObject,'Visible','on');
3176    set(handles.DeleteObject,'Visible','on');
3177    set(handles.ViewObject,'Visible','on');
3178    set(handles.ProjObjectName,'Visible','on');
3179else
3180    set(handles.EditObject,'Visible','off');
3181    set(handles.DeleteObject,'Visible','off');
3182    set(handles.ViewObject,'Visible','off');
3183    if ~ishandle(hset_object)
3184        set(handles.ViewObject,'Value',0);
3185    end
3186    set(handles.ProjObjectName,'Visible','off');
3187end
3188
3189%------------------------------------------------------------------------
3190% --- Executes on button press in ViewObject.
3191%------------------------------------------------------------------------
3192function ViewObject_Callback(hObject, eventdata, handles)
3193
3194UserData=get(handles.series,'UserData');
3195hset_object=findobj(allchild(0),'Tag','set_object');
3196if ~isempty(hset_object)
3197    delete(hset_object)% refresh set_object if already opened
3198end
3199hset_object=set_object(UserData.ProjObject);
3200set(hset_object,'Name','view_object_series')
3201
3202
3203%------------------------------------------------------------------------
3204% --- Executes on button press in EditObject.
3205function EditObject_Callback(hObject, eventdata, handles)
3206%------------------------------------------------------------------------
3207if get(handles.EditObject,'Value')
3208    set(handles.ViewObject,'Value',0)
3209    UserData=get(handles.series,'UserData');
3210    hset_object=set_object(UserData.ProjObject);
3211    set(hset_object,'Name','edit_object_series')
3212    set(get(hset_object,'Children'),'Enable','on')
3213else
3214    hset_object=findobj(allchild(0),'Tag','set_object');
3215    if ~isempty(hset_object)
3216        set(get(hset_object,'Children'),'Enable','off')
3217    end
3218end
3219
3220%------------------------------------------------------------------------
3221% --- Executes on button press in DeleteObject.
3222function DeleteObject_Callback(hObject, eventdata, handles)
3223%------------------------------------------------------------------------
3224SeriesData=get(handles.series,'UserData');
3225SeriesData.ProjObject=[];
3226set(handles.series,'UserData',SeriesData)
3227set(handles.ProjObjectName,'String','')
3228set(handles.ProjObjectName,'Visible','off')
3229set(handles.CheckObject,'Value',0)
3230set(handles.ViewObject,'Visible','off')
3231set(handles.EditObject,'Visible','off')
3232hset_object=findobj(allchild(0),'name','set_object_series');
3233if ~isempty(hset_object)
3234    delete(hset_object)
3235end
3236set(handles.DeleteObject,'Visible','off')
3237
3238%------------------------------------------------------------------------
3239% --- Executed when CheckMask is activated
3240%------------------------------------------------------------------------
3241function CheckMask_Callback(hObject, eventdata, handles)
3242
3243if get(handles.CheckMask,'Value')
3244    InputTable=get(handles.InputTable,'Data');
3245    nbview=size(InputTable,1);
3246    MaskTable=cell(nbview,1); % default
3247    ListMask=cell(nbview,1); % default
3248    MaskData=get(handles.MaskTable,'Data');
3249    MaskData(size(MaskData,1):nbview,1)=cell(size(MaskData,1):nbview,1); % complement if undefined lines
3250    for iview=1:nbview
3251        ListMask{iview,1}=num2str(iview);
3252        RootPath=InputTable{iview,1};
3253        if ~isempty(RootPath)
3254            if isempty(MaskData{iview})
3255                SubDir=InputTable{iview,2};
3256                MaskPath=fullfile(RootPath,[regexprep(SubDir,'\..*','') '.mask']); % take the root part of SubDir, before the first dot '.'
3257                if exist(MaskPath,'dir')
3258                    ListStruct=dir(MaskPath); % look for a mask file
3259                    ListCells=struct2cell(ListStruct); % transform dir struct to a cell arrray
3260                    check_dir=cell2mat(ListCells(4,:)); % =1 for directories, =0 for files
3261                    ListFiles=ListCells(1,:); % list of file and dri names
3262                    ListFiles=ListFiles(~check_dir); % list of file names (excluding dir)
3263                    mdetect=0;
3264                    if ~isempty(ListFiles)
3265                        for ifile=1:numel(ListFiles)
3266                            [tild,tild,MaskFile{ifile},i1_series,i2_series,j1_series,j2_series,MaskNomType,MaskFileType]=find_file_series(MaskPath,ListFiles{ifile},0);
3267                            if strcmp(MaskFileType,'image') && isempty(i2_series) && isempty(j2_series)
3268                                mdetect=1;
3269                                MaskName=ListFiles{ifile};
3270                            end
3271                            if ~strcmp(MaskFile{ifile},MaskFile{1})
3272                                mdetect=0; % cancel detection test in case of multiple masks, use the brower for selection
3273                                break
3274                            end
3275                        end
3276                    end
3277                    if mdetect==1
3278                        MaskName=fullfile(MaskPath,'mask_1.png');
3279                    else
3280                        MaskName=uigetfile_uvmat('select a mask file:',MaskPath,'image');
3281                    end
3282                else
3283                    MaskName=uigetfile_uvmat('select a mask file:',RootPath,'image');
3284                end
3285                MaskTable{iview,1}=MaskName ;
3286                ListMask{iview,1}=num2str(iview);
3287            end
3288        end
3289    end
3290    set(handles.MaskTable,'Data',MaskTable)
3291    set(handles.MaskTable,'Visible','on')
3292    set(handles.MaskBrowse,'Visible','on')
3293    set(handles.ListMask,'Visible','on')
3294    set(handles.ListMask,'String',ListMask)
3295    set(handles.ListMask,'Value',1)
3296else
3297    set(handles.MaskTable,'Visible','off')
3298    set(handles.MaskBrowse,'Visible','off')
3299    set(handles.ListMask,'Visible','off')
3300end
3301
3302%------------------------------------------------------------------------
3303% --- Executes on button press in MaskBrowse.
