source: trunk/src/series.m @ 533

Last change on this file since 533 was 533, checked in by sommeria, 9 years ago

bugs repaired in proj_field

File size: 81.3 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)
62global nb_builtin_ACTION nb_builtin_transform
63% Choose default command line output for series
64handles.output = hObject;
65% Update handles structure
66guidata(hObject, handles);
67%default initial parameters
68drawnow
69set(hObject,'Units','pixels')
70set(handles.PairString,'ColumnName',{'pairs'})
71set(handles.PairString,'ColumnEditable',logical(0))
72set(handles.PairString,'ColumnFormat',{'char'})
73set(handles.PairString,'Data',{''})
74series_ResizeFcn(hObject, eventdata, handles)%resize table according to series GUI size
75set(hObject,'WindowButtonDownFcn',{'mouse_down'})%allows mouse action with right button (zoom for uicontrol display)
76dir_perso=prefdir;
77test_profil_perso=0;
78profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
79if exist(profil_perso,'file')
80     h=load (profil_perso);
81     if isfield(h,'MenuFile')
82          for ifile=1:min(length(h.MenuFile),5)
83              eval(['set(handles.MenuFile_' num2str(ifile) ',''Label'',h.MenuFile{ifile});'])
84          end
85     end
86     test_profil_perso=1;
87end
88
89%check default input data
90if ~exist('param','var')
91    param=[]; %default
92end
93
94%% file name and browser initialisation
95if isfield(param,'transform_str')
96    set(handles.TransformName,'String',param.transform_str)
97end
98if isfield(param,'transform_val')
99    set(handles.TransformName,'Value',param.transform_val);
100else
101     set(handles.TransformName,'Value',1);%default
102end
103if isfield(param,'FileName')
104    InputTable={'','','','',''};
105    set(handles.InputTable,'Data',InputTable)
106    if isfield(param,'FileName_1')
107        display_file_name(handles,param.FileName_1,0)
108        display_file_name(handles,param.FileName,1)
109    else
110        display_file_name(handles,param.FileName,0)
111    end
112end 
113if isfield(param,'incr_i')
114    set(handles.num_incr_i,'String',num2str(param.incr_i))
115end
116if isfield(param,'incr_j')
117    set(handles.num_incr_j,'String',num2str(param.incr_j))
118end
119
120%% fields input initialisation
121if isfield(param,'list_fields')&& isfield(param,'index_fields') &&~isempty(param.list_fields) &&~isempty(param.index_fields)
122    set(handles.FieldName,'String',param.list_fields);% list menu fields
123    set(handles.FieldName,'Value',param.index_fields);% selected string index
124end
125if isfield(param,'Coord_x_str')&& isfield(param,'Coord_x_val')
126        set(handles.Coord_x,'String',param.Coord_x_str);% list menu fields
127    set(handles.Coord_x,'Value',param.Coord_x_val);% selected string index
128end
129if isfield(param,'Coord_y_str')&& isfield(param,'Coord_y_val')
130        set(handles.Coord_y,'String',param.Coord_y_str);% list menu fields
131    set(handles.Coord_y,'Value',param.Coord_y_val);% selected string index
132end
133
134%loads the information stored in prefdir to initiate  the list of ActionName functions
135fct_menu={'check_data_files';'aver_stat';'time_series';'merge_proj';'clean_civ_cmx'};
136transform_menu={'';'phys';'px';'phys_polar'};
137nb_builtin_ACTION=numel(fct_menu); %number of functions
138nb_transform=numel(transform_menu);
139[path_series,name,ext]=fileparts(which('series'));
140path_series=fullfile(path_series,'series');%path of the function 'series'
141addpath (path_series) ; %add the path to UVMAT, (useful in case of change of working directory after civ has been s opened in the working directory)
142path_transform=fullfile(path_series,'transform_field');%path to the field transform functions
143for ilist=1:length(fct_menu)
144    fct_path{ilist,1}=path_series;%paths of the fuctions buil-in in 'series.m'
145end
146
147%% TRANSFORM menu: loads the information stored in prefdir to initiate  the list of field transform functions
148menu_str={'';'sub_field';'phys';'phys_polar'};
149nb_builtin_transform=numel(menu_str); %number of functions
150[path_uvmat,name,ext]=fileparts(which('uvmat'));
151addpath(fullfile(path_uvmat,'transform_field'))
152fct_handle{1,1}=[];
153testexist(1)=1;
154for ilist=2:length(menu_str)
155    if exist(menu_str{ilist},'file')
156        fct_handle{ilist,1}=str2func(menu_str{ilist});
157        testexist(ilist)=1;
158    else
159        testexist(ilist)=0;
160    end
161end
162rmpath(fullfile(path_uvmat,'transform_field'))
163
164%% read the list of transform functions stored in the personal file 'uvmat_perso.mat' in prefdir
165if test_profil_perso
166    if isfield(h,'series_fct') && iscell(h.series_fct)
167         for ilist=1:length(h.series_fct)
168             [path,file]=fileparts(h.series_fct{ilist});
169             fct_path=[fct_path; {path}];%concatene the list of paths
170             fct_menu=[fct_menu; {file}];
171         end
172    end
173    if isfield(h,'transform_fct') && iscell(h.transform_fct)
174        for ilist=1:length(h.transform_fct);
175             [path,file]=fileparts(h.transform_fct{ilist});
176             addpath(path)
177             if exist(file,'file')
178                h_func=str2func(file);
179                testexist=[testexist 1];
180             else
181                h_func=[];
182                testexist=[testexist 0];
183             end
184             fct_handle=[fct_handle; {h_func}];%concatene the list of paths
185             rmpath(path)
186             menu_str=[menu_str; {file}];
187        end
188    end
189end
190fct_menu=[fct_menu;{'more...'}];
191set(handles.ActionName,'String',fct_menu)
192set(handles.ActionName,'UserData',fct_path)% store the list of path in UserData of ACTION
193menu_str=menu_str(find(testexist));
194fct_handle=fct_handle(find(testexist));
195menu_str=[menu_str;{'more...'}];
196set(handles.TransformName,'String',menu_str)
197set(handles.TransformName,'UserData',fct_handle)% store the list of path in UserData of ACTION
198
199%% Adjust the GUI according to the binaries available in PARAM.xml
200path_uvmat=fileparts(which('uvmat')); %path to civ
201addpath (path_uvmat) ; %add the path to civ, (useful in case of change of working directory after civ has been s opened in the working directory)
202errormsg=[];%default error message
203xmlfile='PARAM.xml';
204if exist(xmlfile,'file')
205    try
206        t=xmltree(xmlfile);
207        sparam=convert(t);
208    catch ME
209        errormsg={' Unable to read the file PARAM.xml defining the civx binaries:';ME.message};
210    end
211else
212    errormsg=[xmlfile ' not found: path to civx binaries undefined'];
213end
214if ~isempty(errormsg)
215    msgbox_uvmat('WARNING',errormsg);
216end
217test_batch=0;%default: ,no batch mode available
218if isfield(sparam,'BatchParam') && isfield(sparam.BatchParam,'BatchMode')
219    test_batch=strcmp(sparam.BatchParam.BatchMode,'sge'); %sge is currently the only implemented batch mod
220end
221RUNVal=get(handles.RunMode,'Value');
222if test_batch==0
223   if RUNVal>2
224       set(handles.RunMode,'Value',1)
225   end
226   set(handles.RunMode,'String',{'local';'background'})
227else
228    set(handles.RunMode,'String',{'local';'background';'cluster'})
229end
230
231%------------------------------------------------------------------------
232% --- Outputs from this function are returned to the command line.
233function varargout = series_OutputFcn(hObject, eventdata, handles)
234%------------------------------------------------------------------------
235% varargout  cell array for returning output args (see VARARGOUT);
236% hObject    handle to figure
237% eventdata  reserved - to be defined in a future version of MATLAB
238% handles    structure with handles and user data (see GUIDATA)
239% Get default command line output from handles structure
240varargout{1} = handles.output;
241
242%------------------------------------------------------------------------
243%------------------------------------------------------------------------
244%  II - FUNCTIONS FOR INTRODUCING THE INPUT FILES
245% automatically sets the global properties when the rootfile name is introduced
246% then activate the view-field actionname if selected
247% it is activated either by clicking on the RootPath window or by the
248% browser
249%------------------------------------------------------------------------
250%------------------------------------------------------------------------
251function MenuBrowse_Callback(hObject, eventdata, handles)
252%------------------------------------------------------------------------   
253InputTable=get(handles.InputTable,'Data');
254if isempty(InputTable)
255    RootPathCell={};
256else
257    RootPathCell=InputTable(:,1);
258end
259oldfile=''; %default
260if isempty(RootPathCell)||isequal(RootPathCell,{''})%loads the previously stored file name and set it as default in the file_input box
261     dir_perso=prefdir;
262     profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
263     if exist(profil_perso,'file')
264          h=load (profil_perso);
265         if isfield(h,'filebase')&&ischar(h.filebase)
266                 oldfile=h.filebase;
267         end
268         if isfield(h,'RootPath')&&ischar(h.RootPath)
269                 oldfile=h.RootPath;
270         end
271     end
272else
273     SubDirCell=InputTable(:,2);
274    RootFileCell=InputTable(:,3);
275     oldfile=fullfile(RootPathCell{1},SubDirCell{1},RootFileCell{1});
276 end
277[FileName, PathName, filterindex] = uigetfile( ...
278       {'*.xml;*.xls;*.png;*.tif;*.avi;*.AVI;*.nc', ' (*.xml,*.xls, *.png,*.tif, *.avi,*.nc)';
279       '*.xml',  '.xml files '; ...
280        '*.xls',  '.xls files '; ...
281        '*.png','.png image files'; ...
282        '*.tif','.tif image files'; ...
283        '*.avi;*.AVI','.avi movie files'; ...
284        '*.nc','.netcdf files'; ...
285        '*.*',  'All Files (*.*)'}, ...
286        'Pick a file',oldfile);
287fileinput=[PathName FileName];%complete file name
288if isempty(fileinput),return;end %abandon if no file is introduced by the browser
289[path,name,ext]=fileparts(fileinput);
290if isequal(ext,'.xml')
291    [Param,Heading]=xml2struct(fileinput);
292    if ~strcmp(Heading,'Series')
293        msg_box_uvmat('ERROR','xml file heading is not <Series>')
294    else
295        fill_GUI(Param,handles);%fill the GUI with the parameters retrieved from the xml file
296        if isfield(Param,'CheckObject')&& Param.CheckObject
297            set_object(Param.ProjObject)
298        end
299        set(handles.REFRESH,'UserData',[1:size(Param.InputTable,1)])
300        REFRESH_Callback([],[], handles)
301        return
302    end
303elseif isequal(ext,'.xls')
304    msg_box_uvmat('ERROR','input file type not implemented')%A Faire: ouvrir le fichier pour naviguer
305else
306    display_file_name(handles,fileinput,0)
307end
308
309% --------------------------------------------------------------------
310function MenuFile_1_Callback(hObject, eventdata, handles)
311fileinput=get(handles.MenuFile_1,'Label');
312display_file_name(handles,fileinput,0)
313
314% --------------------------------------------------------------------
315function MenuFile_2_Callback(hObject, eventdata, handles)
316fileinput=get(handles.MenuFile_2,'Label');
317display_file_name(handles,fileinput,0)
318
319% --------------------------------------------------------------------
320function MenuFile_3_Callback(hObject, eventdata, handles)
321fileinput=get(handles.MenuFile_3,'Label');
322display_file_name( handles,fileinput,0)
323
324% --------------------------------------------------------------------
325function MenuFile_4_Callback(hObject, eventdata, handles)
326fileinput=get(handles.MenuFile_4,'Label');
327display_file_name(handles,fileinput,0)
328
329% --------------------------------------------------------------------
330function MenuFile_5_Callback(hObject, eventdata, handles)
331fileinput=get(handles.MenuFile_5,'Label');
332display_file_name(handles,fileinput,0)
333
334% --------------------------------------------------------------------
335function MenuBrowse_insert_Callback(hObject, eventdata, handles)
336InputTable=get(handles.InputTable,'Data');
337RootPathCell=InputTable(:,1);
338SubDirCell=InputTable(:,3);
339RootFileCell=InputTable(:,2);
340oldfile=''; %default
341if isempty(RootPathCell)||isequal(RootPathCell,{''})%loads the previously stored file name and set it as default in the file_input box
342     dir_perso=prefdir;
343     profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
344     if exist(profil_perso,'file')
345          h=load (profil_perso);
346         if isfield(h,'filebase')&ischar(h.filebase)
347                 oldfile=h.filebase;
348         end
349         if isfield(h,'RootPath')&ischar(h.RootPath)
350                 oldfile=h.RootPath;
351         end
352     end
353 else
354     oldfile=fullfile(RootPathCell{1},RootFileCell{1});
355 end
356[FileName, PathName, filterindex] = uigetfile( ...
