source: trunk/src/series.m @ 1030

Last change on this file since 1030 was 1030, checked in by sommeria, 3 years ago

updated for Matlab 2016

File size: 164.2 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 2008-2018, 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,'ActionListUser') && iscell(h.ActionListUser) && isfield(h,'ActionPathListUser') && iscell(h.ActionPathListUser)
220        ActionList=[ActionList;h.ActionListUser];
221        ActionPathList=[ActionPathList;h.ActionPathListUser(:,1)];
222    end
223    %get the menu of transform fct
224    if isfield(h,'TransformListUser') && iscell(h.TransformListUser) && isfield(h,'TransformPathListUser') && iscell(h.TransformPathListUser)
225        TransformList=[TransformList;h.TransformListUser];
226        TransformPathList=[TransformPathList;h.TransformPathListUser];
227    end
228end
229
230%% selection of the input Action fct
231ActionCheckExist=true(size(ActionList)); % initiate the check of the path to the listed action fct
232for ilist=NbBuiltinAction+1:numel(ActionList)%check  the validity of the path of the user defined Action fct
233    ActionCheckExist(ilist)=exist(fullfile(ActionPathList{ilist},[ActionList{ilist} '.m']),'file');
234end
235ActionPathList=ActionPathList(ActionCheckExist,:); % suppress the menu options which are not valid anymore
236ActionList=ActionList(ActionCheckExist);
237set(handles.ActionName,'String',[ActionList;{'more...'}])
238set(handles.ActionName,'UserData',ActionPathList)
239ActionIndex=[];
240if isfield(Param,'ActionName')% copy the selected menu index transferred in Param from uvmat
241    ActionIndex=find(strcmp(Param.ActionName,ActionList),1);
242end
243if isempty(ActionIndex)
244    ActionIndex=1;
245end
246set(handles.ActionName,'Value',ActionIndex)
247set(handles.ActionPath,'String',ActionPathList{ActionIndex})
248set(handles.ActionExt,'Value',1)
249set(handles.ActionExt,'String',ActionExtList)
250
251%% selection of the input transform fct
252TransformCheckExist=true(size(TransformList));
253for ilist=NbBuiltinTransform+1:numel(TransformList)
254    TransformCheckExist(ilist)=exist(fullfile(TransformPathList{ilist},[TransformList{ilist} '.m']),'file');
255end
256TransformPathList=TransformPathList(TransformCheckExist);
257TransformList=TransformList(TransformCheckExist);
258set(handles.TransformName,'String',[TransformList;{'more...'}])
259set(handles.TransformName,'UserData',TransformPathList)
260TransformIndex=[];
261if isfield(Param,'TransformName')% copy the selected menu index transferred in Param from uvmat
262    TransformIndex=find(strcmp(Param.TransformName,TransformList),1);
263end
264if isempty(TransformIndex)
265    TransformIndex=1;
266end
267set(handles.TransformName,'Value',TransformIndex)
268set(handles.TransformPath,'String',TransformPathList{TransformIndex})
269   
270%% fields input initialisation
271if isfield(Param,'list_fields')&& isfield(Param,'index_fields') &&~isempty(Param.list_fields) &&~isempty(Param.index_fields)
272    set(handles.FieldName,'String',Param.list_fields); % list menu fields
273    set(handles.FieldName,'Value',Param.index_fields); % selected string index
274end
275if isfield(Param,'Coordinates')
276    if isfield(Param.Coordinates,'Coord_x')
277        set(handles.Coord_x,'String',Param.Coordinates.Coord_x)
278    end
279    if isfield(Param.Coordinates,'Coord_y')
280        set(handles.Coord_y,'String',Param.Coordinates.Coord_y)
281    end
282    if isfield(Param.Coordinates,'Coord_z')
283        set(handles.Coord_z,'String',Param.Coordinates.Coord_z)
284    end
285end
286
287%% introduce the input file name(s) if defined from input Param,
288set(handles.series,'UserData',SeriesData)% initiate Userdata
289if isfield(Param,'InputFile')
290   
291    %% fill the list of file series
292    InputTable=[{Param.InputFile.RootPath},{Param.InputFile.SubDir},{Param.InputFile.RootFile},{Param.InputFile.NomType},{Param.InputFile.FileExt}];
293    if isempty(find(cellfun('isempty',InputTable)==0)); % if there is no input file, do not introduce input info
294        set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH button to magenta color to indicate that input refresh is needed
295        return
296    end
297    TimeTable=[{Param.InputFile.TimeName},{[]},{[]},{[]},{[]}];
298    if isfield(Param.InputFile,'RootPath_1')
299        InputTable=[InputTable;[{Param.InputFile.RootPath_1},{Param.InputFile.SubDir_1},{Param.InputFile.RootFile_1},{Param.InputFile.NomType_1},{Param.InputFile.FileExt_1}]];
300        TimeTable=[TimeTable; [{Param.InputFile.TimeName_1},{[]},{[]},{[]},{[]}]];
301    end
302    set(handles.InputTable,'Data',InputTable)
303    %% determine the selected reference field indices for pair display
304   
305    [tild,tild,tild,i1,i2,j1,j2]=fileparts_uvmat(Param.InputFile.FileIndex);
306    if isempty(i1)
307        i1=1;
308    end
309    if isempty(i2)
310        i2=i1;
311    end
312    ref_i=floor((i1+i2)/2); % reference image number corresponding to the file
313    % set(handles.num_ref_i,'String',num2str(ref_i));
314    if isempty(j1)
315        j1=1;
316    end
317    if isempty(j2)
318        j2=j1;
319    end
320    ref_j=floor((j1+j2)/2); % reference image number corresponding to the file
321    SeriesData.ref_i=ref_i;
322    SeriesData.ref_j=ref_j;
323    set(handles.series,'UserData',SeriesData)
324    update_rootinfo(handles,Param.HiddenData.i1_series{1},Param.HiddenData.i2_series{1},Param.HiddenData.j1_series{1},Param.HiddenData.j2_series{1},...
325        Param.HiddenData.FileInfo{1},Param.HiddenData.MovieObject{1},1)
326    if isfield(Param,'FileName_1')
327        %         display_file_name(handles,Param,2)
328        update_rootinfo(handles,Param.HiddenData.i1_series{2},Param.HiddenData.i2_series{2},Param.HiddenData.j1_series{2},Param.HiddenData.j2_series{2},...
329            Param.HiddenData.FileInfo{2},Param.HiddenData.MovieObject{2},2)
330    end
331    %% enable field and veltype menus, in accordance with the current action
332    ActionName_Callback([],[], handles)
333   
334    %% set length of waitbar
335    displ_time(handles)
336   
337else
338    set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH button to magenta color to indicate that input refresh is needed
339end
340if isfield(Param,'incr_i')
341    set(handles.num_incr_i,'String',num2str(Param.incr_i))
342else
343    set(handles.num_incr_i,'String','1')
344end
345if isfield(Param,'incr_j')
346    set(handles.num_incr_j,'String',num2str(Param.incr_j))
347else
348    set(handles.num_incr_j,'String','1')
349end
350
351%------------------------------------------------------------------------
352% --- Outputs from this function are returned to the command line.
353function varargout = series_OutputFcn(hObject, eventdata, handles)
354%------------------------------------------------------------------------
355varargout{1} = handles.output;
356
357%------------------------------------------------------------------------
358% --- executed when closing uvmat: delete or desactivate the associated figures if exist
359function closefcn(gcbo,eventdata)
360%------------------------------------------------------------------------
361
362% delete set_object_series if detected
363hh=findobj(allchild(0),'name','view_object_series');
364if ~isempty(hh)
365    delete(hh)
366end
367hh=findobj(allchild(0),'name','edit_object_series');
368if ~isempty(hh)
369    delete(hh)
370end
371
372%delete the bowser if detected
373hh=findobj(allchild(0),'tag','browser');
374if ~isempty(hh)
375    delete(hh)
376end
377
378
379%------------------------------------------------------------------------
380%------------------------------------------------------------------------
381%  II - FUNCTIONS FOR INTRODUCING THE INPUT FILES
382% automatically sets the global properties when the rootfile name is introduced
383% then activate the view-field actionname if selected
384% it is activated either by clicking on the RootPath window or by the
385% browser
386%------------------------------------------------------------------------
387%------------------------------------------------------------------------
388% --- fct activated by the browser under 'Open'
389%------------------------------------------------------------------------ 
390function MenuBrowse_Callback(hObject, eventdata, handles)
391%% look for the previously opened file 'oldfile'
392InputTable=get(handles.InputTable,'Data');
393oldfile=InputTable{1,1};
394if isempty(oldfile)
395    % use a file name stored in prefdir
396    dir_perso=prefdir;
397    profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
398    if exist(profil_perso,'file')
399        h=load (profil_perso);
400        if isfield(h,'RootPath') && ischar(h.RootPath)
401            oldfile=h.RootPath;
402        end
403    end
404end
405%% launch the browser
406fileinput=uigetfile_uvmat('pick an input file in the series',oldfile);
407hh=dir(fileinput);
408if numel(hh)>1
409    msgbox_uvmat('ERROR','invalid input, probably a broken link');
410else
411    if ~isempty(fileinput)
412        display_file_name(handles,fileinput,'one')
413    end
414end
415
416% --------------------------------------------------------------------
417function MenuBrowseAppend_Callback(hObject, eventdata, handles)
418
419%% look for the previously opened file 'oldfile'
420InputTable=get(handles.InputTable,'Data');
421RootPathCell=InputTable(:,1);
422if isempty(RootPathCell{1})% no input file in the table
423     MenuBrowse_Callback(hObject, eventdata, handles)%refresh the input table, not append
424     return
425end
426SubDirCell=InputTable(:,2);
427oldfile=fullfile(RootPathCell{1},SubDirCell{1});
428
429%% use a file name stored in prefdir
430dir_perso=prefdir;
431profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
432if exist(profil_perso,'file')
433    h=load (profil_perso);
434    if isfield(h,'RootPath') && ischar(h.RootPath)
435        oldfile=h.RootPath;
436    end
437end
438
439%% launch the browser
440fileinput=uigetfile_uvmat('pick a file to append in the input table',oldfile);
441hh=dir(fileinput);
442if numel(hh)>1
443    msgbox_uvmat('ERROR','invalid input, probably a broken link');
444else
445    if ~isempty(fileinput)
446        display_file_name(handles,fileinput,'append')
447    end
448end
449
450%------------------------------------------------------------------------
451% --- fct activated by selecting a previous file under the menu Open
452%------------------------------------------------------------------------
453function MenuFile_Callback(hObject, eventdata, handles)
454
455errormsg=display_file_name(handles,get(hObject,'Label'),'one');
456if ~isempty(errormsg)
457    set(hObject,'Label','')
458    MenuFile=[{get(handles.MenuFile_1,'Label')};{get(handles.MenuFile_2,'Label')};...
459        {get(handles.MenuFile_3,'Label')};{get(handles.MenuFile_4,'Label')};{get(handles.MenuFile_5,'Label')}];
460    str_find=strcmp(get(hObject,'Label'),MenuFile);
461    MenuFile(str_find)=[]; % suppress the input file to the list
462    for ifile=1:numel(MenuFile)
463        set(handles.(['MenuFile_' num2str(ifile)]),'Label',MenuFile{ifile});
464    end
465end
466
467%------------------------------------------------------------------------
468% --- fct activated by selecting a previous file under the menu Open/append
469%------------------------------------------------------------------------
470function MenuFile_append_Callback(hObject, eventdata, handles)
471
472InputTable=get(handles.InputTable,'Data');
473if isempty(InputTable{1,1})% no input file in the table
474    display_file_name(handles,get(hObject,'Label'),'one') %refresh the input table, not append
475else
476    display_file_name(handles,get(hObject,'Label'),'append')% append the selected file to the current list of InputTable
477end
478
479%------------------------------------------------------------------------
480% --- fct activated by the browser under 'Open campaign/Browse...'
481%------------------------------------------------------------------------
482function MenuBrowseCampaign_Callback(hObject, eventdata, handles)
483
484%% look for the previously opened file 'oldfile'
485InputTable=get(handles.InputTable,'Data');
486if ~isempty(InputTable)
487oldfile=fullfile(InputTable{1,1},InputTable{1,2});
488else
489    % use a file name stored in prefdir
490    dir_perso=prefdir;
491    profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
492    if exist(profil_perso,'file')
493        h=load (profil_perso);
494        if isfield(h,'MenuCampaign') && ~isempty(h.MenuCampaign)&& ischar(h.MenuCampaign{1})
495            oldfile=h.MenuCampaign{1};
496        end
497    end
498end
499
500OutPut=browse_data(oldfile,'on','on'); % open the GUI browse_data to get select a campaign dir, experiment and device
501NbLines=numel(OutPut.Experiment)*numel(OutPut.DataSeries);
502icount=0;
503for iexp=1:numel(OutPut.Experiment)
504    for idevice=1:numel(OutPut.DataSeries)
505        icount=icount+1;
506        InputTable{icount,1}=fullfile(OutPut.Campaign,OutPut.Experiment{iexp});
507        InputTable{icount,2}=OutPut.DataSeries{idevice};
508        if isempty(InputTable{icount,3})
509            if icount>1
510            InputTable{icount,3}=InputTable{icount-1,3};
511            else
512                InputTable{icount,3}='';
513            end
514        end
515        if isempty(InputTable{icount,4})
516            if icount>1
517            InputTable{icount,4}=InputTable{icount-1,4};
518            else
519                InputTable{icount,4}='';
520            end
521        end
522                if isempty(InputTable{icount,5})
523            if icount>1
524            InputTable{icount,5}=InputTable{icount-1,5};
525            else
526                InputTable{icount,5}='';
527            end
528        end
529    end
530end
531if size(InputTable,1)>icount
532    InputTable(icount+1:size(InputTable,1),:)=[];
533end
534set(handles.InputTable,'Data',InputTable)
535REFRESH_Callback(hObject, eventdata, handles)
536
537% --------------------------------------------------------------------
538function MenuCampaign_Callback(hObject, eventdata, handles)
539% --------------------------------------------------------------------
540
541OutPut=browse_data(get(hObject,'Label'),'on','on'); % open the GUI browse_data to get select a campaign dir, experiment and device
542if ~isfield(OutPut,'Campaign')
543    return
544end
545NbLines=numel(OutPut.Experiment)*numel(OutPut.DataSeries);
546icount=0;
547InputTable=get(handles.InputTable,'Data');
548for iexp=1:numel(OutPut.Experiment)
549    for idevice=1:numel(OutPut.DataSeries)
550        icount=icount+1;
551        InputTable{icount,1}=fullfile(OutPut.Campaign,OutPut.Experiment{iexp});
552        InputTable{icount,2}=OutPut.DataSeries{idevice};
553        if isempty(InputTable{icount,3})
554            if icount>1
555                InputTable{icount,3}=InputTable{icount-1,3};
556            else
557                InputTable{icount,3}='';
558            end
559        end
560        if isempty(InputTable{icount,4})
561            if icount>1
562                InputTable{icount,4}=InputTable{icount-1,4};
563            else
564                InputTable{icount,4}='';
565            end
566        end
567        if isempty(InputTable{icount,5})
568            if icount>1
569                InputTable{icount,5}=InputTable{icount-1,5};
570            else
571                InputTable{icount,5}='';
572            end
573        end
574    end
575end
576if size(InputTable,1)>icount
577    InputTable(icount+1:size(InputTable,1),:)=[];
578end
579set(handles.InputTable,'Data',InputTable)
580REFRESH_Callback(hObject, eventdata, handles)
581
582
583% --- Executes when selected cell(s) is changed in InputTable.
584function InputTable_CellSelectionCallback(hObject, eventdata, handles)
585iline=[];
586if ~isempty(eventdata.Indices)
587    iline=eventdata.Indices(1);
588end
589set(handles.InputLine,'String',num2str(iline));
590
591%------------------------------------------------------------------------
592% --- 'key_press_fcn:' function activated when a key is pressed on the keyboard
593%------------------------------------------------------------------------
594function InputTable_KeyPressFcn(hObject, eventdata, handles)
595set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH button to magenta color to indicate that input refresh is needed
596set(handles.OutputSubDir,'BackgroundColor',[1 0 1])% set edit box OutputSubDir to magenta color to indicate that refresh may be needed
597xx=double(get(handles.series,'CurrentCharacter')); % get the keyboard character
598if ~isempty(xx)
599    switch xx
600        case 31 %downward arrow
601            InputTable=get(handles.InputTable,'Data');
602            iline=str2double(get(handles.InputLine,'String'));
603            if isequal(iline,size(InputTable,1))% arrow downward
604                InputTable=[InputTable;InputTable(iline,:)]; % create a new line as a copy of the last one
605                set(handles.InputTable,'Data',InputTable);
606            end
607        case 127  %key 'Suppress'
608            ClearLine_Callback(hObject, eventdata, handles)
609    end
610end
611
612%------------------------------------------------------------------------
613% --- Executes on button press in REFRESH.
614function REFRESH_Callback(hObject, eventdata, handles)
615%------------------------------------------------------------------------
616InputTable=get(handles.InputTable,'Data');
617set(handles.series,'Pointer','watch') % set the mouse pointer to 'watch'
618set(handles.REFRESH,'BackgroundColor',[1 1 0])% set REFRESH  button to yellow color (indicate activation)
619drawnow
620empty_line=false(size(InputTable,1),1);
621for iline=1:size(InputTable,1)
622    empty_line(iline)= isempty(cell2mat(InputTable(iline,1:3)));
623end
624if ~isempty(find(empty_line));
625    InputTable(empty_line,:)=[]; % remove empty lines
626    set(handles.InputTable,'Data',InputTable)
627    ListTable={'MinIndex_i','MaxIndex_i','MinIndex_j','MaxIndex_j','PairString','TimeTable'};
628    for ilist=1:numel(ListTable)
629        Table=get(handles.(ListTable{ilist}),'Data');
630        Table(empty_line,:)=[]; % remove empty lines
631        set(handles.(ListTable{ilist}),'Data',Table);
632    end
633    set(handles.series,'UserData',[])%refresh the stored info
634end
635nbview=size(InputTable,1);
636for iview=1:nbview
637    RootPath=fullfile(InputTable{iview,1},InputTable{iview,2});
638    if ~exist(RootPath,'dir')
639        i1_series=[];
640        RootFile='';
641    else %scan the input folder
642        InputTable{iview,3}=regexprep(InputTable{iview,3},'^/','');
643            [RootPath,~,RootFile,i1_series,i2_series,j1_series,j2_series,tild,FileInfo,MovieObject]=...
