source: trunk/src/series.m @ 1016

Last change on this file since 1016 was 1016, checked in by sommeria, 6 years ago

bugs repaired for multilevel series

File size: 166.0 KB
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4%'series': master function associated to the GUI series.m for analysis field series 
5%------------------------------------------------------------------------
6% function varargout = series(varargin)
7% associated with the GUI series.fig
8%
9%INPUT
10% param: structure with input parameters (link with the GUI uvmat)
11%      .menu_coord_str: string for the TransformName (menu for coordinate transforms)
12%      .menu_coord_val: value for TransformName (menu for coordinate transforms)
13%      .FileName: input file name
14%      .FileName_1: second input file name
15%      .list_field: menu of input fields
16%      .index_fields: chosen index
17%      .civ1=0 or 1, .interp1,  ... : input civ field type
18%
19
20%=======================================================================
21% Copyright 2008-2017, LEGI UMR 5519 / CNRS UGA G-INP, Grenoble, France
22%   http://www.legi.grenoble-inp.fr
23%   Joel.Sommeria - Joel.Sommeria (A) legi.cnrs.fr
24%
25%     This file is part of the toolbox UVMAT.
26%
27%     UVMAT is free software; you can redistribute it and/or modify
28%     it under the terms of the GNU General Public License as published
29%     by the Free Software Foundation; either version 2 of the license,
30%     or (at your option) any later version.
31%
32%     UVMAT is distributed in the hope that it will be useful,
33%     but WITHOUT ANY WARRANTY; without even the implied warranty of
34%     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
35%     GNU General Public License (see LICENSE.txt) for more details.
36%=======================================================================
37
38%------------------------------------------------------------------------
39%------------------------------------------------------------------------
40%  I - MAIN FUNCTION series
41%------------------------------------------------------------------------
42%------------------------------------------------------------------------
43function varargout = series(varargin)
44
45% Begin initialization code - DO NOT EDIT
46gui_Singleton = 1;
47gui_State = struct('gui_Name',       mfilename, ...
48                   'gui_Singleton',  gui_Singleton, ...
49                   'gui_OpeningFcn', @series_OpeningFcn, ...
50                   'gui_OutputFcn',  @series_OutputFcn, ...
51                   'gui_LayoutFcn',  [] , ...
52                   'gui_Callback',   []);
53if nargin && ischar(varargin{1})
54    gui_State.gui_Callback = str2func(varargin{1});
55end
56
57if nargout
58    [varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:});
59else
60    gui_mainfcn(gui_State, varargin{:});
61end
62% End initialization code - DO NOT EDIT
63
64%--------------------------------------------------------------------------
65% --- Executes just before series is made visible.
66%--------------------------------------------------------------------------
67function series_OpeningFcn(hObject, eventdata, handles,Param)
68
69% Choose default command line output for series
70handles.output = hObject;
71% Update handles structure
72guidata(hObject, handles);
73
74%% initial settings
75% position and  size of the GUI at opening
76set(0,'Unit','points')
77ScreenSize=get(0,'ScreenSize'); % size of the current screen, in points (1/72 inch)
78Width=900; % prefered width of the GUI in points (1/72 inch)
79Height=624; % prefered height of the GUI in points (1/72 inch)
80%adjust to screen size (reduced by a min margin)
81RescaleFactor=min((ScreenSize(3)-80)/Width,(ScreenSize(4)-80)/Height);
82if RescaleFactor>1
83    RescaleFactor=min(RescaleFactor,1);
84end
85Width=Width*RescaleFactor;
86Height=Height*RescaleFactor;
87LeftX=80*RescaleFactor; % position of the left fig side, in pixels (put to the left side, with some margin)
88LowY=round(ScreenSize(4)/2-Height/2); % put at the middle height on the screen
89set(hObject,'Units','points')
90set(hObject,'Position',[LeftX LowY Width Height])% position and size of the GUI at opening
91
92% settings of table MinIndex_j
93set(handles.MinIndex_i,'ColumnFormat',{'numeric'})
94set(handles.MinIndex_i,'ColumnEditable',false)
95set(handles.MinIndex_i,'ColumnName',{'i min'})
96set(handles.MinIndex_i,'Data',[])% initiate Data to double (not cell)
97
98% settings of table MinIndex_j
99set(handles.MinIndex_j,'ColumnFormat',{'numeric'})
100set(handles.MinIndex_j,'ColumnEditable',false)
101set(handles.MinIndex_j,'ColumnName',{'j min'})
102set(handles.MinIndex_j,'Data',[])% initiate Data to double (not cell)
103
104% settings of table MaxIndex_i
105set(handles.MaxIndex_i,'ColumnFormat',{'numeric'})
106set(handles.MaxIndex_i,'ColumnEditable',false)
107set(handles.MaxIndex_i,'ColumnName',{'i max'})
108set(handles.MaxIndex_i,'Data',[])% initiate Data to double (not cell)
109
110% settings of table MaxIndex_j
111set(handles.MaxIndex_j,'ColumnFormat',{'numeric'})
112set(handles.MaxIndex_j,'ColumnEditable',false)
113set(handles.MaxIndex_j,'ColumnName',{'j max'})
114set(handles.MaxIndex_j,'Data',[])% initiate Data to double (not cell)
115
116% settings of table PairString
117set(handles.PairString,'ColumnName',{'pairs'})
118set(handles.PairString,'ColumnEditable',false)
119set(handles.PairString,'ColumnFormat',{'char'})
120set(handles.PairString,'Data',{''})
121
122% settings of table MaskTable
123set(handles.MaskTable,'ColumnName',{'mask name'})
124set(handles.PairString,'ColumnEditable',false)
125set(handles.PairString,'ColumnFormat',{'char'})
126set(handles.PairString,'Data',{''})
127
128series_ResizeFcn(hObject, eventdata, handles)%resize table according to series GUI size
129set(hObject,'WindowButtonDownFcn',{'mouse_down'})%allows mouse action with right button (zoom for uicontrol display)
130set(hObject,'DeleteFcn',{@closefcn})%
131
132% check default input data
133if ~exist('Param','var')
134    Param=[]; % default
135end
136
137%% Read the parameter file series.xml, or created from series.xml.default if it does not exist
138SeriesData=[];
139[path_series,name,ext]=fileparts(which('series'));% path to the GUI series
140xmlfile=fullfile(path_series,'series.xml');
141if ~exist(xmlfile,'file')
142    [success,message]=copyfile(fullfile(path_series,'series.xml.default'),xmlfile);
143end
144if exist(xmlfile,'file')
145    SeriesData.SeriesParam=xml2struct(xmlfile);
146end
147
148%% list of builtin functions in the menu ActionName
149ActionList={'check_data_files';'aver_stat';'time_series';'civ_series';'merge_proj'}; % WARNING: fits with nb_builtin_ACTION=4 in ActionName_callback
150NbBuiltinAction=numel(ActionList);
151set(handles.Action,'UserData',NbBuiltinAction)
152path_series_fct=fullfile(path_series,'series');%path of the functions in subdirectroy 'series'
153[path_series,name,ext]=fileparts(which('series')); % path to the GUI series
154path_series_fct=fullfile(path_series,'series'); % path of the functions in subdirectroy 'series'
155command = ['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))") ' ...
156            'python -c "import fluidimage"'];
157[code, ~] = system(command);
158if code==0
159    ActionExtList={'.m';'.sh';'.py (in dev.)'}; % default choice of extensions (Matlab fct .m or compiled version .sh
160else
161    ActionExtList={'.m';'.sh'};  % python options not installed
162end
163ActionPathList=cell(NbBuiltinAction,1); % initiate the cell matrix of Action fct paths
164ActionPathList(:)={path_series_fct}; % set the default path to series fcts to all list members
165RunModeList={'local';'background'}; % default choice of extensions (Matlab fct .m or compiled version .sh)
166[s,w]=system('oarstat'); % look for cluster system 'oar'
167if isequal(s,0)
168    RunModeList=[RunModeList;{'cluster_oar'}];
169    set(handles.MonitorCluster,'Visible','on'); % make visible button for access to Monika
170    set(handles.num_CPUTime,'Visible','on'); % make visible button for access to Monika
171    set(handles.CPUTime_txt,'Visible','on'); % make visible button for access to Monika
172end
173[s,w]=system('qstat -help'); % look for cluster system 'sge'
174if isequal(s,0)
175    if regexp(w,'^pbs')
176        RunModeList=[RunModeList;{'cluster_pbs'}];
177    elseif regexp(w,'^SGE')
178        RunModeList=[RunModeList;{'cluster_sge'}];
179    else
180        RunModeList=[RunModeList;{'cluster_qstat_unknown'}];
181    end
182end
183set(handles.RunMode,'String',RunModeList)% display the menu of available run modes, local, background or cluster manager
184
185%% list of builtin transform functions in the menu TransformName
186TransformList={'';'sub_field';'phys';'phys_polar'}; % WARNING: must fit with the corresponding menu in uvmat and nb_builtin_transform=4 in  TransformName_callback
187NbBuiltinTransform=numel(TransformList);
188path_transform_fct=fullfile(path_series,'transform_field');
189TransformPathList=cell(NbBuiltinTransform,1); % initiate the cell matrix of Action fct paths
190TransformPathList(:)={path_transform_fct}; % set the default path to series fcts to all list members
191SeriesData.TransformPath=path_transform_fct;% store the standard path for trqnsform functions (needed for compilation)
192
193%% get the user defined functions stored in the personal file uvmat_perso.mat
194dir_perso=prefdir;
195profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
196if exist(profil_perso,'file')
197    h=load (profil_perso);
198    %get the list of previous input files in the upper bar menu Open
199    if isfield(h,'MenuFile')
200        for ifile=1:min(length(h.MenuFile),5)
201            set(handles.(['MenuFile_' num2str(ifile)]),'Label',h.MenuFile{ifile});
202            set(handles.(['MenuFile_' num2str(ifile+5)]),'Label',h.MenuFile{ifile});
203        end
204    end
205    %get the list of previous campaigns in the upper bar menu Open campaign
206    if isfield(h,'MenuCampaign')
207        for ifile=1:min(length(h.MenuCampaign),5)
208            set(handles.(['MenuCampaign_' num2str(ifile)]),'Label',h.MenuCampaign{ifile});
209        end
210    end
211    %get the menu of actions
212%     if isfield(h,'ActionExtListUser') && iscell(h.ActionExtListUser)
213%         ActionExtList=[ActionExtList; h.ActionExtListUser];
214%     end
215    if isfield(h,'ActionListUser') && iscell(h.ActionListUser) && isfield(h,'ActionPathListUser') && iscell(h.ActionPathListUser)
216        ActionList=[ActionList;h.ActionListUser];
217        ActionPathList=[ActionPathList;h.ActionPathListUser(:,1)];
218    end
219    %get the menu of transform fct
220    if isfield(h,'TransformListUser') && iscell(h.TransformListUser) && isfield(h,'TransformPathListUser') && iscell(h.TransformPathListUser)
221        TransformList=[TransformList;h.TransformListUser];
222        TransformPathList=[TransformPathList;h.TransformPathListUser];
223    end
224end
225
226%% selection of the input Action fct
227ActionCheckExist=true(size(ActionList)); % initiate the check of the path to the listed action fct
228for ilist=NbBuiltinAction+1:numel(ActionList)%check  the validity of the path of the user defined Action fct
229    ActionCheckExist(ilist)=exist(fullfile(ActionPathList{ilist},[ActionList{ilist} '.m']),'file');
230end
231ActionPathList=ActionPathList(ActionCheckExist,:); % suppress the menu options which are not valid anymore
232ActionList=ActionList(ActionCheckExist);
233set(handles.ActionName,'String',[ActionList;{'more...'}])
234set(handles.ActionName,'UserData',ActionPathList)
235ActionIndex=[];
236if isfield(Param,'ActionName')% copy the selected menu index transferred in Param from uvmat
237    ActionIndex=find(strcmp(Param.ActionName,ActionList),1);
238end
239if isempty(ActionIndex)
240    ActionIndex=1;
241end
242set(handles.ActionName,'Value',ActionIndex)
243set(handles.ActionPath,'String',ActionPathList{ActionIndex})
244set(handles.ActionExt,'Value',1)
245set(handles.ActionExt,'String',ActionExtList)
246
247%% selection of the input transform fct
248TransformCheckExist=true(size(TransformList));
249for ilist=NbBuiltinTransform+1:numel(TransformList)
250    TransformCheckExist(ilist)=exist(fullfile(TransformPathList{ilist},[TransformList{ilist} '.m']),'file');
251end
252TransformPathList=TransformPathList(TransformCheckExist);
253TransformList=TransformList(TransformCheckExist);
254set(handles.TransformName,'String',[TransformList;{'more...'}])
255set(handles.TransformName,'UserData',TransformPathList)
256TransformIndex=[];
257if isfield(Param,'TransformName')% copy the selected menu index transferred in Param from uvmat
258    TransformIndex=find(strcmp(Param.TransformName,TransformList),1);
259end
260if isempty(TransformIndex)
261    TransformIndex=1;
262end
263set(handles.TransformName,'Value',TransformIndex)
264set(handles.TransformPath,'String',TransformPathList{TransformIndex})
265   
266%% fields input initialisation
267if isfield(Param,'list_fields')&& isfield(Param,'index_fields') &&~isempty(Param.list_fields) &&~isempty(Param.index_fields)
268    set(handles.FieldName,'String',Param.list_fields); % list menu fields
269    set(handles.FieldName,'Value',Param.index_fields); % selected string index
270end
271if isfield(Param,'Coordinates')
272    if isfield(Param.Coordinates,'Coord_x')
273        set(handles.Coord_x,'String',Param.Coordinates.Coord_x)
274    end
275    if isfield(Param.Coordinates,'Coord_y')
276        set(handles.Coord_y,'String',Param.Coordinates.Coord_y)
277    end
278    if isfield(Param.Coordinates,'Coord_z')
279        set(handles.Coord_z,'String',Param.Coordinates.Coord_z)
280    end
281end
282% if isfield(Param,'Coord_x_str') && ischar(Param.Coord_x_str)
283%         set(handles.Coord_x,'String',Param.Coord_x_str); % list menu fields
284% end
285% if isfield(Param,'Coord_y_str')&& ischar(Param.Coord_y_str)
286%         set(handles.Coord_y,'String',Param.Coord_y_str); % list menu fields
287% end
288
289%% introduce the input file name(s) if defined from input Param,
290set(handles.series,'UserData',SeriesData)% initiate Userdata
291if isfield(Param,'InputFile')
292   
293    %% fill the list of file series
294    InputTable=[{Param.InputFile.RootPath},{Param.InputFile.SubDir},{Param.InputFile.RootFile},{Param.InputFile.NomType},{Param.InputFile.FileExt}];
295    if isempty(find(cellfun('isempty',InputTable)==0)); % if there is no input file, do not introduce input info
296        set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH button to magenta color to indicate that input refresh is needed
297        return
298    end
299    TimeTable=[{Param.InputFile.TimeName},{[]},{[]},{[]},{[]}];
300    if isfield(Param.InputFile,'RootPath_1')
301        InputTable=[InputTable;[{Param.InputFile.RootPath_1},{Param.InputFile.SubDir_1},{Param.InputFile.RootFile_1},{Param.InputFile.NomType_1},{Param.InputFile.FileExt_1}]];
302        TimeTable=[TimeTable; [{Param.InputFile.TimeName_1},{[]},{[]},{[]},{[]}]];
303    end
304    set(handles.InputTable,'Data',InputTable)
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=fullfile(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
501
502OutPut=browse_data(oldfile,'on','on'); % open the GUI browse_data to get select a campaign dir, experiment and device
503NbLines=numel(OutPut.Experiment)*numel(OutPut.DataSeries);
504icount=0;
505for iexp=1:numel(OutPut.Experiment)
506    for idevice=1:numel(OutPut.DataSeries)
507        icount=icount+1;
508        InputTable{icount,1}=fullfile(OutPut.Campaign,OutPut.Experiment{iexp});
509        InputTable{icount,2}=OutPut.DataSeries{idevice};
510        if isempty(InputTable{icount,3})
511            if icount>1
512            InputTable{icount,3}=InputTable{icount-1,3};
513            else
514                InputTable{icount,3}='';
515            end
516        end
517        if isempty(InputTable{icount,4})
518            if icount>1
519            InputTable{icount,4}=InputTable{icount-1,4};
520            else
521                InputTable{icount,4}='';
522            end
523        end
524                if isempty(InputTable{icount,5})
525            if icount>1
526            InputTable{icount,5}=InputTable{icount-1,5};
527            else
528                InputTable{icount,5}='';
529            end
530        end
531    end
532end
533if size(InputTable,1)>icount
534    InputTable(icount+1:size(InputTable,1),:)=[];
535end
536set(handles.InputTable,'Data',InputTable)
537REFRESH_Callback(hObject, eventdata, handles)
538
539% --------------------------------------------------------------------
540function MenuCampaign_Callback(hObject, eventdata, handles)
541% --------------------------------------------------------------------
542
543OutPut=browse_data(get(hObject,'Label'),'on','on'); % open the GUI browse_data to get select a campaign dir, experiment and device
544if ~isfield(OutPut,'Campaign')
545    return
546end
547NbLines=numel(OutPut.Experiment)*numel(OutPut.DataSeries);
548icount=0;
549InputTable=get(handles.InputTable,'Data');
550for 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
577end
578if size(InputTable,1)>icount
579    InputTable(icount+1:size(InputTable,1),:)=[];
580end
581set(handles.InputTable,'Data',InputTable)
582REFRESH_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%------------------------------------------------------------------------
618InputTable=get(handles.InputTable,'Data');
619set(handles.series,'Pointer','watch') % set the mouse pointer to 'watch'
620set(handles.REFRESH,'BackgroundColor',[1 1 0])% set REFRESH  button to yellow color (indicate activation)
621drawnow
622empty_line=false(size(InputTable,1),1);
623for iline=1:size(InputTable,1)
624    empty_line(iline)= isempty(cell2mat(InputTable(iline,1:3)));
625end
626if ~isempty(find(empty_line));
627    InputTable(empty_line,:)=[]; % remove empty lines
628    set(handles.InputTable,'Data',InputTable)
629    ListTable={'MinIndex_i','MaxIndex_i','MinIndex_j','MaxIndex_j','PairString','TimeTable'};
630    for ilist=1:numel(ListTable)
631        Table=get(handles.(ListTable{ilist}),'Data');
632        Table(empty_line,:)=[]; % remove empty lines
633        set(handles.(ListTable{ilist}),'Data',Table);
634    end
635    set(handles.series,'UserData',[])%refresh the stored info
636end
637nbview=size(InputTable,1);
638for iview=1:nbview
639    RootPath=fullfile(InputTable{iview,1},InputTable{iview,2});
640    if ~exist(RootPath,'dir')
641        i1_series=[];
642        RootFile='';
643    else %scan the input folder
644        InputTable{iview,3}=regexprep(InputTable{iview,3},'^/','');
645            [RootPath,~,RootFile,i1_series,i2_series,j1_series,j2_series,tild,FileInfo,MovieObject]=...
