source: trunk/src/series.m @ 782

Last change on this file since 782 was 781, checked in by sommeria, 11 years ago
File size: 143.7 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 Joel Sommeria, 2008, LEGI / CNRS-UJF-INPG, sommeria@coriolis-legi.org.
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, TODO: avoid the file checking if Param.i1_series defined
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   
254    %     display_file_name(handles,Param,'one')%refresh the input table
255    update_rootinfo(handles,Param.HiddenData.i1_series{1},Param.HiddenData.i2_series{1},Param.HiddenData.j1_series{1},Param.HiddenData.j2_series{1},...
256        Param.HiddenData.FileInfo{1},Param.HiddenData.MovieObject{1},1)
257    if isfield(Param,'FileName_1')
258
259        %         display_file_name(handles,Param,2)
260        update_rootinfo(handles,Param.HiddenData.i1_series{2},Param.HiddenData.i2_series{2},Param.HiddenData.j1_series{2},Param.HiddenData.j2_series{2},...
261            Param.HiddenData.FileInfo{2},Param.HiddenData.MovieObject{2},2)
262    end
263else
264    set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH button to magenta color to indicate that input refresh is needed
265end
266if isfield(Param,'incr_i')
267    set(handles.num_incr_i,'String',num2str(Param.incr_i))
268end
269if isfield(Param,'incr_j')
270    set(handles.num_incr_j,'String',num2str(Param.incr_j))
271end
272
273%------------------------------------------------------------------------
274% --- Outputs from this function are returned to the command line.
275function varargout = series_OutputFcn(hObject, eventdata, handles)
276%------------------------------------------------------------------------
277varargout{1} = handles.output;
278
279%------------------------------------------------------------------------
280% --- executed when closing uvmat: delete or desactivate the associated figures if exist
281function closefcn(gcbo,eventdata)
282%------------------------------------------------------------------------
283
284% delete set_object_series if detected
285hh=findobj(allchild(0),'name','view_object_series');
286if ~isempty(hh)
287    delete(hh)
288end
289hh=findobj(allchild(0),'name','edit_object_series');
290if ~isempty(hh)
291    delete(hh)
292end
293
294%delete the bowser if detected
295hh=findobj(allchild(0),'tag','browser');
296if ~isempty(hh)
297    delete(hh)
298end
299
300
301%------------------------------------------------------------------------
302%------------------------------------------------------------------------
303%  II - FUNCTIONS FOR INTRODUCING THE INPUT FILES
304% automatically sets the global properties when the rootfile name is introduced
305% then activate the view-field actionname if selected
306% it is activated either by clicking on the RootPath window or by the
307% browser
308%------------------------------------------------------------------------
309%------------------------------------------------------------------------
310% --- fct activated by the browser under 'Open'
311%------------------------------------------------------------------------ 
312function MenuBrowse_Callback(hObject, eventdata, handles)
313%% look for the previously opened file 'oldfile'
314InputTable=get(handles.InputTable,'Data');
315oldfile=InputTable{1,1};
316if isempty(oldfile)
317    % use a file name stored in prefdir
318    dir_perso=prefdir;
319    profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
320    if exist(profil_perso,'file')
321        h=load (profil_perso);
322        if isfield(h,'RootPath') && ischar(h.RootPath)
323            oldfile=h.RootPath;
324        end
325    end
326end
327%% launch the browser
328fileinput=uigetfile_uvmat('pick an input file in the series',oldfile);
329hh=dir(fileinput);
330if numel(hh)>1
331    msgbox_uvmat('ERROR','invalid input, probably a broken link');
332else
333    if ~isempty(fileinput)
334        display_file_name(handles,fileinput,'one')
335    end
336end
337
338% --------------------------------------------------------------------
339function MenuBrowseAppend_Callback(hObject, eventdata, handles)
340
341%% look for the previously opened file 'oldfile'
342InputTable=get(handles.InputTable,'Data');
343RootPathCell=InputTable(:,1);
344if isempty(RootPathCell{1})% no input file in the table
345     MenuBrowse_Callback(hObject, eventdata, handles)%refresh the input table, not append
346     return
347end
348SubDirCell=InputTable(:,2);
349oldfile=fullfile(RootPathCell{1},SubDirCell{1});
350
351%% use a file name stored in prefdir
352dir_perso=prefdir;
353profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
354if exist(profil_perso,'file')
355    h=load (profil_perso);
356    if isfield(h,'RootPath') && ischar(h.RootPath)
357        oldfile=h.RootPath;
358    end
359end
360
361%% launch the browser
362fileinput=uigetfile_uvmat('pick a file to append in the input table',oldfile);
363hh=dir(fileinput);
364if numel(hh)>1
365    msgbox_uvmat('ERROR','invalid input, probably a broken link');
366else
367    if ~isempty(fileinput)
368        display_file_name(handles,fileinput,'append')
369    end
370end
371
372%------------------------------------------------------------------------
373% --- fct activated by selecting a previous file under the menu Open
374%------------------------------------------------------------------------
375function MenuFile_Callback(hObject, eventdata, handles)
376
377errormsg=display_file_name(handles,get(hObject,'Label'),'one');
378if ~isempty(errormsg)
379    set(hObject,'Label','')
380    MenuFile=[{get(handles.MenuFile_1,'Label')};{get(handles.MenuFile_2,'Label')};...
381        {get(handles.MenuFile_3,'Label')};{get(handles.MenuFile_4,'Label')};{get(handles.MenuFile_5,'Label')}];
382    str_find=strcmp(get(hObject,'Label'),MenuFile);
383    MenuFile(str_find)=[];% suppress the input file to the list
384    for ifile=1:numel(MenuFile)
385        set(handles.(['MenuFile_' num2str(ifile)]),'Label',MenuFile{ifile});
386    end
387end
388
389%------------------------------------------------------------------------
390% --- fct activated by selecting a previous file under the menu Open/append
391%------------------------------------------------------------------------
392function MenuFile_append_Callback(hObject, eventdata, handles)
393
394InputTable=get(handles.InputTable,'Data');
395if isempty(InputTable{1,1})% no input file in the table
396    display_file_name(handles,get(hObject,'Label'),'one') %refresh the input table, not append
397else
398    display_file_name(handles,get(hObject,'Label'),'append')% append the selected file to the current list of InputTable
399end
400
401%------------------------------------------------------------------------
402% --- fct activated by the browser under 'Open campaign'
403%------------------------------------------------------------------------
404function MenuBrowseCampaign_Callback(hObject, eventdata, handles)
405
406set(handles.MenuOpenCampaign,'ForegroundColor',[1 1 0])
407drawnow
408InputTable=get(handles.InputTable,'Data');
409RootPath=InputTable{1,1};
410CampaignPath=fileparts(fileparts(RootPath));
411DirFull=uigetfile_uvmat('define this path as the Campaign folder:',CampaignPath,'uigetdir');
412if ~ischar(DirFull)|| ~exist(DirFull,'dir')
413    return
414end
415OutPut=browse_data(DirFull);% open the GUI browse_data to get select a campaign dir, experiment and device
416if ~isfield(OutPut,'Campaign')
417    return
418end
419DirName=fullfile(OutPut.Campaign,OutPut.Experiment{1},OutPut.DataSeries{1});
420ListStruct=dir(DirName); %list files and the dir DataSeries
421% select the first appropriate file in the dir
422FileName='';
423for ilist=1:numel(ListStruct)
424    if ~isequal(ListStruct(ilist).isdir,1)%look for files, not dir
425        FileName=ListStruct(ilist).name;
426        FileType=get_file_type(fullfile(DirName,FileName));
427        switch FileType
428            case {'image','multimage','civx','civdata','netcdf'}
429                break
430        end
431    end
432end
433if isempty(FileName)
434    msgbox_uvmat('ERROR',['no appropriate input file in the DataSeries folder ' fullfile(DirName)])
435    return
436end
437
438%% update the list of campaigns in the menubar
439MenuCampaign=[{get(handles.MenuCampaign_1,'Label')};{get(handles.MenuCampaign_2,'Label')};...
440    {get(handles.MenuCampaign_3,'Label')};{get(handles.MenuCampaign_4,'Label')};{get(handles.MenuCampaign_5,'Label')}];
441check_dir=isempty(find(strcmp(DirFull,MenuCampaign)));
442if check_dir %insert the new campaign in the list if it is not found
443    MenuCampaign(end)=[]; %suppress the last item
444    MenuCampaign=[{DirFull};MenuCampaign];%insert the new campaign
445    for ilist=1:numel(MenuCampaign)
446        set(handles.(['MenuCampaign_' num2str(ilist)]),'Label',MenuCampaign{ilist})
447    end
448    % save the list for future opening:
449    dir_perso=prefdir;
450    profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
451    if exist(profil_perso,'file')
452        save (profil_perso,'MenuCampaign','RootPath','-append'); %store the file names for future opening of uvmat
453    else
454        save (profil_perso,'MenuCampaign','RootPath','-V6'); %store the file names for future opening of uvmat
455    end
456end
457
458%% display the selected field and related information
459if get(handles.CheckAppend,'Value')
460    display_file_name(handles,fullfile(DirName,FileName),'append')
461else
462    display_file_name(handles,fullfile(DirName,FileName),'one')
463end
464set(handles.MenuOpenCampaign,'ForegroundColor',[0 0 0])
465
466% --------------------------------------------------------------------
467function MenuCampaign_Callback(hObject, eventdata, handles)
468% --------------------------------------------------------------------
469set(handles.MenuOpenCampaign,'ForegroundColor',[1 1 0])
470OutPut=browse_data(get(hObject,'Label'));% open the GUI browse_data to get select a campaign dir, experiment and device
471if ~isfield(OutPut,'Campaign')
472    return
473end
474DirName=fullfile(OutPut.Campaign,OutPut.Experiment{1},OutPut.DataSeries{1});
475hdir=dir(DirName); %list files and dirs
476for ilist=1:numel(hdir)
477    if ~isequal(hdir(ilist).isdir,1)%look for files, not dir
478        FileName=hdir(ilist).name;
479        FileType=get_file_type(fullfile(DirName,FileName));
480        switch FileType
481            case {'image','multimage','civx','civdata','netcdf'}
482            break
483        end
484    end
485end
486if get(handles.CheckAppend,'Value')
487    display_file_name(handles,fullfile(DirName,FileName),'append')
488else
489    display_file_name(handles,fullfile(DirName,FileName),'one')
490end
491set(handles.MenuOpenCampaign,'ForegroundColor',[0 0 0])
492
493
494% --- Executes when selected cell(s) is changed in InputTable.
495function InputTable_CellSelectionCallback(hObject, eventdata, handles)
496iline=[];
497if ~isempty(eventdata.Indices)
498    iline=eventdata.Indices(1);
499end
500set(handles.InputTable,'UserData',iline);
501
502%------------------------------------------------------------------------
503% --- 'key_press_fcn:' function activated when a key is pressed on the keyboard
504%------------------------------------------------------------------------
505function InputTable_KeyPressFcn(hObject, eventdata, handles)
506set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH button to magenta color to indicate that input refresh is needed
507xx=double(get(handles.series,'CurrentCharacter')); %get the keyboard character
508switch xx
509    case 31 %downward arrow
510        InputTable=get(handles.InputTable,'Data');
511        iline=get(handles.InputTable,'UserData');
512        if isequal(iline,size(InputTable,1))% arrow downward
513            InputTable=[InputTable;InputTable(iline,:)];% create a new line as a copy of the last one
514            set(handles.InputTable,'Data',InputTable);
515        end
516    case 127  %key 'Suppress'
517         InputTable=get(handles.InputTable,'Data');
518        iline=get(handles.InputTable,'UserData');
519        if iline>1
520            InputTable(iline,:)=[];% suppress the current line if not the first
521            set(handles.InputTable,'Data',InputTable);
522        end
523end
524
525
526%------------------------------------------------------------------------
527% --- Executes on button press in REFRESH.
528function REFRESH_Callback(hObject, eventdata, handles)
529%------------------------------------------------------------------------
530InputTable=get(handles.InputTable,'Data');
531set(handles.series,'Pointer','watch') % set the mouse pointer to 'watch'
532set(handles.REFRESH,'BackgroundColor',[1 1 0])% set REFRESH  button to yellow color (indicate activation)
533drawnow
534empty_line=false(size(InputTable,1),1);
535for iline=1:size(InputTable,1)
536    empty_line(iline)= isempty(cell2mat(InputTable(iline,1:3)));
537end
538if ~isempty(find(empty_line));
539    InputTable(empty_line,:)=[];%remove empty lines
540    set(handles.InputTable,'Data',InputTable)
541    ListTable={'MinIndex_i','MaxIndex_i','MinIndex_j','MaxIndex_j','PairString','TimeTable'};
542    for ilist=1:numel(ListTable)
543        Table=get(handles.(ListTable{ilist}),'Data');
544        Table(empty_line,:)=[];%remove empty lines
545        set(handles.(ListTable{ilist}),'Data',Table);
546    end
547    set(handles.series,'UserData',[])%refresh the stored info
548end
549for iview=1:size(InputTable,1)
550    RootPath=fullfile(InputTable{iview,1},InputTable{iview,2});
551    if ~exist(RootPath,'dir')
552        i1_series=[];
553        RootPath=fileparts(RootPath); %will try the upper folder
554    else %scan the input folder
555        [RootPath,SubDir,RootFile,i1_series,i2_series,j1_series,j2_series,tild,FileType,FileInfo,MovieObject]=...
556            find_file_series(fullfile(InputTable{iview,1},InputTable{iview,2}),[InputTable{iview,3} InputTable{iview,4} InputTable{iview,5}]);
557    end
558    % if no file is found, open a browser
559    if isempty(i1_series)
560        fileinput=uigetfile_uvmat(['wrong input at line ' num2str(iview) ':pick a new input file'],RootPath);
561        if isempty(fileinput)
562            set(handles.REFRESH,'BackgroundColor',[1 0 0])% set REFRESH  back to red color
563            return
564        else
565            display_file_name(handles,fileinput,iview)
566        end
567    else
568       update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileInfo,MovieObject,iview)
569    end
570end
571set(handles.REFRESH,'BackgroundColor',[1 0 0])% set REFRESH  button to red color (indicate activation finished)
572set(handles.series,'Pointer','arrow') % set the mouse pointer to 'watch'
573
574%------------------------------------------------------------------------
575% --- Function called when a new file is opened, either by series_OpeningFcn or by the browser
576function errormsg=display_file_name(handles,Param,iview)
577%------------------------------------------------------------------------ 
578%
579% INPUT:
580% handles: handles of elements in the GUI
581% Param: structure of input parameters, including  input file name and path
582% iview: line index in the input table
583%       or 'one': refresh the list
584%         'append': add a new line to the input table
585set(handles.REFRESH,'BackgroundColor',[1 1 0])% set REFRESH  button to yellow color (indicate activation)
586drawnow
587errormsg='';%default
588if ischar(Param)
589    fileinput=Param;
590else% input set when series is opened (called by the GUI uvmat)
591    fileinput=Param.FileName;
592end
593   
594%% get the input root name, indices, file extension and nomenclature NomType
595if ~exist(fileinput,'file')
596    errormsg=['input file ' fileinput  ' does not exist'];
597    msgbox_uvmat('ERROR',errormsg)
598    set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH  button to magenta color (refresh still needed)
599    return
600end
601
602%% detect root name, nomenclature and indices in the input file name:
603[FilePath,FileName,FileExt]=fileparts(fileinput);
604%%%%%%%%%%%%%%%%%%
605%TODO: case of input by uvmat: do not check agai the input seies %%%%%%%
606%%%%%%%%%%%%%%%%%%%
607% detect the file type, get the movie object if relevant, and look for the corresponding file series:
608% the root name and indices may be corrected by including the first index i1 if a corresponding xml file exists
609[RootPath,SubDir,RootFile,i1_series,i2_series,j1_series,j2_series,NomType,FileType,FileInfo,MovieObject,i1,i2,j1,j2]=find_file_series(FilePath,[FileName FileExt]);
610if isempty(RootFile)&&isempty(i1_series)
611    errormsg='no input file in the series';
612    msgbox_uvmat('ERROR',errormsg)
613    set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH  button to magenta color (end of activation)
614    return
615end
616if strcmp(FileType,'txt')
617    edit(fileinput)
618    set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH  button to  magenta color (end of activation)
619    return
620elseif strcmp(FileType,'xml')
621    editxml(fileinput)
622    set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH  button to magenta  color (end of activation)
623     return
624elseif strcmp(FileType,'figure')
625    open(fileinput)
626    set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH  button to magenta  color (end of activation)
627     return
628end
629
630%% enable other menus and uicontrols
631set(handles.MenuOpenCampaign,'Enable','on')
632set(handles.MenuCampaign_1,'Enable','on')
633set(handles.MenuCampaign_2,'Enable','on')
634set(handles.MenuCampaign_3,'Enable','on')
635set(handles.MenuCampaign_4,'Enable','on')
636set(handles.MenuCampaign_5,'Enable','on')
637set(handles.RUN, 'Enable','On')
638set(handles.RUN,'BackgroundColor',[1 0 0])% set RUN button to red
639set(handles.InputTable,'BackgroundColor',[1 1 0]) % set RootPath edit box  to yellow
640drawnow
641
642
643%% fill the list of file series
644InputTable=get(handles.InputTable,'Data');
645SeriesData=get(handles.series,'UserData');
646if strcmp(iview,'append') % display the input data as a new line in the table
647    iview=size(InputTable,1)+1;% the next line in InputTable becomes the current line
648    InputTable(iview,:)=[{RootPath},{SubDir},{RootFile},{NomType},{FileExt}];
649%     SeriesData.ListViewMenu(iview)=zeros(1,nbview)
650elseif strcmp(iview,'one') % refresh the list of  input  file series
651    iview=1; %the first line in InputTable becomes the current line
652    InputTable={'','','','',''};
653    InputTable(iview,:)=[{RootPath},{SubDir},{RootFile},{NomType},{FileExt}];
654    set(handles.TimeTable,'Data',[{''},{[]},{[]},{[]},{[]}])
655    set(handles.MinIndex_i,'Data',[])
656    set(handles.MaxIndex_i,'Data',[])
657    set(handles.MinIndex_j,'Data',[])
658    set(handles.MaxIndex_j,'Data',[])
659    set(handles.PairString,'Data',{''})
660    SeriesData.CheckPair=0;%reset the list of input lines with pairs
661    SeriesData.i1_series={};
662    SeriesData.i2_series={};
663    SeriesData.j1_series={};
664    SeriesData.j2_series={};
665    SeriesData.FileType={};
666    SeriesData.FileInfo={};
667    SeriesData.Time={};
668end
669set(handles.InputTable,'Data',InputTable)
670
671%% determine the selected reference field indices for pair display
672if isempty(i1)
673    i1=1;
674end
675if isempty(i2)
676    i2=i1;
677end
678ref_i=floor((i1+i2)/2);% reference image number corresponding to the file
679% set(handles.num_ref_i,'String',num2str(ref_i));
680if isempty(j1)
681    j1=1;
682end
683if isempty(j2)
684    j2=j1;
685end
686ref_j=floor((j1+j2)/2);% reference image number corresponding to the file
687SeriesData.ref_i=ref_i;
688SeriesData.ref_j=ref_j;
689
690%% update first and last indices if they do not exist
691Param=read_GUI(handles.series);
692first_j=[];
693if isfield(Param.IndexRange,'first_j'); first_j=Param.IndexRange.first_j; end
694last_j=[];
695if isfield(Param.IndexRange,'last_j'); last_j=Param.IndexRange.last_j; end
696PairString='';
697if isfield(Param.IndexRange,'PairString'); PairString=Param.IndexRange.PairString; end
698[i1,i2,j1,j2] = get_file_index(Param.IndexRange.first_i,first_j,PairString);
699FirstFileName=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},...
