source: trunk/src/series.m @ 523

Last change on this file since 523 was 523, checked in by sommeria, 9 years ago
File size: 93.4 KB
Line 
1%'series': master function associated to the GUI series.m for analysis field series 
2%------------------------------------------------------------------------
3% function varargout = series(varargin)
4% associated with the GUI series.fig
5%
6%INPUT
7% param: structure with input parameters (link with the GUI uvmat)
8%      .menu_coord_str: string for the TransformName (menu for coordinate transforms)
9%      .menu_coord_val: value for TransformName (menu for coordinate transforms)
10%      .FileName: input file name
11%      .FileName_1: second input file name
12%      .list_field: menu of input fields
13%      .index_fields: chosen index
14%      .civ1=0 or 1, .interp1,  ... : input civ field type
15%
16%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
17%  Copyright 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,'ColumnEditable',logical(0))
71set(handles.PairString,'ColumnFormat',{'char'})
72set(handles.PairString,'ColumnWidth',{60})
73set(handles.PairString,'Data',{''})
74set(hObject,'WindowButtonDownFcn',{'mouse_down'})%allows mouse action with right button (zoom for uicontrol display)
75dir_perso=prefdir;
76test_profil_perso=0;
77profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
78if exist(profil_perso,'file')
79     h=load (profil_perso);
80     if isfield(h,'MenuFile')
81          for ifile=1:min(length(h.MenuFile),5)
82              eval(['set(handles.MenuFile_' num2str(ifile) ',''Label'',h.MenuFile{ifile});'])
83          end
84     end
85     test_profil_perso=1;
86end
87
88%check default input data
89if ~exist('param','var')
90    param=[]; %default
91end
92
93%% file name and browser initialisation
94if isfield(param,'menu_coord_str')
95    set(handles.TransformName,'String',param.menu_coord_str)
96end
97if isfield(param,'menu_coord_val')
98    set(handles.TransformName,'Value',param.menu_coord_val);
99else
100     set(handles.TransformName,'Value',1);%default
101end
102if isfield(param,'FileName')
103    InputTable={'','','','',''};
104    set(handles.InputTable,'Data',InputTable)
105    if isfield(param,'FileName_1')
106        display_file_name(handles,param.FileName_1,0)
107        display_file_name(handles,param.FileName,1)
108    else
109        display_file_name(handles,param.FileName,0)
110    end
111end 
112if isfield(param,'incr_i')
113    set(handles.num_incr_i,'String',num2str(param.incr_i))
114end
115if isfield(param,'incr_j')
116    set(handles.num_incr_j,'String',num2str(param.incr_j))
117end
118
119%% fields input initialisation
120if isfield(param,'list_fields')&& isfield(param,'index_fields') &&~isempty(param.list_fields) &&~isempty(param.index_fields)
121    set(handles.FieldName,'String',param.list_fields);% list menu fields
122    set(handles.FieldName,'Value',param.index_fields);% selected string index
123%     FieldCell{1}=param.list_fields{param.index_fields};
124end
125
126%loads the information stored in prefdir to initiate  the list of ActionName functions
127fct_menu={'check_data_files';'aver_stat';'time_series';'merge_proj';'clean_civ_cmx'};
128transform_menu={'';'phys';'px';'phys_polar'};
129nb_builtin_ACTION=numel(fct_menu); %number of functions
130nb_transform=numel(transform_menu);
131[path_series,name,ext]=fileparts(which('series'));
132path_series=fullfile(path_series,'series');%path of the function 'series'
133addpath (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)
134path_transform=fullfile(path_series,'transform_field');%path to the field transform functions
135for ilist=1:length(fct_menu)
136    fct_path{ilist,1}=path_series;%paths of the fuctions buil-in in 'series.m'
137end
138
139%% TRANSFORM menu: loads the information stored in prefdir to initiate  the list of field transform functions
140menu_str={'';'sub_field';'phys';'phys_polar'};
141nb_builtin_transform=numel(menu_str); %number of functions
142[path_uvmat,name,ext]=fileparts(which('uvmat'));
143addpath(fullfile(path_uvmat,'transform_field'))
144fct_handle{1,1}=[];
145testexist(1)=1;
146for ilist=2:length(menu_str)
147    if exist(menu_str{ilist},'file')
148        fct_handle{ilist,1}=str2func(menu_str{ilist});
149        testexist(ilist)=1;
150    else
151        testexist(ilist)=0;
152    end
153end
154rmpath(fullfile(path_uvmat,'transform_field'))
155
156%% read the list of transform functions stored in the personal file 'uvmat_perso.mat' in prefdir
157if test_profil_perso
158    if isfield(h,'series_fct') && iscell(h.series_fct)
159         for ilist=1:length(h.series_fct)
160             [path,file]=fileparts(h.series_fct{ilist});
161             fct_path=[fct_path; {path}];%concatene the list of paths
162             fct_menu=[fct_menu; {file}];
163         end
164    end
165    if isfield(h,'transform_fct') && iscell(h.transform_fct)
166        for ilist=1:length(h.transform_fct);
167             [path,file]=fileparts(h.transform_fct{ilist});
168             addpath(path)
169             if exist(file,'file')
170                h_func=str2func(file);
171                testexist=[testexist 1];
172             else
173                h_func=[];
174                testexist=[testexist 0];
175             end
176             fct_handle=[fct_handle; {h_func}];%concatene the list of paths
177             rmpath(path)
178             menu_str=[menu_str; {file}];
179        end
180    end
181end
182fct_menu=[fct_menu;{'more...'}];
183set(handles.ActionName,'String',fct_menu)
184set(handles.ActionName,'UserData',fct_path)% store the list of path in UserData of ACTION
185menu_str=menu_str(find(testexist));
186fct_handle=fct_handle(find(testexist));
187menu_str=[menu_str;{'more...'}];
188set(handles.TransformName,'String',menu_str)
189set(handles.TransformName,'UserData',fct_handle)% store the list of path in UserData of ACTION
190
191%% Adjust the GUI according to the binaries available in PARAM.xml
192path_uvmat=fileparts(which('uvmat')); %path to civ
193addpath (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)
194errormsg=[];%default error message
195xmlfile='PARAM.xml';
196if exist(xmlfile,'file')
197    try
198        t=xmltree(xmlfile);
199        sparam=convert(t);
200    catch ME
201        errormsg={' Unable to read the file PARAM.xml defining the civx binaries:';ME.message};
202    end
203else
204    errormsg=[xmlfile ' not found: path to civx binaries undefined'];
205end
206if ~isempty(errormsg)
207    msgbox_uvmat('WARNING',errormsg);
208end
209test_batch=0;%default: ,no batch mode available
210if isfield(sparam,'BatchParam') && isfield(sparam.BatchParam,'BatchMode')
211    test_batch=strcmp(sparam.BatchParam.BatchMode,'sge'); %sge is currently the only implemented batch mod
212end
213RUNVal=get(handles.RunMode,'Value');
214if test_batch==0
215   if RUNVal>2
216       set(handles.RunMode,'Value',1)
217   end
218   set(handles.RunMode,'String',{'local';'background'})
219else
220    set(handles.RunMode,'String',{'local';'background';'cluster'})
221end
222
223%------------------------------------------------------------------------
224% --- Outputs from this function are returned to the command line.
225function varargout = series_OutputFcn(hObject, eventdata, handles)
226%------------------------------------------------------------------------
227% varargout  cell array for returning output args (see VARARGOUT);
228% hObject    handle to figure
229% eventdata  reserved - to be defined in a future version of MATLAB
230% handles    structure with handles and user data (see GUIDATA)
231% Get default command line output from handles structure
232varargout{1} = handles.output;
233
234%------------------------------------------------------------------------
235%------------------------------------------------------------------------
236%  II - FUNCTIONS FOR INTRODUCING THE INPUT FILES
237% automatically sets the global properties when the rootfile name is introduced
238% then activate the view-field actionname if selected
239% it is activated either by clicking on the RootPath window or by the
240% browser
241%------------------------------------------------------------------------
242%------------------------------------------------------------------------
243function MenuBrowse_Callback(hObject, eventdata, handles)
244%------------------------------------------------------------------------   
245InputTable=get(handles.InputTable,'Data');
246if isempty(InputTable)
247    RootPathCell={};
248else
249    RootPathCell=InputTable(:,1);
250end
251oldfile=''; %default
252if isempty(RootPathCell)||isequal(RootPathCell,{''})%loads the previously stored file name and set it as default in the file_input box
253     dir_perso=prefdir;
254     profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
255     if exist(profil_perso,'file')
256          h=load (profil_perso);
257         if isfield(h,'filebase')&&ischar(h.filebase)
258                 oldfile=h.filebase;
259         end
260         if isfield(h,'RootPath')&&ischar(h.RootPath)
261                 oldfile=h.RootPath;
262         end
263     end
264else
265     SubDirCell=InputTable(:,2);
266    RootFileCell=InputTable(:,3);
267     oldfile=fullfile(RootPathCell{1},SubDirCell{1},RootFileCell{1});
268 end
269[FileName, PathName, filterindex] = uigetfile( ...
270       {'*.xml;*.xls;*.png;*.tif;*.avi;*.AVI;*.nc', ' (*.xml,*.xls, *.png,*.tif, *.avi,*.nc)';
271       '*.xml',  '.xml files '; ...
272        '*.xls',  '.xls files '; ...
273        '*.png','.png image files'; ...
274        '*.tif','.tif image files'; ...
275        '*.avi;*.AVI','.avi movie files'; ...
276        '*.nc','.netcdf files'; ...
277        '*.*',  'All Files (*.*)'}, ...
278        'Pick a file',oldfile);
279fileinput=[PathName FileName];%complete file name
280if isempty(fileinput),return;end %abandon if no file is introduced by the browser
281[path,name,ext]=fileparts(fileinput);
282if isequal(ext,'.xml')
283    [Param,Heading]=xml2struct(fileinput);
284    if ~strcmp(Heading,'Series')
285        msg_box_uvmat('ERROR','xml file heading is not <Series>')
286    else
287        fill_GUI(Param,handles);%fill the GUI with the parameters retrieved from the xml file
288        if isfield(Param,'CheckObject')&& Param.CheckObject
289            set_object(Param.ProjObject)
290        end
291        set(handles.REFRESH,'UserData',[1:size(Param.InputTable,1)])
292        REFRESH_Callback([],[], handles)
293        return
294    end
295elseif isequal(ext,'.xls')
296    msg_box_uvmat('ERROR','input file type not implemented')%A Faire: ouvrir le fichier pour naviguer
297else
298    display_file_name(handles,fileinput,0)
299end
300
301% --------------------------------------------------------------------
302function MenuFile_1_Callback(hObject, eventdata, handles)
303fileinput=get(handles.MenuFile_1,'Label');
304display_file_name(handles,fileinput,0)
305
306% --------------------------------------------------------------------
307function MenuFile_2_Callback(hObject, eventdata, handles)
308fileinput=get(handles.MenuFile_2,'Label');
309display_file_name(handles,fileinput,0)
310
311% --------------------------------------------------------------------
312function MenuFile_3_Callback(hObject, eventdata, handles)
313fileinput=get(handles.MenuFile_3,'Label');
314display_file_name( handles,fileinput,0)
315
316% --------------------------------------------------------------------
317function MenuFile_4_Callback(hObject, eventdata, handles)
318fileinput=get(handles.MenuFile_4,'Label');
319display_file_name(handles,fileinput,0)
320
321% --------------------------------------------------------------------
322function MenuFile_5_Callback(hObject, eventdata, handles)
323fileinput=get(handles.MenuFile_5,'Label');
324display_file_name(handles,fileinput,0)
325
326% --------------------------------------------------------------------
327function MenuBrowse_insert_Callback(hObject, eventdata, handles)
328InputTable=get(handles.InputTable,'Data');
329RootPathCell=InputTable(:,1);
330SubDirCell=InputTable(:,3);
331RootFileCell=InputTable(:,2);
332oldfile=''; %default
333if isempty(RootPathCell)||isequal(RootPathCell,{''})%loads the previously stored file name and set it as default in the file_input box
334     dir_perso=prefdir;
335     profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
336     if exist(profil_perso,'file')
337          h=load (profil_perso);
338         if isfield(h,'filebase')&ischar(h.filebase)
339                 oldfile=h.filebase;
340         end
341         if isfield(h,'RootPath')&ischar(h.RootPath)
342                 oldfile=h.RootPath;
343         end
344     end
345 else
346     oldfile=fullfile(RootPathCell{1},RootFileCell{1});
347 end
348[FileName, PathName, filterindex] = uigetfile( ...
349       {'*.xml;*.xls;*.png;*.avi;*.AVI;*.nc', ' (*.xml,*.xls, *.png, *.avi,*.nc)';
350       '*.xml',  '.xml files '; ...
351        '*.xls',  '.xls files '; ...
352        '*.png','.png image files'; ...
353        '*.avi;*.AVI','.avi movie files'; ...
354        '*.nc','.netcdf files'; ...
355        '*.*',  'All Files (*.*)'}, ...