646                find_file_series(fullfile(InputTable{iview,1},InputTable{iview,2}),[InputTable{iview,3} InputTable{iview,4} InputTable{iview,5}]);
647    end
648    % if no file is found, open a browser
649    if isempty(RootFile)&& isempty(i1_series)
650        fileinput=uigetfile_uvmat(['wrong input at line ' num2str(iview) ':pick a new input file'],RootPath);
651        if isempty(fileinput)
652            set(handles.REFRESH,'BackgroundColor',[1 0 0])% set REFRESH  back to red color
653            return
654        else
655            display_file_name(handles,fileinput,iview)
656        end
657    else
658       update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileInfo,MovieObject,iview)
659    end
660end
661
662%% update MinIndex_i and MaxIndex_i if the input table content has been reduced in line nbre
663MinIndex_i_table=get(handles.MinIndex_i,'Data'); % retrieve the min indices in the table MinIndex
664set(handles.MinIndex_i,'Data',MinIndex_i_table(1:nbview,:));
665MinIndex_j_table=get(handles.MinIndex_j,'Data'); % retrieve the min indices in the table MinIndex
666set(handles.MinIndex_j,'Data',MinIndex_j_table(1:nbview,:));
667MaxIndex_i_table=get(handles.MaxIndex_i,'Data'); % retrieve the min indices in the table MinIndex
668
669set(handles.MaxIndex_i,'Data',MaxIndex_i_table(1:nbview,:));
670MaxIndex_j_table=get(handles.MaxIndex_j,'Data'); % retrieve the min indices in the table MinIndex
671set(handles.MaxIndex_j,'Data',MaxIndex_j_table(1:nbview,:));
672PairString=get(handles.PairString,'Data'); % retrieve the min indices in the table MinIndex
673set(handles.PairString,'Data',PairString(1:nbview,:));
674TimeTable=get(handles.TimeTable,'Data'); % retrieve the min indices in the table MinIndex
675set(handles.TimeTable,'Data',TimeTable(1:nbview,:));
676
677%% set length of waitbar
678displ_time(handles)
679set(handles.REFRESH,'BackgroundColor',[1 0 0])% set REFRESH  button to red color (indicate activation finished)
680set(handles.series,'Pointer','arrow') % set the mouse pointer to 'watch'
681
682%% enable field and veltype menus, in accordance with the current action
683ActionInput_Callback([],[], handles)
684
685
686%------------------------------------------------------------------------
687% --- Function called when a new file is opened, either by series_OpeningFcn or by the browser
688%------------------------------------------------------------------------
689% INPUT:
690% handles: handles of elements in the GUI
691% Param: structure of input parameters, including  input file name and path
692% iview: line index in the input table
693%       or 'one': refresh the list
694%         'append': add a new line to the input table
695function errormsg=display_file_name(handles,Param,iview)
696 
697set(handles.REFRESH,'BackgroundColor',[1 1 0])% set REFRESH  button to yellow color (indicate activation)
698drawnow
699errormsg=''; % default
700if ischar(Param)
701    fileinput=Param;
702else% input set when series is opened (called by the GUI uvmat)
703    fileinput=Param.FileName;
704end
705   
706%% get the input root name, indices, file extension and nomenclature NomType
707if ~exist(fileinput,'file')
708    errormsg=['input file ' fileinput  ' does not exist'];
709    msgbox_uvmat('ERROR',errormsg)
710    set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH  button to magenta color (refresh still needed)
711    return
712end
713
714%% detect root name, nomenclature and indices in the input file name:
715[FilePath,FileName,FileExt]=fileparts(fileinput);
716%%%%%%%%%%%%%%%%%%
717%TODO: case of input by uvmat: do not check agai the input seies %%%%%%%
718%%%%%%%%%%%%%%%%%%%
719% detect the file type, get the movie object if relevant, and look for the corresponding file series:
720% the root name and indices may be corrected by including the first index i1 if a corresponding xml file exists
721[RootPath,SubDir,RootFile,i1_series,i2_series,j1_series,j2_series,NomType,FileInfo,MovieObject,i1,i2,j1,j2]=find_file_series(FilePath,[FileName FileExt]);
722FileType=FileInfo.FileType;
723if isempty(RootFile)&&isempty(i1_series)
724    errormsg='no input file in the series';
725    msgbox_uvmat('ERROR',errormsg)
726    set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH  button to magenta color (end of activation)
727    return
728end
729if strcmp(FileType,'txt')
730    edit(fileinput)
731    set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH  button to  magenta color (end of activation)
732    return
733elseif strcmp(FileType,'xml')
734    editxml(fileinput)
735    set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH  button to magenta  color (end of activation)
736     return
737elseif strcmp(FileType,'figure')
738    open(fileinput)
739    set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH  button to magenta  color (end of activation)
740     return
741end
742
743%% enable other menus and uicontrols
744% set(handles.MenuOpenCampaign,'Enable','on')
745set(handles.MenuCampaign_1,'Enable','on')
746set(handles.MenuCampaign_2,'Enable','on')
747set(handles.MenuCampaign_3,'Enable','on')
748set(handles.MenuCampaign_4,'Enable','on')
749set(handles.MenuCampaign_5,'Enable','on')
750set(handles.RUN, 'Enable','On')
751set(handles.RUN,'BackgroundColor',[1 0 0])% set RUN button to red
752set(handles.InputTable,'BackgroundColor',[1 1 0]) % set RootPath edit box  to yellow
753drawnow
754
755
756%% fill the list of file series
757InputTable=get(handles.InputTable,'Data');
758SeriesData=get(handles.series,'UserData');
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
761%     InputTable(iview,:)=[{RootPath},{SubDir},{RootFile},{NomType},{FileExt}];
762elseif strcmp(iview,'one') % refresh the list of  input  file series
763    iview=1; % the first line in InputTable becomes the current line
764    InputTable={'','','','',''};
765%     InputTable(iview,:)=[{RootPath},{SubDir},{RootFile},{NomType},{FileExt}];
766    set(handles.TimeTable,'Data',[{''},{[]},{[]},{[]},{[]}])
767    set(handles.MinIndex_i,'Data',[])
768    set(handles.MaxIndex_i,'Data',[])
769    set(handles.MinIndex_j,'Data',[])
770    set(handles.MaxIndex_j,'Data',[])
771    set(handles.PairString,'Data',{''})
772    SeriesData.CheckPair=0; % reset the list of input lines with pairs
773    SeriesData.i1_series={};
774    SeriesData.i2_series={};
775    SeriesData.j1_series={};
776    SeriesData.j2_series={};
777    SeriesData.FileType={};
778    SeriesData.FileInfo={};
779    SeriesData.Time={};
780end
781if isfield(SeriesData,'i1_series')
782    SeriesData.i1_series(iview+1:end)=[];
783    SeriesData.i2_series(iview+1:end)=[];
784    SeriesData.j1_series(iview+1:end)=[];
785    SeriesData.j2_series(iview+1:end)=[];
786    SeriesData.FileType(iview+1:end)=[];
787    SeriesData.FileInfo(iview+1:end)=[];
788    SeriesData.Time(iview+1:end)=[];
789end
790InputTable(iview,:)=[{RootPath},{SubDir},{RootFile},{NomType},{FileExt}];
791if iview >1
792    set(handles.InputLine,'String',num2str(iview))
793end
794set(handles.InputTable,'Data',InputTable)
795
796%% determine the selected reference field indices for pair display
797if isempty(i1)
798    i1=1;
799end
800if isempty(i2)
801    i2=i1;
802end
803ref_i=floor((i1+i2)/2); % reference image number corresponding to the file
804% set(handles.num_ref_i,'String',num2str(ref_i));
805if isempty(j1)
806    j1=1;
807end
808if isempty(j2)
809    j2=j1;
810end
811ref_j=floor((j1+j2)/2); % reference image number corresponding to the file
812SeriesData.ref_i=ref_i;
813SeriesData.ref_j=ref_j;
814
815%% update first and last indices if they do not exist
816Param=read_GUI(handles.series);
817first_j=[];
818if isfield(Param.IndexRange,'first_j'); first_j=Param.IndexRange.first_j; end
819last_j=[];
820if isfield(Param.IndexRange,'last_j'); last_j=Param.IndexRange.last_j; end
821PairString='';
822if isfield(Param.IndexRange,'PairString'); PairString=Param.IndexRange.PairString; end
823[i1,i2,j1,j2] = get_file_index(Param.IndexRange.first_i,first_j,PairString);
824FirstFileName=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},...
825    Param.InputTable{1,5},Param.InputTable{1,4},i1,i2,j1,j2);
826if ~exist(FirstFileName,'file')
827    set(handles.num_first_i,'String',num2str(ref_i))
828    set(handles.num_first_j,'String',num2str(ref_j))
829end
830[i1,i2,j1,j2] = get_file_index(Param.IndexRange.last_i,last_j,PairString);
831LastFileName=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},...
832    Param.InputTable{1,5},Param.InputTable{1,4},i1,i2,j1,j2);
833if ~exist(LastFileName,'file')
834    set(handles.num_last_i,'String',num2str(ref_i))
835    set(handles.num_last_j,'String',num2str(ref_j))
836end
837
838%% update the list of recent files in the menubar and save it for future opening
839MenuFile=[{get(handles.MenuFile_1,'Label')};{get(handles.MenuFile_2,'Label')};...
840    {get(handles.MenuFile_3,'Label')};{get(handles.MenuFile_4,'Label')};{get(handles.MenuFile_5,'Label')}];
841str_find=strcmp(fileinput,MenuFile);
842if isempty(find(str_find,1))
843    MenuFile=[{fileinput};MenuFile]; % insert the current file if not already in the list
844end
845for ifile=1:min(length(MenuFile),5)
846    eval(['set(handles.MenuFile_' num2str(ifile) ',''Label'',MenuFile{ifile});'])
847end
848dir_perso=prefdir;
849profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
850if exist(profil_perso,'file')
851    save (profil_perso,'MenuFile','-append'); % store the file names for future opening of uvmat
852else
853    save (profil_perso,'MenuFile','-V6'); % store the file names for future opening of uvmat
854end
855% save the opened file to initiate future opening
856SeriesData.RefFile{iview}=fileinput; % reference opening file for line iview
857SeriesData.Ref_i1=i1;
858SeriesData.Ref_i2=i2;
859SeriesData.Ref_j1=j1;
860SeriesData.Ref_j2=j2;
861set(handles.series,'UserData',SeriesData)
862
863set(handles.InputTable,'BackgroundColor',[1 1 1])
864
865%% initiate input file series and refresh the current field view:     
866update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileInfo,MovieObject,iview);
867%% enable field and veltype menus, in accordance with the current action
868ActionName_Callback([],[], handles)
869
870%% set length of waitbar
871displ_time(handles)
872
873set(handles.REFRESH,'BackgroundColor',[1 0 0])% set REFRESH  button to red color (end of activation)
874
875%------------------------------------------------------------------------
876% --- Update information about a new field series (indices to scan, timing,
877%     calibration from an xml file
878function update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileInfo,VideoObject,iview)
879%------------------------------------------------------------------------
880InputTable=get(handles.InputTable,'Data');
881
882%% display the min and max indices for the whole file series
883if size(i1_series,2)==2 && min(min(i1_series(:,1,:)))==0
884    MinIndex_j=1; % index j set to 1 by default
885    MaxIndex_j=1;
886    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)
887    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)
888else
889    ref_i=squeeze(max(i1_series(1,:,:),[],2)); % select ref_j index for each ref_i
890    ref_j=squeeze(max(j1_series(1,:,:),[],3)); % select ref_i index for each ref_j
891     MinIndex_i=min(find(ref_i))-1;
892     MaxIndex_i=max(find(ref_i))-1;
893     MaxIndex_j=max(find(ref_j))-1;
894     MinIndex_j=min(find(ref_j))-1;
895    diff_j_max=diff(ref_j);
896    diff_i_max=diff(ref_i);
897    if ~isempty(diff_i_max) && isequal (diff_i_max,diff_i_max(1)*ones(size(diff_i_max)))
898        set(handles.num_incr_i,'String',num2str(diff_i_max(1)))% detect an increment to dispaly by default
899    end
900    if ~isempty(diff_j_max) && isequal (diff_j_max,diff_j_max(1)*ones(size(diff_j_max)))
901        set(handles.num_incr_j,'String',num2str(diff_j_max(1)))
902    end
903end
904if isequal(MinIndex_i,-1)
905    MinIndex_i=0;
906end
907if isequal(MinIndex_j,-1)
908    MinIndex_j=0;
909end
910MinIndex_i_table=get(handles.MinIndex_i,'Data'); % retrieve the min indices in the table MinIndex
911MinIndex_j_table=get(handles.MinIndex_j,'Data'); % retrieve the min indices in the table MinIndex
912MaxIndex_i_table=get(handles.MaxIndex_i,'Data'); % retrieve the min indices in the table MinIndex
913MaxIndex_j_table=get(handles.MaxIndex_j,'Data'); % retrieve the min indices in the table MinIndex
914if ~isempty(MinIndex_i)&&~isempty(MaxIndex_i)
915    MinIndex_i_table(iview,1)=MinIndex_i;
916    MaxIndex_i_table(iview,1)=MaxIndex_i;
917end
918if ~isempty(MinIndex_j)&&~isempty(MaxIndex_j)
919    MinIndex_j_table(iview,1)=MinIndex_j;
920    MaxIndex_j_table(iview,1)=MaxIndex_j;
921end
922set(handles.MinIndex_i,'Data',MinIndex_i_table)%display the min indices in the table MinIndex
923set(handles.MinIndex_j,'Data',MinIndex_j_table)%display the max indices in the table MaxIndex
924set(handles.MaxIndex_i,'Data',MaxIndex_i_table)%display the min indices in the table MinIndex
925set(handles.MaxIndex_j,'Data',MaxIndex_j_table)%display the max indices in the table MaxIndex
926SeriesData=get(handles.series,'UserData');
927
928%% adjust the first and last indices for the selected series, only if requested by the bounds
929% i index, compare input to min index i
930first_i=str2num(get(handles.num_first_i,'String')); % retrieve previous first i
931% ref_i=str2num(get(handles.num_ref_i,'String')); % index i given by the input field
932ref_i=1;
933if isfield(SeriesData,'ref_i')
934    ref_i=SeriesData.ref_i;
935end
936if isempty(first_i)
937    first_i=ref_i; % first_i updated by the input value
938elseif first_i < MinIndex_i
939    first_i=MinIndex_i; % first_i set to the min i index (restricted by oter input lines)
940elseif first_i >MaxIndex_i
941    first_i=MaxIndex_i; % first_i set to the max i index (restricted by oter input lines)
942end
943% j index,  compare input to min index j
944first_j=str2num(get(handles.num_first_j,'String'));
945ref_j=1;
946if isfield(SeriesData,'ref_j')
947    ref_j=SeriesData.ref_j;
948end
949if isempty(first_j)
950    first_j=ref_j; % first_j updated by the input value
951elseif first_j<MinIndex_j
952    first_j=MinIndex_j; % first_j set to the min j index (restricted by oter input lines)
953elseif first_j >MaxIndex_j
954    first_j=MaxIndex_j; % first_j set to the max j index (restricted by oter input lines)
955end
956% i index, compare input to max index i
957last_i=str2num(get(handles.num_last_i,'String'));
958if isempty(last_i)
959    last_i=ref_i;
960elseif last_i > MaxIndex_i
961    last_i=MaxIndex_i;
962elseif last_i<first_i
963    last_i=first_i;
964end
965% j index, compare input to max index j
966last_j=str2num(get(handles.num_last_j,'String'));
967if isempty(last_j)
968    last_j=ref_j;
969elseif last_j>MaxIndex_j
970    last_j=MaxIndex_j;
971elseif last_j<first_j
972    last_j=first_j;
973end
974set(handles.num_first_i,'String',num2str(first_i));
975set(handles.num_first_j,'String',num2str(first_j));
976set(handles.num_last_i,'String',num2str(last_i));
977set(handles.num_last_j,'String',num2str(last_j));
978
979%% number of slices set by default
980NbSlice=[]; % default
981% read  value set by the first series for the append mode (iwiew >1)
982if iview>1 && strcmp(get(handles.num_NbSlice,'Visible'),'on')
983    NbSlice=str2double(get(handles.num_NbSlice,'String'));
984end
985
986%% default time settings
987TimeUnit='';
988% read  value set by the first series for the append mode (iwiew >1)
989if iview>1
990    TimeUnit=get(handles.TimeUnit,'String');
991end
992TimeName='';
993Time=[]; % default
994TimeMin=[];
995TimeFirst=[];
996TimeLast=[];
997TimeMax=[];
998
999%%  read image documentation file if found
1000XmlData=[];
1001check_calib=0;
1002XmlFileName=find_imadoc(InputTable{iview,1},InputTable{iview,2},InputTable{iview,3},InputTable{iview,5});
1003if ~isempty(XmlFileName)
1004    [XmlData,errormsg]=imadoc2struct(XmlFileName);
1005    if ~isempty(errormsg)
1006        msgbox_uvmat('WARNING',['error in reading ' XmlFileName ': ' errormsg]);
1007    end
1008    % read time if available
1009    if isfield(XmlData,'Time')
1010        Time=XmlData.Time;
1011        TimeName='xml';
1012    end
1013    if isfield(XmlData,'Camera')
1014        if isfield(XmlData.Camera,'TimeUnit')&& ~isempty(XmlData.Camera.TimeUnit)
1015            if iview>1 && ~isempty(TimeUnit) && ~strcmp(TimeUnit,XmlData.Camera.TimeUnit)
1016                msgbox_uvmat('WARNING','inconsistent time unit with the first field series');
1017            end
1018            TimeUnit=XmlData.Camera.TimeUnit;
1019        end
1020    end
1021    % number of slices
1022    if isfield(XmlData,'TranslationMotor')&& isfield(XmlData.TranslationMotor,'NbSlice')
1023        NbSlice_motor=XmlData.TranslationMotor.NbSlice;
1024        if ~isempty(NbSlice) && ~isequal(NbSlice_motor,NbSlice)
1025                msgbox_uvmat('WARNING','inconsistent Z numbers of Z indices');
1026        else
1027            NbSlice=NbSlice_motor;
1028        end
1029    end
1030   
1031%     if isfield(XmlData,'GeometryCalib')
1032%         check_calib=1;
1033%         if isfield(XmlData.GeometryCalib,'SliceCoord')
1034%             siz=size(XmlData.GeometryCalib.SliceCoord);
1035%             if ~isempty(NbSlice)&& ~isequal(size(1),NbSlice)
1036%                 msgbox_uvmat('WARNING','inconsistent numbers of Z indices between motor and calibration');
1037%             else
1038%                 NbSlice=siz(1);
1039%             end
1040%         end
1041%     end
1042end
1043if ~isempty(NbSlice)
1044set(handles.num_NbSlice,'String',num2str(NbSlice))
1045set(handles.num_NbSlice,'Visible','on')
1046end
1047
1048%% read timing  from the current file (prioritary)
1049if ~isempty(VideoObject)% case of movies
1050    imainfo=get(VideoObject);
1051    if isempty(j1_series); % frame index along i
1052        Time=zeros(imainfo.NumberOfFrames+1,2);
1053        Time(:,2)=(0:1/imainfo.FrameRate:(imainfo.NumberOfFrames)/imainfo.FrameRate)';
1054    else
1055        Time=[0;ones(size(i1_series,3)-1,1)]*(0:1/imainfo.FrameRate:(imainfo.NumberOfFrames)/imainfo.FrameRate);
1056    end
1057    TimeName='video';
1058end
1059
1060
1061%% determine the min and max times: case of Netcdf files will be treated later in FieldName_Callback
1062if ~isempty(TimeName)
1063    TimeMin=Time(MinIndex_i+1,MinIndex_j+1);
1064    if size(Time)>=[first_i+1 first_j+1]
1065        TimeFirst=Time(first_i+1,first_j+1);
1066    end
1067    if size(Time)>=[last_i+1 last_j+1]
1068        TimeLast=Time(last_i+1,last_j+1);
1069    end
1070    if size(Time)>=[MaxIndex_i+1 MaxIndex_j+1];
1071        TimeMax=Time(MaxIndex_i+1,MaxIndex_j+1);
1072    end
1073end
1074
1075%% update the time table
1076TimeTable=get(handles.TimeTable,'Data');
1077TimeTable{iview,1}=TimeName;
1078TimeTable{iview,2}=TimeMin;
1079TimeTable{iview,3}=TimeFirst;
1080TimeTable{iview,4}=TimeLast;
1081TimeTable{iview,5}=TimeMax;
1082set(handles.TimeTable,'Data',TimeTable)
1083
1084%% update the series info in 'UserData'
1085SeriesData.i1_series{iview}=i1_series;
1086SeriesData.i2_series{iview}=i2_series;
1087SeriesData.j1_series{iview}=j1_series;
1088SeriesData.j2_series{iview}=j2_series;
1089SeriesData.FileType{iview}=FileInfo.FileType;
1090SeriesData.FileInfo{iview}=FileInfo;
1091SeriesData.Time{iview}=Time;
1092
1093SeriesData.TimeName=TimeName;
1094
1095if check_calib
1096    SeriesData.GeometryCalib{iview}=XmlData.GeometryCalib;
1097end
1098set(handles.series,'UserData',SeriesData)
1099
1100%% update pair menus
1101hset_pair=findobj(allchild(0),'Tag','set_pairs');
1102if ~isempty(hset_pair), delete(hset_pair); end % delete the GUI set_pair if opened
1103CheckPair= ~isempty(i2_series)||~isempty(j2_series); % check whether index pairs need to be defined
1104PairString=get(handles.PairString,'Data');
1105if CheckPair% if pairs need to be display for line iview
1106    [ModeMenu,ModeValue]=update_mode(i1_series,i2_series,j2_series);
1107    Menu=update_listpair(i1_series,i2_series,j1_series,j2_series,ModeMenu{ModeValue},Time,TimeUnit,ref_i,ref_j,TimeName,InputTable(iview,:),FileInfo);
1108    PairString{iview,1}=Menu{1};
1109else
1110    PairString{iview,1}=''; % no pair for #iview
1111end
1112set(handles.PairString,'Data',PairString)
1113if isempty(find(cellfun('isempty',get(handles.PairString,'Data'))==0, 1))% if all lines of pairs are empty
1114    set(handles.PairString,'Visible','off')
1115    set(handles.SetPairs,'Visible','off')
1116else
1117    set(handles.PairString,'Visible','on')
1118    set(handles.SetPairs,'Visible','on')
1119end
1120
1121
1122%% display the set of existing files as an image
1123set(handles.FileStatus,'Units','pixels')
1124Position=get(handles.FileStatus,'Position');
1125set(handles.FileStatus,'Units','normalized')
1126%xI=0.5:Position(3)-0.5;
1127nbview=numel(SeriesData.i1_series);
