source: trunk/src/uvmat.m @ 548

Last change on this file since 548 was 548, checked in by sommeria, 8 years ago

various bug repairs

File size: 208.3 KB
Line 
1%'uvmat': function associated with the GUI 'uvmat.fig' for images and data field visualization
2%------------------------------------------------------------------------
3% function huvmat=uvmat(input)
4%
5%OUTPUT
6% huvmat=current handles of the GUI uvmat.fig
7%%
8%
9%INPUT:
10% input: input file name (if character chain), or input image matrix to
11% visualize, or Matlab structure representing  netcdf fieldname (with fieldname
12% ListVarName....)
13%
14%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
15%  Copyright Joel Sommeria,  2008, LEGI / CNRS-UJF-INPG, joel.sommeria@legi.grenoble-inp.fr.
16%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
17%     This open is part of the toolbox UVMAT.
18%
19%     UVMAT is free software; you can redistribute it and/or modify
20%     it under the terms of the GNU General Public License as published by
21%     the Free Software Foundation; either version 2 of the License, or
22%     (at your option) any later version.
23%
24%     UVMAT is distributed in the hope that it will be useful,
25%     but WITHOUT ANY WARRANTY; without even the implied warranty of
26%     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
27%     GNU General Public License (open UVMAT/COPYING.txt) for more details.
28%AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
29%
30% Information stored on the interface:(use 'Export/field in workspace' in
31% the menu bar of uvmat to retrieve it)
32%          .OpenParam: structure containing parameters defined when uvmat is opened
33%                       .PosColorbar: position (1x4 vector)of the colorbar (relative to the fig uvmat)
34%                       .PosSetObject: position of set_object
35%                       .PosGeometryCalib: size of set_object
36%                       .NbBuiltin: nbre of functions always displayed in transform_fct menu
37%          .Object: cell array of structures representing the current projection objects, as produced by 'set_object.m'={[]} by default
38%          .NewSeries: =0/1 flag telling whether a new field series has been opened
39%          .FileName_1: name of the current second field (used to detect a  constant field during file scanning)
40%          .FileType: current file type, as defined by the fct  get_file_type.m)
41%          .i1_series,.i2_series,.j1_series,.j1_series: series of i1,i2,j1,j2 indices detected in the input dir,set by  the fct find_file_series
42%          .MovieObject: current movie object
43%          .TimeUnit: unit for time
44%          .XmlData: cell array of 1 or 2 structures representing the xml files associated with the input fieldname (containing timing  and geometry calibration)
45%          .Field: cell array of 1 or 2 structures representing the current  input field(s)
46%          .PlotAxes: field structure representing the current field plotted  on the main axes  (used for mouse operations)
47%          .HistoAxes: idem for histogram axes
48
49% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%   DATA FLOW  (for run0_Callback) %%%%%%%%%%%%%%%%%%%%:
50%
51%
52% 1) Input filenames are determined by MenuBrowse (first field), MenuBrowse_1
53% (second field), or by the stored file name .FileName_1, or as an input of uvmat.
54% 2) These functions call 'uvmat/display_file_name.m' which detects the file series, and fills the file index boxes
55% 3) Then 'uvmat/update_rootinfo.m' Updates information about a new field series (indices to scan, timing, calibration from an xml file)
56% 4) Then fieldname are opened and visualised by the main sub-function 'uvmat/refresh_field.m'
57% The function first reads the name of the input file(s) (one or two) from the edit boxes  of the GUI
58% It then reads the input file(s) with the function read_field.m and perform the following list of operations:
59%
60%    %%%%%%%%  structure of uvmat/refresh_field.m %%%%%%%%
61%
62%           Main input open       second input open_1       
63%                    |                   | 
64%             read_field.m            read_field.m
65%                    |                   |
66%                 Field{1}            Field{2}               
67%                    |                   |                                 
68%                    --->transform fct<---             transform (e.g. phys.m) and combine input fieldname 
69%                            |                                   
70%                        (calc_tps.m)               calculate tps coefficients (for filter projection or spatial derivatives).
71%                            |
72%                       UvData.Field-------------->histogram
73%               _____________|____________
74%              |                          |                   
75%        proj_field.m               proj_field.m       project the field on the projection objects (use calc_field.m)           
76%              |                          |
77%         UvData.PlotAxes          ViewData.PlotAxes (on view_field)
78%              |                          |
79%       plot_field.m (uvmat)       plot_field.m (view_field)      plot the projected fieldname
80%
81%
82%%%%%%%%%%%%%%    SCALARS: %%%%%%%%%%%%??%%%
83% scalars are displayed either as an image or countour plot, either as a color of
84% velocity vectors. The scalar values in the first case is represented by
85% UvData.Field.A, and by UvData.Field.C in the second case. The corresponding set of X
86% and Y coordinates are represented by UvData.Field.AX and UvData.Field.AY, and .X and
87% .Y for C (the same as velocity vectors). If A is a nxxny matrix (scalar
88% on a regtular grid), then .AX andf.AY contains only two elements, represneting the
89% coordinates of the four image corners. The scalar name is represented by
90% the strings .AName and/or .CName.
91% If the scalar exists in an input open (image or scalar stored under its
92% name in a netcdf open), it is directly read at the level of Field{1}or Field{2}.
93% Else only its name AName is recorded in Field{i}, and its field is then calculated
94%by the fuction calc_scal after the coordinate transform or after projection on an edit_object
95     
96% Properties attached to plotting figures (standard Matlab properties):
97%    'CurrentAxes'= gca or get(gcf,'CurrentAxes');
98%    'CurrentPoint'=get(gcf,'CurrentPoint'): figure coordinates of the point over which the mouse is positioned
99%    'CurrentCharacter'=get(gcf,'CurrentCharacter'): last character typed  over the figure where the mouse is positioned
100%    'WindowButtonMotionFcn': function permanently called by mouse motion over the figure
101%    'KeyPressFcn': function called by pressing a key on the key board
102%    'WindowButtonDownFcn':  function called by pressing the mouse over the  figure
103%    'WindowButtonUpFcn': function called by releasing  the mouse pressure over the  figure
104
105% Properties attached to plotting axes:
106%    'CurrentPoint'=get(gca,'CurrentPoint'); (standard Matlab) same as for the figure, but position in plot coordinates.
107%     AxeData:=get(gca,'UserData');
108%     AxeData.Drawing  = create: create a new object
109%                       = deform: modify an existing object by moving its defining create
110%                      = off: no current drawing action
111%                     = translate: translate an existing object
112%                    = calibration: move a calibration point
113%                    = CheckZoom: isolate a subregion for CheckZoom in=1 if an object is being currently drawn, 0 else (set to 0 by releasing mouse button)
114%            .CurrentOrigin: Origin of a curently drawn edit_object
115%            .CurrentLine: currently drawn menuline (A REVOIR)
116%            .CurrentObject: handle of the currently drawn edit_object
117%            .CurrentRectZoom: current rectangle used for CheckZoom
118
119% Properties attached to projection objects (create, menuline, menuplane...):
120%    'Tag'='proj_object': for all projection objects
121%    ObjectData.Type=...: style of projection object:
122%              .ProjMode
123%              .Coord: defines the position of the object
124%              .XMin,YMin....
125%              .XMax,YMax....
126%              .DX,DY,DZ
127%              .Phi, .Theta, .Psi : Euler angles
128%              .X,.Y,.U,.V.... : field data projected on the object
129%              .IndexObj: index in the list of UvData.Object
130           %during plotting
131%               .plotaxes: handles of the current axes used to plot the  result of field projection on the object
132%               .plothandle: vector of handle(s) of the object graphic represnetation in all the opened plotting axes
133% To each projection object #iobj, corresponds an axis
134% Object{iobj}.plotaxes and nbobj representation graphs  Object{iobj}.plothandles(:) (where nbobj is the
135% nbre of current objects opened in uvmat. Note that Object{iobj}.plothandles(iobj)=[] : an object is not represented in its own projection field;
136
137%------------------------------------------------------------------------
138%------------------------------------------------------------------------
139%  I - MAIN FUNCTION uvmat
140%------------------------------------------------------------------------
141%------------------------------------------------------------------------
142function varargout = uvmat(varargin)
143
144% Begin initialization code - DO NOT EDIT
145gui_Singleton = 1;
146gui_State = struct('gui_Name',          mfilename, ...
147                   'gui_Singleton',     gui_Singleton, ...
148                   'gui_OpeningFcn',    @uvmat_OpeningFcn, ...
149                   'gui_OutputFcn',     @uvmat_OutputFcn, ...
150                   'gui_LayoutFcn',     [], ...
151                   'gui_Callback',      []);
152if nargin && ischar(varargin{1})&& ~isempty(regexp(varargin{1},'_Callback','once'))
153    gui_State.gui_Callback = str2func(varargin{1});
154end
155
156if nargout
157    varargout{1:nargout} = gui_mainfcn(gui_State, varargin{:});
158else
159    gui_mainfcn(gui_State, varargin{:});
160end
161% End initialization code - DO NOT EDIT
162
163%------------------------------------------------------------------------
164% --- Executes just before the GUI uvmat is made visible.
165function uvmat_OpeningFcn(hObject, eventdata, handles, input )
166%------------------------------------------------------------------------
167
168%% Choose default command menuline output for uvmat (standard GUI)
169handles.output = hObject;
170
171%% Update handles structure (standard GUI)
172guidata(hObject, handles);
173
174%% add the path to uvmat (useful if uvmat has been opened in the working directory and a working directory change occured)
175path_uvmat=fileparts(which('uvmat'));
176
177%% set the position of colorbar and ancillary GUIs:
178set(hObject,'Units','Normalized')
179movegui(hObject,'center')
180%UvData.OpenParam.PosColorbar=[0.8450    0.0900    0.0190    0.3600];
181UvData.OpenParam.PosColorbar=[0.805 0.022 0.019 0.445];
182UvData.OpenParam.PosSetObject=[-0.05 -0.03 0.3 0.7]; %position for set_object
183UvData.OpenParam.PosGeometryCalib=[0.95 -0.03 0.28 1 ];%position for geometry_calib (TO IMPROVE)
184% UvData.OpenParam.CalSize=[0.28 1];
185% UvData.PlotAxes=[];%initiate the record of plotted field
186% UvData.axes2=[];
187% UvData.axes1=[];
188AxeData.LimEditBox=1; %initialise AxeData
189set(handles.PlotAxes,'UserData',AxeData)
190
191%% set functions for the mouse and keyboard
192set(hObject,'KeyPressFcn',{'keyboard_callback',handles})%set keyboard action function
193set(hObject,'WindowButtonMotionFcn',{'mouse_motion',handles})%set mouse action functio
194set(hObject,'WindowButtonDownFcn',{'mouse_down'})%set mouse click action function
195set(hObject,'WindowButtonUpFcn',{'mouse_up',handles})
196set(hObject,'DeleteFcn',{@closefcn})%
197
198%% initialisation
199% set(handles.ListObject,'Value',1)% default: empty projection objectproj_field
200% set(handles.ListObject,'String',{''})
201% set(handles.ListObject_1,'Value',1)% default: empty projection objectproj_field
202% set(handles.ListObject_1,'String',{''})
203set(handles.FieldName,'Value',1)
204set(handles.FieldName,'string',{''})
205UvData.Object={[]};
206
207%% TRANSFORM menu: builtin fcts
208transform_menu={'';'sub_field';'phys';'phys_polar'};
209UvData.OpenParam.NbBuiltin=numel(transform_menu); %number of functions
210transform_path=fullfile(path_uvmat,'transform_field');
211path_list=cell(UvData.OpenParam.NbBuiltin,1);
212path_list{1}='';
213for ilist=2:UvData.OpenParam.NbBuiltin
214path_list{ilist}=transform_path; % set transform_path to the path_list
215end
216
217%% load the list of previously browsed files in menus Open, Open_1 and transform_fct
218 dir_perso=prefdir; % path to the directory .matlab for personal data
219 profil_perso=fullfile(dir_perso,'uvmat_perso.mat');% personal data file uvmauvmat_perso.mat' in .matlab
220 if exist(profil_perso,'file')
221     h=load (profil_perso);
222     if isfield(h,'MenuFile')% load the menu of previously opened files
223         for ifile=1:min(length(h.MenuFile),5)
224             eval(['set(handles.MenuFile_' num2str(ifile) ',''Label'',h.MenuFile{ifile});'])
225             eval(['set(handles.MenuFile_' num2str(ifile) '_1,''Label'',h.MenuFile{ifile});'])
226         end
227     end
228     if isfield(h,'transform_fct') && iscell(h.transform_fct) % load the menu of transform fct set by user
229         for ilist=1:length(h.transform_fct);
230             if exist(h.transform_fct{ilist},'file')
231                 [path,file]=fileparts(h.transform_fct{ilist});
232                 transform_menu=[transform_menu; {file}];
233                 path_list=[path_list; {path}];
234             end
235         end
236     end
237 end
238transform_menu=[transform_menu;{'more...'}];%append the option more.. to the menu
239set(handles.transform_fct,'String',transform_menu)% display the menu of transform fcts
240set(handles.transform_fct,'UserData',path_list)% store the corresponding list of path in UserData of uicontrol transform_fct
241set(handles.path_transform,'String','')
242set(handles.path_transform,'UserData',[])
243
244%% case of an input argument for uvmat
245testinputfield=0;
246inputfile=[];
247Field=[];
248if exist('input','var')
249    if ishandle(handles.UVMAT_title)
250        delete(handles.UVMAT_title)
251    end   
252    if isstruct(input)
253        if isfield(input,'InputFile')
254            inputfile=input.InputFile;
255        end
256        if isfield(input,'TimeIndex')
257            set(handles.i1,num2str(input.TimeIndex))
258        end
259        if isfield(input,'FieldsString')
260            UvData.FieldsString=input.FieldsString;
261        end
262    elseif ischar(input)% file name introduced as input
263           inputfile=input;
264    elseif isnumeric(input)%simple matrix introduced as input
265        sizinput=size(input);
266        if sizinput(1)<=1 || sizinput(2)<=1
267            msgbox_uvmat('ERROR','bad input for uvmat: file name, structure or numerical matrix accepted')
268            return
269        end
270        UvData.Field.ListVarName={'A','coord_y','coord_x'};
271        UvData.Field.VarDimName={{'coord_y','coord_x'},'cord_y','coord_x'};
272        UvData.Field.A=input;
273        UvData.Field.coord_x=[0.5 size(input,2)-0.5];
274        UvData.Field.coord_y=[size(input,1)-0.5 0.5];
275        testinputfield=1;
276    end
277else
278    %% check the path and date of modification of all functions in uvmat
279    path_to_uvmat=which ('uvmat');% check the path detected for source file uvmat
280    [infomsg,date_str,svn_info]=check_files;%check the path of the functions called by uvmat.m   
281    date_str=['last modification: ' date_str];
282    if ishandle(handles.UVMAT_title)
283        set(handles.UVMAT_title,'String',...
284            [{'Copyright  LEGI UMR 5519 /CNRS-UJF-Grenoble INP, 2010'};...
285            {'GNU General Public License'};...
286            {path_to_uvmat};...
287            {date_str};...
288            infomsg]);
289    end
290end
291set(handles.uvmat,'UserData',UvData)
292if ~isempty(inputfile)
293    %%%%% display the input field %%%%%%%
294    display_file_name(handles,inputfile)
295    %%%%%%%
296end
297
298set_vec_col_bar(handles) %update the display of color code for vectors
299
300%------------------------------------------------------------------------
301% --- Outputs from this function are returned to the command menuline.
302function varargout = uvmat_OutputFcn(hObject, eventdata, handles)
303varargout{1} = handles.output;% the only output argument is the handle to the GUI figure
304
305%------------------------------------------------------------------------
306% --- executed when closing uvmat: delete or desactivate the associated figures if exist
307function closefcn(gcbo,eventdata)
308%------------------------------------------------------------------------
309hh=findobj(allchild(0),'tag','view_field');
310if ~isempty(hh)
311    delete(hh)
312end
313hh=findobj(allchild(0),'tag','geometry_calib');
314if ~isempty(hh)
315    delete(hh)
316end
317hh=findobj(allchild(0),'tag','set_object');
318if ~isempty(hh)
319    hhh=findobj(hh,'tag','PLOT');
320    set(hhh,'enable','off')
321end
322
323%------------------------------------------------------------------------
324%------------------------------------------------------------------------
325%  II - FUNCTIONS FOR INTRODUCING THE INPUT FILES
326% automatically sets the global properties when the rootfile name is introduced
327% then activate the view-field action if selected
328% it is activated either by clicking on the RootPath window or by the
329% browser
330%------------------------------------------------------------------------
331%------------------------------------------------------------------------
332% --- Executes on the menu Open/Browse...
333% search the files, recognize their type according to their name and fill the rootfile input windows
334function MenuBrowse_Callback(hObject, eventdata, handles)
335[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
336%oldfile=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
337oldfile=fullfile(RootPath,SubDir);
338if isempty(oldfile)||isequal(oldfile,'') %loads the previously stored file name and set it as default in the file_input box
339         dir_perso=prefdir;
340         profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
341         if exist(profil_perso,'file')
342              h=load (profil_perso);
343             if isfield(h,'MenuFile_1')
344                  oldfile=h.MenuFile_1;
345             end
346         end
347end
348[FileName, PathName] = uigetfile({'*.*','All Files(*.*)'},'Pick a file',oldfile);
349if ~ischar(FileName),return,end %abandon if the browser is cancelled
350fileinput=[PathName FileName];%complete file name
351
352%% display the selected field and related information
353display_file_name( handles,fileinput)
354
355% -----------------------------------------------------------------------
356% --- Open again the file whose name has been recorded in MenuFile_1
357function MenuFile_1_Callback(hObject, eventdata, handles)
358%------------------------------------------------------------------------
359fileinput=get(handles.MenuFile_1,'Label');
360display_file_name( handles,fileinput)
361
362% -----------------------------------------------------------------------
363% --- Open again the file whose name has been recorded in MenuFile_2
364function MenuFile_2_Callback(hObject, eventdata, handles)
365%------------------------------------------------------------------------
366fileinput=get(handles.MenuFile_2,'Label');
367display_file_name(handles,fileinput)
368
369% -----------------------------------------------------------------------
370% --- Open again the file whose name has been recorded in MenuFile_3
371function MenuFile_3_Callback(hObject, eventdata, handles)
372%------------------------------------------------------------------------
373fileinput=get(handles.MenuFile_3,'Label');
374display_file_name(handles,fileinput)
375
376% -----------------------------------------------------------------------
377% --- Open again the file whose name has been recorded in MenuFile_4
378function MenuFile_4_Callback(hObject, eventdata, handles)
379%------------------------------------------------------------------------
380fileinput=get(handles.MenuFile_4,'Label');
381display_file_name(handles,fileinput)
382
383% -----------------------------------------------------------------------
384% --- Open again the file whose name has been recorded in MenuFile_5
385function MenuFile_5_Callback(hObject, eventdata, handles)
386%------------------------------------------------------------------------
387fileinput=get(handles.MenuFile_5,'Label');
388display_file_name(handles,fileinput)
389
390%------------------------------------------------------------------------
391% --- Executes on the menu Open/Browse_1 for the second input field,
392%     search the files, recognize their type according to their name and fill the rootfile input windows
393function MenuBrowse_1_Callback(hObject, eventdata, handles)
394%------------------------------------------------------------------------
395RootPath=get(handles.RootPath,'String');
396[FileName, PathName] = uigetfile({'*.*','All Files(*.*)'},'Pick a file',RootPath);
397if ~ischar(FileName),return,end %abandon if the browser is cancelled
398fileinput_1=[PathName FileName];%complete file name
399
400% refresh the current displayed field
401set(handles.SubField,'Value',1)
402display_file_name(handles,fileinput_1,2)
403
404%update list of recent files in the menubar
405MenuFile_1=fileinput_1;
406MenuFile_2=get(handles.MenuFile_1,'Label');
407MenuFile_3=get(handles.MenuFile_2,'Label');
408MenuFile_4=get(handles.MenuFile_3,'Label');
409MenuFile_5=get(handles.MenuFile_4,'Label');
410set(handles.MenuFile_1,'Label',MenuFile_1)
411set(handles.MenuFile_2,'Label',MenuFile_2)
412set(handles.MenuFile_3,'Label',MenuFile_3)
413set(handles.MenuFile_4,'Label',MenuFile_4)
414set(handles.MenuFile_5,'Label',MenuFile_5)
415set(handles.MenuFile_1_1,'Label',MenuFile_1)
416set(handles.MenuFile_2_1,'Label',MenuFile_2)
417set(handles.MenuFile_3_1,'Label',MenuFile_3)
418set(handles.MenuFile_4_1,'Label',MenuFile_4)
419set(handles.MenuFile_5_1,'Label',MenuFile_5)
420dir_perso=prefdir;
421profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
422if exist(profil_perso,'file')
423    save (profil_perso,'MenuFile_1','MenuFile_2','MenuFile_3','MenuFile_4', 'MenuFile_5','-append'); %store the file names for future opening of uvmat
424else
425    txt=ver('MATLAB');
426    Release=txt.Release;
427    relnumb=str2double(Release(3:4));
428    if relnumb >= 14
429        save (profil_perso,'MenuFile_1','MenuFile_2','MenuFile_3','MenuFile_4', 'MenuFile_5','-V6'); %store the file names for future opening of uvmat
430    else
431        save (profil_perso,'MenuFile_1','MenuFile_2','MenuFile_3','MenuFile_4', 'MenuFile_5'); %store the file names for future opening of uvmat
432    end
433end
434
435% -----------------------------------------------------------------------
436% --- Open again as second field the file whose name has been recorded in MenuFile_1
437function MenuFile_1_1_Callback(hObject, eventdata, handles)
438% -----------------------------------------------------------------------
439fileinput_1=get(handles.MenuFile_1_1,'Label');
440set(handles.SubField,'Value',1)
441display_file_name(handles,fileinput_1,2)
442
443% -----------------------------------------------------------------------
444% --- Open again as second field the file whose name has been recorded in MenuFile_2
445function MenuFile_2_1_Callback(hObject, eventdata, handles)
446% -----------------------------------------------------------------------
447fileinput_1=get(handles.MenuFile_2_1,'Label');
448set(handles.SubField,'Value',1)
449display_file_name(handles,fileinput_1,2)
450
451% -----------------------------------------------------------------------
452% --- Open again as second field the file whose name has been recorded in MenuFile_3
453function MenuFile_3_1_Callback(hObject, eventdata, handles)
454% -----------------------------------------------------------------------
455fileinput_1=get(handles.MenuFile_3_1,'Label');
456set(handles.SubField,'Value',1)
457display_file_name(handles,fileinput_1,2)
458
459% -----------------------------------------------------------------------
460% --- Open again as second field the file whose name has been recorded in MenuFile_4
461function MenuFile_4_1_Callback(hObject, eventdata, handles)
462% -----------------------------------------------------------------------
463fileinput_1=get(handles.MenuFile_4_1,'Label');
464set(handles.SubField,'Value',1)
465display_file_name(handles,fileinput_1,2)
466
467% -----------------------------------------------------------------------
468% --- Open again as second field the file whose name has been recorded in MenuFile_5
469function MenuFile_5_1_Callback(hObject, eventdata, handles)
470% -----------------------------------------------------------------------
471fileinput_1=get(handles.MenuFile_5_1,'Label');
472set(handles.SubField,'Value',1)
473display_file_name(handles,fileinput_1,2)
474
475%------------------------------------------------------------------------
476% --- Called by action in RootPath edit box
477function RootPath_Callback(hObject,eventdata,handles)
478%------------------------------------------------------------------------
479% read the current input file name:
480[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
481if ~exist(fullfile(RootPath,SubDir),'dir')
482    msgbox_uvmat('ERROR',['directory ' fullfile(RootPath,SubDir) ' does not exist'])
483    return
484end
485% detect the file type, get the movie object if relevant, and look for the corresponding file series:
486[RootPath,SubDir,RootFile,i1_series,i2_series,j1_series,j2_series,tild,FileType,MovieObject]=find_file_series(fullfile(RootPath,SubDir),[RootFile FileIndices FileExt]);
487% initiate the input file series and refresh the current field view:
488update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileType,MovieObject,1);
489
490%-----------------------------------------------------------------------
491% --- Called by action in RootPath_1 edit box
492function RootPath_1_Callback(hObject,eventdata,handles)
493% -----------------------------------------------------------------------
494% update_rootinfo_1(hObject,eventdata,handles)
495[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes_1(handles);
496if ~exist(fullfile(RootPath,SubDir),'dir')
497    msgbox_uvmat('ERROR',['directory ' fullfile(RootPath,SubDir) ' does not exist'])
498    return
499end
500% detect the file type, get the movie object if relevant, and look for the corresponding file series:
501[RootPath,SubDir,RootFile,i1_series,i2_series,j1_series,j2_series,tild,FileType,MovieObject]=find_file_series(fullfile(RootPath,SubDir),[RootFile FileIndices FileExt]);
502% initiate the input file series and refresh the current field view:
503update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileType,MovieObject,2);
504
505%------------------------------------------------------------------------
506% --- Called by action in RootFile edit box
507function SubDir_Callback(hObject, eventdata, handles)
508%------------------------------------------------------------------------
509%refresh the menu of input fieldname
510Fields_Callback(hObject, eventdata, handles);
511% refresh the current field view
512run0_Callback(hObject, eventdata, handles);
513
514%------------------------------------------------------------------------
515% --- Called by action in RootFile edit box
516function RootFile_Callback(hObject, eventdata, handles)
517%------------------------------------------------------------------------
518RootPath_Callback(hObject,eventdata,handles)
519
520%-----------------------------------------------------------------------
521% --- Called by action in RootFile_1 edit box
522function RootFile_1_Callback(hObject, eventdata, handles)
523% -----------------------------------------------------------------------
524RootPath_1_Callback(hObject,eventdata,handles)
525
526%------------------------------------------------------------------------
527% --- Called by action in FileIndex edit box
528function FileIndex_Callback(hObject, eventdata, handles)
529%------------------------------------------------------------------------
530[tild,tild,tild,i1,i2,j1,j2]=fileparts_uvmat(get(handles.FileIndex,'String'));
531set(handles.i1,'String',num2str(i1));
532set(handles.i2,'String',num2str(i2));
533set(handles.j1,'String',num2str(j1));
534set(handles.j2,'String',num2str(j2));
535
536% refresh the current field view
537run0_Callback(hObject, eventdata, handles)
538
539%------------------------------------------------------------------------
540% --- Called by action in FileIndex_1 edit box
541function FileIndex_1_Callback(hObject, eventdata, handles)
542%------------------------------------------------------------------------
543run0_Callback(hObject, eventdata, handles)
544
545%------------------------------------------------------------------------
546% --- Called by action in NomType edit box
547function NomType_Callback(hObject, eventdata, handles)
548%------------------------------------------------------------------------
