source: trunk/src/series.m @ 837

Last change on this file since 837 was 832, checked in by sommeria, 10 years ago

miinor corrections on 'series'

File size: 143.4 KB
Line 
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
530if ~isempty(xx)
531switch xx
532    case 31 %downward arrow
533        InputTable=get(handles.InputTable,'Data');
534        iline=get(handles.InputTable,'UserData');
535        if isequal(iline,size(InputTable,1))% arrow downward
536            InputTable=[InputTable;InputTable(iline,:)];% create a new line as a copy of the last one
537            set(handles.InputTable,'Data',InputTable);
538        end
539    case 127  %key 'Suppress'
540         InputTable=get(handles.InputTable,'Data');
541        iline=get(handles.InputTable,'UserData');
542        if iline>1
543            InputTable(iline,:)=[];% suppress the current line if not the first
544            set(handles.InputTable,'Data',InputTable);
545        end
546end
547end
548
549%------------------------------------------------------------------------
550% --- Executes on button press in REFRESH.
551function REFRESH_Callback(hObject, eventdata, handles)
552%------------------------------------------------------------------------
553InputTable=get(handles.InputTable,'Data');
554set(handles.series,'Pointer','watch') % set the mouse pointer to 'watch'
555set(handles.REFRESH,'BackgroundColor',[1 1 0])% set REFRESH  button to yellow color (indicate activation)
556drawnow
557empty_line=false(size(InputTable,1),1);
558for iline=1:size(InputTable,1)
559    empty_line(iline)= isempty(cell2mat(InputTable(iline,1:3)));
560end
561if ~isempty(find(empty_line));
562    InputTable(empty_line,:)=[];%remove empty lines
563    set(handles.InputTable,'Data',InputTable)
564    ListTable={'MinIndex_i','MaxIndex_i','MinIndex_j','MaxIndex_j','PairString','TimeTable'};
565    for ilist=1:numel(ListTable)
566        Table=get(handles.(ListTable{ilist}),'Data');
567        Table(empty_line,:)=[];%remove empty lines
568        set(handles.(ListTable{ilist}),'Data',Table);
569    end
570    set(handles.series,'UserData',[])%refresh the stored info
571end
572for iview=1:size(InputTable,1)
573    RootPath=fullfile(InputTable{iview,1},InputTable{iview,2});
574    if ~exist(RootPath,'dir')
575        i1_series=[];
576        RootPath=fileparts(RootPath); %will try the upper folder
577    else %scan the input folder
578        [RootPath,SubDir,RootFile,i1_series,i2_series,j1_series,j2_series,tild,FileInfo,MovieObject]=...
579            find_file_series(fullfile(InputTable{iview,1},InputTable{iview,2}),[InputTable{iview,3} InputTable{iview,4} InputTable{iview,5}]);
580    end
581    % if no file is found, open a browser
582    if isempty(i1_series)
583        fileinput=uigetfile_uvmat(['wrong input at line ' num2str(iview) ':pick a new input file'],RootPath);
584        if isempty(fileinput)
585            set(handles.REFRESH,'BackgroundColor',[1 0 0])% set REFRESH  back to red color
586            return
587        else
588            display_file_name(handles,fileinput,iview)
589        end
590    else
591       update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileInfo,MovieObject,iview)
592    end
593end
594set(handles.REFRESH,'BackgroundColor',[1 0 0])% set REFRESH  button to red color (indicate activation finished)
595set(handles.series,'Pointer','arrow') % set the mouse pointer to 'watch'
596
597%------------------------------------------------------------------------
598% --- Function called when a new file is opened, either by series_OpeningFcn or by the browser
599function errormsg=display_file_name(handles,Param,iview)
600%------------------------------------------------------------------------ 
601%
602% INPUT:
603% handles: handles of elements in the GUI
604% Param: structure of input parameters, including  input file name and path
605% iview: line index in the input table
606%       or 'one': refresh the list
607%         'append': add a new line to the input table
608set(handles.REFRESH,'BackgroundColor',[1 1 0])% set REFRESH  button to yellow color (indicate activation)
609drawnow
610errormsg='';%default
611if ischar(Param)
612    fileinput=Param;
613else% input set when series is opened (called by the GUI uvmat)
614    fileinput=Param.FileName;
615end
616   
617%% get the input root name, indices, file extension and nomenclature NomType
618if ~exist(fileinput,'file')
619    errormsg=['input file ' fileinput  ' does not exist'];
620    msgbox_uvmat('ERROR',errormsg)
621    set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH  button to magenta color (refresh still needed)
622    return
623end
624
625%% detect root name, nomenclature and indices in the input file name:
626[FilePath,FileName,FileExt]=fileparts(fileinput);
627%%%%%%%%%%%%%%%%%%
628%TODO: case of input by uvmat: do not check agai the input seies %%%%%%%
629%%%%%%%%%%%%%%%%%%%
630% detect the file type, get the movie object if relevant, and look for the corresponding file series:
631% the root name and indices may be corrected by including the first index i1 if a corresponding xml file exists
632[RootPath,SubDir,RootFile,i1_series,i2_series,j1_series,j2_series,NomType,FileInfo,MovieObject,i1,i2,j1,j2]=find_file_series(FilePath,[FileName FileExt]);
633FileType=FileInfo.FileType;
634if isempty(RootFile)&&isempty(i1_series)
635    errormsg='no input file in the series';
636    msgbox_uvmat('ERROR',errormsg)
637    set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH  button to magenta color (end of activation)
638    return
639end
640if strcmp(FileType,'txt')
641    edit(fileinput)
642    set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH  button to  magenta color (end of activation)
643    return
644elseif strcmp(FileType,'xml')
645    editxml(fileinput)
646    set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH  button to magenta  color (end of activation)
647     return
648elseif strcmp(FileType,'figure')
649    open(fileinput)
650    set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH  button to magenta  color (end of activation)
651     return
652end
653
654%% enable other menus and uicontrols
655set(handles.MenuOpenCampaign,'Enable','on')
656set(handles.MenuCampaign_1,'Enable','on')
657set(handles.MenuCampaign_2,'Enable','on')
658set(handles.MenuCampaign_3,'Enable','on')
659set(handles.MenuCampaign_4,'Enable','on')
660set(handles.MenuCampaign_5,'Enable','on')
661set(handles.RUN, 'Enable','On')
662set(handles.RUN,'BackgroundColor',[1 0 0])% set RUN button to red
663set(handles.InputTable,'BackgroundColor',[1 1 0]) % set RootPath edit box  to yellow
664drawnow
665
666
667%% fill the list of file series
668InputTable=get(handles.InputTable,'Data');
669SeriesData=get(handles.series,'UserData');
670if strcmp(iview,'append') % display the input data as a new line in the table
671    iview=size(InputTable,1)+1;% the next line in InputTable becomes the current line
672    InputTable(iview,:)=[{RootPath},{SubDir},{RootFile},{NomType},{FileExt}];
673%     SeriesData.ListViewMenu(iview)=zeros(1,nbview)
674elseif strcmp(iview,'one') % refresh the list of  input  file series
675    iview=1; %the first line in InputTable becomes the current line
676    InputTable={'','','','',''};
677    InputTable(iview,:)=[{RootPath},{SubDir},{RootFile},{NomType},{FileExt}];
678    set(handles.TimeTable,'Data',[{''},{[]},{[]},{[]},{[]}])
679    set(handles.MinIndex_i,'Data',[])
680    set(handles.MaxIndex_i,'Data',[])
681    set(handles.MinIndex_j,'Data',[])
682    set(handles.MaxIndex_j,'Data',[])
683    set(handles.PairString,'Data',{''})
684    SeriesData.CheckPair=0;%reset the list of input lines with pairs
685    SeriesData.i1_series={};
686    SeriesData.i2_series={};
687    SeriesData.j1_series={};
688    SeriesData.j2_series={};
689    SeriesData.FileType={};
690    SeriesData.FileInfo={};
691    SeriesData.Time={};
692end
693set(handles.InputTable,'Data',InputTable)
694
695%% determine the selected reference field indices for pair display
696if isempty(i1)
697    i1=1;
698end
699if isempty(i2)
700    i2=i1;
701end
702ref_i=floor((i1+i2)/2);% reference image number corresponding to the file
703% set(handles.num_ref_i,'String',num2str(ref_i));
704if isempty(j1)
705    j1=1;
706end
707if isempty(j2)
708    j2=j1;
709end
710ref_j=floor((j1+j2)/2);% reference image number corresponding to the file
711SeriesData.ref_i=ref_i;
712SeriesData.ref_j=ref_j;
713
714%% update first and last indices if they do not exist
715Param=read_GUI(handles.series);
716first_j=[];
717if isfield(Param.IndexRange,'first_j'); first_j=Param.IndexRange.first_j; end
718last_j=[];
719if isfield(Param.IndexRange,'last_j'); last_j=Param.IndexRange.last_j; end
720PairString='';
721if isfield(Param.IndexRange,'PairString'); PairString=Param.IndexRange.PairString; end
722[i1,i2,j1,j2] = get_file_index(Param.IndexRange.first_i,first_j,PairString);
723FirstFileName=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},...
724    Param.InputTable{1,5},Param.InputTable{1,4},i1,i2,j1,j2);
725if ~exist(FirstFileName,'file')
726    set(handles.num_first_i,'String',num2str(ref_i))
727    set(handles.num_first_j,'String',num2str(ref_j))
728end
729[i1,i2,j1,j2] = get_file_index(Param.IndexRange.last_i,last_j,PairString);
730LastFileName=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},...
731    Param.InputTable{1,5},Param.InputTable{1,4},i1,i2,j1,j2);
732if ~exist(LastFileName,'file')
733    set(handles.num_last_i,'String',num2str(ref_i))
734    set(handles.num_last_j,'String',num2str(ref_j))
735end
736
737%% update the list of recent files in the menubar and save it for future opening
738MenuFile=[{get(handles.MenuFile_1,'Label')};{get(handles.MenuFile_2,'Label')};...
739    {get(handles.MenuFile_3,'Label')};{get(handles.MenuFile_4,'Label')};{get(handles.MenuFile_5,'Label')}];
740str_find=strcmp(fileinput,MenuFile);
741if isempty(find(str_find,1))
742    MenuFile=[{fileinput};MenuFile];%insert the current file if not already in the list
743end
744for ifile=1:min(length(MenuFile),5)
745    eval(['set(handles.MenuFile_' num2str(ifile) ',''Label'',MenuFile{ifile});'])
746end
747dir_perso=prefdir;
748profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
749if exist(profil_perso,'file')
750    save (profil_perso,'MenuFile','-append'); %store the file names for future opening of uvmat
751else
752    save (profil_perso,'MenuFile','-V6'); %store the file names for future opening of uvmat
753end
754% save the opened file to initiate future opening
755SeriesData.RefFile{iview}=fileinput;% reference opening file for line iview
756SeriesData.Ref_i1=i1;
757SeriesData.Ref_i2=i2;
758SeriesData.Ref_j1=j1;
759SeriesData.Ref_j2=j2;
760set(handles.series,'UserData',SeriesData)
761
762set(handles.InputTable,'BackgroundColor',[1 1 1])
763
764%% initiate input file series and refresh the current field view:     
765update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileInfo,MovieObject,iview);
766set(handles.REFRESH,'BackgroundColor',[1 0 0])% set REFRESH  button to red color (end of activation)
767
768%------------------------------------------------------------------------
769% --- Update information about a new field series (indices to scan, timing,
770%     calibration from an xml file
771function update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileInfo,VideoObject,iview)
772%------------------------------------------------------------------------
773InputTable=get(handles.InputTable,'Data');
774
775%% display the min and max indices for the whole file series
776if size(i1_series,2)==2 && min(min(i1_series(:,1,:)))==0
777    MinIndex_j=1;% index j set to 1 by default
778    MaxIndex_j=1;
779    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)
780    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)
781else
782    ref_i=squeeze(max(i1_series(1,:,:),[],2));% select ref_j index for each ref_i
783    ref_j=squeeze(max(j1_series(1,:,:),[],3));% select ref_i index for each ref_j
784     MinIndex_i=min(find(ref_i))-1;
785     MaxIndex_i=max(find(ref_i))-1;
786     MaxIndex_j=max(find(ref_j))-1;
787     MinIndex_j=min(find(ref_j))-1;
788    diff_j_max=diff(ref_j);
789    diff_i_max=diff(ref_i);
790    if ~isempty(diff_i_max) && isequal (diff_i_max,diff_i_max(1)*ones(size(diff_i_max)))
791        set(handles.num_incr_i,'String',num2str(diff_i_max(1)))% detect an increment to dispaly by default
792    end
793    if ~isempty(diff_j_max) && isequal (diff_j_max,diff_j_max(1)*ones(size(diff_j_max)))
794        set(handles.num_incr_j,'String',num2str(diff_j_max(1)))
795    end
796end
797if isequal(MinIndex_i,-1)
798    MinIndex_i=0;
799end
800if isequal(MinIndex_j,-1)
801    MinIndex_j=0;
802end
803MinIndex_i_table=get(handles.MinIndex_i,'Data');%retrieve the min indices in the table MinIndex
804MinIndex_j_table=get(handles.MinIndex_j,'Data');%retrieve the min indices in the table MinIndex
805MaxIndex_i_table=get(handles.MaxIndex_i,'Data');%retrieve the min indices in the table MinIndex
806MaxIndex_j_table=get(handles.MaxIndex_j,'Data');%retrieve the min indices in the table MinIndex
807if ~isempty(MinIndex_i)&&~isempty(MaxIndex_i)
808    MinIndex_i_table(iview,1)=MinIndex_i;
809    MaxIndex_i_table(iview,1)=MaxIndex_i;
810end
811if ~isempty(MinIndex_j)&&~isempty(MaxIndex_j)
812    MinIndex_j_table(iview,1)=MinIndex_j;
813    MaxIndex_j_table(iview,1)=MaxIndex_j;
814end
815set(handles.MinIndex_i,'Data',MinIndex_i_table)%display the min indices in the table MinIndex
816set(handles.MinIndex_j,'Data',MinIndex_j_table)%display the max indices in the table MaxIndex
817set(handles.MaxIndex_i,'Data',MaxIndex_i_table)%display the min indices in the table MinIndex
818set(handles.MaxIndex_j,'Data',MaxIndex_j_table)%display the max indices in the table MaxIndex
819SeriesData=get(handles.series,'UserData');
820
821%% adjust the first and last indices for the selected series, only if requested by the bounds
822% i index, compare input to min index i
823first_i=str2num(get(handles.num_first_i,'String'));%retrieve previous first i
824% ref_i=str2num(get(handles.num_ref_i,'String'));%index i given by the input field
825ref_i=1;
826if isfield(SeriesData,'ref_i')
827ref_i=SeriesData.ref_i;
828end
829if isempty(first_i)
830    first_i=ref_i;% first_i updated by the input value
831elseif first_i < MinIndex_i
832    first_i=MinIndex_i; % first_i set to the min i index (restricted by oter input lines)
833elseif first_i >MaxIndex_i
834    first_i=MaxIndex_i;% first_i set to the max i index (restricted by oter input lines)
835end
836% j index,  compare input to min index j
837first_j=str2num(get(handles.num_first_j,'String'));
838ref_j=1;
839if isfield(SeriesData,'ref_j')
840ref_j=SeriesData.ref_j;
841end
842if isempty(first_j)
843    first_j=ref_j;% first_j updated by the input value
844elseif first_j<MinIndex_j
845    first_j=MinIndex_j; % first_j set to the min j index (restricted by oter input lines)
846elseif first_j >MaxIndex_j
847    first_j=MaxIndex_j; % first_j set to the max j index (restricted by oter input lines)
848end
849% i index, compare input to max index i
850last_i=str2num(get(handles.num_last_i,'String'));
851if isempty(last_i)
852    last_i=ref_i;
853elseif last_i > MaxIndex_i
854    last_i=MaxIndex_i;
855elseif last_i<first_i
856    last_i=first_i;
857end
858% j index, compare input to max index j
859last_j=str2num(get(handles.num_last_j,'String'));
860if isempty(last_j)
861    last_j=ref_j;
862elseif last_j>MaxIndex_j
863    last_j=MaxIndex_j;
864elseif last_j<first_j
865    last_j=first_j;
866end
867set(handles.num_first_i,'String',num2str(first_i));
868set(handles.num_first_j,'String',num2str(first_j));
869set(handles.num_last_i,'String',num2str(last_i));
870set(handles.num_last_j,'String',num2str(last_j));
871
872%% number of slices set by default
873NbSlice=1;%default
874% read  value set by the first series for the append mode (iwiew >1)
875if iview>1 && strcmp(get(handles.num_NbSlice,'Visible'),'on')
876    NbSlice=str2num(get(handles.num_NbSlice,'String'));
877end
878
879%% default time settings
880TimeUnit='';
881% read  value set by the first series for the append mode (iwiew >1)
882if iview>1
883    TimeUnit=get(handles.TimeUnit,'String');
884end
885TimeName='';
886Time=[];%default
887TimeMin=[];
888TimeFirst=[];
889TimeLast=[];
890TimeMax=[];
891
