source: trunk/src/series.m @ 1105

Last change on this file since 1105 was 1105, checked in by sommeria, 3 years ago

replicate repaired again

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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        if get(handles.Replicate,'Value')
1716        PathExpOut=fileparts(ListPath{iexp});
1717        PathExpDeviceOut=ListPath{iexp};
1718        else
1719            PathExpOut=fullfile(PathOut,get(handles.Experiment,'String'));
1720            PathExpDeviceOut=fullfile(PathExpOut,get(handles.Device,'String'))
1721        end
1722        if ~exist(PathExpOut,'dir')
1723            [tild,msg1]=mkdir(PathExpOut);
1724            if ~strcmp(msg1,'')
1725                errormsg=['cannot create ' PathExpOut ': ' msg1]; % error message for directory creation
1726                return
1727            end
1728        end
1729        if ~exist(PathExpDeviceOut,'dir')
1730            [tild,msg1]=mkdir(PathExpDeviceOut);
1731            if ~strcmp(msg1,'')
1732                errormsg=['cannot create ' PathExpDeviceOut ': ' msg1]; % error message for directory creation
1733                return
1734            end
1735        end
1736        SubDirOut=[Param.OutputSubDir Param.OutputDirExt];
1737        SubDirOutNew=SubDirOut;
1738        detect=exist(fullfile(PathExpDeviceOut,SubDirOutNew),'dir'); % test if  the dir  already exist
1739        check_create=1; % need to create the result directory by default
1740        CheckOverwrite=1;
1741        if isfield(Param,'CheckOverwrite')
1742            CheckOverwrite=Param.CheckOverwrite;% will overwrite previous data if it is equal to 1
1743        end
1744        while detect
1745            if CheckOverwrite
1746                comment=', possibly overwrite previous data';
1747            else
1748                comment=', will complement existing result files (no overwriting)';
1749            end
1750            answer=msgbox_uvmat('INPUT_Y-N-Cancel',['use existing ouput directory: ' fullfile(PathExpDeviceOut,SubDirOutNew) comment]);
1751            if strcmp(answer,'Cancel')
1752                break
1753            elseif strcmp(answer,'Yes')
1754                detect=0;
1755                check_create=0;
1756            else
1757                r=regexp(SubDirOutNew,'(?<root>.*\D)(?<num1>\d+)$','names'); % detect whether name ends by a number
1758                if isempty(r)
1759                    r(1).root=[SubDirOutNew '_'];
1760                    r(1).num1='0';
1761                end
1762                SubDirOutNew=[r(1).root num2str(str2num(r(1).num1)+1)]; % increment the index by 1 or put 1
1763                detect=exist(fullfile(PathExpDeviceOut,SubDirOutNew),'dir'); % test if  the dir  already exists
1764                check_create=1;
1765            end
1766        end
1767        if strcmp(answer,'Cancel')
1768            continue
1769        end
1770        Param.OutputDirExt=regexprep(SubDirOutNew,['^' Param.OutputSubDir],'');
1771        Param.OutputRootFile=Param.InputTable{1,3}; % the first sorted RootFile taken for output
1772        OutputDir=fullfile(PathExpDeviceOut,[Param.OutputSubDir Param.OutputDirExt]); % full name (with path) of output directory
1773        if check_create    % create output directory if it does not exist
1774            [tild,msg1]=mkdir(OutputDir);
1775            if ~strcmp(msg1,'')
1776                errormsg=['cannot create ' OutputDir ': ' msg1]; % error message for directory creation
1777                return
1778            end
1779        end
1780       
1781    elseif isfield(Param,'ActionInput')&&isfield(Param.ActionInput,'LogPath')% custom definition of the output dir
1782        OutputDir=Param.ActionInput.LogPath;
1783    end
1784    if isfield(Param,'OutputSubDir')
1785    set(handles.OutputSubDir,'String',Param.OutputSubDir)
1786    set(handles.OutputDirExt,'String',Param.OutputDirExt)
1787    drawnow
1788    end
1789    if get(handles.Replicate,'Value')
1790        set(handles.InputTable,'Data',Param.InputTable)
1791        set(handles.OutputPath,'String',OutputPath)
1792         set(handles.Experiment,'String',ListExpOut{iexp})
1793        set(handles.Device,'String',ListDeviceOut{iexp})
1794        Param.Experiment=ListExpOut{iexp};
1795        Param.Device=ListDeviceOut{iexp};
1796        check_input_file_series(handles)     
1797    end
1798    DirXml=fullfile(OutputDir,'0_XML');
1799    if ~exist(DirXml,'dir')
1800        [~,msg1]=mkdir(DirXml);
1801        if ~strcmp(msg1,'')
1802            errormsg=['cannot create ' DirXml ': ' msg1]; % error message for directory creation
1803            return
1804        end
1805        [success,msg] = fileattrib(DirXml,'+w','g','s'); % allow writing access for the group of users, recursively in the folder
1806        if success==0
1807            msgbox_uvmat('WARNING',{['unable to set group write access to ' DirXml ':']; msg}); % error message for directory creation
1808        end
1809    end
1810    OutputNomType=nomtype2pair(Param.InputTable{1,4}); % nomenclature for output files
1811   
1812    %% get the set of reference input field indices
1813    first_i=1; % first i index to process
1814    last_i=1; % last i index to process
1815    incr_i=1; % increment step in i index
1816    first_j=1; % first j index to process
1817    last_j=1; % last j index to process
1818    incr_j=1; % increment step in j index
1819    if isfield(Param.IndexRange,'first_i')
1820        first_i=Param.IndexRange.first_i;
1821        incr_i=Param.IndexRange.incr_i;
1822        last_i=Param.IndexRange.last_i;
1823    end
1824    if isfield(Param.IndexRange,'incr_j')
1825        first_j=Param.IndexRange.first_j;
1826        last_j=Param.IndexRange.last_j;
1827        incr_j=Param.IndexRange.incr_j;
1828    end
1829    if last_i < first_i || last_j < first_j
1830        errormsg= 'series/Run_Callback:last field index must be larger or equal to the first one';
1831        return
1832    end
1833    %incr_i must be defined, =1 by default, if NbSlice is active
1834    if isempty(incr_i)&& ~isempty(Param.IndexRange.NbSlice)
1835        incr_i=1;
1836        set(handles.num_incr_i,'String','1')
1837    end
1838    % case of no increment i defined: processing is done on the available files found in i1_series
1839    if isempty(incr_i)
1840        if isempty(incr_j)
1841            [ref_j,ref_i]=find(squeeze(SeriesData.i1_series{1}(1,:,:)));
1842            ref_j=ref_j(ref_j>=first_j & ref_j<=last_j);
1843            ref_i=ref_i(ref_i>=first_i & ref_i<=last_i);
1844            ref_j=ref_j-1;
1845            ref_i=ref_i-1;
1846        else
1847            ref_j=first_j:incr_j:last_j;
1848            [tild,ref_i]=find(squeeze(SeriesData.i1_series{1}(1,:,:)));
1849            ref_i=ref_i-1;
1850            ref_i=ref_i(ref_i>=first_i & ref_i<=last_i);
1851        end
1852        % increment i is defined: processing is done on first_i:incr_i:last_i;
1853    else
1854        ref_i=first_i:incr_i:last_i;
1855        if isempty(incr_j)% automatic finding of the existing j indices
1856            [ref_j,tild]=find(squeeze(SeriesData.i1_series{1}(1,:,:)));
1857            ref_j=ref_j-1;
1858            ref_j=ref_j(ref_j>=first_j & ref_j<=last_j);
1859        else
1860            ref_j=first_j:incr_j:last_j;
1861        end
1862    end
1863    nbfield_j=numel(ref_j); % number of j indices
1864    BlockLength=numel(ref_i); % by default, job involves the full set of i field indices
1865    NbProcess=1;
1866    switch RunMode
1867        case 'cluster'
1868            if (isfield(Param.Action, 'CPUTime') && ~isempty(Param.Action.CPUTime))
1869                CPUTime=Param.Action.CPUTime; % Note: CpUTime for one iteration ref_i has to be multiplied by the number of j indices nbfield_j
1870            else
1871                answer=msgbox_uvmat('INPUT_TXT','estimate the CPU time(in minutes) for each value of index i:' ,'');
1872                CPUTime=str2num(answer);
1873                set(handles.num_CPUTime,'String',answer)
1874                Param.Action.CPUTime=CPUTime;
1875            end
1876            JobNumberMax=SeriesData.SeriesParam.ClusterParam.JobNumberMax;
1877            JobCPUTimeAdvised=SeriesData.SeriesParam.ClusterParam.JobCPUTimeAdvised;
1878            if isempty(Param.IndexRange.NbSlice)% if NbSlice is not defined
1879                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.
1880                BlockLength=max(BlockLength,ceil(numel(ref_i)*NbExp/JobNumberMax)); % possibly increase the BlockLength to have less than MaxJobNumber jobs
1881                NbProcess=ceil(numel(ref_i)/BlockLength) ; % nbre of processes sent to oar
1882            else
1883                NbProcess=Param.IndexRange.NbSlice; % the parameter NbSlice sets the nbre of run processes
1884            end
1885            NbCore=min(NbCore,NbProcess); % reduces the number of cores if it exceeds the number of processes
1886        otherwise
1887            if ~isempty(Param.IndexRange.NbSlice)
1888                NbProcess=Param.IndexRange.NbSlice; % the parameter NbSlice sets the nbre of run processes
1889            end
1890    end
1891   
1892    %% record nbre of output files and starting time for computation for status
1893    StatusData=get(handles.status,'UserData');
1894    if isfield(StatusData,'OutputFileMode')
1895        switch StatusData.OutputFileMode
1896            case 'NbInput'
1897                StatusData.NbOutputFile=numel(ref_i)*nbfield_j;
1898            case 'NbInput_i'
1899                StatusData.NbOutputFile=numel(ref_i);
1900            case 'NbSlice'
1901                StatusData.NbOutputFile=str2num(get(handles.num_NbSlice,'String'));
1902        end
1903    end
1904    StatusData.TimeStart=now;
1905    set(handles.status,'UserData',StatusData)
1906   
1907    %% case of a function in Python
1908    if strcmp(ActionExt, '.py (in dev.)')
1909        fprintf([
1910            '\n' ...
1911            '!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n' ...
1912            'The option .py is used. It is still in development.\n' ...
1913            'To try it, first install pyper and the most recent version of fluidimage\n' ...
1914            '(see https://bitbucket.org/fluiddyn/fluidimage).\n' ...
1915            'Warning: there is no direct correspondance between UVMAT and fluidimage parameters\n' ...
1916            '!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n'])
1917        RunMode = 'python';
1918    end
1919   
1920   
1921    %% direct processing on the current Matlab session or creation of command files
1922    filexml=cell(1,NbProcess); % initialisation of the names of the files containing the processing parameters
1923    extxml=cell(1,NbProcess); % initialisation of the set of labels used for the files documenting each process
1924    for iprocess=1:NbProcess
1925        extxml{iprocess}='.xml';
1926    end
1927    for iprocess=1:NbProcess
1928        if ~strcmp(get(handles.RUN,'BusyAction'),'queue')% allow for STOP action
1929            disp('program stopped by user')
1930            return
1931        end
1932        Param.IndexRange.incr_slice=incr_i;
1933        if isempty(Param.IndexRange.NbSlice)
1934            Param.IndexRange.first_i=first_i+(iprocess-1)*BlockLength*incr_i;
1935            if Param.IndexRange.first_i>last_i
1936                NbProcess=iprocess-1; % leave the loop, we are at the end of the calculation
1937                break
1938            end
1939            Param.IndexRange.last_i=min(last_i,first_i+(iprocess)*BlockLength*incr_i-1);
1940        else %multislices (then incr_i is not empty)
1941            Param.IndexRange.first_i= first_i+iprocess-1;
1942            Param.IndexRange.incr_slice=incr_i*Param.IndexRange.NbSlice;
1943        end
1944        for ilist=1:size(Param.InputTable,1)
1945            Param.InputTable{ilist,1}=regexprep(Param.InputTable{ilist,1},'\','/'); % correct path name for PCWIN system
1946        end
1947       
1948        if isfield(Param,'OutputSubDir')
1949            t=struct2xml(Param);
1950            t=set(t,1,'name','Series');
1951            extxml{iprocess}=fullfile_uvmat('','',Param.InputTable{1,3},'.xml',OutputNomType,...
1952                Param.IndexRange.first_i,Param.IndexRange.last_i,first_j,last_j);
1953            filexml{iprocess}=fullfile(OutputDir,'0_XML',extxml{iprocess});
1954            try
1955                save(t, filexml{iprocess}); % save the xml file containing the processing parameters
1956            catch ME
1957                if ~strcmp (RunMode,'local')
1958                    errormsg=['error writting ' filexml{iprocess} ': ' ME.message];
1959                    return
1960                end
1961            end
1962        end
1963        if strcmp (RunMode,'local')
1964            switch ActionExt
1965                case '.m'
1966                    h_fun(Param); % direct launching
1967                   
1968                case '.sh'
1969                    switch computer
1970                        case {'PCWIN','PCWIN64'} %Windows system
1971                            filexml=regexprep(filexml,'\\','\\\\'); % add '\' so that '\' are left as characters
1972                            system([ActionFullName ' ' RunTime ' ' filexml{iprocess}]); % TODO: adapt to DOS system
1973                        case {'GLNX86','GLNXA64','MACI64'}%Linux  system
1974                            system([ActionFullName ' ' RunTime ' ' filexml{iprocess}]);
1975                    end
1976            end
1977        end
1978    end
1979   
1980    if ~strcmp (RunMode,'local') && ~strcmp(RunMode,'python')
1981        %% processing on a different session of the same computer (background) or cluster, create executable files
1982        batch_file_list=cell(NbProcess,1); % initiate the list of executable files
1983        DirExe=fullfile(OutputDir,'0_EXE'); % directory name for executable files
1984        switch computer
1985            case {'PCWIN','PCWIN64'} %Windows system
1986                ExeExt='.bat';
1987            case {'GLNX86','GLNXA64','MACI64'}%Linux  system
1988                ExeExt='.sh';
1989        end
1990        %create subdirectory for executable files
1991        if ~exist(DirExe,'dir')
1992            [tild,msg1]=mkdir(DirExe);
1993            if ~strcmp(msg1,'')
1994                errormsg=['cannot create ' DirExe ': ' msg1]; % error message for directory creation
1995                return
1996            end
1997            [success,msg] = fileattrib(DirExe,'+w','g','s'); % allow writing access for the group of users, recursively in the folder
1998            if success==0
1999                msgbox_uvmat('WARNING',{['unable to set group write access to ' DirExe ':']; msg}); % error message for directory creation
2000            end
2001        end
2002        %create subdirectory for log files
2003        DirLog=fullfile(OutputDir,'0_LOG');
2004        if ~exist(DirLog,'dir')
2005            [tild,msg1]=mkdir(DirLog);
2006            if ~strcmp(msg1,'')
2007                errormsg=['cannot create ' DirLog ': ' msg1]; % error message for directory creation
2008                return
2009            end
2010            [success,msg] = fileattrib(DirLog,'+w','g','s'); % allow writing access for the group of users, recursively in the folder
2011            if success==0
2012                msgbox_uvmat('WARNING',{['unable to set group write access to ' DirLog ':']; msg}); % error message for directory creation
2013            end
2014        end
2015       
2016        %create the executable file
2017        file_exe_global=fullfile_uvmat('','',Param.InputTable{1,3},ExeExt,OutputNomType,...
