source: trunk/src/series.m @ 1150

Last change on this file since 1150 was 1150, checked in by sommeria, 4 months ago

browse_data improved

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1%'series': master function associated to the GUI series.m for analysis field series
2%------------------------------------------------------------------------
3% function varargout = series(varargin)
4% associated with the GUI series.fig
5%
6%INPUT
7% param: structure with input parameters (link with the GUI uvmat)
8%      .menu_coord_str: string for the TransformName (menu for coordinate transforms)
9%      .menu_coord_val: value for TransformName (menu for coordinate transforms)
10%      .FileName: input file name
11%      .FileName_1: second input file name
12%      .list_field: menu of input fields
13%      .index_fields: chosen index
14%      .civ1=0 or 1, .interp1,  ... : input civ field type
15%
16
17%=======================================================================
18% Copyright 2008-2024, LEGI UMR 5519 / CNRS UGA G-INP, Grenoble, France
19%   http://www.legi.grenoble-inp.fr
20%   Joel.Sommeria - Joel.Sommeria (A) univ-grenoble-alpes.fr
21%
22%     This file is part of the toolbox UVMAT.
23%
24%     UVMAT is free software; you can redistribute it and/or modify
25%     it under the terms of the GNU General Public License as published
26%     by the Free Software Foundation; either version 2 of the license,
27%     or (at your option) any later version.
28%
29%     UVMAT is distributed in the hope that it will be useful,
30%     but WITHOUT ANY WARRANTY; without even the implied warranty of
31%     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
32%     GNU General Public License (see LICENSE.txt) for more details.
33%=======================================================================
34
35%------------------------------------------------------------------------
36%------------------------------------------------------------------------
37%  I - MAIN FUNCTION series
38%------------------------------------------------------------------------
39%------------------------------------------------------------------------
40function varargout = series(varargin)
41
42% Begin initialization code - DO NOT EDIT
43gui_Singleton = 1;
44gui_State = struct('gui_Name',       mfilename, ...
45                   'gui_Singleton',  gui_Singleton, ...
46                   'gui_OpeningFcn', @series_OpeningFcn, ...
47                   'gui_OutputFcn',  @series_OutputFcn, ...
48                   'gui_LayoutFcn',  [] , ...
49                   'gui_Callback',   []);
50if nargin && ischar(varargin{1})
51    gui_State.gui_Callback = str2func(varargin{1});
52end
53
54if nargout
55    [varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:});
56else
57    gui_mainfcn(gui_State, varargin{:});
58end
59% End initialization code - DO NOT EDIT
60
61%--------------------------------------------------------------------------
62% --- Executes just before series is made visible.
63%--------------------------------------------------------------------------
64function series_OpeningFcn(hObject, eventdata, handles,Param)
65
66% Choose default command line output for series
67handles.output = hObject;
68% Update handles structure
69guidata(hObject, handles);
70
71%% initial settings
72% position and  size of the GUI at opening
73set(0,'Unit','points')
74ScreenSize=get(0,'ScreenSize'); % size of the current screen, in points (1/72 inch)
75Width=900; % prefered width of the GUI in points (1/72 inch)
76Height=624; % prefered height of the GUI in points (1/72 inch)
77%adjust to screen size (reduced by a min margin)
78RescaleFactor=min((ScreenSize(3)-80)/Width,(ScreenSize(4)-80)/Height);
79if RescaleFactor>1
80    RescaleFactor=min(RescaleFactor,1);
81end
82Width=Width*RescaleFactor;
83Height=Height*RescaleFactor;
84LeftX=80*RescaleFactor; % position of the left fig side, in pixels (put to the left side, with some margin)
85LowY=round(ScreenSize(4)/2-Height/2); % put at the middle height on the screen
86set(hObject,'Units','points')
87set(hObject,'Position',[LeftX LowY Width Height])% position and size of the GUI at opening
88
89% settings of table MinIndex_j
90set(handles.MinIndex_i,'ColumnFormat',{'numeric'})
91set(handles.MinIndex_i,'ColumnEditable',false)
92set(handles.MinIndex_i,'ColumnName',{'i min'})
93set(handles.MinIndex_i,'Data',[])% initiate Data to double (not cell)
94
95% settings of table MinIndex_j
96set(handles.MinIndex_j,'ColumnFormat',{'numeric'})
97set(handles.MinIndex_j,'ColumnEditable',false)
98set(handles.MinIndex_j,'ColumnName',{'j min'})
99set(handles.MinIndex_j,'Data',[])% initiate Data to double (not cell)
100
101% settings of table MaxIndex_i
102set(handles.MaxIndex_i,'ColumnFormat',{'numeric'})
103set(handles.MaxIndex_i,'ColumnEditable',false)
104set(handles.MaxIndex_i,'ColumnName',{'i max'})
105set(handles.MaxIndex_i,'Data',[])% initiate Data to double (not cell)
106
107% settings of table MaxIndex_j
108set(handles.MaxIndex_j,'ColumnFormat',{'numeric'})
109set(handles.MaxIndex_j,'ColumnEditable',false)
110set(handles.MaxIndex_j,'ColumnName',{'j max'})
111set(handles.MaxIndex_j,'Data',[])% initiate Data to double (not cell)
112
113% settings of table PairString
114set(handles.PairString,'ColumnName',{'pairs'})
115set(handles.PairString,'ColumnEditable',false)
116set(handles.PairString,'ColumnFormat',{'char'})
117set(handles.PairString,'Data',{''})
118
119% settings of table MaskTable
120%set(handles.MaskTable,'ColumnName',{'mask name'})
121set(handles.PairString,'ColumnEditable',false)
122set(handles.PairString,'ColumnFormat',{'char'})
123set(handles.PairString,'Data',{''})
124
125series_ResizeFcn(hObject, eventdata, handles)%resize table according to series GUI size
126set(hObject,'WindowButtonDownFcn',{'mouse_down'})%allows mouse action with right button (zoom for uicontrol display)
127set(hObject,'DeleteFcn',{@closefcn})%
128
129% check default input data
130if ~exist('Param','var')
131    Param=[]; % default
132end
133
134%% Read the parameter file series.xml, or created from series.xml.default if it does not exist
135SeriesData=[];
136[path_series,name,ext]=fileparts(which('series'));% path to the GUI series
137xmlfile=fullfile(path_series,'series.xml');
138if ~exist(xmlfile,'file')
139    [success,message]=copyfile(fullfile(path_series,'series.xml.default'),xmlfile);
140end
141if exist(xmlfile,'file')
142    SeriesData.SeriesParam=xml2struct(xmlfile);
143    if ~(isfield(SeriesData.SeriesParam,'ClusterParam')&& isfield(SeriesData.SeriesParam.ClusterParam,'LaunchCmdFcn'))
144        [success,message]=copyfile(xmlfile,fullfile(path_series,'series_old.xml'));% update the file series.xml inot correctly documented
145        delete(xmlfile);
146        [success,message]=copyfile(fullfile(path_series,'series.xml.default'),xmlfile);
147    end
148    SeriesData.SeriesParam=xml2struct(xmlfile);
149end
150
151%% list of builtin functions in the menu ActionName
152ActionList={'check_data_files';'aver_stat';'time_series';'civ_series';'merge_proj'}; % WARNING: fits with nb_builtin_ACTION=4 in ActionName_callback
153NbBuiltinAction=numel(ActionList);
154set(handles.Action,'UserData',NbBuiltinAction)
155path_series_fct=fullfile(path_series,'series');%path of the functions in subdirectroy 'series'
156[path_series,name,ext]=fileparts(which('series')); % path to the GUI series
157path_series_fct=fullfile(path_series,'series'); % path of the functions in subdirectroy 'series'
158ActionExtList={'.m';'.sh';'fluidimage'}; % default choice of extensions (Matlab fct .m or compiled version .sh
159ActionPathList=cell(NbBuiltinAction,1); % initiate the cell matrix of Action fct paths
160ActionPathList(:)={path_series_fct}; % set the default path to series fcts to all list members
161RunModeList={'local';'background'}; % default choice of extensions (Matlab fct .m or compiled version .sh)
162[s,w]=system(SeriesData.SeriesParam.ClusterParam.ExistenceTest); % look for cluster system presence
163if isequal(s,0)
164    RunModeList=[RunModeList;{'cluster'}];
165    set(handles.MonitorCluster,'Visible','on'); % make visible button for access to Monika
166    set(handles.num_CPUTime,'Visible','on'); % make visible button for CPU time estimate for one ref index
167    set(handles.num_CPUTime,'String','')% default CPU time undefined
168    set(handles.CPUTime_txt,'Visible','on'); % make visible button for CPU time title
169end
170set(handles.RunMode,'String',RunModeList)% display the menu of available run modes, local, background or cluster manager
171
172%% list of builtin transform functions in the menu TransformName
173TransformList={'';'sub_field';'phys';'phys_polar'}; % WARNING: must fit with the corresponding menu in uvmat and nb_builtin_transform=4 in  TransformName_callback
174NbBuiltinTransform=numel(TransformList);
175path_transform_fct=fullfile(path_series,'transform_field');
176TransformPathList=cell(NbBuiltinTransform,1); % initiate the cell matrix of Action fct paths
177TransformPathList(:)={path_transform_fct}; % set the default path to series fcts to all list members
178SeriesData.TransformPath=path_transform_fct;% store the standard path for trqnsform functions (needed for compilation)
179
180%% get the user defined functions stored in the personal file uvmat_perso.mat
181dir_perso=prefdir;
182profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
183if exist(profil_perso,'file')
184    h=load (profil_perso);
185    %get the list of previous input files in the upper bar menu Open
186    if isfield(h,'MenuFile')
187        for ifile=1:min(length(h.MenuFile),5)
188            set(handles.(['MenuFile_' num2str(ifile)]),'Label',h.MenuFile{ifile});
189            set(handles.(['MenuFile_' num2str(ifile+5)]),'Label',h.MenuFile{ifile});
190        end
191    end
192    %get the menu of actions
193    if isfield(h,'ActionListUser') && iscell(h.ActionListUser) && isfield(h,'ActionPathListUser') && iscell(h.ActionPathListUser)
194        ActionList=[ActionList;h.ActionListUser];
195        ActionPathList=[ActionPathList;h.ActionPathListUser(:,1)];
196    end
197    %get the menu of transform fct
198    if isfield(h,'TransformListUser') && iscell(h.TransformListUser) && isfield(h,'TransformPathListUser') && iscell(h.TransformPathListUser)
199        TransformList=[TransformList;h.TransformListUser];
200        TransformPathList=[TransformPathList;h.TransformPathListUser];
201    end
202end
203
204%% selection of the input Action fct
205ActionCheckExist=true(size(ActionList)); % initiate the check of the path to the listed action fct
206for ilist=NbBuiltinAction+1:numel(ActionList)%check  the validity of the path of the user defined Action fct
207    ActionCheckExist(ilist)=exist(fullfile(ActionPathList{ilist},[ActionList{ilist} '.m']),'file');
208end
209ActionPathList=ActionPathList(ActionCheckExist,:); % suppress the menu options which are not valid anymore
210ActionList=ActionList(ActionCheckExist);
211set(handles.ActionName,'String',[ActionList;{'more...'}])
212set(handles.ActionName,'UserData',ActionPathList)
213ActionIndex=[];
214if isfield(Param,'ActionName')% copy the selected menu index transferred in Param from uvmat
215    ActionIndex=find(strcmp(Param.ActionName,ActionList),1);
216end
217if isempty(ActionIndex)
218    ActionIndex=1;
219end
220set(handles.ActionName,'Value',ActionIndex)
221set(handles.ActionPath,'String',ActionPathList{ActionIndex})
222set(handles.ActionExt,'Value',1)
223set(handles.ActionExt,'String',ActionExtList)
224
225%% selection of the input transform fct
226TransformCheckExist=true(size(TransformList));
227for ilist=NbBuiltinTransform+1:numel(TransformList)
228    TransformCheckExist(ilist)=exist(fullfile(TransformPathList{ilist},[TransformList{ilist} '.m']),'file');
229end
230TransformPathList=TransformPathList(TransformCheckExist);
231TransformList=TransformList(TransformCheckExist);
232set(handles.TransformName,'String',[TransformList;{'more...'}])
233set(handles.TransformName,'UserData',TransformPathList)
234TransformIndex=[];
235if isfield(Param,'TransformName')% copy the selected menu index transferred in Param from uvmat
236    TransformIndex=find(strcmp(Param.TransformName,TransformList),1);
237end
238if isempty(TransformIndex)
239    TransformIndex=1;
240end
241set(handles.TransformName,'Value',TransformIndex)
242set(handles.TransformPath,'String',TransformPathList{TransformIndex})
243
244%% fields input initialisation
245if isfield(Param,'list_fields')&& isfield(Param,'index_fields') &&~isempty(Param.list_fields) &&~isempty(Param.index_fields)
246    set(handles.FieldName,'String',Param.list_fields); % list menu fields
247    set(handles.FieldName,'Value',Param.index_fields); % selected string index
248end
249if isfield(Param,'Coordinates')
250    if isfield(Param.Coordinates,'Coord_x')
251        set(handles.Coord_x,'String',Param.Coordinates.Coord_x)
252    end
253    if isfield(Param.Coordinates,'Coord_y')
254        set(handles.Coord_y,'String',Param.Coordinates.Coord_y)
255    end
256    if isfield(Param.Coordinates,'Coord_z')
257        set(handles.Coord_z,'String',Param.Coordinates.Coord_z)
258    end
259end
260
261%% introduce the input file name(s) if defined from input Param,
262set(handles.series,'UserData',SeriesData)% initiate Userdata
263if isfield(Param,'InputFile')
264
265    %% fill the list of input file series
266    InputTable=[{Param.InputFile.RootPath},{Param.InputFile.SubDir},{Param.InputFile.RootFile},{Param.InputFile.NomType},{Param.InputFile.FileExt}];
267    if isempty(find(cellfun('isempty',InputTable)==0)) % if there is no input file, do not introduce input info
268        set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH button to magenta color to indicate that input refresh is needed
269        return
270    end
271    TimeTable=[{Param.InputFile.TimeName},{[]},{[]},{[]},{[]}];
272    if isfield(Param.InputFile,'RootPath_1')
273        InputTable=[InputTable;[{Param.InputFile.RootPath_1},{Param.InputFile.SubDir_1},{Param.InputFile.RootFile_1},{Param.InputFile.NomType_1},{Param.InputFile.FileExt_1}]];
274        TimeTable=[TimeTable; [{Param.InputFile.TimeName_1},{[]},{[]},{[]},{[]}]];
275    end
276    set(handles.InputTable,'Data',InputTable)
277
278    %% define the default path for the output files
279    [InputPath,Device,DeviceExt]=fileparts(InputTable{1,1});
280    [InputPath,Experiment,ExperimentExt]=fileparts(InputPath);
281    set(handles.Device,'String',[Device DeviceExt])
282    set(handles.Experiment,'String',[Experiment ExperimentExt])
283    if ~isempty(regexp(InputTable{1,1},'(^http://)|(^https://)'))
284    set(handles.OutputPathBrowse,'Value',1)% an output folder needs to be specified for OpenDAP data
285    end
286
287    %update the output path if needed
288    if ~(isfield(SeriesData,'InputPath') && strcmp(SeriesData.InputPath,InputPath))
289    if get(handles.OutputPathBrowse,'Value')==1  % fix the output path in manual mode
290        OutputPathOld=get(handles.OutputPath,'String');
291        OutputPath=uigetdir(OutputPathOld,'pick a root folder for output data');
292        set(handles.OutputPath,'String',OutputPath)
293    else %reproduce the input path for output
294        set(handles.OutputPath,'String',InputPath)
295    end
296    end
297
298    %% determine the selected reference field indices for pair display
299
300    [tild,tild,tild,i1,i2,j1,j2]=fileparts_uvmat(Param.InputFile.FileIndex);
301    if isempty(i1)
302        i1=1;
303    end
304    if isempty(i2)
305        i2=i1;
306    end
307    ref_i=floor((i1+i2)/2); % reference image number corresponding to the file
308    % set(handles.num_ref_i,'String',num2str(ref_i));
309    if isempty(j1)
310        j1=1;
311    end
312    if isempty(j2)
313        j2=j1;
314    end
315    ref_j=floor((j1+j2)/2); % reference image number corresponding to the file
316    SeriesData.ref_i=ref_i;
317    SeriesData.ref_j=ref_j;
318    set(handles.series,'UserData',SeriesData)
319    update_rootinfo(handles,Param.HiddenData.i1_series{1},Param.HiddenData.i2_series{1},Param.HiddenData.j1_series{1},Param.HiddenData.j2_series{1},...
320        Param.HiddenData.FileInfo{1},Param.HiddenData.MovieObject{1},1)
321    if isfield(Param,'FileName_1')
322        %         display_file_name(handles,Param,2)
323        update_rootinfo(handles,Param.HiddenData.i1_series{2},Param.HiddenData.i2_series{2},Param.HiddenData.j1_series{2},Param.HiddenData.j2_series{2},...
324            Param.HiddenData.FileInfo{2},Param.HiddenData.MovieObject{2},2)
325    end
326    %% enable field and veltype menus, in accordance with the current action
327    ActionName_Callback([],[], handles)
328
329    %% set length of waitbar
330    displ_time(handles)
331
332else
333    set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH button to magenta color to indicate that input refresh is needed
334end
335if isfield(Param,'incr_i')
336    set(handles.num_incr_i,'String',num2str(Param.incr_i))
337else
338    set(handles.num_incr_i,'String','1')
339end
340if isfield(Param,'incr_j')
341    set(handles.num_incr_j,'String',num2str(Param.incr_j))
342else
343    set(handles.num_incr_j,'String','1')
344end
345
346%------------------------------------------------------------------------
347% --- Outputs from this function are returned to the command line.
348function varargout = series_OutputFcn(hObject, eventdata, handles)
349%------------------------------------------------------------------------
350varargout{1} = handles.output;
351
352%------------------------------------------------------------------------
353% --- executed when closing uvmat: delete or desactivate the associated figures if exist
354function closefcn(gcbo,eventdata)
355%------------------------------------------------------------------------
356
357% delete set_object_series if detected
358hh=findobj(allchild(0),'name','view_object_series');
359if ~isempty(hh)
360    delete(hh)
361end
362hh=findobj(allchild(0),'name','edit_object_series');
363if ~isempty(hh)
364    delete(hh)
365end
366
367%delete the bowser if detected
368hh=findobj(allchild(0),'tag','browser');
369if ~isempty(hh)
370    delete(hh)
371end
372
373
374%------------------------------------------------------------------------
375%------------------------------------------------------------------------
376%  II - FUNCTIONS FOR INTRODUCING THE INPUT FILES
377% automatically sets the global properties when the rootfile name is introduced
378% then activate the view-field actionname if selected
379% it is activated either by clicking on the RootPath window or by the
380% browser
381%------------------------------------------------------------------------
382%------------------------------------------------------------------------
383% --- fct activated by the browser under 'Open'
384%------------------------------------------------------------------------
385function MenuBrowse_Callback(hObject, eventdata, handles)
386%% look for the previously opened file 'oldfile'
387InputTable=get(handles.InputTable,'Data');
388oldfile=InputTable{1,1};
389if isempty(oldfile)
390    % use a file name stored in prefdir
391    dir_perso=prefdir;
392    profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
393    if exist(profil_perso,'file')
394        h=load (profil_perso);
395        if isfield(h,'RootPath') && ischar(h.RootPath)
396            oldfile=h.RootPath;
397        end
398    end
399end
400%% launch the browser
401fileinput=uigetfile_uvmat('pick an input file in the series',oldfile);
402hh=dir(fileinput);
403if numel(hh)>1
404    msgbox_uvmat('ERROR','invalid input, probably a broken link');
405else
406    if ~isempty(fileinput)
407        display_file_name(handles,fileinput,'one')
408    end
409end
410
411% --------------------------------------------------------------------
412function MenuBrowseAppend_Callback(hObject, eventdata, handles)
413
414%% look for the previously opened file 'oldfile'
415InputTable=get(handles.InputTable,'Data');
416RootPathCell=InputTable(:,1);
417if isempty(RootPathCell{1})% no input file in the table
418     MenuBrowse_Callback(hObject, eventdata, handles)%refresh the input table, not append
419     return
420end
421SubDirCell=InputTable(:,2);
422oldfile=fullfile(RootPathCell{1},SubDirCell{1});
423
424%% use a file name stored in prefdir
425dir_perso=prefdir;
426profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
427if exist(profil_perso,'file')
428    h=load (profil_perso);
429    if isfield(h,'RootPath') && ischar(h.RootPath)
430        oldfile=h.RootPath;
431    end
432end
433
434%% launch the browser
435fileinput=uigetfile_uvmat('pick a file to append in the input table',oldfile);
436hh=dir(fileinput);
437if numel(hh)>1
438    msgbox_uvmat('ERROR','invalid input, probably a broken link');
439else
440    if ~isempty(fileinput)
441        display_file_name(handles,fileinput,'append')
442    end
443end
444
445%------------------------------------------------------------------------
446% --- fct activated by selecting a previous file under the menu Open
447%------------------------------------------------------------------------
448function MenuFile_Callback(hObject, eventdata, handles)
449
450errormsg=display_file_name(handles,get(hObject,'Label'),'one');
451if ~isempty(errormsg)
452    set(hObject,'Label','')
453    MenuFile=[{get(handles.MenuFile_1,'Label')};{get(handles.MenuFile_2,'Label')};...
454        {get(handles.MenuFile_3,'Label')};{get(handles.MenuFile_4,'Label')};{get(handles.MenuFile_5,'Label')}];
455    str_find=strcmp(get(hObject,'Label'),MenuFile);
456    MenuFile(str_find)=[]; % suppress the input file to the list
457    for ifile=1:numel(MenuFile)
458        set(handles.(['MenuFile_' num2str(ifile)]),'Label',MenuFile{ifile});
459    end
460end
461
462%------------------------------------------------------------------------
463% --- fct activated by selecting a previous file under the menu Open/append
464%------------------------------------------------------------------------
465function MenuFile_append_Callback(hObject, eventdata, handles)
466
467InputTable=get(handles.InputTable,'Data');
468if isempty(InputTable{1,1})% no input file in the table
469    display_file_name(handles,get(hObject,'Label'),'one') %refresh the input table, not append
470else
471    display_file_name(handles,get(hObject,'Label'),'append')% append the selected file to the current list of InputTable
472end
473
474%------------------------------------------------------------------------
475% --- fct activated by the browser under 'Open campaign/Browse...'
476%------------------------------------------------------------------------
477function MenuBrowseCampaign_Callback(hObject, eventdata, handles)
478
479%% look for the previously opened file 'oldfile'
480InputTable=get(handles.InputTable,'Data');
481if ~isempty(InputTable)
482oldfile=[InputTable{1,1} InputTable{1,2}];
483else
484    % use a file name stored in prefdir
485    dir_perso=prefdir;
486    profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
487    if exist(profil_perso,'file')
488        h=load (profil_perso);
489        if isfield(h,'MenuCampaign') && ~isempty(h.MenuCampaign)&& ischar(h.MenuCampaign{1})
490            oldfile=h.MenuCampaign{1};
491        end
492    end
493end
494InputTable{1,1}='...';
495set(handles.InputTable,'Data',InputTable)
496browse_data(oldfile,'on','on'); % open the GUI browse_data to get select a campaign dir, experiment and device
497
498
499
500% --- Executes when selected cell(s) is changed in InputTable.
501function InputTable_CellSelectionCallback(hObject, eventdata, handles)
502iline=[];
503if ~isempty(eventdata.Indices)
504    iline=eventdata.Indices(1);
505end
506set(handles.InputLine,'String',num2str(iline));
507
508%------------------------------------------------------------------------
509% --- 'key_press_fcn:' function activated when a key is pressed on the keyboard
510%------------------------------------------------------------------------
511function InputTable_KeyPressFcn(hObject, eventdata, handles)
512set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH button to magenta color to indicate that input refresh is needed
513set(handles.OutputSubDir,'BackgroundColor',[1 0 1])% set edit box OutputSubDir to magenta color to indicate that refresh may be needed
514xx=double(get(handles.series,'CurrentCharacter')); % get the keyboard character
515if ~isempty(xx)
516    switch xx
517        case 31 %downward arrow
518            InputTable=get(handles.InputTable,'Data');
519            iline=str2double(get(handles.InputLine,'String'));
520            if isequal(iline,size(InputTable,1))% arrow downward
521                InputTable=[InputTable;InputTable(iline,:)]; % create a new line as a copy of the last one
522                set(handles.InputTable,'Data',InputTable);
523            end
524        case 127  %key 'Suppress'
525            ClearLine_Callback(hObject, eventdata, handles)
526    end
527end
528
529%------------------------------------------------------------------------
530% --- Executes on button press in REFRESH.
