source: trunk/src/series.m @ 589

Last change on this file since 589 was 586, checked in by sommeria, 8 years ago

tps_coeff_field introduced and several bugs corrected

File size: 84.3 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)==2 && min(min(i1_series(:,1,:)))==0
596    MinIndex_j=1;
597    MaxIndex_j=1;
598    MinIndex_i=find(i1_series(:,2,:), 1 )-1;
599    MaxIndex_i=find(i1_series(:,2,:), 1, 'last' )-1;
600else
601    pair_max=squeeze(max(i1_series,[],1)); %max on pair index
602    j_max=max(pair_max,[],1);
603    %i_sum=sum(sum(i1_series,2),1);%sum of i1_series on the last index
604    MaxIndex_i=find(j_max, 1, 'last' )-1;% max ref index i
605    MinIndex_i=find(j_max, 1 )-1;% min ref index i
606    diff_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
610    i_max=max(pair_max,[],2);
611    MaxIndex_j=max(find(i_max))-1;% max ref index i
612    MinIndex_j=min(find(i_max))-1;% min ref index i
613    diff_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
620if isequal(MinIndex_i,-1)
621    MinIndex_i=0;
622end
623if isequal(MinIndex_j,-1)
624    MinIndex_j=0;
625end
626MinIndex{iview,1}=MinIndex_i;
627MinIndex{iview,2}=MinIndex_j;
628MaxIndex{iview,1}=MaxIndex_i;
629MaxIndex{iview,2}=MaxIndex_j;
630
631set(handles.MinIndex,'Data',MinIndex)%display the min indices in the table MinIndex
632set(handles.MaxIndex,'Data',MaxIndex)%display the max indices in the table MaxIndex
633
634%% adjust the first and last indices if requested by the bounds
635first_i=str2num(get(handles.num_first_i,'String'));
636ref_i=str2num(get(handles.num_ref_i,'String'));
637ref_j=str2num(get(handles.num_ref_j,'String'));
638if isempty(first_i)
639    first_i=ref_i;
640elseif first_i < MinIndex_i
641    first_i=MinIndex_i;
642elseif first_i >MaxIndex_i
643    first_i=MinIndex_i;
644end
645first_j=str2num(get(handles.num_first_j,'String'));
646if isempty(first_j)
647    first_j=ref_j;
648elseif first_j<MinIndex_j
649    first_j=MinIndex_j;
650elseif first_j >MaxIndex_j
651    first_j=MinIndex_j;
652end
653last_i=str2num(get(handles.num_last_i,'String'));
654if isempty(last_i)
655    last_i=ref_i;
656elseif last_i > MaxIndex_i
657    last_i=MaxIndex_i;
658elseif last_i<first_i
659    last_i=first_i;
660end
661last_j=str2num(get(handles.num_first_j,'String'));
662if isempty(last_j)
663    last_j=ref_j;
664elseif last_j>MaxIndex_j
665    last_j=MaxIndex_j;
666elseif last_i<first_i
667    last_i=first_i;
668end
669set(handles.num_first_i,'String',num2str(first_i));
670set(handles.num_first_j,'String',num2str(first_j));
671set(handles.num_last_i,'String',num2str(last_i));
672set(handles.num_last_j,'String',num2str(last_j));
673
674%% read timing and total frame number from the current file (movie files) may be overrid by xml file
675InputTable=get(handles.InputTable,'Data');
676FileBase=fullfile(InputTable{iview,1},InputTable{iview,3});
677time=[];%default
678% case of movies
679if strcmp(InputTable{iview,4},'*')
680    if ~isempty(VideoObject)
681        imainfo=get(VideoObject);
682        time=(0:1/imainfo.FrameRate:(imainfo.NumberOfFrames-1)/imainfo.FrameRate)';
683       % set(handles.Dt_txt,'String',['Dt=' num2str(1000/imainfo.FrameRate) 'ms']);%display the elementary time interval in millisec
684        ColorType='truecolor';
685    elseif ~isempty(imformats(regexprep(InputTable{iview,5},'^.',''))) || isequal(InputTable{iview,5},'.vol')%&& isequal(NomType,'*')% multi-frame image
686        if ~isempty(InputTable{iview,2})
687            imainfo=imfinfo(fullfile(InputTable{iview,1},InputTable{iview,2},[InputTable{iview,3} InputTable{iview,5}]));
688        else
689            imainfo=imfinfo([FileBase InputTable{iview,5}]);
690        end
691        ColorType=imainfo.ColorType;%='truecolor' for color images
692        if length(imainfo) >1 %case of image with multiple frames
693            nbfield=length(imainfo);
694            nbfield_j=1;
695        end
696    end
697end
698
699%%  read image documentation file  if found%%%%%%%%%%%%%%%%%%%%%%%%%%%
700XmlData=[];
701NbSlice_calib={};
702XmlFileName=find_imadoc(InputTable{iview,1},InputTable{iview,2},InputTable{iview,3},InputTable{iview,5});
703if ~isempty(XmlFileName)
704        [XmlData,warntext]=imadoc2struct(XmlFileName);
705        if isfield(XmlData,'Heading') && isfield(XmlData.Heading,'ImageName') && ischar(XmlData.Heading.ImageName)
706            [PP,FF,ext_ima_read]=fileparts(XmlData.Heading.ImageName);
707        end
708        if isfield(XmlData,'Time')
709            time=XmlData.Time;
710        end
711        if isfield(XmlData,'Camera')
712            if isfield(XmlData.Camera,'NbSlice')&& ~isempty(XmlData.Camera.NbSlice)
713                NbSlice_calib{iview}=XmlData.Camera.NbSlice;% Nbre of slices for Zindex in phys transform
714                if ~isequal(NbSlice_calib{iview},NbSlice_calib{1})
715                    msgbox_uvmat('WARNING','inconsistent number of Z indices for the two field series');
716                end
717            end
718            if isfield(XmlData.Camera,'TimeUnit')&& ~isempty(XmlData.Camera.TimeUnit)
719                TimeUnit=XmlData.Camera.TimeUnit;
720            end
721        end
722        if ~isempty(warntext)
723            msgbox_uvmat('WARNING',warntext)
724        end 
725end
726
727%% update time table
728if ~isempty(time)
729    TimeTable=get(handles.TimeTable,'Data');
730    first_i=str2num(get(handles.num_first_i,'String'));
731    last_i=str2num(get(handles.num_last_i,'String'));
732    first_j=str2num(get(handles.num_first_j,'String'));
733    last_j=str2num(get(handles.num_last_j,'String'));
734    MinIndexTable=get(handles.MinIndex,'Data');
735    MinIndex_i=MinIndexTable{iview,1};
736    MinIndex_j=MinIndexTable{iview,2};
737    MaxIndexTable=get(handles.MaxIndex,'Data');
738    MaxIndex_i=MaxIndexTable{iview,1};
739    MaxIndex_j=MaxIndexTable{iview,2};
740    if isempty(MinIndex_j)% only i index
741        if MinIndex_i>0
742            TimeTable{iview,1}=time(MinIndex_i);
743        end
744        TimeTable{iview,2}=time(first_i);
745        TimeTable{iview,3}=time(last_i);
746        TimeTable{iview,4}=time(MaxIndex_i);
747    elseif ~isempty(time)
748        if MinIndex_i>0
749            TimeTable{iview,1}=time(MinIndex_i,MinIndex_j);
750        end
751        if size(time)>=[last_i last_j]
752            TimeTable{iview,2}=time(first_i,first_j);
753            TimeTable{iview,3}=time(last_i,last_j);
754        end
755        if size(time)>=[MaxIndex_i MaxIndex_j];
756            TimeTable{iview,4}=time(MaxIndex_i,MaxIndex_j);
757        end
758    end
759    set(handles.TimeTable,'Data',TimeTable)
760end
761
762%% number of slices
763NbSlice=1;%default
764if isfield(XmlData,'GeometryCalib') && isfield(XmlData.GeometryCalib,'SliceCoord')
765    siz=size(XmlData.GeometryCalib.SliceCoord);
766    if siz(1)>1
767        NbSlice=siz(1);
768    end
769end
770set(handles.num_NbSlice,'String',num2str(NbSlice))
771   
772%% update pair menus
773set(handles.Pairs,'Visible','on')
774set(handles.PairString,'Visible','on')
775ListView=get(handles.ListView,'String');
776ListView{iview}=num2str(iview);
777set(handles.ListView,'String',ListView);
778set(handles.ListView,'Value',iview)
779update_mode(handles,i1_series,i2_series,j1_series,j2_series,time)
780
781%% update the series info in 'UserData'
782SeriesData=get(handles.series,'UserData');
783SeriesData.i1_series{iview}=i1_series;
784SeriesData.i2_series{iview}=i2_series;
785SeriesData.j1_series{iview}=j1_series;
786SeriesData.j2_series{iview}=j2_series;
787SeriesData.FileType{iview}=FileType;
788SeriesData.Time{iview}=time;
789set(handles.series,'UserData',SeriesData)
790
791%% enable j index visibilitycellfun(@isempty,regexp(PairString,'^j'))
792% state='off';
793check_jindex=~cellfun(@isempty,SeriesData.j1_series); %look for non empty j indices
794if isempty(find(check_jindex))
795    enable_j(handles,'off') % no j index needed
796else
797    PairString=get(handles.PairString,'Data');
798    if isempty(find(cellfun(@isempty,regexp(PairString,'^j'))))% if all pair string begins by j (burst)
799        enable_j(handles,'off') % no j index needed
800    else
801        enable_j(handles,'on')
802    end
803end
804
805%% display the set of existing files as an image
806set(handles.FileStatus,'Units','pixels')
807Position=get(handles.FileStatus,'Position');
808set(handles.FileStatus,'Units','normalized')
809xI=0.5:Position(3)-0.5;
810nbview=numel(SeriesData.i1_series);
811pair_max=cell(1,nbview);
812for iview=1:nbview
813    pair_max{iview}=squeeze(max(SeriesData.i1_series{iview},[],1)); %max on pair index
814    if (strcmp(get(handles.num_first_j,'Visible'),'off')&& size(pair_max{iview},2)~=1)