356        'Pick a file',oldfile);
357fileinput=[PathName FileName];%complete file name
358sizf=size(fileinput);
359if (~ischar(fileinput)|~isequal(sizf(1),1)),return;end
360[path,name,ext]=fileparts(fileinput);
361if isequal(ext,'.xml')
362    msgbox_uvmat('ERROR','input file type not implemented')%A Faire: ouvrir le fichier pour naviguer
363elseif isequal(ext,'.xls')
364    msgbox_uvmat('ERROR','input file type not implemented')%A Faire: ouvrir le fichier pour naviguer
365else
366    display_file_name(handles,fileinput,'append')
367end
368
369% --------------------------------------------------------------------
370function MenuFile_insert_1_Callback(hObject, eventdata, handles)
371% --------------------------------------------------------------------   
372fileinput=get(handles.MenuFile_insert_1,'Label');
373display_file_name(handles,fileinput,'append')
374
375% --------------------------------------------------------------------
376function MenuFile_insert_2_Callback(hObject, eventdata, handles)
377% --------------------------------------------------------------------   
378fileinput=get(handles.MenuFile_insert_2,'Label');
379display_file_name(handles,fileinput,'append')
380
381% --------------------------------------------------------------------
382function MenuFile_insert_3_Callback(hObject, eventdata, handles)
383% --------------------------------------------------------------------   
384fileinput=get(handles.MenuFile_insert_3,'Label');
385display_file_name( handles,fileinput,'append')
386
387% --------------------------------------------------------------------
388function MenuFile_insert_4_Callback(hObject, eventdata, handles)
389% --------------------------------------------------------------------   
390fileinput=get(handles.MenuFile_insert_4,'Label');
391display_file_name( handles,fileinput,'append')
392
393% --------------------------------------------------------------------
394function MenuFile_insert_5_Callback(hObject, eventdata, handles)
395% --------------------------------------------------------------------   
396fileinput=get(handles.MenuFile_insert_5,'Label');
397display_file_name(handles,fileinput,'append')
398
399%------------------------------------------------------------------------
400% --- Executes when entered data in editable cell(s) in InputTable.
401function InputTable_CellEditCallback(hObject, eventdata, handles)
402%------------------------------------------------------------------------
403set(handles.REFRESH,'Visible','on')
404iview=eventdata.Indices(1);
405view_set=get(handles.REFRESH,'UserData');
406if isempty(find(view_set==iview))
407    set(handles.REFRESH,'UserData',[view_set iview])
408end
409%% enable other menus and uicontrols
410set(handles.MenuOpen_insert,'Enable','on')
411set(handles.MenuFile_insert_1,'Enable','on')
412set(handles.MenuFile_insert_2,'Enable','on')
413set(handles.MenuFile_insert_3,'Enable','on')
414set(handles.MenuFile_insert_4,'Enable','on')
415set(handles.MenuFile_insert_5,'Enable','on')
416set(handles.RUN, 'Enable','On')
417set(handles.RUN,'BackgroundColor',[1 0 0])% set RUN button to red
418
419%update the output dir
420% SubDir=sort(InputTable(:,2)); %set of subdirectories sorted in alphabetical order
421% SubDirOut=SubDir{1};
422% if numel(SubDir)>1
423%     for ilist=2:numel(SubDir)
424%         SubDirOut=[SubDirOut '-' SubDir{ilist}];
425%     end
426% end
427% set(handles.OutputSubDir,'String',SubDirOut)
428
429%------------------------------------------------------------------------
430% --- Executes on button press in REFRESH.
431function REFRESH_Callback(hObject, eventdata, handles)
432%------------------------------------------------------------------------
433InputTable=get(handles.InputTable,'Data');
434view_set=get(handles.REFRESH,'UserData');
435set(handles.REFRESH,'BackgroundColor',[0.7 0.7 0.7])% set REFRESH  button to grey color
436drawnow
437for iview=view_set
438    RootPath=fullfile(InputTable{iview,1},InputTable{iview,2});
439    if ~exist(RootPath,'dir')
440        i1_series=[];
441        RootPath=fileparts(RootPath); %will try the upped forldr
442    else
443        [RootPath,SubDir,RootFile,i1_series,i2_series,j1_series,j2_series,tild,FileType,MovieObject]=...
444            find_file_series(fullfile(InputTable{iview,1},InputTable{iview,2}),[InputTable{iview,3} InputTable{iview,4} InputTable{iview,5}]);
445    end
446    if isempty(i1_series)
447        [FileName, PathName, filterindex] = uigetfile( ...
448            {'*.xml;*.xls;*.png;*.tif;*.avi;*.AVI;*.nc', ' (*.xml,*.xls, *.png,*.tif, *.avi,*.nc)';
449            '*.xml',  '.xml files '; ...
450            '*.xls',  '.xls files '; ...
451            '*.png','.png image files'; ...
452            '*.tif','.tif image files'; ...
453            '*.avi;*.AVI','.avi movie files'; ...
454            '*.nc','.netcdf files'; ...
455            '*.*',  'All Files (*.*)'}, ...
456            ['unvalid entry at line ' num2str(iview) ', pick a file'],RootPath);
457        fileinput=[PathName FileName];%complete file name
458        if isempty(fileinput),return;end %abandon if the operation has been cancelled: no input from browser
459        [path,name,ext]=fileparts(fileinput);
460        display_file_name(handles,fileinput,iview)
461    else
462        update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileType,MovieObject,iview)
463    end
464end
465set(handles.REFRESH,'BackgroundColor',[1 0 0])% set REFRESH  button to grey color
466set(handles.REFRESH,'Visible','off')
467set(handles.REFRESH,'UserData',[])
468
469%------------------------------------------------------------------------
470% --- Function called when a new file is opened, either by series_OpeningFcn or by the browser
471function display_file_name(handles,fileinput,iview)
472%------------------------------------------------------------------------ 
473%
474% INPUT:
475% handles: handles of elements in the GUI
476% fielinput: input file name, including path
477% append =0 (refresh the Input table with the new file), ='append' append a new line in the table
478
479%% get the input root name, indices, file extension and nomenclature NomType
480if ~exist(fileinput,'file')
481    msgbox_uvmat('ERROR',['input file ' fileinput  ' does not exist'])
482    return
483end
484
485%% enable other menus and uicontrols
486set(handles.MenuOpen_insert,'Enable','on')
487set(handles.MenuFile_insert_1,'Enable','on')
488set(handles.MenuFile_insert_2,'Enable','on')
489set(handles.MenuFile_insert_3,'Enable','on')
490set(handles.MenuFile_insert_4,'Enable','on')
491set(handles.MenuFile_insert_5,'Enable','on')
492set(handles.RUN, 'Enable','On')
493set(handles.RUN,'BackgroundColor',[1 0 0])% set RUN button to red
494set(handles.InputTable,'BackgroundColor',[1 1 0]) % set RootPath edit box  to yellow
495drawnow
496
497%% detect root name, nomenclature and indices in the input file name:
498[FilePath,FileName,FileExt]=fileparts(fileinput);
499% detect the file type, get the movie object if relevant, and look for the corresponding file series:
500% the root name and indices may be corrected by including the first index i1 if a corresponding xml file exists
501[RootPath,SubDir,RootFile,i1_series,i2_series,j1_series,j2_series,NomType,FileType,MovieObject,i1,i2,j1,j2]=find_file_series(FilePath,[FileName FileExt]);
502if isempty(RootFile)&&isempty(i1_series)
503    errormsg='no input file in the series';
504    return
505end
506
507%% fill the list of file series
508InputTable=get(handles.InputTable,'Data');
509if strcmp(iview,'append') % display the input data as a new line in the table
510     iview=size(InputTable,1);
511     InputTable(iview+1,:)={'','','','',''};
512     InputTable(iview,:)=[{RootPath},{SubDir},{RootFile},{NomType},{FileExt}];
513elseif iview==0 % or re-initialise the list of  input  file series
514    iview=1;
515    InputTable=[{'','','','',''};{'','','','',''}];
516     InputTable(iview,:)=[{RootPath},{SubDir},{RootFile},{NomType},{FileExt}];
517    set(handles.TimeTable,'Data',[{[]},{[]},{[]},{[]}])
518    set(handles.MinIndex,'Data',[{[]},{[]}])
519    set(handles.MaxIndex,'Data',[{[]},{[]}])
520    set(handles.ListView,'Value',1)
521    set(handles.ListView,'String',{'1'})
522end
523nbview=size(InputTable,1);
524set(handles.ListView,'String',mat2cell((1:nbview)',ones(nbview,1)))
525set(handles.ListView,'Value',iview)
526set(handles.InputTable,'Data',InputTable)
527
528%% determine the selected reference field indices for pair display
529ref_i=1; %default ref_i is a reference frame index used to find existing pairs from PIV
530if ~isempty(i1)
531    ref_i=i1;
532    if ~isempty(i2)
533        ref_i=floor((ref_i+i2)/2);% reference image number corresponding to the file
534    end
535end
536set(handles.num_ref_i,'String',num2str(ref_i));
537ref_j=1; %default  ref_j is a reference frame index used to find existing pairs from PIV
538if ~isempty(j1)
539    ref_j=j1;
540    if ~isempty(j2)
541        ref_j=floor((j1+j2)/2);
542    end         
543end
544set(handles.num_ref_j,'String',num2str(ref_j));
545
546%% update the list of recent files in the menubar and save it for future opening
547MenuFile=[{get(handles.MenuFile_1,'Label')};{get(handles.MenuFile_2,'Label')};...
548    {get(handles.MenuFile_3,'Label')};{get(handles.MenuFile_4,'Label')};{get(handles.MenuFile_5,'Label')}];
549str_find=strcmp(fileinput,MenuFile);
550if isempty(find(str_find,1))
551    MenuFile=[{fileinput};MenuFile];%insert the current file if not already in the list
552end
553for ifile=1:min(length(MenuFile),5)
554    eval(['set(handles.MenuFile_' num2str(ifile) ',''Label'',MenuFile{ifile});'])
555    eval(['set(handles.MenuFile_insert_' num2str(ifile) ',''Label'',MenuFile{ifile});'])
556end
557dir_perso=prefdir;
558profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
559if exist(profil_perso,'file')
560    save (profil_perso,'MenuFile','-append'); %store the file names for future opening of uvmat
561else
562    save (profil_perso,'MenuFile','-V6'); %store the file names for future opening of uvmat
563end
564
565set(handles.InputTable,'BackgroundColor',[1 1 1])
566
567%% initiate input file series and refresh the current field view:     
568update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileType,MovieObject,iview);
569
570%------------------------------------------------------------------------
571% --- Update information about a new field series (indices to scan, timing,
572%     calibration from an xml file
573function update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileType,VideoObject,iview)
574%------------------------------------------------------------------------
575%% update the output dir
576InputTable=get(handles.InputTable,'Data');
577SubDir=sort(InputTable(1:end-1,2)); %set of subdirectories sorted in alphabetical order
578SubDirOut=SubDir{1};
579if numel(SubDir)>1
580    for ilist=2:numel(SubDir)