1128j_max=cell(1,nbview);
1129MaxIndex_i=ones(1,nbview); % default
1130MinIndex_i=ones(1,nbview); % default
1131for iline=1:nbview
1132    pair_max=squeeze(max(SeriesData.i1_series{iline},[],1)); % max on pair index
1133    j_max{iline}=max(pair_max,[],1); % max on j index
1134    if ~isempty(j_max{iline})
1135    MaxIndex_i(iline)=max(find(j_max{iline}))-1; % max ref index i
1136    MinIndex_i(iline)=min(find(j_max{iline}))-1; % min ref index i
1137    end
1138end
1139MinIndex_i=min(MinIndex_i);
1140MaxIndex_i=max(MaxIndex_i);
1141range_index=MaxIndex_i-MinIndex_i+1;
1142range_y=max(1,floor(Position(4)/nbview));
1143npx=floor(Position(3));
1144file_indices=MinIndex_i+floor(((0.5:npx-0.5)/npx)*range_index)+1;
1145CData=zeros(nbview*range_y,npx); % initiate the image representing the existing files
1146for iline=1:nbview
1147    ind_y=1+(iline-1)*range_y:iline*range_y;
1148    LineData=zeros(size(file_indices));
1149    file_select=file_indices(file_indices<=numel(j_max{iline}));
1150    ind_select=find(file_indices<=numel(j_max{iline}));
1151    LineData(ind_select)=j_max{iline}(file_select)~=0;
1152    CData(ind_y,:)=ones(size(ind_y'))*LineData;
1153end
1154CData=cat(3,zeros(size(CData)),CData,zeros(size(CData))); % make color images r=0,g,b=0
1155set(handles.FileStatus,'CData',CData);
1156
1157%-----------------------------------------------------------guide -------------
1158%------------------------------------------------------------------------
1159%  III - FUNCTIONS ASSOCIATED TO THE FRAME IndexRange
1160%------------------------------------------------------------------------
1161
1162
1163% ---- determine the menu to put in mode and advice a default choice
1164%------------------------------------------------------------------------
1165function [ModeMenu,ModeValue]=update_mode(i1_series,i2_series,j2_series)
1166%------------------------------------------------------------------------   
1167ModeMenu={''};
1168if isempty(j2_series)% no j pair
1169    ModeValue=1;
1170    if ~isempty(i2_series)
1171        ModeMenu={'series(Di)'}; % pair menu with only option Di
1172    end
1173else %existence of j pairs
1174    pair_max=squeeze(max(i1_series,[],1)); % max on pair index
1175    j_max=max(pair_max,[],1);
1176    MaxIndex_i=find(j_max, 1, 'last' )-1; % max ref index i
1177    MinIndex_i=find(j_max, 1 )-1; % min ref index i
1178    i_max=max(pair_max,[],2);
1179    MaxIndex_j=find(i_max, 1, 'last' )-1; % max ref index i
1180    MinIndex_j=find(i_max, 1 )-1; % min ref index i
1181    if MaxIndex_j==MinIndex_j
1182        ModeValue=1;
1183        ModeMenu={'bursts'};
1184    elseif MaxIndex_i==MinIndex_i
1185        ModeValue=1;
1186        ModeMenu={'series(Dj)'};
1187    else
1188        ModeMenu={'bursts';'series(Dj)'};
1189        if (MaxIndex_j-MinIndex_j)>10
1190            ModeValue=2; % set mode to series(Dj) if more than 10 j values
1191        else
1192            ModeValue=1;
1193        end
1194    end
1195end
1196
1197
1198%------------------------------------------------------------------------
1199function displ_pair=update_listpair(i1_series,i2_series,j1_series,j2_series,mode,time,TimeUnit,ref_i,ref_j,TimeName,InputTable,FileInfo)
1200%------------------------------------------------------------------------
1201displ_pair={};
1202if isempty(TimeUnit)
1203    dtunit='e-03';
1204else
1205    dtunit=['m' TimeUnit];
1206end
1207switch mode
1208    case 'series(Di)'
1209        diff_i=i2_series-i1_series;
1210        min_diff=min(diff_i(diff_i>0));
1211        max_diff=max(diff_i(diff_i>0));
1212        for ipair=min_diff:max_diff
1213            if numel(diff_i(diff_i==ipair))>0
1214                pair_string=['Di= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2)) ];
1215                if ~isempty(time)
1216                    if ref_i<=floor(ipair/2)
1217                        ref_i=floor(ipair/2)+1; % shift ref_i to get the first pair
1218                    end
1219                    Dt=time(ref_i+ceil(ipair/2),ref_j)-time(ref_i-floor(ipair/2),ref_j);
1220                    pair_string=[pair_string ', Dt=' num2str(Dt) ' ' dtunit];
1221                end
1222                displ_pair=[displ_pair;{pair_string}];
1223            end
1224        end
1225        if ~isempty(displ_pair)
1226            displ_pair=[displ_pair;{'Di=*|*'}];
1227        end
1228    case 'series(Dj)'
1229        if isempty(j2_series)
1230            msgbox_uvmat('ERROR','no j1-j2 pair available')
1231            return
1232        end
1233        diff_j=j2_series-j1_series;
1234        min_diff=min(diff_j(diff_j>0));
1235        max_diff=max(diff_j(diff_j>0));
1236        for ipair=min_diff:max_diff
1237            if numel(diff_j(diff_j==ipair))>0
1238                pair_string=['Dj= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2)) ];
1239                if ~isempty(time)
1240                    if ref_j<=floor(ipair/2)
1241                        ref_j=floor(ipair/2)+1; % shift ref_i to get the first pair
1242                    end
1243                    Dt=time(ref_i,ref_j+ceil(ipair/2))-time(ref_i,ref_j-floor(ipair/2));
1244                    pair_string=[pair_string ', Dt=' num2str(Dt) ' ' dtunit];
1245                end
1246                displ_pair=[displ_pair;{pair_string}];
1247            end
1248        end
1249        if ~isempty(displ_pair)
1250            displ_pair=[displ_pair;{'Dj=*|*'}];
1251        end
1252    case 'bursts'
1253        if isempty(j2_series)
1254            msgbox_uvmat('ERROR','no j1-j2 pair available')
1255            return
1256        end
1257        %diff_j=j2_series-j1_series;
1258        min_j1=min(j1_series(j1_series>0));
1259        max_j1=max(j1_series(j1_series>0));
1260        min_j2=min(j2_series(j2_series>0));
1261        max_j2=max(j2_series(j2_series>0));
1262        for pair1=min_j1:min(max_j1,min_j1+20)
1263            for pair2=min_j2:min(max_j2,min_j2+20)
1264                if numel(j1_series(j1_series==pair1))>0 && numel(j2_series(j2_series==pair2))>0
1265                    pair_string=['j= ' num2str(pair1) '-' num2str(pair2)];
1266                    [TimeValue,DtValue]=get_time(ref_i,[],pair_string,InputTable,FileInfo,TimeName,'Dt');
1267                    %Dt=time(ref_i,pair2+1)-time(ref_i,pair1+1);
1268                    pair_string=[pair_string ', Dt=' num2str(DtValue) ' ' dtunit];
1269                    displ_pair=[displ_pair;{pair_string}];
1270                end
1271            end
1272        end
1273        if ~isempty(displ_pair)
1274            displ_pair=[displ_pair;{'j=*-*'}];
1275        end
1276end
1277
1278%------------------------------------------------------------------------
1279function num_first_i_Callback(hObject, eventdata, handles)
1280%------------------------------------------------------------------------
1281num_last_i_Callback(hObject, eventdata, handles)
1282
1283%------------------------------------------------------------------------
1284function num_last_i_Callback(hObject, eventdata, handles)
1285%------------------------------------------------------------------------
1286SeriesData=get(handles.series,'UserData');
1287if ~isfield(SeriesData,'Time')
1288    SeriesData.Time{1}=[];
1289end
1290displ_time(handles);
1291
1292%------------------------------------------------------------------------
1293function num_first_j_Callback(hObject, eventdata, handles)
1294%------------------------------------------------------------------------
1295 num_last_j_Callback(hObject, eventdata, handles)
1296
1297%------------------------------------------------------------------------
1298function num_last_j_Callback(hObject, eventdata, handles)
1299%------------------------------------------------------------------------
1300% first_j=str2num(get(handles.num_first_j,'String'));
1301% last_j=str2num(get(handles.num_last_j,'String'));
1302% ref_j=ceil((first_j+last_j)/2);
1303% set(handles.num_ref_j,'String', num2str(ref_j))
1304% num_ref_j_Callback(hObject, eventdata, handles)
1305SeriesData=get(handles.series,'UserData');
1306if ~isfield(SeriesData,'Time')
1307    SeriesData.Time{1}=[];
1308end
1309displ_time(handles);
1310
1311%------------------------------------------------------------------------
1312% ---- find the times corresponding to the first and last indices of a series
1313function displ_time(handles)
1314%------------------------------------------------------------------------
1315SeriesData=get(handles.series,'UserData'); %
1316if ~isfield(SeriesData,'Time')
1317    return
1318end
1319PairString=get(handles.PairString,'Data');
1320ref_i_1=str2num(get(handles.num_first_i,'String')); % first reference index
1321ref_i_2=str2num(get(handles.num_last_i,'String')); % last reference index
1322ref_j_1=[];ref_j_2=[];
1323if strcmp(get(handles.num_first_j,'Visible'),'on')
1324ref_j_1=str2num(get(handles.num_first_j,'String'));
1325ref_j_2=str2num(get(handles.num_last_j,'String'));
1326end
1327[i1_1,i2_1,j1_1,j2_1] = get_file_index(ref_i_1,ref_j_1,PairString);
1328[i1_2,i2_2,j1_2,j2_2] = get_file_index(ref_i_2,ref_j_2,PairString);
1329TimeTable=get(handles.TimeTable,'Data');
1330%%%%%%
1331%TODO: read time in netcdf file, see ActionName_Callback
1332%%%%%%%
1333%Pairs=get(handles.PairString,'Data');
1334for iview=1:size(TimeTable,1)
1335    if size(SeriesData.Time,1)<iview
1336        break
1337    end
1338    TimeTable{iview,3}=[];
1339    TimeTable{iview,4}=[];
1340    if size(SeriesData.Time{iview},1)>=i2_2+1 && (isempty(ref_j_1)||size(SeriesData.Time{iview},2)>=j2_2+1)
1341        if isempty(ref_j_1)
1342            time_first=(SeriesData.Time{iview}(i1_1+1,2)+SeriesData.Time{iview}(i2_1+1,2))/2;
1343            time_last=(SeriesData.Time{iview}(i1_2+1,2)+SeriesData.Time{iview}(i2_2+1,2))/2;
1344        else
1345            time_first=(SeriesData.Time{iview}(i1_1+1,j1_1+1)+SeriesData.Time{iview}(i2_1+1,j2_1+1))/2;
1346            time_last=(SeriesData.Time{iview}(i1_2+1,j1_2+1)+SeriesData.Time{iview}(i2_2+1,j2_1+1))/2;
1347        end
1348        TimeTable{iview,3}=time_first; % TODO: take into account pairs
1349        TimeTable{iview,4}=time_last; % TODO: take into account pairs
1350    end
1351end
1352set(handles.TimeTable,'Data',TimeTable)
1353
1354%% set the waitbar position with respect to the min and max in the series
1355MinIndex_i=min(get(handles.MinIndex_i,'Data'));
1356MaxIndex_i=max(get(handles.MaxIndex_i,'Data'));
1357pos_first=(ref_i_1-MinIndex_i)/(MaxIndex_i-MinIndex_i+1);
1358pos_last=(ref_i_2-MinIndex_i+1)/(MaxIndex_i-MinIndex_i+1);
1359if isempty(pos_first), pos_first=0; end
1360if isempty(pos_last), pos_last=1; end
1361Position=get(handles.Waitbar,'Position'); % position of the waitbar:= [ x,y, width, height]
1362Position_status=get(handles.FileStatus,'Position');
1363Position(1)=Position_status(1)+Position_status(3)*pos_first;
1364Position(3)=max(Position_status(3)*(pos_last-pos_first),0.001); % width must remain positive
1365set(handles.Waitbar,'Position',Position)
1366update_waitbar(handles.Waitbar,0)
1367
1368%------------------------------------------------------------------------
1369% --- Executes when selected cell(s) is changed in PairString.
1370function PairString_CellSelectionCallback(hObject, eventdata, handles)
1371%------------------------------------------------------------------------   
1372if numel(eventdata.Indices)>=1
1373    PairString=get(hObject,'Data');
1374    if ~isempty(PairString{eventdata.Indices(1)})
1375        SetPairs_Callback(hObject, eventdata.Indices(1), handles)
1376    end
1377end
1378
1379%-------------------------------------
1380function enable_i(handles,state)
1381set(handles.i_txt,'Visible',state)
1382set(handles.num_first_i,'Visible',state)
1383set(handles.num_last_i,'Visible',state)
1384set(handles.num_incr_i,'Visible',state)
1385
1386%-----------------------------------
1387function enable_j(handles,state)
1388set(handles.j_txt,'Visible',state)
1389set(handles.num_first_j,'Visible',state)
1390set(handles.num_last_j,'Visible',state)
1391set(handles.num_incr_j,'Visible',state)
1392set(handles.MinIndex_j,'Visible',state)
1393set(handles.MaxIndex_j,'Visible',state)
1394
1395
1396%%%%%%%%%%%%%%%%%%%%
1397%%  MAIN ActionName FUNCTIONS
1398%%%%%%%%%%%%%%%%%%%%
1399%------------------------------------------------------------------------
1400% --- Executes on button press in RUN.
1401%------------------------------------------------------------------------
1402function RUN_Callback(hObject, eventdata, handles)
1403
1404%% settings of the button RUN
1405if ~isequal(get(handles.ActionInput,'BackgroundColor'),[1 0 0])
1406    msgbox_uvmat('ERROR','first activate the button ActionInput')
1407    return
1408end
1409set(handles.RUN,'BusyAction','queue'); % activation of STOP button will set BusyAction to 'cancel'
1410set(handles.RUN, 'Enable','Off')% avoid further RUN action until the current one is finished
1411set(handles.RUN,'BackgroundColor',[1 1 0])%show activation of RUN by yellow color
1412drawnow
1413set(handles.status,'Value',0)% desable status display if relevant
1414status_Callback([], eventdata, handles)
1415
1416%% launch action
1417errormsg=launch_action(handles);
1418if ~isempty(errormsg)
1419     msgbox_uvmat('ERROR',errormsg)
1420end
1421
1422%% reset the GUI series
1423update_waitbar(handles.Waitbar,1); % put the waitbar to end position to indicate launching is finished
1424set(handles.RUN, 'Enable','On')
1425set(handles.RUN,'BackgroundColor',[1 0 0])
1426set(handles.RUN, 'Value',0)
1427
1428%------------------------------------------------------------------------
1429% --- called by RUN_Callback
1430%------------------------------------------------------------------------
1431% The calculations are launched in three different ways:
1432% RunMode='local': calculation on the local Matlab session, will prevent other actions during that time.
1433% RunMode='background': calculation on the local computer, but in a new Matlab session (with no graphic output).
1434% RunMode='cluster': calculations dispatched in a cluster, using a managing system, 'oar, 'sge, or 'sgb'.
1435% In the latter case, the calculation is split in 'packets' of i index (all j indices are contained in a single packet).
1436% This splitting is possible only if the different calculations in the series are independent. Otherwise the action
1437% function imposes a number of processes NbSlice in input, for instance NbSlice=1 for a time series.
1438% If NbSlice is not imposed, the splitting in packets (jobs) is determined
1439% so that a job is optimum length AdvisedJobCPUTime), and the total job number in any case smaller
1440% than MaxJobNumber (these parameters are defined in the file series.xml in
1441% accordance with the management strategy for the cluster). The jobs are
1442% dispatched in parallel into NbCore processors by the cluster managing system.
1443
1444function errormsg=launch_action(handles)
1445errormsg=''; % default
1446
1447%% read the data on the GUI series
1448Param=read_GUI_series(handles); % displayed parameters
1449SeriesData=get(handles.series,'UserData'); % hidden parameters
1450if isfield(SeriesData,'TransformInput')
1451    Param.TransformInput=SeriesData.TransformInput;
1452end
1453if ~isfield(SeriesData,'i1_series')
1454    errormsg='The input field series needs to be refreshed: press REFRESH';
1455    return
1456end
1457if isfield(Param,'InputFields')&& isfield(Param.InputFields,'FieldName')&& isequal(Param.InputFields.FieldName,'get_field...')
1458    errormsg='input field name(s) not defined, select get_field...';
1459    return
1460end
1461
1462%% select the Action mode, 'local', 'background' or 'cluster' (if available)
1463RunMode='local'; % default (needed for first opening of the GUI series)
1464if isfield(Param.Action,'RunMode')
1465    RunMode=Param.Action.RunMode;
1466    Param.Action=rmfield(Param.Action,'RunMode'); % remove from the recorded xml file to avoid interference during ImportConfig
1467end
1468ActionExt='.m'; % default
1469if isfield(Param.Action,'ActionExt')
1470    ActionExt=Param.Action.ActionExt; % '.m', '.sh' (compiled)  or '.py' (Python)
1471    Param.Action=rmfield(Param.Action,'ActionExt'); % remove from the recorded xml file to avoid interference during ImportConfig
1472end
1473ActionName=Param.Action.ActionName;
1474ActionPath=Param.Action.ActionPath;
1475path_series=fileparts(which('series'));
1476
1477%% create the Action fct handle if RunMode option = 'local'
1478if strcmp(RunMode,'local')
1479    if ~isequal(ActionPath,path_series)
1480        eval(['spath=which(''' ActionName ''');']) %spath = current path of the selected function ACTION
1481        if ~exist(ActionPath,'dir')
1482            errormsg=['The prescribed function path ' ActionPath ' does not exist'];
1483            return
1484        end
1485        if ~isequal(spath,ActionPath)
1486            addpath(ActionPath)% add the prescribed path if not the current one
1487        end
1488    end
1489    eval(['h_fun=@' ActionName ';'])%create a function handle for ACTION
1490    if ~isequal(ActionPath,path_series)
1491        rmpath(ActionPath)% add the prescribed path if not the current one
1492    end
1493end
1494
1495%% Get  parameters from series.xml
1496errormsg=''; % default error message
1497ActionFullName=fullfile(get(handles.ActionPath,'String'),ActionName);
1498
1499%% If a compiled version has been selected (ext .sh) check wether it needs to be recompiled
1500if strcmp(ActionExt,'.sh')
1501    TransformPath='';
1502    if isfield(SeriesData,'TransformPath')
1503        TransformPath=SeriesData.TransformPath;
1504        if isfield(SeriesData,'TransformList')
1505            TransformList=get(handles.TransformName,'String');
1506            TransformIndex=get(handles.TransformName,'Value');
1507            TransformName=TransformList{TransformIndex};
1508            if ~ismember(TransformName,SeriesData.TransformList)
1509                TransformPath='';
1510            end
1511        end
1512    end
1513    if ~isempty(TransformPath)&&...
1514          ~strcmp(TransformPath,get(handles.TransformPath,'String'))% if the transform is not in paths set for compilation
1515        msgbox_uvmat('ERROR', 'compilation not available for this transform function, select .m')
1516        return
1517    end
1518    set(handles.series,'Pointer','watch') % set the mouse pointer to 'watch'
1519    set(handles.ActionExt,'BackgroundColor',[1 1 0])
1520    [mcrmajor, mcrminor] = mcrversion;   
1521    MCRROOT = ['MCRROOT',int2str(mcrmajor),int2str(mcrminor)];
1522    RunTime = getenv(MCRROOT);
1523    ActionNameVersion=[ActionName '_' MCRROOT];
1524    ActionFullName=fullfile(get(handles.ActionPath,'String'),[ActionNameVersion '.sh']);
1525    % compile the .m file if the .sh file does not exist yet
1526    if ~exist(ActionFullName,'file')
1527        answer=msgbox_uvmat('INPUT_Y-N','compiled version has not been created: compile now?');
1528        if strcmp(answer,'Yes')
1529            set(handles.ActionExt,'BackgroundColor',[1 1 0])
1530            path_uvmat=fileparts(which('series'));
1531            currentdir=pwd;
1532            cd(get(handles.ActionPath,'String'))% go to the directory of Action
1533            addpath(path_uvmat)% add the path to uvmat to run the fct 'compile'
1534            compile(ActionName,TransformPath)
1535            cd(currentdir)
1536        else
1537            errormsg='Action launch interrupted';
1538            return
1539        end       
1540    else
1541        sh_file_info=dir(fullfile(get(handles.ActionPath,'String'),[ActionNameVersion '.sh']));
1542        m_file_info=dir(fullfile(get(handles.ActionPath,'String'),[ActionName '.m']));
1543        if isfield(m_file_info,'datenum') && m_file_info.datenum>sh_file_info.datenum
1544            set(handles.ActionExt,'BackgroundColor',[1 1 0])
1545            drawnow
1546            answer=msgbox_uvmat('INPUT_Y-N',[ActionNameVersion '.sh needs to be updated: recompile now?']);
1547            if strcmp(answer,'Yes')
1548                path_uvmat=fileparts(which('series'));
1549                currentdir=pwd;
1550                cd(get(handles.ActionPath,'String'))% go to the directory of Action
1551                addpath(path_uvmat)% add the path to uvmat to run the fct 'compile'
1552                addpath(fullfile(path_uvmat,'transform_field'))% add the path to uvmat to run the fct 'compile'
1553                compile(ActionName,TransformPath)
1554                cd(currentdir)
1555            end
1556        end
1557    end
1558
1559    set(handles.ActionExt,'BackgroundColor',[1 1 1])
1560     set(handles.series,'Pointer','arrow') % set the mouse pointer to 'watch
1561end
1562
1563%% set nbre of cluster cores and processes:
1564% NbCore is the number of computer processors used
1565% NbProcess is the number of independent processes in which the required calculation is split.