644                find_file_series(fullfile(InputTable{iview,1},InputTable{iview,2}),[InputTable{iview,3} InputTable{iview,4} InputTable{iview,5}]);
645    end
646    % if no file is found, open a browser
647    if isempty(RootFile)&& isempty(i1_series)
648        fileinput=uigetfile_uvmat(['wrong input at line ' num2str(iview) ':pick a new input file'],RootPath);
649        if isempty(fileinput)
650            set(handles.REFRESH,'BackgroundColor',[1 0 0])% set REFRESH  back to red color
651            return
652        else
653            display_file_name(handles,fileinput,iview)
654        end
655    else
656       update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileInfo,MovieObject,iview)
657    end
658end
659
660%% update MinIndex_i and MaxIndex_i if the input table content has been reduced in line nbre
661MinIndex_i_table=get(handles.MinIndex_i,'Data'); % retrieve the min indices in the table MinIndex
662set(handles.MinIndex_i,'Data',MinIndex_i_table(1:nbview,:));
663MinIndex_j_table=get(handles.MinIndex_j,'Data'); % retrieve the min indices in the table MinIndex
664set(handles.MinIndex_j,'Data',MinIndex_j_table(1:nbview,:));
665MaxIndex_i_table=get(handles.MaxIndex_i,'Data'); % retrieve the min indices in the table MinIndex
666
667set(handles.MaxIndex_i,'Data',MaxIndex_i_table(1:nbview,:));
668MaxIndex_j_table=get(handles.MaxIndex_j,'Data'); % retrieve the min indices in the table MinIndex
669set(handles.MaxIndex_j,'Data',MaxIndex_j_table(1:nbview,:));
670PairString=get(handles.PairString,'Data'); % retrieve the min indices in the table MinIndex
671set(handles.PairString,'Data',PairString(1:nbview,:));
672TimeTable=get(handles.TimeTable,'Data'); % retrieve the min indices in the table MinIndex
673set(handles.TimeTable,'Data',TimeTable(1:nbview,:));
674
675%% set length of waitbar
676displ_time(handles)
677set(handles.REFRESH,'BackgroundColor',[1 0 0])% set REFRESH  button to red color (indicate activation finished)
678set(handles.series,'Pointer','arrow') % set the mouse pointer to 'watch'
679
680%% enable field and veltype menus, in accordance with the current action
681ActionInput_Callback([],[], handles)
682
683
684%------------------------------------------------------------------------
685% --- Function called when a new file is opened, either by series_OpeningFcn or by the browser
686%------------------------------------------------------------------------
687% INPUT:
688% handles: handles of elements in the GUI
689% Param: structure of input parameters, including  input file name and path
690% iview: line index in the input table
691%       or 'one': refresh the list
692%         'append': add a new line to the input table
693function errormsg=display_file_name(handles,Param,iview)
694 
695set(handles.REFRESH,'BackgroundColor',[1 1 0])% set REFRESH  button to yellow color (indicate activation)
696drawnow
697errormsg=''; % default
698if ischar(Param)
699    fileinput=Param;
700else% input set when series is opened (called by the GUI uvmat)
701    fileinput=Param.FileName;
702end
703   
704%% get the input root name, indices, file extension and nomenclature NomType
705if ~exist(fileinput,'file')
706    errormsg=['input file ' fileinput  ' does not exist'];
707    msgbox_uvmat('ERROR',errormsg)
708    set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH  button to magenta color (refresh still needed)
709    return
710end
711
712%% detect root name, nomenclature and indices in the input file name:
713[FilePath,FileName,FileExt]=fileparts(fileinput);
714%%%%%%%%%%%%%%%%%%
715%TODO: case of input by uvmat: do not check agai the input seies %%%%%%%
716%%%%%%%%%%%%%%%%%%%
717% detect the file type, get the movie object if relevant, and look for the corresponding file series:
718% the root name and indices may be corrected by including the first index i1 if a corresponding xml file exists
719[RootPath,SubDir,RootFile,i1_series,i2_series,j1_series,j2_series,NomType,FileInfo,MovieObject,i1,i2,j1,j2]=find_file_series(FilePath,[FileName FileExt]);
720FileType=FileInfo.FileType;
721if isempty(RootFile)&&isempty(i1_series)
722    errormsg='no input file in the series';
723    msgbox_uvmat('ERROR',errormsg)
724    set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH  button to magenta color (end of activation)
725    return
726end
727if strcmp(FileType,'txt')
728    edit(fileinput)
729    set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH  button to  magenta color (end of activation)
730    return
731elseif strcmp(FileType,'xml')
732    editxml(fileinput)
733    set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH  button to magenta  color (end of activation)
734     return
735elseif strcmp(FileType,'figure')
736    open(fileinput)
737    set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH  button to magenta  color (end of activation)
738     return
739end
740
741%% enable other menus and uicontrols
742% set(handles.MenuOpenCampaign,'Enable','on')
743set(handles.MenuCampaign_1,'Enable','on')
744set(handles.MenuCampaign_2,'Enable','on')
745set(handles.MenuCampaign_3,'Enable','on')
746set(handles.MenuCampaign_4,'Enable','on')
747set(handles.MenuCampaign_5,'Enable','on')
748set(handles.RUN, 'Enable','On')
749set(handles.RUN,'BackgroundColor',[1 0 0])% set RUN button to red
750set(handles.InputTable,'BackgroundColor',[1 1 0]) % set RootPath edit box  to yellow
751drawnow
752
753
754%% fill the list of file series
755InputTable=get(handles.InputTable,'Data');
756SeriesData=get(handles.series,'UserData');
757if strcmp(iview,'append') % display the input data as a new line in the table
758    iview=size(InputTable,1)+1; % the next line in InputTable becomes the current line
759%     InputTable(iview,:)=[{RootPath},{SubDir},{RootFile},{NomType},{FileExt}];
760elseif strcmp(iview,'one') % refresh the list of  input  file series
761    iview=1; % the first line in InputTable becomes the current line
762    InputTable={'','','','',''};
763%     InputTable(iview,:)=[{RootPath},{SubDir},{RootFile},{NomType},{FileExt}];
764    set(handles.TimeTable,'Data',[{''},{[]},{[]},{[]},{[]}])
765    set(handles.MinIndex_i,'Data',[])
766    set(handles.MaxIndex_i,'Data',[])
767    set(handles.MinIndex_j,'Data',[])
768    set(handles.MaxIndex_j,'Data',[])
769    set(handles.PairString,'Data',{''})
770    SeriesData.CheckPair=0; % reset the list of input lines with pairs
771    SeriesData.i1_series={};
772    SeriesData.i2_series={};
773    SeriesData.j1_series={};
774    SeriesData.j2_series={};
775    SeriesData.FileType={};
776    SeriesData.FileInfo={};
777    SeriesData.Time={};
778end
779if isfield(SeriesData,'i1_series')
780    SeriesData.i1_series(iview+1:end)=[];
781    SeriesData.i2_series(iview+1:end)=[];
782    SeriesData.j1_series(iview+1:end)=[];
783    SeriesData.j2_series(iview+1:end)=[];
784    SeriesData.FileType(iview+1:end)=[];
785    SeriesData.FileInfo(iview+1:end)=[];
786    SeriesData.Time(iview+1:end)=[];
787end
788InputTable(iview,:)=[{RootPath},{SubDir},{RootFile},{NomType},{FileExt}];
789if iview >1
790    set(handles.InputLine,'String',num2str(iview))
791end
792set(handles.InputTable,'Data',InputTable)
793
794%% determine the selected reference field indices for pair display
795if isempty(i1)
796    i1=1;
797end
798if isempty(i2)
799    i2=i1;
800end
801ref_i=floor((i1+i2)/2); % reference image number corresponding to the file
802% set(handles.num_ref_i,'String',num2str(ref_i));
803if isempty(j1)
804    j1=1;
805end
806if isempty(j2)
807    j2=j1;
808end
809ref_j=floor((j1+j2)/2); % reference image number corresponding to the file
810SeriesData.ref_i=ref_i;
811SeriesData.ref_j=ref_j;
812
813%% update first and last indices if they do not exist
814Param=read_GUI(handles.series);
815first_j=[];
816if isfield(Param.IndexRange,'first_j'); first_j=Param.IndexRange.first_j; end
817last_j=[];
818if isfield(Param.IndexRange,'last_j'); last_j=Param.IndexRange.last_j; end
819PairString='';
820if isfield(Param.IndexRange,'PairString'); PairString=Param.IndexRange.PairString; end
821[i1,i2,j1,j2] = get_file_index(Param.IndexRange.first_i,first_j,PairString);
822FirstFileName=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},...
823    Param.InputTable{1,5},Param.InputTable{1,4},i1,i2,j1,j2);
824if ~exist(FirstFileName,'file')
825    set(handles.num_first_i,'String',num2str(ref_i))
826    set(handles.num_first_j,'String',num2str(ref_j))
827end
828[i1,i2,j1,j2] = get_file_index(Param.IndexRange.last_i,last_j,PairString);
829LastFileName=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},...
830    Param.InputTable{1,5},Param.InputTable{1,4},i1,i2,j1,j2);
831if ~exist(LastFileName,'file')
832    set(handles.num_last_i,'String',num2str(ref_i))
833    set(handles.num_last_j,'String',num2str(ref_j))
834end
835
836%% update the list of recent files in the menubar and save it for future opening
837MenuFile=[{get(handles.MenuFile_1,'Label')};{get(handles.MenuFile_2,'Label')};...
838    {get(handles.MenuFile_3,'Label')};{get(handles.MenuFile_4,'Label')};{get(handles.MenuFile_5,'Label')}];
839str_find=strcmp(fileinput,MenuFile);
840if isempty(find(str_find,1))
841    MenuFile=[{fileinput};MenuFile]; % insert the current file if not already in the list
842end
843for ifile=1:min(length(MenuFile),5)
844    eval(['set(handles.MenuFile_' num2str(ifile) ',''Label'',MenuFile{ifile});'])
845end
846dir_perso=prefdir;
847profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
848if exist(profil_perso,'file')
849    save (profil_perso,'MenuFile','-append'); % store the file names for future opening of uvmat
850else
851    save (profil_perso,'MenuFile','-V6'); % store the file names for future opening of uvmat
852end
853% save the opened file to initiate future opening
854SeriesData.RefFile{iview}=fileinput; % reference opening file for line iview
855SeriesData.Ref_i1=i1;
856SeriesData.Ref_i2=i2;
857SeriesData.Ref_j1=j1;
858SeriesData.Ref_j2=j2;
859set(handles.series,'UserData',SeriesData)
860
861set(handles.InputTable,'BackgroundColor',[1 1 1])
862
863%% initiate input file series and refresh the current field view:     
864update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileInfo,MovieObject,iview);
865%% enable field and veltype menus, in accordance with the current action
866ActionName_Callback([],[], handles)
867
868%% set length of waitbar
869displ_time(handles)
870
871set(handles.REFRESH,'BackgroundColor',[1 0 0])% set REFRESH  button to red color (end of activation)
872
873%------------------------------------------------------------------------
874% --- Update information about a new field series (indices to scan, timing,
875%     calibration from an xml file
876function update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileInfo,VideoObject,iview)
877%------------------------------------------------------------------------
878InputTable=get(handles.InputTable,'Data');
879
880%% display the min and max indices for the whole file series
881if size(i1_series,2)==2 && min(min(i1_series(:,1,:)))==0
882    MinIndex_j=1; % index j set to 1 by default
883    MaxIndex_j=1;
884    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)
885    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)
886else
887    ref_i=squeeze(max(i1_series(1,:,:),[],2)); % select ref_j index for each ref_i
888    ref_j=squeeze(max(j1_series(1,:,:),[],3)); % select ref_i index for each ref_j
889     MinIndex_i=min(find(ref_i))-1;
890     MaxIndex_i=max(find(ref_i))-1;
891     MaxIndex_j=max(find(ref_j))-1;
892     MinIndex_j=min(find(ref_j))-1;
893    diff_j_max=diff(ref_j);
894    diff_i_max=diff(ref_i);
895    if ~isempty(diff_i_max) && isequal (diff_i_max,diff_i_max(1)*ones(size(diff_i_max)))
896        set(handles.num_incr_i,'String',num2str(diff_i_max(1)))% detect an increment to dispaly by default
897    end
898    if ~isempty(diff_j_max) && isequal (diff_j_max,diff_j_max(1)*ones(size(diff_j_max)))
899        set(handles.num_incr_j,'String',num2str(diff_j_max(1)))
900    end
901end
902if isequal(MinIndex_i,-1)
903    MinIndex_i=0;
904end
905if isequal(MinIndex_j,-1)
906    MinIndex_j=0;
907end
908MinIndex_i_table=get(handles.MinIndex_i,'Data'); % retrieve the min indices in the table MinIndex
909MinIndex_j_table=get(handles.MinIndex_j,'Data'); % retrieve the min indices in the table MinIndex
910MaxIndex_i_table=get(handles.MaxIndex_i,'Data'); % retrieve the min indices in the table MinIndex
911MaxIndex_j_table=get(handles.MaxIndex_j,'Data'); % retrieve the min indices in the table MinIndex
912if ~isempty(MinIndex_i)&&~isempty(MaxIndex_i)
913    MinIndex_i_table(iview,1)=MinIndex_i;
914    MaxIndex_i_table(iview,1)=MaxIndex_i;
915end
916if ~isempty(MinIndex_j)&&~isempty(MaxIndex_j)
917    MinIndex_j_table(iview,1)=MinIndex_j;
918    MaxIndex_j_table(iview,1)=MaxIndex_j;
919end
920set(handles.MinIndex_i,'Data',MinIndex_i_table)%display the min indices in the table MinIndex
921set(handles.MinIndex_j,'Data',MinIndex_j_table)%display the max indices in the table MaxIndex
922set(handles.MaxIndex_i,'Data',MaxIndex_i_table)%display the min indices in the table MinIndex
923set(handles.MaxIndex_j,'Data',MaxIndex_j_table)%display the max indices in the table MaxIndex
924SeriesData=get(handles.series,'UserData');
925
926%% adjust the first and last indices for the selected series, only if requested by the bounds
927% i index, compare input to min index i
928first_i=str2num(get(handles.num_first_i,'String')); % retrieve previous first i
929% ref_i=str2num(get(handles.num_ref_i,'String')); % index i given by the input field
930ref_i=1;
931if isfield(SeriesData,'ref_i')
932    ref_i=SeriesData.ref_i;
933end
934if isempty(first_i)
935    first_i=ref_i; % first_i updated by the input value
936elseif first_i < MinIndex_i
937    first_i=MinIndex_i; % first_i set to the min i index (restricted by oter input lines)
938elseif first_i >MaxIndex_i
939    first_i=MaxIndex_i; % first_i set to the max i index (restricted by oter input lines)
940end
941% j index,  compare input to min index j
942first_j=str2num(get(handles.num_first_j,'String'));
943ref_j=1;
944if isfield(SeriesData,'ref_j')
945    ref_j=SeriesData.ref_j;
946end
947if isempty(first_j)
948    first_j=ref_j; % first_j updated by the input value
949elseif first_j<MinIndex_j
950    first_j=MinIndex_j; % first_j set to the min j index (restricted by oter input lines)
951elseif first_j >MaxIndex_j
952    first_j=MaxIndex_j; % first_j set to the max j index (restricted by oter input lines)
953end
954% i index, compare input to max index i
955last_i=str2num(get(handles.num_last_i,'String'));
956if isempty(last_i)
957    last_i=ref_i;
958elseif last_i > MaxIndex_i
959    last_i=MaxIndex_i;
960elseif last_i<first_i
961    last_i=first_i;
962end
963% j index, compare input to max index j
964last_j=str2num(get(handles.num_last_j,'String'));
965if isempty(last_j)
966    last_j=ref_j;
967elseif last_j>MaxIndex_j
968    last_j=MaxIndex_j;
969elseif last_j<first_j
970    last_j=first_j;
971end
972set(handles.num_first_i,'String',num2str(first_i));
973set(handles.num_first_j,'String',num2str(first_j));
974set(handles.num_last_i,'String',num2str(last_i));
975set(handles.num_last_j,'String',num2str(last_j));
976
977%% number of slices set by default
978NbSlice=[]; % default
979% read  value set by the first series for the append mode (iwiew >1)
980if iview>1 && strcmp(get(handles.num_NbSlice,'Visible'),'on')
981    NbSlice=str2double(get(handles.num_NbSlice,'String'));
982end
983
984%% default time settings
985TimeUnit='';
986% read  value set by the first series for the append mode (iwiew >1)
987if iview>1
988    TimeUnit=get(handles.TimeUnit,'String');
989end
990TimeName='';
991Time=[]; % default
992TimeMin=[];
993TimeFirst=[];
994TimeLast=[];
995TimeMax=[];
996
997%%  read image documentation file if found
998XmlData=[];
999check_calib=0;
1000XmlFileName=find_imadoc(InputTable{iview,1},InputTable{iview,2},InputTable{iview,3},InputTable{iview,5});
1001if ~isempty(XmlFileName)
1002    [XmlData,errormsg]=imadoc2struct(XmlFileName);
1003    if ~isempty(errormsg)
1004        msgbox_uvmat('WARNING',['error in reading ' XmlFileName ': ' errormsg]);
1005    end
1006    % read time if available
1007    if isfield(XmlData,'Time')
1008        Time=XmlData.Time;
1009        TimeName='xml';
1010    end
1011    if isfield(XmlData,'Camera')
1012        if isfield(XmlData.Camera,'TimeUnit')&& ~isempty(XmlData.Camera.TimeUnit)
1013            if iview>1 && ~isempty(TimeUnit) && ~strcmp(TimeUnit,XmlData.Camera.TimeUnit)
1014                msgbox_uvmat('WARNING','inconsistent time unit with the first field series');
1015            end
1016            TimeUnit=XmlData.Camera.TimeUnit;
1017        end
1018    end
1019    % number of slices
1020    if isfield(XmlData,'TranslationMotor')&& isfield(XmlData.TranslationMotor,'NbSlice')
1021        NbSlice_motor=XmlData.TranslationMotor.NbSlice;
1022        if ~isempty(NbSlice) && ~isequal(NbSlice_motor,NbSlice)
1023                msgbox_uvmat('WARNING','inconsistent Z numbers of Z indices');
1024        else
1025            NbSlice=NbSlice_motor;
1026        end
1027    end
1028   
1029%     if isfield(XmlData,'GeometryCalib')
1030%         check_calib=1;
1031%         if isfield(XmlData.GeometryCalib,'SliceCoord')
1032%             siz=size(XmlData.GeometryCalib.SliceCoord);
1033%             if ~isempty(NbSlice)&& ~isequal(size(1),NbSlice)
1034%                 msgbox_uvmat('WARNING','inconsistent numbers of Z indices between motor and calibration');
1035%             else
1036%                 NbSlice=siz(1);
1037%             end
1038%         end
1039%     end
1040end
1041if ~isempty(NbSlice)
1042set(handles.num_NbSlice,'String',num2str(NbSlice))
1043set(handles.num_NbSlice,'Visible','on')
1044end
1045
1046%% read timing  from the current file (prioritary)
1047if ~isempty(VideoObject)% case of movies
1048    imainfo=get(VideoObject);
1049    if isempty(j1_series); % frame index along i
1050        Time=zeros(imainfo.NumberOfFrames+1,2);
1051        Time(:,2)=(0:1/imainfo.FrameRate:(imainfo.NumberOfFrames)/imainfo.FrameRate)';
1052    else
1053        Time=[0;ones(size(i1_series,3)-1,1)]*(0:1/imainfo.FrameRate:(imainfo.NumberOfFrames)/imainfo.FrameRate);
1054    end
1055    TimeName='video';
1056end
1057
1058
1059%% determine the min and max times: case of Netcdf files will be treated later in FieldName_Callback
1060if ~isempty(TimeName)
1061    TimeMin=Time(MinIndex_i+1,MinIndex_j+1);
1062    if size(Time)>=[first_i+1 first_j+1]
1063        TimeFirst=Time(first_i+1,first_j+1);
1064    end
1065    if size(Time)>=[last_i+1 last_j+1]
1066        TimeLast=Time(last_i+1,last_j+1);
1067    end
1068    if size(Time)>=[MaxIndex_i+1 MaxIndex_j+1];
1069        TimeMax=Time(MaxIndex_i+1,MaxIndex_j+1);
1070    end
1071end
1072
1073%% update the time table
1074TimeTable=get(handles.TimeTable,'Data');
1075TimeTable{iview,1}=TimeName;
1076TimeTable{iview,2}=TimeMin;
1077TimeTable{iview,3}=TimeFirst;
1078TimeTable{iview,4}=TimeLast;
1079TimeTable{iview,5}=TimeMax;
1080set(handles.TimeTable,'Data',TimeTable)
1081
1082%% update the series info in 'UserData'
1083SeriesData.i1_series{iview}=i1_series;
1084SeriesData.i2_series{iview}=i2_series;
1085SeriesData.j1_series{iview}=j1_series;
1086SeriesData.j2_series{iview}=j2_series;
1087SeriesData.FileType{iview}=FileInfo.FileType;
1088SeriesData.FileInfo{iview}=FileInfo;
1089SeriesData.Time{iview}=Time;
1090
1091SeriesData.TimeName=TimeName;
1092
1093if check_calib
1094    SeriesData.GeometryCalib{iview}=XmlData.GeometryCalib;
1095end
1096set(handles.series,'UserData',SeriesData)
1097
1098%% update pair menus
1099hset_pair=findobj(allchild(0),'Tag','set_pairs');
1100if ~isempty(hset_pair), delete(hset_pair); end % delete the GUI set_pair if opened
1101CheckPair= ~isempty(i2_series)||~isempty(j2_series); % check whether index pairs need to be defined
1102PairString=get(handles.PairString,'Data');
1103if CheckPair% if pairs need to be display for line iview
1104    [ModeMenu,ModeValue]=update_mode(i1_series,i2_series,j2_series);
1105    Menu=update_listpair(i1_series,i2_series,j1_series,j2_series,ModeMenu{ModeValue},Time,TimeUnit,ref_i,ref_j,TimeName,InputTable(iview,:),FileInfo);
1106    PairString{iview,1}=Menu{1};
1107else
1108    PairString{iview,1}=''; % no pair for #iview
1109end
1110set(handles.PairString,'Data',PairString)
1111if isempty(find(cellfun('isempty',get(handles.PairString,'Data'))==0, 1))% if all lines of pairs are empty
1112    set(handles.PairString,'Visible','off')
1113    set(handles.SetPairs,'Visible','off')
1114else
1115    set(handles.PairString,'Visible','on')
1116    set(handles.SetPairs,'Visible','on')
1117end
1118
1119
1120%% display the set of existing files as an image
1121set(handles.FileStatus,'Units','pixels')
1122Position=get(handles.FileStatus,'Position');
1123set(handles.FileStatus,'Units','normalized')
1124%xI=0.5:Position(3)-0.5;