892%%  read image documentation file if found
893XmlData=[];
894check_calib=0;
895XmlFileName=find_imadoc(InputTable{iview,1},InputTable{iview,2},InputTable{iview,3},InputTable{iview,5});
896if ~isempty(XmlFileName)
897    [XmlData,errormsg]=imadoc2struct(XmlFileName);
898    if ~isempty(errormsg)
899         msgbox_uvmat('WARNING',['error in reading ' XmlFileName ': ' errormsg]);
900    end
901    % read time if available
902    if isfield(XmlData,'Time')
903         Time=XmlData.Time;
904        TimeName='xml';
905    end
906    if isfield(XmlData,'Camera')
907        if isfield(XmlData.Camera,'NbSlice')&& ~isempty(XmlData.Camera.NbSlice)
908            if iview>1 && ~isempty(NbSlice) && ~strcmp(NbSlice,XmlData.Camera.NbSlice)
909                msgbox_uvmat('WARNING','inconsistent number of slices with the first field series');
910            end
911            NbSlice=XmlData.Camera.NbSlice;% Nbre of slices from camera
912        end
913        if isfield(XmlData.Camera,'TimeUnit')&& ~isempty(XmlData.Camera.TimeUnit)
914            if iview>1 && ~isempty(TimeUnit) && ~strcmp(TimeUnit,XmlData.Camera.TimeUnit)
915                msgbox_uvmat('WARNING','inconsistent time unit with the first field series');
916            end
917            TimeUnit=XmlData.Camera.TimeUnit;
918        end
919    end
920    % number of slices
921    if isfield(XmlData,'GeometryCalib')
922        check_calib=1;
923        if isfield(XmlData.GeometryCalib,'SliceCoord')
924            siz=size(XmlData.GeometryCalib.SliceCoord);
925            if siz(1)>1
926                if iview>1 && ~isempty(NbSlice) && ~strcmp(NbSlice,siz(1))
927                    msgbox_uvmat('WARNING','inconsistent number of Z indices with the first field series');
928                end
929                NbSlice=siz(1);
930            end
931        end
932    end
933    set(handles.num_NbSlice,'String',num2str(NbSlice))
934end
935
936%% read timing  from the current file (prioritary)
937if ~isempty(VideoObject)% case of movies
938    imainfo=get(VideoObject);
939    if isempty(j1_series); %frame index along i
940        Time=zeros(imainfo.NumberOfFrames+1,2);
941        Time(:,2)=(0:1/imainfo.FrameRate:(imainfo.NumberOfFrames)/imainfo.FrameRate)';
942    else
943        Time=[0;ones(size(i1_series,3)-1,1)]*(0:1/imainfo.FrameRate:(imainfo.NumberOfFrames)/imainfo.FrameRate);
944    end
945    TimeName='video';
946end
947
948
949%% determine the min and max times: case of Netcdf files will be treated later in FieldName_Callback
950if ~isempty(TimeName)
951    TimeMin=Time(MinIndex_i+1,MinIndex_j+1);
952    if size(Time)>=[first_i+1 first_j+1]
953        TimeFirst=Time(first_i+1,first_j+1);
954    end
955    if size(Time)>=[last_i+1 last_j+1]
956        TimeLast=Time(last_i+1,last_j+1);
957    end
958    if size(Time)>=[MaxIndex_i+1 MaxIndex_j+1];
959        TimeMax=Time(MaxIndex_i+1,MaxIndex_j+1);
960    end
961end
962
963%% update the time table
964TimeTable=get(handles.TimeTable,'Data');
965TimeTable{iview,1}=TimeName;
966TimeTable{iview,2}=TimeMin;
967TimeTable{iview,3}=TimeFirst;
968TimeTable{iview,4}=TimeLast;
969TimeTable{iview,5}=TimeMax;
970set(handles.TimeTable,'Data',TimeTable)
971
972%% update the series info in 'UserData'
973SeriesData.i1_series{iview}=i1_series;
974SeriesData.i2_series{iview}=i2_series;
975SeriesData.j1_series{iview}=j1_series;
976SeriesData.j2_series{iview}=j2_series;
977SeriesData.FileType{iview}=FileInfo.FileType;
978SeriesData.FileInfo{iview}=FileInfo;
979SeriesData.Time{iview}=Time;
980% if ~isempty(TimeName)
981%     SeriesData.TimeSource=TimeSource;
982% end
983if check_calib
984    SeriesData.GeometryCalib{iview}=XmlData.GeometryCalib;
985end
986set(handles.series,'UserData',SeriesData)
987
988%% update pair menus
989hset_pair=findobj(allchild(0),'Tag','set_pairs');
990if ~isempty(hset_pair), delete(hset_pair); end % delete the GUI set_pair if opened
991CheckPair= ~isempty(i2_series)||~isempty(j2_series); % check whether index pairs need to be defined
992PairString=get(handles.PairString,'Data');
993if CheckPair% if pairs need to be display for line iview
994    [ModeMenu,ModeValue]=update_mode(i1_series,i2_series,j2_series);
995    Menu=update_listpair(i1_series,i2_series,j1_series,j2_series,ModeMenu{ModeValue},Time,TimeUnit,ref_i,ref_j,TimeName,InputTable(iview,:),FileInfo);
996    PairString{iview,1}=Menu{1};
997else
998    PairString{iview,1}='';%no pair for #iview
999end
1000set(handles.PairString,'Data',PairString)
1001if isempty(find(cellfun('isempty',get(handles.PairString,'Data'))==0, 1))% if all lines of pairs are empty
1002    set(handles.PairString,'Visible','off')
1003    set(handles.SetPairs,'Visible','off')
1004else
1005    set(handles.PairString,'Visible','on')
1006    set(handles.SetPairs,'Visible','on')
1007end
1008
1009
1010%% display the set of existing files as an image
1011set(handles.FileStatus,'Units','pixels')
1012Position=get(handles.FileStatus,'Position');
1013set(handles.FileStatus,'Units','normalized')
1014%xI=0.5:Position(3)-0.5;
1015nbview=numel(SeriesData.i1_series);
1016j_max=cell(1,nbview);
1017MaxIndex_i=ones(1,nbview);%default
1018MinIndex_i=ones(1,nbview);%default
1019for iline=1:nbview
1020    pair_max=squeeze(max(SeriesData.i1_series{iline},[],1)); %max on pair index
1021    j_max{iline}=max(pair_max,[],1);%max on j index
1022    if ~isempty(j_max{iline})
1023    MaxIndex_i(iline)=max(find(j_max{iline}))-1;% max ref index i
1024    MinIndex_i(iline)=min(find(j_max{iline}))-1;% min ref index i
1025    end
1026end
1027MinIndex_i=min(MinIndex_i);
1028MaxIndex_i=max(MaxIndex_i);
1029range_index=MaxIndex_i-MinIndex_i+1;
1030range_y=max(1,floor(Position(4)/nbview));
1031npx=floor(Position(3));
1032file_indices=MinIndex_i+floor(((0.5:npx-0.5)/npx)*range_index)+1;
1033CData=zeros(nbview*range_y,npx);% initiate the image representing the existing files
1034for iline=1:nbview
1035    ind_y=1+(iline-1)*range_y:iline*range_y;
1036    LineData=zeros(size(file_indices));
1037    file_select=file_indices(file_indices<=numel(j_max{iline}));
1038    ind_select=find(file_indices<=numel(j_max{iline}));
1039    LineData(ind_select)=j_max{iline}(file_select)~=0;
1040    CData(ind_y,:)=ones(size(ind_y'))*LineData;
1041end
1042CData=cat(3,zeros(size(CData)),CData,zeros(size(CData)));%make color images r=0,g,b=0
1043set(handles.FileStatus,'CData',CData);
1044
1045%% enable field and veltype menus, in accordance with the current action
1046ActionName_Callback([],[], handles)
1047
1048%% set length of waitbar
1049displ_time(handles)
1050
1051
1052%-----------------------------------------------------------guide -------------
1053%------------------------------------------------------------------------
1054%  III - FUNCTIONS ASSOCIATED TO THE FRAME IndexRange
1055%------------------------------------------------------------------------
1056
1057
1058% ---- determine the menu to put in mode and advice a default choice
1059%------------------------------------------------------------------------
1060function [ModeMenu,ModeValue]=update_mode(i1_series,i2_series,j2_series)
1061%------------------------------------------------------------------------   
1062ModeMenu={''};
1063if isempty(j2_series)% no j pair
1064    ModeValue=1;
1065    if ~isempty(i2_series)
1066        ModeMenu={'series(Di)'}; % pair menu with only option Di
1067    end
1068else %existence of j pairs
1069    pair_max=squeeze(max(i1_series,[],1)); %max on pair index
1070    j_max=max(pair_max,[],1);
1071    MaxIndex_i=find(j_max, 1, 'last' )-1;% max ref index i
1072    MinIndex_i=find(j_max, 1 )-1;% min ref index i
1073    i_max=max(pair_max,[],2);
1074    MaxIndex_j=find(i_max, 1, 'last' )-1;% max ref index i
1075    MinIndex_j=find(i_max, 1 )-1;% min ref index i
1076    if MaxIndex_j==MinIndex_j
1077        ModeValue=1;
1078        ModeMenu={'bursts'};
1079    elseif MaxIndex_i==MinIndex_i
1080        ModeValue=1;
1081        ModeMenu={'series(Dj)'};
1082    else
1083        ModeMenu={'bursts';'series(Dj)'};
1084        if (MaxIndex_j-MinIndex_j)>10
1085            ModeValue=2;%set mode to series(Dj) if more than 10 j values
1086        else
1087            ModeValue=1;
1088        end
1089    end
1090end
1091
1092
1093%------------------------------------------------------------------------
1094function displ_pair=update_listpair(i1_series,i2_series,j1_series,j2_series,mode,time,TimeUnit,ref_i,ref_j,TimeName,InputTable,FileInfo)
1095%------------------------------------------------------------------------
1096displ_pair={};
1097if isempty(TimeUnit)
1098    dtunit='e-03';
1099else
1100    dtunit=['m' TimeUnit];
1101end
1102switch mode
1103    case 'series(Di)'
1104        diff_i=i2_series-i1_series;
1105        min_diff=min(diff_i(diff_i>0));
1106        max_diff=max(diff_i(diff_i>0));
1107        for ipair=min_diff:max_diff
1108            if numel(diff_i(diff_i==ipair))>0
1109                pair_string=['Di= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2)) ];
1110                if ~isempty(time)
1111                    if ref_i<=floor(ipair/2)
1112                        ref_i=floor(ipair/2)+1;% shift ref_i to get the first pair
1113                    end
1114                    Dt=time(ref_i+ceil(ipair/2),ref_j)-time(ref_i-floor(ipair/2),ref_j);
1115                    pair_string=[pair_string ', Dt=' num2str(Dt) ' ' dtunit];
1116                end
1117                displ_pair=[displ_pair;{pair_string}];
1118            end
1119        end
1120        if ~isempty(displ_pair)
1121            displ_pair=[displ_pair;{'Di=*|*'}];
1122        end
1123    case 'series(Dj)'
1124        if isempty(j2_series)
1125            msgbox_uvmat('ERROR','no j1-j2 pair available')
1126            return
1127        end
1128        diff_j=j2_series-j1_series;
1129        min_diff=min(diff_j(diff_j>0));
1130        max_diff=max(diff_j(diff_j>0));
1131        for ipair=min_diff:max_diff
1132            if numel(diff_j(diff_j==ipair))>0
1133                pair_string=['Dj= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2)) ];
1134                if ~isempty(time)
1135                    if ref_j<=floor(ipair/2)
1136                        ref_j=floor(ipair/2)+1;% shift ref_i to get the first pair
1137                    end
1138                    Dt=time(ref_i,ref_j+ceil(ipair/2))-time(ref_i,ref_j-floor(ipair/2));
1139                    pair_string=[pair_string ', Dt=' num2str(Dt) ' ' dtunit];
1140                end
1141                displ_pair=[displ_pair;{pair_string}];
1142            end
1143        end
1144        if ~isempty(displ_pair)
1145            displ_pair=[displ_pair;{'Dj=*|*'}];
1146        end
1147    case 'bursts'
1148        if isempty(j2_series)
1149            msgbox_uvmat('ERROR','no j1-j2 pair available')
1150            return
1151        end
1152        %diff_j=j2_series-j1_series;
1153        min_j1=min(j1_series(j1_series>0));
1154        max_j1=max(j1_series(j1_series>0));
1155        min_j2=min(j2_series(j2_series>0));
1156        max_j2=max(j2_series(j2_series>0));
1157        for pair1=min_j1:min(max_j1,min_j1+20)
1158            for pair2=min_j2:min(max_j2,min_j2+20)
1159                if numel(j1_series(j1_series==pair1))>0 && numel(j2_series(j2_series==pair2))>0
1160                    pair_string=['j= ' num2str(pair1) '-' num2str(pair2)];
1161                    [TimeValue,DtValue]=get_time(ref_i,[],pair_string,InputTable,FileInfo,TimeName,'Dt');
1162                    %Dt=time(ref_i,pair2+1)-time(ref_i,pair1+1);
1163                    pair_string=[pair_string ', Dt=' num2str(DtValue) ' ' dtunit];
1164                    displ_pair=[displ_pair;{pair_string}];
1165                end
1166            end
1167        end
1168        if ~isempty(displ_pair)
1169            displ_pair=[displ_pair;{'j=*-*'}];
1170        end
1171end
1172
1173%------------------------------------------------------------------------
1174function num_first_i_Callback(hObject, eventdata, handles)
1175%------------------------------------------------------------------------
1176num_last_i_Callback(hObject, eventdata, handles)
1177
1178%------------------------------------------------------------------------
1179function num_last_i_Callback(hObject, eventdata, handles)
1180%------------------------------------------------------------------------
1181SeriesData=get(handles.series,'UserData');
1182if ~isfield(SeriesData,'Time')
1183    SeriesData.Time{1}=[];
1184end
1185displ_time(handles);
1186
1187%------------------------------------------------------------------------
1188function num_first_j_Callback(hObject, eventdata, handles)
1189%------------------------------------------------------------------------
1190 num_last_j_Callback(hObject, eventdata, handles)
1191
1192%------------------------------------------------------------------------
1193function num_last_j_Callback(hObject, eventdata, handles)
1194%------------------------------------------------------------------------
1195% first_j=str2num(get(handles.num_first_j,'String'));
1196% last_j=str2num(get(handles.num_last_j,'String'));
1197% ref_j=ceil((first_j+last_j)/2);
1198% set(handles.num_ref_j,'String', num2str(ref_j))
1199% num_ref_j_Callback(hObject, eventdata, handles)
1200SeriesData=get(handles.series,'UserData');
1201if ~isfield(SeriesData,'Time')
1202    SeriesData.Time{1}=[];
1203end
1204displ_time(handles);
1205
1206%------------------------------------------------------------------------
1207% ---- find the times corresponding to the first and last indices of a series
1208function displ_time(handles)
1209%------------------------------------------------------------------------
1210SeriesData=get(handles.series,'UserData');%
1211if ~isfield(SeriesData,'Time')
1212    return
1213end
1214PairString=get(handles.PairString,'Data');
1215ref_i_1=str2num(get(handles.num_first_i,'String'));%first reference index
1216ref_i_2=str2num(get(handles.num_last_i,'String'));%last reference index
1217ref_j_1=[];ref_j_2=[];
1218if strcmp(get(handles.num_first_j,'Visible'),'on')
1219ref_j_1=str2num(get(handles.num_first_j,'String'));
1220ref_j_2=str2num(get(handles.num_last_j,'String'));
1221end
1222[i1_1,i2_1,j1_1,j2_1] = get_file_index(ref_i_1,ref_j_1,PairString);
1223[i1_2,i2_2,j1_2,j2_2] = get_file_index(ref_i_2,ref_j_2,PairString);
1224TimeTable=get(handles.TimeTable,'Data');
1225%%%%%%
1226%TODO: read time in netcdf file, see ActionName_Callback
1227%%%%%%%
1228%Pairs=get(handles.PairString,'Data');
1229for iview=1:size(TimeTable,1)
1230    if size(SeriesData.Time,1)<iview
1231        break
1232    end
1233    TimeTable{iview,3}=[];
1234    TimeTable{iview,4}=[];
1235    if size(SeriesData.Time{iview},1)>=i2_2+1 && (isempty(ref_j_1)||size(SeriesData.Time{iview},2)>=j2_2+1)
1236        if isempty(ref_j_1)
1237            time_first=(SeriesData.Time{iview}(i1_1+1,2)+SeriesData.Time{iview}(i2_1+1,2))/2;
1238            time_last=(SeriesData.Time{iview}(i1_2+1,2)+SeriesData.Time{iview}(i2_2+1,2))/2;
1239        else
1240            time_first=(SeriesData.Time{iview}(i1_1+1,j1_1+1)+SeriesData.Time{iview}(i2_1+1,j2_1+1))/2;
1241            time_last=(SeriesData.Time{iview}(i1_2+1,j1_2+1)+SeriesData.Time{iview}(i2_2+1,j2_1+1))/2;
1242        end
1243        TimeTable{iview,3}=time_first; %TODO: take into account pairs
1244        TimeTable{iview,4}=time_last; %TODO: take into account pairs
1245    end
1246end
1247set(handles.TimeTable,'Data',TimeTable)
1248
1249%% set the waitbar position with respect to the min and max in the series
1250MinIndex_i=min(get(handles.MinIndex_i,'Data'));
1251MaxIndex_i=max(get(handles.MaxIndex_i,'Data'));
1252pos_first=(ref_i_1-MinIndex_i)/(MaxIndex_i-MinIndex_i+1);
1253pos_last=(ref_i_2-MinIndex_i+1)/(MaxIndex_i-MinIndex_i+1);
1254if isempty(pos_first), pos_first=0; end
1255if isempty(pos_last), pos_last=1; end
1256Position=get(handles.Waitbar,'Position');% position of the waitbar:= [ x,y, width, height]
1257Position_status=get(handles.FileStatus,'Position');
1258Position(1)=Position_status(1)+Position_status(3)*pos_first;
1259Position(3)=max(Position_status(3)*(pos_last-pos_first),0.001);% width must remain positive
1260set(handles.Waitbar,'Position',Position)
1261update_waitbar(handles.Waitbar,0)
1262
1263%------------------------------------------------------------------------
1264% --- Executes when selected cell(s) is changed in PairString.
