source: trunk/src/series.m @ 1022

Last change on this file since 1022 was 1019, checked in by sommeria, 3 years ago

more general cluster commands introduced

File size: 164.4 KB
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4%'series': master function associated to the GUI series.m for analysis field series 
5%------------------------------------------------------------------------
6% function varargout = series(varargin)
7% associated with the GUI series.fig
8%
9%INPUT
10% param: structure with input parameters (link with the GUI uvmat)
11%      .menu_coord_str: string for the TransformName (menu for coordinate transforms)
12%      .menu_coord_val: value for TransformName (menu for coordinate transforms)
13%      .FileName: input file name
14%      .FileName_1: second input file name
15%      .list_field: menu of input fields
16%      .index_fields: chosen index
17%      .civ1=0 or 1, .interp1,  ... : input civ field type
18%
19
20%=======================================================================
21% Copyright 2008-2017, LEGI UMR 5519 / CNRS UGA G-INP, Grenoble, France
22%   http://www.legi.grenoble-inp.fr
23%   Joel.Sommeria - Joel.Sommeria (A) legi.cnrs.fr
24%
25%     This file is part of the toolbox UVMAT.
26%
27%     UVMAT is free software; you can redistribute it and/or modify
28%     it under the terms of the GNU General Public License as published
29%     by the Free Software Foundation; either version 2 of the license,
30%     or (at your option) any later version.
31%
32%     UVMAT is distributed in the hope that it will be useful,
33%     but WITHOUT ANY WARRANTY; without even the implied warranty of
34%     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
35%     GNU General Public License (see LICENSE.txt) for more details.
36%=======================================================================
37
38%------------------------------------------------------------------------
39%------------------------------------------------------------------------
40%  I - MAIN FUNCTION series
41%------------------------------------------------------------------------
42%------------------------------------------------------------------------
43function varargout = series(varargin)
44
45% Begin initialization code - DO NOT EDIT
46gui_Singleton = 1;
47gui_State = struct('gui_Name',       mfilename, ...
48                   'gui_Singleton',  gui_Singleton, ...
49                   'gui_OpeningFcn', @series_OpeningFcn, ...
50                   'gui_OutputFcn',  @series_OutputFcn, ...
51                   'gui_LayoutFcn',  [] , ...
52                   'gui_Callback',   []);
53if nargin && ischar(varargin{1})
54    gui_State.gui_Callback = str2func(varargin{1});
55end
56
57if nargout
58    [varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:});
59else
60    gui_mainfcn(gui_State, varargin{:});
61end
62% End initialization code - DO NOT EDIT
63
64%--------------------------------------------------------------------------
65% --- Executes just before series is made visible.
66%--------------------------------------------------------------------------
67function series_OpeningFcn(hObject, eventdata, handles,Param)
68
69% Choose default command line output for series
70handles.output = hObject;
71% Update handles structure
72guidata(hObject, handles);
73
74%% initial settings
75% position and  size of the GUI at opening
76set(0,'Unit','points')
77ScreenSize=get(0,'ScreenSize'); % size of the current screen, in points (1/72 inch)
78Width=900; % prefered width of the GUI in points (1/72 inch)
79Height=624; % prefered height of the GUI in points (1/72 inch)
80%adjust to screen size (reduced by a min margin)
81RescaleFactor=min((ScreenSize(3)-80)/Width,(ScreenSize(4)-80)/Height);
82if RescaleFactor>1
83    RescaleFactor=min(RescaleFactor,1);
84end
85Width=Width*RescaleFactor;
86Height=Height*RescaleFactor;
87LeftX=80*RescaleFactor; % position of the left fig side, in pixels (put to the left side, with some margin)
88LowY=round(ScreenSize(4)/2-Height/2); % put at the middle height on the screen
89set(hObject,'Units','points')
90set(hObject,'Position',[LeftX LowY Width Height])% position and size of the GUI at opening
91
92% settings of table MinIndex_j
93set(handles.MinIndex_i,'ColumnFormat',{'numeric'})
94set(handles.MinIndex_i,'ColumnEditable',false)
95set(handles.MinIndex_i,'ColumnName',{'i min'})
96set(handles.MinIndex_i,'Data',[])% initiate Data to double (not cell)
97
98% settings of table MinIndex_j
99set(handles.MinIndex_j,'ColumnFormat',{'numeric'})
100set(handles.MinIndex_j,'ColumnEditable',false)
101set(handles.MinIndex_j,'ColumnName',{'j min'})
102set(handles.MinIndex_j,'Data',[])% initiate Data to double (not cell)
103
104% settings of table MaxIndex_i
105set(handles.MaxIndex_i,'ColumnFormat',{'numeric'})
106set(handles.MaxIndex_i,'ColumnEditable',false)
107set(handles.MaxIndex_i,'ColumnName',{'i max'})
108set(handles.MaxIndex_i,'Data',[])% initiate Data to double (not cell)
109
110% settings of table MaxIndex_j
111set(handles.MaxIndex_j,'ColumnFormat',{'numeric'})
112set(handles.MaxIndex_j,'ColumnEditable',false)
113set(handles.MaxIndex_j,'ColumnName',{'j max'})
114set(handles.MaxIndex_j,'Data',[])% initiate Data to double (not cell)
115
116% settings of table PairString
117set(handles.PairString,'ColumnName',{'pairs'})
118set(handles.PairString,'ColumnEditable',false)
119set(handles.PairString,'ColumnFormat',{'char'})
120set(handles.PairString,'Data',{''})
121
122% settings of table MaskTable
123set(handles.MaskTable,'ColumnName',{'mask name'})
124set(handles.PairString,'ColumnEditable',false)
125set(handles.PairString,'ColumnFormat',{'char'})
126set(handles.PairString,'Data',{''})
127
128series_ResizeFcn(hObject, eventdata, handles)%resize table according to series GUI size
129set(hObject,'WindowButtonDownFcn',{'mouse_down'})%allows mouse action with right button (zoom for uicontrol display)
130set(hObject,'DeleteFcn',{@closefcn})%
131
132% check default input data
133if ~exist('Param','var')
134    Param=[]; % default
135end
136
137%% Read the parameter file series.xml, or created from series.xml.default if it does not exist
138SeriesData=[];
139[path_series,name,ext]=fileparts(which('series'));% path to the GUI series
140xmlfile=fullfile(path_series,'series.xml');
141if ~exist(xmlfile,'file')
142    [success,message]=copyfile(fullfile(path_series,'series.xml.default'),xmlfile);
143end
144if exist(xmlfile,'file')
145    SeriesData.SeriesParam=xml2struct(xmlfile);
146    if ~(isfield(SeriesData.SeriesParam,'ClusterParam')&& isfield(SeriesData.SeriesParam.ClusterParam,'LaunchCmdFcn'))
147        [success,message]=copyfile(xmlfile,fullfile(path_series,'series_old.xml'));% update the file series.xml inot correctly documented
148        delete(xmlfile);
149        [success,message]=copyfile(fullfile(path_series,'series.xml.default'),xmlfile);
150    end 
151    SeriesData.SeriesParam=xml2struct(xmlfile);
152end
153
154%% list of builtin functions in the menu ActionName
155ActionList={'check_data_files';'aver_stat';'time_series';'civ_series';'merge_proj'}; % WARNING: fits with nb_builtin_ACTION=4 in ActionName_callback
156NbBuiltinAction=numel(ActionList);
157set(handles.Action,'UserData',NbBuiltinAction)
158path_series_fct=fullfile(path_series,'series');%path of the functions in subdirectroy 'series'
159[path_series,name,ext]=fileparts(which('series')); % path to the GUI series
160path_series_fct=fullfile(path_series,'series'); % path of the functions in subdirectroy 'series'
161command = ['LD_LIBRARY_PATH=$(echo $LD_LIBRARY_PATH | pyp "l = x.split('':''); l = [s for s in l if ''matlab'' not in s]; print('':''.join(l))") ' ...
162            'python -c "import fluidimage"'];
163[code, ~] = system(command);
164if code==0
165    ActionExtList={'.m';'.sh';'.py (in dev.)'}; % default choice of extensions (Matlab fct .m or compiled version .sh
166else
167    ActionExtList={'.m';'.sh'};  % python options not installed
168end
169ActionPathList=cell(NbBuiltinAction,1); % initiate the cell matrix of Action fct paths
170ActionPathList(:)={path_series_fct}; % set the default path to series fcts to all list members
171RunModeList={'local';'background'}; % default choice of extensions (Matlab fct .m or compiled version .sh)
172[s,w]=system(SeriesData.SeriesParam.ClusterParam.ExistenceTest); % look for cluster system presence
173% [s,w]=system('oarstat'); % look for cluster system 'oar'
174if isequal(s,0)
175    RunModeList=[RunModeList;{'cluster'}];
176    set(handles.MonitorCluster,'Visible','on'); % make visible button for access to Monika
177    set(handles.num_CPUTime,'Visible','on'); % make visible button for access to Monika
178    set(handles.CPUTime_txt,'Visible','on'); % make visible button for CPU time estimate for one ref index
179end
180% [s,w]=system('qstat -help'); % look for cluster system 'sge'
181% if isequal(s,0)
182%     if regexp(w,'^pbs')
183%         RunModeList=[RunModeList;{'cluster_pbs'}];
184%     elseif regexp(w,'^SGE')
185%         RunModeList=[RunModeList;{'cluster_sge'}];
186%     else
187%         RunModeList=[RunModeList;{'cluster_qstat_unknown'}];
188%     end
189% end
190set(handles.RunMode,'String',RunModeList)% display the menu of available run modes, local, background or cluster manager
191
192%% list of builtin transform functions in the menu TransformName
193TransformList={'';'sub_field';'phys';'phys_polar'}; % WARNING: must fit with the corresponding menu in uvmat and nb_builtin_transform=4 in  TransformName_callback
194NbBuiltinTransform=numel(TransformList);
195path_transform_fct=fullfile(path_series,'transform_field');
196TransformPathList=cell(NbBuiltinTransform,1); % initiate the cell matrix of Action fct paths
197TransformPathList(:)={path_transform_fct}; % set the default path to series fcts to all list members
198SeriesData.TransformPath=path_transform_fct;% store the standard path for trqnsform functions (needed for compilation)
199
200%% get the user defined functions stored in the personal file uvmat_perso.mat
201dir_perso=prefdir;
202profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
203if exist(profil_perso,'file')
204    h=load (profil_perso);
205    %get the list of previous input files in the upper bar menu Open
206    if isfield(h,'MenuFile')
207        for ifile=1:min(length(h.MenuFile),5)
208            set(handles.(['MenuFile_' num2str(ifile)]),'Label',h.MenuFile{ifile});
209            set(handles.(['MenuFile_' num2str(ifile+5)]),'Label',h.MenuFile{ifile});
210        end
211    end
212    %get the list of previous campaigns in the upper bar menu Open campaign
213    if isfield(h,'MenuCampaign')
214        for ifile=1:min(length(h.MenuCampaign),5)
215            set(handles.(['MenuCampaign_' num2str(ifile)]),'Label',h.MenuCampaign{ifile});
216        end
217    end
218    %get the menu of actions
219%     if isfield(h,'ActionExtListUser') && iscell(h.ActionExtListUser)
220%         ActionExtList=[ActionExtList; h.ActionExtListUser];
221%     end
222    if isfield(h,'ActionListUser') && iscell(h.ActionListUser) && isfield(h,'ActionPathListUser') && iscell(h.ActionPathListUser)
223        ActionList=[ActionList;h.ActionListUser];
224        ActionPathList=[ActionPathList;h.ActionPathListUser(:,1)];
225    end
226    %get the menu of transform fct
227    if isfield(h,'TransformListUser') && iscell(h.TransformListUser) && isfield(h,'TransformPathListUser') && iscell(h.TransformPathListUser)
228        TransformList=[TransformList;h.TransformListUser];
229        TransformPathList=[TransformPathList;h.TransformPathListUser];
230    end
231end
232
233%% selection of the input Action fct
234ActionCheckExist=true(size(ActionList)); % initiate the check of the path to the listed action fct
235for ilist=NbBuiltinAction+1:numel(ActionList)%check  the validity of the path of the user defined Action fct
236    ActionCheckExist(ilist)=exist(fullfile(ActionPathList{ilist},[ActionList{ilist} '.m']),'file');
237end
238ActionPathList=ActionPathList(ActionCheckExist,:); % suppress the menu options which are not valid anymore
239ActionList=ActionList(ActionCheckExist);
240set(handles.ActionName,'String',[ActionList;{'more...'}])
241set(handles.ActionName,'UserData',ActionPathList)
242ActionIndex=[];
243if isfield(Param,'ActionName')% copy the selected menu index transferred in Param from uvmat
244    ActionIndex=find(strcmp(Param.ActionName,ActionList),1);
245end
246if isempty(ActionIndex)
247    ActionIndex=1;
248end
249set(handles.ActionName,'Value',ActionIndex)
250set(handles.ActionPath,'String',ActionPathList{ActionIndex})
251set(handles.ActionExt,'Value',1)
252set(handles.ActionExt,'String',ActionExtList)
253
254%% selection of the input transform fct
255TransformCheckExist=true(size(TransformList));
256for ilist=NbBuiltinTransform+1:numel(TransformList)
257    TransformCheckExist(ilist)=exist(fullfile(TransformPathList{ilist},[TransformList{ilist} '.m']),'file');
258end
259TransformPathList=TransformPathList(TransformCheckExist);
260TransformList=TransformList(TransformCheckExist);
261set(handles.TransformName,'String',[TransformList;{'more...'}])
262set(handles.TransformName,'UserData',TransformPathList)
263TransformIndex=[];
264if isfield(Param,'TransformName')% copy the selected menu index transferred in Param from uvmat
265    TransformIndex=find(strcmp(Param.TransformName,TransformList),1);
266end
267if isempty(TransformIndex)
268    TransformIndex=1;
269end
270set(handles.TransformName,'Value',TransformIndex)
271set(handles.TransformPath,'String',TransformPathList{TransformIndex})
272   
273%% fields input initialisation
274if isfield(Param,'list_fields')&& isfield(Param,'index_fields') &&~isempty(Param.list_fields) &&~isempty(Param.index_fields)
275    set(handles.FieldName,'String',Param.list_fields); % list menu fields
276    set(handles.FieldName,'Value',Param.index_fields); % selected string index
277end
278if isfield(Param,'Coordinates')
279    if isfield(Param.Coordinates,'Coord_x')
280        set(handles.Coord_x,'String',Param.Coordinates.Coord_x)
281    end
282    if isfield(Param.Coordinates,'Coord_y')
283        set(handles.Coord_y,'String',Param.Coordinates.Coord_y)
284    end
285    if isfield(Param.Coordinates,'Coord_z')
286        set(handles.Coord_z,'String',Param.Coordinates.Coord_z)
287    end
288end
289% if isfield(Param,'Coord_x_str') && ischar(Param.Coord_x_str)
290%         set(handles.Coord_x,'String',Param.Coord_x_str); % list menu fields
291% end
292% if isfield(Param,'Coord_y_str')&& ischar(Param.Coord_y_str)
293%         set(handles.Coord_y,'String',Param.Coord_y_str); % list menu fields
294% end
295
296%% introduce the input file name(s) if defined from input Param,
297set(handles.series,'UserData',SeriesData)% initiate Userdata
298if isfield(Param,'InputFile')
299   
300    %% fill the list of file series
301    InputTable=[{Param.InputFile.RootPath},{Param.InputFile.SubDir},{Param.InputFile.RootFile},{Param.InputFile.NomType},{Param.InputFile.FileExt}];
302    if isempty(find(cellfun('isempty',InputTable)==0)); % if there is no input file, do not introduce input info
303        set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH button to magenta color to indicate that input refresh is needed
304        return
305    end
306    TimeTable=[{Param.InputFile.TimeName},{[]},{[]},{[]},{[]}];
307    if isfield(Param.InputFile,'RootPath_1')
308        InputTable=[InputTable;[{Param.InputFile.RootPath_1},{Param.InputFile.SubDir_1},{Param.InputFile.RootFile_1},{Param.InputFile.NomType_1},{Param.InputFile.FileExt_1}]];
309        TimeTable=[TimeTable; [{Param.InputFile.TimeName_1},{[]},{[]},{[]},{[]}]];
310    end
311    set(handles.InputTable,'Data',InputTable)
312    %% determine the selected reference field indices for pair display
313   
314    [tild,tild,tild,i1,i2,j1,j2]=fileparts_uvmat(Param.InputFile.FileIndex);
315    if isempty(i1)
316        i1=1;
317    end
318    if isempty(i2)
319        i2=i1;
320    end
321    ref_i=floor((i1+i2)/2); % reference image number corresponding to the file
322    % set(handles.num_ref_i,'String',num2str(ref_i));
323    if isempty(j1)
324        j1=1;
325    end
326    if isempty(j2)
327        j2=j1;
328    end
329    ref_j=floor((j1+j2)/2); % reference image number corresponding to the file
330    SeriesData.ref_i=ref_i;
331    SeriesData.ref_j=ref_j;
332    set(handles.series,'UserData',SeriesData)
333    update_rootinfo(handles,Param.HiddenData.i1_series{1},Param.HiddenData.i2_series{1},Param.HiddenData.j1_series{1},Param.HiddenData.j2_series{1},...
334        Param.HiddenData.FileInfo{1},Param.HiddenData.MovieObject{1},1)
335    if isfield(Param,'FileName_1')
336        %         display_file_name(handles,Param,2)
337        update_rootinfo(handles,Param.HiddenData.i1_series{2},Param.HiddenData.i2_series{2},Param.HiddenData.j1_series{2},Param.HiddenData.j2_series{2},...
338            Param.HiddenData.FileInfo{2},Param.HiddenData.MovieObject{2},2)
339    end
340    %% enable field and veltype menus, in accordance with the current action
341    ActionName_Callback([],[], handles)
342   
343    %% set length of waitbar
344    displ_time(handles)
345   
346else
347    set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH button to magenta color to indicate that input refresh is needed
348end
349if isfield(Param,'incr_i')
350    set(handles.num_incr_i,'String',num2str(Param.incr_i))
351else
352    set(handles.num_incr_i,'String','1')
353end
354if isfield(Param,'incr_j')
355    set(handles.num_incr_j,'String',num2str(Param.incr_j))
356else
357    set(handles.num_incr_j,'String','1')
358end
359
360%------------------------------------------------------------------------
361% --- Outputs from this function are returned to the command line.
362function varargout = series_OutputFcn(hObject, eventdata, handles)
363%------------------------------------------------------------------------
364varargout{1} = handles.output;
365
366%------------------------------------------------------------------------
367% --- executed when closing uvmat: delete or desactivate the associated figures if exist
368function closefcn(gcbo,eventdata)
369%------------------------------------------------------------------------
370
371% delete set_object_series if detected
372hh=findobj(allchild(0),'name','view_object_series');
373if ~isempty(hh)
374    delete(hh)
375end
376hh=findobj(allchild(0),'name','edit_object_series');
377if ~isempty(hh)
378    delete(hh)
379end
380
381%delete the bowser if detected
382hh=findobj(allchild(0),'tag','browser');
383if ~isempty(hh)
384    delete(hh)
385end
386
387
388%------------------------------------------------------------------------
389%------------------------------------------------------------------------
390%  II - FUNCTIONS FOR INTRODUCING THE INPUT FILES
391% automatically sets the global properties when the rootfile name is introduced
392% then activate the view-field actionname if selected
393% it is activated either by clicking on the RootPath window or by the
394% browser
395%------------------------------------------------------------------------
396%------------------------------------------------------------------------
397% --- fct activated by the browser under 'Open'
398%------------------------------------------------------------------------ 
399function MenuBrowse_Callback(hObject, eventdata, handles)
400%% look for the previously opened file 'oldfile'
401InputTable=get(handles.InputTable,'Data');
402oldfile=InputTable{1,1};
403if isempty(oldfile)
404    % use a file name stored in prefdir
405    dir_perso=prefdir;
406    profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
407    if exist(profil_perso,'file')
408        h=load (profil_perso);
409        if isfield(h,'RootPath') && ischar(h.RootPath)
410            oldfile=h.RootPath;
411        end
412    end
413end
414%% launch the browser
415fileinput=uigetfile_uvmat('pick an input file in the series',oldfile);
416hh=dir(fileinput);
417if numel(hh)>1
418    msgbox_uvmat('ERROR','invalid input, probably a broken link');
419else
420    if ~isempty(fileinput)
421        display_file_name(handles,fileinput,'one')
422    end
423end
424
425% --------------------------------------------------------------------
426function MenuBrowseAppend_Callback(hObject, eventdata, handles)
427
428%% look for the previously opened file 'oldfile'
429InputTable=get(handles.InputTable,'Data');
430RootPathCell=InputTable(:,1);
431if isempty(RootPathCell{1})% no input file in the table
432     MenuBrowse_Callback(hObject, eventdata, handles)%refresh the input table, not append
433     return
434end
435SubDirCell=InputTable(:,2);
436oldfile=fullfile(RootPathCell{1},SubDirCell{1});
437
438%% use a file name stored in prefdir
439dir_perso=prefdir;
440profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
441if exist(profil_perso,'file')
442    h=load (profil_perso);
443    if isfield(h,'RootPath') && ischar(h.RootPath)
444        oldfile=h.RootPath;
445    end
446end
447
448%% launch the browser
449fileinput=uigetfile_uvmat('pick a file to append in the input table',oldfile);
450hh=dir(fileinput);
451if numel(hh)>1
452    msgbox_uvmat('ERROR','invalid input, probably a broken link');
453else
454    if ~isempty(fileinput)
455        display_file_name(handles,fileinput,'append')
456    end
457end
458
459%------------------------------------------------------------------------
460% --- fct activated by selecting a previous file under the menu Open
461%------------------------------------------------------------------------
462function MenuFile_Callback(hObject, eventdata, handles)
463
464errormsg=display_file_name(handles,get(hObject,'Label'),'one');
465if ~isempty(errormsg)
466    set(hObject,'Label','')
467    MenuFile=[{get(handles.MenuFile_1,'Label')};{get(handles.MenuFile_2,'Label')};...
468        {get(handles.MenuFile_3,'Label')};{get(handles.MenuFile_4,'Label')};{get(handles.MenuFile_5,'Label')}];
469    str_find=strcmp(get(hObject,'Label'),MenuFile);
470    MenuFile(str_find)=[]; % suppress the input file to the list
471    for ifile=1:numel(MenuFile)
472        set(handles.(['MenuFile_' num2str(ifile)]),'Label',MenuFile{ifile});
473    end
474end
475
476%------------------------------------------------------------------------
477% --- fct activated by selecting a previous file under the menu Open/append
478%------------------------------------------------------------------------
479function MenuFile_append_Callback(hObject, eventdata, handles)
480
481InputTable=get(handles.InputTable,'Data');
482if isempty(InputTable{1,1})% no input file in the table
483    display_file_name(handles,get(hObject,'Label'),'one') %refresh the input table, not append
484else
485    display_file_name(handles,get(hObject,'Label'),'append')% append the selected file to the current list of InputTable
486end
487
488%------------------------------------------------------------------------
489% --- fct activated by the browser under 'Open campaign/Browse...'