1125nbview=numel(SeriesData.i1_series);
1126j_max=cell(1,nbview);
1127MaxIndex_i=ones(1,nbview); % default
1128MinIndex_i=ones(1,nbview); % default
1129for iline=1:nbview
1130    pair_max=squeeze(max(SeriesData.i1_series{iline},[],1)); % max on pair index
1131    j_max{iline}=max(pair_max,[],1); % max on j index
1132    if ~isempty(j_max{iline})
1133    MaxIndex_i(iline)=max(find(j_max{iline}))-1; % max ref index i
1134    MinIndex_i(iline)=min(find(j_max{iline}))-1; % min ref index i
1135    end
1136end
1137MinIndex_i=min(MinIndex_i);
1138MaxIndex_i=max(MaxIndex_i);
1139range_index=MaxIndex_i-MinIndex_i+1;
1140range_y=max(1,floor(Position(4)/nbview));
1141npx=floor(Position(3));
1142file_indices=MinIndex_i+floor(((0.5:npx-0.5)/npx)*range_index)+1;
1143CData=zeros(nbview*range_y,npx); % initiate the image representing the existing files
1144for iline=1:nbview
1145    ind_y=1+(iline-1)*range_y:iline*range_y;
1146    LineData=zeros(size(file_indices));
1147    file_select=file_indices(file_indices<=numel(j_max{iline}));
1148    ind_select=find(file_indices<=numel(j_max{iline}));
1149    LineData(ind_select)=j_max{iline}(file_select)~=0;
1150    CData(ind_y,:)=ones(size(ind_y'))*LineData;
1151end
1152CData=cat(3,zeros(size(CData)),CData,zeros(size(CData))); % make color images r=0,g,b=0
1153set(handles.FileStatus,'CData',CData);
1154
1155%-----------------------------------------------------------guide -------------
1156%------------------------------------------------------------------------
1157%  III - FUNCTIONS ASSOCIATED TO THE FRAME IndexRange
1158%------------------------------------------------------------------------
1159
1160
1161% ---- determine the menu to put in mode and advice a default choice
1162%------------------------------------------------------------------------
1163function [ModeMenu,ModeValue]=update_mode(i1_series,i2_series,j2_series)
1164%------------------------------------------------------------------------   
1165ModeMenu={''};
1166if isempty(j2_series)% no j pair
1167    ModeValue=1;
1168    if ~isempty(i2_series)
1169        ModeMenu={'series(Di)'}; % pair menu with only option Di
1170    end
1171else %existence of j pairs
1172    pair_max=squeeze(max(i1_series,[],1)); % max on pair index
1173    j_max=max(pair_max,[],1);
1174    MaxIndex_i=find(j_max, 1, 'last' )-1; % max ref index i
1175    MinIndex_i=find(j_max, 1 )-1; % min ref index i
1176    i_max=max(pair_max,[],2);
1177    MaxIndex_j=find(i_max, 1, 'last' )-1; % max ref index i
1178    MinIndex_j=find(i_max, 1 )-1; % min ref index i
1179    if MaxIndex_j==MinIndex_j
1180        ModeValue=1;
1181        ModeMenu={'bursts'};
1182    elseif MaxIndex_i==MinIndex_i
1183        ModeValue=1;
1184        ModeMenu={'series(Dj)'};
1185    else
1186        ModeMenu={'bursts';'series(Dj)'};
1187        if (MaxIndex_j-MinIndex_j)>10
1188            ModeValue=2; % set mode to series(Dj) if more than 10 j values
1189        else
1190            ModeValue=1;
1191        end
1192    end
1193end
1194
1195
1196%------------------------------------------------------------------------
1197function displ_pair=update_listpair(i1_series,i2_series,j1_series,j2_series,mode,time,TimeUnit,ref_i,ref_j,TimeName,InputTable,FileInfo)
1198%------------------------------------------------------------------------
1199displ_pair={};
1200if isempty(TimeUnit)
1201    dtunit='e-03';
1202else
1203    dtunit=['m' TimeUnit];
1204end
1205switch mode
1206    case 'series(Di)'
1207        diff_i=i2_series-i1_series;
1208        min_diff=min(diff_i(diff_i>0));
1209        max_diff=max(diff_i(diff_i>0));
1210        for ipair=min_diff:max_diff
1211            if numel(diff_i(diff_i==ipair))>0
1212                pair_string=['Di= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2)) ];
1213                if ~isempty(time)
1214                    if ref_i<=floor(ipair/2)
1215                        ref_i=floor(ipair/2)+1; % shift ref_i to get the first pair
1216                    end
1217                    Dt=time(ref_i+ceil(ipair/2),ref_j)-time(ref_i-floor(ipair/2),ref_j);
1218                    pair_string=[pair_string ', Dt=' num2str(Dt) ' ' dtunit];
1219                end
1220                displ_pair=[displ_pair;{pair_string}];
1221            end
1222        end
1223        if ~isempty(displ_pair)
1224            displ_pair=[displ_pair;{'Di=*|*'}];
1225        end
1226    case 'series(Dj)'
1227        if isempty(j2_series)
1228            msgbox_uvmat('ERROR','no j1-j2 pair available')
1229            return
1230        end
1231        diff_j=j2_series-j1_series;
1232        min_diff=min(diff_j(diff_j>0));
1233        max_diff=max(diff_j(diff_j>0));
1234        for ipair=min_diff:max_diff
1235            if numel(diff_j(diff_j==ipair))>0
1236                pair_string=['Dj= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2)) ];
1237                if ~isempty(time)
1238                    if ref_j<=floor(ipair/2)
1239                        ref_j=floor(ipair/2)+1; % shift ref_i to get the first pair
1240                    end
1241                    Dt=time(ref_i,ref_j+ceil(ipair/2))-time(ref_i,ref_j-floor(ipair/2));
1242                    pair_string=[pair_string ', Dt=' num2str(Dt) ' ' dtunit];
1243                end
1244                displ_pair=[displ_pair;{pair_string}];
1245            end
1246        end
1247        if ~isempty(displ_pair)
1248            displ_pair=[displ_pair;{'Dj=*|*'}];
1249        end
1250    case 'bursts'
1251        if isempty(j2_series)
1252            msgbox_uvmat('ERROR','no j1-j2 pair available')
1253            return
1254        end
1255        %diff_j=j2_series-j1_series;
1256        min_j1=min(j1_series(j1_series>0));
1257        max_j1=max(j1_series(j1_series>0));
1258        min_j2=min(j2_series(j2_series>0));
1259        max_j2=max(j2_series(j2_series>0));
1260        for pair1=min_j1:min(max_j1,min_j1+20)
1261            for pair2=min_j2:min(max_j2,min_j2+20)
1262                if numel(j1_series(j1_series==pair1))>0 && numel(j2_series(j2_series==pair2))>0
1263                    pair_string=['j= ' num2str(pair1) '-' num2str(pair2)];
1264                    [TimeValue,DtValue]=get_time(ref_i,[],pair_string,InputTable,FileInfo,TimeName,'Dt');
1265                    %Dt=time(ref_i,pair2+1)-time(ref_i,pair1+1);
1266                    pair_string=[pair_string ', Dt=' num2str(DtValue) ' ' dtunit];
1267                    displ_pair=[displ_pair;{pair_string}];
1268                end
1269            end
1270        end
1271        if ~isempty(displ_pair)
1272            displ_pair=[displ_pair;{'j=*-*'}];
1273        end
1274end
1275
1276%------------------------------------------------------------------------
1277function num_first_i_Callback(hObject, eventdata, handles)
1278%------------------------------------------------------------------------
1279num_last_i_Callback(hObject, eventdata, handles)
1280
1281%------------------------------------------------------------------------
1282function num_last_i_Callback(hObject, eventdata, handles)
1283%------------------------------------------------------------------------
1284SeriesData=get(handles.series,'UserData');
1285if ~isfield(SeriesData,'Time')
1286    SeriesData.Time{1}=[];
1287end
1288displ_time(handles);
1289
1290%------------------------------------------------------------------------
1291function num_first_j_Callback(hObject, eventdata, handles)
1292%------------------------------------------------------------------------
1293 num_last_j_Callback(hObject, eventdata, handles)
1294
1295%------------------------------------------------------------------------
1296function num_last_j_Callback(hObject, eventdata, handles)
1297%------------------------------------------------------------------------
1298% first_j=str2num(get(handles.num_first_j,'String'));
1299% last_j=str2num(get(handles.num_last_j,'String'));
1300% ref_j=ceil((first_j+last_j)/2);
1301% set(handles.num_ref_j,'String', num2str(ref_j))
1302% num_ref_j_Callback(hObject, eventdata, handles)
1303SeriesData=get(handles.series,'UserData');
1304if ~isfield(SeriesData,'Time')
1305    SeriesData.Time{1}=[];
1306end
1307displ_time(handles);
1308
1309%------------------------------------------------------------------------
1310% ---- find the times corresponding to the first and last indices of a series
1311function displ_time(handles)
1312%------------------------------------------------------------------------
1313SeriesData=get(handles.series,'UserData'); %
1314if ~isfield(SeriesData,'Time')
1315    return
1316end
1317PairString=get(handles.PairString,'Data');
1318ref_i_1=str2num(get(handles.num_first_i,'String')); % first reference index
1319ref_i_2=str2num(get(handles.num_last_i,'String')); % last reference index
1320ref_j_1=[];ref_j_2=[];
1321if strcmp(get(handles.num_first_j,'Visible'),'on')
1322ref_j_1=str2num(get(handles.num_first_j,'String'));
1323ref_j_2=str2num(get(handles.num_last_j,'String'));
1324end
1325[i1_1,i2_1,j1_1,j2_1] = get_file_index(ref_i_1,ref_j_1,PairString);
1326[i1_2,i2_2,j1_2,j2_2] = get_file_index(ref_i_2,ref_j_2,PairString);
1327TimeTable=get(handles.TimeTable,'Data');
1328%%%%%%
1329%TODO: read time in netcdf file, see ActionName_Callback
1330%%%%%%%
1331%Pairs=get(handles.PairString,'Data');
1332for iview=1:size(TimeTable,1)
1333    if size(SeriesData.Time,1)<iview
1334        break
1335    end
1336    TimeTable{iview,3}=[];
1337    TimeTable{iview,4}=[];
1338    if size(SeriesData.Time{iview},1)>=i2_2+1 && (isempty(ref_j_1)||size(SeriesData.Time{iview},2)>=j2_2+1)
1339        if isempty(ref_j_1)
1340            time_first=(SeriesData.Time{iview}(i1_1+1,2)+SeriesData.Time{iview}(i2_1+1,2))/2;
1341            time_last=(SeriesData.Time{iview}(i1_2+1,2)+SeriesData.Time{iview}(i2_2+1,2))/2;
1342        else
1343            time_first=(SeriesData.Time{iview}(i1_1+1,j1_1+1)+SeriesData.Time{iview}(i2_1+1,j2_1+1))/2;
1344            time_last=(SeriesData.Time{iview}(i1_2+1,j1_2+1)+SeriesData.Time{iview}(i2_2+1,j2_1+1))/2;
1345        end
1346        TimeTable{iview,3}=time_first; % TODO: take into account pairs
1347        TimeTable{iview,4}=time_last; % TODO: take into account pairs
1348    end
1349end
1350set(handles.TimeTable,'Data',TimeTable)
1351
1352%% set the waitbar position with respect to the min and max in the series
1353MinIndex_i=min(get(handles.MinIndex_i,'Data'));
1354MaxIndex_i=max(get(handles.MaxIndex_i,'Data'));
1355pos_first=(ref_i_1-MinIndex_i)/(MaxIndex_i-MinIndex_i+1);
1356pos_last=(ref_i_2-MinIndex_i+1)/(MaxIndex_i-MinIndex_i+1);
1357if isempty(pos_first), pos_first=0; end
1358if isempty(pos_last), pos_last=1; end
1359Position=get(handles.Waitbar,'Position'); % position of the waitbar:= [ x,y, width, height]
1360Position_status=get(handles.FileStatus,'Position');
1361Position(1)=Position_status(1)+Position_status(3)*pos_first;
1362Position(3)=max(Position_status(3)*(pos_last-pos_first),0.001); % width must remain positive
1363set(handles.Waitbar,'Position',Position)
1364update_waitbar(handles.Waitbar,0)
1365
1366%------------------------------------------------------------------------
1367% --- Executes when selected cell(s) is changed in PairString.
1368function PairString_CellSelectionCallback(hObject, eventdata, handles)
1369%------------------------------------------------------------------------   
1370if numel(eventdata.Indices)>=1
1371    PairString=get(hObject,'Data');
1372    if ~isempty(PairString{eventdata.Indices(1)})
1373        SetPairs_Callback(hObject, eventdata.Indices(1), handles)
1374    end
1375end
1376
1377%-------------------------------------
1378function enable_i(handles,state)
1379set(handles.i_txt,'Visible',state)
1380set(handles.num_first_i,'Visible',state)
1381set(handles.num_last_i,'Visible',state)
1382set(handles.num_incr_i,'Visible',state)
1383
1384%-----------------------------------
1385function enable_j(handles,state)
1386set(handles.j_txt,'Visible',state)
1387set(handles.num_first_j,'Visible',state)
1388set(handles.num_last_j,'Visible',state)
1389set(handles.num_incr_j,'Visible',state)
1390set(handles.MinIndex_j,'Visible',state)
1391set(handles.MaxIndex_j,'Visible',state)
1392
1393
1394%%%%%%%%%%%%%%%%%%%%
1395%%  MAIN ActionName FUNCTIONS
1396%%%%%%%%%%%%%%%%%%%%
1397%------------------------------------------------------------------------
1398% --- Executes on button press in RUN.
1399%------------------------------------------------------------------------
1400function RUN_Callback(hObject, eventdata, handles)
1401
1402%% settings of the button RUN
1403if ~isequal(get(handles.ActionInput,'BackgroundColor'),[1 0 0])
1404    msgbox_uvmat('ERROR','first activate the button ActionInput')
1405    return
1406end
1407set(handles.RUN,'BusyAction','queue'); % activation of STOP button will set BusyAction to 'cancel'
1408set(handles.RUN, 'Enable','Off')% avoid further RUN action until the current one is finished
1409set(handles.RUN,'BackgroundColor',[1 1 0])%show activation of RUN by yellow color
1410drawnow
1411set(handles.status,'Value',0)% desable status display if relevant
1412status_Callback([], eventdata, handles)
1413
1414%% launch action
1415errormsg=launch_action(handles);
1416if ~isempty(errormsg)
1417     msgbox_uvmat('ERROR',errormsg)
1418end
1419
1420%% reset the GUI series
1421update_waitbar(handles.Waitbar,1); % put the waitbar to end position to indicate launching is finished
1422set(handles.RUN, 'Enable','On')
1423set(handles.RUN,'BackgroundColor',[1 0 0])
1424set(handles.RUN, 'Value',0)
1425
1426%------------------------------------------------------------------------
1427% --- called by RUN_Callback
1428%------------------------------------------------------------------------
1429% The calculations are launched in three different ways:
1430% RunMode='local': calculation on the local Matlab session, will prevent other actions during that time.
1431% RunMode='background': calculation on the local computer, but in a new Matlab session (with no graphic output).
1432% RunMode='cluster': calculations dispatched in a cluster, using a managing system, 'oar, 'sge, or 'sgb'.
1433% In the latter case, the calculation is split in 'packets' of i index (all j indices are contained in a single packet).
1434% This splitting is possible only if the different calculations in the series are independent. Otherwise the action
1435% function imposes a number of processes NbSlice in input, for instance NbSlice=1 for a time series.
1436% If NbSlice is not imposed, the splitting in packets (jobs) is determined
1437% so that a job is optimum length AdvisedJobCPUTime), and the total job number in any case smaller
1438% than MaxJobNumber (these parameters are defined in the file series.xml in
1439% accordance with the management strategy for the cluster). The jobs are
1440% dispatched in parallel into NbCore processors by the cluster managing system.
1441
1442function errormsg=launch_action(handles)
1443errormsg=''; % default
1444
1445%% read the data on the GUI series
1446Param=read_GUI_series(handles); % displayed parameters
1447SeriesData=get(handles.series,'UserData'); % hidden parameters
1448if isfield(SeriesData,'TransformInput')
1449    Param.TransformInput=SeriesData.TransformInput;
1450end
1451if ~isfield(SeriesData,'i1_series')
1452    errormsg='The input field series needs to be refreshed: press REFRESH';
1453    return
1454end
1455if isfield(Param,'InputFields')&& isfield(Param.InputFields,'FieldName')&& isequal(Param.InputFields.FieldName,'get_field...')
1456    errormsg='input field name(s) not defined, select get_field...';
1457    return
1458end
1459
1460%% select the Action mode, 'local', 'background' or 'cluster' (if available)
1461RunMode='local'; % default (needed for first opening of the GUI series)
1462if isfield(Param.Action,'RunMode')
1463    RunMode=Param.Action.RunMode;
1464    Param.Action=rmfield(Param.Action,'RunMode'); % remove from the recorded xml file to avoid interference during ImportConfig
1465end
1466ActionExt='.m'; % default
1467if isfield(Param.Action,'ActionExt')
1468    ActionExt=Param.Action.ActionExt; % '.m', '.sh' (compiled)  or '.py' (Python)
1469    Param.Action=rmfield(Param.Action,'ActionExt'); % remove from the recorded xml file to avoid interference during ImportConfig
1470end
1471ActionName=Param.Action.ActionName;
1472ActionPath=Param.Action.ActionPath;
1473path_series=fileparts(which('series'));
1474
1475%% create the Action fct handle if RunMode option = 'local'
1476if strcmp(RunMode,'local')
1477    if ~isequal(ActionPath,path_series)
1478        eval(['spath=which(''' ActionName ''');']) %spath = current path of the selected function ACTION
1479        if ~exist(ActionPath,'dir')
1480            errormsg=['The prescribed function path ' ActionPath ' does not exist'];
1481            return
1482        end
1483        if ~isequal(spath,ActionPath)
1484            addpath(ActionPath)% add the prescribed path if not the current one
1485        end
1486    end
1487    eval(['h_fun=@' ActionName ';'])%create a function handle for ACTION
1488    if ~isequal(ActionPath,path_series)
1489        rmpath(ActionPath)% add the prescribed path if not the current one
1490    end
1491end
1492
1493%% Get  parameters from series.xml
1494errormsg=''; % default error message
1495ActionFullName=fullfile(get(handles.ActionPath,'String'),ActionName);
1496
1497%% If a compiled version has been selected (ext .sh) check wether it needs to be recompiled
1498if strcmp(ActionExt,'.sh')
1499    TransformPath='';
1500    if isfield(SeriesData,'TransformPath')
1501        TransformPath=SeriesData.TransformPath;
1502        if isfield(SeriesData,'TransformList')
1503            TransformList=get(handles.TransformName,'String');
1504            TransformIndex=get(handles.TransformName,'Value');
1505            TransformName=TransformList{TransformIndex};
1506            if ~ismember(TransformName,SeriesData.TransformList)
1507                TransformPath='';
1508            end
1509        end
1510    end
1511    if ~isempty(TransformPath)&&...
1512          ~strcmp(TransformPath,get(handles.TransformPath,'String'))% if the transform is not in paths set for compilation
1513        msgbox_uvmat('ERROR', 'compilation not available for this transform function, select .m')
1514        return
1515    end
1516    set(handles.series,'Pointer','watch') % set the mouse pointer to 'watch'
1517    set(handles.ActionExt,'BackgroundColor',[1 1 0])
1518    [mcrmajor, mcrminor] = mcrversion;   
1519    MCRROOT = ['MCRROOT',int2str(mcrmajor),int2str(mcrminor)];
1520    RunTime = getenv(MCRROOT);
1521    ActionNameVersion=[ActionName '_' MCRROOT];
1522    ActionFullName=fullfile(get(handles.ActionPath,'String'),[ActionNameVersion '.sh']);
1523    % compile the .m file if the .sh file does not exist yet
1524    if ~exist(ActionFullName,'file')
1525        answer=msgbox_uvmat('INPUT_Y-N','compiled version has not been created: compile now?');
1526        if strcmp(answer,'Yes')
1527            set(handles.ActionExt,'BackgroundColor',[1 1 0])
1528            path_uvmat=fileparts(which('series'));
1529            currentdir=pwd;
1530            cd(get(handles.ActionPath,'String'))% go to the directory of Action
1531            addpath(path_uvmat)% add the path to uvmat to run the fct 'compile'
1532            compile(ActionName,TransformPath)
1533            cd(currentdir)
1534        else
1535            errormsg='Action launch interrupted';
1536            return
1537        end       
1538    else
1539        sh_file_info=dir(fullfile(get(handles.ActionPath,'String'),[ActionNameVersion '.sh']));
1540        m_file_info=dir(fullfile(get(handles.ActionPath,'String'),[ActionName '.m']));
1541        if isfield(m_file_info,'datenum') && m_file_info.datenum>sh_file_info.datenum
1542            set(handles.ActionExt,'BackgroundColor',[1 1 0])
1543            drawnow
1544            answer=msgbox_uvmat('INPUT_Y-N',[ActionNameVersion '.sh needs to be updated: recompile now?']);
1545            if strcmp(answer,'Yes')
1546                path_uvmat=fileparts(which('series'));
1547                currentdir=pwd;
1548                cd(get(handles.ActionPath,'String'))% go to the directory of Action
1549                addpath(path_uvmat)% add the path to uvmat to run the fct 'compile'
1550                addpath(fullfile(path_uvmat,'transform_field'))% add the path to transform functions to run the fct 'compile'
1551                compile(ActionName,TransformPath)
1552                cd(currentdir)
1553            end
1554        end
1555    end
1556
1557    set(handles.ActionExt,'BackgroundColor',[1 1 1])
1558     set(handles.series,'Pointer','arrow') % set the mouse pointer to 'watch
1559end
1560
1561%% set nbre of cluster cores and processes:
1562% NbCore is the number of computer processors used
1563% NbProcess is the number of independent processes in which the required calculation is split.