3304%------------------------------------------------------------------------
3305function MaskBrowse_Callback(hObject, eventdata, handles)
3306
3307InputTable=get(handles.InputTable,'Data');
3308iview=get(handles.ListMask,'Value');
3309RootPath=InputTable{iview,1};
3310MaskName=uigetfile_uvmat('select a mask file:',RootPath,'image');
3311if ~isempty(MaskName)
3312    MaskTable=get(handles.MaskTable,'Data');
3313    MaskTable{iview,1}=MaskName ;
3314    set(handles.MaskTable,'Data',MaskTable)
3315end
3316
3317%------------------------------------------------------------------------
3318% --- Executes when selected cell(s) is changed in MaskTable.
3319%------------------------------------------------------------------------
3320function MaskTable_CellSelectionCallback(hObject, eventdata, handles)
3321
3322if numel(eventdata.Indices)>=1
3323set(handles.ListMask,'Value',eventdata.Indices(1))
3324end
3325
3326%-------------------------------------------------------------------
3327function MenuHelp_Callback(hObject, eventdata, handles)
3328%-------------------------------------------------------------------
3329
3330
3331% path_to_uvmat=which ('uvmat'); % check the path of uvmat
3332% pathelp=fileparts(path_to_uvmat);
3333% helpfile=fullfile(pathelp,'uvmat_doc','uvmat_doc.html');
3334% 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')
3335% else
3336%     addpath (fullfile(pathelp,'uvmat_doc'))
3337%     web([helpfile '#series'])
3338% end
3339
3340%-------------------------------------------------------------------
3341% --- Executes on selection change in TransformName.
3342function TransformName_Callback(hObject, eventdata, handles)
3343%----------------------------------------------------------------------
3344TransformList=get(handles.TransformName,'String');
3345TransformIndex=get(handles.TransformName,'Value');
3346TransformName=TransformList{TransformIndex};
3347TransformPathList=get(handles.TransformName,'UserData');
3348nb_builtin_transform=4;
3349if isequal(TransformName,'more...');     
3350    FileName=uigetfile_uvmat('Pick a transform function',get(handles.TransformPath,'String'),'.m');
3351    if isempty(FileName)
3352        return     %browser closed without choice
3353    end
3354    [TransformPath,TransformName,TransformExt]=fileparts(FileName); % removes extension .m
3355    if ~strcmp(TransformExt,'.m')
3356        msgbox_uvmat('ERROR','a Matlab function .m must be introduced');
3357        return
3358    end
3359     % insert the choice in the menu
3360    TransformIndex=find(strcmp(TransformName,TransformList),1); % look for the selected function in the menu Action
3361    if isempty(TransformIndex)%the input string does not exist in the menu
3362        TransformIndex= length(TransformList);
3363        TransformList=[TransformList(1:end-1);{TransformName};TransformList(end)]; % the selected function is appended in the menu, before the last item 'more...'