700    Param.InputTable{1,5},Param.InputTable{1,4},i1,i2,j1,j2);
701if ~exist(FirstFileName,'file')
702    set(handles.num_first_i,'String',num2str(ref_i))
703    set(handles.num_first_j,'String',num2str(ref_j))
704end
705[i1,i2,j1,j2] = get_file_index(Param.IndexRange.last_i,last_j,PairString);
706LastFileName=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},...
707    Param.InputTable{1,5},Param.InputTable{1,4},i1,i2,j1,j2);
708if ~exist(LastFileName,'file')
709    set(handles.num_last_i,'String',num2str(ref_i))
710    set(handles.num_last_j,'String',num2str(ref_j))
711end
712
713%% update the list of recent files in the menubar and save it for future opening
714MenuFile=[{get(handles.MenuFile_1,'Label')};{get(handles.MenuFile_2,'Label')};...
715    {get(handles.MenuFile_3,'Label')};{get(handles.MenuFile_4,'Label')};{get(handles.MenuFile_5,'Label')}];
716str_find=strcmp(fileinput,MenuFile);
717if isempty(find(str_find,1))
718    MenuFile=[{fileinput};MenuFile];%insert the current file if not already in the list
719end
720for ifile=1:min(length(MenuFile),5)
721    eval(['set(handles.MenuFile_' num2str(ifile) ',''Label'',MenuFile{ifile});'])
722end
723dir_perso=prefdir;
724profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
725if exist(profil_perso,'file')
726    save (profil_perso,'MenuFile','-append'); %store the file names for future opening of uvmat
727else
728    save (profil_perso,'MenuFile','-V6'); %store the file names for future opening of uvmat
729end
730% save the opened file to initiate future opening
731SeriesData.RefFile{iview}=fileinput;% reference opening file for line iview
732SeriesData.Ref_i1=i1;
733SeriesData.Ref_i2=i2;
734SeriesData.Ref_j1=j1;
735SeriesData.Ref_j2=j2;
736set(handles.series,'UserData',SeriesData)
737
738set(handles.InputTable,'BackgroundColor',[1 1 1])
739
740%% initiate input file series and refresh the current field view:     
741update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileInfo,MovieObject,iview);
742set(handles.REFRESH,'BackgroundColor',[1 0 0])% set REFRESH  button to red color (end of activation)
743
744%------------------------------------------------------------------------
745% --- Update information about a new field series (indices to scan, timing,
746%     calibration from an xml file
747function update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileInfo,VideoObject,iview)
748%------------------------------------------------------------------------
749InputTable=get(handles.InputTable,'Data');
750
751%% display the min and max indices for the whole file series
752if size(i1_series,2)==2 && min(min(i1_series(:,1,:)))==0
753    MinIndex_j=1;% index j set to 1 by default
754    MaxIndex_j=1;
755    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)
756    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)
757else
758    ref_i=squeeze(max(i1_series(1,:,:),[],2));% select ref_j index for each ref_i
759    ref_j=squeeze(max(j1_series(1,:,:),[],3));% select ref_i index for each ref_j
760     MinIndex_i=min(find(ref_i))-1;
761     MaxIndex_i=max(find(ref_i))-1;
762     MaxIndex_j=max(find(ref_j))-1;
763     MinIndex_j=min(find(ref_j))-1;
764    diff_j_max=diff(ref_j);
765    diff_i_max=diff(ref_i);
766    if ~isempty(diff_i_max) && isequal (diff_i_max,diff_i_max(1)*ones(size(diff_i_max)))
767        set(handles.num_incr_i,'String',num2str(diff_i_max(1)))% detect an increment to dispaly by default
768    end
769    if ~isempty(diff_j_max) && isequal (diff_j_max,diff_j_max(1)*ones(size(diff_j_max)))
770        set(handles.num_incr_j,'String',num2str(diff_j_max(1)))
771    end
772end
773if isequal(MinIndex_i,-1)
774    MinIndex_i=0;
775end
776if isequal(MinIndex_j,-1)
777    MinIndex_j=0;
778end
779MinIndex_i_table=get(handles.MinIndex_i,'Data');%retrieve the min indices in the table MinIndex
780MinIndex_j_table=get(handles.MinIndex_j,'Data');%retrieve the min indices in the table MinIndex
781MaxIndex_i_table=get(handles.MaxIndex_i,'Data');%retrieve the min indices in the table MinIndex
782MaxIndex_j_table=get(handles.MaxIndex_j,'Data');%retrieve the min indices in the table MinIndex
783if ~isempty(MinIndex_i)&&~isempty(MaxIndex_i)
784    MinIndex_i_table(iview,1)=MinIndex_i;
785    MaxIndex_i_table(iview,1)=MaxIndex_i;
786end
787if ~isempty(MinIndex_j)&&~isempty(MaxIndex_j)
788    MinIndex_j_table(iview,1)=MinIndex_j;
789    MaxIndex_j_table(iview,1)=MaxIndex_j;
790end
791set(handles.MinIndex_i,'Data',MinIndex_i_table)%display the min indices in the table MinIndex
792set(handles.MinIndex_j,'Data',MinIndex_j_table)%display the max indices in the table MaxIndex
793set(handles.MaxIndex_i,'Data',MaxIndex_i_table)%display the min indices in the table MinIndex
794set(handles.MaxIndex_j,'Data',MaxIndex_j_table)%display the max indices in the table MaxIndex
795SeriesData=get(handles.series,'UserData');
796
797%% adjust the first and last indices for the selected series, only if requested by the bounds
798% i index, compare input to min index i
799first_i=str2num(get(handles.num_first_i,'String'));%retrieve previous first i
800% ref_i=str2num(get(handles.num_ref_i,'String'));%index i given by the input field
801ref_i=1;
802if isfield(SeriesData,'ref_i')
803ref_i=SeriesData.ref_i;
804end
805if isempty(first_i)
806    first_i=ref_i;% first_i updated by the input value
807elseif first_i < MinIndex_i
808    first_i=MinIndex_i; % first_i set to the min i index (restricted by oter input lines)
809elseif first_i >MaxIndex_i
810    first_i=MaxIndex_i;% first_i set to the max i index (restricted by oter input lines)
811end
812% j index,  compare input to min index j
813first_j=str2num(get(handles.num_first_j,'String'));
814ref_j=1;
815if isfield(SeriesData,'ref_j')
816ref_j=SeriesData.ref_j;
817end
818if isempty(first_j)
819    first_j=ref_j;% first_j updated by the input value
820elseif first_j<MinIndex_j
821    first_j=MinIndex_j; % first_j set to the min j index (restricted by oter input lines)
822elseif first_j >MaxIndex_j
823    first_j=MaxIndex_j; % first_j set to the max j index (restricted by oter input lines)
824end
825% i index, compare input to max index i
826last_i=str2num(get(handles.num_last_i,'String'));
827if isempty(last_i)
828    last_i=ref_i;
829elseif last_i > MaxIndex_i
830    last_i=MaxIndex_i;
831elseif last_i<first_i
832    last_i=first_i;
833end
834% j index, compare input to max index j
835last_j=str2num(get(handles.num_last_j,'String'));
836if isempty(last_j)
837    last_j=ref_j;
838elseif last_j>MaxIndex_j
839    last_j=MaxIndex_j;
840elseif last_j<first_j
841    last_j=first_j;
842end
843set(handles.num_first_i,'String',num2str(first_i));
844set(handles.num_first_j,'String',num2str(first_j));
845set(handles.num_last_i,'String',num2str(last_i));
846set(handles.num_last_j,'String',num2str(last_j));
847
848%% number of slices set by default
849NbSlice=1;%default
850% read  value set by the first series for the append mode (iwiew >1)
851if iview>1 && strcmp(get(handles.num_NbSlice,'Visible'),'on')
852    NbSlice=str2num(get(handles.num_NbSlice,'String'));
853end
854
855%% default time settings
856TimeUnit='';
857% read  value set by the first series for the append mode (iwiew >1)
858if iview>1
859    TimeUnit=get(handles.TimeUnit,'String');
860end
861TimeName='';
862Time=[];%default
863TimeMin=[];
864TimeFirst=[];
865TimeLast=[];
866TimeMax=[];
867
868%%  read image documentation file if found
869XmlData=[];
870check_calib=0;
871XmlFileName=find_imadoc(InputTable{iview,1},InputTable{iview,2},InputTable{iview,3},InputTable{iview,5});
872if ~isempty(XmlFileName)
873    [XmlData,errormsg]=imadoc2struct(XmlFileName);
874    if ~isempty(errormsg)
875         msgbox_uvmat('WARNING',['error in reading ' XmlFileName ': ' errormsg]);
876    end
877    % read time if available
878    if isfield(XmlData,'Time')
879         Time=XmlData.Time;
880        TimeName='xml';
881    end
882    if isfield(XmlData,'Camera')
883        if isfield(XmlData.Camera,'NbSlice')&& ~isempty(XmlData.Camera.NbSlice)
884            if iview>1 && ~isempty(NbSlice) && ~strcmp(NbSlice,XmlData.Camera.NbSlice)
885                msgbox_uvmat('WARNING','inconsistent number of slices with the first field series');
886            end
887            NbSlice=XmlData.Camera.NbSlice;% Nbre of slices from camera
888        end
889        if isfield(XmlData.Camera,'TimeUnit')&& ~isempty(XmlData.Camera.TimeUnit)
890            if iview>1 && ~isempty(TimeUnit) && ~strcmp(TimeUnit,XmlData.Camera.TimeUnit)
891                msgbox_uvmat('WARNING','inconsistent time unit with the first field series');
892            end
893            TimeUnit=XmlData.Camera.TimeUnit;
894        end
895    end
896    % number of slices
897    if isfield(XmlData,'GeometryCalib')
898        check_calib=1;
899        if isfield(XmlData.GeometryCalib,'SliceCoord')
900            siz=size(XmlData.GeometryCalib.SliceCoord);
901            if siz(1)>1
902                if iview>1 && ~isempty(NbSlice) && ~strcmp(NbSlice,siz(1))
903                    msgbox_uvmat('WARNING','inconsistent number of Z indices with the first field series');
904                end
905                NbSlice=siz(1);
906            end
907        end
908    end
909    set(handles.num_NbSlice,'String',num2str(NbSlice))
910end
911
912%% read timing  from the current file (prioritary)
913if ~isempty(VideoObject)% case of movies
914    imainfo=get(VideoObject);
915    if isempty(j1_series); %frame index along i
916        Time=zeros(imainfo.NumberOfFrames+1,2);
917        Time(:,2)=(0:1/imainfo.FrameRate:(imainfo.NumberOfFrames)/imainfo.FrameRate)';
918    else
919        Time=[0;ones(size(i1_series,3)-1,1)]*(0:1/imainfo.FrameRate:(imainfo.NumberOfFrames)/imainfo.FrameRate);
920    end
921    TimeName='video';
922end
923
924
925%% determine the min and max times: case of Netcdf files will be treated later in FieldName_Callback
926if ~isempty(TimeName)
927    TimeMin=Time(MinIndex_i+1,MinIndex_j+1);
928    if size(Time)>=[first_i+1 first_j+1]
929        TimeFirst=Time(first_i+1,first_j+1);
930    end
931    if size(Time)>=[last_i+1 last_j+1]
932        TimeLast=Time(last_i+1,last_j+1);
933    end
934    if size(Time)>=[MaxIndex_i+1 MaxIndex_j+1];
935        TimeMax=Time(MaxIndex_i+1,MaxIndex_j+1);
936    end
937end
938
939%% update the time table
940TimeTable=get(handles.TimeTable,'Data');
941TimeTable{iview,1}=TimeName;
942TimeTable{iview,2}=TimeMin;
943TimeTable{iview,3}=TimeFirst;
944TimeTable{iview,4}=TimeLast;
945TimeTable{iview,5}=TimeMax;
946set(handles.TimeTable,'Data',TimeTable)
947
948%% update the series info in 'UserData'
949SeriesData.i1_series{iview}=i1_series;
950SeriesData.i2_series{iview}=i2_series;
951SeriesData.j1_series{iview}=j1_series;
952SeriesData.j2_series{iview}=j2_series;
953SeriesData.FileType{iview}=FileInfo.FileType;
954SeriesData.FileInfo{iview}=FileInfo;
955SeriesData.Time{iview}=Time;
956% if ~isempty(TimeName)
957%     SeriesData.TimeSource=TimeSource;
958% end
959if check_calib
960    SeriesData.GeometryCalib{iview}=XmlData.GeometryCalib;
961end
962set(handles.series,'UserData',SeriesData)
963
964%% update pair menus
965hset_pair=findobj(allchild(0),'Tag','set_pairs');
966if ~isempty(hset_pair), delete(hset_pair); end % delete the GUI set_pair if opened
967CheckPair= ~isempty(i2_series)||~isempty(j2_series); % check whether index pairs need to be defined
968PairString=get(handles.PairString,'Data');
969if CheckPair% if pairs need to be display for line iview
970    [ModeMenu,ModeValue]=update_mode(i1_series,i2_series,j2_series);
971    Menu=update_listpair(i1_series,i2_series,j1_series,j2_series,ModeMenu{ModeValue},Time,TimeUnit,ref_i,ref_j,TimeName,InputTable(iview,:),FileInfo);
972    PairString{iview,1}=Menu{1};
973else
974    PairString{iview,1}='';%no pair for #iview
975end
976set(handles.PairString,'Data',PairString)
977if isempty(find(cellfun('isempty',get(handles.PairString,'Data'))==0, 1))% if all lines of pairs are empty
978    set(handles.PairString,'Visible','off')
979    set(handles.SetPairs,'Visible','off')
980else
981    set(handles.PairString,'Visible','on')
982    set(handles.SetPairs,'Visible','on')
983end
984
985
986%% display the set of existing files as an image
987set(handles.FileStatus,'Units','pixels')
988Position=get(handles.FileStatus,'Position');
989set(handles.FileStatus,'Units','normalized')
990%xI=0.5:Position(3)-0.5;
991nbview=numel(SeriesData.i1_series);
992j_max=cell(1,nbview);
993MaxIndex_i=ones(1,nbview);%default
994MinIndex_i=ones(1,nbview);%default
995for iline=1:nbview
996    pair_max=squeeze(max(SeriesData.i1_series{iline},[],1)); %max on pair index
997    j_max{iline}=max(pair_max,[],1);%max on j index
998    if ~isempty(j_max{iline})
999    MaxIndex_i(iline)=max(find(j_max{iline}))-1;% max ref index i
1000    MinIndex_i(iline)=min(find(j_max{iline}))-1;% min ref index i
1001    end
1002end
1003MinIndex_i=min(MinIndex_i);
1004MaxIndex_i=max(MaxIndex_i);
1005range_index=MaxIndex_i-MinIndex_i+1;
1006range_y=max(1,floor(Position(4)/nbview));
1007npx=floor(Position(3));
1008file_indices=MinIndex_i+floor(((0.5:npx-0.5)/npx)*range_index)+1;
1009CData=zeros(nbview*range_y,npx);% initiate the image representing the existing files
1010for iline=1:nbview
1011    ind_y=1+(iline-1)*range_y:iline*range_y;
1012    LineData=zeros(size(file_indices));
1013    file_select=file_indices(file_indices<=numel(j_max{iline}));
1014    ind_select=find(file_indices<=numel(j_max{iline}));
1015    LineData(ind_select)=j_max{iline}(file_select)~=0;
1016    CData(ind_y,:)=ones(size(ind_y'))*LineData;
1017end
1018CData=cat(3,zeros(size(CData)),CData,zeros(size(CData)));%make color images r=0,g,b=0
1019set(handles.FileStatus,'CData',CData);
1020
1021%% enable field and veltype menus, in accordance with the current action
1022ActionName_Callback([],[], handles)
1023
1024%% set length of waitbar
1025displ_time(handles)
1026
1027
1028% look for netcdf data as input
1029% switch FileType
1030%     case {'civx','civdata'}
1031%         FieldList=[set_field_list('U','V');{'C'}];%standard menu for civx data
1032%         set(handles.Coord_x,'String','X');
1033%         set(handles.Coord_y,'String','Y');
1034%     case 'netcdf'
1035%         ind_x=find(strcmp(get(handles.Coord_x,'String'),FileInfo.ListVarName));
1036%         if isempty(ind_x)
1037%             FieldList={};% new kind of file opened, we need to pick variables with get_field...
1038%             set(handles.Coord_x,'String','')
1039%             set(handles.Coord_y,'String','')
1040%         else
1041%             FileInfo.ListVarName(ind_x)=[];%remove coord-x from the list of variables to display
1042%             ind_y=find(strcmp(get(handles.Coord_y,'String'),FileInfo.ListVarName));
1043%             if isempty(ind_y)
1044%             FieldList={};% new kind of file opened, we need to pick variables with get_field...