1564switch RunMode
1565    case {'local','background'}
1566        NbCore=1; % no need to split the calculation
1567    case 'cluster'
1568        %proposed number of cores to reserve in the cluster
1569        NbCoreAdvised=SeriesData.SeriesParam.ClusterParam.NbCoreAdvised;
1570        NbCoreMax=SeriesData.SeriesParam.ClusterParam.NbCoreMax;
1571        if strcmp(ActionExt,'.m')% case of Matlab function (uncompiled)
1572            warning_string=', preferably use .sh option to save Matlab licences';
1573        else
1574            warning_string=')';
1575        end
1576        answer=msgbox_uvmat('INPUT_TXT',['Number of cores (max ' num2str(NbCoreMax) ', ' warning_string],num2str(NbCoreAdvised));
1577        if isempty(answer)
1578            errormsg='Action launch interrupted by user';
1579            return
1580        end
1581        NbCore=str2double(answer);
1582%         extra_oar=answer{2};
1583%     case {'cluster_pbs', 'cluster_sge', 'cluster_qstat_unknown'}
1584%         if strcmp(ActionExt,'.m')% case of Matlab function (uncompiled)
1585%             NbCore=1; % one core used only (limitation of Matlab licences)
1586%             answer=msgbox_uvmat('INPUT_Y-N','Number of cores =1: select the compiled version .sh for multi-core processing. Proceed with the .m version?');
1587%             if ~strcmp(answer,'Yes')
1588%                 errormsg='Action launch interrupted';
1589%                 return
1590%             end
1591%             extra_oar='';
1592%         else
1593%             answer=inputdlg({'Number of jobs (max 1000)','Queue'},'qsub parameters',1,{'100','piv_debian'});
1594%             NbCore=str2double(answer{1});
1595%             qstat_Queue=answer{2};
1596%             %extra_oar=answer{2}; % TODO : fix this for LMFA cluster. Maybe
1597%             %extrs_oar and extra_pbs are not the best names
1598%         end
1599end
1600if ~isfield(Param.IndexRange,'NbSlice')
1601    Param.IndexRange.NbSlice=[];
1602end
1603
1604%% create the output data directory if needed
1605OutputDir='';
1606if isfield(Param,'OutputSubDir')
1607    SubDirOut=[get(handles.OutputSubDir,'String') Param.OutputDirExt];
1608    SubDirOutNew=SubDirOut;
1609    detect=exist(fullfile(Param.InputTable{1,1},SubDirOutNew),'dir'); % test if  the dir  already exist
1610    check_create=1; % need to create the result directory by default
1611    CheckOverwrite=1;
1612    if isfield(Param,'CheckOverwrite')
1613        CheckOverwrite=Param.CheckOverwrite;
1614    end
1615    while detect
1616        if CheckOverwrite
1617            comment=', possibly overwrite previous data';
1618        else
1619            comment=', will complement existing result files (no overwriting)';
1620        end
1621        answer=msgbox_uvmat('INPUT_Y-N-Cancel',['use existing ouput directory: ' fullfile(Param.InputTable{1,1},SubDirOutNew) comment]);
1622        if strcmp(answer,'Cancel')
1623            return
1624        elseif strcmp(answer,'Yes')
1625            detect=0;
1626            check_create=0;
1627        else
1628            r=regexp(SubDirOutNew,'(?<root>.*\D)(?<num1>\d+)$','names'); % detect whether name ends by a number
1629            if isempty(r)
1630                r(1).root=[SubDirOutNew '_'];
1631                r(1).num1='0';
1632            end
1633            SubDirOutNew=[r(1).root num2str(str2num(r(1).num1)+1)]; % increment the index by 1 or put 1
1634            detect=exist(fullfile(Param.InputTable{1,1},SubDirOutNew),'dir'); % test if  the dir  already exists
1635            check_create=1;
1636        end
1637    end
1638    Param.OutputDirExt=regexprep(SubDirOutNew,Param.OutputSubDir,'');
1639    Param.OutputRootFile=Param.InputTable{1,3}; % the first sorted RootFile taken for output
1640    set(handles.OutputDirExt,'String',Param.OutputDirExt)
1641    OutputDir=fullfile(Param.InputTable{1,1},[Param.OutputSubDir Param.OutputDirExt]); % full name (with path) of output directory
1642    if check_create    % create output directory if it does not exist
1643        [tild,msg1]=mkdir(OutputDir);
1644        if ~strcmp(msg1,'')
1645            errormsg=['cannot create ' OutputDir ': ' msg1]; % error message for directory creation
1646            return
1647        end
1648    end
1649   
1650elseif isfield(Param,'ActionInput')&&isfield(Param.ActionInput,'LogPath')% custom definition of the output dir
1651    OutputDir=Param.ActionInput.LogPath;   
1652end
1653DirXml=fullfile(OutputDir,'0_XML');
1654if ~exist(DirXml,'dir')
1655    [~,msg1]=mkdir(DirXml);
1656    if ~strcmp(msg1,'')
1657        errormsg=['cannot create ' DirXml ': ' msg1]; % error message for directory creation
1658        return
1659    end
1660end
1661OutputNomType=nomtype2pair(Param.InputTable{1,4}); % nomenclature for output files
1662
1663%% get the set of reference input field indices
1664first_i=1; % first i index to process
1665last_i=1; % last i index to process
1666incr_i=1; % increment step in i index
1667first_j=1; % first j index to process
1668last_j=1; % last j index to process
1669incr_j=1; % increment step in j index
1670if isfield(Param.IndexRange,'first_i')
1671    first_i=Param.IndexRange.first_i;
1672    incr_i=Param.IndexRange.incr_i;
1673    last_i=Param.IndexRange.last_i;
1674end
1675if isfield(Param.IndexRange,'incr_j')
1676    first_j=Param.IndexRange.first_j;
1677    last_j=Param.IndexRange.last_j;
1678    incr_j=Param.IndexRange.incr_j;
1679end
1680if last_i < first_i || last_j < first_j
1681    errormsg= 'series/Run_Callback:last field index must be larger or equal to the first one';
1682    return
1683end
1684%incr_i must be defined, =1 by default, if NbSlice is active
1685if isempty(incr_i)&& ~isempty(Param.IndexRange.NbSlice)
1686    incr_i=1;
1687    set(handles.num_incr_i,'String','1')
1688end
1689% case of no increment i defined: processing is done on the available files found in i1_series
1690if isempty(incr_i)
1691    if isempty(incr_j)
1692        [ref_j,ref_i]=find(squeeze(SeriesData.i1_series{1}(1,:,:)));
1693        ref_j=ref_j(ref_j>=first_j & ref_j<=last_j);
1694        ref_i=ref_i(ref_i>=first_i & ref_i<=last_i);
1695        ref_j=ref_j-1;
1696        ref_i=ref_i-1;
1697    else
1698        ref_j=first_j:incr_j:last_j;
1699        [tild,ref_i]=find(squeeze(SeriesData.i1_series{1}(1,:,:)));
1700        ref_i=ref_i-1;
1701        ref_i=ref_i(ref_i>=first_i & ref_i<=last_i);
1702    end
1703    % increment i is defined: processing is done on first_i:incr_i:last_i;
1704else
1705    ref_i=first_i:incr_i:last_i;
1706    if isempty(incr_j)% automatic finding of the existing j indices
1707        [ref_j,tild]=find(squeeze(SeriesData.i1_series{1}(1,:,:)));
1708        ref_j=ref_j-1;
1709        ref_j=ref_j(ref_j>=first_j & ref_j<=last_j);
1710    else
1711        ref_j=first_j:incr_j:last_j;
1712    end
1713end
1714CPUTime=1; % job time estimated at 1 min per iteration (on index i and j) by default
1715if isfield(Param.Action, 'CPUTime') && ~isempty(Param.Action.CPUTime)
1716    CPUTime=Param.Action.CPUTime; % Note: CpUTime for one iteration ref_i has to be multiplied by the number of j indices nbfield_j
1717end
1718nbfield_j=numel(ref_j); % number of j indices
1719BlockLength=numel(ref_i); % by default, job involves the full set of i field indices
1720NbProcess=1;
1721switch RunMode
1722    case 'cluster'
1723        JobNumberMax=SeriesData.SeriesParam.ClusterParam.JobNumberMax;
1724        JobCPUTimeAdvised=SeriesData.SeriesParam.ClusterParam.JobCPUTimeAdvised;
1725        if isempty(Param.IndexRange.NbSlice)% if NbSlice is not defined
1726            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.
1727            BlockLength=max(BlockLength,ceil(numel(ref_i)/JobNumberMax)); % possibly increase the BlockLength to have less than MaxJobNumber jobs
1728            NbProcess=ceil(numel(ref_i)/BlockLength) ; % nbre of processes sent to oar
1729        else
1730            NbProcess=Param.IndexRange.NbSlice; % the parameter NbSlice sets the nbre of run processes
1731        end
1732        NbCore=min(NbCore,NbProcess); % reduces the number of cores if it exceeds the number of processes
1733    otherwise
1734        if ~isempty(Param.IndexRange.NbSlice)
1735            NbProcess=Param.IndexRange.NbSlice; % the parameter NbSlice sets the nbre of run processes
1736        end
1737end
1738
1739%% record nbre of output files and starting time for computation for status
1740StatusData=get(handles.status,'UserData');
1741if isfield(StatusData,'OutputFileMode')
1742    switch StatusData.OutputFileMode
1743        case 'NbInput'
1744            StatusData.NbOutputFile=numel(ref_i)*nbfield_j;
1745        case 'NbInput_i'
1746            StatusData.NbOutputFile=numel(ref_i);
1747        case 'NbSlice'
1748            StatusData.NbOutputFile=str2num(get(handles.num_NbSlice,'String'));
1749    end
1750end
1751StatusData.TimeStart=now;
1752set(handles.status,'UserData',StatusData)
1753
1754%% case of a function in Python
1755if strcmp(ActionExt, '.py (in dev.)')
1756    fprintf([
1757        '\n' ...
1758        '!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n' ...
1759        'The option .py is used. It is still in development.\n' ...
1760        'To try it, first install pyper and the most recent version of fluidimage\n' ...
1761        '(see https://bitbucket.org/fluiddyn/fluidimage).\n' ...
1762        'Warning: there is no direct correspondance between UVMAT and fluidimage parameters\n' ...
1763        '!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n'])
1764    RunMode = 'python';
1765end
1766
1767
1768%% direct processing on the current Matlab session or creation of command files
1769filexml=cell(1,NbProcess); % initialisation of the names of the files containing the processing parameters
1770extxml=cell(1,NbProcess); % initialisation of the set of labels used for the files documenting each process
1771for iprocess=1:NbProcess
1772    extxml{iprocess}='.xml';
1773end
1774for iprocess=1:NbProcess
1775    if ~strcmp(get(handles.RUN,'BusyAction'),'queue')% allow for STOP action
1776        disp('program stopped by user')
1777        return
1778    end
1779    if isempty(Param.IndexRange.NbSlice)
1780        Param.IndexRange.first_i=first_i+(iprocess-1)*BlockLength*incr_i;
1781        if Param.IndexRange.first_i>last_i
1782            NbProcess=iprocess-1; % leave the loop, we are at the end of the calculation
1783            break
1784        end
1785        Param.IndexRange.last_i=min(last_i,first_i+(iprocess)*BlockLength*incr_i-1);
1786    else %multislices (then incr_i is not empty)
1787        Param.IndexRange.first_i= first_i+iprocess-1;
1788        Param.IndexRange.incr_i=incr_i*Param.IndexRange.NbSlice;
1789    end
1790    for ilist=1:size(Param.InputTable,1)
1791        Param.InputTable{ilist,1}=regexprep(Param.InputTable{ilist,1},'\','/'); % correct path name for PCWIN system
1792    end
1793   
1794    if isfield(Param,'OutputSubDir')
1795        t=struct2xml(Param);
1796        t=set(t,1,'name','Series');
1797        extxml{iprocess}=fullfile_uvmat('','',Param.InputTable{1,3},'.xml',OutputNomType,...
1798            Param.IndexRange.first_i,Param.IndexRange.last_i,first_j,last_j);
1799        filexml{iprocess}=fullfile(OutputDir,'0_XML',extxml{iprocess});
1800        try
1801            save(t, filexml{iprocess}); % save the xml file containing the processing parameters
1802        catch ME
1803            if ~strcmp (RunMode,'local')
1804                errormsg=['error writting ' filexml{iprocess} ': ' ME.message];
1805                return
1806            end
1807        end
1808    end
1809    if strcmp (RunMode,'local')
1810        switch ActionExt
1811            case '.m'
1812                h_fun(Param); % direct launching
1813               
1814            case '.sh'
1815                switch computer
1816                    case {'PCWIN','PCWIN64'} %Windows system
1817                        filexml=regexprep(filexml,'\\','\\\\'); % add '\' so that '\' are left as characters
1818                        system([ActionFullName ' ' RunTime ' ' filexml{iprocess}]); % TODO: adapt to DOS system
1819                    case {'GLNX86','GLNXA64','MACI64'}%Linux  system
1820                        system([ActionFullName ' ' RunTime ' ' filexml{iprocess}]);
1821                end
1822        end
1823    end
1824end
1825
1826if ~strcmp (RunMode,'local') && ~strcmp(RunMode,'python')
1827    %% processing on a different session of the same computer (background) or cluster, create executable files
1828    batch_file_list=cell(NbProcess,1); % initiate the list of executable files
1829    DirExe=fullfile(OutputDir,'0_EXE'); % directory name for executable files
1830    switch computer
1831        case {'PCWIN','PCWIN64'} %Windows system
1832            ExeExt='.bat';
1833        case {'GLNX86','GLNXA64','MACI64'}%Linux  system
1834            ExeExt='.sh';
1835    end
1836    %create subdirectory for executable files
1837    if ~exist(DirExe,'dir')
1838        [tild,msg1]=mkdir(DirExe);
1839        if ~strcmp(msg1,'')
1840            errormsg=['cannot create ' DirExe ': ' msg1]; % error message for directory creation
1841            return
1842        end
1843    end
1844    %create subdirectory for log files
1845    DirLog=fullfile(OutputDir,'0_LOG');
1846    if ~exist(DirLog,'dir')
1847        [tild,msg1]=mkdir(DirLog);
1848        if ~strcmp(msg1,'')
1849            errormsg=['cannot create ' DirLog ': ' msg1]; % error message for directory creation
1850            return
1851        end
1852    end
1853   
1854    %create the executable file
1855    file_exe_global=fullfile_uvmat('','',Param.InputTable{1,3},ExeExt,OutputNomType,...
1856        first_i,last_i,first_j,last_j);
1857    file_exe_global=fullfile(OutputDir,'0_EXE',file_exe_global);
1858    filelog_global=fullfile_uvmat('','',Param.InputTable{1,3},'.log',OutputNomType,...
1859        first_i,last_i,first_j,last_j);
1860    filelog_global=fullfile(OutputDir,'0_LOG',filelog_global);
1861
1862    for iprocess=1:NbProcess   
1863        %create the executable file       
1864        batch_file_list{iprocess}=fullfile(OutputDir,'0_EXE',regexprep(extxml{iprocess},'.xml$',ExeExt));
1865       
1866        % set the log file name
1867        filelog{iprocess}=fullfile(OutputDir,'0_LOG',regexprep(extxml{iprocess},'.xml$','.log'));     
1868    end
1869end
1870
1871%% launch the executable files for background or cluster processing
1872
1873switch RunMode
1874   
1875    case 'background'
1876        [fid,message]=fopen(file_exe_global,'w');
1877        if isequal(fid,-1)
1878            errormsg=['creation of ' file_exe_global ':' message];
1879            return
1880        end
1881        switch ActionExt
1882            case '.m'% Matlab function
1883                switch computer
1884                    case {'GLNX86','GLNXA64','MACI64'}
1885                        matlab_ver = ver('MATLAB');
1886                        matlab_version = matlab_ver.Version;
1887                        cmd=[...
1888                            '#!/bin/bash\n'...
1889                            'source /etc/profile\n'...
1890                            'module load matlab/' matlab_version '\n'...% CHOICE OF MATLAB VERSION
1891                            'time_start=$(date +%%s)\n'...
1892                            'matlab -nodisplay -nosplash -nojvm -logfile ''' filelog_global ''' <<END_MATLAB\n'...
1893                            'addpath(''' path_series ''');\n'...
1894                            'addpath(''' Param.Action.ActionPath ''');\n'];
1895                        for iprocess=1:NbProcess
1896                            cmd=[cmd '' Param.Action.ActionName  '(''' filexml{iprocess} ''');\n'];
1897                        end
1898                        cmd=[cmd  'exit\n' 'END_MATLAB\n'...
1899                            'time_end=$(date +%%s)\n'...
1900                            'echo "global time = " $(($time_end - $time_start)) >> ''' filelog_global '''\n'];
1901                        fprintf(fid,cmd); % fill the executable file with the  char string cmd
1902                        fclose(fid); % close the executable filefilelog_global
1903                        system(['chmod +x ' file_exe_global]); % set the file to executable
1904                    case {'PCWIN','PCWIN64'}
1905                        cmd=['matlab -automation -logfile ' regexprep(filelog{iprocess},'\\','\\\\')...
1906                            ' -r "addpath(''' regexprep(path_series,'\\','\\\\') ''');'...
1907                            'addpath(''' regexprep(Param.Action.ActionPath,'\\','\\\\') ''');'];
1908                        for iprocess=1:NbProcess
1909                            cmd=[cmd '' Param.Action.ActionName  '( ''' regexprep(filexml{iprocess},'\\','\\\\') ''');']
1910                        end
1911                        cmd=[cmd ';exit"'];
1912                        fprintf(fid,cmd); % fill the executable file with the  char string cmd
1913                        fclose(fid); % close the executable file
1914                end
1915                system([file_exe_global ' &'])% directly execute the command file
1916            case '.sh' % compiled Matlab function
1917                for iprocess=1:NbProcess
1918                    switch computer
1919                        case {'GLNX86','GLNXA64','MACI64'}
1920                            [fid,message]=fopen(batch_file_list{iprocess},'w'); % create the executable file
1921                            if isequal(fid,-1)
1922                                errormsg=['creation of .bat file: ' message];
1923                                return
1924                            end
1925                            cmd=['#!/bin/bash \n '...
1926                                '#$ -cwd \n '...
1927                                'hostname && date \n '...
1928                                'umask 002 \n'...
1929                                ActionFullName ' ' RunTime ' ' filexml{iprocess}]; % allow writting access to created files for user group
1930                            fprintf(fid,cmd); % fill the executable file with the  char string cmd
1931                            fclose(fid); % close the executable file
1932                            system(['chmod +x ' batch_file_list{iprocess}]); % set the file to executable
1933                            system([batch_file_list{iprocess} ' &'])% directly execute the command file
1934                        case {'PCWIN','PCWIN64'}
1935                            msgbox_uvmat('ERROR','option for compiled Matlab functions not implemented for Windows system')
1936                            return
1937                    end
1938                end
1939                msgbox_uvmat('CONFIRMATION',[ActionFullName ' launched in background: press STATUS to see results'])
1940        end
1941       
1942    case 'cluster' % option 'oar-parexec' used
1943        %create subdirectory for oar commands
1944        for iprocess=1:NbProcess
1945            [fid,message]=fopen(batch_file_list{iprocess},'w'); % create the executable file
1946            if isequal(fid,-1)
1947                errormsg=['creation of .bat file: ' message];
1948                return
1949            end
1950            if  strcmp(ActionExt,'.sh')
1951                cmd=['#!/bin/bash \n '...
1952                    '#$ -cwd \n '...
1953                    'hostname && date \n '...
1954                    'umask 002 \n'...
1955                    ActionFullName ' ' RunTime ' ' filexml{iprocess}]; % allow writting access to created files for user group
1956            else
1957                matlab_ver = ver('MATLAB');
1958                matlab_version = matlab_ver.Version;
1959                cmd=[...
1960                    '#!/bin/bash\n'...
1961                    'source /etc/profile\n'...
1962                    'module load matlab/' matlab_version '\n'...% CHOICE OF MATLAB VERSION
1963                    'matlab -nodisplay -nosplash -nojvm -singleCompThread -logfile ''' filelog{iprocess} ''' <<END_MATLAB\n'...
1964                    'addpath(''' path_series ''');\n'...
1965                    'addpath(''' Param.Action.ActionPath ''');\n'...
1966                    '' Param.Action.ActionName  '(''' filexml{iprocess} ''');\n'...
1967                    'exit\n'...
1968                    'END_MATLAB\n'];
1969            end
1970            fprintf(fid,cmd); % fill the executable file with the  char string cmd
1971            fclose(fid); % close the executable file
1972            system(['chmod +x ' batch_file_list{iprocess}]); % set the file to executable
1973        end
1974        DIR_CLUSTER=fullfile(OutputDir,'0_CLUSTER');
1975        if exist(DIR_CLUSTER,'dir')% delete the content of the dir 0_LOG to allow new input
1976            curdir=pwd;
1977            cd(DIR_CLUSTER)
1978            delete('*')
1979            cd(curdir)
1980        else
1981            [tild,msg1]=mkdir(DIR_CLUSTER);
1982            if ~strcmp(msg1,'')
1983                errormsg=['cannot create ' DIR_CLUSTER ': ' msg1]; % error message for directory creation
1984                return
1985            end
1986        end
1987        % create file containing the list of jobs
1988        ListProcess=fullfile(DIR_CLUSTER,'job_list.txt'); % name of the file containing the list of executables
1989        fid=fopen(ListProcess,'w'); % open it for writting
1990        for iprocess=1:length(batch_file_list)
1991            fprintf(fid,[batch_file_list{iprocess} '\n']); % write list of exe files
1992        end
1993        fclose(fid);
1994        system(['chmod +x ' ListProcess]); % set the file to executable
1995 
1996        CPUTimeProcess=CPUTime*BlockLength*nbfield_j; % estimated CPU time for one individual process (in minutes)
1997        LaunchCmdFcn=SeriesData.SeriesParam.ClusterParam.LaunchCmdFcn;
1998        oar_command=feval(LaunchCmdFcn,ListProcess,ActionFullName,DirLog,NbProcess, NbCore,CPUTimeProcess)
1999        [status,result]=system(oar_command)% execute system command and show the result (ID number of the launched job) on the Matlab command window
2000        filename_oarcommand=fullfile(DIR_CLUSTER,'0_cluster_command'); % keep track of the command in file '0-OAR/0_cluster_command'
2001        fid=fopen(filename_oarcommand,'w');
2002        fprintf(fid,oar_command); % store the command
2003        fprintf(fid,result); % store the result (job ID number)
2004        fclose(fid);
2005        msgbox_uvmat('CONFIRMATION',[ActionFullName ' launched as  ' num2str(NbProcess) ' processes in cluster: press STATUS to see results'])
2006       
2007%     case 'cluster_pbs' % for LMFA Kepler machine:  trqnsferred to fct
2008
2009%         %create subdirectory for pbs command and log files
2010%         DirPBS=fullfile(OutputDir,'0_PBS'); % todo : common name OAR/PBS
2011%         if exist(DirPBS,'dir')% delete the content of the dir 0_LOG to allow new input
2012%             curdir=pwd;
2013%             cd(DirPBS)
2014%             delete('*')
2015%             cd(curdir)
2016%         else
2017%             [tild,msg1]=mkdir(DirPBS);
2018%             if ~strcmp(msg1,'')
2019%                 errormsg=['cannot create ' DirPBS ': ' msg1]; % error message for directory creation
2020%                 return
2021%             end
2022%         end
2023%         max_walltime=3600*20; % 20h max total calculation (cannot exceed 24 h)
2024%         walltime_onejob=1800; % seconds, max estimated time for asingle file index value
2025%         ListProcess=fullfile(DirPBS,'job_list.txt'); % create name of the global executable file
2026%         fid=fopen(ListProcess,'w');
2027%         for iprocess=1:length(batch_file_list)
2028%             fprintf(fid,[batch_file_list{iprocess} '\n']); % list of exe files
2029%         end
2030%         fclose(fid);
2031%         system(['chmod +x ' ListProcess]); % set the file to executable
2032%         pbs_command=['qsub -n CIVX '...