815        pair_max{iview}=squeeze(max(pair_max{iview},[],1)); % consider only the i index
816    end
817    index_min(iview)=find(pair_max{iview}>0, 1 );
818    index_max(iview)=find(pair_max{iview}>0, 1, 'last' );
819end
820index_min=min(index_min);
821index_max=max(index_max);
822range_index=index_max-index_min+1;
823scale_y=Position(4)/nbview;
824scale_x=Position(3)/range_index;
825x=(0.5:range_index-0.5)*Position(3)/range_index;
826% y=(0.5:nbview-0.5)*Position(4)/nbview;
827range_y=max(1,floor(Position(4)/nbview));
828CData=zeros(nbview*range_y,Position(3));
829for iview=1:nbview
830    ind_y=1+(iview-1)*range_y:iview*range_y;
831    LineData=zeros(1,range_index);
832    x_index=find(pair_max{iview}>0)-index_min+1;
833    LineData(x_index)=1;
834    LineData=interp1(x,LineData,xI,'nearest');
835    CData(ind_y,:)=ones(size(ind_y'))*LineData;
836end
837CData=cat(3,zeros(size(CData)),CData,zeros(size(CData)));
838set(handles.FileStatus,'CData',CData);
839
840
841%% enable field and veltype menus, in accordance with the current action
842ActionName_Callback([],[], handles)
843
844%% check for pair display
845check_pairs=0;
846for iview=1:numel(SeriesData.i2_series)
847    if ~isempty(SeriesData.i2_series{iview})||~isempty(SeriesData.j2_series{iview})
848        check_pairs=1;
849    end
850end
851if check_pairs
852    set(handles.Pairs,'Visible','on')
853    set(handles.PairString,'Visible','on')
854else
855    set(handles.Pairs,'Visible','off')
856    set(handles.PairString,'Visible','off')
857end
858
859%% set length of waitbar
860displ_time(handles)
861
862
863%% set default options in menu 'Fields'
864switch FileType
865    case {'civx','civdata'}
866        [FieldList,ColorList]=calc_field;
867        set(handles.FieldName,'String',[{'image'};FieldList;{'get_field...'}]);%standard menu for civx data
868        set(handles.FieldName,'Value',2) % set menu to 'velocity
869        set(handles.Coord_x,'Value',1);
870        set(handles.Coord_x,'String',{'X'});
871        set(handles.Coord_y,'Value',1);
872        set(handles.Coord_y,'String',{'Y'});
873    case 'netcdf'
874        set(handles.FieldName,'Value',1)
875        set(handles.FieldName,'String',{'get_field...'})
876        if isempty(i2_series)
877            i2=[];
878        else
879            i2=i2_series(1,ref_j+1,ref_i+1);
880        end
881        if isempty(j1_series)
882            j1=[];j2=[];
883        else
884            j1=j1_series(1,ref_j+1,ref_i+1);
885            if isempty(j2_series)
886                j2=[];
887            else
888                j2=j2_series(1,ref_j+1,ref_i+1);
889            end
890        end
891        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);
892        hget_field=get_field(FileName);
893        hhget_field=guidata(hget_field);
894        get_field('RUN_Callback',hhget_field.RUN,[],hhget_field);
895    otherwise
896        set(handles.FieldName,'Value',1) % set menu to 'image'
897        set(handles.FieldName,'String',{'image'})
898        set(handles.Coord_x,'Value',1);
899        set(handles.Coord_x,'String',{'AX'});
900        set(handles.Coord_y,'Value',1);
901        set(handles.Coord_y,'String',{'AY'});
902end
903
904%------------------------------------------------------------------------
905function num_first_i_Callback(hObject, eventdata, handles)
906%------------------------------------------------------------------------
907num_last_i_Callback(hObject, eventdata, handles)
908
909%------------------------------------------------------------------------
910function num_last_i_Callback(hObject, eventdata, handles)
911%------------------------------------------------------------------------
912SeriesData=get(handles.series,'UserData');
913if ~isfield(SeriesData,'Time')
914    SeriesData.Time{1}=[];
915end
916displ_time(handles);
917
918%------------------------------------------------------------------------
919function num_first_j_Callback(hObject, eventdata, handles)
920%------------------------------------------------------------------------
921 num_last_j_Callback(hObject, eventdata, handles)
922
923%------------------------------------------------------------------------
924function num_last_j_Callback(hObject, eventdata, handles)
925%------------------------------------------------------------------------
926first_j=str2num(get(handles.num_first_j,'String'));
927last_j=str2num(get(handles.num_last_j,'String'));
928ref_j=ceil((first_j+last_j)/2);
929set(handles.num_ref_j,'String', num2str(ref_j))
930num_ref_j_Callback(hObject, eventdata, handles)
931SeriesData=get(handles.series,'UserData');
932if ~isfield(SeriesData,'Time')
933    SeriesData.Time{1}=[];
934end
935displ_time(handles);
936
937
938%------------------------------------------------------------------------
939% ---- find the times corresponding to the first and last indices of a series
940function displ_time(handles)
941%------------------------------------------------------------------------
942SeriesData=get(handles.series,'UserData');%
943ref_i=[str2num(get(handles.num_first_i,'String')) str2num(get(handles.num_last_i,'String'))];
944ref_j=[str2num(get(handles.num_first_j,'String')) str2num(get(handles.num_last_j,'String'))];
945TimeTable=get(handles.TimeTable,'Data');
946Pairs=get(handles.PairString,'Data');
947for iview=1:size(TimeTable,1)
948    if size(SeriesData.Time,1)<iview
949        break
950    end
951    i1=ref_i;
952    j1=ref_j;
953    i2=ref_i;
954    j2=ref_j;
955    % case of pairs
956    if ~isempty(Pairs{iview,1})
957        r=regexp(Pairs{iview,1},'(?<mode>(Di=)|(Dj=)) -*(?<num1>\d+)\|(?<num2>\d+)','names');
958        if isempty(r)
959            r=regexp(Pairs{iview,1},'(?<num1>\d+)(?<mode>-)(?<num2>\d+)','names');
960        end
961        switch r.mode
962            case 'Di='  %  case 'series(Di)')
963                i1=ref_i-str2num(r.num1);
964                i2=ref_i+str2num(r.num2);
965            case 'Dj='  %  case 'series(Dj)'
966                j1=ref_j-str2num(r.num1);
967                j2=ref_j+str2num(r.num2);
968            case '-'  % case 'bursts'
969                j1=str2num(r.num1)*ones(size(ref_i));
970                j2=str2num(r.num2)*ones(size(ref_i));
971        end
972    end
973    TimeTable{iview,2}=[];
974    TimeTable{iview,3}=[];
975    if size(SeriesData.Time{iview},1)>=i2(2)&&size(SeriesData.Time{iview},1)>=j2(2)
976        if isempty(ref_j)
977            time_first=(SeriesData.Time{iview}(i1(1))+SeriesData.Time{iview}(i2(1)))/2;
978            time_last=(SeriesData.Time{iview}(i1(2))+SeriesData.Time{iview}(i2(2)))/2;
979        else
980            time_first=(SeriesData.Time{iview}(i1(1),j1(1))+SeriesData.Time{iview}(i2(1),j2(1)))/2;
981            time_last=(SeriesData.Time{iview}(i1(2),j1(2))+SeriesData.Time{iview}(i2(2),j2(2)))/2;
982        end
983        TimeTable{iview,2}=time_first; %TODO: take into account pairs
984        TimeTable{iview,3}=time_last; %TODO: take into account pairs
985    end
986end
987set(handles.TimeTable,'Data',TimeTable)
988
989%% set the waitbar position with respect to the min and max in the series
990for iview=1:numel(SeriesData.i1_series)
991    pair_max{iview}=squeeze(max(SeriesData.i1_series{iview},[],1)); %max on pair index
992    if (strcmp(get(handles.num_first_j,'Visible'),'off')&& size(pair_max{iview},2)~=1)
993        pair_max{iview}=squeeze(max(pair_max{iview},[],1)); % consider only the i index
994    end
995    pair_max{iview}=reshape(pair_max{iview},1,[]);
996    index_min(iview)=find(pair_max{iview}>0, 1 );
997    index_max(iview)=find(pair_max{iview}>0, 1, 'last' );
998end
999[index_min,iview_min]=min(index_min);
1000[index_max,iview_max]=min(index_max);
1001if size(SeriesData.i1_series{iview_min},2)==1% movie
1002    index_first=ref_i(1);
1003    index_last=ref_i(2);
1004else
1005    index_first=(ref_i(1)-1)*(size(SeriesData.i1_series{iview_min},1))+ref_j(1)+1;
1006    index_last=(ref_i(2)-1)*(size(SeriesData.i1_series{iview_max},1))+ref_j(2)+1;
1007end
1008range=index_max-index_min+1;
1009coeff_min=(index_first-index_min)/range;
1010coeff_max=(index_last-index_min+1)/range;
1011Position=get(handles.Waitbar,'Position');% position of the waitbar:= [ x,y, width, height]
1012Position_status=get(handles.FileStatus,'Position');
1013Position(1)=coeff_min*Position_status(3)+Position_status(1);
1014Position(3)=Position_status(3)*(coeff_max-coeff_min);
1015set(handles.Waitbar,'Position',Position)
1016update_waitbar(handles.Waitbar,0)
1017
1018%------------------------------------------------------------------------
1019% --- Executes when selected cell(s) is changed in PairString.