3364        set(handles.TransformName,'String',TransformList)
3365        TransformPathList=[TransformPathList;{TransformPath}];
3366    else% the input function already exist, we update its path (possibly new)
3367        TransformPathList{TransformIndex}=TransformPath; %
3368        set(handles.TransformName,'Value',TransformIndex)
3369    end
3370   % save the new menu in the personal file 'uvmat_perso.mat'
3371   dir_perso=prefdir; % personal Matalb directory
3372   profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
3373   if exist(profil_perso,'file')
3374       for ilist=nb_builtin_transform+1:numel(TransformPathList)
3375           TransformListUser{ilist-nb_builtin_transform}=TransformList{ilist};
3376           TransformPathListUser{ilist-nb_builtin_transform}=TransformPathList{ilist};
3377       end
3378       TransformPathListUser=TransformPathListUser';
3379       TransformListUser=TransformListUser';
3380       save (profil_perso,'TransformPathListUser','TransformListUser','-append'); % store the root name for future opening of uvmat
3381   end
3382end
3383
3384%display the current function path
3385set(handles.TransformPath,'String',TransformPathList{TransformIndex}); % show the path to the senlected function
3386set(handles.TransformName,'UserData',TransformPathList);
3387
3388%% create the function handle of the selected fct
3389if ~isempty(TransformName)
3390    if ~exist(TransformPathList{TransformIndex},'dir')
3391        msgbox_uvmat('ERROR',['The prescribed transform function path ' TransformPathList{TransformIndex} ' does not exist']);
3392        return
3393    end
3394    current_dir=pwd; % current working dir
3395    cd(TransformPathList{TransformIndex})
3396    transform_handle=str2func(TransformName);
3397    cd(current_dir)
3398    Field.Action.RUN=0;% indicate that the transform fct is called only to get input param
3399    SeriesData=get(handles.series,'UserData');
3400    ParamIn=[];
3401    if isfield(SeriesData,'TransformInput')
3402        ParamIn.TransformInput=SeriesData.TransformInput;
3403    end
3404    DataOut=feval(transform_handle,Field,ParamIn);% execute the transform fct to get the required conditions
3405    Field.Action.RUN=0; % indicate that the transform fct is called only to get input param
3406    %DataOut=feval(transform_handle,Field,[]); % execute the transform fct to get the required conditions
3407    if isfield(DataOut,'TransformInput')%  used to add transform parameters at selection of the transform fct
3408        SeriesData.TransformInput=DataOut.TransformInput;
3409        set(handles.series,'UserData',SeriesData)
3410    end
3411end
3412
3413%------------------------------------------------------------------------
3414% --- fct activated by the upper bar menu ExportConfig
3415%------------------------------------------------------------------------
3416function MenuDisplayConfig_Callback(hObject, eventdata, handles)
3417
3418global Param
3419Param=read_GUI_series(handles);
3420evalin('base','global Param')%make CurData global in the workspace
3421display('current series config :')
3422evalin('base','Param') %display CurData in the workspace
3423commandwindow; % brings the Matlab command window to the front
3424
3425%------------------------------------------------------------------------
3426% --- fct activated by the upper bar menu InportConfig: import
3427%     menu settings from an xml file (stored in /0_XML for each run)
3428%------------------------------------------------------------------------
3429function MenuImportConfig_Callback(hObject, eventdata, handles)
3430
3431%% use a browser to choose the xml file containing the processing config
3432InputTable=get(handles.InputTable,'Data');
3433oldfile=InputTable{1,1}; % current path in InputTable
3434if isempty(oldfile)
3435    % use a file name stored in prefdir
3436    dir_perso=prefdir;
3437    profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
3438    if exist(profil_perso,'file')
3439        h=load (profil_perso);
3440        if isfield(h,'RootPath') && ischar(h.RootPath)
3441            oldfile=h.RootPath;
3442        end
3443    end
3444end
3445filexml=uigetfile_uvmat('pick a xml parameter file',oldfile,'.xml'); % get the xml file containing processing parameters
3446if isempty(filexml), return, end % quit function if an xml file has not been opened
3447
3448%% fill the GUI series with the content of the xml file
3449[Param,RootTag,errormsg]=xml2struct(filexml); % read the input xml file as a Matlab structure
3450if ~isempty(errormsg)
3451    msgbox_uvmat('ERROR',errormsg);
3452    return
3453end
3454% ask to stop current Action if button RUN is in action (another process is already running)
3455if isequal(get(handles.RUN,'Value'),1)
3456    answer= msgbox_uvmat('INPUT_Y-N','stop current Action process?');
3457    if strcmp(answer,'Yes')
3458        STOP_Callback(hObject, eventdata, handles)
3459    else
3460        return
3461    end
3462end
3463Param.Action.RUN=0; % desactivate the input RUN=1
3464
3465fill_GUI(Param,handles.series)% fill the elements of the GUI series with the input parameters
3466SeriesData=get(handles.series,'UserData');
3467if isfield(Param,'InputFields')
3468    ListField=Param.InputFields.FieldName;
3469    if ischar(ListField),ListField={ListField}; end
3470    set(handles.FieldName,'String',[ListField;{'add_field...'}])
3471     set(handles.FieldName,'Value',1:numel(ListField))
3472     set(handles.FieldName,'Visible','on')
3473end       
3474if isfield(Param,'ActionInput')%  introduce  parameters specific to an Action fct, for instance PIV parameters
3475%     set(handles.ActionInput,'Visible','on')
3476%     set(handles.ActionInput,'Value',0)
3477    Param.ActionInput.ConfigSource=filexml; % record the source of config for future info
3478    SeriesData.ActionInput=Param.ActionInput;
3479end
3480if isfield(Param,'TransformInput')%  introduce  parameters specific to a transform fct
3481    SeriesData.TransformInput=Param.TransformInput;
3482end
3483if isfield(Param,'ProjObject') %introduce projection object if relevant
3484    SeriesData.ProjObject=Param.ProjObject;
3485end
3486set(handles.series,'UserData',SeriesData)
3487if isfield(Param,'CheckObject') && isequal(Param.CheckObject,1)
3488    set(handles.ProjObjectName,'String',Param.ProjObject.Name)
3489    set(handles.ViewObject,'Visible','on')
3490    set(handles.EditObject,'Visible','on')
3491    set(handles.DeleteObject,'Visible','on')
3492else     
3493    set(handles.ProjObjectName,'String','')
3494    set(handles.ProjObjectName,'Visible','off')
3495    set(handles.ViewObject,'Visible','off')
3496    set(handles.EditObject,'Visible','off')
3497    set(handles.DeleteObject,'Visible','off')     
3498end     
3499set(handles.REFRESH,'BackgroundColor',[1 0 1]); % paint REFRESH button in magenta to indicate that it should be activated
3500
3501
3502%------------------------------------------------------------------------
3503% --- Executes when the GUI series is resized.