357       {'*.xml;*.xls;*.png;*.avi;*.AVI;*.nc', ' (*.xml,*.xls, *.png, *.avi,*.nc)';
358       '*.xml',  '.xml files '; ...
359        '*.xls',  '.xls files '; ...
360        '*.png','.png image files'; ...
361        '*.avi;*.AVI','.avi movie files'; ...
362        '*.nc','.netcdf files'; ...
363        '*.*',  'All Files (*.*)'}, ...
364        'Pick a file',oldfile);
365fileinput=[PathName FileName];%complete file name
366sizf=size(fileinput);
367if (~ischar(fileinput)|~isequal(sizf(1),1)),return;end
368[path,name,ext]=fileparts(fileinput);
369if isequal(ext,'.xml')
370    msgbox_uvmat('ERROR','input file type not implemented')%A Faire: ouvrir le fichier pour naviguer
371elseif isequal(ext,'.xls')
372    msgbox_uvmat('ERROR','input file type not implemented')%A Faire: ouvrir le fichier pour naviguer
373else
374    display_file_name(handles,fileinput,'append')
375end
376
377% --------------------------------------------------------------------
378function MenuFile_insert_1_Callback(hObject, eventdata, handles)
379% --------------------------------------------------------------------   
380fileinput=get(handles.MenuFile_insert_1,'Label');
381display_file_name(handles,fileinput,'append')
382
383% --------------------------------------------------------------------
384function MenuFile_insert_2_Callback(hObject, eventdata, handles)
385% --------------------------------------------------------------------   
386fileinput=get(handles.MenuFile_insert_2,'Label');
387display_file_name(handles,fileinput,'append')
388
389% --------------------------------------------------------------------
390function MenuFile_insert_3_Callback(hObject, eventdata, handles)
391% --------------------------------------------------------------------   
392fileinput=get(handles.MenuFile_insert_3,'Label');
393display_file_name( handles,fileinput,'append')
394
395% --------------------------------------------------------------------
396function MenuFile_insert_4_Callback(hObject, eventdata, handles)
397% --------------------------------------------------------------------   
398fileinput=get(handles.MenuFile_insert_4,'Label');
399display_file_name( handles,fileinput,'append')
400
401% --------------------------------------------------------------------
402function MenuFile_insert_5_Callback(hObject, eventdata, handles)
403% --------------------------------------------------------------------   
404fileinput=get(handles.MenuFile_insert_5,'Label');
405display_file_name(handles,fileinput,'append')
406
407%------------------------------------------------------------------------
408% --- Executes when entered data in editable cell(s) in InputTable.
409function InputTable_CellEditCallback(hObject, eventdata, handles)
410%------------------------------------------------------------------------
411set(handles.REFRESH,'Visible','on')
412iview=eventdata.Indices(1);
413view_set=get(handles.REFRESH,'UserData');
414if isempty(find(view_set==iview))
415    set(handles.REFRESH,'UserData',[view_set iview])
416end
417%% enable other menus and uicontrols
418set(handles.MenuOpen_insert,'Enable','on')
419set(handles.MenuFile_insert_1,'Enable','on')
420set(handles.MenuFile_insert_2,'Enable','on')
421set(handles.MenuFile_insert_3,'Enable','on')
422set(handles.MenuFile_insert_4,'Enable','on')
423set(handles.MenuFile_insert_5,'Enable','on')
424set(handles.RUN, 'Enable','On')
425set(handles.RUN,'BackgroundColor',[1 0 0])% set RUN button to red
426
427%update the output dir
428% SubDir=sort(InputTable(:,2)); %set of subdirectories sorted in alphabetical order
429% SubDirOut=SubDir{1};
430% if numel(SubDir)>1
431%     for ilist=2:numel(SubDir)
432%         SubDirOut=[SubDirOut '-' SubDir{ilist}];
433%     end
434% end
435% set(handles.OutputSubDir,'String',SubDirOut)
436
437%------------------------------------------------------------------------
438% --- Executes on button press in REFRESH.
439function REFRESH_Callback(hObject, eventdata, handles)
440%------------------------------------------------------------------------
441InputTable=get(handles.InputTable,'Data');
442view_set=get(handles.REFRESH,'UserData');
443set(handles.REFRESH,'BackgroundColor',[0.7 0.7 0.7])% set REFRESH  button to grey color
444drawnow
445for iview=view_set
446    RootPath=fullfile(InputTable{iview,1},InputTable{iview,2});
447    if ~exist(RootPath,'dir')
448        i1_series=[];
449        RootPath=fileparts(RootPath); %will try the upped forldr
450    else
451        [RootPath,SubDir,RootFile,i1_series,i2_series,j1_series,j2_series,tild,FileType,MovieObject]=...
452            find_file_series(fullfile(InputTable{iview,1},InputTable{iview,2}),[InputTable{iview,3} InputTable{iview,4} InputTable{iview,5}]);
453    end
454    if isempty(i1_series)
455        [FileName, PathName, filterindex] = uigetfile( ...
456            {'*.xml;*.xls;*.png;*.tif;*.avi;*.AVI;*.nc', ' (*.xml,*.xls, *.png,*.tif, *.avi,*.nc)';
457            '*.xml',  '.xml files '; ...
458            '*.xls',  '.xls files '; ...
459            '*.png','.png image files'; ...
460            '*.tif','.tif image files'; ...
461            '*.avi;*.AVI','.avi movie files'; ...
462            '*.nc','.netcdf files'; ...
463            '*.*',  'All Files (*.*)'}, ...
464            ['unvalid entry at line ' num2str(iview) ', pick a file'],RootPath);
465        fileinput=[PathName FileName];%complete file name
466        if isempty(fileinput),return;end %abandon if the operation has been cancelled: no input from browser
467        [path,name,ext]=fileparts(fileinput);
468        display_file_name(handles,fileinput,iview)
469    else
470        update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileType,MovieObject,iview)
471    end
472end
473set(handles.REFRESH,'BackgroundColor',[1 0 0])% set REFRESH  button to grey color
474set(handles.REFRESH,'Visible','off')
475set(handles.REFRESH,'UserData',[])
476
477%------------------------------------------------------------------------
478% --- Function called when a new file is opened, either by series_OpeningFcn or by the browser
479function display_file_name(handles,fileinput,iview)
480%------------------------------------------------------------------------ 
481%
482% INPUT:
483% handles: handles of elements in the GUI
484% fielinput: input file name, including path
485% append =0 (refresh the Input table with the new file), ='append' append a new line in the table
486
487%% get the input root name, indices, file extension and nomenclature NomType
488if ~exist(fileinput,'file')
489    msgbox_uvmat('ERROR',['input file ' fileinput  ' does not exist'])
490    return
491end
492
493%% enable other menus and uicontrols
494set(handles.MenuOpen_insert,'Enable','on')
495set(handles.MenuFile_insert_1,'Enable','on')
496set(handles.MenuFile_insert_2,'Enable','on')
497set(handles.MenuFile_insert_3,'Enable','on')
498set(handles.MenuFile_insert_4,'Enable','on')
499set(handles.MenuFile_insert_5,'Enable','on')
500set(handles.RUN, 'Enable','On')
501set(handles.RUN,'BackgroundColor',[1 0 0])% set RUN button to red
502set(handles.InputTable,'BackgroundColor',[1 1 0]) % set RootPath edit box  to yellow
503drawnow
504
505%% detect root name, nomenclature and indices in the input file name:
506[FilePath,FileName,FileExt]=fileparts(fileinput);
507% detect the file type, get the movie object if relevant, and look for the corresponding file series:
508% the root name and indices may be corrected by including the first index i1 if a corresponding xml file exists
509[RootPath,SubDir,RootFile,i1_series,i2_series,j1_series,j2_series,NomType,FileType,MovieObject,i1,i2,j1,j2]=find_file_series(FilePath,[FileName FileExt]);
510if isempty(RootFile)&&isempty(i1_series)
511    errormsg='no input file in the series';
512    return
513end
514
515%% fill the list of file series
516InputTable=get(handles.InputTable,'Data');
517if strcmp(iview,'append') % display the input data as a new line in the table
518     iview=size(InputTable,1);
519     InputTable(iview+1,:)={'','','','',''};
520     InputTable(iview,:)=[{RootPath},{SubDir},{RootFile},{NomType},{FileExt}];
521elseif iview==0 % or re-initialise the list of  input  file series
522    iview=1;
523    InputTable=[{'','','','',''};{'','','','',''}];
524     InputTable(iview,:)=[{RootPath},{SubDir},{RootFile},{NomType},{FileExt}];
525    set(handles.TimeTable,'Data',[{[]},{[]},{[]},{[]}])
526    set(handles.MinIndex,'Data',[{[]},{[]}])
527    set(handles.MaxIndex,'Data',[{[]},{[]}])
528    set(handles.ListView,'Value',1)
529    set(handles.ListView,'String',{'1'})
530end
531nbview=size(InputTable,1);
532set(handles.ListView,'String',mat2cell((1:nbview)',ones(nbview,1)))
533set(handles.ListView,'Value',iview)
534set(handles.InputTable,'Data',InputTable)
535
536%% determine the selected reference field indices for pair display
537ref_i=1; %default ref_i is a reference frame index used to find existing pairs from PIV
538if ~isempty(i1)
539    ref_i=i1;
540    if ~isempty(i2)
541        ref_i=floor((ref_i+i2)/2);% reference image number corresponding to the file
542    end
543end
544set(handles.num_ref_i,'String',num2str(ref_i));
545ref_j=1; %default  ref_j is a reference frame index used to find existing pairs from PIV
546if ~isempty(j1)
547    ref_j=j1;
548    if ~isempty(j2)
549        ref_j=floor((j1+j2)/2);
550    end         
551end
552set(handles.num_ref_j,'String',num2str(ref_j));
553
554%% update the list of recent files in the menubar and save it for future opening
555MenuFile=[{get(handles.MenuFile_1,'Label')};{get(handles.MenuFile_2,'Label')};...