2018            first_i,last_i,first_j,last_j);
2019        file_exe_global=fullfile(OutputDir,'0_EXE',file_exe_global);
2020        filelog_global=fullfile_uvmat('','',Param.InputTable{1,3},'.log',OutputNomType,...
2021            first_i,last_i,first_j,last_j);
2022        filelog_global=fullfile(OutputDir,'0_LOG',filelog_global);
2023       
2024        for iprocess=1:NbProcess
2025            %create the executable file
2026            batch_file_list{iprocess}=fullfile(OutputDir,'0_EXE',regexprep(extxml{iprocess},'.xml$',ExeExt));
2027           
2028            % set the log file name
2029            filelog{iprocess}=fullfile(OutputDir,'0_LOG',regexprep(extxml{iprocess},'.xml$','.log'));
2030        end
2031    end
2032   
2033    %% launch the executable files for background or cluster processing
2034   
2035    switch RunMode
2036       
2037        case 'background'
2038            [fid,message]=fopen(file_exe_global,'w');
2039            if isequal(fid,-1)
2040                errormsg=['creation of ' file_exe_global ':' message];
2041                return
2042            end
2043            switch ActionExt
2044                case '.m'% Matlab function
2045                    switch computer
2046                        case {'GLNX86','GLNXA64','MACI64'}
2047                            matlab_ver = ver('MATLAB');
2048                            matlab_version = matlab_ver.Version;
2049                            cmd=[...
2050                                '#!/bin/bash\n'...
2051                                'source /etc/profile\n'...
2052                                'module load matlab/' matlab_version '\n'...% CHOICE OF MATLAB VERSION
2053                                'time_start=$(date +%%s)\n'...
2054                                'matlab -nodisplay -nosplash -nojvm -logfile ''' filelog_global ''' <<END_MATLAB\n'...
2055                                'addpath(''' path_series ''');\n'...
2056                                'addpath(''' Param.Action.ActionPath ''');\n'];
2057                            for iprocess=1:NbProcess
2058                                cmd=[cmd '' Param.Action.ActionName  '(''' filexml{iprocess} ''');\n'];
2059                            end
2060                            cmd=[cmd  'exit\n' 'END_MATLAB\n'...
2061                                'time_end=$(date +%%s)\n'...
2062                                'echo "global time = " $(($time_end - $time_start)) >> ''' filelog_global '''\n'];
2063                            fprintf(fid,cmd); % fill the executable file with the  char string cmd
2064                            fclose(fid); % close the executable filefilelog_global
2065                            system(['chmod +x ' file_exe_global]); % set the file to executable
2066                        case {'PCWIN','PCWIN64'}
2067                            cmd=['matlab -automation -logfile ' regexprep(filelog{iprocess},'\\','\\\\')...
2068                                ' -r "addpath(''' regexprep(path_series,'\\','\\\\') ''');'...
2069                                'addpath(''' regexprep(Param.Action.ActionPath,'\\','\\\\') ''');'];
2070                            for iprocess=1:NbProcess
2071                                cmd=[cmd '' Param.Action.ActionName  '( ''' regexprep(filexml{iprocess},'\\','\\\\') ''');']
2072                            end
2073                            cmd=[cmd ';exit"'];
2074                            fprintf(fid,cmd); % fill the executable file with the  char string cmd
2075                            fclose(fid); % close the executable file
2076                    end
2077                    system([file_exe_global ' &'])% directly execute the command file
2078                case '.sh' % compiled Matlab function
2079                    for iprocess=1:NbProcess
2080                        switch computer
2081                            case {'GLNX86','GLNXA64','MACI64'}
2082                                [fid,message]=fopen(batch_file_list{iprocess},'w'); % create the executable file
2083                                if isequal(fid,-1)
2084                                    errormsg=['creation of .bat file: ' message];
2085                                    return
2086                                end
2087                                cmd=['#!/bin/bash \n '...
2088                                    '#$ -cwd \n '...
2089                                    'hostname && date \n '...
2090                                    'umask 002 \n'...
2091                                    ActionFullName ' ' RunTime ' ' filexml{iprocess}]; % allow writting access to created files for user group
2092                                fprintf(fid,cmd); % fill the executable file with the  char string cmd
2093                                fclose(fid); % close the executable file
2094                                system(['chmod +x ' batch_file_list{iprocess}]); % set the file to executable
2095                                system([batch_file_list{iprocess} ' &'])% directly execute the command file
2096                            case {'PCWIN','PCWIN64'}
2097                                msgbox_uvmat('ERROR','option for compiled Matlab functions not implemented for Windows system')
2098                                return
2099                        end
2100                    end
2101                    msgbox_uvmat('CONFIRMATION',[ActionFullName ' launched in background for ' ExpName ': press STATUS to see results'])
2102            end
2103           
2104        case 'cluster' % option 'oar-parexec' used
2105            %create subdirectory for oar commands
2106            for iprocess=1:NbProcess
2107                [fid,message]=fopen(batch_file_list{iprocess},'w'); % create the executable file
2108                if isequal(fid,-1)
2109                    errormsg=['creation of .bat file: ' message];
2110                    return
2111                end
2112                if  strcmp(ActionExt,'.sh')
2113                    cmd=['#!/bin/bash \n '...
2114                        '#$ -cwd \n '...
2115                        'hostname && date \n '...
2116                        'umask 002 \n'...
2117                        ActionFullName ' ' RunTime ' ' filexml{iprocess}]; % allow writting access to created files for user group
2118                else
2119                    matlab_ver = ver('MATLAB');
2120                    matlab_version = matlab_ver.Version;
2121                    cmd=[...
2122                        '#!/bin/bash\n'...
2123                        'source /etc/profile\n'...
2124                        'module load matlab/' matlab_version '\n'...% CHOICE OF MATLAB VERSION
2125                        'matlab -nodisplay -nosplash -nojvm -singleCompThread -logfile ''' filelog{iprocess} ''' <<END_MATLAB\n'...
2126                        'addpath(''' path_series ''');\n'...
2127                        'addpath(''' Param.Action.ActionPath ''');\n'...
2128                        '' Param.Action.ActionName  '(''' filexml{iprocess} ''');\n'...
2129                        'exit\n'...
2130                        'END_MATLAB\n'];
2131                end
2132                fprintf(fid,cmd); % fill the executable file with the  char string cmd
2133                fclose(fid); % close the executable file
2134                system(['chmod +x ' batch_file_list{iprocess}]); % set the file to executable
2135            end
2136            DIR_CLUSTER=fullfile(OutputDir,'0_CLUSTER');
2137            if exist(DIR_CLUSTER,'dir')% delete the content of the dir 0_LOG to allow new input
2138                curdir=pwd;
2139                cd(DIR_CLUSTER)
2140                delete('*')
2141                cd(curdir)
2142            else
2143                [tild,msg1]=mkdir(DIR_CLUSTER);
2144                if ~strcmp(msg1,'')
2145                    errormsg=['cannot create ' DIR_CLUSTER ': ' msg1]; % error message for directory creation
2146                    return
2147                end
2148            end
2149            % create file containing the list of jobs
2150            ListProcess=fullfile(DIR_CLUSTER,'job_list.txt'); % name of the file containing the list of executables
2151            [fid,errormsg]=fopen(ListProcess,'w'); % open it for writting
2152            if isempty(errormsg)
2153            for iprocess=1:length(batch_file_list)
2154                fprintf(fid,[batch_file_list{iprocess} '\n']); % write list of exe files
2155            end
2156            fclose(fid);
2157            system(['chmod +x ' ListProcess]); % set the file to executable
2158            else
2159                errormsg=['error for writting the executable file:' errormsg];
2160            end       
2161            CPUTimeProcess=CPUTime*BlockLength*nbfield_j; % estimated CPU time for one individual process (in minutes)
2162            LaunchCmdFcn=SeriesData.SeriesParam.ClusterParam.LaunchCmdFcn;
2163            oar_command=feval(LaunchCmdFcn,ListProcess,ActionFullName,DirLog,NbProcess, NbCore,CPUTimeProcess)
2164            [status,result]=system(oar_command)% execute system command and show the result (ID number of the launched job) on the Matlab command window
2165            filename_oarcommand=fullfile(DIR_CLUSTER,'0_cluster_command'); % keep track of the command in file '0-OAR/0_cluster_command'
2166            [fid,errormsg]=fopen(filename_oarcommand,'w');
2167            if ~isempty(errormsg)
2168                msgbox_uvmat('ERROR',['cannot create ' filename_oarcommand ': ' errormsg])
2169                return
2170            end
2171            fprintf(fid,oar_command); % store the command
2172            fprintf(fid,result); % store the result (job ID number)
2173            fclose(fid);
2174            if status==0
2175                msgbox_uvmat('CONFIRMATION',[ActionFullName ' launched for ' ExpName ' as ' num2str(NbProcess) ' processes in cluster: press STATUS to see results'])
2176            else
2177                msgbox_uvmat('ERROR',result)
2178            end
2179            %     case 'cluster_pbs' % for LMFA Kepler machine:  trqnsferred to fct
2180           
2181            %         %create subdirectory for pbs command and log files
2182            %         DirPBS=fullfile(OutputDir,'0_PBS'); % todo : common name OAR/PBS
2183            %         if exist(DirPBS,'dir')% delete the content of the dir 0_LOG to allow new input
2184            %             curdir=pwd;
2185            %             cd(DirPBS)
2186            %             delete('*')
2187            %             cd(curdir)
2188            %         else
2189            %             [tild,msg1]=mkdir(DirPBS);
2190            %             if ~strcmp(msg1,'')
2191            %                 errormsg=['cannot create ' DirPBS ': ' msg1]; % error message for directory creation
2192            %                 return
2193            %             end
2194            %         end
2195            %         max_walltime=3600*20; % 20h max total calculation (cannot exceed 24 h)
2196            %         walltime_onejob=1800; % seconds, max estimated time for asingle file index value
2197            %         ListProcess=fullfile(DirPBS,'job_list.txt'); % create name of the global executable file
2198            %         fid=fopen(ListProcess,'w');
2199            %         for iprocess=1:length(batch_file_list)
2200            %             fprintf(fid,[batch_file_list{iprocess} '\n']); % list of exe files
2201            %         end
2202            %         fclose(fid);
2203            %         system(['chmod +x ' ListProcess]); % set the file to executable
2204            %         pbs_command=['qsub -n CIVX '...
2205            %             '-t idempotent --checkpoint ' num2str(walltime_onejob+60) ' '...
2206            %             '-l /core=' num2str(NbCore) ','...
2207            %             'walltime=' datestr(min(1.05*walltime_onejob/86400*max(NbProcess*BlockLength*nbfield_j,NbCore)/NbCore,max_walltime/86400),13) ' '...
2208            %             '-E ' regexprep(ListProcess,'\.txt\>','.stderr') ' '...
2209            %             '-O ' regexprep(ListProcess,'\.txt\>','.log') ' '...
2210            %             extra_qstat ' '...
2211            %             '"oar-parexec -s -f ' ListProcess ' '...
2212            %             '-l ' ListProcess '.log"'];
2213            %         filename_oarcommand=fullfile(DirPBS,'pbs_command');
2214            %         fid=fopen(filename_oarcommand,'w');
2215            %         fprintf(fid,pbs_command);
2216            %         fclose(fid);
2217            %         fprintf(pbs_command); % display in command line
2218            %         %system(pbs_command);
2219            %         msgbox_uvmat('CONFIRMATION',[ActionFullName ' command ready to be launched in cluster'])
2220           
2221        case 'cluster_sge' % for PSMN % TODO: use the standard 'cluster' config with an external fct
2222            % Au PSMN, on ne cr??e pas 1 job avec plusieurs c??urs, mais N jobs de 1 c??urs
2223            % o?? N < 1000.
2224            %create subdirectory for pbs command and log files
2225           
2226            DirSGE=fullfile(OutputDir,'0_SGE');
2227            if exist(DirSGE,'dir')% delete the content of the dir 0_LOG to allow new input
2228                curdir=pwd;
2229                cd(DirSGE)
2230                delete('*')
2231                cd(curdir)
2232            else
2233                [tild,msg1]=mkdir(DirSGE);
2234                if ~strcmp(msg1,'')
2235                    errormsg=['cannot create ' DirSGE ': ' msg1]; % error message for directory creation
2236                    return
2237                end
2238            end
2239            maxImgsPerJob = ceil(length(batch_file_list)/NbCore);
2240            disp(['Max number of jobs: ' num2str(NbCore)])
2241            disp(['Images per job: ' num2str(maxImgsPerJob)])
2242           
2243            iprocess = 1;
2244            imgsInJob = [];
2245            currJobIndex = 1;
2246            done = 0;
2247            while(~done)
2248                if(iprocess <= length(batch_file_list))
2249                    imgsInJob = [imgsInJob, iprocess];
2250                end
2251                if((numel(imgsInJob) >= maxImgsPerJob) || (iprocess == length(batch_file_list)))
2252                    cmd=['#!/bin/sh \n'...
2253                        '#$ -cwd \n'...
2254                        'hostname && date\n']
2255                    for ii=1:numel(imgsInJob)
2256                        cmd=[cmd ActionFullName ' /softs/matlab ' filexml{imgsInJob(ii)} '\n'];
2257                    end
2258                    [fid, message] = fopen([DirSGE '/job' num2str(currJobIndex) '.sh'], 'w');
2259                    fprintf(fid, cmd);
2260                    fclose(fid);
2261                    system(['chmod +x ' DirSGE '/job' num2str(currJobIndex) '.sh'])
2262                    sge_command=['qsub -N civ_' num2str(currJobIndex) ' '...