3504%------------------------------------------------------------------------
3505function series_ResizeFcn(hObject, eventdata, handles)
3506
3507%% input table
3508set(handles.InputTable,'Unit','pixel')
3509Pos=get(handles.InputTable,'Position');
3510set(handles.InputTable,'Unit','normalized')
3511ColumnWidth=round([0.5 0.14 0.14 0.14 0.08]*(Pos(3)-52));
3512ColumnWidth=num2cell(ColumnWidth);
3513set(handles.InputTable,'ColumnWidth',ColumnWidth)
3514
3515%% MinIndex_j and MaxIndex_i
3516unit=get(handles.MinIndex_i,'Unit');
3517set(handles.MinIndex_i,'Unit','pixel')
3518Pos=get(handles.MinIndex_i,'Position');
3519set(handles.MinIndex_i,'Unit',unit)
3520set(handles.MinIndex_i,'ColumnWidth',{Pos(3)-18})
3521set(handles.MaxIndex_i,'ColumnWidth',{Pos(3)-18})
3522set(handles.MinIndex_j,'ColumnWidth',{Pos(3)-18})
3523set(handles.MaxIndex_j,'ColumnWidth',{Pos(3)-18})
3524
3525%% TimeTable
3526set(handles.TimeTable,'Unit','pixel')
3527Pos=get(handles.TimeTable,'Position');
3528set(handles.TimeTable,'Unit','normalized')
3529% ColumnWidth=get(handles.TimeTable,'ColumnWidth');
3530ColumnWidth=num2cell(floor([0.2 0.2 0.2 0.2 0.2]*(Pos(3)-20)));
3531set(handles.TimeTable,'ColumnWidth',ColumnWidth)
3532
3533
3534%% PairString
3535set(handles.PairString,'Unit','pixel')
3536Pos=get(handles.PairString,'Position');
3537set(handles.PairString,'Unit','normalized')
3538set(handles.PairString,'ColumnWidth',{Pos(3)-5})
3539
3540%% MaskTable
3541set(handles.MaskTable,'Unit','pixel')
3542Pos=get(handles.MaskTable,'Position');
3543set(handles.MaskTable,'Unit','normalized')
3544set(handles.MaskTable,'ColumnWidth',{Pos(3)-5})
3545
3546%------------------------------------------------------------------------
3547% --- Executes on button press in status.
3548%------------------------------------------------------------------------
3549function status_Callback(hObject, eventdata, handles)
3550
3551if get(handles.status,'Value')
3552    set(handles.status,'BackgroundColor',[1 1 0])
3553    drawnow
3554    Param=read_GUI(handles.series);
3555    RootPath=fullfile(Param.OutputPath,Param.Experiment,Param.Device);
3556    if ~isfield(Param,'OutputSubDir')   
3557        msgbox_uvmat('ERROR','no standard sub-directory definition for output files, use a browser to check the output')
3558        set(handles.status,'BackgroundColor',[0 1 0])
3559        return
3560    end
3561    OutputSubDir=[Param.OutputSubDir Param.OutputDirExt]; % subdirectory for output files
3562    OutputDir=fullfile(RootPath,OutputSubDir);
3563    if exist(OutputDir,'dir')
3564        uigetfile_uvmat('status_display',OutputDir)
3565    else
3566        msgbox_uvmat('ERROR','output folder not created yet: calculation did not start')
3567        set(handles.status,'BackgroundColor',[0 1 0])
3568    end
3569else
3570    %% delete current display fig if selection is off
3571    set(handles.status,'BackgroundColor',[0 1 0])
3572    hfig=findobj(allchild(0),'name','status_display');
3573    if ~isempty(hfig)
3574        delete(hfig)
3575    end
3576    return
3577end
3578
3579
3580%------------------------------------------------------------------------   
3581% launched by selecting a file on the list
3582%------------------------------------------------------------------------
3583function view_file(hObject, eventdata)
3584
3585list=get(hObject,'String');
3586index=get(hObject,'Value');
3587rootroot=get(hObject,'UserData');
3588selectname=list{index};
3589ind_dot=regexp(selectname,'\.\.\.');
3590if ~isempty(ind_dot)
3591    selectname=selectname(1:ind_dot-1);
3592end
3593FullSelectName=fullfile(rootroot,selectname);
3594if exist(FullSelectName,'dir')% a directory has been selected
3595    ListFiles=dir(FullSelectName);
3596    ListDisplay=cell(numel(ListFiles),1);
3597    for ilist=2:numel(ListDisplay)% suppress the first line '.'