1265function PairString_CellSelectionCallback(hObject, eventdata, handles)
1266%------------------------------------------------------------------------   
1267if numel(eventdata.Indices)>=1
1268    PairString=get(hObject,'Data');
1269    if ~isempty(PairString{eventdata.Indices(1)})
1270        SetPairs_Callback(hObject, eventdata.Indices(1), handles)
1271    end
1272end
1273
1274%-------------------------------------
1275function enable_i(handles,state)
1276set(handles.i_txt,'Visible',state)
1277set(handles.num_first_i,'Visible',state)
1278set(handles.num_last_i,'Visible',state)
1279set(handles.num_incr_i,'Visible',state)
1280
1281%-----------------------------------
1282function enable_j(handles,state)
1283set(handles.j_txt,'Visible',state)
1284set(handles.num_first_j,'Visible',state)
1285set(handles.num_last_j,'Visible',state)
1286set(handles.num_incr_j,'Visible',state)
1287set(handles.MinIndex_j,'Visible',state)
1288set(handles.MaxIndex_j,'Visible',state)
1289
1290
1291%%%%%%%%%%%%%%%%%%%%
1292%%  MAIN ActionName FUNCTIONS
1293%%%%%%%%%%%%%%%%%%%%
1294%------------------------------------------------------------------------
1295% --- Executes on button press in RUN.
1296%------------------------------------------------------------------------
1297function RUN_Callback(hObject, eventdata, handles)
1298
1299%% read the data on the GUI series
1300Param=read_GUI_series(handles);%displayed parameters
1301SeriesData=get(handles.series,'UserData');%hidden parameters
1302if ~isfield(SeriesData,'i1_series')
1303    msgbox_uvmat('ERROR','The input field series needs to be refreshed: press REFRESH')
1304    return
1305end
1306if isfield(Param,'InputFields')&& isequal(Param.InputFields.FieldName,'get_field...')
1307    msgbox_uvmat('ERROR','input field name(s) not defined, select get_field...')
1308    return
1309end
1310
1311%% settings of the button RUN
1312set(handles.RUN,'BusyAction','queue');% activation of STOP button will set BusyAction to 'cancel'
1313set(handles.RUN, 'Enable','Off')% avoid further RUN action until the current one is finished
1314set(handles.RUN,'BackgroundColor',[1 1 0])%show activation of RUN by yellow color
1315drawnow
1316set(handles.status,'Value',0)% desable status display if relevant
1317status_Callback(hObject, eventdata, handles)
1318
1319%% select the Action mode, 'local', 'background' or 'cluster' (if available)
1320RunMode='local';%default (needed for first opening of the GUI series)
1321if isfield(Param.Action,'RunMode')
1322    RunMode=Param.Action.RunMode;
1323    Param.Action=rmfield(Param.Action,'RunMode');%remove from the recorded xml file to avoid interference during ImportConfig
1324end
1325ActionExt='.m';%default
1326if isfield(Param.Action,'ActionExt')
1327    ActionExt=Param.Action.ActionExt;% '.m' or '.sh' (compiled)
1328    Param.Action=rmfield(Param.Action,'ActionExt');%remove from the recorded xml file to avoid interference during ImportConfig
1329end
1330ActionName=Param.Action.ActionName;
1331ActionPath=Param.Action.ActionPath;
1332
1333path_series=fileparts(which('series'));
1334
1335%% create the Action fct handle if RunMode option = 'local'
1336if strcmp(RunMode,'local')
1337    if ~isequal(ActionPath,path_series)
1338        eval(['spath=which(''' ActionName ''');']) %spath = current path of the selected function ACTION
1339        if ~exist(ActionPath,'dir')
1340            msgbox_uvmat('ERROR',['The prescribed function path ' ActionPath ' does not exist']);
1341            return
1342        end
1343        if ~isequal(spath,ActionPath)
1344            addpath(ActionPath)% add the prescribed path if not the current one
1345        end
1346    end
1347    eval(['h_fun=@' ActionName ';'])%create a function handle for ACTION
1348    if ~isequal(ActionPath,path_series)
1349        rmpath(ActionPath)% add the prescribed path if not the current one
1350    end
1351end
1352
1353%% Get RunTime code from the file PARAM.xml (needed to run compiled functions)
1354errormsg='';%default error message
1355xmlfile=fullfile(path_series,'PARAM.xml');
1356test_batch=0;%default: ,no batch mode available
1357if ~exist(xmlfile,'file')
1358    [success,message]=copyfile(fullfile(path_series,'PARAM.xml.default'),xmlfile);
1359end
1360RunTime='';
1361if strcmp(ActionExt,'.sh')
1362    if exist(xmlfile,'file')
1363        s=xml2struct(xmlfile);
1364        if strcmp(RunMode,'cluster_oar') && isfield(s,'BatchParam')
1365            if isfield(s.BatchParam,'RunTime')
1366                RunTime=s.BatchParam.RunTime;
1367            end
1368            if isfield(s.BatchParam,'NbCore')
1369                NbCore=s.BatchParam.NbCore;
1370            end
1371        elseif (strcmp(RunMode,'background')||strcmp(RunMode,'local')) && isfield(s,'RunParam')
1372            if isfield(s.RunParam,'RunTime')
1373                RunTime=s.RunParam.RunTime;
1374            end
1375            if isfield(s.RunParam,'NbCore')
1376                NbCore=s.RunParam.NbCore;
1377            end
1378        end
1379    end
1380    if isempty(RunTime) && strcmp(RunMode,'cluster_oar')
1381        msgbox_uvmat('ERROR','RunTime name not found in PARAM.xml, compiled version .sh cannot run on cluster')
1382        return
1383    end
1384end
1385
1386%% If a compiled version has been selected (ext .sh) check weather it needs to be recompiled
1387if strcmp(ActionExt,'.sh')
1388    TransformPath='';
1389    if ~isempty(get(handles.ActionExt,'UserData'))
1390        TransformPath=get(handles.ActionExt,'UserData');
1391    end
1392    set(handles.series,'Pointer','watch') % set the mouse pointer to 'watch'
1393    set(handles.ActionExt,'BackgroundColor',[1 1 0])
1394    ActionFullName=fullfile(get(handles.ActionPath,'String'),[ActionName '.sh']);
1395    if ~exist(ActionFullName,'file')
1396        answer=msgbox_uvmat('INPUT_Y-N','compiled version has not been created: compile now?');
1397        if strcmp(answer,'Yes')
1398            set(handles.ActionExt,'BackgroundColor',[1 1 0])
1399            path_uvmat=fileparts(which('series'));
1400            currentdir=pwd;
1401            cd(get(handles.ActionPath,'String'))% go to the directory of Action
1402            addpath(path_uvmat)% add the path to uvmat to run the fct 'compile'
1403            compile(ActionName,TransformPath)
1404            cd(currentdir)
1405        end       
1406    else
1407        sh_file_info=dir(fullfile(get(handles.ActionPath,'String'),[ActionName '.sh']));
1408        m_file_info=dir(fullfile(get(handles.ActionPath,'String'),[ActionName '.m']));
1409        if isfield(m_file_info,'datenum') && m_file_info.datenum>sh_file_info.datenum
1410            set(handles.ActionExt,'BackgroundColor',[1 1 0])
1411            drawnow
1412            answer=msgbox_uvmat('INPUT_Y-N',[ActionName '.sh needs to be updated: recompile now?']);
1413            if strcmp(answer,'Yes')
1414                path_uvmat=fileparts(which('series'));
1415                currentdir=pwd;
1416                cd(get(handles.ActionPath,'String'))% go to the directory of Action
1417                addpath(path_uvmat)% add the path to uvmat to run the fct 'compile'
1418                addpath(fullfile(path_uvmat,'transform_field'))% add the path to uvmat to run the fct 'compile'
1419                compile(ActionName,TransformPath)
1420                cd(currentdir)
1421            end
1422        end
1423    end
1424    set(handles.ActionExt,'BackgroundColor',[1 1 1])
1425     set(handles.series,'Pointer','arrow') % set the mouse pointer to 'watch
1426end
1427
1428%% set nbre of cluster cores and processes
1429switch RunMode
1430    case {'local','background'}
1431        NbCore=1;% no need to split the calculation
1432    case 'cluster_oar'
1433        if strcmp(ActionExt,'.m')% case of Matlab function (uncompiled)
1434            NbCore=1;% one core used only (limitation of Matlab licences)
1435            msgbox_uvmat('WARNING','Number of cores =1: select the compiled version civ_matlab.sh for multi-core processing');
1436            extra_oar='';
1437        else
1438            answer=inputdlg({'Number of cores (max 36)','extra oar options'},'oarsub parameter',1,{'12',''});
1439            NbCore=str2double(answer{1});
1440            extra_oar=answer{2};
1441        end
1442end
1443if ~isfield(Param.IndexRange,'NbSlice')
1444    Param.IndexRange.NbSlice=[];
1445end
1446if isempty(Param.IndexRange.NbSlice)
1447    NbProcess=NbCore;% choose one process per core
1448else
1449    NbProcess=Param.IndexRange.NbSlice;% the nbre of run processes is equal to the number of slices
1450    NbCore=min(NbCore,NbProcess);% at least one process per core
1451end
1452
1453%% create the output data directory if needed
1454OutpuDir='';
1455if isfield(Param,'OutputSubDir')
1456    SubDirOut=[get(handles.OutputSubDir,'String') Param.OutputDirExt];
1457    SubDirOutNew=SubDirOut;
1458    detect=exist(fullfile(Param.InputTable{1,1},SubDirOutNew),'dir');% test if  the dir  already exist
1459    check_create=1; %need to create the result directory by default
1460    while detect
1461        answer=msgbox_uvmat('INPUT_Y-N',['use existing ouput directory: ' fullfile(Param.InputTable{1,1},SubDirOutNew) ', possibly delete previous data']);
1462        if strcmp(answer,'Cancel')
1463            errormsg='Cancel';
1464            return
1465        elseif strcmp(answer,'Yes')
1466            detect=0;
1467            check_create=0;
1468        else
1469            r=regexp(SubDirOutNew,'(?<root>.*\D)(?<num1>\d+)$','names');%detect whether name ends by a number
1470            if isempty(r)
1471                r(1).root=[SubDirOutNew '_'];
1472                r(1).num1='0';
1473            end
1474            SubDirOutNew=[r(1).root num2str(str2num(r(1).num1)+1)];%increment the index by 1 or put 1
1475            detect=exist(fullfile(Param.InputTable{1,1},SubDirOutNew),'dir');% test if  the dir  already exists
1476            check_create=1;
1477        end
1478    end
1479    Param.OutputDirExt=regexprep(SubDirOutNew,Param.OutputSubDir,'');
1480    Param.OutputRootFile=Param.InputTable{1,3};% the first sorted RootFile taken for output
1481    set(handles.OutputDirExt,'String',Param.OutputDirExt)
1482    OutputDir=fullfile(Param.InputTable{1,1},[Param.OutputSubDir Param.OutputDirExt]);% full name (with path) of output directory
1483    if check_create    % create output directory if it does not exist
1484        [tild,msg1]=mkdir(OutputDir);
1485        if ~strcmp(msg1,'')
1486            msgbox_uvmat('ERROR',['cannot create ' OutputDir ': ' msg1]);%error message for directory creation
1487            return
1488        end
1489        [success,msg] = fileattrib(OutputDir,'+w','g','s');% allow writing access for the group of users, recursively in the folder 
1490        if success==0
1491            msgbox_uvmat('WARNING',{['unable to set group write access to ' OutputDir ':']; msg1});%error message for directory creation
1492            return
1493        end
1494    end
1495   
1496elseif isfield(Param,'ActionInput')&&isfield(Param.ActionInput,'LogPath')% custom definition of the output dir
1497    OutputDir=Param.ActionInput.LogPath;   
1498end
1499DirXml=fullfile(OutputDir,'0_XML');
1500if ~exist(DirXml,'dir')
1501    [tild,msg1]=mkdir(DirXml);
1502    if ~strcmp(msg1,'')
1503        msgbox_uvmat('ERROR',['cannot create ' DirXml ': ' msg1]);%error message for directory creation
1504        return
1505    end
1506    [success,msg] = fileattrib(DirXml,'+w','g','s');% allow writing access for the group of users, recursively in the folder
1507    if success==0
1508        msgbox_uvmat('WARNING',{['unable to set group write access to ' DirXml ':']; msg});%error message for directory creation
1509    end
1510end
1511OutputNomType=nomtype2pair(Param.InputTable{1,4});% nomenclature for output files
1512
1513%% get the set of reference field indices
1514first_i=1;
1515last_i=1;
1516incr_i=1;
1517first_j=1;
1518last_j=1;
1519incr_j=1;
1520if isfield(Param.IndexRange,'first_i')
1521    first_i=Param.IndexRange.first_i;
1522    incr_i=Param.IndexRange.incr_i;
1523    last_i=Param.IndexRange.last_i;
1524end
1525if isfield(Param.IndexRange,'first_j')
1526    first_j=Param.IndexRange.first_j;
1527    last_j=Param.IndexRange.last_j;
1528    incr_j=Param.IndexRange.incr_j;
1529end
1530if last_i < first_i || last_j < first_j
1531    msgbox_uvmat('ERROR', 'series/Run_Callback:last field index must be larger or equal to the first one')
1532    set(handles.RUN, 'Enable','On'),
1533    set(handles.RUN,'BackgroundColor',[1 0 0])
1534    return
1535end
1536%incr_i must be defined, =1 by default, if NbSlice is active
1537if isempty(incr_i)&& ~isempty(Param.IndexRange.NbSlice)
1538    incr_i=1;
1539    set(handles.num_incr_i,'String','1')
1540end
1541if isempty(incr_i)
1542    if isempty(incr_j)
1543        [ref_j,ref_i]=find(squeeze(SeriesData.i1_series{1}(1,:,:)));
1544        ref_j=ref_j(ref_j>=first_j & ref_j<=last_j);
1545        ref_i=ref_i(ref_i>=first_i & ref_i<=last_i);
1546        ref_j=ref_j-1;
1547        ref_i=ref_i-1;
1548    else
1549        ref_j=first_j:incr_j:last_j;
1550        [tild,ref_i]=find(squeeze(SeriesData.i1_series{1}(1,:,:)));
1551        ref_i=ref_i-1;
1552        ref_i=ref_i(ref_i>=first_i & ref_i<=last_i);
1553    end
1554else
1555    ref_i=first_i:incr_i:last_i;
1556    if isempty(incr_j)
1557        [ref_j,tild]=find(squeeze(SeriesData.i1_series{1}(1,:,:)));
1558        ref_j=ref_j-1;
1559        ref_j=ref_j(ref_j>=first_j & ref_j<=last_j);
1560    else
1561        ref_j=first_j:incr_j:last_j;
1562    end
1563end
1564BlockLength=ceil(numel(ref_i)/NbProcess);
1565nbfield_j=numel(ref_j);
1566
1567%% record nbre of output files and starting time for computation for status
1568StatusData=get(handles.status,'UserData');
1569if isfield(StatusData,'OutputFileMode')
1570    switch StatusData.OutputFileMode
1571        case 'NbInput'
1572            StatusData.NbOutputFile=numel(ref_i)*nbfield_j;
1573        case 'NbInput_i'
1574            StatusData.NbOutputFile=numel(ref_i);
1575        case 'NbSlice'   
1576            StatusData.NbOutputFile=str2num(get(handles.num_NbSlice,'String'));
1577    end
1578end
1579StatusData.TimeStart=now;
1580set(handles.status,'UserData',StatusData)
1581
1582%% direct processing on the current Matlab session
1583if strcmp (RunMode,'local')
1584    for iprocess=1:NbProcess
1585        if isempty(Param.IndexRange.NbSlice)
1586            %Param.IndexRange.first_i=first_i+(iprocess-1)*BlockLength*incr_i;
1587            Param.IndexRange.first_i=ref_i(1+(iprocess-1)*BlockLength);
1588            if Param.IndexRange.first_i>last_i
1589                break
1590            end
1591            Param.IndexRange.last_i=min(ref_i(iprocess*BlockLength),last_i);
1592            %Param.IndexRange.last_i=min(first_i+(iprocess)*BlockLength*incr_i-1,last_i);
1593        else %multislices (then incr_i is not empty)
1594             Param.IndexRange.first_i= first_i+incr_i*(iprocess-1);
1595             Param.IndexRange.incr_i=incr_i*Param.IndexRange.NbSlice;
1596        end
1597        if isfield(Param,'OutputSubDir')
1598        t=struct2xml(Param);
1599        t=set(t,1,'name','Series');
1600        filexml=fullfile_uvmat(DirXml,'',Param.InputTable{1,3},'.xml',OutputNomType,...