581        SubDirOut=[SubDirOut '-' SubDir{ilist}];
582    end
583end
584set(handles.OutputSubDir,'String',SubDirOut)
585
586%% display the min and max indices for the file series
587pair_max=squeeze(max(i1_series,[],1)); %max on pair index
588j_max=max(pair_max,[],1);
589%i_sum=sum(sum(i1_series,2),1);%sum of i1_series on the last index
590MaxIndex_i=max(find(j_max))-1;% max ref index i
591MinIndex_i=min(find(j_max))-1;% min ref index i
592i_max=max(pair_max,[],2);
593MaxIndex_j=max(find(i_max))-1;% max ref index i
594MinIndex_j=min(find(i_max))-1;% min ref index i
595MinIndex=get(handles.MinIndex,'Data');%retrieve the min indices in the table MinIndex
596MaxIndex=get(handles.MaxIndex,'Data');%retrieve the max indices in the table MaxIndex
597MinIndex{iview,1}=MinIndex_i;
598MinIndex{iview,2}=MinIndex_j;
599MaxIndex{iview,1}=MaxIndex_i;
600MaxIndex{iview,2}=MaxIndex_j;
601
602set(handles.MinIndex,'Data',MinIndex)%display the min indices in the table MinIndex
603set(handles.MaxIndex,'Data',MaxIndex)%display the max indices in the table MaxIndex
604
605%% adjust the first and last indices if requested by the bounds
606first_i=str2num(get(handles.num_first_i,'String'));
607ref_i=str2num(get(handles.num_ref_i,'String'));
608ref_j=str2num(get(handles.num_ref_j,'String'));
609if isempty(first_i)
610    first_i=ref_i;
611elseif first_i < MinIndex_i
612    first_i=MinIndex_i;
613end
614first_j=str2num(get(handles.num_first_j,'String'));
615if isempty(first_j)
616    first_j=ref_j;
617elseif first_j<MinIndex_j
618    first_j=MinIndex_j;
619end
620last_i=str2num(get(handles.num_last_i,'String'));
621if isempty(last_i)
622    last_i=ref_i;
623elseif last_i > MaxIndex_i
624    last_i=MaxIndex_i;
625end
626last_j=str2num(get(handles.num_first_j,'String'));
627if isempty(last_j)
628    last_j=ref_j;
629elseif last_j>MaxIndex_j
630    last_j=MaxIndex_j;
631end
632set(handles.num_first_i,'String',num2str(first_i));
633set(handles.num_first_j,'String',num2str(first_j));
634set(handles.num_last_i,'String',num2str(last_i));
635set(handles.num_last_j,'String',num2str(last_j));
636
637%% read timing and total frame number from the current file (movie files) !! may be overrid by xml file
638InputTable=get(handles.InputTable,'Data');
639FileBase=fullfile(InputTable{iview,1},InputTable{iview,3});
640time=[];%default
641% case of movies
642if strcmp(InputTable{iview,4},'*')
643    if ~isempty(VideoObject)
644        imainfo=get(VideoObject);
645        time=(0:1/imainfo.FrameRate:(imainfo.NumberOfFrames-1)/imainfo.FrameRate)';
646        set(handles.Dt_txt,'String',['Dt=' num2str(1000/imainfo.FrameRate) 'ms']);%display the elementary time interval in millisec
647        ColorType='truecolor';
648    elseif ~isempty(imformats(regexprep(InputTable{iview,5},'^.',''))) || isequal(InputTable{iview,5},'.vol')%&& isequal(NomType,'*')% multi-frame image
649        if ~isempty(InputTable{iview,2})
650            imainfo=imfinfo(fullfile(InputTable{iview,1},InputTable{iview,2},[InputTable{iview,3} InputTable{iview,5}]));
651        else
652            imainfo=imfinfo([FileBase InputTable{iview,5}]);
653        end
654        ColorType=imainfo.ColorType;%='truecolor' for color images
655        if length(imainfo) >1 %case of image with multiple frames
656            nbfield=length(imainfo);
657            nbfield_j=1;
658        end
659    end
660end
661
662%%  read image documentation file  if found%%%%%%%%%%%%%%%%%%%%%%%%%%%
663ext_imadoc='';
664if exist([FileBase '.xml'],'file')
665    ext_imadoc='.xml';
666elseif exist([FileBase '.civ'],'file')
667    ext_imadoc='.civ';
668end
669%read the ImaDoc file
670XmlData=[];
671NbSlice_calib={};
672if isequal(ext_imadoc,'.xml')
673        [XmlData,warntext]=imadoc2struct([FileBase '.xml']);
674        if isfield(XmlData,'Heading') && isfield(XmlData.Heading,'ImageName') && ischar(XmlData.Heading.ImageName)
675            [PP,FF,ext_ima_read]=fileparts(XmlData.Heading.ImageName);
676        end
677        if isfield(XmlData,'Time')
678            time=XmlData.Time;
679        end
680        if isfield(XmlData,'Camera')
681            if isfield(XmlData.Camera,'NbSlice')&& ~isempty(XmlData.Camera.NbSlice)
682                NbSlice_calib{iview}=XmlData.Camera.NbSlice;% Nbre of slices for Zindex in phys transform
683                if ~isequal(NbSlice_calib{iview},NbSlice_calib{1})
684                    msgbox_uvmat('WARNING','inconsistent number of Z indices for the two field series');
685                end
686            end
687            if isfield(XmlData.Camera,'TimeUnit')&& ~isempty(XmlData.Camera.TimeUnit)
688                TimeUnit=XmlData.Camera.TimeUnit;
689            end
690        end
691        if ~isempty(warntext)
692            msgbox_uvmat('WARNING',warntext)
693        end 
694elseif isequal(ext_imadoc,'.civ')
695    [error,XmlData.Time,TimeUnit,mode,npx,npy,pxcmx,pxcmy]=read_imatext([FileBase '.civ']);
696    time=XmlData.Time;
697    if error==2, warntext=['no file ' FileBase '.civ'];
698    elseif error==1, warntext='inconsistent number of fields in the .civ file';
699    end 
700end
701
702%% update time table
703if ~isempty(time)
704    TimeTable=get(handles.TimeTable,'Data');
705    first_i=str2num(get(handles.num_first_i,'String'));
706    last_i=str2num(get(handles.num_last_i,'String'));
707    first_j=str2num(get(handles.num_first_j,'String'));
708    last_j=str2num(get(handles.num_last_j,'String'));
709    MinIndexTable=get(handles.MinIndex,'Data');
710    MinIndex_i=MinIndexTable{iview,1};
711    MinIndex_j=MinIndexTable{iview,2};
712    MaxIndexTable=get(handles.MaxIndex,'Data');
713    MaxIndex_i=MaxIndexTable{iview,1};
714    MaxIndex_j=MaxIndexTable{iview,2};
715    if isempty(MinIndex_j)
716        if MinIndex_i>0
717            TimeTable{iview,1}=time(MinIndex_i);
718        end
719        TimeTable{iview,2}=time(first_i);
720        TimeTable{iview,3}=time(last_i);
721        TimeTable{iview,4}=time(MaxIndex_i);
722    elseif ~isempty(time)
723        if MinIndex_i>0
724            TimeTable{iview,1}=time(MinIndex_i,MinIndex_j);
725        end
726        TimeTable{iview,2}=time(first_i,first_j);
727        TimeTable{iview,3}=time(last_i,last_j);
728        TimeTable{iview,4}=time(MaxIndex_i,MaxIndex_j);
729    end
730    set(handles.TimeTable,'Data',TimeTable)
731end
732
733%% number of slices
734NbSlice=1;%default
735if isfield(XmlData,'GeometryCalib') && isfield(XmlData.GeometryCalib,'SliceCoord')
736    siz=size(XmlData.GeometryCalib.SliceCoord);
737    if siz(1)>1
738        NbSlice=siz(1);
739    end
740end
741set(handles.num_NbSlice,'String',num2str(NbSlice))
742   
743%% update pair menus
744set(handles.Pairs,'Visible','on')
745set(handles.PairString,'Visible','on')
746ListView=get(handles.ListView,'String');
747ListView{iview}=num2str(iview);
748set(handles.ListView,'String',ListView);
749set(handles.ListView,'Value',iview)
750update_mode(handles,i1_series,i2_series,j1_series,j2_series,time)
751
752%% update the series info in 'UserData'
753SeriesData=get(handles.series,'UserData');
754SeriesData.i1_series{iview}=i1_series;
755SeriesData.i2_series{iview}=i2_series;
756SeriesData.j1_series{iview}=j1_series;
757SeriesData.j2_series{iview}=j2_series;
758SeriesData.FileType{iview}=FileType;
759SeriesData.Time{iview}=time;
760set(handles.series,'UserData',SeriesData)
761
762%% enable j index visibilitycellfun(@isempty,regexp(PairString,'^j'))
763state='off';
764check_jindex=~cellfun(@isempty,SeriesData.j1_series); %look for non empty j indices
765if isempty(find(check_jindex))
766    enable_j(handles,'off') % no j index needed
767else
768    PairString=get(handles.PairString,'Data');
769    if isempty(find(cellfun(@isempty,regexp(PairString,'^j'))))% if all pair string begins by j (burst)
770        enable_j(handles,'off') % no j index needed
771    else
772        enable_j(handles,'on')
773    end
774end
775
776%% display the set of existing files as an image
777set(handles.FileStatus,'Units','pixels')
778Position=get(handles.FileStatus,'Position');
779set(handles.FileStatus,'Units','normalized')
780xI=0.5:Position(3)-0.5;
781nbview=numel(SeriesData.i1_series);
782pair_max=cell(1,nbview);
783for iview=1:nbview
784    pair_max{iview}=squeeze(max(SeriesData.i1_series{iview},[],1)); %max on pair index
785    index_min(iview)=find(pair_max{iview}>0, 1 );
786    index_max(iview)=find(pair_max{iview}>0, 1, 'last' );
787end
788index_min=min(index_min);
789index_max=max(index_max);
790range_index=index_max-index_min+1;
791scale_y=Position(4)/nbview;
792scale_x=Position(3)/range_index;
793x=(0.5:range_index-0.5)*Position(3)/range_index;
794% y=(0.5:nbview-0.5)*Position(4)/nbview;
795range_y=max(1,floor(Position(4)/nbview));
796CData=zeros(nbview*range_y,Position(3));
797for iview=1:nbview
798    ind_y=1+(iview-1)*range_y:iview*range_y;
799    LineData=zeros(1,range_index);
800    x_index=find(pair_max{iview}>0)-index_min+1;
801    LineData(x_index)=1;
802    LineData=interp1(x,LineData,xI,'nearest');
803    CData(ind_y,:)=ones(size(ind_y'))*LineData;
804end
805CData=cat(3,zeros(size(CData)),CData,zeros(size(CData)));
806set(handles.FileStatus,'CData',CData);
807
808
809%% enable field and veltype menus, in accordance with the current action
810ActionName_Callback([],[], handles)
811
812%% check for pair display
813check_pairs=0;
814for iview=1:numel(SeriesData.i2_series)
815    if ~isempty(SeriesData.i2_series{iview})||~isempty(SeriesData.j2_series{iview})
816        check_pairs=1;
817    end
818end
819if check_pairs
820    set(handles.Pairs,'Visible','on')
821    set(handles.PairString,'Visible','on')
822else
823    set(handles.Pairs,'Visible','off')
824    set(handles.PairString,'Visible','off')
825end
826
827%% set length of waitbar
828displ_time(handles)
829
830
831% %% set default options in menu 'Fields'%% TODO: check VelType
832% if ~testima
833%     testcivx=0;
834%     if isfield(UvData,'FieldsString') && isequal(UvData.FieldsString,{'get_field...'})% field menu defined as input (from get_field)
835%         set(handles_Fields,'Value',1)
836%         set(handles_Fields,'String',{'get_field...'})
837%         UvData=rmfield(UvData,'FieldsString');
838%     else
839%         Data=nc2struct(FileName,'ListGlobalAttribute','Conventions','absolut_time_T0','civ');
840%         if strcmp(Data.Conventions,'uvmat/civdata') ||( ~isempty(Data.absolut_time_T0)&& ~isequal(Data.civ,0))%if the new input is Civx
841%             FieldList=calc_field;
842%             set(handles_Fields,'String',[{'image'};FieldList;{'get_field...'}]);%standard menu for civx data
843%             set(handles_Fields,'Value',2) % set menu to 'velocity'
844%             col_vec=FieldList;
845%             col_vec(1)=[];%remove 'velocity' option for vector color (must be a scalar)
846%             testcivx=1;
847%         end
848%         if ~testcivx
849%             set(handles_Fields,'Value',1) % set menu to 'get_field...