490%------------------------------------------------------------------------
491function MenuBrowseCampaign_Callback(hObject, eventdata, handles)
492
493%% look for the previously opened file 'oldfile'
494InputTable=get(handles.InputTable,'Data');
495if ~isempty(InputTable)
496oldfile=fullfile(InputTable{1,1},InputTable{1,2});
497else
498    % use a file name stored in prefdir
499    dir_perso=prefdir;
500    profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
501    if exist(profil_perso,'file')
502        h=load (profil_perso);
503        if isfield(h,'MenuCampaign') && ~isempty(h.MenuCampaign)&& ischar(h.MenuCampaign{1})
504            oldfile=h.MenuCampaign{1};
505        end
506    end
507end
508
509OutPut=browse_data(oldfile,'on','on'); % open the GUI browse_data to get select a campaign dir, experiment and device
510NbLines=numel(OutPut.Experiment)*numel(OutPut.DataSeries);
511icount=0;
512for iexp=1:numel(OutPut.Experiment)
513    for idevice=1:numel(OutPut.DataSeries)
514        icount=icount+1;
515        InputTable{icount,1}=fullfile(OutPut.Campaign,OutPut.Experiment{iexp});
516        InputTable{icount,2}=OutPut.DataSeries{idevice};
517        if isempty(InputTable{icount,3})
518            if icount>1
519            InputTable{icount,3}=InputTable{icount-1,3};
520            else
521                InputTable{icount,3}='';
522            end
523        end
524        if isempty(InputTable{icount,4})
525            if icount>1
526            InputTable{icount,4}=InputTable{icount-1,4};
527            else
528                InputTable{icount,4}='';
529            end
530        end
531                if isempty(InputTable{icount,5})
532            if icount>1
533            InputTable{icount,5}=InputTable{icount-1,5};
534            else
535                InputTable{icount,5}='';
536            end
537        end
538    end
539end
540if size(InputTable,1)>icount
541    InputTable(icount+1:size(InputTable,1),:)=[];
542end
543set(handles.InputTable,'Data',InputTable)
544REFRESH_Callback(hObject, eventdata, handles)
545
546% --------------------------------------------------------------------
547function MenuCampaign_Callback(hObject, eventdata, handles)
548% --------------------------------------------------------------------
549
550OutPut=browse_data(get(hObject,'Label'),'on','on'); % open the GUI browse_data to get select a campaign dir, experiment and device
551if ~isfield(OutPut,'Campaign')
552    return
553end
554NbLines=numel(OutPut.Experiment)*numel(OutPut.DataSeries);
555icount=0;
556InputTable=get(handles.InputTable,'Data');
557for iexp=1:numel(OutPut.Experiment)
558    for idevice=1:numel(OutPut.DataSeries)
559        icount=icount+1;
560        InputTable{icount,1}=fullfile(OutPut.Campaign,OutPut.Experiment{iexp});
561        InputTable{icount,2}=OutPut.DataSeries{idevice};
562        if isempty(InputTable{icount,3})
563            if icount>1
564                InputTable{icount,3}=InputTable{icount-1,3};
565            else
566                InputTable{icount,3}='';
567            end
568        end
569        if isempty(InputTable{icount,4})
570            if icount>1
571                InputTable{icount,4}=InputTable{icount-1,4};
572            else
573                InputTable{icount,4}='';
574            end
575        end
576        if isempty(InputTable{icount,5})
577            if icount>1
578                InputTable{icount,5}=InputTable{icount-1,5};
579            else
580                InputTable{icount,5}='';
581            end
582        end
583    end
584end
585if size(InputTable,1)>icount
586    InputTable(icount+1:size(InputTable,1),:)=[];
587end
588set(handles.InputTable,'Data',InputTable)
589REFRESH_Callback(hObject, eventdata, handles)
590
591
592% --- Executes when selected cell(s) is changed in InputTable.
593function InputTable_CellSelectionCallback(hObject, eventdata, handles)
594iline=[];
595if ~isempty(eventdata.Indices)
596    iline=eventdata.Indices(1);
597end
598set(handles.InputLine,'String',num2str(iline));
599
600%------------------------------------------------------------------------
601% --- 'key_press_fcn:' function activated when a key is pressed on the keyboard
602%------------------------------------------------------------------------
603function InputTable_KeyPressFcn(hObject, eventdata, handles)
604set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH button to magenta color to indicate that input refresh is needed
605set(handles.OutputSubDir,'BackgroundColor',[1 0 1])% set edit box OutputSubDir to magenta color to indicate that refresh may be needed
606xx=double(get(handles.series,'CurrentCharacter')); % get the keyboard character
607if ~isempty(xx)
608    switch xx
609        case 31 %downward arrow
610            InputTable=get(handles.InputTable,'Data');
611            iline=str2double(get(handles.InputLine,'String'));
612            if isequal(iline,size(InputTable,1))% arrow downward
613                InputTable=[InputTable;InputTable(iline,:)]; % create a new line as a copy of the last one
614                set(handles.InputTable,'Data',InputTable);
615            end
616        case 127  %key 'Suppress'
617            ClearLine_Callback(hObject, eventdata, handles)
618    end
619end
620
621%------------------------------------------------------------------------
622% --- Executes on button press in REFRESH.
623function REFRESH_Callback(hObject, eventdata, handles)
624%------------------------------------------------------------------------
625InputTable=get(handles.InputTable,'Data');
626set(handles.series,'Pointer','watch') % set the mouse pointer to 'watch'
627set(handles.REFRESH,'BackgroundColor',[1 1 0])% set REFRESH  button to yellow color (indicate activation)
628drawnow
629empty_line=false(size(InputTable,1),1);
630for iline=1:size(InputTable,1)
631    empty_line(iline)= isempty(cell2mat(InputTable(iline,1:3)));
632end
633if ~isempty(find(empty_line));
634    InputTable(empty_line,:)=[]; % remove empty lines
635    set(handles.InputTable,'Data',InputTable)
636    ListTable={'MinIndex_i','MaxIndex_i','MinIndex_j','MaxIndex_j','PairString','TimeTable'};
637    for ilist=1:numel(ListTable)
638        Table=get(handles.(ListTable{ilist}),'Data');
639        Table(empty_line,:)=[]; % remove empty lines
640        set(handles.(ListTable{ilist}),'Data',Table);
641    end
642    set(handles.series,'UserData',[])%refresh the stored info
643end
644nbview=size(InputTable,1);
645for iview=1:nbview
646    RootPath=fullfile(InputTable{iview,1},InputTable{iview,2});
647    if ~exist(RootPath,'dir')
648        i1_series=[];
649        RootFile='';
650    else %scan the input folder
651        InputTable{iview,3}=regexprep(InputTable{iview,3},'^/','');
652            [RootPath,~,RootFile,i1_series,i2_series,j1_series,j2_series,tild,FileInfo,MovieObject]=...
653                find_file_series(fullfile(InputTable{iview,1},InputTable{iview,2}),[InputTable{iview,3} InputTable{iview,4} InputTable{iview,5}]);
654    end
655    % if no file is found, open a browser
656    if isempty(RootFile)&& isempty(i1_series)
657        fileinput=uigetfile_uvmat(['wrong input at line ' num2str(iview) ':pick a new input file'],RootPath);
658        if isempty(fileinput)
659            set(handles.REFRESH,'BackgroundColor',[1 0 0])% set REFRESH  back to red color
660            return
661        else
662            display_file_name(handles,fileinput,iview)
663        end
664    else
665       update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileInfo,MovieObject,iview)
666    end
667end
668
669%% update MinIndex_i and MaxIndex_i if the input table content has been reduced in line nbre
670MinIndex_i_table=get(handles.MinIndex_i,'Data'); % retrieve the min indices in the table MinIndex
671set(handles.MinIndex_i,'Data',MinIndex_i_table(1:nbview,:));
672MinIndex_j_table=get(handles.MinIndex_j,'Data'); % retrieve the min indices in the table MinIndex
673set(handles.MinIndex_j,'Data',MinIndex_j_table(1:nbview,:));
674MaxIndex_i_table=get(handles.MaxIndex_i,'Data'); % retrieve the min indices in the table MinIndex
675
676set(handles.MaxIndex_i,'Data',MaxIndex_i_table(1:nbview,:));
677MaxIndex_j_table=get(handles.MaxIndex_j,'Data'); % retrieve the min indices in the table MinIndex
678set(handles.MaxIndex_j,'Data',MaxIndex_j_table(1:nbview,:));
679PairString=get(handles.PairString,'Data'); % retrieve the min indices in the table MinIndex
680set(handles.PairString,'Data',PairString(1:nbview,:));
681TimeTable=get(handles.TimeTable,'Data'); % retrieve the min indices in the table MinIndex
682set(handles.TimeTable,'Data',TimeTable(1:nbview,:));
683
684%% set length of waitbar
685displ_time(handles)
686set(handles.REFRESH,'BackgroundColor',[1 0 0])% set REFRESH  button to red color (indicate activation finished)
687set(handles.series,'Pointer','arrow') % set the mouse pointer to 'watch'
688
689%% enable field and veltype menus, in accordance with the current action
690ActionInput_Callback([],[], handles)
691
692
693%------------------------------------------------------------------------
694% --- Function called when a new file is opened, either by series_OpeningFcn or by the browser
695%------------------------------------------------------------------------
696% INPUT:
697% handles: handles of elements in the GUI
698% Param: structure of input parameters, including  input file name and path
699% iview: line index in the input table
700%       or 'one': refresh the list
701%         'append': add a new line to the input table
702function errormsg=display_file_name(handles,Param,iview)
703 
704set(handles.REFRESH,'BackgroundColor',[1 1 0])% set REFRESH  button to yellow color (indicate activation)
705drawnow
706errormsg=''; % default
707if ischar(Param)
708    fileinput=Param;
709else% input set when series is opened (called by the GUI uvmat)
710    fileinput=Param.FileName;
711end
712   
713%% get the input root name, indices, file extension and nomenclature NomType
714if ~exist(fileinput,'file')
715    errormsg=['input file ' fileinput  ' does not exist'];
716    msgbox_uvmat('ERROR',errormsg)
717    set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH  button to magenta color (refresh still needed)
718    return
719end
720
721%% detect root name, nomenclature and indices in the input file name:
722[FilePath,FileName,FileExt]=fileparts(fileinput);
723%%%%%%%%%%%%%%%%%%
724%TODO: case of input by uvmat: do not check agai the input seies %%%%%%%
725%%%%%%%%%%%%%%%%%%%
726% detect the file type, get the movie object if relevant, and look for the corresponding file series:
727% the root name and indices may be corrected by including the first index i1 if a corresponding xml file exists
728[RootPath,SubDir,RootFile,i1_series,i2_series,j1_series,j2_series,NomType,FileInfo,MovieObject,i1,i2,j1,j2]=find_file_series(FilePath,[FileName FileExt]);
729FileType=FileInfo.FileType;
730if isempty(RootFile)&&isempty(i1_series)
731    errormsg='no input file in the series';
732    msgbox_uvmat('ERROR',errormsg)
733    set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH  button to magenta color (end of activation)
734    return
735end
736if strcmp(FileType,'txt')
737    edit(fileinput)
738    set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH  button to  magenta color (end of activation)
739    return
740elseif strcmp(FileType,'xml')
741    editxml(fileinput)
742    set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH  button to magenta  color (end of activation)
743     return
744elseif strcmp(FileType,'figure')
745    open(fileinput)
746    set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH  button to magenta  color (end of activation)
747     return
748end
749
750%% enable other menus and uicontrols
751% set(handles.MenuOpenCampaign,'Enable','on')
752set(handles.MenuCampaign_1,'Enable','on')
753set(handles.MenuCampaign_2,'Enable','on')
754set(handles.MenuCampaign_3,'Enable','on')
755set(handles.MenuCampaign_4,'Enable','on')
756set(handles.MenuCampaign_5,'Enable','on')
757set(handles.RUN, 'Enable','On')
758set(handles.RUN,'BackgroundColor',[1 0 0])% set RUN button to red
759set(handles.InputTable,'BackgroundColor',[1 1 0]) % set RootPath edit box  to yellow
760drawnow
761
762
763%% fill the list of file series
764InputTable=get(handles.InputTable,'Data');
765SeriesData=get(handles.series,'UserData');
766if strcmp(iview,'append') % display the input data as a new line in the table
767    iview=size(InputTable,1)+1; % the next line in InputTable becomes the current line
768%     InputTable(iview,:)=[{RootPath},{SubDir},{RootFile},{NomType},{FileExt}];
769elseif strcmp(iview,'one') % refresh the list of  input  file series
770    iview=1; % the first line in InputTable becomes the current line
771    InputTable={'','','','',''};
772%     InputTable(iview,:)=[{RootPath},{SubDir},{RootFile},{NomType},{FileExt}];
773    set(handles.TimeTable,'Data',[{''},{[]},{[]},{[]},{[]}])
774    set(handles.MinIndex_i,'Data',[])
775    set(handles.MaxIndex_i,'Data',[])
776    set(handles.MinIndex_j,'Data',[])
777    set(handles.MaxIndex_j,'Data',[])
778    set(handles.PairString,'Data',{''})
779    SeriesData.CheckPair=0; % reset the list of input lines with pairs
780    SeriesData.i1_series={};
781    SeriesData.i2_series={};
782    SeriesData.j1_series={};
783    SeriesData.j2_series={};
784    SeriesData.FileType={};
785    SeriesData.FileInfo={};
786    SeriesData.Time={};
787end
788if isfield(SeriesData,'i1_series')
789    SeriesData.i1_series(iview+1:end)=[];
790    SeriesData.i2_series(iview+1:end)=[];
791    SeriesData.j1_series(iview+1:end)=[];
792    SeriesData.j2_series(iview+1:end)=[];
793    SeriesData.FileType(iview+1:end)=[];
794    SeriesData.FileInfo(iview+1:end)=[];
795    SeriesData.Time(iview+1:end)=[];
796end
797InputTable(iview,:)=[{RootPath},{SubDir},{RootFile},{NomType},{FileExt}];
798if iview >1
799    set(handles.InputLine,'String',num2str(iview))
800end
801set(handles.InputTable,'Data',InputTable)
802
803%% determine the selected reference field indices for pair display
804if isempty(i1)
805    i1=1;
806end
807if isempty(i2)
808    i2=i1;
809end
810ref_i=floor((i1+i2)/2); % reference image number corresponding to the file
811% set(handles.num_ref_i,'String',num2str(ref_i));
812if isempty(j1)
813    j1=1;
814end
815if isempty(j2)
816    j2=j1;
817end
818ref_j=floor((j1+j2)/2); % reference image number corresponding to the file
819SeriesData.ref_i=ref_i;
820SeriesData.ref_j=ref_j;
821
822%% update first and last indices if they do not exist
823Param=read_GUI(handles.series);
824first_j=[];
825if isfield(Param.IndexRange,'first_j'); first_j=Param.IndexRange.first_j; end
826last_j=[];
827if isfield(Param.IndexRange,'last_j'); last_j=Param.IndexRange.last_j; end
828PairString='';
829if isfield(Param.IndexRange,'PairString'); PairString=Param.IndexRange.PairString; end
830[i1,i2,j1,j2] = get_file_index(Param.IndexRange.first_i,first_j,PairString);
831FirstFileName=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},...
832    Param.InputTable{1,5},Param.InputTable{1,4},i1,i2,j1,j2);
833if ~exist(FirstFileName,'file')
834    set(handles.num_first_i,'String',num2str(ref_i))
835    set(handles.num_first_j,'String',num2str(ref_j))
836end
837[i1,i2,j1,j2] = get_file_index(Param.IndexRange.last_i,last_j,PairString);
838LastFileName=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},...
839    Param.InputTable{1,5},Param.InputTable{1,4},i1,i2,j1,j2);
840if ~exist(LastFileName,'file')
841    set(handles.num_last_i,'String',num2str(ref_i))
842    set(handles.num_last_j,'String',num2str(ref_j))
843end
844
845%% update the list of recent files in the menubar and save it for future opening
846MenuFile=[{get(handles.MenuFile_1,'Label')};{get(handles.MenuFile_2,'Label')};...
847    {get(handles.MenuFile_3,'Label')};{get(handles.MenuFile_4,'Label')};{get(handles.MenuFile_5,'Label')}];
848str_find=strcmp(fileinput,MenuFile);
849if isempty(find(str_find,1))
850    MenuFile=[{fileinput};MenuFile]; % insert the current file if not already in the list
851end
852for ifile=1:min(length(MenuFile),5)
853    eval(['set(handles.MenuFile_' num2str(ifile) ',''Label'',MenuFile{ifile});'])
854end
855dir_perso=prefdir;
856profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
857if exist(profil_perso,'file')
858    save (profil_perso,'MenuFile','-append'); % store the file names for future opening of uvmat
859else
860    save (profil_perso,'MenuFile','-V6'); % store the file names for future opening of uvmat
861end
862% save the opened file to initiate future opening
863SeriesData.RefFile{iview}=fileinput; % reference opening file for line iview
864SeriesData.Ref_i1=i1;
865SeriesData.Ref_i2=i2;
866SeriesData.Ref_j1=j1;
867SeriesData.Ref_j2=j2;
868set(handles.series,'UserData',SeriesData)
869
870set(handles.InputTable,'BackgroundColor',[1 1 1])
871
872%% initiate input file series and refresh the current field view:     
873update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileInfo,MovieObject,iview);
874%% enable field and veltype menus, in accordance with the current action
875ActionName_Callback([],[], handles)
876
877%% set length of waitbar
878displ_time(handles)
879
880set(handles.REFRESH,'BackgroundColor',[1 0 0])% set REFRESH  button to red color (end of activation)
881
882%------------------------------------------------------------------------
883% --- Update information about a new field series (indices to scan, timing,
884%     calibration from an xml file
885function update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileInfo,VideoObject,iview)
886%------------------------------------------------------------------------
887InputTable=get(handles.InputTable,'Data');
888
889%% display the min and max indices for the whole file series
890if size(i1_series,2)==2 && min(min(i1_series(:,1,:)))==0
891    MinIndex_j=1; % index j set to 1 by default
892    MaxIndex_j=1;
893    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)
894    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)
895else
896    ref_i=squeeze(max(i1_series(1,:,:),[],2)); % select ref_j index for each ref_i
897    ref_j=squeeze(max(j1_series(1,:,:),[],3)); % select ref_i index for each ref_j
898     MinIndex_i=min(find(ref_i))-1;
899     MaxIndex_i=max(find(ref_i))-1;
900     MaxIndex_j=max(find(ref_j))-1;
901     MinIndex_j=min(find(ref_j))-1;
902    diff_j_max=diff(ref_j);
903    diff_i_max=diff(ref_i);
904    if ~isempty(diff_i_max) && isequal (diff_i_max,diff_i_max(1)*ones(size(diff_i_max)))
905        set(handles.num_incr_i,'String',num2str(diff_i_max(1)))% detect an increment to dispaly by default
906    end
907    if ~isempty(diff_j_max) && isequal (diff_j_max,diff_j_max(1)*ones(size(diff_j_max)))
908        set(handles.num_incr_j,'String',num2str(diff_j_max(1)))
909    end
910end
911if isequal(MinIndex_i,-1)
912    MinIndex_i=0;
913end
914if isequal(MinIndex_j,-1)
915    MinIndex_j=0;
916end
917MinIndex_i_table=get(handles.MinIndex_i,'Data'); % retrieve the min indices in the table MinIndex
918MinIndex_j_table=get(handles.MinIndex_j,'Data'); % retrieve the min indices in the table MinIndex
919MaxIndex_i_table=get(handles.MaxIndex_i,'Data'); % retrieve the min indices in the table MinIndex
920MaxIndex_j_table=get(handles.MaxIndex_j,'Data'); % retrieve the min indices in the table MinIndex
921if ~isempty(MinIndex_i)&&~isempty(MaxIndex_i)
922    MinIndex_i_table(iview,1)=MinIndex_i;
923    MaxIndex_i_table(iview,1)=MaxIndex_i;
924end
925if ~isempty(MinIndex_j)&&~isempty(MaxIndex_j)
926    MinIndex_j_table(iview,1)=MinIndex_j;
927    MaxIndex_j_table(iview,1)=MaxIndex_j;
928end
929set(handles.MinIndex_i,'Data',MinIndex_i_table)%display the min indices in the table MinIndex
930set(handles.MinIndex_j,'Data',MinIndex_j_table)%display the max indices in the table MaxIndex
931set(handles.MaxIndex_i,'Data',MaxIndex_i_table)%display the min indices in the table MinIndex
932set(handles.MaxIndex_j,'Data',MaxIndex_j_table)%display the max indices in the table MaxIndex
933SeriesData=get(handles.series,'UserData');
934
935%% adjust the first and last indices for the selected series, only if requested by the bounds
936% i index, compare input to min index i
937first_i=str2num(get(handles.num_first_i,'String')); % retrieve previous first i
938% ref_i=str2num(get(handles.num_ref_i,'String')); % index i given by the input field
939ref_i=1;
940if isfield(SeriesData,'ref_i')
941    ref_i=SeriesData.ref_i;
942end
943if isempty(first_i)
944    first_i=ref_i; % first_i updated by the input value
945elseif first_i < MinIndex_i
946    first_i=MinIndex_i; % first_i set to the min i index (restricted by oter input lines)
947elseif first_i >MaxIndex_i
948    first_i=MaxIndex_i; % first_i set to the max i index (restricted by oter input lines)
949end
950% j index,  compare input to min index j
951first_j=str2num(get(handles.num_first_j,'String'));
952ref_j=1;
953if isfield(SeriesData,'ref_j')
954    ref_j=SeriesData.ref_j;
955end
956if isempty(first_j)
957    first_j=ref_j; % first_j updated by the input value
958elseif first_j<MinIndex_j
959    first_j=MinIndex_j; % first_j set to the min j index (restricted by oter input lines)
960elseif first_j >MaxIndex_j
961    first_j=MaxIndex_j; % first_j set to the max j index (restricted by oter input lines)
962end
963% i index, compare input to max index i
964last_i=str2num(get(handles.num_last_i,'String'));
965if isempty(last_i)
966    last_i=ref_i;
967elseif last_i > MaxIndex_i
968    last_i=MaxIndex_i;
969elseif last_i<first_i
970    last_i=first_i;
971end
972% j index, compare input to max index j