1045%             set(handles.Coord_x,'String','')
1046%             set(handles.Coord_y,'String','')
1047%             else
1048%                 FileInfo.ListVarName(ind_y)=[];%remove coord-y from the list of variables to display
1049%                 FieldList=(FileInfo.ListVarName)';
1050%             end
1051%         end 
1052%     otherwise
1053%         set(handles.FieldName,'Value',1) % set menu to 'image'
1054%         set(handles.FieldName,'String',{'image'})
1055%         set(handles.Coord_x,'String','AX');
1056%         set(handles.Coord_y,'String','AY');
1057% end
1058% if ismember(FileType,{'civx','civdata','netcdf'})
1059%     PrevMenu=get(handles.FieldName,'String');
1060%     PrevValue=get(handles.FieldName,'Value');
1061%     PrevMenu=PrevMenu(PrevValue(PrevValue<=numel(PrevMenu)));
1062%     FieldValue=[];
1063%     for ilist=1:numel(PrevMenu)
1064%         index_menu=find(strcmp(PrevMenu{ilist},FieldList));
1065%         if ~isempty(index_menu)
1066%             FieldValue=[FieldValue index_menu];
1067%         end
1068%     end
1069%     if isempty(FieldValue)
1070%         FieldValue=1;
1071%     end
1072%     set(handles.FieldName,'Value',FieldValue)
1073%     set(handles.FieldName,'String',[FieldList;{'get_field...'}])
1074% end
1075
1076
1077%-----------------------------------------------------------guide -------------
1078%------------------------------------------------------------------------
1079%  III - FUNCTIONS ASSOCIATED TO THE FRAME IndexRange
1080%------------------------------------------------------------------------
1081
1082
1083% ---- determine the menu to put in mode and advice a default choice
1084%------------------------------------------------------------------------
1085function [ModeMenu,ModeValue]=update_mode(i1_series,i2_series,j2_series)
1086%------------------------------------------------------------------------   
1087ModeMenu={''};
1088if isempty(j2_series)% no j pair
1089    ModeValue=1;
1090    if ~isempty(i2_series)
1091        ModeMenu={'series(Di)'}; % pair menu with only option Di
1092    end
1093else %existence of j pairs
1094    pair_max=squeeze(max(i1_series,[],1)); %max on pair index
1095    j_max=max(pair_max,[],1);
1096    MaxIndex_i=find(j_max, 1, 'last' )-1;% max ref index i
1097    MinIndex_i=find(j_max, 1 )-1;% min ref index i
1098    i_max=max(pair_max,[],2);
1099    MaxIndex_j=find(i_max, 1, 'last' )-1;% max ref index i
1100    MinIndex_j=find(i_max, 1 )-1;% min ref index i
1101    if MaxIndex_j==MinIndex_j
1102        ModeValue=1;
1103        ModeMenu={'bursts'};
1104    elseif MaxIndex_i==MinIndex_i
1105        ModeValue=1;
1106        ModeMenu={'series(Dj)'};
1107    else
1108        ModeMenu={'bursts';'series(Dj)'};
1109        if (MaxIndex_j-MinIndex_j)>10
1110            ModeValue=2;%set mode to series(Dj) if more than 10 j values
1111        else
1112            ModeValue=1;
1113        end
1114    end
1115end
1116
1117
1118%------------------------------------------------------------------------
1119function displ_pair=update_listpair(i1_series,i2_series,j1_series,j2_series,mode,time,TimeUnit,ref_i,ref_j,TimeName,InputTable,FileInfo)
1120%------------------------------------------------------------------------
1121displ_pair={};
1122if isempty(TimeUnit)
1123    dtunit='e-03';
1124else
1125    dtunit=['m' TimeUnit];
1126end
1127switch mode
1128    case 'series(Di)'
1129        diff_i=i2_series-i1_series;
1130        min_diff=min(diff_i(diff_i>0));
1131        max_diff=max(diff_i(diff_i>0));
1132        for ipair=min_diff:max_diff
1133            if numel(diff_i(diff_i==ipair))>0
1134                pair_string=['Di= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2)) ];
1135                if ~isempty(time)
1136                    if ref_i<=floor(ipair/2)
1137                        ref_i=floor(ipair/2)+1;% shift ref_i to get the first pair
1138                    end
1139                    Dt=time(ref_i+ceil(ipair/2),ref_j)-time(ref_i-floor(ipair/2),ref_j);
1140                    pair_string=[pair_string ', Dt=' num2str(Dt) ' ' dtunit];
1141                end
1142                displ_pair=[displ_pair;{pair_string}];
1143            end
1144        end
1145        if ~isempty(displ_pair)
1146            displ_pair=[displ_pair;{'Di=*|*'}];
1147        end
1148    case 'series(Dj)'
1149        if isempty(j2_series)
1150            msgbox_uvmat('ERROR','no j1-j2 pair available')
1151            return
1152        end
1153        diff_j=j2_series-j1_series;
1154        min_diff=min(diff_j(diff_j>0));
1155        max_diff=max(diff_j(diff_j>0));
1156        for ipair=min_diff:max_diff
1157            if numel(diff_j(diff_j==ipair))>0
1158                pair_string=['Dj= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2)) ];
1159                if ~isempty(time)
1160                    if ref_j<=floor(ipair/2)
1161                        ref_j=floor(ipair/2)+1;% shift ref_i to get the first pair
1162                    end
1163                    Dt=time(ref_i,ref_j+ceil(ipair/2))-time(ref_i,ref_j-floor(ipair/2));
1164                    pair_string=[pair_string ', Dt=' num2str(Dt) ' ' dtunit];
1165                end
1166                displ_pair=[displ_pair;{pair_string}];
1167            end
1168        end
1169        if ~isempty(displ_pair)
1170            displ_pair=[displ_pair;{'Dj=*|*'}];
1171        end
1172    case 'bursts'
1173        if isempty(j2_series)
1174            msgbox_uvmat('ERROR','no j1-j2 pair available')
1175            return
1176        end
1177        %diff_j=j2_series-j1_series;
1178        min_j1=min(j1_series(j1_series>0));
1179        max_j1=max(j1_series(j1_series>0));
1180        min_j2=min(j2_series(j2_series>0));
1181        max_j2=max(j2_series(j2_series>0));
1182        for pair1=min_j1:min(max_j1,min_j1+20)
1183            for pair2=min_j2:min(max_j2,min_j2+20)
1184                if numel(j1_series(j1_series==pair1))>0 && numel(j2_series(j2_series==pair2))>0
1185                    pair_string=['j= ' num2str(pair1) '-' num2str(pair2)];
1186                    [TimeValue,DtValue]=get_time(ref_i,[],pair_string,InputTable,FileInfo,TimeName,'Dt');
1187                    %Dt=time(ref_i,pair2+1)-time(ref_i,pair1+1);
1188                    pair_string=[pair_string ', Dt=' num2str(DtValue) ' ' dtunit];
1189                    displ_pair=[displ_pair;{pair_string}];
1190                end
1191            end
1192        end
1193        if ~isempty(displ_pair)
1194            displ_pair=[displ_pair;{'j=*-*'}];
1195        end
1196end
1197
1198%------------------------------------------------------------------------
1199function num_first_i_Callback(hObject, eventdata, handles)
1200%------------------------------------------------------------------------
1201num_last_i_Callback(hObject, eventdata, handles)
1202
1203%------------------------------------------------------------------------
1204function num_last_i_Callback(hObject, eventdata, handles)
1205%------------------------------------------------------------------------
1206SeriesData=get(handles.series,'UserData');
1207if ~isfield(SeriesData,'Time')
1208    SeriesData.Time{1}=[];
1209end
1210displ_time(handles);
1211
1212%------------------------------------------------------------------------
1213function num_first_j_Callback(hObject, eventdata, handles)
1214%------------------------------------------------------------------------
1215 num_last_j_Callback(hObject, eventdata, handles)
1216
1217%------------------------------------------------------------------------
1218function num_last_j_Callback(hObject, eventdata, handles)
1219%------------------------------------------------------------------------
1220% first_j=str2num(get(handles.num_first_j,'String'));
1221% last_j=str2num(get(handles.num_last_j,'String'));
1222% ref_j=ceil((first_j+last_j)/2);
1223% set(handles.num_ref_j,'String', num2str(ref_j))
1224% num_ref_j_Callback(hObject, eventdata, handles)
1225SeriesData=get(handles.series,'UserData');
1226if ~isfield(SeriesData,'Time')
1227    SeriesData.Time{1}=[];
1228end
1229displ_time(handles);
1230
1231%------------------------------------------------------------------------
1232% ---- find the times corresponding to the first and last indices of a series
1233function displ_time(handles)
1234%------------------------------------------------------------------------
1235SeriesData=get(handles.series,'UserData');%
1236if ~isfield(SeriesData,'Time')
1237    return
1238end
1239PairString=get(handles.PairString,'Data');
1240ref_i_1=str2num(get(handles.num_first_i,'String'));%first reference index
1241ref_i_2=str2num(get(handles.num_last_i,'String'));%last reference index
1242ref_j_1=[];ref_j_2=[];
1243if strcmp(get(handles.num_first_j,'Visible'),'on')
1244ref_j_1=str2num(get(handles.num_first_j,'String'));
1245ref_j_2=str2num(get(handles.num_last_j,'String'));
1246end
1247[i1_1,i2_1,j1_1,j2_1] = get_file_index(ref_i_1,ref_j_1,PairString);
1248[i1_2,i2_2,j1_2,j2_2] = get_file_index(ref_i_2,ref_j_2,PairString);
1249TimeTable=get(handles.TimeTable,'Data');
1250%%%%%%
1251%TODO: read time in netcdf file, see ActionName_Callback
1252%%%%%%%
1253%Pairs=get(handles.PairString,'Data');
1254for iview=1:size(TimeTable,1)
1255    if size(SeriesData.Time,1)<iview
1256        break
1257    end
1258    TimeTable{iview,3}=[];
1259    TimeTable{iview,4}=[];
1260    if size(SeriesData.Time{iview},1)>=i2_2+1 && (isempty(ref_j_1)||size(SeriesData.Time{iview},2)>=j2_2+1)
1261        if isempty(ref_j_1)
1262            time_first=(SeriesData.Time{iview}(i1_1+1,2)+SeriesData.Time{iview}(i2_1+1,2))/2;
1263            time_last=(SeriesData.Time{iview}(i1_2+1,2)+SeriesData.Time{iview}(i2_2+1,2))/2;
1264        else
1265            time_first=(SeriesData.Time{iview}(i1_1+1,j1_1+1)+SeriesData.Time{iview}(i2_1+1,j2_1+1))/2;
1266            time_last=(SeriesData.Time{iview}(i1_2+1,j1_2+1)+SeriesData.Time{iview}(i2_2+1,j2_1+1))/2;
1267        end
1268        TimeTable{iview,3}=time_first; %TODO: take into account pairs
1269        TimeTable{iview,4}=time_last; %TODO: take into account pairs
1270    end
1271end
1272set(handles.TimeTable,'Data',TimeTable)
1273
1274%% set the waitbar position with respect to the min and max in the series
1275MinIndex_i=min(get(handles.MinIndex_i,'Data'));
1276MaxIndex_i=max(get(handles.MaxIndex_i,'Data'));
1277pos_first=(ref_i_1-MinIndex_i)/(MaxIndex_i-MinIndex_i+1);
1278pos_last=(ref_i_2-MinIndex_i+1)/(MaxIndex_i-MinIndex_i+1);
1279if isempty(pos_first), pos_first=0; end
1280if isempty(pos_last), pos_last=1; end
1281Position=get(handles.Waitbar,'Position');% position of the waitbar:= [ x,y, width, height]
1282Position_status=get(handles.FileStatus,'Position');
1283Position(1)=Position_status(1)+Position_status(3)*pos_first;
1284Position(3)=max(Position_status(3)*(pos_last-pos_first),0.001);% width must remain positive
1285set(handles.Waitbar,'Position',Position)
1286update_waitbar(handles.Waitbar,0)
1287
1288%------------------------------------------------------------------------
1289% --- Executes when selected cell(s) is changed in PairString.
1290function PairString_CellSelectionCallback(hObject, eventdata, handles)
1291%------------------------------------------------------------------------   
1292if numel(eventdata.Indices)>=1
1293    PairString=get(hObject,'Data');
1294    if ~isempty(PairString{eventdata.Indices(1)})
1295        SetPairs_Callback(hObject, eventdata.Indices(1), handles)
1296    end
1297end
1298
1299%-------------------------------------
1300function enable_i(handles,state)
1301set(handles.i_txt,'Visible',state)
1302set(handles.num_first_i,'Visible',state)
1303set(handles.num_last_i,'Visible',state)
1304set(handles.num_incr_i,'Visible',state)
1305
1306%-----------------------------------
1307function enable_j(handles,state)
1308set(handles.j_txt,'Visible',state)
1309set(handles.num_first_j,'Visible',state)
1310set(handles.num_last_j,'Visible',state)
1311set(handles.num_incr_j,'Visible',state)
1312set(handles.MinIndex_j,'Visible',state)
1313set(handles.MaxIndex_j,'Visible',state)
1314
1315
1316%%%%%%%%%%%%%%%%%%%%
1317%%  MAIN ActionName FUNCTIONS
1318%%%%%%%%%%%%%%%%%%%%
1319%------------------------------------------------------------------------
1320% --- Executes on button press in RUN.
1321%------------------------------------------------------------------------
1322function RUN_Callback(hObject, eventdata, handles)
1323
1324%% read the data on the GUI series
1325Param=read_GUI_series(handles);%displayed parameters
1326SeriesData=get(handles.series,'UserData');%hidden parameters
1327if ~isfield(SeriesData,'i1_series')
1328    msgbox_uvmat('ERROR','The input field series needs to be refreshed: press REFRESH')
1329    return
1330end
1331if isfield(Param,'InputFields')&& isequal(Param.InputFields.FieldName,'get_field...')
1332    msgbox_uvmat('ERROR','input field name(s) not defined, select get_field...')
1333    return
1334end
1335
1336%% settings of the button RUN
1337set(handles.RUN,'BusyAction','queue');% activation of STOP button will set BusyAction to 'cancel'
1338set(handles.RUN, 'Enable','Off')% avoid further RUN action until the current one is finished
1339set(handles.RUN,'BackgroundColor',[1 1 0])%show activation of RUN by yellow color
1340drawnow
1341set(handles.status,'Value',0)% desable status display if relevant
1342status_Callback(hObject, eventdata, handles)
1343
1344%% select the Action mode, 'local', 'background' or 'cluster' (if available)
1345RunMode='local';%default (needed for first opening of the GUI series)
1346if isfield(Param.Action,'RunMode')
1347    RunMode=Param.Action.RunMode;
1348    Param.Action=rmfield(Param.Action,'RunMode');%remove from the recorded xml file to avoid interference during ImportConfig
1349end
1350ActionExt='.m';%default
1351if isfield(Param.Action,'ActionExt')
1352    ActionExt=Param.Action.ActionExt;% '.m' or '.sh' (compiled)
1353    Param.Action=rmfield(Param.Action,'ActionExt');%remove from the recorded xml file to avoid interference during ImportConfig
1354end
1355ActionName=Param.Action.ActionName;
1356ActionPath=Param.Action.ActionPath;
1357
1358path_series=fileparts(which('series'));
1359
1360%% create the Action fct handle if RunMode option = 'local'
1361if strcmp(RunMode,'local')
1362    if ~isequal(ActionPath,path_series)
1363        eval(['spath=which(''' ActionName ''');']) %spath = current path of the selected function ACTION
1364        if ~exist(ActionPath,'dir')
1365            msgbox_uvmat('ERROR',['The prescribed function path ' ActionPath ' does not exist']);
1366            return
1367        end
1368        if ~isequal(spath,ActionPath)
1369            addpath(ActionPath)% add the prescribed path if not the current one
1370        end
1371    end
1372    eval(['h_fun=@' ActionName ';'])%create a function handle for ACTION
1373    if ~isequal(ActionPath,path_series)
1374        rmpath(ActionPath)% add the prescribed path if not the current one
1375    end
1376end
1377
1378%% Get RunTime code from the file PARAM.xml (needed to run compiled functions)
1379errormsg='';%default error message
1380xmlfile=fullfile(path_series,'PARAM.xml');
1381test_batch=0;%default: ,no batch mode available
1382if ~exist(xmlfile,'file')
1383    [success,message]=copyfile(fullfile(path_series,'PARAM.xml.default'),xmlfile);
1384end
1385RunTime='';
1386if strcmp(ActionExt,'.sh')
1387    if exist(xmlfile,'file')
1388        s=xml2struct(xmlfile);
1389        if strcmp(RunMode,'cluster_oar') && isfield(s,'BatchParam')
1390            if isfield(s.BatchParam,'RunTime')
1391                RunTime=s.BatchParam.RunTime;
1392            end
1393            if isfield(s.BatchParam,'NbCore')
1394                NbCore=s.BatchParam.NbCore;
1395            end
1396        elseif (strcmp(RunMode,'background')||strcmp(RunMode,'local')) && isfield(s,'RunParam')
1397            if isfield(s.RunParam,'RunTime')
1398                RunTime=s.RunParam.RunTime;
1399            end
1400            if isfield(s.RunParam,'NbCore')
1401                NbCore=s.RunParam.NbCore;
1402            end
1403        end
1404    end
1405    if isempty(RunTime) && strcmp(RunMode,'cluster_oar')
1406        msgbox_uvmat('ERROR','RunTime name not found in PARAM.xml, compiled version .sh cannot run on cluster')
1407        return
1408    end
1409end
1410
1411%% If a compiled version has been selected (ext .sh) check weather it needs to be recompiled
1412if strcmp(ActionExt,'.sh')
1413    TransformPath='';
1414    if ~isempty(get(handles.ActionExt,'UserData'))
1415        TransformPath=get(handles.ActionExt,'UserData');
1416    end
1417    set(handles.series,'Pointer','watch') % set the mouse pointer to 'watch'
1418    set(handles.ActionExt,'BackgroundColor',[1 1 0])
1419    ActionFullName=fullfile(get(handles.ActionPath,'String'),[ActionName '.sh']);
1420    if ~exist(ActionFullName,'file')
1421        answer=msgbox_uvmat('INPUT_Y-N','compiled version has not been created: compile now?');
1422        if strcmp(answer,'Yes')
1423            set(handles.ActionExt,'BackgroundColor',[1 1 0])
1424            path_uvmat=fileparts(which('series'));
1425            currentdir=pwd;
1426            cd(get(handles.ActionPath,'String'))% go to the directory of Action
1427            addpath(path_uvmat)% add the path to uvmat to run the fct 'compile'
1428            compile(ActionName,TransformPath)
1429            cd(currentdir)
1430        end       
1431    else
1432        sh_file_info=dir(fullfile(get(handles.ActionPath,'String'),[ActionName '.sh']));
1433        m_file_info=dir(fullfile(get(handles.ActionPath,'String'),[ActionName '.m']));
1434        if isfield(m_file_info,'datenum') && m_file_info.datenum>sh_file_info.datenum
1435            set(handles.ActionExt,'BackgroundColor',[1 1 0])
1436            drawnow
1437            answer=msgbox_uvmat('INPUT_Y-N',[ActionName '.sh needs to be updated: recompile now?']);
1438            if strcmp(answer,'Yes')
1439                path_uvmat=fileparts(which('series'));
1440                currentdir=pwd;
1441                cd(get(handles.ActionPath,'String'))% go to the directory of Action
1442                addpath(path_uvmat)% add the path to uvmat to run the fct 'compile'
1443                addpath(fullfile(path_uvmat,'transform_field'))% add the path to uvmat to run the fct 'compile'
1444                compile(ActionName,TransformPath)
1445                cd(currentdir)
1446            end
1447        end
1448    end
1449    set(handles.ActionExt,'BackgroundColor',[1 1 1])
1450     set(handles.series,'Pointer','arrow') % set the mouse pointer to 'watch
1451end
1452
1453%% set nbre of cluster cores and processes
1454switch RunMode
1455    case {'local','background'}
1456        NbCore=1;% no need to split the calculation
1457    case 'cluster_oar'
1458        if strcmp(ActionExt,'.m')% case of Matlab function (uncompiled)
1459            NbCore=1;% one core used only (limitation of Matlab licences)
1460            msgbox_uvmat('WARNING','Number of cores =1: select the compiled version civ_matlab.sh for multi-core processing');
1461            extra_oar='';
1462        else
1463            answer=inputdlg({'Number of cores (max 36)','extra oar options'},'oarsub parameter',1,{'12',''});
1464            NbCore=str2double(answer{1});