2263                        '-q ' qstat_Queue ' '...
2264                        '-e ' fullfile([DirSGE '/job' num2str(currJobIndex) '.out']) ' '...
2265                        '-o ' fullfile([DirSGE '/job' num2str(currJobIndex) '.out']) ' '...
2266                        fullfile([DirSGE '/job' num2str(currJobIndex) '.sh'])];
2267                    fprintf(sge_command); % display in command line
2268                    [status, result] = system(sge_command);
2269                    fprintf(result);
2270                    currJobIndex = currJobIndex + 1;
2271                    imgsInJob = [];
2272                end
2273                if(iprocess == length(batch_file_list))
2274                    done = 1;
2275                end
2276                iprocess = iprocess + 1;
2277            end
2278            msgbox_uvmat('CONFIRMATION',[num2str(currJobIndex-1) ' jobs launched on queue ' qstat_Queue '.'])
2279        case 'python'
2280            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))") ' ...
2281                'python -m fluidimage.run_from_xml ' filexml{iprocess}];
2282            fprintf(['command:\n' command '\n\n'])
2283            system(command, '-echo');
2284    end
2285    if exist(OutputDir,'dir')
2286        [SUCCESS,MESSAGE,MESSAGEID] = fileattrib (OutputDir);
2287        if MESSAGE.GroupWrite~=1
2288            [success,msg] = fileattrib(OutputDir,'+w','g','s'); % allow writing access for the group of users, recursively in the folder
2289            if success==0
2290                msgbox_uvmat('WARNING',{['unable to set group write access to ' OutputDir ':']; msg}); % error message for directory creation
2291            end
2292        end
2293    end
2294end
2295set(handles.Replicate,'BackgroundColor',[0 1 0])
2296
2297%------------------------------------------------------------------------
2298function STOP_Callback(hObject, eventdata, handles)
2299%------------------------------------------------------------------------
2300set(handles.RUN, 'BusyAction','cancel')
2301set(handles.RUN,'BackgroundColor',[1 0 0])
2302set(handles.RUN,'enable','on')
2303set(handles.RUN, 'Value',0)
2304
2305%------------------------------------------------------------------------
2306% --- read parameters from the GUI series
2307%------------------------------------------------------------------------
2308function Param=read_GUI_series(handles)
2309
2310%% read raw parameters from the GUI series
2311Param=read_GUI(handles.series);
2312
2313%% clean the output structure by removing unused information
2314if isfield(Param,'Pairs')
2315    Param=rmfield(Param,'Pairs'); % info Pairs not needed for output
2316end
2317if isfield(Param,'InputLine')
2318    Param=rmfield(Param,'InputLine');
2319end
2320if isfield(Param,'EditObject')
2321    Param=rmfield(Param,'EditObject');
2322end
2323Param.IndexRange.TimeSource=Param.IndexRange.TimeTable{end,1};
2324Param.IndexRange=rmfield(Param.IndexRange,'TimeTable');
2325empty_line=false(size(Param.InputTable,1),1);
2326for iline=1:size(Param.InputTable,1)
2327    empty_line(iline)=isempty(cell2mat(Param.InputTable(iline,1:3)));
2328end
2329Param.InputTable(empty_line,:)=[];
2330
2331%------------------------------------------------------------------------
2332% --- Executes on selection change in ActionName.
2333function ActionName_Callback(hObject, ActionPath, handles)
2334%------------------------------------------------------------------------
2335
2336%% stop any ongoing series processing
2337if isequal(get(handles.RUN,'Value'),1)
2338    answer= msgbox_uvmat('INPUT_Y-N','stop current Action process?');
2339    if strcmp(answer,'Yes')
2340        STOP_Callback(hObject, [], handles)
2341    else
2342        return
2343    end
2344end
2345set(handles.ActionName,'BackgroundColor',[1 1 0])
2346huigetfile=findobj(allchild(0),'tag','status_display');
2347if ~isempty(huigetfile)
2348    delete(huigetfile)
2349end
2350drawnow
2351
2352%% get Action name and path
2353NbBuiltinAction=get(handles.Action,'UserData'); % nbre of functions initially proposed in the menu ActionName (as defined in the Opening fct of series)
2354ActionList=get(handles.ActionName,'String'); % list menu fields
2355ActionIndex=get(handles.ActionName,'Value');
2356if ~isequal(ActionIndex,1)% if we are not just opening series
2357    InputTable=get(handles.InputTable,'Data');
2358    if isempty(InputTable{1,4})
2359        msgbox_uvmat('ERROR','no input file available: use Open in the menu bar')
2360        return
2361    end
2362end
2363ActionName= ActionList{get(handles.ActionName,'Value')}; % selected function name
2364ActionPathList=get(handles.ActionName,'UserData'); % list of recorded paths to functions of the list ActionName
2365
2366%% add a new function to the menu if 'more...' has been selected in the menu ActionName
2367if isequal(ActionName,'more...')
2368    if ~ischar(ActionPath)
2369        ActionPath=get(handles.ActionPath,'String');
2370    end
2371    [FileName, PathName] = uigetfile( ...
2372        {'*.m', ' (*.m)';
2373        '*.m',  '.m files '; ...
2374        '*.*', 'All Files (*.*)'}, ...
2375        'Pick a series processing function ',ActionPath);
2376    if length(FileName)<2
2377        return
2378    end
2379    [tild,ActionName,ActionExt]=fileparts(FileName);
2380   
2381    % insert the choice in the menu ActionName
2382    ActionIndex=find(strcmp(ActionName,ActionList),1); % look for the selected function in the menu Action
2383    PathName=regexprep(PathName,'/$','');
2384    if ~isempty(ActionIndex) && ~strcmp(ActionPathList{ActionIndex},PathName)%compare the path to the existing fct
2385        ActionIndex=[]; % the selected path is different than the recorded one
2386    end
2387    if isempty(ActionIndex)%the qselected fct (with selected path) does not exist in the menu
2388        ActionIndex= length(ActionList);
2389        ActionList=[ActionList(1:end-1);{ActionName};ActionList(end)]; % the selected function is appended in the menu, before the last item 'more...'
2390         ActionPathList=[ActionPathList; PathName];
2391    end
2392   
2393    % record the file extension and extend the path list if it is a new extension
2394    ActionExtList=get(handles.ActionExt,'String');
2395    ActionExtIndex=find(strcmp(ActionExt,ActionExtList), 1);
2396    if isempty(ActionExtIndex)
2397        set(handles.ActionExt,'String',[ActionExtList;{ActionExt}])
2398    end
2399
2400    % remove old Action options in the menu (keeping a menu length <nb_builtin_ACTION+5)
2401    if length(ActionList)>NbBuiltinAction+5; % nb_builtin_ACTION=nbre of functions always remaining in the initial menu
2402        nbremove=length(ActionList)-NbBuiltinAction-5;
2403        ActionList(NbBuiltinAction+1:end-5)=[];
2404        ActionPathList(NbBuiltinAction+1:end-4,:)=[];
2405        ActionIndex=ActionIndex-nbremove;
2406    end
2407   
2408    % record action menu, choice and path
2409    set(handles.ActionName,'Value',ActionIndex)
2410    set(handles.ActionName,'String',ActionList)
2411       set(handles.ActionName,'UserData',ActionPathList);
2412    set(handles.ActionExt,'Value',ActionExtIndex)
2413       
2414    %record the user defined menu additions in personal file profil_perso
2415    dir_perso=prefdir;
2416    profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
2417    if NbBuiltinAction+1<=numel(ActionList)-1
2418        ActionListUser=ActionList(NbBuiltinAction+1:numel(ActionList)-1);
2419        ActionPathListUser=ActionPathList(NbBuiltinAction+1:numel(ActionList)-1);
2420        ActionExtListUser={};
2421        if numel(ActionExtList)>2
2422            ActionExtListUser=ActionExtList(3:end);
2423        end
2424        if exist(profil_perso,'file')
2425            save(profil_perso,'ActionListUser','ActionPathListUser','ActionExtListUser','-append')
2426        else
2427            save(profil_perso,'ActionListUser','ActionPathListUser','ActionExtListUser','-V6')
2428        end
2429    end
2430end
2431
2432%% check the current ActionPath to the selected function
2433ActionPath=ActionPathList{ActionIndex}; % current recorded path
2434set(handles.ActionPath,'String',ActionPath); % show the path to the senlected function
2435
2436%% reinitialise the waitbar
2437update_waitbar(handles.Waitbar,0)
2438
2439%% Put the first line of the selected Action fct as tooltip help
2440try
2441    [fid,errormsg] =fopen([ActionName '.m']);
2442    InputText=textscan(fid,'%s',1,'delimiter','\n');
2443    fclose(fid);
2444    set(handles.ActionName,'ToolTipString',InputText{1}{1})% put the first line of the selected function as tooltip help
2445end
2446set(handles.ActionName,'BackgroundColor',[1 1 1])
2447set(handles.ActionInput,'BackgroundColor',[1 0 1])% set ActionInput button to magenta color to indicate that input refr
2448set(handles.num_CPUTime,'String','')
2449
2450% --- Executes on button press in ActionInput.
2451function ActionInput_Callback(hObject, eventdata, handles)
2452
2453set(handles.ActionInput,'BackgroundColor',[1 1 0])
2454SeriesData=get(handles.series,'UserData'); % info on the input file series
2455
2456%% create the function handle for Action
2457ActionPath=get(handles.ActionPath,'String');
2458ActionList=get(handles.ActionName,'String');
2459ActionName= ActionList{get(handles.ActionName,'Value')}; % selected function name
2460if ~exist(ActionPath,'dir')
2461    ActionName_Callback(handles.ActionName, ActionPath, handles)% update the function
2462    return
2463end
2464current_dir=pwd; % current working dir
2465cd(ActionPath)
2466h_fun=str2func(ActionName);
2467cd(current_dir)
2468
2469%% Activate the Action fct to adapt the configuration of the GUI series and bring specific parameters in SeriesData
2470Param=read_GUI_series(handles); % read the parameters from the GUI series
2471Param.Action.RUN=0;
2472Param.SeriesData=SeriesData;
2473ParamOut=h_fun(Param); % run the selected Action function to get the relevant input
2474
2475
2476%% Visibility of VelType and VelType_1 menus asked by ActionName
2477VelTypeRequest=1; % VelType requested by default
2478VelTypeRequest_1=1; % VelType requested by default
2479if isfield(ParamOut,'VelType')
2480    VelTypeRequest=ismember(ParamOut.VelType,{'on','one','two'});
2481    VelTypeRequest_1=strcmp( ParamOut.VelType,'two');
2482end
2483FieldNameRequest=0;  %hidden by default
2484FieldNameRequest_1=0;  %hidden by default
2485if isfield(ParamOut,'FieldName')
2486    FieldNameRequest=ismember(ParamOut.FieldName,{'on','one','two'});
2487    FieldNameRequest_1=strcmp( ParamOut.FieldName,'two');
2488end
2489
2490%% Detect the types of input files and set menus and default options in 'VelType'
2491if ~isfield(SeriesData,'FileType')
2492    SeriesData.FileType={'none'};
2493end
2494iview_civ=find( strcmp('civx',SeriesData.FileType)|strcmp('civdata',SeriesData.FileType));
2495iview_netcdf=find(strcmp('netcdf',SeriesData.FileType)|strcmp('civx',SeriesData.FileType)|strcmp('civdata',SeriesData.FileType)); % all nc files, icluding civ
2496FieldList=get(handles.FieldName,'String'); % previous list as default
2497if ~iscell(FieldList),FieldList={FieldList};end
2498FieldList_1=get(handles.FieldName_1,'String'); % previous list as default
2499if ~iscell(FieldList_1),FieldList_1={FieldList_1};end
2500CheckList_1=1; % indicate whether FieldName_1 has been updated
2501handles_coord=[handles.Coord_x handles.Coord_y handles.Coord_z handles.Coord_x_title handles.Coord_y_title handles.Coord_z_title];
2502if VelTypeRequest && numel(iview_civ)>=1
2503    menu=set_veltype_display(SeriesData.FileInfo{iview_civ(1)}.CivStage,SeriesData.FileType{iview_civ(1)});
2504    set(handles.VelType,'Value',1)% set first choice by default
2505    set(handles.VelType,'String',[{'*'};menu])
2506    set(handles.VelType,'Visible','on')
2507    set(handles.VelType_title,'Visible','on')
2508    FieldList=set_field_list('U','V'); % standard menu for civx data
2509    if max(get(handles.FieldName,'Value'))>numel(FieldList)
2510        set(handles.FieldName,'Value',1); % velocity vector choice by default
2511    end
2512    if  VelTypeRequest_1 && numel(iview_civ)>=2
2513        menu=set_veltype_display(SeriesData.FileInfo{iview_civ(2)}.CivStage,SeriesData.FileType{iview_civ(2)});
2514        set(handles.VelType_1,'Value',1)% set first choice by default
2515        set(handles.VelType_1,'String',[{'*'};menu])
2516        set(handles.VelType_1,'Visible','on')
2517        set(handles.VelType_title_1,'Visible','on')
2518        FieldList_1=[set_field_list('U','V');{'C'};{'add_field...'}]; % standard menu for civx data
2519        CheckList_1=1;
2520        set(handles.FieldName_1,'Value',1); % velocity vector choice by default
2521    else
2522        set(handles.VelType_1,'Visible','off')
2523        set(handles.VelType_title_1,'Visible','off')
2524    end
2525else
2526    set(handles.VelType,'Visible','off')
2527    set(handles.VelType_title,'Visible','off')
2528end
2529
2530%% Detect the types of input files and set menus and default options in 'FieldName'
2531if (FieldNameRequest || VelTypeRequest) && numel(iview_netcdf)>=1
2532    set(handles.InputFields,'Visible','on')% set the frame InputFields visible
2533    if FieldNameRequest && isfield(SeriesData.FileInfo{iview_netcdf(1)},'ListVarName')
2534        set(handles.FieldName,'Visible','on')
2535        set(handles.Field_text,'Visible','on')
2536        ListVarName=SeriesData.FileInfo{iview_netcdf(1)}.ListVarName;
2537        ind_var=get(handles.FieldName,'Value'); % indices of previously selected variables
2538        for ilist=1:numel(ind_var)
2539            if isempty(find(strcmp(FieldList{ind_var(ilist)},ListVarName)))
2540                FieldList={}; % previous choice not consistent with new input field
2541                set(handles.FieldName,'Value',1)
2542                break
2543            end
2544        end
2545        if ~isempty(FieldList)
2546            if isempty(find(strcmp(get(handles.Coord_x,'String'),ListVarName)))||...