973last_j=str2num(get(handles.num_last_j,'String'));
974if isempty(last_j)
975    last_j=ref_j;
976elseif last_j>MaxIndex_j
977    last_j=MaxIndex_j;
978elseif last_j<first_j
979    last_j=first_j;
980end
981set(handles.num_first_i,'String',num2str(first_i));
982set(handles.num_first_j,'String',num2str(first_j));
983set(handles.num_last_i,'String',num2str(last_i));
984set(handles.num_last_j,'String',num2str(last_j));
985
986%% number of slices set by default
987NbSlice=[]; % default
988% read  value set by the first series for the append mode (iwiew >1)
989if iview>1 && strcmp(get(handles.num_NbSlice,'Visible'),'on')
990    NbSlice=str2double(get(handles.num_NbSlice,'String'));
991end
992
993%% default time settings
994TimeUnit='';
995% read  value set by the first series for the append mode (iwiew >1)
996if iview>1
997    TimeUnit=get(handles.TimeUnit,'String');
998end
999TimeName='';
1000Time=[]; % default
1001TimeMin=[];
1002TimeFirst=[];
1003TimeLast=[];
1004TimeMax=[];
1005
1006%%  read image documentation file if found
1007XmlData=[];
1008check_calib=0;
1009XmlFileName=find_imadoc(InputTable{iview,1},InputTable{iview,2},InputTable{iview,3},InputTable{iview,5});
1010if ~isempty(XmlFileName)
1011    [XmlData,errormsg]=imadoc2struct(XmlFileName);
1012    if ~isempty(errormsg)
1013        msgbox_uvmat('WARNING',['error in reading ' XmlFileName ': ' errormsg]);
1014    end
1015    % read time if available
1016    if isfield(XmlData,'Time')
1017        Time=XmlData.Time;
1018        TimeName='xml';
1019    end
1020    if isfield(XmlData,'Camera')
1021        if isfield(XmlData.Camera,'TimeUnit')&& ~isempty(XmlData.Camera.TimeUnit)
1022            if iview>1 && ~isempty(TimeUnit) && ~strcmp(TimeUnit,XmlData.Camera.TimeUnit)
1023                msgbox_uvmat('WARNING','inconsistent time unit with the first field series');
1024            end
1025            TimeUnit=XmlData.Camera.TimeUnit;
1026        end
1027    end
1028    % number of slices
1029    if isfield(XmlData,'TranslationMotor')&& isfield(XmlData.TranslationMotor,'NbSlice')
1030        NbSlice_motor=XmlData.TranslationMotor.NbSlice;
1031        if ~isempty(NbSlice) && ~isequal(NbSlice_motor,NbSlice)
1032                msgbox_uvmat('WARNING','inconsistent Z numbers of Z indices');
1033        else
1034            NbSlice=NbSlice_motor;
1035        end
1036    end
1037   
1038%     if isfield(XmlData,'GeometryCalib')
1039%         check_calib=1;
1040%         if isfield(XmlData.GeometryCalib,'SliceCoord')
1041%             siz=size(XmlData.GeometryCalib.SliceCoord);
1042%             if ~isempty(NbSlice)&& ~isequal(size(1),NbSlice)
1043%                 msgbox_uvmat('WARNING','inconsistent numbers of Z indices between motor and calibration');
1044%             else
1045%                 NbSlice=siz(1);
1046%             end
1047%         end
1048%     end
1049end
1050if ~isempty(NbSlice)
1051set(handles.num_NbSlice,'String',num2str(NbSlice))
1052set(handles.num_NbSlice,'Visible','on')
1053end
1054
1055%% read timing  from the current file (prioritary)
1056if ~isempty(VideoObject)% case of movies
1057    imainfo=get(VideoObject);
1058    if isempty(j1_series); % frame index along i
1059        Time=zeros(imainfo.NumberOfFrames+1,2);
1060        Time(:,2)=(0:1/imainfo.FrameRate:(imainfo.NumberOfFrames)/imainfo.FrameRate)';
1061    else
1062        Time=[0;ones(size(i1_series,3)-1,1)]*(0:1/imainfo.FrameRate:(imainfo.NumberOfFrames)/imainfo.FrameRate);
1063    end
1064    TimeName='video';
1065end
1066
1067
1068%% determine the min and max times: case of Netcdf files will be treated later in FieldName_Callback
1069if ~isempty(TimeName)
1070    TimeMin=Time(MinIndex_i+1,MinIndex_j+1);
1071    if size(Time)>=[first_i+1 first_j+1]
1072        TimeFirst=Time(first_i+1,first_j+1);
1073    end
1074    if size(Time)>=[last_i+1 last_j+1]
1075        TimeLast=Time(last_i+1,last_j+1);
1076    end
1077    if size(Time)>=[MaxIndex_i+1 MaxIndex_j+1];
1078        TimeMax=Time(MaxIndex_i+1,MaxIndex_j+1);
1079    end
1080end
1081
1082%% update the time table
1083TimeTable=get(handles.TimeTable,'Data');
1084TimeTable{iview,1}=TimeName;
1085TimeTable{iview,2}=TimeMin;
1086TimeTable{iview,3}=TimeFirst;
1087TimeTable{iview,4}=TimeLast;
1088TimeTable{iview,5}=TimeMax;
1089set(handles.TimeTable,'Data',TimeTable)
1090
1091%% update the series info in 'UserData'
1092SeriesData.i1_series{iview}=i1_series;
1093SeriesData.i2_series{iview}=i2_series;
1094SeriesData.j1_series{iview}=j1_series;
1095SeriesData.j2_series{iview}=j2_series;
1096SeriesData.FileType{iview}=FileInfo.FileType;
1097SeriesData.FileInfo{iview}=FileInfo;
1098SeriesData.Time{iview}=Time;
1099
1100SeriesData.TimeName=TimeName;
1101
1102if check_calib
1103    SeriesData.GeometryCalib{iview}=XmlData.GeometryCalib;
1104end
1105set(handles.series,'UserData',SeriesData)
1106
1107%% update pair menus
1108hset_pair=findobj(allchild(0),'Tag','set_pairs');
1109if ~isempty(hset_pair), delete(hset_pair); end % delete the GUI set_pair if opened
1110CheckPair= ~isempty(i2_series)||~isempty(j2_series); % check whether index pairs need to be defined
1111PairString=get(handles.PairString,'Data');
1112if CheckPair% if pairs need to be display for line iview
1113    [ModeMenu,ModeValue]=update_mode(i1_series,i2_series,j2_series);
1114    Menu=update_listpair(i1_series,i2_series,j1_series,j2_series,ModeMenu{ModeValue},Time,TimeUnit,ref_i,ref_j,TimeName,InputTable(iview,:),FileInfo);
1115    PairString{iview,1}=Menu{1};
1116else
1117    PairString{iview,1}=''; % no pair for #iview
1118end
1119set(handles.PairString,'Data',PairString)
1120if isempty(find(cellfun('isempty',get(handles.PairString,'Data'))==0, 1))% if all lines of pairs are empty
1121    set(handles.PairString,'Visible','off')
1122    set(handles.SetPairs,'Visible','off')
1123else
1124    set(handles.PairString,'Visible','on')
1125    set(handles.SetPairs,'Visible','on')
1126end
1127
1128
1129%% display the set of existing files as an image
1130set(handles.FileStatus,'Units','pixels')
1131Position=get(handles.FileStatus,'Position');
1132set(handles.FileStatus,'Units','normalized')
1133%xI=0.5:Position(3)-0.5;
1134nbview=numel(SeriesData.i1_series);
1135j_max=cell(1,nbview);
1136MaxIndex_i=ones(1,nbview); % default
1137MinIndex_i=ones(1,nbview); % default
1138for iline=1:nbview
1139    pair_max=squeeze(max(SeriesData.i1_series{iline},[],1)); % max on pair index
1140    j_max{iline}=max(pair_max,[],1); % max on j index
1141    if ~isempty(j_max{iline})
1142    MaxIndex_i(iline)=max(find(j_max{iline}))-1; % max ref index i
1143    MinIndex_i(iline)=min(find(j_max{iline}))-1; % min ref index i
1144    end
1145end
1146MinIndex_i=min(MinIndex_i);
1147MaxIndex_i=max(MaxIndex_i);
1148range_index=MaxIndex_i-MinIndex_i+1;
1149range_y=max(1,floor(Position(4)/nbview));
1150npx=floor(Position(3));
1151file_indices=MinIndex_i+floor(((0.5:npx-0.5)/npx)*range_index)+1;
1152CData=zeros(nbview*range_y,npx); % initiate the image representing the existing files
1153for iline=1:nbview
1154    ind_y=1+(iline-1)*range_y:iline*range_y;
1155    LineData=zeros(size(file_indices));
1156    file_select=file_indices(file_indices<=numel(j_max{iline}));
1157    ind_select=find(file_indices<=numel(j_max{iline}));
1158    LineData(ind_select)=j_max{iline}(file_select)~=0;
1159    CData(ind_y,:)=ones(size(ind_y'))*LineData;
1160end
1161CData=cat(3,zeros(size(CData)),CData,zeros(size(CData))); % make color images r=0,g,b=0
1162set(handles.FileStatus,'CData',CData);
1163
1164%-----------------------------------------------------------guide -------------
1165%------------------------------------------------------------------------
1166%  III - FUNCTIONS ASSOCIATED TO THE FRAME IndexRange
1167%------------------------------------------------------------------------
1168
1169
1170% ---- determine the menu to put in mode and advice a default choice
1171%------------------------------------------------------------------------
1172function [ModeMenu,ModeValue]=update_mode(i1_series,i2_series,j2_series)
1173%------------------------------------------------------------------------   
1174ModeMenu={''};
1175if isempty(j2_series)% no j pair
1176    ModeValue=1;
1177    if ~isempty(i2_series)
1178        ModeMenu={'series(Di)'}; % pair menu with only option Di
1179    end
1180else %existence of j pairs
1181    pair_max=squeeze(max(i1_series,[],1)); % max on pair index
1182    j_max=max(pair_max,[],1);
1183    MaxIndex_i=find(j_max, 1, 'last' )-1; % max ref index i
1184    MinIndex_i=find(j_max, 1 )-1; % min ref index i
1185    i_max=max(pair_max,[],2);
1186    MaxIndex_j=find(i_max, 1, 'last' )-1; % max ref index i
1187    MinIndex_j=find(i_max, 1 )-1; % min ref index i
1188    if MaxIndex_j==MinIndex_j
1189        ModeValue=1;
1190        ModeMenu={'bursts'};
1191    elseif MaxIndex_i==MinIndex_i
1192        ModeValue=1;
1193        ModeMenu={'series(Dj)'};
1194    else
1195        ModeMenu={'bursts';'series(Dj)'};
1196        if (MaxIndex_j-MinIndex_j)>10
1197            ModeValue=2; % set mode to series(Dj) if more than 10 j values
1198        else
1199            ModeValue=1;
1200        end
1201    end
1202end
1203
1204
1205%------------------------------------------------------------------------
1206function displ_pair=update_listpair(i1_series,i2_series,j1_series,j2_series,mode,time,TimeUnit,ref_i,ref_j,TimeName,InputTable,FileInfo)
1207%------------------------------------------------------------------------
1208displ_pair={};
1209if isempty(TimeUnit)
1210    dtunit='e-03';
1211else
1212    dtunit=['m' TimeUnit];
1213end
1214switch mode
1215    case 'series(Di)'
1216        diff_i=i2_series-i1_series;
1217        min_diff=min(diff_i(diff_i>0));
1218        max_diff=max(diff_i(diff_i>0));
1219        for ipair=min_diff:max_diff
1220            if numel(diff_i(diff_i==ipair))>0
1221                pair_string=['Di= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2)) ];
1222                if ~isempty(time)
1223                    if ref_i<=floor(ipair/2)
1224                        ref_i=floor(ipair/2)+1; % shift ref_i to get the first pair
1225                    end
1226                    Dt=time(ref_i+ceil(ipair/2),ref_j)-time(ref_i-floor(ipair/2),ref_j);
1227                    pair_string=[pair_string ', Dt=' num2str(Dt) ' ' dtunit];
1228                end
1229                displ_pair=[displ_pair;{pair_string}];
1230            end
1231        end
1232        if ~isempty(displ_pair)
1233            displ_pair=[displ_pair;{'Di=*|*'}];
1234        end
1235    case 'series(Dj)'
1236        if isempty(j2_series)
1237            msgbox_uvmat('ERROR','no j1-j2 pair available')
1238            return
1239        end
1240        diff_j=j2_series-j1_series;
1241        min_diff=min(diff_j(diff_j>0));
1242        max_diff=max(diff_j(diff_j>0));
1243        for ipair=min_diff:max_diff
1244            if numel(diff_j(diff_j==ipair))>0
1245                pair_string=['Dj= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2)) ];
1246                if ~isempty(time)
1247                    if ref_j<=floor(ipair/2)
1248                        ref_j=floor(ipair/2)+1; % shift ref_i to get the first pair
1249                    end
1250                    Dt=time(ref_i,ref_j+ceil(ipair/2))-time(ref_i,ref_j-floor(ipair/2));
1251                    pair_string=[pair_string ', Dt=' num2str(Dt) ' ' dtunit];
1252                end
1253                displ_pair=[displ_pair;{pair_string}];
1254            end
1255        end
1256        if ~isempty(displ_pair)
1257            displ_pair=[displ_pair;{'Dj=*|*'}];
1258        end
1259    case 'bursts'
1260        if isempty(j2_series)
1261            msgbox_uvmat('ERROR','no j1-j2 pair available')
1262            return
1263        end
1264        %diff_j=j2_series-j1_series;
1265        min_j1=min(j1_series(j1_series>0));
1266        max_j1=max(j1_series(j1_series>0));
1267        min_j2=min(j2_series(j2_series>0));
1268        max_j2=max(j2_series(j2_series>0));
1269        for pair1=min_j1:min(max_j1,min_j1+20)
1270            for pair2=min_j2:min(max_j2,min_j2+20)
1271                if numel(j1_series(j1_series==pair1))>0 && numel(j2_series(j2_series==pair2))>0
1272                    pair_string=['j= ' num2str(pair1) '-' num2str(pair2)];
1273                    [TimeValue,DtValue]=get_time(ref_i,[],pair_string,InputTable,FileInfo,TimeName,'Dt');
1274                    %Dt=time(ref_i,pair2+1)-time(ref_i,pair1+1);
1275                    pair_string=[pair_string ', Dt=' num2str(DtValue) ' ' dtunit];
1276                    displ_pair=[displ_pair;{pair_string}];
1277                end
1278            end
1279        end
1280        if ~isempty(displ_pair)
1281            displ_pair=[displ_pair;{'j=*-*'}];
1282        end
1283end
1284
1285%------------------------------------------------------------------------
1286function num_first_i_Callback(hObject, eventdata, handles)
1287%------------------------------------------------------------------------
1288num_last_i_Callback(hObject, eventdata, handles)
1289
1290%------------------------------------------------------------------------
1291function num_last_i_Callback(hObject, eventdata, handles)
1292%------------------------------------------------------------------------
1293SeriesData=get(handles.series,'UserData');
1294if ~isfield(SeriesData,'Time')
1295    SeriesData.Time{1}=[];
1296end
1297displ_time(handles);
1298
1299%------------------------------------------------------------------------
1300function num_first_j_Callback(hObject, eventdata, handles)
1301%------------------------------------------------------------------------
1302 num_last_j_Callback(hObject, eventdata, handles)
1303
1304%------------------------------------------------------------------------
1305function num_last_j_Callback(hObject, eventdata, handles)
1306%------------------------------------------------------------------------
1307% first_j=str2num(get(handles.num_first_j,'String'));
1308% last_j=str2num(get(handles.num_last_j,'String'));
1309% ref_j=ceil((first_j+last_j)/2);
1310% set(handles.num_ref_j,'String', num2str(ref_j))
1311% num_ref_j_Callback(hObject, eventdata, handles)
1312SeriesData=get(handles.series,'UserData');
1313if ~isfield(SeriesData,'Time')
1314    SeriesData.Time{1}=[];
1315end
1316displ_time(handles);
1317
1318%------------------------------------------------------------------------
1319% ---- find the times corresponding to the first and last indices of a series
1320function displ_time(handles)
1321%------------------------------------------------------------------------
1322SeriesData=get(handles.series,'UserData'); %
1323if ~isfield(SeriesData,'Time')
1324    return
1325end
1326PairString=get(handles.PairString,'Data');
1327ref_i_1=str2num(get(handles.num_first_i,'String')); % first reference index
1328ref_i_2=str2num(get(handles.num_last_i,'String')); % last reference index
1329ref_j_1=[];ref_j_2=[];
1330if strcmp(get(handles.num_first_j,'Visible'),'on')
1331ref_j_1=str2num(get(handles.num_first_j,'String'));
1332ref_j_2=str2num(get(handles.num_last_j,'String'));
1333end
1334[i1_1,i2_1,j1_1,j2_1] = get_file_index(ref_i_1,ref_j_1,PairString);
1335[i1_2,i2_2,j1_2,j2_2] = get_file_index(ref_i_2,ref_j_2,PairString);
1336TimeTable=get(handles.TimeTable,'Data');
1337%%%%%%
1338%TODO: read time in netcdf file, see ActionName_Callback
1339%%%%%%%
1340%Pairs=get(handles.PairString,'Data');
1341for iview=1:size(TimeTable,1)
1342    if size(SeriesData.Time,1)<iview
1343        break
1344    end
1345    TimeTable{iview,3}=[];
1346    TimeTable{iview,4}=[];
1347    if size(SeriesData.Time{iview},1)>=i2_2+1 && (isempty(ref_j_1)||size(SeriesData.Time{iview},2)>=j2_2+1)
1348        if isempty(ref_j_1)
1349            time_first=(SeriesData.Time{iview}(i1_1+1,2)+SeriesData.Time{iview}(i2_1+1,2))/2;
1350            time_last=(SeriesData.Time{iview}(i1_2+1,2)+SeriesData.Time{iview}(i2_2+1,2))/2;
1351        else
1352            time_first=(SeriesData.Time{iview}(i1_1+1,j1_1+1)+SeriesData.Time{iview}(i2_1+1,j2_1+1))/2;
1353            time_last=(SeriesData.Time{iview}(i1_2+1,j1_2+1)+SeriesData.Time{iview}(i2_2+1,j2_1+1))/2;
1354        end
1355        TimeTable{iview,3}=time_first; % TODO: take into account pairs
1356        TimeTable{iview,4}=time_last; % TODO: take into account pairs
1357    end
1358end
1359set(handles.TimeTable,'Data',TimeTable)
1360
1361%% set the waitbar position with respect to the min and max in the series
1362MinIndex_i=min(get(handles.MinIndex_i,'Data'));
1363MaxIndex_i=max(get(handles.MaxIndex_i,'Data'));
1364pos_first=(ref_i_1-MinIndex_i)/(MaxIndex_i-MinIndex_i+1);
1365pos_last=(ref_i_2-MinIndex_i+1)/(MaxIndex_i-MinIndex_i+1);
1366if isempty(pos_first), pos_first=0; end
1367if isempty(pos_last), pos_last=1; end
1368Position=get(handles.Waitbar,'Position'); % position of the waitbar:= [ x,y, width, height]
1369Position_status=get(handles.FileStatus,'Position');
1370Position(1)=Position_status(1)+Position_status(3)*pos_first;
1371Position(3)=max(Position_status(3)*(pos_last-pos_first),0.001); % width must remain positive
1372set(handles.Waitbar,'Position',Position)
1373update_waitbar(handles.Waitbar,0)
1374
1375%------------------------------------------------------------------------
1376% --- Executes when selected cell(s) is changed in PairString.
1377function PairString_CellSelectionCallback(hObject, eventdata, handles)
1378%------------------------------------------------------------------------   
1379if numel(eventdata.Indices)>=1
1380    PairString=get(hObject,'Data');
1381    if ~isempty(PairString{eventdata.Indices(1)})
1382        SetPairs_Callback(hObject, eventdata.Indices(1), handles)
1383    end
1384end
1385
1386%-------------------------------------
1387function enable_i(handles,state)
1388set(handles.i_txt,'Visible',state)
1389set(handles.num_first_i,'Visible',state)
1390set(handles.num_last_i,'Visible',state)
1391set(handles.num_incr_i,'Visible',state)
1392
1393%-----------------------------------
1394function enable_j(handles,state)
1395set(handles.j_txt,'Visible',state)
1396set(handles.num_first_j,'Visible',state)
1397set(handles.num_last_j,'Visible',state)
1398set(handles.num_incr_j,'Visible',state)
1399set(handles.MinIndex_j,'Visible',state)
1400set(handles.MaxIndex_j,'Visible',state)
1401
1402
1403%%%%%%%%%%%%%%%%%%%%
1404%%  MAIN ActionName FUNCTIONS
1405%%%%%%%%%%%%%%%%%%%%
1406%------------------------------------------------------------------------
1407% --- Executes on button press in RUN.
1408%------------------------------------------------------------------------
1409function RUN_Callback(hObject, eventdata, handles)
1410
1411%% settings of the button RUN
1412if ~isequal(get(handles.ActionInput,'BackgroundColor'),[1 0 0])
1413    msgbox_uvmat('ERROR','first activate the button ActionInput')
1414    return
1415end
1416set(handles.RUN,'BusyAction','queue'); % activation of STOP button will set BusyAction to 'cancel'
1417set(handles.RUN, 'Enable','Off')% avoid further RUN action until the current one is finished
1418set(handles.RUN,'BackgroundColor',[1 1 0])%show activation of RUN by yellow color
1419drawnow
1420set(handles.status,'Value',0)% desable status display if relevant
1421status_Callback([], eventdata, handles)
1422
1423%% launch action
1424errormsg=launch_action(handles);
1425if ~isempty(errormsg)
1426     msgbox_uvmat('ERROR',errormsg)
1427end
1428
1429%% reset the GUI series
1430update_waitbar(handles.Waitbar,1); % put the waitbar to end position to indicate launching is finished
1431set(handles.RUN, 'Enable','On')
1432set(handles.RUN,'BackgroundColor',[1 0 0])
1433set(handles.RUN, 'Value',0)
1434
1435%------------------------------------------------------------------------
1436% --- called by RUN_Callback
1437%------------------------------------------------------------------------
1438% The calculations are launched in three different ways:
1439% RunMode='local': calculation on the local Matlab session, will prevent other actions during that time.
1440% RunMode='background': calculation on the local computer, but in a new Matlab session (with no graphic output).
1441% RunMode='cluster': calculations dispatched in a cluster, using a managing system, 'oar, 'sge, or 'sgb'.
1442% In the latter case, the calculation is split in 'packets' of i index (all j indices are contained in a single packet).
1443% This splitting is possible only if the different calculations in the series are independent. Otherwise the action
1444% function imposes a number of processes NbSlice in input, for instance NbSlice=1 for a time series.
1445% If NbSlice is not imposed, the splitting in packets (jobs) is determined
1446% so that a job is optimum length AdvisedJobCPUTime), and the total job number in any case smaller
1447% than MaxJobNumber (these parameters are defined in the file series.xml in
1448% accordance with the management strategy for the cluster). The jobs are
1449% dispatched in parallel into NbCore processors by the cluster managing system.
1450
1451function errormsg=launch_action(handles)
1452errormsg=''; % default
1453
1454%% read the data on the GUI series
1455Param=read_GUI_series(handles); % displayed parameters
1456SeriesData=get(handles.series,'UserData'); % hidden parameters
1457if isfield(SeriesData,'TransformInput')
1458    Param.TransformInput=SeriesData.TransformInput;
1459end
1460if ~isfield(SeriesData,'i1_series')
1461    errormsg='The input field series needs to be refreshed: press REFRESH';
1462    return
1463end
1464if isfield(Param,'InputFields')&& isfield(Param.InputFields,'FieldName')&& isequal(Param.InputFields.FieldName,'get_field...')