531function REFRESH_Callback(hObject, eventdata, handles)
532%------------------------------------------------------------------------
533check_input_file_series(handles)
534
535%% enable field and veltype menus, in accordance with the current action
536ActionInput_Callback([],[], handles)
537
538%------------------------------------------------------------------------
539% --- check the input file series.
540function check_input_file_series(handles)
541%------------------------------------------------------------------------
542InputTable=get(handles.InputTable,'Data');
543set(handles.series,'Pointer','watch') % set the mouse pointer to 'watch'
544set(handles.REFRESH,'BackgroundColor',[1 1 0])% set REFRESH  button to yellow color (indicate activation)
545drawnow
546empty_line=false(size(InputTable,1),1);
547for iline=1:size(InputTable,1)
548    empty_line(iline)= isempty(cell2mat(InputTable(iline,1:3)));%check the empty lines in the input table
549end
550if ~isempty(find(empty_line,1))
551    InputTable(empty_line,:)=[]; % remove empty lines
552    set(handles.InputTable,'Data',InputTable)
553    ListTable={'MinIndex_i','MaxIndex_i','MinIndex_j','MaxIndex_j','PairString','TimeTable'};
554    for ilist=1:numel(ListTable)
555        Table=get(handles.(ListTable{ilist}),'Data');
556        Table(empty_line,:)=[]; % remove empty lines
557        set(handles.(ListTable{ilist}),'Data',Table);
558    end
559    set(handles.series,'UserData',[])%refresh the stored info
560end
561nbview=size(InputTable,1);
562for iview=1:nbview
563    RootPath=fullfile(InputTable{iview,1},InputTable{iview,2});
564    if ~exist(RootPath,'dir')
565        i1_series=[];
566        RootFile='';
567    else %scan the input folder
568        InputTable{iview,3}=regexprep(InputTable{iview,3},'^/','');%suppress '/' at the beginning of the input name
569        i1=str2double(get(handles.num_first_i,'String'));
570        j1=str2double(get(handles.num_first_j,'String'));
571        j2=[];%default
572        PairString=get(handles.PairString,'Data');
573        if numel(PairString)>=iview
574            checkpair=strfind(PairString{iview},'j=');
575            if checkpair
576                j1=str2double(PairString{iview}(4));
577                j2=str2double(PairString{iview}(6));
578            end
579        end
580        InputFile=fullfile_uvmat('','',InputTable{iview,3},InputTable{iview,5},InputTable{iview,4},i1,[],j1,j2);
581        [RootPath,~,RootFile,i1_series,i2_series,j1_series,j2_series,tild,FileInfo,MovieObject]=...
582                find_file_series(fullfile(InputTable{iview,1},InputTable{iview,2}),InputFile);
583    end
584    % if no file is found, open a browser
585    if isempty(RootFile)&& isempty(i1_series)
586        fileinput=uigetfile_uvmat(['wrong input at line ' num2str(iview) ':pick a new input file'],RootPath);
587        if isempty(fileinput)
588            set(handles.REFRESH,'BackgroundColor',[1 0 0])% set REFRESH  back to red color
589            return
590        else
591            display_file_name(handles,fileinput,iview)
592        end
593    else
594       update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileInfo,MovieObject,iview)
595    end
596end
597
598%% update MinIndex_i and MaxIndex_i if the input table content has been reduced in line nbre
599MinIndex_i_table=get(handles.MinIndex_i,'Data'); % retrieve the min indices in the table MinIndex
600set(handles.MinIndex_i,'Data',MinIndex_i_table(1:nbview,:));
601MinIndex_j_table=get(handles.MinIndex_j,'Data'); % retrieve the min indices in the table MinIndex
602set(handles.MinIndex_j,'Data',MinIndex_j_table(1:nbview,:));
603MaxIndex_i_table=get(handles.MaxIndex_i,'Data'); % retrieve the min indices in the table MinIndex
604
605set(handles.MaxIndex_i,'Data',MaxIndex_i_table(1:nbview,:));
606MaxIndex_j_table=get(handles.MaxIndex_j,'Data'); % retrieve the min indices in the table MinIndex
607set(handles.MaxIndex_j,'Data',MaxIndex_j_table(1:nbview,:));
608PairString=get(handles.PairString,'Data'); % retrieve the min indices in the table MinIndex
609set(handles.PairString,'Data',PairString(1:nbview,:));
610TimeTable=get(handles.TimeTable,'Data'); % retrieve the min indices in the table MinIndex
611set(handles.TimeTable,'Data',TimeTable(1:nbview,:));
612
613%% set length of waitbar
614displ_time(handles)
615set(handles.REFRESH,'BackgroundColor',[1 0 0])% set REFRESH  button to red color (indicate activation finished)
616set(handles.series,'Pointer','arrow') % set the mouse pointer to 'watch'
617
618
619
620%------------------------------------------------------------------------
621% --- Function called when a new file is opened, either by series_OpeningFcn or by the browser
622%------------------------------------------------------------------------
623% INPUT:
624% handles: handles of elements in the GUI
625% Param: structure of input parameters, including  input file name and path
626% iview: line index in the input table
627%       or 'one': refresh the list
628%         'append': add a new line to the input table
629function errormsg=display_file_name(handles,Param,iview)
630
631set(handles.REFRESH,'BackgroundColor',[1 1 0])% set REFRESH  button to yellow color (indicate activation)
632drawnow
633errormsg=''; % default
634if ischar(Param)
635    fileinput=Param;
636else% input set when series is opened (called by the GUI uvmat)
637    fileinput=Param.FileName;
638end
639
640%% get the input root name, indices, file extension and nomenclature NomType
641if isempty(regexp(fileinput,'^http')) && ~exist(fileinput,'file')
642    errormsg=['input file ' fileinput  ' does not exist'];
643    msgbox_uvmat('ERROR',errormsg)
644    set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH  button to magenta color (refresh still needed)
645    return
646end
647
648%% detect root name, nomenclature and indices in the input file name:
649[FilePath,FileName,FileExt]=fileparts(fileinput);
650%%%%%%%%%%%%%%%%%%
651%TODO: case of input by uvmat: do not check agai the input series %%%%%%%
652%%%%%%%%%%%%%%%%%%%
653% detect the file type, get the movie object if relevant, and look for the corresponding file series:
654% the root name and indices may be corrected by including the first index i1 if a corresponding xml file exists
655[RootPath,SubDir,RootFile,i1_series,i2_series,j1_series,j2_series,NomType,FileInfo,MovieObject,i1,i2,j1,j2]=find_file_series(FilePath,[FileName FileExt]);
656FileType=FileInfo.FileType;
657if isempty(RootFile)&&isempty(i1_series)
658    errormsg='no input file in the series';
659    msgbox_uvmat('ERROR',errormsg)
660    set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH  button to magenta color (end of activation)
661    return
662end
663if strcmp(FileType,'txt')
664    edit(fileinput)
665    set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH  button to  magenta color (end of activation)
666    return
667elseif strcmp(FileType,'xml')
668    editxml(fileinput)
669    set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH  button to magenta  color (end of activation)
670     return
671elseif strcmp(FileType,'figure')
672    open(fileinput)
673    set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH  button to magenta  color (end of activation)
674     return
675end
676
677%% enable other menus and uicontrols
678set(handles.RUN, 'Enable','On')
679set(handles.RUN,'BackgroundColor',[1 0 0])% set RUN button to red
680set(handles.InputTable,'BackgroundColor',[1 1 0]) % set RootPath edit box  to yellow
681drawnow
682
683
684%% fill the list of file series
685InputTable=get(handles.InputTable,'Data');
686SeriesData=get(handles.series,'UserData');
687
688if strcmp(iview,'append') % display the input data as a new line in the table
689    iview=size(InputTable,1)+1; % the next line in InputTable becomes the current line
690elseif strcmp(iview,'one') % refresh the list of  input  file series
691    iview=1; % the first line in InputTable becomes the current line
692    InputTable={'','','','',''};
693    set(handles.TimeTable,'Data',[{''},{[]},{[]},{[]},{[]}])
694    set(handles.MinIndex_i,'Data',[])
695    set(handles.MaxIndex_i,'Data',[])
696    set(handles.MinIndex_j,'Data',[])
697    set(handles.MaxIndex_j,'Data',[])
698    set(handles.PairString,'Data',{''})
699    SeriesData.CheckPair=0; % reset the list of input lines with pairs
700    SeriesData.i1_series={};
701    SeriesData.i2_series={};
702    SeriesData.j1_series={};
703    SeriesData.j2_series={};
704    SeriesData.FileType={};
705    SeriesData.FileInfo={};
706    SeriesData.Time={};
707end
708if isfield(SeriesData,'i1_series')
709    SeriesData.i1_series(iview+1:end)=[];
710    SeriesData.i2_series(iview+1:end)=[];
711    SeriesData.j1_series(iview+1:end)=[];
712    SeriesData.j2_series(iview+1:end)=[];
713    SeriesData.FileType(iview+1:end)=[];
714    SeriesData.FileInfo(iview+1:end)=[];
715    SeriesData.Time(iview+1:end)=[];
716end
717InputTable(iview,:)=[{RootPath},{SubDir},{RootFile},{NomType},{FileExt}];
718if iview >1
719    set(handles.InputLine,'String',num2str(iview))
720end
721set(handles.InputTable,'Data',InputTable)
722
723%% determine the selected reference field indices for pair display
724if isempty(i1)
725    i1=1;
726end
727if isempty(i2)
728    i2=i1;
729end
730ref_i=floor((i1+i2)/2); % reference image number corresponding to the file
731% set(handles.num_ref_i,'String',num2str(ref_i));
732if isempty(j1)
733    j1=1;
734end
735if isempty(j2)
736    j2=j1;
737end
738ref_j=floor((j1+j2)/2); % reference image number corresponding to the file
739SeriesData.ref_i=ref_i;
740SeriesData.ref_j=ref_j;
741
742%% update first and last indices if they do not exist
743Param=read_GUI(handles.series);
744first_j=[];
745if isfield(Param.IndexRange,'first_j'); first_j=Param.IndexRange.first_j; end
746last_j=[];
747if isfield(Param.IndexRange,'last_j'); last_j=Param.IndexRange.last_j; end
748PairString='';
749if isfield(Param.IndexRange,'PairString'); PairString=Param.IndexRange.PairString; end
750[i1,i2,j1,j2] = get_file_index(Param.IndexRange.first_i,first_j,PairString);
751FirstFileName=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},...
752    Param.InputTable{1,5},Param.InputTable{1,4},i1,i2,j1,j2);
753if ~exist(FirstFileName,'file')
754    set(handles.num_first_i,'String',num2str(ref_i))
755    set(handles.num_first_j,'String',num2str(ref_j))
756end
757[i1,i2,j1,j2] = get_file_index(Param.IndexRange.last_i,last_j,PairString);
758LastFileName=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},...
759    Param.InputTable{1,5},Param.InputTable{1,4},i1,i2,j1,j2);
760if ~exist(LastFileName,'file')
761    set(handles.num_last_i,'String',num2str(ref_i))
762    set(handles.num_last_j,'String',num2str(ref_j))
763end
764
765%% update the list of recent files in the menubar and save it for future opening
766MenuFile=[{get(handles.MenuFile_1,'Label')};{get(handles.MenuFile_2,'Label')};...
767    {get(handles.MenuFile_3,'Label')};{get(handles.MenuFile_4,'Label')};{get(handles.MenuFile_5,'Label')}];
768str_find=strcmp(fileinput,MenuFile);
769if isempty(find(str_find,1))
770    MenuFile=[{fileinput};MenuFile]; % insert the current file if not already in the list
771end
772for ifile=1:min(length(MenuFile),5)
773    eval(['set(handles.MenuFile_' num2str(ifile) ',''Label'',MenuFile{ifile});'])
774end
775dir_perso=prefdir;
776profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
777if exist(profil_perso,'file')
778    save (profil_perso,'MenuFile','-append'); % store the file names for future opening of uvmat
779else
780    save (profil_perso,'MenuFile','-V6'); % store the file names for future opening of uvmat
781end
782% save the opened file to initiate future opening
783SeriesData.RefFile{iview}=fileinput; % reference opening file for line iview
784SeriesData.Ref_i1=i1;
785SeriesData.Ref_i2=i2;
786SeriesData.Ref_j1=j1;
787SeriesData.Ref_j2=j2;
788
789%% define the path for the output files
790[InputPath,Device,DeviceExt]=fileparts(InputTable{1,1});
791[InputPath,Experiment,ExperimentExt]=fileparts(InputPath);
792set(handles.Device,'String',[Device DeviceExt])
793set(handles.Experiment,'String',[Experiment ExperimentExt])
794if ~isempty(regexp(InputTable{1,1},'(^http://)|(^https://)'))
795    set(handles.OutputPathBrowse,'Value',1)% an output folder needs to be specified for OpenDAP data
796end
797
798%update the output path if needed
799if ~(isfield(SeriesData,'InputPath') && strcmp(SeriesData.InputPath,InputPath))
800    if get(handles.OutputPathBrowse,'Value')==1  % fix the output path in manual mode
801        OutputPathOld=get(handles.OutputPath,'String');
802        OutputPath=uigetdir(OutputPathOld,'pick a root folder for output data');
803        set(handles.OutputPath,'String',OutputPath)
804    else %reproduce the input path for output
805        set(handles.OutputPath,'String',InputPath)
806    end
807    SeriesData.InputPath=InputPath;
808end
809
810set(handles.series,'UserData',SeriesData)
811
812set(handles.InputTable,'BackgroundColor',[1 1 1])
813
814%% initiate input file series and refresh the current field view:
815update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileInfo,MovieObject,iview);
816%% enable field and veltype menus, in accordance with the current action
817ActionName_Callback([],[], handles)
818
819%% set length of waitbar
820displ_time(handles)
821
822set(handles.REFRESH,'BackgroundColor',[1 0 0])% set REFRESH  button to red color (end of activation)
823
824%------------------------------------------------------------------------
825% --- Update information about a new field series (indices to scan, timing,
826%     calibration from an xml file
827function update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileInfo,VideoObject,iview)
828%------------------------------------------------------------------------
829InputTable=get(handles.InputTable,'Data');
830
831%% display the min and max indices for the whole file series
832if size(i1_series,2)==2 && min(min(i1_series(:,1,:)))==0
833    MinIndex_j=1; % index j set to 1 by default
834    MaxIndex_j=1;
835    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)
836    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)
837else
838    ref_i=squeeze(max(i1_series(1,:,:),[],2)); % select ref_j index for each ref_i
839    ref_j=squeeze(max(j1_series(1,:,:),[],3)); % select ref_i index for each ref_j
840     MinIndex_i=min(find(ref_i))-1;
841     MaxIndex_i=max(find(ref_i))-1;
842     MaxIndex_j=max(find(ref_j))-1;
843     MinIndex_j=min(find(ref_j))-1;
844    diff_j_max=diff(ref_j);
845    diff_i_max=diff(ref_i);
846    if ~isempty(diff_i_max) && isequal (diff_i_max,diff_i_max(1)*ones(size(diff_i_max)))
847        set(handles.num_incr_i,'String',num2str(diff_i_max(1)))% detect an increment to dispaly by default
848    end
849    if ~isempty(diff_j_max) && isequal (diff_j_max,diff_j_max(1)*ones(size(diff_j_max)))
850        set(handles.num_incr_j,'String',num2str(diff_j_max(1)))
851    end
852end
853if isequal(MinIndex_i,-1)
854    MinIndex_i=0;
855end
856if isequal(MinIndex_j,-1)
857    MinIndex_j=0;
858end
859MinIndex_i_table=get(handles.MinIndex_i,'Data'); % retrieve the min indices in the table MinIndex
860MinIndex_j_table=get(handles.MinIndex_j,'Data'); % retrieve the min indices in the table MinIndex
861MaxIndex_i_table=get(handles.MaxIndex_i,'Data'); % retrieve the min indices in the table MinIndex
862MaxIndex_j_table=get(handles.MaxIndex_j,'Data'); % retrieve the min indices in the table MinIndex
863if ~isempty(MinIndex_i)&&~isempty(MaxIndex_i)
864    MinIndex_i_table(iview,1)=MinIndex_i;
865    MaxIndex_i_table(iview,1)=MaxIndex_i;
866end
867if ~isempty(MinIndex_j)&&~isempty(MaxIndex_j)
868    MinIndex_j_table(iview,1)=MinIndex_j;
869    MaxIndex_j_table(iview,1)=MaxIndex_j;
870end
871set(handles.MinIndex_i,'Data',MinIndex_i_table)%display the min indices in the table MinIndex
872set(handles.MinIndex_j,'Data',MinIndex_j_table)%display the max indices in the table MaxIndex
873set(handles.MaxIndex_i,'Data',MaxIndex_i_table)%display the min indices in the table MinIndex
874set(handles.MaxIndex_j,'Data',MaxIndex_j_table)%display the max indices in the table MaxIndex
875SeriesData=get(handles.series,'UserData');
876
877%% adjust the first and last indices for the selected series, only if requested by the bounds
878% i index, compare input to min index i
879first_i=str2num(get(handles.num_first_i,'String')); % retrieve previous first i
880% ref_i=str2num(get(handles.num_ref_i,'String')); % index i given by the input field
881ref_i=1;
882if isfield(SeriesData,'ref_i')
883    ref_i=SeriesData.ref_i;
884end
885if isempty(first_i)
886    first_i=ref_i; % first_i updated by the input value
887elseif first_i < MinIndex_i
888    first_i=MinIndex_i; % first_i set to the min i index (restricted by oter input lines)
889elseif first_i >MaxIndex_i
890    first_i=MaxIndex_i; % first_i set to the max i index (restricted by oter input lines)
891end
892% j index,  compare input to min index j
893first_j=str2num(get(handles.num_first_j,'String'));
894ref_j=1;
895if isfield(SeriesData,'ref_j')
896    ref_j=SeriesData.ref_j;
897end
898if isempty(first_j)
899    first_j=ref_j; % first_j updated by the input value
900elseif first_j<MinIndex_j
901    first_j=MinIndex_j; % first_j set to the min j index (restricted by oter input lines)
902elseif first_j >MaxIndex_j
903    first_j=MaxIndex_j; % first_j set to the max j index (restricted by oter input lines)
904end
905% i index, compare input to max index i
906last_i=str2num(get(handles.num_last_i,'String'));
907if isempty(last_i)
908    last_i=ref_i;
909elseif last_i > MaxIndex_i
910    last_i=MaxIndex_i;
911elseif last_i<first_i
912    last_i=first_i;
913end
914% j index, compare input to max index j
915last_j=str2num(get(handles.num_last_j,'String'));
916if isempty(last_j)
917    last_j=ref_j;
918elseif last_j>MaxIndex_j
919    last_j=MaxIndex_j;
920elseif last_j<first_j
921    last_j=first_j;
922end
923set(handles.num_first_i,'String',num2str(first_i));
924set(handles.num_first_j,'String',num2str(first_j));
925set(handles.num_last_i,'String',num2str(last_i));
926set(handles.num_last_j,'String',num2str(last_j));
927
928%% number of slices set by default
929NbSlice=[]; % default
930% read  value set by the first series for the append mode (iwiew >1)
931if iview>1 && strcmp(get(handles.num_NbSlice,'Visible'),'on')
932    NbSlice=str2double(get(handles.num_NbSlice,'String'));
933end
934
935%% default time settings
936TimeUnit='';
937% read  value set by the first series for the append mode (iwiew >1)
938if iview>1
939    TimeUnit=get(handles.TimeUnit,'String');
940end
941TimeName='';
942Time=[]; % default
943TimeMin=[];
944TimeFirst=[];
945TimeLast=[];
946TimeMax=[];
947
948%%  read image documentation file if found
949XmlData=[];
950check_calib=0;
951XmlFileName=find_imadoc(InputTable{iview,1},InputTable{iview,2},InputTable{iview,3},InputTable{iview,5});
952if ~isempty(XmlFileName)
953    [XmlData,errormsg]=imadoc2struct(XmlFileName);
954    if ~isempty(errormsg)
955        msgbox_uvmat('WARNING',['error in reading ' XmlFileName ': ' errormsg]);
956    end
957    % read time if available
958    if isfield(XmlData,'Time')
959        Time=XmlData.Time;
960        TimeName='xml';
961    end
962    if isfield(XmlData,'Camera')
963        if isfield(XmlData.Camera,'TimeUnit')&& ~isempty(XmlData.Camera.TimeUnit)
964            if iview>1 && ~isempty(TimeUnit) && ~strcmp(TimeUnit,XmlData.Camera.TimeUnit)
965                msgbox_uvmat('WARNING','inconsistent time unit with the first field series');
966            end
967            TimeUnit=XmlData.Camera.TimeUnit;
968        end
969    end
970    % number of slices
971    if isfield(XmlData,'TranslationMotor')&& isfield(XmlData.TranslationMotor,'NbSlice')
972        NbSlice_motor=XmlData.TranslationMotor.NbSlice;
973        if ~isempty(NbSlice) && ~isequal(NbSlice_motor,NbSlice)
974                msgbox_uvmat('WARNING','inconsistent Z numbers of Z indices');
975        else
976            NbSlice=NbSlice_motor;
977        end
978    end
979end
980if ~isempty(NbSlice)
981set(handles.num_NbSlice,'String',num2str(NbSlice))
982set(handles.num_NbSlice,'Visible','on')
983end
984
985%% read timing  from the current file (prioritary)
986if ~isempty(VideoObject)% case of movies
987    imainfo=get(VideoObject);
988    if isfield(imainfo,'NumFrames')
989        imainfo.NumberOfFrames=imainfo.NumFrames;
990    end
991    if isempty(j1_series) % frame index along i
992        Time=zeros(imainfo.NumberOfFrames+1,2);
993        Time(:,2)=(0:1/imainfo.FrameRate:(imainfo.NumberOfFrames)/imainfo.FrameRate)';
994    else
995        Time=[0;ones(size(i1_series,3)-1,1)]*(0:1/imainfo.FrameRate:(imainfo.NumberOfFrames)/imainfo.FrameRate);
996    end
997    TimeName='video';
998end
999
1000
1001%% determine the min and max times: case of Netcdf files will be treated later in FieldName_Callback
1002if ~isempty(TimeName)
1003    if size(Time)<[MaxIndex_i+1 MaxIndex_j+1]
1004       msgbox_uvmat('WARNING',['incomplete time info in ' XmlFileName]);
1005    end
1006    TimeMin=Time(MinIndex_i+1,MinIndex_j+1);
1007    if size(Time)>=[first_i+1 first_j+1]
1008        TimeFirst=Time(first_i+1,first_j+1);
1009    end
1010    if size(Time)>=[last_i+1 last_j+1]
1011        TimeLast=Time(last_i+1,last_j+1);
1012    end
1013    if size(Time)>=[MaxIndex_i+1 MaxIndex_j+1]
1014        TimeMax=Time(MaxIndex_i+1,MaxIndex_j+1);
1015    end
1016end
1017
1018%% update the time table
1019TimeTable=get(handles.TimeTable,'Data');
1020TimeTable{iview,1}=TimeName;
1021TimeTable{iview,2}=TimeMin;
1022TimeTable{iview,3}=TimeFirst;
1023TimeTable{iview,4}=TimeLast;
1024TimeTable{iview,5}=TimeMax;
1025set(handles.TimeTable,'Data',TimeTable)
1026
1027%% update the series info in 'UserData'
1028SeriesData.i1_series{iview}=i1_series;
1029SeriesData.i2_series{iview}=i2_series;
1030SeriesData.j1_series{iview}=j1_series;
1031SeriesData.j2_series{iview}=j2_series;
1032SeriesData.FileType{iview}=FileInfo.FileType;
1033SeriesData.FileInfo{iview}=FileInfo;
1034SeriesData.Time{iview}=Time;
1035
1036SeriesData.TimeName=TimeName;
1037
1038if check_calib
1039    SeriesData.GeometryCalib{iview}=XmlData.GeometryCalib;
1040end
1041set(handles.series,'UserData',SeriesData)
1042
1043%% update pair menus
1044hset_pair=findobj(allchild(0),'Tag','set_pairs');
1045if ~isempty(hset_pair), delete(hset_pair); end % delete the GUI set_pair if opened