850%             set(handles_Fields,'String',{'get_field...'})
851%             col_vec={'get_field...'};
852%         end
853%         set(handles.ColorScalar,'String',col_vec)
854%     end
855% end
856% set(handles.uvmat,'UserData',UvData)
857%
858% %% set index navigation options and refresh plots
859% scan_option='i';%default
860% state_j='off'; %default
861% if index==2
862%     if get(handles.scan_j,'Value')
863%         scan_option='j'; %keep the scan option for the second fiel series
864%     end
865%     if strcmp(get(handles.j1,'Visible'),'on')
866%         state_j='on';
867%     end
868% end
869% if ~isempty(j1_series)
870%         state_j='on';
871%         if isequal(nbfield,1) &&index==1
872%             scan_option='j'; %scan j index by default if nbfield=1               
873%         end
874% end
875% if isequal(scan_option,'i')
876%      set(handles.scan_i,'Value',1)
877%      scan_i_Callback([],[], handles);
878% else
879%      set(handles.scan_j,'Value',1)
880%      scan_j_Callback([],[], handles);
881% end
882% set(handles.scan_j,'Visible',state_j)
883% set(handles.j1,'Visible',state_j)
884% set(handles.j2,'Visible',state_j)
885% set(handles.last_j,'Visible',state_j);
886% set(handles.frame_j,'Visible',state_j);
887% set(handles.j_text,'Visible',state_j);
888% if ~isempty(i2_series)||~isempty(j2_series)
889%     set(handles.CheckFixPair,'Visible','on')
890% elseif index==1
891%     set(handles.CheckFixPair,'Visible','off')
892% end
893%
894%
895% mode_Callback(hObject, eventdata, handles)
896%
897% set(handles.REFRESH,'BackgroundColor',[0.7 0.7 0.7])
898% InputTable=get(handles.InputTable,'Data');
899% check_lines=get(handles.REFRESH,'UserData');
900%
901% %% check the indices and FileTypes for each series (limited to the new ones to save time)
902% for ind_list=1:length(check_lines)
903%     if  check_lines(ind_list)
904%         InputLine=InputTable(ind_list,:);
905%         detect_idem=strcmp('"',InputLine);% look for '" (repeat of previous data)
906%         detect_idem=detect_idem(detect_idem>0);
907%         if ~isempty (detect_idem)
908%             InputLine(detect_idem)=InputTable(ind_list-1,detect_idem);
909%             set(handles.InputTable,'Data',InputTable)
910%         end
911%         fileinput=fullfile_uvmat(InputLine{1},InputLine{2},InputLine{3},InputLine{5},InputLine{4},1,2,1,2);
912%         %fileinput=name_generator(fullfile(InputLine{1},InputLine{3}),1,1,InputLine{5},InputLine{4},1,2,2,InputLine{2})
913%         %update file series defined by the selected line
914%         [InputTable{ind_list,3},InputTable{(ind_list),4},errormsg]=update_indices(handles,fileinput,ind_list);
915%         if ~isempty(errormsg)
916%                 msgbox_uvmat('ERROR',errormsg)
917%                 return
918%         end
919%     end
920% end
921% set(handles.InputTable,'Data',InputTable)
922% SeriesData=get(handles.series,'UserData');
923%
924% state_j='off';
925% state_Pairs='off';
926% state_InputFields='off';
927% val=get(handles.ListView,'Value');
928% ListViewString={''};
929% if ~isempty(SeriesData)
930% %     ListViewString={};
931%     for iview=1:size(InputTable,1)
932%         if ~isempty(SeriesData.j1_series{iview})
933%             state_j='on';
934%         end
935%         if ~isempty(SeriesData.i2_series{iview})||~isempty(SeriesData.j2_series{iview})
936%             state_Pairs='on';
937%             ListViewString{iview}=num2str(iview);
938%             if check_lines(iview)
939%                 val=iview;%select the last pair if it is a new entry
940%             end
941%         end
942%         if strcmp(SeriesData.FileType{iview},'civx')||strcmp(SeriesData.FileType{iview},'civdata')
943%             state_InputFields='on';
944%         end
945%     end
946% end
947% set(handles.ListView,'Value',val)
948% set(handles.ListView,'String',ListViewString)
949% if strcmp(state_Pairs,'on')
950%     ListView_Callback(hObject,eventdata,handles)
951% end
952% set(handles.PairString,'Visible',state_Pairs)
953% enable_j(handles,state_j)
954
955%------------------------------------------------------------------------
956function num_first_i_Callback(hObject, eventdata, handles)
957%------------------------------------------------------------------------
958num_last_i_Callback(hObject, eventdata, handles)
959
960%------------------------------------------------------------------------
961function num_last_i_Callback(hObject, eventdata, handles)
962%------------------------------------------------------------------------
963SeriesData=get(handles.series,'UserData');
964if ~isfield(SeriesData,'Time')
965    SeriesData.Time{1}=[];
966end
967displ_time(handles);
968
969%------------------------------------------------------------------------
970function num_first_j_Callback(hObject, eventdata, handles)
971%------------------------------------------------------------------------
972 num_last_j_Callback(hObject, eventdata, handles)
973
974%------------------------------------------------------------------------
975function num_last_j_Callback(hObject, eventdata, handles)
976%------------------------------------------------------------------------
977first_j=str2num(get(handles.num_first_j,'String'));
978last_j=str2num(get(handles.num_last_j,'String'));
979ref_j=ceil((first_j+last_j)/2);
980set(handles.num_ref_j,'String', num2str(ref_j))
981num_ref_j_Callback(hObject, eventdata, handles)
982SeriesData=get(handles.series,'UserData');
983if ~isfield(SeriesData,'Time')
984    SeriesData.Time{1}=[];
985end
986displ_time(handles);
987
988
989%------------------------------------------------------------------------
990% ---- find the times corresponding to the first and last indices of a series
991function displ_time(handles)
992%------------------------------------------------------------------------
993SeriesData=get(handles.series,'UserData');%
994ref_i=[str2num(get(handles.num_first_i,'String')) str2num(get(handles.num_last_i,'String'))];
995ref_j=[str2num(get(handles.num_first_j,'String')) str2num(get(handles.num_last_j,'String'))];
996TimeTable=get(handles.TimeTable,'Data');
997Pairs=get(handles.PairString,'Data');
998for iview=1:size(TimeTable,1)
999    if size(SeriesData.Time,1)<iview
1000        break
1001    end
1002    i1=ref_i;
1003    j1=ref_j;
1004    i2=ref_i;
1005    j2=ref_j;
1006    % case of pairs
1007    if ~isempty(Pairs{iview,1})
1008        r=regexp(Pairs{iview,1},'(?<mode>(Di=)|(Dj=)) -*(?<num1>\d+)\|(?<num2>\d+)','names');
1009        if isempty(r)
1010            r=regexp(Pairs{iview,1},'(?<num1>\d+)(?<mode>-)(?<num2>\d+)','names');
1011        end
1012        switch r.mode
1013            case 'Di='  %  case 'series(Di)')
1014                i1=ref_i-str2num(r.num1);
1015                i2=ref_i+str2num(r.num2);
1016            case 'Dj='  %  case 'series(Dj)'
1017                j1=ref_j-str2num(r.num1);
1018                j2=ref_j+str2num(r.num2);
1019            case '-'  % case 'bursts'
1020                j1=str2num(r.num1)*ones(size(ref_i));
1021                j2=str2num(r.num2)*ones(size(ref_i));
1022        end
1023    end
1024    TimeTable{iview,2}=[];
1025    TimeTable{iview,3}=[];
1026    if size(SeriesData.Time{iview},1)>=i2(2)&&size(SeriesData.Time{iview},1)>=j2(2)
1027        if isempty(ref_j)
1028            time_first=(SeriesData.Time{iview}(i1(1))+SeriesData.Time{iview}(i2(1)))/2;
1029            time_last=(SeriesData.Time{iview}(i1(2))+SeriesData.Time{iview}(i2(2)))/2;
1030        else
1031            time_first=(SeriesData.Time{iview}(i1(1),j1(1))+SeriesData.Time{iview}(i2(1),j2(1)))/2;
1032            time_last=(SeriesData.Time{iview}(i1(2),j1(2))+SeriesData.Time{iview}(i2(2),j2(2)))/2;
1033        end
1034        TimeTable{iview,2}=time_first; %TODO: take into account pairs
1035        TimeTable{iview,3}=time_last; %TODO: take into account pairs
1036    end
1037end
1038set(handles.TimeTable,'Data',TimeTable)
1039
1040%% set the waitbar position with respect to the min and max in the series
1041% for iview=1:numel(SeriesData.i1_series)
1042% [tild,index_min(iview)]=min(SeriesData.i1_series{iview}(SeriesData.i1_series{iview}>0));
1043% [tild,index_max(iview)]=max(SeriesData.i1_series{iview}(SeriesData.i1_series{iview}>0));
1044% end
1045for iview=1:numel(SeriesData.i1_series)
1046    index_min(iview)=min(find(SeriesData.i1_series{iview}(1,2:end,2:end)>0));
1047    index_max(iview)=max(find(SeriesData.i1_series{iview}(1,2:end,2:end)>0));
1048end
1049[index_min,iview_min]=min(index_min);
1050[index_max,iview_max]=min(index_max);
1051index_first=(ref_i(1)-1)*(size(SeriesData.i1_series{iview_min},2)-1)+ref_j(1);
1052index_last=(ref_i(2)-1)*(size(SeriesData.i1_series{iview_max},2)-1)+ref_j(2);
1053range=index_max-index_min+1;
1054coeff_min=(index_first-index_min)/range;
1055coeff_max=(index_last-index_min+1)/range;
1056Position=get(handles.Waitbar,'Position');
1057Position_status=get(handles.FileStatus,'Position');
1058Position(1)=coeff_min*Position_status(3)+Position_status(1);
1059Position(3)=Position_status(3)*(coeff_max-coeff_min);
1060set(handles.Waitbar,'Position',Position)
1061update_waitbar(handles.Waitbar,0)
1062
1063%------------------------------------------------------------------------
1064% --- Executes when selected cell(s) is changed in PairString.
1065function PairString_CellSelectionCallback(hObject, eventdata, handles)
1066%------------------------------------------------------------------------   
1067set(handles.ListView,'Value',eventdata.Indices(1))% detect the selected raw index
1068ListView_Callback ([],[],handles) % update the list of available pairs
1069
1070%------------------------------------------------------------------------
1071%------------------------------------------------------------------------
1072%  III - FUNCTIONS ASSOCIATED TO THE FRAME SET PAIRS
1073%------------------------------------------------------------------------
1074%------------------------------------------------------------------------
1075% --- Executes on selection change in ListView.
1076function ListView_Callback(hObject, eventdata, handles)
1077%------------------------------------------------------------------------   
1078SeriesData=get(handles.series,'UserData');
1079i2_series=[];
1080j2_series=[];
1081iview=get(handles.ListView,'Value');
1082if ~isempty(SeriesData.i2_series{iview})
1083    i2_series=SeriesData.i2_series{iview};
1084end
1085if ~isempty(SeriesData.j2_series{iview})
1086    j2_series=SeriesData.j2_series{iview};
1087end
1088update_mode(handles,SeriesData.i1_series{iview},SeriesData.i2_series{iview},...
1089    SeriesData.j1_series{iview},SeriesData.j2_series{iview},SeriesData.Time{iview})
1090
1091%------------------------------------------------------------------------
1092% --- Executes on button press in mode.
1093function mode_Callback(hObject, eventdata, handles)
1094%------------------------------------------------------------------------       
1095SeriesData=get(handles.series,'UserData');
1096iview=get(handles.ListView,'Value');
1097mode_list=get(handles.mode,'String');
1098mode=mode_list{get(handles.mode,'Value')};
1099if isequal(mode,'bursts')
1100    enable_i(handles,'On')
1101    enable_j(handles,'Off') %do not display j index scanning in burst mode (j is fixed by the burst choice)
1102else
1103    enable_i(handles,'On')
1104    enable_j(handles,'Off')
1105end
1106fill_ListPair(handles,SeriesData.i1_series{iview},SeriesData.i2_series{iview},...
1107    SeriesData.j1_series{iview},SeriesData.j2_series{iview},SeriesData.Time{iview})
1108ListPairs_Callback([],[],handles)
1109
1110%-------------------------------------------------------------
1111% --- Executes on selection in ListPairs.
1112function ListPairs_Callback(hObject,eventdata,handles)
1113%------------------------------------------------------------
1114list_pair=get(handles.ListPairs,'String');%get the menu of image pairs
1115if isempty(list_pair)
1116    string='';
1117else
1118    string=list_pair{get(handles.ListPairs,'Value')};
1119    string=regexprep(string,',.*','');%removes time indication (after ',')
1120end
1121PairString=get(handles.PairString,'Data');
1122iview=get(handles.ListView,'Value');
1123PairString{iview,1}=string;
1124% report the selected pair string to the table PairString
1125set(handles.PairString,'Data',PairString)
1126
1127%------------------------------------------------------------------------
1128function num_ref_i_Callback(hObject, eventdata, handles)
1129%------------------------------------------------------------------------
1130mode_list=get(handles.mode,'String');
1131mode=mode_list{get(handles.mode,'Value')};
1132SeriesData=get(handles.series,'UserData');
1133iview=get(handles.ListView,'Value');
1134fill_ListPair(handles,SeriesData.i1_series{iview},SeriesData.i2_series{iview},...