1601            Param.IndexRange.first_i,Param.IndexRange.last_i,first_j,last_j);
1602        save(t,filexml);
1603        end
1604        switch ActionExt
1605            case '.m'
1606                h_fun(Param);
1607            case '.sh'
1608                switch computer
1609                    case {'PCWIN','PCWIN64'} %Windows system
1610                        filexml=regexprep(filexml,'\\','\\\\');% add '\' so that '\' are left as characters
1611                        system([fullfile(ActionPath,[ActionName '.sh']) ' ' RunTime ' ' filexml]);% TODO: adapt to DOS system
1612                    case {'GLNX86','GLNXA64','MACI64'}%Linux  system
1613                        system([fullfile(ActionPath,[ActionName '.sh']) ' ' RunTime ' ' filexml]);
1614                end
1615        end
1616    end
1617% elseif strcmp(get(handles.OutputDirExt,'Visible'),'off')
1618%     msgbox_uvmat('ERROR',['no output file for Action ' ActionName ', use run mode = local']);% a output dir is needed for background option
1619%     return
1620else
1621    %% processing on a different session of the same computer (background) or cluster, create executable files
1622    batch_file_list=cell(NbProcess,1);% initiate the list of executable files
1623    DirBat=fullfile(OutputDir,'0_EXE');
1624    switch computer
1625        case {'PCWIN','PCWIN64'} %Windows system
1626            ExeExt='.bat';
1627        case {'GLNX86','GLNXA64','MACI64'}%Linux  system
1628           ExeExt='.sh';
1629    end
1630    %create subdirectory for executable files
1631    if ~exist(DirBat,'dir')
1632        [tild,msg1]=mkdir(DirBat);
1633        if ~strcmp(msg1,'')
1634            msgbox_uvmat('ERROR',['cannot create ' DirBat ': ' msg1]);%error message for directory creation
1635            return
1636        end
1637    end
1638    %create subdirectory for log files
1639    DirLog=fullfile(OutputDir,'0_LOG');
1640    if ~exist(DirLog,'dir')
1641        [tild,msg1]=mkdir(DirLog);
1642        if ~strcmp(msg1,'')
1643            msgbox_uvmat('ERROR',['cannot create ' DirLog ': ' msg1]);%error message for directory creation
1644            return
1645        end
1646    end
1647    for iprocess=1:NbProcess
1648        if isempty(Param.IndexRange.NbSlice)% process by blocks of i index
1649            Param.IndexRange.first_i=first_i+(iprocess-1)*BlockLength*incr_i;
1650            if Param.IndexRange.first_i>last_i
1651                NbProcess=iprocess-1;
1652                break% leave the loop, we are at the end of the calculation
1653            end
1654            Param.IndexRange.last_i=min(last_i,first_i+(iprocess)*BlockLength*incr_i-1);
1655        else% process by slices of i index if NbSlice is defined, computation in a single process if NbSlice =1
1656            Param.IndexRange.first_i= first_i+iprocess-1;
1657            Param.IndexRange.incr_i=incr_i*Param.IndexRange.NbSlice;
1658        end
1659        Param.InputTable{1}=regexprep(Param.InputTable{1},'\','/');%correct path name for PCWIN system
1660        % create, fill and save the xml parameter file
1661        t=struct2xml(Param);
1662        t=set(t,1,'name','Series');
1663        filexml=fullfile_uvmat(DirXml,'',Param.InputTable{1,3},'.xml',OutputNomType,...
1664            Param.IndexRange.first_i,Param.IndexRange.last_i,first_j,last_j);
1665        save(t,filexml);% save the parameter file
1666       
1667        %create the executable file
1668         filebat=fullfile_uvmat(DirBat,'',Param.InputTable{1,3},ExeExt,OutputNomType,...
1669           Param.IndexRange.first_i,Param.IndexRange.last_i,first_j,last_j);
1670        batch_file_list{iprocess}=filebat;
1671        [fid,message]=fopen(filebat,'w');% create the executable file
1672        if isequal(fid,-1)
1673            msgbox_uvmat('ERROR', ['creation of .bat file: ' message]);
1674            return
1675        end
1676       
1677        % set the log file name
1678        filelog=fullfile_uvmat(DirLog,'',Param.InputTable{1,3},'.log',OutputNomType,...
1679            Param.IndexRange.first_i,Param.IndexRange.last_i,first_j,last_j);
1680       
1681        % fill and save the executable file
1682        switch ActionExt
1683            case '.m'% Matlab function
1684                switch computer
1685                    case {'GLNX86','GLNXA64','MACI64'}
1686                        cmd=[...
1687                            '#!/bin/bash \n'...
1688                            '. /etc/sysprofile \n'...
1689                            'matlab -nodisplay -nosplash -nojvm -logfile ''' filelog ''' <<END_MATLAB \n'...
1690                            'addpath(''' path_series '''); \n'...
1691                            'addpath(''' Param.Action.ActionPath '''); \n'...
1692                            '' Param.Action.ActionName  '( ''' filexml '''); \n'...
1693                            'exit \n'...
1694                            'END_MATLAB \n'];
1695                        fprintf(fid,cmd);%fill the executable file with the  char string cmd
1696                        fclose(fid);% close the executable file
1697                        system(['chmod +x ' filebat]);% set the file to executable
1698                    case {'PCWIN','PCWIN64'}
1699                        text_matlabscript=['matlab -automation -logfile ' regexprep(filelog,'\\','\\\\')...
1700                            ' -r "addpath(''' regexprep(path_series,'\\','\\\\') ''');'...
1701                            'addpath(''' regexprep(Param.Action.ActionPath,'\\','\\\\') ''');'...
1702                            '' Param.Action.ActionName  '( ''' regexprep(filexml,'\\','\\\\') ''');exit"'];
1703                        fprintf(fid,text_matlabscript);%fill the executable file with the  char string cmd
1704                        fclose(fid);% close the executable file
1705                end
1706            case '.sh' % compiled Matlab function
1707                switch computer
1708                    case {'GLNX86','GLNXA64','MACI64'}
1709                        cmd=['#!/bin/bash \n '...
1710                            '#$ -cwd \n '...
1711                            'hostname && date \n '...
1712                            'umask 002 \n'...
1713                            fullfile(ActionPath,[ActionName '.sh']) ' ' RunTime ' ' filexml];%allow writting access to created files for user group
1714                        fprintf(fid,cmd);%fill the executable file with the  char string cmd
1715                        fclose(fid);% close the executable file
1716                        system(['chmod +x ' filebat]);% set the file to executable
1717                       
1718                    case {'PCWIN','PCWIN64'}   
1719                        fprintf(fid,cmd);
1720                        fclose(fid);
1721                end
1722        end
1723    end
1724end
1725
1726%% launch the executable files for background or cluster processing
1727switch RunMode
1728    case 'background'
1729        for iprocess=1:NbProcess
1730            system([batch_file_list{iprocess} ' &'])% directly execute the command file for each process
1731            msgbox_uvmat('CONFIRMATION',[ActionName 'launched in background: press STATUS to see results'])
1732        end
1733    case 'cluster_oar' % option 'oar-parexec' used
1734        %create subdirectory for oar command and log files
1735        DirOAR=fullfile(OutputDir,'0_OAR');
1736        if exist(DirOAR,'dir')% delete the content of the dir 0_OAR to allow new input
1737            curdir=pwd;
1738            cd(DirOAR)
1739            delete('*')
1740            cd(curdir)
1741        else
1742            [tild,msg1]=mkdir(DirOAR);
1743            if ~strcmp(msg1,'')
1744                msgbox_uvmat('ERROR',['cannot create ' DirOAR ': ' msg1]);%error message for directory creation
1745                return
1746            end
1747        end
1748        max_walltime=3600*20; % 20h max total calculation (cannot exceed 24 h)
1749        walltime_onejob=600;%seconds, max estimated time for asingle file index value
1750        filename_joblist=fullfile(DirOAR,'job_list.txt');%create name of the global executable file
1751        fid=fopen(filename_joblist,'w');
1752        for p=1:length(batch_file_list)
1753            fprintf(fid,[batch_file_list{p} '\n']);% list of exe files
1754        end
1755        fclose(fid);
1756        system(['chmod +x ' filename_joblist]);% set the file to executable
1757        oar_command=['oarsub -n CIVX '...
1758            '-t idempotent --checkpoint ' num2str(walltime_onejob+60) ' '...
1759            '-l /core=' num2str(NbCore) ','...
1760            'walltime=' datestr(min(1.05*walltime_onejob/86400*max(NbProcess*BlockLength*nbfield_j,NbCore)/NbCore,max_walltime/86400),13) ' '...
1761            '-E ' regexprep(filename_joblist,'\.txt\>','.stderr') ' '...
1762            '-O ' regexprep(filename_joblist,'\.txt\>','.stdout') ' '...
1763            extra_oar ' '...
1764            '"oar-parexec -s -f ' filename_joblist ' '...
1765            '-l ' filename_joblist '.log"\n'];
1766        filename_oarcommand=fullfile(DirOAR,'oar_command');
1767        fid=fopen(filename_oarcommand,'w');
1768        fprintf(fid,oar_command);
1769        fclose(fid);
1770        fprintf(oar_command);% display in command line
1771        system(oar_command); 
1772        msgbox_uvmat('CONFIRMATION',[ActionName ' launched in cluster: press STATUS to see results'])
1773end
1774
1775%% reset the GUI series
1776update_waitbar(handles.Waitbar,1); % put the waitbar to end position to indicate launching is finished
1777set(handles.RUN, 'Enable','On')
1778set(handles.RUN,'BackgroundColor',[1 0 0])
1779set(handles.RUN, 'Value',0)
1780
1781%------------------------------------------------------------------------
1782function STOP_Callback(hObject, eventdata, handles)
1783%------------------------------------------------------------------------
1784set(handles.RUN, 'BusyAction','cancel')
1785set(handles.RUN,'BackgroundColor',[1 0 0])
1786set(handles.RUN,'enable','on')
1787set(handles.RUN, 'Value',0)
1788
1789
1790%------------------------------------------------------------------------
1791% --- read parameters from the GUI series
1792%------------------------------------------------------------------------
1793function Param=read_GUI_series(handles)
1794
1795%% read raw parameters from the GUI series
1796Param=read_GUI(handles.series);
1797
1798%% clean the output structure by removing unused information
1799if isfield(Param,'Pairs')
1800    Param=rmfield(Param,'Pairs'); %info Pairs not needed for output
1801end
1802Param.IndexRange=rmfield(Param.IndexRange,'TimeTable');
1803empty_line=false(size(Param.InputTable,1),1);
1804for iline=1:size(Param.InputTable,1)
1805    empty_line(iline)=isempty(cell2mat(Param.InputTable(iline,1:3)));
1806end
1807Param.InputTable(empty_line,:)=[];
1808
1809%------------------------------------------------------------------------
1810% --- Executes on selection change in ActionName.
1811function ActionName_Callback(hObject, eventdata, handles)
1812%------------------------------------------------------------------------
1813
1814%% stop any ongoing series processing
1815if isequal(get(handles.RUN,'Value'),1)
1816    answer= msgbox_uvmat('INPUT_Y-N','stop current Action process?');
1817    if strcmp(answer,'Yes')
1818        STOP_Callback(hObject, eventdata, handles)
1819    else
1820        return
1821    end
1822end
1823set(handles.ActionName,'BackgroundColor',[1 1 0])
1824huigetfile=findobj(allchild(0),'tag','status_display');
1825if ~isempty(huigetfile)
1826    delete(huigetfile)
1827end
1828drawnow
1829
1830%% get Action name and path
1831nb_builtin_ACTION=4; %nbre of functions initially proposed in the menu ActionName (as defined in the Opening fct of series)
1832ActionList=get(handles.ActionName,'String');% list menu fields
1833ActionIndex=get(handles.ActionName,'Value');
1834if ~isequal(ActionIndex,1)% if we are not just opening series
1835    InputTable=get(handles.InputTable,'Data');
1836    if isempty(InputTable{1,4})
1837        msgbox_uvmat('ERROR','no input file available: use Open in the menu bar')
1838        return
1839    end
1840end
1841ActionName= ActionList{get(handles.ActionName,'Value')}; % selected function name
1842ActionPathList=get(handles.ActionName,'UserData');%list of recorded paths to functions of the list ActionName
1843
1844%% add a new function to the menu if 'more...' has been selected in the menu ActionName
1845if isequal(ActionName,'more...')
1846    [FileName, PathName] = uigetfile( ...
1847        {'*.m', ' (*.m)';
1848        '*.m',  '.m files '; ...
1849        '*.*', 'All Files (*.*)'}, ...
1850        'Pick a series processing function ',get(handles.ActionPath,'String'));
1851    if length(FileName)<2
1852        return
1853    end
1854    [ActionPath,ActionName,ActionExt]=fileparts(FileName);
1855   
1856    % insert the choice in the menu ActionName
1857    ActionIndex=find(strcmp(ActionName,ActionList),1);% look for the selected function in the menu Action
1858    if isempty(ActionIndex)%the input string does not exist in the menu
1859        ActionIndex= length(ActionList);
1860        ActionList=[ActionList(1:end-1);{ActionName};ActionList(end)];% the selected function is appended in the menu, before the last item 'more...'
1861        set(handles.ActionName,'String',ActionList)
1862    end
1863   
1864    % record the file extension and extend the path list if it is a new extension
1865    ActionExtList=get(handles.ActionExt,'String');
1866    ActionExtIndex=find(strcmp(ActionExt,ActionExtList), 1);
1867    if isempty(ActionExtIndex)
1868        set(handles.ActionExt,'String',[ActionExtList;{ActionExt}])
1869        ActionExtIndex=numel(ActionExtList)+1;
1870        ActionPathNew=cell(size(ActionPathList,1),1);%new column of ActionPath
1871        ActionPathList=[ActionPathList ActionPathNew];
1872    end
1873    set(handles.ActionName,'UserData',ActionPathList);
1874
1875    % remove old Action options in the menu (keeping a menu length <nb_builtin_ACTION+5)
1876    if length(ActionList)>nb_builtin_ACTION+5; %nb_builtin=nbre of functions always remaining in the initial menu
1877        nbremove=length(ActionList)-nb_builtin_ACTION-5;
1878        ActionList(nb_builtin_ACTION+1:end-5)=[];
1879        ActionPathList(nb_builtin_ACTION+1:end-4,:)=[];
1880        ActionIndex=ActionIndex-nbremove;
1881    end
1882   
1883    % record action menu, choice and path
1884    set(handles.ActionName,'Value',ActionIndex)
1885    set(handles.ActionName,'String',ActionList)
1886    set(handles.ActionExt,'Value',ActionExtIndex)
1887    ActionPathList{ActionIndex,ActionExtIndex}=PathName;
1888       
1889    %record the user defined menu additions in personal file profil_perso
1890    dir_perso=prefdir;
1891    profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
1892    if nb_builtin_ACTION+1<=numel(ActionList)-1
1893        ActionListUser=ActionList(nb_builtin_ACTION+1:numel(ActionList)-1);
1894        ActionPathListUser=ActionPathList(nb_builtin_ACTION+1:numel(ActionList)-1,:);
1895        ActionExtListUser={};
1896        if numel(ActionExtList)>2
1897            ActionExtListUser=ActionExtList(3:end);
1898        end
1899        if exist(profil_perso,'file')
1900            save(profil_perso,'ActionListUser','ActionPathListUser','ActionExtListUser','-append')
1901        else
1902            save(profil_perso,'ActionListUser','ActionPathListUser','ActionExtListUser','-V6')
1903        end
1904    end
1905end
1906
1907%% check the current ActionPath to the selected function
1908ActionPath=ActionPathList{ActionIndex};%current recorded path
1909set(handles.ActionPath,'String',ActionPath); %show the path to the senlected function
1910
1911%% reinitialise the waitbar
1912update_waitbar(handles.Waitbar,0)
1913
1914%% create the function handle for Action
1915path_series=which('series');
1916if ~isequal(ActionPath,path_series)
1917    eval(['spath=which(''' ActionName ''');']) %spath = current path of the selected function ACTION
1918    if ~exist(ActionPath,'dir')
1919        errormsg=['The prescribed function path ' ActionPath ' does not exist'];
1920        return
1921    end
1922    if ~isequal(spath,ActionPath)
1923        addpath(ActionPath)% add the prescribed path if not the current one
1924    end
1925end
1926eval(['h_fun=@' ActionName ';'])%create a function handle for ACTION
1927if ~isequal(ActionPath,path_series)
1928        rmpath(ActionPath)% add the prescribed path if not the current one   
1929end
1930
1931%% Activate the Action fct
1932Param=read_GUI_series(handles);% read the parameters from the GUI series
1933ParamOut=h_fun(Param);%run the selected Action function to get the relevant input
1934
1935%% Put the first line of the selected Action fct as tooltip help
1936try
1937    [fid,errormsg] =fopen([ActionName '.m']);
1938    InputText=textscan(fid,'%s',1,'delimiter','\n');
1939    fclose(fid);
1940    set(handles.ActionName,'ToolTipString',InputText{1}{1})% put the first line of the selected function as tooltip help
1941end
1942
1943
1944%% Visibility of VelType and VelType_1 menus asked by ActionName
1945VelTypeRequest=1;%VelType requested by default
1946VelTypeRequest_1=1;%VelType requested by default
1947if isfield(ParamOut,'VelType')
1948    VelTypeRequest=ismember(ParamOut.VelType,{'on','one','two'});
1949    VelTypeRequest_1=strcmp( ParamOut.VelType,'two');
1950end
1951FieldNameRequest=0;  %hidden by default
1952FieldNameRequest_1=0;  %hidden by default
1953if isfield(ParamOut,'FieldName')
1954    FieldNameRequest=ismember(ParamOut.FieldName,{'on','one','two'});
1955    FieldNameRequest_1=strcmp( ParamOut.FieldName,'two');
1956end
1957
1958%% Detect the types of input files and set menus and default options in 'VelType'
1959SeriesData=get(handles.series,'UserData');% info on the input file series
1960iview_civ=find(strcmp('civx',SeriesData.FileType)|strcmp('civdata',SeriesData.FileType));
1961iview_netcdf=find(strcmp('netcdf',SeriesData.FileType)|strcmp('civx',SeriesData.FileType)|strcmp('civdata',SeriesData.FileType));% all nc files, icluding civ
1962FieldList=get(handles.FieldName,'String');% previous list as default
1963if ~iscell(FieldList),FieldList={FieldList};end
1964FieldList_1=get(handles.FieldName_1,'String');% previous list as default
1965if ~iscell(FieldList_1),FieldList_1={FieldList_1};end
1966CheckList=0;% indicate whether FieldName has been updated
1967CheckList_1=1;% indicate whether FieldName_1 has been updated
1968handles_coord=[handles.Coord_x handles.Coord_y handles.Coord_z handles.Coord_x_title handles.Coord_y_title handles.Coord_z_title];
1969if VelTypeRequest && numel(iview_civ)>=1
1970    menu=set_veltype_display(SeriesData.FileInfo{iview_civ(1)}.CivStage,SeriesData.FileType{iview_civ(1)});
1971    set(handles.VelType,'Value',1)% set first choice by default
1972    set(handles.VelType,'String',[{'*'};menu])
1973    set(handles.VelType,'Visible','on')
1974    set(handles.VelType_title,'Visible','on')
1975    FieldList=[set_field_list('U','V');{'C'};{'get_field...'}];%standard menu for civx data
1976    CheckList=1;
1977    set(handles.FieldName,'Value',1); %velocity vector choice by default
1978    if  VelTypeRequest_1 && numel(iview_civ)>=2
1979        menu=set_veltype_display(SeriesData.FileInfo{iview_civ(2)}.CivStage,SeriesData.FileType{iview_civ(2)});
1980        set(handles.VelType_1,'Value',1)% set first choice by default
1981        set(handles.VelType_1,'String',[{'*'};menu])
1982        set(handles.VelType_1,'Visible','on')
1983        set(handles.VelType_title_1,'Visible','on')
1984        FieldList_1=[set_field_list('U','V');{'C'};{'get_field...'}];%standard menu for civx data
1985        CheckList_1=1;
1986        set(handles.FieldName_1,'Value',1); %velocity vector choice by default
1987    else
1988        set(handles.VelType_1,'Visible','off')
1989        set(handles.VelType_title_1,'Visible','off')
1990    end
1991else
1992    set(handles.VelType,'Visible','off')
1993    set(handles.VelType_title,'Visible','off')
1994end   
1995
1996%% Detect the types of input files and set menus and default options in 'FieldName'
1997if FieldNameRequest && numel(iview_netcdf)>=1
1998    set(handles.InputFields,'Visible','on')
1999    if CheckList==0        % not civ input made
2000        if isfield(SeriesData.FileInfo{iview_netcdf(1)},'ListVarName')
2001        ListVarName=SeriesData.FileInfo{iview_netcdf(1)}.ListVarName;
2002        ind_var=get(handles.FieldName,'Value');%indices of previously selected variables
2003        for ilist=1:numel(ind_var)
2004            if isempty(find(strcmp(FieldList{ind_var(ilist)},ListVarName)))
2005                FieldList={};% previous choice not consistent with new input field
2006                set(handles.FieldName,'Value',1)
2007                break
2008            end
2009        end
2010        if ~isempty(FieldList)
2011            if isempty(find(strcmp(get(handles.Coord_x,'String'),ListVarName)))||...