1046CheckPair= ~isempty(i2_series)||~isempty(j2_series); % check whether index pairs need to be defined
1047PairString=get(handles.PairString,'Data');
1048if CheckPair% if pairs need to be display for line iview
1049    [ModeMenu,ModeValue]=update_mode(i1_series,i2_series,j2_series);
1050    Menu=update_listpair(i1_series,i2_series,j1_series,j2_series,ModeMenu{ModeValue},Time,TimeUnit,ref_i,ref_j,TimeName,InputTable(iview,:),FileInfo);
1051    PairString{iview,1}=Menu{1};
1052else
1053    PairString{iview,1}=''; % no pair for #iview
1054end
1055set(handles.PairString,'Data',PairString)
1056if isempty(find(cellfun('isempty',get(handles.PairString,'Data'))==0, 1))% if all lines of pairs are empty
1057    set(handles.PairString,'Visible','off')
1058    set(handles.SetPairs,'Visible','off')
1059else
1060    set(handles.PairString,'Visible','on')
1061    set(handles.SetPairs,'Visible','on')
1062end
1063
1064
1065%% display the set of existing files as an image
1066set(handles.FileStatus,'Units','pixels')
1067Position=get(handles.FileStatus,'Position');
1068set(handles.FileStatus,'Units','normalized')
1069%xI=0.5:Position(3)-0.5;
1070nbview=numel(SeriesData.i1_series);
1071j_max=cell(1,nbview);
1072MaxIndex_i=ones(1,nbview); % default
1073MinIndex_i=ones(1,nbview); % default
1074for iline=1:nbview
1075    pair_max=squeeze(max(SeriesData.i1_series{iline},[],1)); % max on pair index
1076    j_max{iline}=max(pair_max,[],1); % max on j index
1077    if ~isempty(j_max{iline})
1078    MaxIndex_i(iline)=find(j_max{iline}, 1, 'last' )-1; % max ref index i
1079    MinIndex_i(iline)=find(j_max{iline}, 1 )-1; % min ref index i
1080    end
1081end
1082MinIndex_i=min(MinIndex_i);
1083MaxIndex_i=max(MaxIndex_i);
1084range_index=MaxIndex_i-MinIndex_i+1;
1085range_y=max(1,floor(Position(4)/nbview));
1086npx=floor(Position(3));
1087file_indices=MinIndex_i+floor(((0.5:npx-0.5)/npx)*range_index)+1;
1088CData=zeros(nbview*range_y,npx); % initiate the image representing the existing files
1089for iline=1:nbview
1090    ind_y=1+(iline-1)*range_y:iline*range_y;
1091    LineData=zeros(size(file_indices));
1092    file_select=file_indices(file_indices<=numel(j_max{iline}));
1093    ind_select=file_indices<=numel(j_max{iline});
1094    LineData(ind_select)=j_max{iline}(file_select)~=0;
1095    CData(ind_y,:)=ones(size(ind_y'))*LineData;
1096end
1097CData=cat(3,zeros(size(CData)),CData,zeros(size(CData))); % make color images r=0,g,b=0
1098set(handles.FileStatus,'CData',CData);
1099
1100%-----------------------------------------------------------guide -------------
1101%------------------------------------------------------------------------
1102%  III - FUNCTIONS ASSOCIATED TO THE FRAME IndexRange
1103%------------------------------------------------------------------------
1104
1105
1106% ---- determine the menu to put in mode and advice a default choice
1107%------------------------------------------------------------------------
1108function [ModeMenu,ModeValue]=update_mode(i1_series,i2_series,j2_series)
1109%------------------------------------------------------------------------
1110ModeMenu={''};
1111if isempty(j2_series)% no j pair
1112    ModeValue=1;
1113    if ~isempty(i2_series)
1114        ModeMenu={'series(Di)'}; % pair menu with only option Di
1115    end
1116else %existence of j pairs
1117    pair_max=squeeze(max(i1_series,[],1)); % max on pair index
1118    j_max=max(pair_max,[],1);
1119    MaxIndex_i=find(j_max, 1, 'last' )-1; % max ref index i
1120    MinIndex_i=find(j_max, 1 )-1; % min ref index i
1121    i_max=max(pair_max,[],2);
1122    MaxIndex_j=find(i_max, 1, 'last' )-1; % max ref index i
1123    MinIndex_j=find(i_max, 1 )-1; % min ref index i
1124    if MaxIndex_j==MinIndex_j
1125        ModeValue=1;
1126        ModeMenu={'bursts'};
1127    elseif MaxIndex_i==MinIndex_i
1128        ModeValue=1;
1129        ModeMenu={'series(Dj)'};
1130    else
1131        ModeMenu={'bursts';'series(Dj)'};
1132        if (MaxIndex_j-MinIndex_j)>10
1133            ModeValue=2; % set mode to series(Dj) if more than 10 j values
1134        else
1135            ModeValue=1;
1136        end
1137    end
1138end
1139
1140
1141%------------------------------------------------------------------------
1142%fill the menu of possible pairs as input
1143function displ_pair=update_listpair(i1_series,i2_series,j1_series,j2_series,mode,time,TimeUnit,ref_i,ref_j,TimeName,InputTable,FileInfo)
1144%------------------------------------------------------------------------
1145displ_pair={};
1146if isempty(TimeUnit)
1147    dtunit='e-03';
1148else
1149    dtunit=['m' TimeUnit];
1150end
1151switch mode
1152    case 'series(Di)'
1153        diff_i=i2_series-i1_series;
1154        min_diff=min(diff_i(diff_i>0));
1155        max_diff=max(diff_i(diff_i>0));
1156        for ipair=min_diff:max_diff
1157            if ~isempty(find(diff_i==ipair,1))% if the considered difference exists as input
1158                pair_string=['Di= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2)) ];
1159                if size(time,1)>=ref_i+ceil(ipair/2)
1160                    if ref_i<=floor(ipair/2)
1161                        ref_i=floor(ipair/2)+1; % shift ref_i to get the first pair
1162                    end
1163                    Dt=time(ref_i+ceil(ipair/2),ref_j)-time(ref_i-floor(ipair/2),ref_j);
1164                    pair_string=[pair_string ', Dt=' num2str(Dt) ' ' dtunit];
1165                end
1166                displ_pair=[displ_pair;{pair_string}];
1167            end
1168        end
1169        if ~isempty(displ_pair)
1170            displ_pair=[displ_pair;{'Di=*|*'}];
1171        end
1172    case 'series(Dj)'
1173        if isempty(j2_series)
1174            msgbox_uvmat('ERROR','no j1-j2 pair available')
1175            return
1176        end
1177        diff_j=j2_series-j1_series;
1178        min_diff=min(diff_j(diff_j>0));
1179        max_diff=max(diff_j(diff_j>0));
1180        for ipair=min_diff:max_diff
1181            if numel(diff_j(diff_j==ipair))>0
1182                pair_string=['Dj= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2)) ];
1183                if ~isempty(time)
1184                    if ref_j<=floor(ipair/2)
1185                        ref_j=floor(ipair/2)+1; % shift ref_i to get the first pair
1186                    end
1187                    Dt=time(ref_i,ref_j+ceil(ipair/2))-time(ref_i,ref_j-floor(ipair/2));
1188                    pair_string=[pair_string ', Dt=' num2str(Dt) ' ' dtunit];
1189                end
1190                displ_pair=[displ_pair;{pair_string}];
1191            end
1192        end
1193        if ~isempty(displ_pair)
1194            displ_pair=[displ_pair;{'Dj=*|*'}];
1195        end
1196    case 'bursts'
1197        if isempty(j2_series)
1198            msgbox_uvmat('ERROR','no j1-j2 pair available')
1199            return
1200        end
1201        %diff_j=j2_series-j1_series;
1202        min_j1=min(j1_series(j1_series>0));
1203        max_j1=max(j1_series(j1_series>0));
1204        min_j2=min(j2_series(j2_series>0));
1205        max_j2=max(j2_series(j2_series>0));
1206        for pair1=min_j1:min(max_j1,min_j1+20)
1207            for pair2=min_j2:min(max_j2,min_j2+20)
1208                if numel(j1_series(j1_series==pair1))>0 && numel(j2_series(j2_series==pair2))>0
1209                    pair_string=['j= ' num2str(pair1) '-' num2str(pair2)];
1210                    [TimeValue,DtValue]=get_time(ref_i,[],pair_string,InputTable,FileInfo,TimeName,'Dt');
1211                    %Dt=time(ref_i,pair2+1)-time(ref_i,pair1+1);
1212                    pair_string=[pair_string ', Dt=' num2str(DtValue) ' ' dtunit];
1213                    displ_pair=[displ_pair;{pair_string}];
1214                end
1215            end
1216        end
1217        if ~isempty(displ_pair)
1218            displ_pair=[displ_pair;{'j=*-*'}];
1219        end
1220end
1221
1222%------------------------------------------------------------------------
1223function num_first_i_Callback(hObject, eventdata, handles)
1224%------------------------------------------------------------------------
1225num_last_i_Callback(hObject, eventdata, handles)
1226
1227%------------------------------------------------------------------------
1228function num_last_i_Callback(hObject, eventdata, handles)
1229%------------------------------------------------------------------------
1230SeriesData=get(handles.series,'UserData');
1231if ~isfield(SeriesData,'Time')
1232    SeriesData.Time{1}=[];
1233end
1234displ_time(handles);
1235
1236%------------------------------------------------------------------------
1237function num_first_j_Callback(hObject, eventdata, handles)
1238%------------------------------------------------------------------------
1239 num_last_j_Callback(hObject, eventdata, handles)
1240
1241%------------------------------------------------------------------------
1242function num_last_j_Callback(hObject, eventdata, handles)
1243%------------------------------------------------------------------------
1244SeriesData=get(handles.series,'UserData');
1245if ~isfield(SeriesData,'Time')
1246    SeriesData.Time{1}=[];
1247end
1248displ_time(handles);
1249
1250%------------------------------------------------------------------------
1251% ---- find the times corresponding to the first and last indices of a series
1252function displ_time(handles)
1253%------------------------------------------------------------------------
1254SeriesData=get(handles.series,'UserData'); %
1255if ~isfield(SeriesData,'Time')
1256    return
1257end
1258PairString=get(handles.PairString,'Data');
1259ref_i_1=str2num(get(handles.num_first_i,'String')); % first reference index
1260ref_i_2=str2num(get(handles.num_last_i,'String')); % last reference index
1261ref_j_1=[];ref_j_2=[];
1262if strcmp(get(handles.num_first_j,'Visible'),'on')
1263ref_j_1=str2num(get(handles.num_first_j,'String'));
1264ref_j_2=str2num(get(handles.num_last_j,'String'));
1265end
1266[i1_1,i2_1,j1_1,j2_1] = get_file_index(ref_i_1,ref_j_1,PairString);
1267[i1_2,i2_2,j1_2,j2_2] = get_file_index(ref_i_2,ref_j_2,PairString);
1268TimeTable=get(handles.TimeTable,'Data');
1269%%%%%%
1270%TODO: read time in netcdf file, see ActionName_Callback
1271%%%%%%%
1272%Pairs=get(handles.PairString,'Data');
1273for iview=1:size(TimeTable,1)
1274    if numel(SeriesData.Time)<iview
1275        break
1276    end
1277    TimeTable{iview,3}=[];
1278    TimeTable{iview,4}=[];
1279    if size(SeriesData.Time{iview},1)>=i2_2+1 && (isempty(ref_j_1)||size(SeriesData.Time{iview},2)>=j2_2+1)
1280        if isempty(ref_j_1)
1281            time_first=(SeriesData.Time{iview}(i1_1+1,2)+SeriesData.Time{iview}(i2_1+1,2))/2;
1282            time_last=(SeriesData.Time{iview}(i1_2+1,2)+SeriesData.Time{iview}(i2_2+1,2))/2;
1283        else
1284            time_first=(SeriesData.Time{iview}(i1_1+1,j1_1+1)+SeriesData.Time{iview}(i2_1+1,j2_1+1))/2;
1285            time_last=(SeriesData.Time{iview}(i1_2+1,j1_2+1)+SeriesData.Time{iview}(i2_2+1,j2_1+1))/2;
1286        end
1287        TimeTable{iview,3}=time_first; % TODO: take into account pairs
1288        TimeTable{iview,4}=time_last; % TODO: take into account pairs
1289    end
1290end
1291set(handles.TimeTable,'Data',TimeTable)
1292
1293%% set the waitbar position with respect to the min and max in the series
1294MinIndex_i=min(get(handles.MinIndex_i,'Data'));
1295MaxIndex_i=max(get(handles.MaxIndex_i,'Data'));
1296pos_first=(ref_i_1-MinIndex_i)/(MaxIndex_i-MinIndex_i+1);
1297pos_last=(ref_i_2-MinIndex_i+1)/(MaxIndex_i-MinIndex_i+1);
1298if isempty(pos_first), pos_first=0; end
1299if isempty(pos_last), pos_last=1; end
1300Position=get(handles.Waitbar,'Position'); % position of the waitbar:= [ x,y, width, height]
1301Position_status=get(handles.FileStatus,'Position');
1302Position(1)=Position_status(1)+Position_status(3)*pos_first;
1303Position(3)=max(Position_status(3)*(pos_last-pos_first),0.001); % width must remain positive
1304set(handles.Waitbar,'Position',Position)
1305update_waitbar(handles.Waitbar,0)
1306
1307%------------------------------------------------------------------------
1308% --- Executes when selected cell(s) is changed in PairString.
1309function PairString_CellSelectionCallback(hObject, eventdata, handles)
1310%------------------------------------------------------------------------
1311if numel(eventdata.Indices)>=1
1312    PairString=get(hObject,'Data');
1313    if ~isempty(PairString{eventdata.Indices(1)})
1314        SetPairs_Callback(hObject, eventdata.Indices(1), handles)
1315    end
1316end
1317
1318%-------------------------------------
1319function enable_i(handles,state)
1320set(handles.i_txt,'Visible',state)
1321set(handles.num_first_i,'Visible',state)
1322set(handles.num_last_i,'Visible',state)
1323set(handles.num_incr_i,'Visible',state)
1324
1325%-----------------------------------
1326function enable_j(handles,state)
1327set(handles.j_txt,'Visible',state)
1328set(handles.num_first_j,'Visible',state)
1329set(handles.num_last_j,'Visible',state)
1330set(handles.num_incr_j,'Visible',state)
1331set(handles.MinIndex_j,'Visible',state)
1332set(handles.MaxIndex_j,'Visible',state)
1333
1334
1335%%%%%%%%%%%%%%%%%%%%
1336%%  MAIN ActionName FUNCTIONS
1337%%%%%%%%%%%%%%%%%%%%
1338%------------------------------------------------------------------------
1339% --- Executes on button press in RUN.
1340%------------------------------------------------------------------------
1341function RUN_Callback(hObject, eventdata, handles)
1342
1343%% settings of the button RUN
1344if ~isequal(get(handles.ActionInput,'BackgroundColor'),[1 0 0])
1345    msgbox_uvmat('ERROR','first activate the button ActionInput')
1346    return
1347end
1348set(handles.RUN,'BusyAction','queue'); % activation of STOP button will set BusyAction to 'cancel'
1349set(handles.RUN, 'Enable','Off')% avoid further RUN action until the current one is finished
1350set(handles.RUN,'BackgroundColor',[1 1 0])%show activation of RUN by yellow color
1351drawnow
1352set(handles.status,'Value',0)% desable status display if relevant
1353status_Callback([], eventdata, handles)
1354
1355%% launch action
1356errormsg=launch_action(handles);
1357if ~isempty(errormsg)
1358     msgbox_uvmat('ERROR',errormsg)
1359end
1360
1361%% reset the GUI series
1362update_waitbar(handles.Waitbar,1); % put the waitbar to end position to indicate launching is finished
1363set(handles.RUN, 'Enable','On')
1364set(handles.RUN,'BackgroundColor',[1 0 0])
1365set(handles.RUN, 'Value',0)
1366
1367%------------------------------------------------------------------------
1368% --- called by RUN_Callback
1369%------------------------------------------------------------------------
1370% The calculations are launched in three different ways:
1371% RunMode='local': calculation on the local Matlab session, will prevent other actions during that time.
1372% RunMode='background': calculation on the local computer, but in a new Matlab session (with no graphic output).
1373% RunMode='cluster': calculations dispatched in a cluster, using a managing system, 'oar, 'sge, or 'sgb'.
1374% In the latter case, the calculation is split in 'packets' of i index (all j indices are contained in a single packet).
1375% This splitting is possible only if the different calculations in the series are independent. Otherwise the action
1376% function imposes a number of processes NbSlice in input, for instance NbSlice=1 for a time series.
1377% If NbSlice is not imposed, the splitting in packets (jobs) is determined
1378% so that a job is optimum length AdvisedJobCPUTime), and the total job number in any case smaller
1379% than MaxJobNumber (these parameters are defined in the file series.xml in
1380% accordance with the management strategy for the cluster). The jobs are
1381% dispatched in parallel into NbCore processors by the cluster managing system.
1382
1383function errormsg=launch_action(handles)
1384errormsg=''; % default
1385
1386%% read the data on the GUI series
1387Param=read_GUI_series(handles); % displayed parameters
1388SeriesData=get(handles.series,'UserData'); % hidden parameters
1389if isfield(SeriesData,'TransformInput')
1390    Param.TransformInput=SeriesData.TransformInput;
1391end
1392if isfield(SeriesData,'ProjObject')
1393    Param.ProjObject=SeriesData.ProjObject;
1394end
1395if ~isfield(SeriesData,'i1_series')
1396    errormsg='The input field series needs to be refreshed: press REFRESH';
1397    return
1398end
1399if isfield(Param,'InputFields')&& isfield(Param.InputFields,'FieldName')&& isequal(Param.InputFields.FieldName,'add_field...')
1400    errormsg='input field name(s) not defined, select add_field...';
1401    return
1402end
1403
1404%% select the Action mode, 'local', 'background' or 'cluster' (if available)
1405RunMode='local'; % default (needed for first opening of the GUI series)
1406if isfield(Param.Action,'RunMode')
1407    RunMode=Param.Action.RunMode;
1408    Param.Action=rmfield(Param.Action,'RunMode'); % remove from the recorded xml file to avoid interference during ImportConfig
1409    Param.RunMode=RunMode; % keep track of the mode
1410end
1411ActionExt='.m'; % default
1412if isfield(Param.Action,'ActionExt')
1413    ActionExt=Param.Action.ActionExt; % '.m', '.sh' (compiled)  or 'fluidimage' (Python)
1414    Param.Action=rmfield(Param.Action,'ActionExt'); % remove from the recorded xml file to avoid interference during ImportConfig
1415end
1416ActionName=Param.Action.ActionName;
1417ActionPath=Param.Action.ActionPath;
1418path_series=fileparts(which('series'));
1419
1420%% create the Action fct handle if RunMode option = 'local'
1421if strcmp(RunMode,'local')
1422    current_dir=pwd; % current working dir
1423cd(ActionPath)
1424h_fun=str2func(ActionName);% create the function handle for the function ActionName
1425cd(current_dir)
1426    % if ~isequal(ActionPath,path_series)
1427    %
1428    %     %eval(['spath=which(''' ActionName ''');']) %spath = current path of the selected function ACTION
1429    %     if ~exist(ActionPath,'dir')
1430    %         errormsg=['The prescribed function path ' ActionPath ' does not exist'];
1431    %         return
1432    %     end
1433    %     spath=fileparts(which(ActionName));
1434    %     if ~strcmp(spath,ActionPath)
1435    %         addpath(ActionPath)% add the prescribed path if not the current one
1436    %     end
1437    % end
1438    % eval(['h_fun=@' ActionName ';'])%create a function handle for ACTION
1439    % if ~isequal(ActionPath,path_series)
1440    %     rmpath(ActionPath)% add the prescribed path if not the current one
1441    % end
1442 end
1443
1444%% Get  parameters from series.xml
1445errormsg=''; % default error message
1446ActionFullName=fullfile(get(handles.ActionPath,'String'),ActionName);
1447
1448%% If a compiled version has been selected (ext .sh) check wether it needs to be recompiled
1449if strcmp(ActionExt,'.sh')
1450    TransformPath='';
1451    if isfield(SeriesData,'TransformPath')
1452        TransformPath=SeriesData.TransformPath;
1453        if isfield(SeriesData,'TransformList')
1454            TransformList=get(handles.TransformName,'String');
1455            TransformIndex=get(handles.TransformName,'Value');
1456            TransformName=TransformList{TransformIndex};
1457            if ~ismember(TransformName,SeriesData.TransformList)
1458                TransformPath='';
1459            end
1460        end
1461    end
1462    if ~isempty(TransformPath)&&...
1463          ~strcmp(TransformPath,get(handles.TransformPath,'String'))% if the transform is not in paths set for compilation
1464        msgbox_uvmat('ERROR', 'compilation not available for this transform function, select .m')
1465        return
1466    end
1467    set(handles.series,'Pointer','watch') % set the mouse pointer to 'watch'
1468    set(handles.ActionExt,'BackgroundColor',[1 1 0])
1469    [mcrmajor, mcrminor] = mcrversion;
1470    MCRROOT = ['MCRROOT',int2str(mcrmajor),int2str(mcrminor)];
1471    RunTime = getenv('MCRROOT'); % Just variable MCRROOT with no version in it's name
1472    if strcmp(RunTime,'')
1473        RunTime = getenv(MCRROOT); % Use specialize MCRROOT with version
1474    end
1475    ActionNameVersion=[ActionName '_' MCRROOT];
1476    ActionFullName=fullfile(get(handles.ActionPath,'String'),[ActionNameVersion '.sh']);
1477    % compile the .m file if the .sh file does not exist yet
1478    if ~exist(ActionFullName,'file')
1479        answer=msgbox_uvmat('INPUT_Y-N','compiled version has not been created: compile now?');
1480        if strcmp(answer,'Yes')
1481            set(handles.ActionExt,'BackgroundColor',[1 1 0])
1482            path_uvmat=fileparts(which('series'));
1483            currentdir=pwd;
1484            cd(get(handles.ActionPath,'String'))% go to the directory of Action
1485            addpath(path_uvmat)% add the path to uvmat to run the fct 'compile'
1486            compile(ActionName,TransformPath)
1487            cd(currentdir)
1488        else
1489            errormsg='Action launch interrupted';
1490            return
1491        end
1492    else
1493        sh_file_info=dir(fullfile(get(handles.ActionPath,'String'),[ActionNameVersion '.sh']));
1494        m_file_info=dir(fullfile(get(handles.ActionPath,'String'),[ActionName '.m']));
1495        if isfield(m_file_info,'datenum') && m_file_info.datenum>sh_file_info.datenum
1496            set(handles.ActionExt,'BackgroundColor',[1 1 0])
1497            drawnow
1498            answer=msgbox_uvmat('INPUT_Y-N',[ActionNameVersion '.sh needs to be updated: recompile now?']);
1499            if strcmp(answer,'Yes')
1500                path_uvmat=fileparts(which('series'));
1501                currentdir=pwd;
1502                cd(get(handles.ActionPath,'String'))% go to the directory of Action
1503                addpath(path_uvmat)% add the path to uvmat to run the fct 'compile'
1504                addpath(fullfile(path_uvmat,'transform_field'))% add the path to transform functions to run the fct 'compile'
1505                compile(ActionName,TransformPath)
1506                cd(currentdir)
1507            end
1508        end
1509    end
1510
1511    set(handles.ActionExt,'BackgroundColor',[1 1 1])
1512     set(handles.series,'Pointer','arrow') % set the mouse pointer to 'watch
1513end
1514
1515%% set nbre of cluster cores and processes:
1516% NbCore is the number of computer processors used
1517% NbProcess is the number of independent processes in which the required calculation is split.