1135    SeriesData.j1_series{iview},SeriesData.j2_series{iview},SeriesData.Time{iview});% update the menu of pairs depending on the available netcdf files
1136ListPairs_Callback([],[],handles)
1137
1138%------------------------------------------------------------------------
1139function num_ref_j_Callback(hObject, eventdata, handles)
1140%------------------------------------------------------------------------
1141num_ref_i_Callback(hObject, eventdata, handles)
1142
1143%------------------------------------------------------------------------
1144function update_mode(handles,i1_series,i2_series,j1_series,j2_series,time)
1145%------------------------------------------------------------------------   
1146% check_burst=0;
1147if isempty(j2_series)% no j pair
1148    if isempty(i2_series)
1149        set(handles.mode,'Value',1)
1150        set(handles.mode,'String',{''})% no pair menu to display
1151    else   
1152        set(handles.mode,'Value',1)
1153        set(handles.mode,'String',{'series(Di)'}) % pair menu with only option Di
1154    end
1155else %existence of j pairs
1156    pair_max=squeeze(max(i1_series,[],1)); %max on pair index
1157    j_max=max(pair_max,[],1);
1158    MaxIndex_i=max(find(j_max))-1;% max ref index i
1159    MinIndex_i=min(find(j_max))-1;% min ref index i
1160    i_max=max(pair_max,[],2);
1161    MaxIndex_j=max(find(i_max))-1;% max ref index i
1162    MinIndex_j=min(find(i_max))-1;% min ref index i
1163    if MaxIndex_j==MinIndex_j
1164        set(handles.mode,'Value',1);
1165        set(handles.mode,'String',{'bursts'})
1166%         check_burst=1;
1167    elseif MaxIndex_i==MinIndex_i
1168        set(handles.mode,'Value',1);
1169        set(handles.mode,'String',{'series(Dj)'})
1170    else
1171        set(handles.mode,'String',{'bursts';'series(Dj)'})
1172        if (MaxIndex_j-MinIndex_j)>10
1173            set(handles.mode,'Value',2);%set mode to series(Dj) if more than 10 j values
1174        else
1175            set(handles.mode,'Value',1);
1176%             check_burst=1;
1177        end
1178    end
1179end
1180% if check_burst
1181%     enable_i(handles,'On')
1182%     enable_j(handles,'Off') %do not display j index scanning in burst mode (j is fixed by the burst choice)
1183% else
1184%     enable_i(handles,'On')
1185%     if isempty(j1_series)
1186%          enable_j(handles,'Off')
1187%     else
1188%         enable_j(handles,'On')
1189%     end
1190% end
1191fill_ListPair(handles,i1_series,i2_series,j1_series,j2_series,time)
1192ListPairs_Callback([],[],handles)
1193
1194%--------------------------------------------------------------
1195% determine the menu for civ1 pairstring depending on existing netcdf files
1196% with the reference indices num_ref_i and num_ref_j
1197%----------------------------------------------------------------
1198function fill_ListPair(handles,i1_series,i2_series,j1_series,j2_series,time)
1199
1200mode_list=get(handles.mode,'String');
1201mode=mode_list{get(handles.mode,'Value')};
1202ref_i=str2num(get(handles.num_ref_i,'String'));
1203if isempty(ref_i)
1204    ref_i=1;
1205end
1206if strcmp(get(handles.num_ref_j,'Visible'),'on')
1207    ref_j=str2num(get(handles.num_ref_j,'String'));
1208    if isempty(ref_j)
1209        ref_j=1;
1210    end
1211else
1212    ref_j=1;
1213end
1214TimeUnit=get(handles.TimeUnit,'String');
1215if length(TimeUnit)>=1
1216    dtunit=['m' TimeUnit];
1217else
1218    dtunit='e-03';
1219end
1220
1221displ_pair={};
1222if strcmp(mode,'series(Di)')
1223    if isempty(i2_series)
1224        msgbox_uvmat('ERROR','no i1-i2 pair available')
1225        return
1226    end
1227    diff_i=i2_series-i1_series;
1228    min_diff=min(diff_i(diff_i>0));
1229    max_diff=max(diff_i(diff_i>0));
1230    for ipair=min_diff:max_diff
1231        if numel(diff_i(diff_i==ipair))>0
1232            pair_string=['Di= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2)) ];
1233            if ~isempty(time)
1234                if ref_i<=floor(ipair/2)
1235                    ref_i=floor(ipair/2)+1;% shift ref_i to get the first pair
1236                end
1237                Dt=time(ref_i+ceil(ipair/2),ref_j)-time(ref_i-floor(ipair/2),ref_j);
1238                pair_string=[pair_string ', Dt=' num2str(Dt) ' ' dtunit];
1239            end
1240            displ_pair=[displ_pair;{pair_string}];
1241        end
1242    end
1243    if ~isempty(displ_pair)
1244        displ_pair=[displ_pair;{'Di=*|*'}];
1245    end
1246elseif strcmp(mode,'series(Dj)')
1247    if isempty(j2_series)
1248        msgbox_uvmat('ERROR','no j1-j2 pair available')
1249        return
1250    end
1251    diff_j=j2_series-j1_series;
1252    min_diff=min(diff_j(diff_j>0));
1253    max_diff=max(diff_j(diff_j>0));
1254    for ipair=min_diff:max_diff
1255        if numel(diff_j(diff_j==ipair))>0
1256            pair_string=['Dj= ' num2str(-floor(ipair/2)) '|' num2str(ceil(ipair/2)) ];
1257            if ~isempty(time)
1258                if ref_j<=floor(ipair/2)
1259                    ref_j=floor(ipair/2)+1;% shift ref_i to get the first pair
1260                end
1261                Dt=time(ref_i,ref_j+ceil(ipair/2))-time(ref_i,ref_j-floor(ipair/2));
1262                pair_string=[pair_string ', Dt=' num2str(Dt) ' ' dtunit];
1263            end
1264            displ_pair=[displ_pair;{pair_string}];
1265        end
1266    end
1267    if ~isempty(displ_pair)
1268        displ_pair=[displ_pair;{'Dj=*|*'}];
1269    end
1270elseif strcmp(mode,'bursts')
1271    if isempty(j2_series)
1272        msgbox_uvmat('ERROR','no j1-j2 pair available')
1273        return
1274    end
1275    diff_j=j2_series-j1_series;
1276    min_j1=min(j1_series(j1_series>0));
1277    max_j1=max(j1_series(j1_series>0));
1278    min_j2=min(j2_series(j2_series>0));
1279    max_j2=max(j2_series(j2_series>0));
1280    for pair1=min_j1:min(max_j1,min_j1+20)
1281        for pair2=min_j2:min(max_j2,min_j2+20)
1282        if numel(j1_series(j1_series==pair1))>0 && numel(j2_series(j2_series==pair2))>0
1283            displ_pair=[displ_pair;{['j= ' num2str(pair1) '-' num2str(pair2)]}];
1284        end
1285        end
1286    end
1287    if ~isempty(displ_pair)
1288        displ_pair=[displ_pair;{'j=*-*'}];
1289    end
1290end
1291set(handles.num_ref_i,'String',num2str(ref_i)) % update ref_i and ref_j
1292set(handles.num_ref_j,'String',num2str(ref_j))
1293
1294%% display list of pairstring
1295displ_pair_list=get(handles.ListPairs,'String');
1296NewVal=[];
1297if ~isempty(displ_pair_list)
1298Val=get(handles.ListPairs,'Value');
1299NewVal=find(strcmp(displ_pair_list{Val},displ_pair),1);% look at the previous display in the new menu displ_pï¿œir
1300end
1301if ~isempty(NewVal)
1302    set(handles.ListPairs,'Value',NewVal)
1303else
1304    set(handles.ListPairs,'Value',1)
1305end
1306set(handles.ListPairs,'String',displ_pair)
1307
1308%-------------------------------------
1309function enable_i(handles,state)
1310set(handles.i_txt,'Visible',state)
1311set(handles.num_first_i,'Visible',state)
1312set(handles.num_last_i,'Visible',state)
1313set(handles.num_incr_i,'Visible',state)
1314% set(handles.num_MaxIndex_i,'Visible',state)
1315set(handles.num_ref_i,'Visible',state)
1316set(handles.ref_i_text,'Visible',state)
1317
1318%-----------------------------------
1319function enable_j(handles,state)
1320set(handles.j_txt,'Visible',state)
1321% set(handles.num_MinIndex_j,'Visible',state)
1322set(handles.num_first_j,'Visible',state)
1323set(handles.num_last_j,'Visible',state)
1324set(handles.num_incr_j,'Visible',state)
1325% set(handles.num_MaxIndex_j,'Visible',state)
1326set(handles.num_ref_j,'Visible',state)
1327set(handles.ref_j_text,'Visible',state)
1328
1329%-----------------------------------
1330% function view_FieldMenu(handles,state)
1331% % set(handles.FieldName,'Visible',state)
1332% % set(handles.Field_text,'Visible',state)
1333% set(handles.InputFields,'Visible',state)
1334
1335% %-----------------------------------
1336% function view_FieldMenu_1(handles,state)
1337% set(handles.FieldName_1,'Visible',state)
1338% set(handles.Field_text_1,'Visible',state)
1339
1340
1341%%%%%%%%%%%%%%%%%%%%
1342%%  MAIN ActionName FUNCTIONS
1343%%%%%%%%%%%%%%%%%%%%
1344%------------------------------------------------------------------------
1345% --- Executes on button press in RUN.
1346function RUN_Callback(hObject, eventdata, handles)
1347%------------------------------------------------------------------------
1348set(handles.RUN,'BusyAction','queue');
1349set(0,'CurrentFigure',handles.series)
1350set(handles.RUN, 'Enable','Off')
1351set(handles.RUN,'BackgroundColor',[0.831 0.816 0.784])
1352drawnow
1353[h_fun,Series,filexml,errormsg]=prepare_jobs(handles);
1354if ~isempty(errormsg)
1355    msgbox_uvmat('ERROR',errormsg)
1356    return
1357end
1358RunModeList=get(handles.RunMode,'String');
1359RunMode=RunModeList{get(handles.RunMode,'Value')};
1360
1361switch RunMode
1362    case 'local'
1363        Series=h_fun(Series);
1364        if ~isempty(filexml)
1365            t=struct2xml(Series);
1366            t=set(t,1,'name','Series');
1367            save(t,filexml);
1368        end
1369    case 'background'
1370        if isempty(filexml)
1371            Series=h_fun(Series);% no background in the absence of output file
1372        else
1373            % update the xml file after interactive input with the function
1374            Series.Specific='?';
1375            Series=h_fun(Series);
1376            t=struct2xml(Series);
1377            t=set(t,1,'name','Series');
1378            save(t,filexml);
1379            path_uvmat=fileparts(which('uvmat'));
1380           
1381            filename_bat=regexprep(filexml,'.xml$','.bat');
1382            [fid,message]=fopen(filename_bat,'w');
1383            if isequal(fid,-1)
1384                msgbox_uvmat('ERROR', ['creation of .bat file: ' message]);
1385                return
1386            end
1387            path_fct=get(handles.ActionPath,'String');
1388            filelog=regexprep(filexml,'.xml$','.log');
1389       
1390            switch computer
1391                case {'GLNX86','GLNXA64','MACI64'}
1392                    text_matlabscript=[...
1393                        '#!/bin/bash \n'...
1394                        '. /etc/sysprofile \n'...
1395                        'matlab -nodisplay -nosplash -nojvm -logfile ''' filelog ''' <<END_MATLAB \n'...
1396                        'addpath(''' path_uvmat '''); \n'...
1397                        'addpath(''' Series.Action.ActionPath '''); \n'...
1398                        '' Series.Action.ActionName  '( ''' filexml '''); \n'...
1399                        'exit \n'...
1400                        'END_MATLAB \n'];
1401                    fprintf(fid,text_matlabscript);
1402                    fclose(fid);
1403                    system(['chmod +x ' filename_bat]);% set the file to executable
1404                    system(['. ' filename_bat ' &']);%execute fct
1405                   
1406                case {'PCWIN','PCWIN64'}
1407                    text_matlabscript=['matlab -automation -logfile ' regexprep(filelog,'\\','\\\\')...
1408                        ' -r "addpath(''' regexprep(path_uvmat,'\\','\\\\') ''');'...
1409                        'addpath(''' regexprep(Series.Action.ActionPath,'\\','\\\\') ''');'...
1410                        '' Series.Action.ActionName  '( ''' regexprep(filexml,'\\','\\\\') ''');exit"'];
1411                    fprintf(fid,text_matlabscript);
1412                    fclose(fid);
1413                    dos([filename_bat ' &']);
1414            end
1415        end
1416        update_waitbar(handles.Waitbar,1); % put the waitbar to end position to indicate lounching is finished
1417end
1418
1419set(handles.RUN, 'Enable','On')
1420set(handles.RUN,'BackgroundColor',[1 0 0])
1421
1422%------------------------------------------------------------------------
1423function STOP_Callback(hObject, eventdata, handles)
1424%------------------------------------------------------------------------
1425set(handles.RUN, 'BusyAction','cancel')
1426set(handles.RUN,'BackgroundColor',[1 0 0])
1427set(handles.RUN,'enable','on')
1428% set(handles.BATCH,'BackgroundColor',[1 0 0])
1429% set(handles.BATCH,'enable','on')
1430
1431%------------------------------------------------------------------------
1432% --- Executes on button press in BATCH.
1433function BATCH_Callback(hObject, eventdata, handles)
1434%------------------------------------------------------------------------   
1435
1436
1437% %------------------------------------------------------------------------
1438% % --- Executes on button press in BIN.
1439% function BIN_Callback(hObject, eventdata, handles)
1440% %------------------------------------------------------------------------
1441%     cmd=['#!/bin/bash \n '...
1442%         '#$ -cwd \n '...
1443%         'hostname && date \n '...
1444%         'umask 002 \n'...
1445%         Param.xml.CivmBin ' ' Param.xml.RunTime ' ' filename_xml ' ' OutputFile '.nc'];
1446%     
1447%------------------------------------------------------------------------
1448% --- Main launch command, called by RUN and BATCH
1449function [h_fun,Series,filexml,errormsg]=prepare_jobs(handles,run)
1450%INPUT:
1451% handles: handles of graphic objects on the GUI series
1452% run=0, just to display parameters for MenuExport/GUI config
1453% run=1 (default) prepare the computation
1454
1455%------------------------------------------------------------------------
1456h_fun=[];
1457filexml='';
1458errormsg='';
1459if ~exist('run','var')
1460    run=1;
1461end
1462%% Read parameters from series
1463Series=read_GUI(handles.series);
1464if isfield(Series,'Pairs')
1465Series=rmfield(Series,'Pairs'); %info Pairs not needed for output
1466end
1467
1468%% read index ranges
1469first_i=1;
1470last_i=1;
1471incr_i=1;
1472first_j=1;
1473last_j=1;
1474incr_j=1;
1475if isfield(Series.IndexRange,'first_i')
1476    first_i=Series.IndexRange.first_i;
1477    incr_i=Series.IndexRange.incr_i;
1478    last_i=Series.IndexRange.last_i;
1479end
1480if isfield(Series.IndexRange,'first_j')
1481    first_j=Series.IndexRange.first_j;
1482    incr_j=Series.IndexRange.incr_j;
1483    last_j=Series.IndexRange.last_j;
1484end
1485
1486%% read input file parameters and set menus
1487menu_coord_state=get(handles.TransformName,'Visible');
1488if isequal(menu_coord_state,'on')
1489    menu_index=get(handles.TransformName,'Value');
1490    transform_list=get(handles.TransformName,'UserData');
1491    Series.FieldTransform.TransformHandle=transform_list{menu_index};% transform function handles
1492end
1493
1494if last_i < first_i | last_j < first_j , msgbox_uvmat('ERROR','last field number must be larger than the first one'),...
1495    set(handles.RUN, 'Enable','On'), set(handles.RUN,'BackgroundColor',[1 0 0]),return,end;
1496
1497%% projection object
1498if isfield(Series,'CheckObject')
1499    if Series.CheckObject
1500        hset_object=findobj(allchild(0),'tag','set_object');
1501        Series.ProjObject=read_GUI(hset_object);
1502        CheckObject_Callback([], [], handles)
1503    end
1504else
1505    Series.CheckObject=0;
1506end
1507
1508%% get_field GUI
1509if isfield(Series,'InputFields')&&isfield(Series.InputFields,'Field')
1510    if strcmp(Series.InputFields.Field,'get_field...')