3598        ListDisplay{ilist-1}=ListFiles(ilist).name;
3599    end
3600    set(hObject,'Value',1)
3601    set(hObject,'String',ListDisplay)
3602    if strcmp(selectname,'..')
3603        FullSelectName=fileparts(fileparts(FullSelectName));
3604    end
3605    set(hObject,'UserData',FullSelectName)
3606    hfig=get(hObject,'parent');
3607    htitlebox=findobj(hfig,'tag','titlebox');   
3608    set(htitlebox,'String',FullSelectName)
3609elseif exist(FullSelectName,'file')%visualise the vel field if it exists
3610    FileInfo=get_file_info(FullSelectName);   
3611    if strcmp(FileInfo.FileType,'txt')
3612        edit(FullSelectName)
3613    elseif strcmp(FileInfo.FileType,'xml')
3614        editxml(FullSelectName)
3615    else
3616        uvmat(FullSelectName)
3617    end
3618    set(gcbo,'Value',1)
3619end
3620
3621
3622%------------------------------------------------------------------------   
3623% launched by refreshing the status figure
3624%------------------------------------------------------------------------
3625function refresh_GUI(hfig)
3626
3627htitlebox=findobj(hfig,'tag','titlebox');
3628hlist=findobj(hfig,'tag','list');
3629hseries=findobj(allchild(0),'tag','series');
3630hstatus=findobj(hseries,'tag','status');
3631StatusData=get(hstatus,'UserData');
3632OutputDir=get(htitlebox,'String');
3633if ischar(OutputDir),OutputDir={OutputDir};end
3634ListFiles=dir(OutputDir{1});
3635if numel(ListFiles)<1
3636    return
3637end
3638ListFiles(1)=[]; % removes the first line ='.'
3639ListDisplay=cell(numel(ListFiles),1);
3640testrecent=0;
3641datnum=zeros(numel(ListDisplay),1);
3642for ilist=1:numel(ListDisplay)
3643    ListDisplay{ilist}=ListFiles(ilist).name;
3644      if ~ListFiles(ilist).isdir && isfield(ListFiles(ilist),'datenum')
3645            datnum(ilist)=ListFiles(ilist).datenum; % only available in recent matlab versions
3646            testrecent=1;
3647       end
3648end
3649set(hlist,'String',ListDisplay)
3650
3651%% Look at date of creation
3652ListDisplay=ListDisplay(datnum~=0);
3653datnum=datnum(datnum~=0); % keep the non zero values corresponding to existing files
3654NbOutputFile=[];
3655if isempty(datnum)
3656    if testrecent
3657        message='no civ result created yet';
3658    else
3659        message='';
3660    end
3661else
3662    [first,indfirst]=min(datnum);
3663    [last,indlast]=max(datnum);
3664    NbOutputFile_str='?';
3665    NbOutputFile=[];
3666    if isfield(StatusData,'NbOutputFile')
3667        NbOutputFile=StatusData.NbOutputFile;
3668        NbOutputFile_str=num2str(NbOutputFile);
3669    end
3670    message={[num2str(numel(datnum)) ' file(s) done over ' NbOutputFile_str] ;['oldest modification:  ' ListDisplay{indfirst} ' : ' datestr(first)];...
3671        ['latest modification:  ' ListDisplay{indlast} ' : ' datestr(last)]};
3672end
3673set(htitlebox,'String', [OutputDir{1};message])
3674
3675%% update the waitbar
3676hwaitbar=findobj(hfig,'tag','waitbar');
3677if ~isempty(NbOutputFile)
3678    BarPosition=get(hwaitbar,'Position');
3679    BarPosition(3)=0.9*numel(datnum)/NbOutputFile;
3680    set(hwaitbar,'Position',BarPosition)
3681end
3682
3683%------------------------------------------------------------------------
3684% --- Executes on selection change in ActionExt.
3685%------------------------------------------------------------------------
3686function ActionExt_Callback(hObject, eventdata, handles)
3687
3688ActionExtList=get(handles.ActionExt,'String');
3689ActionExt=ActionExtList{get(handles.ActionExt,'Value')};
3690if strcmp(ActionExt,'.py (in dev.)')
3691    set(handles.RunMode,'Value',2)
3692end
3693
3694
3695function num_NbSlice_Callback(hObject, eventdata, handles)
3696NbSlice=str2num(get(handles.num_NbSlice,'String'));
3697
3698%------------------------------------------------------------------------
3699% --- set the visibility of relevant velocity type menus:
3700function menu=set_veltype_display(Civ,FileType)
3701%------------------------------------------------------------------------
3702if ~exist('FileType','var')
3703    FileType='civx';
3704end
3705switch FileType
3706    case 'civx'
3707        menu={'civ1';'interp1';'filter1';'civ2';'interp2';'filter2'};
3708        if isequal(Civ,0)
3709            imax=0;
3710        elseif isequal(Civ,1) || isequal(Civ,2)
3711            imax=1;
3712        elseif isequal(Civ,3)
3713            imax=3;
3714        elseif isequal(Civ,4) || isequal(Civ,5)
3715            imax=4;
3716        elseif isequal(Civ,6) %patch2
3717            imax=6;
3718        end
3719    case 'civdata'
3720        menu={'civ1';'filter1';'civ2';'filter2'};
3721        if isequal(Civ,0)
3722            imax=0;
3723        elseif isequal(Civ,1) || isequal(Civ,2)
3724            imax=1;
3725        elseif isequal(Civ,3)
3726            imax=2;
3727        elseif isequal(Civ,4) || isequal(Civ,5)
3728            imax=3;
3729        else%if isequal(Civ,6) %patch2
3730            imax=4;
3731        end
3732end
3733menu=menu(1:imax);
3734
3735
3736% --- Executes on mouse motion over figure - except title and menu.