2547                    isempty(find(strcmp(get(handles.Coord_y,'String'),ListVarName)))
2548                FieldList={};
2549                set(handles.Coord_x,'String','')
2550                set(handles.Coord_y,'String','')
2551            end
2552            Coord_z=get(handles.Coord_z,'String');
2553            if ~isempty(Coord_z) && isempty(find(strcmp(Coord_z,ListVarName)))
2554                FieldList={};
2555                set(handles.Coord_z,'String','')
2556            end
2557        end
2558    else
2559        set(handles.FieldName,'Visible','off')
2560        set(handles.Field_text,'Visible','off')
2561    end
2562   
2563    set(handles_coord,'Visible','on')
2564    if isempty(find(strcmp('add_field...',FieldList)))
2565        FieldList=[FieldList;{'add_field...'}];%add 'add_field...' to the menu FieldName if it is not already
2566    end
2567    if FieldNameRequest_1 && numel(iview_netcdf)>=2
2568        set(handles.FieldName_1,'Visible','on')
2569        if CheckList_1==0        % not civ input made
2570            ListVarName=SeriesData.FileInfo{iview_netcdf(2)}.ListVarName;
2571            ind_var=get(handles.FieldName,'Value'); % indices of previously selected variables
2572            for ilist=1:numel(ind_var)
2573                if isempty(find(strcmp(FieldList{ind_var(ilist)},ListVarName)))
2574                    FieldList_1={}; % previous choice not consistent with new input field
2575                    set(handles.FieldName_1,'Value',1)
2576                    break
2577                end
2578            end
2579            warn_coord=0;
2580            if isempty(find(strcmp(get(handles.Coord_x,'String'),ListVarName)))||...
2581                    isempty(find(strcmp(get(handles.Coord_y,'String'),ListVarName)))
2582                warn_coord=1;
2583            end
2584            if ~isempty(Coord_z) && isempty(find(strcmp(Coord_z,ListVarName)))
2585                FieldList_1={};
2586                warn_coord=1;
2587            end
2588            if warn_coord
2589                msgbox_uvmat('WARNING','coordinate names do not exist in the second netcdf input file')
2590            end
2591           
2592            set(handles.FieldName_1,'Visible','on')
2593            set(handles.FieldName_1,'Value',1)
2594            set(handles.FieldName_1,'String',FieldList_1)
2595        end
2596    else
2597        set(handles.FieldName_1,'Visible','off')
2598    end
2599    if isempty(FieldList)
2600        set(handles.Field_text,'Visible','off')
2601        set(handles.FieldName,'Visible','off')
2602    else
2603        set(handles.Field_text,'Visible','on')
2604        set(handles.FieldName,'Visible','on')
2605        set(handles.FieldName,'String',FieldList)
2606    end
2607else
2608    set(handles.InputFields,'Visible','off')
2609end
2610
2611%% Introduce visibility of file overwrite option
2612if isfield(ParamOut,'CheckOverwriteVisible')&& strcmp(ParamOut.CheckOverwriteVisible,'on')
2613    set(handles.CheckOverwrite,'Visible','on')
2614else
2615    set(handles.CheckOverwrite,'Visible','off')
2616end
2617
2618%% Check whether alphabetical sorting of input Subdir is allowed by the Action fct  (for multiples series entries)
2619if isfield(ParamOut,'AllowInputSort')&&isequal(ParamOut.AllowInputSort,'on')&& size(Param.InputTable,1)>1
2620    [tild,iview]=sort(Param.InputTable(:,2)); % subdirectories sorted in alphabetical order
2621    set(handles.InputTable,'Data',Param.InputTable(iview,:));
2622    MinIndex_i=get(handles.MinIndex_i,'Data');
2623    MinIndex_j=get(handles.MinIndex_j,'Data');
2624    MaxIndex_i=get(handles.MaxIndex_i,'Data');
2625    MaxIndex_j=get(handles.MaxIndex_j,'Data');
2626    set(handles.MinIndex_i,'Data',MinIndex_i(iview,:));
2627    set(handles.MinIndex_j,'Data',MinIndex_j(iview,:));
2628    set(handles.MaxIndex_i,'Data',MaxIndex_i(iview,:));
2629    set(handles.MaxIndex_j,'Data',MaxIndex_j(iview,:));
2630    TimeTable=get(handles.TimeTable,'Data');
2631    if size(TimeTable,1)<size(Param.InputTable,1)%if the time table is not complete, copy the missing lines from the previous ones
2632        for iline=size(TimeTable,1)+1:size(Param.InputTable,1)
2633            TimeTable(iline,:)=TimeTable(iline-1,:);
2634        end
2635    end
2636    set(handles.TimeTable,'Data',TimeTable(iview,:));% sort the time tables
2637    PairString=get(handles.PairString,'Data');
2638    set(handles.PairString,'Data',PairString(iview,:));
2639end
2640
2641%% Impose the whole input file index range if requested
2642if isfield(ParamOut,'WholeIndexRange')&&isequal(ParamOut.WholeIndexRange,'on')
2643    MinIndex_i=get(handles.MinIndex_i,'Data');
2644    MinIndex_j=get(handles.MinIndex_j,'Data');
2645    MaxIndex_i=get(handles.MaxIndex_i,'Data');
2646    MaxIndex_j=get(handles.MaxIndex_j,'Data');
2647    set(handles.num_first_i,'String',num2str(MinIndex_i(1)))% set first as the min index (for the first line)
2648    set(handles.num_last_i,'String',num2str(MaxIndex_i(1)))% set last as the max index (for the first line)
2649    set(handles.num_incr_i,'String','1')
2650    set(handles.num_first_j,'String',num2str(MinIndex_j(1)))% set first as the min index (for the first line)
2651    set(handles.num_last_j,'String',num2str(MaxIndex_j(1)))% set last as the max index (for the first line)
2652    set(handles.num_incr_j,'String','1')
2653else  % check index ranges
2654    first_i=1;last_i=1;first_j=1;last_j=1;
2655    if isfield(Param.IndexRange,'first_i')
2656        first_i=Param.IndexRange.first_i;
2657        last_i=Param.IndexRange.last_i;
2658    end
2659    if isfield(Param.IndexRange,'first_j')
2660        first_j=Param.IndexRange.first_j;
2661        last_j=Param.IndexRange.last_j;
2662    end
2663    if last_i < first_i || last_j < first_j , msgbox_uvmat('ERROR','last field number must be larger than the first one'),...
2664            set(handles.RUN, 'Enable','On'), set(handles.RUN,'BackgroundColor',[1 0 0]),return,end
2665end
2666
2667%% enable or desable j index visibility
2668status_j='on'; % default
2669if isfield(SeriesData,'j1_series') && isempty(find(~cellfun(@isempty,SeriesData.j1_series), 1)) % case of empty j indices
2670    status_j='off'; % no j index needed
2671elseif strcmp(get(handles.PairString,'Visible'),'on')
2672    check_burst=cellfun(@isempty,regexp(get(handles.PairString,'Data'),'^j')); % =0 for burst case, 1 otherwise
2673    if isempty(find(check_burst, 1))% if all pair string begins by j (burst)
2674        status_j='off'; % no j index needed for bust case
2675    end
2676end
2677enable_j(handles,status_j) % no j index needed
2678if isfield(ParamOut,'j_index_1')&& isfield(ParamOut,'j_index_2')%strcmp(ParamOut.Desable_j_index,'on')
2679    %status_j='off';
2680    set(handles.num_first_j,'String',num2str(ParamOut.j_index_1))
2681    set(handles.num_last_j,'String',num2str(ParamOut.j_index_2))
2682    set(handles.num_first_j,'enable','off')
2683    set(handles.num_last_j,'enable','off')
2684    set(handles.num_incr_j,'visible','off')
2685else
2686    set(handles.num_first_j,'enable','on')
2687    set(handles.num_last_j,'enable','on')
2688    set(handles.num_incr_j,'visible',status_j)
2689end
2690
2691%% NbSlice visibility
2692if isfield(ParamOut,'NbSlice') && (strcmp(ParamOut.NbSlice,'on')||isnumeric(ParamOut.NbSlice))
2693    set(handles.num_NbSlice,'Visible','on')
2694    set(handles.NbSlice_title,'Visible','on')
2695else
2696    set(handles.num_NbSlice,'Visible','off')
2697    set(handles.NbSlice_title,'Visible','off')
2698end
2699if isfield(ParamOut,'NbSlice') && isnumeric(ParamOut.NbSlice)
2700    set(handles.num_NbSlice,'String',num2str(ParamOut.NbSlice))
2701    set(handles.num_NbSlice,'Enable','off'); % NbSlice set by the activation of the Action function
2702else
2703    set(handles.num_NbSlice,'Enable','on'); % NbSlice can be modified on the GUI series
2704end
2705
2706%% Visibility of FieldTransform menu
2707FieldTransformVisible='off';  %hidden by default
2708if isfield(ParamOut,'FieldTransform')
2709    if ~strcmp(ParamOut.FieldTransform,'off')
2710    FieldTransformVisible='on'; 
2711    end
2712    if iscell(ParamOut.FieldTransform)
2713        SeriesData.TransformList=ParamOut.FieldTransform;
2714    end
2715    TransformName_Callback([],[], handles)
2716end
2717set(handles.FieldTransform,'Visible',FieldTransformVisible)
2718if isfield(ParamOut,'TransformPath')% record the path of transform function requested for compilation
2719    set(handles.TransformPath,'UserData',ParamOut.TransformPath)
2720else
2721    set(handles.TransformPath,'UserData',[])
2722end
2723
2724%% Visibility of projection object
2725ProjObjectVisible='off';  %hidden by default
2726if isfield(ParamOut,'ProjObject')
2727    ProjObjectVisible=ParamOut.ProjObject;
2728end
2729set(handles.CheckObject,'Visible',ProjObjectVisible)
2730if ~get(handles.CheckObject,'Value')
2731    ProjObjectVisible='off';
2732end
2733set(handles.ProjObjectName,'Visible',ProjObjectVisible)
2734set(handles.DeleteObject,'Visible',ProjObjectVisible)
2735set(handles.ViewObject,'Visible',ProjObjectVisible)
2736set(handles.EditObject,'Visible',ProjObjectVisible)
2737
2738%% Visibility of mask input
2739MaskVisible='off';  %hidden by default
2740if isfield(ParamOut,'Mask')
2741    MaskVisible=ParamOut.Mask;
2742end
2743set(handles.CheckMask,'Visible',MaskVisible);
2744%% Setting of expected iteration time
2745if isfield(ParamOut,'CPUTime')
2746    set(handles.num_CPUTime,'String',num2str(ParamOut.CPUTime));
2747end
2748
2749%% definition of the path for the output files
2750InputTable=get(handles.InputTable,'Data');
2751[OutputPath,Device,DeviceExt]=fileparts(InputTable{1,1});
2752[OutputPath,Experiment,ExperimentExt]=fileparts(OutputPath);
2753set(handles.Device,'String',[Device DeviceExt])
2754set(handles.Device,'Visible','on')
2755set(handles.Device_title,'Visible','on')
2756set(handles.Experiment,'String',[Experiment ExperimentExt])
2757set(handles.Experiment,'Visible','on')
2758set(handles.Experiment_title,'Visible','on')
2759set(handles.Experiment_title,'Visible','on')
2760set(handles.OutputPath,'Visible','on')
2761set(handles.OutputPathBrowse,'Visible','on')
2762   
2763%% definition of the subdirectory containing the output files
2764
2765if  ~(isfield(SeriesData,'ActionName') && strcmp(ActionName,SeriesData.ActionName))
2766    OutputDirExt='.series'; % default
2767    if isfield(ParamOut,'OutputDirExt')&&~isempty(ParamOut.OutputDirExt)
2768        OutputDirExt=ParamOut.OutputDirExt;
2769    end
2770    set(handles.OutputDirExt,'String',OutputDirExt)
2771end
2772OutputDirVisible='off';
2773OutputSubDirMode='auto'; % default
2774SubDirOut='';
2775if isfield(ParamOut,'OutputSubDirMode')
2776    OutputSubDirMode=ParamOut.OutputSubDirMode;
2777end
2778switch OutputSubDirMode
2779    case 'auto' % default
2780        OutputDirVisible='on';
2781        SubDir=InputTable(1:end,2); % set of subdirectories
2782        SubDirOut=SubDir{1};
2783        if numel(SubDir)>1
2784            for ilist=2:numel(SubDir)
2785                SubDirOut=[SubDirOut '-' regexprep(SubDir{ilist},'^/','')];
2786            end
2787        end
2788    case 'one'
2789        OutputDirVisible='on';
2790        SubDirOut=InputTable{1,2}; % use the first subdir name (+OutputDirExt) as output  subdirectory
2791    case 'two'
2792        OutputDirVisible='on';   
2793        SubDir=InputTable(1:2,2); % set of subdirectories
2794        SubDirOut=SubDir{1};
2795        if numel(SubDir)>1
2796                SubDirOut=[SubDirOut '-' regexprep(SubDir{2},'^/','')];
2797        end
2798    case 'last'
2799        OutputDirVisible='on';
2800        SubDirOut=InputTable{end,2}; % use the last subdir name (+OutputDirExt) as output  subdirectory
2801end
2802set(handles.OutputSubDir,'String',SubDirOut)
2803set(handles.OutputSubDir,'BackgroundColor',[1 1 1])% set edit box to white color to indicate refreshment
2804set(handles.OutputDirExt,'Visible',OutputDirVisible)
2805set(handles.OutputSubDir,'Visible',OutputDirVisible)
2806% set(handles.OutputDir_title,'Visible',OutputDirVisible)
2807SeriesData.ActionName=ActionName; % record ActionName for next use
2808
2809
2810%% visibility of the run mode (local or background or cluster)
2811if strcmp(OutputSubDirMode,'none')
2812    RunModeVisible='off'; % only local mode available if no output file is produced
2813else
2814    RunModeVisible='on';
2815end
2816set(handles.RunMode,'Visible',RunModeVisible)
2817set(handles.ActionExt,'Visible',RunModeVisible)
2818set(handles.RunMode_title,'Visible',RunModeVisible)
2819set(handles.ActionExt_title,'Visible',RunModeVisible)
2820
2821
2822%% Expected nbre of output files
2823if isfield(ParamOut,'OutputFileMode')
2824    StatusData.OutputFileMode=ParamOut.OutputFileMode;
2825    set(handles.status,'UserData',StatusData)
2826end
2827
2828%% definition of an additional parameter set, determined by an ancillary GUI
2829if isfield(ParamOut,'ActionInput')
2830%     set(handles.ActionInput,'Visible','on')
2831    ParamOut.ActionInput.Program=ActionName; % record the program in ActionInput
2832    SeriesData.ActionInput=ParamOut.ActionInput;
2833else
2834%     set(handles.ActionInput,'Visible','off')
2835    if isfield(SeriesData,'ActionInput')
2836        SeriesData=rmfield(SeriesData,'ActionInput');
2837    end
2838end
2839set(handles.series,'UserData',SeriesData)
2840set(handles.ActionInput,'BackgroundColor',[1 0 0])
2841
2842
2843%------------------------------------------------------------------------
2844% --- Executes on button press in RefreshField.