549i1=str2num(get(handles.i1,'String'));
550i2=str2num(get(handles.i2,'String'));
551j1=str2num(get(handles.j1,'String'));
552j2=str2num(get(handles.j2,'String'));
553FileIndex=fullfile_uvmat('','','','',get(handles.NomType,'String'),i1,i2,j1,j2);
554set(handles.FileIndex,'String',FileIndex)
555% refresh the current settings and refresh the field view
556RootPath_Callback(hObject,eventdata,handles)
557
558%------------------------------------------------------------------------
559% --- Called by action in NomType edit box
560function NomType_1_Callback(hObject, eventdata, handles)
561%------------------------------------------------------------------------
562i1=str2num(get(handles.i1,'String'));
563i2=str2num(get(handles.i2,'String'));
564j1=str2num(get(handles.j1,'String'));
565j2=str2num(get(handles.j2,'String'));
566FileIndex=fullfile_uvmat('','','','',get(handles.NomType_1,'String'),i1,i2,j1,j2);
567set(handles.FileIndex_1,'String',FileIndex)
568% refresh the current settings and refresh the field view
569RootPath_1_Callback(hObject,eventdata,handles)
570
571%------------------------------------------------------------------------
572% --- Fills the edit boxes RootPath, RootFile,NomType...from an input file name 'fileinput'
573function display_file_name(handles,fileinput,index)
574%------------------------------------------------------------------------
575%% look for the input file existence
576if ~exist(fileinput,'file')
577    msgbox_uvmat('ERROR',['input file ' fileinput  ' does not exist'])
578    return
579end
580
581%% set the mouse pointer to 'watch'
582set(handles.uvmat,'Pointer','watch')
583set(handles.RootPath,'BackgroundColor',[1 1 0])
584drawnow
585
586%% define the relevant handles for the first field series (index=1) or the second file series (index=2)
587if ~exist('index','var')
588    index=1;
589end
590if index==1
591    handles_RootPath=handles.RootPath;
592    handles_SubDir=handles.SubDir;
593    handles_RootFile=handles.RootFile;
594    handles_FileIndex=handles.FileIndex;
595    handles_NomType=handles.NomType;
596    handles_FileExt=handles.FileExt;
597elseif index==2
598    handles_RootPath=handles.RootPath_1;
599    handles_SubDir=handles.SubDir_1;
600    handles_RootFile=handles.RootFile_1;
601    handles_FileIndex=handles.FileIndex_1;
602    handles_NomType=handles.NomType_1;
603    handles_FileExt=handles.FileExt_1;
604    set(handles.RootPath_1,'Visible','on')
605    set(handles.RootFile_1,'Visible','on')
606    set(handles.SubDir_1,'Visible','on');
607    set(handles.FileIndex_1,'Visible','on');
608    set(handles.FileExt_1,'Visible','on');
609    set(handles.NomType_1,'Visible','on');
610end
611
612%% detect root name, nomenclature and indices in the input file name:
613[FilePath,FileName,FileExt]=fileparts(fileinput);
614% detect the file type, get the movie object if relevant, and look for the corresponding file series:
615% the root name and indices may be corrected by including the first index i1 if a corresponding xml file exists
616[RootPath,SubDir,RootFile,i1_series,i2_series,j1_series,j2_series,NomType,FileType,MovieObject,i1,i2,j1,j2]=find_file_series(FilePath,[FileName FileExt]);
617
618%% open the file or fill the GUI uvmat according to the detected file type
619switch FileType
620    case ''
621        msgbox_uvmat('ERROR','invalid input file type')
622    case 'txt'
623        edit(fileinput)
624    case 'figure'                           %display matlab figure
625        hfig=open(fileinput);
626        set(hfig,'WindowButtonMotionFcn','mouse_motion')%set mouse action functio
627        set(hfig,'WindowButtonUpFcn','mouse_up')%set mouse click action function
628        set(hfig,'WindowButtonUpFcn','mouse_down')%set mouse click action function
629    case 'xml'                % edit xml files
630        t=xmltree(fileinput);
631        % the xml file marks a project or project link, open datatree_browser
632        if strcmp(get(t,1,'name'),'Project')&& exist(regexprep(fileinput,'.xml$',''),'dir')
633            datatree_browser(fileinput)
634        else % other xml file, open the xml editor
635            editxml(fileinput);
636        end
637    case 'xls'% Excel file opended by editxml
638        editxml(fileinput);
639    otherwise
640        set(handles_RootPath,'String',RootPath);
641        rootname=fullfile(RootPath,SubDir,RootFile);
642        set(handles_SubDir,'String',['/' SubDir]);
643        set(handles_RootFile,'String',['/' RootFile]); %display the separator
644        indices=fileinput(length(rootname)+1:end);
645        indices(end-length(FileExt)+1:end)=[]; %remove extension
646        set(handles_FileIndex,'String',indices);
647        set(handles_NomType,'String',NomType);
648        set(handles_FileExt,'String',FileExt);
649        if index==1
650            % fill file index counters if the first file series is opened
651            set(handles.i1,'String',num2str(i1));
652            set(handles.i2,'String',num2str(i2));
653            set(handles.j1,'String',num2stra(j1,NomType));
654            set(handles.j2,'String',num2stra(j2,NomType));
655        else %read the current field index to synchronise with the first series
656            i1_s=str2num(get(handles.i1,'String'));
657            i2_0=str2num(get(handles.i2,'String'));
658            if ~isempty(i2_0)
659                i2_s=i2_0;
660            else
661               i2_s=i2;
662            end
663            j1_0=stra2num(get(handles.j1,'String'));
664            if ~isempty(j1_0)
665                j1_s=j1_0;
666            else
667                j1_s=j1;
668            end
669            j2_0=stra2num(get(handles.j2,'String'));
670            if ~isempty(j2_0)
671                j2_s=j2_0;
672            else
673                j2_s=j2;
674            end
675        end
676       
677        % synchronise indices of the second  input file if it exists
678        if get(handles.SubField,'Value')==1% if the subfield button is activated, update the field numbers
679            Input=read_GUI(handles.InputFile);
680            if ~isfield(Input,'RootPath_1')||strcmp(Input.RootPath_1,'"')
681                Input.RootPath_1=Input.RootPath;
682            end
683            if ~isfield(Input,'SubDir_1')||strcmp(Input.SubDir_1,'"')
684                Input.SubDir_1=Input.SubDir;
685            end
686            if ~isfield(Input,'RootFile_1')||strcmp(Input.RootFile_1,'"')
687                Input.RootFile_1=Input.RootFile;
688            end
689            if ~isfield(Input,'FileExt_1')||strcmp(Input.FileExt_1,'"')
690                Input.FileExt_1=Input.FileExt;
691            end
692            if ~isfield(Input,'NomType_1')||strcmp(Input.NomType_1,'"')
693                Input.NomType_1=Input.NomType;
694            end
695            %updtate the indices of the second field series to correspond to the newly opened one
696            FileName_1=fullfile_uvmat(Input.RootPath_1,Input.SubDir_1,Input.RootFile_1,Input.FileExt_1,Input.NomType_1,i1_s,i2_s,j1_s,j2_s);
697            if exist(FileName_1,'file')
698                FileIndex_1=fullfile_uvmat('','','','',Input.NomType_1,i1_s,i2_s,j1_s,j2_s);
699            else
700                FileIndex_1=fullfile_uvmat('','','','',Input.NomType_1,i1,i2,j1,j2);
701                msgbox_uvmat('WARNING','unable to synchronise the indices of the two series')
702            end
703            set(handles.FileIndex_1,'String',FileIndex_1)
704        end
705       
706        %enable other menus
707        set(handles.MenuOpen_1,'Enable','on')
708        set(handles.MenuFile_1_1,'Enable','on')
709        set(handles.MenuFile_2_1,'Enable','on')
710        set(handles.MenuFile_3_1,'Enable','on')
711        set(handles.MenuFile_4_1,'Enable','on')
712        set(handles.MenuFile_5_1,'Enable','on')
713        set(handles.MenuExport,'Enable','on')
714        set(handles.MenuExportFigure,'Enable','on')
715        set(handles.MenuExportMovie,'Enable','on')
716        set(handles.MenuTools,'Enable','on')
717
718        % initiate input file series and refresh the current field view:     
719        update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileType,MovieObject,index);
720
721end
722
723%% update list of recent files in the menubar and save it for future opening
724MenuFile=[{get(handles.MenuFile_1,'Label')};{get(handles.MenuFile_2,'Label')};...
725    {get(handles.MenuFile_3,'Label')};{get(handles.MenuFile_4,'Label')};{get(handles.MenuFile_5,'Label')}];
726str_find=strcmp(fileinput,MenuFile);
727if isempty(find(str_find,1))
728    MenuFile=[{fileinput};MenuFile];%insert the current file if not already in the list
729end
730for ifile=1:min(length(MenuFile),5)
731    eval(['set(handles.MenuFile_' num2str(ifile) ',''Label'',MenuFile{ifile});'])
732    eval(['set(handles.MenuFile_' num2str(ifile) '_1,''Label'',MenuFile{ifile});'])
733end
734dir_perso=prefdir;
735profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
736if exist(profil_perso,'file')
737    save (profil_perso,'MenuFile','-append'); %store the file names for future opening of uvmat
738else
739    save (profil_perso,'MenuFile','-V6'); %store the file names for future opening of uvmat
740end
741
742%% set back the mouse pointer to arrow
743set(handles.uvmat,'Pointer','arrow')
744
745
746%------------------------------------------------------------------------
747% --- Update information about a new field series (indices to scan, timing,
748%     calibration from an xml file, then refresh current plots
749
750function update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileType,VideoObject,index)
751%------------------------------------------------------------------------
752%% define the relevant handles depending on the index (1=first file series, 2= second file series)
753if ~exist('index','var')
754    index=1;
755end
756if index==1
757    handles_RootPath=handles.RootPath;
758    handles_Fields=handles.FieldName;
759elseif index==2
760    handles_RootPath=handles.RootPath_1;
761    handles_Fields=handles.FieldName_1;
762end
763
764set(handles_RootPath,'BackgroundColor',[1 1 0])
765drawnow
766set(handles.FieldName,'UserData',[])% reinialize data from uvmat opening
767UvData=get(handles.uvmat,'UserData');%huvmat=handles of the uvmat interface
768UvData.NewSeries=1; %flag for run0: begin a new series
769UvData.FileName_1='';% name of the current second field (used to detect a  constant field during file scanning)
770UvData.FileType{index}=FileType;
771UvData.i1_series{index}=i1_series;
772UvData.i2_series{index}=i2_series;
773UvData.j1_series{index}=j1_series;
774UvData.j2_series{index}=j2_series;
775set(handles.FixVelType,'Value',0); %desactivate fixed veltype
776if index==1
777    [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
778else
779    [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes_1(handles);
780end
781FileName=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
782FileBase=fullfile(RootPath,RootFile);
783if ~exist(FileName,'file')
784   msgbox_uvmat('ERROR',['input file ' FileName ' not found']);
785    return
786end
787
788%% read timing and total frame number from the current file (movie files) !! may be overrid by xml file
789XmlData.Time=[];%default
790XmlData.GeometryCalib=[];%default
791TimeUnit='';%default
792Time=[];
793% testima=0; %test for image input
794imainfo=[];
795ColorType='falsecolor'; %default
796% hhh=[];
797UvData.MovieObject{index}=VideoObject;
798if ~isempty(VideoObject)
799    imainfo=get(VideoObject);
800%     testima=1;
801    TimeUnit='s';
802    if isempty(j1_series); %frame index along i
803        Time=(0:1/imainfo.FrameRate:(imainfo.NumberOfFrames)/imainfo.FrameRate)';
804    else
805        Time=ones(size(i1_series,1),1)*(0:1/imainfo.FrameRate:(imainfo.NumberOfFrames)/imainfo.FrameRate);
806    end
807    set(handles.Dt_txt,'String',['Dt=' num2str(1000/imainfo.FrameRate) 'ms']);%display the elementary time interval in millisec
808    ColorType='truecolor';
809elseif ~isempty(FileExt(2:end))&&(~isempty(imformats(FileExt(2:end))) || isequal(FileExt,'.vol'))%&& isequal(NomType,'*')% multi-frame image
810%     testima=1;
811    if ~isequal(SubDir,'')
812        imainfo=imfinfo([fullfile(RootPath,SubDir,RootFile) FileIndices FileExt]);
813    else
814        imainfo=imfinfo([FileBase FileIndices FileExt]);
815    end
816    ColorType=imainfo.ColorType;%='truecolor' for color images
817end
818if isfield(imainfo,'Width') && isfield(imainfo,'Height')
819    if length(imainfo)>1
820        set(handles.num_Npx,'String',num2str(imainfo(1).Width));%fills nbre of pixels x box
821        set(handles.num_Npy,'String',num2str(imainfo(1).Height));%fills nbre of pixels x box
822    else
823        set(handles.num_Npx,'String',num2str(imainfo.Width));%fills nbre of pixels x box
824        set(handles.num_Npy,'String',num2str(imainfo.Height));%fills nbre of pixels x box
825    end
826else
827    set(handles.num_Npx,'String','');%fills nbre of pixels x box
828    set(handles.num_Npy,'String','');%fills nbre of pixels x box
829end
830set(handles.CheckBW,'Value',strcmp(ColorType,'grayscale'))% select handles.CheckBW if grayscale image
831
832%% read parameters (time, geometric calibration..) from a documentation file (.xml advised)
833XmlFileName=find_imadoc(RootPath,SubDir,RootFile,FileExt);
834[tild,tild,DocExt]=fileparts(XmlFileName);
835warntext='';%default warning message
836NbSlice=1;%default
837set(handles.RootPath,'BackgroundColor',[1 1 1])
838if ~isempty(XmlFileName)
839    set(handles.view_xml,'Visible','on')
840    set(handles.view_xml,'BackgroundColor',[1 1 0])
841    set(handles.view_xml,'String','view .xml')
842    drawnow
843    [XmlDataRead,warntext]=imadoc2struct(XmlFileName);
844    if ~isempty(warntext)
845        msgbox_uvmat('WARNING',warntext)
846    end
847    if isempty(XmlDataRead)
848        set(handles.view_xml,'Visible','off')
849    else
850        set(handles.view_xml,'String',['view ' DocExt])   
851        XmlData=XmlDataRead;
852        if isfield(XmlData,'TimeUnit')
853            if isfield(XmlData,'TimeUnit')&& ~isempty(XmlData.TimeUnit)
854                TimeUnit=XmlData.TimeUnit;
855            end
856        end
857        set(handles.view_xml,'BackgroundColor',[1 1 1])
858        drawnow
859        if isfield(XmlData, 'GeometryCalib') && ~isempty(XmlData.GeometryCalib)
860            if isfield(XmlData.GeometryCalib,'VolumeScan') && isequal(XmlData.GeometryCalib.VolumeScan,'y')
861                set (handles.num_NbSlice,'String','volume')
862            end
863            hgeometry_calib=findobj('tag','geometry_calib');
864            if ~isempty(hgeometry_calib)
865                GUserData=get(hgeometry_calib,'UserData');
866                if ~(isfield(GUserData,'XmlInputFile') && strcmp(GUserData.XmlInputFile,XmlFileName))
867                    answer=msgbox_uvmat('INPUT_Y-N','replace the display of geometry_calib with the new input data?');
868                    if strcmp(answer,'Yes')
869                        geometry_calib(XmlFileName);%diplay the new calibration points and parameters in geometry_calib
870                    end
871                end
872            end
873        end
874    end
875end
876if ~(isfield(XmlData,'Time')&& ~isempty(XmlData.Time))
877    XmlData.Time=Time; %time set by video
878end
879
880%% store last index in handles.lat_i and .last_j
881nbfield=max(max(max(i2_series)));
882if isempty(nbfield)
883    nbfield=max(max(max(i1_series)));
884end
885nbfield_j=max(max(max(j2_series)));
886if isempty(nbfield_j)
887    nbfield_j=max(max(max(j2_series)));
888end
889if ~isempty(XmlData.Time)
890    %transform .Time to a column vector if it is a line vector the nomenclature uses a single index
891    if isequal(size(XmlData.Time,1),1)
892        NomType=get(handles.NomType,'String');
893        XmlData.Time=(XmlData.Time)';
894    end
895end
896last_i_cell=get(handles.last_i,'String');
897if isempty(nbfield)
898    last_i_cell{1}='';
899else
900    last_i_cell{1}=num2str(nbfield);
901end
902set(handles.last_i,'String',last_i_cell)
903last_j_cell=get(handles.last_j,'String');
904if isempty(nbfield_j)
905     last_j_cell{1}='';
906else
907     last_j_cell{1}=num2str(nbfield_j);
908end
909set(handles.last_j,'String',last_j_cell);
910
911%% store geometric calibration in UvData
912if isfield(XmlData,'GeometryCalib')
913    GeometryCalib=XmlData.GeometryCalib;
914    if isempty(GeometryCalib)
915        set(handles.pxcm,'String','')
916        set(handles.pycm,'String','')
917        set(handles.transform_fct,'Value',1); %  no transform by default
918    else
919        if (isfield(GeometryCalib,'R')&& ~isequal(GeometryCalib.R(2,1),0) && ~isequal(GeometryCalib.R(1,2),0)) ||...
920            (isfield(GeometryCalib,'kappa1')&& ~isequal(GeometryCalib.kappa1,0))
921            set(handles.pxcm,'String','var')
922            set(handles.pycm,'String','var')
923        elseif isfield(GeometryCalib,'fx_fy')
924            pixcmx=GeometryCalib.fx_fy(1);%*GeometryCalib.R(1,1)*GeometryCalib.sx/(GeometryCalib.Tz*GeometryCalib.dpx);
925            pixcmy=GeometryCalib.fx_fy(2);%*GeometryCalib.R(2,2)/(GeometryCalib.Tz*GeometryCalib.dpy);
926            set(handles.pxcm,'String',num2str(pixcmx))
927            set(handles.pycm,'String',num2str(pixcmy))
928        end
929        if ~get(handles.CheckFixLimits,'Value')
930            set(handles.transform_fct,'Value',3); % phys transform by default if fixedLimits is off
931        end
932        if isfield(GeometryCalib,'SliceCoord')           
933           siz=size(GeometryCalib.SliceCoord);
934           if siz(1)>1
935               NbSlice=siz(1);
936               set(handles.slices,'Visible','on')
937               set(handles.slices,'Value',1)
938           end
939           if isfield(GeometryCalib,'VolumeScan') && isequal(GeometryCalib.VolumeScan,'y')
940               set(handles.num_NbSlice,'String','volume')
941           else
942               set(handles.num_NbSlice,'String',num2str(NbSlice))
943           end
944           slices_Callback([],[], handles)
945        end           
946    end
947end
948
949%% update the data attached to the uvmat interface
950if ~isempty(TimeUnit)
951    set(handles.time_txt,'String',['time (' TimeUnit ')'])
952end
953UvData.TimeUnit=TimeUnit;
954UvData.XmlData{index}=XmlData;
955UvData.NewSeries=1;
956% UvData.MovieObject=MovieObject;
957
958%display warning message
959if ~isequal(warntext,'')
960    msgbox_uvmat('WARNING',warntext);
961end
962
963%% set default options in menu 'FieldName'
964switch FileType
965    case {'civx','civdata'}
966        [FieldList,ColorList]=calc_field;
967        set(handles_Fields,'String',[{'image'};FieldList;{'get_field...'}]);%standard menu for civx data
968        set(handles_Fields,'Value',2) % set menu to 'velocity
969        set(handles.ColorScalar,'Value',1)
970        set(handles.ColorScalar,'String',ColorList)
971        set(handles.Vectors,'Visible','on')
972        set(handles.Coord_x,'Value',1);
973        set(handles.Coord_x,'String',{'X'});
974        set(handles.Coord_y,'Value',1);
975        set(handles.Coord_y,'String',{'Y'});
976    case 'netcdf'
977        set(handles_Fields,'Value',1)
978        set(handles_Fields,'String',{'get_field...'})
979        hget_field=get_field(FileName);
980        hhget_field=guidata(hget_field);
981        get_field('RUN_Callback',hhget_field.RUN,[],hhget_field);
982    otherwise
983        set(handles_Fields,'Value',1) % set menu to 'image'
984        set(handles_Fields,'String',{'image'})
985        set(handles.Coord_x,'Value',1);
986        set(handles.Coord_x,'String',{'AX'});
987        set(handles.Coord_y,'Value',1);
988        set(handles.Coord_y,'String',{'AY'});
989end
990set(handles.uvmat,'UserData',UvData)
991
992%% set index navigation options and refresh plots
993scan_option='i';%default
994state_j='off'; %default
995if index==2
996    if get(handles.scan_j,'Value')
997        scan_option='j'; %keep the scan option for the second file series
998    end
999    if strcmp(get(handles.j1,'Visible'),'on')
1000        state_j='on';
1001    end
1002end
1003[ref_j,ref_i]=find(squeeze(i1_series(1,:,:)));
1004if ~isempty(j1_series)
1005        state_j='on';
1006        if index==1
1007            if isequal(ref_i,ref_i(1)*ones(size(ref_j)))% if ref_i is always equal to its first value
1008                scan_option='j'; %scan j indext               
1009            end
1010        end
1011end
1012if isequal(scan_option,'i')
1013    diff_ref_i=diff(ref_i,1);
1014    if isempty(diff_ref_i)
1015        diff_ref_i=1;
1016    end
1017    if isequal (diff_ref_i,diff_ref_i(1)*ones(size(diff_ref_i)))
1018        set(handles.num_IndexIncrement,'String',num2str(diff_ref_i(1)))
1019    end
1020     set(handles.scan_i,'Value',1)
1021     scan_i_Callback([],[], handles);
1022else
1023    diff_ref_j=diff(ref_j);
1024    if isempty(diff_ref_j)
1025        diff_ref_j=1;
1026    end
1027    if isequal (diff_ref_j,diff_ref_j(1)*ones(size(diff_ref_j)))
1028        set(handles.num_IndexIncrement,'String',num2str(diff_ref_j(1)))
1029    end
1030     set(handles.scan_j,'Value',1)
1031     scan_j_Callback([],[], handles);
1032end
1033set(handles.scan_j,'Visible',state_j)
1034set(handles.j1,'Visible',state_j)
1035set(handles.j2,'Visible',state_j)
1036set(handles.last_j,'Visible',state_j);
1037set(handles.frame_j,'Visible',state_j);
1038set(handles.j_text,'Visible',state_j);
1039if ~isempty(i2_series)||~isempty(j2_series)
1040    set(handles.CheckFixPair,'Visible','on')
1041elseif index==1
1042    set(handles.CheckFixPair,'Visible','off')
1043end
1044
1045%% apply the effect of the transform fct and view the field 
1046transform=get(handles.path_transform,'UserData');
1047if index==2 && (~isa(transform,'function_handle')||nargin(transform)<3)
1048    set(handles.transform_fct,'value',2); % set transform to sub_field if the current fct doe not accept two input fields
1049end
1050transform_fct_Callback([],[],handles)
1051mask_test=get(handles.CheckMask,'value');
1052if mask_test
1053    MaskData=get(handles.CheckMask,'UserData');
1054    if isfield(MaskData,'maskhandle') && ishandle(MaskData.maskhandle)
1055          delete(MaskData.maskhandle)    %delete old mask
1056    end
1057    CheckMask_Callback([],[],handles)
1058end
1059
1060%------------------------------------------------------------------------
1061% --- switch file index scanning options scan_i and scan_j in an exclusive way
1062function scan_i_Callback(hObject, eventdata, handles)
1063%------------------------------------------------------------------------
1064if get(handles.scan_i,'Value')==1
1065    set(handles.scan_i,'BackgroundColor',[1 1 0])
1066    set(handles.scan_j,'Value',0)
1067else
1068    set(handles.scan_i,'BackgroundColor',[0.831 0.816 0.784])
1069    set(handles.scan_j,'Value',1)
1070end
1071scan_j_Callback(hObject, eventdata, handles)
1072
1073%------------------------------------------------------------------------
1074% --- switch file index scanning options scan_i and scan_j in an exclusive way
1075function scan_j_Callback(hObject, eventdata, handles)
1076%------------------------------------------------------------------------
1077if get(handles.scan_j,'Value')==1
1078    set(handles.scan_j,'BackgroundColor',[1 1 0])
1079    set(handles.scan_i,'Value',0)
1080    set(handles.scan_i,'BackgroundColor',[0.831 0.816 0.784])
1081%     NomType=get(handles.NomType,'String');
1082%     switch NomType
1083%     case {'_1_1-2','#_ab','%3dab'},% pair with j index
1084%         set(handles.CheckFixPair,'Visible','on')% option fixed pair on/off made visible (choice of avaible pair with buttons + and - if ='off')
1085%     otherwise
1086%         set(handles.CheckFixPair,'Visible','off')
1087%     end
1088else
1089    set(handles.scan_j,'BackgroundColor',[0.831 0.816 0.784])
1090    set(handles.scan_i,'Value',1)
1091    set(handles.scan_i,'BackgroundColor',[1 1 0])
1092    set(handles.CheckFixPair,'Visible','off')
1093end
1094
1095%------------------------------------------------------------------------
1096function i1_Callback(hObject, eventdata, handles)
1097%------------------------------------------------------------------------
1098update_ij(handles,1)
1099
1100%------------------------------------------------------------------------
1101function i2_Callback(hObject, eventdata, handles)
1102%------------------------------------------------------------------------
1103update_ij(handles,2)
1104
1105%------------------------------------------------------------------------
1106function j1_Callback(hObject, eventdata, handles)
1107%------------------------------------------------------------------------
1108update_ij(handles,3)
1109
1110%------------------------------------------------------------------------
1111function j2_Callback(hObject, eventdata, handles)
1112%------------------------------------------------------------------------
1113update_ij(handles,4)
1114
1115%------------------------------------------------------------------------
1116%--- update the index display after action on edit boxes i1, i2, j1 or j2
1117function update_ij(handles,index_rank)
1118NomType=get(handles.NomType,'String');
1119indices=get(handles.FileIndex,'String');
1120[tild,tild,tild,i1,i2,j1,j2]=fileparts_uvmat(indices);% the indices for the second series taken from FileIndex
1121switch index_rank
1122    case 1
1123        indices=fullfile_uvmat('','','','',NomType,stra2num(get(handles.i1,'String')),i2,j1,j2);
1124        set(handles.i1,'BackgroundColor',[0.7 0.7 0.7])% mark the edit box in grey, then RUN0 will mark it in white for confirmation
1125    case 2
1126        indices=fullfile_uvmat('','','','',NomType,i1,stra2num(get(handles.i2,'String')),j1,j2);
1127        set(handles.i2,'BackgroundColor',[0.7 0.7 0.7])% mark the edit box in grey, then RUN0 will mark it in white for confirmation
1128    case 3
1129        indices=fullfile_uvmat('','','','',NomType,i1,i2,stra2num(get(handles.j1,'String')),j2);
1130        set(handles.j1,'BackgroundColor',[0.7 0.7 0.7])% mark the edit box in grey, then RUN0 will mark it in white for confirmation
1131    case 4
1132        indices=fullfile_uvmat('','','','',NomType,i1,i2,j1,stra2num(get(handles.j2,'String')));
1133        set(handles.j2,'BackgroundColor',[0.7 0.7 0.7])% mark the edit box in grey, then RUN0 will mark it in white for confirmation
1134end
1135set(handles.FileIndex,'String',indices)
1136set(handles.FileIndex,'BackgroundColor',[0.7 0.7 0.7])% mark the edit box in grey, then RUN0 will mark it in white for confirmation
1137% update the second index if relevant
1138if strcmp(get(handles.FileIndex_1,'Visible'),'on')
1139    NomType_1=get(handles.NomType_1,'String');
1140    indices_1=get(handles.FileIndex_1,'String');
1141    [tild,tild,tild,i1_1,i2_1,j1_1,j2_1]=fileparts_uvmat(indices_1);% the indices for the second series taken from FileIndex_1
1142    switch index_rank
1143        case 1
1144            indices_1=fullfile_uvmat('','','','',NomType_1,stra2num(get(handles.i1,'String')),i2_1,j1_1,j2_1);
1145        case 2
1146            indices_1=fullfile_uvmat('','','','',NomType_1,i1_1,stra2num(get(handles.i2,'String')),j1_1,j2_1);
1147        case 3
1148            indices_1=fullfile_uvmat('','','','',NomType_1,i1_1,i2_1,stra2num(get(handles.j1,'String')),j2_1);
1149        case 4
1150            indices_1=fullfile_uvmat('','','','',NomType_1,i1_1,i2_1,j1_1,stra2num(get(handles.j2,'String')));
1151    end
1152    set(handles.FileIndex_1,'String',indices_1)
1153    set(handles.FileIndex_1,'BackgroundColor',[0.7 0.7 0.7])% mark the edit box in grey, then RUN0 will mark it in white for confirmation
1154end
1155   
1156%------------------------------------------------------------------------
1157
1158%------------------------------------------------------------------------
1159function slices_Callback(hObject, eventdata, handles)
1160%------------------------------------------------------------------------
1161if get(handles.slices,'Value')==1
1162    set(handles.slices,'BackgroundColor',[1 1 0])
1163    set(handles.num_NbSlice,'Visible','on')
1164    set(handles.z_text,'Visible','on')
1165    set(handles.z_index,'Visible','on')
1166    num_NbSlice_Callback(hObject, eventdata, handles)
1167else
1168    set(handles.num_NbSlice,'Visible','off')
1169    set(handles.slices,'BackgroundColor',[0.7 0.7 0.7])
1170    set(handles.z_text,'Visible','off')
1171    set(handles.z_index,'Visible','off')
1172    set(handles.masklevel,'Value',1)
1173    set(handles.masklevel,'String',{'1'})
1174end
1175
1176%------------------------------------------------------------------------
1177function num_NbSlice_Callback(hObject, eventdata, handles)
1178%------------------------------------------------------------------------
1179nb_slice_str=get(handles.num_NbSlice,'String');
1180if isequal(nb_slice_str,'volume')
1181    num=stra2num(get(handles.j1,'String'));
1182    last_j=get(handles.last_j,'String');
1183    nbslice=str2double(last_j{1});
1184else
1185    num=str2double(get(handles.i1,'String'));
1186    nbslice=str2double(get(handles.num_NbSlice,'String'));
1187end
1188z=mod(num-1,nbslice)+1;
1189set(handles.z_index,'String',num2str(z))
1190for ilist=1:nbslice
1191    list_index{ilist,1}=num2str(ilist);
1192end   
1193set(handles.masklevel,'String',list_index)
1194set(handles.masklevel,'Value',z)
1195
1196%------------------------------------------------------------------------
1197% --- Executes on button press in view_xml.