1566switch RunMode
1567    case {'local','background'}
1568        NbCore=1; % no need to split the calculation
1569    case 'cluster_oar'
1570        %proposed number of cores to reserve in the cluster
1571        NbCoreAdvised=SeriesData.SeriesParam.OarParam.NbCoreAdvised;
1572        NbCoreMax=SeriesData.SeriesParam.OarParam.NbCoreMax;
1573        if strcmp(ActionExt,'.m')% case of Matlab function (uncompiled)
1574            warning_string=', preferably use .sh option to save Matlab licences';
1575        else
1576            warning_string=')';
1577        end
1578        answer=inputdlg({['Number of cores (max ' num2str(NbCoreMax) warning_string],'extra oar options'},'oarsub parameter',1,{num2str(NbCoreAdvised),''});
1579        if isempty(answer)
1580            errormsg='Action launch interrupted by user';
1581            return
1582        end
1583        NbCore=str2double(answer{1});
1584        extra_oar=answer{2};
1585    case {'cluster_pbs', 'cluster_sge', 'cluster_qstat_unknown'}
1586        if strcmp(ActionExt,'.m')% case of Matlab function (uncompiled)
1587            NbCore=1; % one core used only (limitation of Matlab licences)
1588            answer=msgbox_uvmat('INPUT_Y-N','Number of cores =1: select the compiled version .sh for multi-core processing. Proceed with the .m version?');
1589            if ~strcmp(answer,'Yes')
1590                errormsg='Action launch interrupted';
1591                return
1592            end
1593            extra_oar='';
1594        else
1595            answer=inputdlg({'Number of jobs (max 1000)','Queue'},'qsub parameters',1,{'100','piv_debian'});
1596            NbCore=str2double(answer{1});
1597            qstat_Queue=answer{2};
1598            %extra_oar=answer{2}; % TODO : fix this for LMFA cluster. Maybe
1599            %extrs_oar and extra_pbs are not the best names
1600        end
1601end
1602if ~isfield(Param.IndexRange,'NbSlice')
1603    Param.IndexRange.NbSlice=[];
1604end
1605
1606%% create the output data directory if needed
1607OutputDir='';
1608if isfield(Param,'OutputSubDir')
1609    SubDirOut=[get(handles.OutputSubDir,'String') Param.OutputDirExt];
1610    SubDirOutNew=SubDirOut;
1611    detect=exist(fullfile(Param.InputTable{1,1},SubDirOutNew),'dir'); % test if  the dir  already exist
1612    check_create=1; % need to create the result directory by default
1613    CheckOverwrite=1;
1614    if isfield(Param,'CheckOverwrite')
1615        CheckOverwrite=Param.CheckOverwrite;
1616    end
1617    while detect
1618        if CheckOverwrite
1619            comment=', possibly overwrite previous data';
1620        else
1621            comment=', will complement existing result files (no overwriting)';
1622        end
1623        answer=msgbox_uvmat('INPUT_Y-N-Cancel',['use existing ouput directory: ' fullfile(Param.InputTable{1,1},SubDirOutNew) comment]);
1624        if strcmp(answer,'Cancel')
1625            return
1626        elseif strcmp(answer,'Yes')
1627            detect=0;
1628            check_create=0;
1629        else
1630            r=regexp(SubDirOutNew,'(?<root>.*\D)(?<num1>\d+)$','names'); % detect whether name ends by a number
1631            if isempty(r)
1632                r(1).root=[SubDirOutNew '_'];
1633                r(1).num1='0';
1634            end
1635            SubDirOutNew=[r(1).root num2str(str2num(r(1).num1)+1)]; % increment the index by 1 or put 1
1636            detect=exist(fullfile(Param.InputTable{1,1},SubDirOutNew),'dir'); % test if  the dir  already exists
1637            check_create=1;
1638        end
1639    end
1640    Param.OutputDirExt=regexprep(SubDirOutNew,Param.OutputSubDir,'');
1641    Param.OutputRootFile=Param.InputTable{1,3}; % the first sorted RootFile taken for output
1642    set(handles.OutputDirExt,'String',Param.OutputDirExt)
1643    OutputDir=fullfile(Param.InputTable{1,1},[Param.OutputSubDir Param.OutputDirExt]); % full name (with path) of output directory
1644    if check_create    % create output directory if it does not exist
1645        [tild,msg1]=mkdir(OutputDir);
1646        if ~strcmp(msg1,'')
1647            errormsg=['cannot create ' OutputDir ': ' msg1]; % error message for directory creation
1648            return
1649        end
1650    end
1651   
1652elseif isfield(Param,'ActionInput')&&isfield(Param.ActionInput,'LogPath')% custom definition of the output dir
1653    OutputDir=Param.ActionInput.LogPath;   
1654end
1655DirXml=fullfile(OutputDir,'0_XML');
1656if ~exist(DirXml,'dir')
1657    [~,msg1]=mkdir(DirXml);
1658    if ~strcmp(msg1,'')
1659        errormsg=['cannot create ' DirXml ': ' msg1]; % error message for directory creation
1660        return
1661    end
1662end
1663OutputNomType=nomtype2pair(Param.InputTable{1,4}); % nomenclature for output files
1664
1665%% get the set of reference input field indices
1666first_i=1; % first i index to process
1667last_i=1; % last i index to process
1668incr_i=1; % increment step in i index
1669first_j=1; % first j index to process
1670last_j=1; % last j index to process
1671incr_j=1; % increment step in j index
1672if isfield(Param.IndexRange,'first_i')
1673    first_i=Param.IndexRange.first_i;
1674    incr_i=Param.IndexRange.incr_i;
1675    last_i=Param.IndexRange.last_i;
1676end
1677if isfield(Param.IndexRange,'incr_j')
1678    first_j=Param.IndexRange.first_j;
1679    last_j=Param.IndexRange.last_j;
1680    incr_j=Param.IndexRange.incr_j;
1681end
1682if last_i < first_i || last_j < first_j
1683    errormsg= 'series/Run_Callback:last field index must be larger or equal to the first one';
1684    return
1685end
1686%incr_i must be defined, =1 by default, if NbSlice is active
1687if isempty(incr_i)&& ~isempty(Param.IndexRange.NbSlice)
1688    incr_i=1;
1689    set(handles.num_incr_i,'String','1')
1690end
1691% case of no increment i defined: processing is done on the available files found in i1_series
1692if isempty(incr_i)
1693    if isempty(incr_j)
1694        [ref_j,ref_i]=find(squeeze(SeriesData.i1_series{1}(1,:,:)));
1695        ref_j=ref_j(ref_j>=first_j & ref_j<=last_j);
1696        ref_i=ref_i(ref_i>=first_i & ref_i<=last_i);
1697        ref_j=ref_j-1;
1698        ref_i=ref_i-1;
1699    else
1700        ref_j=first_j:incr_j:last_j;
1701        [tild,ref_i]=find(squeeze(SeriesData.i1_series{1}(1,:,:)));
1702        ref_i=ref_i-1;
1703        ref_i=ref_i(ref_i>=first_i & ref_i<=last_i);
1704    end
1705    % increment i is defined: processing is done on first_i:incr_i:last_i;
1706else
1707    ref_i=first_i:incr_i:last_i;
1708    if isempty(incr_j)% automatic finding of the existing j indices
1709        [ref_j,tild]=find(squeeze(SeriesData.i1_series{1}(1,:,:)));
1710        ref_j=ref_j-1;
1711        ref_j=ref_j(ref_j>=first_j & ref_j<=last_j);
1712    else
1713        ref_j=first_j:incr_j:last_j;
1714    end
1715end
1716CPUTime=1; % job time estimated at 1 min per iteration (on index i and j) by default
1717if isfield(Param.Action, 'CPUTime') && ~isempty(Param.Action.CPUTime)
1718    CPUTime=Param.Action.CPUTime; % Note: CpUTime for one iteration ref_i has to be multiplied by the number of j indices nbfield_j
1719end
1720nbfield_j=numel(ref_j); % number of j indices
1721BlockLength=numel(ref_i); % by default, job involves the full set of i field indices
1722NbProcess=1;
1723switch RunMode
1724    case {'cluster_oar','cluster_pbs','cluster_sge','cluster_qstat_unknown'}
1725        JobNumberMax=SeriesData.SeriesParam.OarParam.JobNumberMax;
1726        JobCPUTimeAdvised=SeriesData.SeriesParam.OarParam.JobCPUTimeAdvised;
1727        if isempty(Param.IndexRange.NbSlice)% if NbSlice is not defined
1728            BlockLength= ceil(JobCPUTimeAdvised/(CPUTime*nbfield_j)); % iterations are grouped in sets with length BlockLength  such that the typical CPU time of a job is MinJobNumber.
1729            BlockLength=max(BlockLength,ceil(numel(ref_i)/JobNumberMax)); % possibly increase the BlockLength to have less than MaxJobNumber jobs
1730            NbProcess=ceil(numel(ref_i)/BlockLength) ; % nbre of processes sent to oar
1731        else
1732            NbProcess=Param.IndexRange.NbSlice; % the parameter NbSlice sets the nbre of run processes
1733        end
1734        NbCore=min(NbCore,NbProcess); % reduces the number of cores if it exceeds the number of processes
1735    otherwise
1736        if ~isempty(Param.IndexRange.NbSlice)
1737            NbProcess=Param.IndexRange.NbSlice; % the parameter NbSlice sets the nbre of run processes
1738        end
1739end
1740
1741%% record nbre of output files and starting time for computation for status
1742StatusData=get(handles.status,'UserData');
1743if isfield(StatusData,'OutputFileMode')
1744    switch StatusData.OutputFileMode
1745        case 'NbInput'
1746            StatusData.NbOutputFile=numel(ref_i)*nbfield_j;
1747        case 'NbInput_i'
1748            StatusData.NbOutputFile=numel(ref_i);
1749        case 'NbSlice'
1750            StatusData.NbOutputFile=str2num(get(handles.num_NbSlice,'String'));
1751    end
1752end
1753StatusData.TimeStart=now;
1754set(handles.status,'UserData',StatusData)
1755
1756%% case of a function in Python
1757if strcmp(ActionExt, '.py (in dev.)')
1758    fprintf([
1759        '\n' ...
1760        '!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n' ...
1761        'The option .py is used. It is still in development.\n' ...
1762        'To try it, first install pyper and the most recent version of fluidimage\n' ...
1763        '(see https://bitbucket.org/fluiddyn/fluidimage).\n' ...
1764        'Warning: there is no direct correspondance between UVMAT and fluidimage parameters\n' ...
1765        '!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n'])
1766    RunMode = 'python';
1767end
1768
1769
1770%% direct processing on the current Matlab session or creation of command files
1771filexml=cell(1,NbProcess); % initialisation of the names of the files containing the processing parameters
1772extxml=cell(1,NbProcess); % initialisation of the set of labels used for the files documenting each process
1773for iprocess=1:NbProcess
1774    extxml{iprocess}='.xml';
1775end
1776for iprocess=1:NbProcess
1777    if ~strcmp(get(handles.RUN,'BusyAction'),'queue')% allow for STOP action
1778        disp('program stopped by user')
1779        return
1780    end
1781    if isempty(Param.IndexRange.NbSlice)
1782        Param.IndexRange.first_i=first_i+(iprocess-1)*BlockLength*incr_i;
1783        if Param.IndexRange.first_i>last_i
1784            NbProcess=iprocess-1; % leave the loop, we are at the end of the calculation
1785            break
1786        end
1787        Param.IndexRange.last_i=min(last_i,first_i+(iprocess)*BlockLength*incr_i-1);
1788    else %multislices (then incr_i is not empty)
1789        Param.IndexRange.first_i= first_i+iprocess-1;
1790        Param.IndexRange.incr_i=incr_i*Param.IndexRange.NbSlice;
1791    end
1792    for ilist=1:size(Param.InputTable,1)
1793        Param.InputTable{ilist,1}=regexprep(Param.InputTable{ilist,1},'\','/'); % correct path name for PCWIN system
1794    end
1795   
1796    if isfield(Param,'OutputSubDir')
1797        t=struct2xml(Param);
1798        t=set(t,1,'name','Series');
1799        extxml{iprocess}=fullfile_uvmat('','',Param.InputTable{1,3},'.xml',OutputNomType,...
1800            Param.IndexRange.first_i,Param.IndexRange.last_i,first_j,last_j);
1801        filexml{iprocess}=fullfile(OutputDir,'0_XML',extxml{iprocess});
1802        try
1803            save(t, filexml{iprocess}); % save the xml file containing the processing parameters
1804        catch ME
1805            if ~strcmp (RunMode,'local')
1806                errormsg=['error writting ' filexml{iprocess} ': ' ME.message];
1807                return
1808            end
1809        end
1810    end
1811    if strcmp (RunMode,'local')
1812        switch ActionExt
1813            case '.m'
1814                h_fun(Param); % direct launching
1815               
1816            case '.sh'
1817                switch computer
1818                    case {'PCWIN','PCWIN64'} %Windows system
1819                        filexml=regexprep(filexml,'\\','\\\\'); % add '\' so that '\' are left as characters
1820                        system([ActionFullName ' ' RunTime ' ' filexml{iprocess}]); % TODO: adapt to DOS system
1821                    case {'GLNX86','GLNXA64','MACI64'}%Linux  system
1822                        system([ActionFullName ' ' RunTime ' ' filexml{iprocess}]);
1823                end
1824        end
1825    end
1826end
1827
1828if ~strcmp (RunMode,'local') && ~strcmp(RunMode,'python')
1829    %% processing on a different session of the same computer (background) or cluster, create executable files
1830    batch_file_list=cell(NbProcess,1); % initiate the list of executable files
1831    DirExe=fullfile(OutputDir,'0_EXE'); % directory name for executable files
1832    switch computer
1833        case {'PCWIN','PCWIN64'} %Windows system
1834            ExeExt='.bat';
1835        case {'GLNX86','GLNXA64','MACI64'}%Linux  system
1836            ExeExt='.sh';
1837    end
1838    %create subdirectory for executable files
1839    if ~exist(DirExe,'dir')
1840        [tild,msg1]=mkdir(DirExe);
1841        if ~strcmp(msg1,'')
1842            errormsg=['cannot create ' DirExe ': ' msg1]; % error message for directory creation
1843            return
1844        end
1845    end
1846    %create subdirectory for log files
1847    DirLog=fullfile(OutputDir,'0_LOG');
1848    if ~exist(DirLog,'dir')
1849        [tild,msg1]=mkdir(DirLog);
1850        if ~strcmp(msg1,'')
1851            errormsg=['cannot create ' DirLog ': ' msg1]; % error message for directory creation
1852            return
1853        end
1854    end
1855   
1856    %create the executable file
1857    file_exe_global=fullfile_uvmat('','',Param.InputTable{1,3},ExeExt,OutputNomType,...
1858        first_i,last_i,first_j,last_j);
1859    file_exe_global=fullfile(OutputDir,'0_EXE',file_exe_global);
1860    filelog_global=fullfile_uvmat('','',Param.InputTable{1,3},'.log',OutputNomType,...
1861        first_i,last_i,first_j,last_j);
1862    filelog_global=fullfile(OutputDir,'0_LOG',filelog_global);
1863
1864    for iprocess=1:NbProcess   
1865        %create the executable file       
1866        batch_file_list{iprocess}=fullfile(OutputDir,'0_EXE',regexprep(extxml{iprocess},'.xml$',ExeExt));
1867       
1868        % set the log file name
1869        filelog{iprocess}=fullfile(OutputDir,'0_LOG',regexprep(extxml{iprocess},'.xml$','.log'));     
1870    end
1871end
1872
1873%% launch the executable files for background or cluster processing
1874
1875switch RunMode
1876   
1877    case 'background'
1878        [fid,message]=fopen(file_exe_global,'w');
1879        if isequal(fid,-1)
1880            errormsg=['creation of ' file_exe_global ':' message];
1881            return
1882        end
1883        switch ActionExt
1884            case '.m'% Matlab function
1885                switch computer
1886                    case {'GLNX86','GLNXA64','MACI64'}
1887                        matlab_ver = ver('MATLAB');
1888                        matlab_version = matlab_ver.Version;
1889                        cmd=[...
1890                            '#!/bin/bash\n'...
1891                            'source /etc/profile\n'...
1892                            'module load matlab/' matlab_version '\n'...% CHOICE OF MATLAB VERSION
1893                            'time_start=$(date +%%s)\n'...
1894                            'matlab -nodisplay -nosplash -nojvm -logfile ''' filelog_global ''' <<END_MATLAB\n'...
1895                            'addpath(''' path_series ''');\n'...
1896                            'addpath(''' Param.Action.ActionPath ''');\n'];
1897                        for iprocess=1:NbProcess
1898                            cmd=[cmd '' Param.Action.ActionName  '(''' filexml{iprocess} ''');\n'];
1899                        end
1900                        cmd=[cmd  'exit\n' 'END_MATLAB\n'...
1901                            'time_end=$(date +%%s)\n'...
1902                            'echo "global time = " $(($time_end - $time_start)) >> ''' filelog_global '''\n'];
1903                        fprintf(fid,cmd); % fill the executable file with the  char string cmd
1904                        fclose(fid); % close the executable filefilelog_global
1905                        system(['chmod +x ' file_exe_global]); % set the file to executable
1906                    case {'PCWIN','PCWIN64'}
1907                        cmd=['matlab -automation -logfile ' regexprep(filelog{iprocess},'\\','\\\\')...
1908                            ' -r "addpath(''' regexprep(path_series,'\\','\\\\') ''');'...
1909                            'addpath(''' regexprep(Param.Action.ActionPath,'\\','\\\\') ''');'];
1910                        for iprocess=1:NbProcess
1911                            cmd=[cmd '' Param.Action.ActionName  '( ''' regexprep(filexml{iprocess},'\\','\\\\') ''');']
1912                        end
1913                        cmd=[cmd ';exit"'];
1914                        fprintf(fid,cmd); % fill the executable file with the  char string cmd
1915                        fclose(fid); % close the executable file
1916                end
1917                system([file_exe_global ' &'])% directly execute the command file
1918            case '.sh' % compiled Matlab function
1919                for iprocess=1:NbProcess
1920                    switch computer
1921                        case {'GLNX86','GLNXA64','MACI64'}
1922                            [fid,message]=fopen(batch_file_list{iprocess},'w'); % create the executable file
1923                            if isequal(fid,-1)
1924                                errormsg=['creation of .bat file: ' message];
1925                                return
1926                            end
1927                            cmd=['#!/bin/bash \n '...
1928                                '#$ -cwd \n '...
1929                                'hostname && date \n '...
1930                                'umask 002 \n'...
1931                                ActionFullName ' ' RunTime ' ' filexml{iprocess}]; % allow writting access to created files for user group
1932                            fprintf(fid,cmd); % fill the executable file with the  char string cmd
1933                            fclose(fid); % close the executable file
1934                            system(['chmod +x ' batch_file_list{iprocess}]); % set the file to executable
1935                            system([batch_file_list{iprocess} ' &'])% directly execute the command file
1936                        case {'PCWIN','PCWIN64'}
1937                            msgbox_uvmat('ERROR','option for compiled Matlab functions not implemented for Windows system')
1938                            return
1939                    end
1940                end
1941                msgbox_uvmat('CONFIRMATION',[ActionFullName ' launched in background: press STATUS to see results'])
1942        end
1943       
1944    case 'cluster_oar' % option 'oar-parexec' used
1945        %create subdirectory for oar commands
1946        for iprocess=1:NbProcess
1947            [fid,message]=fopen(batch_file_list{iprocess},'w'); % create the executable file
1948            if isequal(fid,-1)
1949                errormsg=['creation of .bat file: ' message];
1950                return
1951            end
1952            if  strcmp(ActionExt,'.sh')
1953                cmd=['#!/bin/bash \n '...
1954                    '#$ -cwd \n '...
1955                    'hostname && date \n '...
1956                    'umask 002 \n'...
1957                    ActionFullName ' ' RunTime ' ' filexml{iprocess}]; % allow writting access to created files for user group
1958            else
1959                matlab_ver = ver('MATLAB');
1960                matlab_version = matlab_ver.Version;
1961                cmd=[...
1962                    '#!/bin/bash\n'...
1963                    'source /etc/profile\n'...
1964                    'module load matlab/' matlab_version '\n'...% CHOICE OF MATLAB VERSION
1965                    'matlab -nodisplay -nosplash -nojvm -singleCompThread -logfile ''' filelog{iprocess} ''' <<END_MATLAB\n'...
1966                    'addpath(''' path_series ''');\n'...
1967                    'addpath(''' Param.Action.ActionPath ''');\n'...
1968                    '' Param.Action.ActionName  '(''' filexml{iprocess} ''');\n'...
1969                    'exit\n'...
1970                    'END_MATLAB\n'];
1971            end
1972            fprintf(fid,cmd); % fill the executable file with the  char string cmd
1973            fclose(fid); % close the executable file
1974            system(['chmod +x ' batch_file_list{iprocess}]); % set the file to executable
1975        end
1976        DirOAR=fullfile(OutputDir,'0_OAR');
1977        if exist(DirOAR,'dir')% delete the content of the dir 0_LOG to allow new input
1978            curdir=pwd;
1979            cd(DirOAR)
1980            delete('*')
1981            cd(curdir)
1982        else
1983            [tild,msg1]=mkdir(DirOAR);
1984            if ~strcmp(msg1,'')
1985                errormsg=['cannot create ' DirOAR ': ' msg1]; % error message for directory creation
1986                return
1987            end
1988        end
1989        % create file containing the list of jobs
1990        filename_joblist=fullfile(DirOAR,'job_list.txt'); % name of the file containing the list of executables
1991        fid=fopen(filename_joblist,'w'); % open it for writting
1992        for iprocess=1:length(batch_file_list)
1993            fprintf(fid,[batch_file_list{iprocess} '\n']); % write list of exe files
1994        end
1995        fclose(fid);
1996        system(['chmod +x ' filename_joblist]); % set the file to executable
1997       
1998        filename_log=fullfile(DirLog,'job_list.stdout'); % file for output messages of the master oar process
1999        filename_errors=fullfile(DirLog,'job_list.stderr'); % file for error messages of the master oar process
2000        % the command job_list.txt contains the list of NbProcess independent individual jobs
2001        % in which the total calculation has been split. Those are written as executable files .sh in the folder /O_EXE.
2002        %  These individual jobs are grouped by the system as oar jobs on the NbCore processors.
2003        %  For each processor, the oar job must stop after the walltime which has been set, which is limited to 24 h.
2004        %  However, the oar job is automatically restarted (option 'idempotent') provided the individual jobs are
2005        % shorter than the wall time: in the time interval 'checkpoint' (WallTimeOneJob) before the end of the allowed duration,
2006        %  the oar job restarts when an individual job ends.
2007        WallTimeMax=SeriesData.SeriesParam.OarParam.WallTimeMax;
2008        JobTime=CPUTime*BlockLength*nbfield_j; % estimated CPU time for one individual job (in minutes)
2009        % wall time (in hours ) for each oar job, allowing 10 individual jobs, but limited to 23 h:
2010        WallTimeTotal=min(WallTimeMax,4*JobTime/60);
2011        %disp(['WallTimeTotal: ' num2str(WallTimeTotal) ' hours'])
2012        % estimated time of an individual job (in min), with a margin of error
2013        WallTimeOneJob=min(4*JobTime+10,WallTimeTotal*60/2); % estimated max time of an individual job for checkpoint
2014        disp(['WallTimeOneJob: ' num2str(WallTimeOneJob) ' minutes'])
2015        if NbProcess>=8
2016            bigiojob_string=['+{type = ' char(39) 'bigiojob' char(39) '}/licence=1'];% char(39) is quote - bigiojob limit UVmat parallel launch on cluster to avoid saturation of disk access to data
2017        else
2018            bigiojob_string='';
2019        end
2020        oar_command=['oarsub -n UVmat_' ActionFullName ' '...
2021            '-t idempotent --checkpoint ' num2str(WallTimeOneJob*60) ' '...
2022            '-l "/core=' num2str(NbCore)...
2023            bigiojob_string... % char(39) is quote - bigiojob limit UVmat parallel launch on cluster
2024            ',walltime=' datestr(WallTimeTotal/24,13) '" '...