556    {get(handles.MenuFile_3,'Label')};{get(handles.MenuFile_4,'Label')};{get(handles.MenuFile_5,'Label')}];
557str_find=strcmp(fileinput,MenuFile);
558if isempty(find(str_find,1))
559    MenuFile=[{fileinput};MenuFile];%insert the current file if not already in the list
560end
561for ifile=1:min(length(MenuFile),5)
562    eval(['set(handles.MenuFile_' num2str(ifile) ',''Label'',MenuFile{ifile});'])
563    eval(['set(handles.MenuFile_insert_' num2str(ifile) ',''Label'',MenuFile{ifile});'])
564end
565dir_perso=prefdir;
566profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
567if exist(profil_perso,'file')
568    save (profil_perso,'MenuFile','-append'); %store the file names for future opening of uvmat
569else
570    save (profil_perso,'MenuFile','-V6'); %store the file names for future opening of uvmat
571end
572
573set(handles.InputTable,'BackgroundColor',[1 1 1])
574
575%% initiate input file series and refresh the current field view:     
576update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileType,MovieObject,iview);
577
578%------------------------------------------------------------------------
579% --- Update information about a new field series (indices to scan, timing,
580%     calibration from an xml file
581function update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileType,VideoObject,iview)
582%------------------------------------------------------------------------
583%% update the output dir
584InputTable=get(handles.InputTable,'Data');
585SubDir=sort(InputTable(1:end-1,2)); %set of subdirectories sorted in alphabetical order
586SubDirOut=SubDir{1};
587if numel(SubDir)>1
588    for ilist=2:numel(SubDir)
589        SubDirOut=[SubDirOut '-' SubDir{ilist}];
590    end
591end
592set(handles.OutputSubDir,'String',SubDirOut)
593
594%% display the min and max indices for the file series
595if size(i1_series,2)==1
596    MinIndex_j=1;
597    MaxIndex_j=1;
598    MinIndex_i=min(find(i1_series));
599    MaxIndex_i=max(find(i1_series));
600else
601pair_max=squeeze(max(i1_series,[],1)); %max on pair index
602j_max=max(pair_max,[],1);
603%i_sum=sum(sum(i1_series,2),1);%sum of i1_series on the last index
604MaxIndex_i=max(find(j_max))-1;% max ref index i
605MinIndex_i=min(find(j_max))-1;% min ref index i
606diff_i_max=diff(j_max);
607    if isequal (diff_i_max,diff_i_max(1)*ones(size(diff_i_max)))
608        set(handles.num_incr_i,'String',num2str(diff_i_max(1)))
609    end
610i_max=max(pair_max,[],2);
611MaxIndex_j=max(find(i_max))-1;% max ref index i
612MinIndex_j=min(find(i_max))-1;% min ref index i
613diff_j_max=diff(i_max);
614    if isequal (diff_j_max,diff_j_max(1)*ones(size(diff_j_max)))
615        set(handles.num_incr_j,'String',num2str(diff_j_max(1)))
616    end
617end
618MinIndex=get(handles.MinIndex,'Data');%retrieve the min indices in the table MinIndex
619MaxIndex=get(handles.MaxIndex,'Data');%retrieve the max indices in the table MaxIndex
620MinIndex{iview,1}=MinIndex_i;
621MinIndex{iview,2}=MinIndex_j;
622MaxIndex{iview,1}=MaxIndex_i;
623MaxIndex{iview,2}=MaxIndex_j;
624
625set(handles.MinIndex,'Data',MinIndex)%display the min indices in the table MinIndex
626set(handles.MaxIndex,'Data',MaxIndex)%display the max indices in the table MaxIndex
627
628%% adjust the first and last indices if requested by the bounds
629first_i=str2num(get(handles.num_first_i,'String'));
630ref_i=str2num(get(handles.num_ref_i,'String'));
631ref_j=str2num(get(handles.num_ref_j,'String'));
632if isempty(first_i)
633    first_i=ref_i;
634elseif first_i < MinIndex_i
635    first_i=MinIndex_i;
636elseif first_i >MaxIndex_i
637    first_i=MinIndex_i;
638end
639first_j=str2num(get(handles.num_first_j,'String'));
640if isempty(first_j)
641    first_j=ref_j;
642elseif first_j<MinIndex_j
643    first_j=MinIndex_j;
644elseif first_j >MaxIndex_j
645    first_j=MinIndex_j;
646end
647last_i=str2num(get(handles.num_last_i,'String'));
648if isempty(last_i)
649    last_i=ref_i;
650elseif last_i > MaxIndex_i
651    last_i=MaxIndex_i;
652elseif last_i<first_i
653    last_i=first_i;
654end
655last_j=str2num(get(handles.num_first_j,'String'));
656if isempty(last_j)
657    last_j=ref_j;
658elseif last_j>MaxIndex_j
659    last_j=MaxIndex_j;
660elseif last_i<first_i
661    last_i=first_i;
662end
663set(handles.num_first_i,'String',num2str(first_i));
664set(handles.num_first_j,'String',num2str(first_j));
665set(handles.num_last_i,'String',num2str(last_i));
666set(handles.num_last_j,'String',num2str(last_j));
667
668%% read timing and total frame number from the current file (movie files) may be overrid by xml file
669InputTable=get(handles.InputTable,'Data');
670FileBase=fullfile(InputTable{iview,1},InputTable{iview,3});
671time=[];%default
672% case of movies
673if strcmp(InputTable{iview,4},'*')
674    if ~isempty(VideoObject)
675        imainfo=get(VideoObject);
676        time=(0:1/imainfo.FrameRate:(imainfo.NumberOfFrames-1)/imainfo.FrameRate)';
677       % set(handles.Dt_txt,'String',['Dt=' num2str(1000/imainfo.FrameRate) 'ms']);%display the elementary time interval in millisec
678        ColorType='truecolor';
679    elseif ~isempty(imformats(regexprep(InputTable{iview,5},'^.',''))) || isequal(InputTable{iview,5},'.vol')%&& isequal(NomType,'*')% multi-frame image
680        if ~isempty(InputTable{iview,2})
681            imainfo=imfinfo(fullfile(InputTable{iview,1},InputTable{iview,2},[InputTable{iview,3} InputTable{iview,5}]));
682        else
683            imainfo=imfinfo([FileBase InputTable{iview,5}]);
684        end
685        ColorType=imainfo.ColorType;%='truecolor' for color images
686        if length(imainfo) >1 %case of image with multiple frames
687            nbfield=length(imainfo);
688            nbfield_j=1;
689        end
690    end
691end
692
693%%  read image documentation file  if found%%%%%%%%%%%%%%%%%%%%%%%%%%%
694XmlData=[];
695NbSlice_calib={};
696XmlFileName=find_imadoc(InputTable{iview,1},InputTable{iview,2},InputTable{iview,3},InputTable{iview,5});
697if ~isempty(XmlFileName)
698        [XmlData,warntext]=imadoc2struct(XmlFileName);
699        if isfield(XmlData,'Heading') && isfield(XmlData.Heading,'ImageName') && ischar(XmlData.Heading.ImageName)
700            [PP,FF,ext_ima_read]=fileparts(XmlData.Heading.ImageName);
701        end
702        if isfield(XmlData,'Time')
703            time=XmlData.Time;
704        end
705        if isfield(XmlData,'Camera')
706            if isfield(XmlData.Camera,'NbSlice')&& ~isempty(XmlData.Camera.NbSlice)
707                NbSlice_calib{iview}=XmlData.Camera.NbSlice;% Nbre of slices for Zindex in phys transform
708                if ~isequal(NbSlice_calib{iview},NbSlice_calib{1})
709                    msgbox_uvmat('WARNING','inconsistent number of Z indices for the two field series');
710                end
711            end
712            if isfield(XmlData.Camera,'TimeUnit')&& ~isempty(XmlData.Camera.TimeUnit)
713                TimeUnit=XmlData.Camera.TimeUnit;
714            end
715        end
716        if ~isempty(warntext)
717            msgbox_uvmat('WARNING',warntext)
718        end 
719end
720
721%% update time table
722if ~isempty(time)
723    TimeTable=get(handles.TimeTable,'Data');
724    first_i=str2num(get(handles.num_first_i,'String'));
725    last_i=str2num(get(handles.num_last_i,'String'));
726    first_j=str2num(get(handles.num_first_j,'String'));
727    last_j=str2num(get(handles.num_last_j,'String'));
728    MinIndexTable=get(handles.MinIndex,'Data');
729    MinIndex_i=MinIndexTable{iview,1};
730    MinIndex_j=MinIndexTable{iview,2};
731    MaxIndexTable=get(handles.MaxIndex,'Data');
732    MaxIndex_i=MaxIndexTable{iview,1};
733    MaxIndex_j=MaxIndexTable{iview,2};
734    if isempty(MinIndex_j)
735        if MinIndex_i>0
736            TimeTable{iview,1}=time(MinIndex_i);
737        end
738        TimeTable{iview,2}=time(first_i);
739        TimeTable{iview,3}=time(last_i);
740        TimeTable{iview,4}=time(MaxIndex_i);
741    elseif ~isempty(time)
742        if MinIndex_i>0
743            TimeTable{iview,1}=time(MinIndex_i,MinIndex_j);
744        end
745        TimeTable{iview,2}=time(first_i,first_j);
746        TimeTable{iview,3}=time(last_i,last_j);
747        TimeTable{iview,4}=time(MaxIndex_i,MaxIndex_j);
748    end
749    set(handles.TimeTable,'Data',TimeTable)
750end
751
752%% number of slices
753NbSlice=1;%default
754if isfield(XmlData,'GeometryCalib') && isfield(XmlData.GeometryCalib,'SliceCoord')
755    siz=size(XmlData.GeometryCalib.SliceCoord);
756    if siz(1)>1
757        NbSlice=siz(1);
758    end
759end
760set(handles.num_NbSlice,'String',num2str(NbSlice))
761   
762%% update pair menus
763set(handles.Pairs,'Visible','on')
764set(handles.PairString,'Visible','on')
765ListView=get(handles.ListView,'String');
766ListView{iview}=num2str(iview);
767set(handles.ListView,'String',ListView);
768set(handles.ListView,'Value',iview)
769update_mode(handles,i1_series,i2_series,j1_series,j2_series,time)
770
771%% update the series info in 'UserData'
772SeriesData=get(handles.series,'UserData');
773SeriesData.i1_series{iview}=i1_series;
774SeriesData.i2_series{iview}=i2_series;
775SeriesData.j1_series{iview}=j1_series;
776SeriesData.j2_series{iview}=j2_series;
777SeriesData.FileType{iview}=FileType;
778SeriesData.Time{iview}=time;
779set(handles.series,'UserData',SeriesData)
780
781%% enable j index visibilitycellfun(@isempty,regexp(PairString,'^j'))
782state='off';
783check_jindex=~cellfun(@isempty,SeriesData.j1_series); %look for non empty j indices
784if isempty(find(check_jindex))
785    enable_j(handles,'off') % no j index needed
786else
787    PairString=get(handles.PairString,'Data');
788    if isempty(find(cellfun(@isempty,regexp(PairString,'^j'))))% if all pair string begins by j (burst)
789        enable_j(handles,'off') % no j index needed
790    else
791        enable_j(handles,'on')
792    end
793end
794
795%% display the set of existing files as an image
796set(handles.FileStatus,'Units','pixels')
797Position=get(handles.FileStatus,'Position');
798set(handles.FileStatus,'Units','normalized')
799xI=0.5:Position(3)-0.5;
800nbview=numel(SeriesData.i1_series);
801pair_max=cell(1,nbview);
802for iview=1:nbview
803    pair_max{iview}=squeeze(max(SeriesData.i1_series{iview},[],1)); %max on pair index
804    if (strcmp(get(handles.num_first_j,'Visible'),'off')&& size(pair_max{iview},2)~=1)
805        pair_max{iview}=squeeze(max(pair_max{iview},[],1)); % consider only the i index
806    end
807    index_min(iview)=find(pair_max{iview}>0, 1 );
808    index_max(iview)=find(pair_max{iview}>0, 1, 'last' );
809end
810index_min=min(index_min);