1465            extra_oar=answer{2};
1466        end
1467end
1468if ~isfield(Param.IndexRange,'NbSlice')
1469    Param.IndexRange.NbSlice=[];
1470end
1471if isempty(Param.IndexRange.NbSlice)
1472    NbProcess=NbCore;% choose one process per core
1473else
1474    NbProcess=Param.IndexRange.NbSlice;% the nbre of run processes is equal to the number of slices
1475    NbCore=min(NbCore,NbProcess);% at least one process per core
1476end
1477
1478%% create the output data directory if needed
1479if isfield(Param,'OutputSubDir')
1480    SubDirOut=[get(handles.OutputSubDir,'String') Param.OutputDirExt];
1481    SubDirOutNew=SubDirOut;
1482    detect=exist(fullfile(Param.InputTable{1,1},SubDirOutNew),'dir');% test if  the dir  already exist
1483    check_create=1; %need to create the result directory by default
1484    while detect
1485        answer=msgbox_uvmat('INPUT_Y-N',['use existing ouput directory: ' fullfile(Param.InputTable{1,1},SubDirOutNew) ', possibly delete previous data']);
1486        if strcmp(answer,'Cancel')
1487            errormsg='Cancel';
1488            return
1489        elseif strcmp(answer,'Yes')
1490            detect=0;
1491            check_create=0;
1492        else
1493            r=regexp(SubDirOutNew,'(?<root>.*\D)(?<num1>\d+)$','names');%detect whether name ends by a number
1494            if isempty(r)
1495                r(1).root=[SubDirOutNew '_'];
1496                r(1).num1='0';
1497            end
1498            SubDirOutNew=[r(1).root num2str(str2num(r(1).num1)+1)];%increment the index by 1 or put 1
1499            detect=exist(fullfile(Param.InputTable{1,1},SubDirOutNew),'dir');% test if  the dir  already exists
1500            check_create=1;
1501        end
1502    end
1503    Param.OutputDirExt=regexprep(SubDirOutNew,Param.OutputSubDir,'');
1504    Param.OutputRootFile=Param.InputTable{1,3};% the first sorted RootFile taken for output
1505    set(handles.OutputDirExt,'String',Param.OutputDirExt)
1506    OutputDir=fullfile(Param.InputTable{1,1},[Param.OutputSubDir Param.OutputDirExt]);% full name (with path) of output directory
1507    if check_create    % create output directory if it does not exist
1508        [tild,msg1]=mkdir(OutputDir);
1509        if ~strcmp(msg1,'')
1510            msgbox_uvmat('ERROR',['cannot create ' OutputDir ': ' msg1]);%error message for directory creation
1511            return
1512        end
1513        [success,msg] = fileattrib(OutputDir,'+w','g','s');% allow writing access for the group of users, recursively in the folder 
1514        if success==0
1515            msgbox_uvmat('WARNING',{['unable to set group write access to ' OutputDir ':']; msg1});%error message for directory creation
1516            return
1517        end
1518    end
1519    OutputNomType=nomtype2pair(Param.InputTable{1,4});% nomenclature for output files
1520    DirXml=fullfile(OutputDir,'0_XML');
1521    if ~exist(DirXml,'dir')
1522        [tild,msg1]=mkdir(DirXml);
1523        if ~strcmp(msg1,'')
1524            msgbox_uvmat('ERROR',['cannot create ' DirXml ': ' msg1]);%error message for directory creation
1525            return
1526        end
1527        [success,msg] = fileattrib(DirXml,'+w','g','s');% allow writing access for the group of users, recursively in the folder
1528        if success==0
1529            msgbox_uvmat('WARNING',{['unable to set group write access to ' DirXml ':']; msg});%error message for directory creation
1530        end
1531    end
1532end
1533       
1534%% get the set of reference field indices
1535first_i=1;
1536last_i=1;
1537incr_i=1;
1538first_j=1;
1539last_j=1;
1540incr_j=1;
1541if isfield(Param.IndexRange,'first_i')
1542    first_i=Param.IndexRange.first_i;
1543    incr_i=Param.IndexRange.incr_i;
1544    last_i=Param.IndexRange.last_i;
1545end
1546if isfield(Param.IndexRange,'first_j')
1547    first_j=Param.IndexRange.first_j;
1548    last_j=Param.IndexRange.last_j;
1549    incr_j=Param.IndexRange.incr_j;
1550end
1551if last_i < first_i || last_j < first_j
1552    msgbox_uvmat('ERROR', 'series/Run_Callback:last field index must be larger or equal to the first one')
1553    set(handles.RUN, 'Enable','On'),
1554    set(handles.RUN,'BackgroundColor',[1 0 0])
1555    return
1556end
1557%incr_i must be defined, =1 by default, if NbSlice is active
1558if isempty(incr_i)&& ~isempty(Param.IndexRange.NbSlice)
1559    incr_i=1;
1560    set(handles.num_incr_i,'String','1')
1561end
1562if isempty(incr_i)
1563    if isempty(incr_j)
1564        [ref_j,ref_i]=find(squeeze(SeriesData.i1_series{1}(1,:,:)));
1565        ref_j=ref_j(ref_j>=first_j & ref_j<=last_j);
1566        ref_i=ref_i(ref_i>=first_i & ref_i<=last_i);
1567        ref_j=ref_j-1;
1568        ref_i=ref_i-1;
1569    else
1570        ref_j=first_j:incr_j:last_j;
1571        [tild,ref_i]=find(squeeze(SeriesData.i1_series{1}(1,:,:)));
1572        ref_i=ref_i-1;
1573        ref_i=ref_i(ref_i>=first_i & ref_i<=last_i);
1574    end
1575else
1576    ref_i=first_i:incr_i:last_i;
1577    if isempty(incr_j)
1578        [ref_j,tild]=find(squeeze(SeriesData.i1_series{1}(1,:,:)));
1579        ref_j=ref_j-1;
1580        ref_j=ref_j(ref_j>=first_j & ref_j<=last_j);
1581    else
1582        ref_j=first_j:incr_j:last_j;
1583    end
1584end
1585BlockLength=ceil(numel(ref_i)/NbProcess);
1586nbfield_j=numel(ref_j);
1587
1588%% record nbre of output files and starting time for computation for status
1589StatusData=get(handles.status,'UserData');
1590if isfield(StatusData,'OutputFileMode')
1591    switch StatusData.OutputFileMode
1592        case 'NbInput'
1593            StatusData.NbOutputFile=numel(ref_i)*nbfield_j;
1594        case 'NbInput_i'
1595            StatusData.NbOutputFile=numel(ref_i);
1596        case 'NbSlice'   
1597            StatusData.NbOutputFile=str2num(get(handles.num_NbSlice,'String'));
1598    end
1599end
1600StatusData.TimeStart=now;
1601set(handles.status,'UserData',StatusData)
1602
1603%% direct processing on the current Matlab session
1604if strcmp (RunMode,'local')
1605    for iprocess=1:NbProcess
1606        if isempty(Param.IndexRange.NbSlice)
1607            %Param.IndexRange.first_i=first_i+(iprocess-1)*BlockLength*incr_i;
1608            Param.IndexRange.first_i=ref_i(1+(iprocess-1)*BlockLength);
1609            if Param.IndexRange.first_i>last_i
1610                break
1611            end
1612            Param.IndexRange.last_i=min(ref_i(iprocess*BlockLength),last_i);
1613            %Param.IndexRange.last_i=min(first_i+(iprocess)*BlockLength*incr_i-1,last_i);
1614        else %multislices (then incr_i is not empty)
1615             Param.IndexRange.first_i= first_i+incr_i*(iprocess-1);
1616             Param.IndexRange.incr_i=incr_i*Param.IndexRange.NbSlice;
1617        end
1618        if isfield(Param,'OutputSubDir')
1619        t=struct2xml(Param);
1620        t=set(t,1,'name','Series');
1621        filexml=fullfile_uvmat(DirXml,'',Param.InputTable{1,3},'.xml',OutputNomType,...
1622            Param.IndexRange.first_i,Param.IndexRange.last_i,first_j,last_j);
1623        save(t,filexml);
1624        end
1625        switch ActionExt
1626            case '.m'
1627                h_fun(Param);
1628            case '.sh'
1629                switch computer
1630                    case {'PCWIN','PCWIN64'} %Windows system
1631                        filexml=regexprep(filexml,'\\','\\\\');% add '\' so that '\' are left as characters
1632                        system([fullfile(ActionPath,[ActionName '.sh']) ' ' RunTime ' ' filexml]);% TODO: adapt to DOS system
1633                    case {'GLNX86','GLNXA64','MACI64'}%Linux  system
1634                        system([fullfile(ActionPath,[ActionName '.sh']) ' ' RunTime ' ' filexml]);
1635                end
1636        end
1637    end
1638elseif strcmp(get(handles.OutputDirExt,'Visible'),'off')
1639    msgbox_uvmat('ERROR',['no output file for Action ' ActionName ', use run mode = local']);% a output dir is needed for background option
1640    return
1641else
1642    %% processing on a different session of the same computer (background) or cluster, create executable files
1643    batch_file_list=cell(NbProcess,1);% initiate the list of executable files
1644    DirBat=fullfile(OutputDir,'0_EXE');
1645    switch computer
1646        case {'PCWIN','PCWIN64'} %Windows system
1647            ExeExt='.bat';
1648        case {'GLNX86','GLNXA64','MACI64'}%Linux  system
1649           ExeExt='.sh';
1650    end
1651    %create subdirectory for executable files
1652    if ~exist(DirBat,'dir')
1653        [tild,msg1]=mkdir(DirBat);
1654        if ~strcmp(msg1,'')
1655            msgbox_uvmat('ERROR',['cannot create ' DirBat ': ' msg1]);%error message for directory creation
1656            return
1657        end
1658    end
1659    %create subdirectory for log files
1660    DirLog=fullfile(OutputDir,'0_LOG');
1661    if ~exist(DirLog,'dir')
1662        [tild,msg1]=mkdir(DirLog);
1663        if ~strcmp(msg1,'')
1664            msgbox_uvmat('ERROR',['cannot create ' DirLog ': ' msg1]);%error message for directory creation
1665            return
1666        end
1667    end
1668    for iprocess=1:NbProcess
1669        if isempty(Param.IndexRange.NbSlice)% process by blocks of i index
1670            Param.IndexRange.first_i=first_i+(iprocess-1)*BlockLength*incr_i;
1671            if Param.IndexRange.first_i>last_i
1672                NbProcess=iprocess-1;
1673                break% leave the loop, we are at the end of the calculation
1674            end
1675            Param.IndexRange.last_i=min(last_i,first_i+(iprocess)*BlockLength*incr_i-1);
1676        else% process by slices of i index if NbSlice is defined, computation in a single process if NbSlice =1
1677            Param.IndexRange.first_i= first_i+iprocess-1;
1678            Param.IndexRange.incr_i=incr_i*Param.IndexRange.NbSlice;
1679        end
1680       
1681        % create, fill and save the xml parameter file
1682        t=struct2xml(Param);
1683        t=set(t,1,'name','Series');
1684        filexml=fullfile_uvmat(DirXml,'',Param.InputTable{1,3},'.xml',OutputNomType,...
1685            Param.IndexRange.first_i,Param.IndexRange.last_i,first_j,last_j);
1686        save(t,filexml);% save the parameter file
1687       
1688        %create the executable file
1689         filebat=fullfile_uvmat(DirBat,'',Param.InputTable{1,3},ExeExt,OutputNomType,...
1690           Param.IndexRange.first_i,Param.IndexRange.last_i,first_j,last_j);
1691        batch_file_list{iprocess}=filebat;
1692        [fid,message]=fopen(filebat,'w');% create the executable file
1693        if isequal(fid,-1)
1694            msgbox_uvmat('ERROR', ['creation of .bat file: ' message]);
1695            return
1696        end
1697       
1698        % set the log file name
1699        filelog=fullfile_uvmat(DirLog,'',Param.InputTable{1,3},'.log',OutputNomType,...
1700            Param.IndexRange.first_i,Param.IndexRange.last_i,first_j,last_j);
1701       
1702        % fill and save the executable file
1703        switch ActionExt
1704            case '.m'% Matlab function
1705                switch computer
1706                    case {'GLNX86','GLNXA64','MACI64'}
1707                        cmd=[...
1708                            '#!/bin/bash \n'...
1709                            '. /etc/sysprofile \n'...
1710                            'matlab -nodisplay -nosplash -nojvm -logfile ''' filelog ''' <<END_MATLAB \n'...
1711                            'addpath(''' path_series '''); \n'...
1712                            'addpath(''' Param.Action.ActionPath '''); \n'...
1713                            '' Param.Action.ActionName  '( ''' filexml '''); \n'...
1714                            'exit \n'...
1715                            'END_MATLAB \n'];
1716                        fprintf(fid,cmd);%fill the executable file with the  char string cmd
1717                        fclose(fid);% close the executable file
1718                        system(['chmod +x ' filebat]);% set the file to executable
1719                    case {'PCWIN','PCWIN64'}
1720                        text_matlabscript=['matlab -automation -logfile ' regexprep(filelog,'\\','\\\\')...
1721                            ' -r "addpath(''' regexprep(path_series,'\\','\\\\') ''');'...
1722                            'addpath(''' regexprep(Param.Action.ActionPath,'\\','\\\\') ''');'...
1723                            '' Param.Action.ActionName  '( ''' regexprep(filexml,'\\','\\\\') ''');exit"'];
1724                        fprintf(fid,text_matlabscript);%fill the executable file with the  char string cmd
1725                        fclose(fid);% close the executable file
1726                end
1727            case '.sh' % compiled Matlab function
1728                switch computer
1729                    case {'GLNX86','GLNXA64','MACI64'}
1730                        cmd=['#!/bin/bash \n '...
1731                            '#$ -cwd \n '...
1732                            'hostname && date \n '...
1733                            'umask 002 \n'...
1734                            fullfile(ActionPath,[ActionName '.sh']) ' ' RunTime ' ' filexml];%allow writting access to created files for user group
1735                        fprintf(fid,cmd);%fill the executable file with the  char string cmd
1736                        fclose(fid);% close the executable file
1737                        system(['chmod +x ' filebat]);% set the file to executable
1738                       
1739                    case {'PCWIN','PCWIN64'}   
1740                        fprintf(fid,cmd);
1741                        fclose(fid);
1742                end
1743        end
1744    end
1745end
1746
1747%% launch the executable files for background or cluster processing
1748switch RunMode
1749    case 'background'
1750        for iprocess=1:NbProcess
1751            system([batch_file_list{iprocess} ' &'])% directly execute the command file for each process
1752            msgbox_uvmat('CONFIRMATION',[ActionName 'launched in background: press STATUS to see results'])
1753        end
1754    case 'cluster_oar' % option 'oar-parexec' used
1755        %create subdirectory for oar command and log files
1756        DirOAR=fullfile(OutputDir,'0_OAR');
1757        if exist(DirOAR,'dir')% delete the content of the dir 0_OAR to allow new input
1758            curdir=pwd;
1759            cd(DirOAR)
1760            delete('*')
1761            cd(curdir)
1762        else
1763            [tild,msg1]=mkdir(DirOAR);
1764            if ~strcmp(msg1,'')
1765                msgbox_uvmat('ERROR',['cannot create ' DirOAR ': ' msg1]);%error message for directory creation
1766                return
1767            end
1768        end
1769        max_walltime=3600*20; % 20h max total calculation (cannot exceed 24 h)
1770        walltime_onejob=600;%seconds, max estimated time for asingle file index value
1771        filename_joblist=fullfile(DirOAR,'job_list.txt');%create name of the global executable file
1772        fid=fopen(filename_joblist,'w');
1773        for p=1:length(batch_file_list)
1774            fprintf(fid,[batch_file_list{p} '\n']);% list of exe files
1775        end
1776        fclose(fid);
1777        system(['chmod +x ' filename_joblist]);% set the file to executable
1778        oar_command=['oarsub -n CIVX '...
1779            '-t idempotent --checkpoint ' num2str(walltime_onejob+60) ' '...
1780            '-l /core=' num2str(NbCore) ','...
1781            'walltime=' datestr(min(1.05*walltime_onejob/86400*max(NbProcess*BlockLength*nbfield_j,NbCore)/NbCore,max_walltime/86400),13) ' '...
1782            '-E ' regexprep(filename_joblist,'\.txt\>','.stderr') ' '...
1783            '-O ' regexprep(filename_joblist,'\.txt\>','.stdout') ' '...
1784            extra_oar ' '...
1785            '"oar-parexec -s -f ' filename_joblist ' '...
1786            '-l ' filename_joblist '.log"\n'];
1787        filename_oarcommand=fullfile(DirOAR,'oar_command');
1788        fid=fopen(filename_oarcommand,'w');
1789        fprintf(fid,oar_command);
1790        fclose(fid);
1791        fprintf(oar_command);% display in command line
1792        system(oar_command); 
1793        msgbox_uvmat('CONFIRMATION',[ActionName ' launched in cluster: press STATUS to see results'])
1794end
1795
1796%% reset the GUI series
1797update_waitbar(handles.Waitbar,1); % put the waitbar to end position to indicate launching is finished
1798set(handles.RUN, 'Enable','On')
1799set(handles.RUN,'BackgroundColor',[1 0 0])
1800set(handles.RUN, 'Value',0)
1801
1802%------------------------------------------------------------------------
1803function STOP_Callback(hObject, eventdata, handles)
1804%------------------------------------------------------------------------
1805set(handles.RUN, 'BusyAction','cancel')
1806set(handles.RUN,'BackgroundColor',[1 0 0])
1807set(handles.RUN,'enable','on')
1808set(handles.RUN, 'Value',0)
1809
1810
1811%------------------------------------------------------------------------
1812% --- read parameters from the GUI series
1813%------------------------------------------------------------------------
1814function Param=read_GUI_series(handles)
1815
1816%% read raw parameters from the GUI series
1817Param=read_GUI(handles.series);
1818
1819%% clean the output structure by removing unused information
1820if isfield(Param,'Pairs')
1821    Param=rmfield(Param,'Pairs'); %info Pairs not needed for output
1822end
1823Param.IndexRange=rmfield(Param.IndexRange,'TimeTable');
1824empty_line=false(size(Param.InputTable,1),1);
1825for iline=1:size(Param.InputTable,1)
1826    empty_line(iline)=isempty(cell2mat(Param.InputTable(iline,1:3)));
1827end
1828Param.InputTable(empty_line,:)=[];
1829
1830%------------------------------------------------------------------------
1831% --- Executes on selection change in ActionName.
1832function ActionName_Callback(hObject, eventdata, handles)
1833%------------------------------------------------------------------------
1834
1835%% stop any ongoing series processing
1836if isequal(get(handles.RUN,'Value'),1)
1837    answer= msgbox_uvmat('INPUT_Y-N','stop current Action process?');
1838    if strcmp(answer,'Yes')
1839        STOP_Callback(hObject, eventdata, handles)
1840    else
1841        return
1842    end
1843end
1844set(handles.ActionName,'BackgroundColor',[1 1 0])
1845huigetfile=findobj(allchild(0),'tag','status_display');
1846if ~isempty(huigetfile)
1847    delete(huigetfile)
1848end
1849drawnow
1850
1851%% get Action name and path
1852nb_builtin_ACTION=4; %nbre of functions initially proposed in the menu ActionName (as defined in the Opening fct of series)
1853ActionList=get(handles.ActionName,'String');% list menu fields
1854ActionIndex=get(handles.ActionName,'Value');
1855if ~isequal(ActionIndex,1)% if we are not just opening series
1856    InputTable=get(handles.InputTable,'Data');
1857    if isempty(InputTable{1,4})
1858        msgbox_uvmat('ERROR','no input file available: use Open in the menu bar')
1859        return
1860    end
1861end
1862ActionName= ActionList{get(handles.ActionName,'Value')}; % selected function name
1863ActionPathList=get(handles.ActionName,'UserData');%list of recorded paths to functions of the list ActionName
1864
1865%% add a new function to the menu if 'more...' has been selected in the menu ActionName
1866if isequal(ActionName,'more...')