2025            '-E ' filename_errors ' '...
2026            '-O ' filename_log ' '...
2027            extra_oar ' '...
2028            '"oar-parexec -s -f ' filename_joblist ' '...
2029            '-l ' filename_joblist '.log"'];
2030       
2031        fprintf(oar_command); % display  system command on the Matlab command window
2032        [status,result]=system(oar_command)% execute system command and show the result (ID number of the launched job) on the Matlab command window
2033        filename_oarcommand=fullfile(DirOAR,'0_oar_command'); % keep track of the command in file '0-OAR/0_oar_command'
2034        fid=fopen(filename_oarcommand,'w');
2035        fprintf(fid,oar_command); % store the command
2036        fprintf(fid,result); % store the result (job ID number)
2037        fclose(fid);
2038        msgbox_uvmat('CONFIRMATION',[ActionFullName ' launched as  ' num2str(NbProcess) ' processes in cluster: press STATUS to see results'])
2039       
2040    case 'cluster_pbs' % for LMFA Kepler machine
2041        %create subdirectory for pbs command and log files
2042        DirPBS=fullfile(OutputDir,'0_PBS'); % todo : common name OAR/PBS
2043        if exist(DirPBS,'dir')% delete the content of the dir 0_LOG to allow new input
2044            curdir=pwd;
2045            cd(DirPBS)
2046            delete('*')
2047            cd(curdir)
2048        else
2049            [tild,msg1]=mkdir(DirPBS);
2050            if ~strcmp(msg1,'')
2051                errormsg=['cannot create ' DirPBS ': ' msg1]; % error message for directory creation
2052                return
2053            end
2054        end
2055        max_walltime=3600*20; % 20h max total calculation (cannot exceed 24 h)
2056        walltime_onejob=1800; % seconds, max estimated time for asingle file index value
2057        filename_joblist=fullfile(DirPBS,'job_list.txt'); % create name of the global executable file
2058        fid=fopen(filename_joblist,'w');
2059        for iprocess=1:length(batch_file_list)
2060            fprintf(fid,[batch_file_list{iprocess} '\n']); % list of exe files
2061        end
2062        fclose(fid);
2063        system(['chmod +x ' filename_joblist]); % set the file to executable
2064        pbs_command=['qsub -n CIVX '...
2065            '-t idempotent --checkpoint ' num2str(walltime_onejob+60) ' '...
2066            '-l /core=' num2str(NbCore) ','...
2067            'walltime=' datestr(min(1.05*walltime_onejob/86400*max(NbProcess*BlockLength*nbfield_j,NbCore)/NbCore,max_walltime/86400),13) ' '...
2068            '-E ' regexprep(filename_joblist,'\.txt\>','.stderr') ' '...
2069            '-O ' regexprep(filename_joblist,'\.txt\>','.log') ' '...
2070            extra_qstat ' '...
2071            '"oar-parexec -s -f ' filename_joblist ' '...
2072            '-l ' filename_joblist '.log"'];
2073        filename_oarcommand=fullfile(DirPBS,'pbs_command');
2074        fid=fopen(filename_oarcommand,'w');
2075        fprintf(fid,pbs_command);
2076        fclose(fid);
2077        fprintf(pbs_command); % display in command line
2078        %system(pbs_command);
2079        msgbox_uvmat('CONFIRMATION',[ActionFullName ' command ready to be launched in cluster'])
2080
2081     case 'cluster_sge' % for PSMN
2082        % Au PSMN, on ne cr??e pas 1 job avec plusieurs c??urs, mais N jobs de 1 c??urs
2083        % o?? N < 1000.
2084        %create subdirectory for pbs command and log files
2085
2086        DirSGE=fullfile(OutputDir,'0_SGE');
2087        if exist(DirSGE,'dir')% delete the content of the dir 0_LOG to allow new input
2088            curdir=pwd;
2089            cd(DirSGE)
2090            delete('*')
2091            cd(curdir)
2092        else
2093            [tild,msg1]=mkdir(DirSGE);
2094            if ~strcmp(msg1,'')
2095                errormsg=['cannot create ' DirSGE ': ' msg1]; % error message for directory creation
2096                return
2097            end
2098        end
2099        maxImgsPerJob = ceil(length(batch_file_list)/NbCore);
2100        disp(['Max number of jobs: ' num2str(NbCore)])
2101        disp(['Images per job: ' num2str(maxImgsPerJob)])
2102       
2103        iprocess = 1;
2104        imgsInJob = [];
2105        currJobIndex = 1;
2106        done = 0;
2107        while(~done)
2108            if(iprocess <= length(batch_file_list))
2109                imgsInJob = [imgsInJob, iprocess];
2110            end
2111            if((numel(imgsInJob) >= maxImgsPerJob) || (iprocess == length(batch_file_list)))
2112                cmd=['#!/bin/sh \n'...
2113                     '#$ -cwd \n'...
2114                     'hostname && date\n']
2115                for ii=1:numel(imgsInJob)
2116                    cmd=[cmd ActionFullName ' /softs/matlab ' filexml{imgsInJob(ii)} '\n'];
2117                end
2118                [fid, message] = fopen([DirSGE '/job' num2str(currJobIndex) '.sh'], 'w');
2119                fprintf(fid, cmd);
2120                fclose(fid);
2121                system(['chmod +x ' DirSGE '/job' num2str(currJobIndex) '.sh'])
2122                sge_command=['qsub -N civ_' num2str(currJobIndex) ' '...
2123                    '-q ' qstat_Queue ' '...
2124                    '-e ' fullfile([DirSGE '/job' num2str(currJobIndex) '.out']) ' '...
2125                    '-o ' fullfile([DirSGE '/job' num2str(currJobIndex) '.out']) ' '...
2126                    fullfile([DirSGE '/job' num2str(currJobIndex) '.sh'])];
2127                fprintf(sge_command); % display in command line
2128                [status, result] = system(sge_command);
2129                fprintf(result);
2130                currJobIndex = currJobIndex + 1;
2131                imgsInJob = [];
2132            end
2133            if(iprocess == length(batch_file_list))
2134                done = 1;
2135            end
2136            iprocess = iprocess + 1;
2137        end
2138        msgbox_uvmat('CONFIRMATION',[num2str(currJobIndex-1) ' jobs launched on queue ' qstat_Queue '.'])
2139    case 'python'
2140        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))") ' ...
2141            'python -m fluidimage.run_from_xml ' filexml{iprocess}];
2142        fprintf(['command:\n' command '\n\n'])
2143        system(command, '-echo');
2144end
2145if exist(OutputDir,'dir')
2146    [SUCCESS,MESSAGE,MESSAGEID] = fileattrib (OutputDir);
2147    if MESSAGE.GroupWrite~=1
2148    [success,msg] = fileattrib(OutputDir,'+w','g','s'); % allow writing access for the group of users, recursively in the folder
2149    if success==0
2150        msgbox_uvmat('WARNING',{['unable to set group write access to ' OutputDir ':']; msg}); % error message for directory creation
2151    end
2152    end
2153end
2154
2155%------------------------------------------------------------------------
2156function STOP_Callback(hObject, eventdata, handles)
2157%------------------------------------------------------------------------
2158set(handles.RUN, 'BusyAction','cancel')
2159set(handles.RUN,'BackgroundColor',[1 0 0])
2160set(handles.RUN,'enable','on')
2161set(handles.RUN, 'Value',0)
2162
2163%------------------------------------------------------------------------
2164% --- read parameters from the GUI series
2165%------------------------------------------------------------------------
2166function Param=read_GUI_series(handles)
2167
2168%% read raw parameters from the GUI series
2169Param=read_GUI(handles.series);
2170
2171%% clean the output structure by removing unused information
2172if isfield(Param,'Pairs')
2173    Param=rmfield(Param,'Pairs'); % info Pairs not needed for output
2174end
2175if isfield(Param,'InputLine')
2176    Param=rmfield(Param,'InputLine');
2177end
2178if isfield(Param,'EditObject')
2179    Param=rmfield(Param,'EditObject');
2180end
2181Param.IndexRange.TimeSource=Param.IndexRange.TimeTable{end,1};
2182Param.IndexRange=rmfield(Param.IndexRange,'TimeTable');
2183empty_line=false(size(Param.InputTable,1),1);
2184for iline=1:size(Param.InputTable,1)
2185    empty_line(iline)=isempty(cell2mat(Param.InputTable(iline,1:3)));
2186end
2187Param.InputTable(empty_line,:)=[];
2188
2189%------------------------------------------------------------------------
2190% --- Executes on selection change in ActionName.
2191function ActionName_Callback(hObject, eventdata, handles)
2192%------------------------------------------------------------------------
2193
2194%% stop any ongoing series processing
2195if isequal(get(handles.RUN,'Value'),1)
2196    answer= msgbox_uvmat('INPUT_Y-N','stop current Action process?');
2197    if strcmp(answer,'Yes')
2198        STOP_Callback(hObject, eventdata, handles)
2199    else
2200        return
2201    end
2202end
2203set(handles.ActionName,'BackgroundColor',[1 1 0])
2204huigetfile=findobj(allchild(0),'tag','status_display');
2205if ~isempty(huigetfile)
2206    delete(huigetfile)
2207end
2208drawnow
2209
2210%% get Action name and path
2211NbBuiltinAction=get(handles.Action,'UserData'); % nbre of functions initially proposed in the menu ActionName (as defined in the Opening fct of series)
2212ActionList=get(handles.ActionName,'String'); % list menu fields
2213ActionIndex=get(handles.ActionName,'Value');
2214if ~isequal(ActionIndex,1)% if we are not just opening series
2215    InputTable=get(handles.InputTable,'Data');
2216    if isempty(InputTable{1,4})
2217        msgbox_uvmat('ERROR','no input file available: use Open in the menu bar')
2218        return
2219    end
2220end
2221ActionName= ActionList{get(handles.ActionName,'Value')}; % selected function name
2222ActionPathList=get(handles.ActionName,'UserData'); % list of recorded paths to functions of the list ActionName
2223
2224%% add a new function to the menu if 'more...' has been selected in the menu ActionName
2225if isequal(ActionName,'more...')
2226    [FileName, PathName] = uigetfile( ...
2227        {'*.m', ' (*.m)';
2228        '*.m',  '.m files '; ...
2229        '*.*', 'All Files (*.*)'}, ...
2230        'Pick a series processing function ',get(handles.ActionPath,'String'));
2231    if length(FileName)<2
2232        return
2233    end
2234    [tild,ActionName,ActionExt]=fileparts(FileName);
2235   
2236    % insert the choice in the menu ActionName
2237    ActionIndex=find(strcmp(ActionName,ActionList),1); % look for the selected function in the menu Action
2238    PathName=regexprep(PathName,'/$','');
2239    if ~isempty(ActionIndex) && ~strcmp(ActionPathList{ActionIndex},PathName)%compare the path to the existing fct
2240        ActionIndex=[]; % the selected path is different than the recorded one
2241    end
2242    if isempty(ActionIndex)%the qselected fct (with selected path) does not exist in the menu
2243        ActionIndex= length(ActionList);
2244        ActionList=[ActionList(1:end-1);{ActionName};ActionList(end)]; % the selected function is appended in the menu, before the last item 'more...'
2245         ActionPathList=[ActionPathList; PathName];
2246    end
2247   
2248    % record the file extension and extend the path list if it is a new extension
2249    ActionExtList=get(handles.ActionExt,'String');
2250    ActionExtIndex=find(strcmp(ActionExt,ActionExtList), 1);
2251    if isempty(ActionExtIndex)
2252        set(handles.ActionExt,'String',[ActionExtList;{ActionExt}])
2253    end
2254
2255    % remove old Action options in the menu (keeping a menu length <nb_builtin_ACTION+5)
2256    if length(ActionList)>NbBuiltinAction+5; % nb_builtin_ACTION=nbre of functions always remaining in the initial menu
2257        nbremove=length(ActionList)-NbBuiltinAction-5;
2258        ActionList(NbBuiltinAction+1:end-5)=[];
2259        ActionPathList(NbBuiltinAction+1:end-4,:)=[];
2260        ActionIndex=ActionIndex-nbremove;
2261    end
2262   
2263    % record action menu, choice and path
2264    set(handles.ActionName,'Value',ActionIndex)
2265    set(handles.ActionName,'String',ActionList)
2266       set(handles.ActionName,'UserData',ActionPathList);
2267    set(handles.ActionExt,'Value',ActionExtIndex)
2268       
2269    %record the user defined menu additions in personal file profil_perso
2270    dir_perso=prefdir;
2271    profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
2272    if NbBuiltinAction+1<=numel(ActionList)-1
2273        ActionListUser=ActionList(NbBuiltinAction+1:numel(ActionList)-1);
2274        ActionPathListUser=ActionPathList(NbBuiltinAction+1:numel(ActionList)-1);
2275        ActionExtListUser={};
2276        if numel(ActionExtList)>2
2277            ActionExtListUser=ActionExtList(3:end);
2278        end
2279        if exist(profil_perso,'file')
2280            save(profil_perso,'ActionListUser','ActionPathListUser','ActionExtListUser','-append')
2281        else
2282            save(profil_perso,'ActionListUser','ActionPathListUser','ActionExtListUser','-V6')
2283        end
2284    end
2285end
2286
2287%% check the current ActionPath to the selected function
2288ActionPath=ActionPathList{ActionIndex}; % current recorded path
2289set(handles.ActionPath,'String',ActionPath); % show the path to the senlected function
2290
2291%% reinitialise the waitbar
2292update_waitbar(handles.Waitbar,0)
2293
2294%% Put the first line of the selected Action fct as tooltip help
2295try
2296    [fid,errormsg] =fopen([ActionName '.m']);
2297    InputText=textscan(fid,'%s',1,'delimiter','\n');
2298    fclose(fid);
2299    set(handles.ActionName,'ToolTipString',InputText{1}{1})% put the first line of the selected function as tooltip help
2300end
2301set(handles.ActionName,'BackgroundColor',[1 1 1])
2302set(handles.ActionInput,'BackgroundColor',[1 0 1])% set ActionInput button to magenta color to indicate that input refr
2303
2304
2305% --- Executes on button press in ActionInput.
2306function ActionInput_Callback(hObject, eventdata, handles)
2307
2308set(handles.ActionInput,'BackgroundColor',[1 1 0])
2309
2310%% create the function handle for Action
2311ActionPath=get(handles.ActionPath,'String');
2312ActionList=get(handles.ActionName,'String');
2313ActionName= ActionList{get(handles.ActionName,'Value')}; % selected function name
2314if ~exist(ActionPath,'dir')
2315    msgbox_uvmat('ERROR',['The prescribed function path ' ActionPath ' does not exist']);
2316    return
2317end
2318current_dir=pwd; % current working dir
2319cd(ActionPath)
2320h_fun=str2func(ActionName);
2321cd(current_dir)
2322
2323%% Activate the Action fct to adapt the configuration of the GUI series and bring specific parameters in SeriesData
2324Param=read_GUI_series(handles); % read the parameters from the GUI series
2325Param.Action.RUN=0;
2326ParamOut=h_fun(Param); % run the selected Action function to get the relevant input
2327
2328
2329%% Visibility of VelType and VelType_1 menus asked by ActionName
2330VelTypeRequest=1; % VelType requested by default
2331VelTypeRequest_1=1; % VelType requested by default
2332if isfield(ParamOut,'VelType')
2333    VelTypeRequest=ismember(ParamOut.VelType,{'on','one','two'});
2334    VelTypeRequest_1=strcmp( ParamOut.VelType,'two');
2335end
2336FieldNameRequest=0;  %hidden by default
2337FieldNameRequest_1=0;  %hidden by default
2338if isfield(ParamOut,'FieldName')
2339    FieldNameRequest=ismember(ParamOut.FieldName,{'on','one','two'});
2340    FieldNameRequest_1=strcmp( ParamOut.FieldName,'two');
2341end
2342
2343%% Detect the types of input files and set menus and default options in 'VelType'
2344SeriesData=get(handles.series,'UserData'); % info on the input file series
2345iview_civ=find(strcmp('civx',SeriesData.FileType)|strcmp('civdata',SeriesData.FileType));
2346iview_netcdf=find(strcmp('netcdf',SeriesData.FileType)|strcmp('civx',SeriesData.FileType)|strcmp('civdata',SeriesData.FileType)); % all nc files, icluding civ
2347FieldList=get(handles.FieldName,'String'); % previous list as default
2348if ~iscell(FieldList),FieldList={FieldList};end
2349FieldList_1=get(handles.FieldName_1,'String'); % previous list as default
2350if ~iscell(FieldList_1),FieldList_1={FieldList_1};end
2351%CheckList=0; % indicate whether FieldName has been updated
2352CheckList_1=1; % indicate whether FieldName_1 has been updated
2353handles_coord=[handles.Coord_x handles.Coord_y handles.Coord_z handles.Coord_x_title handles.Coord_y_title handles.Coord_z_title];
2354if VelTypeRequest && numel(iview_civ)>=1
2355    menu=set_veltype_display(SeriesData.FileInfo{iview_civ(1)}.CivStage,SeriesData.FileType{iview_civ(1)});
2356    set(handles.VelType,'Value',1)% set first choice by default
2357    set(handles.VelType,'String',[{'*'};menu])
2358    set(handles.VelType,'Visible','on')
2359    set(handles.VelType_title,'Visible','on')
2360    FieldList=[set_field_list('U','V');{'C'};{'get_field...'}]; % standard menu for civx data
2361    %CheckList=1;
2362    set(handles.FieldName,'Value',1); % velocity vector choice by default
2363    if  VelTypeRequest_1 && numel(iview_civ)>=2
2364        menu=set_veltype_display(SeriesData.FileInfo{iview_civ(2)}.CivStage,SeriesData.FileType{iview_civ(2)});
2365        set(handles.VelType_1,'Value',1)% set first choice by default
2366        set(handles.VelType_1,'String',[{'*'};menu])
2367        set(handles.VelType_1,'Visible','on')
2368        set(handles.VelType_title_1,'Visible','on')
2369        FieldList_1=[set_field_list('U','V');{'C'};{'get_field...'}]; % standard menu for civx data
2370        CheckList_1=1;
2371        set(handles.FieldName_1,'Value',1); % velocity vector choice by default
2372    else
2373        set(handles.VelType_1,'Visible','off')
2374        set(handles.VelType_title_1,'Visible','off')
2375    end
2376else
2377    set(handles.VelType,'Visible','off')
2378    set(handles.VelType_title,'Visible','off')
2379end
2380
2381%% Detect the types of input files and set menus and default options in 'FieldName'
2382if (FieldNameRequest || VelTypeRequest) && numel(iview_netcdf)>=1
2383    set(handles.InputFields,'Visible','on')% set the frame InputFields visible
2384    if FieldNameRequest && isfield(SeriesData.FileInfo{iview_netcdf(1)},'ListVarName')
2385        set(handles.FieldName,'Visible','on')
2386        ListVarName=SeriesData.FileInfo{iview_netcdf(1)}.ListVarName;
2387        ind_var=get(handles.FieldName,'Value'); % indices of previously selected variables
2388        for ilist=1:numel(ind_var)
2389            if isempty(find(strcmp(FieldList{ind_var(ilist)},ListVarName)))
2390                FieldList={}; % previous choice not consistent with new input field
2391                set(handles.FieldName,'Value',1)
2392                break
2393            end
2394        end
2395        if ~isempty(FieldList)
2396            if isempty(find(strcmp(get(handles.Coord_x,'String'),ListVarName)))||...
2397                    isempty(find(strcmp(get(handles.Coord_y,'String'),ListVarName)))
2398                FieldList={};
2399                set(handles.Coord_x,'String','')
2400                set(handles.Coord_y,'String','')
2401            end
2402            Coord_z=get(handles.Coord_z,'String');
2403            if ~isempty(Coord_z) && isempty(find(strcmp(Coord_z,ListVarName)))
2404                FieldList={};
2405                set(handles.Coord_z,'String','')
2406            end
2407        end
2408    else
2409        set(handles.FieldName,'Visible','off')
2410    end
2411   
2412    set(handles_coord,'Visible','on')
2413    FieldList=[FieldList;{'get_field...'}];
2414    if FieldNameRequest_1 && numel(iview_netcdf)>=2
2415        set(handles.FieldName_1,'Visible','on')
2416        if CheckList_1==0        % not civ input made
2417            ListVarName=SeriesData.FileInfo{iview_netcdf(2)}.ListVarName;
2418            ind_var=get(handles.FieldName,'Value'); % indices of previously selected variables
2419            for ilist=1:numel(ind_var)
2420                if isempty(find(strcmp(FieldList{ind_var(ilist)},ListVarName)))
2421                    FieldList_1={}; % previous choice not consistent with new input field
2422                    set(handles.FieldName_1,'Value',1)
2423                    break
2424                end
2425            end
2426            warn_coord=0;
2427            if isempty(find(strcmp(get(handles.Coord_x,'String'),ListVarName)))||...