1020function PairString_CellSelectionCallback(hObject, eventdata, handles)
1021%------------------------------------------------------------------------   
1022set(handles.ListView,'Value',eventdata.Indices(1))% detect the selected raw index
1023ListView_Callback ([],[],handles) % update the list of available pairs
1024
1025%------------------------------------------------------------------------
1026%------------------------------------------------------------------------
1027%  III - FUNCTIONS ASSOCIATED TO THE FRAME SET PAIRS
1028%------------------------------------------------------------------------
1029%------------------------------------------------------------------------
1030% --- Executes on selection change in ListView.
1031function ListView_Callback(hObject, eventdata, handles)
1032%------------------------------------------------------------------------   
1033SeriesData=get(handles.series,'UserData');
1034i2_series=[];
1035j2_series=[];
1036iview=get(handles.ListView,'Value');
1037if ~isempty(SeriesData.i2_series{iview})
1038    i2_series=SeriesData.i2_series{iview};
1039end
1040if ~isempty(SeriesData.j2_series{iview})
1041    j2_series=SeriesData.j2_series{iview};
1042end
1043update_mode(handles,SeriesData.i1_series{iview},SeriesData.i2_series{iview},...
1044    SeriesData.j1_series{iview},SeriesData.j2_series{iview},SeriesData.Time{iview})
1045
1046%------------------------------------------------------------------------
1047% --- Executes on button press in mode.
1048function mode_Callback(hObject, eventdata, handles)
1049%------------------------------------------------------------------------       
1050SeriesData=get(handles.series,'UserData');
1051iview=get(handles.ListView,'Value');
1052mode_list=get(handles.mode,'String');
1053mode=mode_list{get(handles.mode,'Value')};
1054if isequal(mode,'bursts')
1055    enable_i(handles,'On')
1056    enable_j(handles,'Off') %do not display j index scanning in burst mode (j is fixed by the burst choice)
1057else
1058    enable_i(handles,'On')
1059    enable_j(handles,'Off')
1060end
1061fill_ListPair(handles,SeriesData.i1_series{iview},SeriesData.i2_series{iview},...
1062    SeriesData.j1_series{iview},SeriesData.j2_series{iview},SeriesData.Time{iview})
1063ListPairs_Callback([],[],handles)
1064
1065%-------------------------------------------------------------
1066% --- Executes on selection in ListPairs.
1067function ListPairs_Callback(hObject,eventdata,handles)
1068%------------------------------------------------------------
1069list_pair=get(handles.ListPairs,'String');%get the menu of image pairs
1070if isempty(list_pair)
1071    string='';
1072else
1073    string=list_pair{get(handles.ListPairs,'Value')};
1074    string=regexprep(string,',.*','');%removes time indication (after ',')
1075end
1076PairString=get(handles.PairString,'Data');
1077iview=get(handles.ListView,'Value');
1078PairString{iview,1}=string;
1079% report the selected pair string to the table PairString
1080set(handles.PairString,'Data',PairString)
1081
1082%------------------------------------------------------------------------
1083function num_ref_i_Callback(hObject, eventdata, handles)
1084%------------------------------------------------------------------------
1085mode_list=get(handles.mode,'String');
1086mode=mode_list{get(handles.mode,'Value')};
1087SeriesData=get(handles.series,'UserData');
1088iview=get(handles.ListView,'Value');
1089fill_ListPair(handles,SeriesData.i1_series{iview},SeriesData.i2_series{iview},...
1090    SeriesData.j1_series{iview},SeriesData.j2_series{iview},SeriesData.Time{iview});% update the menu of pairs depending on the available netcdf files
1091ListPairs_Callback([],[],handles)
1092
1093%------------------------------------------------------------------------
1094function num_ref_j_Callback(hObject, eventdata, handles)
1095%------------------------------------------------------------------------
1096num_ref_i_Callback(hObject, eventdata, handles)
1097
1098%------------------------------------------------------------------------
1099function update_mode(handles,i1_series,i2_series,j1_series,j2_series,time)
1100%------------------------------------------------------------------------   
1101% check_burst=0;
1102if isempty(j2_series)% no j pair
1103    if isempty(i2_series)
1104        set(handles.mode,'Value',1)
1105        set(handles.mode,'String',{''})% no pair menu to display
1106    else   
1107        set(handles.mode,'Value',1)
1108        set(handles.mode,'String',{'series(Di)'}) % pair menu with only option Di
1109    end
1110else %existence of j pairs
1111    pair_max=squeeze(max(i1_series,[],1)); %max on pair index
1112    j_max=max(pair_max,[],1);
1113    MaxIndex_i=max(find(j_max))-1;% max ref index i
1114    MinIndex_i=min(find(j_max))-1;% min ref index i
1115    i_max=max(pair_max,[],2);
1116    MaxIndex_j=max(find(i_max))-1;% max ref index i
1117    MinIndex_j=min(find(i_max))-1;% min ref index i
1118    if MaxIndex_j==MinIndex_j
1119        set(handles.mode,'Value',1);
1120        set(handles.mode,'String',{'bursts'})
1121%         check_burst=1;
1122    elseif MaxIndex_i==MinIndex_i
1123        set(handles.mode,'Value',1);
1124        set(handles.mode,'String',{'series(Dj)'})
1125    else
1126        set(handles.mode,'String',{'bursts';'series(Dj)'})
1127        if (MaxIndex_j-MinIndex_j)>10
1128            set(handles.mode,'Value',2);%set mode to series(Dj) if more than 10 j values
1129        else
1130            set(handles.mode,'Value',1);
1131%             check_burst=1;
1132        end
1133    end
1134end
1135% if check_burst
1136%     enable_i(handles,'On')
1137%     enable_j(handles,'Off') %do not display j index scanning in burst mode (j is fixed by the burst choice)
1138% else
1139%     enable_i(handles,'On')
1140%     if isempty(j1_series)
1141%          enable_j(handles,'Off')
1142%     else
1143%         enable_j(handles,'On')
1144%     end
1145% end
1146fill_ListPair(handles,i1_series,i2_series,j1_series,j2_series,time)
1147ListPairs_Callback([],[],handles)
1148
1149%--------------------------------------------------------------
1150% determine the menu for civ1 pairstring depending on existing netcdf files
1151% with the reference indices num_ref_i and num_ref_j
1152%----------------------------------------------------------------
1153function fill_ListPair(handles,i1_series,i2_series,j1_series,j2_series,time)
1154
1155mode_list=get(handles.mode,'String');
1156mode=mode_list{get(handles.mode,'Value')};
1157ref_i=str2num(get(handles.num_ref_i,'String'));
1158if isempty(ref_i)
1159    ref_i=1;
1160end
1161if strcmp(get(handles.num_ref_j,'Visible'),'on')
1162    ref_j=str2num(get(handles.num_ref_j,'String'));
1163    if isempty(ref_j)
1164        ref_j=1;
1165    end
1166else
1167    ref_j=1;
1168end
1169TimeUnit=get(handles.TimeUnit,'String');
1170if length(TimeUnit)>=1
1171    dtunit=['m' TimeUnit];
1172else
1173    dtunit='e-03';
1174end
1175
1176displ_pair={};
1177if strcmp(mode,'series(Di)')
1178    if isempty(i2_series)
1179        msgbox_uvmat('ERROR','no i1-i2 pair available')
1180        return
1181    end
1182    diff_i=i2_series-i1_series;
1183    min_diff=min(diff_i(diff_i>0));
1184    max_diff=max(diff_i(diff_i>0));
1185    for ipair=min_diff:max_diff
1186        if numel(diff_i(diff_i==ipair))>0
1187            pair_string=['Di= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2)) ];
1188            if ~isempty(time)
1189                if ref_i<=floor(ipair/2)
1190                    ref_i=floor(ipair/2)+1;% shift ref_i to get the first pair
1191                end
1192                Dt=time(ref_i+ceil(ipair/2),ref_j)-time(ref_i-floor(ipair/2),ref_j);
1193                pair_string=[pair_string ', Dt=' num2str(Dt) ' ' dtunit];