1198function view_xml_Callback(hObject, eventdata, handles)
1199%------------------------------------------------------------------------
1200%[FileName,RootPath,FileBase,FileIndices,FileExt]=read_file_boxes(handles);
1201 [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
1202FileBase=fullfile(RootPath,RootFile);
1203option=get(handles.view_xml,'String');
1204if isequal(option,'view .xml')
1205    FileXml=fullfile(RootPath,[SubDir '.xml']);
1206    if ~exist(FileXml,'file')% case of civ files , removes the extension for subdir
1207        FileXml=fullfile(RootPath,[regexprep(SubDir,'\..+$','') '.xml']);
1208    end
1209    heditxml=editxml(FileXml);
1210end
1211
1212%------------------------------------------------------------------------
1213% --- Executes on button press in CheckMask.
1214function CheckMask_Callback(hObject, eventdata, handles)
1215%------------------------------------------------------------------------
1216%case of view mask selection
1217if isequal(get(handles.CheckMask,'Value'),1)
1218     [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
1219     FileBase=fullfile(RootPath,RootFile);
1220    num_i1=stra2num(get(handles.i1,'String'));
1221    num_j1=stra2num(get(handles.j1,'String'));
1222    currentdir=pwd; 
1223    cd(RootPath);
1224    maskfiles=dir('*_*mask_*.png');%look for a mask file
1225    cd(currentdir);%come back to the working directory
1226    mdetect=0;
1227    if ~isempty(maskfiles)
1228        for ilist=1:length(maskfiles)
1229            maskname=maskfiles(ilist).name;% take the first mask file in the list
1230            [tild,tild,tild,tild,tild,tild,tild,MaskExt,Mask_NomType{ilist}]=fileparts_uvmat(maskname);
1231             [tild,Name]=fileparts(maskname);
1232            Namedouble=double(Name);
1233            val=(48>Namedouble)|(Namedouble>57);% select the non-numerical characters
1234            ind_mask=findstr('mask',Name);
1235            i=ind_mask-1;
1236            while val(i)==0 && i>0
1237                i=i-1;
1238            end
1239            nbmask_str=str2num(Name(i+1:ind_mask-1));
1240            if ~isempty(nbmask_str)
1241                nbslice(ilist)=nbmask_str; % number of different masks (slices)
1242            end
1243        end
1244        if isequal(min(nbslice),max(nbslice))
1245            nbslice=nbslice(1);
1246        else
1247            msgbox_uvmat('ERROR','several inconsistent mask sets coexist in the current image directory')
1248            return
1249        end
1250        if ~isempty(nbslice) && Name(i)=='_'
1251            Mask.Base=[FileBase Name(i:ind_mask+3)];
1252            Mask.NbSlice=nbslice;
1253            num_i1=mod(num_i1-1,nbslice)+1;
1254            Mask.NomType=regexprep(Mask_NomType{1},'0','');%remove '0' in nom type for masks
1255            [RootPath,RootFile]=fileparts(Mask.Base);
1256            maskname=fullfile_uvmat(RootPath,'',RootFile,'.png',Mask.NomType,num_i1,[],num_j1);
1257            %maskname=name_generator(Mask.Base,num_i1,num_j1,'.png',Mask.NomType);%
1258            mdetect=exist(maskname,'file');
1259            if mdetect
1260                set(handles.num_NbSlice,'String',Name(i+1:ind_mask-1));
1261                set(handles.num_NbSlice,'BackgroundColor',[1 1 0])
1262                set(handles.CheckMask,'UserData',Mask);
1263                set(handles.CheckMask,'BackgroundColor',[1 1 0])
1264                if nbslice > 1
1265                    set(handles.slices,'value',1)
1266                    slices_Callback(hObject, eventdata, handles)
1267                end
1268            end
1269        end
1270    end
1271    errormsg=[];%default
1272    if mdetect==0
1273        [FileName, PathName, filterindex] = uigetfile( ...
1274            {'*.png', ' (*.png)';
1275            '*.png',  '.png files '; ...
1276            '*.*', 'All Files (*.*)'}, ...
1277            'Pick a mask file *.png',FileBase);
1278        if ~ischar(FileName),return,end %abandon if the browser is cancelled
1279        maskname=fullfile(PathName,FileName);
1280        [RootDir,SubDir,RootFile,tild,tild,tild,tild,tild,Mask.NomType]=fileparts_uvmat(maskname);
1281        Mask.Base=fullfile(RootDir,SubDir,RootFile);
1282        Mask.NbSlice=1;
1283        set(handles.CheckMask,'UserData',Mask);
1284        set(handles.CheckMask,'BackgroundColor',[1 1 0])
1285    end
1286    if isempty(errormsg)
1287        errormsg=update_mask(handles,num_i1,num_j1);
1288    end
1289    if ~isempty(errormsg)
1290            set(handles.CheckMask,'Value',0)
1291            set(handles.CheckMask,'BackgroundColor',[0.7 0.7 0.7])
1292     end
1293else % desactivate mask display
1294    MaskData=get(handles.CheckMask,'UserData');
1295    if isfield(MaskData,'maskhandle') && ishandle(MaskData.maskhandle)
1296          delete(MaskData.maskhandle)   
1297    end
1298    set(handles.CheckMask,'UserData',[])   
1299    UvData=get(handles.uvmat,'UserData');
1300    if isfield(UvData,'MaskName')
1301        UvData=rmfield(UvData,'MaskName');
1302        set(handles.uvmat,'UserData',UvData)
1303    end
1304    set(handles.CheckMask,'BackgroundColor',[0.7 0.7 0.7])
1305end
1306
1307%------------------------------------------------------------------------
1308function errormsg=update_mask(handles,num_i1,num_j1)
1309%------------------------------------------------------------------------
1310errormsg=[];%default
1311MaskData=get(handles.CheckMask,'UserData');
1312if isfield(MaskData,'maskhandle')&& ishandle(MaskData.maskhandle)
1313    uistack(MaskData.maskhandle,'top');
1314end
1315num_i1_mask=mod(num_i1-1,MaskData.NbSlice)+1;
1316[RootPath,RootFile]=fileparts(MaskData.Base);
1317MaskName=fullfile_uvmat(RootPath,'',RootFile,'.png',MaskData.NomType,num_i1_mask,[],num_j1);
1318UvData=get(handles.uvmat,'UserData');
1319%update mask image if the mask is new
1320if ~ (isfield(UvData,'MaskName') && isequal(UvData.MaskName,MaskName))
1321    UvData.MaskName=MaskName; %update the recorded name on UvData
1322    set(handles.uvmat,'UserData',UvData);
1323    if ~exist(MaskName,'file')
1324        if isfield(MaskData,'maskhandle')&& ishandle(MaskData.maskhandle)
1325            delete(MaskData.maskhandle)   
1326        end
1327    else
1328        %read mask image
1329        [Mask,tild,errormsg] = read_field(MaskName,'image');
1330%         Mask.AName='image';
1331%         Mask.A=imread(MaskName);
1332        if ~isempty(errormsg)
1333            return
1334        end
1335        npxy=size(Mask.A);
1336        if length(npxy)>2
1337            errormsg=[MaskName ' is not a grey scale image'];
1338            return
1339        elseif ~isa(Mask.A,'uint8')
1340            errormsg=[MaskName ' is not a 8 bit grey level image'];
1341            return
1342        end
1343%         Mask.AX=[0.5 npxy(2)-0.5];
1344%         Mask.AY=[npxy(1)-0.5 0.5 ];
1345%         Mask.CoordUnit='pixel';
1346        if isequal(get(handles.slices,'Value'),1)
1347           NbSlice=str2num(get(handles.num_NbSlice,'String'));
1348           num_i1=str2num(get(handles.i1,'String'));
1349           Mask.ZIndex=mod(num_i1-1,NbSlice)+1;
1350        end
1351        %px to phys or other transform on field
1352         menu_transform=get(handles.transform_fct,'String');
1353        choice_value=get(handles.transform_fct,'Value');
1354        transform_name=menu_transform{choice_value};%name of the transform fct  given by the menu 'transform_fct'
1355%         transform_list=get(handles.transform_fct,'UserData');
1356%         transform=transform_list{choice_value};
1357        transform=get(handles.path_transform,'UserData');
1358        if  ~isequal(transform_name,'') && ~isequal(transform_name,'px')
1359            if isfield(UvData,'XmlData') && isfield(UvData.XmlData{1},'GeometryCalib')%use geometry calib recorded from the ImaDoc xml file as first priority
1360                Calib=UvData.XmlData{1}.GeometryCalib;
1361                Mask=transform(Mask,UvData.XmlData{1});
1362            end
1363        end
1364        flagmask=Mask.A < 200;
1365       
1366        %make brown color image
1367        imflag(:,:,1)=0.9*flagmask;
1368        imflag(:,:,2)=0.7*flagmask;
1369        imflag(:,:,3)=zeros(size(flagmask));
1370       
1371        %update mask image
1372        hmask=[]; %default
1373        if isfield(MaskData,'maskhandle')&& ishandle(MaskData.maskhandle)
1374            hmask=MaskData.maskhandle;
1375        end
1376        if ~isempty(hmask)
1377            set(hmask,'CData',imflag)   
1378            set(hmask,'AlphaData',flagmask*0.6)
1379            set(hmask,'XData',Mask.AX);
1380            set(hmask,'YData',Mask.AY);
1381%             uistack(hmask,'top')
1382        else
1383            axes(handles.PlotAxes)
1384            hold on   
1385            size(flagmask)
1386           % MaskData.maskhandle=image(Mask.AX,Mask.AY,imflag,'Tag','mask','HitTest','off','AlphaData',0.6*flagmask);
1387            MaskData.maskhandle=image(Mask.AX,Mask.AY,imflag,'Tag','mask','HitTest','off','AlphaData',0.6*ones(size(flagmask)));
1388%             set(MaskData.maskhandle,'AlphaData',0.6*flagmask)
1389            set(handles.CheckMask,'UserData',MaskData)
1390        end
1391    end
1392end
1393
1394%------------------------------------------------------------------------
1395%------------------------------------------------------------------------
1396% III - MAIN REFRESH FUNCTIONS : 'FRAME PLOT'
1397%------------------------------------------------------------------------
1398
1399%------------------------------------------------------------------------
1400% --- Executes on button press in runplus: make one step forward and call
1401% --- run0. The step forward is along the fieldname series 1 or 2 depending on
1402% --- the scan_i and scan_j check box (exclusive each other)
1403function runplus_Callback(hObject, eventdata, handles)
1404%------------------------------------------------------------------------
1405set(handles.runplus,'BackgroundColor',[1 1 0])%paint the command button in yellow
1406drawnow
1407%TODO: introduce the option: increment ='*' to move to the next available view
1408increment=str2num(get(handles.num_IndexIncrement,'String')); %get the field increment d
1409% if isnan(increment)
1410%     set(handles.num_IndexIncrement,'String','1')%default value
1411%     increment=1;
1412% end
1413errormsg=runpm(hObject,eventdata,handles,increment);
1414if ~isempty(errormsg)
1415    msgbox_uvmat('ERROR',errormsg);
1416end
1417set(handles.runplus,'BackgroundColor',[1 0 0])%paint the command button back to red
1418
1419%------------------------------------------------------------------------
1420% --- Executes on button press in runmin: make one step backward and call
1421% --- run0. The step backward is along the fieldname series 1 or 2 depending on
1422% --- the scan_i and scan_j check box (exclusive each other)
1423function runmin_Callback(hObject, eventdata, handles)
1424%------------------------------------------------------------------------
1425set(handles.runmin,'BackgroundColor',[1 1 0])%paint the command button in yellow
1426drawnow
1427increment=-str2num(get(handles.num_IndexIncrement,'String')); %get the field increment d
1428% if isnan(increment)
1429%     set(handles.num_IndexIncrement,'String','1')%default value
1430%     increment=1;
1431% end
1432errormsg=runpm(hObject,eventdata,handles,increment);
1433if ~isempty(errormsg)
1434    msgbox_uvmat('ERROR',errormsg);
1435end
1436set(handles.runmin,'BackgroundColor',[1 0 0])%paint the command button back to red
1437
1438%------------------------------------------------------------------------
1439% -- Executes on button press in Movie: make a series of +> steps
1440function Movie_Callback(hObject, eventdata, handles)
1441%------------------------------------------------------------------------
1442set(handles.Movie,'BackgroundColor',[1 1 0])%paint the command button in yellow
1443drawnow
1444increment=str2num(get(handles.num_IndexIncrement,'String')); %get the field increment d
1445% if isnan(increment)
1446%     set(handles.num_IndexIncrement,'String','1')%default value
1447%     increment=1;
1448% end
1449set(handles.STOP,'Visible','on')
1450set(handles.speed,'Visible','on')
1451set(handles.speed_txt,'Visible','on')
1452set(handles.Movie,'BusyAction','queue')
1453UvData=get(handles.uvmat,'UserData');
1454
1455while get(handles.Movie,'Value')==1 && get(handles.speed,'Value')~=0 && isequal(get(handles.Movie,'BusyAction'),'queue') % enable STOP command
1456        errormsg=runpm(hObject,eventdata,handles,increment);
1457        if ~isempty(errormsg)
1458            set(handles.Movie,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1459            return
1460        end
1461        pause(1.02-get(handles.speed,'Value'))% wait for next image
1462end
1463if isfield(UvData,'aviobj') && ~isempty( UvData.aviobj),
1464    UvData.aviobj=close(UvData.aviobj);
1465   set(handles.uvmat,'UserData',UvData);
1466end
1467set(handles.Movie,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1468
1469%------------------------------------------------------------------------
1470% -- Executes on button press in Movie: make a series of <- steps
1471function MovieBackward_Callback(hObject, eventdata, handles)
1472%------------------------------------------------------------------------
1473set(handles.MovieBackward,'BackgroundColor',[1 1 0])%paint the command button in yellow
1474drawnow
1475increment=-str2num(get(handles.num_IndexIncrement,'String')); %get the field increment d
1476set(handles.STOP,'Visible','on')
1477set(handles.speed,'Visible','on')
1478set(handles.speed_txt,'Visible','on')
1479set(handles.MovieBackward,'BusyAction','queue')
1480UvData=get(handles.uvmat,'UserData');
1481
1482while get(handles.MovieBackward,'Value')==1 && get(handles.speed,'Value')~=0 && isequal(get(handles.MovieBackward,'BusyAction'),'queue') % enable STOP command
1483        errormsg=runpm(hObject,eventdata,handles,increment);
1484        if ~isempty(errormsg)
1485            set(handles.MovieBackward,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1486            return
1487        end
1488        pause(1.02-get(handles.speed,'Value'))% wait for next image
1489end
1490if isfield(UvData,'aviobj') && ~isempty( UvData.aviobj),
1491    UvData.aviobj=close(UvData.aviobj);
1492   set(handles.uvmat,'UserData',UvData);
1493end
1494set(handles.MovieBackward,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1495
1496%------------------------------------------------------------------------
1497function STOP_Callback(hObject, eventdata, handles)
1498%------------------------------------------------------------------------
1499set(handles.movie_pair,'BusyAction','Cancel')
1500set(handles.movie_pair,'value',0)
1501set(handles.Movie,'BusyAction','Cancel')
1502set(handles.MovieBackward,'BusyAction','Cancel')
1503set(handles.MenuExportMovie,'BusyAction','Cancel')
1504set(handles.movie_pair,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1505set(handles.Movie,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1506set(handles.MovieBackward,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1507
1508%------------------------------------------------------------------------
1509% --- function activated by runplus and run minus
1510function errormsg=runpm(hObject,eventdata,handles,increment)
1511%------------------------------------------------------------------------
1512errormsg='';%default
1513%% check for movie pair status
1514movie_status=get(handles.movie_pair,'Value');
1515if isequal(movie_status,1)
1516    STOP_Callback(hObject, eventdata, handles)%interrupt movie pair if active
1517end
1518
1519%% read the current input file name(s) and field indices
1520InputFile=read_GUI(handles.InputFile);
1521InputFile.RootFile=regexprep(InputFile.RootFile,'^[\\/]|[\\/]$','');%suppress possible / or \ separator at the beginning or the end of the string
1522InputFile.SubDir=regexprep(InputFile.SubDir,'^[\\/]|[\\/]$','');%suppress possible / or \ separator at the beginning or the end of the string
1523FileExt=InputFile.FileExt;
1524NomType=get(handles.NomType,'String');
1525i1=str2num(get(handles.i1,'String'));%read the field indices (for movie, it is not given by the file name)
1526i2=[];%default
1527if strcmp(get(handles.i2,'Visible'),'on')
1528    i2=str2num(get(handles.i2,'String'));
1529end
1530j1=[];
1531if strcmp(get(handles.j1,'Visible'),'on')
1532    j1=stra2num(get(handles.j1,'String'));
1533end
1534j2=j1;
1535if strcmp(get(handles.j2,'Visible'),'on')
1536    j2=stra2num(get(handles.j2,'String'));
1537end
1538sub_value= get(handles.SubField,'Value');
1539if sub_value % a second input file has been entered
1540     [InputFile.RootPath_1,InputFile.SubDir_1,InputFile.RootFile_1,InputFile.FileIndex_1,InputFile.FileExt_1,InputFile.NomType_1]=read_file_boxes_1(handles);   
1541    [tild,tild,tild,i1_1,i2_1,j1_1,j2_1]=fileparts_uvmat(InputFile.FileIndex_1);% the indices for the second series taken from FileIndex_1
1542else
1543    filename_1=[];
1544end   
1545
1546%% increment (or decrement) the field indices and update the input filename(s)
1547if isempty(increment)
1548    set(handles.CheckFixPair,'Value',0)
1549end
1550CheckFixPair=get(handles.CheckFixPair,'Value')||(isempty(i2)&&isempty(j2));
1551
1552% the pair i1-i2 or j1-j2 is imposed (check box CheckFixPair selected)
1553        i1_1=i1;
1554        i2_1=i2;
1555        j1_1=j1;
1556        j2_1=j2;
1557if CheckFixPair
1558    if get(handles.scan_i,'Value')==1% case of scanning along index i
1559        i1=i1+increment;
1560        i2=i2+increment;
1561        if sub_value
1562            i1_1=i1_1+increment;
1563            i2_1=i2_1+increment;
1564        end
1565       
1566    else % case of scanning along index j (burst numbers)
1567        j1=j1+increment;
1568        j2=j2+increment;
1569        if sub_value
1570            j1_1=j1_1+increment;
1571            j2_1=j2_1+increment;
1572        end
1573    end
1574   
1575% the pair i1-i2 or j1-j2 is free (check box CheckFixPair not selected): the list of existing indices recorded in UvData is used
1576else
1577    UvData=get(handles.uvmat,'UserData');
1578    ref_i=i1;
1579    if ~isempty(i2)
1580        ref_i=floor((i1+i2)/2);% current reference index i
1581    end
1582    ref_j=1;
1583    if ~isempty(j1)
1584        ref_j=j1;
1585        if ~isempty(j2)
1586            ref_j=floor((j1+j2)/2);% current reference index j
1587        end
1588    end
1589    if ~isempty(increment)
1590        if get(handles.scan_i,'Value')==1% case of scanning along index i
1591            ref_i=ref_i+increment;% increment the current reference index i
1592        else % case of scanning along index j (burst numbers)
1593            ref_j=ref_j+increment;% increment the current reference index j if scan_j option is used
1594        end
1595    else % free increment
1596        runaction=get(gcbo,'tag');
1597        if strcmp(runaction,'runplus')||strcmp(runaction,'Movie')% if runplus or movie is activated
1598            step=1;
1599        else
1600            step=-1;
1601        end
1602        if get(handles.scan_i,'Value')==1% case of scanning along index i
1603            ref_i=ref_i+step;
1604            while ref_i>=0  && size(UvData.i1_series{1},3)>=ref_i+1 && UvData.i1_series{1}(1,ref_j+1,ref_i+1)==0
1605                ref_i=ref_i+step;
1606            end
1607        else % case of scanning along index j (burst numbers)
1608            ref_j=ref_j+step;
1609            while ref_j>=0  && size(UvData.i1_series{1},2)>=ref_j+1 && UvData.i1_series{1}(1,ref_j+1,ref_i+1)==0
1610                ref_j=ref_j+step;
1611            end
1612        end
1613    end
1614    if ref_i<0
1615        errormsg='minimum i index reached';
1616    elseif ref_j<0
1617        errormsg='minimum j index reached';
1618    elseif ref_i+1>size(UvData.i1_series{1},3)
1619        errormsg='maximum i index reached (reload the input file to update the index bound)';
1620    elseif ref_j+1>size(UvData.i1_series{1},2)
1621        errormsg='maximum j index reached (reload the input file to update the index bound)';
1622    end
1623    if ~isempty(errormsg),return,end
1624    siz=size(UvData.i1_series{1});
1625    ref_indices=ref_i*siz(1)*siz(2)+ref_j*siz(1)+1:ref_i*siz(1)*siz(2)+(ref_j+1)*siz(1);
1626    i1_subseries=UvData.i1_series{1}(ref_indices);
1627    ref_indices=ref_indices(i1_subseries>0);
1628    if isempty(ref_indices)% case of pairs (free index i)
1629        ref_indices=ref_i*siz(1)*siz(2)+1:(ref_i+1)*siz(1)*siz(2);
1630        i1_subseries=UvData.i1_series{1}(ref_indices);
1631        ref_indices=ref_indices(i1_subseries>0);
1632    end
1633    if isempty(ref_indices),errormsg='no next frame: set num_IndexIncrement =''*'' to reach the next existing file';return
1634    end
1635    i1=UvData.i1_series{1}(ref_indices(end));
1636    if ~isempty(UvData.i2_series{1})
1637        i2=UvData.i2_series{1}(ref_indices(end));
1638    end
1639    if ~isempty(UvData.j1_series{1})
1640        j1=UvData.j1_series{1}(ref_indices(end));
1641    end
1642    if ~isempty(UvData.j2_series{1})
1643        j2=UvData.j2_series{1}(ref_indices(end));
1644    end
1645   
1646    % case of a second file series
1647    if sub_value
1648        ref_i_1=i1_1;
1649        if ~isempty(i2_1)
1650            ref_i_1=floor((i1_1+i2_1)/2);% current reference index i
1651        end
1652        ref_j_1=1;
1653        if ~isempty(j1_1)
1654            ref_j_1=j1_1;
1655            if ~isempty(j2_1)
1656                ref_j_1=floor((j1_1+j2_1)/2);% current reference index j
1657            end
1658        end
1659        if ~isempty(increment)
1660            if get(handles.scan_i,'Value')==1% case of scanning along index i
1661                ref_i_1=ref_i_1+increment;% increment the current reference index i
1662            else % case of scanning along index j (burst numbers)
1663                ref_j_1=ref_j_1+increment;% increment the current reference index j if scan_j option is used
1664            end
1665        else % free increment, synchronise the ref indices with the first series
1666            ref_i_1=ref_i;
1667            ref_j_1=ref_j;
1668        end
1669        if numel(UvData.i1_series)==1
1670            UvData.i1_series{2}=UvData.i1_series{1};
1671            UvData.j1_series{2}=UvData.j1_series{1};
1672            UvData.i2_series{2}=UvData.i2_series{1};
1673            UvData.j2_series{2}=UvData.j2_series{1};
1674        end
1675        if ref_i_1<0
1676            errormsg='minimum i index reached';
1677        elseif ref_j_1<0
1678            errormsg='minimum j index reached';
1679        elseif ref_i_1+1>size(UvData.i1_series{2},3)
1680            errormsg='maximum i index reached for the second series (reload the input file to update the index bound)';
1681        elseif ref_j_1+1>size(UvData.i1_series{2},2)
1682            errormsg='maximum j index reached for the second series(reload the input file to update the index bound)';
1683        end
1684        if ~isempty(errormsg),return,end
1685        siz=size(UvData.i1_series{2});