1511        hget_field=findobj(allchild(0),'name','get_field');
1512        Series.GetField=read_GUI(hget_field);
1513    end
1514end
1515
1516if ~run
1517    return
1518end
1519
1520%% defining the ActionName function handle
1521list_action=get(handles.ActionName,'String');% list menu action
1522index=get(handles.ActionName,'Value');
1523action= list_action{index}; % selected string
1524%Series.Action=action;%name of the processing programme
1525Series.hseries=handles.series; % handles to the series GUI
1526path_series=which('series');
1527list_path=get(handles.ActionName,'UserData');
1528fct_path=list_path{index}; %path stored for the function ACTION
1529if ~isequal(fct_path,path_series)
1530    eval(['spath=which(''' action ''');']) %spath = current path of the selected function ACTION
1531    if ~exist(fct_path,'dir')
1532        errormsg=['The prescribed function path ' fct_path ' does not exist'];
1533        return
1534    end
1535    if ~isequal(spath,fct_path)
1536        addpath(fct_path)% add the prescribed path if not the current one
1537    end
1538end
1539eval(['h_fun=@' action ';'])%create a function handle for ACTION
1540if ~isequal(fct_path,path_series)
1541        rmpath(fct_path)% add the prescribed path if not the current one   
1542end
1543
1544%% create the output data directory and write in it the xml file from the GUI config
1545%determine the root file corresponding to the first sub dir
1546if isfield(Series,'OutputSubDir')
1547    SubDirOut=[Series.OutputSubDir Series.OutputDirExt];
1548    SubDirOutNew=SubDirOut;
1549    iview=1;
1550    SeriesData=get(handles.series,'UserData');
1551    if size(Series.InputTable,1)>1 && isfield(SeriesData,'AllowInputSort') && isfield(SeriesData.AllowInputSort)
1552        [tild,iview]=sort(Series.InputTable(:,2)); %subdirectories sorted in alphabetical order
1553        Series.InputTable=Series.InputTable(iview,:);
1554    end
1555    detect=exist(fullfile(Series.InputTable{1,1},SubDirOutNew),'dir');% test if  the dir  already exist
1556    check_create=1; %need to create the result directory by default
1557    while detect
1558        answer=msgbox_uvmat('INPUT_Y-N',['use existing ouput directory: ' fullfile(Series.InputTable{1,1},SubDirOutNew) ', possibly delete previous data']);
1559        if isequal(answer,'Yes')
1560            detect=0;
1561            check_create=0;
1562        else
1563            r=regexp(SubDirOutNew,'(?<root>.*\D)(?<num1>\d+)$','names');%detect whether name ends by a number
1564            if isempty(r)
1565                r(1).root=[SubDirOutNew '_'];
1566                r(1).num1='0';
1567            end
1568            SubDirOutNew=[r(1).root num2str(str2num(r(1).num1)+1)];%increment the index by 1 or put 1
1569            detect=exist(fullfile(Series.InputTable{1,1},SubDirOutNew),'dir');% test if  the dir  already exists   
1570            check_create=1;
1571        end
1572    end
1573    Series.OutputDirExt=regexprep(SubDirOutNew,Series.OutputSubDir,'');
1574 %   Series.OutputSubDir=SubDirOutNew;
1575 %   Series.OutputDir=fullfile(Series.InputTable{1,1},Series.OutputSubDir);%directory set for output results
1576    Series.OutputRootFile=Series.InputTable{1,3};% the first sorted RootFile taken for output
1577    set(handles.OutputDirExt,'String',Series.OutputDirExt)
1578    % create output directory
1579    OutputDir=fullfile(Series.InputTable{1,1},[Series.OutputSubDir Series.OutputDirExt]);
1580    if check_create
1581        [tild,msg1]=mkdir(OutputDir);
1582        if ~strcmp(msg1,'')
1583            errormsg=['cannot create ' OutputDir ': ' msg1];%error message for directory creation
1584            return
1585        end
1586    end
1587    filexml=fullfile(OutputDir,[Series.InputTable{1,3} '.xml']);% name of the parameter xml file set in this directory
1588end
1589%removes redondant information
1590Series.IndexRange=rmfield(Series.IndexRange,'TimeTable');
1591Series.IndexRange=rmfield(Series.IndexRange,'MinIndex');
1592Series.IndexRange=rmfield(Series.IndexRange,'MaxIndex');
1593%removes empty lines of InputTable
1594empty_line=zeros(size(Series.InputTable,1),1);
1595for iline=1:size(Series.InputTable,1)
1596    empty_line(iline)=isequal(Series.InputTable(iline,1:3),{'','',''});
1597end
1598Series.InputTable(find(empty_line),:)=[];
1599
1600%------------------------------------------------------------------------
1601% --- Executes on selection change in ActionName.
1602function ActionName_Callback(hObject, eventdata, handles)
1603%------------------------------------------------------------------------
1604global nb_builtin_ACTION
1605list_ACTION=get(handles.ActionName,'String');% list menu fields
1606index_ACTION=get(handles.ActionName,'Value');% selected string index
1607ACTION= list_ACTION{index_ACTION}; % selected function name
1608path_series=which('series');%path to series.m
1609list_path=get(handles.ActionName,'UserData');%list of recorded paths to functions of the list ACTION
1610default_file=fullfile(list_path{end},ACTION);
1611% add a new function to the menu if the selected item is 'more...'
1612if isequal(ACTION,'more...')
1613    pathfct=fileparts(path_series);
1614    [FileName, PathName, filterindex] = uigetfile( ...
1615       {'*.m', ' (*.m)';
1616        '*.m',  '.m files '; ...
1617        '*.*', 'All Files (*.*)'}, ...
1618        'Pick a file',default_file);
1619    if length(FileName)<2
1620        return
1621    end
1622    [pp,ACTION,ext_fct]=fileparts(FileName);%(end-1:end);
1623    if ~isequal(ext_fct,'.m')
1624        msgbox_uvmat('ERROR','a Matlab function .m must be introduced');
1625        return
1626    end
1627   
1628   % insert the choice in the actionname menu
1629   menu_str=update_menu(handles.ActionName,ACTION);%new action menu in which the new item has been appended if needed
1630   index_ACTION=get(handles.ActionName,'Value');% currently selected index in the list
1631   list_path{index_ACTION}=PathName;
1632   if length(menu_str)>nb_builtin_ACTION+5; %nb_builtin=nbre of functions always remaining in the initial menu
1633       nbremove=length(menu_str)-nb_builtin_ACTION-5;
1634       menu_str(nb_builtin_ACTION+1:end-5)=[];
1635       list_path(nb_builtin_ACTION+1:end-4)=[];
1636       index_ACTION=index_ACTION-nbremove;
1637       set(handles.ActionName,'Value',index_ACTION)
1638       set(handles.ActionName,'String',menu_str)
1639   end
1640   list_path{index_ACTION}=PathName;
1641   set(handles.ActionName,'UserData',list_path);
1642   set(handles.ActionPath,'enable','inactive')% indicate that the current path is accessible (not 'off')
1643   
1644   %record the current menu in personal file profil_perso
1645   dir_perso=prefdir;
1646   profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
1647   for ilist=nb_builtin_ACTION+1:length(menu_str)-1
1648       series_fct{ilist-nb_builtin_ACTION}=fullfile(list_path{ilist},[menu_str{ilist} '.m']);     
1649   end
1650   if nb_builtin_ACTION+1<=length(menu_str)-1
1651       if exist(profil_perso,'file')% && nb_builtin_ACTION+1>=length(menu_str)-1
1652           save(profil_perso,'series_fct','-append')
1653       else
1654           txt=ver('MATLAB');
1655           Release=txt.Release;
1656           relnumb=str2num(Release(3:4));
1657           if relnumb >= 14%recent relaese of Matlab
1658               save(profil_perso,'series_fct','-V6')
1659           else
1660               save(profil_perso, 'series_fct')
1661           end
1662       end
1663   end
1664end
1665
1666%check the current ActionPath to the selected function
1667PathName=list_path{index_ACTION};%current recorded path
1668set(handles.ActionPath,'String',PathName); %show the path to the senlected function
1669
1670%reinitialise the waitbar
1671update_waitbar(handles.Waitbar,0)
1672
1673%default setting for the visibility of the GUI elements
1674set(handles.num_NbSlice,'Visible','off')
1675set(handles.NbSlice_title,'Visible','off')
1676set(handles.VelType,'Visible','off');
1677set(handles.VelType_text,'Visible','off');
1678set(handles.VelType_1,'Visible','off');
1679set(handles.VelType_text_1,'Visible','off');
1680set(handles.InputFields,'Visible','off')
1681set(handles.FieldName_1,'Visible','off')
1682%view_FieldMenu_1(handles,'off')
1683set(handles.FieldTransform,'Visible','off')
1684set(handles.CheckObject,'Visible','off');
1685set(handles.ProjObject,'Visible','off');
1686set(handles.CheckMask,'Visible','off')
1687set(handles.Mask,'Visible','off')
1688set(handles.OutputDirExt,'Visible','off')
1689set(handles.OutputSubDir,'Visible','off')
1690set(handles.OutputDir_title,'Visible','off')
1691%set the displayed GUI item needed for input parameters
1692if ~isequal(path_series,PathName)
1693    addpath(PathName)
1694end
1695eval(['h_function=@' ACTION ';']);
1696try
1697    [fid,errormsg] =fopen([ACTION '.m']);
1698    InputText=textscan(fid,'%s',1,'delimiter','\n');
1699    fclose(fid)
1700    set(handles.ActionName,'ToolTipString',InputText{1}{1})% put the first line of the selected function as tooltip help
1701end
1702if ~isequal(path_series,PathName)
1703    rmpath(PathName)
1704end
1705varargout=h_function();
1706Param_list={};
1707
1708InputTable=get(handles.InputTable,'Data');
1709nbview=size(InputTable,1);
1710SeriesData=get(handles.series,'UserData');
1711nb_civ=numel(find(strcmp('civx',SeriesData.FileType)|strcmp('civdata',SeriesData.FileType)));
1712nb_netcdf=numel(find(strcmp('netcdf',SeriesData.FileType)));
1713for ilist=1:length(varargout)-1
1714    switch varargout{ilist}
1715        case 'AllowInputSort'
1716            if isequal(lower(varargout{ilist+1}),'on')% sort the input table by alphabetical order of the SubDir
1717                SeriesData.AllowInputSort=1;
1718                set(handles.series,'UserData',SeriesData)
1719            end                     
1720        case 'WholeIndexRange'
1721            if isequal(lower(varargout{ilist+1}),'on')% set by default the input index range from min to max
1722                MinIndex=get(handles.MinIndex,'Data');
1723                MaxIndex=get(handles.MaxIndex,'Data');
1724                if ~isempty(MinIndex)
1725                    set(handles.num_first_i,'String',num2str(MinIndex{1}))
1726                    set(handles.num_last_i,'String',num2str(MaxIndex{1}))
1727                    set(handles.num_incr_i,'String','1')
1728                    if size(MinIndex,2)>=2
1729                        set(handles.num_first_j,'String',num2str(MinIndex{1,2}))
1730                        set(handles.num_last_j,'String',num2str(MaxIndex{1,2}))
1731                        set(handles.num_incr_j,'String','1')
1732                    end
1733                end
1734            end           
1735        case 'NbSlice'   %hidden by default
1736            if isequal(lower(varargout{ilist+1}),'on')
1737                set(handles.num_NbSlice,'Visible','on')
1738                set(handles.NbSlice_title,'Visible','on')
1739            end
1740        case 'VelType'   %hidden by default
1741             if isequal(lower(varargout{ilist+1}),'one') || isequal(lower(varargout{ilist+1}),'two')
1742                if nb_civ>=1
1743                    set(handles.VelType,'Visible','on')
1744                    set(handles.VelType_text,'Visible','on');
1745                end
1746             end
1747            if isequal(lower(varargout{ilist+1}),'two')
1748                if nb_civ>=2
1749                    set(handles.VelType_1,'Visible','on')
1750                    set(handles.VelType_text_1,'Visible','on');
1751                end
1752            end
1753        case 'FieldName'   %hidden by default
1754            if isequal(lower(varargout{ilist+1}),'one')||isequal(lower(varargout{ilist+1}),'two')
1755                if (nb_civ+nb_netcdf)>=1
1756                 set(handles.FieldName,'Visible','on') % test for MenuBorser
1757                 set(handles.InputFields,'Visible','on')
1758                end
1759            end
1760            if isequal(lower(varargout{ilist+1}),'two')
1761                if (nb_civ+nb_netcdf)>=1
1762                set(handles.FieldName_1,'Visible','on')
1763                end
1764            end
1765        case 'FieldTransform'   %hidden by default
1766            if isequal(lower(varargout{ilist+1}),'on')
1767                set(handles.TransformName,'Enable','on')
1768                set(handles.FieldTransform,'Visible','on')
1769                TransformName_Callback([],[], handles)
1770            end
1771        case 'ProjObject'   %hidden by default
1772            if isequal(lower(varargout{ilist+1}),'on')   
1773                set(handles.CheckObject,'Visible','on')
1774                set(handles.ProjObject,'Visible','on')
1775            end
1776        case 'Mask'   %hidden by default
1777            if isequal(lower(varargout{ilist+1}),'on')   
1778                set(handles.Mask,'Visible','on')
1779                 set(handles.CheckMask,'Visible','on');
1780            end 
1781        case 'OutputDirExt'
1782            if ~isempty(varargout{ilist+1})
1783            set(handles.OutputDirExt,'String',varargout{ilist+1})
1784            set(handles.OutputDirExt,'Visible','on')
1785            set(handles.OutputSubDir,'Visible','on')
1786            set(handles.OutputDir_title,'Visible','on') 
1787            end
1788    end
1789end
1790if ~isempty(Param_list)
1791    set(handles.ParamKey,'String',Param_list)
1792    set(handles.ParamVal,'Visible','on')
1793end
1794
1795%------------------------------------------------------------------------
1796% --- Executes on selection change in FieldName.