2845function RefreshField_Callback(hObject, eventdata, handles)
2846%------------------------------------------------------------------------
2847set(handles.FieldName,'String',{'add_field...'});
2848set(handles.FieldName,'Value',1);
2849FieldName_Callback(hObject, eventdata, handles)
2850
2851
2852%------------------------------------------------------------------------
2853% --- Executes on selection change in FieldName.
2854function FieldName_Callback(hObject, eventdata, handles)
2855%------------------------------------------------------------------------
2856FieldListInit=get(handles.FieldName,'String');
2857field_index=get(handles.FieldName,'Value');
2858field=FieldListInit{field_index(1)};
2859if isequal(field,'add_field...')
2860    FieldListInit(field_index(1))=[];
2861    SeriesData=get(handles.series,'UserData');
2862    % input line for which the field choice is relevant
2863    iview=find(ismember(SeriesData.FileType,{'netcdf','civx','civdata'})); % all nc files, icluding civ
2864    hget_field=findobj(allchild(0),'name','get_field');
2865    if ~isempty(hget_field)
2866        delete(hget_field)%delete opened versions of get_field
2867    end
2868    Param=read_GUI(handles.series);
2869    InputTable=Param.InputTable(iview,:);
2870    % check the existence of the first file in the series
2871    first_j=[];last_j=[];MinIndex_j=1;MaxIndex_j=1; % default setting for index j
2872    if isfield(Param.IndexRange,'first_j') % if index j is used     
2873        first_j=Param.IndexRange.first_j;
2874        last_j=Param.IndexRange.last_j;
2875        MinIndex_j=Param.IndexRange.MinIndex_j(iview);
2876        MaxIndex_j=Param.IndexRange.MaxIndex_j(iview);
2877    end
2878    PairString='';
2879    if isfield(Param.IndexRange,'PairString'); PairString=Param.IndexRange.PairString{iview}; end
2880    [i1,i2,j1,j2] = get_file_index(Param.IndexRange.first_i,first_j,PairString);
2881    LineIndex=iview(1);
2882    if numel(iview)>1     
2883        answer=msgbox_uvmat('INPUT_TXT',['select the line of the input table:' num2str(iview)] ,num2str(iview(1)));
2884        LineIndex=str2num(answer);
2885    end
2886    FirstFileName=fullfile_uvmat(InputTable{LineIndex,1},InputTable{LineIndex,2},InputTable{LineIndex,3},...
2887        InputTable{LineIndex,5},InputTable{LineIndex,4},i1,i2,j1,j2);
2888    if exist(FirstFileName,'file') || ~isempty(regexp(InputTable{LineIndex,1},'^http'))
2889        ParamIn.Title='get_field: pick input variables and coordinates for series processing';
2890        ParamIn.SeriesInput=1;
2891        GetFieldData=get_field(FirstFileName,ParamIn);
2892        FieldList={};
2893        if isfield(GetFieldData,'FieldOption')% if a field has been selected
2894        switch GetFieldData.FieldOption
2895            case 'vectors'
2896                UName=GetFieldData.PanelVectors.vector_x;
2897                VName=GetFieldData.PanelVectors.vector_y;
2898                YName={GetFieldData.Coordinates.Coord_y};
2899                FieldList={['vec(' UName ',' VName ')'];...
2900                    ['norm(' UName ',' VName ')'];...
2901                    UName;VName};
2902                set(handles.VelType,'Visible','off')
2903            case {'scalar'}
2904                FieldList=GetFieldData.PanelScalar.scalar;
2905                YName={GetFieldData.Coordinates.Coord_y};
2906                if ischar(FieldList)
2907                    FieldList={FieldList};
2908                end
2909                set(handles.VelType,'Visible','off')
2910            case 'civdata...'
2911                FieldList=[set_field_list('U','V') ;{'C'}];
2912                set(handles.FieldName,'Value',1) % set menu to 'velocity
2913                XName='X';
2914                YName='y';
2915                set(handles.VelType,'Visible','on')
2916        end
2917        set(handles.FieldName,'Value',1)
2918        set(handles.FieldName,'String',[FieldListInit; FieldList; {'add_field...'}]);
2919        if ~strcmp(GetFieldData.FieldOption,'civdata...')
2920           if ~isempty(regexp(FieldList{1},'^vec'))
2921                set(handles.FieldName,'Value',1)
2922           else
2923                set(handles.FieldName,'Value',1:numel(FieldList))%select all input fields by default
2924           end
2925            XName=GetFieldData.Coordinates.Coord_x;
2926            YName=GetFieldData.Coordinates.Coord_y;
2927            TimeNameStr=GetFieldData.Time.SwitchVarIndexTime;
2928            % get the time info                     
2929            TimeTable=get(handles.TimeTable,'Data');
2930            switch TimeNameStr
2931                case 'file index'
2932                    TimeName='';
2933                case 'attribute'
2934                    TimeName=['att:' GetFieldData.Time.TimeName];
2935                    % update the time table
2936                    TimeTable{LineIndex,2}=get_time(Param.IndexRange.MinIndex_i(LineIndex),MinIndex_j,PairString,InputTable,SeriesData.FileInfo{LineIndex},GetFieldData.Time.TimeName);  % Min time     
2937                    TimeTable{LineIndex,3}=get_time(Param.IndexRange.first_i,first_j,PairString,InputTable,SeriesData.FileInfo{LineIndex},GetFieldData.Time.TimeName);  % first time             
2938                    TimeTable{LineIndex,4}=get_time(Param.IndexRange.last_i,last_j,PairString,InputTable,SeriesData.FileInfo{LineIndex},GetFieldData.Time.TimeName);  % last time                     
2939                    TimeTable{LineIndex,5}=get_time(Param.IndexRange.MaxIndex_i(LineIndex),MaxIndex_j,PairString,InputTable,SeriesData.FileInfo{LineIndex},GetFieldData.Time.TimeName);  % Max time
2940                case 'variable'
2941                    set(handles.TimeName,'String',['var:' GetFieldData.Time.TimeName])
2942                    set(handles.NomType,'String','*')
2943                    set(handles.RootFile,'String',[get(handles.RootFile,'String') get(handles.FileIndex,'String')])% A VERIFIER !!!!!!
2944                    set(handles.FileIndex,'String','')
2945                    ParamIn.TimeVarName=GetFieldData.Time.TimeName;
2946                case 'matrix_index'
2947                    TimeName=['dim:' GetFieldData.Time.TimeName];
2948                    set(handles.NomType,'String','*')
2949                    set(handles.RootFile,'String',[get(handles.RootFile,'String') get(handles.FileIndex,'String')])
2950                    set(handles.FileIndex,'String','')
2951                    ParamIn.TimeDimName=GetFieldData.Time.TimeName;
2952            end
2953            TimeTable{LineIndex,1}=TimeName;
2954            set(handles.TimeTable,'Data',TimeTable);
2955        end
2956        set(handles.Coord_x,'String',XName)
2957        set(handles.Coord_y,'String',YName)
2958        set(handles.Coord_x,'Visible','on')
2959        set(handles.Coord_y,'Visible','on')
2960        end
2961    else
2962        msgbox_uvmat('ERROR',[FirstFileName ' does not exist'])
2963    end
2964end
2965
2966
2967function [TimeValue,DtValue]=get_time(ref_i,ref_j,PairString,InputTable,FileInfo,TimeName,DtName)
2968[i1,i2,j1,j2] = get_file_index(ref_i,ref_j,PairString);
2969FileName=fullfile_uvmat(InputTable{1},InputTable{2},InputTable{3},InputTable{5},InputTable{4},i1,i2,j1,j2);
2970Data=nc2struct(FileName,[]);
2971TimeValue=[];
2972DtValue=[];
2973if isequal(FileInfo.FileType,'civdata')
2974    if ismember(TimeName,{'civ1','filter1'})
2975        if isfield(Data,'Civ1_Time')
2976        TimeValue=Data.Civ1_Time;
2977        end
2978        if isfield(Data,'Civ1_Dt')
2979        DtValue=Data.Civ1_Dt;
2980        end
2981    else
2982        if isfield(Data,'Civ2_Time')
2983        TimeValue=Data.Civ2_Time;
2984        end
2985        if isfield(Data,'Civ2_Dt')
2986        DtValue=Data.Civ2_Dt;
2987        end
2988    end
2989else
2990    if ~isempty(TimeName)&& isfield(Data,TimeName)
2991        TimeValue=Data.(TimeName);
2992    end
2993    if exist('DtName','var') && isfield(Data,DtName)
2994        DtValue=Data.(DtName);
2995    end
2996end
2997
2998%------------------------------------------------------------------------
2999% --- Executes on selection change in FieldName_1.
3000function FieldName_1_Callback(hObject, eventdata, handles)
3001%------------------------------------------------------------------------
3002field_str=get(handles.FieldName_1,'String');
3003field_index=get(handles.FieldName_1,'Value');
3004field=field_str{field_index(1)};
3005if isequal(field,'add_field...')
3006    hget_field=findobj(allchild(0),'name','get_field');
3007    if ~isempty(hget_field)
3008        delete(hget_field)%delete opened versions of get_field
3009    end
3010    Param=read_GUI(handles.series);
3011    Param.InputTable=Param.InputTable(1,:);
3012    % check the existence of the first file in the series
3013    first_j=[];
3014    if isfield(Param.IndexRange,'first_j'); first_j=Param.IndexRange.first_j; end
3015    if isfield(Param.IndexRange,'last_j'); last_j=Param.IndexRange.last_j; end
3016    PairString='';
3017    if isfield(Param.IndexRange,'PairString'); PairString=Param.IndexRange.PairString; end
3018    [i1,i2,j1,j2] = get_file_index(Param.IndexRange.first_i,first_j,PairString);
3019    FirstFileName=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},...
3020        Param.InputTable{1,5},Param.InputTable{1,4},i1,i2,j1,j2);
3021    if exist(FirstFileName,'file')
3022        ParamIn.SeriesInput=1;
3023        GetFieldData=get_field(FirstFileName,ParamIn);
3024        FieldList={};
3025        switch GetFieldData.FieldOption
3026            case 'vectors'
3027                UName=GetFieldData.PanelVectors.vector_x;
3028                VName=GetFieldData.PanelVectors.vector_y;
3029                FieldList={['vec(' UName ',' VName ')'];...
3030                    ['norm(' UName ',' VName ')'];...
3031                    UName;VName};
3032            case {'scalar','pick variables'}
3033                FieldList=GetFieldData.PanelScalar.scalar;
3034                if ischar(FieldList)
3035                    FieldList={FieldList};
3036                end
3037            case '1D plot'
3038
3039            case 'civdata...'
3040                FieldList=set_field_list('U','V','C');
3041                set(handles.FieldName,'Value',2) % set menu to 'velocity
3042        end
3043        if ~strcmp(GetFieldData.FieldOption,'civdata...')
3044            TimeNameStr=GetFieldData.Time.SwitchVarIndexTime;
3045            switch TimeNameStr
3046                case 'file index'
3047                    set(handles.TimeName,'String','');
3048                case 'attribute'
3049                    set(handles.TimeName,'String',['att:' GetFieldData.Time.TimeName]);
3050                case 'variable'
3051                    set(handles.TimeName,'String',['var:' GetFieldData.Time.TimeName])
3052                    set(handles.NomType,'String','*')
3053                    set(handles.RootFile,'String',[get(handles.RootFile,'String') get(handles.FileIndex,'String')])% A VERIFIER !!!!!!
3054                    set(handles.FileIndex,'String','')
3055                    ParamIn.TimeVarName=GetFieldData.Time.TimeName;
3056                case 'matrix_index'
3057                    set(handles.TimeName,'String',['dim:' GetFieldData.Time.TimeName]);
3058                    set(handles.NomType,'String','*')
3059                    set(handles.RootFile,'String',[get(handles.RootFile,'String') get(handles.FileIndex,'String')])
3060                    set(handles.FileIndex,'String','')
3061                    ParamIn.TimeDimName=GetFieldData.Time.TimeName;
3062            end
3063        end
3064        set(handles.FieldName_1,'Value',1)
3065        set(handles.FieldName_1,'String',[FieldList; {'add_field...'}]);
3066    end
3067end   
3068
3069
3070%%%%%%%%%%%%%
3071function [ind_remove]=find_pairs(dirpair,ind_i,last_i)
3072indsel=ind_i;
3073indiff=diff(ind_i); % test index increment to detect multiplets (several pairs with the same index ind_i) and holes in the series
3074indiff=[1 indiff last_i-ind_i(end)+1]; % for testing gaps with the imposed bounds
3075if ~isempty(indiff)
3076    indiff2=diff(indiff);
3077    indiffp=[indiff2 1];
3078    indiffm=[1 indiff2];
3079    ind_multi_m=find((indiff==0)&(indiffm<0))-1; % indices of first members of multiplets
3080    ind_multi_p=find((indiff==0)&(indiffp>0)); % indices of last members of multiplets
3081    %for each multiplet, select the most recent file
3082    ind_remove=[];
3083    for i=1:length(ind_multi_m)
3084        ind_pairs=ind_multi_m(i):ind_multi_p(i);
3085        for imulti=1:length(ind_pairs)
3086            datepair(imulti)=datenum(dirpair(ind_pairs(imulti)).date); % dates of creation
3087        end
3088        [datenew,indsort2]=sort(datepair); % sort the multiplet by creation date
3089        ind_s=indsort2(1:end-1); %
3090        ind_remove=[ind_remove ind_pairs(ind_s)]; % remove these indices, leave the last one
3091    end
3092end
3093
3094%------------------------------------------------------------------------
3095% --- determine the list of index pairstring of processing file
3096function [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)
3097%------------------------------------------------------------------------
3098num_i1=num_i; % set of first image numbers by default
3099num_i2=num_i;
3100num_j1=num_j;
3101num_j2=num_j;
3102num_i_out=num_i;
3103num_j_out=num_j;
3104% if isequal (NomType,'_1-2_1') || isequal (NomType,'_1-2')
3105if isequal(mode,'series(Di)')
3106    num_i1_line=num_i+ind_shift(3); % set of first image numbers
3107    num_i2_line=num_i+ind_shift(4);
3108    % adjust the first and last field number
3109        indsel=find(num_i1_line >= 1);
3110    num_i_out=num_i(indsel);
3111    num_i1_line=num_i1_line(indsel);
3112    num_i2_line=num_i2_line(indsel);
3113    num_j1=meshgrid(num_j,ones(size(num_i1_line)));
3114    num_j2=meshgrid(num_j,ones(size(num_i1_line)));
3115    [xx,num_i1]=meshgrid(num_j,num_i1_line);
3116    [xx,num_i2]=meshgrid(num_j,num_i2_line);
3117elseif isequal (mode,'series(Dj)')||isequal (mode,'bursts')
3118    if isequal(mode,'bursts') %case of bursts (png_old or png_2D)
3119        num_j1=ind_shift(1)*ones(size(num_i));
3120        num_j2=ind_shift(2)*ones(size(num_i));
3121    else
3122        num_j1_col=num_j+ind_shift(1); % set of first image numbers
3123        num_j2_col=num_j+ind_shift(2);
3124        % adjust the first field number
3125        indsel=find((num_j1_col >= 1));   
3126        num_j_out=num_j(indsel);
3127        num_j1_col=num_j1_col(indsel);
3128        num_j2_col=num_j2_col(indsel);
3129        [num_i1,num_j1]=meshgrid(num_i,num_j1_col);
3130        [num_i2,num_j2]=meshgrid(num_i,num_j2_col);
3131    end   
3132end
3133
3134%------------------------------------------------------------------------
3135% --- Executes on button press in CheckObject.