1686        ref_indices=ref_i_1*siz(1)*siz(2)+ref_j_1*siz(1)+1:ref_i_1*siz(1)*siz(2)+(ref_j_1+1)*siz(1);
1687        i1_subseries=UvData.i1_series{2}(ref_indices);
1688        ref_indices=ref_indices(i1_subseries>0);
1689        if isempty(ref_indices)% case of pairs (free index i)
1690            ref_indices=ref_i_1*siz(1)*siz(2)+1:(ref_i_1+1)*siz(1)*siz(2);
1691            i1_subseries=UvData.i1_series{2}(ref_indices);
1692            ref_indices=ref_indices(i1_subseries>0);
1693        end
1694        i1_1=UvData.i1_series{2}(ref_indices(end));
1695        if ~isempty(UvData.i2_series{2})
1696            i2_1=UvData.i2_series{2}(ref_indices(end));
1697        end
1698        if ~isempty(UvData.j1_series{2})
1699            j1_1=UvData.j1_series{2}(ref_indices(end));
1700        end
1701        if ~isempty(UvData.j2_series{2})
1702            j2_1=UvData.j2_series{1}(ref_indices(end));
1703        end   
1704    else% the second series (if needed) is the same file as the first
1705        i1_1=i1;
1706        i2_1=i2;
1707        j1_1=j1;
1708        j2_1=j2;
1709    end
1710end
1711filename=fullfile_uvmat(InputFile.RootPath,InputFile.SubDir,InputFile.RootFile,FileExt,NomType,i1,i2,j1,j2);
1712if sub_value
1713    filename_1=fullfile_uvmat(InputFile.RootPath_1,InputFile.SubDir_1,InputFile.RootFile_1,InputFile.FileExt_1,InputFile.NomType_1,i1_1,i2_1,j1_1,j2_1);
1714end
1715
1716%% refresh plots
1717errormsg=refresh_field(handles,filename,filename_1,i1,i2,j1,j2,i1_1,i2_1,j1_1,j2_1);
1718
1719%% update the index counters if the index move is successfull
1720if isempty(errormsg)
1721    set(handles.i1,'String',num2stra(i1,NomType,1));
1722    if isequal(i2,i1)
1723        set(handles.i2,'String','');
1724    else
1725        set(handles.i2,'String',num2stra(i2,NomType,1));
1726    end
1727    set(handles.j1,'String',num2stra(j1,NomType,2));
1728    if isequal(j2,j1)
1729        set(handles.j2,'String','');
1730    else
1731        set(handles.j2,'String',num2stra(j2,NomType,2));
1732    end
1733    indices=fullfile_uvmat('','','','',NomType,i1,i2,j1,j2);
1734    set(handles.FileIndex,'String',indices);
1735    if ~isempty(filename_1)
1736        indices_1=fullfile_uvmat('','','','',InputFile.NomType_1,i1_1,i2_1,j1_1,j2_1);
1737        set(handles.FileIndex_1,'String',indices_1);
1738    end
1739    if isequal(movie_status,1)
1740        set(handles.movie_pair,'Value',1)
1741        movie_pair_Callback(hObject, eventdata, handles); %reactivate moviepair if it was activated
1742    end
1743end
1744
1745%------------------------------------------------------------------------
1746% --- Executes on button press in movie_pair: create an alternating movie with two view
1747function movie_pair_Callback(hObject, eventdata, handles)
1748%------------------------------------------------------------------------
1749%% stop movie action if the movie_pair button is off
1750if ~get(handles.movie_pair,'value')
1751    set(handles.movie_pair,'BusyAction','Cancel')%stop movie pair if button is 'off'
1752    set(handles.i2,'String','')
1753    set(handles.j2,'String','')
1754    return
1755else
1756    set(handles.movie_pair,'BusyAction','queue')
1757end
1758
1759%% initialisation
1760set(handles.movie_pair,'BackgroundColor',[1 1 0])%paint the command button in yellow
1761drawnow
1762list_fields=get(handles.FieldName,'String');% list menu fields
1763index_fields=get(handles.FieldName,'Value');% selected string index
1764FieldName=list_fields{index_fields}; % selected field
1765UvData=get(handles.uvmat,'UserData');
1766if isequal(FieldName,'image')
1767    index=1;
1768    [RootPath,SubDir,RootFile,FileIndices,Ext]=read_file_boxes(handles);
1769    NomType=get(handles.NomType,'String');
1770else
1771    list_fields=get(handles.FieldName_1,'String');% list menu fields
1772    index_fields=get(handles.FieldName_1,'Value');% selected string index
1773    FieldName=list_fields{index_fields}; % selected field
1774    if isequal(FieldName,'image')
1775        index=2;
1776        [RootPath,tild,RootFile,FileIndex_1,Ext,NomType]=read_file_boxes_1(handles);
1777    else
1778        msgbox_uvmat('ERROR','an image or movie must be first introduced as input')
1779        set(handles.movie_pair,'BackgroundColor',[1 0 0])%paint the command button in red
1780        set(handles.movie_pair,'Value',0)
1781        return
1782    end
1783end
1784num_i1=str2num(get(handles.i1,'String'));
1785num_j1=stra2num(get(handles.j1,'String'));
1786num_i2=str2num(get(handles.i2,'String'));
1787num_j2=stra2num(get(handles.j2,'String'));
1788if isempty(num_j2)
1789    if isempty(num_i2)   
1790        msgbox_uvmat('ERROR', 'a second image index i2 or j2 is needed to show the pair as a movie')
1791        set(handles.movie_pair,'BackgroundColor',[1 0 0])%paint the command button in red
1792         set(handles.movie_pair,'Value',0)
1793        return
1794    else
1795        num_j2=num_j1;%repeat the index i1 by default
1796    end
1797end
1798if isempty(num_i2)
1799    num_i2=num_i1;%repeat the index i1 by default
1800end
1801imaname_1=fullfile_uvmat(RootPath,SubDir,RootFile,Ext,NomType,num_i2,[],num_j2);
1802if strcmp(NomType,'*')
1803    num_frame=num_i2;
1804else
1805    num_frame=num_j2;
1806end
1807if ~exist(imaname_1,'file')
1808      msgbox_uvmat('ERROR',['second input open (-)  ' imaname_1 ' not found']);
1809      set(handles.movie_pair,'BackgroundColor',[1 0 0])%paint the command button in red
1810       set(handles.movie_pair,'Value',0)
1811      return
1812end
1813
1814%% get the first image
1815%Field.AName='image';
1816if index==1
1817    Field_a=UvData.Field;% movie on the second field
1818else
1819    Field_a=UvData.Field_1;% movie on the first field
1820end
1821
1822%% read the second image
1823MovieObject=[];
1824if numel(UvData.MovieObject)>=index
1825    MovieObject=UvData.MovieObject{index};
1826end
1827[Field_b,ParamOut,errormsg] = read_field(imaname_1,UvData.FileType{index},MovieObject,num_frame)
1828% Field_b.AX=Field_a.AX;
1829% Field_b.AY=Field_a.AY;
1830% % z index
1831% nbslice=str2double(get(handles.num_NbSlice,'String'));
1832% if ~isempty(nbslice)
1833%     Field_b.ZIndex=mod(num_i2-1,nbslice)+1;
1834% end
1835% Field_b.CoordUnit='pixel';
1836%
1837% %% determine the input file type
1838% if (test_1 && isfield(UvData,'MovieObject')&& numel(UvData.MovieObject>=2))||(~test_1 && ~isempty(UvData.MovieObject{1}))
1839%     FileType='movie';
1840% elseif isequal(lower(Ext),'.avi')
1841%     FileType='avi';
1842% elseif isequal(lower(Ext),'.vol')
1843%     FileType='vol';
1844% else
1845%    form=imformats(Ext(2:end));
1846%    if ~isempty(form)% if the extension corresponds to an image format recognized by Matlab
1847%        if isequal(NomType,'*');
1848%            FileType='multimage';
1849%        else
1850%            FileType='image';
1851%        end
1852%    end
1853% end
1854% switch FileType
1855%         case 'movie'
1856%             if test_1
1857%                 Field_b.A=read(UvData.MovieObject{2},num_i2);
1858%             else
1859%                 Field_b.A=read(UvData.MovieObject{1},num_i2);
1860%             end
1861%         case 'avi'
1862%             mov=aviread(imaname_1,num_i2);
1863%             Field_b.A=frame2im(mov(1));
1864%         case 'vol'
1865%             Field_b.A=imread(imaname_1);
1866%         case 'multimage'
1867%             Field_b.A=imread(imaname_1,num_i2);
1868%         case 'image'
1869%             Field_b.A=imread(imaname_1);
1870% end
1871% if get(handles.slices,'Value')
1872%     Field.ZIndex=str2double(get(handles.z_index,'String'));
1873% end
1874
1875%px to phys or other transform on field
1876% menu_transform=get(handles.transform_fct,'String');
1877% choice_value=get(handles.transform_fct,'Value');
1878% transform_name=menu_transform{choice_value};%name of the transform fct  given by the menu 'transform_fct'
1879% transform_list=get(handles.transform_fct,'UserData');
1880transform=get(handles.path_transform,'UserData');
1881if  ~isempty(transform)
1882    if isfield(UvData,'XmlData') && numel(UvData.XmlData)>=index %use geometry calib recorded from the ImaDoc xml file as first priority
1883        if index==2
1884        Field_a=transform(Field_a,UvData.XmlData{index});%the first field has been stored without transform
1885        end
1886        Field_b=transform(Field_b,UvData.XmlData{index});
1887    end
1888end
1889
1890 % make movie until movie speed is set to 0 or STOP is activated
1891hima=findobj(handles.PlotAxes,'Tag','ima');% %handles.PlotAxes =main plotting window (A GENERALISER)
1892set(handles.STOP,'Visible','on')
1893set(handles.speed,'Visible','on')
1894set(handles.speed_txt,'Visible','on')
1895while get(handles.speed,'Value')~=0 && isequal(get(handles.movie_pair,'BusyAction'),'queue')%isequal(get(handles.run0,'BusyAction'),'queue'); % enable STOP command
1896    % read and plot the series of images in non erase mode
1897    set(hima,'CData',Field_b.A);
1898    pause(1.02-get(handles.speed,'Value'));% wait for next image
1899    set(hima,'CData',Field_a.A);
1900    pause(1.02-get(handles.speed,'Value'));% wait for next image
1901end
1902set(handles.movie_pair,'BackgroundColor',[1 0 0])%paint the command button in red
1903 set(handles.movie_pair,'Value',0)
1904
1905%------------------------------------------------------------------------
1906% --- Executes on button press in run0.
1907function run0_Callback(hObject, eventdata, handles)
1908%------------------------------------------------------------------------
1909set(handles.run0,'BackgroundColor',[1 1 0])%paint the command button in yellow
1910drawnow
1911[RootPath,SubDir,RootFile,FileIndex,FileExt]=read_file_boxes(handles);
1912filename=[fullfile(RootPath,SubDir,RootFile) FileIndex FileExt];
1913filename_1='';%default
1914FileIndex_1='';
1915if get(handles.SubField,'Value')
1916    [RootPath_1,SubDir_1,RootFile_1,FileIndex_1,FileExt_1]=read_file_boxes_1(handles);
1917    filename_1=[fullfile(RootPath_1,SubDir_1,RootFile_1) FileIndex_1 FileExt_1];
1918end
1919num_i1=stra2num(get(handles.i1,'String'));
1920num_i2=stra2num(get(handles.i2,'String'));
1921num_j1=stra2num(get(handles.j1,'String'));
1922num_j2=stra2num(get(handles.j2,'String'));
1923[tild,tild,tild,i1_1,i2_1,j1_1,j2_1]=fileparts_uvmat(FileIndex_1);
1924
1925errormsg=refresh_field(handles,filename,filename_1,num_i1,num_i2,num_j1,num_j2,i1_1,i2_1,j1_1,j2_1);
1926
1927if ~isempty(errormsg)
1928      msgbox_uvmat('ERROR',errormsg);
1929else
1930    set(handles.i1,'BackgroundColor',[1 1 1])
1931    set(handles.i2,'BackgroundColor',[1 1 1])
1932    set(handles.j1,'BackgroundColor',[1 1 1])
1933    set(handles.j2,'BackgroundColor',[1 1 1])
1934    set(handles.FileIndex,'BackgroundColor',[1 1 1])
1935    set(handles.FileIndex_1,'BackgroundColor',[1 1 1])
1936end   
1937set(handles.run0,'BackgroundColor',[1 0 0])
1938
1939
1940%------------------------------------------------------------------------
1941% --- read the input files and refresh all the plots, including projection.
1942% OUTPUT:
1943%  errormsg: error message char string  =[] by default
1944% INPUT:
1945% filename: first input file (=[] in the absence of input file)
1946% filename_1: second input file (=[] in the asbsenc of secodn input file)
1947% num_i1,num_i2,num_j1,num_j2; frame indices
1948% Field: structure describing an optional input field (then replace the input file)
1949
1950function errormsg=refresh_field(handles,FileName,FileName_1,num_i1,num_i2,num_j1,num_j2,i1_1,i2_1,j1_1,j2_1)
1951%------------------------------------------------------------------------
1952
1953%% initialisation
1954abstime=[];
1955abstime_1=[];
1956dt=[];
1957if ~exist('Field','var')
1958    Field={};
1959end
1960UvData=get(handles.uvmat,'UserData');
1961if ishandle(handles.UVMAT_title) %remove title panel on uvmat
1962    delete(handles.UVMAT_title)
1963end
1964
1965%% determine the main input file information for action
1966if ~exist(FileName,'file')
1967    errormsg=['input file ' FileName ' does not exist'];
1968    return
1969end
1970NomType=get(handles.NomType,'String');
1971NomType_1='';
1972if strcmp(get(handles.NomType_1,'Visible'),'on')
1973    NomType_1=get(handles.NomType_1,'String');
1974end
1975%update the z position index
1976nbslice_str=get(handles.num_NbSlice,'String');
1977if isequal(nbslice_str,'volume')%NOT USED
1978    z_index=num_j1;
1979    set(handles.z_index,'String',num2str(z_index))
1980else
1981    nbslice=str2num(nbslice_str);
1982    z_index=mod(num_i1-1,nbslice)+1;
1983    set(handles.z_index,'String',num2str(z_index))
1984end
1985% refresh menu for save_mask if relevant
1986masknumber=get(handles.masklevel,'String');
1987if length(masknumber)>=z_index
1988    set(handles.masklevel,'Value',z_index)
1989end
1990
1991%% test for need of tps
1992check_proj_tps=0;
1993if  (strcmp(UvData.FileType{1},'civdata')||strcmp(UvData.FileType{1},'civx'))
1994    for iobj=1:numel(UvData.Object)
1995        if isfield(UvData.Object{iobj},'ProjMode')&& strcmp(UvData.Object{iobj}.ProjMode,'filter')
1996            check_proj_tps=1;
1997            break
1998        end
1999    end
2000end
2001
2002%% read the first input field
2003ParamIn.ColorVar='';%default variable name for vector color
2004frame_index=1;%default
2005FieldName='';%default
2006VelType='';%default
2007switch UvData.FileType{1}
2008    case {'civx','civdata','netcdf'};
2009        list_fields=get(handles.FieldName,'String');% list menu fields
2010        FieldName= list_fields{get(handles.FieldName,'Value')}; % selected field
2011        if ~strcmp(FieldName,'get_field...')
2012            if get(handles.FixVelType,'Value')
2013                VelTypeList=get(handles.VelType,'String');
2014                VelType=VelTypeList{get(handles.VelType,'Value')};
2015            end
2016        end
2017        if ~isempty(regexp(FieldName,'^vec('))
2018            list_code=get(handles.ColorCode,'String');% list menu fields
2019            index_code=get(handles.ColorCode,'Value');% selected string index
2020            if  ~strcmp(list_code{index_code},'black') &&  ~strcmp(list_code{index_code},'white')
2021                list_code=get(handles.ColorScalar,'String');% list menu fields
2022                index_code=get(handles.ColorScalar,'Value');% selected string index
2023                ParamIn.ColorVar= list_code{index_code}; % selected field
2024            end
2025        end
2026    case {'video','mmreader'}
2027        ParamIn=UvData.MovieObject{1};     
2028        if ~strcmp(NomType,'*')
2029            frame_index=num_j1;%frame index for movies or multimage
2030        else
2031            frame_index=num_i1;
2032        end
2033    case 'multimage'
2034        if ~strcmp(NomType,'*')
2035            frame_index=num_j1;%frame index for movies or multimage
2036        else
2037            frame_index=num_i1;
2038        end
2039    case 'vol' %TODO: update
2040        if isfield(UvData.XmlData,'Npy') && isfield(UvData.XmlData,'Npx')
2041            ParamIn.Npy=UvData.XmlData.Npy;
2042            ParamIn.Npx=UvData.XmlData.Npx;
2043        else           
2044            errormsg='Npx and Npy need to be defined in the xml file for volume images .vol';
2045            return
2046        end
2047end
2048if isstruct (ParamIn)
2049    ParamIn.FieldName=FieldName;
2050    ParamIn.VelType=VelType;
2051    XNameMenu=get(handles.Coord_x,'String');
2052    ParamIn.Coord_x=XNameMenu(get(handles.Coord_x,'Value'));
2053    YNameMenu=get(handles.Coord_y,'String');
2054    ParamIn.Coord_y=YNameMenu(get(handles.Coord_y,'Value'));
2055end
2056check_tps = 0;         
2057if strcmp(UvData.FileType{1},'civdata')&&~strcmp(ParamIn.FieldName,'velocity')&&~strcmp(ParamIn.FieldName,'get_field...')
2058       check_tps=1;%tps needed to get the requested field
2059end
2060[Field{1},ParamOut,errormsg] = read_field(FileName,UvData.FileType{1},ParamIn,frame_index);
2061if ~isempty(errormsg)
2062    errormsg=['uvmat / refresh_field / read_field( ' FileName ') / ' errormsg];
2063    return
2064end 
2065if isfield(ParamOut,'Npx')&& isfield(ParamOut,'Npy')
2066    set(handles.num_Npx,'String',num2str(ParamOut.Npx));% display image size on the interface
2067    set(handles.num_Npy,'String',num2str(ParamOut.Npy));
2068end
2069if isfield(ParamOut,'TimeIndex')% case of time obtained from get_field
2070    set(handles.i1,'String',num2str(ParamOut.TimeIndex))
2071end
2072if isfield(ParamOut,'TimeValue')
2073    Field{1}.Time=ParamOut.TimeValue;% case of time obtained from get_field
2074end
2075Field{1}.ZIndex=z_index; %used for multiplane 3D calibration
2076% end
2077
2078%% choose and read a second field FileName_1 if defined
2079VelType_1=[];%default
2080FieldName_1=[];
2081ParamIn_1=[];
2082ParamOut_1=[];
2083frame_index_1=1;
2084if ~isempty(FileName_1)
2085    if ~exist(FileName_1,'file')
2086        errormsg=['second file ' FileName_1 ' does not exist'];
2087        return
2088    end
2089    Name=FileName_1;
2090    switch UvData.FileType{2}
2091        case {'civx','civdata','netcdf'};
2092            list_fields=get(handles.FieldName_1,'String');% list menu fields
2093            if ischar(list_fields),list_fields={list_fields};end
2094            FieldName_1= list_fields{get(handles.FieldName_1,'Value')}; % selected field
2095            if ~strcmp(FieldName,'get_field...')
2096                if get(handles.FixVelType,'Value')
2097                    VelTypeList=get(handles.VelType_1,'String');
2098                    VelType_1=VelTypeList{get(handles.VelType_1,'Value')};% read the velocity type.
2099                end
2100            end
2101            if strcmp(FieldName_1,'velocity')&& strcmp(get(handles.ColorCode,'Visible'),'on')
2102                list_code=get(handles.ColorCode,'String');% list menu fields
2103                index_code=get(handles.ColorCode,'Value');% selected string index
2104                if  ~strcmp(list_code{index_code},'black') &&  ~strcmp(list_code{index_code},'white')
2105                    list_code=get(handles.ColorScalar,'String');% list menu fields
2106                    index_code=get(handles.ColorScalar,'Value');% selected string index
2107                    ParamIn_1.ColorVar= list_code{index_code}; % selected field for vector color display                 
2108                end
2109            end
2110        case {'video','mmreader'}
2111            ParamIn_1=UvData.MovieObject{2};
2112                        if ~strcmp(NomType_1,'*')
2113                frame_index_1=j1_1;%frame index for movies or multimage
2114            else
2115                frame_index_1=i1_1;
2116            end 
2117         case 'multimage'
2118            if ~strcmp(NomType_1,'*')
2119                frame_index_1=j1_1;%frame index for movies or multimage
2120            else
2121                frame_index_1=i1_1;
2122            end   
2123        case 'vol' %TODO: update
2124            if isfield(UvData.XmlData,'Npy') && isfield(UvData.XmlData,'Npx')
2125                ParamIn_1.Npy=UvData.XmlData.Npy;
2126                ParamIn_1.Npx=UvData.XmlData.Npx;
2127            else
2128                errormsg='Npx and Npy need to be defined in the xml file for volume images .vol';
2129                return
2130            end
2131    end
2132    if isequal(get(handles.NomType_1,'Visible'),'on')
2133    NomType_1=get(handles.NomType_1,'String');
2134    else
2135        NomType_1=get(handles.NomType,'String');
2136    end
2137    test_keepdata_1=0;% test for keeping the previous stored data if the input files are unchanged
2138    if ~isequal(NomType_1,'*')&& isfield(UvData,'FileName_1')
2139           test_keepdata_1= strcmp(FileName_1,UvData.FileName_1) ;%&& strcmp(FieldName_1,UvData.FieldName_1);
2140    end
2141    if test_keepdata_1
2142        Field{2}=UvData.Field_1;% keep the stored field
2143        ParamOut_1=UvData.ParamOut_1;
2144    else
2145        if isempty(ParamIn_1) || isstruct(ParamIn_1)
2146        ParamIn_1.FieldName=FieldName_1;
2147        ParamIn_1.VelType=VelType_1;
2148        ParamIn_1.GUIName='get_field_1';
2149        end 
2150        [Field{2},ParamOut_1,errormsg] = read_field(Name,UvData.FileType{2},ParamIn_1,frame_index_1);
2151        if ~isempty(errormsg)
2152            errormsg=['error in reading ' FieldName_1 ' in ' FileName_1 ': ' errormsg];
2153            return
2154        end
2155        if isstruct(ParamOut_1)&&~strcmp(ParamOut_1.FieldName,'get_field...')&& (strcmp(UvData.FileType{2},'civdata')||strcmp(UvData.FileType{2},'civx'))...
2156                &&~strcmp(ParamOut_1.FieldName,'velocity') && ~strcmp(ParamOut_1.FieldName,'get_field...')
2157            if ~check_proj_tps
2158             %   Field{2}=calc_field([{ParamOut_1.FieldName} {ParamOut_1.ColorVar}],Field{2});
2159            end
2160        end
2161    end
2162    Field{2}.ZIndex=z_index;%used for multi-plane 3D calibration
2163end
2164
2165%% update uvmat interface
2166if isfield(ParamOut,'Npx')
2167    set(handles.num_Npx,'String',num2str(ParamOut.Npx));% display image size on the interface
2168    set(handles.num_Npy,'String',num2str(ParamOut.Npy));
2169elseif isfield(ParamOut_1,'Npx')
2170    set(handles.num_Npx,'String',num2str(ParamOut_1.Npx));% display image size on the interface
2171    set(handles.num_Npy,'String',num2str(ParamOut_1.Npy));
2172end
2173
2174%% update the display menu for the first velocity type (first menuline)
2175test_veltype=0;
2176% if ~isequal(FileType,'netcdf')|| isequal(FieldName,'get_field...')
2177if (strcmp(UvData.FileType{1},'civx')||strcmp(UvData.FileType{1},'civdata'))&& ~strcmp(FieldName,'get_field...')
2178    test_veltype=1;
2179    set(handles.VelType,'Visible','on')
2180    set(handles.VelType_1,'Visible','on')
2181    set(handles.FixVelType,'Visible','on')
2182    menu=set_veltype_display(ParamOut.CivStage,UvData.FileType{1});
2183    index_menu=strcmp(ParamOut.VelType,menu);%look for VelType in  the menu
2184    index_val=find(index_menu,1);
2185    if isempty(index_val)
2186        index_val=1;
2187    end
2188    set(handles.VelType,'Value',index_val)
2189    if ~get(handles.SubField,'value')
2190        set(handles.VelType,'String',menu)
2191        set(handles.VelType_1,'Value',1)
2192        set(handles.VelType_1,'String',[{''};menu])
2193    end
2194else
2195    set(handles.VelType,'Visible','off')
2196end
2197% display the FieldName menu from the input file and pick the selected one:
2198% if isstruct(ParamOut)
2199%     field_index=strcmp(ParamOut.FieldName,ParamOut.FieldList);
2200%     set(handles.FieldName,'String',ParamOut.FieldList); %update the field menu
2201%     set(handles.FieldName,'Value',find(field_index,1))
2202% end
2203
2204%% update the display menu for the second velocity type (second menuline)
2205test_veltype_1=0;
2206if isempty(FileName_1)
2207%     set(handles.FieldName_1,'Value',1); %update the field menu
2208%     if isstruct(ParamOut)
2209%     set(handles.FieldName_1,'String',[{''};ParamOut.FieldList]); %update the field menu
2210%     end
2211elseif ~test_keepdata_1
2212    if (~strcmp(UvData.FileType{2},'netcdf')&&~strcmp(UvData.FileType{2},'civdata')&&~strcmp(UvData.FileType{2},'civx'))|| isequal(FieldName_1,'get_field...')