1518% switch RunMode
1519%     case {'local','background'}
1520%         NbCore=1; % no need to split the calculation
1521%     case 'cluster'
1522%         %proposed number of cores to reserve in the cluster
1523%         NbCoreAdvised=SeriesData.SeriesParam.ClusterParam.NbCoreAdvised;
1524%         NbCoreMax=min(NbProcess,SeriesData.SeriesParam.ClusterParam.NbCoreMax);
1525%         if NbCoreMax~=1
1526%             if strcmp(ActionExt,'.m')% case of Matlab function (uncompiled)
1527%                 warning_string=', preferably use .sh option to save Matlab licences';
1528%             else
1529%                 warning_string=')';
1530%             end
1531%             answer=msgbox_uvmat('INPUT_TXT',['Number of cores (max ' num2str(NbCoreMax) ', ' warning_string],num2str(NbCoreAdvised));
1532%             if isempty(answer)
1533%                 errormsg='Action launch interrupted by user';
1534%                 return
1535%             end
1536%             NbCore=str2double(answer);
1537%             if NbCore > NbCoreMax
1538%                 NbCore=NbCoreMax;
1539%             end
1540%         else
1541%             NbCore=1;
1542%         end
1543% end
1544if ~isfield(Param.IndexRange,'NbSlice')
1545    Param.IndexRange.NbSlice=[];
1546end
1547OutputPath=get(handles.OutputPath,'String');
1548
1549%% Look for processing on multiple experiments set by the GUI browse_data
1550NbExp=1;% initiate the number of experiments set by the GUI browse_data, =1 otherwise
1551if get(handles.Replicate,'Value')
1552    hh=findobj(allchild(0),'Tag','browse_data');
1553    if isempty(hh)
1554        set(handles.Replicate,'Value',0)
1555    else
1556        set(handles.Replicate,'BackgroundColor',[1 1 0])%paint Relicate button in yellow
1557        BrowseData=guidata(hh);
1558        SourceDir=get(BrowseData.SourceDir,'String');
1559        ListExp=get(BrowseData.ListExperiments,'String');
1560        ExpIndices=get(BrowseData.ListExperiments,'Value');
1561        ListExp=ListExp(ExpIndices);
1562        ListDevices=get(BrowseData.ListDevices,'String');
1563        DeviceIndices=get(BrowseData.ListDevices,'Value');
1564        ListDevices=ListDevices(DeviceIndices);
1565        ListDataSeries=get(BrowseData.DataSeries,'String');
1566        DataSeriesIndices=get(BrowseData.DataSeries,'Value');
1567        ListDataSeries=ListDataSeries(DataSeriesIndices);
1568        NbExp=0; % counter of the number of experiments set by the GUI browse_data
1569        for iexp=1:numel(ListExp)
1570            if ~isempty(regexp(ListExp{iexp},'^\+/'))% if it is a folder
1571               %if strcmp(get(BrowseData.DataSeries,'enable'),'off') %case of a multiple input line for series
1572%                     NbExp=NbExp+1;
1573%                     ExpIndex{NbExp}=iexp;
1574%                     for idevice=1:numel(ListDevices)
1575%                         lpath= fullfile(SourceDir,regexprep(ListExp{iexp},'^\+/',''),...
1576%                             regexprep(ListDevices{idevice},'^\+/',''));
1577%                         lpathout=fullfile(OutputPath,regexprep(ListExp{iexp},'^\+/',''),...
1578%                             regexprep(ListDevices{idevice},'^\+/',''));
1579%                         ldir=regexprep(ListDataSeries{idevice},'^\+/','');
1580%                         ListPath{idevice,NbExp}=lpath;
1581%                         ListPathOut{idevice,NbExp}=lpathout;
1582%                         ListSubdir{idevice,NbExp}=ldir;
1583%                     end
1584                %else
1585                    for idevice=1:numel(ListDevices)
1586                        if ~isempty(regexp(ListDevices{idevice},'^\+/'))% if it is a folder
1587                            for isubdir=1:numel(ListDataSeries)
1588                                if ~isempty(regexp(ListDataSeries{isubdir},'^\+/'))% if it is a folder
1589                                    lpath= fullfile(SourceDir,regexprep(ListExp{iexp},'^\+/',''),...
1590                                        regexprep(ListDevices{idevice},'^\+/',''));
1591                                    lpathout= fullfile(OutputPath,regexprep(ListExp{iexp},'^\+/',''),...
1592                                        regexprep(ListDevices{idevice},'^\+/',''));
1593                                    ldir= regexprep(ListDataSeries{isubdir},'^\+/','');
1594                                    if exist(fullfile(lpath,ldir),'dir')
1595                                        NbExp=NbExp+1;
1596                                        ExpIndex(NbExp)=ExpIndices(iexp);
1597                                        DeviceIndex(NbExp)=DeviceIndices(idevice);
1598                                        ListPath{NbExp}=lpath;
1599                                        ListPathOut{NbExp}=lpathout;
1600                                        ListDeviceOut{NbExp}=regexprep(ListDevices{idevice},'^\+/','');
1601                                        ListExpOut{NbExp}=regexprep(ListExp{iexp},'^\+/','');
1602                                        ListSubdir{NbExp}=ldir;
1603                                    end
1604                                end
1605                            end
1606                        end
1607                    end
1608%                 end
1609            end
1610        end
1611        answer=msgbox_uvmat('INPUT_Y-N-Cancel',['replicate the processing on ' num2str(NbExp) ' data series']);
1612        if strcmp(answer,'Cancel')||strcmp(answer,'No')
1613            return
1614        end
1615    end
1616end
1617
1618%%%%%%%%%%%%%%%%%%% LOOP ON EXPERIMENTS POSSIBLY SET BY THE GUI browse_data, NbExp=1 otherwise %%%%%%%%%
1619
1620for iexp=1:NbExp
1621    if get(handles.Replicate,'Value')
1622        if ~strcmp(get(handles.RUN,'BusyAction'),'queue')% allow for STOP action
1623            disp('program stopped by user')
1624            return
1625        end
1626        set(BrowseData.ListExperiments,'Value',ExpIndex(iexp))
1627        set(BrowseData.ListDevices,'Value',DeviceIndex(iexp))
1628        Param.InputTable(:,1)=ListPath(:,iexp);
1629        Param.InputTable(:,2)=ListSubdir(:,iexp);
1630        OutputSubDir=unique(ListSubdir(:,iexp));
1631        Param.OutputSubDir=OutputSubDir{1};
1632        if numel(OutputSubDir)>1% case
1633            for iout=2:numel(OutputSubDir)
1634                Param.OutputSubDir=[Param.OutputSubDir '-' OutputSubDir{iout}];
1635            end
1636        end
1637    end
1638    [xx,ExpName]=fileparts(Param.InputTable{1,1});
1639    Param.IndexRange.first_i=str2num(get(handles.num_first_i,'String'));%reset the firrst_i and last_i for multiple experiments, modified by the splitting into NbProcess
1640    Param.IndexRange.last_i=str2num(get(handles.num_last_i,'String'));
1641
1642    %% create the output data directory if needed, after checking its existence
1643    OutputDir='';
1644    answer='';
1645    if isfield(Param,'OutputSubDir')&& isfield(Param,'OutputDirExt')% possibly update the output dir if it already exists
1646        PathOut=get(handles.OutputPath,'String');
1647        if ~exist(PathOut,'dir') % test if  the dir  already exist
1648            PathOut=uigetdir(PathOut,'pick the output root path');
1649            set(handles.OutputPath,'String',PathOut);
1650        end
1651        if get(handles.Replicate,'Value')
1652        PathExpOut=fileparts(ListPath{iexp});
1653        PathExpDeviceOut=ListPath{iexp};
1654        else
1655            PathExpOut=fullfile(PathOut,get(handles.Experiment,'String'));
1656            PathExpDeviceOut=fullfile(PathExpOut,get(handles.Device,'String'))
1657        end
1658        if ~exist(PathExpOut,'dir')
1659            [tild,msg1]=mkdir(PathExpOut);
1660            if ~strcmp(msg1,'')
1661                errormsg=['cannot create ' PathExpOut ': ' msg1]; % error message for directory creation
1662                return
1663            end
1664        end
1665        if ~exist(PathExpDeviceOut,'dir')
1666            [tild,msg1]=mkdir(PathExpDeviceOut);
1667            if ~strcmp(msg1,'')
1668                errormsg=['cannot create ' PathExpDeviceOut ': ' msg1]; % error message for directory creation
1669                return
1670            end
1671        end
1672
1673        SubDirOut=[Param.OutputSubDir Param.OutputDirExt];
1674        SubDirOutNew=SubDirOut;
1675        detect=exist(fullfile(PathExpDeviceOut,SubDirOutNew),'dir'); % test if  the dir  already exist
1676        check_create=1; % need to create the result directory by default
1677        CheckOverwrite=1;
1678        if isfield(Param,'CheckOverwrite')
1679            CheckOverwrite=Param.CheckOverwrite;% will overwrite previous data if it is equal to 1
1680        end
1681        while detect
1682            if CheckOverwrite
1683                comment=', possibly overwrite previous data';
1684            else
1685                comment=', will complement existing result files (no overwriting)';
1686            end
1687            answer=msgbox_uvmat('INPUT_Y-N-Cancel',['use existing ouput directory: ' fullfile(PathExpDeviceOut,SubDirOutNew) comment]);
1688            if strcmp(answer,'Cancel')
1689                break
1690            elseif strcmp(answer,'Yes')
1691                detect=0;
1692                check_create=0;
1693            else
1694                r=regexp(SubDirOutNew,'(?<root>.*\D)(?<num1>\d+)$','names'); % detect whether name ends by a number
1695                if isempty(r)
1696                    r(1).root=[SubDirOutNew '_'];
1697                    r(1).num1='0';
1698                end
1699                SubDirOutNew=[r(1).root num2str(str2num(r(1).num1)+1)]; % increment the index by 1 or put 1
1700                detect=exist(fullfile(PathExpDeviceOut,SubDirOutNew),'dir'); % test if  the dir  already exists
1701                check_create=1;
1702            end
1703        end
1704        if strcmp(answer,'Cancel')
1705            continue
1706        end
1707        Param.OutputDirExt=regexprep(SubDirOutNew,['^' Param.OutputSubDir],'');
1708        Param.OutputRootFile=Param.InputTable{1,3}; % the first sorted RootFile taken for output
1709        OutputDir=fullfile(PathExpDeviceOut,[Param.OutputSubDir Param.OutputDirExt]); % full name (with path) of output directory
1710        if check_create    % create output directory if it does not exist
1711            [tild,msg1]=mkdir(OutputDir);
1712            if ~strcmp(msg1,'')
1713                errormsg=['cannot create ' OutputDir ': ' msg1]; % error message for directory creation
1714                return
1715            end
1716        end
1717
1718    elseif isfield(Param,'ActionInput')&&isfield(Param.ActionInput,'LogPath')% custom definition of the output dir
1719        OutputDir=Param.ActionInput.LogPath;
1720    end
1721    if isfield(Param,'OutputSubDir')&& isfield(Param,'OutputDirExt')
1722        set(handles.OutputSubDir,'String',Param.OutputSubDir)
1723        set(handles.OutputDirExt,'String',Param.OutputDirExt)
1724        drawnow
1725    end
1726    if get(handles.Replicate,'Value')
1727        set(handles.InputTable,'Data',Param.InputTable)
1728        set(handles.OutputPath,'String',OutputPath)
1729         set(handles.Experiment,'String',ListExpOut{iexp})
1730        set(handles.Device,'String',ListDeviceOut{iexp})
1731        Param.Experiment=ListExpOut{iexp};
1732        Param.Device=ListDeviceOut{iexp};
1733        check_input_file_series(handles)
1734    end
1735    DirXml=fullfile(OutputDir,'0_XML');
1736    if ~exist(DirXml,'dir')
1737        [~,msg1]=mkdir(DirXml);
1738        if ~strcmp(msg1,'')
1739            errormsg=['cannot create ' DirXml ': ' msg1]; % error message for directory creation
1740            return
1741        end
1742        [success,msg] = fileattrib(DirXml,'+w','g','s'); % allow writing access for the group of users, recursively in the folder
1743        if success==0
1744            msgbox_uvmat('WARNING',{['unable to set group write access to ' DirXml ':']; msg}); % error message for directory creation
1745        end
1746    end
1747    OutputNomType=nomtype2pair(Param.InputTable{1,4}); % nomenclature for output files
1748
1749    %% get the set of reference input field indices
1750    first_i=1; % first i index to process
1751    last_i=1; % last i index to process
1752    incr_i=1; % increment step in i index
1753    first_j=1; % first j index to process
1754    last_j=1; % last j index to process
1755    incr_j=1; % increment step in j index
1756    if isfield(Param.IndexRange,'first_i')
1757        first_i=Param.IndexRange.first_i;
1758        incr_i=Param.IndexRange.incr_i;
1759        last_i=Param.IndexRange.last_i;
1760    end
1761    if isfield(Param.IndexRange,'incr_j')
1762        first_j=Param.IndexRange.first_j;
1763        last_j=Param.IndexRange.last_j;
1764        incr_j=Param.IndexRange.incr_j;
1765    end
1766    if last_i < first_i || last_j < first_j
1767        errormsg= 'series/Run_Callback:last field index must be larger or equal to the first one';
1768        return
1769    end
1770    %incr_i must be defined, =1 by default, if NbSlice is active
1771    if isempty(incr_i)&& ~isempty(Param.IndexRange.NbSlice)
1772        incr_i=1;
1773        set(handles.num_incr_i,'String','1')
1774    end
1775    % case of no increment i defined: processing is done on the available files found in i1_series
1776    if isempty(incr_i)
1777        if isempty(incr_j)
1778            [ref_j,ref_i]=find(squeeze(SeriesData.i1_series{1}(1,:,:)));
1779            ref_j=ref_j(ref_j>=first_j & ref_j<=last_j);
1780            ref_i=ref_i(ref_i>=first_i & ref_i<=last_i);
1781            ref_j=ref_j-1;
1782            ref_i=ref_i-1;
1783        else
1784            ref_j=first_j:incr_j:last_j;
1785            [tild,ref_i]=find(squeeze(SeriesData.i1_series{1}(1,:,:)));
1786            ref_i=ref_i-1;
1787            ref_i=ref_i(ref_i>=first_i & ref_i<=last_i);
1788        end
1789        % increment i is defined: processing is done on first_i:incr_i:last_i;
1790    else
1791        ref_i=first_i:incr_i:last_i;
1792        if isempty(incr_j)% automatic finding of the existing j indices
1793            [ref_j,tild]=find(squeeze(SeriesData.i1_series{1}(1,:,:)));
1794            ref_j=ref_j-1;
1795            ref_j=ref_j(ref_j>=first_j & ref_j<=last_j);
1796        else
1797            ref_j=first_j:incr_j:last_j;
1798        end
1799    end
1800    nbfield_j=numel(ref_j); % number of j indices
1801    BlockLength=numel(ref_i); % by default, job involves the full set of i field indicesNbProcess
1802    NbProcess=1;
1803    NbCore=1;
1804    switch RunMode
1805        case 'cluster'
1806            if (isfield(Param.Action, 'CPUTime') && ~isempty(Param.Action.CPUTime) && isnumeric(Param.Action.CPUTime))
1807                CPUTime=Param.Action.CPUTime; % Note: CpUTime for one iteration ref_i has to be multiplied by the number of j indices nbfield_j
1808            else
1809                answer=msgbox_uvmat('INPUT_TXT','estimate the CPU time(in minutes) for each value of index i:' ,'');
1810                CPUTime=str2num(answer);
1811                set(handles.num_CPUTime,'String',answer)
1812                Param.Action.CPUTime=CPUTime;
1813            end
1814            JobNumberMax=SeriesData.SeriesParam.ClusterParam.JobNumberMax;
1815            JobCPUTimeAdvised=SeriesData.SeriesParam.ClusterParam.JobCPUTimeAdvised;
1816            if isempty(Param.IndexRange.NbSlice)% if NbSlice is not defined
1817                BlockLength= ceil(JobCPUTimeAdvised/(CPUTime*nbfield_j)); % iterations are grouped in sets with length BlockLength  such that the typical CPU time of a job is JobCPUTimeAdvised.
1818                BlockLength=max(BlockLength,ceil(numel(ref_i)*NbExp/JobNumberMax)); % possibly increase the BlockLength to have less than MaxJobNumber jobs
1819                NbProcess=ceil(numel(ref_i)/BlockLength) ; % nbre of processes sent to oar
1820            else
1821                NbProcess=Param.IndexRange.NbSlice; % the parameter NbSlice sets the nbre of run processes
1822            end
1823
1824            %         %proposed number of cores to reserve in the cluster
1825            NbCoreAdvised=SeriesData.SeriesParam.ClusterParam.NbCoreAdvised;
1826            NbCoreMax=min(NbProcess,SeriesData.SeriesParam.ClusterParam.NbCoreMax);% reduces the number of cores if it exceeds the number of processes
1827            if NbCoreMax~=1
1828                if strcmp(ActionExt,'.m')% case of Matlab function (uncompiled)
1829                    warning_string=', preferably use .sh option to save Matlab licences';
1830                else
1831                    warning_string=')';
1832                end
1833                answer=msgbox_uvmat('INPUT_TXT',['Number of cores (max ' num2str(NbCoreMax) ', ' warning_string],num2str(NbCoreAdvised));
1834                if isempty(answer)
1835                    errormsg='Action launch interrupted by user';
1836                    return
1837                end
1838                NbCore=str2double(answer);
1839                if NbCore > NbCoreMax
1840                    NbCore=NbCoreMax;
1841                end
1842            end
1843        otherwise
1844            if ~isempty(Param.IndexRange.NbSlice)
1845                NbProcess=Param.IndexRange.NbSlice; % the parameter NbSlice sets the nbre of run processes
1846            end
1847    end
1848
1849    %% record nbre of output files and starting time for computation for status
1850    StatusData=get(handles.status,'UserData');
1851    if isfield(StatusData,'OutputFileMode')
1852        switch StatusData.OutputFileMode
1853            case 'NbInput'
1854                StatusData.NbOutputFile=numel(ref_i)*nbfield_j;
1855            case 'NbInput_i'
1856                StatusData.NbOutputFile=numel(ref_i);
1857            case 'NbSlice'
1858                StatusData.NbOutputFile=str2num(get(handles.num_NbSlice,'String'));
1859        end
1860    end
1861    StatusData.TimeStart=now;
1862    set(handles.status,'UserData',StatusData)
1863
1864    %% case of a function in Python
1865    if strcmp(ActionExt, 'fluidimage')
1866        fprintf([
1867            '\n' ...
1868            '!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n' ...
1869            'The computation should be done by fluidimage (https://fluidimage.readthedocs.io).\n' ...
1870            'Warning: Fluidimage parameters will be guessed from UVmat parameters but \n' ...
1871            'there is no direct correspondance between UVMAT and fluidimage parameters.\n' ...
1872            'Please report issues here https://foss.heptapod.net/fluiddyn/fluidimage/-/issues\n' ...
1873            '!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n'])
1874        RunMode = 'python';
1875    end
1876
1877
1878    %% direct processing on the current Matlab session or creation of command files
1879    filexml=cell(1,NbProcess); % initialisation of the names of the files containing the processing parameters
1880    extxml=cell(1,NbProcess); % initialisation of the set of labels used for the files documenting each process
1881    for iprocess=1:NbProcess
1882        extxml{iprocess}='.xml';
1883    end
1884    for iprocess=1:NbProcess
1885        if ~strcmp(get(handles.RUN,'BusyAction'),'queue')% allow for STOP action
1886            disp('program stopped by user')
1887            return
1888        end
1889        Param.IndexRange.incr_slice=incr_i;
1890        if isempty(Param.IndexRange.NbSlice)
1891            Param.IndexRange.first_i=first_i+(iprocess-1)*BlockLength*incr_i;
1892            if Param.IndexRange.first_i>last_i
1893                NbProcess=iprocess-1; % leave the loop, we are at the end of the calculation
1894                break
1895            end
1896            Param.IndexRange.last_i=min(last_i,first_i+(iprocess)*BlockLength*incr_i-1);
1897        else %multislices (then incr_i is not empty)
1898            Param.IndexRange.first_i= first_i+iprocess-1;
1899            Param.IndexRange.incr_slice=incr_i*Param.IndexRange.NbSlice;
1900        end
1901        for ilist=1:size(Param.InputTable,1)
1902            Param.InputTable{ilist,1}=regexprep(Param.InputTable{ilist,1},'\','/'); % correct path name for PCWIN system
1903        end
1904
1905        if isfield(Param,'OutputSubDir')
1906            t=struct2xml(Param);
1907            t=set(t,1,'name','Series');
1908            extxml{iprocess}=fullfile_uvmat('','',Param.InputTable{1,3},'.xml',OutputNomType,...
1909                Param.IndexRange.first_i,Param.IndexRange.last_i,first_j,last_j);
1910            filexml{iprocess}=fullfile(OutputDir,'0_XML',extxml{iprocess});
1911            try
1912                save(t, filexml{iprocess}); % save the xml file containing the processing parameters
1913            catch ME
1914                if ~strcmp (RunMode,'local')
1915                    errormsg=['error writting ' filexml{iprocess} ': ' ME.message];
1916                    return
1917                end
1918            end
1919        end
1920        if strcmp (RunMode,'local')
1921            switch ActionExt
1922                case '.m'
1923                    h_fun(Param); % direct launching
1924
1925                case '.sh'
1926                    switch computer
1927                        case {'PCWIN','PCWIN64'} %Windows system
1928                            filexml=regexprep(filexml,'\\','\\\\'); % add '\' so that '\' are left as characters
1929                            system([ActionFullName ' ' RunTime ' ' filexml{iprocess}]); % TODO: adapt to DOS system
1930                        case {'GLNX86','GLNXA64','MACI64'}%Linux  system
1931                            system([ActionFullName ' ' RunTime ' ' filexml{iprocess}]);
1932                    end
1933            end
1934        end
1935    end
1936
1937    if ~strcmp (RunMode,'local') && ~strcmp(RunMode,'python')
1938        %% processing on a different session of the same computer (background) or cluster, create executable files
1939        batch_file_list=cell(NbProcess,1); % initiate the list of executable files
1940        DirExe=fullfile(OutputDir,'0_EXE'); % directory name for executable files
1941        switch computer
1942            case {'PCWIN','PCWIN64'} %Windows system
1943                ExeExt='.bat';
1944            case {'GLNX86','GLNXA64','MACI64'}%Linux  system
1945                ExeExt='.sh';
1946        end
1947        %create subdirectory for executable files
1948        if ~exist(DirExe,'dir')
1949            [tild,msg1]=mkdir(DirExe);
1950            if ~strcmp(msg1,'')
1951                errormsg=['cannot create ' DirExe ': ' msg1]; % error message for directory creation
1952                return
1953            end
1954            [success,msg] = fileattrib(DirExe,'+w','g','s'); % allow writing access for the group of users, recursively in the folder
1955            if success==0
1956                msgbox_uvmat('WARNING',{['unable to set group write access to ' DirExe ':']; msg}); % error message for directory creation
1957            end
1958        end
1959        %create subdirectory for log files
1960        DirLog=fullfile(OutputDir,'0_LOG');
1961        if ~exist(DirLog,'dir')
1962            [tild,msg1]=mkdir(DirLog);
1963            if ~strcmp(msg1,'')
1964                errormsg=['cannot create ' DirLog ': ' msg1]; % error message for directory creation
1965                return
1966            end
1967            [success,msg] = fileattrib(DirLog,'+w','g','s'); % allow writing access for the group of users, recursively in the folder
1968            if success==0
1969                msgbox_uvmat('WARNING',{['unable to set group write access to ' DirLog ':']; msg}); % error message for directory creation
1970            end
1971        end
1972
1973        %create the executable and log file names
1974        file_exe_global=fullfile_uvmat('','',Param.InputTable{1,3},ExeExt,OutputNomType,...
1975            first_i,last_i,first_j,last_j);
1976        file_exe_global=fullfile(OutputDir,'0_EXE',file_exe_global);
1977        filelog_global=fullfile_uvmat('','',Param.InputTable{1,3},'.log',OutputNomType,...
1978            first_i,last_i,first_j,last_j);
1979        filelog_global=fullfile(OutputDir,'0_LOG',filelog_global);
1980
1981        for iprocess=1:NbProcess
1982            batch_file_list{iprocess}=fullfile(OutputDir,'0_EXE',regexprep(extxml{iprocess},'.xml$',ExeExt)); % executable file names
1983            filelog{iprocess}=fullfile(OutputDir,'0_LOG',regexprep(extxml{iprocess},'.xml$','.log'));% corresponding log file names
1984        end
1985    end
1986
1987    %% launch the executable files for background or cluster processing
1988
1989    switch RunMode
1990
1991        case 'background'
1992            [fid,message]=fopen(file_exe_global,'w');
1993            if isequal(fid,-1)
1994                errormsg=['creation of ' file_exe_global ':' message];
1995                return
1996            end
1997            switch ActionExt
1998                case '.m'% Matlab function
1999                    switch computer
2000                        case {'GLNX86','GLNXA64','MACI64'}
2001                            cmd=command_launch_matlab(filelog_global,path_series,Param.Action.ActionPath,Param.Action.ActionName,filexml,'background');
2002                            fprintf(fid,cmd); % fill the executable file with the  char string cmd
2003                            fclose(fid); % close the executable filefilelog_global
2004                            system(['chmod +x ' file_exe_global]); % set the file to executable
2005                        case {'PCWIN','PCWIN64'}
2006                            cmd=['matlab -automation -logfile ' regexprep(filelog{iprocess},'\\','\\\\')...
2007                                ' -r "addpath(''' regexprep(path_series,'\\','\\\\') ''');'...