3136function CheckObject_Callback(hObject, eventdata, handles)
3137%------------------------------------------------------------------------
3138hset_object=findobj(allchild(0),'tag','set_object'); % find the set_object interface handle
3139if get(handles.CheckObject,'Value')
3140    SeriesData=get(handles.series,'UserData');
3141    if isfield(SeriesData,'ProjObject') && ~isempty(SeriesData.ProjObject)
3142        set(handles.ViewObject,'Value',1)
3143        ViewObject_Callback(hObject, eventdata, handles)
3144    else
3145        if ishandle(hset_object)
3146            uistack(hset_object,'top')% show the GUI set_object if opened
3147        else
3148            %get the object file
3149            InputTable=get(handles.InputTable,'Data');
3150            defaultname=InputTable{1,1};
3151            if isempty(defaultname)
3152                defaultname={''};
3153            end
3154            fileinput=uigetfile_uvmat('pick a xml object file (or use uvmat to create it)',defaultname,'.xml');
3155            if isempty(fileinput)% exit if no object file is selected
3156                set(handles.CheckObject,'Value',0)
3157                return
3158            end
3159            %read the file
3160            data=xml2struct(fileinput);
3161            if ~isfield(data,'Type')
3162                msgbox_uvmat('ERROR',[fileinput ' is not an object xml file'])
3163                set(handles.CheckObject,'Value',0)
3164                return
3165            end
3166            if ~isfield(data,'ProjMode')
3167                data.ProjMode='none';
3168            end
3169            hset_object=set_object(data); % call the set_object interface
3170            set(hset_object,'Name','set_object_series')% name to distinguish from set_object used with uvmat
3171        end
3172        ProjObject=read_GUI(hset_object);
3173        set(handles.ProjObjectName,'String',ProjObject.Name); % display the object name
3174        SeriesData=get(handles.series,'UserData');
3175        SeriesData.ProjObject=ProjObject;
3176        set(handles.series,'UserData',SeriesData);
3177    end
3178    set(handles.EditObject,'Visible','on');
3179    set(handles.DeleteObject,'Visible','on');
3180    set(handles.ViewObject,'Visible','on');
3181    set(handles.ProjObjectName,'Visible','on');
3182else
3183    set(handles.EditObject,'Visible','off');
3184    set(handles.DeleteObject,'Visible','off');
3185    set(handles.ViewObject,'Visible','off');
3186    if ~ishandle(hset_object)
3187        set(handles.ViewObject,'Value',0);
3188    end
3189    set(handles.ProjObjectName,'Visible','off');
3190end
3191
3192%------------------------------------------------------------------------
3193% --- Executes on button press in ViewObject.
3194%------------------------------------------------------------------------
3195function ViewObject_Callback(hObject, eventdata, handles)
3196
3197UserData=get(handles.series,'UserData');
3198hset_object=findobj(allchild(0),'Tag','set_object');
3199if ~isempty(hset_object)
3200    delete(hset_object)% refresh set_object if already opened
3201end
3202hset_object=set_object(UserData.ProjObject);
3203set(hset_object,'Name','view_object_series')
3204
3205
3206%------------------------------------------------------------------------
3207% --- Executes on button press in EditObject.
3208function EditObject_Callback(hObject, eventdata, handles)
3209%------------------------------------------------------------------------
3210if get(handles.EditObject,'Value')
3211    set(handles.ViewObject,'Value',0)
3212    UserData=get(handles.series,'UserData');
3213    hset_object=set_object(UserData.ProjObject);
3214    set(hset_object,'Name','edit_object_series')
3215    set(get(hset_object,'Children'),'Enable','on')
3216else
3217    hset_object=findobj(allchild(0),'Tag','set_object');
3218    if ~isempty(hset_object)
3219        set(get(hset_object,'Children'),'Enable','off')
3220    end
3221end
3222
3223%------------------------------------------------------------------------
3224% --- Executes on button press in DeleteObject.
3225function DeleteObject_Callback(hObject, eventdata, handles)
3226%------------------------------------------------------------------------
3227SeriesData=get(handles.series,'UserData');
3228SeriesData.ProjObject=[];
3229set(handles.series,'UserData',SeriesData)
3230set(handles.ProjObjectName,'String','')
3231set(handles.ProjObjectName,'Visible','off')
3232set(handles.CheckObject,'Value',0)
3233set(handles.ViewObject,'Visible','off')
3234set(handles.EditObject,'Visible','off')
3235hset_object=findobj(allchild(0),'name','set_object_series');
3236if ~isempty(hset_object)
3237    delete(hset_object)
3238end
3239set(handles.DeleteObject,'Visible','off')
3240
3241%------------------------------------------------------------------------
3242% --- Executed when CheckMask is activated
3243%------------------------------------------------------------------------
3244function CheckMask_Callback(hObject, eventdata, handles)
3245
3246if get(handles.CheckMask,'Value')
3247    InputTable=get(handles.InputTable,'Data');
3248    nbview=size(InputTable,1);
3249    MaskTable=cell(nbview,1); % default
3250    ListMask=cell(nbview,1); % default
3251    MaskData=get(handles.MaskTable,'Data');
3252    MaskData(size(MaskData,1):nbview,1)=cell(size(MaskData,1):nbview,1); % complement if undefined lines
3253    for iview=1:nbview
3254        ListMask{iview,1}=num2str(iview);
3255        RootPath=InputTable{iview,1};
3256        if ~isempty(RootPath)
3257            if isempty(MaskData{iview})
3258                SubDir=InputTable{iview,2};
3259                MaskPath=fullfile(RootPath,[regexprep(SubDir,'\..*','') '.mask']); % take the root part of SubDir, before the first dot '.'
3260                if exist(MaskPath,'dir')
3261                    ListStruct=dir(MaskPath); % look for a mask file
3262                    ListCells=struct2cell(ListStruct); % transform dir struct to a cell arrray
3263                    check_dir=cell2mat(ListCells(4,:)); % =1 for directories, =0 for files
3264                    ListFiles=ListCells(1,:); % list of file and dri names
3265                    ListFiles=ListFiles(~check_dir); % list of file names (excluding dir)
3266                    mdetect=0;
3267                    if ~isempty(ListFiles)
3268                        for ifile=1:numel(ListFiles)
3269                            [tild,tild,MaskFile{ifile},i1_series,i2_series,j1_series,j2_series,MaskNomType,MaskFileType]=find_file_series(MaskPath,ListFiles{ifile},0);
3270                            if strcmp(MaskFileType,'image') && isempty(i2_series) && isempty(j2_series)
3271                                mdetect=1;
3272                                MaskName=ListFiles{ifile};
3273                            end
3274                            if ~strcmp(MaskFile{ifile},MaskFile{1})
3275                                mdetect=0; % cancel detection test in case of multiple masks, use the brower for selection
3276                                break
3277                            end
3278                        end
3279                    end
3280                    if mdetect==1
3281                        MaskName=fullfile(MaskPath,'mask_1.png');
3282                    else
3283                        MaskName=uigetfile_uvmat('select a mask file:',MaskPath,'image');
3284                    end
3285                else
3286                    MaskName=uigetfile_uvmat('select a mask file:',RootPath,'image');
3287                end
3288                MaskTable{iview,1}=MaskName ;
3289                ListMask{iview,1}=num2str(iview);
3290            end
3291        end
3292    end
3293    set(handles.MaskTable,'Data',MaskTable)
3294    set(handles.MaskTable,'Visible','on')
3295    set(handles.MaskBrowse,'Visible','on')
3296    set(handles.ListMask,'Visible','on')
3297    set(handles.ListMask,'String',ListMask)
3298    set(handles.ListMask,'Value',1)
3299else
3300    set(handles.MaskTable,'Visible','off')
3301    set(handles.MaskBrowse,'Visible','off')
3302    set(handles.ListMask,'Visible','off')
3303end
3304
3305%------------------------------------------------------------------------
3306% --- Executes on button press in MaskBrowse.
3307%------------------------------------------------------------------------
3308function MaskBrowse_Callback(hObject, eventdata, handles)
3309
3310InputTable=get(handles.InputTable,'Data');
3311iview=get(handles.ListMask,'Value');
3312RootPath=InputTable{iview,1};
3313MaskName=uigetfile_uvmat('select a mask file:',RootPath,'image');
3314if ~isempty(MaskName)
3315    MaskTable=get(handles.MaskTable,'Data');
3316    MaskTable{iview,1}=MaskName ;
3317    set(handles.MaskTable,'Data',MaskTable)
3318end
3319
3320%------------------------------------------------------------------------
3321% --- Executes when selected cell(s) is changed in MaskTable.
3322%------------------------------------------------------------------------
3323function MaskTable_CellSelectionCallback(hObject, eventdata, handles)
3324
3325if numel(eventdata.Indices)>=1
3326set(handles.ListMask,'Value',eventdata.Indices(1))
3327end
3328
3329%-------------------------------------------------------------------
3330function MenuHelp_Callback(hObject, eventdata, handles)
3331%-------------------------------------------------------------------
3332
3333
3334% path_to_uvmat=which ('uvmat'); % check the path of uvmat
3335% pathelp=fileparts(path_to_uvmat);
3336% helpfile=fullfile(pathelp,'uvmat_doc','uvmat_doc.html');
3337% 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')
3338% else
3339%     addpath (fullfile(pathelp,'uvmat_doc'))
3340%     web([helpfile '#series'])
3341% end
3342
3343%-------------------------------------------------------------------
3344% --- Executes on selection change in TransformName.
3345function TransformName_Callback(hObject, eventdata, handles)
3346%----------------------------------------------------------------------
3347TransformList=get(handles.TransformName,'String');
3348TransformIndex=get(handles.TransformName,'Value');
3349TransformName=TransformList{TransformIndex};
3350TransformPathList=get(handles.TransformName,'UserData');
3351nb_builtin_transform=4;
3352if isequal(TransformName,'more...');     
3353    FileName=uigetfile_uvmat('Pick a transform function',get(handles.TransformPath,'String'),'.m');
3354    if isempty(FileName)
3355        return     %browser closed without choice
3356    end
3357    [TransformPath,TransformName,TransformExt]=fileparts(FileName); % removes extension .m
3358    if ~strcmp(TransformExt,'.m')
3359        msgbox_uvmat('ERROR','a Matlab function .m must be introduced');
3360        return
3361    end
3362     % insert the choice in the menu
3363    TransformIndex=find(strcmp(TransformName,TransformList),1); % look for the selected function in the menu Action
3364    if isempty(TransformIndex)%the input string does not exist in the menu
3365        TransformIndex= length(TransformList);
3366        TransformList=[TransformList(1:end-1);{TransformName};TransformList(end)]; % the selected function is appended in the menu, before the last item 'more...'