1867    [FileName, PathName] = uigetfile( ...
1868        {'*.m', ' (*.m)';
1869        '*.m',  '.m files '; ...
1870        '*.*', 'All Files (*.*)'}, ...
1871        'Pick a series processing function ',get(handles.ActionPath,'String'));
1872    if length(FileName)<2
1873        return
1874    end
1875    [ActionPath,ActionName,ActionExt]=fileparts(FileName);
1876   
1877    % insert the choice in the menu ActionName
1878    ActionIndex=find(strcmp(ActionName,ActionList),1);% look for the selected function in the menu Action
1879    if isempty(ActionIndex)%the input string does not exist in the menu
1880        ActionIndex= length(ActionList);
1881        ActionList=[ActionList(1:end-1);{ActionName};ActionList(end)];% the selected function is appended in the menu, before the last item 'more...'
1882        set(handles.ActionName,'String',ActionList)
1883    end
1884   
1885    % record the file extension and extend the path list if it is a new extension
1886    ActionExtList=get(handles.ActionExt,'String');
1887    ActionExtIndex=find(strcmp(ActionExt,ActionExtList), 1);
1888    if isempty(ActionExtIndex)
1889        set(handles.ActionExt,'String',[ActionExtList;{ActionExt}])
1890        ActionExtIndex=numel(ActionExtList)+1;
1891        ActionPathNew=cell(size(ActionPathList,1),1);%new column of ActionPath
1892        ActionPathList=[ActionPathList ActionPathNew];
1893    end
1894    set(handles.ActionName,'UserData',ActionPathList);
1895
1896    % remove old Action options in the menu (keeping a menu length <nb_builtin_ACTION+5)
1897    if length(ActionList)>nb_builtin_ACTION+5; %nb_builtin=nbre of functions always remaining in the initial menu
1898        nbremove=length(ActionList)-nb_builtin_ACTION-5;
1899        ActionList(nb_builtin_ACTION+1:end-5)=[];
1900        ActionPathList(nb_builtin_ACTION+1:end-4,:)=[];
1901        ActionIndex=ActionIndex-nbremove;
1902    end
1903   
1904    % record action menu, choice and path
1905    set(handles.ActionName,'Value',ActionIndex)
1906    set(handles.ActionName,'String',ActionList)
1907    set(handles.ActionExt,'Value',ActionExtIndex)
1908    ActionPathList{ActionIndex,ActionExtIndex}=PathName;
1909       
1910    %record the user defined menu additions in personal file profil_perso
1911    dir_perso=prefdir;
1912    profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
1913    if nb_builtin_ACTION+1<=numel(ActionList)-1
1914        ActionListUser=ActionList(nb_builtin_ACTION+1:numel(ActionList)-1);
1915        ActionPathListUser=ActionPathList(nb_builtin_ACTION+1:numel(ActionList)-1,:);
1916        ActionExtListUser={};
1917        if numel(ActionExtList)>2
1918            ActionExtListUser=ActionExtList(3:end);
1919        end
1920        if exist(profil_perso,'file')
1921            save(profil_perso,'ActionListUser','ActionPathListUser','ActionExtListUser','-append')
1922        else
1923            save(profil_perso,'ActionListUser','ActionPathListUser','ActionExtListUser','-V6')
1924        end
1925    end
1926end
1927
1928%% check the current ActionPath to the selected function
1929ActionPath=ActionPathList{ActionIndex};%current recorded path
1930set(handles.ActionPath,'String',ActionPath); %show the path to the senlected function
1931
1932%% reinitialise the waitbar
1933update_waitbar(handles.Waitbar,0)
1934
1935%% create the function handle for Action
1936path_series=which('series');
1937if ~isequal(ActionPath,path_series)
1938    eval(['spath=which(''' ActionName ''');']) %spath = current path of the selected function ACTION
1939    if ~exist(ActionPath,'dir')
1940        errormsg=['The prescribed function path ' ActionPath ' does not exist'];
1941        return
1942    end
1943    if ~isequal(spath,ActionPath)
1944        addpath(ActionPath)% add the prescribed path if not the current one
1945    end
1946end
1947eval(['h_fun=@' ActionName ';'])%create a function handle for ACTION
1948if ~isequal(ActionPath,path_series)
1949        rmpath(ActionPath)% add the prescribed path if not the current one   
1950end
1951
1952%% Activate the Action fct
1953Param=read_GUI_series(handles);% read the parameters from the GUI series
1954ParamOut=h_fun(Param);%run the selected Action function to get the relevant input
1955
1956%% Put the first line of the selected Action fct as tooltip help
1957try
1958    [fid,errormsg] =fopen([ActionName '.m']);
1959    InputText=textscan(fid,'%s',1,'delimiter','\n');
1960    fclose(fid);
1961    set(handles.ActionName,'ToolTipString',InputText{1}{1})% put the first line of the selected function as tooltip help
1962end
1963
1964
1965%% Visibility of VelType and VelType_1 menus asked by ActionName
1966VelTypeRequest=1;%VelType requested by default
1967VelTypeRequest_1=1;%VelType requested by default
1968if isfield(ParamOut,'VelType')
1969    VelTypeRequest=ismember(ParamOut.VelType,{'on','one','two'});
1970    VelTypeRequest_1=strcmp( ParamOut.VelType,'two');
1971end
1972FieldNameRequest=0;  %hidden by default
1973FieldNameRequest_1=0;  %hidden by default
1974if isfield(ParamOut,'FieldName')
1975    FieldNameRequest=ismember(ParamOut.FieldName,{'on','one','two'});
1976    FieldNameRequest_1=strcmp( ParamOut.FieldName,'two');
1977end
1978
1979%% Detect the types of input files and set menus and default options in 'VelType'
1980SeriesData=get(handles.series,'UserData');% info on the input file series
1981iview_civ=find(strcmp('civx',SeriesData.FileType)|strcmp('civdata',SeriesData.FileType));
1982iview_netcdf=find(strcmp('netcdf',SeriesData.FileType)|strcmp('civx',SeriesData.FileType)|strcmp('civdata',SeriesData.FileType));% all nc files, icluding civ
1983FieldList=get(handles.FieldName,'String');% previous list as default
1984if ~iscell(FieldList),FieldList={FieldList};end
1985FieldList_1=get(handles.FieldName_1,'String');% previous list as default
1986if ~iscell(FieldList_1),FieldList_1={FieldList_1};end
1987CheckList=0;% indicate whether FieldName has been updated
1988CheckList_1=1;% indicate whether FieldName_1 has been updated
1989handles_coord=[handles.Coord_x handles.Coord_y handles.Coord_z handles.Coord_x_title handles.Coord_y_title handles.Coord_z_title];
1990if VelTypeRequest && numel(iview_civ)>=1
1991    menu=set_veltype_display(SeriesData.FileInfo{iview_civ(1)}.CivStage,SeriesData.FileType{iview_civ(1)});
1992    set(handles.VelType,'Value',1)% set first choice by default
1993    set(handles.VelType,'String',[{'*'};menu])
1994    set(handles.VelType,'Visible','on')
1995    set(handles.VelType_title,'Visible','on')
1996    FieldList=[set_field_list('U','V');{'C'};{'get_field...'}];%standard menu for civx data
1997    CheckList=1;
1998    set(handles.FieldName,'Value',1); %velocity vector choice by default
1999    if  VelTypeRequest_1 && numel(iview_civ)>=2
2000        menu=set_veltype_display(SeriesData.FileInfo{iview_civ(2)}.CivStage,SeriesData.FileType{iview_civ(2)});
2001        set(handles.VelType_1,'Value',1)% set first choice by default
2002        set(handles.VelType_1,'String',[{'*'};menu])
2003        set(handles.VelType_1,'Visible','on')
2004        set(handles.VelType_title_1,'Visible','on')
2005        FieldList_1=[set_field_list('U','V');{'C'};{'get_field...'}];%standard menu for civx data
2006        CheckList_1=1;
2007        set(handles.FieldName_1,'Value',1); %velocity vector choice by default
2008    else
2009        set(handles.VelType_1,'Visible','off')
2010        set(handles.VelType_title_1,'Visible','off')
2011    end
2012else
2013    set(handles.VelType,'Visible','off')
2014    set(handles.VelType_title,'Visible','off')
2015end   
2016
2017%% Detect the types of input files and set menus and default options in 'FieldName'
2018if FieldNameRequest && numel(iview_netcdf)>=1
2019    set(handles.InputFields,'Visible','on')
2020%     set(handles.FieldName,'Visible','on')
2021    if CheckList==0        % not civ input made
2022        ListVarName=SeriesData.FileInfo{iview_netcdf(1)}.ListVarName;
2023        ind_var=get(handles.FieldName,'Value');%indices of previously selected variables
2024        for ilist=1:numel(ind_var)
2025            if isempty(find(strcmp(FieldList{ind_var(ilist)},ListVarName)))
2026                FieldList={};% previous choice not consistent with new input field
2027                set(handles.FieldName,'Value',1)
2028                break
2029            end
2030        end
2031        if ~isempty(FieldList)
2032            if isempty(find(strcmp(get(handles.Coord_x,'String'),ListVarName)))||...
2033                    isempty(find(strcmp(get(handles.Coord_y,'String'),ListVarName)))
2034                FieldList={};
2035                set(handles.Coord_x,'String','')
2036                set(handles.Coord_y,'String','')
2037            end
2038            Coord_z=get(handles.Coord_z,'String');
2039            if ~isempty(Coord_z) && isempty(find(strcmp(Coord_z,ListVarName)))
2040                FieldList={};
2041                set(handles.Coord_z,'String','')
2042            end
2043        end
2044        set(handles_coord,'Visible','on')
2045        FieldList=[FieldList;{'get_field...'}];
2046        if FieldNameRequest_1 && numel(iview_netcdf)>=2
2047            set(handles.FieldName_1,'Visible','on')
2048            if CheckList_1==0        % not civ input made
2049                ListVarName=SeriesData.FileInfo{iview_netcdf(2)}.ListVarName;
2050                ind_var=get(handles.FieldName,'Value');%indices of previously selected variables
2051                for ilist=1:numel(ind_var)
2052                    if isempty(find(strcmp(FieldList{ind_var(ilist)},ListVarName)))
2053                        FieldList_1={};% previous choice not consistent with new input field
2054                        set(handles.FieldName_1,'Value',1)
2055                        break
2056                    end
2057                end
2058                warn_coord=0;
2059                if isempty(find(strcmp(get(handles.Coord_x,'String'),ListVarName)))||...
2060                        isempty(find(strcmp(get(handles.Coord_y,'String'),ListVarName)))
2061                    warn_coord=1;
2062                end
2063                if ~isempty(Coord_z) && isempty(find(strcmp(Coord_z,ListVarName)))
2064                    FieldList_1={};
2065                    warn_coord=1;
2066                end
2067                if warn_coord
2068                    msgbox_uvmat('WARNING','coordiante names do not exist in the second netcdf input file')
2069                end
2070                set(handles.FieldName,'String',[FieldList;{'get_field...'}])
2071                set(handles.FieldName_1,'Visible','on')
2072                set(handles.FieldName_1,'Value',1)
2073                set(handles.FieldName_1,'String',FieldList_1)
2074            end
2075        else
2076            set(handles.FieldName_1,'Visible','off')
2077        end
2078    else
2079        set(handles_coord,'Visible','off')% no coord display for civ data
2080    end
2081    set(handles.FieldName,'String',FieldList)
2082else
2083    set(handles.InputFields,'Visible','off')
2084end
2085
2086
2087%% Check whether alphabetical sorting of input Subdir is allowed by the Action fct  (for multiples series entries)
2088if isfield(ParamOut,'AllowInputSort')&&isequal(ParamOut.AllowInputSort,'on')&& size(Param.InputTable,1)>1
2089    [tild,iview]=sort(InputTable(:,2)); %subdirectories sorted in alphabetical order
2090    set(handles.InputTable,'Data',InputTable(iview,:));
2091    MinIndex_i=get(handles.MinIndex_i,'Data');
2092    MinIndex_j=get(handles.MinIndex_j,'Data');
2093    MaxIndex_i=get(handles.MaxIndex_i,'Data');
2094    MaxIndex_j=get(handles.MaxIndex_j,'Data');
2095    set(handles.MinIndex_i,'Data',MinIndex_i(iview,:));
2096    set(handles.MinIndex_j,'Data',MinIndex_j(iview,:));
2097    set(handles.MaxIndex_i,'Data',MaxIndex_i(iview,:));
2098    set(handles.MaxIndex_j,'Data',MaxIndex_j(iview,:));
2099    TimeTable=get(handles.TimeTable,'Data');
2100    set(handles.TimeTable,'Data',TimeTable(iview,:));
2101    PairString=get(handles.PairString,'Data');
2102    set(handles.PairString,'Data',PairString(iview,:));
2103end
2104
2105%% Impose the whole input file index range if requested
2106if isfield(ParamOut,'WholeIndexRange')&&isequal(ParamOut.WholeIndexRange,'on')
2107    MinIndex_i=get(handles.MinIndex_i,'Data');
2108    MinIndex_j=get(handles.MinIndex_j,'Data');
2109    MaxIndex_i=get(handles.MaxIndex_i,'Data');
2110    MaxIndex_j=get(handles.MaxIndex_j,'Data');
2111    set(handles.num_first_i,'String',num2str(MinIndex_i(1)))% set first as the min index (for the first line)
2112    set(handles.num_last_i,'String',num2str(MaxIndex_i(1)))% set last as the max index (for the first line)
2113    set(handles.num_incr_i,'String','1')
2114    set(handles.num_first_j,'String',num2str(MinIndex_j(1)))% set first as the min index (for the first line)
2115    set(handles.num_last_j,'String',num2str(MaxIndex_j(1)))% set last as the max index (for the first line)
2116    set(handles.num_incr_j,'String','1')
2117else  % check index ranges
2118    first_i=1;last_i=1;first_j=1;last_j=1;
2119    if isfield(Param.IndexRange,'first_i')
2120        first_i=Param.IndexRange.first_i;
2121        last_i=Param.IndexRange.last_i;
2122    end
2123    if isfield(Param.IndexRange,'first_j')
2124        first_j=Param.IndexRange.first_j;
2125        last_j=Param.IndexRange.last_j;
2126    end
2127    if last_i < first_i || last_j < first_j , msgbox_uvmat('ERROR','last field number must be larger than the first one'),...
2128            set(handles.RUN, 'Enable','On'), set(handles.RUN,'BackgroundColor',[1 0 0]),return,end;
2129end
2130
2131%% enable or desable j index visibility
2132status_j='on';%default
2133if isfield(ParamOut,'Desable_j_index')&&isequal(ParamOut.Desable_j_index,'on')
2134    status_j='off';
2135end
2136if isempty(find(~cellfun(@isempty,SeriesData.j1_series), 1)); % case of empty j indices
2137    status_j='off'; % no j index needed
2138elseif strcmp(get(handles.PairString,'Visible'),'on')
2139    check_burst=cellfun(@isempty,regexp(get(handles.PairString,'Data'),'^j'));%=0 for burst case, 1 otherwise
2140    if isempty(find(check_burst, 1))% if all pair string begins by j (burst)
2141        status_j='off'; % no j index needed for bust case
2142    end
2143end
2144enable_j(handles,status_j) % no j index needed
2145
2146
2147%% NbSlice visibility
2148NbSliceVisible='off';%default
2149if isfield(ParamOut,'NbSlice') && isequal(ParamOut.NbSlice,'on')
2150    NbSliceVisible='on';
2151    set(handles.num_NbProcess,'String',get(handles.num_NbSlice,'String'))% the nbre of processes is imposed as the nbre of slices
2152else
2153    set(handles.num_NbProcess,'String','')% free nbre of processes
2154end
2155set(handles.num_NbSlice,'Visible',NbSliceVisible)
2156set(handles.NbSlice_title,'Visible',NbSliceVisible)
2157
2158
2159
2160%% Visibility of FieldTransform menu
2161FieldTransformVisible='off';  %hidden by default
2162if isfield(ParamOut,'FieldTransform')
2163    FieldTransformVisible=ParamOut.FieldTransform; 
2164    TransformName_Callback([],[], handles)
2165end
2166set(handles.FieldTransform,'Visible',FieldTransformVisible)
2167if isfield(ParamOut,'TransformPath')
2168    set(handles.ActionExt,'UserData',ParamOut.TransformPath)
2169else
2170    set(handles.ActionExt,'UserData',[])
2171end
2172
2173%% Visibility of projection object
2174ProjObjectVisible='off';  %hidden by default
2175if isfield(ParamOut,'ProjObject')
2176    ProjObjectVisible=ParamOut.ProjObject;
2177end
2178set(handles.CheckObject,'Visible',ProjObjectVisible)
2179if ~get(handles.CheckObject,'Value')
2180    ProjObjectVisible='off';
2181end
2182set(handles.ProjObject,'Visible',ProjObjectVisible)
2183set(handles.DeleteObject,'Visible',ProjObjectVisible)
2184set(handles.ViewObject,'Visible',ProjObjectVisible)
2185set(handles.EditObject,'Visible',ProjObjectVisible)
2186
2187%% Visibility of mask input
2188MaskVisible='off';  %hidden by default
2189if isfield(ParamOut,'Mask')
2190    MaskVisible=ParamOut.Mask;
2191end
2192set(handles.CheckMask,'Visible',MaskVisible);
2193
2194%% definition of the directory containing the output files
2195OutputDirVisible='off';
2196if isfield(ParamOut,'OutputDirExt')&&~isempty(ParamOut.OutputDirExt)
2197    OutputSubDirMode='all';%default
2198    if isfield(ParamOut,'OutputSubDirMode')
2199        OutputSubDirMode=ParamOut.OutputSubDirMode;
2200    end
2201    set(handles.OutputDirExt,'String',ParamOut.OutputDirExt)
2202    OutputDirVisible='on';
2203    SubDir=InputTable(1:end,2); %set of subdirectories sorted in alphabetical order
2204    if strcmp(OutputSubDirMode,'last')
2205        SubDirOut=SubDir{end};
2206    else
2207        SubDirOut=SubDir{1};
2208        if ~strcmp(OutputSubDirMode,'first')  && numel(SubDir)>1
2209            for ilist=2:numel(SubDir)
2210                SubDirOut=[SubDirOut '-' SubDir{ilist}];
2211            end
2212        end
2213    end
2214    set(handles.OutputSubDir,'String',SubDirOut)
2215end
2216set(handles.OutputDirExt,'Visible',OutputDirVisible)
2217set(handles.OutputSubDir,'Visible',OutputDirVisible)
2218set(handles.OutputDir_title,'Visible',OutputDirVisible)
2219set(handles.RunMode,'Visible',OutputDirVisible)
2220set(handles.ActionExt,'Visible',OutputDirVisible)
2221set(handles.RunMode_title,'Visible',OutputDirVisible)
2222set(handles.ActionExt_title,'Visible',OutputDirVisible)
2223
2224
2225%% Expected nbre of output files
2226if isfield(ParamOut,'OutputFileMode')
2227    StatusData.OutputFileMode=ParamOut.OutputFileMode;
2228    set(handles.status,'UserData',StatusData)
2229end
2230
2231%% definition of an additional parameter set, determined by an ancillary GUI
2232if isfield(ParamOut,'ActionInput')
2233    set(handles.ActionInput,'Visible','on')
2234    ParamOut.ActionInput.Program=ActionName; % record the program in ActionInput
2235    SeriesData.ActionInput=ParamOut.ActionInput;
2236else
2237    set(handles.ActionInput,'Visible','off')
2238    if isfield(SeriesData,'ActionInput')
2239        SeriesData=rmfield(SeriesData,'ActionInput');
2240    end
2241end
2242set(handles.series,'UserData',SeriesData)
2243set(handles.ActionName,'BackgroundColor',[1 1 1])
2244
2245%------------------------------------------------------------------------
2246% --- Executes on button press in ActionInput.