1465    errormsg='input field name(s) not defined, select get_field...';
1466    return
1467end
1468
1469%% select the Action mode, 'local', 'background' or 'cluster' (if available)
1470RunMode='local'; % default (needed for first opening of the GUI series)
1471if isfield(Param.Action,'RunMode')
1472    RunMode=Param.Action.RunMode;
1473    Param.Action=rmfield(Param.Action,'RunMode'); % remove from the recorded xml file to avoid interference during ImportConfig
1474end
1475ActionExt='.m'; % default
1476if isfield(Param.Action,'ActionExt')
1477    ActionExt=Param.Action.ActionExt; % '.m', '.sh' (compiled)  or '.py' (Python)
1478    Param.Action=rmfield(Param.Action,'ActionExt'); % remove from the recorded xml file to avoid interference during ImportConfig
1479end
1480ActionName=Param.Action.ActionName;
1481ActionPath=Param.Action.ActionPath;
1482path_series=fileparts(which('series'));
1483
1484%% create the Action fct handle if RunMode option = 'local'
1485if strcmp(RunMode,'local')
1486    if ~isequal(ActionPath,path_series)
1487        eval(['spath=which(''' ActionName ''');']) %spath = current path of the selected function ACTION
1488        if ~exist(ActionPath,'dir')
1489            errormsg=['The prescribed function path ' ActionPath ' does not exist'];
1490            return
1491        end
1492        if ~isequal(spath,ActionPath)
1493            addpath(ActionPath)% add the prescribed path if not the current one
1494        end
1495    end
1496    eval(['h_fun=@' ActionName ';'])%create a function handle for ACTION
1497    if ~isequal(ActionPath,path_series)
1498        rmpath(ActionPath)% add the prescribed path if not the current one
1499    end
1500end
1501
1502%% Get  parameters from series.xml
1503errormsg=''; % default error message
1504ActionFullName=fullfile(get(handles.ActionPath,'String'),ActionName);
1505
1506%% If a compiled version has been selected (ext .sh) check wether it needs to be recompiled
1507if strcmp(ActionExt,'.sh')
1508    TransformPath='';
1509    if isfield(SeriesData,'TransformPath')
1510        TransformPath=SeriesData.TransformPath;
1511        if isfield(SeriesData,'TransformList')
1512            TransformList=get(handles.TransformName,'String');
1513            TransformIndex=get(handles.TransformName,'Value');
1514            TransformName=TransformList{TransformIndex};
1515            if ~ismember(TransformName,SeriesData.TransformList)
1516                TransformPath='';
1517            end
1518        end
1519    end
1520    if ~isempty(TransformPath)&&...
1521          ~strcmp(TransformPath,get(handles.TransformPath,'String'))% if the transform is not in paths set for compilation
1522        msgbox_uvmat('ERROR', 'compilation not available for this transform function, select .m')
1523        return
1524    end
1525    set(handles.series,'Pointer','watch') % set the mouse pointer to 'watch'
1526    set(handles.ActionExt,'BackgroundColor',[1 1 0])
1527    [mcrmajor, mcrminor] = mcrversion;   
1528    MCRROOT = ['MCRROOT',int2str(mcrmajor),int2str(mcrminor)];
1529    RunTime = getenv(MCRROOT);
1530    ActionNameVersion=[ActionName '_' MCRROOT];
1531    ActionFullName=fullfile(get(handles.ActionPath,'String'),[ActionNameVersion '.sh']);
1532    % compile the .m file if the .sh file does not exist yet
1533    if ~exist(ActionFullName,'file')
1534        answer=msgbox_uvmat('INPUT_Y-N','compiled version has not been created: compile now?');
1535        if strcmp(answer,'Yes')
1536            set(handles.ActionExt,'BackgroundColor',[1 1 0])
1537            path_uvmat=fileparts(which('series'));
1538            currentdir=pwd;
1539            cd(get(handles.ActionPath,'String'))% go to the directory of Action
1540            addpath(path_uvmat)% add the path to uvmat to run the fct 'compile'
1541            compile(ActionName,TransformPath)
1542            cd(currentdir)
1543        else
1544            errormsg='Action launch interrupted';
1545            return
1546        end       
1547    else
1548        sh_file_info=dir(fullfile(get(handles.ActionPath,'String'),[ActionNameVersion '.sh']));
1549        m_file_info=dir(fullfile(get(handles.ActionPath,'String'),[ActionName '.m']));
1550        if isfield(m_file_info,'datenum') && m_file_info.datenum>sh_file_info.datenum
1551            set(handles.ActionExt,'BackgroundColor',[1 1 0])
1552            drawnow
1553            answer=msgbox_uvmat('INPUT_Y-N',[ActionNameVersion '.sh needs to be updated: recompile now?']);
1554            if strcmp(answer,'Yes')
1555                path_uvmat=fileparts(which('series'));
1556                currentdir=pwd;
1557                cd(get(handles.ActionPath,'String'))% go to the directory of Action
1558                addpath(path_uvmat)% add the path to uvmat to run the fct 'compile'
1559                addpath(fullfile(path_uvmat,'transform_field'))% add the path to uvmat to run the fct 'compile'
1560                compile(ActionName,TransformPath)
1561                cd(currentdir)
1562            end
1563        end
1564    end
1565
1566    set(handles.ActionExt,'BackgroundColor',[1 1 1])
1567     set(handles.series,'Pointer','arrow') % set the mouse pointer to 'watch
1568end
1569
1570%% set nbre of cluster cores and processes:
1571% NbCore is the number of computer processors used
1572% NbProcess is the number of independent processes in which the required calculation is split.
1573switch RunMode
1574    case {'local','background'}
1575        NbCore=1; % no need to split the calculation
1576    case 'cluster'
1577        %proposed number of cores to reserve in the cluster
1578        NbCoreAdvised=SeriesData.SeriesParam.ClusterParam.NbCoreAdvised;
1579        NbCoreMax=SeriesData.SeriesParam.ClusterParam.NbCoreMax;
1580        if strcmp(ActionExt,'.m')% case of Matlab function (uncompiled)
1581            warning_string=', preferably use .sh option to save Matlab licences';
1582        else
1583            warning_string=')';
1584        end
1585        answer=msgbox_uvmat('INPUT_TXT',['Number of cores (max ' num2str(NbCoreMax) ', ' warning_string],num2str(NbCoreAdvised));
1586        if isempty(answer)
1587            errormsg='Action launch interrupted by user';
1588            return
1589        end
1590        NbCore=str2double(answer);
1591%         extra_oar=answer{2};
1592%     case {'cluster_pbs', 'cluster_sge', 'cluster_qstat_unknown'}
1593%         if strcmp(ActionExt,'.m')% case of Matlab function (uncompiled)
1594%             NbCore=1; % one core used only (limitation of Matlab licences)
1595%             answer=msgbox_uvmat('INPUT_Y-N','Number of cores =1: select the compiled version .sh for multi-core processing. Proceed with the .m version?');
1596%             if ~strcmp(answer,'Yes')
1597%                 errormsg='Action launch interrupted';
1598%                 return
1599%             end
1600%             extra_oar='';
1601%         else
1602%             answer=inputdlg({'Number of jobs (max 1000)','Queue'},'qsub parameters',1,{'100','piv_debian'});
1603%             NbCore=str2double(answer{1});
1604%             qstat_Queue=answer{2};
1605%             %extra_oar=answer{2}; % TODO : fix this for LMFA cluster. Maybe
1606%             %extrs_oar and extra_pbs are not the best names
1607%         end
1608end
1609if ~isfield(Param.IndexRange,'NbSlice')
1610    Param.IndexRange.NbSlice=[];
1611end
1612
1613%% create the output data directory if needed
1614OutputDir='';
1615if isfield(Param,'OutputSubDir')
1616    SubDirOut=[get(handles.OutputSubDir,'String') Param.OutputDirExt];
1617    SubDirOutNew=SubDirOut;
1618    detect=exist(fullfile(Param.InputTable{1,1},SubDirOutNew),'dir'); % test if  the dir  already exist
1619    check_create=1; % need to create the result directory by default
1620    CheckOverwrite=1;
1621    if isfield(Param,'CheckOverwrite')
1622        CheckOverwrite=Param.CheckOverwrite;
1623    end
1624    while detect
1625        if CheckOverwrite
1626            comment=', possibly overwrite previous data';
1627        else
1628            comment=', will complement existing result files (no overwriting)';
1629        end
1630        answer=msgbox_uvmat('INPUT_Y-N-Cancel',['use existing ouput directory: ' fullfile(Param.InputTable{1,1},SubDirOutNew) comment]);
1631        if strcmp(answer,'Cancel')
1632            return
1633        elseif strcmp(answer,'Yes')
1634            detect=0;
1635            check_create=0;
1636        else
1637            r=regexp(SubDirOutNew,'(?<root>.*\D)(?<num1>\d+)$','names'); % detect whether name ends by a number
1638            if isempty(r)
1639                r(1).root=[SubDirOutNew '_'];
1640                r(1).num1='0';
1641            end
1642            SubDirOutNew=[r(1).root num2str(str2num(r(1).num1)+1)]; % increment the index by 1 or put 1
1643            detect=exist(fullfile(Param.InputTable{1,1},SubDirOutNew),'dir'); % test if  the dir  already exists
1644            check_create=1;
1645        end
1646    end
1647    Param.OutputDirExt=regexprep(SubDirOutNew,Param.OutputSubDir,'');
1648    Param.OutputRootFile=Param.InputTable{1,3}; % the first sorted RootFile taken for output
1649    set(handles.OutputDirExt,'String',Param.OutputDirExt)
1650    OutputDir=fullfile(Param.InputTable{1,1},[Param.OutputSubDir Param.OutputDirExt]); % full name (with path) of output directory
1651    if check_create    % create output directory if it does not exist
1652        [tild,msg1]=mkdir(OutputDir);
1653        if ~strcmp(msg1,'')
1654            errormsg=['cannot create ' OutputDir ': ' msg1]; % error message for directory creation
1655            return
1656        end
1657    end
1658   
1659elseif isfield(Param,'ActionInput')&&isfield(Param.ActionInput,'LogPath')% custom definition of the output dir
1660    OutputDir=Param.ActionInput.LogPath;   
1661end
1662DirXml=fullfile(OutputDir,'0_XML');
1663if ~exist(DirXml,'dir')
1664    [~,msg1]=mkdir(DirXml);
1665    if ~strcmp(msg1,'')
1666        errormsg=['cannot create ' DirXml ': ' msg1]; % error message for directory creation
1667        return
1668    end
1669end
1670OutputNomType=nomtype2pair(Param.InputTable{1,4}); % nomenclature for output files
1671
1672%% get the set of reference input field indices
1673first_i=1; % first i index to process
1674last_i=1; % last i index to process
1675incr_i=1; % increment step in i index
1676first_j=1; % first j index to process
1677last_j=1; % last j index to process
1678incr_j=1; % increment step in j index
1679if isfield(Param.IndexRange,'first_i')
1680    first_i=Param.IndexRange.first_i;
1681    incr_i=Param.IndexRange.incr_i;
1682    last_i=Param.IndexRange.last_i;
1683end
1684if isfield(Param.IndexRange,'incr_j')
1685    first_j=Param.IndexRange.first_j;
1686    last_j=Param.IndexRange.last_j;
1687    incr_j=Param.IndexRange.incr_j;
1688end
1689if last_i < first_i || last_j < first_j
1690    errormsg= 'series/Run_Callback:last field index must be larger or equal to the first one';
1691    return
1692end
1693%incr_i must be defined, =1 by default, if NbSlice is active
1694if isempty(incr_i)&& ~isempty(Param.IndexRange.NbSlice)
1695    incr_i=1;
1696    set(handles.num_incr_i,'String','1')
1697end
1698% case of no increment i defined: processing is done on the available files found in i1_series
1699if isempty(incr_i)
1700    if isempty(incr_j)
1701        [ref_j,ref_i]=find(squeeze(SeriesData.i1_series{1}(1,:,:)));
1702        ref_j=ref_j(ref_j>=first_j & ref_j<=last_j);
1703        ref_i=ref_i(ref_i>=first_i & ref_i<=last_i);
1704        ref_j=ref_j-1;
1705        ref_i=ref_i-1;
1706    else
1707        ref_j=first_j:incr_j:last_j;
1708        [tild,ref_i]=find(squeeze(SeriesData.i1_series{1}(1,:,:)));
1709        ref_i=ref_i-1;
1710        ref_i=ref_i(ref_i>=first_i & ref_i<=last_i);
1711    end
1712    % increment i is defined: processing is done on first_i:incr_i:last_i;
1713else
1714    ref_i=first_i:incr_i:last_i;
1715    if isempty(incr_j)% automatic finding of the existing j indices
1716        [ref_j,tild]=find(squeeze(SeriesData.i1_series{1}(1,:,:)));
1717        ref_j=ref_j-1;
1718        ref_j=ref_j(ref_j>=first_j & ref_j<=last_j);
1719    else
1720        ref_j=first_j:incr_j:last_j;
1721    end
1722end
1723CPUTime=1; % job time estimated at 1 min per iteration (on index i and j) by default
1724if isfield(Param.Action, 'CPUTime') && ~isempty(Param.Action.CPUTime)
1725    CPUTime=Param.Action.CPUTime; % Note: CpUTime for one iteration ref_i has to be multiplied by the number of j indices nbfield_j
1726end
1727nbfield_j=numel(ref_j); % number of j indices
1728BlockLength=numel(ref_i); % by default, job involves the full set of i field indices
1729NbProcess=1;
1730switch RunMode
1731    case 'cluster'
1732        JobNumberMax=SeriesData.SeriesParam.ClusterParam.JobNumberMax;
1733        JobCPUTimeAdvised=SeriesData.SeriesParam.ClusterParam.JobCPUTimeAdvised;
1734        if isempty(Param.IndexRange.NbSlice)% if NbSlice is not defined
1735            BlockLength= ceil(JobCPUTimeAdvised/(CPUTime*nbfield_j)); % iterations are grouped in sets with length BlockLength  such that the typical CPU time of a job is MinJobNumber.
1736            BlockLength=max(BlockLength,ceil(numel(ref_i)/JobNumberMax)); % possibly increase the BlockLength to have less than MaxJobNumber jobs
1737            NbProcess=ceil(numel(ref_i)/BlockLength) ; % nbre of processes sent to oar
1738        else
1739            NbProcess=Param.IndexRange.NbSlice; % the parameter NbSlice sets the nbre of run processes
1740        end
1741        NbCore=min(NbCore,NbProcess); % reduces the number of cores if it exceeds the number of processes
1742    otherwise
1743        if ~isempty(Param.IndexRange.NbSlice)
1744            NbProcess=Param.IndexRange.NbSlice; % the parameter NbSlice sets the nbre of run processes
1745        end
1746end
1747
1748%% record nbre of output files and starting time for computation for status
1749StatusData=get(handles.status,'UserData');
1750if isfield(StatusData,'OutputFileMode')
1751    switch StatusData.OutputFileMode
1752        case 'NbInput'
1753            StatusData.NbOutputFile=numel(ref_i)*nbfield_j;
1754        case 'NbInput_i'
1755            StatusData.NbOutputFile=numel(ref_i);
1756        case 'NbSlice'
1757            StatusData.NbOutputFile=str2num(get(handles.num_NbSlice,'String'));
1758    end
1759end
1760StatusData.TimeStart=now;
1761set(handles.status,'UserData',StatusData)
1762
1763%% case of a function in Python
1764if strcmp(ActionExt, '.py (in dev.)')
1765    fprintf([
1766        '\n' ...
1767        '!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n' ...
1768        'The option .py is used. It is still in development.\n' ...
1769        'To try it, first install pyper and the most recent version of fluidimage\n' ...
1770        '(see https://bitbucket.org/fluiddyn/fluidimage).\n' ...
1771        'Warning: there is no direct correspondance between UVMAT and fluidimage parameters\n' ...
1772        '!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n'])
1773    RunMode = 'python';
1774end
1775
1776
1777%% direct processing on the current Matlab session or creation of command files
1778filexml=cell(1,NbProcess); % initialisation of the names of the files containing the processing parameters
1779extxml=cell(1,NbProcess); % initialisation of the set of labels used for the files documenting each process
1780for iprocess=1:NbProcess
1781    extxml{iprocess}='.xml';
1782end
1783for iprocess=1:NbProcess
1784    if ~strcmp(get(handles.RUN,'BusyAction'),'queue')% allow for STOP action
1785        disp('program stopped by user')
1786        return
1787    end
1788    if isempty(Param.IndexRange.NbSlice)
1789        Param.IndexRange.first_i=first_i+(iprocess-1)*BlockLength*incr_i;
1790        if Param.IndexRange.first_i>last_i
1791            NbProcess=iprocess-1; % leave the loop, we are at the end of the calculation
1792            break
1793        end
1794        Param.IndexRange.last_i=min(last_i,first_i+(iprocess)*BlockLength*incr_i-1);
1795    else %multislices (then incr_i is not empty)
1796        Param.IndexRange.first_i= first_i+iprocess-1;
1797        Param.IndexRange.incr_i=incr_i*Param.IndexRange.NbSlice;
1798    end
1799    for ilist=1:size(Param.InputTable,1)
1800        Param.InputTable{ilist,1}=regexprep(Param.InputTable{ilist,1},'\','/'); % correct path name for PCWIN system
1801    end
1802   
1803    if isfield(Param,'OutputSubDir')
1804        t=struct2xml(Param);
1805        t=set(t,1,'name','Series');
1806        extxml{iprocess}=fullfile_uvmat('','',Param.InputTable{1,3},'.xml',OutputNomType,...
1807            Param.IndexRange.first_i,Param.IndexRange.last_i,first_j,last_j);
1808        filexml{iprocess}=fullfile(OutputDir,'0_XML',extxml{iprocess});
1809        try
1810            save(t, filexml{iprocess}); % save the xml file containing the processing parameters
1811        catch ME
1812            if ~strcmp (RunMode,'local')
1813                errormsg=['error writting ' filexml{iprocess} ': ' ME.message];
1814                return
1815            end
1816        end
1817    end
1818    if strcmp (RunMode,'local')
1819        switch ActionExt
1820            case '.m'
1821                h_fun(Param); % direct launching
1822               
1823            case '.sh'
1824                switch computer
1825                    case {'PCWIN','PCWIN64'} %Windows system
1826                        filexml=regexprep(filexml,'\\','\\\\'); % add '\' so that '\' are left as characters
1827                        system([ActionFullName ' ' RunTime ' ' filexml{iprocess}]); % TODO: adapt to DOS system
1828                    case {'GLNX86','GLNXA64','MACI64'}%Linux  system
1829                        system([ActionFullName ' ' RunTime ' ' filexml{iprocess}]);
1830                end
1831        end
1832    end
1833end
1834
1835if ~strcmp (RunMode,'local') && ~strcmp(RunMode,'python')
1836    %% processing on a different session of the same computer (background) or cluster, create executable files
1837    batch_file_list=cell(NbProcess,1); % initiate the list of executable files
1838    DirExe=fullfile(OutputDir,'0_EXE'); % directory name for executable files
1839    switch computer
1840        case {'PCWIN','PCWIN64'} %Windows system
1841            ExeExt='.bat';
1842        case {'GLNX86','GLNXA64','MACI64'}%Linux  system
1843            ExeExt='.sh';
1844    end
1845    %create subdirectory for executable files
1846    if ~exist(DirExe,'dir')
1847        [tild,msg1]=mkdir(DirExe);
1848        if ~strcmp(msg1,'')
1849            errormsg=['cannot create ' DirExe ': ' msg1]; % error message for directory creation
1850            return
1851        end
1852    end
1853    %create subdirectory for log files
1854    DirLog=fullfile(OutputDir,'0_LOG');
1855    if ~exist(DirLog,'dir')
1856        [tild,msg1]=mkdir(DirLog);
1857        if ~strcmp(msg1,'')
1858            errormsg=['cannot create ' DirLog ': ' msg1]; % error message for directory creation
1859            return
1860        end
1861    end
1862   
1863    %create the executable file
1864    file_exe_global=fullfile_uvmat('','',Param.InputTable{1,3},ExeExt,OutputNomType,...
1865        first_i,last_i,first_j,last_j);
1866    file_exe_global=fullfile(OutputDir,'0_EXE',file_exe_global);
1867    filelog_global=fullfile_uvmat('','',Param.InputTable{1,3},'.log',OutputNomType,...
1868        first_i,last_i,first_j,last_j);
1869    filelog_global=fullfile(OutputDir,'0_LOG',filelog_global);
1870
1871    for iprocess=1:NbProcess   
1872        %create the executable file       
1873        batch_file_list{iprocess}=fullfile(OutputDir,'0_EXE',regexprep(extxml{iprocess},'.xml$',ExeExt));
1874       
1875        % set the log file name
1876        filelog{iprocess}=fullfile(OutputDir,'0_LOG',regexprep(extxml{iprocess},'.xml$','.log'));     
1877    end
1878end
1879
1880%% launch the executable files for background or cluster processing
1881
1882switch RunMode
1883   
1884    case 'background'
1885        [fid,message]=fopen(file_exe_global,'w');
1886        if isequal(fid,-1)
1887            errormsg=['creation of ' file_exe_global ':' message];
1888            return
1889        end
1890        switch ActionExt
1891            case '.m'% Matlab function
1892                switch computer
1893                    case {'GLNX86','GLNXA64','MACI64'}
1894                        matlab_ver = ver('MATLAB');
1895                        matlab_version = matlab_ver.Version;
1896                        cmd=[...
1897                            '#!/bin/bash\n'...
1898                            'source /etc/profile\n'...
1899                            'module load matlab/' matlab_version '\n'...% CHOICE OF MATLAB VERSION
1900                            'time_start=$(date +%%s)\n'...
1901                            'matlab -nodisplay -nosplash -nojvm -logfile ''' filelog_global ''' <<END_MATLAB\n'...
1902                            'addpath(''' path_series ''');\n'...
1903                            'addpath(''' Param.Action.ActionPath ''');\n'];
1904                        for iprocess=1:NbProcess
1905                            cmd=[cmd '' Param.Action.ActionName  '(''' filexml{iprocess} ''');\n'];
1906                        end
1907                        cmd=[cmd  'exit\n' 'END_MATLAB\n'...
1908                            'time_end=$(date +%%s)\n'...
1909                            'echo "global time = " $(($time_end - $time_start)) >> ''' filelog_global '''\n'];
1910                        fprintf(fid,cmd); % fill the executable file with the  char string cmd
1911                        fclose(fid); % close the executable filefilelog_global
1912                        system(['chmod +x ' file_exe_global]); % set the file to executable
1913                    case {'PCWIN','PCWIN64'}
1914                        cmd=['matlab -automation -logfile ' regexprep(filelog{iprocess},'\\','\\\\')...
1915                            ' -r "addpath(''' regexprep(path_series,'\\','\\\\') ''');'...