2213        set(handles.VelType_1,'Visible','off')
2214    else
2215        test_veltype_1=1;
2216        set(handles.VelType_1,'Visible','on')
2217        menu=set_veltype_display(ParamOut_1.CivStage,UvData.FileType{2});
2218        index_menu=strcmp(ParamOut_1.VelType,menu);
2219        set(handles.VelType_1,'Value',1+find(index_menu,1))
2220        set(handles.VelType_1,'String',[{''};menu])
2221    end
2222    % update the second field menu: the same quantity
2223    if isstruct(ParamOut_1)
2224    set(handles.FieldName_1,'String',[{''};ParamOut_1.FieldList]); %update the field menu
2225    % display the FieldName menu from the input file and pick the selected one:
2226    field_index=strcmp(ParamOut_1.FieldName,ParamOut_1.FieldList);
2227    set(handles.FieldName_1,'Value',find(field_index,1)+1) 
2228    end
2229   
2230end
2231if test_veltype||test_veltype_1
2232     set(handles.FixVelType,'Visible','on')
2233else
2234     set(handles.FixVelType,'Visible','off')
2235end
2236
2237% field_index=strcmp(ParamOut_1.FieldName,ParamOut_1.FieldList);
2238% set(handles.FieldName,'String',ParamOut.FieldList); %update the field menu
2239% set(handles.FieldName,'Value',find(field_index,1))
2240   
2241%% introduce w as background image by default for a new series (only for nbdim=2)
2242if ~isfield(UvData,'NewSeries')
2243    UvData.NewSeries=1;
2244end
2245%put W as background image by default if NbDim=2:
2246if  UvData.NewSeries && isequal(get(handles.SubField,'Value'),0) && isfield(Field{1},'W') && ~isempty(Field{1}.W) && ~isequal(Field{1}.NbDim,3);
2247        set(handles.SubField,'Value',1);
2248        set(handles.RootPath_1,'String','"')
2249        set(handles.RootFile_1,'String','"')
2250        set(handles.SubDir_1,'String','"');
2251         indices=fullfile_uvmat('','','','',NomType,num_i1,num_i2,num_j1,num_j2);
2252        set(handles.FileIndex_1,'String',indices)
2253        set(handles.FileExt_1,'String','"');
2254        set(handles.FieldName_1,'Visible','on');
2255        set(handles.FieldName_1,'Visible','on');
2256        set(handles.RootPath_1,'Visible','on')
2257        set(handles.RootFile_1,'Visible','on')
2258        set(handles.SubDir_1,'Visible','on');
2259        set(handles.FileIndex_1,'Visible','on');
2260        set(handles.FileExt_1,'Visible','on');
2261        set(handles.FieldName_1,'Visible','on');
2262        Field{1}.AName='w';
2263end           
2264
2265%% display time
2266testimedoc=0;
2267TimeUnit='';
2268if isfield(Field{1},'Time')
2269    abstime=Field{1}.Time;%time read from the netcdf input file
2270end
2271if numel(Field)==2 && isfield(Field{2},'Time')
2272    abstime_1=Field{2}.Time;%time read from the netcdf input file
2273end
2274if isfield(Field{1},'Dt')
2275    dt=Field{1}.Dt;%dt read from the netcdf input file
2276    if isfield(Field{1},'TimeUnit')
2277       TimeUnit=Field{1}.TimeUnit;
2278    end
2279elseif numel(Field)==2 && isfield(Field{2},'Dt')%dt obtained from the second field if not defined in the first
2280    dt=Field{2}.Dt;%dt read from the netcdf input file
2281    if isfield(Field{2},'TimeUnit')
2282       TimeUnit=Field{2}.TimeUnit;
2283    end
2284end
2285% time from xml file overset previous result
2286if isfield(UvData,'XmlData') && isfield(UvData.XmlData{1},'Time')
2287    if isempty(num_i2)||isnan(num_i2)
2288        num_i2=num_i1;
2289    end
2290    if isempty(num_j1)||isnan(num_j1)
2291        num_j1=1;
2292    end
2293    if isempty(num_j2)||isnan(num_j2)
2294        num_j2=num_j1;
2295    end
2296    siz=size(UvData.XmlData{1}.Time);
2297    if ~isempty(num_i1)&& ~isempty(num_i2)&&siz(1)>=max(num_i1,num_i2) && siz(2)>=max(num_j1,num_j2)
2298        abstime=(UvData.XmlData{1}.Time(num_i1,num_j1)+UvData.XmlData{1}.Time(num_i2,num_j2))/2;%overset the time read from files
2299        dt=(UvData.XmlData{1}.Time(num_i2,num_j2)-UvData.XmlData{1}.Time(num_i1,num_j1));
2300        Field{1}.Dt=dt;
2301        if isfield(UvData.XmlData{1},'TimeUnit')
2302            TimeUnit=UvData.XmlData{1}.TimeUnit;
2303        end
2304    end
2305    if numel(UvData.XmlData)==2
2306        if isempty(i2_1)
2307            i2_1=num_i1;
2308        end
2309        if isempty(j1_1)
2310            j1_1=1;
2311        end
2312        if isempty(j2_1)
2313            j2_1=j1_1;
2314        end
2315        siz=size(UvData.XmlData{2}.Time);
2316        if ~isempty(i1_1) && siz(1)>=max(i1_1,i2_1) && siz(2)>=max(j1_1,j2_1)
2317            abstime_1=(UvData.XmlData{2}.Time(i1_1,j1_1)+UvData.XmlData{2}.Time(i2_1,j2_1))/2;%overset the time read from files
2318            Field{2}.Dt=(UvData.XmlData{2}.Time(i2_1,j2_1)-UvData.XmlData{2}.Time(i1_1,j1_1));
2319        end
2320    end
2321end
2322if ~isequal(numel(abstime),1)
2323    abstime=[];
2324end
2325if ~isequal(numel(abstime_1),1)
2326      abstime_1=[];
2327end 
2328set(handles.abs_time,'String',num2str(abstime,5))
2329set(handles.abs_time_1,'String',num2str(abstime_1,5))
2330if isempty(dt)||isequal(dt,0)
2331    set(handles.Dt_txt,'String','')
2332else
2333    if  isempty(TimeUnit)
2334        set(handles.Dt_txt,'String',['Dt=' num2str(1000*dt,3) '  10^(-3)'] )
2335    else
2336        set(handles.Dt_txt,'String',['Dt=' num2str(1000*dt,3) '  m' TimeUnit] )
2337    end
2338end
2339
2340
2341%% store the current open names, fieldname and vel types in uvmat interface
2342UvData.FileName_1=FileName_1;
2343UvData.ParamOut_1=ParamOut_1;
2344if numel(Field)==2
2345UvData.Field_1=Field{2}; %store the second field for possible use at next RUN
2346end
2347
2348%% apply coordinate transform or other user fct
2349transform=get(handles.path_transform,'UserData');
2350if isempty(transform)
2351    UvData.Field=Field{1};
2352else
2353    XmlData=[];%default
2354    XmlData_1=[];%default
2355    if isfield(UvData,'XmlData')%use geometry calib recorded from the ImaDoc xml file as first priority
2356        XmlData=UvData.XmlData{1};
2357        if numel(UvData.XmlData)==2
2358            XmlData_1=UvData.XmlData{2};
2359        end
2360    end
2361    transform=get(handles.path_transform,'UserData');
2362    switch nargin(transform)
2363        case 4
2364            if length(Field)==2
2365                UvData.Field=transform(Field{1},XmlData,Field{2},XmlData_1);
2366            else
2367                UvData.Field=transform(Field{1},XmlData);
2368            end
2369        case 3
2370            if length(Field)==2
2371                UvData.Field=transform(Field{1},XmlData,Field{2});
2372            else
2373                UvData.Field=transform(Field{1},XmlData);
2374            end
2375        case 2
2376            UvData.Field=transform(Field{1},XmlData);
2377        case 1
2378            UvData.Field=transform(Field{1});
2379    end
2380end
2381
2382%% calculate tps coefficients if needed
2383UvData.Field=calc_tps(UvData.Field,check_proj_tps);
2384
2385%% analyse input field
2386%test_x=0;
2387%test_z=0;% test for unstructured z coordinate
2388%[errormsg,ListDimName,DimValue,VarDimIndex]=check_field_structure(UvData.Field);% check the input field structure
2389% if ~isempty(errormsg)
2390%     errormsg=['error in uvmat/refresh_field/check_field_structure: ' errormsg];% display error
2391%     return
2392% end
2393[CellInfo,NbDimArray,errormsg]=find_field_cells(UvData.Field);% analyse  the input field structure
2394if ~isempty(errormsg)
2395    errormsg=['uvmat /refresh_field / find_field_cells / ' errormsg];% display error
2396    return
2397end
2398
2399NbDim=max(NbDimArray);% spatial dimension of the input field
2400imax=find(NbDimArray==NbDim);% indices of field cells to consider
2401if isfield(UvData.Field,'NbDim')
2402    NbDim=double(UvData.Field.NbDim);% deal with plane fields containing z coordinates
2403end
2404
2405
2406%% get bounds and mesh (needed  to propose default options for projection objects)
2407if NbDim>1
2408    CoordMax=zeros(numel(imax),NbDim);
2409    CoordMin=zeros(numel(imax),NbDim);
2410    Mesh=zeros(numel(imax),NbDim);
2411    for ind=1:numel(imax)
2412        XName=UvData.Field.ListVarName{CellInfo{imax(ind)}.CoordIndex(end)};
2413        YName=UvData.Field.ListVarName{CellInfo{imax(ind)}.CoordIndex(end-1)};
2414        CoordMax(ind,NbDim)=max(max(UvData.Field.(XName)));
2415        CoordMin(ind,NbDim)=min(min(UvData.Field.(XName)));
2416        CoordMax(ind,NbDim-1)=max(max(UvData.Field.(YName)));
2417        CoordMin(ind,NbDim-1)=min(min(UvData.Field.(YName)));
2418        %         test_x=1;%test for unstructured coordinates
2419        if NbDim==3
2420            ZName=UvData.Field.ListVarName{CellInfo{imax(ind)}.CoordIndex(1)};
2421            CoordMax(imax(ind),1)=max(max(UvData.Field.(ZName)));
2422            CoordMin(ind,1)=min(min(UvData.Field.(ZName)));
2423        end
2424       
2425        switch CellInfo{imax(ind)}.CoordType
2426           
2427            case 'scattered' %unstructured coordinates
2428                NbPoints=CellInfo{imax(ind)}.CoordSize;% nbre of points
2429                Mesh(ind,:)=(prod(CoordMax(ind,:)-CoordMin(ind,:))/NbPoints)^(1/NbDim); %(volume or area per point)^(1/NbDim)
2430            case 'grid'%structured coordinate
2431                NbPoints=CellInfo{imax(ind)}.CoordSize;% nbre of points in each direction
2432                Mesh(ind,:)=min((CoordMax(ind,:)-CoordMin(ind,:))./(NbPoints-1));               
2433        end
2434    end
2435    UvData.Field.Mesh=min(Mesh);
2436    UvData.Field.XMax=max(CoordMax(ind,end));
2437    UvData.Field.XMin=min(CoordMin(ind,end));
2438    UvData.Field.YMax=max(CoordMax(ind,end-1));
2439    UvData.Field.YMin=max(CoordMin(ind,end-1));
2440    if NbDim==3
2441        UvData.Field.ZMax=max(CoordMax(ind,1));
2442        UvData.Field.ZMin=max(CoordMin(ind,1));
2443    end
2444    % adjust the mesh to a value 1, 2 , 5 *10^n
2445    ord=10^(floor(log10(UvData.Field.Mesh)));%order of magnitude
2446    if UvData.Field.Mesh/ord>=5
2447        UvData.Field.Mesh=5*ord;
2448    elseif UvData.Field.Mesh/ord>=2
2449        UvData.Field.Mesh=2*ord;
2450    else
2451        UvData.Field.Mesh=ord;
2452    end
2453    % default projection plane
2454    if isempty(UvData.Object{1})
2455        UvData.Object{1}.Type='plane';%main plotting plane
2456        UvData.Object{1}.ProjMode='projection';%main plotting plane
2457        UvData.Object{1}.DisplayHandle.uvmat=[]; %plane not visible in uvmat
2458        UvData.Object{1}.DisplayHandle.view_field=[]; %plane not visible in uvmat
2459    end
2460    %% 3D case (menuvolume)
2461    if NbDim==3% && UvData.NewSeries
2462        test_set_object=1;
2463        hset_object=findobj(allchild(0),'tag','set_object');% look for the set_object GUI
2464        ZBounds(1)=UvData.Field.ZMin; %minimum for the Z slider
2465        ZBounds(2)=UvData.Field.ZMax;%maximum for the Z slider
2466        if ~isempty(hset_object) %if set_object is detected
2467            delete(hset_object);% delete the GUI set_object if it does not fit
2468        end
2469        if test_set_object% reinitiate the GUI set_object
2470            delete_object(1);% delete the current projection object in the list UvData.Object, delete its graphic representations and update the list displayed in handles.ListObject and 2
2471            UvData.Object{1}.NbDim=NbDim;%test for 3D objects
2472            UvData.Object{1}.RangeZ=UvData.Field.Mesh;%main plotting plane
2473            UvData.Object{1}.Coord(1,3)=(UvData.Field.ZMin+UvData.Field.ZMax)/2;%section at a middle plane chosen
2474            UvData.Object{1}.Angle=[0 0 0];
2475            UvData.Object{1}.HandlesDisplay=plot(0,0,'Tag','proj_object');% A REVOIR
2476            UvData.Object{1}.Name='1-PLANE';
2477            UvData.Object{1}.enable_plot=1;
2478            set_object(UvData.Object{1},handles,ZBounds);
2479            set(handles.ListObject,'Value',1);
2480            set(handles.ListObject,'String',{'1-PLANE'});
2481            set(handles.edit_object,'Value',1)% put the plane in edit mode to enable the z cursor
2482            edit_object_Callback([],[], handles)
2483        end
2484        %multilevel case (single menuplane in a 3D space)
2485    elseif isfield(UvData,'Z')
2486        if isfield(UvData,'CoordType')&& isequal(UvData.CoordType,'phys') && isfield(UvData,'XmlData')
2487            XmlData=UvData.XmlData{1};
2488            if isfield(XmlData,'PlanePos')
2489                UvData.Object{1}.Coord=XmlData.PlanePos(UvData.ZIndex,:);
2490            end
2491            if isfield(XmlData,'PlaneAngle')
2492                siz=size(XmlData.PlaneAngle);
2493                indangle=min(siz(1),UvData.ZIndex);%take first angle if a single angle is defined (translating scanning)
2494                UvData.Object{1}.PlaneAngle=XmlData.PlaneAngle(indangle,:);
2495            end
2496        elseif isfield(UvData,'ZIndex')
2497            UvData.Object{1}.ZObject=UvData.ZIndex;
2498        end
2499    end
2500end
2501
2502testnewseries=UvData.NewSeries;
2503UvData.NewSeries=0;% put to 0 the test for a new field series (set by RootPath_callback)
2504set(handles.uvmat,'UserData',UvData)
2505
2506%% reset the min and max of scalar if only the mask is displayed(TODO: check the need)
2507% if isfield(UvData,'Mask')&& ~isfield(UvData,'A')
2508%     set(handles.num_MinA,'String','0')
2509%     set(handles.num_MaxA,'String','255')
2510% end
2511
2512%% usual 1D (x,y) plots
2513if NbDim<=1
2514    set(handles.Objects,'Visible','off')
2515    set(handles.ListObject_1_title,'Visible','off')
2516    set(handles.ListObject_1,'Visible','off')
2517    [PlotType,PlotParamOut]=plot_field(UvData.Field,handles.PlotAxes,read_GUI(handles.uvmat));
2518    write_plot_param(handles,PlotParamOut) %update the auto plot parameters
2519   
2520%% 2D or 3D fieldname are generally projected
2521else
2522    set(handles.Objects,'Visible','on')
2523    set(handles.ListObject_1_title,'Visible','on')
2524    set(handles.ListObject_1,'Visible','on')
2525   
2526    %% Plot the projections on the selected  projection objects
2527    % main projection object (uvmat display)
2528    list_object=get(handles.ListObject_1,'String');
2529    if isequal(list_object,{''})||isequal(list_object,' ')%refresh list of objects if the menu is empty
2530        set(handles.ListObject,'Value',1)
2531        set(handles.ListObject,'String',{'plane'})
2532        UvData.Object{1}.Type='plane';%main plotting plane
2533        UvData.Object{1}.ProjMode='projection';%main plotting plane
2534        UvData.Object{1}.DisplayHandle.uvmat=[]; %plane not visible in uvmat
2535        UvData.Object{1}.DisplayHandle.view_field=[]; %plane not visible in uvmat
2536        set(handles.ListObject_1,'Value',1)
2537        set(handles.ListObject_1,'String',{'plane'})
2538    end
2539    IndexObj(1)=get(handles.ListObject_1,'Value');%selected projection object for main view
2540    if IndexObj(1)> numel(UvData.Object)
2541        IndexObj(1)=1;%select the first object if the selected one does not exist
2542        set(handles.ListObject_1,'Value',1)
2543    end
2544    IndexObj(2)=get(handles.ListObject,'Value');%selected projection object for main view
2545    if isequal(IndexObj(2),IndexObj(1))
2546        IndexObj(2)=[];
2547    end
2548    plot_handles{1}=handles;
2549    if isfield(UvData,'plotaxes')%case of movies
2550        haxes(1)=UvData.plotaxes;
2551    else
2552        haxes(1)=handles.PlotAxes;
2553    end
2554    PlotParam{1}=read_GUI(handles.uvmat);
2555    %default settings if vectors not visible
2556    if ~isfield(PlotParam{1},'Vectors')
2557        PlotParam{1}.Vectors.MaxVec=1;
2558        PlotParam{1}.Vectors.MinVec=0;
2559        PlotParam{1}.Vectors.CheckFixVecColor=1;
2560        PlotParam{1}.Vectors.ColCode1=0.33;
2561        PlotParam{1}.Vectors.ColCode2=0.66;
2562        PlotParam{1}.Vectors.ColorScalar={''};
2563        PlotParam{1}.Vectors.ColorCode= {'rgb'};
2564    end
2565    PosColorbar{1}=UvData.OpenParam.PosColorbar;%prescribe the colorbar position on the uvmat interface
2566   
2567    %% second projection object (view_field display)
2568    if length( IndexObj)>=2
2569        view_field_handle=findobj(allchild(0),'tag','view_field');%handles of the view_field GUI
2570        if ~isempty(view_field_handle)
2571            plot_handles{2}=guidata(view_field_handle);
2572            haxes(2)=plot_handles{2}.PlotAxes;
2573            PlotParam{2}=read_GUI(handles.uvmat);%read plotting parameters on the uvmat interface
2574            PosColorbar{2}='*'; %TODO: deal with colorbar position on view_field
2575        end
2576    end
2577   
2578    %% loop on the projection objects: one or two
2579   
2580    for imap=1:numel(IndexObj)
2581        iobj=IndexObj(imap);
2582        [ObjectData,errormsg]=proj_field(UvData.Field,UvData.Object{iobj});% project field on the object
2583        if ~isempty(errormsg)
2584            return
2585        end
2586        if testnewseries
2587            PlotParam{imap}.Scalar.CheckBW=[]; %B/W option depends on the input field (image or scalar)
2588            if isfield(ObjectData,'CoordUnit')
2589                PlotParam{imap}.Coordinates.CheckFixAspectRatio=1;% set x and y scaling equal if CoordUnit is defined (common unit for x and y)
2590                PlotParam{imap}.Coordinates.AspectRatio=1; %set aspect ratio to 1
2591            end
2592        end
2593        %use of mask (TODO: check)
2594        if isfield(ObjectData,'NbDim') && isequal(ObjectData.NbDim,2) && isfield(ObjectData,'Mask') && isfield(ObjectData,'A')
2595            flag_mask=double(ObjectData.Mask>200);%=0 for masked regions
2596            AX=ObjectData.AX;%x coordiantes for the scalar field
2597            AY=ObjectData.AY;%y coordinates for the scalar field
2598            MaskX=ObjectData.MaskX;%x coordiantes for the mask
2599            MaskY=ObjectData.MaskY;%y coordiantes for the mask
2600            if ~isequal(MaskX,AX)||~isequal(MaskY,AY)
2601                nxy=size(flag_mask);
2602                sizpx=(ObjectData.MaskX(end)-ObjectData.MaskX(1))/(nxy(2)-1);%size of a mask pixel
2603                sizpy=(ObjectData.MaskY(1)-ObjectData.MaskY(end))/(nxy(1)-1);
2604                x_mask=ObjectData.MaskX(1):sizpx:ObjectData.MaskX(end); % pixel x coordinates for image display
2605                y_mask=ObjectData.MaskY(1):-sizpy:ObjectData.MaskY(end);% pixel x coordinates for image display
2606                %project on the positions of the scalar
2607                npxy=size(ObjectData.A);
2608                dxy(1)=(ObjectData.AY(end)-ObjectData.AY(1))/(npxy(1)-1);%grid mesh in y
2609                dxy(2)=(ObjectData.AX(end)-ObjectData.AX(1))/(npxy(2)-1);%grid mesh in x
2610                xi=ObjectData.AX(1):dxy(2):ObjectData.AX(end);
2611                yi=ObjectData.AY(1):dxy(1):ObjectData.AY(end);
2612                [XI,YI]=meshgrid(xi,yi);% creates the matrix of regular coordinates
2613                flag_mask = interp2(x_mask,y_mask,flag_mask,XI,YI);
2614            end
2615            AClass=class(ObjectData.A);
2616            ObjectData.A=flag_mask.*double(ObjectData.A);
2617            ObjectData.A=feval(AClass,ObjectData.A);
2618%             ind_off=[];
2619%             if isfield(ObjectData,'ListVarName')
2620%                 for ilist=1:length(ObjectData.ListVarName)
2621%                     if isequal(ObjectData.ListVarName{ilist},'Mask')||isequal(ObjectData.ListVarName{ilist},'MaskX')||isequal(ObjectData.ListVarName{ilist},'MaskY')
2622%                         ind_off=[ind_off ilist];
2623%                     end
2624%                 end
2625%                 ObjectData.ListVarName(ind_off)=[];
2626%                 VarDimIndex(ind_off)=[];
2627%                 ind_off=[];
2628%             
2629%             end
2630        end
2631        if ~isempty(ObjectData)
2632            PlotType='none'; %default
2633            if imap==2 && isempty(view_field_handle)
2634                view_field(ObjectData)
2635            else
2636                [PlotType,PlotParamOut]=plot_field(ObjectData,haxes(imap),PlotParam{imap},PosColorbar{imap});
2637                write_plot_param(plot_handles{imap},PlotParamOut) %update the auto plot parameters
2638                if isfield(Field,'Mesh')&&~isempty(Field.Mesh)
2639                    ObjectData.Mesh=Field.Mesh; % gives an estimated mesh size (useful for mouse action on the plot)
2640                end
2641            end
2642        end
2643    end
2644   
2645    %% update the mask
2646    if isequal(get(handles.CheckMask,'Value'),1)%if the mask option is on
2647        update_mask(handles,num_i1,num_i2);
2648    end
2649   
2650    %% prepare the menus of histograms and plot them (histogram of the whole volume in 3D case)
2651    menu_histo=(UvData.Field.ListVarName)';%list of field variables to be displayed for the menu of histogram display
2652    ind_skip=[];
2653    % nb_histo=1;
2654    Ustring='';
2655    Vstring='';
2656    % suppress coordinates from the histogram menu
2657    for ivar=1:numel(menu_histo)%l loop on field variables:
2658        if isfield(UvData.Field,'VarAttribute') && numel(UvData.Field.VarAttribute)>=ivar && isfield(UvData.Field.VarAttribute{ivar},'Role')
2659            Role=UvData.Field.VarAttribute{ivar}.Role;
2660            switch Role
2661                case {'coord_x','coord_y','coord_z','dimvar'}
2662                    ind_skip=[ind_skip ivar];
2663                case {'vector_x'}
2664                    Ustring=UvData.Field.ListVarName{ivar};
2665                    ind_skip=[ind_skip ivar];
2666                case {'vector_y'}
2667                    Vstring=UvData.Field.ListVarName{ivar};
2668                    ind_skip=[ind_skip ivar];
2669            end
2670        end
2671        DimCell=UvData.Field.VarDimName{ivar};
2672        DimName='';
2673        if ischar(DimCell)
2674            DimName=DimCell;
2675        elseif iscell(DimCell)&& numel(DimCell)==1
2676            DimName=DimCell{1};
2677        end
2678        if strcmp(DimName,menu_histo{ivar})
2679            ind_skip=[ind_skip ivar];
2680        end
2681    end
2682    menu_histo(ind_skip)=[];% remove skipped items
2683    if ~isempty(Ustring)
2684        menu_histo=[{[Ustring ',' Vstring]};menu_histo];% add U, V at the beginning if they exist
2685    end
2686   
2687    %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
2688    % display menus and plot histograms
2689    test_v=0;
2690    if ~isempty(menu_histo)
2691        set(handles.histo1_menu,'Value',1)
2692        set(handles.histo1_menu,'String',menu_histo)
2693        histo1_menu_Callback(handles.histo1_menu, [], handles)% plot first histogram
2694    end
2695end
2696
2697%------------------------------------------------------------------------
2698function histo1_menu_Callback(hObject, eventdata, handles)
2699%--------------------------------------------
2700histo_menu=get(handles.histo1_menu,'String');
2701histo_value=get(handles.histo1_menu,'Value');
2702FieldName=histo_menu{histo_value};
2703
2704UvData=get(handles.uvmat,'UserData');
2705Field=UvData.Field;
2706r=regexp(FieldName,'(?<var1>.*)(?<sep>,)(?<var2>.*)','names');
2707FieldName_2='';
2708if ~isempty(r)
2709    FieldName=r.var1;
2710    FieldName_2=r.var2;
2711end
2712if ~isfield(UvData.Field,FieldName)
2713    msgbox_uvmat('ERROR',['no field  ' FieldName ' for histogram'])
2714    return
2715end
2716FieldHisto=Field.(FieldName);
2717if isfield(Field,'FF') && ~isempty(Field.FF) && isequal(size(Field.FF),size(FieldHisto))
2718    indsel=find(Field.FF==0);%find values marked as false
2719    if ~isempty(indsel)
2720        FieldHisto=FieldHisto(indsel);
2721        if ~isempty(FieldName_2)
2722            FieldHisto(:,:,2)=Field.(FieldName_2)(indsel);
2723        end
2724    end
2725end
2726if isempty(Field)
2727    msgbox_uvmat('ERROR',['empty field ' FieldName])
2728else
2729    nxy=size(FieldHisto);
2730    Amin=double(min(min(min(FieldHisto))));%min of field value
2731    Amax=double(max(max(max(FieldHisto))));%max of field value
2732    if isequal(Amin,Amax)
2733        cla(handles.HistoAxes)
2734    else
2735        Histo.ListVarName={FieldName,'histo'};
2736        if isfield(Field,'NbDim') && isequal(Field.NbDim,3)
2737            Histo.VarDimName={FieldName,FieldName}; %dimensions for the histogram
2738        else
2739            if numel(nxy)==2
2740                Histo.VarDimName={FieldName,FieldName}; %dimensions for the histogram
2741            else
2742                Histo.VarDimName={FieldName,{FieldName,'component'}}; %dimensions for the histogram
2743            end
2744        end
2745        %unit
2746        units=[]; %default
2747        for ivar=1:numel(Field.ListVarName)
2748            if strcmp(Field.ListVarName{ivar},FieldName)
2749                if isfield(Field,'VarAttribute') && numel(Field.VarAttribute)>=ivar && isfield(Field.VarAttribute{ivar},'units')
2750                    units=Field.VarAttribute{ivar}.units;
2751                    break
2752                end
2753            end
2754        end
2755        if ~isempty(units)
2756            Histo.VarAttribute{1}.units=units;
2757        end
2758        eval(['Histo.' FieldName '=linspace(Amin,Amax,50);'])%absissa values for histo
2759        if isfield(Field,'NbDim') && isequal(Field.NbDim,3)
2760            C=reshape(double(FieldHisto),1,[]);% reshape in a vector
2761            Histo.histo(:,1)=hist(C, Histo.(FieldName));  %calculate histogram
2762        else
2763            for col=1:size(FieldHisto,3)
2764                B=FieldHisto(:,:,col);
2765                C=reshape(double(B),1,nxy(1)*nxy(2));% reshape in a vector
2766                Histo.histo(:,col)=hist(C, Histo.(FieldName));  %calculate histogram
2767            end
2768        end
2769        plot_field(Histo,handles.HistoAxes);
2770        hlegend=legend;
2771        if isempty(FieldName_2)
2772        set(hlegend,'String',FieldName)
2773        else
2774            set(hlegend,'String',{FieldName;FieldName_2})
2775        end
2776    end
2777end
2778
2779%-------------------------------------------------------------------
2780% --- translate coordinate to matrix index
2781%-------------------------------------------------------------------
2782function [indx,indy]=pos2ind(x0,rangx0,nxy)
2783indx=1+round((nxy(2)-1)*(x0-rangx0(1))/(rangx0(2)-rangx0(1)));% index x of pixel 
2784indy=1+round((nxy(1)-1)*(y12-rangy0(1))/(rangy0(2)-rangy0(1)));% index y of pixel
2785
2786
2787%-------------------------------------------------------------------
2788% --- Executes on button press in 'CheckZoom'.