811index_max=max(index_max);
812range_index=index_max-index_min+1;
813scale_y=Position(4)/nbview;
814scale_x=Position(3)/range_index;
815x=(0.5:range_index-0.5)*Position(3)/range_index;
816% y=(0.5:nbview-0.5)*Position(4)/nbview;
817range_y=max(1,floor(Position(4)/nbview));
818CData=zeros(nbview*range_y,Position(3));
819for iview=1:nbview
820    ind_y=1+(iview-1)*range_y:iview*range_y;
821    LineData=zeros(1,range_index);
822    x_index=find(pair_max{iview}>0)-index_min+1;
823    LineData(x_index)=1;
824    LineData=interp1(x,LineData,xI,'nearest');
825    CData(ind_y,:)=ones(size(ind_y'))*LineData;
826end
827CData=cat(3,zeros(size(CData)),CData,zeros(size(CData)));
828set(handles.FileStatus,'CData',CData);
829
830
831%% enable field and veltype menus, in accordance with the current action
832ActionName_Callback([],[], handles)
833
834%% check for pair display
835check_pairs=0;
836for iview=1:numel(SeriesData.i2_series)
837    if ~isempty(SeriesData.i2_series{iview})||~isempty(SeriesData.j2_series{iview})
838        check_pairs=1;
839    end
840end
841if check_pairs
842    set(handles.Pairs,'Visible','on')
843    set(handles.PairString,'Visible','on')
844else
845    set(handles.Pairs,'Visible','off')
846    set(handles.PairString,'Visible','off')
847end
848
849%% set length of waitbar
850displ_time(handles)
851
852
853%% set default options in menu 'Fields'
854switch FileType
855    case {'civx','civdata'}
856        [FieldList,ColorList]=calc_field;
857        set(handles.FieldName,'String',[{'image'};FieldList;{'get_field...'}]);%standard menu for civx data
858        set(handles.FieldName,'Value',2) % set menu to 'velocity
859        set(handles.Coord_x,'Value',1);
860        set(handles.Coord_x,'String',{'X'});
861        set(handles.Coord_y,'Value',1);
862        set(handles.Coord_y,'String',{'Y'});
863    case 'netcdf'
864        set(handles.FieldName,'Value',1)
865        set(handles.FieldName,'String',{'get_field...'})
866        if isempty(i2_series)
867            i2=[];
868        else
869            i2=i2_series(1,ref_j+1,ref_i+1);
870        end
871        if isempty(j1_series)
872            j1=[];j2=[];
873        else
874            j1=j1_series(1,ref_j+1,ref_i+1);
875            if isempty(j2_series)
876                j2=[];
877            else
878                j2=j2_series(1,ref_j+1,ref_i+1);
879            end
880        end
881        FileName=fullfile_uvmat(InputTable{iview,1},InputTable{iview,2},InputTable{iview,3},InputTable{iview,5},InputTable{iview,4},i1_series(1,ref_j+1,ref_i+1),i2,j1,j2);
882        hget_field=get_field(FileName);
883        hhget_field=guidata(hget_field);
884        get_field('RUN_Callback',hhget_field.RUN,[],hhget_field);
885    otherwise
886        set(handles.FieldName,'Value',1) % set menu to 'image'
887        set(handles.FieldName,'String',{'image'})
888        set(handles.Coord_x,'Value',1);
889        set(handles.Coord_x,'String',{'AX'});
890        set(handles.Coord_y,'Value',1);
891        set(handles.Coord_y,'String',{'AY'});
892end
893
894%------------------------------------------------------------------------
895function num_first_i_Callback(hObject, eventdata, handles)
896%------------------------------------------------------------------------
897num_last_i_Callback(hObject, eventdata, handles)
898
899%------------------------------------------------------------------------
900function num_last_i_Callback(hObject, eventdata, handles)
901%------------------------------------------------------------------------
902SeriesData=get(handles.series,'UserData');
903if ~isfield(SeriesData,'Time')
904    SeriesData.Time{1}=[];
905end
906displ_time(handles);
907
908%------------------------------------------------------------------------
909function num_first_j_Callback(hObject, eventdata, handles)
910%------------------------------------------------------------------------
911 num_last_j_Callback(hObject, eventdata, handles)
912
913%------------------------------------------------------------------------
914function num_last_j_Callback(hObject, eventdata, handles)
915%------------------------------------------------------------------------
916first_j=str2num(get(handles.num_first_j,'String'));
917last_j=str2num(get(handles.num_last_j,'String'));
918ref_j=ceil((first_j+last_j)/2);
919set(handles.num_ref_j,'String', num2str(ref_j))
920num_ref_j_Callback(hObject, eventdata, handles)
921SeriesData=get(handles.series,'UserData');
922if ~isfield(SeriesData,'Time')
923    SeriesData.Time{1}=[];
924end
925displ_time(handles);
926
927
928%------------------------------------------------------------------------
929% ---- find the times corresponding to the first and last indices of a series
930function displ_time(handles)
931%------------------------------------------------------------------------
932SeriesData=get(handles.series,'UserData');%
933ref_i=[str2num(get(handles.num_first_i,'String')) str2num(get(handles.num_last_i,'String'))];
934ref_j=[str2num(get(handles.num_first_j,'String')) str2num(get(handles.num_last_j,'String'))];
935TimeTable=get(handles.TimeTable,'Data');
936Pairs=get(handles.PairString,'Data');
937for iview=1:size(TimeTable,1)
938    if size(SeriesData.Time,1)<iview
939        break
940    end
941    i1=ref_i;
942    j1=ref_j;
943    i2=ref_i;
944    j2=ref_j;
945    % case of pairs
946    if ~isempty(Pairs{iview,1})
947        r=regexp(Pairs{iview,1},'(?<mode>(Di=)|(Dj=)) -*(?<num1>\d+)\|(?<num2>\d+)','names');
948        if isempty(r)
949            r=regexp(Pairs{iview,1},'(?<num1>\d+)(?<mode>-)(?<num2>\d+)','names');
950        end
951        switch r.mode
952            case 'Di='  %  case 'series(Di)')
953                i1=ref_i-str2num(r.num1);
954                i2=ref_i+str2num(r.num2);
955            case 'Dj='  %  case 'series(Dj)'
956                j1=ref_j-str2num(r.num1);
957                j2=ref_j+str2num(r.num2);
958            case '-'  % case 'bursts'
959                j1=str2num(r.num1)*ones(size(ref_i));
960                j2=str2num(r.num2)*ones(size(ref_i));
961        end
962    end
963    TimeTable{iview,2}=[];
964    TimeTable{iview,3}=[];
965    if size(SeriesData.Time{iview},1)>=i2(2)&&size(SeriesData.Time{iview},1)>=j2(2)
966        if isempty(ref_j)
967            time_first=(SeriesData.Time{iview}(i1(1))+SeriesData.Time{iview}(i2(1)))/2;
968            time_last=(SeriesData.Time{iview}(i1(2))+SeriesData.Time{iview}(i2(2)))/2;
969        else
970            time_first=(SeriesData.Time{iview}(i1(1),j1(1))+SeriesData.Time{iview}(i2(1),j2(1)))/2;
971            time_last=(SeriesData.Time{iview}(i1(2),j1(2))+SeriesData.Time{iview}(i2(2),j2(2)))/2;
972        end
973        TimeTable{iview,2}=time_first; %TODO: take into account pairs
974        TimeTable{iview,3}=time_last; %TODO: take into account pairs
975    end
976end
977set(handles.TimeTable,'Data',TimeTable)
978
979%% set the waitbar position with respect to the min and max in the series
980for iview=1:numel(SeriesData.i1_series)
981    pair_max{iview}=squeeze(max(SeriesData.i1_series{iview},[],1)); %max on pair index
982    if (strcmp(get(handles.num_first_j,'Visible'),'off')&& size(pair_max{iview},2)~=1)
983        pair_max{iview}=squeeze(max(pair_max{iview},[],1)); % consider only the i index
984    end
985    pair_max{iview}=reshape(pair_max{iview},1,[]);
986    index_min(iview)=find(pair_max{iview}>0, 1 );
987    index_max(iview)=find(pair_max{iview}>0, 1, 'last' );
988end
989[index_min,iview_min]=min(index_min);
990[index_max,iview_max]=min(index_max);
991if size(SeriesData.i1_series{iview_min},2)==1% movie
992    index_first=ref_i(1);
993    index_last=ref_i(2);
994else
995    index_first=(ref_i(1)-1)*(size(SeriesData.i1_series{iview_min},1))+ref_j(1)+1;
996    index_last=(ref_i(2)-1)*(size(SeriesData.i1_series{iview_max},1))+ref_j(2)+1;
997end
998range=index_max-index_min+1;
999coeff_min=(index_first-index_min)/range;
1000coeff_max=(index_last-index_min+1)/range;
1001Position=get(handles.Waitbar,'Position');% position of the waitbar:= [ x,y, width, height]
1002Position_status=get(handles.FileStatus,'Position');
1003Position(1)=coeff_min*Position_status(3)+Position_status(1);
1004Position(3)=Position_status(3)*(coeff_max-coeff_min);
1005set(handles.Waitbar,'Position',Position)
1006update_waitbar(handles.Waitbar,0)
1007
1008%------------------------------------------------------------------------
1009% --- Executes when selected cell(s) is changed in PairString.
1010function PairString_CellSelectionCallback(hObject, eventdata, handles)
1011%------------------------------------------------------------------------   
1012set(handles.ListView,'Value',eventdata.Indices(1))% detect the selected raw index
1013ListView_Callback ([],[],handles) % update the list of available pairs
1014
1015%------------------------------------------------------------------------
1016%------------------------------------------------------------------------
1017%  III - FUNCTIONS ASSOCIATED TO THE FRAME SET PAIRS
1018%------------------------------------------------------------------------
1019%------------------------------------------------------------------------
1020% --- Executes on selection change in ListView.
1021function ListView_Callback(hObject, eventdata, handles)
1022%------------------------------------------------------------------------   
1023SeriesData=get(handles.series,'UserData');
1024i2_series=[];
1025j2_series=[];
1026iview=get(handles.ListView,'Value');
1027if ~isempty(SeriesData.i2_series{iview})
1028    i2_series=SeriesData.i2_series{iview};
1029end
1030if ~isempty(SeriesData.j2_series{iview})
1031    j2_series=SeriesData.j2_series{iview};
1032end
1033update_mode(handles,SeriesData.i1_series{iview},SeriesData.i2_series{iview},...
1034    SeriesData.j1_series{iview},SeriesData.j2_series{iview},SeriesData.Time{iview})
1035
1036%------------------------------------------------------------------------
1037% --- Executes on button press in mode.
1038function mode_Callback(hObject, eventdata, handles)
1039%------------------------------------------------------------------------       
1040SeriesData=get(handles.series,'UserData');
1041iview=get(handles.ListView,'Value');
1042mode_list=get(handles.mode,'String');
1043mode=mode_list{get(handles.mode,'Value')};
1044if isequal(mode,'bursts')
1045    enable_i(handles,'On')
1046    enable_j(handles,'Off') %do not display j index scanning in burst mode (j is fixed by the burst choice)
1047else
1048    enable_i(handles,'On')
1049    enable_j(handles,'Off')
1050end
1051fill_ListPair(handles,SeriesData.i1_series{iview},SeriesData.i2_series{iview},...