1916                            'addpath(''' regexprep(Param.Action.ActionPath,'\\','\\\\') ''');'];
1917                        for iprocess=1:NbProcess
1918                            cmd=[cmd '' Param.Action.ActionName  '( ''' regexprep(filexml{iprocess},'\\','\\\\') ''');']
1919                        end
1920                        cmd=[cmd ';exit"'];
1921                        fprintf(fid,cmd); % fill the executable file with the  char string cmd
1922                        fclose(fid); % close the executable file
1923                end
1924                system([file_exe_global ' &'])% directly execute the command file
1925            case '.sh' % compiled Matlab function
1926                for iprocess=1:NbProcess
1927                    switch computer
1928                        case {'GLNX86','GLNXA64','MACI64'}
1929                            [fid,message]=fopen(batch_file_list{iprocess},'w'); % create the executable file
1930                            if isequal(fid,-1)
1931                                errormsg=['creation of .bat file: ' message];
1932                                return
1933                            end
1934                            cmd=['#!/bin/bash \n '...
1935                                '#$ -cwd \n '...
1936                                'hostname && date \n '...
1937                                'umask 002 \n'...
1938                                ActionFullName ' ' RunTime ' ' filexml{iprocess}]; % allow writting access to created files for user group
1939                            fprintf(fid,cmd); % fill the executable file with the  char string cmd
1940                            fclose(fid); % close the executable file
1941                            system(['chmod +x ' batch_file_list{iprocess}]); % set the file to executable
1942                            system([batch_file_list{iprocess} ' &'])% directly execute the command file
1943                        case {'PCWIN','PCWIN64'}
1944                            msgbox_uvmat('ERROR','option for compiled Matlab functions not implemented for Windows system')
1945                            return
1946                    end
1947                end
1948                msgbox_uvmat('CONFIRMATION',[ActionFullName ' launched in background: press STATUS to see results'])
1949        end
1950       
1951    case 'cluster' % option 'oar-parexec' used
1952        %create subdirectory for oar commands
1953        for iprocess=1:NbProcess
1954            [fid,message]=fopen(batch_file_list{iprocess},'w'); % create the executable file
1955            if isequal(fid,-1)
1956                errormsg=['creation of .bat file: ' message];
1957                return
1958            end
1959            if  strcmp(ActionExt,'.sh')
1960                cmd=['#!/bin/bash \n '...
1961                    '#$ -cwd \n '...
1962                    'hostname && date \n '...
1963                    'umask 002 \n'...
1964                    ActionFullName ' ' RunTime ' ' filexml{iprocess}]; % allow writting access to created files for user group
1965            else
1966                matlab_ver = ver('MATLAB');
1967                matlab_version = matlab_ver.Version;
1968                cmd=[...
1969                    '#!/bin/bash\n'...
1970                    'source /etc/profile\n'...
1971                    'module load matlab/' matlab_version '\n'...% CHOICE OF MATLAB VERSION
1972                    'matlab -nodisplay -nosplash -nojvm -singleCompThread -logfile ''' filelog{iprocess} ''' <<END_MATLAB\n'...
1973                    'addpath(''' path_series ''');\n'...
1974                    'addpath(''' Param.Action.ActionPath ''');\n'...
1975                    '' Param.Action.ActionName  '(''' filexml{iprocess} ''');\n'...
1976                    'exit\n'...
1977                    'END_MATLAB\n'];
1978            end
1979            fprintf(fid,cmd); % fill the executable file with the  char string cmd
1980            fclose(fid); % close the executable file
1981            system(['chmod +x ' batch_file_list{iprocess}]); % set the file to executable
1982        end
1983        DIR_CLUSTER=fullfile(OutputDir,'0_CLUSTER');
1984        if exist(DIR_CLUSTER,'dir')% delete the content of the dir 0_LOG to allow new input
1985            curdir=pwd;
1986            cd(DIR_CLUSTER)
1987            delete('*')
1988            cd(curdir)
1989        else
1990            [tild,msg1]=mkdir(DIR_CLUSTER);
1991            if ~strcmp(msg1,'')
1992                errormsg=['cannot create ' DIR_CLUSTER ': ' msg1]; % error message for directory creation
1993                return
1994            end
1995        end
1996        % create file containing the list of jobs
1997        ListProcess=fullfile(DIR_CLUSTER,'job_list.txt'); % name of the file containing the list of executables
1998        fid=fopen(ListProcess,'w'); % open it for writting
1999        for iprocess=1:length(batch_file_list)
2000            fprintf(fid,[batch_file_list{iprocess} '\n']); % write list of exe files
2001        end
2002        fclose(fid);
2003        system(['chmod +x ' ListProcess]); % set the file to executable
2004 
2005        CPUTimeProcess=CPUTime*BlockLength*nbfield_j; % estimated CPU time for one individual process (in minutes)
2006        LaunchCmdFcn=SeriesData.SeriesParam.ClusterParam.LaunchCmdFcn;
2007        oar_command=feval(LaunchCmdFcn,ListProcess,ActionFullName,DirLog,NbProcess, NbCore,CPUTimeProcess)
2008        [status,result]=system(oar_command)% execute system command and show the result (ID number of the launched job) on the Matlab command window
2009        filename_oarcommand=fullfile(DIR_CLUSTER,'0_cluster_command'); % keep track of the command in file '0-OAR/0_cluster_command'
2010        fid=fopen(filename_oarcommand,'w');
2011        fprintf(fid,oar_command); % store the command
2012        fprintf(fid,result); % store the result (job ID number)
2013        fclose(fid);
2014        msgbox_uvmat('CONFIRMATION',[ActionFullName ' launched as  ' num2str(NbProcess) ' processes in cluster: press STATUS to see results'])
2015       
2016%     case 'cluster_pbs' % for LMFA Kepler machine:  trqnsferred to fct
2017
2018%         %create subdirectory for pbs command and log files
2019%         DirPBS=fullfile(OutputDir,'0_PBS'); % todo : common name OAR/PBS
2020%         if exist(DirPBS,'dir')% delete the content of the dir 0_LOG to allow new input
2021%             curdir=pwd;
2022%             cd(DirPBS)
2023%             delete('*')
2024%             cd(curdir)
2025%         else
2026%             [tild,msg1]=mkdir(DirPBS);
2027%             if ~strcmp(msg1,'')
2028%                 errormsg=['cannot create ' DirPBS ': ' msg1]; % error message for directory creation
2029%                 return
2030%             end
2031%         end
2032%         max_walltime=3600*20; % 20h max total calculation (cannot exceed 24 h)
2033%         walltime_onejob=1800; % seconds, max estimated time for asingle file index value
2034%         ListProcess=fullfile(DirPBS,'job_list.txt'); % create name of the global executable file
2035%         fid=fopen(ListProcess,'w');
2036%         for iprocess=1:length(batch_file_list)
2037%             fprintf(fid,[batch_file_list{iprocess} '\n']); % list of exe files
2038%         end
2039%         fclose(fid);
2040%         system(['chmod +x ' ListProcess]); % set the file to executable
2041%         pbs_command=['qsub -n CIVX '...
2042%             '-t idempotent --checkpoint ' num2str(walltime_onejob+60) ' '...
2043%             '-l /core=' num2str(NbCore) ','...
2044%             'walltime=' datestr(min(1.05*walltime_onejob/86400*max(NbProcess*BlockLength*nbfield_j,NbCore)/NbCore,max_walltime/86400),13) ' '...
2045%             '-E ' regexprep(ListProcess,'\.txt\>','.stderr') ' '...
2046%             '-O ' regexprep(ListProcess,'\.txt\>','.log') ' '...
2047%             extra_qstat ' '...
2048%             '"oar-parexec -s -f ' ListProcess ' '...
2049%             '-l ' ListProcess '.log"'];
2050%         filename_oarcommand=fullfile(DirPBS,'pbs_command');
2051%         fid=fopen(filename_oarcommand,'w');
2052%         fprintf(fid,pbs_command);
2053%         fclose(fid);
2054%         fprintf(pbs_command); % display in command line
2055%         %system(pbs_command);
2056%         msgbox_uvmat('CONFIRMATION',[ActionFullName ' command ready to be launched in cluster'])
2057
2058     case 'cluster_sge' % for PSMN % TODO: use the standard 'cluster' config with an external fct
2059        % Au PSMN, on ne cr??e pas 1 job avec plusieurs c??urs, mais N jobs de 1 c??urs
2060        % o?? N < 1000.
2061        %create subdirectory for pbs command and log files
2062
2063        DirSGE=fullfile(OutputDir,'0_SGE');
2064        if exist(DirSGE,'dir')% delete the content of the dir 0_LOG to allow new input
2065            curdir=pwd;
2066            cd(DirSGE)
2067            delete('*')
2068            cd(curdir)
2069        else
2070            [tild,msg1]=mkdir(DirSGE);
2071            if ~strcmp(msg1,'')
2072                errormsg=['cannot create ' DirSGE ': ' msg1]; % error message for directory creation
2073                return
2074            end
2075        end
2076        maxImgsPerJob = ceil(length(batch_file_list)/NbCore);
2077        disp(['Max number of jobs: ' num2str(NbCore)])
2078        disp(['Images per job: ' num2str(maxImgsPerJob)])
2079       
2080        iprocess = 1;
2081        imgsInJob = [];
2082        currJobIndex = 1;
2083        done = 0;
2084        while(~done)
2085            if(iprocess <= length(batch_file_list))
2086                imgsInJob = [imgsInJob, iprocess];
2087            end
2088            if((numel(imgsInJob) >= maxImgsPerJob) || (iprocess == length(batch_file_list)))
2089                cmd=['#!/bin/sh \n'...
2090                     '#$ -cwd \n'...
2091                     'hostname && date\n']
2092                for ii=1:numel(imgsInJob)
2093                    cmd=[cmd ActionFullName ' /softs/matlab ' filexml{imgsInJob(ii)} '\n'];
2094                end
2095                [fid, message] = fopen([DirSGE '/job' num2str(currJobIndex) '.sh'], 'w');
2096                fprintf(fid, cmd);
2097                fclose(fid);
2098                system(['chmod +x ' DirSGE '/job' num2str(currJobIndex) '.sh'])
2099                sge_command=['qsub -N civ_' num2str(currJobIndex) ' '...
2100                    '-q ' qstat_Queue ' '...
2101                    '-e ' fullfile([DirSGE '/job' num2str(currJobIndex) '.out']) ' '...
2102                    '-o ' fullfile([DirSGE '/job' num2str(currJobIndex) '.out']) ' '...
2103                    fullfile([DirSGE '/job' num2str(currJobIndex) '.sh'])];
2104                fprintf(sge_command); % display in command line
2105                [status, result] = system(sge_command);
2106                fprintf(result);
2107                currJobIndex = currJobIndex + 1;
2108                imgsInJob = [];
2109            end
2110            if(iprocess == length(batch_file_list))
2111                done = 1;
2112            end
2113            iprocess = iprocess + 1;
2114        end
2115        msgbox_uvmat('CONFIRMATION',[num2str(currJobIndex-1) ' jobs launched on queue ' qstat_Queue '.'])
2116    case 'python'
2117        command = ['LD_LIBRARY_PATH=$(echo $LD_LIBRARY_PATH | pyp "l = x.split('':''); l = [s for s in l if ''matlab'' not in s]; print('':''.join(l))") ' ...
2118            'python -m fluidimage.run_from_xml ' filexml{iprocess}];
2119        fprintf(['command:\n' command '\n\n'])
2120        system(command, '-echo');
2121end
2122if exist(OutputDir,'dir')
2123    [SUCCESS,MESSAGE,MESSAGEID] = fileattrib (OutputDir);
2124    if MESSAGE.GroupWrite~=1
2125    [success,msg] = fileattrib(OutputDir,'+w','g','s'); % allow writing access for the group of users, recursively in the folder
2126    if success==0
2127        msgbox_uvmat('WARNING',{['unable to set group write access to ' OutputDir ':']; msg}); % error message for directory creation
2128    end
2129    end
2130end
2131
2132%------------------------------------------------------------------------
2133function STOP_Callback(hObject, eventdata, handles)
2134%------------------------------------------------------------------------
2135set(handles.RUN, 'BusyAction','cancel')
2136set(handles.RUN,'BackgroundColor',[1 0 0])
2137set(handles.RUN,'enable','on')
2138set(handles.RUN, 'Value',0)
2139
2140%------------------------------------------------------------------------
2141% --- read parameters from the GUI series
2142%------------------------------------------------------------------------
2143function Param=read_GUI_series(handles)
2144
2145%% read raw parameters from the GUI series
2146Param=read_GUI(handles.series);
2147
2148%% clean the output structure by removing unused information
2149if isfield(Param,'Pairs')
2150    Param=rmfield(Param,'Pairs'); % info Pairs not needed for output
2151end
2152if isfield(Param,'InputLine')
2153    Param=rmfield(Param,'InputLine');
2154end
2155if isfield(Param,'EditObject')
2156    Param=rmfield(Param,'EditObject');
2157end
2158Param.IndexRange.TimeSource=Param.IndexRange.TimeTable{end,1};
2159Param.IndexRange=rmfield(Param.IndexRange,'TimeTable');
2160empty_line=false(size(Param.InputTable,1),1);
2161for iline=1:size(Param.InputTable,1)
2162    empty_line(iline)=isempty(cell2mat(Param.InputTable(iline,1:3)));
2163end
2164Param.InputTable(empty_line,:)=[];
2165
2166%------------------------------------------------------------------------
2167% --- Executes on selection change in ActionName.
2168function ActionName_Callback(hObject, eventdata, handles)
2169%------------------------------------------------------------------------
2170
2171%% stop any ongoing series processing
2172if isequal(get(handles.RUN,'Value'),1)
2173    answer= msgbox_uvmat('INPUT_Y-N','stop current Action process?');
2174    if strcmp(answer,'Yes')
2175        STOP_Callback(hObject, eventdata, handles)
2176    else
2177        return
2178    end
2179end
2180set(handles.ActionName,'BackgroundColor',[1 1 0])
2181huigetfile=findobj(allchild(0),'tag','status_display');
2182if ~isempty(huigetfile)
2183    delete(huigetfile)
2184end
2185drawnow
2186
2187%% get Action name and path
2188NbBuiltinAction=get(handles.Action,'UserData'); % nbre of functions initially proposed in the menu ActionName (as defined in the Opening fct of series)
2189ActionList=get(handles.ActionName,'String'); % list menu fields
2190ActionIndex=get(handles.ActionName,'Value');
2191if ~isequal(ActionIndex,1)% if we are not just opening series
2192    InputTable=get(handles.InputTable,'Data');
2193    if isempty(InputTable{1,4})
2194        msgbox_uvmat('ERROR','no input file available: use Open in the menu bar')
2195        return
2196    end
2197end
2198ActionName= ActionList{get(handles.ActionName,'Value')}; % selected function name
2199ActionPathList=get(handles.ActionName,'UserData'); % list of recorded paths to functions of the list ActionName
2200
2201%% add a new function to the menu if 'more...' has been selected in the menu ActionName
2202if isequal(ActionName,'more...')
2203    [FileName, PathName] = uigetfile( ...
2204        {'*.m', ' (*.m)';
2205        '*.m',  '.m files '; ...
2206        '*.*', 'All Files (*.*)'}, ...
2207        'Pick a series processing function ',get(handles.ActionPath,'String'));
2208    if length(FileName)<2
2209        return
2210    end
2211    [tild,ActionName,ActionExt]=fileparts(FileName);
2212   
2213    % insert the choice in the menu ActionName
2214    ActionIndex=find(strcmp(ActionName,ActionList),1); % look for the selected function in the menu Action
2215    PathName=regexprep(PathName,'/$','');
2216    if ~isempty(ActionIndex) && ~strcmp(ActionPathList{ActionIndex},PathName)%compare the path to the existing fct
2217        ActionIndex=[]; % the selected path is different than the recorded one
2218    end
2219    if isempty(ActionIndex)%the qselected fct (with selected path) does not exist in the menu
2220        ActionIndex= length(ActionList);
2221        ActionList=[ActionList(1:end-1);{ActionName};ActionList(end)]; % the selected function is appended in the menu, before the last item 'more...'
2222         ActionPathList=[ActionPathList; PathName];
2223    end
2224   
2225    % record the file extension and extend the path list if it is a new extension
2226    ActionExtList=get(handles.ActionExt,'String');
2227    ActionExtIndex=find(strcmp(ActionExt,ActionExtList), 1);
2228    if isempty(ActionExtIndex)
2229        set(handles.ActionExt,'String',[ActionExtList;{ActionExt}])
2230    end
2231
2232    % remove old Action options in the menu (keeping a menu length <nb_builtin_ACTION+5)
2233    if length(ActionList)>NbBuiltinAction+5; % nb_builtin_ACTION=nbre of functions always remaining in the initial menu
2234        nbremove=length(ActionList)-NbBuiltinAction-5;
2235        ActionList(NbBuiltinAction+1:end-5)=[];
2236        ActionPathList(NbBuiltinAction+1:end-4,:)=[];
2237        ActionIndex=ActionIndex-nbremove;
2238    end
2239   
2240    % record action menu, choice and path
2241    set(handles.ActionName,'Value',ActionIndex)
2242    set(handles.ActionName,'String',ActionList)
2243       set(handles.ActionName,'UserData',ActionPathList);
2244    set(handles.ActionExt,'Value',ActionExtIndex)
2245       
2246    %record the user defined menu additions in personal file profil_perso
2247    dir_perso=prefdir;
2248    profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
2249    if NbBuiltinAction+1<=numel(ActionList)-1
2250        ActionListUser=ActionList(NbBuiltinAction+1:numel(ActionList)-1);
2251        ActionPathListUser=ActionPathList(NbBuiltinAction+1:numel(ActionList)-1);
2252        ActionExtListUser={};
2253        if numel(ActionExtList)>2
2254            ActionExtListUser=ActionExtList(3:end);
2255        end
2256        if exist(profil_perso,'file')
2257            save(profil_perso,'ActionListUser','ActionPathListUser','ActionExtListUser','-append')
2258        else
2259            save(profil_perso,'ActionListUser','ActionPathListUser','ActionExtListUser','-V6')
2260        end
2261    end
2262end
2263
2264%% check the current ActionPath to the selected function
2265ActionPath=ActionPathList{ActionIndex}; % current recorded path
2266set(handles.ActionPath,'String',ActionPath); % show the path to the senlected function
2267
2268%% reinitialise the waitbar
2269update_waitbar(handles.Waitbar,0)
2270
2271%% Put the first line of the selected Action fct as tooltip help
2272try
2273    [fid,errormsg] =fopen([ActionName '.m']);
2274    InputText=textscan(fid,'%s',1,'delimiter','\n');
2275    fclose(fid);
2276    set(handles.ActionName,'ToolTipString',InputText{1}{1})% put the first line of the selected function as tooltip help
2277end
2278set(handles.ActionName,'BackgroundColor',[1 1 1])
2279set(handles.ActionInput,'BackgroundColor',[1 0 1])% set ActionInput button to magenta color to indicate that input refr
2280
2281
2282% --- Executes on button press in ActionInput.
2283function ActionInput_Callback(hObject, eventdata, handles)
2284
2285set(handles.ActionInput,'BackgroundColor',[1 1 0])
2286
2287%% create the function handle for Action
2288ActionPath=get(handles.ActionPath,'String');
2289ActionList=get(handles.ActionName,'String');
2290ActionName= ActionList{get(handles.ActionName,'Value')}; % selected function name
2291if ~exist(ActionPath,'dir')
2292    msgbox_uvmat('ERROR',['The prescribed function path ' ActionPath ' does not exist']);
2293    return
2294end
2295current_dir=pwd; % current working dir
2296cd(ActionPath)
2297h_fun=str2func(ActionName);
2298cd(current_dir)
2299
2300%% Activate the Action fct to adapt the configuration of the GUI series and bring specific parameters in SeriesData
2301Param=read_GUI_series(handles); % read the parameters from the GUI series
2302Param.Action.RUN=0;
2303ParamOut=h_fun(Param); % run the selected Action function to get the relevant input
2304
2305
2306%% Visibility of VelType and VelType_1 menus asked by ActionName
2307VelTypeRequest=1; % VelType requested by default
2308VelTypeRequest_1=1; % VelType requested by default
2309if isfield(ParamOut,'VelType')
2310    VelTypeRequest=ismember(ParamOut.VelType,{'on','one','two'});
2311    VelTypeRequest_1=strcmp( ParamOut.VelType,'two');
2312end
2313FieldNameRequest=0;  %hidden by default
2314FieldNameRequest_1=0;  %hidden by default
2315if isfield(ParamOut,'FieldName')
2316    FieldNameRequest=ismember(ParamOut.FieldName,{'on','one','two'});
2317    FieldNameRequest_1=strcmp( ParamOut.FieldName,'two');
2318end
2319
2320%% Detect the types of input files and set menus and default options in 'VelType'
2321SeriesData=get(handles.series,'UserData'); % info on the input file series
2322iview_civ=find(strcmp('civx',SeriesData.FileType)|strcmp('civdata',SeriesData.FileType));
2323iview_netcdf=find(strcmp('netcdf',SeriesData.FileType)|strcmp('civx',SeriesData.FileType)|strcmp('civdata',SeriesData.FileType)); % all nc files, icluding civ
2324FieldList=get(handles.FieldName,'String'); % previous list as default
2325if ~iscell(FieldList),FieldList={FieldList};end
2326FieldList_1=get(handles.FieldName_1,'String'); % previous list as default
2327if ~iscell(FieldList_1),FieldList_1={FieldList_1};end
2328%CheckList=0; % indicate whether FieldName has been updated
2329CheckList_1=1; % indicate whether FieldName_1 has been updated
2330handles_coord=[handles.Coord_x handles.Coord_y handles.Coord_z handles.Coord_x_title handles.Coord_y_title handles.Coord_z_title];
2331if VelTypeRequest && numel(iview_civ)>=1
2332    menu=set_veltype_display(SeriesData.FileInfo{iview_civ(1)}.CivStage,SeriesData.FileType{iview_civ(1)});
2333    set(handles.VelType,'Value',1)% set first choice by default
2334    set(handles.VelType,'String',[{'*'};menu])
2335    set(handles.VelType,'Visible','on')
2336    set(handles.VelType_title,'Visible','on')
2337    FieldList=[set_field_list('U','V');{'C'};{'get_field...'}]; % standard menu for civx data
2338    %CheckList=1;
2339    set(handles.FieldName,'Value',1); % velocity vector choice by default
2340    if  VelTypeRequest_1 && numel(iview_civ)>=2
2341        menu=set_veltype_display(SeriesData.FileInfo{iview_civ(2)}.CivStage,SeriesData.FileType{iview_civ(2)});
2342        set(handles.VelType_1,'Value',1)% set first choice by default
2343        set(handles.VelType_1,'String',[{'*'};menu])
2344        set(handles.VelType_1,'Visible','on')
2345        set(handles.VelType_title_1,'Visible','on')
2346        FieldList_1=[set_field_list('U','V');{'C'};{'get_field...'}]; % standard menu for civx data
2347        CheckList_1=1;
2348        set(handles.FieldName_1,'Value',1); % velocity vector choice by default
2349    else
2350        set(handles.VelType_1,'Visible','off')
2351        set(handles.VelType_title_1,'Visible','off')
2352    end
2353else
2354    set(handles.VelType,'Visible','off')
2355    set(handles.VelType_title,'Visible','off')
2356end
2357
2358%% Detect the types of input files and set menus and default options in 'FieldName'
2359if (FieldNameRequest || VelTypeRequest) && numel(iview_netcdf)>=1
2360    set(handles.InputFields,'Visible','on')% set the frame InputFields visible
2361    if FieldNameRequest && isfield(SeriesData.FileInfo{iview_netcdf(1)},'ListVarName')
2362        set(handles.FieldName,'Visible','on')
2363        ListVarName=SeriesData.FileInfo{iview_netcdf(1)}.ListVarName;
2364        ind_var=get(handles.FieldName,'Value'); % indices of previously selected variables
2365        for ilist=1:numel(ind_var)
2366            if isempty(find(strcmp(FieldList{ind_var(ilist)},ListVarName)))
2367                FieldList={}; % previous choice not consistent with new input field
2368                set(handles.FieldName,'Value',1)
2369                break
2370            end
2371        end
2372        if ~isempty(FieldList)
2373            if isempty(find(strcmp(get(handles.Coord_x,'String'),ListVarName)))||...