2012                    isempty(find(strcmp(get(handles.Coord_y,'String'),ListVarName)))
2013                FieldList={};
2014                set(handles.Coord_x,'String','')
2015                set(handles.Coord_y,'String','')
2016            end
2017            Coord_z=get(handles.Coord_z,'String');
2018            if ~isempty(Coord_z) && isempty(find(strcmp(Coord_z,ListVarName)))
2019                FieldList={};
2020                set(handles.Coord_z,'String','')
2021            end
2022        end
2023        set(handles_coord,'Visible','on')
2024        FieldList=[FieldList;{'get_field...'}];
2025        if FieldNameRequest_1 && numel(iview_netcdf)>=2
2026            set(handles.FieldName_1,'Visible','on')
2027            if CheckList_1==0        % not civ input made
2028                ListVarName=SeriesData.FileInfo{iview_netcdf(2)}.ListVarName;
2029                ind_var=get(handles.FieldName,'Value');%indices of previously selected variables
2030                for ilist=1:numel(ind_var)
2031                    if isempty(find(strcmp(FieldList{ind_var(ilist)},ListVarName)))
2032                        FieldList_1={};% previous choice not consistent with new input field
2033                        set(handles.FieldName_1,'Value',1)
2034                        break
2035                    end
2036                end
2037                warn_coord=0;
2038                if isempty(find(strcmp(get(handles.Coord_x,'String'),ListVarName)))||...
2039                        isempty(find(strcmp(get(handles.Coord_y,'String'),ListVarName)))
2040                    warn_coord=1;
2041                end
2042                if ~isempty(Coord_z) && isempty(find(strcmp(Coord_z,ListVarName)))
2043                    FieldList_1={};
2044                    warn_coord=1;
2045                end
2046                if warn_coord
2047                    msgbox_uvmat('WARNING','coordiante names do not exist in the second netcdf input file')
2048                end
2049                set(handles.FieldName,'String',[FieldList;{'get_field...'}])
2050                set(handles.FieldName_1,'Visible','on')
2051                set(handles.FieldName_1,'Value',1)
2052                set(handles.FieldName_1,'String',FieldList_1)
2053            end
2054        else
2055            set(handles.FieldName_1,'Visible','off')
2056        end
2057        end
2058    else
2059        set(handles_coord,'Visible','off')% no coord display for civ data
2060    end
2061    set(handles.FieldName,'String',FieldList)
2062else
2063    set(handles.InputFields,'Visible','off')
2064end
2065
2066
2067%% Check whether alphabetical sorting of input Subdir is allowed by the Action fct  (for multiples series entries)
2068if isfield(ParamOut,'AllowInputSort')&&isequal(ParamOut.AllowInputSort,'on')&& size(Param.InputTable,1)>1
2069    [tild,iview]=sort(InputTable(:,2)); %subdirectories sorted in alphabetical order
2070    set(handles.InputTable,'Data',InputTable(iview,:));
2071    MinIndex_i=get(handles.MinIndex_i,'Data');
2072    MinIndex_j=get(handles.MinIndex_j,'Data');
2073    MaxIndex_i=get(handles.MaxIndex_i,'Data');
2074    MaxIndex_j=get(handles.MaxIndex_j,'Data');
2075    set(handles.MinIndex_i,'Data',MinIndex_i(iview,:));
2076    set(handles.MinIndex_j,'Data',MinIndex_j(iview,:));
2077    set(handles.MaxIndex_i,'Data',MaxIndex_i(iview,:));
2078    set(handles.MaxIndex_j,'Data',MaxIndex_j(iview,:));
2079    TimeTable=get(handles.TimeTable,'Data');
2080    set(handles.TimeTable,'Data',TimeTable(iview,:));
2081    PairString=get(handles.PairString,'Data');
2082    set(handles.PairString,'Data',PairString(iview,:));
2083end
2084
2085%% Impose the whole input file index range if requested
2086if isfield(ParamOut,'WholeIndexRange')&&isequal(ParamOut.WholeIndexRange,'on')
2087    MinIndex_i=get(handles.MinIndex_i,'Data');
2088    MinIndex_j=get(handles.MinIndex_j,'Data');
2089    MaxIndex_i=get(handles.MaxIndex_i,'Data');
2090    MaxIndex_j=get(handles.MaxIndex_j,'Data');
2091    set(handles.num_first_i,'String',num2str(MinIndex_i(1)))% set first as the min index (for the first line)
2092    set(handles.num_last_i,'String',num2str(MaxIndex_i(1)))% set last as the max index (for the first line)
2093    set(handles.num_incr_i,'String','1')
2094    set(handles.num_first_j,'String',num2str(MinIndex_j(1)))% set first as the min index (for the first line)
2095    set(handles.num_last_j,'String',num2str(MaxIndex_j(1)))% set last as the max index (for the first line)
2096    set(handles.num_incr_j,'String','1')
2097else  % check index ranges
2098    first_i=1;last_i=1;first_j=1;last_j=1;
2099    if isfield(Param.IndexRange,'first_i')
2100        first_i=Param.IndexRange.first_i;
2101        last_i=Param.IndexRange.last_i;
2102    end
2103    if isfield(Param.IndexRange,'first_j')
2104        first_j=Param.IndexRange.first_j;
2105        last_j=Param.IndexRange.last_j;
2106    end
2107    if last_i < first_i || last_j < first_j , msgbox_uvmat('ERROR','last field number must be larger than the first one'),...
2108            set(handles.RUN, 'Enable','On'), set(handles.RUN,'BackgroundColor',[1 0 0]),return,end;
2109end
2110
2111%% enable or desable j index visibility
2112status_j='on';%default
2113if isfield(ParamOut,'Desable_j_index')&&isequal(ParamOut.Desable_j_index,'on')
2114    status_j='off';
2115end
2116if isempty(find(~cellfun(@isempty,SeriesData.j1_series), 1)); % case of empty j indices
2117    status_j='off'; % no j index needed
2118elseif strcmp(get(handles.PairString,'Visible'),'on')
2119    check_burst=cellfun(@isempty,regexp(get(handles.PairString,'Data'),'^j'));%=0 for burst case, 1 otherwise
2120    if isempty(find(check_burst, 1))% if all pair string begins by j (burst)
2121        status_j='off'; % no j index needed for bust case
2122    end
2123end
2124enable_j(handles,status_j) % no j index needed
2125
2126
2127%% NbSlice visibility
2128NbSliceVisible='off';%default
2129if isfield(ParamOut,'NbSlice') && isequal(ParamOut.NbSlice,'on')
2130    NbSliceVisible='on';
2131    set(handles.num_NbProcess,'String',get(handles.num_NbSlice,'String'))% the nbre of processes is imposed as the nbre of slices
2132else
2133    set(handles.num_NbProcess,'String','')% free nbre of processes
2134end
2135set(handles.num_NbSlice,'Visible',NbSliceVisible)
2136set(handles.NbSlice_title,'Visible',NbSliceVisible)
2137
2138
2139
2140%% Visibility of FieldTransform menu
2141FieldTransformVisible='off';  %hidden by default
2142if isfield(ParamOut,'FieldTransform')
2143    FieldTransformVisible=ParamOut.FieldTransform; 
2144    TransformName_Callback([],[], handles)
2145end
2146set(handles.FieldTransform,'Visible',FieldTransformVisible)
2147if isfield(ParamOut,'TransformPath')
2148    set(handles.ActionExt,'UserData',ParamOut.TransformPath)
2149else
2150    set(handles.ActionExt,'UserData',[])
2151end
2152
2153%% Visibility of projection object
2154ProjObjectVisible='off';  %hidden by default
2155if isfield(ParamOut,'ProjObject')
2156    ProjObjectVisible=ParamOut.ProjObject;
2157end
2158set(handles.CheckObject,'Visible',ProjObjectVisible)
2159if ~get(handles.CheckObject,'Value')
2160    ProjObjectVisible='off';
2161end
2162set(handles.ProjObject,'Visible',ProjObjectVisible)
2163set(handles.DeleteObject,'Visible',ProjObjectVisible)
2164set(handles.ViewObject,'Visible',ProjObjectVisible)
2165set(handles.EditObject,'Visible',ProjObjectVisible)
2166
2167%% Visibility of mask input
2168MaskVisible='off';  %hidden by default
2169if isfield(ParamOut,'Mask')
2170    MaskVisible=ParamOut.Mask;
2171end
2172set(handles.CheckMask,'Visible',MaskVisible);
2173
2174%% definition of the directory containing the output files
2175SubDirOut='';%default
2176OutputDirExt='.series'; %default
2177if isfield(ParamOut,'OutputDirExt')&&~isempty(ParamOut.OutputDirExt)
2178    OutputDirExt=ParamOut.OutputDirExt;
2179end
2180set(handles.OutputDirExt,'String',OutputDirExt)
2181OutputDirVisible='off';
2182OutputSubDirMode='auto';%default
2183if isfield(ParamOut,'OutputSubDirMode')
2184    OutputSubDirMode=ParamOut.OutputSubDirMode;
2185end
2186switch OutputSubDirMode
2187    case 'auto';%default
2188        OutputDirVisible='on';
2189        SubDir=InputTable(1:end,2); %set of subdirectories
2190        SubDirOut=SubDir{1};
2191        if numel(SubDir)>1
2192            for ilist=2:numel(SubDir)
2193                SubDirOut=[SubDirOut '-' SubDir{ilist}];
2194            end
2195        end
2196    case 'first'
2197        OutputDirVisible='on';
2198        SubDirOut=InputTable{1,2}; %use the first subdir name (+OutputDirExt) as output  subdirectory
2199    case 'last'
2200        OutputDirVisible='on';
2201        SubDirOut=InputTable{end,2}; %use the last subdir name (+OutputDirExt) as output  subdirectory
2202end
2203set(handles.OutputSubDir,'String',SubDirOut)
2204set(handles.OutputDirExt,'Visible',OutputDirVisible)
2205set(handles.OutputSubDir,'Visible',OutputDirVisible)
2206set(handles.OutputDir_title,'Visible',OutputDirVisible)
2207
2208%% visibility of the run mode (local or background or cluster)
2209if strcmp(OutputSubDirMode,'none')
2210    RunModeVisible='off';% only local mode available if no output file is produced
2211else
2212     RunModeVisible='on';
2213end
2214set(handles.RunMode,'Visible',RunModeVisible)
2215set(handles.ActionExt,'Visible',RunModeVisible)
2216set(handles.RunMode_title,'Visible',RunModeVisible)
2217set(handles.ActionExt_title,'Visible',RunModeVisible)
2218
2219
2220%% Expected nbre of output files
2221if isfield(ParamOut,'OutputFileMode')
2222    StatusData.OutputFileMode=ParamOut.OutputFileMode;
2223    set(handles.status,'UserData',StatusData)
2224end
2225
2226%% definition of an additional parameter set, determined by an ancillary GUI
2227if isfield(ParamOut,'ActionInput')
2228    set(handles.ActionInput,'Visible','on')
2229    ParamOut.ActionInput.Program=ActionName; % record the program in ActionInput
2230    SeriesData.ActionInput=ParamOut.ActionInput;
2231else
2232    set(handles.ActionInput,'Visible','off')
2233    if isfield(SeriesData,'ActionInput')
2234        SeriesData=rmfield(SeriesData,'ActionInput');
2235    end
2236end
2237set(handles.series,'UserData',SeriesData)
2238set(handles.ActionName,'BackgroundColor',[1 1 1])
2239
2240%------------------------------------------------------------------------
2241% --- Executes on button press in ActionInput.
2242function ActionInput_Callback(hObject, eventdata, handles)
2243%------------------------------------------------------------------------
2244% if get(handles.ActionInput,'Value')
2245ActionName_Callback(hObject, eventdata, handles)
2246% end
2247
2248%------------------------------------------------------------------------
2249% --- Executes on selection change in FieldName.
2250function FieldName_Callback(hObject, eventdata, handles)
2251%------------------------------------------------------------------------
2252field_str=get(handles.FieldName,'String');
2253field_index=get(handles.FieldName,'Value');
2254field=field_str{field_index(1)};
2255if isequal(field,'get_field...')
2256    SeriesData=get(handles.series,'UserData');
2257    % input line for which the field choice is relevant
2258    iview=find(strcmp('netcdf',SeriesData.FileType)|strcmp('civx',SeriesData.FileType)|strcmp('civdata',SeriesData.FileType));% all nc files, icluding civ
2259    hget_field=findobj(allchild(0),'name','get_field');
2260    if ~isempty(hget_field)
2261        delete(hget_field)%delete opened versions of get_field
2262    end
2263    Param=read_GUI(handles.series);
2264    InputTable=Param.InputTable(iview,:);
2265    % check the existence of the first file in the series
2266    first_j=[];last_j=[];MinIndex_j=1;MaxIndex_j=1;%default setting for index j
2267    if isfield(Param.IndexRange,'first_j');% if index j is used
2268        first_j=Param.IndexRange.first_j;
2269        last_j=Param.IndexRange.last_j;
2270        MinIndex_j=Param.IndexRange.MinIndex_j(iview);
2271        MaxIndex_j=Param.IndexRange.MaxIndex_j(iview);
2272    end
2273    PairString='';
2274    if isfield(Param.IndexRange,'PairString'); PairString=Param.IndexRange.PairString{iview}; end
2275    [i1,i2,j1,j2] = get_file_index(Param.IndexRange.first_i,first_j,PairString);
2276    FirstFileName=fullfile_uvmat(InputTable{1},InputTable{2},InputTable{3},...
2277        InputTable{5},InputTable{4},i1,i2,j1,j2);
2278    if exist(FirstFileName,'file')
2279        ParamIn.Title='get_field: pick input variables and coordinates for series processing';
2280        ParamIn.SeriesInput=1;
2281        GetFieldData=get_field(FirstFileName,ParamIn);
2282        FieldList={};
2283        switch GetFieldData.FieldOption
2284            case 'vectors'
2285                UName=GetFieldData.PanelVectors.vector_x;
2286                VName=GetFieldData.PanelVectors.vector_y;
2287                YName={GetFieldData.Coordinates.Coord_y};
2288                FieldList={['vec(' UName ',' VName ')'];...
2289                    ['norm(' UName ',' VName ')'];...
2290                    UName;VName};
2291            case {'scalar'}
2292                FieldList=GetFieldData.PanelScalar.scalar;
2293                YName={GetFieldData.Coordinates.Coord_y};
2294                if ischar(FieldList)
2295                    FieldList={FieldList};
2296                end
2297            case 'civdata...'
2298                FieldList=[set_field_list('U','V') ;{'C'}];
2299                set(handles.FieldName,'Value',1) % set menu to 'velocity
2300                XName='X';
2301                YName='y';
2302                set(handles.VelType,'visible','on')
2303                set(handles.VelType_title,'visible','on')
2304        end
2305        set(handles.FieldName,'Value',1)
2306        set(handles.FieldName,'String',[FieldList; {'get_field...'}]);
2307        if ~strcmp(GetFieldData.FieldOption,'civdata...')