1052    SeriesData.j1_series{iview},SeriesData.j2_series{iview},SeriesData.Time{iview})
1053ListPairs_Callback([],[],handles)
1054
1055%-------------------------------------------------------------
1056% --- Executes on selection in ListPairs.
1057function ListPairs_Callback(hObject,eventdata,handles)
1058%------------------------------------------------------------
1059list_pair=get(handles.ListPairs,'String');%get the menu of image pairs
1060if isempty(list_pair)
1061    string='';
1062else
1063    string=list_pair{get(handles.ListPairs,'Value')};
1064    string=regexprep(string,',.*','');%removes time indication (after ',')
1065end
1066PairString=get(handles.PairString,'Data');
1067iview=get(handles.ListView,'Value');
1068PairString{iview,1}=string;
1069% report the selected pair string to the table PairString
1070set(handles.PairString,'Data',PairString)
1071
1072%------------------------------------------------------------------------
1073function num_ref_i_Callback(hObject, eventdata, handles)
1074%------------------------------------------------------------------------
1075mode_list=get(handles.mode,'String');
1076mode=mode_list{get(handles.mode,'Value')};
1077SeriesData=get(handles.series,'UserData');
1078iview=get(handles.ListView,'Value');
1079fill_ListPair(handles,SeriesData.i1_series{iview},SeriesData.i2_series{iview},...
1080    SeriesData.j1_series{iview},SeriesData.j2_series{iview},SeriesData.Time{iview});% update the menu of pairs depending on the available netcdf files
1081ListPairs_Callback([],[],handles)
1082
1083%------------------------------------------------------------------------
1084function num_ref_j_Callback(hObject, eventdata, handles)
1085%------------------------------------------------------------------------
1086num_ref_i_Callback(hObject, eventdata, handles)
1087
1088%------------------------------------------------------------------------
1089function update_mode(handles,i1_series,i2_series,j1_series,j2_series,time)
1090%------------------------------------------------------------------------   
1091% check_burst=0;
1092if isempty(j2_series)% no j pair
1093    if isempty(i2_series)
1094        set(handles.mode,'Value',1)
1095        set(handles.mode,'String',{''})% no pair menu to display
1096    else   
1097        set(handles.mode,'Value',1)
1098        set(handles.mode,'String',{'series(Di)'}) % pair menu with only option Di
1099    end
1100else %existence of j pairs
1101    pair_max=squeeze(max(i1_series,[],1)); %max on pair index
1102    j_max=max(pair_max,[],1);
1103    MaxIndex_i=max(find(j_max))-1;% max ref index i
1104    MinIndex_i=min(find(j_max))-1;% min ref index i
1105    i_max=max(pair_max,[],2);
1106    MaxIndex_j=max(find(i_max))-1;% max ref index i
1107    MinIndex_j=min(find(i_max))-1;% min ref index i
1108    if MaxIndex_j==MinIndex_j
1109        set(handles.mode,'Value',1);
1110        set(handles.mode,'String',{'bursts'})
1111%         check_burst=1;
1112    elseif MaxIndex_i==MinIndex_i
1113        set(handles.mode,'Value',1);
1114        set(handles.mode,'String',{'series(Dj)'})
1115    else
1116        set(handles.mode,'String',{'bursts';'series(Dj)'})
1117        if (MaxIndex_j-MinIndex_j)>10
1118            set(handles.mode,'Value',2);%set mode to series(Dj) if more than 10 j values
1119        else
1120            set(handles.mode,'Value',1);
1121%             check_burst=1;
1122        end
1123    end
1124end
1125% if check_burst
1126%     enable_i(handles,'On')
1127%     enable_j(handles,'Off') %do not display j index scanning in burst mode (j is fixed by the burst choice)
1128% else
1129%     enable_i(handles,'On')
1130%     if isempty(j1_series)
1131%          enable_j(handles,'Off')
1132%     else
1133%         enable_j(handles,'On')
1134%     end
1135% end
1136fill_ListPair(handles,i1_series,i2_series,j1_series,j2_series,time)
1137ListPairs_Callback([],[],handles)
1138
1139%--------------------------------------------------------------
1140% determine the menu for civ1 pairstring depending on existing netcdf files
1141% with the reference indices num_ref_i and num_ref_j
1142%----------------------------------------------------------------
1143function fill_ListPair(handles,i1_series,i2_series,j1_series,j2_series,time)
1144
1145mode_list=get(handles.mode,'String');
1146mode=mode_list{get(handles.mode,'Value')};
1147ref_i=str2num(get(handles.num_ref_i,'String'));
1148if isempty(ref_i)
1149    ref_i=1;
1150end
1151if strcmp(get(handles.num_ref_j,'Visible'),'on')
1152    ref_j=str2num(get(handles.num_ref_j,'String'));
1153    if isempty(ref_j)
1154        ref_j=1;
1155    end
1156else
1157    ref_j=1;
1158end
1159TimeUnit=get(handles.TimeUnit,'String');
1160if length(TimeUnit)>=1
1161    dtunit=['m' TimeUnit];
1162else
1163    dtunit='e-03';
1164end
1165
1166displ_pair={};
1167if strcmp(mode,'series(Di)')
1168    if isempty(i2_series)
1169        msgbox_uvmat('ERROR','no i1-i2 pair available')
1170        return
1171    end
1172    diff_i=i2_series-i1_series;
1173    min_diff=min(diff_i(diff_i>0));
1174    max_diff=max(diff_i(diff_i>0));
1175    for ipair=min_diff:max_diff
1176        if numel(diff_i(diff_i==ipair))>0
1177            pair_string=['Di= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2)) ];
1178            if ~isempty(time)
1179                if ref_i<=floor(ipair/2)
1180                    ref_i=floor(ipair/2)+1;% shift ref_i to get the first pair
1181                end
1182                Dt=time(ref_i+ceil(ipair/2),ref_j)-time(ref_i-floor(ipair/2),ref_j);
1183                pair_string=[pair_string ', Dt=' num2str(Dt) ' ' dtunit];
1184            end
1185            displ_pair=[displ_pair;{pair_string}];
1186        end
1187    end
1188    if ~isempty(displ_pair)
1189        displ_pair=[displ_pair;{'Di=*|*'}];
1190    end
1191elseif strcmp(mode,'series(Dj)')
1192    if isempty(j2_series)
1193        msgbox_uvmat('ERROR','no j1-j2 pair available')
1194        return
1195    end
1196    diff_j=j2_series-j1_series;
1197    min_diff=min(diff_j(diff_j>0));
1198    max_diff=max(diff_j(diff_j>0));
1199    for ipair=min_diff:max_diff
1200        if numel(diff_j(diff_j==ipair))>0
1201            pair_string=['Dj= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2)) ];
1202            if ~isempty(time)
1203                if ref_j<=floor(ipair/2)
1204                    ref_j=floor(ipair/2)+1;% shift ref_i to get the first pair
1205                end
1206                Dt=time(ref_i,ref_j+ceil(ipair/2))-time(ref_i,ref_j-floor(ipair/2));
1207                pair_string=[pair_string ', Dt=' num2str(Dt) ' ' dtunit];
1208            end
1209            displ_pair=[displ_pair;{pair_string}];
1210        end
1211    end
1212    if ~isempty(displ_pair)
1213        displ_pair=[displ_pair;{'Dj=*|*'}];
1214    end
1215elseif strcmp(mode,'bursts')
1216    if isempty(j2_series)
1217        msgbox_uvmat('ERROR','no j1-j2 pair available')
1218        return
1219    end
1220    diff_j=j2_series-j1_series;
1221    min_j1=min(j1_series(j1_series>0));
1222    max_j1=max(j1_series(j1_series>0));
1223    min_j2=min(j2_series(j2_series>0));
1224    max_j2=max(j2_series(j2_series>0));
1225    for pair1=min_j1:min(max_j1,min_j1+20)
1226        for pair2=min_j2:min(max_j2,min_j2+20)
1227        if numel(j1_series(j1_series==pair1))>0 && numel(j2_series(j2_series==pair2))>0
1228            displ_pair=[displ_pair;{['j= ' num2str(pair1) '-' num2str(pair2)]}];
1229        end
1230        end
1231    end
1232    if ~isempty(displ_pair)
1233        displ_pair=[displ_pair;{'j=*-*'}];
1234    end
1235end
1236set(handles.num_ref_i,'String',num2str(ref_i)) % update ref_i and ref_j
1237set(handles.num_ref_j,'String',num2str(ref_j))
1238
1239%% display list of pairstring
1240displ_pair_list=get(handles.ListPairs,'String');
1241NewVal=[];
1242if ~isempty(displ_pair_list)
1243Val=get(handles.ListPairs,'Value');
1244NewVal=find(strcmp(displ_pair_list{Val},displ_pair),1);% look at the previous display in the new menu displ_pï¿œir
1245end
1246if ~isempty(NewVal)
1247    set(handles.ListPairs,'Value',NewVal)
1248else
1249    set(handles.ListPairs,'Value',1)
1250end
1251set(handles.ListPairs,'String',displ_pair)
1252
1253%-------------------------------------
1254function enable_i(handles,state)
1255set(handles.i_txt,'Visible',state)
1256set(handles.num_first_i,'Visible',state)
1257set(handles.num_last_i,'Visible',state)
1258set(handles.num_incr_i,'Visible',state)
1259% set(handles.num_MaxIndex_i,'Visible',state)
1260set(handles.num_ref_i,'Visible',state)
1261set(handles.ref_i_text,'Visible',state)
1262
1263%-----------------------------------
1264function enable_j(handles,state)
1265set(handles.j_txt,'Visible',state)
1266set(handles.num_first_j,'Visible',state)
1267set(handles.num_last_j,'Visible',state)
1268set(handles.num_incr_j,'Visible',state)
1269set(handles.num_ref_j,'Visible',state)
1270set(handles.ref_j_text,'Visible',state)
1271% if strcmp(state,'off')
1272%     set(handles.MinIndex,'ColumnName',{'imax'})
1273% set(handles.MinIndex,'ColumnEditable',logical(0))
1274% else
1275%         set(handles.MinIndex,'ColumnName',{'imax','jmax'})
1276% end
1277
1278
1279%%%%%%%%%%%%%%%%%%%%
1280%%  MAIN ActionName FUNCTIONS
1281%%%%%%%%%%%%%%%%%%%%
1282%------------------------------------------------------------------------
1283% --- Executes on button press in RUN.