1797function FieldName_Callback(hObject, eventdata, handles)
1798%------------------------------------------------------------------------
1799field_str=get(handles.FieldName,'String');
1800field_index=get(handles.FieldName,'Value');
1801field=field_str{field_index(1)};
1802if isequal(field,'get_field...')   
1803     hget_field=findobj(allchild(0),'name','get_field');
1804     if ~isempty(hget_field)
1805         delete(hget_field)%delete opened versions of get_field
1806     end
1807     filecell=get_file_series(read_GUI(handles.series));
1808     if exist(filecell{1,1},'file')
1809        get_field(filecell{1,1})
1810     end
1811elseif isequal(field,'more...')
1812    str=calc_field;
1813    [ind_answer,v] = listdlg('PromptString','Select a file:',...
1814                'SelectionMode','single',...
1815                'ListString',str);
1816       % edit the choice in the fields and actionname menu
1817     scalar=cell2mat(str(ind_answer));
1818     update_menu(handles.FieldName,scalar)
1819end
1820
1821%------------------------------------------------------------------------
1822% --- Executes on selection change in FieldName_1.
1823function FieldName_1_Callback(hObject, eventdata, handles)
1824%------------------------------------------------------------------------
1825field_str=get(handles.FieldName_1,'String');
1826field_index=get(handles.FieldName_1,'Value');
1827field=field_str{field_index};
1828if isequal(field,'get_field...')   
1829     hget_field=findobj(allchild(0),'name','get_field_1');
1830     if ~isempty(hget_field)
1831         delete(hget_field)
1832     end
1833     SeriesData=get(handles.series,'UserData');
1834     filename=SeriesData.CurrentInputFile_1;
1835     if exist(filename,'file')
1836        hget_field=get_field(filename);
1837        set(hget_field,'name','get_field_1')
1838     end
1839elseif isequal(field,'more...')
1840    str=calc_field;
1841    [ind_answer,v] = listdlg('PromptString','Select a file:',...
1842                'SelectionMode','single',...
1843                'ListString',str);
1844       % edit the choice in the fields and actionname menu
1845     scalar=cell2mat(str(ind_answer));
1846     update_menu(handles.FieldName_1,scalar)
1847end   
1848
1849
1850%%%%%%%%%%%%%
1851function [ind_remove]=find_pairs(dirpair,ind_i,last_i)
1852indsel=ind_i;
1853indiff=diff(ind_i); %test index increment to detect multiplets (several pairs with the same index ind_i) and holes in the series
1854indiff=[1 indiff last_i-ind_i(end)+1];%for testing gaps with the imposed bounds
1855if ~isempty(indiff)
1856    indiff2=diff(indiff);
1857    indiffp=[indiff2 1];
1858    indiffm=[1 indiff2];
1859    ind_multi_m=find((indiff==0)&(indiffm<0))-1;%indices of first members of multiplets
1860    ind_multi_p=find((indiff==0)&(indiffp>0));%indices of last members of multiplets
1861    %for each multiplet, select the most recent file
1862    ind_remove=[];
1863    for i=1:length(ind_multi_m)
1864        ind_pairs=ind_multi_m(i):ind_multi_p(i);
1865        for imulti=1:length(ind_pairs)
1866            datepair(imulti)=datenum(dirpair(ind_pairs(imulti)).date);%dates of creation
1867        end
1868        [datenew,indsort2]=sort(datepair); %sort the multiplet by creation date
1869        ind_s=indsort2(1:end-1);%
1870        ind_remove=[ind_remove ind_pairs(ind_s)];%remove these indices, leave the last one
1871    end
1872end
1873
1874%------------------------------------------------------------------------
1875% --- determine the list of index pairstring of processing file
1876function [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)
1877%------------------------------------------------------------------------
1878num_i1=num_i;% set of first image numbers by default
1879num_i2=num_i;
1880num_j1=num_j;
1881num_j2=num_j;
1882num_i_out=num_i;
1883num_j_out=num_j;
1884% if isequal (NomType,'_1-2_1') || isequal (NomType,'_1-2')
1885if isequal(mode,'series(Di)')
1886    num_i1_line=num_i+ind_shift(3);% set of first image numbers
1887    num_i2_line=num_i+ind_shift(4);
1888    % adjust the first and last field number
1889        indsel=find(num_i1_line >= 1);
1890    num_i_out=num_i(indsel);
1891    num_i1_line=num_i1_line(indsel);
1892    num_i2_line=num_i2_line(indsel);
1893    num_j1=meshgrid(num_j,ones(size(num_i1_line)));
1894    num_j2=meshgrid(num_j,ones(size(num_i1_line)));
1895    [xx,num_i1]=meshgrid(num_j,num_i1_line);
1896    [xx,num_i2]=meshgrid(num_j,num_i2_line);
1897elseif isequal (mode,'series(Dj)')||isequal (mode,'bursts')
1898    if isequal(mode,'bursts') %case of bursts (png_old or png_2D)
1899        num_j1=ind_shift(1)*ones(size(num_i));
1900        num_j2=ind_shift(2)*ones(size(num_i));
1901    else
1902        num_j1_col=num_j+ind_shift(1);% set of first image numbers
1903        num_j2_col=num_j+ind_shift(2);
1904        % adjust the first field number
1905        indsel=find((num_j1_col >= 1));   
1906        num_j_out=num_j(indsel);
1907        num_j1_col=num_j1_col(indsel);
1908        num_j2_col=num_j2_col(indsel);
1909        [num_i1,num_j1]=meshgrid(num_i,num_j1_col);
1910        [num_i2,num_j2]=meshgrid(num_i,num_j2_col);
1911    end   
1912end
1913
1914%------------------------------------------------------------------------
1915% --- Executes on button press in CheckObject.
1916function CheckObject_Callback(hObject, eventdata, handles)
1917%------------------------------------------------------------------------
1918% SeriesData=get(handles.series,'UserData');
1919value=get(handles.CheckObject,'Value');
1920if value
1921     set(handles.CheckObject,'BackgroundColor',[1 1 0])%put unactivated buttons to yellow
1922     hset_object=findobj(allchild(0),'tag','set_object');%find the set_object interface handle
1923     if ishandle(hset_object)
1924         uistack(hset_object,'top')% show the GUI set_object if opened
1925     else
1926         %get the object file
1927         InputTable=get(handles.InputTable,'Data');
1928         defaultname=InputTable{1,1};
1929         if isempty(defaultname)
1930            defaultname={''};
1931         end
1932        [FileName, PathName, filterindex] = uigetfile( ...
1933       {'*.xml;*.mat', ' (*.xml,*.mat)';
1934       '*.xml',  '.xml files '; ...
1935        '*.mat',  '.mat matlab files '}, ...
1936        'Pick an xml object file (or use uvmat to create it)',defaultname);
1937        fileinput=[PathName FileName];%complete file name
1938        sizf=size(fileinput);
1939        if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end
1940        %read the file
1941        data=xml2struct(fileinput);
1942        if ~isfield(data,'Type')
1943             msgbox_uvmat('ERROR',[fileinput ' is not an object xml file'])
1944             return
1945        end
1946        if ~isfield(data,'ProjMode')
1947             data.ProjMode='none';
1948        end
1949        hset_object=set_object(data);% call the set_object interface
1950     end
1951     Object=read_GUI(hset_object);
1952     set(handles.ProjObject,'String',Object.Name);%display the object name
1953else
1954    set(handles.CheckObject,'BackgroundColor',[0.7 0.7 0.7])%put activated buttons to green
1955end
1956%set(handles.series,'UserData',SeriesData)
1957
1958%--------------------------------------------------------------
1959function CheckMask_Callback(hObject, eventdata, handles)
1960value=get(handles.CheckMask,'Value');
1961if value
1962    msgbox_uvmat('ERROR','not implemented yet')
1963end
1964%--------------------------------------------------------------
1965
1966%-------------------------------------------------------------------
1967%'uv_ncbrowser': interactively calls the netcdf file browser 'get_field.m'
1968function ncbrowser_uvmat(hObject, eventdata)
1969%-------------------------------------------------------------------
1970     bla=get(gcbo,'String');
1971     ind=get(gcbo,'Value');
1972     filename=cell2mat(bla(ind));
1973      blank=find(filename==' ');
1974      filename=filename(1:blank-1);
1975     get_field(filename)
1976
1977% ------------------------------------------------------------------
1978function MenuHelp_Callback(hObject, eventdata, handles)
1979%-------------------------------------------------------------------
1980path_to_uvmat=which ('uvmat');% check the path of uvmat
1981pathelp=fileparts(path_to_uvmat);
1982helpfile=fullfile(pathelp,'uvmat_doc','uvmat_doc.html');
1983if isempty(dir(helpfile)), msgbox_uvmat('ERROR','Please put the help file uvmat_doc.html in the sub-directory /uvmat_doc of the UVMAT package')
1984else
1985    addpath (fullfile(pathelp,'uvmat_doc'))
1986    web([helpfile '#series'])
1987end
1988
1989%-------------------------------------------------------------------
1990% --- Executes on selection change in TransformName.
1991function TransformName_Callback(hObject, eventdata, handles)
1992%-------------------------------------------------------------------
1993global nb_transform
1994
1995menu=get(handles.TransformName,'String');
1996ind_coord=get(handles.TransformName,'Value');
1997coord_option=menu{ind_coord};
1998list_transform=get(handles.TransformName,'UserData');
1999ff=functions(list_transform{end});
2000if isequal(coord_option,'more...');
2001    coord_fct='';
2002    prompt = {'Enter the name of the transform function'};
2003    dlg_title = 'user defined transform';
2004    num_lines= 1;
2005    [FileName, PathName, filterindex] = uigetfile( ...
2006       {'*.m', ' (*.m)';
2007        '*.m',  '.m files '; ...
2008        '*.*', 'All Files (*.*)'}, ...
2009        'Pick a file', ff.file);
2010    if isequal(PathName(end),'/')||isequal(PathName(end),'\')
2011        PathName(end)=[];
2012    end
2013    transform_selected =fullfile(PathName,FileName);
2014    if ~exist(transform_selected,'file')
2015          return
2016    end
2017    [ppp,transform,xt_fct]=fileparts(FileName);% removes extension .m
2018    if ~isequal(ext_fct,'.m')
2019        msgbox_uvmat('ERROR','a Matlab function .m must be introduced');
2020        return
2021    end
2022   menu=update_menu(handles.TransformName,transform);%add the selected fct to the menu
2023   ind_coord=get(handles.TransformName,'Value');
2024   addpath(PathName)
2025   list_transform{ind_coord}=str2func(transform);% create the function handle corresponding to the newly seleced function
2026   set(handles.TransformName,'UserData',list_transform)
2027   rmpath(PathName)
2028   % save the new menu in the personal file 'uvmat_perso.mat'
2029   dir_perso=prefdir;%personal Matalb directory
2030   profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
2031   if exist(profil_perso,'file')
2032       for ilist=nb_transform+1:numel(list_transform)
2033           ff=functions(list_transform{ilist});
2034           transform_fct{ilist-nb_transform}=ff.file;
2035       end
2036        save (profil_perso,'transform_fct','-append'); %store the root name for future opening of uvmat
2037   end
2038end
2039
2040%check the current ActionPath to the selected function
2041if ~isempty(list_transform{ind_coord})
2042    func=functions(list_transform{ind_coord});
2043    set(handles.TransformPath,'String',fileparts(func.file)); %show the path to the senlected function
2044else
2045    set(handles.TransformPath,'String',''); %show the path to the senlected function
2046end
2047
2048% %------------------------------------------------------------------------
2049% % --- Executes on button press in REFRESH.