2308            set(handles.FieldName,'Value',1:numel(FieldList))%select all input fields by default
2309            set(handles.VelType,'visible','off')
2310            set(handles.VelType_title,'visible','off')
2311            XName=GetFieldData.Coordinates.Coord_x;
2312            YName=GetFieldData.Coordinates.Coord_y;
2313            TimeNameStr=GetFieldData.Time.SwitchVarIndexTime;
2314            % get the time info                     
2315            TimeTable=get(handles.TimeTable,'Data');
2316            switch TimeNameStr
2317                case 'file index'
2318                    TimeName='';
2319                case 'attribute'
2320                    TimeName=['att:' GetFieldData.Time.TimeName];
2321                    % update the time table
2322                    TimeTable{iview,2}=get_time(Param.IndexRange.MinIndex_i(iview),MinIndex_j,PairString,InputTable,SeriesData.FileInfo{iview},GetFieldData.Time.TimeName);  % Min time     
2323                    TimeTable{iview,3}=get_time(Param.IndexRange.first_i,first_j,PairString,InputTable,SeriesData.FileInfo{iview},GetFieldData.Time.TimeName);  % first time             
2324                    TimeTable{iview,4}=get_time(Param.IndexRange.last_i,last_j,PairString,InputTable,SeriesData.FileInfo{iview},GetFieldData.Time.TimeName);  % last time                     
2325                    TimeTable{iview,5}=get_time(Param.IndexRange.MaxIndex_i(iview),MaxIndex_j,PairString,InputTable,SeriesData.FileInfo{iview},GetFieldData.Time.TimeName);  % Max time
2326                case 'variable'
2327                    set(handles.TimeName,'String',['var:' GetFieldData.Time.TimeName])
2328                    set(handles.NomType,'String','*')
2329                    set(handles.RootFile,'String',[get(handles.RootFile,'String') get(handles.FileIndex,'String')])% A VERIFIER !!!!!!
2330                    set(handles.FileIndex,'String','')
2331                    ParamIn.TimeVarName=GetFieldData.Time.TimeName;
2332                case 'matrix_index'
2333                    TimeName=['dim:' GetFieldData.Time.TimeName];
2334                    set(handles.NomType,'String','*')
2335                    set(handles.RootFile,'String',[get(handles.RootFile,'String') get(handles.FileIndex,'String')])
2336                    set(handles.FileIndex,'String','')
2337                    ParamIn.TimeDimName=GetFieldData.Time.TimeName;
2338            end
2339            TimeTable{iview,1}=TimeName;
2340            set(handles.TimeTable,'Data',TimeTable);
2341        end
2342        set(handles.Coord_x,'String',XName)
2343        set(handles.Coord_y,'String',YName)
2344    else
2345        msgbox_uvmat('ERROR',[FirstFileName ' does not exist'])
2346    end
2347end
2348
2349function [TimeValue,DtValue]=get_time(ref_i,ref_j,PairString,InputTable,FileInfo,TimeName,DtName)
2350[i1,i2,j1,j2] = get_file_index(ref_i,ref_j,PairString);
2351FileName=fullfile_uvmat(InputTable{1},InputTable{2},InputTable{3},InputTable{5},InputTable{4},i1,i2,j1,j2);
2352Data=nc2struct(FileName,[]);
2353TimeValue=[];
2354DtValue=[];
2355if isequal(FileInfo.FileType,'civdata')
2356    if ismember(TimeName,{'civ1','filter1'})
2357        TimeValue=Data.Civ1_Time;
2358        DtValue=Data.Civ1_Dt;
2359    else
2360        TimeValue=Data.Civ2_Time;
2361        DtValue=Data.Civ2_Dt;
2362    end
2363else
2364    if ~isempty(TimeName)&& isfield(Data,TimeName)
2365        TimeValue=Data.(TimeName);
2366    end
2367    if exist('DtName','var') && isfield(Data,DtName)
2368        DtValue=Data.(DtName);
2369    end
2370end
2371
2372%------------------------------------------------------------------------
2373% --- Executes on selection change in FieldName_1.
2374function FieldName_1_Callback(hObject, eventdata, handles)
2375%------------------------------------------------------------------------
2376field_str=get(handles.FieldName_1,'String');
2377field_index=get(handles.FieldName_1,'Value');
2378field=field_str{field_index(1)};
2379if isequal(field,'get_field...')
2380    hget_field=findobj(allchild(0),'name','get_field');
2381    if ~isempty(hget_field)
2382        delete(hget_field)%delete opened versions of get_field
2383    end
2384    Param=read_GUI(handles.series);
2385    Param.InputTable=Param.InputTable(1,:);
2386    % check the existence of the first file in the series
2387    first_j=[];
2388    if isfield(Param.IndexRange,'first_j'); first_j=Param.IndexRange.first_j; end
2389    if isfield(Param.IndexRange,'last_j'); last_j=Param.IndexRange.last_j; end
2390    PairString='';
2391    if isfield(Param.IndexRange,'PairString'); PairString=Param.IndexRange.PairString; end
2392    [i1,i2,j1,j2] = get_file_index(Param.IndexRange.first_i,first_j,PairString);
2393    FirstFileName=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},...
2394        Param.InputTable{1,5},Param.InputTable{1,4},i1,i2,j1,j2);
2395    if exist(FirstFileName,'file')
2396        ParamIn.SeriesInput=1;
2397        GetFieldData=get_field(FirstFileName,ParamIn);
2398        FieldList={};
2399        switch GetFieldData.FieldOption
2400            case 'vectors'
2401                UName=GetFieldData.PanelVectors.vector_x;
2402                VName=GetFieldData.PanelVectors.vector_y;
2403                FieldList={['vec(' UName ',' VName ')'];...
2404                    ['norm(' UName ',' VName ')'];...
2405                    UName;VName};
2406            case {'scalar','pick variables'}
2407                FieldList=GetFieldData.PanelScalar.scalar;
2408                if ischar(FieldList)
2409                    FieldList={FieldList};
2410                end
2411            case '1D plot'
2412
2413            case 'civdata...'
2414                FieldList=set_field_list('U','V','C');
2415                set(handles.FieldName,'Value',2) % set menu to 'velocity
2416        end
2417        if ~strcmp(GetFieldData.FieldOption,'civdata...')
2418            TimeNameStr=GetFieldData.Time.SwitchVarIndexTime;
2419            switch TimeNameStr
2420                case 'file index'
2421                    set(handles.TimeName,'String','');
2422                case 'attribute'
2423                    set(handles.TimeName,'String',['att:' GetFieldData.Time.TimeName]);
2424                case 'variable'
2425                    set(handles.TimeName,'String',['var:' GetFieldData.Time.TimeName])
2426                    set(handles.NomType,'String','*')
2427                    set(handles.RootFile,'String',[get(handles.RootFile,'String') get(handles.FileIndex,'String')])% A VERIFIER !!!!!!
2428                    set(handles.FileIndex,'String','')
2429                    ParamIn.TimeVarName=GetFieldData.Time.TimeName;
2430                case 'matrix_index'
2431                    set(handles.TimeName,'String',['dim:' GetFieldData.Time.TimeName]);
2432                    set(handles.NomType,'String','*')
2433                    set(handles.RootFile,'String',[get(handles.RootFile,'String') get(handles.FileIndex,'String')])
2434                    set(handles.FileIndex,'String','')
2435                    ParamIn.TimeDimName=GetFieldData.Time.TimeName;
2436            end
2437        end
2438        set(handles.FieldName_1,'Value',1)
2439        set(handles.FieldName_1,'String',[FieldList; {'get_field...'}]);
2440    end
2441end   
2442
2443
2444%%%%%%%%%%%%%
2445function [ind_remove]=find_pairs(dirpair,ind_i,last_i)
2446indsel=ind_i;
2447indiff=diff(ind_i); %test index increment to detect multiplets (several pairs with the same index ind_i) and holes in the series
2448indiff=[1 indiff last_i-ind_i(end)+1];%for testing gaps with the imposed bounds
2449if ~isempty(indiff)
2450    indiff2=diff(indiff);
2451    indiffp=[indiff2 1];
2452    indiffm=[1 indiff2];
2453    ind_multi_m=find((indiff==0)&(indiffm<0))-1;%indices of first members of multiplets
2454    ind_multi_p=find((indiff==0)&(indiffp>0));%indices of last members of multiplets
2455    %for each multiplet, select the most recent file
2456    ind_remove=[];
2457    for i=1:length(ind_multi_m)
2458        ind_pairs=ind_multi_m(i):ind_multi_p(i);
2459        for imulti=1:length(ind_pairs)
2460            datepair(imulti)=datenum(dirpair(ind_pairs(imulti)).date);%dates of creation
2461        end
2462        [datenew,indsort2]=sort(datepair); %sort the multiplet by creation date
2463        ind_s=indsort2(1:end-1);%
2464        ind_remove=[ind_remove ind_pairs(ind_s)];%remove these indices, leave the last one
2465    end
2466end
2467
2468%------------------------------------------------------------------------
2469% --- determine the list of index pairstring of processing file
2470function [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)
2471%------------------------------------------------------------------------
2472num_i1=num_i;% set of first image numbers by default
2473num_i2=num_i;
2474num_j1=num_j;
2475num_j2=num_j;
2476num_i_out=num_i;
2477num_j_out=num_j;
2478% if isequal (NomType,'_1-2_1') || isequal (NomType,'_1-2')
2479if isequal(mode,'series(Di)')
2480    num_i1_line=num_i+ind_shift(3);% set of first image numbers
2481    num_i2_line=num_i+ind_shift(4);
2482    % adjust the first and last field number
2483        indsel=find(num_i1_line >= 1);
2484    num_i_out=num_i(indsel);
2485    num_i1_line=num_i1_line(indsel);
2486    num_i2_line=num_i2_line(indsel);
2487    num_j1=meshgrid(num_j,ones(size(num_i1_line)));
2488    num_j2=meshgrid(num_j,ones(size(num_i1_line)));
2489    [xx,num_i1]=meshgrid(num_j,num_i1_line);
2490    [xx,num_i2]=meshgrid(num_j,num_i2_line);
2491elseif isequal (mode,'series(Dj)')||isequal (mode,'bursts')
2492    if isequal(mode,'bursts') %case of bursts (png_old or png_2D)
2493        num_j1=ind_shift(1)*ones(size(num_i));
2494        num_j2=ind_shift(2)*ones(size(num_i));
2495    else
2496        num_j1_col=num_j+ind_shift(1);% set of first image numbers
2497        num_j2_col=num_j+ind_shift(2);
2498        % adjust the first field number
2499        indsel=find((num_j1_col >= 1));   
2500        num_j_out=num_j(indsel);
2501        num_j1_col=num_j1_col(indsel);
2502        num_j2_col=num_j2_col(indsel);
2503        [num_i1,num_j1]=meshgrid(num_i,num_j1_col);
2504        [num_i2,num_j2]=meshgrid(num_i,num_j2_col);
2505    end   
2506end
2507
2508%------------------------------------------------------------------------
2509% --- Executes on button press in CheckObject.
2510function CheckObject_Callback(hObject, eventdata, handles)
2511%------------------------------------------------------------------------
2512hset_object=findobj(allchild(0),'tag','set_object');%find the set_object interface handle
2513if get(handles.CheckObject,'Value')
2514    SeriesData=get(handles.series,'UserData');
2515    if isfield(SeriesData,'ProjObject') && ~isempty(SeriesData.ProjObject)
2516        set(handles.ViewObject,'Value',1)
2517        ViewObject_Callback(hObject, eventdata, handles)
2518    else
2519        if ishandle(hset_object)
2520            uistack(hset_object,'top')% show the GUI set_object if opened
2521        else
2522            %get the object file
2523            InputTable=get(handles.InputTable,'Data');
2524            defaultname=InputTable{1,1};
2525            if isempty(defaultname)
2526                defaultname={''};
2527            end
2528            fileinput=uigetfile_uvmat('pick a xml object file (or use uvmat to create it)',defaultname,'.xml');
2529            if isempty(fileinput)% exit if no object file is selected
2530                set(handles.CheckObject,'Value',0)
2531                return
2532            end
2533            %read the file
2534            data=xml2struct(fileinput);
2535            if ~isfield(data,'Type')
2536                msgbox_uvmat('ERROR',[fileinput ' is not an object xml file'])
2537                set(handles.CheckObject,'Value',0)
2538                return
2539            end
2540            if ~isfield(data,'ProjMode')
2541                data.ProjMode='none';
2542            end
2543            hset_object=set_object(data);% call the set_object interface
2544            set(hset_object,'Name','set_object_series')% name to distinguish from set_object used with uvmat
2545        end
2546        ProjObject=read_GUI(hset_object);
2547        set(handles.ProjObject,'String',ProjObject.Name);%display the object name
2548        SeriesData=get(handles.series,'UserData');
2549        SeriesData.ProjObject=ProjObject;
2550        set(handles.series,'UserData',SeriesData);
2551    end
2552    set(handles.EditObject,'Visible','on');
2553    set(handles.DeleteObject,'Visible','on');
2554    set(handles.ViewObject,'Visible','on');
2555    set(handles.ProjObject,'Visible','on');
2556else
2557    set(handles.EditObject,'Visible','off');
2558    set(handles.DeleteObject,'Visible','off');
2559    set(handles.ViewObject,'Visible','off');
2560    if ~ishandle(hset_object)
2561        set(handles.ViewObject,'Value',0);
2562    end
2563    set(handles.ProjObject,'Visible','off');
2564end
2565
2566%------------------------------------------------------------------------
2567% --- Executes on button press in ViewObject.
2568%------------------------------------------------------------------------
2569function ViewObject_Callback(hObject, eventdata, handles)
2570
2571UserData=get(handles.series,'UserData');
2572hset_object=findobj(allchild(0),'Tag','set_object');
2573if ~isempty(hset_object)
2574    delete(hset_object)% refresh set_object if already opened
2575end
2576hset_object=set_object(UserData.ProjObject);
2577set(hset_object,'Name','view_object_series')
2578
2579
2580%------------------------------------------------------------------------
2581% --- Executes on button press in EditObject.
2582function EditObject_Callback(hObject, eventdata, handles)
2583%------------------------------------------------------------------------
2584if get(handles.EditObject,'Value')
2585    set(handles.ViewObject,'Value',0)
2586        UserData=get(handles.series,'UserData');
2587    hset_object=set_object(UserData.ProjObject);
2588    set(hset_object,'Name','edit_object_series')
2589    set(get(hset_object,'Children'),'Enable','on')
2590else
2591    hset_object=findobj(allchild(0),'Tag','set_object');
2592    if ~isempty(hset_object)
2593        set(get(hset_object,'Children'),'Enable','off')
2594    end
2595end
2596
2597%------------------------------------------------------------------------
2598% --- Executes on button press in DeleteObject.
2599function DeleteObject_Callback(hObject, eventdata, handles)
2600%------------------------------------------------------------------------
2601SeriesData=get(handles.series,'UserData');
2602SeriesData.ProjObject=[];
2603set(handles.series,'UserData',SeriesData)
2604set(handles.ProjObject,'String','')
2605set(handles.ProjObject,'Visible','off')
2606set(handles.CheckObject,'Value',0)
2607set(handles.ViewObject,'Visible','off')
2608set(handles.EditObject,'Visible','off')
2609hset_object=findobj(allchild(0),'name','set_object_series');
2610if ~isempty(hset_object)
2611    delete(hset_object)
2612end
2613set(handles.DeleteObject,'Visible','off')
2614
2615%------------------------------------------------------------------------
2616% --- Executed when CheckMask is activated
2617%------------------------------------------------------------------------
2618function CheckMask_Callback(hObject, eventdata, handles)
2619
2620if get(handles.CheckMask,'Value')
2621    InputTable=get(handles.InputTable,'Data');
2622    nbview=size(InputTable,1);
2623    MaskTable=cell(nbview,1);%default
2624    ListMask=cell(nbview,1);%default
2625    MaskData=get(handles.MaskTable,'Data');
2626    MaskData(size(MaskData,1):nbview,1)=cell(size(MaskData,1):nbview,1);%complement if undefined lines
2627    for iview=1:nbview
2628        ListMask{iview,1}=num2str(iview);
2629        RootPath=InputTable{iview,1};
2630        if ~isempty(RootPath)
2631            if isempty(MaskData{iview})
2632                SubDir=InputTable{iview,2};
2633                MaskPath=fullfile(RootPath,[regexprep(SubDir,'\..*','') '.mask']);%take the root part of SubDir, before the first dot '.'
2634                if exist(MaskPath,'dir')
2635                    ListStruct=dir(MaskPath);%look for a mask file
2636                    ListCells=struct2cell(ListStruct);% transform dir struct to a cell arrray
2637                    check_dir=cell2mat(ListCells(4,:));% =1 for directories, =0 for files
2638                    ListFiles=ListCells(1,:);%list of file and dri names
2639                    ListFiles=ListFiles(~check_dir);%list of file names (excluding dir)
2640                    mdetect=0;
2641                    if ~isempty(ListFiles)
2642                        for ifile=1:numel(ListFiles)
2643                            [tild,tild,MaskFile{ifile},i1_series,i2_series,j1_series,j2_series,MaskNomType,MaskFileType]=find_file_series(MaskPath,ListFiles{ifile},0);
2644                            if strcmp(MaskFileType,'image') && isempty(i2_series) && isempty(j2_series)
2645                                mdetect=1;
2646                                MaskName=ListFiles{ifile};
2647                            end
2648                            if ~strcmp(MaskFile{ifile},MaskFile{1})
2649                                mdetect=0;% cancel detection test in case of multiple masks, use the brower for selection
2650                                break
2651                            end
2652                        end
2653                    end
2654                    if mdetect==1
2655                        MaskName=fullfile(MaskPath,'mask_1.png');
2656                    else
2657                        MaskName=uigetfile_uvmat('select a mask file:',MaskPath,'image');
2658                    end
2659                else
2660                    MaskName=uigetfile_uvmat('select a mask file:',RootPath,'image');
2661                end
2662                MaskTable{iview,1}=MaskName ;
2663                ListMask{iview,1}=num2str(iview);
2664            end
2665        end
2666    end
2667    set(handles.MaskTable,'Data',MaskTable)
2668    set(handles.MaskTable,'Visible','on')
2669    set(handles.MaskBrowse,'Visible','on')
2670    set(handles.ListMask,'Visible','on')
2671    set(handles.ListMask,'String',ListMask)
2672    set(handles.ListMask,'Value',1)
2673else
2674    set(handles.MaskTable,'Visible','off')
2675    set(handles.MaskBrowse,'Visible','off')
2676    set(handles.ListMask,'Visible','off')
2677end
2678
2679%------------------------------------------------------------------------
2680% --- Executes on button press in MaskBrowse.