2033%             '-t idempotent --checkpoint ' num2str(walltime_onejob+60) ' '...
2034%             '-l /core=' num2str(NbCore) ','...
2035%             'walltime=' datestr(min(1.05*walltime_onejob/86400*max(NbProcess*BlockLength*nbfield_j,NbCore)/NbCore,max_walltime/86400),13) ' '...
2036%             '-E ' regexprep(ListProcess,'\.txt\>','.stderr') ' '...
2037%             '-O ' regexprep(ListProcess,'\.txt\>','.log') ' '...
2038%             extra_qstat ' '...
2039%             '"oar-parexec -s -f ' ListProcess ' '...
2040%             '-l ' ListProcess '.log"'];
2041%         filename_oarcommand=fullfile(DirPBS,'pbs_command');
2042%         fid=fopen(filename_oarcommand,'w');
2043%         fprintf(fid,pbs_command);
2044%         fclose(fid);
2045%         fprintf(pbs_command); % display in command line
2046%         %system(pbs_command);
2047%         msgbox_uvmat('CONFIRMATION',[ActionFullName ' command ready to be launched in cluster'])
2048
2049     case 'cluster_sge' % for PSMN % TODO: use the standard 'cluster' config with an external fct
2050        % Au PSMN, on ne cr??e pas 1 job avec plusieurs c??urs, mais N jobs de 1 c??urs
2051        % o?? N < 1000.
2052        %create subdirectory for pbs command and log files
2053
2054        DirSGE=fullfile(OutputDir,'0_SGE');
2055        if exist(DirSGE,'dir')% delete the content of the dir 0_LOG to allow new input
2056            curdir=pwd;
2057            cd(DirSGE)
2058            delete('*')
2059            cd(curdir)
2060        else
2061            [tild,msg1]=mkdir(DirSGE);
2062            if ~strcmp(msg1,'')
2063                errormsg=['cannot create ' DirSGE ': ' msg1]; % error message for directory creation
2064                return
2065            end
2066        end
2067        maxImgsPerJob = ceil(length(batch_file_list)/NbCore);
2068        disp(['Max number of jobs: ' num2str(NbCore)])
2069        disp(['Images per job: ' num2str(maxImgsPerJob)])
2070       
2071        iprocess = 1;
2072        imgsInJob = [];
2073        currJobIndex = 1;
2074        done = 0;
2075        while(~done)
2076            if(iprocess <= length(batch_file_list))
2077                imgsInJob = [imgsInJob, iprocess];
2078            end
2079            if((numel(imgsInJob) >= maxImgsPerJob) || (iprocess == length(batch_file_list)))
2080                cmd=['#!/bin/sh \n'...
2081                     '#$ -cwd \n'...
2082                     'hostname && date\n']
2083                for ii=1:numel(imgsInJob)
2084                    cmd=[cmd ActionFullName ' /softs/matlab ' filexml{imgsInJob(ii)} '\n'];
2085                end
2086                [fid, message] = fopen([DirSGE '/job' num2str(currJobIndex) '.sh'], 'w');
2087                fprintf(fid, cmd);
2088                fclose(fid);
2089                system(['chmod +x ' DirSGE '/job' num2str(currJobIndex) '.sh'])
2090                sge_command=['qsub -N civ_' num2str(currJobIndex) ' '...
2091                    '-q ' qstat_Queue ' '...
2092                    '-e ' fullfile([DirSGE '/job' num2str(currJobIndex) '.out']) ' '...
2093                    '-o ' fullfile([DirSGE '/job' num2str(currJobIndex) '.out']) ' '...
2094                    fullfile([DirSGE '/job' num2str(currJobIndex) '.sh'])];
2095                fprintf(sge_command); % display in command line
2096                [status, result] = system(sge_command);
2097                fprintf(result);
2098                currJobIndex = currJobIndex + 1;
2099                imgsInJob = [];
2100            end
2101            if(iprocess == length(batch_file_list))
2102                done = 1;
2103            end
2104            iprocess = iprocess + 1;
2105        end
2106        msgbox_uvmat('CONFIRMATION',[num2str(currJobIndex-1) ' jobs launched on queue ' qstat_Queue '.'])
2107    case 'python'
2108        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))") ' ...
2109            'python -m fluidimage.run_from_xml ' filexml{iprocess}];
2110        fprintf(['command:\n' command '\n\n'])
2111        system(command, '-echo');
2112end
2113if exist(OutputDir,'dir')
2114    [SUCCESS,MESSAGE,MESSAGEID] = fileattrib (OutputDir);
2115    if MESSAGE.GroupWrite~=1
2116    [success,msg] = fileattrib(OutputDir,'+w','g','s'); % allow writing access for the group of users, recursively in the folder
2117    if success==0
2118        msgbox_uvmat('WARNING',{['unable to set group write access to ' OutputDir ':']; msg}); % error message for directory creation
2119    end
2120    end
2121end
2122
2123%------------------------------------------------------------------------
2124function STOP_Callback(hObject, eventdata, handles)
2125%------------------------------------------------------------------------
2126set(handles.RUN, 'BusyAction','cancel')
2127set(handles.RUN,'BackgroundColor',[1 0 0])
2128set(handles.RUN,'enable','on')
2129set(handles.RUN, 'Value',0)
2130
2131%------------------------------------------------------------------------
2132% --- read parameters from the GUI series
2133%------------------------------------------------------------------------
2134function Param=read_GUI_series(handles)
2135
2136%% read raw parameters from the GUI series
2137Param=read_GUI(handles.series);
2138
2139%% clean the output structure by removing unused information
2140if isfield(Param,'Pairs')
2141    Param=rmfield(Param,'Pairs'); % info Pairs not needed for output
2142end
2143if isfield(Param,'InputLine')
2144    Param=rmfield(Param,'InputLine');
2145end
2146if isfield(Param,'EditObject')
2147    Param=rmfield(Param,'EditObject');
2148end
2149Param.IndexRange.TimeSource=Param.IndexRange.TimeTable{end,1};
2150Param.IndexRange=rmfield(Param.IndexRange,'TimeTable');
2151empty_line=false(size(Param.InputTable,1),1);
2152for iline=1:size(Param.InputTable,1)
2153    empty_line(iline)=isempty(cell2mat(Param.InputTable(iline,1:3)));
2154end
2155Param.InputTable(empty_line,:)=[];
2156
2157%------------------------------------------------------------------------
2158% --- Executes on selection change in ActionName.
2159function ActionName_Callback(hObject, eventdata, handles)
2160%------------------------------------------------------------------------
2161
2162%% stop any ongoing series processing
2163if isequal(get(handles.RUN,'Value'),1)
2164    answer= msgbox_uvmat('INPUT_Y-N','stop current Action process?');
2165    if strcmp(answer,'Yes')
2166        STOP_Callback(hObject, eventdata, handles)
2167    else
2168        return
2169    end
2170end
2171set(handles.ActionName,'BackgroundColor',[1 1 0])
2172huigetfile=findobj(allchild(0),'tag','status_display');
2173if ~isempty(huigetfile)
2174    delete(huigetfile)
2175end
2176drawnow
2177
2178%% get Action name and path
2179NbBuiltinAction=get(handles.Action,'UserData'); % nbre of functions initially proposed in the menu ActionName (as defined in the Opening fct of series)
2180ActionList=get(handles.ActionName,'String'); % list menu fields
2181ActionIndex=get(handles.ActionName,'Value');
2182if ~isequal(ActionIndex,1)% if we are not just opening series
2183    InputTable=get(handles.InputTable,'Data');
2184    if isempty(InputTable{1,4})
2185        msgbox_uvmat('ERROR','no input file available: use Open in the menu bar')
2186        return
2187    end
2188end
2189ActionName= ActionList{get(handles.ActionName,'Value')}; % selected function name
2190ActionPathList=get(handles.ActionName,'UserData'); % list of recorded paths to functions of the list ActionName
2191
2192%% add a new function to the menu if 'more...' has been selected in the menu ActionName
2193if isequal(ActionName,'more...')
2194    [FileName, PathName] = uigetfile( ...
2195        {'*.m', ' (*.m)';
2196        '*.m',  '.m files '; ...
2197        '*.*', 'All Files (*.*)'}, ...
2198        'Pick a series processing function ',get(handles.ActionPath,'String'));
2199    if length(FileName)<2
2200        return
2201    end
2202    [tild,ActionName,ActionExt]=fileparts(FileName);
2203   
2204    % insert the choice in the menu ActionName
2205    ActionIndex=find(strcmp(ActionName,ActionList),1); % look for the selected function in the menu Action
2206    PathName=regexprep(PathName,'/$','');
2207    if ~isempty(ActionIndex) && ~strcmp(ActionPathList{ActionIndex},PathName)%compare the path to the existing fct
2208        ActionIndex=[]; % the selected path is different than the recorded one
2209    end
2210    if isempty(ActionIndex)%the qselected fct (with selected path) does not exist in the menu
2211        ActionIndex= length(ActionList);
2212        ActionList=[ActionList(1:end-1);{ActionName};ActionList(end)]; % the selected function is appended in the menu, before the last item 'more...'
2213         ActionPathList=[ActionPathList; PathName];
2214    end
2215   
2216    % record the file extension and extend the path list if it is a new extension
2217    ActionExtList=get(handles.ActionExt,'String');
2218    ActionExtIndex=find(strcmp(ActionExt,ActionExtList), 1);
2219    if isempty(ActionExtIndex)
2220        set(handles.ActionExt,'String',[ActionExtList;{ActionExt}])
2221    end
2222
2223    % remove old Action options in the menu (keeping a menu length <nb_builtin_ACTION+5)
2224    if length(ActionList)>NbBuiltinAction+5; % nb_builtin_ACTION=nbre of functions always remaining in the initial menu
2225        nbremove=length(ActionList)-NbBuiltinAction-5;
2226        ActionList(NbBuiltinAction+1:end-5)=[];
2227        ActionPathList(NbBuiltinAction+1:end-4,:)=[];
2228        ActionIndex=ActionIndex-nbremove;
2229    end
2230   
2231    % record action menu, choice and path
2232    set(handles.ActionName,'Value',ActionIndex)
2233    set(handles.ActionName,'String',ActionList)
2234       set(handles.ActionName,'UserData',ActionPathList);
2235    set(handles.ActionExt,'Value',ActionExtIndex)
2236       
2237    %record the user defined menu additions in personal file profil_perso
2238    dir_perso=prefdir;
2239    profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
2240    if NbBuiltinAction+1<=numel(ActionList)-1
2241        ActionListUser=ActionList(NbBuiltinAction+1:numel(ActionList)-1);
2242        ActionPathListUser=ActionPathList(NbBuiltinAction+1:numel(ActionList)-1);
2243        ActionExtListUser={};
2244        if numel(ActionExtList)>2
2245            ActionExtListUser=ActionExtList(3:end);
2246        end
2247        if exist(profil_perso,'file')
2248            save(profil_perso,'ActionListUser','ActionPathListUser','ActionExtListUser','-append')
2249        else
2250            save(profil_perso,'ActionListUser','ActionPathListUser','ActionExtListUser','-V6')
2251        end
2252    end
2253end
2254
2255%% check the current ActionPath to the selected function
2256ActionPath=ActionPathList{ActionIndex}; % current recorded path
2257set(handles.ActionPath,'String',ActionPath); % show the path to the senlected function
2258
2259%% reinitialise the waitbar
2260update_waitbar(handles.Waitbar,0)
2261
2262%% Put the first line of the selected Action fct as tooltip help
2263try
2264    [fid,errormsg] =fopen([ActionName '.m']);
2265    InputText=textscan(fid,'%s',1,'delimiter','\n');
2266    fclose(fid);
2267    set(handles.ActionName,'ToolTipString',InputText{1}{1})% put the first line of the selected function as tooltip help
2268end
2269set(handles.ActionName,'BackgroundColor',[1 1 1])
2270set(handles.ActionInput,'BackgroundColor',[1 0 1])% set ActionInput button to magenta color to indicate that input refr
2271
2272
2273% --- Executes on button press in ActionInput.
2274function ActionInput_Callback(hObject, eventdata, handles)
2275
2276set(handles.ActionInput,'BackgroundColor',[1 1 0])
2277
2278%% create the function handle for Action
2279ActionPath=get(handles.ActionPath,'String');
2280ActionList=get(handles.ActionName,'String');
2281ActionName= ActionList{get(handles.ActionName,'Value')}; % selected function name
2282if ~exist(ActionPath,'dir')
2283    msgbox_uvmat('ERROR',['The prescribed function path ' ActionPath ' does not exist']);
2284    return
2285end
2286current_dir=pwd; % current working dir
2287cd(ActionPath)
2288h_fun=str2func(ActionName);
2289cd(current_dir)
2290
2291%% Activate the Action fct to adapt the configuration of the GUI series and bring specific parameters in SeriesData
2292Param=read_GUI_series(handles); % read the parameters from the GUI series
2293Param.Action.RUN=0;
2294ParamOut=h_fun(Param); % run the selected Action function to get the relevant input
2295
2296
2297%% Visibility of VelType and VelType_1 menus asked by ActionName
2298VelTypeRequest=1; % VelType requested by default
2299VelTypeRequest_1=1; % VelType requested by default
2300if isfield(ParamOut,'VelType')
2301    VelTypeRequest=ismember(ParamOut.VelType,{'on','one','two'});
2302    VelTypeRequest_1=strcmp( ParamOut.VelType,'two');
2303end
2304FieldNameRequest=0;  %hidden by default
2305FieldNameRequest_1=0;  %hidden by default
2306if isfield(ParamOut,'FieldName')
2307    FieldNameRequest=ismember(ParamOut.FieldName,{'on','one','two'});
2308    FieldNameRequest_1=strcmp( ParamOut.FieldName,'two');
2309end
2310
2311%% Detect the types of input files and set menus and default options in 'VelType'
2312SeriesData=get(handles.series,'UserData'); % info on the input file series
2313iview_civ=find(strcmp('civx',SeriesData.FileType)|strcmp('civdata',SeriesData.FileType));
2314iview_netcdf=find(strcmp('netcdf',SeriesData.FileType)|strcmp('civx',SeriesData.FileType)|strcmp('civdata',SeriesData.FileType)); % all nc files, icluding civ
2315FieldList=get(handles.FieldName,'String'); % previous list as default
2316if ~iscell(FieldList),FieldList={FieldList};end
2317FieldList_1=get(handles.FieldName_1,'String'); % previous list as default
2318if ~iscell(FieldList_1),FieldList_1={FieldList_1};end
2319CheckList_1=1; % indicate whether FieldName_1 has been updated
2320handles_coord=[handles.Coord_x handles.Coord_y handles.Coord_z handles.Coord_x_title handles.Coord_y_title handles.Coord_z_title];
2321if VelTypeRequest && numel(iview_civ)>=1
2322    menu=set_veltype_display(SeriesData.FileInfo{iview_civ(1)}.CivStage,SeriesData.FileType{iview_civ(1)});
2323    set(handles.VelType,'Value',1)% set first choice by default
2324    set(handles.VelType,'String',[{'*'};menu])
2325    set(handles.VelType,'Visible','on')
2326    set(handles.VelType_title,'Visible','on')
2327    FieldList=set_field_list('U','V'); % standard menu for civx data
2328    %CheckList=1;
2329    set(handles.FieldName,'Value',1); % velocity vector choice by default
2330    if  VelTypeRequest_1 && numel(iview_civ)>=2
2331        menu=set_veltype_display(SeriesData.FileInfo{iview_civ(2)}.CivStage,SeriesData.FileType{iview_civ(2)});
2332        set(handles.VelType_1,'Value',1)% set first choice by default
2333        set(handles.VelType_1,'String',[{'*'};menu])
2334        set(handles.VelType_1,'Visible','on')
2335        set(handles.VelType_title_1,'Visible','on')
2336        FieldList_1=[set_field_list('U','V');{'C'};{'get_field...'}]; % standard menu for civx data
2337        CheckList_1=1;
2338        set(handles.FieldName_1,'Value',1); % velocity vector choice by default
2339    else
2340        set(handles.VelType_1,'Visible','off')
2341        set(handles.VelType_title_1,'Visible','off')
2342    end
2343else
2344    set(handles.VelType,'Visible','off')
2345    set(handles.VelType_title,'Visible','off')
2346end
2347
2348%% Detect the types of input files and set menus and default options in 'FieldName'
2349if (FieldNameRequest || VelTypeRequest) && numel(iview_netcdf)>=1
2350    set(handles.InputFields,'Visible','on')% set the frame InputFields visible
2351    if FieldNameRequest && isfield(SeriesData.FileInfo{iview_netcdf(1)},'ListVarName')
2352        set(handles.FieldName,'Visible','on')
2353        ListVarName=SeriesData.FileInfo{iview_netcdf(1)}.ListVarName;
2354        ind_var=get(handles.FieldName,'Value'); % indices of previously selected variables
2355        for ilist=1:numel(ind_var)
2356            if isempty(find(strcmp(FieldList{ind_var(ilist)},ListVarName)))
2357                FieldList={}; % previous choice not consistent with new input field
2358                set(handles.FieldName,'Value',1)
2359                break
2360            end
2361        end
2362        if ~isempty(FieldList)
2363            if isempty(find(strcmp(get(handles.Coord_x,'String'),ListVarName)))||...
2364                    isempty(find(strcmp(get(handles.Coord_y,'String'),ListVarName)))
2365                FieldList={};
2366                set(handles.Coord_x,'String','')
2367                set(handles.Coord_y,'String','')
2368            end
2369            Coord_z=get(handles.Coord_z,'String');
2370            if ~isempty(Coord_z) && isempty(find(strcmp(Coord_z,ListVarName)))
2371                FieldList={};
2372                set(handles.Coord_z,'String','')
2373            end
2374        end
2375    else
2376        set(handles.FieldName,'Visible','off')
2377    end
2378   
2379    set(handles_coord,'Visible','on')
2380    if isempty(find(strcmp('get_field...',FieldList)))
2381    FieldList=[FieldList;{'get_field...'}];%add 'get_field...' to the menu FieldName if it is not already
2382    end
2383    if FieldNameRequest_1 && numel(iview_netcdf)>=2
2384        set(handles.FieldName_1,'Visible','on')
2385        if CheckList_1==0        % not civ input made
2386            ListVarName=SeriesData.FileInfo{iview_netcdf(2)}.ListVarName;
2387            ind_var=get(handles.FieldName,'Value'); % indices of previously selected variables
2388            for ilist=1:numel(ind_var)
2389                if isempty(find(strcmp(FieldList{ind_var(ilist)},ListVarName)))
2390                    FieldList_1={}; % previous choice not consistent with new input field
2391                    set(handles.FieldName_1,'Value',1)
2392                    break
2393                end
2394            end
2395            warn_coord=0;
2396            if isempty(find(strcmp(get(handles.Coord_x,'String'),ListVarName)))||...
2397                    isempty(find(strcmp(get(handles.Coord_y,'String'),ListVarName)))
2398                warn_coord=1;
2399            end
2400            if ~isempty(Coord_z) && isempty(find(strcmp(Coord_z,ListVarName)))
2401                FieldList_1={};
2402                warn_coord=1;
2403            end
2404            if warn_coord
2405                msgbox_uvmat('WARNING','coordinate names do not exist in the second netcdf input file')
2406            end
2407           
2408            set(handles.FieldName_1,'Visible','on')
2409            set(handles.FieldName_1,'Value',1)
2410            set(handles.FieldName_1,'String',FieldList_1)
2411        end
2412    else
2413        set(handles.FieldName_1,'Visible','off')
2414    end
2415    if isempty(FieldList)
2416        set(handles.FieldName,'Visible','off')
2417    else
2418        set(handles.FieldName,'Visible','on')
2419        set(handles.FieldName,'String',FieldList)
2420    end
2421else
2422    set(handles.InputFields,'Visible','off')
2423end
2424
2425%% Introduce visibility of file overwrite option
2426if isfield(ParamOut,'CheckOverwriteVisible')&& strcmp(ParamOut.CheckOverwriteVisible,'on')
2427    set(handles.CheckOverwrite,'Visible','on')
2428else
2429    set(handles.CheckOverwrite,'Visible','off')
2430end
2431
2432%% Check whether alphabetical sorting of input Subdir is allowed by the Action fct  (for multiples series entries)
2433if isfield(ParamOut,'AllowInputSort')&&isequal(ParamOut.AllowInputSort,'on')&& size(Param.InputTable,1)>1
2434    [tild,iview]=sort(Param.InputTable(:,2)); % subdirectories sorted in alphabetical order
2435    set(handles.InputTable,'Data',Param.InputTable(iview,:));
2436    MinIndex_i=get(handles.MinIndex_i,'Data');
2437    MinIndex_j=get(handles.MinIndex_j,'Data');
2438    MaxIndex_i=get(handles.MaxIndex_i,'Data');
2439    MaxIndex_j=get(handles.MaxIndex_j,'Data');
2440    set(handles.MinIndex_i,'Data',MinIndex_i(iview,:));
2441    set(handles.MinIndex_j,'Data',MinIndex_j(iview,:));
2442    set(handles.MaxIndex_i,'Data',MaxIndex_i(iview,:));
2443    set(handles.MaxIndex_j,'Data',MaxIndex_j(iview,:));
2444    TimeTable=get(handles.TimeTable,'Data');
2445    set(handles.TimeTable,'Data',TimeTable(iview,:));
2446    PairString=get(handles.PairString,'Data');
2447    set(handles.PairString,'Data',PairString(iview,:));
2448end
2449
2450%% Impose the whole input file index range if requested
2451if isfield(ParamOut,'WholeIndexRange')&&isequal(ParamOut.WholeIndexRange,'on')
2452    MinIndex_i=get(handles.MinIndex_i,'Data');
2453    MinIndex_j=get(handles.MinIndex_j,'Data');
2454    MaxIndex_i=get(handles.MaxIndex_i,'Data');
2455    MaxIndex_j=get(handles.MaxIndex_j,'Data');
2456    set(handles.num_first_i,'String',num2str(MinIndex_i(1)))% set first as the min index (for the first line)
2457    set(handles.num_last_i,'String',num2str(MaxIndex_i(1)))% set last as the max index (for the first line)
2458    set(handles.num_incr_i,'String','1')
2459    set(handles.num_first_j,'String',num2str(MinIndex_j(1)))% set first as the min index (for the first line)
2460    set(handles.num_last_j,'String',num2str(MaxIndex_j(1)))% set last as the max index (for the first line)
2461    set(handles.num_incr_j,'String','1')
2462else  % check index ranges
2463    first_i=1;last_i=1;first_j=1;last_j=1;
2464    if isfield(Param.IndexRange,'first_i')
2465        first_i=Param.IndexRange.first_i;
2466        last_i=Param.IndexRange.last_i;
2467    end
2468    if isfield(Param.IndexRange,'first_j')
2469        first_j=Param.IndexRange.first_j;
2470        last_j=Param.IndexRange.last_j;
2471    end
2472    if last_i < first_i || last_j < first_j , msgbox_uvmat('ERROR','last field number must be larger than the first one'),...