3737% function series_WindowButtonMotionFcn(hObject, eventdata, handles)
3738% set(hObject,'Pointer','arrow');
3739
3740
3741% --- Executes on button press in SetPairs.
3742function SetPairs_Callback(hObject, eventdata, handles)
3743
3744%% delete previous occurrence of 'set_pairs'
3745hfig=findobj(allchild(0),'Tag','set_pairs');
3746if ~isempty(hfig)
3747delete(hfig)
3748end
3749
3750%% create the GUI set_pairs
3751set(0,'Unit','points')
3752ScreenSize=get(0,'ScreenSize'); % get the size of the screen, to put the fig on the upper right
3753Width=220; % fig width in points (1/72 inch)
3754Height=min(0.8*ScreenSize(4),300);
3755Left=ScreenSize(3)- Width-40; % right edge close to the right, with margin=40
3756Bottom=ScreenSize(4)-Height-40; % put fig at top right
3757hfig=findobj(allchild(0),'Tag','set_slice');
3758if ~isempty(hfig),delete(hfig), end; % delete existing version of the GUI
3759hfig=figure('name','set_pairs','tag','set_pairs','MenuBar','none','NumberTitle','off','Unit','points','Position',[Left,Bottom,Width,Height]);
3760BackgroundColor=get(hfig,'Color');
3761SeriesData=get(handles.series,'UserData');
3762TimeUnit=get(handles.TimeUnit,'String');
3763PairString=get(handles.PairString,'Data');
3764ListViewLines=find(cellfun('isempty',PairString)==0); % find list of non empty pairs
3765ListViewMenu=cell(numel(ListViewLines),1);
3766%iview=get(handles.PairString,'Value');
3767iview=[];
3768for ilist=1:numel(ListViewLines)
3769    ListViewMenu{ilist}=num2str(ListViewLines(ilist));
3770end
3771if isempty(iview)
3772    ListViewValue=numel(ListViewLines); % we work by default on the pair option for the last line which requires pairs
3773    iview=ListViewLines(end);
3774else
3775    ListViewValue=find(ListViewLines==iview);
3776end
3777ref_i=str2num(get(handles.num_first_i,'String'));
3778ref_j=1; % default
3779if strcmp(get(handles.num_first_j,'String'),'Visible')
3780    ref_j=str2num(get(handles.num_first_j,'String'));
3781end
3782[ModeMenu,ModeValue]=update_mode(SeriesData.i1_series{1},SeriesData.i2_series{1},SeriesData.j2_series{1});
3783InputTable=get(handles.InputTable,'Data');
3784displ_pair=update_listpair(SeriesData.i1_series{1},SeriesData.i2_series{1},SeriesData.j1_series{1},SeriesData.j2_series{1},ModeMenu{ModeValue},...
3785                                                 SeriesData.Time{1},TimeUnit,ref_i,ref_j,SeriesData.TimeName,InputTable,SeriesData.FileInfo{1});
3786for iline=1:size(InputTable,1)
3787    viewcell{iline}=num2str(iline);
3788end
3789viewcell=viewcell';
3790ModeMenu={'bursts';'series(Dj)'};
3791ModeValue=1;                                               
3792                   %i1_series,i2_series,j1_series,j2_series,mode,time,TimeUnit,ref_i,ref_j,TimeName,InputTable,FileInfo                             
3793% first raw of the GUI
3794uicontrol('Style','text','Units','normalized', 'Position', [0.05 0.88 0.5 0.1],'BackgroundColor',BackgroundColor,...
3795    'String','row to edit #','FontUnits','points','FontSize',12,'FontWeight','bold','ForegroundColor','blue','HorizontalAlignment','right'); % title
3796uicontrol('Style','popupmenu','Units','normalized', 'Position', [0.54 0.8 0.3 0.2],'BackgroundColor',[1 1 1],...
3797    'Callback',@(hObject,eventdata)ListView_Callback(hObject,eventdata),'String',viewcell,'Value',1,'FontUnits','points','FontSize',12,'FontWeight','bold',...
3798    'Tag','ListView','TooltipString','''ListView'':choice of the file series w for pair display');
3799% second raw of the GUI
3800uicontrol('Style','text','Units','normalized', 'Position', [0.05 0.79 0.7 0.1],'BackgroundColor',BackgroundColor,...