3367        set(handles.TransformName,'String',TransformList)
3368        TransformPathList=[TransformPathList;{TransformPath}];
3369    else% the input function already exist, we update its path (possibly new)
3370        TransformPathList{TransformIndex}=TransformPath; %
3371        set(handles.TransformName,'Value',TransformIndex)
3372    end
3373   % save the new menu in the personal file 'uvmat_perso.mat'
3374   dir_perso=prefdir; % personal Matalb directory
3375   profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
3376   if exist(profil_perso,'file')
3377       for ilist=nb_builtin_transform+1:numel(TransformPathList)
3378           TransformListUser{ilist-nb_builtin_transform}=TransformList{ilist};
3379           TransformPathListUser{ilist-nb_builtin_transform}=TransformPathList{ilist};
3380       end
3381       TransformPathListUser=TransformPathListUser';
3382       TransformListUser=TransformListUser';
3383       save (profil_perso,'TransformPathListUser','TransformListUser','-append'); % store the root name for future opening of uvmat
3384   end
3385end
3386
3387%display the current function path
3388set(handles.TransformPath,'String',TransformPathList{TransformIndex}); % show the path to the senlected function
3389set(handles.TransformName,'UserData',TransformPathList);
3390
3391%% create the function handle of the selected fct
3392if ~isempty(TransformName)
3393    if ~exist(TransformPathList{TransformIndex},'dir')
3394        msgbox_uvmat('ERROR',['The prescribed transform function path ' TransformPathList{TransformIndex} ' does not exist']);
3395        return
3396    end
3397    current_dir=pwd; % current working dir
3398    cd(TransformPathList{TransformIndex})
3399    transform_handle=str2func(TransformName);
3400    cd(current_dir)
3401    Field.Action.RUN=0;% indicate that the transform fct is called only to get input param
3402    SeriesData=get(handles.series,'UserData');
3403    ParamIn=[];
3404    if isfield(SeriesData,'TransformInput')
3405        ParamIn.TransformInput=SeriesData.TransformInput;
3406    end
3407    DataOut=feval(transform_handle,Field,ParamIn);% execute the transform fct to get the required conditions
3408    Field.Action.RUN=0; % indicate that the transform fct is called only to get input param
3409    %DataOut=feval(transform_handle,Field,[]); % execute the transform fct to get the required conditions
3410    if isfield(DataOut,'TransformInput')%  used to add transform parameters at selection of the transform fct
3411        SeriesData.TransformInput=DataOut.TransformInput;
3412        set(handles.series,'UserData',SeriesData)
3413    end
3414end
3415
3416%------------------------------------------------------------------------
3417% --- fct activated by the upper bar menu ExportConfig
3418%------------------------------------------------------------------------
3419function MenuDisplayConfig_Callback(hObject, eventdata, handles)
3420
3421global Param
3422Param=read_GUI_series(handles);
3423evalin('base','global Param')%make CurData global in the workspace
3424display('current series config :')
3425evalin('base','Param') %display CurData in the workspace
3426commandwindow; % brings the Matlab command window to the front
3427
3428%------------------------------------------------------------------------
3429% --- fct activated by the upper bar menu InportConfig: import
3430%     menu settings from an xml file (stored in /0_XML for each run)
3431%------------------------------------------------------------------------
3432function MenuImportConfig_Callback(hObject, eventdata, handles)
3433
3434%% use a browser to choose the xml file containing the processing config
3435InputTable=get(handles.InputTable,'Data');
3436oldfile=InputTable{1,1}; % current path in InputTable
3437if isempty(oldfile)
3438    % use a file name stored in prefdir
3439    dir_perso=prefdir;
3440    profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
3441    if exist(profil_perso,'file')
3442        h=load (profil_perso);
3443        if isfield(h,'RootPath') && ischar(h.RootPath)
3444            oldfile=h.RootPath;
3445        end
3446    end
3447end
3448filexml=uigetfile_uvmat('pick a xml parameter file',oldfile,'.xml'); % get the xml file containing processing parameters
3449if isempty(filexml), return, end % quit function if an xml file has not been opened
3450
3451%% fill the GUI series with the content of the xml file
3452[Param,RootTag,errormsg]=xml2struct(filexml); % read the input xml file as a Matlab structure
3453if ~isempty(errormsg)
3454    msgbox_uvmat('ERROR',errormsg);
3455    return
3456end
3457% ask to stop current Action if button RUN is in action (another process is already running)
3458if isequal(get(handles.RUN,'Value'),1)
3459    answer= msgbox_uvmat('INPUT_Y-N','stop current Action process?');
3460    if strcmp(answer,'Yes')
3461        STOP_Callback(hObject, eventdata, handles)
3462    else
3463        return
3464    end
3465end
3466Param.Action.RUN=0; % desactivate the input RUN=1
3467
3468fill_GUI(Param,handles.series)% fill the elements of the GUI series with the input parameters
3469SeriesData=get(handles.series,'UserData');
3470if isfield(Param,'InputFields')
3471    ListField=Param.InputFields.FieldName;
3472    if ischar(ListField),ListField={ListField}; end
3473    set(handles.FieldName,'String',[ListField;{'add_field...'}])
3474     set(handles.FieldName,'Value',1:numel(ListField))
3475     set(handles.FieldName,'Visible','on')
3476end       
3477if isfield(Param,'ActionInput')%  introduce  parameters specific to an Action fct, for instance PIV parameters
3478%     set(handles.ActionInput,'Visible','on')
3479%     set(handles.ActionInput,'Value',0)
3480    Param.ActionInput.ConfigSource=filexml; % record the source of config for future info
3481    SeriesData.ActionInput=Param.ActionInput;
3482end
3483if isfield(Param,'TransformInput')%  introduce  parameters specific to a transform fct
3484    SeriesData.TransformInput=Param.TransformInput;
3485end
3486if isfield(Param,'ProjObject') %introduce projection object if relevant
3487    SeriesData.ProjObject=Param.ProjObject;
3488end
3489set(handles.series,'UserData',SeriesData)
3490if isfield(Param,'CheckObject') && isequal(Param.CheckObject,1)
3491    set(handles.ProjObjectName,'String',Param.ProjObject.Name)
3492    set(handles.ViewObject,'Visible','on')
3493    set(handles.EditObject,'Visible','on')
3494    set(handles.DeleteObject,'Visible','on')
3495else     
3496    set(handles.ProjObjectName,'String','')
3497    set(handles.ProjObjectName,'Visible','off')
3498    set(handles.ViewObject,'Visible','off')
3499    set(handles.EditObject,'Visible','off')
3500    set(handles.DeleteObject,'Visible','off')     
3501end     
3502set(handles.REFRESH,'BackgroundColor',[1 0 1]); % paint REFRESH button in magenta to indicate that it should be activated
3503
3504
3505%------------------------------------------------------------------------
3506% --- Executes when the GUI series is resized.
3507%------------------------------------------------------------------------
3508function series_ResizeFcn(hObject, eventdata, handles)
3509
3510%% input table
3511set(handles.InputTable,'Unit','pixel')
3512Pos=get(handles.InputTable,'Position');
3513set(handles.InputTable,'Unit','normalized')
3514ColumnWidth=round([0.5 0.14 0.14 0.14 0.08]*(Pos(3)-52));
3515ColumnWidth=num2cell(ColumnWidth);
3516set(handles.InputTable,'ColumnWidth',ColumnWidth)
3517
3518%% MinIndex_j and MaxIndex_i
3519unit=get(handles.MinIndex_i,'Unit');
3520set(handles.MinIndex_i,'Unit','pixel')
3521Pos=get(handles.MinIndex_i,'Position');
3522set(handles.MinIndex_i,'Unit',unit)
3523set(handles.MinIndex_i,'ColumnWidth',{Pos(3)-18})
3524set(handles.MaxIndex_i,'ColumnWidth',{Pos(3)-18})
3525set(handles.MinIndex_j,'ColumnWidth',{Pos(3)-18})
3526set(handles.MaxIndex_j,'ColumnWidth',{Pos(3)-18})
3527
3528%% TimeTable
3529set(handles.TimeTable,'Unit','pixel')
3530Pos=get(handles.TimeTable,'Position');
3531set(handles.TimeTable,'Unit','normalized')
3532% ColumnWidth=get(handles.TimeTable,'ColumnWidth');
3533ColumnWidth=num2cell(floor([0.2 0.2 0.2 0.2 0.2]*(Pos(3)-20)));
3534set(handles.TimeTable,'ColumnWidth',ColumnWidth)
3535
3536
3537%% PairString
3538set(handles.PairString,'Unit','pixel')
3539Pos=get(handles.PairString,'Position');
3540set(handles.PairString,'Unit','normalized')
3541set(handles.PairString,'ColumnWidth',{Pos(3)-5})
3542
3543%% MaskTable
3544set(handles.MaskTable,'Unit','pixel')
3545Pos=get(handles.MaskTable,'Position');
3546set(handles.MaskTable,'Unit','normalized')
3547set(handles.MaskTable,'ColumnWidth',{Pos(3)-5})
3548
3549%------------------------------------------------------------------------
3550% --- Executes on button press in status.
3551%------------------------------------------------------------------------
3552function status_Callback(hObject, eventdata, handles)
3553
3554if get(handles.status,'Value')
3555    set(handles.status,'BackgroundColor',[1 1 0])
3556    drawnow
3557    Param=read_GUI(handles.series);
3558    RootPath=fullfile(Param.OutputPath,Param.Experiment,Param.Device);
3559    if ~isfield(Param,'OutputSubDir')   
3560        msgbox_uvmat('ERROR','no standard sub-directory definition for output files, use a browser to check the output')
3561        set(handles.status,'BackgroundColor',[0 1 0])
3562        return
3563    end
3564    OutputSubDir=[Param.OutputSubDir Param.OutputDirExt]; % subdirectory for output files
3565    OutputDir=fullfile(RootPath,OutputSubDir);
3566    if exist(OutputDir,'dir')
3567        uigetfile_uvmat('status_display',OutputDir)
3568    else
3569        msgbox_uvmat('ERROR','output folder not created yet: calculation did not start')
3570        set(handles.status,'BackgroundColor',[0 1 0])
3571    end
3572else
3573    %% delete current display fig if selection is off
3574    set(handles.status,'BackgroundColor',[0 1 0])
3575    hfig=findobj(allchild(0),'name','status_display');
3576    if ~isempty(hfig)
3577        delete(hfig)
3578    end
3579    return
3580end
3581
3582
3583%------------------------------------------------------------------------   
3584% launched by selecting a file on the list
3585%------------------------------------------------------------------------
3586function view_file(hObject, eventdata)
3587
3588list=get(hObject,'String');
3589index=get(hObject,'Value');
3590rootroot=get(hObject,'UserData');
3591selectname=list{index};
3592ind_dot=regexp(selectname,'\.\.\.');
3593if ~isempty(ind_dot)
3594    selectname=selectname(1:ind_dot-1);
3595end
3596FullSelectName=fullfile(rootroot,selectname);
3597if exist(FullSelectName,'dir')% a directory has been selected
3598    ListFiles=dir(FullSelectName);
3599    ListDisplay=cell(numel(ListFiles),1);
3600    for ilist=2:numel(ListDisplay)% suppress the first line '.'
3601        ListDisplay{ilist-1}=ListFiles(ilist).name;
3602    end
3603    set(hObject,'Value',1)
3604    set(hObject,'String',ListDisplay)
3605    if strcmp(selectname,'..')
3606        FullSelectName=fileparts(fileparts(FullSelectName));
3607    end
3608    set(hObject,'UserData',FullSelectName)
3609    hfig=get(hObject,'parent');
3610    htitlebox=findobj(hfig,'tag','titlebox');   
3611    set(htitlebox,'String',FullSelectName)
3612elseif exist(FullSelectName,'file')%visualise the vel field if it exists
3613    FileInfo=get_file_info(FullSelectName);   
3614    if strcmp(FileInfo.FileType,'txt')
3615        edit(FullSelectName)
3616    elseif strcmp(FileInfo.FileType,'xml')
3617        editxml(FullSelectName)
3618    else
3619        uvmat(FullSelectName)
3620    end
3621    set(gcbo,'Value',1)
3622end
3623
3624
3625%------------------------------------------------------------------------   
3626% launched by refreshing the status figure
3627%------------------------------------------------------------------------
3628function refresh_GUI(hfig)
3629
3630htitlebox=findobj(hfig,'tag','titlebox');
3631hlist=findobj(hfig,'tag','list');
3632hseries=findobj(allchild(0),'tag','series');
3633hstatus=findobj(hseries,'tag','status');
3634StatusData=get(hstatus,'UserData');
3635OutputDir=get(htitlebox,'String');
3636if ischar(OutputDir),OutputDir={OutputDir};end
3637ListFiles=dir(OutputDir{1});
3638if numel(ListFiles)<1
3639    return
3640end
3641ListFiles(1)=[]; % removes the first line ='.'
3642ListDisplay=cell(numel(ListFiles),1);
3643testrecent=0;
3644datnum=zeros(numel(ListDisplay),1);
3645for ilist=1:numel(ListDisplay)
3646    ListDisplay{ilist}=ListFiles(ilist).name;
3647      if ~ListFiles(ilist).isdir && isfield(ListFiles(ilist),'datenum')
3648            datnum(ilist)=ListFiles(ilist).datenum; % only available in recent matlab versions
3649            testrecent=1;
3650       end
3651end
3652set(hlist,'String',ListDisplay)
3653
3654%% Look at date of creation
3655ListDisplay=ListDisplay(datnum~=0);
3656datnum=datnum(datnum~=0); % keep the non zero values corresponding to existing files
3657NbOutputFile=[];
3658if isempty(datnum)
3659    if testrecent
3660        message='no civ result created yet';
3661    else
3662        message='';
3663    end
3664else
3665    [first,indfirst]=min(datnum);
3666    [last,indlast]=max(datnum);
3667    NbOutputFile_str='?';
3668    NbOutputFile=[];
3669    if isfield(StatusData,'NbOutputFile')
3670        NbOutputFile=StatusData.NbOutputFile;
3671        NbOutputFile_str=num2str(NbOutputFile);
3672    end
3673    message={[num2str(numel(datnum)) ' file(s) done over ' NbOutputFile_str] ;['oldest modification:  ' ListDisplay{indfirst} ' : ' datestr(first)];...
3674        ['latest modification:  ' ListDisplay{indlast} ' : ' datestr(last)]};
3675end
3676set(htitlebox,'String', [OutputDir{1};message])
3677
3678%% update the waitbar
3679hwaitbar=findobj(hfig,'tag','waitbar');
3680if ~isempty(NbOutputFile)
3681    BarPosition=get(hwaitbar,'Position');
3682    BarPosition(3)=0.9*numel(datnum)/NbOutputFile;
3683    set(hwaitbar,'Position',BarPosition)
3684end
3685
3686%------------------------------------------------------------------------
3687% --- Executes on selection change in ActionExt.
3688%------------------------------------------------------------------------
3689function ActionExt_Callback(hObject, eventdata, handles)
3690
3691ActionExtList=get(handles.ActionExt,'String');
3692ActionExt=ActionExtList{get(handles.ActionExt,'Value')};
3693if strcmp(ActionExt,'.py (in dev.)')
3694    set(handles.RunMode,'Value',2)
3695end
3696
3697
3698function num_NbSlice_Callback(hObject, eventdata, handles)
3699NbSlice=str2num(get(handles.num_NbSlice,'String'));
3700
3701%------------------------------------------------------------------------
3702% --- set the visibility of relevant velocity type menus:
3703function menu=set_veltype_display(Civ,FileType)
3704%------------------------------------------------------------------------
3705if ~exist('FileType','var')
3706    FileType='civx';
3707end
3708switch FileType
3709    case 'civx'
3710        menu={'civ1';'interp1';'filter1';'civ2';'interp2';'filter2'};
3711        if isequal(Civ,0)
3712            imax=0;
3713        elseif isequal(Civ,1) || isequal(Civ,2)
3714            imax=1;
3715        elseif isequal(Civ,3)
3716            imax=3;
3717        elseif isequal(Civ,4) || isequal(Civ,5)
3718            imax=4;
3719        elseif isequal(Civ,6) %patch2
3720            imax=6;
3721        end
3722    case 'civdata'
3723        menu={'civ1';'filter1';'civ2';'filter2'};
3724        if isequal(Civ,0)
3725            imax=0;
3726        elseif isequal(Civ,1) || isequal(Civ,2)
3727            imax=1;
3728        elseif isequal(Civ,3)
3729            imax=2;
3730        elseif isequal(Civ,4) || isequal(Civ,5)
3731            imax=3;
3732        else%if isequal(Civ,6) %patch2
3733            imax=4;
3734        end
3735end
3736menu=menu(1:imax);
3737
3738
3739% --- Executes on mouse motion over figure - except title and menu.