2374                    isempty(find(strcmp(get(handles.Coord_y,'String'),ListVarName)))
2375                FieldList={};
2376                set(handles.Coord_x,'String','')
2377                set(handles.Coord_y,'String','')
2378            end
2379            Coord_z=get(handles.Coord_z,'String');
2380            if ~isempty(Coord_z) && isempty(find(strcmp(Coord_z,ListVarName)))
2381                FieldList={};
2382                set(handles.Coord_z,'String','')
2383            end
2384        end
2385    else
2386        set(handles.FieldName,'Visible','off')
2387    end
2388   
2389    set(handles_coord,'Visible','on')
2390    FieldList=[FieldList;{'get_field...'}];
2391    if FieldNameRequest_1 && numel(iview_netcdf)>=2
2392        set(handles.FieldName_1,'Visible','on')
2393        if CheckList_1==0        % not civ input made
2394            ListVarName=SeriesData.FileInfo{iview_netcdf(2)}.ListVarName;
2395            ind_var=get(handles.FieldName,'Value'); % indices of previously selected variables
2396            for ilist=1:numel(ind_var)
2397                if isempty(find(strcmp(FieldList{ind_var(ilist)},ListVarName)))
2398                    FieldList_1={}; % previous choice not consistent with new input field
2399                    set(handles.FieldName_1,'Value',1)
2400                    break
2401                end
2402            end
2403            warn_coord=0;
2404            if isempty(find(strcmp(get(handles.Coord_x,'String'),ListVarName)))||...
2405                    isempty(find(strcmp(get(handles.Coord_y,'String'),ListVarName)))
2406                warn_coord=1;
2407            end
2408            if ~isempty(Coord_z) && isempty(find(strcmp(Coord_z,ListVarName)))
2409                FieldList_1={};
2410                warn_coord=1;
2411            end
2412            if warn_coord
2413                msgbox_uvmat('WARNING','coordinate names do not exist in the second netcdf input file')
2414            end
2415           
2416            set(handles.FieldName_1,'Visible','on')
2417            set(handles.FieldName_1,'Value',1)
2418            set(handles.FieldName_1,'String',FieldList_1)
2419        end
2420    else
2421        set(handles.FieldName_1,'Visible','off')
2422    end
2423    if isempty(FieldList)
2424        set(handles.FieldName,'Visible','off')
2425    else
2426        set(handles.FieldName,'Visible','on')
2427        set(handles.FieldName,'String',FieldList)
2428    end
2429else
2430    set(handles.InputFields,'Visible','off')
2431end
2432
2433%% Introduce visibility of file overwrite option
2434if isfield(ParamOut,'CheckOverwriteVisible')&& strcmp(ParamOut.CheckOverwriteVisible,'on')
2435    set(handles.CheckOverwrite,'Visible','on')
2436else
2437    set(handles.CheckOverwrite,'Visible','off')
2438end
2439
2440%% Check whether alphabetical sorting of input Subdir is allowed by the Action fct  (for multiples series entries)
2441if isfield(ParamOut,'AllowInputSort')&&isequal(ParamOut.AllowInputSort,'on')&& size(Param.InputTable,1)>1
2442    [tild,iview]=sort(Param.InputTable(:,2)); % subdirectories sorted in alphabetical order
2443    set(handles.InputTable,'Data',Param.InputTable(iview,:));
2444    MinIndex_i=get(handles.MinIndex_i,'Data');
2445    MinIndex_j=get(handles.MinIndex_j,'Data');
2446    MaxIndex_i=get(handles.MaxIndex_i,'Data');
2447    MaxIndex_j=get(handles.MaxIndex_j,'Data');
2448    set(handles.MinIndex_i,'Data',MinIndex_i(iview,:));
2449    set(handles.MinIndex_j,'Data',MinIndex_j(iview,:));
2450    set(handles.MaxIndex_i,'Data',MaxIndex_i(iview,:));
2451    set(handles.MaxIndex_j,'Data',MaxIndex_j(iview,:));
2452    TimeTable=get(handles.TimeTable,'Data');
2453    set(handles.TimeTable,'Data',TimeTable(iview,:));
2454    PairString=get(handles.PairString,'Data');
2455    set(handles.PairString,'Data',PairString(iview,:));
2456end
2457
2458%% Impose the whole input file index range if requested
2459if isfield(ParamOut,'WholeIndexRange')&&isequal(ParamOut.WholeIndexRange,'on')
2460    MinIndex_i=get(handles.MinIndex_i,'Data');
2461    MinIndex_j=get(handles.MinIndex_j,'Data');
2462    MaxIndex_i=get(handles.MaxIndex_i,'Data');
2463    MaxIndex_j=get(handles.MaxIndex_j,'Data');
2464    set(handles.num_first_i,'String',num2str(MinIndex_i(1)))% set first as the min index (for the first line)
2465    set(handles.num_last_i,'String',num2str(MaxIndex_i(1)))% set last as the max index (for the first line)
2466    set(handles.num_incr_i,'String','1')
2467    set(handles.num_first_j,'String',num2str(MinIndex_j(1)))% set first as the min index (for the first line)
2468    set(handles.num_last_j,'String',num2str(MaxIndex_j(1)))% set last as the max index (for the first line)
2469    set(handles.num_incr_j,'String','1')
2470else  % check index ranges
2471    first_i=1;last_i=1;first_j=1;last_j=1;
2472    if isfield(Param.IndexRange,'first_i')
2473        first_i=Param.IndexRange.first_i;
2474        last_i=Param.IndexRange.last_i;
2475    end
2476    if isfield(Param.IndexRange,'first_j')
2477        first_j=Param.IndexRange.first_j;
2478        last_j=Param.IndexRange.last_j;
2479    end
2480    if last_i < first_i || last_j < first_j , msgbox_uvmat('ERROR','last field number must be larger than the first one'),...
2481            set(handles.RUN, 'Enable','On'), set(handles.RUN,'BackgroundColor',[1 0 0]),return,end;
2482end
2483
2484%% enable or desable j index visibility
2485status_j='on'; % default
2486if isempty(find(~cellfun(@isempty,SeriesData.j1_series), 1)); % case of empty j indices
2487    status_j='off'; % no j index needed
2488elseif strcmp(get(handles.PairString,'Visible'),'on')
2489    check_burst=cellfun(@isempty,regexp(get(handles.PairString,'Data'),'^j')); % =0 for burst case, 1 otherwise
2490    if isempty(find(check_burst, 1))% if all pair string begins by j (burst)
2491        status_j='off'; % no j index needed for bust case
2492    end
2493end
2494enable_j(handles,status_j) % no j index needed
2495if isfield(ParamOut,'j_index_1')&& isfield(ParamOut,'j_index_2')%strcmp(ParamOut.Desable_j_index,'on')
2496    %status_j='off';
2497    set(handles.num_first_j,'String',num2str(ParamOut.j_index_1))
2498    set(handles.num_last_j,'String',num2str(ParamOut.j_index_2))
2499    set(handles.num_first_j,'enable','off')
2500    set(handles.num_last_j,'enable','off')
2501    set(handles.num_incr_j,'visible','off')
2502else
2503    set(handles.num_first_j,'enable','on')
2504    set(handles.num_last_j,'enable','on')
2505    set(handles.num_incr_j,'visible',status_j)
2506end
2507
2508%% NbSlice visibility
2509if isfield(ParamOut,'NbSlice') && (strcmp(ParamOut.NbSlice,'on')||isnumeric(ParamOut.NbSlice))
2510    set(handles.num_NbSlice,'Visible','on')
2511    set(handles.NbSlice_title,'Visible','on')
2512else
2513    set(handles.num_NbSlice,'Visible','off')
2514    set(handles.NbSlice_title,'Visible','off')
2515end
2516if isfield(ParamOut,'NbSlice') && isnumeric(ParamOut.NbSlice)
2517    set(handles.num_NbSlice,'String',num2str(ParamOut.NbSlice))
2518    set(handles.num_NbSlice,'Enable','off'); % NbSlice set by the activation of the Action function
2519else
2520    set(handles.num_NbSlice,'Enable','on'); % NbSlice can be modified on the GUI series
2521end
2522
2523%% Visibility of FieldTransform menu
2524FieldTransformVisible='off';  %hidden by default
2525if isfield(ParamOut,'FieldTransform')
2526    if ~strcmp(ParamOut.FieldTransform,'off')
2527    FieldTransformVisible='on'; 
2528    end
2529    if iscell(ParamOut.FieldTransform)
2530        SeriesData.TransformList=ParamOut.FieldTransform;
2531    end
2532    TransformName_Callback([],[], handles)
2533end
2534set(handles.FieldTransform,'Visible',FieldTransformVisible)
2535if isfield(ParamOut,'TransformPath');% record the path of transform function requested for compilation
2536    set(handles.TransformPath,'UserData',ParamOut.TransformPath)
2537else
2538    set(handles.TransformPath,'UserData',[])
2539end
2540
2541%% Visibility of projection object
2542ProjObjectVisible='off';  %hidden by default
2543if isfield(ParamOut,'ProjObject')
2544    ProjObjectVisible=ParamOut.ProjObject;
2545end
2546set(handles.CheckObject,'Visible',ProjObjectVisible)
2547if ~get(handles.CheckObject,'Value')
2548    ProjObjectVisible='off';
2549end
2550set(handles.ProjObject,'Visible',ProjObjectVisible)
2551set(handles.DeleteObject,'Visible',ProjObjectVisible)
2552set(handles.ViewObject,'Visible',ProjObjectVisible)
2553set(handles.EditObject,'Visible',ProjObjectVisible)
2554
2555%% Visibility of mask input
2556MaskVisible='off';  %hidden by default
2557if isfield(ParamOut,'Mask')
2558    MaskVisible=ParamOut.Mask;
2559end
2560set(handles.CheckMask,'Visible',MaskVisible);
2561
2562%% definition of the directory containing the output files
2563if  ~(isfield(SeriesData,'ActionName') && strcmp(ActionName,SeriesData.ActionName))
2564    OutputDirExt='.series'; % default
2565    if isfield(ParamOut,'OutputDirExt')&&~isempty(ParamOut.OutputDirExt)
2566        OutputDirExt=ParamOut.OutputDirExt;
2567    end
2568    set(handles.OutputDirExt,'String',OutputDirExt)
2569end
2570OutputDirVisible='off';
2571OutputSubDirMode='auto'; % default
2572SubDirOut='';
2573if isfield(ParamOut,'OutputSubDirMode')
2574    OutputSubDirMode=ParamOut.OutputSubDirMode;
2575end
2576InputTable=get(handles.InputTable,'Data');
2577switch OutputSubDirMode
2578    case 'auto'; % default
2579        OutputDirVisible='on';
2580        SubDir=InputTable(1:end,2); % set of subdirectories
2581        SubDirOut=SubDir{1};
2582        if numel(SubDir)>1
2583            for ilist=2:numel(SubDir)
2584                SubDirOut=[SubDirOut '-' regexprep(SubDir{ilist},'^/','')];
2585            end
2586        end
2587    case 'one'
2588        OutputDirVisible='on';
2589        SubDirOut=InputTable{1,2}; % use the first subdir name (+OutputDirExt) as output  subdirectory
2590    case 'two'
2591        OutputDirVisible='on';   
2592        SubDir=InputTable(1:2,2); % set of subdirectories
2593        SubDirOut=SubDir{1};
2594        if numel(SubDir)>1
2595                SubDirOut=[SubDirOut '-' regexprep(SubDir{2},'^/','')];
2596        end
2597    case 'last'
2598        OutputDirVisible='on';
2599        SubDirOut=InputTable{end,2}; % use the last subdir name (+OutputDirExt) as output  subdirectory
2600end
2601set(handles.OutputSubDir,'String',SubDirOut)
2602set(handles.OutputSubDir,'BackgroundColor',[1 1 1])% set edit box to white color to indicate refreshment
2603set(handles.OutputDirExt,'Visible',OutputDirVisible)
2604set(handles.OutputSubDir,'Visible',OutputDirVisible)
2605%set(handles.CheckOverwrite,'Visible',OutputDirVisible)
2606set(handles.OutputDir_title,'Visible',OutputDirVisible)
2607SeriesData.ActionName=ActionName; % record ActionName for next use
2608
2609
2610%% visibility of the run mode (local or background or cluster)
2611if strcmp(OutputSubDirMode,'none')
2612    RunModeVisible='off'; % only local mode available if no output file is produced
2613else
2614    RunModeVisible='on';
2615end
2616set(handles.RunMode,'Visible',RunModeVisible)
2617set(handles.ActionExt,'Visible',RunModeVisible)
2618set(handles.RunMode_title,'Visible',RunModeVisible)
2619set(handles.ActionExt_title,'Visible',RunModeVisible)
2620
2621
2622%% Expected nbre of output files
2623if isfield(ParamOut,'OutputFileMode')
2624    StatusData.OutputFileMode=ParamOut.OutputFileMode;
2625    set(handles.status,'UserData',StatusData)
2626end
2627
2628%% definition of an additional parameter set, determined by an ancillary GUI
2629if isfield(ParamOut,'ActionInput')
2630%     set(handles.ActionInput,'Visible','on')
2631    ParamOut.ActionInput.Program=ActionName; % record the program in ActionInput
2632    SeriesData.ActionInput=ParamOut.ActionInput;
2633else
2634%     set(handles.ActionInput,'Visible','off')
2635    if isfield(SeriesData,'ActionInput')
2636        SeriesData=rmfield(SeriesData,'ActionInput');
2637    end
2638end
2639set(handles.series,'UserData',SeriesData)
2640set(handles.ActionInput,'BackgroundColor',[1 0 0])
2641
2642%------------------------------------------------------------------------
2643% --- Executes on selection change in FieldName.
2644function FieldName_Callback(hObject, eventdata, handles)
2645%------------------------------------------------------------------------
2646field_str=get(handles.FieldName,'String');
2647field_index=get(handles.FieldName,'Value');
2648field=field_str{field_index(1)};
2649if isequal(field,'get_field...')
2650    SeriesData=get(handles.series,'UserData');
2651    % input line for which the field choice is relevant
2652    iview=find(ismember(SeriesData.FileType,{'netcdf','civx','civdata'})); % all nc files, icluding civ
2653    hget_field=findobj(allchild(0),'name','get_field');
2654    if ~isempty(hget_field)
2655        delete(hget_field)%delete opened versions of get_field
2656    end
2657    Param=read_GUI(handles.series);
2658    InputTable=Param.InputTable(iview,:);
2659    % check the existence of the first file in the series
2660    first_j=[];last_j=[];MinIndex_j=1;MaxIndex_j=1; % default setting for index j
2661    if isfield(Param.IndexRange,'first_j'); % if index j is used     
2662        first_j=Param.IndexRange.first_j;
2663        last_j=Param.IndexRange.last_j;
2664        MinIndex_j=Param.IndexRange.MinIndex_j(iview);
2665        MaxIndex_j=Param.IndexRange.MaxIndex_j(iview);
2666    end
2667    PairString='';
2668    if isfield(Param.IndexRange,'PairString'); PairString=Param.IndexRange.PairString{iview}; end
2669    [i1,i2,j1,j2] = get_file_index(Param.IndexRange.first_i,first_j,PairString);
2670    LineIndex=iview(1);
2671    if numel(iview)>1     
2672        answer=msgbox_uvmat('INPUT_TXT',['select the line of the input table:' num2str(iview)] ,num2str(iview(1)));
2673        LineIndex=str2num(answer);
2674%         InputLine=str2num(get(handles.InputLine,'String'));
2675%         if ismember(InputLine,iview)
2676%             LineIndex=InputLine;
2677%         end
2678    end
2679    FirstFileName=fullfile_uvmat(InputTable{LineIndex,1},InputTable{LineIndex,2},InputTable{LineIndex,3},...
2680        InputTable{LineIndex,5},InputTable{LineIndex,4},i1,i2,j1,j2);
2681    if exist(FirstFileName,'file')
2682        ParamIn.Title='get_field: pick input variables and coordinates for series processing';
2683        ParamIn.SeriesInput=1;
2684        GetFieldData=get_field(FirstFileName,ParamIn);
2685        FieldList={};
2686        if isfield(GetFieldData,'FieldOption')% if a field has been selected
2687        switch GetFieldData.FieldOption
2688            case 'vectors'
2689                UName=GetFieldData.PanelVectors.vector_x;
2690                VName=GetFieldData.PanelVectors.vector_y;
2691                YName={GetFieldData.Coordinates.Coord_y};
2692                FieldList={['vec(' UName ',' VName ')'];...
2693                    ['norm(' UName ',' VName ')'];...
2694                    UName;VName};
2695            case {'scalar'}
2696                FieldList=GetFieldData.PanelScalar.scalar;
2697                YName={GetFieldData.Coordinates.Coord_y};
2698                if ischar(FieldList)
2699                    FieldList={FieldList};
2700                end
2701            case 'civdata...'
2702                FieldList=[set_field_list('U','V') ;{'C'}];
2703                set(handles.FieldName,'Value',1) % set menu to 'velocity
2704                XName='X';
2705                YName='y';
2706        end
2707        set(handles.FieldName,'Value',1)
2708        set(handles.FieldName,'String',[FieldList; {'get_field...'}]);
2709        if ~strcmp(GetFieldData.FieldOption,'civdata...')
2710           if ~isempty(regexp(FieldList{1},'^vec'))
2711                set(handles.FieldName,'Value',1)
2712           else
2713                set(handles.FieldName,'Value',1:numel(FieldList))%select all input fields by default
2714           end
2715            XName=GetFieldData.Coordinates.Coord_x;
2716            YName=GetFieldData.Coordinates.Coord_y;
2717            TimeNameStr=GetFieldData.Time.SwitchVarIndexTime;
2718            % get the time info                     
2719            TimeTable=get(handles.TimeTable,'Data');
2720            switch TimeNameStr
2721                case 'file index'
2722                    TimeName='';
2723                case 'attribute'
2724                    TimeName=['att:' GetFieldData.Time.TimeName];
2725                    % update the time table
2726                    TimeTable{LineIndex,2}=get_time(Param.IndexRange.MinIndex_i(LineIndex),MinIndex_j,PairString,InputTable,SeriesData.FileInfo{LineIndex},GetFieldData.Time.TimeName);  % Min time     
2727                    TimeTable{LineIndex,3}=get_time(Param.IndexRange.first_i,first_j,PairString,InputTable,SeriesData.FileInfo{LineIndex},GetFieldData.Time.TimeName);  % first time             
2728                    TimeTable{LineIndex,4}=get_time(Param.IndexRange.last_i,last_j,PairString,InputTable,SeriesData.FileInfo{LineIndex},GetFieldData.Time.TimeName);  % last time                     
2729                    TimeTable{LineIndex,5}=get_time(Param.IndexRange.MaxIndex_i(LineIndex),MaxIndex_j,PairString,InputTable,SeriesData.FileInfo{LineIndex},GetFieldData.Time.TimeName);  % Max time
2730                case 'variable'
2731                    set(handles.TimeName,'String',['var:' GetFieldData.Time.TimeName])
2732                    set(handles.NomType,'String','*')
2733                    set(handles.RootFile,'String',[get(handles.RootFile,'String') get(handles.FileIndex,'String')])% A VERIFIER !!!!!!
2734                    set(handles.FileIndex,'String','')
2735                    ParamIn.TimeVarName=GetFieldData.Time.TimeName;
2736                case 'matrix_index'
2737                    TimeName=['dim:' GetFieldData.Time.TimeName];
2738                    set(handles.NomType,'String','*')
2739                    set(handles.RootFile,'String',[get(handles.RootFile,'String') get(handles.FileIndex,'String')])
2740                    set(handles.FileIndex,'String','')
2741                    ParamIn.TimeDimName=GetFieldData.Time.TimeName;
2742            end
2743            TimeTable{LineIndex,1}=TimeName;
2744            set(handles.TimeTable,'Data',TimeTable);
2745        end
2746        set(handles.Coord_x,'String',XName)
2747        set(handles.Coord_y,'String',YName)
2748        set(handles.Coord_x,'Visible','on')
2749        set(handles.Coord_y,'Visible','on')
2750        end
2751    else
2752        msgbox_uvmat('ERROR',[FirstFileName ' does not exist'])
2753    end
2754end
2755
2756
2757function [TimeValue,DtValue]=get_time(ref_i,ref_j,PairString,InputTable,FileInfo,TimeName,DtName)
2758[i1,i2,j1,j2] = get_file_index(ref_i,ref_j,PairString);
2759FileName=fullfile_uvmat(InputTable{1},InputTable{2},InputTable{3},InputTable{5},InputTable{4},i1,i2,j1,j2);
2760Data=nc2struct(FileName,[]);
2761TimeValue=[];
2762DtValue=[];
2763if isequal(FileInfo.FileType,'civdata')
2764    if ismember(TimeName,{'civ1','filter1'})
2765        if isfield(Data,'Civ1_Time')
2766        TimeValue=Data.Civ1_Time;
2767        end
2768        if isfield(Data,'Civ1_Dt')
2769        DtValue=Data.Civ1_Dt;
2770        end
2771    else
2772        if isfield(Data,'Civ2_Time')
2773        TimeValue=Data.Civ2_Time;
2774        end
2775        if isfield(Data,'Civ2_Dt')
2776        DtValue=Data.Civ2_Dt;
2777        end
2778    end
2779else
2780    if ~isempty(TimeName)&& isfield(Data,TimeName)
2781        TimeValue=Data.(TimeName);
2782    end
2783    if exist('DtName','var') && isfield(Data,DtName)
2784        DtValue=Data.(DtName);
2785    end
2786end
2787
2788%------------------------------------------------------------------------
2789% --- Executes on selection change in FieldName_1.
2790function FieldName_1_Callback(hObject, eventdata, handles)
2791%------------------------------------------------------------------------
2792field_str=get(handles.FieldName_1,'String');
2793field_index=get(handles.FieldName_1,'Value');
2794field=field_str{field_index(1)};
2795if isequal(field,'get_field...')