2428                    isempty(find(strcmp(get(handles.Coord_y,'String'),ListVarName)))
2429                warn_coord=1;
2430            end
2431            if ~isempty(Coord_z) && isempty(find(strcmp(Coord_z,ListVarName)))
2432                FieldList_1={};
2433                warn_coord=1;
2434            end
2435            if warn_coord
2436                msgbox_uvmat('WARNING','coordinate names do not exist in the second netcdf input file')
2437            end
2438           
2439            set(handles.FieldName_1,'Visible','on')
2440            set(handles.FieldName_1,'Value',1)
2441            set(handles.FieldName_1,'String',FieldList_1)
2442        end
2443    else
2444        set(handles.FieldName_1,'Visible','off')
2445    end
2446    if isempty(FieldList)
2447        set(handles.FieldName,'Visible','off')
2448    else
2449        set(handles.FieldName,'Visible','on')
2450        set(handles.FieldName,'String',FieldList)
2451    end
2452else
2453    set(handles.InputFields,'Visible','off')
2454end
2455
2456%% Introduce visibility of file overwrite option
2457if isfield(ParamOut,'CheckOverwriteVisible')&& strcmp(ParamOut.CheckOverwriteVisible,'on')
2458    set(handles.CheckOverwrite,'Visible','on')
2459else
2460    set(handles.CheckOverwrite,'Visible','off')
2461end
2462
2463%% Check whether alphabetical sorting of input Subdir is allowed by the Action fct  (for multiples series entries)
2464if isfield(ParamOut,'AllowInputSort')&&isequal(ParamOut.AllowInputSort,'on')&& size(Param.InputTable,1)>1
2465    [tild,iview]=sort(Param.InputTable(:,2)); % subdirectories sorted in alphabetical order
2466    set(handles.InputTable,'Data',Param.InputTable(iview,:));
2467    MinIndex_i=get(handles.MinIndex_i,'Data');
2468    MinIndex_j=get(handles.MinIndex_j,'Data');
2469    MaxIndex_i=get(handles.MaxIndex_i,'Data');
2470    MaxIndex_j=get(handles.MaxIndex_j,'Data');
2471    set(handles.MinIndex_i,'Data',MinIndex_i(iview,:));
2472    set(handles.MinIndex_j,'Data',MinIndex_j(iview,:));
2473    set(handles.MaxIndex_i,'Data',MaxIndex_i(iview,:));
2474    set(handles.MaxIndex_j,'Data',MaxIndex_j(iview,:));
2475    TimeTable=get(handles.TimeTable,'Data');
2476    set(handles.TimeTable,'Data',TimeTable(iview,:));
2477    PairString=get(handles.PairString,'Data');
2478    set(handles.PairString,'Data',PairString(iview,:));
2479end
2480
2481%% Impose the whole input file index range if requested
2482if isfield(ParamOut,'WholeIndexRange')&&isequal(ParamOut.WholeIndexRange,'on')
2483    MinIndex_i=get(handles.MinIndex_i,'Data');
2484    MinIndex_j=get(handles.MinIndex_j,'Data');
2485    MaxIndex_i=get(handles.MaxIndex_i,'Data');
2486    MaxIndex_j=get(handles.MaxIndex_j,'Data');
2487    set(handles.num_first_i,'String',num2str(MinIndex_i(1)))% set first as the min index (for the first line)
2488    set(handles.num_last_i,'String',num2str(MaxIndex_i(1)))% set last as the max index (for the first line)
2489    set(handles.num_incr_i,'String','1')
2490    set(handles.num_first_j,'String',num2str(MinIndex_j(1)))% set first as the min index (for the first line)
2491    set(handles.num_last_j,'String',num2str(MaxIndex_j(1)))% set last as the max index (for the first line)
2492    set(handles.num_incr_j,'String','1')
2493else  % check index ranges
2494    first_i=1;last_i=1;first_j=1;last_j=1;
2495    if isfield(Param.IndexRange,'first_i')
2496        first_i=Param.IndexRange.first_i;
2497        last_i=Param.IndexRange.last_i;
2498    end
2499    if isfield(Param.IndexRange,'first_j')
2500        first_j=Param.IndexRange.first_j;
2501        last_j=Param.IndexRange.last_j;
2502    end
2503    if last_i < first_i || last_j < first_j , msgbox_uvmat('ERROR','last field number must be larger than the first one'),...
2504            set(handles.RUN, 'Enable','On'), set(handles.RUN,'BackgroundColor',[1 0 0]),return,end;
2505end
2506
2507%% enable or desable j index visibility
2508status_j='on'; % default
2509if isempty(find(~cellfun(@isempty,SeriesData.j1_series), 1)); % case of empty j indices
2510    status_j='off'; % no j index needed
2511elseif strcmp(get(handles.PairString,'Visible'),'on')
2512    check_burst=cellfun(@isempty,regexp(get(handles.PairString,'Data'),'^j')); % =0 for burst case, 1 otherwise
2513    if isempty(find(check_burst, 1))% if all pair string begins by j (burst)
2514        status_j='off'; % no j index needed for bust case
2515    end
2516end
2517enable_j(handles,status_j) % no j index needed
2518if isfield(ParamOut,'j_index_1')&& isfield(ParamOut,'j_index_2')%strcmp(ParamOut.Desable_j_index,'on')
2519    %status_j='off';
2520    set(handles.num_first_j,'String',num2str(ParamOut.j_index_1))
2521    set(handles.num_last_j,'String',num2str(ParamOut.j_index_2))
2522    set(handles.num_first_j,'enable','off')
2523    set(handles.num_last_j,'enable','off')
2524    set(handles.num_incr_j,'visible','off')
2525else
2526    set(handles.num_first_j,'enable','on')
2527    set(handles.num_last_j,'enable','on')
2528    set(handles.num_incr_j,'visible',status_j)
2529end
2530
2531%% NbSlice visibility
2532if isfield(ParamOut,'NbSlice') && (strcmp(ParamOut.NbSlice,'on')||isnumeric(ParamOut.NbSlice))
2533    set(handles.num_NbSlice,'Visible','on')
2534    set(handles.NbSlice_title,'Visible','on')
2535else
2536    set(handles.num_NbSlice,'Visible','off')
2537    set(handles.NbSlice_title,'Visible','off')
2538end
2539if isfield(ParamOut,'NbSlice') && isnumeric(ParamOut.NbSlice)
2540    set(handles.num_NbSlice,'String',num2str(ParamOut.NbSlice))
2541    set(handles.num_NbSlice,'Enable','off'); % NbSlice set by the activation of the Action function
2542else
2543    set(handles.num_NbSlice,'Enable','on'); % NbSlice can be modified on the GUI series
2544end
2545
2546%% Visibility of FieldTransform menu
2547FieldTransformVisible='off';  %hidden by default
2548if isfield(ParamOut,'FieldTransform')
2549    if ~strcmp(ParamOut.FieldTransform,'off')
2550    FieldTransformVisible='on'; 
2551    end
2552    if iscell(ParamOut.FieldTransform)
2553        SeriesData.TransformList=ParamOut.FieldTransform;
2554    end
2555    TransformName_Callback([],[], handles)
2556end
2557set(handles.FieldTransform,'Visible',FieldTransformVisible)
2558if isfield(ParamOut,'TransformPath');% record the path of transform function requested for compilation
2559    set(handles.TransformPath,'UserData',ParamOut.TransformPath)
2560else
2561    set(handles.TransformPath,'UserData',[])
2562end
2563
2564%% Visibility of projection object
2565ProjObjectVisible='off';  %hidden by default
2566if isfield(ParamOut,'ProjObject')
2567    ProjObjectVisible=ParamOut.ProjObject;
2568end
2569set(handles.CheckObject,'Visible',ProjObjectVisible)
2570if ~get(handles.CheckObject,'Value')
2571    ProjObjectVisible='off';
2572end
2573set(handles.ProjObject,'Visible',ProjObjectVisible)
2574set(handles.DeleteObject,'Visible',ProjObjectVisible)
2575set(handles.ViewObject,'Visible',ProjObjectVisible)
2576set(handles.EditObject,'Visible',ProjObjectVisible)
2577
2578%% Visibility of mask input
2579MaskVisible='off';  %hidden by default
2580if isfield(ParamOut,'Mask')
2581    MaskVisible=ParamOut.Mask;
2582end
2583set(handles.CheckMask,'Visible',MaskVisible);
2584
2585%% definition of the directory containing the output files
2586if  ~(isfield(SeriesData,'ActionName') && strcmp(ActionName,SeriesData.ActionName))
2587    OutputDirExt='.series'; % default
2588    if isfield(ParamOut,'OutputDirExt')&&~isempty(ParamOut.OutputDirExt)
2589        OutputDirExt=ParamOut.OutputDirExt;
2590    end
2591    set(handles.OutputDirExt,'String',OutputDirExt)
2592end
2593OutputDirVisible='off';
2594OutputSubDirMode='auto'; % default
2595SubDirOut='';
2596if isfield(ParamOut,'OutputSubDirMode')
2597    OutputSubDirMode=ParamOut.OutputSubDirMode;
2598end
2599InputTable=get(handles.InputTable,'Data');
2600switch OutputSubDirMode
2601    case 'auto'; % default
2602        OutputDirVisible='on';
2603        SubDir=InputTable(1:end,2); % set of subdirectories
2604        SubDirOut=SubDir{1};
2605        if numel(SubDir)>1
2606            for ilist=2:numel(SubDir)
2607                SubDirOut=[SubDirOut '-' regexprep(SubDir{ilist},'^/','')];
2608            end
2609        end
2610    case 'one'
2611        OutputDirVisible='on';
2612        SubDirOut=InputTable{1,2}; % use the first subdir name (+OutputDirExt) as output  subdirectory
2613    case 'two'
2614        OutputDirVisible='on';   
2615        SubDir=InputTable(1:2,2); % set of subdirectories
2616        SubDirOut=SubDir{1};
2617        if numel(SubDir)>1
2618                SubDirOut=[SubDirOut '-' regexprep(SubDir{2},'^/','')];
2619        end
2620    case 'last'
2621        OutputDirVisible='on';
2622        SubDirOut=InputTable{end,2}; % use the last subdir name (+OutputDirExt) as output  subdirectory
2623end
2624set(handles.OutputSubDir,'String',SubDirOut)
2625set(handles.OutputSubDir,'BackgroundColor',[1 1 1])% set edit box to white color to indicate refreshment
2626set(handles.OutputDirExt,'Visible',OutputDirVisible)
2627set(handles.OutputSubDir,'Visible',OutputDirVisible)
2628%set(handles.CheckOverwrite,'Visible',OutputDirVisible)
2629set(handles.OutputDir_title,'Visible',OutputDirVisible)
2630SeriesData.ActionName=ActionName; % record ActionName for next use
2631
2632
2633%% visibility of the run mode (local or background or cluster)
2634if strcmp(OutputSubDirMode,'none')
2635    RunModeVisible='off'; % only local mode available if no output file is produced
2636else
2637    RunModeVisible='on';
2638end
2639set(handles.RunMode,'Visible',RunModeVisible)
2640set(handles.ActionExt,'Visible',RunModeVisible)
2641set(handles.RunMode_title,'Visible',RunModeVisible)
2642set(handles.ActionExt_title,'Visible',RunModeVisible)
2643
2644
2645%% Expected nbre of output files
2646if isfield(ParamOut,'OutputFileMode')
2647    StatusData.OutputFileMode=ParamOut.OutputFileMode;
2648    set(handles.status,'UserData',StatusData)
2649end
2650
2651%% definition of an additional parameter set, determined by an ancillary GUI
2652if isfield(ParamOut,'ActionInput')
2653%     set(handles.ActionInput,'Visible','on')
2654    ParamOut.ActionInput.Program=ActionName; % record the program in ActionInput
2655    SeriesData.ActionInput=ParamOut.ActionInput;
2656else
2657%     set(handles.ActionInput,'Visible','off')
2658    if isfield(SeriesData,'ActionInput')
2659        SeriesData=rmfield(SeriesData,'ActionInput');
2660    end
2661end
2662set(handles.series,'UserData',SeriesData)
2663set(handles.ActionInput,'BackgroundColor',[1 0 0])
2664
2665%------------------------------------------------------------------------
2666% --- Executes on selection change in FieldName.
2667function FieldName_Callback(hObject, eventdata, handles)
2668%------------------------------------------------------------------------
2669field_str=get(handles.FieldName,'String');
2670field_index=get(handles.FieldName,'Value');
2671field=field_str{field_index(1)};
2672if isequal(field,'get_field...')
2673    SeriesData=get(handles.series,'UserData');
2674    % input line for which the field choice is relevant
2675    iview=find(ismember(SeriesData.FileType,{'netcdf','civx','civdata'})); % all nc files, icluding civ
2676    hget_field=findobj(allchild(0),'name','get_field');
2677    if ~isempty(hget_field)
2678        delete(hget_field)%delete opened versions of get_field
2679    end
2680    Param=read_GUI(handles.series);
2681    InputTable=Param.InputTable(iview,:);
2682    % check the existence of the first file in the series
2683    first_j=[];last_j=[];MinIndex_j=1;MaxIndex_j=1; % default setting for index j
2684    if isfield(Param.IndexRange,'first_j'); % if index j is used     
2685        first_j=Param.IndexRange.first_j;
2686        last_j=Param.IndexRange.last_j;
2687        MinIndex_j=Param.IndexRange.MinIndex_j(iview);
2688        MaxIndex_j=Param.IndexRange.MaxIndex_j(iview);
2689    end
2690    PairString='';
2691    if isfield(Param.IndexRange,'PairString'); PairString=Param.IndexRange.PairString{iview}; end
2692    [i1,i2,j1,j2] = get_file_index(Param.IndexRange.first_i,first_j,PairString);
2693    LineIndex=iview(1);
2694    if numel(iview)>1     
2695        answer=msgbox_uvmat('INPUT_TXT',['select the line of the input table:' num2str(iview)] ,num2str(iview(1)));
2696        LineIndex=str2num(answer);
2697%         InputLine=str2num(get(handles.InputLine,'String'));
2698%         if ismember(InputLine,iview)
2699%             LineIndex=InputLine;
2700%         end
2701    end
2702    FirstFileName=fullfile_uvmat(InputTable{LineIndex,1},InputTable{LineIndex,2},InputTable{LineIndex,3},...
2703        InputTable{LineIndex,5},InputTable{LineIndex,4},i1,i2,j1,j2);
2704    if exist(FirstFileName,'file')
2705        ParamIn.Title='get_field: pick input variables and coordinates for series processing';
2706        ParamIn.SeriesInput=1;
2707        GetFieldData=get_field(FirstFileName,ParamIn);
2708        FieldList={};
2709        if isfield(GetFieldData,'FieldOption')% if a field has been selected
2710        switch GetFieldData.FieldOption
2711            case 'vectors'
2712                UName=GetFieldData.PanelVectors.vector_x;
2713                VName=GetFieldData.PanelVectors.vector_y;
2714                YName={GetFieldData.Coordinates.Coord_y};
2715                FieldList={['vec(' UName ',' VName ')'];...
2716                    ['norm(' UName ',' VName ')'];...
2717                    UName;VName};
2718            case {'scalar'}
2719                FieldList=GetFieldData.PanelScalar.scalar;
2720                YName={GetFieldData.Coordinates.Coord_y};
2721                if ischar(FieldList)
2722                    FieldList={FieldList};
2723                end
2724            case 'civdata...'
2725                FieldList=[set_field_list('U','V') ;{'C'}];
2726                set(handles.FieldName,'Value',1) % set menu to 'velocity
2727                XName='X';
2728                YName='y';
2729        end
2730        set(handles.FieldName,'Value',1)
2731        set(handles.FieldName,'String',[FieldList; {'get_field...'}]);
2732        if ~strcmp(GetFieldData.FieldOption,'civdata...')
2733           if ~isempty(regexp(FieldList{1},'^vec'))
2734                set(handles.FieldName,'Value',1)
2735           else
2736                set(handles.FieldName,'Value',1:numel(FieldList))%select all input fields by default
2737           end
2738            XName=GetFieldData.Coordinates.Coord_x;
2739            YName=GetFieldData.Coordinates.Coord_y;
2740            TimeNameStr=GetFieldData.Time.SwitchVarIndexTime;
2741            % get the time info                     
2742            TimeTable=get(handles.TimeTable,'Data');
2743            switch TimeNameStr
2744                case 'file index'
2745                    TimeName='';
2746                case 'attribute'
2747                    TimeName=['att:' GetFieldData.Time.TimeName];
2748                    % update the time table
2749                    TimeTable{LineIndex,2}=get_time(Param.IndexRange.MinIndex_i(LineIndex),MinIndex_j,PairString,InputTable,SeriesData.FileInfo{LineIndex},GetFieldData.Time.TimeName);  % Min time     
2750                    TimeTable{LineIndex,3}=get_time(Param.IndexRange.first_i,first_j,PairString,InputTable,SeriesData.FileInfo{LineIndex},GetFieldData.Time.TimeName);  % first time             
2751                    TimeTable{LineIndex,4}=get_time(Param.IndexRange.last_i,last_j,PairString,InputTable,SeriesData.FileInfo{LineIndex},GetFieldData.Time.TimeName);  % last time                     
2752                    TimeTable{LineIndex,5}=get_time(Param.IndexRange.MaxIndex_i(LineIndex),MaxIndex_j,PairString,InputTable,SeriesData.FileInfo{LineIndex},GetFieldData.Time.TimeName);  % Max time
2753                case 'variable'
2754                    set(handles.TimeName,'String',['var:' GetFieldData.Time.TimeName])
2755                    set(handles.NomType,'String','*')
2756                    set(handles.RootFile,'String',[get(handles.RootFile,'String') get(handles.FileIndex,'String')])% A VERIFIER !!!!!!
2757                    set(handles.FileIndex,'String','')
2758                    ParamIn.TimeVarName=GetFieldData.Time.TimeName;
2759                case 'matrix_index'
2760                    TimeName=['dim:' GetFieldData.Time.TimeName];
2761                    set(handles.NomType,'String','*')
2762                    set(handles.RootFile,'String',[get(handles.RootFile,'String') get(handles.FileIndex,'String')])
2763                    set(handles.FileIndex,'String','')
2764                    ParamIn.TimeDimName=GetFieldData.Time.TimeName;
2765            end
2766            TimeTable{LineIndex,1}=TimeName;
2767            set(handles.TimeTable,'Data',TimeTable);
2768        end
2769        set(handles.Coord_x,'String',XName)
2770        set(handles.Coord_y,'String',YName)
2771        set(handles.Coord_x,'Visible','on')
2772        set(handles.Coord_y,'Visible','on')
2773        end
2774    else
2775        msgbox_uvmat('ERROR',[FirstFileName ' does not exist'])
2776    end
2777end
2778
2779
2780function [TimeValue,DtValue]=get_time(ref_i,ref_j,PairString,InputTable,FileInfo,TimeName,DtName)
2781[i1,i2,j1,j2] = get_file_index(ref_i,ref_j,PairString);
2782FileName=fullfile_uvmat(InputTable{1},InputTable{2},InputTable{3},InputTable{5},InputTable{4},i1,i2,j1,j2);
2783Data=nc2struct(FileName,[]);
2784TimeValue=[];
2785DtValue=[];
2786if isequal(FileInfo.FileType,'civdata')
2787    if ismember(TimeName,{'civ1','filter1'})
2788        if isfield(Data,'Civ1_Time')
2789        TimeValue=Data.Civ1_Time;
2790        end
2791        if isfield(Data,'Civ1_Dt')
2792        DtValue=Data.Civ1_Dt;
2793        end
2794    else
2795        if isfield(Data,'Civ2_Time')
2796        TimeValue=Data.Civ2_Time;
2797        end
2798        if isfield(Data,'Civ2_Dt')
2799        DtValue=Data.Civ2_Dt;
2800        end
2801    end
2802else
2803    if ~isempty(TimeName)&& isfield(Data,TimeName)
2804        TimeValue=Data.(TimeName);
2805    end
2806    if exist('DtName','var') && isfield(Data,DtName)
2807        DtValue=Data.(DtName);
2808    end
2809end
2810
2811%------------------------------------------------------------------------
2812% --- Executes on selection change in FieldName_1.
2813function FieldName_1_Callback(hObject, eventdata, handles)
2814%------------------------------------------------------------------------
2815field_str=get(handles.FieldName_1,'String');
2816field_index=get(handles.FieldName_1,'Value');
2817field=field_str{field_index(1)};
2818if isequal(field,'get_field...')
2819    hget_field=findobj(allchild(0),'name','get_field');
2820    if ~isempty(hget_field)
2821        delete(hget_field)%delete opened versions of get_field
2822    end
2823    Param=read_GUI(handles.series);
2824    Param.InputTable=Param.InputTable(1,:);
2825    % check the existence of the first file in the series
2826    first_j=[];
2827    if isfield(Param.IndexRange,'first_j'); first_j=Param.IndexRange.first_j; end
2828    if isfield(Param.IndexRange,'last_j'); last_j=Param.IndexRange.last_j; end
2829    PairString='';
2830    if isfield(Param.IndexRange,'PairString'); PairString=Param.IndexRange.PairString; end
2831    [i1,i2,j1,j2] = get_file_index(Param.IndexRange.first_i,first_j,PairString);
2832    FirstFileName=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},...
2833        Param.InputTable{1,5},Param.InputTable{1,4},i1,i2,j1,j2);
2834    if exist(FirstFileName,'file')
2835        ParamIn.SeriesInput=1;
2836        GetFieldData=get_field(FirstFileName,ParamIn);
2837        FieldList={};
2838        switch GetFieldData.FieldOption
2839            case 'vectors'
2840                UName=GetFieldData.PanelVectors.vector_x;
2841                VName=GetFieldData.PanelVectors.vector_y;
2842                FieldList={['vec(' UName ',' VName ')'];...
2843                    ['norm(' UName ',' VName ')'];...
2844                    UName;VName};
2845            case {'scalar','pick variables'}
2846                FieldList=GetFieldData.PanelScalar.scalar;
2847                if ischar(FieldList)
2848                    FieldList={FieldList};
2849                end
2850            case '1D plot'
2851
2852            case 'civdata...'
2853                FieldList=set_field_list('U','V','C');
2854                set(handles.FieldName,'Value',2) % set menu to 'velocity
2855        end
2856        if ~strcmp(GetFieldData.FieldOption,'civdata...')
2857            TimeNameStr=GetFieldData.Time.SwitchVarIndexTime;
2858            switch TimeNameStr
2859                case 'file index'
2860                    set(handles.TimeName,'String','');
2861                case 'attribute'
2862                    set(handles.TimeName,'String',['att:' GetFieldData.Time.TimeName]);
2863                case 'variable'
2864                    set(handles.TimeName,'String',['var:' GetFieldData.Time.TimeName])
2865                    set(handles.NomType,'String','*')
2866                    set(handles.RootFile,'String',[get(handles.RootFile,'String') get(handles.FileIndex,'String')])% A VERIFIER !!!!!!