3740% function series_WindowButtonMotionFcn(hObject, eventdata, handles)
3741% set(hObject,'Pointer','arrow');
3742
3743
3744% --- Executes on button press in SetPairs.
3745function SetPairs_Callback(hObject, eventdata, handles)
3746
3747%% delete previous occurrence of 'set_pairs'
3748hfig=findobj(allchild(0),'Tag','set_pairs');
3749if ~isempty(hfig)
3750delete(hfig)
3751end
3752
3753%% create the GUI set_pairs
3754set(0,'Unit','points')
3755ScreenSize=get(0,'ScreenSize'); % get the size of the screen, to put the fig on the upper right
3756Width=220; % fig width in points (1/72 inch)
3757Height=min(0.8*ScreenSize(4),300);
3758Left=ScreenSize(3)- Width-40; % right edge close to the right, with margin=40
3759Bottom=ScreenSize(4)-Height-40; % put fig at top right
3760hfig=findobj(allchild(0),'Tag','set_slice');
3761if ~isempty(hfig),delete(hfig), end; % delete existing version of the GUI
3762hfig=figure('name','set_pairs','tag','set_pairs','MenuBar','none','NumberTitle','off','Unit','points','Position',[Left,Bottom,Width,Height]);
3763BackgroundColor=get(hfig,'Color');
3764SeriesData=get(handles.series,'UserData');
3765TimeUnit=get(handles.TimeUnit,'String');
3766PairString=get(handles.PairString,'Data');
3767ListViewLines=find(cellfun('isempty',PairString)==0); % find list of non empty pairs
3768ListViewMenu=cell(numel(ListViewLines),1);
3769%iview=get(handles.PairString,'Value');
3770iview=[];
3771for ilist=1:numel(ListViewLines)
3772    ListViewMenu{ilist}=num2str(ListViewLines(ilist));
3773end
3774if isempty(iview)
3775    ListViewValue=numel(ListViewLines); % we work by default on the pair option for the last line which requires pairs
3776    iview=ListViewLines(end);
3777else
3778    ListViewValue=find(ListViewLines==iview);
3779end
3780ref_i=str2num(get(handles.num_first_i,'String'));
3781ref_j=1; % default
3782if strcmp(get(handles.num_first_j,'String'),'Visible')
3783    ref_j=str2num(get(handles.num_first_j,'String'));
3784end
3785[ModeMenu,ModeValue]=update_mode(SeriesData.i1_series{1},SeriesData.i2_series{1},SeriesData.j2_series{1});
3786InputTable=get(handles.InputTable,'Data');
3787displ_pair=update_listpair(SeriesData.i1_series{1},SeriesData.i2_series{1},SeriesData.j1_series{1},SeriesData.j2_series{1},ModeMenu{ModeValue},...
3788                                                 SeriesData.Time{1},TimeUnit,ref_i,ref_j,SeriesData.TimeName,InputTable,SeriesData.FileInfo{1});
3789for iline=1:size(InputTable,1)
3790    viewcell{iline}=num2str(iline);
3791end
3792viewcell=viewcell';
3793ModeMenu={'bursts';'series(Dj)'};
3794ModeValue=1;                                               
3795                   %i1_series,i2_series,j1_series,j2_series,mode,time,TimeUnit,ref_i,ref_j,TimeName,InputTable,FileInfo                             
3796% first raw of the GUI
3797uicontrol('Style','text','Units','normalized', 'Position', [0.05 0.88 0.5 0.1],'BackgroundColor',BackgroundColor,...
3798    'String','row to edit #','FontUnits','points','FontSize',12,'FontWeight','bold','ForegroundColor','blue','HorizontalAlignment','right'); % title
3799uicontrol('Style','popupmenu','Units','normalized', 'Position', [0.54 0.8 0.3 0.2],'BackgroundColor',[1 1 1],...
3800    'Callback',@(hObject,eventdata)ListView_Callback(hObject,eventdata),'String',viewcell,'Value',1,'FontUnits','points','FontSize',12,'FontWeight','bold',...
3801    'Tag','ListView','TooltipString','''ListView'':choice of the file series w for pair display');
3802% second raw of the GUI
3803uicontrol('Style','text','Units','normalized', 'Position', [0.05 0.79 0.7 0.1],'BackgroundColor',BackgroundColor,...
3804    'String','mode of index pairing:','FontUnits','points','FontSize',12,'FontWeight','bold','ForegroundColor','blue','HorizontalAlignment','left'); % title
3805uicontrol('Style','popupmenu','Units','normalized', 'Position', [0.05 0.62 0.9 0.2],'BackgroundColor',[1 1 1],...
3806    'Callback',@(hObject,eventdata)Mode_Callback(hObject,eventdata),'String',ModeMenu,'Value',ModeValue,'FontUnits','points','FontSize',12,'FontWeight','bold',...
3807    'Tag','Mode','TooltipString','''Mode'': choice of the image pair mode');
3808% third raw
3809uicontrol('Style','text','Units','normalized', 'Position', [0.05 0.6 0.7 0.1],'BackgroundColor',BackgroundColor,...
3810    'String','pair choice:','FontUnits','points','FontSize',12,'FontWeight','bold','ForegroundColor','blue','HorizontalAlignment','left'); % title
3811uicontrol('Style','listbox','Units','normalized', 'Position', [0.05 0.42 0.9 0.2],'BackgroundColor',[1 1 1],...
3812    'Callback',@(hObject,eventdata)ListPair_Callback(hObject,eventdata),'String',displ_pair,'Value',1,'FontUnits','points','FontSize',12,'FontWeight','bold',...
3813    'Tag','ListPair','TooltipString','''ListPair'': menu for selecting the image pair');
3814uicontrol('Style','text','Units','normalized', 'Position', [0.1 0.22 0.8 0.1],'BackgroundColor',BackgroundColor,...
3815    'String','ref_i           ref_j','FontUnits','points','FontSize',12,'FontWeight','bold','ForegroundColor','blue','HorizontalAlignment','center'); % title
3816uicontrol('Style','edit','Units','normalized', 'Position', [0.15 0.17 0.3 0.08],'BackgroundColor',[1 1 1],...
3817    'Callback',@(hObject,eventdata)num_ref_i_Callback(hObject,eventdata),'String',num2str(ref_i),'FontUnits','points','FontSize',12,'FontWeight','bold',...
3818    'Tag','num_ref_i','TooltipString','''num_ref_i'': reference field index i used to display dt in ''list_pair_civ''');
3819uicontrol('Style','edit','Units','normalized', 'Position', [0.55 0.17 0.3 0.08],'BackgroundColor',[1 1 1],...
3820    'Callback',@(hObject,eventdata)num_ref_j_Callback(hObject,eventdata),'String',num2str(ref_j),'FontUnits','points','FontSize',12,'FontWeight','bold',...
3821    'Tag','num_ref_j','TooltipString','''num_ref_j'': reference field index i used to display dt in ''list_pair_civ''');
3822uicontrol('Style','pushbutton','Units','normalized', 'Position', [0.01 0.01 0.3 0.12],'BackgroundColor',[0 1 0],...
3823    'Callback',@(hObject,eventdata)OK_Callback(hObject,eventdata),'String','OK','FontUnits','points','FontSize',12,'FontWeight','bold',...
3824    'Tag','OK','TooltipString','''OK'': validate the choice');
3825%  last raw  of the GUI: pushbuttons
3826% 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),...
3827%     'FontWeight','bold','FontUnits','points','FontSize',12,'TooltipString','''OK'': apply the output to the current field series in uvmat');
3828drawnow
3829
3830%------------------------------------------------------------------------
3831function ListView_Callback(hObject,eventdata)
3832Mode_Callback(hObject,eventdata)
3833
3834%------------------------------------------------------------------------   
3835function Mode_Callback(hObject,eventdata)
3836%% get input info
3837hseries=findobj(allchild(0),'tag','series'); % handles of the GUI series
3838hhseries=guidata(hseries); % handles of the elements in the GUI series
3839TimeUnit=get(hhseries.TimeUnit,'String');
3840SeriesData=get(hseries,'UserData');
3841mode_list=get(hObject,'String');
3842mode=mode_list{get(hObject,'Value')};
3843hListView=findobj(get(hObject,'parent'),'Tag','ListView');
3844iview=get(hListView,'Value');
3845i1_series=SeriesData.i1_series{iview};
3846i2_series=SeriesData.i2_series{iview};
3847j1_series=SeriesData.j1_series{iview};
3848j2_series=SeriesData.j2_series{iview};
3849
3850%% enable j index visibility after the new choice
3851
3852if strcmp(mode,'series(Dj)')
3853   status_j='on'; % default
3854else
3855       status_j='off'; % no j index needed for bust case
3856end
3857enable_j(hhseries,status_j) % no j index needed
3858
3859%% get the reference indices for the time interval Dt
3860href_i=findobj(get(hObject,'parent'),'Tag','ref_i');
3861ref_i=[];ref_j=[];
3862if strcmp(get(href_i,'Visible'),'on')
3863    ref_i=str2num(get(href_i,'String'));
3864end
3865if isempty(ref_i)
3866    ref_i=1;
3867end
3868if isempty(ref_j)
3869    ref_j=1;
3870end
3871
3872%% update the menu ListPair
3873Menu=update_listpair(i1_series,i2_series,j1_series,j2_series,mode,SeriesData.Time{iview},TimeUnit,ref_i,ref_j,SeriesData.FileInfo);
3874hlist_pairs=findobj(get(hObject,'parent'),'Tag','ListPair');
3875set(hlist_pairs,'Value',1)% set the first choice by default in ListPair
3876set(hlist_pairs,'String',Menu)% set the menu in ListPair
3877ListPair_Callback(hlist_pairs,[])% apply the default choice in ListPair
3878
3879%-------------------------------------------------------------
3880% --- Executes on selection in ListPair.
3881function ListPair_Callback(hObject,eventdata)
3882%------------------------------------------------------------
3883list_pair=get(hObject,'String'); % get the menu of image pairs
3884if isempty(list_pair)
3885    string='';
3886else
3887    string=list_pair{get(hObject,'Value')};
3888   % string=regexprep(string,',.*',''); % removes time indication (after ',')
3889end
3890hseries=findobj(allchild(0),'tag','series');
3891hPairString=findobj(hseries,'tag','PairString');
3892PairString=get(hPairString,'Data');
3893hListView=findobj(get(hObject,'parent'),'Tag','ListView');
3894iview=get(hListView,'Value');
3895PairString{iview,1}=string;
3896% report the selected pair string to the table PairString
3897set(hPairString,'Data',PairString)
3898
3899
3900%------------------------------------------------------------------------
3901function num_ref_i_Callback(hObject, eventdata)
3902%------------------------------------------------------------------------
3903Mode_Callback([],[])
3904
3905%------------------------------------------------------------------------
3906function num_ref_j_Callback(hObject, eventdata)
3907%------------------------------------------------------------------------
3908Mode_Callback([],[])
3909
3910%------------------------------------------------------------------------
3911function OK_Callback(hObject, eventdata)
3912%------------------------------------------------------------------------
3913delete(get(hObject,'parent'))
3914
3915
3916%------------------------------------------------------------------------
3917% --- Executes on button press in ClearLine.
3918%------------------------------------------------------------------------
3919function ClearLine_Callback(hObject, eventdata, handles)
3920InputTable=get(handles.InputTable,'Data');
3921iline=str2double(get(handles.InputLine,'String'));
3922if size(InputTable,1)>1
3923    InputTable(iline,:)=[]; % suppress the current line if not the first
3924    set(handles.InputTable,'Data',InputTable);
3925end
3926set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH button to magenta color to indicate that input refr
3927
3928
3929% --- Executes on button press in MonitorCluster.
3930function MonitorCluster_Callback(hObject, eventdata, handles)
3931
3932[rr,ss]=system('oarstat |grep N=UVmat');% check the list of jobs launched with uvmat
3933if isempty(ss)
3934   disp( 'no job presently submitted with uvmat')
3935else
3936    disp('format: R/W=run/wait, time lapsed, R=nbre of cores,W=walltime')
3937    disp(ss)
3938end
3939
3940
3941function OutputSubDir_Callback(hObject, eventdata, handles)
3942set(handles.OutputSubDir,'BackgroundColor',[1 1 1])
3943
3944
3945% --- Executes on button press in CheckOverwrite.
3946function CheckOverwrite_Callback(hObject, eventdata, handles)
3947
3948% --- Executes on button press in TestCPUTime.
3949function TestCPUTime_Callback(hObject, eventdata, handles)
3950% hObject    handle to TestCPUTime (see GCBO)
3951% eventdata  reserved - to be defined in a future version of MATLAB
3952% handles    structure with handles and user data (see GUIDATA)
3953
3954
3955% --- Executes on button press in DiskQuota.
3956function DiskQuota_Callback(hObject, eventdata, handles)
3957SeriesData=get(handles.series,'UserData');
3958system(SeriesData.SeriesParam.DiskQuotaCmd)
3959
3960
3961% --- Executes on button press in Replicate.
3962function Replicate_Callback(hObject, eventdata, handles)
3963if get(handles.Replicate,'Value')
3964    InputTable=get(handles.InputTable,'Data');
3965    for ilist=1:size(InputTable,1)
3966        InputDir{ilist}=fullfile(InputTable{ilist,1},InputTable{ilist,2});
3967    end
3968    browse_data(InputDir)
3969else
3970    hh=findobj(allchild(0),'Tag','browse_data');
3971    if ~isempty(hh)
3972        delete(hh)
3973    end
3974end
3975
3976
3977
3978
3979function OutputPath_Callback(hObject, eventdata, handles)
3980
3981
3982function Experiment_Callback(hObject, eventdata, handles)
3983
3984
3985function Device_Callback(hObject, eventdata, handles)
3986
3987
3988% --- Executes on button press in OutputPathBrowse.
3989function OutputPathBrowse_Callback(hObject, eventdata, handles)
3990CheckValue=get(handles.OutputPathBrowse,'Value');
3991if CheckValue
3992OutputPath=uigetdir(get(handles.OutputPath,'String'));
3993set(handles.OutputPath,'String',OutputPath)
3994else
3995    InputTable=get(handles.InputTable,'Data');
3996    set(handles.OutputPath,'String',InputTable{1,1})
3997end
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