2008                                'addpath(''' regexprep(Param.Action.ActionPath,'\\','\\\\') ''');'];
2009                            for iprocess=1:NbProcess
2010                                cmd=[cmd '' Param.Action.ActionName  '( ''' regexprep(filexml{iprocess},'\\','\\\\') ''');']
2011                            end
2012                            cmd=[cmd ';exit"'];
2013                            fprintf(fid,cmd); % fill the executable file with the  char string cmd
2014                            fclose(fid); % close the executable file
2015                    end
2016                    system([file_exe_global ' &'])% directly execute the command file
2017                case '.sh' % compiled Matlab function
2018                    for iprocess=1:NbProcess
2019                        switch computer
2020                            case {'GLNX86','GLNXA64','MACI64'}
2021                                [fid,message]=fopen(batch_file_list{iprocess},'w'); % create the executable file
2022                                if isequal(fid,-1)
2023                                    errormsg=['creation of .bat file: ' message];
2024                                    return
2025                                end
2026                                cmd=['#!/bin/bash \n '...
2027                                    '#$ -cwd \n '...
2028                                    'hostname && date \n '...
2029                                    'umask 002 \n'...
2030                                    ActionFullName ' ' RunTime ' ' filexml{iprocess}]; % allow writting access to created files for user group
2031                                fprintf(fid,cmd); % fill the executable file with the  char string cmd
2032                                fclose(fid); % close the executable file
2033                                system(['chmod +x ' batch_file_list{iprocess}]); % set the file to executable
2034                                system([batch_file_list{iprocess} ' &'])% directly execute the command file
2035                            case {'PCWIN','PCWIN64'}
2036                                msgbox_uvmat('ERROR','option for compiled Matlab functions not implemented for Windows system')
2037                                return
2038                        end
2039                    end
2040                    msgbox_uvmat('CONFIRMATION',[ActionFullName ' launched in background for ' ExpName ': press STATUS to see results'])
2041            end
2042
2043        case 'cluster' % option 'oar-parexec' used
2044            %create subdirectory for oar commands
2045            for iprocess=1:NbProcess
2046                [fid,message]=fopen(batch_file_list{iprocess},'w'); % create the executable file
2047                if isequal(fid,-1)
2048                    errormsg=['creation of .bat file: ' message];
2049                    return
2050                end
2051                if  strcmp(ActionExt,'.sh')
2052                    cmd=['#!/bin/bash \n '...
2053                        '#$ -cwd \n '...
2054                        'hostname && date \n '...
2055                        'umask 002 \n'...
2056                        ActionFullName ' ' RunTime ' ' filexml{iprocess}]; % allow writting access to created files for user group
2057                else
2058                    cmd=command_launch_matlab(filelog_global,path_series,Param.Action.ActionPath,Param.Action.ActionName,filexml{iprocess},'cluster');
2059 
2060                end
2061                fprintf(fid,cmd); % fill the executable file with the  char string cmd
2062                fclose(fid); % close the executable file
2063                system(['chmod +x ' batch_file_list{iprocess}]); % set the file to executable
2064            end
2065            DIR_CLUSTER=fullfile(OutputDir,'0_CLUSTER');
2066            if exist(DIR_CLUSTER,'dir')% delete the content of the dir 0_LOG to allow new input
2067                curdir=pwd;
2068                cd(DIR_CLUSTER)
2069                delete('*')
2070                cd(curdir)
2071            else
2072                [tild,msg1]=mkdir(DIR_CLUSTER);
2073                if ~strcmp(msg1,'')
2074                    errormsg=['cannot create ' DIR_CLUSTER ': ' msg1]; % error message for directory creation
2075                    return
2076                end
2077            end
2078            % create file containing the list of jobs
2079            ListProcess=fullfile(DIR_CLUSTER,'job_list.txt'); % name of the file containing the list of executables
2080            [fid,errormsg]=fopen(ListProcess,'w'); % open it for writting
2081            if isempty(errormsg)
2082            for iprocess=1:length(batch_file_list)
2083                fprintf(fid,[batch_file_list{iprocess} '\n']); % write list of exe files
2084            end
2085            fclose(fid);
2086            system(['chmod +x ' ListProcess]); % set the file to executable
2087            else
2088                errormsg=['error for writting the executable file:' errormsg];
2089            end
2090            CPUTimeProcess=CPUTime*BlockLength*nbfield_j; % estimated CPU time for one individual process (in minutes)
2091            LaunchCmdFcn=SeriesData.SeriesParam.ClusterParam.LaunchCmdFcn;% command obtained from the function
2092            oar_command=feval(LaunchCmdFcn,ListProcess,ActionFullName,DirLog,NbProcess, NbCore,CPUTimeProcess)
2093            [status,result]=system(oar_command)% execute system command and show the result (ID number of the launched job) on the Matlab command window
2094            filename_oarcommand=fullfile(DIR_CLUSTER,'0_cluster_command'); % keep track of the command in file '0-OAR/0_cluster_command'
2095            [fid,errormsg]=fopen(filename_oarcommand,'w');
2096            if ~isempty(errormsg)
2097                msgbox_uvmat('ERROR',['cannot create ' filename_oarcommand ': ' errormsg])
2098                return
2099            end
2100            fprintf(fid,oar_command); % store the command
2101            fprintf(fid,result); % store the result (job ID number)
2102            fclose(fid);
2103            if status==0
2104                msgbox_uvmat('CONFIRMATION',[ActionFullName ' launched for ' ExpName ' as ' num2str(NbProcess) ' processes in cluster: press STATUS to see results'])
2105            else
2106                msgbox_uvmat('ERROR',result)
2107            end
2108            %     case 'cluster_pbs' % for LMFA Kepler machine:  trqnsferred to fct
2109
2110            %         %create subdirectory for pbs command and log files
2111            %         DirPBS=fullfile(OutputDir,'0_PBS'); % todo : common name OAR/PBS
2112            %         if exist(DirPBS,'dir')% delete the content of the dir 0_LOG to allow new input
2113            %             curdir=pwd;
2114            %             cd(DirPBS)
2115            %             delete('*')
2116            %             cd(curdir)
2117            %         else
2118            %             [tild,msg1]=mkdir(DirPBS);
2119            %             if ~strcmp(msg1,'')
2120            %                 errormsg=['cannot create ' DirPBS ': ' msg1]; % error message for directory creation
2121            %                 return
2122            %             end
2123            %         end
2124            %         max_walltime=3600*20; % 20h max total calculation (cannot exceed 24 h)
2125            %         walltime_onejob=1800; % seconds, max estimated time for asingle file index value
2126            %         ListProcess=fullfile(DirPBS,'job_list.txt'); % create name of the global executable file
2127            %         fid=fopen(ListProcess,'w');
2128            %         for iprocess=1:length(batch_file_list)
2129            %             fprintf(fid,[batch_file_list{iprocess} '\n']); % list of exe files
2130            %         end
2131            %         fclose(fid);
2132            %         system(['chmod +x ' ListProcess]); % set the file to executable
2133            %         pbs_command=['qsub -n CIVX '...
2134            %             '-t idempotent --checkpoint ' num2str(walltime_onejob+60) ' '...
2135            %             '-l /core=' num2str(NbCore) ','...
2136            %             'walltime=' datestr(min(1.05*walltime_onejob/86400*max(NbProcess*BlockLength*nbfield_j,NbCore)/NbCore,max_walltime/86400),13) ' '...
2137            %             '-E ' regexprep(ListProcess,'\.txt\>','.stderr') ' '...
2138            %             '-O ' regexprep(ListProcess,'\.txt\>','.log') ' '...
2139            %             extra_qstat ' '...
2140            %             '"oar-parexec -s -f ' ListProcess ' '...
2141            %             '-l ' ListProcess '.log"'];
2142            %         filename_oarcommand=fullfile(DirPBS,'pbs_command');
2143            %         fid=fopen(filename_oarcommand,'w');
2144            %         fprintf(fid,pbs_command);
2145            %         fclose(fid);
2146            %         fprintf(pbs_command); % display in command line
2147            %         %system(pbs_command);
2148            %         msgbox_uvmat('CONFIRMATION',[ActionFullName ' command ready to be launched in cluster'])
2149
2150        case 'cluster_sge' % for PSMN % TODO: use the standard 'cluster' config with an external fct
2151            % Au PSMN, on ne cr??e pas 1 job avec plusieurs c??urs, mais N jobs de 1 c??urs
2152            % o?? N < 1000.
2153            %create subdirectory for pbs command and log files
2154
2155            DirSGE=fullfile(OutputDir,'0_SGE');
2156            if exist(DirSGE,'dir')% delete the content of the dir 0_LOG to allow new input
2157                curdir=pwd;
2158                cd(DirSGE)
2159                delete('*')
2160                cd(curdir)
2161            else
2162                [tild,msg1]=mkdir(DirSGE);
2163                if ~strcmp(msg1,'')
2164                    errormsg=['cannot create ' DirSGE ': ' msg1]; % error message for directory creation
2165                    return
2166                end
2167            end
2168            maxImgsPerJob = ceil(length(batch_file_list)/NbCore);
2169            disp(['Max number of jobs: ' num2str(NbCore)])
2170            disp(['Images per job: ' num2str(maxImgsPerJob)])
2171
2172            iprocess = 1;
2173            imgsInJob = [];
2174            currJobIndex = 1;
2175            done = 0;
2176            while(~done)
2177                if(iprocess <= length(batch_file_list))
2178                    imgsInJob = [imgsInJob, iprocess];
2179                end
2180                if((numel(imgsInJob) >= maxImgsPerJob) || (iprocess == length(batch_file_list)))
2181                    cmd=['#!/bin/sh \n'...
2182                        '#$ -cwd \n'...
2183                        'hostname && date\n']
2184                    for ii=1:numel(imgsInJob)
2185                        cmd=[cmd ActionFullName ' /softs/matlab ' filexml{imgsInJob(ii)} '\n'];
2186                    end
2187                    [fid, message] = fopen([DirSGE '/job' num2str(currJobIndex) '.sh'], 'w');
2188                    fprintf(fid, cmd);
2189                    fclose(fid);
2190                    system(['chmod +x ' DirSGE '/job' num2str(currJobIndex) '.sh'])
2191                    sge_command=['qsub -N civ_' num2str(currJobIndex) ' '...
2192                        '-q ' qstat_Queue ' '...
2193                        '-e ' fullfile([DirSGE '/job' num2str(currJobIndex) '.out']) ' '...
2194                        '-o ' fullfile([DirSGE '/job' num2str(currJobIndex) '.out']) ' '...
2195                        fullfile([DirSGE '/job' num2str(currJobIndex) '.sh'])];
2196                    fprintf(sge_command); % display in command line
2197                    [status, result] = system(sge_command);
2198                    fprintf(result);
2199                    currJobIndex = currJobIndex + 1;
2200                    imgsInJob = [];
2201                end
2202                if(iprocess == length(batch_file_list))
2203                    done = 1;
2204                end
2205                iprocess = iprocess + 1;
2206            end
2207            msgbox_uvmat('CONFIRMATION',[num2str(currJobIndex-1) ' jobs launched on queue ' qstat_Queue '.'])
2208        case 'python'
2209            command = command_launch_python(filexml{iprocess});
2210            fprintf(['command:\n' command '\n\n'])
2211            [status, result] = call_command_clean(command);
2212    end
2213    if exist(OutputDir,'dir')
2214        [SUCCESS,MESSAGE,MESSAGEID] = fileattrib (OutputDir);
2215        if MESSAGE.GroupWrite~=1
2216            [success,msg] = fileattrib(OutputDir,'+w','g','s'); % allow writing access for the group of users, recursively in the folder
2217            if success==0
2218                msgbox_uvmat('WARNING',{['unable to set group write access to ' OutputDir ':']; msg}); % error message for directory creation
2219            end
2220        end
2221    end
2222end
2223set(handles.Replicate,'BackgroundColor',[0 1 0])
2224
2225%------------------------------------------------------------------------
2226function STOP_Callback(hObject, eventdata, handles)
2227%------------------------------------------------------------------------
2228set(handles.RUN, 'BusyAction','cancel')
2229set(handles.RUN,'BackgroundColor',[1 0 0])
2230set(handles.RUN,'enable','on')
2231set(handles.RUN, 'Value',0)
2232
2233%------------------------------------------------------------------------
2234% --- read parameters from the GUI series
2235%------------------------------------------------------------------------
2236function Param=read_GUI_series(handles)
2237
2238%% read raw parameters from the GUI series
2239Param=read_GUI(handles.series);
2240
2241%% clean the output structure by removing unused information
2242if isfield(Param,'Pairs')
2243    Param=rmfield(Param,'Pairs'); % info Pairs not needed for output
2244end
2245if isfield(Param,'InputLine')
2246    Param=rmfield(Param,'InputLine');
2247end
2248if isfield(Param,'EditObject')
2249    Param=rmfield(Param,'EditObject');
2250end
2251Param.IndexRange.TimeSource=Param.IndexRange.TimeTable{end,1};
2252Param.IndexRange=rmfield(Param.IndexRange,'TimeTable');
2253empty_line=false(size(Param.InputTable,1),1);
2254for iline=1:size(Param.InputTable,1)
2255    empty_line(iline)=isempty(cell2mat(Param.InputTable(iline,1:3)));
2256end
2257Param.InputTable(empty_line,:)=[];
2258
2259%------------------------------------------------------------------------
2260% --- Executes on selection change in ActionName.
2261function ActionName_Callback(hObject, ActionPath, handles)
2262%------------------------------------------------------------------------
2263
2264%% stop any ongoing series processing
2265if isequal(get(handles.RUN,'Value'),1)
2266    answer= msgbox_uvmat('INPUT_Y-N','stop current Action process?');
2267    if strcmp(answer,'Yes')
2268        STOP_Callback(hObject, [], handles)
2269    else
2270        return
2271    end
2272end
2273set(handles.ActionName,'BackgroundColor',[1 1 0])
2274huigetfile=findobj(allchild(0),'tag','status_display');
2275if ~isempty(huigetfile)
2276    delete(huigetfile)
2277end
2278drawnow
2279
2280%% get Action name and path
2281NbBuiltinAction=get(handles.Action,'UserData'); % nbre of functions initially proposed in the menu ActionName (as defined in the Opening fct of series)
2282ActionList=get(handles.ActionName,'String'); % list menu fields
2283ActionIndex=get(handles.ActionName,'Value');
2284if ~isequal(ActionIndex,1)% if we are not just opening series
2285    InputTable=get(handles.InputTable,'Data');
2286    if isempty(InputTable{1,4})
2287        msgbox_uvmat('ERROR','no input file available: use Open in the menu bar')
2288        return
2289    end
2290end
2291ActionName= ActionList{get(handles.ActionName,'Value')}; % selected function name
2292ActionPathList=get(handles.ActionName,'UserData'); % list of recorded paths to functions of the list ActionName
2293
2294%% add a new function to the menu if 'more...' has been selected in the menu ActionName
2295if isequal(ActionName,'more...')
2296    if ~ischar(ActionPath)
2297        ActionPath=get(handles.ActionPath,'String');
2298    end
2299    [FileName, PathName] = uigetfile( ...
2300        {'*.m', ' (*.m)';
2301        '*.m',  '.m files '; ...
2302        '*.*', 'All Files (*.*)'}, ...
2303        'Pick a series processing function ',ActionPath);
2304    if length(FileName)<2
2305        return
2306    end
2307    [tild,ActionName,ActionExt]=fileparts(FileName);
2308
2309    % insert the choice in the menu ActionName
2310    ActionIndex=find(strcmp(ActionName,ActionList),1); % look for the selected function in the menu Action
2311    PathName=regexprep(PathName,'/$','');
2312    if ~isempty(ActionIndex) && ~strcmp(ActionPathList{ActionIndex},PathName)%compare the path to the existing fct
2313        ActionIndex=[]; % the selected path is different than the recorded one
2314    end
2315    if isempty(ActionIndex)%the qselected fct (with selected path) does not exist in the menu
2316        ActionIndex= length(ActionList);
2317        ActionList=[ActionList(1:end-1);{ActionName};ActionList(end)]; % the selected function is appended in the menu, before the last item 'more...'
2318         ActionPathList=[ActionPathList; PathName];
2319    end
2320
2321    % record the file extension and extend the path list if it is a new extension
2322    ActionExtList=get(handles.ActionExt,'String');
2323    ActionExtIndex=find(strcmp(ActionExt,ActionExtList), 1);
2324    if isempty(ActionExtIndex)
2325        set(handles.ActionExt,'String',[ActionExtList;{ActionExt}])
2326    end
2327
2328    % remove old Action options in the menu (keeping a menu length <nb_builtin_ACTION+5)
2329    if length(ActionList)>NbBuiltinAction+5% nb_builtin_ACTION=nbre of functions always remaining in the initial menu
2330        nbremove=length(ActionList)-NbBuiltinAction-5;
2331        ActionList(NbBuiltinAction+1:end-5)=[];
2332        ActionPathList(NbBuiltinAction+1:end-4,:)=[];
2333        ActionIndex=ActionIndex-nbremove;
2334    end
2335
2336    % record action menu, choice and path
2337    set(handles.ActionName,'Value',ActionIndex)
2338    set(handles.ActionName,'String',ActionList)
2339       set(handles.ActionName,'UserData',ActionPathList);
2340    set(handles.ActionExt,'Value',ActionExtIndex)
2341
2342    %record the user defined menu additions in personal file profil_perso
2343    dir_perso=prefdir;
2344    profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
2345    if NbBuiltinAction+1<=numel(ActionList)-1
2346        ActionListUser=ActionList(NbBuiltinAction+1:numel(ActionList)-1);
2347        ActionPathListUser=ActionPathList(NbBuiltinAction+1:numel(ActionList)-1);
2348        ActionExtListUser={};
2349        if numel(ActionExtList)>2
2350            ActionExtListUser=ActionExtList(3:end);
2351        end
2352        if exist(profil_perso,'file')
2353            save(profil_perso,'ActionListUser','ActionPathListUser','ActionExtListUser','-append')
2354        else
2355            save(profil_perso,'ActionListUser','ActionPathListUser','ActionExtListUser','-V6')
2356        end
2357    end
2358end
2359
2360%% check the current ActionPath to the selected function
2361ActionPath=ActionPathList{ActionIndex}; % current recorded path
2362set(handles.ActionPath,'String',ActionPath); % show the path to the selected function
2363
2364%% reinitialise the waitbar
2365update_waitbar(handles.Waitbar,0)
2366
2367%% Put the first line of the selected Action fct as tooltip help
2368try
2369    [fid,errormsg] =fopen([fullfile(ActionPath,ActionName) '.m']);
2370    InputText=textscan(fid,'%s',1,'delimiter','\n');
2371    fclose(fid);
2372    set(handles.ActionName,'ToolTipString',InputText{1}{1})% put the first line of the selected function as tooltip help
2373end
2374set(handles.ActionName,'BackgroundColor',[1 1 1])
2375set(handles.ActionInput,'BackgroundColor',[1 0 1])% set ActionInput button to magenta color to indicate that input refr
2376set(handles.num_CPUTime,'String','')
2377
2378% --- Executes on button press in ActionInput.
2379function ActionInput_Callback(hObject, eventdata, handles)
2380
2381set(handles.ActionInput,'BackgroundColor',[1 1 0])
2382SeriesData=get(handles.series,'UserData'); % info on the input file series
2383
2384%% create the function handle for Action
2385ActionPath=get(handles.ActionPath,'String');
2386ActionList=get(handles.ActionName,'String');
2387ActionName= ActionList{get(handles.ActionName,'Value')}; % selected function name
2388if ~exist(ActionPath,'dir')
2389    ActionName_Callback(handles.ActionName, ActionPath, handles)% update the function
2390    return
2391end
2392current_dir=pwd; % current working dir
2393cd(ActionPath)
2394h_fun=str2func(ActionName);% create the function handle for the function ActionName
2395cd(current_dir)
2396
2397%% Activate the Action fct to adapt the configuration of the GUI series and bring specific parameters in SeriesData
2398Param=read_GUI_series(handles); % read the parameters from the GUI series
2399Param.Action.RUN=0;
2400Param.SeriesData=SeriesData;
2401ParamOut=h_fun(Param); % run the selected Action function to get the relevant input
2402
2403
2404%% Visibility of VelType and VelType_1 menus asked by ActionName
2405VelTypeRequest=1; % VelType requested by default
2406VelTypeRequest_1=1; % VelType requested by default
2407if isfield(ParamOut,'VelType')
2408    VelTypeRequest=ismember(ParamOut.VelType,{'on','one','two'});
2409    VelTypeRequest_1=strcmp( ParamOut.VelType,'two');
2410end
2411FieldNameRequest=0;  %hidden by default
2412FieldNameRequest_1=0;  %hidden by default
2413if isfield(ParamOut,'FieldName')
2414    FieldNameRequest=ismember(ParamOut.FieldName,{'on','one','two'});
2415    FieldNameRequest_1=strcmp( ParamOut.FieldName,'two');
2416end
2417
2418%% Detect the types of input files and set menus and default options in 'VelType'
2419if ~isfield(SeriesData,'FileType')
2420    SeriesData.FileType={'none'};
2421end
2422iview_civ=find( strcmp('civx',SeriesData.FileType)|strcmp('civdata',SeriesData.FileType));
2423iview_netcdf=find(strcmp('netcdf',SeriesData.FileType)|strcmp('civx',SeriesData.FileType)|strcmp('civdata',SeriesData.FileType)); % all nc files, icluding civ
2424FieldList=get(handles.FieldName,'String'); % previous list as default
2425if ~iscell(FieldList),FieldList={FieldList};end
2426FieldList_1=get(handles.FieldName_1,'String'); % previous list as default
2427if ~iscell(FieldList_1),FieldList_1={FieldList_1};end
2428CheckPivData_1=0; % indicate whether FieldName_1 has been updated with civ data, 0 by default
2429handles_coord=[handles.Coord_x handles.Coord_y handles.Coord_z handles.Coord_x_title handles.Coord_y_title handles.Coord_z_title];
2430if VelTypeRequest && numel(iview_civ)>=1
2431    menu=set_veltype_display(SeriesData.FileInfo{iview_civ(1)}.CivStage,SeriesData.FileType{iview_civ(1)});
2432    set(handles.VelType,'Value',1)% set first choice by default
2433    set(handles.VelType,'String',[{'*'};menu])
2434    set(handles.VelType,'Visible','on')
2435    set(handles.VelType_title,'Visible','on')
2436    FieldList=set_field_list('U','V'); % standard menu for civx data
2437    if max(get(handles.FieldName,'Value'))>numel(FieldList)
2438        set(handles.FieldName,'Value',1); % velocity vector choice by default
2439    end
2440    if  VelTypeRequest_1 && numel(iview_civ)>=2
2441        menu=set_veltype_display(SeriesData.FileInfo{iview_civ(2)}.CivStage,SeriesData.FileType{iview_civ(2)});
2442        set(handles.VelType_1,'Value',1)% set first choice by default
2443        set(handles.VelType_1,'String',[{'*'};menu])
2444        set(handles.VelType_1,'Visible','on')
2445        set(handles.VelType_title_1,'Visible','on')
2446        FieldList_1=[set_field_list('U','V');{'C'};{'add_field...'}]; % standard menu for civx data
2447        CheckPivData_1=1;
2448        set(handles.FieldName_1,'Value',1); % velocity vector choice by default
2449    else
2450        set(handles.VelType_1,'Visible','off')
2451        set(handles.VelType_title_1,'Visible','off')
2452    end
2453else
2454    set(handles.VelType,'Visible','off')
2455    set(handles.VelType_title,'Visible','off')
2456end
2457
2458%% Detect the types of input files and set menus and default options in 'FieldName'
2459if (FieldNameRequest || VelTypeRequest) && numel(iview_netcdf)>=1
2460    set(handles.InputFields,'Visible','on')% set the frame InputFields visible
2461    if FieldNameRequest && isfield(SeriesData.FileInfo{iview_netcdf(1)},'ListVarName')
2462        set(handles.FieldName,'Visible','on')
2463        set(handles.Field_text,'Visible','on')
2464        ListVarName=SeriesData.FileInfo{iview_netcdf(1)}.ListVarName;
2465        ind_var=get(handles.FieldName,'Value'); % indices of previously selected variables
2466        for ilist=1:numel(ind_var)
2467            if isempty(find(strcmp(FieldList{ind_var(ilist)},ListVarName)))
2468                FieldList={}; % previous choice not consistent with new input field
2469                set(handles.FieldName,'Value',1)
2470                break
2471            end
2472        end
2473        if ~isempty(FieldList)iview_netcdf
2474            if isempty(find(strcmp(get(handles.Coord_x,'String'),ListVarName)))||...