2247function ActionInput_Callback(hObject, eventdata, handles)
2248%------------------------------------------------------------------------
2249% if get(handles.ActionInput,'Value')
2250ActionName_Callback(hObject, eventdata, handles)
2251% end
2252
2253%------------------------------------------------------------------------
2254% --- Executes on selection change in FieldName.
2255function FieldName_Callback(hObject, eventdata, handles)
2256%------------------------------------------------------------------------
2257field_str=get(handles.FieldName,'String');
2258field_index=get(handles.FieldName,'Value');
2259field=field_str{field_index(1)};
2260if isequal(field,'get_field...')
2261    SeriesData=get(handles.series,'UserData');
2262    % input line for which the field choice is relevant
2263    iview=find(strcmp('netcdf',SeriesData.FileType)|strcmp('civx',SeriesData.FileType)|strcmp('civdata',SeriesData.FileType));% all nc files, icluding civ
2264    hget_field=findobj(allchild(0),'name','get_field');
2265    if ~isempty(hget_field)
2266        delete(hget_field)%delete opened versions of get_field
2267    end
2268    Param=read_GUI(handles.series);
2269    InputTable=Param.InputTable(iview,:);
2270    % check the existence of the first file in the series
2271    first_j=[];last_j=[];MinIndex_j=1;MaxIndex_j=1;%default setting for index j
2272    if isfield(Param.IndexRange,'first_j');% if index j is used
2273        first_j=Param.IndexRange.first_j;
2274        last_j=Param.IndexRange.last_j;
2275        MinIndex_j=Param.IndexRange.MinIndex_j(iview);
2276        MaxIndex_j=Param.IndexRange.MaxIndex_j(iview);
2277    end
2278    PairString='';
2279    if isfield(Param.IndexRange,'PairString'); PairString=Param.IndexRange.PairString{iview}; end
2280    [i1,i2,j1,j2] = get_file_index(Param.IndexRange.first_i,first_j,PairString);
2281    FirstFileName=fullfile_uvmat(InputTable{1},InputTable{2},InputTable{3},...
2282        InputTable{5},InputTable{4},i1,i2,j1,j2);
2283    if exist(FirstFileName,'file')
2284        ParamIn.Title='get_field: pick input variables and coordinates for series processing';
2285        ParamIn.SeriesInput=1;
2286        GetFieldData=get_field(FirstFileName,ParamIn);
2287        FieldList={};
2288        switch GetFieldData.FieldOption
2289            case 'vectors'
2290                UName=GetFieldData.PanelVectors.vector_x;
2291                VName=GetFieldData.PanelVectors.vector_y;
2292                YName={GetFieldData.Coordinates.Coord_y};
2293                FieldList={['vec(' UName ',' VName ')'];...
2294                    ['norm(' UName ',' VName ')'];...
2295                    UName;VName};
2296            case {'scalar'}
2297                FieldList=GetFieldData.PanelScalar.scalar;
2298                YName={GetFieldData.Coordinates.Coord_y};
2299                if ischar(FieldList)
2300                    FieldList={FieldList};
2301                end
2302            case 'civdata...'
2303                FieldList=[set_field_list('U','V') ;{'C'}];
2304                set(handles.FieldName,'Value',1) % set menu to 'velocity
2305                XName='X';
2306                YName='y';
2307                set(handles.VelType,'visible','on')
2308                set(handles.VelType_title,'visible','on')
2309        end
2310        set(handles.FieldName,'Value',1)
2311        set(handles.FieldName,'String',[FieldList; {'get_field...'}]);
2312        if ~strcmp(GetFieldData.FieldOption,'civdata...')
2313            set(handles.FieldName,'Value',1:numel(FieldList))%select all input fields by default
2314            set(handles.VelType,'visible','off')
2315            set(handles.VelType_title,'visible','off')
2316            XName=GetFieldData.Coordinates.Coord_x;
2317            YName=GetFieldData.Coordinates.Coord_y;
2318            TimeNameStr=GetFieldData.Time.SwitchVarIndexTime;
2319            % get the time info                     
2320            TimeTable=get(handles.TimeTable,'Data');
2321            switch TimeNameStr
2322                case 'file index'
2323                    TimeName='';
2324                case 'attribute'
2325                    TimeName=['att:' GetFieldData.Time.TimeName];
2326                    % update the time table
2327                    TimeTable{iview,2}=get_time(Param.IndexRange.MinIndex_i(iview),MinIndex_j,PairString,InputTable,SeriesData.FileInfo{iview},GetFieldData.Time.TimeName);  % Min time     
2328                    TimeTable{iview,3}=get_time(Param.IndexRange.first_i,first_j,PairString,InputTable,SeriesData.FileInfo{iview},GetFieldData.Time.TimeName);  % first time             
2329                    TimeTable{iview,4}=get_time(Param.IndexRange.last_i,last_j,PairString,InputTable,SeriesData.FileInfo{iview},GetFieldData.Time.TimeName);  % last time                     
2330                    TimeTable{iview,5}=get_time(Param.IndexRange.MaxIndex_i(iview),MaxIndex_j,PairString,InputTable,SeriesData.FileInfo{iview},GetFieldData.Time.TimeName);  % Max time
2331                case 'variable'
2332                    set(handles.TimeName,'String',['var:' GetFieldData.Time.TimeName])
2333                    set(handles.NomType,'String','*')
2334                    set(handles.RootFile,'String',[get(handles.RootFile,'String') get(handles.FileIndex,'String')])% A VERIFIER !!!!!!
2335                    set(handles.FileIndex,'String','')
2336                    ParamIn.TimeVarName=GetFieldData.Time.TimeName;
2337                case 'matrix_index'
2338                    TimeName=['dim:' GetFieldData.Time.TimeName];
2339                    set(handles.NomType,'String','*')
2340                    set(handles.RootFile,'String',[get(handles.RootFile,'String') get(handles.FileIndex,'String')])
2341                    set(handles.FileIndex,'String','')
2342                    ParamIn.TimeDimName=GetFieldData.Time.TimeName;
2343            end
2344            TimeTable{iview,1}=TimeName;
2345            set(handles.TimeTable,'Data',TimeTable);
2346        end
2347        set(handles.Coord_x,'String',XName)
2348        set(handles.Coord_y,'String',YName)
2349    end
2350end
2351
2352function [TimeValue,DtValue]=get_time(ref_i,ref_j,PairString,InputTable,FileInfo,TimeName,DtName)
2353[i1,i2,j1,j2] = get_file_index(ref_i,ref_j,PairString);
2354FileName=fullfile_uvmat(InputTable{1},InputTable{2},InputTable{3},InputTable{5},InputTable{4},i1,i2,j1,j2);
2355Data=nc2struct(FileName,[]);
2356TimeValue=[];
2357DtValue=[];
2358if isequal(FileInfo.FileType,'civdata')
2359    if ismember(TimeName,{'civ1','filter1'})
2360        TimeValue=Data.Civ1_Time;
2361        DtValue=Data.Civ1_Dt;
2362    else
2363        TimeValue=Data.Civ2_Time;
2364        DtValue=Data.Civ2_Dt;
2365    end
2366else
2367    if ~isempty(TimeName)&& isfield(Data,TimeName)
2368        TimeValue=Data.(TimeName);
2369    end
2370    if exist('DtName','var') && isfield(Data,DtName)
2371        DtValue=Data.(DtName);
2372    end
2373end
2374
2375%------------------------------------------------------------------------
2376% --- Executes on selection change in FieldName_1.
2377function FieldName_1_Callback(hObject, eventdata, handles)
2378%------------------------------------------------------------------------
2379field_str=get(handles.FieldName_1,'String');
2380field_index=get(handles.FieldName_1,'Value');
2381field=field_str{field_index(1)};
2382if isequal(field,'get_field...')
2383    hget_field=findobj(allchild(0),'name','get_field');
2384    if ~isempty(hget_field)
2385        delete(hget_field)%delete opened versions of get_field
2386    end
2387    Param=read_GUI(handles.series);
2388    Param.InputTable=Param.InputTable(1,:);
2389    % check the existence of the first file in the series
2390    first_j=[];
2391    if isfield(Param.IndexRange,'first_j'); first_j=Param.IndexRange.first_j; end
2392    if isfield(Param.IndexRange,'last_j'); last_j=Param.IndexRange.last_j; end
2393    PairString='';
2394    if isfield(Param.IndexRange,'PairString'); PairString=Param.IndexRange.PairString; end
2395    [i1,i2,j1,j2] = get_file_index(Param.IndexRange.first_i,first_j,PairString);
2396    FirstFileName=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},...
2397        Param.InputTable{1,5},Param.InputTable{1,4},i1,i2,j1,j2);
2398    if exist(FirstFileName,'file')
2399        ParamIn.SeriesInput=1;
2400        GetFieldData=get_field(FirstFileName,ParamIn);
2401        FieldList={};
2402        switch GetFieldData.FieldOption
2403            case 'vectors'
2404                UName=GetFieldData.PanelVectors.vector_x;
2405                VName=GetFieldData.PanelVectors.vector_y;
2406                FieldList={['vec(' UName ',' VName ')'];...
2407                    ['norm(' UName ',' VName ')'];...
2408                    UName;VName};
2409            case {'scalar','pick variables'}
2410                FieldList=GetFieldData.PanelScalar.scalar;
2411                if ischar(FieldList)
2412                    FieldList={FieldList};
2413                end
2414            case '1D plot'
2415
2416            case 'civdata...'
2417                FieldList=set_field_list('U','V','C');
2418                set(handles.FieldName,'Value',2) % set menu to 'velocity
2419        end
2420        if ~strcmp(GetFieldData.FieldOption,'civdata...')
2421            TimeNameStr=GetFieldData.Time.SwitchVarIndexTime;
2422            switch TimeNameStr
2423                case 'file index'
2424                    set(handles.TimeName,'String','');
2425                case 'attribute'
2426                    set(handles.TimeName,'String',['att:' GetFieldData.Time.TimeName]);
2427                case 'variable'
2428                    set(handles.TimeName,'String',['var:' GetFieldData.Time.TimeName])
2429                    set(handles.NomType,'String','*')
2430                    set(handles.RootFile,'String',[get(handles.RootFile,'String') get(handles.FileIndex,'String')])% A VERIFIER !!!!!!
2431                    set(handles.FileIndex,'String','')
2432                    ParamIn.TimeVarName=GetFieldData.Time.TimeName;
2433                case 'matrix_index'
2434                    set(handles.TimeName,'String',['dim:' GetFieldData.Time.TimeName]);
2435                    set(handles.NomType,'String','*')
2436                    set(handles.RootFile,'String',[get(handles.RootFile,'String') get(handles.FileIndex,'String')])
2437                    set(handles.FileIndex,'String','')
2438                    ParamIn.TimeDimName=GetFieldData.Time.TimeName;
2439            end
2440        end
2441        set(handles.FieldName_1,'Value',1)
2442        set(handles.FieldName_1,'String',[FieldList; {'get_field...'}]);
2443    end
2444end   
2445
2446
2447%%%%%%%%%%%%%
2448function [ind_remove]=find_pairs(dirpair,ind_i,last_i)
2449indsel=ind_i;
2450indiff=diff(ind_i); %test index increment to detect multiplets (several pairs with the same index ind_i) and holes in the series
2451indiff=[1 indiff last_i-ind_i(end)+1];%for testing gaps with the imposed bounds
2452if ~isempty(indiff)
2453    indiff2=diff(indiff);
2454    indiffp=[indiff2 1];
2455    indiffm=[1 indiff2];
2456    ind_multi_m=find((indiff==0)&(indiffm<0))-1;%indices of first members of multiplets
2457    ind_multi_p=find((indiff==0)&(indiffp>0));%indices of last members of multiplets
2458    %for each multiplet, select the most recent file
2459    ind_remove=[];
2460    for i=1:length(ind_multi_m)
2461        ind_pairs=ind_multi_m(i):ind_multi_p(i);
2462        for imulti=1:length(ind_pairs)
2463            datepair(imulti)=datenum(dirpair(ind_pairs(imulti)).date);%dates of creation
2464        end
2465        [datenew,indsort2]=sort(datepair); %sort the multiplet by creation date
2466        ind_s=indsort2(1:end-1);%
2467        ind_remove=[ind_remove ind_pairs(ind_s)];%remove these indices, leave the last one
2468    end
2469end
2470
2471%------------------------------------------------------------------------
2472% --- determine the list of index pairstring of processing file
2473function [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)
2474%------------------------------------------------------------------------
2475num_i1=num_i;% set of first image numbers by default
2476num_i2=num_i;
2477num_j1=num_j;
2478num_j2=num_j;
2479num_i_out=num_i;
2480num_j_out=num_j;
2481% if isequal (NomType,'_1-2_1') || isequal (NomType,'_1-2')
2482if isequal(mode,'series(Di)')
2483    num_i1_line=num_i+ind_shift(3);% set of first image numbers
2484    num_i2_line=num_i+ind_shift(4);
2485    % adjust the first and last field number
2486        indsel=find(num_i1_line >= 1);
2487    num_i_out=num_i(indsel);
2488    num_i1_line=num_i1_line(indsel);
2489    num_i2_line=num_i2_line(indsel);
2490    num_j1=meshgrid(num_j,ones(size(num_i1_line)));
2491    num_j2=meshgrid(num_j,ones(size(num_i1_line)));
2492    [xx,num_i1]=meshgrid(num_j,num_i1_line);
2493    [xx,num_i2]=meshgrid(num_j,num_i2_line);
2494elseif isequal (mode,'series(Dj)')||isequal (mode,'bursts')
2495    if isequal(mode,'bursts') %case of bursts (png_old or png_2D)
2496        num_j1=ind_shift(1)*ones(size(num_i));
2497        num_j2=ind_shift(2)*ones(size(num_i));
2498    else
2499        num_j1_col=num_j+ind_shift(1);% set of first image numbers
2500        num_j2_col=num_j+ind_shift(2);
2501        % adjust the first field number
2502        indsel=find((num_j1_col >= 1));   
2503        num_j_out=num_j(indsel);
2504        num_j1_col=num_j1_col(indsel);
2505        num_j2_col=num_j2_col(indsel);
2506        [num_i1,num_j1]=meshgrid(num_i,num_j1_col);
2507        [num_i2,num_j2]=meshgrid(num_i,num_j2_col);
2508    end   
2509end
2510
2511%------------------------------------------------------------------------
2512% --- Executes on button press in CheckObject.
2513function CheckObject_Callback(hObject, eventdata, handles)
2514%------------------------------------------------------------------------
2515hset_object=findobj(allchild(0),'tag','set_object');%find the set_object interface handle
2516if get(handles.CheckObject,'Value')
2517    SeriesData=get(handles.series,'UserData');
2518    if isfield(SeriesData,'ProjObject') && ~isempty(SeriesData.ProjObject)
2519        set(handles.ViewObject,'Value',1)
2520        ViewObject_Callback(hObject, eventdata, handles)
2521    else
2522        if ishandle(hset_object)
2523            uistack(hset_object,'top')% show the GUI set_object if opened
2524        else
2525            %get the object file
2526            InputTable=get(handles.InputTable,'Data');
2527            defaultname=InputTable{1,1};
2528            if isempty(defaultname)
2529                defaultname={''};
2530            end
2531            fileinput=uigetfile_uvmat('pick a xml object file (or use uvmat to create it)',defaultname,'.xml');
2532            if isempty(fileinput)% exit if no object file is selected
2533                set(handles.CheckObject,'Value',0)
2534                return
2535            end
2536            %read the file
2537            data=xml2struct(fileinput);
2538            if ~isfield(data,'Type')
2539                msgbox_uvmat('ERROR',[fileinput ' is not an object xml file'])
2540                set(handles.CheckObject,'Value',0)
2541                return
2542            end
2543            if ~isfield(data,'ProjMode')
2544                data.ProjMode='none';
2545            end
2546            hset_object=set_object(data);% call the set_object interface
2547            set(hset_object,'Name','set_object_series')% name to distinguish from set_object used with uvmat
2548        end
2549        ProjObject=read_GUI(hset_object);
2550        set(handles.ProjObject,'String',ProjObject.Name);%display the object name
2551        SeriesData=get(handles.series,'UserData');
2552        SeriesData.ProjObject=ProjObject;
2553        set(handles.series,'UserData',SeriesData);
2554    end
2555    set(handles.EditObject,'Visible','on');
2556    set(handles.DeleteObject,'Visible','on');
2557    set(handles.ViewObject,'Visible','on');
2558    set(handles.ProjObject,'Visible','on');
2559else
2560    set(handles.EditObject,'Visible','off');
2561    set(handles.DeleteObject,'Visible','off');
2562    set(handles.ViewObject,'Visible','off');
2563    if ~ishandle(hset_object)
2564        set(handles.ViewObject,'Value',0);
2565    end
2566    set(handles.ProjObject,'Visible','off');
2567end
2568
2569%------------------------------------------------------------------------
2570% --- Executes on button press in ViewObject.
2571%------------------------------------------------------------------------
2572function ViewObject_Callback(hObject, eventdata, handles)
2573
2574UserData=get(handles.series,'UserData');
2575hset_object=findobj(allchild(0),'Tag','set_object');
2576if ~isempty(hset_object)
2577    delete(hset_object)% refresh set_object if already opened
2578end
2579hset_object=set_object(UserData.ProjObject);
2580set(hset_object,'Name','view_object_series')
2581
2582
2583%------------------------------------------------------------------------
2584% --- Executes on button press in EditObject.
2585function EditObject_Callback(hObject, eventdata, handles)
2586%------------------------------------------------------------------------
2587if get(handles.EditObject,'Value')
2588    set(handles.ViewObject,'Value',0)
2589        UserData=get(handles.series,'UserData');
2590    hset_object=set_object(UserData.ProjObject);
2591    set(hset_object,'Name','edit_object_series')
2592    set(get(hset_object,'Children'),'Enable','on')
2593else
2594    hset_object=findobj(allchild(0),'Tag','set_object');
2595    if ~isempty(hset_object)
2596        set(get(hset_object,'Children'),'Enable','off')
2597    end
2598end
2599
2600%------------------------------------------------------------------------
2601% --- Executes on button press in DeleteObject.