1194            end
1195            displ_pair=[displ_pair;{pair_string}];
1196        end
1197    end
1198    if ~isempty(displ_pair)
1199        displ_pair=[displ_pair;{'Di=*|*'}];
1200    end
1201elseif strcmp(mode,'series(Dj)')
1202    if isempty(j2_series)
1203        msgbox_uvmat('ERROR','no j1-j2 pair available')
1204        return
1205    end
1206    diff_j=j2_series-j1_series;
1207    min_diff=min(diff_j(diff_j>0));
1208    max_diff=max(diff_j(diff_j>0));
1209    for ipair=min_diff:max_diff
1210        if numel(diff_j(diff_j==ipair))>0
1211            pair_string=['Dj= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2)) ];
1212            if ~isempty(time)
1213                if ref_j<=floor(ipair/2)
1214                    ref_j=floor(ipair/2)+1;% shift ref_i to get the first pair
1215                end
1216                Dt=time(ref_i,ref_j+ceil(ipair/2))-time(ref_i,ref_j-floor(ipair/2));
1217                pair_string=[pair_string ', Dt=' num2str(Dt) ' ' dtunit];
1218            end
1219            displ_pair=[displ_pair;{pair_string}];
1220        end
1221    end
1222    if ~isempty(displ_pair)
1223        displ_pair=[displ_pair;{'Dj=*|*'}];
1224    end
1225elseif strcmp(mode,'bursts')
1226    if isempty(j2_series)
1227        msgbox_uvmat('ERROR','no j1-j2 pair available')
1228        return
1229    end
1230    diff_j=j2_series-j1_series;
1231    min_j1=min(j1_series(j1_series>0));
1232    max_j1=max(j1_series(j1_series>0));
1233    min_j2=min(j2_series(j2_series>0));
1234    max_j2=max(j2_series(j2_series>0));
1235    for pair1=min_j1:min(max_j1,min_j1+20)
1236        for pair2=min_j2:min(max_j2,min_j2+20)
1237        if numel(j1_series(j1_series==pair1))>0 && numel(j2_series(j2_series==pair2))>0
1238            displ_pair=[displ_pair;{['j= ' num2str(pair1) '-' num2str(pair2)]}];
1239        end
1240        end
1241    end
1242    if ~isempty(displ_pair)
1243        displ_pair=[displ_pair;{'j=*-*'}];
1244    end
1245end
1246set(handles.num_ref_i,'String',num2str(ref_i)) % update ref_i and ref_j
1247set(handles.num_ref_j,'String',num2str(ref_j))
1248
1249%% display list of pairstring
1250displ_pair_list=get(handles.ListPairs,'String');
1251NewVal=[];
1252if ~isempty(displ_pair_list)
1253Val=get(handles.ListPairs,'Value');
1254NewVal=find(strcmp(displ_pair_list{Val},displ_pair),1);% look at the previous display in the new menu displ_pï¿œir
1255end
1256if ~isempty(NewVal)
1257    set(handles.ListPairs,'Value',NewVal)
1258else
1259    set(handles.ListPairs,'Value',1)
1260end
1261set(handles.ListPairs,'String',displ_pair)
1262
1263%-------------------------------------
1264function enable_i(handles,state)
1265set(handles.i_txt,'Visible',state)
1266set(handles.num_first_i,'Visible',state)
1267set(handles.num_last_i,'Visible',state)
1268set(handles.num_incr_i,'Visible',state)
1269% set(handles.num_MaxIndex_i,'Visible',state)
1270set(handles.num_ref_i,'Visible',state)
1271set(handles.ref_i_text,'Visible',state)
1272
1273%-----------------------------------
1274function enable_j(handles,state)
1275set(handles.j_txt,'Visible',state)
1276set(handles.num_first_j,'Visible',state)
1277set(handles.num_last_j,'Visible',state)
1278set(handles.num_incr_j,'Visible',state)
1279set(handles.num_ref_j,'Visible',state)
1280set(handles.ref_j_text,'Visible',state)
1281% if strcmp(state,'off')
1282%     set(handles.MinIndex,'ColumnName',{'imax'})
1283% set(handles.MinIndex,'ColumnEditable',logical(0))
1284% else
1285%         set(handles.MinIndex,'ColumnName',{'imax','jmax'})
1286% end
1287
1288
1289%%%%%%%%%%%%%%%%%%%%
1290%%  MAIN ActionName FUNCTIONS
1291%%%%%%%%%%%%%%%%%%%%
1292%------------------------------------------------------------------------
1293% --- Executes on button press in RUN.
1294function RUN_Callback(hObject, eventdata, handles)
1295%------------------------------------------------------------------------
1296set(handles.RUN,'BusyAction','queue');
1297set(0,'CurrentFigure',handles.series)
1298set(handles.RUN, 'Enable','Off')
1299set(handles.RUN,'BackgroundColor',[0.831 0.816 0.784])
1300drawnow
1301[h_fun,Series,filexml,errormsg]=prepare_jobs(handles);
1302if ~isempty(errormsg)
1303    msgbox_uvmat('ERROR',errormsg)
1304    return
1305end
1306RunModeList=get(handles.RunMode,'String');
1307RunMode=RunModeList{get(handles.RunMode,'Value')};
1308
1309switch RunMode
1310    case 'local'
1311        Series=h_fun(Series);
1312        if ~isempty(filexml)
1313            t=struct2xml(Series);
1314            t=set(t,1,'name','Series');
1315            save(t,filexml);
1316        end
1317    case 'background'
1318        if isempty(filexml)
1319            Series=h_fun(Series);% no background in the absence of output file
1320        else
1321            % update the xml file after interactive input with the function
1322            Series.Specific='?';
1323            Series=h_fun(Series);
1324            t=struct2xml(Series);
1325            t=set(t,1,'name','Series');
1326            save(t,filexml);
1327            path_uvmat=fileparts(which('uvmat'));
1328           
1329            filename_bat=regexprep(filexml,'.xml$','.bat');
1330            [fid,message]=fopen(filename_bat,'w');
1331            if isequal(fid,-1)
1332                msgbox_uvmat('ERROR', ['creation of .bat file: ' message]);
1333                return
1334            end
1335            path_fct=get(handles.ActionPath,'String');
1336            filelog=regexprep(filexml,'.xml$','.log');
1337       
1338            switch computer
1339                case {'GLNX86','GLNXA64','MACI64'}
1340                    text_matlabscript=[...
1341                        '#!/bin/bash \n'...
1342                        '. /etc/sysprofile \n'...
1343                        'matlab -nodisplay -nosplash -nojvm -logfile ''' filelog ''' <<END_MATLAB \n'...
1344                        'addpath(''' path_uvmat '''); \n'...
1345                        'addpath(''' Series.Action.ActionPath '''); \n'...
1346                        '' Series.Action.ActionName  '( ''' filexml '''); \n'...
1347                        'exit \n'...
1348                        'END_MATLAB \n'];
1349                    fprintf(fid,text_matlabscript);
1350                    fclose(fid);
1351                    system(['chmod +x ' filename_bat]);% set the file to executable
1352                    system(['. ' filename_bat ' &']);%execute fct
1353                   
1354                case {'PCWIN','PCWIN64'}
1355                    text_matlabscript=['matlab -automation -logfile ' regexprep(filelog,'\\','\\\\')...
1356                        ' -r "addpath(''' regexprep(path_uvmat,'\\','\\\\') ''');'...
1357                        'addpath(''' regexprep(Series.Action.ActionPath,'\\','\\\\') ''');'...
1358                        '' Series.Action.ActionName  '( ''' regexprep(filexml,'\\','\\\\') ''');exit"'];
1359                    fprintf(fid,text_matlabscript);
1360                    fclose(fid);
1361                    dos([filename_bat ' &']);
1362            end
1363        end
1364        update_waitbar(handles.Waitbar,1); % put the waitbar to end position to indicate lounching is finished
1365end
1366
1367set(handles.RUN, 'Enable','On')
1368set(handles.RUN,'BackgroundColor',[1 0 0])
1369
1370%------------------------------------------------------------------------
1371function STOP_Callback(hObject, eventdata, handles)
1372%------------------------------------------------------------------------
1373set(handles.RUN, 'BusyAction','cancel')
1374set(handles.RUN,'BackgroundColor',[1 0 0])
1375set(handles.RUN,'enable','on')
1376
1377% %------------------------------------------------------------------------
1378% % --- Executes on button press in BIN.