2789%-------------------------------------------------------------------
2790function CheckZoom_Callback(hObject, eventdata, handles)
2791
2792if (get(handles.CheckZoom,'Value') == 1);
2793    set(handles.CheckZoom,'BackgroundColor',[1 1 0])
2794    set(handles.CheckFixLimits,'Value',1)% propose by default fixed limits for the plotting axes
2795    set(handles.CheckFixLimits,'BackgroundColor',[1 1 0])
2796else
2797    set(handles.CheckZoom,'BackgroundColor',[0.7 0.7 0.7])
2798end
2799
2800%-------------------------------------------------------------------
2801% --- Executes on button press in 'CheckFixLimits'.
2802%-------------------------------------------------------------------
2803function CheckFixLimits_Callback(hObject, eventdata, handles)
2804test=get(handles.CheckFixLimits,'Value');
2805if test
2806    set(handles.CheckFixLimits,'BackgroundColor',[1 1 0])
2807else
2808    set(handles.CheckFixLimits,'BackgroundColor',[0.7 0.7 0.7])
2809    update_plot(handles);
2810end
2811
2812%-------------------------------------------------------------------
2813% --- Executes on button press in CheckFixAspectRatio.
2814function CheckFixAspectRatio_Callback(hObject, eventdata, handles)
2815%-------------------------------------------------------------------
2816if get(handles.CheckFixAspectRatio,'Value')
2817    set(handles.CheckFixAspectRatio,'BackgroundColor',[1 1 0])
2818    update_plot(handles);
2819else
2820    set(handles.CheckFixAspectRatio,'BackgroundColor',[0.7 0.7 0.7])
2821    update_plot(handles);
2822end
2823
2824%-------------------------------------------------------------------
2825function num_AspectRatio_Callback(hObject, eventdata, handles)
2826%-------------------------------------------------------------------
2827set(handles.CheckFixAspectRatio,'Value',1)% select the fixed aspect ratio button
2828set(handles.CheckFixAspectRatio,'BackgroundColor',[1 1 0])% mark in yellow
2829update_plot(handles);
2830%-------------------------------------------------------------------
2831
2832%-------------------------------------------------------------------
2833
2834
2835
2836%-------------------------------------------------------------------
2837%----Executes on button press in 'record': records the current flags of manual correction.
2838%-------------------------------------------------------------------
2839function record_Callback(hObject, eventdata, handles)
2840% [filebase,num_i1,num_j1,num_i2,num_j2,Ext,NomType,SubDir]=read_input_file(handles);
2841[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
2842FileName=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
2843%FileName=read_file_boxes(handles);
2844[erread,message]=fileattrib(FileName);
2845if ~isempty(message) && ~isequal(message.UserWrite,1)
2846     msgbox_uvmat('ERROR',['no writting access to ' FileName])
2847     return
2848end
2849test_civ2=isequal(get(handles.civ2,'BackgroundColor'),[1 1 0]);
2850test_civ1=isequal(get(handles.VelType,'BackgroundColor'),[1 1 0]);
2851if ~test_civ2 && ~test_civ1
2852    msgbox_uvmat('ERROR','manual correction only possible for CIV1 or CIV2 velocity fields')
2853end
2854if test_civ2
2855    nbname='nb_vectors2';
2856   flagname='vec2_FixFlag';
2857   attrname='fix2';
2858end
2859if test_civ1
2860    nbname='nb_vectors';
2861   flagname='vec_FixFlag';
2862   attrname='fix';
2863end
2864%write fix flags in the netcdf file
2865UvData=get(handles.uvmat,'UserData');
2866hhh=which('netcdf.open');% look for built-in matlab netcdf library
2867if ~isequal(hhh,'')% case of new builtin Matlab netcdf library
2868    nc=netcdf.open(FileName,'NC_WRITE');
2869    netcdf.reDef(nc);
2870    netcdf.putAtt(nc,netcdf.getConstant('NC_GLOBAL'),attrname,1);
2871    dimid = netcdf.inqDimID(nc,nbname);
2872    try
2873        varid = netcdf.inqVarID(nc,flagname);% look for already existing fixflag variable
2874    catch
2875        varid=netcdf.defVar(nc,flagname,'double',dimid);%create fixflag variable if it does not exist
2876    end
2877    netcdf.endDef(nc);
2878    netcdf.putVar(nc,varid,UvData.PlotAxes.FF);
2879    netcdf.close(nc); 
2880else %old netcdf library
2881    netcdf_toolbox(FileName,AxeData,attrname,nbname,flagname)
2882end
2883
2884%-------------------------------------------------------------------
2885%----Correct the netcdf file, using toolbox (old versions of Matlab).
2886%-------------------------------------------------------------------
2887function netcdf_toolbox(FileName,AxeData,attrname,nbname,flagname)
2888nc=netcdf(FileName,'write'); %open netcdf file
2889result=redef(nc);
2890eval(['nc.' attrname '=1;']);
2891theDim=nc(nbname) ;% get the number of velocity vectors
2892nb_vectors=size(theDim);
2893var_FixFlag=ncvar(flagname,nc);% var_FixFlag will be written as the netcdf variable vec_FixFlag
2894var_FixFlag(1:nb_vectors)=AxeData.FF;%
2895fin=close(nc);
2896
2897%-------------------------------------------------------------------
2898% --- Executes on button press in SubField
2899function SubField_Callback(hObject, eventdata, handles)
2900%-------------------------------------------------------------------
2901UvData=get(handles.uvmat,'UserData');
2902if get(handles.SubField,'Value')==0% if the subfield button is desactivated   
2903    set(handles.RootPath_1,'String','')
2904    set(handles.RootFile_1,'String','')
2905    set(handles.SubDir_1,'String','');
2906    set(handles.FileIndex_1,'String','');
2907    set(handles.FileExt_1,'String','');
2908    set(handles.RootPath_1,'Visible','off')
2909    set(handles.RootFile_1,'Visible','off')
2910    set(handles.SubDir_1,'Visible','off');
2911    set(handles.NomType_1,'Visible','off');
2912    set(handles.abs_time_1,'Visible','off')
2913    set(handles.FileIndex_1,'Visible','off');
2914    set(handles.FileExt_1,'Visible','off');
2915    set(handles.FieldName_1,'Value',1);%set to blank state
2916    set(handles.VelType_1,'Value',1);%set to blank state
2917    set(handles.num_Opacity,'String','')% desactivate opacity setting
2918    if ~strcmp(get(handles.VelType,'Visible'),'on')
2919        set(handles.VelType_1,'Visible','off')
2920    end
2921    if isfield(UvData,'XmlData_1')
2922        UvData=rmfield(UvData,'XmlData_1');
2923    end
2924    set(handles.uvmat,'UserData',UvData);
2925    transform_fct_list=get(handles.transform_fct,'String');
2926    transform_fct=transform_fct_list(get(handles.transform_fct,'Value'));
2927    if strcmp(transform_fct,'sub_field')
2928        set(handles.transform_fct,'Value',1)%suppress the sub_field transform
2929        transform_fct_Callback(hObject, eventdata, handles);
2930    else
2931        run0_Callback(hObject, eventdata, handles)
2932    end 
2933else
2934    MenuBrowse_1_Callback(hObject, eventdata, handles)
2935end
2936
2937%------------------------------------------------------------------------
2938% --- read the data displayed for the input rootfile windows (new): TODO use read_GUI
2939
2940function [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles)
2941%------------------------------------------------------------------------
2942InputFile=read_GUI(handles.InputFile);
2943RootPath=InputFile.RootPath;
2944SubDir=regexprep(InputFile.SubDir,'/|\','');
2945RootFile=regexprep(InputFile.RootFile,'/|\','');
2946FileIndices=InputFile.FileIndex;
2947FileExt=InputFile.FileExt;
2948
2949
2950%------------------------------------------------------------------------
2951% ---- read the data displayed for the second input rootfile windows
2952function [RootPath_1,SubDir_1,RootFile_1,FileIndex_1,FileExt_1,NomType_1]=read_file_boxes_1(handles)
2953%------------------------------------------------------------------------
2954RootPath_1=get(handles.RootPath_1,'String'); % read the data from the file1_input window
2955if isequal(get(handles.RootPath_1,'Visible'),'off') || isequal(RootPath_1,'"')
2956    RootPath_1=get(handles.RootPath,'String');
2957end;
2958SubDir_1=get(handles.SubDir_1,'String');
2959if isequal(get(handles.SubDir_1,'Visible'),'off')|| isequal(SubDir_1,'"')
2960    SubDir_1=get(handles.SubDir,'String');
2961end
2962SubDir_1=regexprep(SubDir_1,'\<[\\/]|[\\/]\>','');%suppress possible / or \ separator at the beginning or the end of the string
2963RootFile_1=get(handles.RootFile_1,'String');
2964if isequal(get(handles.RootFile_1,'Visible'),'off') || isequal(RootFile_1,'"')
2965    RootFile_1=get(handles.RootFile,'String');
2966end
2967RootFile_1=regexprep(RootFile_1,'\<[\\/]|[\\/]\>','');%suppress possible / or \ separator at the beginning or the end of the string
2968FileIndex_1=get(handles.FileIndex_1,'String');
2969if isequal(get(handles.FileIndex_1,'Visible'),'off')|| isequal(FileIndex_1,'"')
2970    FileIndex_1=get(handles.FileIndex,'String');
2971end
2972FileExt_1=get(handles.FileExt_1,'String');
2973if isequal(get(handles.FileExt_1,'Visible'),'off') || isequal(FileExt_1,'"')
2974    FileExt_1=get(handles.FileExt,'String');%read FileExt by default
2975end
2976NomType_1=get(handles.NomType_1,'String');
2977if isequal(get(handles.NomType_1,'Visible'),'off') || isequal(NomType_1,'"')
2978    NomType_1=get(handles.NomType,'String');%read FileExt by default
2979end
2980%------------------------------------------------------------------------
2981% --- Executes on menu selection FieldName
2982function FieldName_Callback(hObject, eventdata, handles)
2983%------------------------------------------------------------------------
2984list_fields=get(handles.FieldName,'String');% list menu fields
2985index_fields=get(handles.FieldName,'Value');% selected string index
2986field= list_fields{index_fields(1)}; % selected string
2987if isequal(field,'get_field...')
2988    set(handles.FixVelType,'visible','off')
2989    set(handles.VelType,'visible','off')
2990    set(handles.VelType_1,'visible','off')
2991    [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
2992    FileName=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
2993    hget_field=findobj(allchild(0),'name','get_field');
2994    if ~isempty(hget_field)
2995        delete(hget_field)
2996    end
2997    get_field(FileName);
2998    return %no further action
2999end
3000
3001UvData=get(handles.uvmat,'UserData');
3002
3003%read the rootfile input display
3004[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
3005FileName=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
3006[tild,tild,tild,i1,i2,j1,j2,tild,NomType]=fileparts_uvmat(['xxx' get(handles.FileIndex,'String') FileExt]);
3007if isequal(field,'image')
3008    if  isfield(UvData.Field,'Civ2_ImageA')%get the corresponding input image in the netcdf file
3009        imagename=UvData.Field.Civ2_ImageA;
3010    elseif isfield(UvData.Field,'Civ1_ImageA')%
3011        imagename=UvData.Field.Civ1_ImageA;
3012    else
3013        SubDirBase=regexprep(SubDir,'\..*','');%take the root part of SubDir, before the first dot '.'
3014        imagename=fullfile_uvmat(RootPath,SubDirBase,RootFile,'.png',NomType,i1,[],j1,[]);
3015    end
3016    if ~exist(imagename,'file')
3017        [FileName,PathName] = uigetfile( ...
3018            {'*.png;*.jpg;*.tif;*.avi;*.AVI;*.vol', ' (*.png, .tif, *.avi,*.vol)';
3019            '*.jpg',' jpeg image files'; ...
3020            '*.png','.png image files'; ...
3021            '*.tif','.tif image files'; ...
3022            '*.avi;*.AVI','.avi movie files'; ...
3023            '*.vol','.volume images (png)'; ...
3024            '*.*',  'All Files (*.*)'}, ...
3025            'Pick an image',imagename);
3026        if ~ischar(FileName),return,end %abandon if the browser is cancelled
3027        imagename=[PathName FileName];
3028    end
3029     % display the selected field and related information
3030    display_file_name(handles,imagename)%display the image
3031    return
3032else
3033    ext=get(handles.FileExt,'String');
3034    if ~isequal(ext,'.nc') %find the new NomType if the previous display was not already a netcdf file
3035        [FileName,PathName] = uigetfile( ...
3036            {'*.nc', ' (*.nc)';
3037            '*.nc',' netcdf files'; ...
3038            '*.*',  'All Files (*.*)'}, ...
3039            'Pick a netcdf file',FileBase);
3040        if ~ischar(FileName),return,end %abandon if the browser is cancelled
3041        FullFileName=[PathName FileName];
3042        % display the selected field and related information
3043        display_file_name( handles,FullFileName)
3044        return
3045    end
3046end
3047indices=fullfile_uvmat('','','','',NomType,i1,i2,j1,j2);
3048set(handles.FileIndex,'String',indices)
3049% set(handles.NomType,'String',NomType)
3050
3051%common to Fields_1_Callback
3052list_fields_1=get(handles.FieldName_1,'String');% list menu fields
3053field_1='';
3054if ~isempty(list_fields_1)
3055field_1= list_fields_1{get(handles.FieldName_1,'Value')}; % selected string
3056end
3057if isequal(field,'image')||isequal(field_1,'image')
3058    set(handles.TitleNpxy,'Visible','on')% visible npx,pxcm... buttons
3059    set(handles.num_Npx,'Visible','on')
3060    set(handles.num_Npy,'Visible','on')
3061else
3062    set(handles.TitleNpxy,'Visible','off')% visible npx,pxcm... buttons
3063    set(handles.num_Npx,'Visible','off')
3064    set(handles.num_Npy,'Visible','off')
3065end
3066if ~(isfield(UvData,'NewSeries')&&isequal(UvData.NewSeries,1))
3067    run0_Callback(hObject, eventdata, handles)
3068end
3069
3070%---------------------------------------------------
3071% --- Executes on menu selection FieldName
3072function FieldName_1_Callback(hObject, eventdata, handles)
3073%-------------------------------------------------
3074%% read input data
3075check_new=~get(handles.SubField,'Value'); %check_new=1 if a second field was not previously entered
3076UvData=get(handles.uvmat,'UserData');
3077if check_new && isfield(UvData,'XmlData')
3078    UvData.XmlData{2}=UvData.XmlData{1};
3079end
3080if isfield(UvData,'Field_1')
3081    UvData=rmfield(UvData,'Field_1');% remove the stored second field (a new one needs to be read)
3082end
3083UvData.FileName_1='';% desactivate the use of a constant second file
3084list_fields=get(handles.FieldName,'String');% list menu fields
3085field= list_fields{get(handles.FieldName,'Value')}; % selected string
3086list_fields=get(handles.FieldName_1,'String');% list menu fields
3087field_1= list_fields{get(handles.FieldName_1,'Value')}; % selected string for the second field
3088if isempty(field_1)%||(numel(UvData.FileType)>=2 && strcmp(UvData.FileType{2},'image'))
3089    set(handles.SubField,'Value',0)
3090    SubField_Callback(hObject, eventdata, handles)
3091    return
3092else
3093    set(handles.SubField,'Value',1)%state that a second field is now entered
3094end
3095
3096%% read the rootfile input display
3097[RootPath_1,SubDir_1,RootFile_1,FileIndex_1,FileExt_1]=read_file_boxes_1(handles);
3098FileName_1=[fullfile(RootPath_1,SubDir_1,RootFile_1) FileIndex_1 FileExt_1];
3099[tild,tild,tild,i1,i2,j1,j2]=fileparts_uvmat(get(handles.FileIndex,'String'));
3100switch field_1
3101    case 'get_field...'
3102        set_veltype_display(0) % no veltype display
3103        hget_field=findobj(allchild(0),'name','get_field_1');
3104        if ~isempty(hget_field)
3105            delete(hget_field)
3106        end
3107        hget_field=get_field(FileName_1);
3108        set(hget_field,'name','get_field_1')
3109        hhget_field=guidata(hget_field);
3110        set(hhget_field.list_fig,'Value',1)
3111        set(hhget_field.list_fig,'String',{'uvmat'})
3112        if check_new
3113            UvData.FileType{2}=UvData.FileType{1};
3114            set(handles.FileIndex_1,'String',get(handles.FileIndex,'String'))
3115              set(handles.uvmat,'UserData',UvData)
3116        end
3117    case 'image'
3118        % get the image name corresponding to the current netcdf name (no unique correspondance)
3119        if  isfield(UvData.Field,'Civ2_ImageA')%get the corresponding input image in the netcdf file
3120            imagename=UvData.Field.Civ2_ImageA;
3121        elseif isfield(UvData.Field,'Civ1_ImageA')%
3122            imagename=UvData.Field.Civ1_ImageA;
3123        else
3124            SubDirBase=regexprep(SubDir_1,'\..*','');%take the root part of SubDir, before the first dot '.'
3125            imagename=fullfile_uvmat(RootPath_1,SubDirBase,RootFile_1,'.png',get(handles.NomType,'String'),i1,[],j1);
3126        end
3127        if ~exist(imagename,'file') % browse for images if it is not found
3128            [FileName,PathName] = uigetfile( ...
3129                {'*.png;*.jpg;*.tif;*.avi;*.AVI;*.vol', ' (*.png, .tif, *.avi,*.vol)';
3130                '*.jpg',' jpeg image files'; ...
3131                '*.png','.png image files'; ...
3132                '*.tif','.tif image files'; ...
3133                '*.avi;*.AVI','.avi movie files'; ...
3134                '*.vol','.volume images (png)'; ...
3135                '*.*',  'All Files (*.*)'}, ...
3136                'Pick an image',imagename);
3137            if ~ischar(FileName),return,end %abandon if the browser is cancelled
3138            imagename=[PathName FileName];
3139        end
3140        if ~ischar(imagename)% quit if the browser has  been closed
3141            set(handles.SubField,'Value',0)
3142        else %valid browser input:  display the selected image
3143            set(handles.TitleNpxy,'Visible','on')% visible npx,pxcm... buttons
3144            set(handles.num_Npx,'Visible','on')
3145            set(handles.num_Npy,'Visible','on')
3146            display_file_name(handles,imagename,2)%display the imag
3147        end
3148    otherwise
3149        if check_new
3150            UvData.FileType{2}=UvData.FileType{1};
3151            set(handles.FileIndex_1,'String',get(handles.FileIndex,'String'))
3152            set(handles.FileExt_1,'String',get(handles.FileExt,'String'))
3153        end
3154        if ~isequal(field,'image')
3155            set(handles.TitleNpxy,'Visible','off')% visible npx,pxcm... buttons
3156            set(handles.num_Npx,'Visible','off')
3157            set(handles.num_Npy,'Visible','off')
3158        end
3159        set(handles.uvmat,'UserData',UvData)
3160        if ~(isfield(UvData,'NewSeries')&&isequal(UvData.NewSeries,1))
3161            run0_Callback(hObject, eventdata, handles)
3162        end
3163end
3164
3165%------------------------------------------------------------------------
3166% --- set the visibility of relevant velocity type menus:
3167function menu=set_veltype_display(Civ,FileType)
3168%------------------------------------------------------------------------
3169if ~exist('FileType','var')
3170    FileType='civx';
3171end
3172switch FileType
3173    case 'civx'
3174        menu={'civ1';'interp1';'filter1';'civ2';'interp2';'filter2'};
3175        if isequal(Civ,0)
3176            imax=0;
3177        elseif isequal(Civ,1) || isequal(Civ,2)
3178            imax=1;
3179        elseif isequal(Civ,3)
3180            imax=3;
3181        elseif isequal(Civ,4) || isequal(Civ,5)
3182            imax=4;
3183        elseif isequal(Civ,6) %patch2
3184            imax=6;
3185        end
3186    case 'civdata'
3187        menu={'civ1';'filter1';'civ2';'filter2'};
3188        if isequal(Civ,0)
3189            imax=0;
3190        elseif isequal(Civ,1) || isequal(Civ,2)
3191            imax=1;
3192        elseif isequal(Civ,3)
3193            imax=2;
3194        elseif isequal(Civ,4) || isequal(Civ,5)
3195            imax=3;
3196        elseif isequal(Civ,6) %patch2
3197            imax=4;
3198        end
3199end
3200menu=menu(1:imax);
3201
3202%------------------------------------------------------------------------
3203% --- Executes on button press in FixVelType.
3204function FixVelType_Callback(hObject, eventdata, handles)
3205%------------------------------------------------------------------------
3206% refresh the current plot if the fixed  veltype is unselected
3207if ~get(handles.FixVelType,'Value')
3208    run0_Callback(hObject, eventdata, handles)
3209end
3210
3211%------------------------------------------------------------------------
3212% --- Executes on button press in VelType.
3213function VelType_Callback(hObject, eventdata, handles)
3214%------------------------------------------------------------------------
3215set(handles.FixVelType,'Value',1)
3216run0_Callback(hObject, eventdata, handles)
3217
3218%------------------------------------------------------------------------
3219% --- Executes on choice selection in VelType_1.
3220function VelType_1_Callback(hObject, eventdata, handles)
3221%------------------------------------------------------------------------
3222set(handles.FixVelType,'Value',1)% the velocity type is now imposed by the GUI (not automatic)
3223UvData=get(handles.uvmat,'UserData');
3224set(handles.run0,'BackgroundColor',[1 1 0])%paint run0 button in yellow to indicate its activation
3225drawnow   
3226InputFile=read_GUI(handles.InputFile);% read the input file parameters
3227[RootPath,SubDir,RootFile,FileIndex,FileExt]=read_file_boxes(handles);
3228[RootPath_1,SubDir_1,RootFile_1,FileIndex_1,FileExt_1]=read_file_boxes_1(handles);
3229FileName=[fullfile(RootPath,SubDir,RootFile) FileIndex FileExt];% name of the first input file
3230
3231check_refresh=0;
3232if isempty(InputFile.VelType_1)
3233        FileName_1='';% we plot the first input field without the second field
3234        set(handles.SubField,'Value',0)
3235        SubField_Callback(hObject, eventdata, handles)% activate SubField_Callback and refresh current display, removing the second field
3236elseif get(handles.SubField,'Value')% if subfield is already 'on'
3237     FileName_1=[fullfile(RootPath_1,SubDir_1,RootFile_1) FileIndex_1 FileExt_1];% name of the second input file
3238     check_refresh=1;%will refresh the current display
3239else% we introduce the same file (with a different field) for the second series
3240     FileName_1=FileName;% we compare two fields in the same file
3241     UvData.FileType{2}=UvData.FileType{1};
3242     UvData.XmlData{2}= UvData.XmlData{1};
3243     set(handles.SubField,'Value',1)
3244     transform=get(handles.path_transform,'UserData');
3245     if (~isa(transform,'function_handle')||nargin(transform)<3)
3246        set(handles.transform_fct,'value',2); % set transform to sub_field if the current fct doe not accept two input fields
3247        transform_fct_Callback(hObject, eventdata, handles)% activate transform_fct_Callback and refresh current display
3248     else
3249         check_refresh=1;
3250     end 
3251end
3252
3253% refresh the current display if it has not been done previously
3254if check_refresh
3255    UvData.FileName_1='';% desactivate the use of a constant second file
3256    set(handles.uvmat,'UserData',UvData)
3257    num_i1=stra2num(get(handles.i1,'String'));
3258    num_i2=stra2num(get(handles.i2,'String'));
3259    num_j1=stra2num(get(handles.j1,'String'));
3260    num_j2=stra2num(get(handles.j2,'String'));
3261    [tild,tild,tild,i1_1,i2_1,j1_1,j2_1]=fileparts_uvmat(['xx' FileIndex_1]);
3262    errormsg=refresh_field(handles,FileName,FileName_1,num_i1,num_i2,num_j1,num_j2,i1_1,i2_1,j1_1,j2_1);
3263    if ~isempty(errormsg)
3264        msgbox_uvmat('ERROR',errormsg);
3265    else
3266        set(handles.i1,'BackgroundColor',[1 1 1])
3267        set(handles.i2,'BackgroundColor',[1 1 1])
3268        set(handles.j1,'BackgroundColor',[1 1 1])
3269        set(handles.j2,'BackgroundColor',[1 1 1])
3270        set(handles.FileIndex,'BackgroundColor',[1 1 1])
3271        set(handles.FileIndex_1,'BackgroundColor',[1 1 1])
3272    end
3273    set(handles.run0,'BackgroundColor',[1 0 0])
3274end
3275
3276%-----------------------------------------------
3277% --- reset civ buttons
3278function reset_vel_type(handles_civ0,handle1)
3279for ibutton=1:length(handles_civ0)
3280    set(handles_civ0(ibutton),'BackgroundColor',[0.831 0.816 0.784])
3281    set(handles_civ0(ibutton),'Value',0)
3282end
3283if exist('handle1','var')%handles of selected button
3284        set(handle1,'BackgroundColor',[1 1 0]) 
3285end
3286
3287%-------------------------------------------------------
3288% --- Executes on button press in MENUVOLUME.