2602function DeleteObject_Callback(hObject, eventdata, handles)
2603%------------------------------------------------------------------------
2604SeriesData=get(handles.series,'UserData');
2605SeriesData.ProjObject=[];
2606set(handles.series,'UserData',SeriesData)
2607set(handles.ProjObject,'String','')
2608set(handles.ProjObject,'Visible','off')
2609set(handles.CheckObject,'Value',0)
2610set(handles.ViewObject,'Visible','off')
2611set(handles.EditObject,'Visible','off')
2612hset_object=findobj(allchild(0),'name','set_object_series');
2613if ~isempty(hset_object)
2614    delete(hset_object)
2615end
2616set(handles.DeleteObject,'Visible','off')
2617
2618%------------------------------------------------------------------------
2619% --- Executed when CheckMask is activated
2620%------------------------------------------------------------------------
2621function CheckMask_Callback(hObject, eventdata, handles)
2622
2623if get(handles.CheckMask,'Value')
2624    InputTable=get(handles.InputTable,'Data');
2625    nbview=size(InputTable,1);
2626    MaskTable=cell(nbview,1);%default
2627    ListMask=cell(nbview,1);%default
2628    MaskData=get(handles.MaskTable,'Data');
2629    MaskData(size(MaskData,1):nbview,1)=cell(size(MaskData,1):nbview,1);%complement if undefined lines
2630    for iview=1:nbview
2631        ListMask{iview,1}=num2str(iview);
2632        RootPath=InputTable{iview,1};
2633        if ~isempty(RootPath)
2634            if isempty(MaskData{iview})
2635                SubDir=InputTable{iview,2};
2636                MaskPath=fullfile(RootPath,[regexprep(SubDir,'\..*','') '.mask']);%take the root part of SubDir, before the first dot '.'
2637                if exist(MaskPath,'dir')
2638                    ListStruct=dir(MaskPath);%look for a mask file
2639                    ListCells=struct2cell(ListStruct);% transform dir struct to a cell arrray
2640                    check_dir=cell2mat(ListCells(4,:));% =1 for directories, =0 for files
2641                    ListFiles=ListCells(1,:);%list of file and dri names
2642                    ListFiles=ListFiles(~check_dir);%list of file names (excluding dir)
2643                    mdetect=0;
2644                    if ~isempty(ListFiles)
2645                        for ifile=1:numel(ListFiles)
2646                            [tild,tild,MaskFile{ifile},i1_series,i2_series,j1_series,j2_series,MaskNomType,MaskFileType]=find_file_series(MaskPath,ListFiles{ifile},0);
2647                            if strcmp(MaskFileType,'image') && isempty(i2_series) && isempty(j2_series)
2648                                mdetect=1;
2649                                MaskName=ListFiles{ifile};
2650                            end
2651                            if ~strcmp(MaskFile{ifile},MaskFile{1})
2652                                mdetect=0;% cancel detection test in case of multiple masks, use the brower for selection
2653                                break
2654                            end
2655                        end
2656                    end
2657                    if mdetect==1
2658                        MaskName=fullfile(MaskPath,'mask_1.png');
2659                    else
2660                        MaskName=uigetfile_uvmat('select a mask file:',MaskPath,'image');
2661                    end
2662                else
2663                    MaskName=uigetfile_uvmat('select a mask file:',RootPath,'image');
2664                end
2665                MaskTable{iview,1}=MaskName ;
2666                ListMask{iview,1}=num2str(iview);
2667            end
2668        end
2669    end
2670    set(handles.MaskTable,'Data',MaskTable)
2671    set(handles.MaskTable,'Visible','on')
2672    set(handles.MaskBrowse,'Visible','on')
2673    set(handles.ListMask,'Visible','on')
2674    set(handles.ListMask,'String',ListMask)
2675    set(handles.ListMask,'Value',1)
2676else
2677    set(handles.MaskTable,'Visible','off')
2678    set(handles.MaskBrowse,'Visible','off')
2679    set(handles.ListMask,'Visible','off')
2680end
2681
2682%------------------------------------------------------------------------
2683% --- Executes on button press in MaskBrowse.
2684%------------------------------------------------------------------------
2685function MaskBrowse_Callback(hObject, eventdata, handles)
2686
2687InputTable=get(handles.InputTable,'Data');
2688iview=get(handles.ListMask,'Value');
2689RootPath=InputTable{iview,1};
2690MaskName=uigetfile_uvmat('select a mask file:',RootPath,'image');
2691if ~isempty(MaskName)
2692    MaskTable=get(handles.MaskTable,'Data');
2693    MaskTable{iview,1}=MaskName ;
2694    set(handles.MaskTable,'Data',MaskTable)
2695end
2696
2697%------------------------------------------------------------------------
2698% --- Executes when selected cell(s) is changed in MaskTable.
2699%------------------------------------------------------------------------
2700function MaskTable_CellSelectionCallback(hObject, eventdata, handles)
2701
2702if numel(eventdata.Indices)>=1
2703set(handles.ListMask,'Value',eventdata.Indices(1))
2704end
2705
2706%-------------------------------------------------------------------
2707function MenuHelp_Callback(hObject, eventdata, handles)
2708%-------------------------------------------------------------------
2709
2710
2711% path_to_uvmat=which ('uvmat');% check the path of uvmat
2712% pathelp=fileparts(path_to_uvmat);
2713% helpfile=fullfile(pathelp,'uvmat_doc','uvmat_doc.html');
2714% 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')
2715% else
2716%     addpath (fullfile(pathelp,'uvmat_doc'))
2717%     web([helpfile '#series'])
2718% end
2719
2720%-------------------------------------------------------------------
2721% --- Executes on selection change in TransformName.
2722function TransformName_Callback(hObject, eventdata, handles)
2723%----------------------------------------------------------------------
2724TransformList=get(handles.TransformName,'String');
2725TransformIndex=get(handles.TransformName,'Value');
2726TransformName=TransformList{TransformIndex};
2727TransformPathList=get(handles.TransformName,'UserData');
2728nb_builtin_transform=4;
2729if isequal(TransformName,'more...');     
2730    FileName=uigetfile_uvmat('Pick a transform function',get(handles.TransformPath,'String'),'.m');
2731    if isempty(FileName)
2732        return     %browser closed without choice
2733    end
2734    [TransformPath,TransformName,TransformExt]=fileparts(FileName);% removes extension .m
2735    if ~strcmp(TransformExt,'.m')
2736        msgbox_uvmat('ERROR','a Matlab function .m must be introduced');
2737        return
2738    end
2739     % insert the choice in the menu
2740    TransformIndex=find(strcmp(TransformName,TransformList),1);% look for the selected function in the menu Action
2741    if isempty(TransformIndex)%the input string does not exist in the menu
2742        TransformIndex= length(TransformList);
2743        TransformList=[TransformList(1:end-1);{TransformName};TransformList(end)];% the selected function is appended in the menu, before the last item 'more...'
2744        set(handles.TransformName,'String',TransformList)
2745        TransformPathList=[TransformPathList;{TransformPath}];
2746    else% the input function already exist, we update its path (possibly new)
2747        TransformPathList{TransformIndex}=TransformPath;%
2748        set(handles.TransformName,'Value',TransformIndex)
2749    end
2750   % save the new menu in the personal file 'uvmat_perso.mat'
2751   dir_perso=prefdir;%personal Matalb directory
2752   profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
2753   if exist(profil_perso,'file')
2754       for ilist=nb_builtin_transform+1:numel(TransformPathList)
2755           TransformListUser{ilist-nb_builtin_transform}=TransformList{ilist};
2756           TransformPathListUser{ilist-nb_builtin_transform}=TransformPathList{ilist};
2757       end
2758       TransformPathListUser=TransformPathListUser';
2759       TransformListUser=TransformListUser';
2760       save (profil_perso,'TransformPathListUser','TransformListUser','-append'); %store the root name for future opening of uvmat
2761   end
2762end
2763
2764%display the current function path
2765set(handles.TransformPath,'String',TransformPathList{TransformIndex}); %show the path to the senlected function
2766set(handles.TransformName,'UserData',TransformPathList);
2767
2768%------------------------------------------------------------------------
2769% --- fct activated by the upper bar menu ExportConfig
2770%------------------------------------------------------------------------
2771function MenuDisplayConfig_Callback(hObject, eventdata, handles)
2772
2773global Param
2774Param=read_GUI_series(handles);
2775evalin('base','global Param')%make CurData global in the workspace
2776display('current series config :')
2777evalin('base','Param') %display CurData in the workspace
2778commandwindow; %brings the Matlab command window to the front
2779
2780%------------------------------------------------------------------------
2781% --- fct activated by the upper bar menu InportConfig: import
2782%     menu settings from an xml file (stored in /0_XML for each run)
2783%------------------------------------------------------------------------
2784function MenuImportConfig_Callback(hObject, eventdata, handles)
2785
2786%% use a starting file name for browserr
2787InputTable=get(handles.InputTable,'Data');
2788oldfile=InputTable{1,1};
2789if isempty(oldfile)
2790    % use a file name stored in prefdir
2791    dir_perso=prefdir;
2792    profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
2793    if exist(profil_perso,'file')
2794        h=load (profil_perso);
2795        if isfield(h,'RootPath') && ischar(h.RootPath)
2796            oldfile=h.RootPath;
2797        end
2798    end
2799end
2800filexml=uigetfile_uvmat('pick a xml parameter file',oldfile,'.xml');% get the xml file containing processing parameters
2801%proceed only if a file has been introduced by the browser
2802if ~isempty(filexml)
2803    Param=xml2struct(filexml);% read the input xml file as a Matlab structure
2804    % ask to stop current Action if button RUN is in action (another process is already running)
2805    if isequal(get(handles.RUN,'Value'),1)
2806        answer= msgbox_uvmat('INPUT_Y-N','stop current Action process?');
2807        if strcmp(answer,'Yes')
2808            STOP_Callback(hObject, eventdata, handles)
2809        else
2810            return
2811        end
2812    end
2813    Param.Action.RUN=0; %desactivate the input RUN=1
2814    fill_GUI(Param,handles.series)% fill the elements of the GUI series with the input parameters
2815    SeriesData=get(handles.series,'UserData');
2816    if isfield(Param,'InputFields')
2817        ListField=Param.InputFields.FieldName;
2818        set(handles.FieldName,'String',[ListField;{'get-field...'}])
2819         set(handles.FieldName,'Value',1:numel(ListField))
2820    end       
2821    if isfield(Param,'ActionInput')%  introduce  parameters specific to an Action fct, for instance PIV parameters
2822        set(handles.ActionInput,'Visible','on')
2823        set(handles.ActionInput,'Value',0)
2824        Param.ActionInput.ConfigSource=filexml;% record the source of config for future info
2825        SeriesData.ActionInput=Param.ActionInput;
2826    end
2827    if isfield(Param,'ProjObject') %introduce projection object if relevant
2828        SeriesData.ProjObject=Param.ProjObject;
2829    end
2830    set(handles.series,'UserData',SeriesData)
2831    if isfield(Param,'CheckObject') && isequal(Param.CheckObject,1)
2832        set(handles.ProjObject,'String',Param.ProjObject.Name)
2833        set(handles.ViewObject,'Visible','on')
2834        set(handles.EditObject,'Visible','on')
2835        set(handles.DeleteObject,'Visible','on')
2836    else     
2837        set(handles.ProjObject,'String','')
2838        set(handles.ProjObject,'Visible','off')
2839        set(handles.ViewObject,'Visible','off')
2840        set(handles.EditObject,'Visible','off')
2841        set(handles.DeleteObject,'Visible','off')     
2842    end     
2843    set(handles.REFRESH,'BackgroundColor',[1 0 1]); %paint REFRESH button in magenta to indicate that it should be activated
2844end
2845
2846
2847
2848% --------------------------------------------------------------------
2849function MenuImportParam_Callback(hObject, eventdata, handles)
2850%% use a starting file name for browserr
2851InputTable=get(handles.InputTable,'Data');
2852oldfile=InputTable{1,1};
2853if isempty(oldfile)
2854    % use a file name stored in prefdir
2855    dir_perso=prefdir;
2856    profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
2857    if exist(profil_perso,'file')
2858        h=load (profil_perso);
2859        if isfield(h,'RootPath') && ischar(h.RootPath)
2860            oldfile=h.RootPath;
2861        end
2862    end
2863end
2864filexml=uigetfile_uvmat('pick a xml parameter file',oldfile,'.xml');% get the xml file containing processing parameters
2865%proceed only if a file has been introduced by the browser
2866if ~isempty(filexml)
2867    Param=xml2struct(filexml);% read the input xml file as a Matlab structure
2868    % ask to stop current Action if button RUN is in action (another process is already running)
2869    if isequal(get(handles.RUN,'Value'),1)
2870        answer= msgbox_uvmat('INPUT_Y-N','stop current Action process?');
2871        if strcmp(answer,'Yes')
2872            STOP_Callback(hObject, eventdata, handles)
2873        else
2874            return
2875        end
2876    end
2877    Param.Action.RUN=0; %desactivate the input RUN=1
2878    if ~isfield(Param,'InputTable')||~isfield(Param,'IndexRange')
2879        msgbox_uvmat('ERROR','invalid config file: open a file in a folder ''/0_XML''')
2880        return
2881    end
2882    Param=rmfield(Param,'InputTable');% do not refresh Input files and index range
2883    Param=rmfield(Param,'IndexRange'); 
2884    fill_GUI(Param,handles.series)% fill the elements of the GUI series with the input parameters
2885    SeriesData=get(handles.series,'UserData');
2886    if isfield(Param,'InputFields')
2887        ListField=Param.InputFields.FieldName;
2888        set(handles.FieldName,'String',[ListField;{'get-field...'}])
2889         set(handles.FieldName,'Value',1:numel(ListField))
2890    end       
2891    if isfield(Param,'ActionInput')%  introduce  parameters specific to an Action fct, for instance PIV parameters
2892        set(handles.ActionInput,'Visible','on')
2893        set(handles.ActionInput,'Value',0)
2894        Param.ActionInput.ConfigSource=filexml;% record the source of config for future info
2895        SeriesData.ActionInput=Param.ActionInput;
2896    end
2897    if isfield(Param,'ProjObject') %introduce projection object if relevant
2898        SeriesData.ProjObject=Param.ProjObject;
2899    end
2900    set(handles.series,'UserData',SeriesData)
2901    if isfield(Param,'CheckObject') && isequal(Param.CheckObject,1)
2902        set(handles.ProjObject,'String',Param.ProjObject.Name)
2903        set(handles.ViewObject,'Visible','on')
2904        set(handles.EditObject,'Visible','on')
2905        set(handles.DeleteObject,'Visible','on')
2906    else     
2907        set(handles.ProjObject,'String','')
2908        set(handles.ProjObject,'Visible','off')
2909        set(handles.ViewObject,'Visible','off')
2910        set(handles.EditObject,'Visible','off')
2911        set(handles.DeleteObject,'Visible','off')     
2912    end     
2913    set(handles.REFRESH,'BackgroundColor',[1 0 1]); %paint REFRESH button in magenta to indicate that it should be activated
2914end
2915
2916
2917
2918%------------------------------------------------------------------------
2919% --- Executes when the GUI series is resized.
2920%------------------------------------------------------------------------
2921function series_ResizeFcn(hObject, eventdata, handles)
2922
2923%% input table
2924set(handles.InputTable,'Unit','pixel')
2925Pos=get(handles.InputTable,'Position');
2926set(handles.InputTable,'Unit','normalized')
2927ColumnWidth=round([0.5 0.14 0.14 0.14 0.08]*(Pos(3)-52));
2928ColumnWidth=num2cell(ColumnWidth);
2929set(handles.InputTable,'ColumnWidth',ColumnWidth)
2930
2931%% MinIndex_j and MaxIndex_i
2932unit=get(handles.MinIndex_i,'Unit');
2933set(handles.MinIndex_i,'Unit','pixel')
2934Pos=get(handles.MinIndex_i,'Position');
2935set(handles.MinIndex_i,'Unit',unit)
2936set(handles.MinIndex_i,'ColumnWidth',{Pos(3)-18})
2937set(handles.MaxIndex_i,'ColumnWidth',{Pos(3)-18})
2938set(handles.MinIndex_j,'ColumnWidth',{Pos(3)-18})
2939set(handles.MaxIndex_j,'ColumnWidth',{Pos(3)-18})
2940
2941%% TimeTable
2942set(handles.TimeTable,'Unit','pixel')
2943Pos=get(handles.TimeTable,'Position');
2944set(handles.TimeTable,'Unit','normalized')
2945% ColumnWidth=get(handles.TimeTable,'ColumnWidth');
2946ColumnWidth=num2cell(floor([0.2 0.2 0.2 0.2 0.2]*(Pos(3)-20)));
2947set(handles.TimeTable,'ColumnWidth',ColumnWidth)
2948
2949
2950%% PairString
2951set(handles.PairString,'Unit','pixel')
2952Pos=get(handles.PairString,'Position');
2953set(handles.PairString,'Unit','normalized')
2954set(handles.PairString,'ColumnWidth',{Pos(3)-5})
2955
2956%% MaskTable
2957set(handles.MaskTable,'Unit','pixel')
2958Pos=get(handles.MaskTable,'Position');
2959set(handles.MaskTable,'Unit','normalized')
2960set(handles.MaskTable,'ColumnWidth',{Pos(3)-5})
2961
2962%------------------------------------------------------------------------
2963% --- Executes on button press in status.
2964%------------------------------------------------------------------------
2965function status_Callback(hObject, eventdata, handles)
2966
2967if get(handles.status,'Value')
2968    set(handles.status,'BackgroundColor',[1 1 0])
2969    drawnow
2970    Param=read_GUI(handles.series);
2971    RootPath=Param.InputTable{1,1};
2972    if ~isfield(Param,'OutputSubDir')   
2973        msgbox_uvmat('ERROR','no directory defined for output files')
2974        return
2975    end
2976    OutputSubDir=[Param.OutputSubDir Param.OutputDirExt];% subdirectory for output files
2977    OutputDir=fullfile(RootPath,OutputSubDir);
2978    if exist(OutputDir,'dir')
2979        uigetfile_uvmat('status_display',OutputDir)
2980    else
2981        msgbox_uvmat('ERROR','output folder not created yet: calculation did not start')
2982        set(handles.status,'BackgroundColor',[0 1 0])
2983    end
2984else
2985    %% delete current display fig if selection is off
2986    set(handles.status,'BackgroundColor',[0 1 0])
2987    hfig=findobj(allchild(0),'name','status_display');
2988    if ~isempty(hfig)
2989        delete(hfig)
2990    end
2991    return
2992end
2993
2994
2995%------------------------------------------------------------------------   
2996% launched by selecting a file on the list
2997%------------------------------------------------------------------------
2998function view_file(hObject, eventdata)
2999
3000list=get(hObject,'String');
3001index=get(hObject,'Value');
3002rootroot=get(hObject,'UserData');
3003selectname=list{index};
3004ind_dot=regexp(selectname,'\.\.\.');
3005if ~isempty(ind_dot)
3006    selectname=selectname(1:ind_dot-1);
3007end
3008FullSelectName=fullfile(rootroot,selectname);
3009if exist(FullSelectName,'dir')% a directory has been selected
3010    ListFiles=dir(FullSelectName);
3011    ListDisplay=cell(numel(ListFiles),1);
3012    for ilist=2:numel(ListDisplay)% suppress the first line '.'