2475                    isempty(find(strcmp(get(handles.Coord_y,'String'),ListVarName)))
2476                FieldList={};
2477                set(handles.Coord_x,'String','')
2478                set(handles.Coord_y,'String','')
2479            end
2480            Coord_z=get(handles.Coord_z,'String');
2481            if ~isempty(Coord_z) && isempty(find(strcmp(Coord_z,ListVarName)))REFRESH
2482                FieldList={};
2483                set(handles.Coord_z,'String','')
2484            end
2485        end
2486    else
2487        set(handles.FieldName,'Visible','off')
2488        set(handles.Field_text,'Visible','off')
2489    end
2490    set(handles_coord,'Visible','on')
2491    if isempty(find(strcmp('add_field...',FieldList)))
2492        FieldList=[FieldList;{'add_field...'}];%add 'add_field...' to the menu FieldName if it is not already
2493    end
2494    if FieldNameRequest_1 && numel(iview_netcdf)>=2
2495        set(handles.FieldName_1,'Visible','on')
2496        set(handles.Field_text_1,'Visible','on')
2497        if CheckPivData_1==0        % not civ input made
2498            FieldList_1={'add_field...'}
2499            ListVarName=SeriesData.FileInfo{iview_netcdf(2)}.ListVarName;
2500            ind_var=get(handles.FieldName,'Value'); % indices of previously selected variables
2501            for ilist=1:numel(ind_var)
2502                if isempty(find(strcmp(FieldList{ind_var(ilist)},ListVarName)))
2503                    %FieldList_1={}; % previous choice not consistent with new input field
2504                    set(handles.FieldName_1,'Value',1)
2505                    break
2506                end
2507            end
2508            warn_coord=0;
2509            if isempty(find(strcmp(get(handles.Coord_x,'String'),ListVarName)))||...
2510                    isempty(find(strcmp(get(handles.Coord_y,'String'),ListVarName)))
2511                warn_coord=1;
2512            end
2513            if ~isempty(Coord_z) && isempty(find(strcmp(Coord_z,ListVarName)))
2514                FieldList_1={'add_field...'};
2515                warn_coord=1;
2516            end
2517            if warn_coord
2518                msgbox_uvmat('WARNING','coordinate names do not exist in the second netcdf input file')
2519            end
2520
2521            set(handles.FieldName_1,'Visible','on')
2522            set(handles.FieldName_1,'Value',1)
2523            set(handles.FieldName_1,'String',FieldList_1)
2524        end
2525    else
2526        set(handles.FieldName_1,'Visible','off')
2527    end
2528    if isempty(FieldList)
2529        set(handles.Field_text,'Visible','off')
2530        set(handles.FieldName,'Visible','off')
2531    else
2532        set(handles.Field_text,'Visible','on')
2533        set(handles.FieldName,'Visible','on')
2534        set(handles.FieldName,'String',FieldList)
2535    end
2536else
2537    set(handles.InputFields,'Visible','off')
2538end
2539
2540%% Introduce visibility of file overwrite option
2541if isfield(ParamOut,'CheckOverwriteVisible')&& strcmp(ParamOut.CheckOverwriteVisible,'on')
2542    set(handles.CheckOverwrite,'Visible','on')
2543else
2544    set(handles.CheckOverwrite,'Visible','off')
2545end
2546
2547%% Check whether alphabetical sorting of input Subdir is allowed by the Action fct  (for multiples series entries)
2548if isfield(ParamOut,'AllowInputSort')&&isequal(ParamOut.AllowInputSort,'on')&& size(Param.InputTable,1)>1
2549    [tild,iview]=sort(Param.InputTable(:,2)); % subdirectories sorted in alphabetical order
2550    set(handles.InputTable,'Data',Param.InputTable(iview,:));
2551    MinIndex_i=get(handles.MinIndex_i,'Data');
2552    MinIndex_j=get(handles.MinIndex_j,'Data');
2553    MaxIndex_i=get(handles.MaxIndex_i,'Data');
2554    MaxIndex_j=get(handles.MaxIndex_j,'Data');
2555    set(handles.MinIndex_i,'Data',MinIndex_i(iview,:));
2556    set(handles.MinIndex_j,'Data',MinIndex_j(iview,:));
2557    set(handles.MaxIndex_i,'Data',MaxIndex_i(iview,:));
2558    set(handles.MaxIndex_j,'Data',MaxIndex_j(iview,:));
2559    TimeTable=get(handles.TimeTable,'Data');
2560    if size(TimeTable,1)<size(Param.InputTable,1)%if the time table is not complete, copy the missing lines from the previous ones
2561        for iline=size(TimeTable,1)+1:size(Param.InputTable,1)
2562            TimeTable(iline,:)=TimeTable(iline-1,:);
2563        end
2564    end
2565    set(handles.TimeTable,'Data',TimeTable(iview,:));% sort the time tables
2566    PairString=get(handles.PairString,'Data');
2567    set(handles.PairString,'Data',PairString(iview,:));
2568end
2569
2570%% Impose the whole input file index range if requested
2571if ~isfield(ParamOut,'WholeIndexRange')
2572    ParamOut.WholeIndexRange='off';
2573end
2574if ~isfield(ParamOut,'WholeIndexRange_j')
2575    ParamOut.WholeIndexRange_j='off';
2576end
2577
2578if strcmp(ParamOut.WholeIndexRange,'on')
2579    MinIndex_i=get(handles.MinIndex_i,'Data');
2580    MaxIndex_i=get(handles.MaxIndex_i,'Data');
2581    set(handles.num_first_i,'String',num2str(MinIndex_i(1)))% set first as the min index (for the first line)
2582    set(handles.num_last_i,'String',num2str(MaxIndex_i(1)))% set last as the max index (for the first line)
2583    set(handles.num_incr_i,'String','1')
2584else
2585    first_i=1;last_i=1;
2586    if isfield(Param.IndexRange,'first_i')
2587        first_i=Param.IndexRange.first_i;
2588        last_i=Param.IndexRange.last_i;
2589    end
2590end
2591if strcmp(ParamOut.WholeIndexRange,'on')||strcmp(ParamOut.WholeIndexRange_j,'on')
2592    MinIndex_j=get(handles.MinIndex_j,'Data');
2593    MaxIndex_j=get(handles.MaxIndex_j,'Data');
2594    set(handles.num_first_j,'String',num2str(MinIndex_j(1)))% set first as the min index (for the first line)
2595    set(handles.num_last_j,'String',num2str(MaxIndex_j(1)))% set last as the max index (for the first line)
2596    set(handles.num_incr_j,'String','1')
2597else  % check index ranges
2598    first_j=1;last_j=1;
2599    if isfield(Param.IndexRange,'first_j')
2600        first_j=Param.IndexRange.first_j;
2601        last_j=Param.IndexRange.last_j;
2602    end
2603    if last_i < first_i || last_j < first_j , msgbox_uvmat('ERROR','last field number must be larger than the first one'),...
2604            set(handles.RUN, 'Enable','On'), set(handles.RUN,'BackgroundColor',[1 0 0]),return,end
2605end
2606
2607%% enable or desable j index visibility
2608status_j='on'; % default
2609if isfield(SeriesData,'j1_series') && isempty(find(~cellfun(@isempty,SeriesData.j1_series), 1)) % case of empty j indices
2610    status_j='off'; % no j index needed
2611elseif strcmp(get(handles.PairString,'Visible'),'on')
2612    check_burst=cellfun(@isempty,regexp(get(handles.PairString,'Data'),'^j')); % =0 for burst case, 1 otherwise
2613    if isempty(find(check_burst, 1))% if all pair string begins by j (burst)
2614        status_j='off'; % no j index needed for bust case
2615    end
2616end
2617enable_j(handles,status_j) % no j index needed
2618if isfield(ParamOut,'j_index_1')&& isfield(ParamOut,'j_index_2')%strcmp(ParamOut.Desable_j_index,'on')
2619    %status_j='off';
2620    set(handles.num_first_j,'String',num2str(ParamOut.j_index_1))
2621    set(handles.num_last_j,'String',num2str(ParamOut.j_index_2))
2622    % set(handles.num_first_j,'enable','off')
2623    % set(handles.num_last_j,'enable','off')
2624    set(handles.num_first_j,'visible','off')
2625    set(handles.num_last_j,'visible','off')
2626    set(handles.num_incr_j,'visible','off')
2627else
2628    set(handles.num_first_j,'visible','on')
2629    set(handles.num_last_j,'visible','on')
2630    set(handles.num_incr_j,'visible',status_j)
2631end
2632
2633%% NbSlice visibility
2634% if isfield(ParamOut,'OutputFileMode')&& strcmp(ParamOut.OutputFileMode,'NbSlice')
2635%     ParamOut.NbSlice='on';
2636% end
2637if isfield(ParamOut,'NbSlice') && (strcmp(ParamOut.NbSlice,'on')||isnumeric(ParamOut.NbSlice))
2638    set(handles.num_NbSlice,'Visible','on')
2639    set(handles.NbSlice_title,'Visible','on')
2640    if isnumeric(ParamOut.NbSlice)
2641        set(handles.num_NbSlice,'String',num2str(ParamOut.NbSlice))
2642    end
2643else
2644    set(handles.num_NbSlice,'Visible','off')
2645    set(handles.NbSlice_title,'Visible','off')
2646end
2647if isfield(ParamOut,'NbSlice') && isnumeric(ParamOut.NbSlice)
2648    set(handles.num_NbSlice,'String',num2str(ParamOut.NbSlice))
2649    set(handles.num_NbSlice,'Enable','off'); % NbSlice set by the activation of the Action function
2650else
2651    set(handles.num_NbSlice,'Enable','on'); % NbSlice can be modified on the GUI series
2652end
2653
2654%% Visibility of FieldTransform menu
2655FieldTransformVisible='off';  %hidden by default
2656if isfield(ParamOut,'FieldTransform')
2657    if ~strcmp(ParamOut.FieldTransform,'off')
2658    FieldTransformVisible='on';
2659    end
2660    if iscell(ParamOut.FieldTransform)
2661        SeriesData.TransformList=ParamOut.FieldTransform;
2662    end
2663    TransformName_Callback([],[], handles)
2664end
2665set(handles.FieldTransform,'Visible',FieldTransformVisible)
2666if isfield(ParamOut,'TransformPath')% record the path of transform function requested for compilation
2667    set(handles.TransformPath,'UserData',ParamOut.TransformPath)
2668else
2669    set(handles.TransformPath,'UserData',[])
2670end
2671
2672%% Visibility of projection object
2673ProjObjectVisible='off';  %hidden by default
2674if isfield(ParamOut,'ProjObject')
2675    ProjObjectVisible=ParamOut.ProjObject;
2676end
2677set(handles.CheckObject,'Visible',ProjObjectVisible)
2678if ~get(handles.CheckObject,'Value')
2679    ProjObjectVisible='off';
2680end
2681set(handles.ProjObjectName,'Visible',ProjObjectVisible)
2682set(handles.DeleteObject,'Visible',ProjObjectVisible)
2683set(handles.ViewObject,'Visible',ProjObjectVisible)
2684set(handles.EditObject,'Visible',ProjObjectVisible)
2685
2686%% Visibility of mask input
2687MaskVisible='off';  %hidden by default
2688if isfield(ParamOut,'Mask')
2689    MaskVisible=ParamOut.Mask;
2690end
2691set(handles.CheckMask,'Visible',MaskVisible);
2692%% Setting of expected iteration time
2693if isfield(ParamOut,'CPUTime')
2694    set(handles.num_CPUTime,'String',num2str(ParamOut.CPUTime));
2695end
2696
2697%% definition of the path for the output files
2698InputTable=get(handles.InputTable,'Data');
2699[OutputPath,Device,DeviceExt]=fileparts(InputTable{1,1});
2700[OutputPath,Experiment,ExperimentExt]=fileparts(OutputPath);
2701set(handles.Device,'String',[Device DeviceExt])
2702set(handles.Device,'Visible','on')
2703set(handles.Device_title,'Visible','on')
2704set(handles.Experiment,'String',[Experiment ExperimentExt])
2705set(handles.Experiment,'Visible','on')
2706set(handles.Experiment_title,'Visible','on')
2707set(handles.Experiment_title,'Visible','on')
2708set(handles.OutputPath,'Visible','on')
2709set(handles.OutputPathBrowse,'Visible','on')
2710
2711%% definition of the subdirectory containing the output files
2712
2713if  ~(isfield(SeriesData,'ActionName') && strcmp(ActionName,SeriesData.ActionName))
2714    OutputDirExt='.series'; % default
2715    if isfield(ParamOut,'OutputDirExt')&&~isempty(ParamOut.OutputDirExt)
2716        OutputDirExt=ParamOut.OutputDirExt;
2717    end
2718    set(handles.OutputDirExt,'String',OutputDirExt)
2719end
2720OutputDirVisible='off';
2721OutputSubDirMode='auto'; % default
2722SubDirOut='';
2723if isfield(ParamOut,'OutputSubDirMode')
2724    OutputSubDirMode=ParamOut.OutputSubDirMode;
2725end
2726switch OutputSubDirMode
2727    case 'auto' % default
2728        OutputDirVisible='on';
2729        SubDir=InputTable(1:end,2); % set of subdirectories
2730        SubDirOut=SubDir{1};
2731        if numel(SubDir)>1
2732            for ilist=2:numel(SubDir)
2733                SubDirOut=[SubDirOut '-' regexprep(SubDir{ilist},'^/','')];
2734            end
2735        end
2736    case 'one'
2737        OutputDirVisible='on';
2738        SubDirOut=InputTable{1,2}; % use the first subdir name (+OutputDirExt) as output  subdirectory
2739    case 'two'
2740        OutputDirVisible='on';
2741        SubDir=InputTable(1:2,2); % set of subdirectories
2742        SubDirOut=SubDir{1};
2743        if numel(SubDir)>1
2744                SubDirOut=[SubDirOut '-' regexprep(SubDir{2},'^/','')];
2745        end
2746    case 'last'
2747        OutputDirVisible='on';
2748        SubDirOut=InputTable{end,2}; % use the last subdir name (+OutputDirExt) as output  subdirectory
2749end
2750set(handles.OutputSubDir,'String',SubDirOut)
2751set(handles.OutputSubDir,'BackgroundColor',[1 1 1])% set edit box to white color to indicate refreshment
2752set(handles.OutputDirExt,'Visible',OutputDirVisible)
2753set(handles.OutputSubDir,'Visible',OutputDirVisible)
2754% set(handles.OutputDir_title,'Visible',OutputDirVisible)
2755SeriesData.ActionName=ActionName; % record ActionName for next use
2756
2757
2758%% visibility of the run mode (local or background or cluster)
2759if strcmp(OutputSubDirMode,'none')
2760    RunModeVisible='off'; % only local mode available if no output file is produced
2761else
2762    RunModeVisible='on';
2763end
2764set(handles.RunMode,'Visible',RunModeVisible)
2765set(handles.ActionExt,'Visible',RunModeVisible)
2766set(handles.RunMode_title,'Visible',RunModeVisible)
2767set(handles.ActionExt_title,'Visible',RunModeVisible)
2768
2769
2770%% Expected nbre of output files
2771if isfield(ParamOut,'OutputFileMode')
2772    StatusData.OutputFileMode=ParamOut.OutputFileMode;
2773    set(handles.status,'UserData',StatusData)
2774end
2775
2776%% definition of an additional parameter set, determined by an ancillary GUI
2777if isfield(ParamOut,'ActionInput')
2778%     set(handles.ActionInput,'Visible','on')
2779    ParamOut.ActionInput.Program=ActionName; % record the program in ActionInput
2780    SeriesData.ActionInput=ParamOut.ActionInput;
2781else
2782%     set(handles.ActionInput,'Visible','off')
2783    if isfield(SeriesData,'ActionInput')
2784        SeriesData=rmfield(SeriesData,'ActionInput');
2785    end
2786end
2787set(handles.series,'UserData',SeriesData)
2788set(handles.ActionInput,'BackgroundColor',[1 0 0])
2789
2790
2791%------------------------------------------------------------------------
2792% --- Executes on button press in RefreshField.
2793function RefreshField_Callback(hObject, eventdata, handles)
2794%------------------------------------------------------------------------
2795set(handles.FieldName,'String',{'add_field...'});
2796set(handles.FieldName,'Value',1);
2797FieldName_Callback(hObject, eventdata, handles)
2798
2799
2800%------------------------------------------------------------------------
2801% --- Executes on selection change in FieldName.
2802function FieldName_Callback(hObject, eventdata, handles)
2803%------------------------------------------------------------------------
2804FieldListInit=get(handles.FieldName,'String');
2805field_index=get(handles.FieldName,'Value');
2806field=FieldListInit{field_index(1)};
2807if isequal(field,'add_field...')
2808    FieldListInit(field_index(1))=[];
2809    SeriesData=get(handles.series,'UserData');
2810    % input line for which the field choice is relevant
2811    iview=find(ismember(SeriesData.FileType,{'netcdf','civx','civdata'})); % all nc files, icluding civ
2812    hget_field=findobj(allchild(0),'name','get_field');
2813    if ~isempty(hget_field)
2814        delete(hget_field)%delete opened versions of get_field
2815    end
2816    Param=read_GUI(handles.series);
2817    InputTable=Param.InputTable(iview,:);
2818    % check the existence of the first file in the series
2819    first_j=[];last_j=[];MinIndex_j=1;MaxIndex_j=1; % default setting for index j
2820    if isfield(Param.IndexRange,'first_j') % if index j is used
2821        first_j=Param.IndexRange.first_j;
2822        last_j=Param.IndexRange.last_j;
2823        MinIndex_j=Param.IndexRange.MinIndex_j(iview);
2824        MaxIndex_j=Param.IndexRange.MaxIndex_j(iview);
2825    end
2826    PairString='';
2827    if isfield(Param.IndexRange,'PairString'); PairString=Param.IndexRange.PairString{iview}; end
2828    [i1,i2,j1,j2] = get_file_index(Param.IndexRange.first_i,first_j,PairString);
2829    LineIndex=iview(1);
2830    if numel(iview)>1
2831        answer=msgbox_uvmat('INPUT_TXT',['select the line of the input table:' num2str(iview)] ,num2str(iview(1)));
2832        LineIndex=str2num(answer);
2833    end
2834    FirstFileName=fullfile_uvmat(InputTable{LineIndex,1},InputTable{LineIndex,2},InputTable{LineIndex,3},...
2835        InputTable{LineIndex,5},InputTable{LineIndex,4},i1,i2,j1,j2);
2836    if exist(FirstFileName,'file') || ~isempty(regexp(InputTable{LineIndex,1},'^http'))
2837        ParamIn.Title='get_field: pick input variables and coordinates for series processing';
2838        ParamIn.SeriesInput=1;
2839        GetFieldData=get_field(FirstFileName,ParamIn);
2840        FieldList={};
2841        if isfield(GetFieldData,'FieldOption')% if a field has been selected
2842        switch GetFieldData.FieldOption
2843            case 'vectors'
2844                UName=GetFieldData.PanelVectors.vector_x;
2845                VName=GetFieldData.PanelVectors.vector_y;
2846                YName={GetFieldData.Coordinates.Coord_y};
2847                FieldList={['vec(' UName ',' VName ')'];...
2848                    ['norm(' UName ',' VName ')'];...
2849                    UName;VName};
2850                set(handles.VelType,'Visible','off')
2851            case {'scalar'}
2852                FieldList=GetFieldData.PanelScalar.scalar;
2853                YName={GetFieldData.Coordinates.Coord_y};
2854                if ischar(FieldList)
2855                    FieldList={FieldList};
2856                end
2857                set(handles.VelType,'Visible','off')
2858            case 'civdata...'
2859                FieldList=[set_field_list('U','V') ;{'C'}];
2860                set(handles.FieldName,'Value',1) % set menu to 'velocity
2861                XName='X';
2862                YName='y';
2863                set(handles.VelType,'Visible','on')
2864        end
2865        set(handles.FieldName,'Value',1)
2866        set(handles.FieldName,'String',[FieldListInit; FieldList; {'add_field...'}]);
2867        if ~strcmp(GetFieldData.FieldOption,'civdata...')
2868           if ~isempty(regexp(FieldList{1},'^vec'))
2869                set(handles.FieldName,'Value',1)
2870           else
2871                set(handles.FieldName,'Value',1:numel(FieldList))%select all input fields by default
2872           end
2873            XName=GetFieldData.Coordinates.Coord_x;
2874            YName=GetFieldData.Coordinates.Coord_y;
2875            TimeNameStr=GetFieldData.Time.SwitchVarIndexTime;
2876            % get the time info
2877            TimeTable=get(handles.TimeTable,'Data');
2878            switch TimeNameStr
2879                case 'file index'
2880                    TimeName='';
2881                case 'attribute'
2882                    TimeName=['att:' GetFieldData.Time.TimeName];
2883                    % update the time table
2884                    TimeTable{LineIndex,2}=get_time(Param.IndexRange.MinIndex_i(LineIndex),MinIndex_j,PairString,InputTable,SeriesData.FileInfo{LineIndex},GetFieldData.Time.TimeName);  % Min time
2885                    TimeTable{LineIndex,3}=get_time(Param.IndexRange.first_i,first_j,PairString,InputTable,SeriesData.FileInfo{LineIndex},GetFieldData.Time.TimeName);  % first time
2886                    TimeTable{LineIndex,4}=get_time(Param.IndexRange.last_i,last_j,PairString,InputTable,SeriesData.FileInfo{LineIndex},GetFieldData.Time.TimeName);  % last time
2887                    TimeTable{LineIndex,5}=get_time(Param.IndexRange.MaxIndex_i(LineIndex),MaxIndex_j,PairString,InputTable,SeriesData.FileInfo{LineIndex},GetFieldData.Time.TimeName);  % Max time
2888                case 'variable'
2889                    set(handles.TimeName,'String',['var:' GetFieldData.Time.TimeName])
2890                    set(handles.NomType,'String','*')
2891                    set(handles.RootFile,'String',[get(handles.RootFile,'String') get(handles.FileIndex,'String')])% A VERIFIER !!!!!!
2892                    set(handles.FileIndex,'String','')
2893                    ParamIn.TimeVarName=GetFieldData.Time.TimeName;
2894                case 'matrix_index'
2895                    TimeName=['dim:' GetFieldData.Time.TimeName];
2896                    set(handles.NomType,'String','*')
2897                    set(handles.RootFile,'String',[get(handles.RootFile,'String') get(handles.FileIndex,'String')])
2898                    set(handles.FileIndex,'String','')
2899                    ParamIn.TimeDimName=GetFieldData.Time.TimeName;
2900            end
2901            TimeTable{LineIndex,1}=TimeName;
2902            set(handles.TimeTable,'Data',TimeTable);
2903        end
2904        set(handles.Coord_x,'String',XName)
2905        set(handles.Coord_y,'String',YName)
2906        set(handles.Coord_x,'Visible','on')
2907        set(handles.Coord_y,'Visible','on')
2908        end
2909    else
2910        msgbox_uvmat('ERROR',[FirstFileName ' does not exist'])
2911    end
2912end
2913
2914
2915function [TimeValue,DtValue]=get_time(ref_i,ref_j,PairString,InputTable,FileInfo,TimeName,DtName)
2916[i1,i2,j1,j2] = get_file_index(ref_i,ref_j,PairString);
2917FileName=fullfile_uvmat(InputTable{1},InputTable{2},InputTable{3},InputTable{5},InputTable{4},i1,i2,j1,j2);
2918%Data=nc2struct(FileName,[]);
2919TimeValue=[];
2920DtValue=[];
2921switch FileInfo.FileType
2922    case 'civdata'
2923    Data=nc2struct(FileName,[]);
2924    if ismember(TimeName,{'civ1','filter1'})
2925        if isfield(Data,'Civ1_Time')
2926        TimeValue=Data.Civ1_Time;
2927        end
2928        if isfield(Data,'Civ1_Dt')
2929        DtValue=Data.Civ1_Dt;
2930        end
2931    else
2932        if isfield(Data,'Civ2_Time')
2933        TimeValue=Data.Civ2_Time;
2934        end
2935        if isfield(Data,'Civ2_Dt')
2936        DtValue=Data.Civ2_Dt;
2937        end
2938    end
2939    case 'pivdata_fluidimage'
2940      TimeValue=ref_i;%default
2941      DtValue=1;%default
2942    case 'netcdf'
2943        Data=nc2struct(FileName,[]);
2944    if ~isempty(TimeName)&& isfield(Data,TimeName)
2945        TimeValue=Data.(TimeName);
2946    end
2947    if exist('DtName','var') && isfield(Data,DtName)
2948        DtValue=Data.(DtName);
2949    end
2950end
2951
2952%------------------------------------------------------------------------
2953% --- Executes on selection change in FieldName_1.
2954function FieldName_1_Callback(hObject, eventdata, handles)
2955%------------------------------------------------------------------------
2956field_str=get(handles.FieldName_1,'String');
2957field_index=get(handles.FieldName_1,'Value');
2958field=field_str{field_index(1)};
2959if strcmp(field,'add_field...')