3289%-------------------------------------------------------
3290function VOLUME_Callback(hObject, eventdata, handles)
3291%errordlg('command VOL not implemented yet')
3292if ishandle(handles.UVMAT_title)
3293    delete(handles.UVMAT_title)
3294end
3295UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
3296if isequal(get(handles.VOLUME,'Value'),1)
3297    set(handles.CheckZoom,'Value',0)
3298    set(handles.CheckZoom,'BackgroundColor',[0.7 0.7 0.7])
3299    set(handles.edit_vect,'Value',0)
3300    edit_vect_Callback(hObject, eventdata, handles)
3301    set(handles.edit_object,'Value',0)
3302    set(handles.edit_object,'BackgroundColor',[0.7 0.7 0.7])
3303%     set(handles.cal,'Value',0)
3304%     set(handles.cal,'BackgroundColor',[0 1 0])
3305    set(handles.edit_vect,'Value',0)
3306    edit_vect_Callback(hObject, eventdata, handles)
3307    %initiate set_object GUI
3308    data.Name='VOLUME';
3309    if isfield(UvData,'CoordType')
3310        data.CoordType=UvData.CoordType;
3311    end
3312    if isfield(UvData.Field,'Mesh')&~isempty(UvData.Field.Mesh)
3313        data.RangeX=[UvData.Field.XMin UvData.Field.XMax];
3314        data.RangeY=[UvData.Field.YMin UvData.Field.YMax];
3315        data.DX=UvData.Field.Mesh;
3316        data.DY=UvData.Field.Mesh;
3317    elseif isfield(UvData.Field,'AX')&isfield(UvData.Field,'AY')& isfield(UvData.Field,'A')%only image
3318        np=size(UvData.Field.A);
3319        meshx=(UvData.Field.AX(end)-UvData.Field.AX(1))/np(2);
3320        meshy=abs(UvData.Field.AY(end)-UvData.Field.AY(1))/np(1);
3321        data.RangeY=max(meshx,meshy);
3322        data.RangeX=max(meshx,meshy);
3323        data.DX=max(meshx,meshy);
3324    end
3325    data.ParentButton=handles.VOLUME;
3326    PlotHandles=get_plot_handles(handles);%get the handles of the interface elements setting the plotting parameters
3327    [hset_object,UvData.sethandles]=set_object(data,PlotHandles);% call the set_object interface with action on haxes,
3328                                                      % associate the set_object interface handle to the plotting axes
3329    set(hset_object,'Position',get(handles.uvmat,'Position')+UvData.OpenParam.PosSetObject)
3330    UvData.MouseAction='create_object';
3331else
3332    set(handles.VOLUME,'BackgroundColor',[0 1 0])
3333end
3334set(handles.uvmat,'UserData',UvData)
3335
3336%-------------------------------------------------------
3337function edit_vect_Callback(hObject, eventdata, handles)
3338%-------------------------------------------------------
3339%
3340% UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
3341if isequal(get(handles.edit_vect,'Value'),1)
3342    test_civ2=isequal(get(handles.civ2,'BackgroundColor'),[1 1 0]);
3343    test_civ1=isequal(get(handles.VelType,'BackgroundColor'),[1 1 0]);
3344    if ~test_civ2 && ~test_civ1
3345        msgbox_uvmat('ERROR','manual correction only possible for CIV1 or CIV2 velocity fields')
3346    end
3347    set(handles.record,'Visible','on')
3348    set(handles.edit_vect,'BackgroundColor',[1 1 0])
3349    set(handles.edit_object,'Value',0)
3350    set(handles.CheckZoom,'Value',0)
3351    set(handles.CheckZoom,'BackgroundColor',[0.7 0.7 0.7])
3352%     set(handles.create,'Value',0)
3353%     set(handles.create,'BackgroundColor',[0 1 0])
3354    set(handles.edit_object,'BackgroundColor',[0.7 0.7 0.7])
3355    set(gcf,'Pointer','arrow')
3356%     UvData.MouseAction='edit_vect';
3357else
3358    set(handles.record,'Visible','off')
3359    set(handles.edit_vect,'BackgroundColor',[0.7 0.7 0.7])
3360end
3361
3362%----------------------------------------------
3363function save_mask_Callback(hObject, eventdata, handles)
3364%-----------------------------------------------------------------------
3365UvData=get(handles.uvmat,'UserData');
3366
3367flag=1;
3368npx=size(UvData.Field.A,2);
3369npy=size(UvData.Field.A,1);
3370xi=0.5:npx-0.5;
3371yi=0.5:npy-0.5;
3372[Xi,Yi]=meshgrid(xi,yi);
3373if isfield(UvData,'Object')
3374    for iobj=1:length(UvData.Object)
3375        ObjectData=UvData.Object{iobj};
3376        if isfield(ObjectData,'ProjMode') &&(isequal(ObjectData.ProjMode,'mask_inside')||isequal(ObjectData.ProjMode,'mask_outside'));
3377            flagobj=1;
3378            testphys=0; %coordinates in pixels by default
3379            if isfield(ObjectData,'CoordType') && isequal(ObjectData.CoordType,'phys')
3380                if isfield(UvData,'XmlData')&& isfield(UvData.XmlData{1},'GeometryCalib')
3381                    Calib=UvData.XmlData{1}.GeometryCalib;
3382                    testphys=1;
3383                end
3384            end
3385            if isfield(ObjectData,'Coord')& isfield(ObjectData,'Style')
3386                if isequal(ObjectData.Type,'polygon')
3387                    X=ObjectData.Coord(:,1);
3388                    Y=ObjectData.Coord(:,2);
3389                    if testphys
3390                        [X,Y]=px_XYZ(Calib,X,Y,0);% to generalise with 3D cases
3391                    end
3392                    flagobj=~inpolygon(Xi,Yi,X',Y');%=0 inside the polygon, 1 outside                 
3393                elseif isequal(ObjectData.Type,'ellipse')
3394                    if testphys
3395                        %[X,Y]=px_XYZ(Calib,X,Y,0);% TODO:create a polygon boundary and transform to phys
3396                    end
3397                    RangeX=max(ObjectData.RangeX);
3398                    RangeY=max(ObjectData.RangeY);
3399                    X2Max=RangeX*RangeX;
3400                    Y2Max=RangeY*RangeY;
3401                    distX=(Xi-ObjectData.Coord(1,1));
3402                    distY=(Yi-ObjectData.Coord(1,2));
3403                    flagobj=(distX.*distX/X2Max+distY.*distY/Y2Max)>1;
3404                elseif isequal(ObjectData.Type,'rectangle')
3405                    if testphys
3406                        %[X,Y]=px_XYZ(Calib,X,Y,0);% TODO:create a polygon boundary and transform to phys
3407                    end
3408                    distX=abs(Xi-ObjectData.Coord(1,1));
3409                    distY=abs(Yi-ObjectData.Coord(1,2));
3410                    flagobj=distX>max(ObjectData.RangeX) | distY>max(ObjectData.RangeY);
3411                end
3412                if isequal(ObjectData.ProjMode,'mask_outside')
3413                    flagobj=~flagobj;
3414                end
3415                flag=flag & flagobj;
3416            end
3417        end
3418    end
3419end
3420% flag=~flag;
3421%mask name
3422RootPath=get(handles.RootPath,'String');
3423RootFile=get(handles.RootFile,'String');
3424RootFile=regexprep(RootFile,'\<[\\/]|[\\/]\>','');%suppress possible / or \ separator at the beginning or the end of the string
3425filebase=fullfile(RootPath,RootFile);
3426list=get(handles.masklevel,'String');
3427masknumber=num2str(length(list));
3428maskindex=get(handles.masklevel,'Value');
3429mask_name=fullfile_uvmat(RootPath,SubDir,[RootFile '_' masknumber 'mask'],'.png','_1',maskindex);
3430%mask_name=name_generator([filebase '_' masknumber 'mask'],maskindex,1,'.png','_i');
3431imflag=uint8(255*(0.392+0.608*flag));% =100 for flag=0 (vectors not computed when 20<imflag<200)
3432imflag=flipdim(imflag,1);
3433% imflag=uint8(255*flag);% =0 for flag=0 (vectors=0 when 20<imflag<200)
3434msgbox_uvmat('CONFIRMATION',[mask_name ' saved'])
3435imwrite(imflag,mask_name,'BitDepth',8);
3436
3437%display the mask
3438figure;
3439vec=linspace(0,1,256);%define a linear greyscale colormap
3440map=[vec' vec' vec'];
3441colormap(map)
3442
3443image(imflag);
3444
3445%-------------------------------------------------------------------
3446%-------------------------------------------------------------------
3447%  - FUNCTIONS FOR SETTING PLOTTING PARAMETERS
3448
3449%------------------------------------------------------------------
3450%-------------------------------------------------------------
3451% --- Executes on selection change in transform_fct.
3452
3453function transform_fct_Callback(hObject, eventdata, handles)
3454%-------------------------------------------------------------
3455UvData=get(handles.uvmat,'UserData');
3456menu=get(handles.transform_fct,'String');refresh
3457ichoice=get(handles.transform_fct,'Value');%item number in the menu
3458transform_name=menu{ichoice};% choice of the transform fct
3459list_path=get(handles.transform_fct,'UserData');
3460
3461%% add a new item to the menu if the option 'more...' has been selected
3462prev_path=fullfile(get(handles.path_transform,'String'));
3463if ~exist(prev_path,'dir')
3464    prev_path=fullfile(fileparts(which('uvmat')),'transform_field');
3465end
3466if strcmp(transform_name,'more...');
3467    [FileName, PathName] = uigetfile( ...
3468        {'*.m', ' (*.m)';
3469        '*.m',  '.m files '; ...
3470        '*.*', 'All Files (*.*)'}, ...
3471        'Pick the transform function', prev_path);
3472    if ~ischar(FileName),return,end %abandon if the browser is cancelled
3473    path_transform_fct =fullfile(PathName,FileName);
3474    if isempty(regexp(FileName,'.m$'))% detect file extension .m
3475        msgbox_uvmat('ERROR','a Matlab function .m must be introduced');
3476        return
3477    else
3478        transform_name=regexprep(FileName,'.m','');
3479    end
3480    ichoice=find(strcmp(transform_name,menu),1);%look for the selected fct in the existing menu
3481    if isempty(ichoice)% if the item is not found, add it to the menu (before 'more...' and select it)
3482        menu=[menu(1:end-1);{transform_name};{'more...'}];
3483        ichoice=numel(menu)-1;   
3484    end
3485    list_path{ichoice}=PathName;%update the list fo fct paths
3486    set(handles.transform_fct,'String',menu)
3487    set(handles.transform_fct,'Value',ichoice)
3488   
3489    % save the new menu in the personal file 'uvmat_perso.mat'
3490    dir_perso=prefdir;%personal Matalb directory
3491    profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
3492    if exist(profil_perso,'file')
3493        nb_builtin=UvData.OpenParam.NbBuiltin;% number of 'builtin' (basic) transform fcts in uvmat
3494        if nb_builtin<numel(list_path)
3495        for ilist=nb_builtin+1:numel(list_path)
3496            transform_fct{ilist-nb_builtin}=[fullfile(list_path{ilist},menu{ilist}) '.m'];
3497        end
3498        save (profil_perso,'transform_fct','-append'); %store the root name for future opening of uvmat
3499        end
3500    end
3501end
3502
3503%% create the function handle of the selected fct
3504
3505if isempty(list_path{ichoice})% case of no selected fct
3506    transform_handle=[];
3507else
3508    if ~exist(list_path{ichoice},'dir')
3509        msgbox_uvmat('ERROR','invalid fct path: select the transform fct again with the option more...')
3510        return
3511    end
3512    current_dir=pwd;%current working dir
3513    cd(list_path{ichoice})
3514    transform_handle=str2func(transform_name);
3515    cd(current_dir)
3516end
3517set(handles.path_transform,'String',list_path{ichoice})
3518set(handles.path_transform,'UserData',transform_handle)
3519set(handles.transform_fct,'UserData',list_path)
3520
3521%% update the ToolTip string of the menu transform_fct with the first line of the selected fct file
3522if isempty(list_path{ichoice})% case of no selected fct
3523    set(handles.transform_fct,'ToolTipString','transform_fct:choose a transform function')
3524else
3525    try
3526        [fid,errormsg] =fopen([fullfile(list_path{ichoice},transform_name) '.m']);
3527        InputText=textscan(fid,'%s',1,'delimiter','\n');
3528        fclose(fid)
3529        set(handles.transform_fct,'ToolTipString',['transform_fct: ' InputText{1}{1}])% put the first line of the selected function as tooltip help
3530    end
3531end
3532
3533%% adapt the GUI to the input/output conditions of the selected transform fct
3534DataOut=[];
3535CoordUnit='';
3536CoordUnitPrev='';
3537if isfield(UvData,'Field')&&isfield(UvData.Field,'CoordUnit')
3538    CoordUnitPrev=UvData.Field.CoordUnit;
3539end
3540if ~isempty(list_path{ichoice})
3541    if nargin(transform_handle)>1 && isfield(UvData,'XmlData')&&~isempty(UvData.XmlData)
3542        XmlData=UvData.XmlData{1};
3543        DataOut=feval(transform_handle,'*',XmlData);
3544        if isfield(DataOut,'CoordUnit')
3545            CoordUnit=DataOut.CoordUnit;
3546        end
3547        if isfield(DataOut,'InputFieldType')
3548            UvData.InputFieldType=DataOut.InputFieldType;
3549        end
3550    else
3551        DataOut=feval(transform_handle,'*');
3552    end
3553end
3554
3555
3556%% delete drawn objects if the output CooordUnit is different from the previous one
3557if ~strcmp(CoordUnit,CoordUnitPrev)
3558    set(handles.CheckFixLimits,'Value',0)
3559set(handles.CheckFixLimits,'BackgroundColor',[0.7 0.7 0.7])
3560    hother=findobj('Tag','proj_object');%find all the proj objects
3561    for iobj=1:length(hother)
3562        delete_object(hother(iobj))
3563    end
3564    hother=findobj('Tag','DeformPoint');%find all the proj objects
3565    for iobj=1:length(hother)
3566        delete_object(hother(iobj))
3567    end
3568    hh=findobj('Tag','calib_points');
3569    if ~isempty(hh)
3570        delete(hh)
3571    end
3572    hhh=findobj('Tag','calib_marker');
3573    if ~isempty(hhh)
3574        delete(hhh)
3575    end
3576%     if isfield(UvData,'Object')
3577%         UvData.Object=UvData.Object(1);
3578%     end
3579    set(handles.ListObject,'Value',1)
3580    set(handles.ListObject,'String',{''})
3581    set(handles.ListObject_1,'Value',1)
3582    set(handles.ListObject_1,'String',{''})
3583    set(handles.ViewObject,'value',0)
3584    ViewObject_Callback(hObject, eventdata, handles)
3585    set(handles.ViewField,'value',0)
3586    ViewField_Callback(hObject, eventdata, handles)
3587    set(handles.edit_object,'Value',0)
3588    edit_object_Callback(hObject, eventdata, handles)
3589    UvData.Object={[]};
3590end
3591set(handles.uvmat,'UserData',UvData)
3592
3593%% refresh the current plot
3594if isempty(list_path{ichoice}) || nargin(transform_handle)<3
3595    set(handles.SubField,'Value',0)
3596    SubField_Callback(hObject, eventdata, handles)
3597else
3598    run0_Callback(hObject, eventdata, handles)
3599end
3600
3601%------------------------------------------------
3602%CALLBACKS FOR PLOTTING PARAMETERS
3603%-------------------------------------------------
3604%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3605% Plot coordinates
3606%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3607%------------------------------------------------------------------------
3608function num_MinX_Callback(hObject, eventdata, handles)
3609%------------------------------------------------------------------------
3610set(handles.CheckFixLimits,'Value',1) %suppress auto mode
3611set(handles.CheckFixLimits,'BackgroundColor',[1 1 0])
3612update_plot(handles);
3613
3614%------------------------------------------------------------------------
3615function num_MaxX_Callback(hObject, eventdata, handles)
3616%------------------------------------------------------------------------
3617set(handles.CheckFixLimits,'Value',1) %suppress auto mode
3618set(handles.CheckFixLimits,'BackgroundColor',[1 1 0])
3619update_plot(handles);
3620
3621%------------------------------------------------------------------------
3622function num_MinY_Callback(hObject, eventdata, handles)
3623%------------------------------------------
3624set(handles.CheckFixLimits,'Value',1) %suppress auto mode
3625set(handles.CheckFixLimits,'BackgroundColor',[1 1 0])
3626update_plot(handles);
3627
3628%------------------------------------------------------------------------
3629function num_MaxY_Callback(hObject, eventdata, handles)
3630%------------------------------------------------------------------------
3631set(handles.CheckFixLimits,'Value',1) %suppress auto mode
3632set(handles.CheckFixLimits,'BackgroundColor',[1 1 0])
3633update_plot(handles);
3634
3635%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3636% Scalar or image representation
3637%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3638%------------------------------------------------------------------------
3639function num_MinA_Callback(hObject, eventdata, handles)
3640%------------------------------------------
3641set(handles.CheckFixScalar,'Value',1) %suppress auto mode
3642set(handles.CheckFixScalar,'BackgroundColor',[1 1 0])
3643MinA=str2double(get(handles.num_MinA,'String'));
3644MaxA=str2double(get(handles.num_MaxA,'String'));
3645if MinA>MaxA% switch minA and maxA in case of error
3646    MinA_old=MinA;
3647    MinA=MaxA;
3648    MaxA=MinA_old;
3649    set(handles.num_MinA,'String',num2str(MinA,5));
3650    set(handles.num_MaxA,'String',num2str(MaxA,5));
3651end
3652update_plot(handles);
3653
3654%------------------------------------------------------------------------
3655function num_MaxA_Callback(hObject, eventdata, handles)
3656%------------------------------------------------------------------------
3657set(handles.CheckFixScalar,'Value',1) %suppress auto mode
3658set(handles.CheckFixScalar,'BackgroundColor',[1 1 0])
3659MinA=str2double(get(handles.num_MinA,'String'));
3660MaxA=str2double(get(handles.num_MaxA,'String'));
3661if MinA>MaxA% switch minA and maxA in case of error
3662        MinA_old=MinA;
3663    MinA=MaxA;
3664    MaxA=MinA_old;
3665    set(handles.num_MinA,'String',num2str(MinA,5));
3666    set(handles.num_MaxA,'String',num2str(MaxA,5));
3667end
3668update_plot(handles);
3669
3670%------------------------------------------------------------------------
3671function CheckFixScalar_Callback(hObject, eventdata, handles)
3672%------------------------------------------------------------------------
3673test=get(handles.CheckFixScalar,'Value');
3674if test
3675    set(handles.CheckFixScalar,'BackgroundColor',[1 1 0])
3676else
3677    set(handles.CheckFixScalar,'BackgroundColor',[0.7 0.7 0.7])
3678    update_plot(handles);
3679end
3680
3681%-------------------------------------------------------------------
3682function CheckBW_Callback(hObject, eventdata, handles)
3683%-------------------------------------------------------------------
3684update_plot(handles);
3685
3686%-------------------------------------------------------------------
3687function num_Opacity_Callback(hObject, eventdata, handles)
3688update_plot(handles);
3689%-------------------------------------------------------------------
3690
3691%-------------------------------------------------------------------
3692function ListContour_Callback(hObject, eventdata, handles)
3693%-------------------------------------------------------------------
3694val=get(handles.ListContour,'Value');
3695if val==2
3696    set(handles.interval_txt,'Visible','on')
3697    set(handles.num_IncrA,'Visible','on')
3698else
3699    set(handles.interval_txt,'Visible','off')
3700    set(handles.num_IncrA,'Visible','off')
3701end
3702update_plot(handles);
3703
3704%-------------------------------------------------------------------
3705function num_IncrA_Callback(hObject, eventdata, handles)
3706%-------------------------------------------------------------------
3707update_plot(handles);
3708
3709
3710%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3711% Vector representation
3712%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3713%-------------------------------------------------------------------
3714function CheckHideWarning_Callback(hObject, eventdata, handles)
3715%-------------------------------------------------------------------
3716update_plot(handles);
3717
3718%-------------------------------------------------------------------
3719function CheckHideFalse_Callback(hObject, eventdata, handles)
3720%-------------------------------------------------------------------
3721update_plot(handles);
3722
3723%-------------------------------------------------------------------
3724function num_VecScale_Callback(hObject, eventdata, handles)
3725%-------------------------------------------------------------------
3726set(handles.CheckFixVectors,'Value',1);
3727set(handles.CheckFixVectors,'BackgroundColor',[1 1 0])
3728update_plot(handles);
3729
3730%-------------------------------------------------------------------
3731function CheckFixVectors_Callback(hObject, eventdata, handles)
3732%-------------------------------------------------------------------
3733test=get(handles.CheckFixVectors,'Value');
3734if test
3735    set(handles.CheckFixVectors,'BackgroundColor',[1 1 0])
3736else
3737    update_plot(handles);
3738    %set(handles.num_VecScale,'String',num2str(ScalOut.num_VecScale,3))
3739    set(handles.CheckFixVectors,'BackgroundColor',[0.7 0.7 0.7])
3740end
3741
3742%------------------------------------------------------------------------
3743% --- Executes on selection change in CheckDecimate4 (nb_vec/4).
3744function CheckDecimate4_Callback(hObject, eventdata, handles)
3745%------------------------------------------------------------------------
3746update_plot(handles);
3747
3748%------------------------------------------------------------------------
3749% --- Executes on selection change in ColorCode menu
3750function ColorCode_Callback(hObject, eventdata, handles)
3751%------------------------------------------------------------------------
3752% edit the choice for color code
3753update_color_code_boxes(handles);
3754update_plot(handles);
3755
3756%------------------------------------------------------------------------
3757function update_color_code_boxes(handles)
3758%------------------------------------------------------------------------
3759list_code=get(handles.ColorCode,'String');% list menu fields
3760colcode= list_code{get(handles.ColorCode,'Value')}; % selected field
3761enable_slider='off';%default
3762enable_bounds='off';%default
3763enable_scalar='off';%default
3764switch colcode
3765    case {'rgb','bgr'}
3766        enable_slider='on';
3767        enable_bounds='on';
3768        enable_scalar='on';
3769    case '64 colors'
3770        enable_bounds='on';
3771        enable_scalar='on';
3772end
3773set(handles.Slider1,'Visible',enable_slider)
3774set(handles.Slider2,'Visible', enable_slider)
3775set(handles.num_ColCode1,'Visible',enable_slider)
3776set(handles.num_ColCode2,'Visible',enable_slider)
3777set(handles.TitleColCode1,'Visible',enable_slider)
3778set(handles.TitleColCode2,'Visible',enable_slider)
3779set(handles.CheckFixVecColor,'Visible',enable_bounds)
3780set(handles.num_MinVec,'Visible',enable_bounds)
3781set(handles.num_MaxVec,'Visible',enable_bounds)
3782set(handles.ColorScalar,'Visible',enable_scalar)
3783set_vec_col_bar(handles)
3784
3785%------------------------------------------------------------------
3786% --- Executes on selection change in ColorScalar: choice of the color code.
3787function ColorScalar_Callback(hObject, eventdata, handles)
3788%------------------------------------------------------------------
3789% edit the choice for color code
3790list_scalar=get(handles.ColorScalar,'String');% list menu fields
3791col_scalar= list_scalar{get(handles.ColorScalar,'Value')}; % selected field
3792if isequal(col_scalar,'ima_cor')
3793    set(handles.CheckFixVecColor,'Value',1)%fixed scale by default
3794    ColorCode='rgb';
3795    set(handles.num_MinVec,'String','0')
3796    set(handles.num_MaxVec,'String','1')
3797    set(handles.num_ColCode1,'String','0.333')
3798    set(handles.num_ColCode2,'String','0.666')
3799else
3800    set(handles.CheckFixVecColor,'Value',0)%auto scale between min,max by default
3801    ColorCode='64 colors';
3802end
3803ColorCodeList=get(handles.ColorCode,'String');
3804ichoice=find(strcmp(ColorCode,ColorCodeList),1);
3805set(handles.ColorCode,'Value',ichoice)% set color code in the menu
3806
3807update_color_code_boxes(handles);
3808%replot the current graph
3809run0_Callback(hObject, eventdata, handles)
3810
3811%----------------------------------------------------------------
3812% -- Executes on slider movement to set the color code
3813%
3814function Slider1_Callback(hObject, eventdata, handles)
3815%------------------------------------------------------------------
3816slider1=get(handles.Slider1,'Value');
3817min_val=str2num(get(handles.num_MinVec,'String'));
3818max_val=str2num(get(handles.num_MaxVec,'String'));
3819col=min_val+(max_val-min_val)*slider1;
3820set(handles.num_ColCode1,'String',num2str(col))
3821if(get(handles.Slider2,'Value') < col)%move also the second slider at the same value if needed
3822    set(handles.Slider2,'Value',col)
3823    set(handles.num_ColCode2,'String',num2str(col))
3824end
3825set_vec_col_bar(handles)
3826update_plot(handles);
3827
3828%----------------------------------------------------------------
3829% Executes on slider movement to set the color code
3830%----------------------------------------------------------------
3831function Slider2_Callback(hObject, eventdata, handles)
3832slider2=get(handles.Slider2,'Value');
3833min_val=str2num(get(handles.num_MinVec,'String'));
3834max_val=str2num(get(handles.num_MaxVec,'String'));
3835col=min_val+(max_val-min_val)*slider2;
3836set(handles.num_ColCode2,'String',num2str(col))
3837if(get(handles.Slider1,'Value') > col)%move also the first slider at the same value if needed
3838    set(handles.Slider1,'Value',col)
3839    set(handles.num_ColCode1,'String',num2str(col))
3840end
3841set_vec_col_bar(handles)
3842update_plot(handles);
3843
3844%----------------------------------------------------------------
3845% --- Execute on return carriage on the edit box corresponding to slider 1
3846%----------------------------------------------------------------
3847function num_ColCode1_Callback(hObject, eventdata, handles)
3848set_vec_col_bar(handles)
3849update_plot(handles);
3850
3851%----------------------------------------------------------------
3852% --- Execute on return carriage on the edit box corresponding to slider 2
3853%----------------------------------------------------------------
3854function num_ColCode2_Callback(hObject, eventdata, handles)
3855set_vec_col_bar(handles)
3856update_plot(handles);
3857%------------------------------------------------------------------------
3858%-------------------------------------------------------
3859% --- Executes on button press in CheckFixVecColor.