1284function RUN_Callback(hObject, eventdata, handles)
1285%------------------------------------------------------------------------
1286set(handles.RUN,'BusyAction','queue');
1287set(0,'CurrentFigure',handles.series)
1288set(handles.RUN, 'Enable','Off')
1289set(handles.RUN,'BackgroundColor',[0.831 0.816 0.784])
1290drawnow
1291[h_fun,Series,filexml,errormsg]=prepare_jobs(handles);
1292if ~isempty(errormsg)
1293    msgbox_uvmat('ERROR',errormsg)
1294    return
1295end
1296RunModeList=get(handles.RunMode,'String');
1297RunMode=RunModeList{get(handles.RunMode,'Value')};
1298
1299switch RunMode
1300    case 'local'
1301        Series=h_fun(Series);
1302        if ~isempty(filexml)
1303            t=struct2xml(Series);
1304            t=set(t,1,'name','Series');
1305            save(t,filexml);
1306        end
1307    case 'background'
1308        if isempty(filexml)
1309            Series=h_fun(Series);% no background in the absence of output file
1310        else
1311            % update the xml file after interactive input with the function
1312            Series.Specific='?';
1313            Series=h_fun(Series);
1314            t=struct2xml(Series);
1315            t=set(t,1,'name','Series');
1316            save(t,filexml);
1317            path_uvmat=fileparts(which('uvmat'));
1318           
1319            filename_bat=regexprep(filexml,'.xml$','.bat');
1320            [fid,message]=fopen(filename_bat,'w');
1321            if isequal(fid,-1)
1322                msgbox_uvmat('ERROR', ['creation of .bat file: ' message]);
1323                return
1324            end
1325            path_fct=get(handles.ActionPath,'String');
1326            filelog=regexprep(filexml,'.xml$','.log');
1327       
1328            switch computer
1329                case {'GLNX86','GLNXA64','MACI64'}
1330                    text_matlabscript=[...
1331                        '#!/bin/bash \n'...
1332                        '. /etc/sysprofile \n'...
1333                        'matlab -nodisplay -nosplash -nojvm -logfile ''' filelog ''' <<END_MATLAB \n'...
1334                        'addpath(''' path_uvmat '''); \n'...
1335                        'addpath(''' Series.Action.ActionPath '''); \n'...
1336                        '' Series.Action.ActionName  '( ''' filexml '''); \n'...
1337                        'exit \n'...
1338                        'END_MATLAB \n'];
1339                    fprintf(fid,text_matlabscript);
1340                    fclose(fid);
1341                    system(['chmod +x ' filename_bat]);% set the file to executable
1342                    system(['. ' filename_bat ' &']);%execute fct
1343                   
1344                case {'PCWIN','PCWIN64'}
1345                    text_matlabscript=['matlab -automation -logfile ' regexprep(filelog,'\\','\\\\')...
1346                        ' -r "addpath(''' regexprep(path_uvmat,'\\','\\\\') ''');'...
1347                        'addpath(''' regexprep(Series.Action.ActionPath,'\\','\\\\') ''');'...
1348                        '' Series.Action.ActionName  '( ''' regexprep(filexml,'\\','\\\\') ''');exit"'];
1349                    fprintf(fid,text_matlabscript);
1350                    fclose(fid);
1351                    dos([filename_bat ' &']);
1352            end
1353        end
1354        update_waitbar(handles.Waitbar,1); % put the waitbar to end position to indicate lounching is finished
1355end
1356
1357set(handles.RUN, 'Enable','On')
1358set(handles.RUN,'BackgroundColor',[1 0 0])
1359
1360%------------------------------------------------------------------------
1361function STOP_Callback(hObject, eventdata, handles)
1362%------------------------------------------------------------------------
1363set(handles.RUN, 'BusyAction','cancel')
1364set(handles.RUN,'BackgroundColor',[1 0 0])
1365set(handles.RUN,'enable','on')
1366% set(handles.BATCH,'BackgroundColor',[1 0 0])
1367% set(handles.BATCH,'enable','on')
1368
1369%------------------------------------------------------------------------
1370% --- Executes on button press in BATCH.
1371function BATCH_Callback(hObject, eventdata, handles)
1372%------------------------------------------------------------------------   
1373
1374
1375% %------------------------------------------------------------------------
1376% % --- Executes on button press in BIN.
1377% function BIN_Callback(hObject, eventdata, handles)
1378% %------------------------------------------------------------------------
1379%     cmd=['#!/bin/bash \n '...
1380%         '#$ -cwd \n '...
1381%         'hostname && date \n '...
1382%         'umask 002 \n'...
1383%         Param.xml.CivmBin ' ' Param.xml.RunTime ' ' filename_xml ' ' OutputFile '.nc'];
1384%     
1385%------------------------------------------------------------------------
1386% --- Main launch command, called by RUN and BATCH
1387function [h_fun,Series,filexml,errormsg]=prepare_jobs(handles,run)
1388%INPUT:
1389% handles: handles of graphic objects on the GUI series
1390% run=0, just to display parameters for MenuExport/GUI config
1391% run=1 (default) prepare the computation
1392
1393%------------------------------------------------------------------------
1394h_fun=[];
1395filexml='';
1396errormsg='';
1397if ~exist('run','var')
1398    run=1;
1399end
1400%% Read parameters from series
1401Series=read_GUI(handles.series);
1402if isfield(Series,'Pairs')
1403Series=rmfield(Series,'Pairs'); %info Pairs not needed for output
1404end
1405
1406%% read index ranges
1407first_i=1;
1408last_i=1;
1409incr_i=1;
1410first_j=1;
1411last_j=1;
1412incr_j=1;
1413if isfield(Series.IndexRange,'first_i')
1414    first_i=Series.IndexRange.first_i;
1415    incr_i=Series.IndexRange.incr_i;
1416    last_i=Series.IndexRange.last_i;
1417end
1418if isfield(Series.IndexRange,'first_j')
1419    first_j=Series.IndexRange.first_j;
1420    incr_j=Series.IndexRange.incr_j;
1421    last_j=Series.IndexRange.last_j;
1422end
1423
1424%% read input file parameters and set menus
1425menu_coord_state=get(handles.TransformName,'Visible');
1426if isequal(menu_coord_state,'on')
1427    menu_index=get(handles.TransformName,'Value');
1428    transform_list=get(handles.TransformName,'UserData');
1429    Series.FieldTransform.TransformHandle=transform_list{menu_index};% transform function handles
1430end
1431
1432if last_i < first_i | last_j < first_j , msgbox_uvmat('ERROR','last field number must be larger than the first one'),...
1433    set(handles.RUN, 'Enable','On'), set(handles.RUN,'BackgroundColor',[1 0 0]),return,end;
1434
1435%% projection object
1436if isfield(Series,'CheckObject')
1437    if Series.CheckObject
1438        hset_object=findobj(allchild(0),'tag','set_object');
1439        Series.ProjObject=read_GUI(hset_object);
1440        CheckObject_Callback([], [], handles)
1441    end
1442else
1443    Series.CheckObject=0;
1444end
1445
1446%% get_field GUI
1447if isfield(Series,'InputFields')&&isfield(Series.InputFields,'Field')
1448    if strcmp(Series.InputFields.Field,'get_field...')
1449        hget_field=findobj(allchild(0),'name','get_field');
1450        Series.GetField=read_GUI(hget_field);
1451    end
1452end
1453
1454if ~run
1455    return
1456end
1457
1458%% defining the ActionName function handle
1459list_action=get(handles.ActionName,'String');% list menu action
1460index=get(handles.ActionName,'Value');
1461action= list_action{index}; % selected string
1462%Series.Action=action;%name of the processing programme
1463Series.hseries=handles.series; % handles to the series GUI
1464path_series=which('series');
1465list_path=get(handles.ActionName,'UserData');
1466fct_path=list_path{index}; %path stored for the function ACTION
1467if ~isequal(fct_path,path_series)
1468    eval(['spath=which(''' action ''');']) %spath = current path of the selected function ACTION
1469    if ~exist(fct_path,'dir')
1470        errormsg=['The prescribed function path ' fct_path ' does not exist'];
1471        return
1472    end
1473    if ~isequal(spath,fct_path)
1474        addpath(fct_path)% add the prescribed path if not the current one
1475    end
1476end
1477eval(['h_fun=@' action ';'])%create a function handle for ACTION
1478if ~isequal(fct_path,path_series)
1479        rmpath(fct_path)% add the prescribed path if not the current one   
1480end
1481
1482%% create the output data directory and write in it the xml file from the GUI config
1483%determine the root file corresponding to the first sub dir
1484if isfield(Series,'OutputSubDir')
1485    SubDirOut=[Series.OutputSubDir Series.OutputDirExt];
1486    SubDirOutNew=SubDirOut;
1487    iview=1;
1488    SeriesData=get(handles.series,'UserData');
1489    if size(Series.InputTable,1)>1 && isfield(SeriesData,'AllowInputSort') && isfield(SeriesData.AllowInputSort)
1490        [tild,iview]=sort(Series.InputTable(:,2)); %subdirectories sorted in alphabetical order
1491        Series.InputTable=Series.InputTable(iview,:);
1492    end
1493    detect=exist(fullfile(Series.InputTable{1,1},SubDirOutNew),'dir');% test if  the dir  already exist
1494    check_create=1; %need to create the result directory by default
1495    while detect
1496        answer=msgbox_uvmat('INPUT_Y-N',['use existing ouput directory: ' fullfile(Series.InputTable{1,1},SubDirOutNew) ', possibly delete previous data']);
1497        if isequal(answer,'Yes')
1498            detect=0;
1499            check_create=0;
1500        else
1501            r=regexp(SubDirOutNew,'(?<root>.*\D)(?<num1>\d+)$','names');%detect whether name ends by a number
1502            if isempty(r)
1503                r(1).root=[SubDirOutNew '_'];
1504                r(1).num1='0';
1505            end
1506            SubDirOutNew=[r(1).root num2str(str2num(r(1).num1)+1)];%increment the index by 1 or put 1
1507            detect=exist(fullfile(Series.InputTable{1,1},SubDirOutNew),'dir');% test if  the dir  already exists   
1508            check_create=1;
1509        end
1510    end
1511    Series.OutputDirExt=regexprep(SubDirOutNew,Series.OutputSubDir,'');
1512 %   Series.OutputSubDir=SubDirOutNew;
1513 %   Series.OutputDir=fullfile(Series.InputTable{1,1},Series.OutputSubDir);%directory set for output results
1514    Series.OutputRootFile=Series.InputTable{1,3};% the first sorted RootFile taken for output
1515    set(handles.OutputDirExt,'String',Series.OutputDirExt)
1516    % create output directory
1517    OutputDir=fullfile(Series.InputTable{1,1},[Series.OutputSubDir Series.OutputDirExt]);
1518    if check_create
1519        [tild,msg1]=mkdir(OutputDir);
1520        if ~strcmp(msg1,'')
1521            errormsg=['cannot create ' OutputDir ': ' msg1];%error message for directory creation
1522            return
1523        end
1524    end
1525    filexml=fullfile(OutputDir,[Series.InputTable{1,3} '.xml']);% name of the parameter xml file set in this directory
1526end
1527%removes redondant information
1528Series.IndexRange=rmfield(Series.IndexRange,'TimeTable');
1529Series.IndexRange=rmfield(Series.IndexRange,'MinIndex');
1530Series.IndexRange=rmfield(Series.IndexRange,'MaxIndex');
1531%removes empty lines of InputTable
1532empty_line=zeros(size(Series.InputTable,1),1);
1533for iline=1:size(Series.InputTable,1)
1534    empty_line(iline)=isequal(Series.InputTable(iline,1:3),{'','',''});
1535end
1536Series.InputTable(find(empty_line),:)=[];
1537
1538%------------------------------------------------------------------------
1539% --- Executes on selection change in ActionName.
1540function ActionName_Callback(hObject, eventdata, handles)
1541%------------------------------------------------------------------------
1542global nb_builtin_ACTION
1543list_ACTION=get(handles.ActionName,'String');% list menu fields
1544index_ACTION=get(handles.ActionName,'Value');% selected string index
1545ACTION= list_ACTION{index_ACTION}; % selected function name
1546path_series=which('series');%path to series.m
1547list_path=get(handles.ActionName,'UserData');%list of recorded paths to functions of the list ACTION
1548default_file=fullfile(list_path{end},ACTION);
1549% add a new function to the menu if the selected item is 'more...'