2796    hget_field=findobj(allchild(0),'name','get_field');
2797    if ~isempty(hget_field)
2798        delete(hget_field)%delete opened versions of get_field
2799    end
2800    Param=read_GUI(handles.series);
2801    Param.InputTable=Param.InputTable(1,:);
2802    % check the existence of the first file in the series
2803    first_j=[];
2804    if isfield(Param.IndexRange,'first_j'); first_j=Param.IndexRange.first_j; end
2805    if isfield(Param.IndexRange,'last_j'); last_j=Param.IndexRange.last_j; end
2806    PairString='';
2807    if isfield(Param.IndexRange,'PairString'); PairString=Param.IndexRange.PairString; end
2808    [i1,i2,j1,j2] = get_file_index(Param.IndexRange.first_i,first_j,PairString);
2809    FirstFileName=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},...
2810        Param.InputTable{1,5},Param.InputTable{1,4},i1,i2,j1,j2);
2811    if exist(FirstFileName,'file')
2812        ParamIn.SeriesInput=1;
2813        GetFieldData=get_field(FirstFileName,ParamIn);
2814        FieldList={};
2815        switch GetFieldData.FieldOption
2816            case 'vectors'
2817                UName=GetFieldData.PanelVectors.vector_x;
2818                VName=GetFieldData.PanelVectors.vector_y;
2819                FieldList={['vec(' UName ',' VName ')'];...
2820                    ['norm(' UName ',' VName ')'];...
2821                    UName;VName};
2822            case {'scalar','pick variables'}
2823                FieldList=GetFieldData.PanelScalar.scalar;
2824                if ischar(FieldList)
2825                    FieldList={FieldList};
2826                end
2827            case '1D plot'
2828
2829            case 'civdata...'
2830                FieldList=set_field_list('U','V','C');
2831                set(handles.FieldName,'Value',2) % set menu to 'velocity
2832        end
2833        if ~strcmp(GetFieldData.FieldOption,'civdata...')
2834            TimeNameStr=GetFieldData.Time.SwitchVarIndexTime;
2835            switch TimeNameStr
2836                case 'file index'
2837                    set(handles.TimeName,'String','');
2838                case 'attribute'
2839                    set(handles.TimeName,'String',['att:' GetFieldData.Time.TimeName]);
2840                case 'variable'
2841                    set(handles.TimeName,'String',['var:' GetFieldData.Time.TimeName])
2842                    set(handles.NomType,'String','*')
2843                    set(handles.RootFile,'String',[get(handles.RootFile,'String') get(handles.FileIndex,'String')])% A VERIFIER !!!!!!
2844                    set(handles.FileIndex,'String','')
2845                    ParamIn.TimeVarName=GetFieldData.Time.TimeName;
2846                case 'matrix_index'
2847                    set(handles.TimeName,'String',['dim:' GetFieldData.Time.TimeName]);
2848                    set(handles.NomType,'String','*')
2849                    set(handles.RootFile,'String',[get(handles.RootFile,'String') get(handles.FileIndex,'String')])
2850                    set(handles.FileIndex,'String','')
2851                    ParamIn.TimeDimName=GetFieldData.Time.TimeName;
2852            end
2853        end
2854        set(handles.FieldName_1,'Value',1)
2855        set(handles.FieldName_1,'String',[FieldList; {'get_field...'}]);
2856    end
2857end   
2858
2859
2860%%%%%%%%%%%%%
2861function [ind_remove]=find_pairs(dirpair,ind_i,last_i)
2862indsel=ind_i;
2863indiff=diff(ind_i); % test index increment to detect multiplets (several pairs with the same index ind_i) and holes in the series
2864indiff=[1 indiff last_i-ind_i(end)+1]; % for testing gaps with the imposed bounds
2865if ~isempty(indiff)
2866    indiff2=diff(indiff);
2867    indiffp=[indiff2 1];
2868    indiffm=[1 indiff2];
2869    ind_multi_m=find((indiff==0)&(indiffm<0))-1; % indices of first members of multiplets
2870    ind_multi_p=find((indiff==0)&(indiffp>0)); % indices of last members of multiplets
2871    %for each multiplet, select the most recent file
2872    ind_remove=[];
2873    for i=1:length(ind_multi_m)
2874        ind_pairs=ind_multi_m(i):ind_multi_p(i);
2875        for imulti=1:length(ind_pairs)
2876            datepair(imulti)=datenum(dirpair(ind_pairs(imulti)).date); % dates of creation
2877        end
2878        [datenew,indsort2]=sort(datepair); % sort the multiplet by creation date
2879        ind_s=indsort2(1:end-1); %
2880        ind_remove=[ind_remove ind_pairs(ind_s)]; % remove these indices, leave the last one
2881    end
2882end
2883
2884%------------------------------------------------------------------------
2885% --- determine the list of index pairstring of processing file
2886function [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)
2887%------------------------------------------------------------------------
2888num_i1=num_i; % set of first image numbers by default
2889num_i2=num_i;
2890num_j1=num_j;
2891num_j2=num_j;
2892num_i_out=num_i;
2893num_j_out=num_j;
2894% if isequal (NomType,'_1-2_1') || isequal (NomType,'_1-2')
2895if isequal(mode,'series(Di)')
2896    num_i1_line=num_i+ind_shift(3); % set of first image numbers
2897    num_i2_line=num_i+ind_shift(4);
2898    % adjust the first and last field number
2899        indsel=find(num_i1_line >= 1);
2900    num_i_out=num_i(indsel);
2901    num_i1_line=num_i1_line(indsel);
2902    num_i2_line=num_i2_line(indsel);
2903    num_j1=meshgrid(num_j,ones(size(num_i1_line)));
2904    num_j2=meshgrid(num_j,ones(size(num_i1_line)));
2905    [xx,num_i1]=meshgrid(num_j,num_i1_line);
2906    [xx,num_i2]=meshgrid(num_j,num_i2_line);
2907elseif isequal (mode,'series(Dj)')||isequal (mode,'bursts')
2908    if isequal(mode,'bursts') %case of bursts (png_old or png_2D)
2909        num_j1=ind_shift(1)*ones(size(num_i));
2910        num_j2=ind_shift(2)*ones(size(num_i));
2911    else
2912        num_j1_col=num_j+ind_shift(1); % set of first image numbers
2913        num_j2_col=num_j+ind_shift(2);
2914        % adjust the first field number
2915        indsel=find((num_j1_col >= 1));   
2916        num_j_out=num_j(indsel);
2917        num_j1_col=num_j1_col(indsel);
2918        num_j2_col=num_j2_col(indsel);
2919        [num_i1,num_j1]=meshgrid(num_i,num_j1_col);
2920        [num_i2,num_j2]=meshgrid(num_i,num_j2_col);
2921    end   
2922end
2923
2924%------------------------------------------------------------------------
2925% --- Executes on button press in CheckObject.
2926function CheckObject_Callback(hObject, eventdata, handles)
2927%------------------------------------------------------------------------
2928hset_object=findobj(allchild(0),'tag','set_object'); % find the set_object interface handle
2929if get(handles.CheckObject,'Value')
2930    SeriesData=get(handles.series,'UserData');
2931    if isfield(SeriesData,'ProjObject') && ~isempty(SeriesData.ProjObject)
2932        set(handles.ViewObject,'Value',1)
2933        ViewObject_Callback(hObject, eventdata, handles)
2934    else
2935        if ishandle(hset_object)
2936            uistack(hset_object,'top')% show the GUI set_object if opened
2937        else
2938            %get the object file
2939            InputTable=get(handles.InputTable,'Data');
2940            defaultname=InputTable{1,1};
2941            if isempty(defaultname)
2942                defaultname={''};
2943            end
2944            fileinput=uigetfile_uvmat('pick a xml object file (or use uvmat to create it)',defaultname,'.xml');
2945            if isempty(fileinput)% exit if no object file is selected
2946                set(handles.CheckObject,'Value',0)
2947                return
2948            end
2949            %read the file
2950            data=xml2struct(fileinput);
2951            if ~isfield(data,'Type')
2952                msgbox_uvmat('ERROR',[fileinput ' is not an object xml file'])
2953                set(handles.CheckObject,'Value',0)
2954                return
2955            end
2956            if ~isfield(data,'ProjMode')
2957                data.ProjMode='none';
2958            end
2959            hset_object=set_object(data); % call the set_object interface
2960            set(hset_object,'Name','set_object_series')% name to distinguish from set_object used with uvmat
2961        end
2962        ProjObject=read_GUI(hset_object);
2963        set(handles.ProjObject,'String',ProjObject.Name); % display the object name
2964        SeriesData=get(handles.series,'UserData');
2965        SeriesData.ProjObject=ProjObject;
2966        set(handles.series,'UserData',SeriesData);
2967    end
2968    set(handles.EditObject,'Visible','on');
2969    set(handles.DeleteObject,'Visible','on');
2970    set(handles.ViewObject,'Visible','on');
2971    set(handles.ProjObject,'Visible','on');
2972else
2973    set(handles.EditObject,'Visible','off');
2974    set(handles.DeleteObject,'Visible','off');
2975    set(handles.ViewObject,'Visible','off');
2976    if ~ishandle(hset_object)
2977        set(handles.ViewObject,'Value',0);
2978    end
2979    set(handles.ProjObject,'Visible','off');
2980end
2981
2982%------------------------------------------------------------------------
2983% --- Executes on button press in ViewObject.
2984%------------------------------------------------------------------------
2985function ViewObject_Callback(hObject, eventdata, handles)
2986
2987UserData=get(handles.series,'UserData');
2988hset_object=findobj(allchild(0),'Tag','set_object');
2989if ~isempty(hset_object)
2990    delete(hset_object)% refresh set_object if already opened
2991end
2992hset_object=set_object(UserData.ProjObject);
2993set(hset_object,'Name','view_object_series')
2994
2995
2996%------------------------------------------------------------------------
2997% --- Executes on button press in EditObject.
2998function EditObject_Callback(hObject, eventdata, handles)
2999%------------------------------------------------------------------------
3000if get(handles.EditObject,'Value')
3001    set(handles.ViewObject,'Value',0)
3002    UserData=get(handles.series,'UserData');
3003    hset_object=set_object(UserData.ProjObject);
3004    set(hset_object,'Name','edit_object_series')
3005    set(get(hset_object,'Children'),'Enable','on')
3006else
3007    hset_object=findobj(allchild(0),'Tag','set_object');
3008    if ~isempty(hset_object)
3009        set(get(hset_object,'Children'),'Enable','off')
3010    end
3011end
3012
3013%------------------------------------------------------------------------
3014% --- Executes on button press in DeleteObject.
3015function DeleteObject_Callback(hObject, eventdata, handles)
3016%------------------------------------------------------------------------
3017SeriesData=get(handles.series,'UserData');
3018SeriesData.ProjObject=[];
3019set(handles.series,'UserData',SeriesData)
3020set(handles.ProjObject,'String','')
3021set(handles.ProjObject,'Visible','off')
3022set(handles.CheckObject,'Value',0)
3023set(handles.ViewObject,'Visible','off')
3024set(handles.EditObject,'Visible','off')
3025hset_object=findobj(allchild(0),'name','set_object_series');
3026if ~isempty(hset_object)
3027    delete(hset_object)
3028end
3029set(handles.DeleteObject,'Visible','off')
3030
3031%------------------------------------------------------------------------
3032% --- Executed when CheckMask is activated
3033%------------------------------------------------------------------------
3034function CheckMask_Callback(hObject, eventdata, handles)
3035
3036if get(handles.CheckMask,'Value')
3037    InputTable=get(handles.InputTable,'Data');
3038    nbview=size(InputTable,1);
3039    MaskTable=cell(nbview,1); % default
3040    ListMask=cell(nbview,1); % default
3041    MaskData=get(handles.MaskTable,'Data');
3042    MaskData(size(MaskData,1):nbview,1)=cell(size(MaskData,1):nbview,1); % complement if undefined lines
3043    for iview=1:nbview
3044        ListMask{iview,1}=num2str(iview);
3045        RootPath=InputTable{iview,1};
3046        if ~isempty(RootPath)
3047            if isempty(MaskData{iview})
3048                SubDir=InputTable{iview,2};
3049                MaskPath=fullfile(RootPath,[regexprep(SubDir,'\..*','') '.mask']); % take the root part of SubDir, before the first dot '.'
3050                if exist(MaskPath,'dir')
3051                    ListStruct=dir(MaskPath); % look for a mask file
3052                    ListCells=struct2cell(ListStruct); % transform dir struct to a cell arrray
3053                    check_dir=cell2mat(ListCells(4,:)); % =1 for directories, =0 for files
3054                    ListFiles=ListCells(1,:); % list of file and dri names
3055                    ListFiles=ListFiles(~check_dir); % list of file names (excluding dir)
3056                    mdetect=0;
3057                    if ~isempty(ListFiles)
3058                        for ifile=1:numel(ListFiles)
3059                            [tild,tild,MaskFile{ifile},i1_series,i2_series,j1_series,j2_series,MaskNomType,MaskFileType]=find_file_series(MaskPath,ListFiles{ifile},0);
3060                            if strcmp(MaskFileType,'image') && isempty(i2_series) && isempty(j2_series)
3061                                mdetect=1;
3062                                MaskName=ListFiles{ifile};
3063                            end
3064                            if ~strcmp(MaskFile{ifile},MaskFile{1})
3065                                mdetect=0; % cancel detection test in case of multiple masks, use the brower for selection
3066                                break
3067                            end
3068                        end
3069                    end
3070                    if mdetect==1
3071                        MaskName=fullfile(MaskPath,'mask_1.png');
3072                    else
3073                        MaskName=uigetfile_uvmat('select a mask file:',MaskPath,'image');
3074                    end
3075                else
3076                    MaskName=uigetfile_uvmat('select a mask file:',RootPath,'image');
3077                end
3078                MaskTable{iview,1}=MaskName ;
3079                ListMask{iview,1}=num2str(iview);
3080            end
3081        end
3082    end
3083    set(handles.MaskTable,'Data',MaskTable)
3084    set(handles.MaskTable,'Visible','on')
3085    set(handles.MaskBrowse,'Visible','on')
3086    set(handles.ListMask,'Visible','on')
3087    set(handles.ListMask,'String',ListMask)
3088    set(handles.ListMask,'Value',1)
3089else
3090    set(handles.MaskTable,'Visible','off')
3091    set(handles.MaskBrowse,'Visible','off')
3092    set(handles.ListMask,'Visible','off')
3093end
3094
3095%------------------------------------------------------------------------
3096% --- Executes on button press in MaskBrowse.
3097%------------------------------------------------------------------------
3098function MaskBrowse_Callback(hObject, eventdata, handles)
3099
3100InputTable=get(handles.InputTable,'Data');
3101iview=get(handles.ListMask,'Value');
3102RootPath=InputTable{iview,1};
3103MaskName=uigetfile_uvmat('select a mask file:',RootPath,'image');
3104if ~isempty(MaskName)
3105    MaskTable=get(handles.MaskTable,'Data');
3106    MaskTable{iview,1}=MaskName ;
3107    set(handles.MaskTable,'Data',MaskTable)
3108end
3109
3110%------------------------------------------------------------------------
3111% --- Executes when selected cell(s) is changed in MaskTable.
3112%------------------------------------------------------------------------
3113function MaskTable_CellSelectionCallback(hObject, eventdata, handles)
3114
3115if numel(eventdata.Indices)>=1
3116set(handles.ListMask,'Value',eventdata.Indices(1))
3117end
3118
3119%-------------------------------------------------------------------
3120function MenuHelp_Callback(hObject, eventdata, handles)
3121%-------------------------------------------------------------------
3122
3123
3124% path_to_uvmat=which ('uvmat'); % check the path of uvmat
3125% pathelp=fileparts(path_to_uvmat);
3126% helpfile=fullfile(pathelp,'uvmat_doc','uvmat_doc.html');
3127% 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')
3128% else
3129%     addpath (fullfile(pathelp,'uvmat_doc'))
3130%     web([helpfile '#series'])
3131% end
3132
3133%-------------------------------------------------------------------
3134% --- Executes on selection change in TransformName.
3135function TransformName_Callback(hObject, eventdata, handles)
3136%----------------------------------------------------------------------
3137TransformList=get(handles.TransformName,'String');
3138TransformIndex=get(handles.TransformName,'Value');
3139TransformName=TransformList{TransformIndex};
3140TransformPathList=get(handles.TransformName,'UserData');
3141nb_builtin_transform=4;
3142if isequal(TransformName,'more...');     
3143    FileName=uigetfile_uvmat('Pick a transform function',get(handles.TransformPath,'String'),'.m');
3144    if isempty(FileName)
3145        return     %browser closed without choice
3146    end
3147    [TransformPath,TransformName,TransformExt]=fileparts(FileName); % removes extension .m
3148    if ~strcmp(TransformExt,'.m')
3149        msgbox_uvmat('ERROR','a Matlab function .m must be introduced');
3150        return
3151    end
3152     % insert the choice in the menu
3153    TransformIndex=find(strcmp(TransformName,TransformList),1); % look for the selected function in the menu Action
3154    if isempty(TransformIndex)%the input string does not exist in the menu
3155        TransformIndex= length(TransformList);
3156        TransformList=[TransformList(1:end-1);{TransformName};TransformList(end)]; % the selected function is appended in the menu, before the last item 'more...'
3157        set(handles.TransformName,'String',TransformList)
3158        TransformPathList=[TransformPathList;{TransformPath}];
3159    else% the input function already exist, we update its path (possibly new)
3160        TransformPathList{TransformIndex}=TransformPath; %
3161        set(handles.TransformName,'Value',TransformIndex)
3162    end
3163   % save the new menu in the personal file 'uvmat_perso.mat'
3164   dir_perso=prefdir; % personal Matalb directory
3165   profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
3166   if exist(profil_perso,'file')
3167       for ilist=nb_builtin_transform+1:numel(TransformPathList)
3168           TransformListUser{ilist-nb_builtin_transform}=TransformList{ilist};
3169           TransformPathListUser{ilist-nb_builtin_transform}=TransformPathList{ilist};
3170       end
3171       TransformPathListUser=TransformPathListUser';
3172       TransformListUser=TransformListUser';
3173       save (profil_perso,'TransformPathListUser','TransformListUser','-append'); % store the root name for future opening of uvmat
3174   end
3175end
3176
3177%display the current function path
3178set(handles.TransformPath,'String',TransformPathList{TransformIndex}); % show the path to the senlected function
3179set(handles.TransformName,'UserData',TransformPathList);
3180
3181%% create the function handle of the selected fct
3182if ~isempty(TransformName)
3183    if ~exist(TransformPathList{TransformIndex},'dir')
3184        msgbox_uvmat('ERROR',['The prescribed transform function path ' TransformPathList{TransformIndex} ' does not exist']);
3185        return
3186    end
3187    current_dir=pwd; % current working dir
3188    cd(TransformPathList{TransformIndex})
3189    transform_handle=str2func(TransformName);
3190    cd(current_dir)
3191    Field.Action.RUN=0;% indicate that the transform fct is called only to get input param
3192    SeriesData=get(handles.series,'UserData');
3193    ParamIn=[];
3194    if isfield(SeriesData,'TransformInput')
3195        ParamIn.TransformInput=SeriesData.TransformInput;
3196    end
3197    DataOut=feval(transform_handle,Field,ParamIn);% execute the transform fct to get the required conditions
3198    Field.Action.RUN=0; % indicate that the transform fct is called only to get input param
3199    DataOut=feval(transform_handle,Field,[]); % execute the transform fct to get the required conditions
3200    if isfield(DataOut,'TransformInput')%  used to add transform parameters at selection of the transform fct
3201        SeriesData.TransformInput=DataOut.TransformInput;
3202        set(handles.series,'UserData',SeriesData)
3203    end
3204end
3205
3206%------------------------------------------------------------------------
3207% --- fct activated by the upper bar menu ExportConfig
3208%------------------------------------------------------------------------
3209function MenuDisplayConfig_Callback(hObject, eventdata, handles)
3210
3211global Param
3212Param=read_GUI_series(handles);
3213evalin('base','global Param')%make CurData global in the workspace
3214display('current series config :')
3215evalin('base','Param') %display CurData in the workspace
3216commandwindow; % brings the Matlab command window to the front
3217
3218%------------------------------------------------------------------------
3219% --- fct activated by the upper bar menu InportConfig: import
3220%     menu settings from an xml file (stored in /0_XML for each run)
3221%------------------------------------------------------------------------
3222function MenuImportConfig_Callback(hObject, eventdata, handles)
3223
3224%% use a browser to choose the xml file containing the processing config
3225InputTable=get(handles.InputTable,'Data');
3226oldfile=InputTable{1,1}; % current path in InputTable
3227if isempty(oldfile)
3228    % use a file name stored in prefdir
3229    dir_perso=prefdir;
3230    profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
3231    if exist(profil_perso,'file')
3232        h=load (profil_perso);
3233        if isfield(h,'RootPath') && ischar(h.RootPath)
3234            oldfile=h.RootPath;
3235        end
3236    end
3237end
3238filexml=uigetfile_uvmat('pick a xml parameter file',oldfile,'.xml'); % get the xml file containing processing parameters
3239if isempty(filexml), return, end % quit function if an xml file has not been opened
3240
3241%% fill the GUI series with the content of the xml file
3242Param=xml2struct(filexml); % read the input xml file as a Matlab structure
3243
3244% ask to stop current Action if button RUN is in action (another process is already running)
3245if isequal(get(handles.RUN,'Value'),1)
3246    answer= msgbox_uvmat('INPUT_Y-N','stop current Action process?');
3247    if strcmp(answer,'Yes')
3248        STOP_Callback(hObject, eventdata, handles)
3249    else
3250        return
3251    end
3252end
3253Param.Action.RUN=0; % desactivate the input RUN=1
3254
3255fill_GUI(Param,handles.series)% fill the elements of the GUI series with the input parameters
3256SeriesData=get(handles.series,'UserData');
3257if isfield(Param,'InputFields')
3258    ListField=Param.InputFields.FieldName;
3259    if ischar(ListField),ListField={ListField}; end
3260    set(handles.FieldName,'String',[ListField;{'get-field...'}])
3261     set(handles.FieldName,'Value',1:numel(ListField))
3262     set(handles.FieldName,'Visible','on')
3263end       
3264if isfield(Param,'ActionInput')%  introduce  parameters specific to an Action fct, for instance PIV parameters
3265%     set(handles.ActionInput,'Visible','on')
3266%     set(handles.ActionInput,'Value',0)
3267    Param.ActionInput.ConfigSource=filexml; % record the source of config for future info
3268    SeriesData.ActionInput=Param.ActionInput;
3269end
3270if isfield(Param,'TransformInput')%  introduce  parameters specific to a transform fct
3271    SeriesData.TransformInput=Param.TransformInput;
3272end
3273if isfield(Param,'ProjObject') %introduce projection object if relevant
3274    SeriesData.ProjObject=Param.ProjObject;
3275end
3276set(handles.series,'UserData',SeriesData)
3277if isfield(Param,'CheckObject') && isequal(Param.CheckObject,1)
3278    set(handles.ProjObject,'String',Param.ProjObject.Name)
3279    set(handles.ViewObject,'Visible','on')
3280    set(handles.EditObject,'Visible','on')
3281    set(handles.DeleteObject,'Visible','on')
3282else     
3283    set(handles.ProjObject,'String','')
3284    set(handles.ProjObject,'Visible','off')
3285    set(handles.ViewObject,'Visible','off')
3286    set(handles.EditObject,'Visible','off')
3287    set(handles.DeleteObject,'Visible','off')     
3288end     
3289set(handles.REFRESH,'BackgroundColor',[1 0 1]); % paint REFRESH button in magenta to indicate that it should be activated
3290
3291
3292%------------------------------------------------------------------------
3293% --- Executes when the GUI series is resized.