2050%     function REFRESH_INDICES_Callback(hObject, eventdata, handles)
2051% %------------------------------------------------------------------------       
2052% % hObject    handle to REFRESH (see GCBO)
2053% % eventdata  reserved - to be defined in a future version of MATLAB
2054% % handles    structure with handles and user data (see GUIDATA)
2055% set(handles.REFRESH,'BackgroundColor',[0.7 0.7 0.7])
2056% InputTable=get(handles.InputTable,'Data');
2057% check_lines=get(handles.REFRESH,'UserData');
2058%
2059% %% check the indices and FileTypes for each series (limited to the new ones to save time)
2060% for ind_list=1:length(check_lines)
2061%     if  check_lines(ind_list)
2062%         InputLine=InputTable(ind_list,:);
2063%         detect_idem=strcmp('"',InputLine);% look for '" (repeat of previous data)
2064%         detect_idem=detect_idem(detect_idem>0);
2065%         if ~isempty (detect_idem)
2066%             InputLine(detect_idem)=InputTable(ind_list-1,detect_idem);
2067%             set(handles.InputTable,'Data',InputTable)
2068%         end
2069%         fileinput=fullfile_uvmat(InputLine{1},InputLine{2},InputLine{3},InputLine{5},InputLine{4},1,2,1,2);
2070%         %fileinput=name_generator(fullfile(InputLine{1},InputLine{3}),1,1,InputLine{5},InputLine{4},1,2,2,InputLine{2})
2071%         %update file series defined by the selected line
2072%         [InputTable{ind_list,3},InputTable{(ind_list),4},errormsg]=update_indices(handles,fileinput,ind_list);
2073%         if ~isempty(errormsg)
2074%                 msgbox_uvmat('ERROR',errormsg)
2075%                 return
2076%         end
2077%     end
2078% end
2079% set(handles.InputTable,'Data',InputTable)
2080% SeriesData=get(handles.series,'UserData');
2081%
2082% state_j='off';
2083% state_Pairs='off';
2084% state_InputFields='off';
2085% val=get(handles.ListView,'Value');
2086% ListViewString={''};
2087% if ~isempty(SeriesData)
2088% %     ListViewString={};
2089%     for iview=1:size(InputTable,1)
2090%         if ~isempty(SeriesData.j1_series{iview})
2091%             state_j='on';
2092%         end
2093%         if ~isempty(SeriesData.i2_series{iview})||~isempty(SeriesData.j2_series{iview})
2094%             state_Pairs='on';
2095%             ListViewString{iview}=num2str(iview);
2096%             if check_lines(iview)
2097%                 val=iview;%select the last pair if it is a new entry
2098%             end
2099%         end
2100%         if strcmp(SeriesData.FileType{iview},'civx')||strcmp(SeriesData.FileType{iview},'civdata')
2101%             state_InputFields='on';
2102%         end
2103%     end
2104% end
2105% set(handles.ListView,'Value',val)
2106% set(handles.ListView,'String',ListViewString)
2107% if strcmp(state_Pairs,'on')
2108%     ListView_Callback(hObject,eventdata,handles)
2109% end
2110% set(handles.PairString,'Visible',state_Pairs)
2111% enable_j(handles,state_j)
2112% set(handles.REFRESH,'BackgroundColor',[1 0 0])
2113% set(handles.REFRESH,'visible','off')
2114
2115% -----------------------------------------------------------------------
2116% --- Update min and max indices of a file series by scanning with find_file_series
2117% --- which also changes the root file and NomType in case of movie. Also adjust the string representation of indices (e.g;
2118% --- 1 or 001 by the function find_file_series
2119% --- This function also dispaly the set of availbale files in the series
2120% --- and the menus appropriate to the file type as well as timing possibly set
2121% --- by an xml image documentation file
2122function [RootFile,NomType,errormsg]=update_indices(handles,fileinput,iview)
2123% -----------------------------------------------------------------------
2124%% look for min and max indices existing in the file series and update SeriesData
2125errormsg='';
2126[FilePath,FileName,FileExt]=fileparts(fileinput);
2127% detect the file type, get the movie object if relevant, and look for the corresponding file series:
2128% the root name and indices may be corrected by including the first index i1 if a corresponding xml file exists
2129[RootPath,SubDir,RootFile,i1_series,i2_series,j1_series,j2_series,NomType,FileType,Object,i1,i2,j1,j2]=find_file_series(FilePath,[FileName FileExt]);
2130if isempty(RootFile)&&isempty(i1_series)
2131    errormsg='no input file in the series';
2132    return
2133end
2134
2135%% adjust the min and max indices common to all the file series
2136MinIndex=get(handles.MinIndex,'Data');
2137MaxIndex=get(handles.MaxIndex,'Data');
2138MinIndex_i=min(i1_series(i1_series>0));
2139if ~isempty(i2_series)
2140    MaxIndex_i=max(i2_series(i2_series>0));
2141else
2142    MaxIndex_i=max(i1_series(i1_series>0));
2143end
2144MinIndex_j=min(j1_series(j1_series>0));
2145if ~isempty(j2_series)
2146    MaxIndex_j=max(j2_series(j2_series>0));
2147else
2148    MaxIndex_j=max(j1_series(j1_series>0));
2149end
2150MinIndex{iview,1}=MinIndex_i;
2151MinIndex{iview,2}=MinIndex_j;
2152MaxIndex{iview,1}=MaxIndex_i;
2153MaxIndex{iview,2}=MaxIndex_j;
2154set(handles.MinIndex,'Data',MinIndex)
2155set(handles.MaxIndex,'Data',MaxIndex)
2156SeriesData=get(handles.series,'UserData');
2157SeriesData.i1_series{iview}=i1_series;
2158SeriesData.i2_series{iview}=i2_series;
2159SeriesData.j1_series{iview}=j1_series;
2160SeriesData.j2_series{iview}=j2_series;
2161SeriesData.FileType{iview}=FileType;
2162
2163%% display the set of existing files as an image
2164set(handles.Waitbar,'Units','pixels')
2165pos=get(handles.Waitbar,'Position');
2166xima=0.5:pos(3)-0.5;% pixel positions on the image representing the existing file indices
2167yima=0.5:pos(4)-0.5;
2168[XIma,YIma]=meshgrid(xima,yima);
2169nb_i=size(i1_series,3);
2170nb_j=size(i1_series,2);
2171ind_i=(0.5:nb_i-0.5)*pos(3)/nb_i;
2172ind_j=(0.5:nb_j-0.5)*pos(4)/nb_j;
2173[Ind_i,Ind_j]=meshgrid(ind_i,ind_j);
2174CData=zeros([size(XIma) 3]);
2175file_ima=double((i1_series(:,:,1)>0)');
2176if numel(file_ima)>=2
2177if size(file_ima,1)==1
2178    CLine=interp1(ind_i,file_ima,xima,'nearest');
2179    CData(:,:,2)=ones(size(yima'))*CLine;
2180else
2181    CData(:,:,2)=interp2(Ind_i,Ind_j,file_ima,XIma,YIma,'nearest');
2182end
2183set(handles.Waitbar,'CData',CData)
2184end
2185set(handles.Waitbar,'Units','normalized')
2186
2187%% enable field and veltype menus
2188% testfield=isequal(get(handles.FieldName,'enable'),'on');
2189% testfield_1=isequal(get(handles.FieldName_1,'enable'),'on');
2190% testveltype=isequal(get(handles.VelType,'enable'),'on');
2191% testveltype_1=isequal(get(handles.VelType_1,'enable'),'on');
2192% testtransform=isequal(get(handles.TransformName,'Enable'),'on');
2193% testnc=0;
2194% testnc_1=0;
2195% testcivx=0;
2196% testcivx_1=0;
2197% testima=0; %test for image input
2198% if isequal(lower(FileExt),'.avi') %.avi file
2199%     testima=1;
2200% elseif ~isempty(imformats(FileExt(2:end)))
2201%     testima=1;
2202% elseif isequal(FileExt,'.vol')
2203%      testima=1;
2204% end
2205%TODO: update
2206% if length(FileExtCell)==1 || length(FileExtCell)>2
2207%     for iview=1:length(FileExtCell)
2208%         if isequal(FileExtCell{iview},'.nc')
2209%             testnc=1;
2210%         end
2211%         if isequal(FileTypeCell{iview},'civx')
2212%             testcivx=1;
2213%         end
2214%     end
2215% elseif length(FileExtCell)==2
2216%     testnc=isequal(FileExtCell{1},'.nc');
2217%     testnc_1=isequal(FileExtCell{2},'.nc');
2218%     testcivx=isequal(FileTypeCell{1},'civx');
2219%     testcivx_1=isequal(FileTypeCell{2},'civx');
2220% end
2221switch FileType
2222    case {'civx','civdata'}
2223    %view_FieldMenu(handles,'on')
2224    menustr=get(handles.FieldName,'String');
2225    if isequal(menustr,{'get_field...'})
2226        set(handles.FieldName,'String',{'get_field...';'velocity';'vort';'div';'more...'})
2227    end
2228    set(handles.VelType,'Visible','on')
2229    set(handles.FieldTransform,'Visible','on')
2230    %      view_TRANSFORM(handles,'on')
2231    %     TODO: second menu
2232    %           view_FieldMenu_1(handles,'on')
2233    %     if testcivx_1
2234    %         menustr=get(handles.FieldName_1,'String');
2235    %         if isequal(menustr,{'get_field...'})
2236    %             set(handles.FieldName_1,'String',{'get_field...';'velocity';'vort';'div';'more...'})
2237    %         end
2238    %     else
2239    %         set(handles.FieldName_1,'Value',1)
2240    %         set(handles.FieldName_1,'String',{'get_field...'})
2241    %     set(handles.VelType_1,'Visible','on')
2242    %     set(handles.VelType_text_1,'Visible','on');
2243    %     end
2244    %     view_FieldMenu_1(handles,'off')
2245    case 'netcdf'
2246  %  view_FieldMenu(handles,'on')
2247    set(handles.FieldName,'Value',1)
2248    set(handles.FieldName,'String',{'get_field...'})
2249    set(handles.FieldTransform,'Visible','off')
2250    %     view_TRANSFORM(handles,'off')
2251    case {'image','multimage','video'}
2252%    view_FieldMenu(handles,'off')
2253 %   view_FieldMenu_1(handles,'off')
2254    set(handles.VelType,'Visible','off')
2255    set(handles.VelType_text,'Visible','off');
2256end
2257
2258
2259%TODO:update
2260% if ~isequal(FileExt,'.nc') && ~isequal(FileExt,'.cdf') && ~testima
2261%     msgbox_uvmat('ERROR',['invalid input file extension ' FileExt])
2262%     return
2263% end 
2264
2265%%  read image documentation file  if found%%%%%%%%%%%%%%%%%%%%%%%%%%%
2266ext_imadoc='';
2267FileBase=fullfile(RootPath,RootFile);
2268if isequal(FileExt,'.xml')||isequal(FileExt,'.civ')
2269    ext_imadoc=FileExt;
2270elseif exist([FileBase '.xml'],'file')
2271    ext_imadoc='.xml';
2272elseif exist([FileBase '.civ'],'file')
2273    ext_imadoc='.civ';
2274end
2275%read the ImaDoc file
2276XmlData=[];
2277NbSlice_calib={};
2278if isequal(ext_imadoc,'.xml')
2279        [XmlData,warntext]=imadoc2struct([FileBase '.xml']);
2280        if isfield(XmlData,'Heading') && isfield(XmlData.Heading,'ImageName') && ischar(XmlData.Heading.ImageName)
2281            [PP,FF,ext_ima_read]=fileparts(XmlData.Heading.ImageName);
2282        end
2283        if isfield(XmlData,'Time')
2284            time{iview}=XmlData.Time;
2285        end
2286        if isfield(XmlData,'Camera')
2287            if isfield(XmlData.Camera,'NbSlice')&& ~isempty(XmlData.Camera.NbSlice)
2288                NbSlice_calib{iview}=XmlData.Camera.NbSlice;% Nbre of slices for Zindex in phys transform
2289                if ~isequal(NbSlice_calib{iview},NbSlice_calib{1})
2290                    msgbox_uvmat('WARNING','inconsistent number of Z indices for the two field series');
2291                end
2292            end
2293            if isfield(XmlData.Camera,'TimeUnit')&& ~isempty(XmlData.Camera.TimeUnit)
2294                TimeUnit=XmlData.Camera.TimeUnit;
2295            end
2296        end
2297        if ~isempty(warntext)
2298            msgbox_uvmat('WARNING',warntext)
2299        end 
2300elseif isequal(ext_imadoc,'.civ')
2301    [error,XmlData.Time,TimeUnit,mode,npx,npy,pxcmx,pxcmy]=read_imatext([FileBase '.civ']);
2302    time{iview}=XmlData.Time;
2303    if error==2, warntext=['no file ' FileBase '.civ'];
2304    elseif error==1, warntext='inconsistent number of fields in the .civ file';
2305    end 
2306end
2307
2308%% update time table
2309TimeTable=get(handles.TimeTable,'Data');
2310TimeTable{iview,1}=time(MinIndex_i,MinIndex_j);
2311TimeTable{iview,4}=time(MaxIndex_i,MaxIndex_j);
2312set(handles.TimeTable,'Data',TimeTable)
2313
2314%% number of slices
2315if isfield(XmlData,'GeometryCalib') && isfield(XmlData.GeometryCalib,'SliceCoord')
2316       siz=size(XmlData.GeometryCalib.SliceCoord);
2317       if siz(1)>1
2318           NbSlice=siz(1);
2319       else
2320           NbSlice=1;
2321       end
2322       set(handles.num_NbSlice,'String',num2str(NbSlice))
2323end
2324% set(handles.mode,'Visible','off') % do not show index pairstring by default
2325set(handles.PairString,'Visible','off')
2326% set(handles.num_ref_i,'Visible','off')
2327% set(handles.ref_i_text,'Visible','off')
2328testpair=0;
2329%set the menus of image pairstring and default selection for series
2330%list pairstring if relevant
2331% Val=get(handles.NomType,'Value');
2332% synchronise_view(handles,Val)
2333
2334% if ~isfield(SeriesData,'j1_series')||isempty(SeriesData.j1_series{index})
2335%     state_j='off'; %no need for j index
2336% else
2337%     state_j='on'; %case of j index
2338% end
2339% show index pairstring if files exist
2340set(handles.series,'UserData',SeriesData)
2341
2342
2343% --------------------------------------------------------------------
2344function MenuExportConfig_Callback(hObject, eventdata, handles)
2345global Series
2346[tild,Series,errormsg]=prepare_jobs(handles,0);
2347% Series=read_GUI(handles.series);
2348
2349evalin('base','global Series')%make CurData global in the workspace
2350display('current series config :')
2351evalin('base','Series') %display CurData in the workspace
2352commandwindow; %brings the Matlab command window to the front
2353
2354
2355% --- Executes on selection change in RunMode.
2356function RunMode_Callback(hObject, eventdata, handles)
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