3013        ListDisplay{ilist-1}=ListFiles(ilist).name;
3014    end
3015    set(hObject,'Value',1)
3016    set(hObject,'String',ListDisplay)
3017    if strcmp(selectname,'..')
3018        FullSelectName=fileparts(fileparts(FullSelectName));
3019    end
3020    set(hObject,'UserData',FullSelectName)
3021    hfig=get(hObject,'parent');
3022    htitlebox=findobj(hfig,'tag','titlebox');   
3023    set(htitlebox,'String',FullSelectName)
3024elseif exist(FullSelectName,'file')%visualise the vel field if it exists
3025    FileType=get_file_type(FullSelectName);
3026    if strcmp(FileType,'txt')
3027        edit(FullSelectName)
3028    elseif strcmp(FileType,'xml')
3029        editxml(FullSelectName)
3030    else
3031        uvmat(FullSelectName)
3032    end
3033    set(gcbo,'Value',1)
3034end
3035
3036
3037%------------------------------------------------------------------------   
3038% launched by refreshing the status figure
3039%------------------------------------------------------------------------
3040function refresh_GUI(hfig)
3041
3042htitlebox=findobj(hfig,'tag','titlebox');
3043hlist=findobj(hfig,'tag','list');
3044hseries=findobj(allchild(0),'tag','series');
3045hstatus=findobj(hseries,'tag','status');
3046StatusData=get(hstatus,'UserData');
3047OutputDir=get(htitlebox,'String');
3048if ischar(OutputDir),OutputDir={OutputDir};end
3049ListFiles=dir(OutputDir{1});
3050if numel(ListFiles)<1
3051    return
3052end
3053ListFiles(1)=[];%removes the first line ='.'
3054ListDisplay=cell(numel(ListFiles),1);
3055testrecent=0;
3056datnum=zeros(numel(ListDisplay),1);
3057for ilist=1:numel(ListDisplay)
3058    ListDisplay{ilist}=ListFiles(ilist).name;
3059      if ~ListFiles(ilist).isdir && isfield(ListFiles(ilist),'datenum')
3060            datnum(ilist)=ListFiles(ilist).datenum;%only available in recent matlab versions
3061            testrecent=1;
3062       end
3063end
3064set(hlist,'String',ListDisplay)
3065
3066%% Look at date of creation
3067ListDisplay=ListDisplay(datnum~=0);
3068datnum=datnum(datnum~=0);%keep the non zero values corresponding to existing files
3069NbOutputFile=[];
3070if isempty(datnum)
3071    if testrecent
3072        message='no civ result created yet';
3073    else
3074        message='';
3075    end
3076else
3077    [first,indfirst]=min(datnum);
3078    [last,indlast]=max(datnum);
3079    NbOutputFile_str='?';
3080    NbOutputFile=[];
3081    if isfield(StatusData,'NbOutputFile')
3082        NbOutputFile=StatusData.NbOutputFile;
3083        NbOutputFile_str=num2str(NbOutputFile);
3084    end
3085    message={[num2str(numel(datnum)) ' file(s) done over ' NbOutputFile_str] ;['oldest modification:  ' ListDisplay{indfirst} ' : ' datestr(first)];...
3086        ['latest modification:  ' ListDisplay{indlast} ' : ' datestr(last)]};
3087end
3088set(htitlebox,'String', [OutputDir{1};message])
3089
3090%% update the waitbar
3091hwaitbar=findobj(hfig,'tag','waitbar');
3092if ~isempty(NbOutputFile)
3093    BarPosition=get(hwaitbar,'Position');
3094    BarPosition(3)=0.9*numel(datnum)/NbOutputFile;
3095    set(hwaitbar,'Position',BarPosition)
3096end
3097
3098%------------------------------------------------------------------------
3099% --- Executes on selection change in ActionExt.
3100%------------------------------------------------------------------------
3101function ActionExt_Callback(hObject, eventdata, handles)
3102
3103ActionExtList=get(handles.ActionExt,'String');
3104ActionExt=ActionExtList{get(handles.ActionExt,'Value')};
3105ActionList=get(handles.ActionName,'String');
3106ActionName=ActionList{get(handles.ActionName,'Value')};
3107% TransformPath='';
3108% if ~isempty(get(handles.ActionExt,'UserData'))
3109%     TransformPath=get(handles.ActionExt,'UserData');
3110% end
3111% if strcmp(ActionExt,'.sh')
3112%     set(handles.series,'Pointer','watch') % set the mouse pointer to 'watch'
3113%     set(handles.ActionExt,'BackgroundColor',[1 1 0])
3114%     ActionFullName=fullfile(get(handles.ActionPath,'String'),[ActionName '.sh']);
3115%     if ~exist(ActionFullName,'file')
3116%         answer=msgbox_uvmat('INPUT_Y-N','compiled version has not been created: compile now?');
3117%         if strcmp(answer,'Yes')
3118%             set(handles.ActionExt,'BackgroundColor',[1 1 0])
3119%             path_uvmat=fileparts(which('series'));
3120%             currentdir=pwd;
3121%             cd(get(handles.ActionPath,'String'))% go to the directory of Action
3122%             %  addpath(get(handles.TransformPath,'String'))
3123%             addpath(path_uvmat)% add the path to uvmat to run the fct 'compile'
3124%            % addpath(fullfile(path_uvmat,'transform_field'))% add the path to uvmat to run the fct 'compile'
3125%             compile(ActionName,TransformPath)
3126%             cd(currentdir)
3127%         end       
3128%     else
3129%         sh_file_info=dir(fullfile(get(handles.ActionPath,'String'),[ActionName '.sh']));
3130%         m_file_info=dir(fullfile(get(handles.ActionPath,'String'),[ActionName '.m']));
3131%         if isfield(m_file_info,'datenum') && m_file_info.datenum>sh_file_info.datenum
3132%             set(handles.ActionExt,'BackgroundColor',[1 1 0])
3133%             drawnow
3134%             answer=msgbox_uvmat('INPUT_Y-N',[ActionName '.sh needs to be updated: recompile now?']);
3135%             if strcmp(answer,'Yes')
3136%                 path_uvmat=fileparts(which('series'));
3137%                 currentdir=pwd;
3138%                 cd(get(handles.ActionPath,'String'))% go to the directory of Action
3139%                 %  addpath(get(handles.TransformPath,'String'))
3140%                 addpath(path_uvmat)% add the path to uvmat to run the fct 'compile'
3141%                 addpath(fullfile(path_uvmat,'transform_field'))% add the path to uvmat to run the fct 'compile'
3142%                 compile(ActionName,TransformPath)
3143%                 cd(currentdir)
3144%             end
3145%         end
3146%     end
3147%     set(handles.ActionExt,'BackgroundColor',[1 1 1])
3148%      set(handles.series,'Pointer','arrow') % set the mouse pointer to 'watch
3149% end
3150
3151
3152function num_NbProcess_Callback(hObject, eventdata, handles)
3153
3154
3155function num_NbSlice_Callback(hObject, eventdata, handles)
3156NbSlice=str2num(get(handles.num_NbSlice,'String'));
3157set(handles.num_NbProcess,'String',num2str(NbSlice))
3158
3159%------------------------------------------------------------------------
3160% --- set the visibility of relevant velocity type menus:
3161function menu=set_veltype_display(Civ,FileType)
3162%------------------------------------------------------------------------
3163if ~exist('FileType','var')
3164    FileType='civx';
3165end
3166switch FileType
3167    case 'civx'
3168        menu={'civ1';'interp1';'filter1';'civ2';'interp2';'filter2'};
3169        if isequal(Civ,0)
3170            imax=0;
3171        elseif isequal(Civ,1) || isequal(Civ,2)
3172            imax=1;
3173        elseif isequal(Civ,3)
3174            imax=3;
3175        elseif isequal(Civ,4) || isequal(Civ,5)
3176            imax=4;
3177        elseif isequal(Civ,6) %patch2
3178            imax=6;
3179        end
3180    case 'civdata'
3181        menu={'civ1';'filter1';'civ2';'filter2'};
3182        if isequal(Civ,0)
3183            imax=0;
3184        elseif isequal(Civ,1) || isequal(Civ,2)
3185            imax=1;
3186        elseif isequal(Civ,3)
3187            imax=2;
3188        elseif isequal(Civ,4) || isequal(Civ,5)
3189            imax=3;
3190        elseif isequal(Civ,6) %patch2
3191            imax=4;
3192        end
3193end
3194menu=menu(1:imax);
3195
3196
3197% --- Executes on mouse motion over figure - except title and menu.
3198function series_WindowButtonMotionFcn(hObject, eventdata, handles)
3199set(hObject,'Pointer','arrow');
3200
3201
3202% --- Executes on button press in SetPairs.
3203function SetPairs_Callback(hObject, iview, handles)
3204
3205%% delete previous occurrence of 'set_pairs'
3206hfig=findobj(allchild(0),'Tag','set_pairs');
3207if ~isempty(hfig)
3208delete(hfig)
3209end
3210
3211%% create the GUI set_pairs
3212set(0,'Unit','points')
3213ScreenSize=get(0,'ScreenSize');% get the size of the screen, to put the fig on the upper right
3214Width=220;% fig width in points (1/72 inch)
3215Height=min(0.8*ScreenSize(4),300);
3216Left=ScreenSize(3)- Width-40; %right edge close to the right, with margin=40
3217Bottom=ScreenSize(4)-Height-40; %put fig at top right
3218hfig=findobj(allchild(0),'Tag','set_slice');
3219if ~isempty(hfig),delete(hfig), end; %delete existing version of the GUI
3220hfig=figure('name','set_pairs','tag','set_pairs','MenuBar','none','NumberTitle','off','Unit','points','Position',[Left,Bottom,Width,Height]);
3221BackgroundColor=get(hfig,'Color');
3222SeriesData=get(handles.series,'UserData');
3223TimeUnit=get(handles.TimeUnit,'String');
3224PairString=get(handles.PairString,'Data');
3225ListViewLines=find(cellfun('isempty',PairString)==0);%find list of non empty pairs
3226ListViewMenu=cell(numel(ListViewLines),1);
3227for ilist=1:numel(ListViewLines)
3228    ListViewMenu{ilist}=num2str(ListViewLines(ilist));
3229end
3230if isempty(iview)
3231    ListViewValue=numel(ListViewLines);% we work by default on the pair option for the last line which requires pairs
3232    iview=ListViewLines(end);
3233else
3234    ListViewValue=find(ListViewLines==iview);
3235end
3236ref_i=str2num(get(handles.num_first_i,'String'));
3237ref_j=str2num(get(handles.num_first_j,'String'));
3238[ModeMenu,ModeValue]=update_mode(SeriesData.i1_series{iview},SeriesData.i2_series{iview},SeriesData.j2_series{iview});
3239displ_pair=update_listpair(SeriesData.i1_series{iview},SeriesData.i2_series{iview},SeriesData.j1_series{iview},SeriesData.j2_series{iview},ModeMenu{ModeValue},...
3240                                                     SeriesData.Time{iview},TimeUnit,ref_i,ref_j,SeriesData.FileInfo{iview});
3241% first raw of the GUI
3242uicontrol('Style','text','Units','normalized', 'Position', [0.05 0.88 0.5 0.1],'BackgroundColor',BackgroundColor,...
3243    'String','row to edit #','FontUnits','points','FontSize',12,'FontWeight','bold','ForegroundColor','blue','HorizontalAlignment','right');%title
3244uicontrol('Style','popupmenu','Units','normalized', 'Position', [0.54 0.8 0.3 0.2],'BackgroundColor',[1 1 1],...
3245    'Callback',@(hObject,eventdata)ListView_Callback(hObject,eventdata),'String',ListViewMenu,'Value',ListViewValue,'FontUnits','points','FontSize',12,'FontWeight','bold',...
3246    'Tag','ListView','TooltipString','''ListView'':choice of the file series w for pair display');
3247% second raw of the GUI
3248uicontrol('Style','text','Units','normalized', 'Position', [0.05 0.79 0.7 0.1],'BackgroundColor',BackgroundColor,...
3249    'String','mode of index pairing:','FontUnits','points','FontSize',12,'FontWeight','bold','ForegroundColor','blue','HorizontalAlignment','left');%title
3250uicontrol('Style','popupmenu','Units','normalized', 'Position', [0.05 0.62 0.9 0.2],'BackgroundColor',[1 1 1],...
3251    'Callback',@(hObject,eventdata)Mode_Callback(hObject,eventdata),'String',ModeMenu,'Value',ModeValue,'FontUnits','points','FontSize',12,'FontWeight','bold',...
3252    'Tag','Mode','TooltipString','''Mode'': choice of the image pair mode');
3253% third raw
3254uicontrol('Style','text','Units','normalized', 'Position', [0.05 0.6 0.7 0.1],'BackgroundColor',BackgroundColor,...
3255    'String','pair choice:','FontUnits','points','FontSize',12,'FontWeight','bold','ForegroundColor','blue','HorizontalAlignment','left');%title
3256uicontrol('Style','listbox','Units','normalized', 'Position', [0.05 0.42 0.9 0.2],'BackgroundColor',[1 1 1],...
3257    'Callback',@(hObject,eventdata)ListPair_Callback(hObject,eventdata),'String',displ_pair,'Value',1,'FontUnits','points','FontSize',12,'FontWeight','bold',...
3258    'Tag','ListPair','TooltipString','''ListPair'': menu for selecting the image pair');
3259uicontrol('Style','text','Units','normalized', 'Position', [0.1 0.22 0.8 0.1],'BackgroundColor',BackgroundColor,...
3260    'String','ref_i           ref_j','FontUnits','points','FontSize',12,'FontWeight','bold','ForegroundColor','blue','HorizontalAlignment','center');%title
3261uicontrol('Style','edit','Units','normalized', 'Position', [0.15 0.17 0.3 0.08],'BackgroundColor',[1 1 1],...
3262    'Callback',@(hObject,eventdata)num_ref_i_Callback(hObject,eventdata),'String',num2str(ref_i),'FontUnits','points','FontSize',12,'FontWeight','bold',...
3263    'Tag','num_ref_i','TooltipString','''num_ref_i'': reference field index i used to display dt in ''list_pair_civ''');
3264uicontrol('Style','edit','Units','normalized', 'Position', [0.55 0.17 0.3 0.08],'BackgroundColor',[1 1 1],...
3265    'Callback',@(hObject,eventdata)num_ref_j_Callback(hObject,eventdata),'String',num2str(ref_j),'FontUnits','points','FontSize',12,'FontWeight','bold',...
3266    'Tag','num_ref_j','TooltipString','''num_ref_j'': reference field index i used to display dt in ''list_pair_civ''');
3267%  last raw  of the GUI: pushbuttons
3268% 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),...
3269%     'FontWeight','bold','FontUnits','points','FontSize',12,'TooltipString','''OK'': apply the output to the current field series in uvmat');
3270drawnow
3271
3272%------------------------------------------------------------------------
3273function ListView_Callback(hObject,eventdata)
3274Mode_Callback(hObject,eventdata)
3275
3276%------------------------------------------------------------------------   
3277function Mode_Callback(hObject,eventdata)
3278%% get input info
3279hseries=findobj(allchild(0),'tag','series');%handles of the GUI series
3280hhseries=guidata(hseries);%handles of the elements in the GUI series
3281TimeUnit=get(hhseries.TimeUnit,'String');
3282SeriesData=get(hseries,'UserData');
3283mode_list=get(hObject,'String');
3284mode=mode_list{get(hObject,'Value')};
3285hListView=findobj(get(hObject,'parent'),'Tag','ListView');
3286iview=get(hListView,'Value');
3287i1_series=SeriesData.i1_series{iview};
3288i2_series=SeriesData.i2_series{iview};
3289j1_series=SeriesData.j1_series{iview};
3290j2_series=SeriesData.j2_series{iview};
3291
3292%% enable j index visibility after the new choice
3293status_j='on';%default
3294if isempty(find(~cellfun(@isempty,SeriesData.j1_series), 1)); % case of empty j indices
3295    status_j='off'; % no j index needed
3296elseif strcmp(get(handles.PairString,'Visible'),'on')
3297    check_burst=cellfun(@isempty,regexp(PairString,'^j'));%=0 for burst case, 1 otherwise
3298    if isempty(find(check_burst, 1))% if all pair string begins by j (burst)
3299        status_j='off'; % no j index needed for bust case
3300    end
3301end
3302enable_j(handles,status_j) % no j index needed
3303
3304%% get the reference indices for the time interval Dt
3305href_i=findobj(get(hObject,'parent'),'Tag','ref_i');
3306ref_i=[];ref_j=[];
3307if strcmp(get(href_i,'Visible'),'on')
3308    ref_i=str2num(get(href_i,'String'));
3309end
3310if isempty(ref_i)
3311    ref_i=1;
3312end
3313if isempty(ref_j)
3314    ref_j=1;
3315end
3316
3317%% update the menu ListPair
3318Menu=update_listpair(i1_series,i2_series,j1_series,j2_series,mode,SeriesData.Time{iview},TimeUnit,ref_i,ref_j,FileInfo);
3319hlist_pairs=findobj(get(hObject,'parent'),'Tag','ListPair');
3320set(hlist_pairs,'Value',1)% set the first choice by default in ListPair
3321set(hlist_pairs,'String',Menu)% set the menu in ListPair
3322ListPair_Callback(hlist_pairs,[])% apply the default choice in ListPair
3323
3324%-------------------------------------------------------------
3325% --- Executes on selection in ListPair.
3326function ListPair_Callback(hObject,eventdata)
3327%------------------------------------------------------------
3328list_pair=get(hObject,'String');%get the menu of image pairs
3329if isempty(list_pair)
3330    string='';
3331else
3332    string=list_pair{get(hObject,'Value')};
3333   % string=regexprep(string,',.*','');%removes time indication (after ',')
3334end
3335hseries=findobj(allchild(0),'tag','series');
3336hPairString=findobj(hseries,'tag','PairString');
3337PairString=get(hPairString,'Data');
3338hListView=findobj(get(hObject,'parent'),'Tag','ListView');
3339iview=get(hListView,'Value');
3340PairString{iview,1}=string;
3341% report the selected pair string to the table PairString
3342set(hPairString,'Data',PairString)
3343
3344
3345%------------------------------------------------------------------------
3346function num_ref_i_Callback(hObject, eventdata)
3347%------------------------------------------------------------------------
3348Mode_Callback([],[])
3349
3350%------------------------------------------------------------------------
3351function num_ref_j_Callback(hObject, eventdata)
3352%------------------------------------------------------------------------
3353Mode_Callback([],[])
3354
3355
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