2960    %iview=find(ismember(SeriesData.FileType,{'netcdf','civx','civdata'})); % all nc files, icluding civ
2961    hget_field=findobj(allchild(0),'name','get_field');
2962    if ~isempty(hget_field)
2963        delete(hget_field)%delete opened versions of get_field
2964    end
2965    Param=read_GUI(handles.series);
2966    InputTable=Param.InputTable(2,:);
2967    % check the existence of the first file in the series
2968    first_j=[];
2969    if isfield(Param.IndexRange,'first_j'); first_j=Param.IndexRange.first_j; end
2970    if isfield(Param.IndexRange,'last_j'); last_j=Param.IndexRange.last_j; end
2971    PairString='';
2972    if isfield(Param.IndexRange,'PairString'); PairString=Param.IndexRange.PairString; end
2973    [i1,i2,j1,j2] = get_file_index(Param.IndexRange.first_i,first_j,PairString);
2974    FirstFileName=fullfile_uvmat(Param.InputTable{2,1},Param.InputTable{2,2},Param.InputTable{2,3},...
2975        Param.InputTable{2,5},Param.InputTable{2,4},i1,i2,j1,j2);
2976    if exist(FirstFileName,'file')
2977        ParamIn.SeriesInput=1;
2978        GetFieldData=get_field(FirstFileName,ParamIn);
2979        FieldList={};
2980        switch GetFieldData.FieldOption
2981            case 'vectors'
2982                UName=GetFieldData.PanelVectors.vector_x;
2983                VName=GetFieldData.PanelVectors.vector_y;
2984                FieldList={['vec(' UName ',' VName ')'];...
2985                    ['norm(' UName ',' VName ')'];...
2986                    UName;VName};
2987            case {'scalar','pick variables'}
2988                FieldList=GetFieldData.PanelScalar.scalar;
2989                if ischar(FieldList)
2990                    FieldList={FieldList};
2991                end
2992            case '1D plot'
2993
2994            case 'civdata...'
2995                FieldList=set_field_list('U','V','C');
2996                set(handles.FieldName,'Value',2) % set menu to 'velocity
2997        end
2998        set(handles.FieldName_1,'Value',1)
2999        set(handles.FieldName_1,'String',[FieldList; {'add_field...'}]);
3000    end
3001end
3002
3003
3004%%%%%%%%%%%%%
3005function [ind_remove]=find_pairs(dirpair,ind_i,last_i)
3006indsel=ind_i;
3007indiff=diff(ind_i); % test index increment to detect multiplets (several pairs with the same index ind_i) and holes in the series
3008indiff=[1 indiff last_i-ind_i(end)+1]; % for testing gaps with the imposed bounds
3009if ~isempty(indiff)
3010    indiff2=diff(indiff);
3011    indiffp=[indiff2 1];
3012    indiffm=[1 indiff2];
3013    ind_multi_m=find((indiff==0)&(indiffm<0))-1; % indices of first members of multiplets
3014    ind_multi_p=find((indiff==0)&(indiffp>0)); % indices of last members of multiplets
3015    %for each multiplet, select the most recent file
3016    ind_remove=[];
3017    for i=1:length(ind_multi_m)
3018        ind_pairs=ind_multi_m(i):ind_multi_p(i);
3019        for imulti=1:length(ind_pairs)
3020            datepair(imulti)=datenum(dirpair(ind_pairs(imulti)).date); % dates of creation
3021        end
3022        [datenew,indsort2]=sort(datepair); % sort the multiplet by creation date
3023        ind_s=indsort2(1:end-1); %
3024        ind_remove=[ind_remove ind_pairs(ind_s)]; % remove these indices, leave the last one
3025    end
3026end
3027
3028%------------------------------------------------------------------------
3029% --- determine the list of index pairstring of processing file
3030function [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)
3031%------------------------------------------------------------------------
3032num_i1=num_i; % set of first image numbers by default
3033num_i2=num_i;
3034num_j1=num_j;
3035num_j2=num_j;
3036num_i_out=num_i;
3037num_j_out=num_j;
3038% if isequal (NomType,'_1-2_1') || isequal (NomType,'_1-2')
3039if isequal(mode,'series(Di)')
3040    num_i1_line=num_i+ind_shift(3); % set of first image numbers
3041    num_i2_line=num_i+ind_shift(4);
3042    % adjust the first and last field number
3043        indsel=find(num_i1_line >= 1);
3044    num_i_out=num_i(indsel);
3045    num_i1_line=num_i1_line(indsel);
3046    num_i2_line=num_i2_line(indsel);
3047    num_j1=meshgrid(num_j,ones(size(num_i1_line)));
3048    num_j2=meshgrid(num_j,ones(size(num_i1_line)));
3049    [xx,num_i1]=meshgrid(num_j,num_i1_line);
3050    [xx,num_i2]=meshgrid(num_j,num_i2_line);
3051elseif isequal (mode,'series(Dj)')||isequal (mode,'bursts')
3052    if isequal(mode,'bursts') %case of bursts (png_old or png_2D)
3053        num_j1=ind_shift(1)*ones(size(num_i));
3054        num_j2=ind_shift(2)*ones(size(num_i));
3055    else
3056        num_j1_col=num_j+ind_shift(1); % set of first image numbers
3057        num_j2_col=num_j+ind_shift(2);
3058        % adjust the first field number
3059        indsel=find((num_j1_col >= 1));
3060        num_j_out=num_j(indsel);
3061        num_j1_col=num_j1_col(indsel);
3062        num_j2_col=num_j2_col(indsel);
3063        [num_i1,num_j1]=meshgrid(num_i,num_j1_col);
3064        [num_i2,num_j2]=meshgrid(num_i,num_j2_col);
3065    end
3066end
3067
3068%------------------------------------------------------------------------
3069% --- Executes on button press in CheckObject.
3070function CheckObject_Callback(hObject, eventdata, handles)
3071%------------------------------------------------------------------------
3072hset_object=findobj(allchild(0),'tag','set_object'); % find the set_object interface handle
3073if get(handles.CheckObject,'Value')
3074    SeriesData=get(handles.series,'UserData');
3075    if isfield(SeriesData,'ProjObject') && ~isempty(SeriesData.ProjObject)% a projection object is already loaded in the GUI series
3076        set(handles.ViewObject,'Value',1)
3077        ViewObject_Callback(hObject, eventdata, handles)
3078    else
3079        if ishandle(hset_object)% a projection object is already displayed in a GUI set_object
3080            uistack(hset_object,'top')% show the GUI set_object if opened
3081        else
3082            %get the object file
3083            InputTable=get(handles.InputTable,'Data');
3084            defaultname=InputTable{1,1};
3085            if isempty(defaultname)
3086                defaultname={''};
3087            end
3088            fileinput=uigetfile_uvmat('pick a xml object file (or use uvmat to create it)',defaultname,'.xml');
3089            if isempty(fileinput)% exit if no object file is selected
3090                set(handles.CheckObject,'Value',0)
3091                return
3092            end
3093            %read the file
3094            data=xml2struct(fileinput);
3095            if ~isfield(data,'Type')
3096                msgbox_uvmat('ERROR',[fileinput ' is not an object xml file'])
3097                set(handles.CheckObject,'Value',0)
3098                return
3099            end
3100            if ~isfield(data,'ProjMode')
3101                data.ProjMode='none';
3102            end
3103            hset_object=set_object(data); % call the set_object interface
3104            set(hset_object,'Name','set_object_series')% name to distinguish from set_object used with uvmat
3105        end
3106        ProjObject=read_GUI(hset_object);
3107        set(handles.ProjObjectName,'String',ProjObject.Name); % display the object name
3108        SeriesData=get(handles.series,'UserData');
3109        SeriesData.ProjObject=ProjObject;
3110        set(handles.series,'UserData',SeriesData);
3111    end
3112    set(handles.EditObject,'Visible','on');
3113    set(handles.DeleteObject,'Visible','on');
3114    set(handles.ViewObject,'Visible','on');
3115    set(handles.ProjObjectName,'Visible','on');
3116else
3117    set(handles.EditObject,'Visible','off');
3118    set(handles.DeleteObject,'Visible','off');
3119    set(handles.ViewObject,'Visible','off');
3120    if ~ishandle(hset_object)
3121        set(handles.ViewObject,'Value',0);
3122    end
3123    set(handles.ProjObjectName,'Visible','off');
3124end
3125
3126%------------------------------------------------------------------------
3127% --- Executes on button press in ViewObject.
3128%------------------------------------------------------------------------
3129function ViewObject_Callback(hObject, eventdata, handles)
3130
3131UserData=get(handles.series,'UserData');
3132hset_object=findobj(allchild(0),'Tag','set_object');
3133if ~isempty(hset_object)
3134    delete(hset_object)% refresh set_object if already opened
3135end
3136hset_object=set_object(UserData.ProjObject);
3137set(hset_object,'Name','view_object_series')
3138
3139
3140%------------------------------------------------------------------------
3141% --- Executes on button press in EditObject.
3142function EditObject_Callback(hObject, eventdata, handles)
3143%------------------------------------------------------------------------
3144if get(handles.EditObject,'Value')
3145    set(handles.ViewObject,'Value',0)
3146    UserData=get(handles.series,'UserData');
3147    if isfield(UserData,'ProjObject')
3148    hset_object=set_object(UserData.ProjObject);
3149    set(hset_object,'Name','edit_object_series')
3150    set(get(hset_object,'Children'),'Enable','on')
3151    else
3152        msgbox_uvmat('ERROR','no projection object available');
3153    end
3154else
3155    hset_object=findobj(allchild(0),'Tag','set_object');
3156    if ~isempty(hset_object)
3157        set(get(hset_object,'Children'),'Enable','off')
3158    end
3159end
3160
3161%------------------------------------------------------------------------
3162% --- Executes on button press in DeleteObject.
3163function DeleteObject_Callback(hObject, eventdata, handles)
3164%------------------------------------------------------------------------
3165SeriesData=get(handles.series,'UserData');
3166SeriesData.ProjObject=[];
3167set(handles.series,'UserData',SeriesData)
3168set(handles.ProjObjectName,'String','')
3169set(handles.ProjObjectName,'Visible','off')
3170set(handles.CheckObject,'Value',0)
3171set(handles.ViewObject,'Visible','off')
3172set(handles.EditObject,'Visible','off')
3173hset_object=findobj(allchild(0),'name','set_object_series');
3174if ~isempty(hset_object)
3175    delete(hset_object)
3176end
3177set(handles.DeleteObject,'Visible','off')
3178
3179%------------------------------------------------------------------------
3180% --- Executed when CheckMask is activated
3181%------------------------------------------------------------------------
3182function CheckMask_Callback(hObject, eventdata, handles)
3183
3184
3185if get(handles.CheckMask,'Value')
3186    set(handles.DeleteMask,'Visible','on')
3187    Param=read_GUI_series(handles); % displayed parameters
3188    NbView=size(Param.InputTable,1);
3189    MaskTable=cell(NbView,2);
3190   
3191    RootPath=Param.InputTable{1,1};
3192    first_j=[];% note that the function will propose to cover the whole range of indices
3193    if isfield(Param.IndexRange,'first_j'); first_j=Param.IndexRange.first_j; end
3194    last_j=[];
3195    if isfield(Param.IndexRange,'last_j'); last_j=Param.IndexRange.last_j; end
3196    PairString='';
3197    if isfield(Param.IndexRange,'PairString'); PairString=Param.IndexRange.PairString; end
3198    [i1,i2,j1,j2] = get_file_index(Param.IndexRange.first_i,first_j,PairString);
3199    %checkmask=zeros(NbView,1);
3200    for iview=1:NbView
3201        checkmask=0;
3202        FirstFileName=fullfile_uvmat(Param.InputTable{iview,1},Param.InputTable{iview,2},Param.InputTable{iview,3},...
3203            Param.InputTable{iview,5},Param.InputTable{iview,4},i1,i2,j1,j2);
3204        Data=nc2struct(FirstFileName);
3205        if isfield(Data,'Civ2_Mask')
3206            MaskTable{iview,1}=Data.Civ2_Mask;
3207            checkmask=1;
3208        end
3209        if ~checkmask
3210            MaskTable{iview,1}=uigetfile_uvmat('select a mask file:',Param.InputTable{iview,1},'image');
3211        end
3212    end
3213    for iview=1:NbView
3214        [Path,Name]=fileparts(MaskTable{iview,1});
3215        Name=regexprep(Name,'_\d+','');
3216        maskfiles=dir(fullfile(Path,[Name '_*.png']));%look for mask files       
3217        if ~isempty(maskfiles)
3218            for ilist=1:numel(maskfiles)
3219                r=regexp(maskfiles(ilist).name,'_(?<num1>\d+)','names');%look for burst pairs
3220                index(ilist)=str2double(r.num1);
3221            end
3222            MaskTable{iview,2}=max(index);
3223        end
3224    end
3225    set(handles.MaskTable,'Data',MaskTable)
3226    set(handles.CheckMask,'Value',0)
3227end
3228%       
3229% if ~isempty(NewMask)
3230%     if isempty(MaskList)
3231%         MaskList={NewMask};
3232%     else
3233%     MaskList={MaskList;NewMask};
3234%     end
3235%     set(handles.Mask,'String',MaskList)
3236% end
3237% end
3238% %     MaskTable=cell(nbview,1); % default
3239% %     ListMask=cell(nbview,1); % default
3240% %     MaskData=get(handles.MaskTable,'Data');
3241% %     MaskData(size(MaskData,1):nbview,1)=cell(size(MaskData,1):nbview,1); % complement if undefined lines
3242%     for iview=1:nbview
3243%         ListMask{iview,1}=num2str(iview);
3244%         RootPath=InputTable{iview,1};
3245%         if ~isempty(RootPath)
3246%             if isempty(MaskData{iview})
3247%                 SubDir=InputTable{iview,2};
3248%                 MaskPath=fullfile(RootPath,[regexprep(SubDir,'\..*','') '.mask']); % take the root part of SubDir, before the first dot '.'
3249%                 if exist(MaskPath,'dir')
3250%                     ListStruct=dir(MaskPath); % look for a mask file
3251%                     ListCells=struct2cell(ListStruct); % transform dir struct to a cell arrray
3252%                     check_dir=cell2mat(ListCells(4,:)); % =1 for directories, =0 for files
3253%                     ListFiles=ListCells(1,:); % list of file and dri names
3254%                     ListFiles=ListFiles(~check_dir); % list of file names (excluding dir)
3255%                     mdetect=0;
3256%                     if ~isempty(ListFiles)
3257%                         for ifile=1:numel(ListFiles)
3258%                             [tild,tild,MaskFile{ifile},i1_series,i2_series,j1_series,j2_series,MaskNomType,MaskFileType]=find_file_series(MaskPath,ListFiles{ifile},0);
3259%                             if strcmp(MaskFileType,'image') && isempty(i2_series) && isempty(j2_series)
3260%                                 mdetect=1;
3261%                                 MaskName=ListFiles{ifile};
3262%                             end
3263%                             if ~strcmp(MaskFile{ifile},MaskFile{1})
3264%                                 mdetect=0; % cancel detection test in case of multiple masks, use the brower for selection
3265%                                 break
3266%                             end
3267%                         end
3268%                     end
3269%                     if mdetect==1
3270%                         MaskName=fullfile(MaskPath,'mask_1.png');
3271%                     else
3272%                         MaskName=uigetfile_uvmat('select a mask file:',MaskPath,'image');
3273%                     end
3274%                 else
3275%                     MaskName=uigetfile_uvmat('select a mask file:',RootPath,'image');
3276%                 end
3277%                 MaskTable{iview,1}=MaskName ;
3278%                 ListMask{iview,1}=num2str(iview);
3279%             end
3280%         end
3281%     end
3282%     set(handles.MaskTable,'Data',MaskTable)
3283%     set(handles.MaskTable,'Visible','on')
3284%     set(handles.MaskBrowse,'Visible','on')
3285%     set(handles.ListMask,'Visible','on')
3286%     set(handles.ListMask,'String',ListMask)
3287%     set(handles.ListMask,'Value',1)
3288
3289
3290
3291%------------------------------------------------------------------------
3292% --- Executes when selected cell(s) is changed in MaskTable.
3293%------------------------------------------------------------------------
3294function MaskTable_CellSelectionCallback(hObject, eventdata, handles)
3295
3296if numel(eventdata.Indices)>=1
3297set(handles.ListMask,'Value',eventdata.Indices(1))
3298end
3299
3300%-------------------------------------------------------------------
3301function MenuHelp_Callback(hObject, eventdata, handles)
3302%-------------------------------------------------------------------
3303
3304
3305% path_to_uvmat=which ('uvmat'); % check the path of uvmat
3306% pathelp=fileparts(path_to_uvmat);
3307% helpfile=fullfile(pathelp,'uvmat_doc','uvmat_doc.html');
3308% 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')
3309% else
3310%     addpath (fullfile(pathelp,'uvmat_doc'))
3311%     web([helpfile '#series'])
3312% end
3313
3314%-------------------------------------------------------------------
3315% --- Executes on selection change in TransformName.
3316function TransformName_Callback(hObject, eventdata, handles)
3317%----------------------------------------------------------------------
3318TransformList=get(handles.TransformName,'String');
3319TransformIndex=get(handles.TransformName,'Value');
3320TransformName=TransformList{TransformIndex};
3321TransformPathList=get(handles.TransformName,'UserData');
3322nb_builtin_transform=4;
3323
3324%% browse transform functions with the input menu option more...
3325if isequal(TransformName,'more...')% browse transform functions
3326    FileName=uigetfile_uvmat('Pick a transform function',get(handles.TransformPath,'String'),'.m');
3327    if isempty(FileName)
3328        return     %browser closed without choice
3329    end
3330    [TransformPath,TransformName,TransformExt]=fileparts(FileName); % removes extension .m
3331    if ~strcmp(TransformExt,'.m')
3332        msgbox_uvmat('ERROR','a Matlab function .m must be introduced');
3333        return
3334    end
3335     % insert the choice in the menu
3336    TransformIndex=find(strcmp(TransformName,TransformList),1); % look for the selected function in the menu Action
3337    if isempty(TransformIndex)%the input string does not exist in the menu
3338        TransformIndex= length(TransformList);
3339        TransformList=[TransformList(1:end-1);{TransformName};TransformList(end)]; % the selected function is appended in the menu, before the last item 'more...'
3340        set(handles.TransformName,'String',TransformList)
3341        TransformPathList=[TransformPathList;{TransformPath}];
3342    else% the input function already exist, we update its path (possibly new)
3343        TransformPathList{TransformIndex}=TransformPath; %
3344        set(handles.TransformName,'Value',TransformIndex)
3345    end
3346   % save the new menu in the personal file 'uvmat_perso.mat'
3347   dir_perso=prefdir; % personal Matalb directory
3348   profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
3349   if exist(profil_perso,'file')
3350       for ilist=nb_builtin_transform+1:numel(TransformPathList)
3351           TransformListUser{ilist-nb_builtin_transform}=TransformList{ilist};
3352           TransformPathListUser{ilist-nb_builtin_transform}=TransformPathList{ilist};
3353       end
3354       TransformPathListUser=TransformPathListUser';
3355       TransformListUser=TransformListUser';
3356       save (profil_perso,'TransformPathListUser','TransformListUser','-append'); % store the root name for future opening of uvmat
3357   end
3358end
3359
3360%% display the current function path
3361set(handles.TransformPath,'String',TransformPathList{TransformIndex}); % show the path to the senlected function
3362set(handles.TransformName,'UserData',TransformPathList);
3363
3364%% create the function handle of the selected fct
3365if ~isempty(TransformName)
3366    if ~exist(TransformPathList{TransformIndex},'dir')
3367        msgbox_uvmat('ERROR',['The prescribed transform function path ' TransformPathList{TransformIndex} ' does not exist']);
3368        return
3369    end
3370    current_dir=pwd; % current working dir
3371    cd(TransformPathList{TransformIndex})
3372    transform_handle=str2func(TransformName);
3373    cd(current_dir)
3374    Field.Action.RUN=0;% indicate that the transform fct is called only to get input param
3375    SeriesData=get(handles.series,'UserData');
3376    ParamIn=[];
3377    if isfield(SeriesData,'TransformInput')
3378        ParamIn.TransformInput=SeriesData.TransformInput;
3379    end
3380    DataOut=feval(transform_handle,Field,ParamIn);% execute the transform fct to get its input parameters
3381    if isfield(DataOut,'TransformInput')%  used to add transform parameters at selection of the transform fct
3382        SeriesData.TransformInput=DataOut.TransformInput;
3383        set(handles.series,'UserData',SeriesData)
3384    end
3385end
3386
3387%------------------------------------------------------------------------
3388% --- fct activated by the upper bar menu ExportConfig
3389%------------------------------------------------------------------------
3390function MenuDisplayConfig_Callback(hObject, eventdata, handles)
3391
3392global Param
3393Param=read_GUI_series(handles);
3394evalin('base','global Param')%make CurData global in the workspace
3395display('current series config :')
3396evalin('base','Param') %display CurData in the workspace
3397commandwindow; % brings the Matlab command window to the front
3398
3399%------------------------------------------------------------------------
3400% --- fct activated by the upper bar menu InportConfig: import
3401%     menu settings from an xml file (stored in /0_XML for each run)
3402%------------------------------------------------------------------------
3403function MenuImportConfig_Callback(hObject, eventdata, handles)
3404
3405%% use a browser to choose the xml file containing the processing config
3406InputTable=get(handles.InputTable,'Data');
3407oldfile=InputTable{1,1}; % current path in InputTable
3408if isempty(oldfile)
3409    % use a file name stored in prefdir
3410    dir_perso=prefdir;
3411    profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
3412    if exist(profil_perso,'file')
3413        h=load (profil_perso);
3414        if isfield(h,'RootPath') && ischar(h.RootPath)
3415            oldfile=h.RootPath;
3416        end
3417    end
3418end
3419filexml=uigetfile_uvmat('pick a xml parameter file',oldfile,'.xml'); % get the xml file containing processing parameters
3420if isempty(filexml), return, end % quit function if an xml file has not been opened
3421
3422%% fill the GUI series with the content of the xml file
3423[Param,RootTag,errormsg]=xml2struct(filexml); % read the input xml file as a Matlab structure
3424if ~isempty(errormsg)
3425    msgbox_uvmat('ERROR',errormsg);
3426    return
3427end
3428% ask to stop current Action if button RUN is in action (another process is already running)
3429if isequal(get(handles.RUN,'Value'),1)
3430    answer= msgbox_uvmat('INPUT_Y-N','stop current Action process?');
3431    if strcmp(answer,'Yes')
3432        STOP_Callback(hObject, eventdata, handles)
3433    else
3434        return
3435    end
3436end
3437Param.Action.RUN=0; % desactivate the input RUN=1
3438
3439fill_GUI(Param,handles.series)% fill the elements of the GUI series with the input parameters
3440SeriesData=get(handles.series,'UserData');
3441if isfield(Param,'InputFields')
3442    ListField=Param.InputFields.FieldName;
3443    if ischar(ListField),ListField={ListField}; end
3444    set(handles.FieldName,'String',[ListField;{'add_field...'}])
3445     set(handles.FieldName,'Value',1:numel(ListField))
3446     set(handles.FieldName,'Visible','on')
3447end
3448if isfield(Param,'ActionInput')%  introduce  parameters specific to an Action fct, for instance PIV parameters
3449%     set(handles.ActionInput,'Visible','on')
3450%     set(handles.ActionInput,'Value',0)
3451    Param.ActionInput.ConfigSource=filexml; % record the source of config for future info
3452    SeriesData.ActionInput=Param.ActionInput;
3453end
3454if isfield(Param,'TransformInput')%  introduce  parameters specific to a transform fct
3455    SeriesData.TransformInput=Param.TransformInput;
3456end
3457if isfield(Param,'ProjObject') %introduce projection object if relevant
3458    SeriesData.ProjObject=Param.ProjObject;
3459end
3460set(handles.series,'UserData',SeriesData)
3461if isfield(Param,'CheckObject') && isequal(Param.CheckObject,1)
3462    set(handles.ProjObjectName,'String',Param.ProjObject.Name)
3463    set(handles.ViewObject,'Visible','on')
3464    set(handles.EditObject,'Visible','on')
3465    set(handles.DeleteObject,'Visible','on')
3466else
3467    set(handles.ProjObjectName,'String','')
3468    set(handles.ProjObjectName,'Visible','off')
3469    set(handles.ViewObject,'Visible','off')
3470    set(handles.EditObject,'Visible','off')
3471    set(handles.DeleteObject,'Visible','off')
3472end
3473set(handles.REFRESH,'BackgroundColor',[1 0 1]); % paint REFRESH button in magenta to indicate that it should be activated
3474
3475
3476%------------------------------------------------------------------------
3477% --- Executes when the GUI series is resized.