1379% function BIN_Callback(hObject, eventdata, handles)
1380% %------------------------------------------------------------------------
1381%     cmd=['#!/bin/bash \n '...
1382%         '#$ -cwd \n '...
1383%         'hostname && date \n '...
1384%         'umask 002 \n'...
1385%         Param.xml.CivmBin ' ' Param.xml.RunTime ' ' filename_xml ' ' OutputFile '.nc'];
1386%     
1387%------------------------------------------------------------------------
1388% --- Main launch command, called by RUN and BATCH
1389function [h_fun,Series,filexml,errormsg]=prepare_jobs(handles,run)
1390%INPUT:
1391% handles: handles of graphic objects on the GUI series
1392% run=0, just to display parameters for MenuExport/GUI config
1393% run=1 (default) prepare the computation
1394
1395%------------------------------------------------------------------------
1396h_fun=[];
1397filexml='';
1398errormsg='';
1399if ~exist('run','var')
1400    run=1;
1401end
1402%% Read parameters from series
1403Series=read_GUI(handles.series);
1404if isfield(Series,'Pairs')
1405Series=rmfield(Series,'Pairs'); %info Pairs not needed for output
1406end
1407
1408%% read index ranges
1409first_i=1;
1410last_i=1;
1411incr_i=1;
1412first_j=1;
1413last_j=1;
1414incr_j=1;
1415if isfield(Series.IndexRange,'first_i')
1416    first_i=Series.IndexRange.first_i;
1417    incr_i=Series.IndexRange.incr_i;
1418    last_i=Series.IndexRange.last_i;
1419end
1420if isfield(Series.IndexRange,'first_j')
1421    first_j=Series.IndexRange.first_j;
1422    incr_j=Series.IndexRange.incr_j;
1423    last_j=Series.IndexRange.last_j;
1424end
1425
1426%% read input file parameters and set menus
1427menu_coord_state=get(handles.TransformName,'Visible');
1428if isequal(menu_coord_state,'on')
1429    menu_index=get(handles.TransformName,'Value');
1430    transform_list=get(handles.TransformName,'UserData');
1431    Series.FieldTransform.TransformHandle=transform_list{menu_index};% transform function handles
1432end
1433
1434if last_i < first_i | last_j < first_j , msgbox_uvmat('ERROR','last field number must be larger than the first one'),...
1435    set(handles.RUN, 'Enable','On'), set(handles.RUN,'BackgroundColor',[1 0 0]),return,end;
1436
1437%% projection object
1438if isfield(Series,'CheckObject')
1439    if Series.CheckObject
1440        hset_object=findobj(allchild(0),'tag','set_object');
1441        Series.ProjObject=read_GUI(hset_object);
1442        CheckObject_Callback([], [], handles)
1443    end
1444else
1445    Series.CheckObject=0;
1446end
1447
1448%% get_field GUI
1449if isfield(Series,'InputFields')&&isfield(Series.InputFields,'Field')
1450    if strcmp(Series.InputFields.Field,'get_field...')
1451        hget_field=findobj(allchild(0),'name','get_field');
1452        Series.GetField=read_GUI(hget_field);
1453    end
1454end
1455
1456if ~run
1457    return
1458end
1459
1460%% defining the ActionName function handle
1461list_action=get(handles.ActionName,'String');% list menu action
1462index=get(handles.ActionName,'Value');
1463action= list_action{index}; % selected string
1464Series.hseries=handles.series; % handles to the series GUI
1465path_series=which('series');
1466list_path=get(handles.ActionName,'UserData');
1467fct_path=list_path{index}; %path stored for the function ACTION
1468if ~isequal(fct_path,path_series)
1469    eval(['spath=which(''' action ''');']) %spath = current path of the selected function ACTION
1470    if ~exist(fct_path,'dir')
1471        errormsg=['The prescribed function path ' fct_path ' does not exist'];
1472        return
1473    end
1474    if ~isequal(spath,fct_path)
1475        addpath(fct_path)% add the prescribed path if not the current one
1476    end
1477end
1478eval(['h_fun=@' action ';'])%create a function handle for ACTION
1479if ~isequal(fct_path,path_series)
1480        rmpath(fct_path)% add the prescribed path if not the current one   
1481end
1482
1483%% create the output data directory and write in it the xml file from the GUI config
1484%determine the root file corresponding to the first sub dir
1485if isfield(Series,'OutputSubDir')
1486    SubDirOut=[Series.OutputSubDir Series.OutputDirExt];
1487    SubDirOutNew=SubDirOut;
1488    iview=1;
1489    SeriesData=get(handles.series,'UserData');
1490    if size(Series.InputTable,1)>1 && isfield(SeriesData,'AllowInputSort') && isfield(SeriesData.AllowInputSort)
1491        [tild,iview]=sort(Series.InputTable(:,2)); %subdirectories sorted in alphabetical order
1492        Series.InputTable=Series.InputTable(iview,:);
1493    end
1494    detect=exist(fullfile(Series.InputTable{1,1},SubDirOutNew),'dir');% test if  the dir  already exist
1495    check_create=1; %need to create the result directory by default
1496    while detect
1497        answer=msgbox_uvmat('INPUT_Y-N',['use existing ouput directory: ' fullfile(Series.InputTable{1,1},SubDirOutNew) ', possibly delete previous data']);
1498        if isequal(answer,'Yes')
1499            detect=0;
1500            check_create=0;
1501        else
1502            r=regexp(SubDirOutNew,'(?<root>.*\D)(?<num1>\d+)$','names');%detect whether name ends by a number
1503            if isempty(r)
1504                r(1).root=[SubDirOutNew '_'];
1505                r(1).num1='0';
1506            end
1507            SubDirOutNew=[r(1).root num2str(str2num(r(1).num1)+1)];%increment the index by 1 or put 1
1508            detect=exist(fullfile(Series.InputTable{1,1},SubDirOutNew),'dir');% test if  the dir  already exists   
1509            check_create=1;
1510        end
1511    end
1512    Series.OutputDirExt=regexprep(SubDirOutNew,Series.OutputSubDir,'');
1513    Series.OutputRootFile=Series.InputTable{1,3};% the first sorted RootFile taken for output
1514    set(handles.OutputDirExt,'String',Series.OutputDirExt)
1515    % create output directory
1516    OutputDir=fullfile(Series.InputTable{1,1},[Series.OutputSubDir Series.OutputDirExt]);
1517    if check_create
1518        [tild,msg1]=mkdir(OutputDir);
1519        if ~strcmp(msg1,'')
1520            errormsg=['cannot create ' OutputDir ': ' msg1];%error message for directory creation
1521            return
1522        end
1523    end
1524    filexml=fullfile(OutputDir,[Series.InputTable{1,3} '.xml']);% name of the parameter xml file set in this directory
1525end
1526%removes redondant information
1527Series.IndexRange=rmfield(Series.IndexRange,'TimeTable');
1528Series.IndexRange=rmfield(Series.IndexRange,'MinIndex');
1529Series.IndexRange=rmfield(Series.IndexRange,'MaxIndex');
1530%removes empty lines of InputTable
1531empty_line=zeros(size(Series.InputTable,1),1);
1532for iline=1:size(Series.InputTable,1)
1533    empty_line(iline)=isequal(Series.InputTable(iline,1:3),{'','',''});
1534end
1535Series.InputTable(find(empty_line),:)=[];
1536
1537%------------------------------------------------------------------------
1538% --- Executes on selection change in ActionName.
1539function ActionName_Callback(hObject, eventdata, handles)
1540%------------------------------------------------------------------------
1541global nb_builtin_ACTION
1542list_ACTION=get(handles.ActionName,'String');% list menu fields
1543index_ACTION=get(handles.ActionName,'Value');% selected string index
1544ACTION= list_ACTION{index_ACTION}; % selected function name
1545path_series=which('series');%path to series.m
1546list_path=get(handles.ActionName,'UserData');%list of recorded paths to functions of the list ACTION
1547default_file=fullfile(list_path{end},ACTION);
1548% add a new function to the menu if the selected item is 'more...'
1549if isequal(ACTION,'more...')
1550    pathfct=fileparts(path_series);
1551    [FileName, PathName, filterindex] = uigetfile( ...
1552       {'*.m', ' (*.m)';
1553        '*.m',  '.m files '; ...
1554        '*.*', 'All Files (*.*)'}, ...