2681%------------------------------------------------------------------------
2682function MaskBrowse_Callback(hObject, eventdata, handles)
2683
2684InputTable=get(handles.InputTable,'Data');
2685iview=get(handles.ListMask,'Value');
2686RootPath=InputTable{iview,1};
2687MaskName=uigetfile_uvmat('select a mask file:',RootPath,'image');
2688if ~isempty(MaskName)
2689    MaskTable=get(handles.MaskTable,'Data');
2690    MaskTable{iview,1}=MaskName ;
2691    set(handles.MaskTable,'Data',MaskTable)
2692end
2693
2694%------------------------------------------------------------------------
2695% --- Executes when selected cell(s) is changed in MaskTable.
2696%------------------------------------------------------------------------
2697function MaskTable_CellSelectionCallback(hObject, eventdata, handles)
2698
2699if numel(eventdata.Indices)>=1
2700set(handles.ListMask,'Value',eventdata.Indices(1))
2701end
2702
2703%-------------------------------------------------------------------
2704function MenuHelp_Callback(hObject, eventdata, handles)
2705%-------------------------------------------------------------------
2706
2707
2708% path_to_uvmat=which ('uvmat');% check the path of uvmat
2709% pathelp=fileparts(path_to_uvmat);
2710% helpfile=fullfile(pathelp,'uvmat_doc','uvmat_doc.html');
2711% 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')
2712% else
2713%     addpath (fullfile(pathelp,'uvmat_doc'))
2714%     web([helpfile '#series'])
2715% end
2716
2717%-------------------------------------------------------------------
2718% --- Executes on selection change in TransformName.
2719function TransformName_Callback(hObject, eventdata, handles)
2720%----------------------------------------------------------------------
2721TransformList=get(handles.TransformName,'String');
2722TransformIndex=get(handles.TransformName,'Value');
2723TransformName=TransformList{TransformIndex};
2724TransformPathList=get(handles.TransformName,'UserData');
2725nb_builtin_transform=4;
2726if isequal(TransformName,'more...');     
2727    FileName=uigetfile_uvmat('Pick a transform function',get(handles.TransformPath,'String'),'.m');
2728    if isempty(FileName)
2729        return     %browser closed without choice
2730    end
2731    [TransformPath,TransformName,TransformExt]=fileparts(FileName);% removes extension .m
2732    if ~strcmp(TransformExt,'.m')
2733        msgbox_uvmat('ERROR','a Matlab function .m must be introduced');
2734        return
2735    end
2736     % insert the choice in the menu
2737    TransformIndex=find(strcmp(TransformName,TransformList),1);% look for the selected function in the menu Action
2738    if isempty(TransformIndex)%the input string does not exist in the menu
2739        TransformIndex= length(TransformList);
2740        TransformList=[TransformList(1:end-1);{TransformName};TransformList(end)];% the selected function is appended in the menu, before the last item 'more...'
2741        set(handles.TransformName,'String',TransformList)
2742        TransformPathList=[TransformPathList;{TransformPath}];
2743    else% the input function already exist, we update its path (possibly new)
2744        TransformPathList{TransformIndex}=TransformPath;%
2745        set(handles.TransformName,'Value',TransformIndex)
2746    end
2747   % save the new menu in the personal file 'uvmat_perso.mat'
2748   dir_perso=prefdir;%personal Matalb directory
2749   profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
2750   if exist(profil_perso,'file')
2751       for ilist=nb_builtin_transform+1:numel(TransformPathList)
2752           TransformListUser{ilist-nb_builtin_transform}=TransformList{ilist};
2753           TransformPathListUser{ilist-nb_builtin_transform}=TransformPathList{ilist};
2754       end
2755       TransformPathListUser=TransformPathListUser';
2756       TransformListUser=TransformListUser';
2757       save (profil_perso,'TransformPathListUser','TransformListUser','-append'); %store the root name for future opening of uvmat
2758   end
2759end
2760
2761%display the current function path
2762set(handles.TransformPath,'String',TransformPathList{TransformIndex}); %show the path to the senlected function
2763set(handles.TransformName,'UserData',TransformPathList);
2764
2765%------------------------------------------------------------------------
2766% --- fct activated by the upper bar menu ExportConfig
2767%------------------------------------------------------------------------
2768function MenuDisplayConfig_Callback(hObject, eventdata, handles)
2769
2770global Param
2771Param=read_GUI_series(handles);
2772evalin('base','global Param')%make CurData global in the workspace
2773display('current series config :')
2774evalin('base','Param') %display CurData in the workspace
2775commandwindow; %brings the Matlab command window to the front
2776
2777%------------------------------------------------------------------------
2778% --- fct activated by the upper bar menu InportConfig: import
2779%     menu settings from an xml file (stored in /0_XML for each run)
2780%------------------------------------------------------------------------
2781function MenuImportConfig_Callback(hObject, eventdata, handles)
2782
2783%% use a starting file name for browserr
2784InputTable=get(handles.InputTable,'Data');
2785oldfile=InputTable{1,1};
2786if isempty(oldfile)
2787    % use a file name stored in prefdir
2788    dir_perso=prefdir;
2789    profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
2790    if exist(profil_perso,'file')
2791        h=load (profil_perso);
2792        if isfield(h,'RootPath') && ischar(h.RootPath)
2793            oldfile=h.RootPath;
2794        end
2795    end
2796end
2797filexml=uigetfile_uvmat('pick a xml parameter file',oldfile,'.xml');% get the xml file containing processing parameters
2798%proceed only if a file has been introduced by the browser
2799if ~isempty(filexml)
2800    Param=xml2struct(filexml);% read the input xml file as a Matlab structure
2801    % ask to stop current Action if button RUN is in action (another process is already running)
2802    if isequal(get(handles.RUN,'Value'),1)
2803        answer= msgbox_uvmat('INPUT_Y-N','stop current Action process?');
2804        if strcmp(answer,'Yes')
2805            STOP_Callback(hObject, eventdata, handles)
2806        else
2807            return
2808        end
2809    end
2810    Param.Action.RUN=0; %desactivate the input RUN=1
2811    fill_GUI(Param,handles.series)% fill the elements of the GUI series with the input parameters
2812    SeriesData=get(handles.series,'UserData');
2813    if isfield(Param,'InputFields')
2814        ListField=Param.InputFields.FieldName;
2815        if ischar(ListField),ListField={ListField}; end
2816        set(handles.FieldName,'String',[ListField;{'get-field...'}])
2817         set(handles.FieldName,'Value',1:numel(ListField))
2818         set(handles.FieldName,'Visible','on')
2819    end       
2820    if isfield(Param,'ActionInput')%  introduce  parameters specific to an Action fct, for instance PIV parameters
2821        set(handles.ActionInput,'Visible','on')
2822        set(handles.ActionInput,'Value',0)
2823        Param.ActionInput.ConfigSource=filexml;% record the source of config for future info
2824        SeriesData.ActionInput=Param.ActionInput;
2825    end
2826    if isfield(Param,'ProjObject') %introduce projection object if relevant
2827        SeriesData.ProjObject=Param.ProjObject;
2828    end
2829    set(handles.series,'UserData',SeriesData)
2830    if isfield(Param,'CheckObject') && isequal(Param.CheckObject,1)
2831        set(handles.ProjObject,'String',Param.ProjObject.Name)
2832        set(handles.ViewObject,'Visible','on')
2833        set(handles.EditObject,'Visible','on')
2834        set(handles.DeleteObject,'Visible','on')
2835    else     
2836        set(handles.ProjObject,'String','')
2837        set(handles.ProjObject,'Visible','off')
2838        set(handles.ViewObject,'Visible','off')
2839        set(handles.EditObject,'Visible','off')
2840        set(handles.DeleteObject,'Visible','off')     
2841    end     
2842    set(handles.REFRESH,'BackgroundColor',[1 0 1]); %paint REFRESH button in magenta to indicate that it should be activated
2843end
2844
2845
2846
2847% --------------------------------------------------------------------
2848% function MenuImportParam_Callback(hObject, eventdata, handles)
2849% %% use a starting file name for browserr
2850% InputTable=get(handles.InputTable,'Data');
2851% oldfile=InputTable{1,1};
2852% if isempty(oldfile)
2853%     % use a file name stored in prefdir
2854%     dir_perso=prefdir;
2855%     profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
2856%     if exist(profil_perso,'file')
2857%         h=load (profil_perso);
2858%         if isfield(h,'RootPath') && ischar(h.RootPath)
2859%             oldfile=h.RootPath;
2860%         end
2861%     end
2862% end
2863% filexml=uigetfile_uvmat('pick a xml parameter file',oldfile,'.xml');% get the xml file containing processing parameters
2864% %proceed only if a file has been introduced by the browser
2865% if ~isempty(filexml)
2866%     Param=xml2struct(filexml);% read the input xml file as a Matlab structure
2867%     % ask to stop current Action if button RUN is in action (another process is already running)
2868%     if isequal(get(handles.RUN,'Value'),1)
2869%         answer= msgbox_uvmat('INPUT_Y-N','stop current Action process?');
2870%         if strcmp(answer,'Yes')
2871%             STOP_Callback(hObject, eventdata, handles)
2872%         else
2873%             return
2874%         end
2875%     end
2876%     Param.Action.RUN=0; %desactivate the input RUN=1
2877%     if ~isfield(Param,'InputTable')||~isfield(Param,'IndexRange')
2878%         msgbox_uvmat('ERROR','invalid config file: open a file in a folder ''/0_XML''')
2879%         return
2880%     end
2881%     Param=rmfield(Param,'InputTable');% do not refresh Input files and index range
2882%     Param=rmfield(Param,'IndexRange'); 
2883%     fill_GUI(Param,handles.series)% fill the elements of the GUI series with the input parameters
2884%     SeriesData=get(handles.series,'UserData');
2885%     if isfield(Param,'InputFields')
2886%         ListField=Param.InputFields.FieldName;
2887%         set(handles.FieldName,'String',[ListField;{'get-field...'}])
2888%          set(handles.FieldName,'Value',1:numel(ListField))
2889%     end       
2890%     if isfield(Param,'ActionInput')%  introduce  parameters specific to an Action fct, for instance PIV parameters
2891%         set(handles.ActionInput,'Visible','on')
2892%         set(handles.ActionInput,'Value',0)
2893%         Param.ActionInput.ConfigSource=filexml;% record the source of config for future info
2894%         SeriesData.ActionInput=Param.ActionInput;
2895%     end
2896%     if isfield(Param,'ProjObject') %introduce projection object if relevant
2897%         SeriesData.ProjObject=Param.ProjObject;
2898%     end
2899%     set(handles.series,'UserData',SeriesData)
2900%     if isfield(Param,'CheckObject') && isequal(Param.CheckObject,1)
2901%         set(handles.ProjObject,'String',Param.ProjObject.Name)
2902%         set(handles.ViewObject,'Visible','on')
2903%         set(handles.EditObject,'Visible','on')
2904%         set(handles.DeleteObject,'Visible','on')
2905%     else     
2906%         set(handles.ProjObject,'String','')
2907%         set(handles.ProjObject,'Visible','off')
2908%         set(handles.ViewObject,'Visible','off')
2909%         set(handles.EditObject,'Visible','off')
2910%         set(handles.DeleteObject,'Visible','off')     
2911%     end     
2912%     set(handles.REFRESH,'BackgroundColor',[1 0 1]); %paint REFRESH button in magenta to indicate that it should be activated
2913% end
2914
2915
2916
2917%------------------------------------------------------------------------
2918% --- Executes when the GUI series is resized.
2919%------------------------------------------------------------------------
2920function series_ResizeFcn(hObject, eventdata, handles)
2921
2922%% input table
2923set(handles.InputTable,'Unit','pixel')
2924Pos=get(handles.InputTable,'Position');
2925set(handles.InputTable,'Unit','normalized')
2926ColumnWidth=round([0.5 0.14 0.14 0.14 0.08]*(Pos(3)-52));
2927ColumnWidth=num2cell(ColumnWidth);
2928set(handles.InputTable,'ColumnWidth',ColumnWidth)
2929
2930%% MinIndex_j and MaxIndex_i
2931unit=get(handles.MinIndex_i,'Unit');
2932set(handles.MinIndex_i,'Unit','pixel')
2933Pos=get(handles.MinIndex_i,'Position');
2934set(handles.MinIndex_i,'Unit',unit)
2935set(handles.MinIndex_i,'ColumnWidth',{Pos(3)-18})
2936set(handles.MaxIndex_i,'ColumnWidth',{Pos(3)-18})
2937set(handles.MinIndex_j,'ColumnWidth',{Pos(3)-18})
2938set(handles.MaxIndex_j,'ColumnWidth',{Pos(3)-18})
2939
2940%% TimeTable
2941set(handles.TimeTable,'Unit','pixel')
2942Pos=get(handles.TimeTable,'Position');
2943set(handles.TimeTable,'Unit','normalized')
2944% ColumnWidth=get(handles.TimeTable,'ColumnWidth');
2945ColumnWidth=num2cell(floor([0.2 0.2 0.2 0.2 0.2]*(Pos(3)-20)));
2946set(handles.TimeTable,'ColumnWidth',ColumnWidth)
2947
2948
2949%% PairString
2950set(handles.PairString,'Unit','pixel')
2951Pos=get(handles.PairString,'Position');
2952set(handles.PairString,'Unit','normalized')
2953set(handles.PairString,'ColumnWidth',{Pos(3)-5})
2954
2955%% MaskTable
2956set(handles.MaskTable,'Unit','pixel')
2957Pos=get(handles.MaskTable,'Position');
2958set(handles.MaskTable,'Unit','normalized')
2959set(handles.MaskTable,'ColumnWidth',{Pos(3)-5})
2960
2961%------------------------------------------------------------------------
2962% --- Executes on button press in status.
2963%------------------------------------------------------------------------
2964function status_Callback(hObject, eventdata, handles)
2965
2966if get(handles.status,'Value')
2967    set(handles.status,'BackgroundColor',[1 1 0])
2968    drawnow
2969    Param=read_GUI(handles.series);
2970    RootPath=Param.InputTable{1,1};
2971    if ~isfield(Param,'OutputSubDir')   
2972        msgbox_uvmat('ERROR','no standard sub-directory definition for output files, use a browser to check the output')
2973        return
2974    end
2975    OutputSubDir=[Param.OutputSubDir Param.OutputDirExt];% subdirectory for output files
2976    OutputDir=fullfile(RootPath,OutputSubDir);
2977    if exist(OutputDir,'dir')
2978        uigetfile_uvmat('status_display',OutputDir)
2979    else
2980        msgbox_uvmat('ERROR','output folder not created yet: calculation did not start')
2981        set(handles.status,'BackgroundColor',[0 1 0])
2982    end
2983else
2984    %% delete current display fig if selection is off
2985    set(handles.status,'BackgroundColor',[0 1 0])
2986    hfig=findobj(allchild(0),'name','status_display');
2987    if ~isempty(hfig)
2988        delete(hfig)
2989    end
2990    return
2991end
2992
2993
2994%------------------------------------------------------------------------   
2995% launched by selecting a file on the list
2996%------------------------------------------------------------------------
2997function view_file(hObject, eventdata)
2998
2999list=get(hObject,'String');
3000index=get(hObject,'Value');
3001rootroot=get(hObject,'UserData');
3002selectname=list{index};
3003ind_dot=regexp(selectname,'\.\.\.');
3004if ~isempty(ind_dot)
3005    selectname=selectname(1:ind_dot-1);
3006end
3007FullSelectName=fullfile(rootroot,selectname);
3008if exist(FullSelectName,'dir')% a directory has been selected
3009    ListFiles=dir(FullSelectName);
3010    ListDisplay=cell(numel(ListFiles),1);
3011    for ilist=2:numel(ListDisplay)% suppress the first line '.'
3012        ListDisplay{ilist-1}=ListFiles(ilist).name;
3013    end
3014    set(hObject,'Value',1)
3015    set(hObject,'String',ListDisplay)
3016    if strcmp(selectname,'..')