2867                    set(handles.FileIndex,'String','')
2868                    ParamIn.TimeVarName=GetFieldData.Time.TimeName;
2869                case 'matrix_index'
2870                    set(handles.TimeName,'String',['dim:' GetFieldData.Time.TimeName]);
2871                    set(handles.NomType,'String','*')
2872                    set(handles.RootFile,'String',[get(handles.RootFile,'String') get(handles.FileIndex,'String')])
2873                    set(handles.FileIndex,'String','')
2874                    ParamIn.TimeDimName=GetFieldData.Time.TimeName;
2875            end
2876        end
2877        set(handles.FieldName_1,'Value',1)
2878        set(handles.FieldName_1,'String',[FieldList; {'get_field...'}]);
2879    end
2880end   
2881
2882
2883%%%%%%%%%%%%%
2884function [ind_remove]=find_pairs(dirpair,ind_i,last_i)
2885indsel=ind_i;
2886indiff=diff(ind_i); % test index increment to detect multiplets (several pairs with the same index ind_i) and holes in the series
2887indiff=[1 indiff last_i-ind_i(end)+1]; % for testing gaps with the imposed bounds
2888if ~isempty(indiff)
2889    indiff2=diff(indiff);
2890    indiffp=[indiff2 1];
2891    indiffm=[1 indiff2];
2892    ind_multi_m=find((indiff==0)&(indiffm<0))-1; % indices of first members of multiplets
2893    ind_multi_p=find((indiff==0)&(indiffp>0)); % indices of last members of multiplets
2894    %for each multiplet, select the most recent file
2895    ind_remove=[];
2896    for i=1:length(ind_multi_m)
2897        ind_pairs=ind_multi_m(i):ind_multi_p(i);
2898        for imulti=1:length(ind_pairs)
2899            datepair(imulti)=datenum(dirpair(ind_pairs(imulti)).date); % dates of creation
2900        end
2901        [datenew,indsort2]=sort(datepair); % sort the multiplet by creation date
2902        ind_s=indsort2(1:end-1); %
2903        ind_remove=[ind_remove ind_pairs(ind_s)]; % remove these indices, leave the last one
2904    end
2905end
2906
2907%------------------------------------------------------------------------
2908% --- determine the list of index pairstring of processing file
2909function [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)
2910%------------------------------------------------------------------------
2911num_i1=num_i; % set of first image numbers by default
2912num_i2=num_i;
2913num_j1=num_j;
2914num_j2=num_j;
2915num_i_out=num_i;
2916num_j_out=num_j;
2917% if isequal (NomType,'_1-2_1') || isequal (NomType,'_1-2')
2918if isequal(mode,'series(Di)')
2919    num_i1_line=num_i+ind_shift(3); % set of first image numbers
2920    num_i2_line=num_i+ind_shift(4);
2921    % adjust the first and last field number
2922        indsel=find(num_i1_line >= 1);
2923    num_i_out=num_i(indsel);
2924    num_i1_line=num_i1_line(indsel);
2925    num_i2_line=num_i2_line(indsel);
2926    num_j1=meshgrid(num_j,ones(size(num_i1_line)));
2927    num_j2=meshgrid(num_j,ones(size(num_i1_line)));
2928    [xx,num_i1]=meshgrid(num_j,num_i1_line);
2929    [xx,num_i2]=meshgrid(num_j,num_i2_line);
2930elseif isequal (mode,'series(Dj)')||isequal (mode,'bursts')
2931    if isequal(mode,'bursts') %case of bursts (png_old or png_2D)
2932        num_j1=ind_shift(1)*ones(size(num_i));
2933        num_j2=ind_shift(2)*ones(size(num_i));
2934    else
2935        num_j1_col=num_j+ind_shift(1); % set of first image numbers
2936        num_j2_col=num_j+ind_shift(2);
2937        % adjust the first field number
2938        indsel=find((num_j1_col >= 1));   
2939        num_j_out=num_j(indsel);
2940        num_j1_col=num_j1_col(indsel);
2941        num_j2_col=num_j2_col(indsel);
2942        [num_i1,num_j1]=meshgrid(num_i,num_j1_col);
2943        [num_i2,num_j2]=meshgrid(num_i,num_j2_col);
2944    end   
2945end
2946
2947%------------------------------------------------------------------------
2948% --- Executes on button press in CheckObject.
2949function CheckObject_Callback(hObject, eventdata, handles)
2950%------------------------------------------------------------------------
2951hset_object=findobj(allchild(0),'tag','set_object'); % find the set_object interface handle
2952if get(handles.CheckObject,'Value')
2953    SeriesData=get(handles.series,'UserData');
2954    if isfield(SeriesData,'ProjObject') && ~isempty(SeriesData.ProjObject)
2955        set(handles.ViewObject,'Value',1)
2956        ViewObject_Callback(hObject, eventdata, handles)
2957    else
2958        if ishandle(hset_object)
2959            uistack(hset_object,'top')% show the GUI set_object if opened
2960        else
2961            %get the object file
2962            InputTable=get(handles.InputTable,'Data');
2963            defaultname=InputTable{1,1};
2964            if isempty(defaultname)
2965                defaultname={''};
2966            end
2967            fileinput=uigetfile_uvmat('pick a xml object file (or use uvmat to create it)',defaultname,'.xml');
2968            if isempty(fileinput)% exit if no object file is selected
2969                set(handles.CheckObject,'Value',0)
2970                return
2971            end
2972            %read the file
2973            data=xml2struct(fileinput);
2974            if ~isfield(data,'Type')
2975                msgbox_uvmat('ERROR',[fileinput ' is not an object xml file'])
2976                set(handles.CheckObject,'Value',0)
2977                return
2978            end
2979            if ~isfield(data,'ProjMode')
2980                data.ProjMode='none';
2981            end
2982            hset_object=set_object(data); % call the set_object interface
2983            set(hset_object,'Name','set_object_series')% name to distinguish from set_object used with uvmat
2984        end
2985        ProjObject=read_GUI(hset_object);
2986        set(handles.ProjObject,'String',ProjObject.Name); % display the object name
2987        SeriesData=get(handles.series,'UserData');
2988        SeriesData.ProjObject=ProjObject;
2989        set(handles.series,'UserData',SeriesData);
2990    end
2991    set(handles.EditObject,'Visible','on');
2992    set(handles.DeleteObject,'Visible','on');
2993    set(handles.ViewObject,'Visible','on');
2994    set(handles.ProjObject,'Visible','on');
2995else
2996    set(handles.EditObject,'Visible','off');
2997    set(handles.DeleteObject,'Visible','off');
2998    set(handles.ViewObject,'Visible','off');
2999    if ~ishandle(hset_object)
3000        set(handles.ViewObject,'Value',0);
3001    end
3002    set(handles.ProjObject,'Visible','off');
3003end
3004
3005%------------------------------------------------------------------------
3006% --- Executes on button press in ViewObject.
3007%------------------------------------------------------------------------
3008function ViewObject_Callback(hObject, eventdata, handles)
3009
3010UserData=get(handles.series,'UserData');
3011hset_object=findobj(allchild(0),'Tag','set_object');
3012if ~isempty(hset_object)
3013    delete(hset_object)% refresh set_object if already opened
3014end
3015hset_object=set_object(UserData.ProjObject);
3016set(hset_object,'Name','view_object_series')
3017
3018
3019%------------------------------------------------------------------------
3020% --- Executes on button press in EditObject.
3021function EditObject_Callback(hObject, eventdata, handles)
3022%------------------------------------------------------------------------
3023if get(handles.EditObject,'Value')
3024    set(handles.ViewObject,'Value',0)
3025    UserData=get(handles.series,'UserData');
3026    hset_object=set_object(UserData.ProjObject);
3027    set(hset_object,'Name','edit_object_series')
3028    set(get(hset_object,'Children'),'Enable','on')
3029else
3030    hset_object=findobj(allchild(0),'Tag','set_object');
3031    if ~isempty(hset_object)
3032        set(get(hset_object,'Children'),'Enable','off')
3033    end
3034end
3035
3036%------------------------------------------------------------------------
3037% --- Executes on button press in DeleteObject.
3038function DeleteObject_Callback(hObject, eventdata, handles)
3039%------------------------------------------------------------------------
3040SeriesData=get(handles.series,'UserData');
3041SeriesData.ProjObject=[];
3042set(handles.series,'UserData',SeriesData)
3043set(handles.ProjObject,'String','')
3044set(handles.ProjObject,'Visible','off')
3045set(handles.CheckObject,'Value',0)
3046set(handles.ViewObject,'Visible','off')
3047set(handles.EditObject,'Visible','off')
3048hset_object=findobj(allchild(0),'name','set_object_series');
3049if ~isempty(hset_object)
3050    delete(hset_object)
3051end
3052set(handles.DeleteObject,'Visible','off')
3053
3054%------------------------------------------------------------------------
3055% --- Executed when CheckMask is activated
3056%------------------------------------------------------------------------
3057function CheckMask_Callback(hObject, eventdata, handles)
3058
3059if get(handles.CheckMask,'Value')
3060    InputTable=get(handles.InputTable,'Data');
3061    nbview=size(InputTable,1);
3062    MaskTable=cell(nbview,1); % default
3063    ListMask=cell(nbview,1); % default
3064    MaskData=get(handles.MaskTable,'Data');
3065    MaskData(size(MaskData,1):nbview,1)=cell(size(MaskData,1):nbview,1); % complement if undefined lines
3066    for iview=1:nbview
3067        ListMask{iview,1}=num2str(iview);
3068        RootPath=InputTable{iview,1};
3069        if ~isempty(RootPath)
3070            if isempty(MaskData{iview})
3071                SubDir=InputTable{iview,2};
3072                MaskPath=fullfile(RootPath,[regexprep(SubDir,'\..*','') '.mask']); % take the root part of SubDir, before the first dot '.'
3073                if exist(MaskPath,'dir')
3074                    ListStruct=dir(MaskPath); % look for a mask file
3075                    ListCells=struct2cell(ListStruct); % transform dir struct to a cell arrray
3076                    check_dir=cell2mat(ListCells(4,:)); % =1 for directories, =0 for files
3077                    ListFiles=ListCells(1,:); % list of file and dri names
3078                    ListFiles=ListFiles(~check_dir); % list of file names (excluding dir)
3079                    mdetect=0;
3080                    if ~isempty(ListFiles)
3081                        for ifile=1:numel(ListFiles)
3082                            [tild,tild,MaskFile{ifile},i1_series,i2_series,j1_series,j2_series,MaskNomType,MaskFileType]=find_file_series(MaskPath,ListFiles{ifile},0);
3083                            if strcmp(MaskFileType,'image') && isempty(i2_series) && isempty(j2_series)
3084                                mdetect=1;
3085                                MaskName=ListFiles{ifile};
3086                            end
3087                            if ~strcmp(MaskFile{ifile},MaskFile{1})
3088                                mdetect=0; % cancel detection test in case of multiple masks, use the brower for selection
3089                                break
3090                            end
3091                        end
3092                    end
3093                    if mdetect==1
3094                        MaskName=fullfile(MaskPath,'mask_1.png');
3095                    else
3096                        MaskName=uigetfile_uvmat('select a mask file:',MaskPath,'image');
3097                    end
3098                else
3099                    MaskName=uigetfile_uvmat('select a mask file:',RootPath,'image');
3100                end
3101                MaskTable{iview,1}=MaskName ;
3102                ListMask{iview,1}=num2str(iview);
3103            end
3104        end
3105    end
3106    set(handles.MaskTable,'Data',MaskTable)
3107    set(handles.MaskTable,'Visible','on')
3108    set(handles.MaskBrowse,'Visible','on')
3109    set(handles.ListMask,'Visible','on')
3110    set(handles.ListMask,'String',ListMask)
3111    set(handles.ListMask,'Value',1)
3112else
3113    set(handles.MaskTable,'Visible','off')
3114    set(handles.MaskBrowse,'Visible','off')
3115    set(handles.ListMask,'Visible','off')
3116end
3117
3118%------------------------------------------------------------------------
3119% --- Executes on button press in MaskBrowse.
3120%------------------------------------------------------------------------
3121function MaskBrowse_Callback(hObject, eventdata, handles)
3122
3123InputTable=get(handles.InputTable,'Data');
3124iview=get(handles.ListMask,'Value');
3125RootPath=InputTable{iview,1};
3126MaskName=uigetfile_uvmat('select a mask file:',RootPath,'image');
3127if ~isempty(MaskName)
3128    MaskTable=get(handles.MaskTable,'Data');
3129    MaskTable{iview,1}=MaskName ;
3130    set(handles.MaskTable,'Data',MaskTable)
3131end
3132
3133%------------------------------------------------------------------------
3134% --- Executes when selected cell(s) is changed in MaskTable.
3135%------------------------------------------------------------------------
3136function MaskTable_CellSelectionCallback(hObject, eventdata, handles)
3137
3138if numel(eventdata.Indices)>=1
3139set(handles.ListMask,'Value',eventdata.Indices(1))
3140end
3141
3142%-------------------------------------------------------------------
3143function MenuHelp_Callback(hObject, eventdata, handles)
3144%-------------------------------------------------------------------
3145
3146
3147% path_to_uvmat=which ('uvmat'); % check the path of uvmat
3148% pathelp=fileparts(path_to_uvmat);
3149% helpfile=fullfile(pathelp,'uvmat_doc','uvmat_doc.html');
3150% 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')
3151% else
3152%     addpath (fullfile(pathelp,'uvmat_doc'))
3153%     web([helpfile '#series'])
3154% end
3155
3156%-------------------------------------------------------------------
3157% --- Executes on selection change in TransformName.
3158function TransformName_Callback(hObject, eventdata, handles)
3159%----------------------------------------------------------------------
3160TransformList=get(handles.TransformName,'String');
3161TransformIndex=get(handles.TransformName,'Value');
3162TransformName=TransformList{TransformIndex};
3163TransformPathList=get(handles.TransformName,'UserData');
3164nb_builtin_transform=4;
3165if isequal(TransformName,'more...');     
3166    FileName=uigetfile_uvmat('Pick a transform function',get(handles.TransformPath,'String'),'.m');
3167    if isempty(FileName)
3168        return     %browser closed without choice
3169    end
3170    [TransformPath,TransformName,TransformExt]=fileparts(FileName); % removes extension .m
3171    if ~strcmp(TransformExt,'.m')
3172        msgbox_uvmat('ERROR','a Matlab function .m must be introduced');
3173        return
3174    end
3175     % insert the choice in the menu
3176    TransformIndex=find(strcmp(TransformName,TransformList),1); % look for the selected function in the menu Action
3177    if isempty(TransformIndex)%the input string does not exist in the menu
3178        TransformIndex= length(TransformList);
3179        TransformList=[TransformList(1:end-1);{TransformName};TransformList(end)]; % the selected function is appended in the menu, before the last item 'more...'
3180        set(handles.TransformName,'String',TransformList)
3181        TransformPathList=[TransformPathList;{TransformPath}];
3182    else% the input function already exist, we update its path (possibly new)
3183        TransformPathList{TransformIndex}=TransformPath; %
3184        set(handles.TransformName,'Value',TransformIndex)
3185    end
3186   % save the new menu in the personal file 'uvmat_perso.mat'
3187   dir_perso=prefdir; % personal Matalb directory
3188   profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
3189   if exist(profil_perso,'file')
3190       for ilist=nb_builtin_transform+1:numel(TransformPathList)
3191           TransformListUser{ilist-nb_builtin_transform}=TransformList{ilist};
3192           TransformPathListUser{ilist-nb_builtin_transform}=TransformPathList{ilist};
3193       end
3194       TransformPathListUser=TransformPathListUser';
3195       TransformListUser=TransformListUser';
3196       save (profil_perso,'TransformPathListUser','TransformListUser','-append'); % store the root name for future opening of uvmat
3197   end
3198end
3199
3200%display the current function path
3201set(handles.TransformPath,'String',TransformPathList{TransformIndex}); % show the path to the senlected function
3202set(handles.TransformName,'UserData',TransformPathList);
3203
3204%% create the function handle of the selected fct
3205if ~isempty(TransformName)
3206    if ~exist(TransformPathList{TransformIndex},'dir')
3207        msgbox_uvmat('ERROR',['The prescribed transform function path ' TransformPathList{TransformIndex} ' does not exist']);
3208        return
3209    end
3210    current_dir=pwd; % current working dir
3211    cd(TransformPathList{TransformIndex})
3212    transform_handle=str2func(TransformName);
3213    cd(current_dir)
3214    Field.Action.RUN=0;% indicate that the transform fct is called only to get input param
3215    SeriesData=get(handles.series,'UserData');
3216    ParamIn=[];
3217    if isfield(SeriesData,'TransformInput')
3218        ParamIn.TransformInput=SeriesData.TransformInput;
3219    end
3220    DataOut=feval(transform_handle,Field,ParamIn);% execute the transform fct to get the required conditions
3221    Field.Action.RUN=0; % indicate that the transform fct is called only to get input param
3222    DataOut=feval(transform_handle,Field,[]); % execute the transform fct to get the required conditions
3223    if isfield(DataOut,'TransformInput')%  used to add transform parameters at selection of the transform fct
3224        SeriesData.TransformInput=DataOut.TransformInput;
3225        set(handles.series,'UserData',SeriesData)
3226    end
3227end
3228
3229%------------------------------------------------------------------------
3230% --- fct activated by the upper bar menu ExportConfig
3231%------------------------------------------------------------------------
3232function MenuDisplayConfig_Callback(hObject, eventdata, handles)
3233
3234global Param
3235Param=read_GUI_series(handles);
3236evalin('base','global Param')%make CurData global in the workspace
3237display('current series config :')
3238evalin('base','Param') %display CurData in the workspace
3239commandwindow; % brings the Matlab command window to the front
3240
3241%------------------------------------------------------------------------
3242% --- fct activated by the upper bar menu InportConfig: import
3243%     menu settings from an xml file (stored in /0_XML for each run)
3244%------------------------------------------------------------------------
3245function MenuImportConfig_Callback(hObject, eventdata, handles)
3246
3247%% use a browser to choose the xml file containing the processing config
3248InputTable=get(handles.InputTable,'Data');
3249oldfile=InputTable{1,1}; % current path in InputTable
3250if isempty(oldfile)
3251    % use a file name stored in prefdir
3252    dir_perso=prefdir;
3253    profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
3254    if exist(profil_perso,'file')
3255        h=load (profil_perso);
3256        if isfield(h,'RootPath') && ischar(h.RootPath)
3257            oldfile=h.RootPath;
3258        end
3259    end
3260end
3261filexml=uigetfile_uvmat('pick a xml parameter file',oldfile,'.xml'); % get the xml file containing processing parameters
3262if isempty(filexml), return, end % quit function if an xml file has not been opened
3263
3264%% fill the GUI series with the content of the xml file
3265Param=xml2struct(filexml); % read the input xml file as a Matlab structure
3266
3267% ask to stop current Action if button RUN is in action (another process is already running)
3268if isequal(get(handles.RUN,'Value'),1)
3269    answer= msgbox_uvmat('INPUT_Y-N','stop current Action process?');
3270    if strcmp(answer,'Yes')
3271        STOP_Callback(hObject, eventdata, handles)
3272    else
3273        return
3274    end
3275end
3276Param.Action.RUN=0; % desactivate the input RUN=1
3277
3278fill_GUI(Param,handles.series)% fill the elements of the GUI series with the input parameters
3279SeriesData=get(handles.series,'UserData');
3280if isfield(Param,'InputFields')
3281    ListField=Param.InputFields.FieldName;
3282    if ischar(ListField),ListField={ListField}; end
3283    set(handles.FieldName,'String',[ListField;{'get-field...'}])
3284     set(handles.FieldName,'Value',1:numel(ListField))
3285     set(handles.FieldName,'Visible','on')
3286end       
3287if isfield(Param,'ActionInput')%  introduce  parameters specific to an Action fct, for instance PIV parameters
3288%     set(handles.ActionInput,'Visible','on')
3289%     set(handles.ActionInput,'Value',0)
3290    Param.ActionInput.ConfigSource=filexml; % record the source of config for future info
3291    SeriesData.ActionInput=Param.ActionInput;
3292end
3293if isfield(Param,'TransformInput')%  introduce  parameters specific to a transform fct
3294    SeriesData.TransformInput=Param.TransformInput;
3295end
3296if isfield(Param,'ProjObject') %introduce projection object if relevant
3297    SeriesData.ProjObject=Param.ProjObject;
3298end
3299set(handles.series,'UserData',SeriesData)
3300if isfield(Param,'CheckObject') && isequal(Param.CheckObject,1)
3301    set(handles.ProjObject,'String',Param.ProjObject.Name)
3302    set(handles.ViewObject,'Visible','on')
3303    set(handles.EditObject,'Visible','on')
3304    set(handles.DeleteObject,'Visible','on')
3305else     
3306    set(handles.ProjObject,'String','')
3307    set(handles.ProjObject,'Visible','off')
3308    set(handles.ViewObject,'Visible','off')
3309    set(handles.EditObject,'Visible','off')
3310    set(handles.DeleteObject,'Visible','off')     
3311end     
3312set(handles.REFRESH,'BackgroundColor',[1 0 1]); % paint REFRESH button in magenta to indicate that it should be activated
3313
3314
3315%------------------------------------------------------------------------
3316% --- Executes when the GUI series is resized.