1550if isequal(ACTION,'more...')
1551    pathfct=fileparts(path_series);
1552    [FileName, PathName, filterindex] = uigetfile( ...
1553       {'*.m', ' (*.m)';
1554        '*.m',  '.m files '; ...
1555        '*.*', 'All Files (*.*)'}, ...
1556        'Pick a file',default_file);
1557    if length(FileName)<2
1558        return
1559    end
1560    [pp,ACTION,ext_fct]=fileparts(FileName);%(end-1:end);
1561    if ~isequal(ext_fct,'.m')
1562        msgbox_uvmat('ERROR','a Matlab function .m must be introduced');
1563        return
1564    end
1565   
1566   % insert the choice in the actionname menu
1567   menu_str=update_menu(handles.ActionName,ACTION);%new action menu in which the new item has been appended if needed
1568   index_ACTION=get(handles.ActionName,'Value');% currently selected index in the list
1569   list_path{index_ACTION}=PathName;
1570   if length(menu_str)>nb_builtin_ACTION+5; %nb_builtin=nbre of functions always remaining in the initial menu
1571       nbremove=length(menu_str)-nb_builtin_ACTION-5;
1572       menu_str(nb_builtin_ACTION+1:end-5)=[];
1573       list_path(nb_builtin_ACTION+1:end-4)=[];
1574       index_ACTION=index_ACTION-nbremove;
1575       set(handles.ActionName,'Value',index_ACTION)
1576       set(handles.ActionName,'String',menu_str)
1577   end
1578   list_path{index_ACTION}=PathName;
1579   set(handles.ActionName,'UserData',list_path);
1580   set(handles.ActionPath,'enable','inactive')% indicate that the current path is accessible (not 'off')
1581   
1582   %record the current menu in personal file profil_perso
1583   dir_perso=prefdir;
1584   profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
1585   for ilist=nb_builtin_ACTION+1:length(menu_str)-1
1586       series_fct{ilist-nb_builtin_ACTION}=fullfile(list_path{ilist},[menu_str{ilist} '.m']);     
1587   end
1588   if nb_builtin_ACTION+1<=length(menu_str)-1
1589       if exist(profil_perso,'file')% && nb_builtin_ACTION+1>=length(menu_str)-1
1590           save(profil_perso,'series_fct','-append')
1591       else
1592           txt=ver('MATLAB');
1593           Release=txt.Release;
1594           relnumb=str2num(Release(3:4));
1595           if relnumb >= 14%recent relaese of Matlab
1596               save(profil_perso,'series_fct','-V6')
1597           else
1598               save(profil_perso, 'series_fct')
1599           end
1600       end
1601   end
1602end
1603
1604%check the current ActionPath to the selected function
1605PathName=list_path{index_ACTION};%current recorded path
1606set(handles.ActionPath,'String',PathName); %show the path to the senlected function
1607
1608%reinitialise the waitbar
1609update_waitbar(handles.Waitbar,0)
1610
1611%default setting for the visibility of the GUI elements
1612set(handles.num_NbSlice,'Visible','off')
1613set(handles.NbSlice_title,'Visible','off')
1614set(handles.VelType,'Visible','off');
1615set(handles.VelType_text,'Visible','off');
1616set(handles.VelType_1,'Visible','off');
1617set(handles.VelType_text_1,'Visible','off');
1618set(handles.InputFields,'Visible','off')
1619set(handles.FieldName_1,'Visible','off')
1620%view_FieldMenu_1(handles,'off')
1621set(handles.FieldTransform,'Visible','off')
1622set(handles.CheckObject,'Visible','off');
1623set(handles.ProjObject,'Visible','off');
1624set(handles.CheckMask,'Visible','off')
1625set(handles.Mask,'Visible','off')
1626set(handles.OutputDirExt,'Visible','off')
1627set(handles.OutputSubDir,'Visible','off')
1628set(handles.OutputDir_title,'Visible','off')
1629%set the displayed GUI item needed for input parameters
1630if ~isequal(path_series,PathName)
1631    addpath(PathName)
1632end
1633eval(['h_function=@' ACTION ';']);
1634try
1635    [fid,errormsg] =fopen([ACTION '.m']);
1636    InputText=textscan(fid,'%s',1,'delimiter','\n');
1637    fclose(fid)
1638    set(handles.ActionName,'ToolTipString',InputText{1}{1})% put the first line of the selected function as tooltip help
1639end
1640if ~isequal(path_series,PathName)
1641    rmpath(PathName)
1642end
1643varargout=h_function();
1644Param_list={};
1645
1646InputTable=get(handles.InputTable,'Data');
1647nbview=size(InputTable,1);
1648SeriesData=get(handles.series,'UserData');
1649nb_civ=numel(find(strcmp('civx',SeriesData.FileType)|strcmp('civdata',SeriesData.FileType)));
1650nb_netcdf=numel(find(strcmp('netcdf',SeriesData.FileType)));
1651for ilist=1:length(varargout)-1
1652    switch varargout{ilist}
1653        case 'AllowInputSort'
1654            if isequal(lower(varargout{ilist+1}),'on')% sort the input table by alphabetical order of the SubDir
1655                SeriesData.AllowInputSort=1;
1656                set(handles.series,'UserData',SeriesData)
1657            end                     
1658        case 'WholeIndexRange'
1659            if isequal(lower(varargout{ilist+1}),'on')% set by default the input index range from min to max
1660                MinIndex=get(handles.MinIndex,'Data');
1661                MaxIndex=get(handles.MaxIndex,'Data');
1662                if ~isempty(MinIndex)
1663                    set(handles.num_first_i,'String',num2str(MinIndex{1}))
1664                    set(handles.num_last_i,'String',num2str(MaxIndex{1}))
1665                    set(handles.num_incr_i,'String','1')
1666                    if size(MinIndex,2)>=2
1667                        set(handles.num_first_j,'String',num2str(MinIndex{1,2}))
1668                        set(handles.num_last_j,'String',num2str(MaxIndex{1,2}))
1669                        set(handles.num_incr_j,'String','1')
1670                    end
1671                end
1672            end           
1673        case 'NbSlice'   %hidden by default
1674            if isequal(lower(varargout{ilist+1}),'on')
1675                set(handles.num_NbSlice,'Visible','on')
1676                set(handles.NbSlice_title,'Visible','on')
1677            end
1678        case 'VelType'   %hidden by default
1679             if isequal(lower(varargout{ilist+1}),'one') || isequal(lower(varargout{ilist+1}),'two')
1680                if nb_civ>=1
1681                    set(handles.VelType,'Visible','on')
1682                    set(handles.VelType_text,'Visible','on');
1683                end
1684             end
1685            if isequal(lower(varargout{ilist+1}),'two')
1686                if nb_civ>=2
1687                    set(handles.VelType_1,'Visible','on')
1688                    set(handles.VelType_text_1,'Visible','on');
1689                end
1690            end
1691        case 'FieldName'   %hidden by default
1692            if isequal(lower(varargout{ilist+1}),'one')||isequal(lower(varargout{ilist+1}),'two')
1693                if (nb_civ+nb_netcdf)>=1
1694                 set(handles.FieldName,'Visible','on') % test for MenuBorser
1695                 set(handles.InputFields,'Visible','on')
1696                end
1697            end
1698            if isequal(lower(varargout{ilist+1}),'two')
1699                if (nb_civ+nb_netcdf)>=1
1700                set(handles.FieldName_1,'Visible','on')
1701                end
1702            end
1703        case 'FieldTransform'   %hidden by default
1704            if isequal(lower(varargout{ilist+1}),'on')
1705                set(handles.TransformName,'Enable','on')
1706                set(handles.FieldTransform,'Visible','on')
1707                TransformName_Callback([],[], handles)
1708            end
1709        case 'ProjObject'   %hidden by default
1710            if isequal(lower(varargout{ilist+1}),'on')   
1711                set(handles.CheckObject,'Visible','on')
1712                set(handles.ProjObject,'Visible','on')
1713            end
1714        case 'Mask'   %hidden by default
1715            if isequal(lower(varargout{ilist+1}),'on')   
1716                set(handles.Mask,'Visible','on')
1717                 set(handles.CheckMask,'Visible','on');
1718            end 
1719        case 'OutputDirExt'
1720            if ~isempty(varargout{ilist+1})
1721            set(handles.OutputDirExt,'String',varargout{ilist+1})
1722            set(handles.OutputDirExt,'Visible','on')
1723            set(handles.OutputSubDir,'Visible','on')
1724            set(handles.OutputDir_title,'Visible','on') 
1725            end
1726    end
1727end
1728if ~isempty(Param_list)
1729    set(handles.ParamKey,'String',Param_list)
1730    set(handles.ParamVal,'Visible','on')
1731end
1732
1733%------------------------------------------------------------------------
1734% --- Executes on selection change in FieldName.
1735function FieldName_Callback(hObject, eventdata, handles)
1736%------------------------------------------------------------------------
1737field_str=get(handles.FieldName,'String');
1738field_index=get(handles.FieldName,'Value');
1739field=field_str{field_index(1)};
1740if isequal(field,'get_field...')   
1741     hget_field=findobj(allchild(0),'name','get_field');
1742     if ~isempty(hget_field)
1743         delete(hget_field)%delete opened versions of get_field
1744     end
1745     filecell=get_file_series(read_GUI(handles.series));
1746     if exist(filecell{1,1},'file')
1747        get_field(filecell{1,1})
1748     end
1749elseif isequal(field,'more...')
1750    str=calc_field;
1751    [ind_answer,v] = listdlg('PromptString','Select a file:',...
1752                'SelectionMode','single',...
1753                'ListString',str);
1754       % edit the choice in the fields and actionname menu
1755     scalar=cell2mat(str(ind_answer));
1756     update_menu(handles.FieldName,scalar)
1757end
1758
1759%------------------------------------------------------------------------
1760% --- Executes on selection change in FieldName_1.
1761function FieldName_1_Callback(hObject, eventdata, handles)
1762%------------------------------------------------------------------------
1763field_str=get(handles.FieldName_1,'String');
1764field_index=get(handles.FieldName_1,'Value');
1765field=field_str{field_index};
1766if isequal(field,'get_field...')   
1767     hget_field=findobj(allchild(0),'name','get_field_1');
1768     if ~isempty(hget_field)
1769         delete(hget_field)
1770     end
1771     SeriesData=get(handles.series,'UserData');
1772     filename=SeriesData.CurrentInputFile_1;
1773     if exist(filename,'file')
1774        hget_field=get_field(filename);
1775        set(hget_field,'name','get_field_1')
1776     end
1777elseif isequal(field,'more...')
1778    str=calc_field;
1779    [ind_answer,v] = listdlg('PromptString','Select a file:',...
1780                'SelectionMode','single',...