3801    'String','mode of index pairing:','FontUnits','points','FontSize',12,'FontWeight','bold','ForegroundColor','blue','HorizontalAlignment','left'); % title
3802uicontrol('Style','popupmenu','Units','normalized', 'Position', [0.05 0.62 0.9 0.2],'BackgroundColor',[1 1 1],...
3803    'Callback',@(hObject,eventdata)Mode_Callback(hObject,eventdata),'String',ModeMenu,'Value',ModeValue,'FontUnits','points','FontSize',12,'FontWeight','bold',...
3804    'Tag','Mode','TooltipString','''Mode'': choice of the image pair mode');
3805% third raw
3806uicontrol('Style','text','Units','normalized', 'Position', [0.05 0.6 0.7 0.1],'BackgroundColor',BackgroundColor,...
3807    'String','pair choice:','FontUnits','points','FontSize',12,'FontWeight','bold','ForegroundColor','blue','HorizontalAlignment','left'); % title
3808uicontrol('Style','listbox','Units','normalized', 'Position', [0.05 0.42 0.9 0.2],'BackgroundColor',[1 1 1],...
3809    'Callback',@(hObject,eventdata)ListPair_Callback(hObject,eventdata),'String',displ_pair,'Value',1,'FontUnits','points','FontSize',12,'FontWeight','bold',...
3810    'Tag','ListPair','TooltipString','''ListPair'': menu for selecting the image pair');
3811uicontrol('Style','text','Units','normalized', 'Position', [0.1 0.22 0.8 0.1],'BackgroundColor',BackgroundColor,...
3812    'String','ref_i           ref_j','FontUnits','points','FontSize',12,'FontWeight','bold','ForegroundColor','blue','HorizontalAlignment','center'); % title
3813uicontrol('Style','edit','Units','normalized', 'Position', [0.15 0.17 0.3 0.08],'BackgroundColor',[1 1 1],...
3814    'Callback',@(hObject,eventdata)num_ref_i_Callback(hObject,eventdata),'String',num2str(ref_i),'FontUnits','points','FontSize',12,'FontWeight','bold',...
3815    'Tag','num_ref_i','TooltipString','''num_ref_i'': reference field index i used to display dt in ''list_pair_civ''');
3816uicontrol('Style','edit','Units','normalized', 'Position', [0.55 0.17 0.3 0.08],'BackgroundColor',[1 1 1],...
3817    'Callback',@(hObject,eventdata)num_ref_j_Callback(hObject,eventdata),'String',num2str(ref_j),'FontUnits','points','FontSize',12,'FontWeight','bold',...
3818    'Tag','num_ref_j','TooltipString','''num_ref_j'': reference field index i used to display dt in ''list_pair_civ''');
3819uicontrol('Style','pushbutton','Units','normalized', 'Position', [0.01 0.01 0.3 0.12],'BackgroundColor',[0 1 0],...
3820    'Callback',@(hObject,eventdata)OK_Callback(hObject,eventdata),'String','OK','FontUnits','points','FontSize',12,'FontWeight','bold',...
3821    'Tag','OK','TooltipString','''OK'': validate the choice');
3822%  last raw  of the GUI: pushbuttons
3823% 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),...
3824%     'FontWeight','bold','FontUnits','points','FontSize',12,'TooltipString','''OK'': apply the output to the current field series in uvmat');
3825drawnow
3826
3827%------------------------------------------------------------------------
3828function ListView_Callback(hObject,eventdata)
3829Mode_Callback(hObject,eventdata)
3830
3831%------------------------------------------------------------------------   
3832function Mode_Callback(hObject,eventdata)
3833%% get input info
3834hseries=findobj(allchild(0),'tag','series'); % handles of the GUI series
3835hhseries=guidata(hseries); % handles of the elements in the GUI series
3836TimeUnit=get(hhseries.TimeUnit,'String');
3837SeriesData=get(hseries,'UserData');
3838mode_list=get(hObject,'String');
3839mode=mode_list{get(hObject,'Value')};
3840hListView=findobj(get(hObject,'parent'),'Tag','ListView');
3841iview=get(hListView,'Value');
3842i1_series=SeriesData.i1_series{iview};
3843i2_series=SeriesData.i2_series{iview};
3844j1_series=SeriesData.j1_series{iview};
3845j2_series=SeriesData.j2_series{iview};
3846
3847%% enable j index visibility after the new choice
3848
3849if strcmp(mode,'series(Dj)')
3850   status_j='on'; % default
3851else
3852       status_j='off'; % no j index needed for bust case
3853end
3854enable_j(hhseries,status_j) % no j index needed
3855
3856%% get the reference indices for the time interval Dt
3857href_i=findobj(get(hObject,'parent'),'Tag','ref_i');
3858ref_i=[];ref_j=[];
3859if strcmp(get(href_i,'Visible'),'on')
3860    ref_i=str2num(get(href_i,'String'));
3861end
3862if isempty(ref_i)
3863    ref_i=1;
3864end
3865if isempty(ref_j)
3866    ref_j=1;
3867end
3868
3869%% update the menu ListPair
3870Menu=update_listpair(i1_series,i2_series,j1_series,j2_series,mode,SeriesData.Time{iview},TimeUnit,ref_i,ref_j,SeriesData.FileInfo);
3871hlist_pairs=findobj(get(hObject,'parent'),'Tag','ListPair');
3872set(hlist_pairs,'Value',1)% set the first choice by default in ListPair
3873set(hlist_pairs,'String',Menu)% set the menu in ListPair
3874ListPair_Callback(hlist_pairs,[])% apply the default choice in ListPair
3875
3876%-------------------------------------------------------------
3877% --- Executes on selection in ListPair.