3478%------------------------------------------------------------------------
3479function series_ResizeFcn(hObject, eventdata, handles)
3480
3481%% input table
3482set(handles.InputTable,'Unit','pixel')
3483Pos=get(handles.InputTable,'Position');
3484set(handles.InputTable,'Unit','normalized')
3485ColumnWidth=round([0.5 0.14 0.14 0.14 0.08]*(Pos(3)-52));
3486ColumnWidth=num2cell(ColumnWidth);
3487set(handles.InputTable,'ColumnWidth',ColumnWidth)
3488
3489%% MaskTable
3490set(handles.MaskTable,'Unit','pixel')
3491Pos=get(handles.MaskTable,'Position');
3492set(handles.MaskTable,'Unit','normalized')
3493ColumnWidth=round([0.9 0.1]*(Pos(3)-52));
3494ColumnWidth=num2cell(ColumnWidth);
3495set(handles.MaskTable,'ColumnWidth',ColumnWidth)
3496
3497%% MinIndex_j and MaxIndex_i
3498unit=get(handles.MinIndex_i,'Unit');
3499set(handles.MinIndex_i,'Unit','pixel')
3500Pos=get(handles.MinIndex_i,'Position');
3501set(handles.MinIndex_i,'Unit',unit)
3502set(handles.MinIndex_i,'ColumnWidth',{Pos(3)-18})
3503set(handles.MaxIndex_i,'ColumnWidth',{Pos(3)-18})
3504set(handles.MinIndex_j,'ColumnWidth',{Pos(3)-18})
3505set(handles.MaxIndex_j,'ColumnWidth',{Pos(3)-18})
3506
3507%% TimeTable
3508set(handles.TimeTable,'Unit','pixel')
3509Pos=get(handles.TimeTable,'Position');
3510set(handles.TimeTable,'Unit','normalized')
3511% ColumnWidth=get(handles.TimeTable,'ColumnWidth');
3512ColumnWidth=num2cell(floor([0.2 0.2 0.2 0.2 0.2]*(Pos(3)-20)));
3513set(handles.TimeTable,'ColumnWidth',ColumnWidth)
3514
3515
3516%% PairString
3517set(handles.PairString,'Unit','pixel')
3518Pos=get(handles.PairString,'Position');
3519set(handles.PairString,'Unit','normalized')
3520set(handles.PairString,'ColumnWidth',{Pos(3)-5})
3521
3522%% MaskTable
3523% % set(handles.MaskTable,'Unit','pixel')
3524% % Pos=get(handles.MaskTable,'Position');
3525% % set(handles.MaskTable,'Unit','normalized')
3526% % set(handles.MaskTable,'ColumnWidth',{Pos(3)-5})
3527
3528%------------------------------------------------------------------------
3529% --- Executes on button press in status.
3530%------------------------------------------------------------------------
3531function status_Callback(hObject, eventdata, handles)
3532
3533if get(handles.status,'Value')
3534    set(handles.status,'BackgroundColor',[1 1 0])
3535    drawnow
3536    Param=read_GUI(handles.series);
3537    RootPath=fullfile(Param.OutputPath,Param.Experiment,Param.Device);
3538    if ~isfield(Param,'OutputSubDir')
3539        msgbox_uvmat('ERROR','no standard sub-directory definition for output files, use a browser to check the output')
3540        set(handles.status,'BackgroundColor',[0 1 0])
3541        return
3542    end
3543    OutputSubDir=[Param.OutputSubDir Param.OutputDirExt]; % subdirectory for output files
3544    OutputDir=fullfile(RootPath,OutputSubDir);
3545    if exist(OutputDir,'dir')
3546        uigetfile_uvmat('status_display',OutputDir)
3547    else
3548        msgbox_uvmat('ERROR','output folder not created yet: calculation did not start')
3549        set(handles.status,'BackgroundColor',[0 1 0])
3550    end
3551else
3552    %% delete current display fig if selection is off
3553    set(handles.status,'BackgroundColor',[0 1 0])
3554    hfig=findobj(allchild(0),'name','status_display');
3555    if ~isempty(hfig)
3556        delete(hfig)
3557    end
3558    return
3559end
3560
3561
3562%------------------------------------------------------------------------
3563% launched by selecting a file on the list
3564%------------------------------------------------------------------------
3565function view_file(hObject, eventdata)
3566
3567list=get(hObject,'String');
3568index=get(hObject,'Value');
3569rootroot=get(hObject,'UserData');
3570selectname=list{index};
3571ind_dot=regexp(selectname,'\.\.\.');
3572if ~isempty(ind_dot)
3573    selectname=selectname(1:ind_dot-1);
3574end
3575FullSelectName=fullfile(rootroot,selectname);
3576if exist(FullSelectName,'dir')% a directory has been selected
3577    ListFiles=dir(FullSelectName);
3578    ListDisplay=cell(numel(ListFiles),1);
3579    for ilist=2:numel(ListDisplay)% suppress the first line '.'
3580        ListDisplay{ilist-1}=ListFiles(ilist).name;
3581    end
3582    set(hObject,'Value',1)
3583    set(hObject,'String',ListDisplay)
3584    if strcmp(selectname,'..')
3585        FullSelectName=fileparts(fileparts(FullSelectName));
3586    end
3587    set(hObject,'UserData',FullSelectName)
3588    hfig=get(hObject,'parent');
3589    htitlebox=findobj(hfig,'tag','titlebox');
3590    set(htitlebox,'String',FullSelectName)
3591elseif exist(FullSelectName,'file')%visualise the vel field if it exists
3592    FileInfo=get_file_info(FullSelectName);
3593    if strcmp(FileInfo.FileType,'txt')
3594        edit(FullSelectName)
3595    elseif strcmp(FileInfo.FileType,'xml')
3596        editxml(FullSelectName)
3597    else
3598        uvmat(FullSelectName)
3599    end
3600    set(gcbo,'Value',1)
3601end
3602
3603
3604%------------------------------------------------------------------------
3605% launched by refreshing the status figure
3606%------------------------------------------------------------------------
3607function refresh_GUI(hfig)
3608
3609htitlebox=findobj(hfig,'tag','titlebox');
3610hlist=findobj(hfig,'tag','list');
3611hseries=findobj(allchild(0),'tag','series');
3612hstatus=findobj(hseries,'tag','status');
3613StatusData=get(hstatus,'UserData');
3614OutputDir=get(htitlebox,'String');
3615if ischar(OutputDir),OutputDir={OutputDir};end
3616ListFiles=dir(OutputDir{1});
3617if numel(ListFiles)<1
3618    return
3619end
3620ListFiles(1)=[]; % removes the first line ='.'
3621ListDisplay=cell(numel(ListFiles),1);
3622testrecent=0;
3623datnum=zeros(numel(ListDisplay),1);
3624for ilist=1:numel(ListDisplay)
3625    ListDisplay{ilist}=ListFiles(ilist).name;
3626      if ~ListFiles(ilist).isdir && isfield(ListFiles(ilist),'datenum')
3627            datnum(ilist)=ListFiles(ilist).datenum; % only available in recent matlab versions
3628            testrecent=1;
3629       end
3630end
3631set(hlist,'String',ListDisplay)
3632
3633%% Look at date of creation
3634ListDisplay=ListDisplay(datnum~=0);
3635datnum=datnum(datnum~=0); % keep the non zero values corresponding to existing files
3636NbOutputFile=[];
3637if isempty(datnum)
3638    if testrecent
3639        message='no civ result created yet';
3640    else
3641        message='';
3642    end
3643else
3644    [first,indfirst]=min(datnum);
3645    [last,indlast]=max(datnum);
3646    NbOutputFile_str='?';
3647    NbOutputFile=[];
3648    if isfield(StatusData,'NbOutputFile')
3649        NbOutputFile=StatusData.NbOutputFile;
3650        NbOutputFile_str=num2str(NbOutputFile);
3651    end
3652    message={[num2str(numel(datnum)) ' file(s) done over ' NbOutputFile_str] ;['oldest modification:  ' ListDisplay{indfirst} ' : ' datestr(first)];...
3653        ['latest modification:  ' ListDisplay{indlast} ' : ' datestr(last)]};
3654end
3655set(htitlebox,'String', [OutputDir{1};message])
3656
3657%% update the waitbar
3658hwaitbar=findobj(hfig,'tag','waitbar');
3659if ~isempty(NbOutputFile)
3660    BarPosition=get(hwaitbar,'Position');
3661    BarPosition(3)=0.9*numel(datnum)/NbOutputFile;
3662    set(hwaitbar,'Position',BarPosition)
3663end
3664
3665%------------------------------------------------------------------------
3666% --- Executes on selection change in ActionExt.
3667%------------------------------------------------------------------------
3668function ActionExt_Callback(hObject, eventdata, handles)
3669
3670ActionExtList=get(handles.ActionExt,'String');
3671ActionExt=ActionExtList{get(handles.ActionExt,'Value')};
3672if strcmp(ActionExt,'fluidimage')
3673    set(handles.RunMode,'Value',2)
3674end
3675
3676
3677function num_NbSlice_Callback(hObject, eventdata, handles)
3678NbSlice=str2num(get(handles.num_NbSlice,'String'));
3679
3680%------------------------------------------------------------------------
3681% --- set the visibility of relevant velocity type menus:
3682function menu=set_veltype_display(Civ,FileType)
3683%------------------------------------------------------------------------
3684if ~exist('FileType','var')
3685    FileType='civx';
3686end
3687switch FileType
3688    case 'civx'
3689        menu={'civ1';'interp1';'filter1';'civ2';'interp2';'filter2'};
3690        if isequal(Civ,0)
3691            imax=0;
3692        elseif isequal(Civ,1) || isequal(Civ,2)
3693            imax=1;
3694        elseif isequal(Civ,3)
3695            imax=3;
3696        elseif isequal(Civ,4) || isequal(Civ,5)
3697            imax=4;
3698        elseif isequal(Civ,6) %patch2
3699            imax=6;
3700        end
3701    case 'civdata'
3702        menu={'civ1';'filter1';'civ2';'filter2'};
3703        if isequal(Civ,0)
3704            imax=0;
3705        elseif isequal(Civ,1) || isequal(Civ,2)
3706            imax=1;
3707        elseif isequal(Civ,3)
3708            imax=2;
3709        elseif isequal(Civ,4) || isequal(Civ,5)
3710            imax=3;
3711        else%if isequal(Civ,6) %patch2
3712            imax=4;
3713        end
3714end
3715menu=menu(1:imax);
3716
3717
3718% --- Executes on mouse motion over figure - except title and menu.
3719% function series_WindowButtonMotionFcn(hObject, eventdata, handles)
3720% set(hObject,'Pointer','arrow');
3721
3722
3723% --- Executes on button press in SetPairs.
3724function SetPairs_Callback(hObject, eventdata, handles)
3725
3726%% delete previous occurrence of 'set_pairs'
3727hfig=findobj(allchild(0),'Tag','set_pairs');
3728if ~isempty(hfig)
3729delete(hfig)
3730end
3731
3732%% create the GUI set_pairs
3733set(0,'Unit','points')
3734ScreenSize=get(0,'ScreenSize'); % get the size of the screen, to put the fig on the upper right
3735Width=220; % fig width in points (1/72 inch)
3736Height=min(0.8*ScreenSize(4),300);
3737Left=ScreenSize(3)- Width-40; % right edge close to the right, with margin=40
3738Bottom=ScreenSize(4)-Height-40; % put fig at top right
3739hfig=findobj(allchild(0),'Tag','set_slice');
3740if ~isempty(hfig),delete(hfig), end; % delete existing version of the GUI
3741hfig=figure('name','set_pairs','tag','set_pairs','MenuBar','none','NumberTitle','off','Unit','points','Position',[Left,Bottom,Width,Height]);
3742BackgroundColor=get(hfig,'Color');
3743SeriesData=get(handles.series,'UserData');
3744TimeUnit=get(handles.TimeUnit,'String');
3745PairString=get(handles.PairString,'Data');
3746ListViewLines=find(cellfun('isempty',PairString)==0); % find list of non empty pairs
3747ListViewMenu=cell(numel(ListViewLines),1);
3748%iview=get(handles.PairString,'Value');
3749iview=[];
3750for ilist=1:numel(ListViewLines)
3751    ListViewMenu{ilist}=num2str(ListViewLines(ilist));
3752end
3753if isempty(iview)
3754    ListViewValue=numel(ListViewLines); % we work by default on the pair option for the last line which requires pairs
3755    iview=ListViewLines(end);
3756else
3757    ListViewValue=find(ListViewLines==iview);
3758end
3759ref_i=str2num(get(handles.num_first_i,'String'));
3760ref_j=1; % default
3761if strcmp(get(handles.num_first_j,'String'),'Visible')
3762    ref_j=str2num(get(handles.num_first_j,'String'));
3763end
3764[ModeMenu,ModeValue]=update_mode(SeriesData.i1_series{1},SeriesData.i2_series{1},SeriesData.j2_series{1});
3765InputTable=get(handles.InputTable,'Data');
3766displ_pair=update_listpair(SeriesData.i1_series{1},SeriesData.i2_series{1},SeriesData.j1_series{1},SeriesData.j2_series{1},ModeMenu{ModeValue},...
3767                                                 SeriesData.Time{1},TimeUnit,ref_i,ref_j,SeriesData.TimeName,InputTable,SeriesData.FileInfo{1});
3768for iline=1:size(InputTable,1)
3769    viewcell{iline}=num2str(iline);
3770end
3771viewcell=viewcell';
3772ModeMenu={'bursts';'series(Dj)'};
3773ModeValue=1;
3774                   %i1_series,i2_series,j1_series,j2_series,mode,time,TimeUnit,ref_i,ref_j,TimeName,InputTable,FileInfo
3775% first raw of the GUI
3776uicontrol('Style','text','Units','normalized', 'Position', [0.05 0.88 0.5 0.1],'BackgroundColor',BackgroundColor,...
3777    'String','row to edit #','FontUnits','points','FontSize',12,'FontWeight','bold','ForegroundColor','blue','HorizontalAlignment','right'); % title
3778uicontrol('Style','popupmenu','Units','normalized', 'Position', [0.54 0.8 0.3 0.2],'BackgroundColor',[1 1 1],...
3779    'Callback',@(hObject,eventdata)ListView_Callback(hObject,eventdata),'String',viewcell,'Value',1,'FontUnits','points','FontSize',12,'FontWeight','bold',...
3780    'Tag','ListView','TooltipString','''ListView'':choice of the file series w for pair display');
3781% second raw of the GUI
3782uicontrol('Style','text','Units','normalized', 'Position', [0.05 0.79 0.7 0.1],'BackgroundColor',BackgroundColor,...
3783    'String','mode of index pairing:','FontUnits','points','FontSize',12,'FontWeight','bold','ForegroundColor','blue','HorizontalAlignment','left'); % title
3784uicontrol('Style','popupmenu','Units','normalized', 'Position', [0.05 0.62 0.9 0.2],'BackgroundColor',[1 1 1],...
3785    'Callback',@(hObject,eventdata)Mode_Callback(hObject,eventdata),'String',ModeMenu,'Value',ModeValue,'FontUnits','points','FontSize',12,'FontWeight','bold',...
3786    'Tag','Mode','TooltipString','''Mode'': choice of the image pair mode');
3787% third raw
3788uicontrol('Style','text','Units','normalized', 'Position', [0.05 0.6 0.7 0.1],'BackgroundColor',BackgroundColor,...
3789    'String','pair choice:','FontUnits','points','FontSize',12,'FontWeight','bold','ForegroundColor','blue','HorizontalAlignment','left'); % title
3790uicontrol('Style','listbox','Units','normalized', 'Position', [0.05 0.42 0.9 0.2],'BackgroundColor',[1 1 1],...
3791    'Callback',@(hObject,eventdata)ListPair_Callback(hObject,eventdata),'String',displ_pair,'Value',1,'FontUnits','points','FontSize',12,'FontWeight','bold',...
3792    'Tag','ListPair','TooltipString','''ListPair'': menu for selecting the image pair');
3793uicontrol('Style','text','Units','normalized', 'Position', [0.1 0.22 0.8 0.1],'BackgroundColor',BackgroundColor,...
3794    'String','ref_i           ref_j','FontUnits','points','FontSize',12,'FontWeight','bold','ForegroundColor','blue','HorizontalAlignment','center'); % title
3795uicontrol('Style','edit','Units','normalized', 'Position', [0.15 0.17 0.3 0.08],'BackgroundColor',[1 1 1],...
3796    'Callback',@(hObject,eventdata)num_ref_i_Callback(hObject,eventdata),'String',num2str(ref_i),'FontUnits','points','FontSize',12,'FontWeight','bold',...
3797    'Tag','num_ref_i','TooltipString','''num_ref_i'': reference field index i used to display dt in ''list_pair_civ''');
3798uicontrol('Style','edit','Units','normalized', 'Position', [0.55 0.17 0.3 0.08],'BackgroundColor',[1 1 1],...
3799    'Callback',@(hObject,eventdata)num_ref_j_Callback(hObject,eventdata),'String',num2str(ref_j),'FontUnits','points','FontSize',12,'FontWeight','bold',...
3800    'Tag','num_ref_j','TooltipString','''num_ref_j'': reference field index i used to display dt in ''list_pair_civ''');
3801uicontrol('Style','pushbutton','Units','normalized', 'Position', [0.01 0.01 0.3 0.12],'BackgroundColor',[0 1 0],...
3802    'Callback',@(hObject,eventdata)OK_Callback(hObject,eventdata),'String','OK','FontUnits','points','FontSize',12,'FontWeight','bold',...
3803    'Tag','OK','TooltipString','''OK'': validate the choice');
3804%  last raw  of the GUI: pushbuttons
3805% 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),...
3806%     'FontWeight','bold','FontUnits','points','FontSize',12,'TooltipString','''OK'': apply the output to the current field series in uvmat');
3807drawnow
3808
3809%------------------------------------------------------------------------
3810function ListView_Callback(hObject,eventdata)
3811Mode_Callback(hObject,eventdata)
3812
3813%------------------------------------------------------------------------
3814function Mode_Callback(hObject,eventdata)
3815%% get input info
3816hseries=findobj(allchild(0),'tag','series'); % handles of the GUI series
3817hhseries=guidata(hseries); % handles of the elements in the GUI series
3818TimeUnit=get(hhseries.TimeUnit,'String');
3819SeriesData=get(hseries,'UserData');
3820mode_list=get(hObject,'String');
3821mode=mode_list{get(hObject,'Value')};
3822hListView=findobj(get(hObject,'parent'),'Tag','ListView');
3823iview=get(hListView,'Value');
3824i1_series=SeriesData.i1_series{iview};
3825i2_series=SeriesData.i2_series{iview};
3826j1_series=SeriesData.j1_series{iview};
3827j2_series=SeriesData.j2_series{iview};
3828
3829%% enable j index visibility after the new choice
3830
3831if strcmp(mode,'series(Dj)')
3832   status_j='on'; % default
3833else
3834       status_j='off'; % no j index needed for bust case
3835end
3836enable_j(hhseries,status_j) % no j index needed
3837
3838%% get the reference indices for the time interval Dt
3839href_i=findobj(get(hObject,'parent'),'Tag','ref_i');
3840ref_i=[];ref_j=[];
3841if strcmp(get(href_i,'Visible'),'on')
3842    ref_i=str2num(get(href_i,'String'));
3843end
3844if isempty(ref_i)
3845    ref_i=1;
3846end
3847if isempty(ref_j)
3848    ref_j=1;
3849end
3850
3851%% update the menu ListPair
3852Menu=update_listpair(i1_series,i2_series,j1_series,j2_series,mode,SeriesData.Time{iview},TimeUnit,ref_i,ref_j,SeriesData.FileInfo);
3853hlist_pairs=findobj(get(hObject,'parent'),'Tag','ListPair');
3854set(hlist_pairs,'Value',1)% set the first choice by default in ListPair
3855set(hlist_pairs,'String',Menu)% set the menu in ListPair
3856ListPair_Callback(hlist_pairs,[])% apply the default choice in ListPair
3857
3858%-------------------------------------------------------------
3859% --- Executes on selection in ListPair.
3860function ListPair_Callback(hObject,eventdata)
3861%------------------------------------------------------------
3862list_pair=get(hObject,'String'); % get the menu of image pairs
3863if isempty(list_pair)
3864    string='';
3865else
3866    string=list_pair{get(hObject,'Value')};
3867   % string=regexprep(string,',.*',''); % removes time indication (after ',')
3868end
3869hseries=findobj(allchild(0),'tag','series');
3870hPairString=findobj(hseries,'tag','PairString');
3871PairString=get(hPairString,'Data');
3872hListView=findobj(get(hObject,'parent'),'Tag','ListView');
3873iview=get(hListView,'Value');
3874PairString{iview,1}=string;
3875% report the selected pair string to the table PairString
3876set(hPairString,'Data',PairString)
3877
3878
3879%------------------------------------------------------------------------
3880function num_ref_i_Callback(hObject, eventdata)
3881%------------------------------------------------------------------------
3882Mode_Callback([],[])
3883
3884%------------------------------------------------------------------------
3885function num_ref_j_Callback(hObject, eventdata)
3886%------------------------------------------------------------------------
3887Mode_Callback([],[])
3888
3889%------------------------------------------------------------------------
3890function OK_Callback(hObject, eventdata)
3891%------------------------------------------------------------------------
3892delete(get(hObject,'parent'))
3893
3894
3895%------------------------------------------------------------------------
3896% --- Executes on button press in ClearLine.
3897%------------------------------------------------------------------------
3898function ClearLine_Callback(hObject, eventdata, handles)
3899InputTable=get(handles.InputTable,'Data');
3900iline=str2double(get(handles.InputLine,'String'));
3901if size(InputTable,1)>1
3902    InputTable(iline,:)=[]; % suppress the current line if not the first
3903    set(handles.InputTable,'Data',InputTable);
3904end
3905set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH button to magenta color to indicate that input refr
3906
3907
3908% --- Executes on button press in MonitorCluster.
3909function MonitorCluster_Callback(hObject, eventdata, handles)
3910
3911[rr,ss]=system('oarstat |grep N=UVmat');% check the list of jobs launched with uvmat
3912if isempty(ss)
3913   disp( 'no job presently submitted with uvmat')
3914else
3915    disp('format: R/W=run/wait, time lapsed, R=nbre of cores,W=walltime')
3916    disp(ss)
3917end
3918
3919
3920function OutputSubDir_Callback(hObject, eventdata, handles)
3921set(handles.OutputSubDir,'BackgroundColor',[1 1 1])
3922
3923
3924% --- Executes on button press in CheckOverwrite.
3925function CheckOverwrite_Callback(hObject, eventdata, handles)
3926
3927% --- Executes on button press in TestCPUTime.
3928function TestCPUTime_Callback(hObject, eventdata, handles)
3929% hObject    handle to TestCPUTime (see GCBO)
3930% eventdata  reserved - to be defined in a future version of MATLAB
3931% handles    structure with handles and user data (see GUIDATA)
3932
3933
3934% --- Executes on button press in DiskQuota.
3935function DiskQuota_Callback(hObject, eventdata, handles)
3936SeriesData=get(handles.series,'UserData');
3937system(SeriesData.SeriesParam.DiskQuotaCmd)
3938
3939
3940% --- Executes on button press in Replicate.
3941function Replicate_Callback(hObject, eventdata, handles)
3942if get(handles.Replicate,'Value')
3943    InputTable=get(handles.InputTable,'Data');
3944    for ilist=1:size(InputTable,1)
3945        InputDir{ilist}=fullfile(InputTable{ilist,1},InputTable{ilist,2});
3946    end
3947    browse_data(InputDir)
3948else
3949    hh=findobj(allchild(0),'Tag','browse_data');
3950    if ~isempty(hh)
3951        delete(hh)
3952    end
3953end
3954
3955
3956
3957
3958function OutputPath_Callback(hObject, eventdata, handles)
3959
3960
3961function Experiment_Callback(hObject, eventdata, handles)
3962
3963
3964function Device_Callback(hObject, eventdata, handles)
3965
3966
3967% --- Executes on button press in OutputPathBrowse.
3968function OutputPathBrowse_Callback(hObject, eventdata, handles)
3969CheckValue=get(handles.OutputPathBrowse,'Value');
3970if CheckValue
3971OutputPath=uigetdir(get(handles.OutputPath,'String'));
3972set(handles.OutputPath,'String',OutputPath)
3973else
3974    InputTable=get(handles.InputTable,'Data');
3975    set(handles.OutputPath,'String',InputTable{1,1})
3976end
3977
3978
3979
3980% --- Executes on button press in DeleteMask.
3981function DeleteMask_Callback(hObject, eventdata, handles)
3982set(handles.MaskTable,'Data',{})
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