1781                'ListString',str);
1782       % edit the choice in the fields and actionname menu
1783     scalar=cell2mat(str(ind_answer));
1784     update_menu(handles.FieldName_1,scalar)
1785end   
1786
1787
1788%%%%%%%%%%%%%
1789function [ind_remove]=find_pairs(dirpair,ind_i,last_i)
1790indsel=ind_i;
1791indiff=diff(ind_i); %test index increment to detect multiplets (several pairs with the same index ind_i) and holes in the series
1792indiff=[1 indiff last_i-ind_i(end)+1];%for testing gaps with the imposed bounds
1793if ~isempty(indiff)
1794    indiff2=diff(indiff);
1795    indiffp=[indiff2 1];
1796    indiffm=[1 indiff2];
1797    ind_multi_m=find((indiff==0)&(indiffm<0))-1;%indices of first members of multiplets
1798    ind_multi_p=find((indiff==0)&(indiffp>0));%indices of last members of multiplets
1799    %for each multiplet, select the most recent file
1800    ind_remove=[];
1801    for i=1:length(ind_multi_m)
1802        ind_pairs=ind_multi_m(i):ind_multi_p(i);
1803        for imulti=1:length(ind_pairs)
1804            datepair(imulti)=datenum(dirpair(ind_pairs(imulti)).date);%dates of creation
1805        end
1806        [datenew,indsort2]=sort(datepair); %sort the multiplet by creation date
1807        ind_s=indsort2(1:end-1);%
1808        ind_remove=[ind_remove ind_pairs(ind_s)];%remove these indices, leave the last one
1809    end
1810end
1811
1812%------------------------------------------------------------------------
1813% --- determine the list of index pairstring of processing file
1814function [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)
1815%------------------------------------------------------------------------
1816num_i1=num_i;% set of first image numbers by default
1817num_i2=num_i;
1818num_j1=num_j;
1819num_j2=num_j;
1820num_i_out=num_i;
1821num_j_out=num_j;
1822% if isequal (NomType,'_1-2_1') || isequal (NomType,'_1-2')
1823if isequal(mode,'series(Di)')
1824    num_i1_line=num_i+ind_shift(3);% set of first image numbers
1825    num_i2_line=num_i+ind_shift(4);
1826    % adjust the first and last field number
1827        indsel=find(num_i1_line >= 1);
1828    num_i_out=num_i(indsel);
1829    num_i1_line=num_i1_line(indsel);
1830    num_i2_line=num_i2_line(indsel);
1831    num_j1=meshgrid(num_j,ones(size(num_i1_line)));
1832    num_j2=meshgrid(num_j,ones(size(num_i1_line)));
1833    [xx,num_i1]=meshgrid(num_j,num_i1_line);
1834    [xx,num_i2]=meshgrid(num_j,num_i2_line);
1835elseif isequal (mode,'series(Dj)')||isequal (mode,'bursts')
1836    if isequal(mode,'bursts') %case of bursts (png_old or png_2D)
1837        num_j1=ind_shift(1)*ones(size(num_i));
1838        num_j2=ind_shift(2)*ones(size(num_i));
1839    else
1840        num_j1_col=num_j+ind_shift(1);% set of first image numbers
1841        num_j2_col=num_j+ind_shift(2);
1842        % adjust the first field number
1843        indsel=find((num_j1_col >= 1));   
1844        num_j_out=num_j(indsel);
1845        num_j1_col=num_j1_col(indsel);
1846        num_j2_col=num_j2_col(indsel);
1847        [num_i1,num_j1]=meshgrid(num_i,num_j1_col);
1848        [num_i2,num_j2]=meshgrid(num_i,num_j2_col);
1849    end   
1850end
1851
1852%------------------------------------------------------------------------
1853% --- Executes on button press in CheckObject.
1854function CheckObject_Callback(hObject, eventdata, handles)
1855%------------------------------------------------------------------------
1856% SeriesData=get(handles.series,'UserData');
1857value=get(handles.CheckObject,'Value');
1858if value
1859     set(handles.CheckObject,'BackgroundColor',[1 1 0])%put unactivated buttons to yellow
1860     hset_object=findobj(allchild(0),'tag','set_object');%find the set_object interface handle
1861     if ishandle(hset_object)
1862         uistack(hset_object,'top')% show the GUI set_object if opened
1863     else
1864         %get the object file
1865         InputTable=get(handles.InputTable,'Data');
1866         defaultname=InputTable{1,1};
1867         if isempty(defaultname)
1868            defaultname={''};
1869         end
1870        [FileName, PathName, filterindex] = uigetfile( ...
1871       {'*.xml;*.mat', ' (*.xml,*.mat)';
1872       '*.xml',  '.xml files '; ...
1873        '*.mat',  '.mat matlab files '}, ...
1874        'Pick an xml object file (or use uvmat to create it)',defaultname);
1875        fileinput=[PathName FileName];%complete file name
1876        sizf=size(fileinput);
1877        if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end
1878        %read the file
1879        data=xml2struct(fileinput);
1880        if ~isfield(data,'Type')
1881             msgbox_uvmat('ERROR',[fileinput ' is not an object xml file'])
1882             return
1883        end
1884        if ~isfield(data,'ProjMode')
1885             data.ProjMode='none';
1886        end
1887        hset_object=set_object(data);% call the set_object interface
1888     end
1889     Object=read_GUI(hset_object);
1890     set(handles.ProjObject,'String',Object.Name);%display the object name
1891else
1892    set(handles.CheckObject,'BackgroundColor',[0.7 0.7 0.7])%put activated buttons to green
1893end
1894%set(handles.series,'UserData',SeriesData)
1895
1896%--------------------------------------------------------------
1897function CheckMask_Callback(hObject, eventdata, handles)
1898value=get(handles.CheckMask,'Value');
1899if value
1900    msgbox_uvmat('ERROR','not implemented yet')
1901end
1902%--------------------------------------------------------------
1903
1904%-------------------------------------------------------------------
1905%'uv_ncbrowser': interactively calls the netcdf file browser 'get_field.m'
1906function ncbrowser_uvmat(hObject, eventdata)
1907%-------------------------------------------------------------------
1908     bla=get(gcbo,'String');
1909     ind=get(gcbo,'Value');
1910     filename=cell2mat(bla(ind));
1911      blank=find(filename==' ');
1912      filename=filename(1:blank-1);
1913     get_field(filename)
1914
1915% ------------------------------------------------------------------
1916function MenuHelp_Callback(hObject, eventdata, handles)
1917%-------------------------------------------------------------------
1918path_to_uvmat=which ('uvmat');% check the path of uvmat
1919pathelp=fileparts(path_to_uvmat);
1920helpfile=fullfile(pathelp,'uvmat_doc','uvmat_doc.html');
1921if isempty(dir(helpfile)), msgbox_uvmat('ERROR','Please put the help file uvmat_doc.html in the sub-directory /uvmat_doc of the UVMAT package')
1922else
1923    addpath (fullfile(pathelp,'uvmat_doc'))
1924    web([helpfile '#series'])
1925end
1926
1927%-------------------------------------------------------------------
1928% --- Executes on selection change in TransformName.
1929function TransformName_Callback(hObject, eventdata, handles)
1930%-------------------------------------------------------------------
1931global nb_transform
1932
1933menu=get(handles.TransformName,'String');
1934ind_coord=get(handles.TransformName,'Value');
1935coord_option=menu{ind_coord};
1936list_transform=get(handles.TransformName,'UserData');
1937ff=functions(list_transform{end});
1938if isequal(coord_option,'more...');
1939    coord_fct='';
1940    prompt = {'Enter the name of the transform function'};
1941    dlg_title = 'user defined transform';
1942    num_lines= 1;
1943    [FileName, PathName, filterindex] = uigetfile( ...
1944       {'*.m', ' (*.m)';
1945        '*.m',  '.m files '; ...
1946        '*.*', 'All Files (*.*)'}, ...
1947        'Pick a file', ff.file);
1948    if isequal(PathName(end),'/')||isequal(PathName(end),'\')
1949        PathName(end)=[];
1950    end
1951    transform_selected =fullfile(PathName,FileName);
1952    if ~exist(transform_selected,'file')
1953          return
1954    end
1955    [ppp,transform,xt_fct]=fileparts(FileName);% removes extension .m
1956    if ~isequal(ext_fct,'.m')
1957        msgbox_uvmat('ERROR','a Matlab function .m must be introduced');
1958        return
1959    end
1960   menu=update_menu(handles.TransformName,transform);%add the selected fct to the menu
1961   ind_coord=get(handles.TransformName,'Value');
1962   addpath(PathName)
1963   list_transform{ind_coord}=str2func(transform);% create the function handle corresponding to the newly seleced function
1964   set(handles.TransformName,'UserData',list_transform)
1965   rmpath(PathName)
1966   % save the new menu in the personal file 'uvmat_perso.mat'
1967   dir_perso=prefdir;%personal Matalb directory
1968   profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
1969   if exist(profil_perso,'file')
1970       for ilist=nb_transform+1:numel(list_transform)
1971           ff=functions(list_transform{ilist});
1972           transform_fct{ilist-nb_transform}=ff.file;
1973       end
1974        save (profil_perso,'transform_fct','-append'); %store the root name for future opening of uvmat
1975   end
1976end
1977
1978%check the current ActionPath to the selected function
1979if ~isempty(list_transform{ind_coord})
1980    func=functions(list_transform{ind_coord});
1981    set(handles.TransformPath,'String',fileparts(func.file)); %show the path to the senlected function
1982else
1983    set(handles.TransformPath,'String',''); %show the path to the senlected function
1984end
1985
1986
1987
1988% --------------------------------------------------------------------
1989function MenuExportConfig_Callback(hObject, eventdata, handles)
1990global Series
1991[tild,Series,errormsg]=prepare_jobs(handles,0);
1992% Series=read_GUI(handles.series);
1993
1994evalin('base','global Series')%make CurData global in the workspace
1995display('current series config :')
1996evalin('base','Series') %display CurData in the workspace
1997commandwindow; %brings the Matlab command window to the front
1998
1999
2000% --- Executes on selection change in RunMode.
2001function RunMode_Callback(hObject, eventdata, handles)
2002
2003% --- Executes on selection change in Coord_x.
2004function Coord_x_Callback(hObject, eventdata, handles)
2005
2006
2007% --- Executes on selection change in Coord_y.
2008function Coord_y_Callback(hObject, eventdata, handles)
2009
2010
2011
2012% --- Executes when series is resized.
2013function series_ResizeFcn(hObject, eventdata, handles)
2014%% input table
2015set(handles.InputTable,'Unit','pixel')
2016Pos=get(handles.InputTable,'Position');
2017set(handles.InputTable,'Unit','normalized')
2018ColumnWidth=round([0.5 0.14 0.14 0.14 0.08]*(Pos(3)-52));
2019ColumnWidth=num2cell(ColumnWidth);
2020set(handles.InputTable,'ColumnWidth',ColumnWidth)
2021
2022%% MinIndex and MaxIndex
2023set(handles.MinIndex,'Unit','pixel')
2024Pos=get(handles.MinIndex,'Position');
2025set(handles.MinIndex,'Unit','normalized')
2026ColumnWidth=get(handles.MinIndex,'ColumnWidth');
2027if numel(ColumnWidth)==2
2028    ColumnWidth=num2cell(floor([0.5 0.5]*(Pos(3)-20)));
2029else
2030    ColumnWidth={Pos(3)-5};
2031end   
2032set(handles.MinIndex,'ColumnWidth',ColumnWidth)
2033set(handles.MaxIndex,'ColumnWidth',ColumnWidth)
2034
2035%% TimeTable
2036set(handles.TimeTable,'Unit','pixel')
2037Pos=get(handles.TimeTable,'Position');
2038set(handles.TimeTable,'Unit','normalized')
2039ColumnWidth=get(handles.TimeTable,'ColumnWidth');
2040ColumnWidth=num2cell(floor([0.25 0.25 0.25 0.25]*(Pos(3)-20)));
2041set(handles.TimeTable,'ColumnWidth',ColumnWidth)
2042
2043
2044%% PairString
2045set(handles.PairString,'Unit','pixel')
2046Pos=get(handles.PairString,'Position');
2047set(handles.PairString,'Unit','normalized')
2048set(handles.PairString,'ColumnWidth',{Pos(3)-5})
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