1555        'Pick a file',default_file);
1556    if length(FileName)<2
1557        return
1558    end
1559    [pp,ACTION,ext_fct]=fileparts(FileName);%(end-1:end);
1560    if ~isequal(ext_fct,'.m')
1561        msgbox_uvmat('ERROR','a Matlab function .m must be introduced');
1562        return
1563    end
1564   
1565   % insert the choice in the actionname menu
1566   menu_str=update_menu(handles.ActionName,ACTION);%new action menu in which the new item has been appended if needed
1567   index_ACTION=get(handles.ActionName,'Value');% currently selected index in the list
1568   list_path{index_ACTION}=PathName;
1569   if length(menu_str)>nb_builtin_ACTION+5; %nb_builtin=nbre of functions always remaining in the initial menu
1570       nbremove=length(menu_str)-nb_builtin_ACTION-5;
1571       menu_str(nb_builtin_ACTION+1:end-5)=[];
1572       list_path(nb_builtin_ACTION+1:end-4)=[];
1573       index_ACTION=index_ACTION-nbremove;
1574       set(handles.ActionName,'Value',index_ACTION)
1575       set(handles.ActionName,'String',menu_str)
1576   end
1577   list_path{index_ACTION}=PathName;
1578   set(handles.ActionName,'UserData',list_path);
1579   set(handles.ActionPath,'enable','inactive')% indicate that the current path is accessible (not 'off')
1580   
1581   %record the current menu in personal file profil_perso
1582   dir_perso=prefdir;
1583   profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
1584   for ilist=nb_builtin_ACTION+1:length(menu_str)-1
1585       series_fct{ilist-nb_builtin_ACTION}=fullfile(list_path{ilist},[menu_str{ilist} '.m']);     
1586   end
1587   if nb_builtin_ACTION+1<=length(menu_str)-1
1588       if exist(profil_perso,'file')% && nb_builtin_ACTION+1>=length(menu_str)-1
1589           save(profil_perso,'series_fct','-append')
1590       else
1591           txt=ver('MATLAB');
1592           Release=txt.Release;
1593           relnumb=str2num(Release(3:4));
1594           if relnumb >= 14%recent relaese of Matlab
1595               save(profil_perso,'series_fct','-V6')
1596           else
1597               save(profil_perso, 'series_fct')
1598           end
1599       end
1600   end
1601end
1602
1603%check the current ActionPath to the selected function
1604PathName=list_path{index_ACTION};%current recorded path
1605set(handles.ActionPath,'String',PathName); %show the path to the senlected function
1606
1607%reinitialise the waitbar
1608update_waitbar(handles.Waitbar,0)
1609
1610%default setting for the visibility of the GUI elements
1611set(handles.num_NbSlice,'Visible','off')
1612set(handles.NbSlice_title,'Visible','off')
1613set(handles.VelType,'Visible','off');
1614set(handles.VelType_text,'Visible','off');
1615set(handles.VelType_1,'Visible','off');
1616set(handles.VelType_text_1,'Visible','off');
1617set(handles.InputFields,'Visible','off')
1618set(handles.FieldName_1,'Visible','off')
1619%view_FieldMenu_1(handles,'off')
1620set(handles.FieldTransform,'Visible','off')
1621set(handles.CheckObject,'Visible','off');
1622set(handles.ProjObject,'Visible','off');
1623set(handles.CheckMask,'Visible','off')
1624set(handles.Mask,'Visible','off')
1625set(handles.OutputDirExt,'Visible','off')
1626set(handles.OutputSubDir,'Visible','off')
1627set(handles.OutputDir_title,'Visible','off')
1628%set the displayed GUI item needed for input parameters
1629if ~isequal(path_series,PathName)
1630    addpath(PathName)
1631end
1632eval(['h_function=@' ACTION ';']);
1633try
1634    [fid,errormsg] =fopen([ACTION '.m']);
1635    InputText=textscan(fid,'%s',1,'delimiter','\n');
1636    fclose(fid);
1637    set(handles.ActionName,'ToolTipString',InputText{1}{1})% put the first line of the selected function as tooltip help
1638end
1639if ~isequal(path_series,PathName)
1640    rmpath(PathName)
1641end
1642varargout=h_function();
1643Param_list={};
1644
1645InputTable=get(handles.InputTable,'Data');
1646nbview=size(InputTable,1);
1647SeriesData=get(handles.series,'UserData');
1648nb_civ=numel(find(strcmp('civx',SeriesData.FileType)|strcmp('civdata',SeriesData.FileType)));
1649nb_netcdf=numel(find(strcmp('netcdf',SeriesData.FileType)));
1650for ilist=1:length(varargout)-1
1651    switch varargout{ilist}
1652        case 'AllowInputSort'
1653            if isequal(lower(varargout{ilist+1}),'on')% sort the input table by alphabetical order of the SubDir
1654                SeriesData.AllowInputSort=1;
1655                set(handles.series,'UserData',SeriesData)
1656            end                     
1657        case 'WholeIndexRange'
1658            if isequal(lower(varargout{ilist+1}),'on')% set by default the input index range from min to max
1659                MinIndex=get(handles.MinIndex,'Data');
1660                MaxIndex=get(handles.MaxIndex,'Data');
1661                if ~isempty(MinIndex)
1662                    set(handles.num_first_i,'String',num2str(MinIndex{1}))
1663                    set(handles.num_last_i,'String',num2str(MaxIndex{1}))
1664                    set(handles.num_incr_i,'String','1')
1665                    if size(MinIndex,2)>=2
1666                        set(handles.num_first_j,'String',num2str(MinIndex{1,2}))
1667                        set(handles.num_last_j,'String',num2str(MaxIndex{1,2}))
1668                        set(handles.num_incr_j,'String','1')
1669                    end
1670                end
1671            end           
1672        case 'NbSlice'   %hidden by default
1673            if isequal(lower(varargout{ilist+1}),'on')
1674                set(handles.num_NbSlice,'Visible','on')
1675                set(handles.NbSlice_title,'Visible','on')
1676            end
1677        case 'VelType'   %hidden by default
1678             if isequal(lower(varargout{ilist+1}),'one') || isequal(lower(varargout{ilist+1}),'two')
1679                if nb_civ>=1
1680                    set(handles.VelType,'Visible','on')
1681                    set(handles.VelType_text,'Visible','on');
1682                end
1683             end
1684            if isequal(lower(varargout{ilist+1}),'two')
1685                if nb_civ>=2
1686                    set(handles.VelType_1,'Visible','on')
1687                    set(handles.VelType_text_1,'Visible','on');
1688                end
1689            end
1690        case 'FieldName'   %hidden by default
1691            if isequal(lower(varargout{ilist+1}),'one')||isequal(lower(varargout{ilist+1}),'two')
1692                if (nb_civ+nb_netcdf)>=1
1693                 set(handles.FieldName,'Visible','on') % test for MenuBorser
1694                 set(handles.InputFields,'Visible','on')
1695                end
1696            end
1697            if isequal(lower(varargout{ilist+1}),'two')
1698                if (nb_civ+nb_netcdf)>=1
1699                set(handles.FieldName_1,'Visible','on')
1700                end
1701            end
1702        case 'FieldTransform'   %hidden by default
1703            if isequal(lower(varargout{ilist+1}),'on')
1704                set(handles.TransformName,'Enable','on')
1705                set(handles.FieldTransform,'Visible','on')
1706                TransformName_Callback([],[], handles)
1707            end
1708        case 'ProjObject'   %hidden by default
1709            if isequal(lower(varargout{ilist+1}),'on')   
1710                set(handles.CheckObject,'Visible','on')
1711                set(handles.ProjObject,'Visible','on')
1712            end
1713        case 'Mask'   %hidden by default
1714            if isequal(lower(varargout{ilist+1}),'on')   
1715                set(handles.Mask,'Visible','on')
1716                 set(handles.CheckMask,'Visible','on');
1717            end 
1718        case 'OutputDirExt'
1719            if ~isempty(varargout{ilist+1})
1720            set(handles.OutputDirExt,'String',varargout{ilist+1})
1721            set(handles.OutputDirExt,'Visible','on')
1722            set(handles.OutputSubDir,'Visible','on')
1723            set(handles.OutputDir_title,'Visible','on') 
1724            end
1725    end
1726end
1727if ~isempty(Param_list)
1728    set(handles.ParamKey,'String',Param_list)
1729    set(handles.ParamVal,'Visible','on')
1730end
1731
1732%------------------------------------------------------------------------
1733% --- Executes on selection change in FieldName.
1734function FieldName_Callback(hObject, eventdata, handles)
1735%------------------------------------------------------------------------
1736field_str=get(handles.FieldName,'String');
1737field_index=get(handles.FieldName,'Value');
1738field=field_str{field_index(1)};
1739if isequal(field,'get_field...')   
1740     hget_field=findobj(allchild(0),'name','get_field');
1741     if ~isempty(hget_field)
1742         delete(hget_field)%delete opened versions of get_field
1743     end
1744     filecell=get_file_series(read_GUI(handles.series));
1745     if exist(filecell{1,1},'file')
1746        get_field(filecell{1,1})
1747     end
1748elseif isequal(field,'more...')
1749    str=calc_field;
1750    [ind_answer,v] = listdlg('PromptString','Select a file:',...
