source: trunk/src/series.m @ 824

Last change on this file since 824 was 824, checked in by sommeria, 9 years ago

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