3017        FullSelectName=fileparts(fileparts(FullSelectName));
3018    end
3019    set(hObject,'UserData',FullSelectName)
3020    hfig=get(hObject,'parent');
3021    htitlebox=findobj(hfig,'tag','titlebox');   
3022    set(htitlebox,'String',FullSelectName)
3023elseif exist(FullSelectName,'file')%visualise the vel field if it exists
3024    FileInfo=get_file_info(FullSelectName);   
3025    if strcmp(FileInfo.FileType,'txt')
3026        edit(FullSelectName)
3027    elseif strcmp(FileInfo.FileType,'xml')
3028        editxml(FullSelectName)
3029    else
3030        uvmat(FullSelectName)
3031    end
3032    set(gcbo,'Value',1)
3033end
3034
3035
3036%------------------------------------------------------------------------   
3037% launched by refreshing the status figure
3038%------------------------------------------------------------------------
3039function refresh_GUI(hfig)
3040
3041htitlebox=findobj(hfig,'tag','titlebox');
3042hlist=findobj(hfig,'tag','list');
3043hseries=findobj(allchild(0),'tag','series');
3044hstatus=findobj(hseries,'tag','status');
3045StatusData=get(hstatus,'UserData');
3046OutputDir=get(htitlebox,'String');
3047if ischar(OutputDir),OutputDir={OutputDir};end
3048ListFiles=dir(OutputDir{1});
3049if numel(ListFiles)<1
3050    return
3051end
3052ListFiles(1)=[];%removes the first line ='.'
3053ListDisplay=cell(numel(ListFiles),1);
3054testrecent=0;
3055datnum=zeros(numel(ListDisplay),1);
3056for ilist=1:numel(ListDisplay)
3057    ListDisplay{ilist}=ListFiles(ilist).name;
3058      if ~ListFiles(ilist).isdir && isfield(ListFiles(ilist),'datenum')
3059            datnum(ilist)=ListFiles(ilist).datenum;%only available in recent matlab versions
3060            testrecent=1;
3061       end
3062end
3063set(hlist,'String',ListDisplay)
3064
3065%% Look at date of creation
3066ListDisplay=ListDisplay(datnum~=0);
3067datnum=datnum(datnum~=0);%keep the non zero values corresponding to existing files
3068NbOutputFile=[];
3069if isempty(datnum)
3070    if testrecent
3071        message='no civ result created yet';
3072    else
3073        message='';
3074    end
3075else
3076    [first,indfirst]=min(datnum);
3077    [last,indlast]=max(datnum);
3078    NbOutputFile_str='?';
3079    NbOutputFile=[];
3080    if isfield(StatusData,'NbOutputFile')
3081        NbOutputFile=StatusData.NbOutputFile;
3082        NbOutputFile_str=num2str(NbOutputFile);
3083    end
3084    message={[num2str(numel(datnum)) ' file(s) done over ' NbOutputFile_str] ;['oldest modification:  ' ListDisplay{indfirst} ' : ' datestr(first)];...
3085        ['latest modification:  ' ListDisplay{indlast} ' : ' datestr(last)]};
3086end
3087set(htitlebox,'String', [OutputDir{1};message])
3088
3089%% update the waitbar
3090hwaitbar=findobj(hfig,'tag','waitbar');
3091if ~isempty(NbOutputFile)
3092    BarPosition=get(hwaitbar,'Position');
3093    BarPosition(3)=0.9*numel(datnum)/NbOutputFile;
3094    set(hwaitbar,'Position',BarPosition)
3095end
3096
3097%------------------------------------------------------------------------
3098% --- Executes on selection change in ActionExt.
3099%------------------------------------------------------------------------
3100function ActionExt_Callback(hObject, eventdata, handles)
3101
3102ActionExtList=get(handles.ActionExt,'String');
3103ActionExt=ActionExtList{get(handles.ActionExt,'Value')};
3104ActionList=get(handles.ActionName,'String');
3105ActionName=ActionList{get(handles.ActionName,'Value')};
3106% TransformPath='';
3107% if ~isempty(get(handles.ActionExt,'UserData'))
3108%     TransformPath=get(handles.ActionExt,'UserData');
3109% end
3110% if strcmp(ActionExt,'.sh')
3111%     set(handles.series,'Pointer','watch') % set the mouse pointer to 'watch'
3112%     set(handles.ActionExt,'BackgroundColor',[1 1 0])
3113%     ActionFullName=fullfile(get(handles.ActionPath,'String'),[ActionName '.sh']);
3114%     if ~exist(ActionFullName,'file')
3115%         answer=msgbox_uvmat('INPUT_Y-N','compiled version has not been created: compile now?');
3116%         if strcmp(answer,'Yes')
3117%             set(handles.ActionExt,'BackgroundColor',[1 1 0])
3118%             path_uvmat=fileparts(which('series'));
3119%             currentdir=pwd;
3120%             cd(get(handles.ActionPath,'String'))% go to the directory of Action
3121%             %  addpath(get(handles.TransformPath,'String'))
3122%             addpath(path_uvmat)% add the path to uvmat to run the fct 'compile'
3123%            % addpath(fullfile(path_uvmat,'transform_field'))% add the path to uvmat to run the fct 'compile'
3124%             compile(ActionName,TransformPath)
3125%             cd(currentdir)
3126%         end       
3127%     else
3128%         sh_file_info=dir(fullfile(get(handles.ActionPath,'String'),[ActionName '.sh']));
3129%         m_file_info=dir(fullfile(get(handles.ActionPath,'String'),[ActionName '.m']));
3130%         if isfield(m_file_info,'datenum') && m_file_info.datenum>sh_file_info.datenum
3131%             set(handles.ActionExt,'BackgroundColor',[1 1 0])
3132%             drawnow
3133%             answer=msgbox_uvmat('INPUT_Y-N',[ActionName '.sh needs to be updated: recompile now?']);
3134%             if strcmp(answer,'Yes')
3135%                 path_uvmat=fileparts(which('series'));
3136%                 currentdir=pwd;
3137%                 cd(get(handles.ActionPath,'String'))% go to the directory of Action
3138%                 %  addpath(get(handles.TransformPath,'String'))
3139%                 addpath(path_uvmat)% add the path to uvmat to run the fct 'compile'
3140%                 addpath(fullfile(path_uvmat,'transform_field'))% add the path to uvmat to run the fct 'compile'
3141%                 compile(ActionName,TransformPath)
3142%                 cd(currentdir)
3143%             end
3144%         end
3145%     end
3146%     set(handles.ActionExt,'BackgroundColor',[1 1 1])
3147%      set(handles.series,'Pointer','arrow') % set the mouse pointer to 'watch
3148% end
3149
3150
3151function num_NbProcess_Callback(hObject, eventdata, handles)
3152
3153
3154function num_NbSlice_Callback(hObject, eventdata, handles)
3155NbSlice=str2num(get(handles.num_NbSlice,'String'));
3156set(handles.num_NbProcess,'String',num2str(NbSlice))
3157
3158%------------------------------------------------------------------------
3159% --- set the visibility of relevant velocity type menus:
3160function menu=set_veltype_display(Civ,FileType)
3161%------------------------------------------------------------------------
3162if ~exist('FileType','var')
3163    FileType='civx';
3164end
3165switch FileType
3166    case 'civx'
3167        menu={'civ1';'interp1';'filter1';'civ2';'interp2';'filter2'};
3168        if isequal(Civ,0)
3169            imax=0;
3170        elseif isequal(Civ,1) || isequal(Civ,2)
3171            imax=1;
3172        elseif isequal(Civ,3)
3173            imax=3;
3174        elseif isequal(Civ,4) || isequal(Civ,5)
3175            imax=4;
3176        elseif isequal(Civ,6) %patch2
3177            imax=6;
3178        end
3179    case 'civdata'
3180        menu={'civ1';'filter1';'civ2';'filter2'};
3181        if isequal(Civ,0)
3182            imax=0;
3183        elseif isequal(Civ,1) || isequal(Civ,2)
3184            imax=1;
3185        elseif isequal(Civ,3)
3186            imax=2;
3187        elseif isequal(Civ,4) || isequal(Civ,5)
3188            imax=3;
3189        elseif isequal(Civ,6) %patch2
3190            imax=4;
3191        end
3192end
3193menu=menu(1:imax);
3194
3195
3196% --- Executes on mouse motion over figure - except title and menu.
3197function series_WindowButtonMotionFcn(hObject, eventdata, handles)
3198set(hObject,'Pointer','arrow');
3199
3200
3201% --- Executes on button press in SetPairs.
3202function SetPairs_Callback(hObject, iview, handles)
3203
3204%% delete previous occurrence of 'set_pairs'
3205hfig=findobj(allchild(0),'Tag','set_pairs');
3206if ~isempty(hfig)
3207delete(hfig)
3208end
3209
3210%% create the GUI set_pairs
3211set(0,'Unit','points')
3212ScreenSize=get(0,'ScreenSize');% get the size of the screen, to put the fig on the upper right
3213Width=220;% fig width in points (1/72 inch)
3214Height=min(0.8*ScreenSize(4),300);
3215Left=ScreenSize(3)- Width-40; %right edge close to the right, with margin=40
3216Bottom=ScreenSize(4)-Height-40; %put fig at top right
3217hfig=findobj(allchild(0),'Tag','set_slice');
3218if ~isempty(hfig),delete(hfig), end; %delete existing version of the GUI
3219hfig=figure('name','set_pairs','tag','set_pairs','MenuBar','none','NumberTitle','off','Unit','points','Position',[Left,Bottom,Width,Height]);
3220BackgroundColor=get(hfig,'Color');
3221SeriesData=get(handles.series,'UserData');
3222TimeUnit=get(handles.TimeUnit,'String');
3223PairString=get(handles.PairString,'Data');
3224ListViewLines=find(cellfun('isempty',PairString)==0);%find list of non empty pairs
3225ListViewMenu=cell(numel(ListViewLines),1);
3226for ilist=1:numel(ListViewLines)
3227    ListViewMenu{ilist}=num2str(ListViewLines(ilist));
3228end
3229if isempty(iview)
3230    ListViewValue=numel(ListViewLines);% we work by default on the pair option for the last line which requires pairs
3231    iview=ListViewLines(end);
3232else
3233    ListViewValue=find(ListViewLines==iview);
3234end
3235ref_i=str2num(get(handles.num_first_i,'String'));
3236ref_j=str2num(get(handles.num_first_j,'String'));
3237[ModeMenu,ModeValue]=update_mode(SeriesData.i1_series{iview},SeriesData.i2_series{iview},SeriesData.j2_series{iview});
3238displ_pair=update_listpair(SeriesData.i1_series{iview},SeriesData.i2_series{iview},SeriesData.j1_series{iview},SeriesData.j2_series{iview},ModeMenu{ModeValue},...
3239                                                     SeriesData.Time{iview},TimeUnit,ref_i,ref_j,SeriesData.FileInfo{iview});
3240% first raw of the GUI
3241uicontrol('Style','text','Units','normalized', 'Position', [0.05 0.88 0.5 0.1],'BackgroundColor',BackgroundColor,...
3242    'String','row to edit #','FontUnits','points','FontSize',12,'FontWeight','bold','ForegroundColor','blue','HorizontalAlignment','right');%title
3243uicontrol('Style','popupmenu','Units','normalized', 'Position', [0.54 0.8 0.3 0.2],'BackgroundColor',[1 1 1],...
3244    'Callback',@(hObject,eventdata)ListView_Callback(hObject,eventdata),'String',ListViewMenu,'Value',ListViewValue,'FontUnits','points','FontSize',12,'FontWeight','bold',...
3245    'Tag','ListView','TooltipString','''ListView'':choice of the file series w for pair display');
3246% second raw of the GUI
3247uicontrol('Style','text','Units','normalized', 'Position', [0.05 0.79 0.7 0.1],'BackgroundColor',BackgroundColor,...
3248    'String','mode of index pairing:','FontUnits','points','FontSize',12,'FontWeight','bold','ForegroundColor','blue','HorizontalAlignment','left');%title
3249uicontrol('Style','popupmenu','Units','normalized', 'Position', [0.05 0.62 0.9 0.2],'BackgroundColor',[1 1 1],...
3250    'Callback',@(hObject,eventdata)Mode_Callback(hObject,eventdata),'String',ModeMenu,'Value',ModeValue,'FontUnits','points','FontSize',12,'FontWeight','bold',...
3251    'Tag','Mode','TooltipString','''Mode'': choice of the image pair mode');
3252% third raw
3253uicontrol('Style','text','Units','normalized', 'Position', [0.05 0.6 0.7 0.1],'BackgroundColor',BackgroundColor,...
3254    'String','pair choice:','FontUnits','points','FontSize',12,'FontWeight','bold','ForegroundColor','blue','HorizontalAlignment','left');%title
3255uicontrol('Style','listbox','Units','normalized', 'Position', [0.05 0.42 0.9 0.2],'BackgroundColor',[1 1 1],...
3256    'Callback',@(hObject,eventdata)ListPair_Callback(hObject,eventdata),'String',displ_pair,'Value',1,'FontUnits','points','FontSize',12,'FontWeight','bold',...
3257    'Tag','ListPair','TooltipString','''ListPair'': menu for selecting the image pair');
3258uicontrol('Style','text','Units','normalized', 'Position', [0.1 0.22 0.8 0.1],'BackgroundColor',BackgroundColor,...
3259    'String','ref_i           ref_j','FontUnits','points','FontSize',12,'FontWeight','bold','ForegroundColor','blue','HorizontalAlignment','center');%title
3260uicontrol('Style','edit','Units','normalized', 'Position', [0.15 0.17 0.3 0.08],'BackgroundColor',[1 1 1],...
3261    'Callback',@(hObject,eventdata)num_ref_i_Callback(hObject,eventdata),'String',num2str(ref_i),'FontUnits','points','FontSize',12,'FontWeight','bold',...
3262    'Tag','num_ref_i','TooltipString','''num_ref_i'': reference field index i used to display dt in ''list_pair_civ''');
3263uicontrol('Style','edit','Units','normalized', 'Position', [0.55 0.17 0.3 0.08],'BackgroundColor',[1 1 1],...
3264    'Callback',@(hObject,eventdata)num_ref_j_Callback(hObject,eventdata),'String',num2str(ref_j),'FontUnits','points','FontSize',12,'FontWeight','bold',...
3265    'Tag','num_ref_j','TooltipString','''num_ref_j'': reference field index i used to display dt in ''list_pair_civ''');
3266%  last raw  of the GUI: pushbuttons
3267% 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),...
3268%     'FontWeight','bold','FontUnits','points','FontSize',12,'TooltipString','''OK'': apply the output to the current field series in uvmat');
3269drawnow
3270
3271%------------------------------------------------------------------------
3272function ListView_Callback(hObject,eventdata)
3273Mode_Callback(hObject,eventdata)
3274
3275%------------------------------------------------------------------------   
3276function Mode_Callback(hObject,eventdata)
3277%% get input info
3278hseries=findobj(allchild(0),'tag','series');%handles of the GUI series
3279hhseries=guidata(hseries);%handles of the elements in the GUI series
3280TimeUnit=get(hhseries.TimeUnit,'String');
3281SeriesData=get(hseries,'UserData');
3282mode_list=get(hObject,'String');
3283mode=mode_list{get(hObject,'Value')};
3284hListView=findobj(get(hObject,'parent'),'Tag','ListView');
3285iview=get(hListView,'Value');
3286i1_series=SeriesData.i1_series{iview};
3287i2_series=SeriesData.i2_series{iview};
3288j1_series=SeriesData.j1_series{iview};
3289j2_series=SeriesData.j2_series{iview};
3290
3291%% enable j index visibility after the new choice
3292status_j='on';%default
3293if isempty(find(~cellfun(@isempty,SeriesData.j1_series), 1)); % case of empty j indices
3294    status_j='off'; % no j index needed
3295elseif strcmp(get(handles.PairString,'Visible'),'on')
3296    check_burst=cellfun(@isempty,regexp(PairString,'^j'));%=0 for burst case, 1 otherwise
3297    if isempty(find(check_burst, 1))% if all pair string begins by j (burst)
3298        status_j='off'; % no j index needed for bust case
3299    end
3300end
3301enable_j(handles,status_j) % no j index needed
3302
3303%% get the reference indices for the time interval Dt
3304href_i=findobj(get(hObject,'parent'),'Tag','ref_i');
3305ref_i=[];ref_j=[];
3306if strcmp(get(href_i,'Visible'),'on')
3307    ref_i=str2num(get(href_i,'String'));
3308end
3309if isempty(ref_i)
3310    ref_i=1;
3311end
3312if isempty(ref_j)
3313    ref_j=1;
3314end
3315
3316%% update the menu ListPair
3317Menu=update_listpair(i1_series,i2_series,j1_series,j2_series,mode,SeriesData.Time{iview},TimeUnit,ref_i,ref_j,FileInfo);
3318hlist_pairs=findobj(get(hObject,'parent'),'Tag','ListPair');
3319set(hlist_pairs,'Value',1)% set the first choice by default in ListPair
3320set(hlist_pairs,'String',Menu)% set the menu in ListPair
3321ListPair_Callback(hlist_pairs,[])% apply the default choice in ListPair
3322
3323%-------------------------------------------------------------
3324% --- Executes on selection in ListPair.
3325function ListPair_Callback(hObject,eventdata)
3326%------------------------------------------------------------
3327list_pair=get(hObject,'String');%get the menu of image pairs
3328if isempty(list_pair)
3329    string='';
3330else
3331    string=list_pair{get(hObject,'Value')};
3332   % string=regexprep(string,',.*','');%removes time indication (after ',')
3333end
3334hseries=findobj(allchild(0),'tag','series');
3335hPairString=findobj(hseries,'tag','PairString');
3336PairString=get(hPairString,'Data');
3337hListView=findobj(get(hObject,'parent'),'Tag','ListView');
3338iview=get(hListView,'Value');
3339PairString{iview,1}=string;
3340% report the selected pair string to the table PairString
3341set(hPairString,'Data',PairString)
3342
3343
3344%------------------------------------------------------------------------
3345function num_ref_i_Callback(hObject, eventdata)
3346%------------------------------------------------------------------------
3347Mode_Callback([],[])
3348
3349%------------------------------------------------------------------------
3350function num_ref_j_Callback(hObject, eventdata)
3351%------------------------------------------------------------------------
3352Mode_Callback([],[])
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