1751                'SelectionMode','single',...
1752                'ListString',str);
1753       % edit the choice in the fields and actionname menu
1754     scalar=cell2mat(str(ind_answer));
1755     update_menu(handles.FieldName,scalar)
1756end
1757
1758%------------------------------------------------------------------------
1759% --- Executes on selection change in FieldName_1.
1760function FieldName_1_Callback(hObject, eventdata, handles)
1761%------------------------------------------------------------------------
1762field_str=get(handles.FieldName_1,'String');
1763field_index=get(handles.FieldName_1,'Value');
1764field=field_str{field_index};
1765if isequal(field,'get_field...')   
1766     hget_field=findobj(allchild(0),'name','get_field_1');
1767     if ~isempty(hget_field)
1768         delete(hget_field)
1769     end
1770     SeriesData=get(handles.series,'UserData');
1771     filename=SeriesData.CurrentInputFile_1;
1772     if exist(filename,'file')
1773        hget_field=get_field(filename);
1774        set(hget_field,'name','get_field_1')
1775     end
1776elseif isequal(field,'more...')
1777    str=calc_field;
1778    [ind_answer,v] = listdlg('PromptString','Select a file:',...
1779                'SelectionMode','single',...
1780                'ListString',str);
1781       % edit the choice in the fields and actionname menu
1782     scalar=cell2mat(str(ind_answer));
1783     update_menu(handles.FieldName_1,scalar)
1784end   
1785
1786
1787%%%%%%%%%%%%%
1788function [ind_remove]=find_pairs(dirpair,ind_i,last_i)
1789indsel=ind_i;
1790indiff=diff(ind_i); %test index increment to detect multiplets (several pairs with the same index ind_i) and holes in the series
1791indiff=[1 indiff last_i-ind_i(end)+1];%for testing gaps with the imposed bounds
1792if ~isempty(indiff)
1793    indiff2=diff(indiff);
1794    indiffp=[indiff2 1];
1795    indiffm=[1 indiff2];
1796    ind_multi_m=find((indiff==0)&(indiffm<0))-1;%indices of first members of multiplets
1797    ind_multi_p=find((indiff==0)&(indiffp>0));%indices of last members of multiplets
1798    %for each multiplet, select the most recent file
1799    ind_remove=[];
1800    for i=1:length(ind_multi_m)
1801        ind_pairs=ind_multi_m(i):ind_multi_p(i);
1802        for imulti=1:length(ind_pairs)
1803            datepair(imulti)=datenum(dirpair(ind_pairs(imulti)).date);%dates of creation
1804        end
1805        [datenew,indsort2]=sort(datepair); %sort the multiplet by creation date
1806        ind_s=indsort2(1:end-1);%
1807        ind_remove=[ind_remove ind_pairs(ind_s)];%remove these indices, leave the last one
1808    end
1809end
1810
1811%------------------------------------------------------------------------
1812% --- determine the list of index pairstring of processing file
1813function [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)
1814%------------------------------------------------------------------------
1815num_i1=num_i;% set of first image numbers by default
1816num_i2=num_i;
1817num_j1=num_j;
1818num_j2=num_j;
1819num_i_out=num_i;
1820num_j_out=num_j;
1821% if isequal (NomType,'_1-2_1') || isequal (NomType,'_1-2')
1822if isequal(mode,'series(Di)')
1823    num_i1_line=num_i+ind_shift(3);% set of first image numbers
1824    num_i2_line=num_i+ind_shift(4);
1825    % adjust the first and last field number
1826        indsel=find(num_i1_line >= 1);
1827    num_i_out=num_i(indsel);
1828    num_i1_line=num_i1_line(indsel);
1829    num_i2_line=num_i2_line(indsel);
1830    num_j1=meshgrid(num_j,ones(size(num_i1_line)));
1831    num_j2=meshgrid(num_j,ones(size(num_i1_line)));
1832    [xx,num_i1]=meshgrid(num_j,num_i1_line);
1833    [xx,num_i2]=meshgrid(num_j,num_i2_line);
1834elseif isequal (mode,'series(Dj)')||isequal (mode,'bursts')
1835    if isequal(mode,'bursts') %case of bursts (png_old or png_2D)
1836        num_j1=ind_shift(1)*ones(size(num_i));
1837        num_j2=ind_shift(2)*ones(size(num_i));
1838    else
1839        num_j1_col=num_j+ind_shift(1);% set of first image numbers
1840        num_j2_col=num_j+ind_shift(2);
1841        % adjust the first field number
1842        indsel=find((num_j1_col >= 1));   
1843        num_j_out=num_j(indsel);
1844        num_j1_col=num_j1_col(indsel);
1845        num_j2_col=num_j2_col(indsel);
1846        [num_i1,num_j1]=meshgrid(num_i,num_j1_col);
1847        [num_i2,num_j2]=meshgrid(num_i,num_j2_col);
1848    end   
1849end
1850
1851%------------------------------------------------------------------------
1852% --- Executes on button press in CheckObject.
1853function CheckObject_Callback(hObject, eventdata, handles)
1854%------------------------------------------------------------------------
1855value=get(handles.CheckObject,'Value');
1856if value
1857     set(handles.CheckObject,'BackgroundColor',[1 1 0])%put unactivated buttons to yellow
1858     hset_object=findobj(allchild(0),'tag','set_object');%find the set_object interface handle
1859     if ishandle(hset_object)
1860         uistack(hset_object,'top')% show the GUI set_object if opened
1861     else
1862         %get the object file
1863         InputTable=get(handles.InputTable,'Data');
1864         defaultname=InputTable{1,1};
1865         if isempty(defaultname)
1866            defaultname={''};
1867         end
1868        [FileName, PathName, filterindex] = uigetfile( ...
1869       {'*.xml;*.mat', ' (*.xml,*.mat)';
1870       '*.xml',  '.xml files '; ...
1871        '*.mat',  '.mat matlab files '}, ...
1872        'Pick an xml object file (or use uvmat to create it)',defaultname);
1873        fileinput=[PathName FileName];%complete file name
1874        sizf=size(fileinput);
1875        if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end
1876        %read the file
1877        data=xml2struct(fileinput);
1878        if ~isfield(data,'Type')
1879             msgbox_uvmat('ERROR',[fileinput ' is not an object xml file'])
1880             return
1881        end
1882        if ~isfield(data,'ProjMode')
1883             data.ProjMode='none';
1884        end
1885        hset_object=set_object(data);% call the set_object interface
1886     end
1887     Object=read_GUI(hset_object);
1888     set(handles.ProjObject,'String',Object.Name);%display the object name
1889else
1890    set(handles.CheckObject,'BackgroundColor',[0.7 0.7 0.7])%put activated buttons to green
1891end
1892%set(handles.series,'UserData',SeriesData)
1893
1894%--------------------------------------------------------------
1895function CheckMask_Callback(hObject, eventdata, handles)
1896value=get(handles.CheckMask,'Value');
1897if value
1898    msgbox_uvmat('ERROR','not implemented yet')
1899end
1900%--------------------------------------------------------------
1901
1902%-------------------------------------------------------------------
1903%'uv_ncbrowser': interactively calls the netcdf file browser 'get_field.m'
1904function ncbrowser_uvmat(hObject, eventdata)
1905%-------------------------------------------------------------------
1906     bla=get(gcbo,'String');
1907     ind=get(gcbo,'Value');
1908     filename=cell2mat(bla(ind));
1909      blank=find(filename==' ');
1910      filename=filename(1:blank-1);
1911     get_field(filename)
1912
1913% ------------------------------------------------------------------
1914function MenuHelp_Callback(hObject, eventdata, handles)
1915%-------------------------------------------------------------------
1916path_to_uvmat=which ('uvmat');% check the path of uvmat
1917pathelp=fileparts(path_to_uvmat);
1918helpfile=fullfile(pathelp,'uvmat_doc','uvmat_doc.html');
1919if isempty(dir(helpfile)), msgbox_uvmat('ERROR','Please put the help file uvmat_doc.html in the sub-directory /uvmat_doc of the UVMAT package')
1920else
1921    addpath (fullfile(pathelp,'uvmat_doc'))
1922    web([helpfile '#series'])
1923end
1924
1925%-------------------------------------------------------------------
1926% --- Executes on selection change in TransformName.
1927function TransformName_Callback(hObject, eventdata, handles)
1928%-------------------------------------------------------------------
1929global nb_transform
1930
1931menu=get(handles.TransformName,'String');
1932ind_coord=get(handles.TransformName,'Value');
1933coord_option=menu{ind_coord};
1934list_transform=get(handles.TransformName,'UserData');
1935ff=functions(list_transform{end});
1936if isequal(coord_option,'more...');
1937    coord_fct='';
1938    prompt = {'Enter the name of the transform function'};
1939    dlg_title = 'user defined transform';
1940    num_lines= 1;
1941    [FileName, PathName, filterindex] = uigetfile( ...