3878function ListPair_Callback(hObject,eventdata)
3879%------------------------------------------------------------
3880list_pair=get(hObject,'String'); % get the menu of image pairs
3881if isempty(list_pair)
3882    string='';
3883else
3884    string=list_pair{get(hObject,'Value')};
3885   % string=regexprep(string,',.*',''); % removes time indication (after ',')
3886end
3887hseries=findobj(allchild(0),'tag','series');
3888hPairString=findobj(hseries,'tag','PairString');
3889PairString=get(hPairString,'Data');
3890hListView=findobj(get(hObject,'parent'),'Tag','ListView');
3891iview=get(hListView,'Value');
3892PairString{iview,1}=string;
3893% report the selected pair string to the table PairString
3894set(hPairString,'Data',PairString)
3895
3896
3897%------------------------------------------------------------------------
3898function num_ref_i_Callback(hObject, eventdata)
3899%------------------------------------------------------------------------
3900Mode_Callback([],[])
3901
3902%------------------------------------------------------------------------
3903function num_ref_j_Callback(hObject, eventdata)
3904%------------------------------------------------------------------------
3905Mode_Callback([],[])
3906
3907%------------------------------------------------------------------------
3908function OK_Callback(hObject, eventdata)
3909%------------------------------------------------------------------------
3910delete(get(hObject,'parent'))
3911
3912
3913%------------------------------------------------------------------------
3914% --- Executes on button press in ClearLine.
3915%------------------------------------------------------------------------
3916function ClearLine_Callback(hObject, eventdata, handles)
3917InputTable=get(handles.InputTable,'Data');
3918iline=str2double(get(handles.InputLine,'String'));
3919if size(InputTable,1)>1
3920    InputTable(iline,:)=[]; % suppress the current line if not the first
3921    set(handles.InputTable,'Data',InputTable);
3922end
3923set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH button to magenta color to indicate that input refr
3924
3925
3926% --- Executes on button press in MonitorCluster.
3927function MonitorCluster_Callback(hObject, eventdata, handles)
3928
3929[rr,ss]=system('oarstat |grep N=UVmat');% check the list of jobs launched with uvmat
3930if isempty(ss)
3931   disp( 'no job presently submitted with uvmat')
3932else
3933    disp('format: R/W=run/wait, time lapsed, R=nbre of cores,W=walltime')
3934    disp(ss)
3935end
3936
3937
3938function OutputSubDir_Callback(hObject, eventdata, handles)
3939set(handles.OutputSubDir,'BackgroundColor',[1 1 1])
3940
3941
3942% --- Executes on button press in CheckOverwrite.
3943function CheckOverwrite_Callback(hObject, eventdata, handles)
3944
3945% --- Executes on button press in TestCPUTime.
3946function TestCPUTime_Callback(hObject, eventdata, handles)
3947% hObject    handle to TestCPUTime (see GCBO)
3948% eventdata  reserved - to be defined in a future version of MATLAB
3949% handles    structure with handles and user data (see GUIDATA)
3950
3951
3952% --- Executes on button press in DiskQuota.
3953function DiskQuota_Callback(hObject, eventdata, handles)
3954SeriesData=get(handles.series,'UserData');
3955system(SeriesData.SeriesParam.DiskQuotaCmd)
3956
3957
3958% --- Executes on button press in Replicate.
3959function Replicate_Callback(hObject, eventdata, handles)
3960if get(handles.Replicate,'Value')
3961    InputTable=get(handles.InputTable,'Data');
3962    for ilist=1:size(InputTable,1)
3963        InputDir{ilist}=fullfile(InputTable{ilist,1},InputTable{ilist,2});
3964    end
3965    browse_data(InputDir)
3966else
3967    hh=findobj(allchild(0),'Tag','browse_data');
3968    if ~isempty(hh)
3969        delete(hh)
3970    end
3971end
3972
3973
3974
3975
3976function OutputPath_Callback(hObject, eventdata, handles)
3977
3978
3979function Experiment_Callback(hObject, eventdata, handles)
3980
3981
3982function Device_Callback(hObject, eventdata, handles)
3983
3984
3985% --- Executes on button press in OutputPathBrowse.
3986function OutputPathBrowse_Callback(hObject, eventdata, handles)
3987CheckValue=get(handles.OutputPathBrowse,'Value');
3988if CheckValue
3989OutputPath=uigetdir(get(handles.OutputPath,'String'));
3990set(handles.OutputPath,'String',OutputPath)
3991else
3992    InputTable=get(handles.InputTable,'Data');
3993    set(handles.OutputPath,'String',InputTable{1,1})
3994end
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