2473            set(handles.RUN, 'Enable','On'), set(handles.RUN,'BackgroundColor',[1 0 0]),return,end;
2474end
2475
2476%% enable or desable j index visibility
2477status_j='on'; % default
2478if isempty(find(~cellfun(@isempty,SeriesData.j1_series), 1)); % case of empty j indices
2479    status_j='off'; % no j index needed
2480elseif strcmp(get(handles.PairString,'Visible'),'on')
2481    check_burst=cellfun(@isempty,regexp(get(handles.PairString,'Data'),'^j')); % =0 for burst case, 1 otherwise
2482    if isempty(find(check_burst, 1))% if all pair string begins by j (burst)
2483        status_j='off'; % no j index needed for bust case
2484    end
2485end
2486enable_j(handles,status_j) % no j index needed
2487if isfield(ParamOut,'j_index_1')&& isfield(ParamOut,'j_index_2')%strcmp(ParamOut.Desable_j_index,'on')
2488    %status_j='off';
2489    set(handles.num_first_j,'String',num2str(ParamOut.j_index_1))
2490    set(handles.num_last_j,'String',num2str(ParamOut.j_index_2))
2491    set(handles.num_first_j,'enable','off')
2492    set(handles.num_last_j,'enable','off')
2493    set(handles.num_incr_j,'visible','off')
2494else
2495    set(handles.num_first_j,'enable','on')
2496    set(handles.num_last_j,'enable','on')
2497    set(handles.num_incr_j,'visible',status_j)
2498end
2499
2500%% NbSlice visibility
2501if isfield(ParamOut,'NbSlice') && (strcmp(ParamOut.NbSlice,'on')||isnumeric(ParamOut.NbSlice))
2502    set(handles.num_NbSlice,'Visible','on')
2503    set(handles.NbSlice_title,'Visible','on')
2504else
2505    set(handles.num_NbSlice,'Visible','off')
2506    set(handles.NbSlice_title,'Visible','off')
2507end
2508if isfield(ParamOut,'NbSlice') && isnumeric(ParamOut.NbSlice)
2509    set(handles.num_NbSlice,'String',num2str(ParamOut.NbSlice))
2510    set(handles.num_NbSlice,'Enable','off'); % NbSlice set by the activation of the Action function
2511else
2512    set(handles.num_NbSlice,'Enable','on'); % NbSlice can be modified on the GUI series
2513end
2514
2515%% Visibility of FieldTransform menu
2516FieldTransformVisible='off';  %hidden by default
2517if isfield(ParamOut,'FieldTransform')
2518    if ~strcmp(ParamOut.FieldTransform,'off')
2519    FieldTransformVisible='on'; 
2520    end
2521    if iscell(ParamOut.FieldTransform)
2522        SeriesData.TransformList=ParamOut.FieldTransform;
2523    end
2524    TransformName_Callback([],[], handles)
2525end
2526set(handles.FieldTransform,'Visible',FieldTransformVisible)
2527if isfield(ParamOut,'TransformPath');% record the path of transform function requested for compilation
2528    set(handles.TransformPath,'UserData',ParamOut.TransformPath)
2529else
2530    set(handles.TransformPath,'UserData',[])
2531end
2532
2533%% Visibility of projection object
2534ProjObjectVisible='off';  %hidden by default
2535if isfield(ParamOut,'ProjObject')
2536    ProjObjectVisible=ParamOut.ProjObject;
2537end
2538set(handles.CheckObject,'Visible',ProjObjectVisible)
2539if ~get(handles.CheckObject,'Value')
2540    ProjObjectVisible='off';
2541end
2542set(handles.ProjObject,'Visible',ProjObjectVisible)
2543set(handles.DeleteObject,'Visible',ProjObjectVisible)
2544set(handles.ViewObject,'Visible',ProjObjectVisible)
2545set(handles.EditObject,'Visible',ProjObjectVisible)
2546
2547%% Visibility of mask input
2548MaskVisible='off';  %hidden by default
2549if isfield(ParamOut,'Mask')
2550    MaskVisible=ParamOut.Mask;
2551end
2552set(handles.CheckMask,'Visible',MaskVisible);
2553
2554%% definition of the directory containing the output files
2555if  ~(isfield(SeriesData,'ActionName') && strcmp(ActionName,SeriesData.ActionName))
2556    OutputDirExt='.series'; % default
2557    if isfield(ParamOut,'OutputDirExt')&&~isempty(ParamOut.OutputDirExt)
2558        OutputDirExt=ParamOut.OutputDirExt;
2559    end
2560    set(handles.OutputDirExt,'String',OutputDirExt)
2561end
2562OutputDirVisible='off';
2563OutputSubDirMode='auto'; % default
2564SubDirOut='';
2565if isfield(ParamOut,'OutputSubDirMode')
2566    OutputSubDirMode=ParamOut.OutputSubDirMode;
2567end
2568InputTable=get(handles.InputTable,'Data');
2569switch OutputSubDirMode
2570    case 'auto'; % default
2571        OutputDirVisible='on';
2572        SubDir=InputTable(1:end,2); % set of subdirectories
2573        SubDirOut=SubDir{1};
2574        if numel(SubDir)>1
2575            for ilist=2:numel(SubDir)
2576                SubDirOut=[SubDirOut '-' regexprep(SubDir{ilist},'^/','')];
2577            end
2578        end
2579    case 'one'
2580        OutputDirVisible='on';
2581        SubDirOut=InputTable{1,2}; % use the first subdir name (+OutputDirExt) as output  subdirectory
2582    case 'two'
2583        OutputDirVisible='on';   
2584        SubDir=InputTable(1:2,2); % set of subdirectories
2585        SubDirOut=SubDir{1};
2586        if numel(SubDir)>1
2587                SubDirOut=[SubDirOut '-' regexprep(SubDir{2},'^/','')];
2588        end
2589    case 'last'
2590        OutputDirVisible='on';
2591        SubDirOut=InputTable{end,2}; % use the last subdir name (+OutputDirExt) as output  subdirectory
2592end
2593set(handles.OutputSubDir,'String',SubDirOut)
2594set(handles.OutputSubDir,'BackgroundColor',[1 1 1])% set edit box to white color to indicate refreshment
2595set(handles.OutputDirExt,'Visible',OutputDirVisible)
2596set(handles.OutputSubDir,'Visible',OutputDirVisible)
2597%set(handles.CheckOverwrite,'Visible',OutputDirVisible)
2598set(handles.OutputDir_title,'Visible',OutputDirVisible)
2599SeriesData.ActionName=ActionName; % record ActionName for next use
2600
2601
2602%% visibility of the run mode (local or background or cluster)
2603if strcmp(OutputSubDirMode,'none')
2604    RunModeVisible='off'; % only local mode available if no output file is produced
2605else
2606    RunModeVisible='on';
2607end
2608set(handles.RunMode,'Visible',RunModeVisible)
2609set(handles.ActionExt,'Visible',RunModeVisible)
2610set(handles.RunMode_title,'Visible',RunModeVisible)
2611set(handles.ActionExt_title,'Visible',RunModeVisible)
2612
2613
2614%% Expected nbre of output files
2615if isfield(ParamOut,'OutputFileMode')
2616    StatusData.OutputFileMode=ParamOut.OutputFileMode;
2617    set(handles.status,'UserData',StatusData)
2618end
2619
2620%% definition of an additional parameter set, determined by an ancillary GUI
2621if isfield(ParamOut,'ActionInput')
2622%     set(handles.ActionInput,'Visible','on')
2623    ParamOut.ActionInput.Program=ActionName; % record the program in ActionInput
2624    SeriesData.ActionInput=ParamOut.ActionInput;
2625else
2626%     set(handles.ActionInput,'Visible','off')
2627    if isfield(SeriesData,'ActionInput')
2628        SeriesData=rmfield(SeriesData,'ActionInput');
2629    end
2630end
2631set(handles.series,'UserData',SeriesData)
2632set(handles.ActionInput,'BackgroundColor',[1 0 0])
2633
2634%------------------------------------------------------------------------
2635% --- Executes on selection change in FieldName.
2636function FieldName_Callback(hObject, eventdata, handles)
2637%------------------------------------------------------------------------
2638field_str=get(handles.FieldName,'String');
2639field_index=get(handles.FieldName,'Value');
2640field=field_str{field_index(1)};
2641if isequal(field,'get_field...')
2642    SeriesData=get(handles.series,'UserData');
2643    % input line for which the field choice is relevant
2644    iview=find(ismember(SeriesData.FileType,{'netcdf','civx','civdata'})); % all nc files, icluding civ
2645    hget_field=findobj(allchild(0),'name','get_field');
2646    if ~isempty(hget_field)
2647        delete(hget_field)%delete opened versions of get_field
2648    end
2649    Param=read_GUI(handles.series);
2650    InputTable=Param.InputTable(iview,:);
2651    % check the existence of the first file in the series
2652    first_j=[];last_j=[];MinIndex_j=1;MaxIndex_j=1; % default setting for index j
2653    if isfield(Param.IndexRange,'first_j'); % if index j is used     
2654        first_j=Param.IndexRange.first_j;
2655        last_j=Param.IndexRange.last_j;
2656        MinIndex_j=Param.IndexRange.MinIndex_j(iview);
2657        MaxIndex_j=Param.IndexRange.MaxIndex_j(iview);
2658    end
2659    PairString='';
2660    if isfield(Param.IndexRange,'PairString'); PairString=Param.IndexRange.PairString{iview}; end
2661    [i1,i2,j1,j2] = get_file_index(Param.IndexRange.first_i,first_j,PairString);
2662    LineIndex=iview(1);
2663    if numel(iview)>1     
2664        answer=msgbox_uvmat('INPUT_TXT',['select the line of the input table:' num2str(iview)] ,num2str(iview(1)));
2665        LineIndex=str2num(answer);
2666%         InputLine=str2num(get(handles.InputLine,'String'));
2667%         if ismember(InputLine,iview)
2668%             LineIndex=InputLine;
2669%         end
2670    end
2671    FirstFileName=fullfile_uvmat(InputTable{LineIndex,1},InputTable{LineIndex,2},InputTable{LineIndex,3},...
2672        InputTable{LineIndex,5},InputTable{LineIndex,4},i1,i2,j1,j2);
2673    if exist(FirstFileName,'file')
2674        ParamIn.Title='get_field: pick input variables and coordinates for series processing';
2675        ParamIn.SeriesInput=1;
2676        GetFieldData=get_field(FirstFileName,ParamIn);
2677        FieldList={};
2678        if isfield(GetFieldData,'FieldOption')% if a field has been selected
2679        switch GetFieldData.FieldOption
2680            case 'vectors'
2681                UName=GetFieldData.PanelVectors.vector_x;
2682                VName=GetFieldData.PanelVectors.vector_y;
2683                YName={GetFieldData.Coordinates.Coord_y};
2684                FieldList={['vec(' UName ',' VName ')'];...
2685                    ['norm(' UName ',' VName ')'];...
2686                    UName;VName};
2687                set(handles.VelType,'Visible','off')
2688            case {'scalar'}
2689                FieldList=GetFieldData.PanelScalar.scalar;
2690                YName={GetFieldData.Coordinates.Coord_y};
2691                if ischar(FieldList)
2692                    FieldList={FieldList};
2693                end
2694                set(handles.VelType,'Visible','off')
2695            case 'civdata...'
2696                FieldList=[set_field_list('U','V') ;{'C'}];
2697                set(handles.FieldName,'Value',1) % set menu to 'velocity
2698                XName='X';
2699                YName='y';
2700                set(handles.VelType,'Visible','on')
2701        end
2702        set(handles.FieldName,'Value',1)
2703        set(handles.FieldName,'String',[FieldList; {'get_field...'}]);
2704        if ~strcmp(GetFieldData.FieldOption,'civdata...')
2705           if ~isempty(regexp(FieldList{1},'^vec'))
2706                set(handles.FieldName,'Value',1)
2707           else
2708                set(handles.FieldName,'Value',1:numel(FieldList))%select all input fields by default
2709           end
2710            XName=GetFieldData.Coordinates.Coord_x;
2711            YName=GetFieldData.Coordinates.Coord_y;
2712            TimeNameStr=GetFieldData.Time.SwitchVarIndexTime;
2713            % get the time info                     
2714            TimeTable=get(handles.TimeTable,'Data');
2715            switch TimeNameStr
2716                case 'file index'
2717                    TimeName='';
2718                case 'attribute'
2719                    TimeName=['att:' GetFieldData.Time.TimeName];
2720                    % update the time table
2721                    TimeTable{LineIndex,2}=get_time(Param.IndexRange.MinIndex_i(LineIndex),MinIndex_j,PairString,InputTable,SeriesData.FileInfo{LineIndex},GetFieldData.Time.TimeName);  % Min time     
2722                    TimeTable{LineIndex,3}=get_time(Param.IndexRange.first_i,first_j,PairString,InputTable,SeriesData.FileInfo{LineIndex},GetFieldData.Time.TimeName);  % first time             
2723                    TimeTable{LineIndex,4}=get_time(Param.IndexRange.last_i,last_j,PairString,InputTable,SeriesData.FileInfo{LineIndex},GetFieldData.Time.TimeName);  % last time                     
2724                    TimeTable{LineIndex,5}=get_time(Param.IndexRange.MaxIndex_i(LineIndex),MaxIndex_j,PairString,InputTable,SeriesData.FileInfo{LineIndex},GetFieldData.Time.TimeName);  % Max time
2725                case 'variable'
2726                    set(handles.TimeName,'String',['var:' GetFieldData.Time.TimeName])
2727                    set(handles.NomType,'String','*')
2728                    set(handles.RootFile,'String',[get(handles.RootFile,'String') get(handles.FileIndex,'String')])% A VERIFIER !!!!!!
2729                    set(handles.FileIndex,'String','')
2730                    ParamIn.TimeVarName=GetFieldData.Time.TimeName;
2731                case 'matrix_index'
2732                    TimeName=['dim:' GetFieldData.Time.TimeName];
2733                    set(handles.NomType,'String','*')
2734                    set(handles.RootFile,'String',[get(handles.RootFile,'String') get(handles.FileIndex,'String')])
2735                    set(handles.FileIndex,'String','')
2736                    ParamIn.TimeDimName=GetFieldData.Time.TimeName;
2737            end
2738            TimeTable{LineIndex,1}=TimeName;
2739            set(handles.TimeTable,'Data',TimeTable);
2740        end
2741        set(handles.Coord_x,'String',XName)
2742        set(handles.Coord_y,'String',YName)
2743        set(handles.Coord_x,'Visible','on')
2744        set(handles.Coord_y,'Visible','on')
2745        end
2746    else
2747        msgbox_uvmat('ERROR',[FirstFileName ' does not exist'])
2748    end
2749end
2750
2751
2752function [TimeValue,DtValue]=get_time(ref_i,ref_j,PairString,InputTable,FileInfo,TimeName,DtName)
2753[i1,i2,j1,j2] = get_file_index(ref_i,ref_j,PairString);
2754FileName=fullfile_uvmat(InputTable{1},InputTable{2},InputTable{3},InputTable{5},InputTable{4},i1,i2,j1,j2);
2755Data=nc2struct(FileName,[]);
2756TimeValue=[];
2757DtValue=[];
2758if isequal(FileInfo.FileType,'civdata')
2759    if ismember(TimeName,{'civ1','filter1'})
2760        if isfield(Data,'Civ1_Time')
2761        TimeValue=Data.Civ1_Time;
2762        end
2763        if isfield(Data,'Civ1_Dt')
2764        DtValue=Data.Civ1_Dt;
2765        end
2766    else
2767        if isfield(Data,'Civ2_Time')
2768        TimeValue=Data.Civ2_Time;
2769        end
2770        if isfield(Data,'Civ2_Dt')
2771        DtValue=Data.Civ2_Dt;
2772        end
2773    end
2774else
2775    if ~isempty(TimeName)&& isfield(Data,TimeName)
2776        TimeValue=Data.(TimeName);
2777    end
2778    if exist('DtName','var') && isfield(Data,DtName)
2779        DtValue=Data.(DtName);
2780    end
2781end
2782
2783%------------------------------------------------------------------------
2784% --- Executes on selection change in FieldName_1.
2785function FieldName_1_Callback(hObject, eventdata, handles)
2786%------------------------------------------------------------------------
2787field_str=get(handles.FieldName_1,'String');
2788field_index=get(handles.FieldName_1,'Value');
2789field=field_str{field_index(1)};
2790if isequal(field,'get_field...')
2791    hget_field=findobj(allchild(0),'name','get_field');
2792    if ~isempty(hget_field)
2793        delete(hget_field)%delete opened versions of get_field
2794    end
2795    Param=read_GUI(handles.series);
2796    Param.InputTable=Param.InputTable(1,:);
2797    % check the existence of the first file in the series
2798    first_j=[];
2799    if isfield(Param.IndexRange,'first_j'); first_j=Param.IndexRange.first_j; end
2800    if isfield(Param.IndexRange,'last_j'); last_j=Param.IndexRange.last_j; end
2801    PairString='';
2802    if isfield(Param.IndexRange,'PairString'); PairString=Param.IndexRange.PairString; end
2803    [i1,i2,j1,j2] = get_file_index(Param.IndexRange.first_i,first_j,PairString);
2804    FirstFileName=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},...
2805        Param.InputTable{1,5},Param.InputTable{1,4},i1,i2,j1,j2);
2806    if exist(FirstFileName,'file')
2807        ParamIn.SeriesInput=1;
2808        GetFieldData=get_field(FirstFileName,ParamIn);
2809        FieldList={};
2810        switch GetFieldData.FieldOption
2811            case 'vectors'
2812                UName=GetFieldData.PanelVectors.vector_x;
2813                VName=GetFieldData.PanelVectors.vector_y;
2814                FieldList={['vec(' UName ',' VName ')'];...
2815                    ['norm(' UName ',' VName ')'];...
2816                    UName;VName};
2817            case {'scalar','pick variables'}
2818                FieldList=GetFieldData.PanelScalar.scalar;
2819                if ischar(FieldList)
2820                    FieldList={FieldList};
2821                end
2822            case '1D plot'
2823
2824            case 'civdata...'
2825                FieldList=set_field_list('U','V','C');
2826                set(handles.FieldName,'Value',2) % set menu to 'velocity
2827        end
2828        if ~strcmp(GetFieldData.FieldOption,'civdata...')
2829            TimeNameStr=GetFieldData.Time.SwitchVarIndexTime;
2830            switch TimeNameStr
2831                case 'file index'
2832                    set(handles.TimeName,'String','');
2833                case 'attribute'
2834                    set(handles.TimeName,'String',['att:' GetFieldData.Time.TimeName]);
2835                case 'variable'
2836                    set(handles.TimeName,'String',['var:' GetFieldData.Time.TimeName])
2837                    set(handles.NomType,'String','*')
2838                    set(handles.RootFile,'String',[get(handles.RootFile,'String') get(handles.FileIndex,'String')])% A VERIFIER !!!!!!