1942       {'*.m', ' (*.m)';
1943        '*.m',  '.m files '; ...
1944        '*.*', 'All Files (*.*)'}, ...
1945        'Pick a file', ff.file);
1946    if isequal(PathName(end),'/')||isequal(PathName(end),'\')
1947        PathName(end)=[];
1948    end
1949    transform_selected =fullfile(PathName,FileName);
1950    if ~exist(transform_selected,'file')
1951          return
1952    end
1953    [ppp,transform,xt_fct]=fileparts(FileName);% removes extension .m
1954    if ~isequal(ext_fct,'.m')
1955        msgbox_uvmat('ERROR','a Matlab function .m must be introduced');
1956        return
1957    end
1958   menu=update_menu(handles.TransformName,transform);%add the selected fct to the menu
1959   ind_coord=get(handles.TransformName,'Value');
1960   addpath(PathName)
1961   list_transform{ind_coord}=str2func(transform);% create the function handle corresponding to the newly seleced function
1962   set(handles.TransformName,'UserData',list_transform)
1963   rmpath(PathName)
1964   % save the new menu in the personal file 'uvmat_perso.mat'
1965   dir_perso=prefdir;%personal Matalb directory
1966   profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
1967   if exist(profil_perso,'file')
1968       for ilist=nb_transform+1:numel(list_transform)
1969           ff=functions(list_transform{ilist});
1970           transform_fct{ilist-nb_transform}=ff.file;
1971       end
1972        save (profil_perso,'transform_fct','-append'); %store the root name for future opening of uvmat
1973   end
1974end
1975
1976%check the current ActionPath to the selected function
1977if ~isempty(list_transform{ind_coord})
1978    func=functions(list_transform{ind_coord});
1979    set(handles.TransformPath,'String',fileparts(func.file)); %show the path to the senlected function
1980else
1981    set(handles.TransformPath,'String',''); %show the path to the senlected function
1982end
1983
1984
1985
1986% --------------------------------------------------------------------
1987function MenuExportConfig_Callback(hObject, eventdata, handles)
1988global Series
1989[tild,Series,errormsg]=prepare_jobs(handles,0);
1990% Series=read_GUI(handles.series);
1991
1992evalin('base','global Series')%make CurData global in the workspace
1993display('current series config :')
1994evalin('base','Series') %display CurData in the workspace
1995commandwindow; %brings the Matlab command window to the front
1996
1997
1998% --- Executes on selection change in RunMode.
1999function RunMode_Callback(hObject, eventdata, handles)
2000
2001% --- Executes on selection change in Coord_x.
2002function Coord_x_Callback(hObject, eventdata, handles)
2003
2004
2005% --- Executes on selection change in Coord_y.
2006function Coord_y_Callback(hObject, eventdata, handles)
2007
2008
2009
2010% --- Executes when series is resized.
2011function series_ResizeFcn(hObject, eventdata, handles)
2012%% input table
2013set(handles.InputTable,'Unit','pixel')
2014Pos=get(handles.InputTable,'Position');
2015set(handles.InputTable,'Unit','normalized')
2016ColumnWidth=round([0.5 0.14 0.14 0.14 0.08]*(Pos(3)-52));
2017ColumnWidth=num2cell(ColumnWidth);
2018set(handles.InputTable,'ColumnWidth',ColumnWidth)
2019
2020%% MinIndex and MaxIndex
2021set(handles.MinIndex,'Unit','pixel')
2022Pos=get(handles.MinIndex,'Position');
2023set(handles.MinIndex,'Unit','normalized')
2024ColumnWidth=get(handles.MinIndex,'ColumnWidth');
2025if numel(ColumnWidth)==2
2026    ColumnWidth=num2cell(floor([0.5 0.5]*(Pos(3)-20)));
2027else
2028    ColumnWidth={Pos(3)-5};
2029end   
2030set(handles.MinIndex,'ColumnWidth',ColumnWidth)
2031set(handles.MaxIndex,'ColumnWidth',ColumnWidth)
2032
2033%% TimeTable
2034set(handles.TimeTable,'Unit','pixel')
2035Pos=get(handles.TimeTable,'Position');
2036set(handles.TimeTable,'Unit','normalized')
2037ColumnWidth=get(handles.TimeTable,'ColumnWidth');
2038ColumnWidth=num2cell(floor([0.25 0.25 0.25 0.25]*(Pos(3)-20)));
2039set(handles.TimeTable,'ColumnWidth',ColumnWidth)
2040
2041
2042%% PairString
2043set(handles.PairString,'Unit','pixel')
2044Pos=get(handles.PairString,'Position');
2045set(handles.PairString,'Unit','normalized')
2046set(handles.PairString,'ColumnWidth',{Pos(3)-5})
2047
2048
2049% --- Executes on button press in status.
2050function status_Callback(hObject, eventdata, handles)
2051val=get(handles.status,'Value');
2052if val==0
2053    set(handles.status,'BackgroundColor',[0 1 0])
2054    hfig=findobj(allchild(0),'name','series_status');
2055    if ~isempty(hfig)
2056        delete(hfig)
2057    end
2058    return
2059end
2060set(handles.status,'BackgroundColor',[1 1 0])
2061drawnow
2062% listtype={'civ1','fix1','patch1','civ2','fix2','patch2'};
2063% Param.CheckCiv1=get(handles.CheckCiv1,'Value');
2064% Param.CheckFix1=get(handles.CheckFix1,'Value');
2065% Param.CheckPatch1=get(handles.CheckPatch1,'Value');
2066% Param.CheckCiv2=get(handles.CheckCiv2,'Value');
2067% Param.CheckFix2=get(handles.CheckFix2,'Value');
2068% Param.CheckPatch2=get(handles.CheckPatch2,'Value');
2069% box_test=[Param.CheckCiv1 Param.CheckFix1 Param.CheckPatch1 Param.CheckCiv2 Param.CheckFix2 Param.CheckPatch2];
2070%
2071% option_civ=find(box_test,1,'last');%last selected option (non-zero index of box_test)
2072% filecell=get(handles.civ,'UserData');%retrieve the list of output files expected for PIV
2073% test_new=0;
2074% if ~isfield(filecell,'nc')
2075%     test_new=1;
2076%     [ref_i,ref_j,errormsg]=find_ref_indices(handles);
2077%     if ~isempty(errormsg)
2078%         msgbox_uvmat('ERROR',errormsg)
2079%         return
2080%     end
2081%     filecell=set_civ_filenames(handles,ref_i,ref_j,box_test);%determine the output file expected from the GUI status
2082% end
2083% if ~isequal(box_test(4:6),[0 0 0])
2084%     civ_files=filecell.nc.civ2;%case of civ2 operations
2085% else
2086%     civ_files=filecell.nc.civ1;
2087% end
2088hfig=findobj(allchild(0),'name','series_status');
2089if isempty(hfig)
2090    hfig=figure('DeleteFcn',@stop_status);
2091    set(hfig,'MenuBar','none')% suppress the menu bar
2092    set(hfig,'NumberTitle','off')%suppress the fig number in the title
2093    set(hfig,'name','series_status')
2094    set(hfig,'tag','series_status')
2095%    set(hfig,'UserData',civ_files)
2096    hlist= uicontrol('Style','listbox','Units','normalized', 'Position',[0.05 0.09 0.9 0.71], 'Callback', {'open_uvmat'},'tag','list');
2097    uicontrol('Style','edit','Units','normalized', 'Position', [0.05 0.87 0.9 0.1],'tag','msgbox','Max',2,'String','checking files...');
2098    uicontrol('Style','frame','Units','normalized', 'Position', [0.05 0.81 0.9 0.05]);
2099    uicontrol('Style','pushbutton','Units','normalized', 'Position', [0.7 0.01 0.2 0.07],'String','Close','FontWeight','bold','FontUnits','normalized','FontSize',0.9,'Callback',@close_GUI);
2100    hrefresh=uicontrol('Style','pushbutton','Units','normalized', 'Position', [0.1 0.01 0.2 0.07],'String','Refresh','FontWeight','bold','FontUnits','normalized','FontSize',0.9,'Callback',@refresh_GUI);
2101    BarPosition=[0.05 0.81 0.01 0.05];
2102    uicontrol('Style','frame','Units','normalized', 'Position',BarPosition ,'BackgroundColor',[1 0 0],'tag','waitbar');
2103    drawnow
2104end
2105StatusData.time_ref=get(handles.RUN,'UserData');% get the time of launch
2106% StatusData.option_civ=option_civ;
2107set(hrefresh,'UserData',StatusData)
2108Param=read_GUI(handles.series);
2109RootPath=Param.InputTable{1,1};
2110SubDir=Param.InputTable{1,2};
2111OutputSubDir=[Param.OutputSubDir Param.OutputDirExt];% subdirectory for output files
2112OutputDir=fullfile(RootPath,SubDir,OutputSubDir);
2113set(hlist,'UserData',OutputDir)
2114%refresh_GUI(hrefresh,[])
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