3294%------------------------------------------------------------------------
3295function series_ResizeFcn(hObject, eventdata, handles)
3296
3297%% input table
3298set(handles.InputTable,'Unit','pixel')
3299Pos=get(handles.InputTable,'Position');
3300set(handles.InputTable,'Unit','normalized')
3301ColumnWidth=round([0.5 0.14 0.14 0.14 0.08]*(Pos(3)-52));
3302ColumnWidth=num2cell(ColumnWidth);
3303set(handles.InputTable,'ColumnWidth',ColumnWidth)
3304
3305%% MinIndex_j and MaxIndex_i
3306unit=get(handles.MinIndex_i,'Unit');
3307set(handles.MinIndex_i,'Unit','pixel')
3308Pos=get(handles.MinIndex_i,'Position');
3309set(handles.MinIndex_i,'Unit',unit)
3310set(handles.MinIndex_i,'ColumnWidth',{Pos(3)-18})
3311set(handles.MaxIndex_i,'ColumnWidth',{Pos(3)-18})
3312set(handles.MinIndex_j,'ColumnWidth',{Pos(3)-18})
3313set(handles.MaxIndex_j,'ColumnWidth',{Pos(3)-18})
3314
3315%% TimeTable
3316set(handles.TimeTable,'Unit','pixel')
3317Pos=get(handles.TimeTable,'Position');
3318set(handles.TimeTable,'Unit','normalized')
3319% ColumnWidth=get(handles.TimeTable,'ColumnWidth');
3320ColumnWidth=num2cell(floor([0.2 0.2 0.2 0.2 0.2]*(Pos(3)-20)));
3321set(handles.TimeTable,'ColumnWidth',ColumnWidth)
3322
3323
3324%% PairString
3325set(handles.PairString,'Unit','pixel')
3326Pos=get(handles.PairString,'Position');
3327set(handles.PairString,'Unit','normalized')
3328set(handles.PairString,'ColumnWidth',{Pos(3)-5})
3329
3330%% MaskTable
3331set(handles.MaskTable,'Unit','pixel')
3332Pos=get(handles.MaskTable,'Position');
3333set(handles.MaskTable,'Unit','normalized')
3334set(handles.MaskTable,'ColumnWidth',{Pos(3)-5})
3335
3336%------------------------------------------------------------------------
3337% --- Executes on button press in status.
3338%------------------------------------------------------------------------
3339function status_Callback(hObject, eventdata, handles)
3340
3341if get(handles.status,'Value')
3342    set(handles.status,'BackgroundColor',[1 1 0])
3343    drawnow
3344    Param=read_GUI(handles.series);
3345    RootPath=Param.InputTable{1,1};
3346    if ~isfield(Param,'OutputSubDir')   
3347        msgbox_uvmat('ERROR','no standard sub-directory definition for output files, use a browser to check the output')
3348        set(handles.status,'BackgroundColor',[0 1 0])
3349        return
3350    end
3351    OutputSubDir=[Param.OutputSubDir Param.OutputDirExt]; % subdirectory for output files
3352    OutputDir=fullfile(RootPath,OutputSubDir);
3353    if exist(OutputDir,'dir')
3354        uigetfile_uvmat('status_display',OutputDir)
3355    else
3356        msgbox_uvmat('ERROR','output folder not created yet: calculation did not start')
3357        set(handles.status,'BackgroundColor',[0 1 0])
3358    end
3359else
3360    %% delete current display fig if selection is off
3361    set(handles.status,'BackgroundColor',[0 1 0])
3362    hfig=findobj(allchild(0),'name','status_display');
3363    if ~isempty(hfig)
3364        delete(hfig)
3365    end
3366    return
3367end
3368
3369
3370%------------------------------------------------------------------------   
3371% launched by selecting a file on the list
3372%------------------------------------------------------------------------
3373function view_file(hObject, eventdata)
3374
3375list=get(hObject,'String');
3376index=get(hObject,'Value');
3377rootroot=get(hObject,'UserData');
3378selectname=list{index};
3379ind_dot=regexp(selectname,'\.\.\.');
3380if ~isempty(ind_dot)
3381    selectname=selectname(1:ind_dot-1);
3382end
3383FullSelectName=fullfile(rootroot,selectname);
3384if exist(FullSelectName,'dir')% a directory has been selected
3385    ListFiles=dir(FullSelectName);
3386    ListDisplay=cell(numel(ListFiles),1);
3387    for ilist=2:numel(ListDisplay)% suppress the first line '.'
3388        ListDisplay{ilist-1}=ListFiles(ilist).name;
3389    end
3390    set(hObject,'Value',1)
3391    set(hObject,'String',ListDisplay)
3392    if strcmp(selectname,'..')
3393        FullSelectName=fileparts(fileparts(FullSelectName));
3394    end
3395    set(hObject,'UserData',FullSelectName)
3396    hfig=get(hObject,'parent');
3397    htitlebox=findobj(hfig,'tag','titlebox');   
3398    set(htitlebox,'String',FullSelectName)
3399elseif exist(FullSelectName,'file')%visualise the vel field if it exists
3400    FileInfo=get_file_info(FullSelectName);   
3401    if strcmp(FileInfo.FileType,'txt')
3402        edit(FullSelectName)
3403    elseif strcmp(FileInfo.FileType,'xml')
3404        editxml(FullSelectName)
3405    else
3406        uvmat(FullSelectName)
3407    end
3408    set(gcbo,'Value',1)
3409end
3410
3411
3412%------------------------------------------------------------------------   
3413% launched by refreshing the status figure
3414%------------------------------------------------------------------------
3415function refresh_GUI(hfig)
3416
3417htitlebox=findobj(hfig,'tag','titlebox');
3418hlist=findobj(hfig,'tag','list');
3419hseries=findobj(allchild(0),'tag','series');
3420hstatus=findobj(hseries,'tag','status');
3421StatusData=get(hstatus,'UserData');
3422OutputDir=get(htitlebox,'String');
3423if ischar(OutputDir),OutputDir={OutputDir};end
3424ListFiles=dir(OutputDir{1});
3425if numel(ListFiles)<1
3426    return
3427end
3428ListFiles(1)=[]; % removes the first line ='.'
3429ListDisplay=cell(numel(ListFiles),1);
3430testrecent=0;
3431datnum=zeros(numel(ListDisplay),1);
3432for ilist=1:numel(ListDisplay)
3433    ListDisplay{ilist}=ListFiles(ilist).name;
3434      if ~ListFiles(ilist).isdir && isfield(ListFiles(ilist),'datenum')
3435            datnum(ilist)=ListFiles(ilist).datenum; % only available in recent matlab versions
3436            testrecent=1;
3437       end
3438end
3439set(hlist,'String',ListDisplay)
3440
3441%% Look at date of creation
3442ListDisplay=ListDisplay(datnum~=0);
3443datnum=datnum(datnum~=0); % keep the non zero values corresponding to existing files
3444NbOutputFile=[];
3445if isempty(datnum)
3446    if testrecent
3447        message='no civ result created yet';
3448    else
3449        message='';
3450    end
3451else
3452    [first,indfirst]=min(datnum);
3453    [last,indlast]=max(datnum);
3454    NbOutputFile_str='?';
3455    NbOutputFile=[];
3456    if isfield(StatusData,'NbOutputFile')
3457        NbOutputFile=StatusData.NbOutputFile;
3458        NbOutputFile_str=num2str(NbOutputFile);
3459    end
3460    message={[num2str(numel(datnum)) ' file(s) done over ' NbOutputFile_str] ;['oldest modification:  ' ListDisplay{indfirst} ' : ' datestr(first)];...
3461        ['latest modification:  ' ListDisplay{indlast} ' : ' datestr(last)]};
3462end
3463set(htitlebox,'String', [OutputDir{1};message])
3464
3465%% update the waitbar
3466hwaitbar=findobj(hfig,'tag','waitbar');
3467if ~isempty(NbOutputFile)
3468    BarPosition=get(hwaitbar,'Position');
3469    BarPosition(3)=0.9*numel(datnum)/NbOutputFile;
3470    set(hwaitbar,'Position',BarPosition)
3471end
3472
3473%------------------------------------------------------------------------
3474% --- Executes on selection change in ActionExt.
3475%------------------------------------------------------------------------
3476function ActionExt_Callback(hObject, eventdata, handles)
3477
3478ActionExtList=get(handles.ActionExt,'String');
3479ActionExt=ActionExtList{get(handles.ActionExt,'Value')};
3480if strcmp(ActionExt,'.py (in dev.)')
3481    set(handles.RunMode,'Value',2)
3482end
3483
3484%function num_NbProcess_Callback(hObject, eventdata, handles)
3485
3486
3487function num_NbSlice_Callback(hObject, eventdata, handles)
3488NbSlice=str2num(get(handles.num_NbSlice,'String'));
3489%set(handles.num_NbProcess,'String',num2str(NbSlice))
3490
3491%------------------------------------------------------------------------
3492% --- set the visibility of relevant velocity type menus:
3493function menu=set_veltype_display(Civ,FileType)
3494%------------------------------------------------------------------------
3495if ~exist('FileType','var')
3496    FileType='civx';
3497end
3498switch FileType
3499    case 'civx'
3500        menu={'civ1';'interp1';'filter1';'civ2';'interp2';'filter2'};
3501        if isequal(Civ,0)
3502            imax=0;
3503        elseif isequal(Civ,1) || isequal(Civ,2)
3504            imax=1;
3505        elseif isequal(Civ,3)
3506            imax=3;
3507        elseif isequal(Civ,4) || isequal(Civ,5)
3508            imax=4;
3509        elseif isequal(Civ,6) %patch2
3510            imax=6;
3511        end
3512    case 'civdata'
3513        menu={'civ1';'filter1';'civ2';'filter2'};
3514        if isequal(Civ,0)
3515            imax=0;
3516        elseif isequal(Civ,1) || isequal(Civ,2)
3517            imax=1;
3518        elseif isequal(Civ,3)
3519            imax=2;
3520        elseif isequal(Civ,4) || isequal(Civ,5)
3521            imax=3;
3522        else%if isequal(Civ,6) %patch2
3523            imax=4;
3524        end
3525end
3526menu=menu(1:imax);
3527
3528
3529% --- Executes on mouse motion over figure - except title and menu.
3530function series_WindowButtonMotionFcn(hObject, eventdata, handles)
3531set(hObject,'Pointer','arrow');
3532
3533
3534% --- Executes on button press in SetPairs.
3535function SetPairs_Callback(hObject, eventdata, handles)
3536
3537%% delete previous occurrence of 'set_pairs'
3538hfig=findobj(allchild(0),'Tag','set_pairs');
3539if ~isempty(hfig)
3540delete(hfig)
3541end
3542
3543%% create the GUI set_pairs
3544set(0,'Unit','points')
3545ScreenSize=get(0,'ScreenSize'); % get the size of the screen, to put the fig on the upper right
3546Width=220; % fig width in points (1/72 inch)
3547Height=min(0.8*ScreenSize(4),300);
3548Left=ScreenSize(3)- Width-40; % right edge close to the right, with margin=40
3549Bottom=ScreenSize(4)-Height-40; % put fig at top right
3550hfig=findobj(allchild(0),'Tag','set_slice');
3551if ~isempty(hfig),delete(hfig), end; % delete existing version of the GUI
3552hfig=figure('name','set_pairs','tag','set_pairs','MenuBar','none','NumberTitle','off','Unit','points','Position',[Left,Bottom,Width,Height]);
3553BackgroundColor=get(hfig,'Color');
3554SeriesData=get(handles.series,'UserData');
3555TimeUnit=get(handles.TimeUnit,'String');
3556PairString=get(handles.PairString,'Data');
3557ListViewLines=find(cellfun('isempty',PairString)==0); % find list of non empty pairs
3558ListViewMenu=cell(numel(ListViewLines),1);
3559%iview=get(handles.PairString,'Value');
3560iview=[];
3561for ilist=1:numel(ListViewLines)
3562    ListViewMenu{ilist}=num2str(ListViewLines(ilist));
3563end
3564if isempty(iview)
3565    ListViewValue=numel(ListViewLines); % we work by default on the pair option for the last line which requires pairs
3566    iview=ListViewLines(end);
3567else
3568    ListViewValue=find(ListViewLines==iview);
3569end
3570ref_i=str2num(get(handles.num_first_i,'String'));
3571ref_j=1; % default
3572if strcmp(get(handles.num_first_j,'String'),'Visible')
3573    ref_j=str2num(get(handles.num_first_j,'String'));
3574end
3575[ModeMenu,ModeValue]=update_mode(SeriesData.i1_series{1},SeriesData.i2_series{1},SeriesData.j2_series{1});
3576InputTable=get(handles.InputTable,'Data');
3577displ_pair=update_listpair(SeriesData.i1_series{1},SeriesData.i2_series{1},SeriesData.j1_series{1},SeriesData.j2_series{1},ModeMenu{ModeValue},...
3578                                                 SeriesData.Time{1},TimeUnit,ref_i,ref_j,SeriesData.TimeName,InputTable,SeriesData.FileInfo{1});
3579for iline=1:size(InputTable,1)
3580    viewcell{iline}=num2str(iline);
3581end
3582viewcell=viewcell';
3583ModeMenu={'bursts';'series(Dj)'};
3584ModeValue=1;                                               
3585                   %i1_series,i2_series,j1_series,j2_series,mode,time,TimeUnit,ref_i,ref_j,TimeName,InputTable,FileInfo                             
3586% first raw of the GUI
3587uicontrol('Style','text','Units','normalized', 'Position', [0.05 0.88 0.5 0.1],'BackgroundColor',BackgroundColor,...
3588    'String','row to edit #','FontUnits','points','FontSize',12,'FontWeight','bold','ForegroundColor','blue','HorizontalAlignment','right'); % title
3589uicontrol('Style','popupmenu','Units','normalized', 'Position', [0.54 0.8 0.3 0.2],'BackgroundColor',[1 1 1],...
3590    'Callback',@(hObject,eventdata)ListView_Callback(hObject,eventdata),'String',viewcell,'Value',1,'FontUnits','points','FontSize',12,'FontWeight','bold',...
3591    'Tag','ListView','TooltipString','''ListView'':choice of the file series w for pair display');
3592% second raw of the GUI
3593uicontrol('Style','text','Units','normalized', 'Position', [0.05 0.79 0.7 0.1],'BackgroundColor',BackgroundColor,...
3594    'String','mode of index pairing:','FontUnits','points','FontSize',12,'FontWeight','bold','ForegroundColor','blue','HorizontalAlignment','left'); % title
3595uicontrol('Style','popupmenu','Units','normalized', 'Position', [0.05 0.62 0.9 0.2],'BackgroundColor',[1 1 1],...
3596    'Callback',@(hObject,eventdata)Mode_Callback(hObject,eventdata),'String',ModeMenu,'Value',ModeValue,'FontUnits','points','FontSize',12,'FontWeight','bold',...
3597    'Tag','Mode','TooltipString','''Mode'': choice of the image pair mode');
3598% third raw
3599uicontrol('Style','text','Units','normalized', 'Position', [0.05 0.6 0.7 0.1],'BackgroundColor',BackgroundColor,...
3600    'String','pair choice:','FontUnits','points','FontSize',12,'FontWeight','bold','ForegroundColor','blue','HorizontalAlignment','left'); % title
3601uicontrol('Style','listbox','Units','normalized', 'Position', [0.05 0.42 0.9 0.2],'BackgroundColor',[1 1 1],...
3602    'Callback',@(hObject,eventdata)ListPair_Callback(hObject,eventdata),'String',displ_pair,'Value',1,'FontUnits','points','FontSize',12,'FontWeight','bold',...
3603    'Tag','ListPair','TooltipString','''ListPair'': menu for selecting the image pair');
3604uicontrol('Style','text','Units','normalized', 'Position', [0.1 0.22 0.8 0.1],'BackgroundColor',BackgroundColor,...
3605    'String','ref_i           ref_j','FontUnits','points','FontSize',12,'FontWeight','bold','ForegroundColor','blue','HorizontalAlignment','center'); % title
3606uicontrol('Style','edit','Units','normalized', 'Position', [0.15 0.17 0.3 0.08],'BackgroundColor',[1 1 1],...
3607    'Callback',@(hObject,eventdata)num_ref_i_Callback(hObject,eventdata),'String',num2str(ref_i),'FontUnits','points','FontSize',12,'FontWeight','bold',...
3608    'Tag','num_ref_i','TooltipString','''num_ref_i'': reference field index i used to display dt in ''list_pair_civ''');
3609uicontrol('Style','edit','Units','normalized', 'Position', [0.55 0.17 0.3 0.08],'BackgroundColor',[1 1 1],...
3610    'Callback',@(hObject,eventdata)num_ref_j_Callback(hObject,eventdata),'String',num2str(ref_j),'FontUnits','points','FontSize',12,'FontWeight','bold',...
3611    'Tag','num_ref_j','TooltipString','''num_ref_j'': reference field index i used to display dt in ''list_pair_civ''');
3612uicontrol('Style','pushbutton','Units','normalized', 'Position', [0.01 0.01 0.3 0.12],'BackgroundColor',[0 1 0],...
3613    'Callback',@(hObject,eventdata)OK_Callback(hObject,eventdata),'String','OK','FontUnits','points','FontSize',12,'FontWeight','bold',...
3614    'Tag','OK','TooltipString','''OK'': validate the choice');
3615%  last raw  of the GUI: pushbuttons
3616% 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),...
3617%     'FontWeight','bold','FontUnits','points','FontSize',12,'TooltipString','''OK'': apply the output to the current field series in uvmat');
3618drawnow
3619
3620%------------------------------------------------------------------------
3621function ListView_Callback(hObject,eventdata)
3622Mode_Callback(hObject,eventdata)
3623
3624%------------------------------------------------------------------------   
3625function Mode_Callback(hObject,eventdata)
3626%% get input info
3627hseries=findobj(allchild(0),'tag','series'); % handles of the GUI series
3628hhseries=guidata(hseries); % handles of the elements in the GUI series
3629TimeUnit=get(hhseries.TimeUnit,'String');
3630SeriesData=get(hseries,'UserData');
3631mode_list=get(hObject,'String');
3632mode=mode_list{get(hObject,'Value')};
3633hListView=findobj(get(hObject,'parent'),'Tag','ListView');
3634iview=get(hListView,'Value');
3635i1_series=SeriesData.i1_series{iview};
3636i2_series=SeriesData.i2_series{iview};
3637j1_series=SeriesData.j1_series{iview};
3638j2_series=SeriesData.j2_series{iview};
3639
3640%% enable j index visibility after the new choice
3641
3642if strcmp(mode,'series(Dj)')
3643   status_j='on'; % default
3644else
3645       status_j='off'; % no j index needed for bust case
3646end
3647enable_j(hhseries,status_j) % no j index needed
3648
3649%% get the reference indices for the time interval Dt
3650href_i=findobj(get(hObject,'parent'),'Tag','ref_i');
3651ref_i=[];ref_j=[];
3652if strcmp(get(href_i,'Visible'),'on')
3653    ref_i=str2num(get(href_i,'String'));
3654end
3655if isempty(ref_i)
3656    ref_i=1;
3657end
3658if isempty(ref_j)
3659    ref_j=1;
3660end
3661
3662%% update the menu ListPair
3663Menu=update_listpair(i1_series,i2_series,j1_series,j2_series,mode,SeriesData.Time{iview},TimeUnit,ref_i,ref_j,SeriesData.FileInfo);
3664hlist_pairs=findobj(get(hObject,'parent'),'Tag','ListPair');
3665set(hlist_pairs,'Value',1)% set the first choice by default in ListPair
3666set(hlist_pairs,'String',Menu)% set the menu in ListPair
3667ListPair_Callback(hlist_pairs,[])% apply the default choice in ListPair
3668
3669%-------------------------------------------------------------
3670% --- Executes on selection in ListPair.
3671function ListPair_Callback(hObject,eventdata)
3672%------------------------------------------------------------
3673list_pair=get(hObject,'String'); % get the menu of image pairs
3674if isempty(list_pair)
3675    string='';
3676else
3677    string=list_pair{get(hObject,'Value')};
3678   % string=regexprep(string,',.*',''); % removes time indication (after ',')
3679end
3680hseries=findobj(allchild(0),'tag','series');
3681hPairString=findobj(hseries,'tag','PairString');
3682PairString=get(hPairString,'Data');
3683hListView=findobj(get(hObject,'parent'),'Tag','ListView');
3684iview=get(hListView,'Value');
3685PairString{iview,1}=string;
3686% report the selected pair string to the table PairString
3687set(hPairString,'Data',PairString)
3688
3689
3690%------------------------------------------------------------------------
3691function num_ref_i_Callback(hObject, eventdata)
3692%------------------------------------------------------------------------
3693Mode_Callback([],[])
3694
3695%------------------------------------------------------------------------
3696function num_ref_j_Callback(hObject, eventdata)
3697%------------------------------------------------------------------------
3698Mode_Callback([],[])
3699
3700%------------------------------------------------------------------------
3701function OK_Callback(hObject, eventdata)
3702%------------------------------------------------------------------------
3703delete(get(hObject,'parent'))
3704
3705
3706%------------------------------------------------------------------------
3707% --- Executes on button press in ClearLine.
3708%------------------------------------------------------------------------
3709function ClearLine_Callback(hObject, eventdata, handles)
3710InputTable=get(handles.InputTable,'Data');
3711iline=str2double(get(handles.InputLine,'String'));
3712if size(InputTable,1)>1
3713    InputTable(iline,:)=[]; % suppress the current line if not the first
3714    set(handles.InputTable,'Data',InputTable);
3715end
3716set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH button to magenta color to indicate that input refr
3717
3718
3719% --- Executes on button press in MonitorCluster.
3720function MonitorCluster_Callback(hObject, eventdata, handles)
3721disp('format: R/W=run/wait, time lapsed, R=nbre of cores,W=walltime')
3722system('oarstat |grep N=UVmat')% check the list of jobs launched with uvmat
3723
3724
3725function OutputSubDir_Callback(hObject, eventdata, handles)
3726set(handles.OutputSubDir,'BackgroundColor',[1 1 1])
3727
3728
3729% --- Executes on button press in CheckOverwrite.
3730function CheckOverwrite_Callback(hObject, eventdata, handles)
3731
3732% --- Executes on button press in TestCPUTime.
3733function TestCPUTime_Callback(hObject, eventdata, handles)
3734% hObject    handle to TestCPUTime (see GCBO)
3735% eventdata  reserved - to be defined in a future version of MATLAB
3736% handles    structure with handles and user data (see GUIDATA)
3737
3738
3739% --- Executes on button press in DiskQuota.
3740function DiskQuota_Callback(hObject, eventdata, handles)
3741SeriesData=get(handles.series,'UserData');
3742system(SeriesData.SeriesParam.DiskQuotaCmd)
3743
3744
3745
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