2839                    set(handles.FileIndex,'String','')
2840                    ParamIn.TimeVarName=GetFieldData.Time.TimeName;
2841                case 'matrix_index'
2842                    set(handles.TimeName,'String',['dim:' GetFieldData.Time.TimeName]);
2843                    set(handles.NomType,'String','*')
2844                    set(handles.RootFile,'String',[get(handles.RootFile,'String') get(handles.FileIndex,'String')])
2845                    set(handles.FileIndex,'String','')
2846                    ParamIn.TimeDimName=GetFieldData.Time.TimeName;
2847            end
2848        end
2849        set(handles.FieldName_1,'Value',1)
2850        set(handles.FieldName_1,'String',[FieldList; {'get_field...'}]);
2851    end
2852end   
2853
2854
2855%%%%%%%%%%%%%
2856function [ind_remove]=find_pairs(dirpair,ind_i,last_i)
2857indsel=ind_i;
2858indiff=diff(ind_i); % test index increment to detect multiplets (several pairs with the same index ind_i) and holes in the series
2859indiff=[1 indiff last_i-ind_i(end)+1]; % for testing gaps with the imposed bounds
2860if ~isempty(indiff)
2861    indiff2=diff(indiff);
2862    indiffp=[indiff2 1];
2863    indiffm=[1 indiff2];
2864    ind_multi_m=find((indiff==0)&(indiffm<0))-1; % indices of first members of multiplets
2865    ind_multi_p=find((indiff==0)&(indiffp>0)); % indices of last members of multiplets
2866    %for each multiplet, select the most recent file
2867    ind_remove=[];
2868    for i=1:length(ind_multi_m)
2869        ind_pairs=ind_multi_m(i):ind_multi_p(i);
2870        for imulti=1:length(ind_pairs)
2871            datepair(imulti)=datenum(dirpair(ind_pairs(imulti)).date); % dates of creation
2872        end
2873        [datenew,indsort2]=sort(datepair); % sort the multiplet by creation date
2874        ind_s=indsort2(1:end-1); %
2875        ind_remove=[ind_remove ind_pairs(ind_s)]; % remove these indices, leave the last one
2876    end
2877end
2878
2879%------------------------------------------------------------------------
2880% --- determine the list of index pairstring of processing file
2881function [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)
2882%------------------------------------------------------------------------
2883num_i1=num_i; % set of first image numbers by default
2884num_i2=num_i;
2885num_j1=num_j;
2886num_j2=num_j;
2887num_i_out=num_i;
2888num_j_out=num_j;
2889% if isequal (NomType,'_1-2_1') || isequal (NomType,'_1-2')
2890if isequal(mode,'series(Di)')
2891    num_i1_line=num_i+ind_shift(3); % set of first image numbers
2892    num_i2_line=num_i+ind_shift(4);
2893    % adjust the first and last field number
2894        indsel=find(num_i1_line >= 1);
2895    num_i_out=num_i(indsel);
2896    num_i1_line=num_i1_line(indsel);
2897    num_i2_line=num_i2_line(indsel);
2898    num_j1=meshgrid(num_j,ones(size(num_i1_line)));
2899    num_j2=meshgrid(num_j,ones(size(num_i1_line)));
2900    [xx,num_i1]=meshgrid(num_j,num_i1_line);
2901    [xx,num_i2]=meshgrid(num_j,num_i2_line);
2902elseif isequal (mode,'series(Dj)')||isequal (mode,'bursts')
2903    if isequal(mode,'bursts') %case of bursts (png_old or png_2D)
2904        num_j1=ind_shift(1)*ones(size(num_i));
2905        num_j2=ind_shift(2)*ones(size(num_i));
2906    else
2907        num_j1_col=num_j+ind_shift(1); % set of first image numbers
2908        num_j2_col=num_j+ind_shift(2);
2909        % adjust the first field number
2910        indsel=find((num_j1_col >= 1));   
2911        num_j_out=num_j(indsel);
2912        num_j1_col=num_j1_col(indsel);
2913        num_j2_col=num_j2_col(indsel);
2914        [num_i1,num_j1]=meshgrid(num_i,num_j1_col);
2915        [num_i2,num_j2]=meshgrid(num_i,num_j2_col);
2916    end   
2917end
2918
2919%------------------------------------------------------------------------
2920% --- Executes on button press in CheckObject.
2921function CheckObject_Callback(hObject, eventdata, handles)
2922%------------------------------------------------------------------------
2923hset_object=findobj(allchild(0),'tag','set_object'); % find the set_object interface handle
2924if get(handles.CheckObject,'Value')
2925    SeriesData=get(handles.series,'UserData');
2926    if isfield(SeriesData,'ProjObject') && ~isempty(SeriesData.ProjObject)
2927        set(handles.ViewObject,'Value',1)
2928        ViewObject_Callback(hObject, eventdata, handles)
2929    else
2930        if ishandle(hset_object)
2931            uistack(hset_object,'top')% show the GUI set_object if opened
2932        else
2933            %get the object file
2934            InputTable=get(handles.InputTable,'Data');
2935            defaultname=InputTable{1,1};
2936            if isempty(defaultname)
2937                defaultname={''};
2938            end
2939            fileinput=uigetfile_uvmat('pick a xml object file (or use uvmat to create it)',defaultname,'.xml');
2940            if isempty(fileinput)% exit if no object file is selected
2941                set(handles.CheckObject,'Value',0)
2942                return
2943            end
2944            %read the file
2945            data=xml2struct(fileinput);
2946            if ~isfield(data,'Type')
2947                msgbox_uvmat('ERROR',[fileinput ' is not an object xml file'])
2948                set(handles.CheckObject,'Value',0)
2949                return
2950            end
2951            if ~isfield(data,'ProjMode')
2952                data.ProjMode='none';
2953            end
2954            hset_object=set_object(data); % call the set_object interface
2955            set(hset_object,'Name','set_object_series')% name to distinguish from set_object used with uvmat
2956        end
2957        ProjObject=read_GUI(hset_object);
2958        set(handles.ProjObject,'String',ProjObject.Name); % display the object name
2959        SeriesData=get(handles.series,'UserData');
2960        SeriesData.ProjObject=ProjObject;
2961        set(handles.series,'UserData',SeriesData);
2962    end
2963    set(handles.EditObject,'Visible','on');
2964    set(handles.DeleteObject,'Visible','on');
2965    set(handles.ViewObject,'Visible','on');
2966    set(handles.ProjObject,'Visible','on');
2967else
2968    set(handles.EditObject,'Visible','off');
2969    set(handles.DeleteObject,'Visible','off');
2970    set(handles.ViewObject,'Visible','off');
2971    if ~ishandle(hset_object)
2972        set(handles.ViewObject,'Value',0);
2973    end
2974    set(handles.ProjObject,'Visible','off');
2975end
2976
2977%------------------------------------------------------------------------
2978% --- Executes on button press in ViewObject.
2979%------------------------------------------------------------------------
2980function ViewObject_Callback(hObject, eventdata, handles)
2981
2982UserData=get(handles.series,'UserData');
2983hset_object=findobj(allchild(0),'Tag','set_object');
2984if ~isempty(hset_object)
2985    delete(hset_object)% refresh set_object if already opened
2986end
2987hset_object=set_object(UserData.ProjObject);
2988set(hset_object,'Name','view_object_series')
2989
2990
2991%------------------------------------------------------------------------
2992% --- Executes on button press in EditObject.
2993function EditObject_Callback(hObject, eventdata, handles)
2994%------------------------------------------------------------------------
2995if get(handles.EditObject,'Value')
2996    set(handles.ViewObject,'Value',0)
2997    UserData=get(handles.series,'UserData');
2998    hset_object=set_object(UserData.ProjObject);
2999    set(hset_object,'Name','edit_object_series')
3000    set(get(hset_object,'Children'),'Enable','on')
3001else
3002    hset_object=findobj(allchild(0),'Tag','set_object');
3003    if ~isempty(hset_object)
3004        set(get(hset_object,'Children'),'Enable','off')
3005    end
3006end
3007
3008%------------------------------------------------------------------------
3009% --- Executes on button press in DeleteObject.
3010function DeleteObject_Callback(hObject, eventdata, handles)
3011%------------------------------------------------------------------------
3012SeriesData=get(handles.series,'UserData');
3013SeriesData.ProjObject=[];
3014set(handles.series,'UserData',SeriesData)
3015set(handles.ProjObject,'String','')
3016set(handles.ProjObject,'Visible','off')
3017set(handles.CheckObject,'Value',0)
3018set(handles.ViewObject,'Visible','off')
3019set(handles.EditObject,'Visible','off')
3020hset_object=findobj(allchild(0),'name','set_object_series');
3021if ~isempty(hset_object)
3022    delete(hset_object)
3023end
3024set(handles.DeleteObject,'Visible','off')
3025
3026%------------------------------------------------------------------------
3027% --- Executed when CheckMask is activated
3028%------------------------------------------------------------------------
3029function CheckMask_Callback(hObject, eventdata, handles)
3030
3031if get(handles.CheckMask,'Value')
3032    InputTable=get(handles.InputTable,'Data');
3033    nbview=size(InputTable,1);
3034    MaskTable=cell(nbview,1); % default
3035    ListMask=cell(nbview,1); % default
3036    MaskData=get(handles.MaskTable,'Data');
3037    MaskData(size(MaskData,1):nbview,1)=cell(size(MaskData,1):nbview,1); % complement if undefined lines
3038    for iview=1:nbview
3039        ListMask{iview,1}=num2str(iview);
3040        RootPath=InputTable{iview,1};
3041        if ~isempty(RootPath)
3042            if isempty(MaskData{iview})
3043                SubDir=InputTable{iview,2};
3044                MaskPath=fullfile(RootPath,[regexprep(SubDir,'\..*','') '.mask']); % take the root part of SubDir, before the first dot '.'
3045                if exist(MaskPath,'dir')
3046                    ListStruct=dir(MaskPath); % look for a mask file
3047                    ListCells=struct2cell(ListStruct); % transform dir struct to a cell arrray
3048                    check_dir=cell2mat(ListCells(4,:)); % =1 for directories, =0 for files
3049                    ListFiles=ListCells(1,:); % list of file and dri names
3050                    ListFiles=ListFiles(~check_dir); % list of file names (excluding dir)
3051                    mdetect=0;
3052                    if ~isempty(ListFiles)
3053                        for ifile=1:numel(ListFiles)
3054                            [tild,tild,MaskFile{ifile},i1_series,i2_series,j1_series,j2_series,MaskNomType,MaskFileType]=find_file_series(MaskPath,ListFiles{ifile},0);
3055                            if strcmp(MaskFileType,'image') && isempty(i2_series) && isempty(j2_series)
3056                                mdetect=1;
3057                                MaskName=ListFiles{ifile};
3058                            end
3059                            if ~strcmp(MaskFile{ifile},MaskFile{1})
3060                                mdetect=0; % cancel detection test in case of multiple masks, use the brower for selection
3061                                break
3062                            end
3063                        end
3064                    end
3065                    if mdetect==1
3066                        MaskName=fullfile(MaskPath,'mask_1.png');
3067                    else
3068                        MaskName=uigetfile_uvmat('select a mask file:',MaskPath,'image');
3069                    end
3070                else
3071                    MaskName=uigetfile_uvmat('select a mask file:',RootPath,'image');
3072                end
3073                MaskTable{iview,1}=MaskName ;
3074                ListMask{iview,1}=num2str(iview);
3075            end
3076        end
3077    end
3078    set(handles.MaskTable,'Data',MaskTable)
3079    set(handles.MaskTable,'Visible','on')
3080    set(handles.MaskBrowse,'Visible','on')
3081    set(handles.ListMask,'Visible','on')
3082    set(handles.ListMask,'String',ListMask)
3083    set(handles.ListMask,'Value',1)
3084else
3085    set(handles.MaskTable,'Visible','off')
3086    set(handles.MaskBrowse,'Visible','off')
3087    set(handles.ListMask,'Visible','off')
3088end
3089
3090%------------------------------------------------------------------------
3091% --- Executes on button press in MaskBrowse.
3092%------------------------------------------------------------------------
3093function MaskBrowse_Callback(hObject, eventdata, handles)
3094
3095InputTable=get(handles.InputTable,'Data');
3096iview=get(handles.ListMask,'Value');
3097RootPath=InputTable{iview,1};
3098MaskName=uigetfile_uvmat('select a mask file:',RootPath,'image');
3099if ~isempty(MaskName)
3100    MaskTable=get(handles.MaskTable,'Data');
3101    MaskTable{iview,1}=MaskName ;
3102    set(handles.MaskTable,'Data',MaskTable)
3103end
3104
3105%------------------------------------------------------------------------
3106% --- Executes when selected cell(s) is changed in MaskTable.
3107%------------------------------------------------------------------------
3108function MaskTable_CellSelectionCallback(hObject, eventdata, handles)
3109
3110if numel(eventdata.Indices)>=1
3111set(handles.ListMask,'Value',eventdata.Indices(1))
3112end
3113
3114%-------------------------------------------------------------------
3115function MenuHelp_Callback(hObject, eventdata, handles)
3116%-------------------------------------------------------------------
3117
3118
3119% path_to_uvmat=which ('uvmat'); % check the path of uvmat
3120% pathelp=fileparts(path_to_uvmat);
3121% helpfile=fullfile(pathelp,'uvmat_doc','uvmat_doc.html');
3122% 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')
3123% else
3124%     addpath (fullfile(pathelp,'uvmat_doc'))
3125%     web([helpfile '#series'])
3126% end
3127
3128%-------------------------------------------------------------------
3129% --- Executes on selection change in TransformName.
3130function TransformName_Callback(hObject, eventdata, handles)
3131%----------------------------------------------------------------------
3132TransformList=get(handles.TransformName,'String');
3133TransformIndex=get(handles.TransformName,'Value');
3134TransformName=TransformList{TransformIndex};
3135TransformPathList=get(handles.TransformName,'UserData');
3136nb_builtin_transform=4;
3137if isequal(TransformName,'more...');     
3138    FileName=uigetfile_uvmat('Pick a transform function',get(handles.TransformPath,'String'),'.m');
3139    if isempty(FileName)
3140        return     %browser closed without choice
3141    end
3142    [TransformPath,TransformName,TransformExt]=fileparts(FileName); % removes extension .m
3143    if ~strcmp(TransformExt,'.m')
3144        msgbox_uvmat('ERROR','a Matlab function .m must be introduced');
3145        return
3146    end
3147     % insert the choice in the menu
3148    TransformIndex=find(strcmp(TransformName,TransformList),1); % look for the selected function in the menu Action
3149    if isempty(TransformIndex)%the input string does not exist in the menu
3150        TransformIndex= length(TransformList);
3151        TransformList=[TransformList(1:end-1);{TransformName};TransformList(end)]; % the selected function is appended in the menu, before the last item 'more...'
3152        set(handles.TransformName,'String',TransformList)
3153        TransformPathList=[TransformPathList;{TransformPath}];
3154    else% the input function already exist, we update its path (possibly new)
3155        TransformPathList{TransformIndex}=TransformPath; %
3156        set(handles.TransformName,'Value',TransformIndex)
3157    end
3158   % save the new menu in the personal file 'uvmat_perso.mat'
3159   dir_perso=prefdir; % personal Matalb directory
3160   profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
3161   if exist(profil_perso,'file')
3162       for ilist=nb_builtin_transform+1:numel(TransformPathList)
3163           TransformListUser{ilist-nb_builtin_transform}=TransformList{ilist};
3164           TransformPathListUser{ilist-nb_builtin_transform}=TransformPathList{ilist};
3165       end
3166       TransformPathListUser=TransformPathListUser';
3167       TransformListUser=TransformListUser';
3168       save (profil_perso,'TransformPathListUser','TransformListUser','-append'); % store the root name for future opening of uvmat
3169   end
3170end
3171
3172%display the current function path
3173set(handles.TransformPath,'String',TransformPathList{TransformIndex}); % show the path to the senlected function
3174set(handles.TransformName,'UserData',TransformPathList);
3175
3176%% create the function handle of the selected fct
3177if ~isempty(TransformName)
3178    if ~exist(TransformPathList{TransformIndex},'dir')
3179        msgbox_uvmat('ERROR',['The prescribed transform function path ' TransformPathList{TransformIndex} ' does not exist']);
3180        return
3181    end
3182    current_dir=pwd; % current working dir
3183    cd(TransformPathList{TransformIndex})
3184    transform_handle=str2func(TransformName);
3185    cd(current_dir)
3186    Field.Action.RUN=0;% indicate that the transform fct is called only to get input param
3187    SeriesData=get(handles.series,'UserData');
3188    ParamIn=[];
3189    if isfield(SeriesData,'TransformInput')
3190        ParamIn.TransformInput=SeriesData.TransformInput;
3191    end
3192    DataOut=feval(transform_handle,Field,ParamIn);% execute the transform fct to get the required conditions
3193    Field.Action.RUN=0; % indicate that the transform fct is called only to get input param
3194    DataOut=feval(transform_handle,Field,[]); % execute the transform fct to get the required conditions
3195    if isfield(DataOut,'TransformInput')%  used to add transform parameters at selection of the transform fct
3196        SeriesData.TransformInput=DataOut.TransformInput;
3197        set(handles.series,'UserData',SeriesData)
3198    end
3199end
3200
3201%------------------------------------------------------------------------
3202% --- fct activated by the upper bar menu ExportConfig
3203%------------------------------------------------------------------------
3204function MenuDisplayConfig_Callback(hObject, eventdata, handles)
3205
3206global Param
3207Param=read_GUI_series(handles);
3208evalin('base','global Param')%make CurData global in the workspace
3209display('current series config :')
3210evalin('base','Param') %display CurData in the workspace
3211commandwindow; % brings the Matlab command window to the front
3212
3213%------------------------------------------------------------------------
3214% --- fct activated by the upper bar menu InportConfig: import
3215%     menu settings from an xml file (stored in /0_XML for each run)
3216%------------------------------------------------------------------------
3217function MenuImportConfig_Callback(hObject, eventdata, handles)
3218
3219%% use a browser to choose the xml file containing the processing config
3220InputTable=get(handles.InputTable,'Data');
3221oldfile=InputTable{1,1}; % current path in InputTable
3222if isempty(oldfile)
3223    % use a file name stored in prefdir
3224    dir_perso=prefdir;
3225    profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
3226    if exist(profil_perso,'file')
3227        h=load (profil_perso);
3228        if isfield(h,'RootPath') && ischar(h.RootPath)
3229            oldfile=h.RootPath;
3230        end
3231    end
3232end
3233filexml=uigetfile_uvmat('pick a xml parameter file',oldfile,'.xml'); % get the xml file containing processing parameters
3234if isempty(filexml), return, end % quit function if an xml file has not been opened
3235
3236%% fill the GUI series with the content of the xml file
3237Param=xml2struct(filexml); % read the input xml file as a Matlab structure
3238
3239% ask to stop current Action if button RUN is in action (another process is already running)
3240if isequal(get(handles.RUN,'Value'),1)
3241    answer= msgbox_uvmat('INPUT_Y-N','stop current Action process?');
3242    if strcmp(answer,'Yes')
3243        STOP_Callback(hObject, eventdata, handles)
3244    else
3245        return
3246    end
3247end
3248Param.Action.RUN=0; % desactivate the input RUN=1
3249
3250fill_GUI(Param,handles.series)% fill the elements of the GUI series with the input parameters
3251SeriesData=get(handles.series,'UserData');
3252if isfield(Param,'InputFields')
3253    ListField=Param.InputFields.FieldName;
3254    if ischar(ListField),ListField={ListField}; end
3255    set(handles.FieldName,'String',[ListField;{'get-field...'}])
3256     set(handles.FieldName,'Value',1:numel(ListField))
3257     set(handles.FieldName,'Visible','on')
3258end       
3259if isfield(Param,'ActionInput')%  introduce  parameters specific to an Action fct, for instance PIV parameters
3260%     set(handles.ActionInput,'Visible','on')
3261%     set(handles.ActionInput,'Value',0)
3262    Param.ActionInput.ConfigSource=filexml; % record the source of config for future info
3263    SeriesData.ActionInput=Param.ActionInput;
3264end
3265if isfield(Param,'TransformInput')%  introduce  parameters specific to a transform fct
3266    SeriesData.TransformInput=Param.TransformInput;
3267end
3268if isfield(Param,'ProjObject') %introduce projection object if relevant
3269    SeriesData.ProjObject=Param.ProjObject;
3270end
3271set(handles.series,'UserData',SeriesData)
3272if isfield(Param,'CheckObject') && isequal(Param.CheckObject,1)
3273    set(handles.ProjObject,'String',Param.ProjObject.Name)
3274    set(handles.ViewObject,'Visible','on')
3275    set(handles.EditObject,'Visible','on')
3276    set(handles.DeleteObject,'Visible','on')
3277else     
3278    set(handles.ProjObject,'String','')
3279    set(handles.ProjObject,'Visible','off')
3280    set(handles.ViewObject,'Visible','off')
3281    set(handles.EditObject,'Visible','off')
3282    set(handles.DeleteObject,'Visible','off')     
3283end     
3284set(handles.REFRESH,'BackgroundColor',[1 0 1]); % paint REFRESH button in magenta to indicate that it should be activated
3285
3286
3287%------------------------------------------------------------------------
3288% --- Executes when the GUI series is resized.