3317%------------------------------------------------------------------------
3318function series_ResizeFcn(hObject, eventdata, handles)
3319
3320%% input table
3321set(handles.InputTable,'Unit','pixel')
3322Pos=get(handles.InputTable,'Position');
3323set(handles.InputTable,'Unit','normalized')
3324ColumnWidth=round([0.5 0.14 0.14 0.14 0.08]*(Pos(3)-52));
3325ColumnWidth=num2cell(ColumnWidth);
3326set(handles.InputTable,'ColumnWidth',ColumnWidth)
3327
3328%% MinIndex_j and MaxIndex_i
3329unit=get(handles.MinIndex_i,'Unit');
3330set(handles.MinIndex_i,'Unit','pixel')
3331Pos=get(handles.MinIndex_i,'Position');
3332set(handles.MinIndex_i,'Unit',unit)
3333set(handles.MinIndex_i,'ColumnWidth',{Pos(3)-18})
3334set(handles.MaxIndex_i,'ColumnWidth',{Pos(3)-18})
3335set(handles.MinIndex_j,'ColumnWidth',{Pos(3)-18})
3336set(handles.MaxIndex_j,'ColumnWidth',{Pos(3)-18})
3337
3338%% TimeTable
3339set(handles.TimeTable,'Unit','pixel')
3340Pos=get(handles.TimeTable,'Position');
3341set(handles.TimeTable,'Unit','normalized')
3342% ColumnWidth=get(handles.TimeTable,'ColumnWidth');
3343ColumnWidth=num2cell(floor([0.2 0.2 0.2 0.2 0.2]*(Pos(3)-20)));
3344set(handles.TimeTable,'ColumnWidth',ColumnWidth)
3345
3346
3347%% PairString
3348set(handles.PairString,'Unit','pixel')
3349Pos=get(handles.PairString,'Position');
3350set(handles.PairString,'Unit','normalized')
3351set(handles.PairString,'ColumnWidth',{Pos(3)-5})
3352
3353%% MaskTable
3354set(handles.MaskTable,'Unit','pixel')
3355Pos=get(handles.MaskTable,'Position');
3356set(handles.MaskTable,'Unit','normalized')
3357set(handles.MaskTable,'ColumnWidth',{Pos(3)-5})
3358
3359%------------------------------------------------------------------------
3360% --- Executes on button press in status.
3361%------------------------------------------------------------------------
3362function status_Callback(hObject, eventdata, handles)
3363
3364if get(handles.status,'Value')
3365    set(handles.status,'BackgroundColor',[1 1 0])
3366    drawnow
3367    Param=read_GUI(handles.series);
3368    RootPath=Param.InputTable{1,1};
3369    if ~isfield(Param,'OutputSubDir')   
3370        msgbox_uvmat('ERROR','no standard sub-directory definition for output files, use a browser to check the output')
3371        set(handles.status,'BackgroundColor',[0 1 0])
3372        return
3373    end
3374    OutputSubDir=[Param.OutputSubDir Param.OutputDirExt]; % subdirectory for output files
3375    OutputDir=fullfile(RootPath,OutputSubDir);
3376    if exist(OutputDir,'dir')
3377        uigetfile_uvmat('status_display',OutputDir)
3378    else
3379        msgbox_uvmat('ERROR','output folder not created yet: calculation did not start')
3380        set(handles.status,'BackgroundColor',[0 1 0])
3381    end
3382else
3383    %% delete current display fig if selection is off
3384    set(handles.status,'BackgroundColor',[0 1 0])
3385    hfig=findobj(allchild(0),'name','status_display');
3386    if ~isempty(hfig)
3387        delete(hfig)
3388    end
3389    return
3390end
3391
3392
3393%------------------------------------------------------------------------   
3394% launched by selecting a file on the list
3395%------------------------------------------------------------------------
3396function view_file(hObject, eventdata)
3397
3398list=get(hObject,'String');
3399index=get(hObject,'Value');
3400rootroot=get(hObject,'UserData');
3401selectname=list{index};
3402ind_dot=regexp(selectname,'\.\.\.');
3403if ~isempty(ind_dot)
3404    selectname=selectname(1:ind_dot-1);
3405end
3406FullSelectName=fullfile(rootroot,selectname);
3407if exist(FullSelectName,'dir')% a directory has been selected
3408    ListFiles=dir(FullSelectName);
3409    ListDisplay=cell(numel(ListFiles),1);
3410    for ilist=2:numel(ListDisplay)% suppress the first line '.'
3411        ListDisplay{ilist-1}=ListFiles(ilist).name;
3412    end
3413    set(hObject,'Value',1)
3414    set(hObject,'String',ListDisplay)
3415    if strcmp(selectname,'..')
3416        FullSelectName=fileparts(fileparts(FullSelectName));
3417    end
3418    set(hObject,'UserData',FullSelectName)
3419    hfig=get(hObject,'parent');
3420    htitlebox=findobj(hfig,'tag','titlebox');   
3421    set(htitlebox,'String',FullSelectName)
3422elseif exist(FullSelectName,'file')%visualise the vel field if it exists
3423    FileInfo=get_file_info(FullSelectName);   
3424    if strcmp(FileInfo.FileType,'txt')
3425        edit(FullSelectName)
3426    elseif strcmp(FileInfo.FileType,'xml')
3427        editxml(FullSelectName)
3428    else
3429        uvmat(FullSelectName)
3430    end
3431    set(gcbo,'Value',1)
3432end
3433
3434
3435%------------------------------------------------------------------------   
3436% launched by refreshing the status figure
3437%------------------------------------------------------------------------
3438function refresh_GUI(hfig)
3439
3440htitlebox=findobj(hfig,'tag','titlebox');
3441hlist=findobj(hfig,'tag','list');
3442hseries=findobj(allchild(0),'tag','series');
3443hstatus=findobj(hseries,'tag','status');
3444StatusData=get(hstatus,'UserData');
3445OutputDir=get(htitlebox,'String');
3446if ischar(OutputDir),OutputDir={OutputDir};end
3447ListFiles=dir(OutputDir{1});
3448if numel(ListFiles)<1
3449    return
3450end
3451ListFiles(1)=[]; % removes the first line ='.'
3452ListDisplay=cell(numel(ListFiles),1);
3453testrecent=0;
3454datnum=zeros(numel(ListDisplay),1);
3455for ilist=1:numel(ListDisplay)
3456    ListDisplay{ilist}=ListFiles(ilist).name;
3457      if ~ListFiles(ilist).isdir && isfield(ListFiles(ilist),'datenum')
3458            datnum(ilist)=ListFiles(ilist).datenum; % only available in recent matlab versions
3459            testrecent=1;
3460       end
3461end
3462set(hlist,'String',ListDisplay)
3463
3464%% Look at date of creation
3465ListDisplay=ListDisplay(datnum~=0);
3466datnum=datnum(datnum~=0); % keep the non zero values corresponding to existing files
3467NbOutputFile=[];
3468if isempty(datnum)
3469    if testrecent
3470        message='no civ result created yet';
3471    else
3472        message='';
3473    end
3474else
3475    [first,indfirst]=min(datnum);
3476    [last,indlast]=max(datnum);
3477    NbOutputFile_str='?';
3478    NbOutputFile=[];
3479    if isfield(StatusData,'NbOutputFile')
3480        NbOutputFile=StatusData.NbOutputFile;
3481        NbOutputFile_str=num2str(NbOutputFile);
3482    end
3483    message={[num2str(numel(datnum)) ' file(s) done over ' NbOutputFile_str] ;['oldest modification:  ' ListDisplay{indfirst} ' : ' datestr(first)];...
3484        ['latest modification:  ' ListDisplay{indlast} ' : ' datestr(last)]};
3485end
3486set(htitlebox,'String', [OutputDir{1};message])
3487
3488%% update the waitbar
3489hwaitbar=findobj(hfig,'tag','waitbar');
3490if ~isempty(NbOutputFile)
3491    BarPosition=get(hwaitbar,'Position');
3492    BarPosition(3)=0.9*numel(datnum)/NbOutputFile;
3493    set(hwaitbar,'Position',BarPosition)
3494end
3495
3496%------------------------------------------------------------------------
3497% --- Executes on selection change in ActionExt.
3498%------------------------------------------------------------------------
3499function ActionExt_Callback(hObject, eventdata, handles)
3500
3501ActionExtList=get(handles.ActionExt,'String');
3502ActionExt=ActionExtList{get(handles.ActionExt,'Value')};
3503if strcmp(ActionExt,'.py (in dev.)')
3504    set(handles.RunMode,'Value',2)
3505end
3506
3507%function num_NbProcess_Callback(hObject, eventdata, handles)
3508
3509
3510function num_NbSlice_Callback(hObject, eventdata, handles)
3511NbSlice=str2num(get(handles.num_NbSlice,'String'));
3512%set(handles.num_NbProcess,'String',num2str(NbSlice))
3513
3514%------------------------------------------------------------------------
3515% --- set the visibility of relevant velocity type menus:
3516function menu=set_veltype_display(Civ,FileType)
3517%------------------------------------------------------------------------
3518if ~exist('FileType','var')
3519    FileType='civx';
3520end
3521switch FileType
3522    case 'civx'
3523        menu={'civ1';'interp1';'filter1';'civ2';'interp2';'filter2'};
3524        if isequal(Civ,0)
3525            imax=0;
3526        elseif isequal(Civ,1) || isequal(Civ,2)
3527            imax=1;
3528        elseif isequal(Civ,3)
3529            imax=3;
3530        elseif isequal(Civ,4) || isequal(Civ,5)
3531            imax=4;
3532        elseif isequal(Civ,6) %patch2
3533            imax=6;
3534        end
3535    case 'civdata'
3536        menu={'civ1';'filter1';'civ2';'filter2'};
3537        if isequal(Civ,0)
3538            imax=0;
3539        elseif isequal(Civ,1) || isequal(Civ,2)
3540            imax=1;
3541        elseif isequal(Civ,3)
3542            imax=2;
3543        elseif isequal(Civ,4) || isequal(Civ,5)
3544            imax=3;
3545        else%if isequal(Civ,6) %patch2
3546            imax=4;
3547        end
3548end
3549menu=menu(1:imax);
3550
3551
3552% --- Executes on mouse motion over figure - except title and menu.
3553function series_WindowButtonMotionFcn(hObject, eventdata, handles)
3554set(hObject,'Pointer','arrow');
3555
3556
3557% --- Executes on button press in SetPairs.
3558function SetPairs_Callback(hObject, eventdata, handles)
3559
3560%% delete previous occurrence of 'set_pairs'
3561hfig=findobj(allchild(0),'Tag','set_pairs');
3562if ~isempty(hfig)
3563delete(hfig)
3564end
3565
3566%% create the GUI set_pairs
3567set(0,'Unit','points')
3568ScreenSize=get(0,'ScreenSize'); % get the size of the screen, to put the fig on the upper right
3569Width=220; % fig width in points (1/72 inch)
3570Height=min(0.8*ScreenSize(4),300);
3571Left=ScreenSize(3)- Width-40; % right edge close to the right, with margin=40
3572Bottom=ScreenSize(4)-Height-40; % put fig at top right
3573hfig=findobj(allchild(0),'Tag','set_slice');
3574if ~isempty(hfig),delete(hfig), end; % delete existing version of the GUI
3575hfig=figure('name','set_pairs','tag','set_pairs','MenuBar','none','NumberTitle','off','Unit','points','Position',[Left,Bottom,Width,Height]);
3576BackgroundColor=get(hfig,'Color');
3577SeriesData=get(handles.series,'UserData');
3578TimeUnit=get(handles.TimeUnit,'String');
3579PairString=get(handles.PairString,'Data');
3580ListViewLines=find(cellfun('isempty',PairString)==0); % find list of non empty pairs
3581ListViewMenu=cell(numel(ListViewLines),1);
3582%iview=get(handles.PairString,'Value');
3583iview=[];
3584for ilist=1:numel(ListViewLines)
3585    ListViewMenu{ilist}=num2str(ListViewLines(ilist));
3586end
3587if isempty(iview)
3588    ListViewValue=numel(ListViewLines); % we work by default on the pair option for the last line which requires pairs
3589    iview=ListViewLines(end);
3590else
3591    ListViewValue=find(ListViewLines==iview);
3592end
3593ref_i=str2num(get(handles.num_first_i,'String'));
3594ref_j=1; % default
3595if strcmp(get(handles.num_first_j,'String'),'Visible')
3596    ref_j=str2num(get(handles.num_first_j,'String'));
3597end
3598[ModeMenu,ModeValue]=update_mode(SeriesData.i1_series{1},SeriesData.i2_series{1},SeriesData.j2_series{1});
3599InputTable=get(handles.InputTable,'Data');
3600displ_pair=update_listpair(SeriesData.i1_series{1},SeriesData.i2_series{1},SeriesData.j1_series{1},SeriesData.j2_series{1},ModeMenu{ModeValue},...
3601                                                 SeriesData.Time{1},TimeUnit,ref_i,ref_j,SeriesData.TimeName,InputTable,SeriesData.FileInfo{1});
3602for iline=1:size(InputTable,1)
3603    viewcell{iline}=num2str(iline);
3604end
3605viewcell=viewcell';
3606ModeMenu={'bursts';'series(Dj)'};
3607ModeValue=1;                                               
3608                   %i1_series,i2_series,j1_series,j2_series,mode,time,TimeUnit,ref_i,ref_j,TimeName,InputTable,FileInfo                             
3609% first raw of the GUI
3610uicontrol('Style','text','Units','normalized', 'Position', [0.05 0.88 0.5 0.1],'BackgroundColor',BackgroundColor,...
3611    'String','row to edit #','FontUnits','points','FontSize',12,'FontWeight','bold','ForegroundColor','blue','HorizontalAlignment','right'); % title
3612uicontrol('Style','popupmenu','Units','normalized', 'Position', [0.54 0.8 0.3 0.2],'BackgroundColor',[1 1 1],...
3613    'Callback',@(hObject,eventdata)ListView_Callback(hObject,eventdata),'String',viewcell,'Value',1,'FontUnits','points','FontSize',12,'FontWeight','bold',...
3614    'Tag','ListView','TooltipString','''ListView'':choice of the file series w for pair display');
3615% second raw of the GUI
3616uicontrol('Style','text','Units','normalized', 'Position', [0.05 0.79 0.7 0.1],'BackgroundColor',BackgroundColor,...
3617    'String','mode of index pairing:','FontUnits','points','FontSize',12,'FontWeight','bold','ForegroundColor','blue','HorizontalAlignment','left'); % title
3618uicontrol('Style','popupmenu','Units','normalized', 'Position', [0.05 0.62 0.9 0.2],'BackgroundColor',[1 1 1],...
3619    'Callback',@(hObject,eventdata)Mode_Callback(hObject,eventdata),'String',ModeMenu,'Value',ModeValue,'FontUnits','points','FontSize',12,'FontWeight','bold',...
3620    'Tag','Mode','TooltipString','''Mode'': choice of the image pair mode');
3621% third raw
3622uicontrol('Style','text','Units','normalized', 'Position', [0.05 0.6 0.7 0.1],'BackgroundColor',BackgroundColor,...
3623    'String','pair choice:','FontUnits','points','FontSize',12,'FontWeight','bold','ForegroundColor','blue','HorizontalAlignment','left'); % title
3624uicontrol('Style','listbox','Units','normalized', 'Position', [0.05 0.42 0.9 0.2],'BackgroundColor',[1 1 1],...
3625    'Callback',@(hObject,eventdata)ListPair_Callback(hObject,eventdata),'String',displ_pair,'Value',1,'FontUnits','points','FontSize',12,'FontWeight','bold',...
3626    'Tag','ListPair','TooltipString','''ListPair'': menu for selecting the image pair');
3627uicontrol('Style','text','Units','normalized', 'Position', [0.1 0.22 0.8 0.1],'BackgroundColor',BackgroundColor,...
3628    'String','ref_i           ref_j','FontUnits','points','FontSize',12,'FontWeight','bold','ForegroundColor','blue','HorizontalAlignment','center'); % title
3629uicontrol('Style','edit','Units','normalized', 'Position', [0.15 0.17 0.3 0.08],'BackgroundColor',[1 1 1],...
3630    'Callback',@(hObject,eventdata)num_ref_i_Callback(hObject,eventdata),'String',num2str(ref_i),'FontUnits','points','FontSize',12,'FontWeight','bold',...
3631    'Tag','num_ref_i','TooltipString','''num_ref_i'': reference field index i used to display dt in ''list_pair_civ''');
3632uicontrol('Style','edit','Units','normalized', 'Position', [0.55 0.17 0.3 0.08],'BackgroundColor',[1 1 1],...
3633    'Callback',@(hObject,eventdata)num_ref_j_Callback(hObject,eventdata),'String',num2str(ref_j),'FontUnits','points','FontSize',12,'FontWeight','bold',...
3634    'Tag','num_ref_j','TooltipString','''num_ref_j'': reference field index i used to display dt in ''list_pair_civ''');
3635uicontrol('Style','pushbutton','Units','normalized', 'Position', [0.01 0.01 0.3 0.12],'BackgroundColor',[0 1 0],...
3636    'Callback',@(hObject,eventdata)OK_Callback(hObject,eventdata),'String','OK','FontUnits','points','FontSize',12,'FontWeight','bold',...
3637    'Tag','OK','TooltipString','''OK'': validate the choice');
3638%  last raw  of the GUI: pushbuttons
3639% 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),...
3640%     'FontWeight','bold','FontUnits','points','FontSize',12,'TooltipString','''OK'': apply the output to the current field series in uvmat');
3641drawnow
3642
3643%------------------------------------------------------------------------
3644function ListView_Callback(hObject,eventdata)
3645Mode_Callback(hObject,eventdata)
3646
3647%------------------------------------------------------------------------   
3648function Mode_Callback(hObject,eventdata)
3649%% get input info
3650hseries=findobj(allchild(0),'tag','series'); % handles of the GUI series
3651hhseries=guidata(hseries); % handles of the elements in the GUI series
3652TimeUnit=get(hhseries.TimeUnit,'String');
3653SeriesData=get(hseries,'UserData');
3654mode_list=get(hObject,'String');
3655mode=mode_list{get(hObject,'Value')};
3656hListView=findobj(get(hObject,'parent'),'Tag','ListView');
3657iview=get(hListView,'Value');
3658i1_series=SeriesData.i1_series{iview};
3659i2_series=SeriesData.i2_series{iview};
3660j1_series=SeriesData.j1_series{iview};
3661j2_series=SeriesData.j2_series{iview};
3662
3663%% enable j index visibility after the new choice
3664
3665if strcmp(mode,'series(Dj)')
3666   status_j='on'; % default
3667else
3668       status_j='off'; % no j index needed for bust case
3669end
3670enable_j(hhseries,status_j) % no j index needed
3671
3672%% get the reference indices for the time interval Dt
3673href_i=findobj(get(hObject,'parent'),'Tag','ref_i');
3674ref_i=[];ref_j=[];
3675if strcmp(get(href_i,'Visible'),'on')
3676    ref_i=str2num(get(href_i,'String'));
3677end
3678if isempty(ref_i)
3679    ref_i=1;
3680end
3681if isempty(ref_j)
3682    ref_j=1;
3683end
3684
3685%% update the menu ListPair
3686Menu=update_listpair(i1_series,i2_series,j1_series,j2_series,mode,SeriesData.Time{iview},TimeUnit,ref_i,ref_j,SeriesData.FileInfo);
3687hlist_pairs=findobj(get(hObject,'parent'),'Tag','ListPair');
3688set(hlist_pairs,'Value',1)% set the first choice by default in ListPair
3689set(hlist_pairs,'String',Menu)% set the menu in ListPair
3690ListPair_Callback(hlist_pairs,[])% apply the default choice in ListPair
3691
3692%-------------------------------------------------------------
3693% --- Executes on selection in ListPair.
3694function ListPair_Callback(hObject,eventdata)
3695%------------------------------------------------------------
3696list_pair=get(hObject,'String'); % get the menu of image pairs
3697if isempty(list_pair)
3698    string='';
3699else
3700    string=list_pair{get(hObject,'Value')};
3701   % string=regexprep(string,',.*',''); % removes time indication (after ',')
3702end
3703hseries=findobj(allchild(0),'tag','series');
3704hPairString=findobj(hseries,'tag','PairString');
3705PairString=get(hPairString,'Data');
3706hListView=findobj(get(hObject,'parent'),'Tag','ListView');
3707iview=get(hListView,'Value');
3708PairString{iview,1}=string;
3709% report the selected pair string to the table PairString
3710set(hPairString,'Data',PairString)
3711
3712
3713%------------------------------------------------------------------------
3714function num_ref_i_Callback(hObject, eventdata)
3715%------------------------------------------------------------------------
3716Mode_Callback([],[])
3717
3718%------------------------------------------------------------------------
3719function num_ref_j_Callback(hObject, eventdata)
3720%------------------------------------------------------------------------
3721Mode_Callback([],[])
3722
3723%------------------------------------------------------------------------
3724function OK_Callback(hObject, eventdata)
3725%------------------------------------------------------------------------
3726delete(get(hObject,'parent'))
3727
3728
3729%------------------------------------------------------------------------
3730% --- Executes on button press in ClearLine.
3731%------------------------------------------------------------------------
3732function ClearLine_Callback(hObject, eventdata, handles)
3733InputTable=get(handles.InputTable,'Data');
3734iline=str2double(get(handles.InputLine,'String'));
3735if size(InputTable,1)>1
3736    InputTable(iline,:)=[]; % suppress the current line if not the first
3737    set(handles.InputTable,'Data',InputTable);
3738end
3739set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH button to magenta color to indicate that input refr
3740
3741
3742% --- Executes on button press in MonitorCluster.
3743function MonitorCluster_Callback(hObject, eventdata, handles)
3744disp('format: R/W=run/wait, time lapsed, R=nbre of cores,W=walltime')
3745system('oarstat |grep N=UVmat')% check the list of jobs launched with uvmat
3746
3747
3748function OutputSubDir_Callback(hObject, eventdata, handles)
3749set(handles.OutputSubDir,'BackgroundColor',[1 1 1])
3750
3751
3752% --- Executes on button press in CheckOverwrite.
3753function CheckOverwrite_Callback(hObject, eventdata, handles)
3754
3755% --- Executes on button press in TestCPUTime.
3756function TestCPUTime_Callback(hObject, eventdata, handles)
3757% hObject    handle to TestCPUTime (see GCBO)
3758% eventdata  reserved - to be defined in a future version of MATLAB
3759% handles    structure with handles and user data (see GUIDATA)
3760
3761
3762% --- Executes on button press in DiskQuota.
3763function DiskQuota_Callback(hObject, eventdata, handles)
3764SeriesData=get(handles.series,'UserData');
3765system(SeriesData.SeriesParam.DiskQuotaCmd)
3766
3767
3768
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