3289%------------------------------------------------------------------------
3290function series_ResizeFcn(hObject, eventdata, handles)
3291
3292%% input table
3293set(handles.InputTable,'Unit','pixel')
3294Pos=get(handles.InputTable,'Position');
3295set(handles.InputTable,'Unit','normalized')
3296ColumnWidth=round([0.5 0.14 0.14 0.14 0.08]*(Pos(3)-52));
3297ColumnWidth=num2cell(ColumnWidth);
3298set(handles.InputTable,'ColumnWidth',ColumnWidth)
3299
3300%% MinIndex_j and MaxIndex_i
3301unit=get(handles.MinIndex_i,'Unit');
3302set(handles.MinIndex_i,'Unit','pixel')
3303Pos=get(handles.MinIndex_i,'Position');
3304set(handles.MinIndex_i,'Unit',unit)
3305set(handles.MinIndex_i,'ColumnWidth',{Pos(3)-18})
3306set(handles.MaxIndex_i,'ColumnWidth',{Pos(3)-18})
3307set(handles.MinIndex_j,'ColumnWidth',{Pos(3)-18})
3308set(handles.MaxIndex_j,'ColumnWidth',{Pos(3)-18})
3309
3310%% TimeTable
3311set(handles.TimeTable,'Unit','pixel')
3312Pos=get(handles.TimeTable,'Position');
3313set(handles.TimeTable,'Unit','normalized')
3314% ColumnWidth=get(handles.TimeTable,'ColumnWidth');
3315ColumnWidth=num2cell(floor([0.2 0.2 0.2 0.2 0.2]*(Pos(3)-20)));
3316set(handles.TimeTable,'ColumnWidth',ColumnWidth)
3317
3318
3319%% PairString
3320set(handles.PairString,'Unit','pixel')
3321Pos=get(handles.PairString,'Position');
3322set(handles.PairString,'Unit','normalized')
3323set(handles.PairString,'ColumnWidth',{Pos(3)-5})
3324
3325%% MaskTable
3326set(handles.MaskTable,'Unit','pixel')
3327Pos=get(handles.MaskTable,'Position');
3328set(handles.MaskTable,'Unit','normalized')
3329set(handles.MaskTable,'ColumnWidth',{Pos(3)-5})
3330
3331%------------------------------------------------------------------------
3332% --- Executes on button press in status.
3333%------------------------------------------------------------------------
3334function status_Callback(hObject, eventdata, handles)
3335
3336if get(handles.status,'Value')
3337    set(handles.status,'BackgroundColor',[1 1 0])
3338    drawnow
3339    Param=read_GUI(handles.series);
3340    RootPath=Param.InputTable{1,1};
3341    if ~isfield(Param,'OutputSubDir')   
3342        msgbox_uvmat('ERROR','no standard sub-directory definition for output files, use a browser to check the output')
3343        set(handles.status,'BackgroundColor',[0 1 0])
3344        return
3345    end
3346    OutputSubDir=[Param.OutputSubDir Param.OutputDirExt]; % subdirectory for output files
3347    OutputDir=fullfile(RootPath,OutputSubDir);
3348    if exist(OutputDir,'dir')
3349        uigetfile_uvmat('status_display',OutputDir)
3350    else
3351        msgbox_uvmat('ERROR','output folder not created yet: calculation did not start')
3352        set(handles.status,'BackgroundColor',[0 1 0])
3353    end
3354else
3355    %% delete current display fig if selection is off
3356    set(handles.status,'BackgroundColor',[0 1 0])
3357    hfig=findobj(allchild(0),'name','status_display');
3358    if ~isempty(hfig)
3359        delete(hfig)
3360    end
3361    return
3362end
3363
3364
3365%------------------------------------------------------------------------   
3366% launched by selecting a file on the list
3367%------------------------------------------------------------------------
3368function view_file(hObject, eventdata)
3369
3370list=get(hObject,'String');
3371index=get(hObject,'Value');
3372rootroot=get(hObject,'UserData');
3373selectname=list{index};
3374ind_dot=regexp(selectname,'\.\.\.');
3375if ~isempty(ind_dot)
3376    selectname=selectname(1:ind_dot-1);
3377end
3378FullSelectName=fullfile(rootroot,selectname);
3379if exist(FullSelectName,'dir')% a directory has been selected
3380    ListFiles=dir(FullSelectName);
3381    ListDisplay=cell(numel(ListFiles),1);
3382    for ilist=2:numel(ListDisplay)% suppress the first line '.'
3383        ListDisplay{ilist-1}=ListFiles(ilist).name;
3384    end
3385    set(hObject,'Value',1)
3386    set(hObject,'String',ListDisplay)
3387    if strcmp(selectname,'..')
3388        FullSelectName=fileparts(fileparts(FullSelectName));
3389    end
3390    set(hObject,'UserData',FullSelectName)
3391    hfig=get(hObject,'parent');
3392    htitlebox=findobj(hfig,'tag','titlebox');   
3393    set(htitlebox,'String',FullSelectName)
3394elseif exist(FullSelectName,'file')%visualise the vel field if it exists
3395    FileInfo=get_file_info(FullSelectName);   
3396    if strcmp(FileInfo.FileType,'txt')
3397        edit(FullSelectName)
3398    elseif strcmp(FileInfo.FileType,'xml')
3399        editxml(FullSelectName)
3400    else
3401        uvmat(FullSelectName)
3402    end
3403    set(gcbo,'Value',1)
3404end
3405
3406
3407%------------------------------------------------------------------------   
3408% launched by refreshing the status figure
3409%------------------------------------------------------------------------
3410function refresh_GUI(hfig)
3411
3412htitlebox=findobj(hfig,'tag','titlebox');
3413hlist=findobj(hfig,'tag','list');
3414hseries=findobj(allchild(0),'tag','series');
3415hstatus=findobj(hseries,'tag','status');
3416StatusData=get(hstatus,'UserData');
3417OutputDir=get(htitlebox,'String');
3418if ischar(OutputDir),OutputDir={OutputDir};end
3419ListFiles=dir(OutputDir{1});
3420if numel(ListFiles)<1
3421    return
3422end
3423ListFiles(1)=[]; % removes the first line ='.'
3424ListDisplay=cell(numel(ListFiles),1);
3425testrecent=0;
3426datnum=zeros(numel(ListDisplay),1);
3427for ilist=1:numel(ListDisplay)
3428    ListDisplay{ilist}=ListFiles(ilist).name;
3429      if ~ListFiles(ilist).isdir && isfield(ListFiles(ilist),'datenum')
3430            datnum(ilist)=ListFiles(ilist).datenum; % only available in recent matlab versions
3431            testrecent=1;
3432       end
3433end
3434set(hlist,'String',ListDisplay)
3435
3436%% Look at date of creation
3437ListDisplay=ListDisplay(datnum~=0);
3438datnum=datnum(datnum~=0); % keep the non zero values corresponding to existing files
3439NbOutputFile=[];
3440if isempty(datnum)
3441    if testrecent
3442        message='no civ result created yet';
3443    else
3444        message='';
3445    end
3446else
3447    [first,indfirst]=min(datnum);
3448    [last,indlast]=max(datnum);
3449    NbOutputFile_str='?';
3450    NbOutputFile=[];
3451    if isfield(StatusData,'NbOutputFile')
3452        NbOutputFile=StatusData.NbOutputFile;
3453        NbOutputFile_str=num2str(NbOutputFile);
3454    end
3455    message={[num2str(numel(datnum)) ' file(s) done over ' NbOutputFile_str] ;['oldest modification:  ' ListDisplay{indfirst} ' : ' datestr(first)];...
3456        ['latest modification:  ' ListDisplay{indlast} ' : ' datestr(last)]};
3457end
3458set(htitlebox,'String', [OutputDir{1};message])
3459
3460%% update the waitbar
3461hwaitbar=findobj(hfig,'tag','waitbar');
3462if ~isempty(NbOutputFile)
3463    BarPosition=get(hwaitbar,'Position');
3464    BarPosition(3)=0.9*numel(datnum)/NbOutputFile;
3465    set(hwaitbar,'Position',BarPosition)
3466end
3467
3468%------------------------------------------------------------------------
3469% --- Executes on selection change in ActionExt.
3470%------------------------------------------------------------------------
3471function ActionExt_Callback(hObject, eventdata, handles)
3472
3473ActionExtList=get(handles.ActionExt,'String');
3474ActionExt=ActionExtList{get(handles.ActionExt,'Value')};
3475if strcmp(ActionExt,'.py (in dev.)')
3476    set(handles.RunMode,'Value',2)
3477end
3478
3479%function num_NbProcess_Callback(hObject, eventdata, handles)
3480
3481
3482function num_NbSlice_Callback(hObject, eventdata, handles)
3483NbSlice=str2num(get(handles.num_NbSlice,'String'));
3484%set(handles.num_NbProcess,'String',num2str(NbSlice))
3485
3486%------------------------------------------------------------------------
3487% --- set the visibility of relevant velocity type menus:
3488function menu=set_veltype_display(Civ,FileType)
3489%------------------------------------------------------------------------
3490if ~exist('FileType','var')
3491    FileType='civx';
3492end
3493switch FileType
3494    case 'civx'
3495        menu={'civ1';'interp1';'filter1';'civ2';'interp2';'filter2'};
3496        if isequal(Civ,0)
3497            imax=0;
3498        elseif isequal(Civ,1) || isequal(Civ,2)
3499            imax=1;
3500        elseif isequal(Civ,3)
3501            imax=3;
3502        elseif isequal(Civ,4) || isequal(Civ,5)
3503            imax=4;
3504        elseif isequal(Civ,6) %patch2
3505            imax=6;
3506        end
3507    case 'civdata'
3508        menu={'civ1';'filter1';'civ2';'filter2'};
3509        if isequal(Civ,0)
3510            imax=0;
3511        elseif isequal(Civ,1) || isequal(Civ,2)
3512            imax=1;
3513        elseif isequal(Civ,3)
3514            imax=2;
3515        elseif isequal(Civ,4) || isequal(Civ,5)
3516            imax=3;
3517        else%if isequal(Civ,6) %patch2
3518            imax=4;
3519        end
3520end
3521menu=menu(1:imax);
3522
3523
3524% --- Executes on mouse motion over figure - except title and menu.
3525function series_WindowButtonMotionFcn(hObject, eventdata, handles)
3526set(hObject,'Pointer','arrow');
3527
3528
3529% --- Executes on button press in SetPairs.
3530function SetPairs_Callback(hObject, eventdata, handles)
3531
3532%% delete previous occurrence of 'set_pairs'
3533hfig=findobj(allchild(0),'Tag','set_pairs');
3534if ~isempty(hfig)
3535delete(hfig)
3536end
3537
3538%% create the GUI set_pairs
3539set(0,'Unit','points')
3540ScreenSize=get(0,'ScreenSize'); % get the size of the screen, to put the fig on the upper right
3541Width=220; % fig width in points (1/72 inch)
3542Height=min(0.8*ScreenSize(4),300);
3543Left=ScreenSize(3)- Width-40; % right edge close to the right, with margin=40
3544Bottom=ScreenSize(4)-Height-40; % put fig at top right
3545hfig=findobj(allchild(0),'Tag','set_slice');
3546if ~isempty(hfig),delete(hfig), end; % delete existing version of the GUI
3547hfig=figure('name','set_pairs','tag','set_pairs','MenuBar','none','NumberTitle','off','Unit','points','Position',[Left,Bottom,Width,Height]);
3548BackgroundColor=get(hfig,'Color');
3549SeriesData=get(handles.series,'UserData');
3550TimeUnit=get(handles.TimeUnit,'String');
3551PairString=get(handles.PairString,'Data');
3552ListViewLines=find(cellfun('isempty',PairString)==0); % find list of non empty pairs
3553ListViewMenu=cell(numel(ListViewLines),1);
3554%iview=get(handles.PairString,'Value');
3555iview=[];
3556for ilist=1:numel(ListViewLines)
3557    ListViewMenu{ilist}=num2str(ListViewLines(ilist));
3558end
3559if isempty(iview)
3560    ListViewValue=numel(ListViewLines); % we work by default on the pair option for the last line which requires pairs
3561    iview=ListViewLines(end);
3562else
3563    ListViewValue=find(ListViewLines==iview);
3564end
3565ref_i=str2num(get(handles.num_first_i,'String'));
3566ref_j=1; % default
3567if strcmp(get(handles.num_first_j,'String'),'Visible')
3568    ref_j=str2num(get(handles.num_first_j,'String'));
3569end
3570[ModeMenu,ModeValue]=update_mode(SeriesData.i1_series{1},SeriesData.i2_series{1},SeriesData.j2_series{1});
3571InputTable=get(handles.InputTable,'Data');
3572displ_pair=update_listpair(SeriesData.i1_series{1},SeriesData.i2_series{1},SeriesData.j1_series{1},SeriesData.j2_series{1},ModeMenu{ModeValue},...
3573                                                 SeriesData.Time{1},TimeUnit,ref_i,ref_j,SeriesData.TimeName,InputTable,SeriesData.FileInfo{1});
3574for iline=1:size(InputTable,1)
3575    viewcell{iline}=num2str(iline);
3576end
3577viewcell=viewcell';
3578ModeMenu={'bursts';'series(Dj)'};
3579ModeValue=1;                                               
3580                   %i1_series,i2_series,j1_series,j2_series,mode,time,TimeUnit,ref_i,ref_j,TimeName,InputTable,FileInfo                             
3581% first raw of the GUI
3582uicontrol('Style','text','Units','normalized', 'Position', [0.05 0.88 0.5 0.1],'BackgroundColor',BackgroundColor,...
3583    'String','row to edit #','FontUnits','points','FontSize',12,'FontWeight','bold','ForegroundColor','blue','HorizontalAlignment','right'); % title
3584uicontrol('Style','popupmenu','Units','normalized', 'Position', [0.54 0.8 0.3 0.2],'BackgroundColor',[1 1 1],...
3585    'Callback',@(hObject,eventdata)ListView_Callback(hObject,eventdata),'String',viewcell,'Value',1,'FontUnits','points','FontSize',12,'FontWeight','bold',...
3586    'Tag','ListView','TooltipString','''ListView'':choice of the file series w for pair display');
3587% second raw of the GUI
3588uicontrol('Style','text','Units','normalized', 'Position', [0.05 0.79 0.7 0.1],'BackgroundColor',BackgroundColor,...
3589    'String','mode of index pairing:','FontUnits','points','FontSize',12,'FontWeight','bold','ForegroundColor','blue','HorizontalAlignment','left'); % title
3590uicontrol('Style','popupmenu','Units','normalized', 'Position', [0.05 0.62 0.9 0.2],'BackgroundColor',[1 1 1],...
3591    'Callback',@(hObject,eventdata)Mode_Callback(hObject,eventdata),'String',ModeMenu,'Value',ModeValue,'FontUnits','points','FontSize',12,'FontWeight','bold',...
3592    'Tag','Mode','TooltipString','''Mode'': choice of the image pair mode');
3593% third raw
3594uicontrol('Style','text','Units','normalized', 'Position', [0.05 0.6 0.7 0.1],'BackgroundColor',BackgroundColor,...
3595    'String','pair choice:','FontUnits','points','FontSize',12,'FontWeight','bold','ForegroundColor','blue','HorizontalAlignment','left'); % title
3596uicontrol('Style','listbox','Units','normalized', 'Position', [0.05 0.42 0.9 0.2],'BackgroundColor',[1 1 1],...
3597    'Callback',@(hObject,eventdata)ListPair_Callback(hObject,eventdata),'String',displ_pair,'Value',1,'FontUnits','points','FontSize',12,'FontWeight','bold',...
3598    'Tag','ListPair','TooltipString','''ListPair'': menu for selecting the image pair');
3599uicontrol('Style','text','Units','normalized', 'Position', [0.1 0.22 0.8 0.1],'BackgroundColor',BackgroundColor,...
3600    'String','ref_i           ref_j','FontUnits','points','FontSize',12,'FontWeight','bold','ForegroundColor','blue','HorizontalAlignment','center'); % title
3601uicontrol('Style','edit','Units','normalized', 'Position', [0.15 0.17 0.3 0.08],'BackgroundColor',[1 1 1],...
3602    'Callback',@(hObject,eventdata)num_ref_i_Callback(hObject,eventdata),'String',num2str(ref_i),'FontUnits','points','FontSize',12,'FontWeight','bold',...
3603    'Tag','num_ref_i','TooltipString','''num_ref_i'': reference field index i used to display dt in ''list_pair_civ''');
3604uicontrol('Style','edit','Units','normalized', 'Position', [0.55 0.17 0.3 0.08],'BackgroundColor',[1 1 1],...
3605    'Callback',@(hObject,eventdata)num_ref_j_Callback(hObject,eventdata),'String',num2str(ref_j),'FontUnits','points','FontSize',12,'FontWeight','bold',...
3606    'Tag','num_ref_j','TooltipString','''num_ref_j'': reference field index i used to display dt in ''list_pair_civ''');
3607uicontrol('Style','pushbutton','Units','normalized', 'Position', [0.01 0.01 0.3 0.12],'BackgroundColor',[0 1 0],...
3608    'Callback',@(hObject,eventdata)OK_Callback(hObject,eventdata),'String','OK','FontUnits','points','FontSize',12,'FontWeight','bold',...
3609    'Tag','OK','TooltipString','''OK'': validate the choice');
3610%  last raw  of the GUI: pushbuttons
3611% 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),...
3612%     'FontWeight','bold','FontUnits','points','FontSize',12,'TooltipString','''OK'': apply the output to the current field series in uvmat');
3613drawnow
3614
3615%------------------------------------------------------------------------
3616function ListView_Callback(hObject,eventdata)
3617Mode_Callback(hObject,eventdata)
3618
3619%------------------------------------------------------------------------   
3620function Mode_Callback(hObject,eventdata)
3621%% get input info
3622hseries=findobj(allchild(0),'tag','series'); % handles of the GUI series
3623hhseries=guidata(hseries); % handles of the elements in the GUI series
3624TimeUnit=get(hhseries.TimeUnit,'String');
3625SeriesData=get(hseries,'UserData');
3626mode_list=get(hObject,'String');
3627mode=mode_list{get(hObject,'Value')};
3628hListView=findobj(get(hObject,'parent'),'Tag','ListView');
3629iview=get(hListView,'Value');
3630i1_series=SeriesData.i1_series{iview};
3631i2_series=SeriesData.i2_series{iview};
3632j1_series=SeriesData.j1_series{iview};
3633j2_series=SeriesData.j2_series{iview};
3634
3635%% enable j index visibility after the new choice
3636
3637if strcmp(mode,'series(Dj)')
3638   status_j='on'; % default
3639else
3640       status_j='off'; % no j index needed for bust case
3641end
3642enable_j(hhseries,status_j) % no j index needed
3643
3644%% get the reference indices for the time interval Dt
3645href_i=findobj(get(hObject,'parent'),'Tag','ref_i');
3646ref_i=[];ref_j=[];
3647if strcmp(get(href_i,'Visible'),'on')
3648    ref_i=str2num(get(href_i,'String'));
3649end
3650if isempty(ref_i)
3651    ref_i=1;
3652end
3653if isempty(ref_j)
3654    ref_j=1;
3655end
3656
3657%% update the menu ListPair
3658Menu=update_listpair(i1_series,i2_series,j1_series,j2_series,mode,SeriesData.Time{iview},TimeUnit,ref_i,ref_j,SeriesData.FileInfo);
3659hlist_pairs=findobj(get(hObject,'parent'),'Tag','ListPair');
3660set(hlist_pairs,'Value',1)% set the first choice by default in ListPair
3661set(hlist_pairs,'String',Menu)% set the menu in ListPair
3662ListPair_Callback(hlist_pairs,[])% apply the default choice in ListPair
3663
3664%-------------------------------------------------------------
3665% --- Executes on selection in ListPair.
3666function ListPair_Callback(hObject,eventdata)
3667%------------------------------------------------------------
3668list_pair=get(hObject,'String'); % get the menu of image pairs
3669if isempty(list_pair)
3670    string='';
3671else
3672    string=list_pair{get(hObject,'Value')};
3673   % string=regexprep(string,',.*',''); % removes time indication (after ',')
3674end
3675hseries=findobj(allchild(0),'tag','series');
3676hPairString=findobj(hseries,'tag','PairString');
3677PairString=get(hPairString,'Data');
3678hListView=findobj(get(hObject,'parent'),'Tag','ListView');
3679iview=get(hListView,'Value');
3680PairString{iview,1}=string;
3681% report the selected pair string to the table PairString
3682set(hPairString,'Data',PairString)
3683
3684
3685%------------------------------------------------------------------------
3686function num_ref_i_Callback(hObject, eventdata)
3687%------------------------------------------------------------------------
3688Mode_Callback([],[])
3689
3690%------------------------------------------------------------------------
3691function num_ref_j_Callback(hObject, eventdata)
3692%------------------------------------------------------------------------
3693Mode_Callback([],[])
3694
3695%------------------------------------------------------------------------
3696function OK_Callback(hObject, eventdata)
3697%------------------------------------------------------------------------
3698delete(get(hObject,'parent'))
3699
3700
3701%------------------------------------------------------------------------
3702% --- Executes on button press in ClearLine.
3703%------------------------------------------------------------------------
3704function ClearLine_Callback(hObject, eventdata, handles)
3705InputTable=get(handles.InputTable,'Data');
3706iline=str2double(get(handles.InputLine,'String'));
3707if size(InputTable,1)>1
3708    InputTable(iline,:)=[]; % suppress the current line if not the first
3709    set(handles.InputTable,'Data',InputTable);
3710end
3711set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH button to magenta color to indicate that input refr
3712
3713
3714% --- Executes on button press in MonitorCluster.
3715function MonitorCluster_Callback(hObject, eventdata, handles)
3716disp('format: R/W=run/wait, time lapsed, R=nbre of cores,W=walltime')
3717system('oarstat |grep N=UVmat')% check the list of jobs launched with uvmat
3718
3719
3720function OutputSubDir_Callback(hObject, eventdata, handles)
3721set(handles.OutputSubDir,'BackgroundColor',[1 1 1])
3722
3723
3724% --- Executes on button press in CheckOverwrite.
3725function CheckOverwrite_Callback(hObject, eventdata, handles)
3726
3727% --- Executes on button press in TestCPUTime.
3728function TestCPUTime_Callback(hObject, eventdata, handles)
3729% hObject    handle to TestCPUTime (see GCBO)
3730% eventdata  reserved - to be defined in a future version of MATLAB
3731% handles    structure with handles and user data (see GUIDATA)
3732
3733
3734% --- Executes on button press in DiskQuota.
3735function DiskQuota_Callback(hObject, eventdata, handles)
3736SeriesData=get(handles.series,'UserData');
3737system(SeriesData.SeriesParam.DiskQuotaCmd)
3738
3739
3740
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