3860%-------------------------------------------------------
3861function VecColBar_Callback(hObject, eventdata, handles)
3862set_vec_col_bar(handles)
3863
3864%------------------------------------------------------------------------
3865% --- Executes on button press in CheckFixVecColor.
3866function CheckFixVecColor_Callback(hObject, eventdata, handles)
3867%------------------------------------------------------------------------
3868if ~get(handles.CheckFixVecColor,'Value')
3869    update_plot(handles);
3870end
3871
3872%------------------------------------------------------------------------
3873% --- Executes on selection change in num_MaxVec.
3874function num_MinVec_Callback(hObject, eventdata, handles)
3875%------------------------------------------------------------------------
3876max_vec_Callback(hObject, eventdata, handles)
3877
3878%------------------------------------------------------------------------
3879% --- Executes on selection change in num_MaxVec.
3880function num_MaxVec_Callback(hObject, eventdata, handles)
3881%------------------------------------------------------------------------
3882set(handles.CheckFixVecColor,'Value',1)
3883CheckFixVecColor_Callback(hObject, eventdata, handles)
3884min_val=str2num(get(handles.num_MinVec,'String'));
3885max_val=str2num(get(handles.num_MaxVec,'String'));
3886slider1=get(handles.Slider1,'Value');
3887slider2=get(handles.Slider2,'Value');
3888colcode1=min_val+(max_val-min_val)*slider1;
3889colcode2=min_val+(max_val-min_val)*slider2;
3890set(handles.num_ColCode1,'String',num2str(colcode1))
3891set(handles.num_ColCode2,'String',num2str(colcode2))
3892update_plot(handles);
3893
3894%------------------------------------------------------------------------
3895% --- update the display of color code for vectors (on vecColBar)
3896function set_vec_col_bar(handles)
3897%------------------------------------------------------------------------
3898%get the image of the color display button 'VecColBar' in pixels
3899set(handles.VecColBar,'Unit','pixel');
3900pos_vert=get(handles.VecColBar,'Position');
3901set(handles.VecColBar,'Unit','Normalized');
3902width=ceil(pos_vert(3));
3903height=ceil(pos_vert(4));
3904
3905%get slider indications
3906list=get(handles.ColorCode,'String');
3907ichoice=get(handles.ColorCode,'Value');
3908colcode.ColorCode=list{ichoice};
3909colcode.MinVec=str2num(get(handles.num_MinVec,'String'));
3910colcode.MaxVec=str2num(get(handles.num_MaxVec,'String'));
3911test3color=strcmp(colcode.ColorCode,'rgb') || strcmp(colcode.ColorCode,'bgr');
3912if test3color
3913    colcode.ColCode1=str2num(get(handles.num_ColCode1,'String'));
3914    colcode.ColCode2=str2num(get(handles.num_ColCode2,'String'));
3915end
3916vec_C=colcode.MinVec+(colcode.MaxVec-colcode.MinVec)*(0.5:width-0.5)/width;%sample of vec_C values from min to max
3917[colorlist,col_vec]=set_col_vec(colcode,vec_C);
3918oneheight=ones(1,height);
3919A1=colorlist(col_vec,1)*oneheight;
3920A2=colorlist(col_vec,2)*oneheight;
3921A3=colorlist(col_vec,3)*oneheight;
3922A(:,:,1)=A1';
3923A(:,:,2)=A2';
3924A(:,:,3)=A3';
3925set(handles.VecColBar,'Cdata',A)
3926
3927%-------------------------------------------------------------------
3928function update_plot(handles)
3929%-------------------------------------------------------------------
3930UvData=get(handles.uvmat,'UserData');
3931AxeData=UvData.PlotAxes;% retrieve the current plotted data
3932PlotParam=read_GUI(handles.uvmat);
3933[tild,PlotParamOut]= plot_field(AxeData,handles.PlotAxes,PlotParam);
3934write_plot_param(handles,PlotParamOut); %update the auto plot parameters
3935
3936%------------------------------------------------------------------------
3937%------------------------------------------------------------------------
3938%   SELECTION AND EDITION OF PROJECTION OBJECTS
3939%------------------------------------------------------------------------
3940%------------------------------------------------------------------------
3941
3942% --- Executes on selection change in ListObject_1.
3943function ListObject_1_Callback(hObject, eventdata, handles)
3944list_str=get(handles.ListObject,'String');
3945UvData=get(handles.uvmat,'UserData');
3946ObjectData=UvData.Object{get(handles.ListObject_1,'Value')};
3947
3948%% update the projection plot on uvmat
3949ProjData= proj_field(UvData.Field,ObjectData);%project the current input field on object ObjectData
3950plot_field(ProjData,handles.PlotAxes,read_GUI(handles.uvmat));% plot the projected field;
3951%replot all the objects within the new projected field
3952for IndexObj=1:numel(list_str)
3953        hobject=UvData.Object{IndexObj}.DisplayHandle.uvmat;
3954        if isempty(hobject) || ~ishandle(hobject)
3955            hobject=handles.PlotAxes;
3956        end
3957        if isequal(IndexObj,get(handles.ListObject,'Value'))
3958            objectcolor='m'; %paint in magenta the currently selected object in ListObject
3959        else
3960            objectcolor='b';
3961        end
3962        UvData.Object{IndexObj}.DisplayHandle.uvmat=plot_object(UvData.Object{IndexObj},ObjectData,hobject,objectcolor);%draw the object in uvmat     
3963end
3964set(handles.uvmat,'UserData',UvData)
3965
3966%% display the object parameters if the GUI set_object is already opened
3967if ~get(handles.ViewObject,'Value')
3968    ZBounds=0; % default
3969    if isfield(UvData.Field,'ZMin') && isfield(UvData.Field,'ZMax')
3970        ZBounds(1)=UvData.Field.ZMin; %minimum for the Z slider
3971        ZBounds(2)=UvData.Field.ZMax;%maximum for the Z slider
3972    end
3973    ObjectData.Name=list_str{get(handles.ListObject_1,'Value')};
3974    set_object(ObjectData,[],ZBounds);
3975    set(handles.ViewObject,'Value',1)% show that the selected object in ListObject_1 is currently visualised
3976end
3977
3978%  desactivate the edit object mode
3979set(handles.edit_object,'Value',0)
3980set(handles.edit_object,'BackgroundColor',[0.7,0.7,0.7])
3981
3982%------------------------------------------------------------------------
3983% --- Executes on selection change in ListObject.
3984function ListObject_Callback(hObject, eventdata, handles)
3985%------------------------------------------------------------------------
3986list_str=get(handles.ListObject,'String');
3987IndexObj=get(handles.ListObject,'Value');%present object selection
3988
3989%% The object  is displayed in set_object if this GUI is already opened
3990UvData=get(handles.uvmat,'UserData');
3991ObjectData=UvData.Object{IndexObj};
3992hset_object=findobj(allchild(0),'tag','set_object');
3993if ~isempty(hset_object)
3994    ZBounds=0; % default
3995    if isfield(UvData.Field,'ZMin') && isfield(UvData.Field,'ZMax')
3996        ZBounds(1)=UvData.Field.ZMin; %minimum for the Z slider
3997        ZBounds(2)=UvData.Field.ZMax;%maximum for the Z slider
3998    end
3999    ObjectData.Name=list_str{IndexObj};
4000    set_object(ObjectData,[],ZBounds);
4001    set(handles.ViewField,'Value',1)% show that the selected object in ListObject is currently visualised
4002end
4003
4004%%  desactivate the edit object mode
4005set(handles.edit_object,'Value',0)
4006set(handles.edit_object,'BackgroundColor',[0.7,0.7,0.7])
4007
4008%% update the  plot on view_field if view_field is already openened
4009hview_field=findobj(allchild(0),'tag','view_field');
4010if isempty(hview_field)
4011    hhview_field.PlotAxes=[];
4012else
4013    Data=get(hview_field,'UserData');
4014    hhview_field=guidata(hview_field);
4015    ProjData= proj_field(UvData.Field,ObjectData);%project the current interface field on ObjectData
4016    [PlotType,PlotParam]=plot_field(ProjData,hhview_field.PlotAxes,read_GUI(hview_field));%read plotting parameters on the uvmat interfachhview_fiel
4017    write_plot_param(hhview_field,PlotParam); %update the display of plotting parameters for the current object
4018    haxes=findobj(hview_field,'tag','axes3');
4019    pos=get(hview_field,'Position'); 
4020    if strcmp(get(haxes,'Visible'),'off')%sempty(PlotParam.Coordinates)% case of no plot display (pure text table)
4021        h_TableDisplay=findobj(hview_field,'tag','TableDisplay');
4022        pos_table=get(h_TableDisplay,'Position');
4023        set(hview_field,'Position',[pos(1)+pos(3)-pos_table(3) pos(2)+pos(4)-pos_table(4) pos_table(3) pos_table(4)])
4024        drawnow% needed to change position before the next command
4025        set(hview_field,'UserData',Data);% restore the previously stored GUI position after GUI resizing
4026    else
4027        set(hview_field,'Position',Data.GUISize)% return to the previously stored GUI position and size
4028    end
4029end
4030
4031%% update the color of the graphic object representation: the selected object in magenta, others in blue
4032update_object_color(handles.PlotAxes,hhview_field.PlotAxes,UvData.Object{IndexObj}.DisplayHandle.uvmat)
4033
4034%------------------------------------------------------------------------
4035%--- update the color representation of objects (indicating the selected ones)
4036function update_object_color(axes_uvmat,axes_view_field,DisplayHandle)
4037%------------------------------------------------------------------------
4038if isempty(axes_view_field)% case with no view_field plot
4039hother=[findobj(axes_uvmat,'Tag','proj_object');findobj(axes_uvmat,'Tag','DeformPoint')];%find all the proj object and deform point representations
4040else
4041hother=[findobj(axes_uvmat,'Tag','proj_object') ;findobj(axes_view_field,'Tag','proj_object');... %find all the proj object representations
4042findobj(axes_uvmat,'Tag','DeformPoint'); findobj(axes_view_field,'Tag','DeformPoint')];%find all the deform point representations
4043end
4044for iobj=1:length(hother)
4045    if isequal(get(hother(iobj),'Type'),'rectangle')||isequal(get(hother(iobj),'Type'),'patch')
4046        set(hother(iobj),'EdgeColor','b')
4047        if isequal(get(hother(iobj),'FaceColor'),'m')
4048            set(hother(iobj),'FaceColor','b')
4049        end
4050    elseif isequal(get(hother(iobj),'Type'),'image')
4051        Acolor=get(hother(iobj),'CData');
4052        Acolor(:,:,1)=zeros(size(Acolor,1),size(Acolor,2));
4053        set(hother(iobj),'CData',Acolor);
4054    else
4055        set(hother(iobj),'Color','b')
4056    end
4057    set(hother(iobj),'Selected','off')
4058end
4059if ishandle(DisplayHandle)
4060    linetype=get(DisplayHandle,'Type');
4061    if isequal(linetype,'line')
4062        set(DisplayHandle,'Color','m'); %set the selected object to magenta color
4063    elseif isequal(linetype,'rectangle')
4064        set(DisplayHandle,'EdgeColor','m'); %set the selected object to magenta color
4065    elseif isequal(linetype,'patch')
4066        set(DisplayHandle,'FaceColor','m'); %set the selected object to magenta color
4067    end
4068    SubObjectData=get(DisplayHandle,'UserData');
4069    if isfield(SubObjectData,'SubObject') & ishandle(SubObjectData.SubObject)
4070        for iobj=1:length(SubObjectData.SubObject)
4071            hsub=SubObjectData.SubObject(iobj);
4072            if isequal(get(hsub,'Type'),'rectangle')
4073                set(hsub,'EdgeColor','m'); %set the selected object to magenta color
4074            elseif isequal(get(hsub,'Type'),'image')
4075                Acolor=get(hsub,'CData');
4076                Acolor(:,:,1)=Acolor(:,:,3);
4077                set(hsub,'CData',Acolor);
4078            else
4079                set(hsub,'Color','m')
4080            end
4081        end
4082    end
4083    if isfield(SubObjectData,'DeformPoint') & ishandle(SubObjectData.DeformPoint)
4084        set(SubObjectData.DeformPoint,'Color','m')
4085    end
4086end
4087
4088%-------------------------------------------------------------------
4089% --- Executes on selection change in edit_object.
4090function edit_object_Callback(hObject, eventdata, handles)
4091%-------------------------------------------------------------------
4092UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
4093hset_object=findobj(allchild(0),'Tag','set_object');
4094if get(handles.edit_object,'Value')
4095    set(handles.edit_object,'BackgroundColor',[1,1,0]) 
4096    %suppress the other options
4097    set(handles.CheckZoom,'Value',0)
4098    CheckZoom_Callback(hObject, eventdata, handles)
4099    hgeometry_calib=findobj(allchild(0),'tag','geometry_calib');
4100    if ishandle(hgeometry_calib)
4101        hhgeometry_calib=guidata(hgeometry_calib);
4102        set(hhgeometry_calib.edit_append,'Value',0)% desactivate mouse action in geometry_calib
4103        set(hhgeometry_calib.edit_append,'BackgroundColor',[0.7 0.7 0.7])
4104    end
4105    set(handles.ViewObject,'value',1)
4106    ViewObject_Callback(hObject, eventdata, handles)
4107else % desctivate object edit mode
4108    set(handles.edit_object,'BackgroundColor',[0.7,0.7,0.7]) 
4109    if ~isempty(hset_object)% open the
4110        hhset_object=guidata(hset_object);
4111        set(hhset_object.PLOT,'enable','off');
4112        set(get(hset_object,'children'),'enable','inactive')
4113    end
4114end
4115
4116
4117%------------------------------------------------------------------------
4118% --- Executes on button press in ViewObject.
4119function ViewObject_Callback(hObject, eventdata, handles)
4120%------------------------------------------------------------------------
4121check_view=get(handles.ViewObject,'Value');
4122
4123if check_view %activate set_object   
4124    IndexObj=get(handles.ListObject,'Value');
4125    list_object=get(handles.ListObject,'String');
4126    UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
4127    UvData.Object{IndexObj}.Name=list_object{IndexObj};
4128    if numel(UvData.Object)<IndexObj;% error in UvData
4129        msgbox_uvmat('ERROR','invalid object list')
4130        return
4131    end
4132    ZBounds=0; % default
4133    if isfield(UvData.Field,'ZMin') && isfield(UvData.Field,'ZMax')
4134        ZBounds(1)=UvData.Field.ZMin; %minimum for the Z slider
4135        ZBounds(2)=UvData.Field.ZMax;%maximum for the Z slider
4136    end
4137%     set(handles.ListObject_1,'Value',IndexObj);%restore ListObject selection after set_object deletion
4138    data=UvData.Object{IndexObj};
4139    if ~isfield(data,'Type')% default plane
4140        data.Type='plane';
4141    end
4142%     if isfield(UvData,'Field')
4143%         Field=UvData.Field;
4144%         if isfield(UvData.Field,'Mesh')&&~isempty(UvData.Field.Mesh)
4145%             data.RangeX=[UvData.Field.XMin UvData.Field.XMax];
4146%             if strcmp(data.Type,'line')||strcmp(data.Type,'polyline')
4147%                 data.RangeY=UvData.Field.Mesh;
4148%             else
4149%                 data.RangeY=[UvData.Field.YMin UvData.Field.YMax];
4150%             end
4151%             data.DX=UvData.Field.Mesh;
4152%             data.DY=UvData.Field.Mesh;
4153%         end
4154%         if isfield(Field,'NbDim')&& isequal(Field.NbDim,3)
4155%             data.Coord=[0 0 0]; %default
4156%         end
4157%         if isfield(Field,'CoordUnit')
4158%             data.CoordUnit=Field.CoordUnit;
4159%         end
4160%     end
4161    hset_object=set_object(data,[],ZBounds);
4162    hhset_object=guidata(hset_object);
4163    if get(handles.edit_object,'Value')% edit mode
4164        set(hhset_object.PLOT,'Enable','on')
4165        set(get(hset_object,'children'),'enable','on')
4166    else
4167        set(hhset_object.PLOT,'Enable','off')
4168        set(get(hset_object,'children'),'enable','inactive')% deactivate the GUI except SAVE
4169        set(hhset_object.SAVE,'Enable','on')
4170    end
4171else
4172    hset_object=findobj(allchild(0),'tag','set_object');
4173    if ~isempty(hset_object)
4174        delete(hset_object)% delete existing version of set_object
4175    end
4176end
4177 
4178
4179%------------------------------------------------------------------------
4180% --- Executes on button press in ViewField.
4181function ViewField_Callback(hObject, eventdata, handles)
4182%------------------------------------------------------------------------
4183check_view=get(handles.ViewField,'Value');
4184
4185if check_view
4186    IndexObj=get(handles.ListObject,'Value');
4187    UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
4188    if numel(UvData.Object)<IndexObj(end);% error in UvData
4189        msgbox_uvmat('ERROR','invalid object list')
4190        return
4191    end
4192    ZBounds=0; % default
4193    if isfield(UvData.Field,'ZMin') && isfield(UvData.Field,'ZMax')
4194        ZBounds(1)=UvData.Field.ZMin; %minimum for the Z slider
4195        ZBounds(2)=UvData.Field.ZMax;%maximum for the Z slider
4196    end
4197    set(handles.ListObject,'Value',IndexObj);%restore ListObject selection after set_object deletion
4198    if ~isfield(UvData.Object{IndexObj(1)},'Type')% default plane
4199        UvData.Object{IndexObj(1)}.Type='plane';
4200    end
4201    list_object=get(handles.ListObject,'String');
4202    UvData.Object{IndexObj(end)}.Name=list_object{IndexObj(end)};
4203   
4204    %% show the projection of the selected object on view_field
4205    ProjData= proj_field(UvData.Field,UvData.Object{IndexObj});%project the current field on ObjectData
4206    hview_field=findobj(allchild(0),'tag','view_field');
4207    if isempty(hview_field)
4208        hview_field=view_field;
4209    end
4210    hhview_field=guidata(hview_field);
4211    [PlotType,PlotParam]=plot_field(ProjData,hhview_field.PlotAxes,read_GUI(hview_field));%read plotting parameters on the GUI view_field);
4212    write_plot_param(hhview_field,PlotParam); %update the display of plotting parameters for the current object
4213    haxes=findobj(hview_field,'tag','axes3');
4214    pos=get(hview_field,'Position');
4215    if strcmp(get(haxes,'Visible'),'off')%sempty(PlotParam.Coordinates)% case of no plot display (pure text table)
4216        h_TableDisplay=findobj(hview_field,'tag','TableDisplay');
4217        pos_table=get(h_TableDisplay,'Position');
4218        set(hview_field,'Position',[pos(1)+pos(3)-pos_table(3) pos(2)+pos(4)-pos_table(4) pos_table(3) pos_table(4)])
4219    else
4220        Data=get(hview_field,'UserData');
4221        set(hview_field,'Position',Data.GUISize)% restore the size of view_field for plots
4222    end
4223else
4224    hview_field=findobj(allchild(0),'tag','view_field');
4225    if ~isempty(hview_field)
4226        delete(hview_field)% delete existing version of set_object
4227    end
4228end
4229
4230
4231%------------------------------------------------------------------------
4232% --- Executes on button press in delete_object.
4233function delete_object_Callback(hObject, eventdata, handles)
4234%------------------------------------------------------------------------
4235IndexObj=get(handles.ListObject,'Value');%projection object selected for view_field
4236IndexObj_1=get(handles.ListObject_1,'Value');%projection object selected for uvmat plot
4237if IndexObj>1 && ~isequal(IndexObj,IndexObj_1) % do not delete the object used for the uvmat plot
4238    delete_object(IndexObj)
4239end
4240
4241%------------------------------------------------------------------------
4242%------------------------------------------------------------------------
4243%  II - TOOLS FROM THE UPPER MENU BAR
4244%------------------------------------------------------------------------
4245%------------------------------------------------------------------------
4246
4247%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
4248% Export  Menu Callbacks
4249%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
4250%------------------------------------------------------------------------
4251% --- Executes on button press in Menu/Export/field in workspace.
4252function MenuExportField_Callback(hObject, eventdata, handles)
4253%------------------------------------------------------------------------
4254global Data_uvmat
4255Data_uvmat=get(handles.uvmat,'UserData');
4256evalin('base','global Data_uvmat')%make CurData global in the workspace
4257display('current field :')
4258evalin('base','Data_uvmat') %display CurData in the workspace
4259commandwindow; %brings the Matlab command window to the front
4260
4261%------------------------------------------------------------------------
4262% --- Executes on button press in Menu/Export/extract figure.
4263function MenuExportFigure_Callback(hObject, eventdata, handles)
4264%------------------------------------------------------------------------
4265% huvmat=get(handles.MenuExport,'parent');
4266hfig=figure;
4267copyobj(handles.PlotAxes,hfig);
4268map=colormap(handles.PlotAxes);
4269colormap(map);%transmit the current colormap to the zoom fig
4270colorbar
4271
4272% --------------------------------------------------------------------
4273function MenuExportAxis_Callback(hObject, eventdata, handles)
4274answer=msgbox_uvmat('CONFIRMATION','select a figure/axis on which the current uvmat plot will be exported')
4275if strcmp(answer,'Yes')
4276hchild=get(handles.PlotAxes,'children');
4277copyobj(hchild,gca);
4278end
4279
4280%------------------------------------------------------------------------
4281% --------------------------------------------------------------------
4282function MenuExportMovie_Callback(hObject, eventdata, handles)
4283% --------------------------------------------------------------------
4284set(handles.MenuExportMovie,'BusyAction','queue')% activate the button
4285huvmat=get(handles.run0,'parent');
4286UvData=get(huvmat,'UserData');
4287%[xx,xx,FileBase]=read_file_boxes(handles);
4288[RootPath,SubDir,RootFile,FileIndex,FileExt]=read_file_boxes(handles);
4289FileBase=fullfile(RootPath,RootFile);
4290 %read the current input file name
4291prompt = {'movie file name';'frames per second';'frame resolution (*[512x384] pixels)';'axis position relative to the frame';'total frame number (starting from the current uvmat display)'};
4292dlg_title = 'select properties of the output avi movie';
4293num_lines= 1;
4294def     = {[FileBase '_out.avi'];'10';'1';'[0.03 0.05 0.95 0.92]';'10'};
4295answer = inputdlg(prompt,dlg_title,num_lines,def,'on');
4296aviname=answer{1};
4297fps=str2double(answer{2});
4298% check for existing file with output name aviname
4299if exist(aviname,'file')
4300    backup=aviname;
4301    testexist=2;
4302    while testexist==2
4303        backup=[backup '~'];
4304        testexist=exist(backup,'file');     
4305    end
4306    [success,message]=copyfile(aviname,backup);%make backup of the existing file
4307    if isequal(success,1)
4308        delete(aviname)%delete existing file
4309    else
4310        msgbox_uvmat('ERROR',message)
4311        return
4312    end
4313end
4314%create avi open
4315aviobj=avifile(aviname,'Compression','None','fps',fps);
4316
4317%display first view for tests
4318newfig=figure;
4319newaxes=copyobj(handles.PlotAxes,newfig);%new plotting axes in the new figure
4320set(newaxes,'Tag','movieaxes')
4321nbpix=[512 384]*str2double(answer{3});
4322set(gcf,'Position',[1 1 nbpix])% resolution XVGA
4323set(newaxes,'Position',eval(answer{4}));
4324map=colormap(handles.PlotAxes);
4325colormap(map);%transmit the current colormap to the zoom fig
4326msgbox_uvmat('INPUT_Y-N',{['adjust figure ' num2str(newfig) ' with its matlab edit menu '] ;...
4327        ['then press OK to get the avi movie as a copy of figure ' num2str(newfig) ' display']});
4328UvData.plotaxes=newaxes;% the axis in the new figure becomes the current main plotting axes
4329set(huvmat,'UserData',UvData);
4330increment=str2num(get(handles.num_IndexIncrement,'String')); %get the field increment d
4331set(handles.STOP,'Visible','on')
4332set(handles.speed,'Visible','on')
4333set(handles.speed_txt,'Visible','on')
4334set(handles.Movie,'BusyAction','queue')
4335
4336%imin=str2double(get(handles.i1,'String'));
4337imax=str2double(answer{5});
4338% if isfield(UvData,'Time')
4339htitle=get(newaxes,'Title');
4340xlim=get(newaxes,'XLim');
4341ylim=get(newaxes,'YLim');
4342set(htitle,'Position',[xlim(2)+0.07*(xlim(2)-xlim(1)) ylim(2)-0.05*(ylim(2)-ylim(1)) 0])
4343time_str=get(handles.abs_time,'String');
4344set(htitle,'String',['t=' time_str])
4345set(handles.speed,'Value',1)
4346for i=1:imax
4347    if get(handles.speed,'Value')~=0 && isequal(get(handles.MenuExportMovie,'BusyAction'),'queue') % enable STOP command
4348            runpm(hObject,eventdata,handles,increment)% run plus
4349            drawnow
4350            time_str=get(handles.abs_time,'String');
4351            if ishandle(htitle)
4352             set(htitle,'String',['t=' time_str])
4353            end
4354            mov=getframe(newfig);
4355            aviobj=addframe(aviobj,mov);
4356    end
4357end
4358aviobj=close(aviobj);
4359UvData=rmfield(UvData,'plotaxes');
4360%UvData.Object{1}.plotaxes=handles.PlotAxes;
4361set(huvmat,'UserData',UvData);
4362msgbox_uvmat('CONFIRMATION',{['movie ' aviname ' created '];['with ' num2str(imax) ' frames']})
4363
4364
4365%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
4366% Projection Objects Menu Callbacks
4367%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
4368
4369% -----------------------------------------------------------------------
4370function Menupoints_Callback(hObject, eventdata, handles)
4371%------------------------------------------------------------------------
4372data.Type='points';
4373data.ProjMode='projection';%default
4374data.ProjModeMenu={};% do not restrict ProjMode menus
4375create_object(data,handles)
4376
4377% -----------------------------------------------------------------------
4378function Menuline_Callback(hObject, eventdata, handles)
4379%------------------------------------------------------------------------
4380data.Type='line';
4381data.ProjMode='projection';%default
4382data.ProjModeMenu={};% do not restrict ProjMode menus
4383create_object(data,handles)
4384
4385%------------------------------------------------------------------------
4386function Menupolyline_Callback(hObject, eventdata, handles)
4387%------------------------------------------------------------------------
4388data.Type='polyline';
4389data.ProjMode='projection';%default
4390data.ProjModeMenu={};% do not restrict ProjMode menus
4391create_object(data,handles)
4392
4393%------------------------------------------------------------------------
4394function Menupolygon_Callback(hObject, eventdata, handles)
4395%------------------------------------------------------------------------
4396data.Type='polygon';
4397data.ProjMode='inside';%default
4398data.ProjModeMenu={};% do not restrict ProjMode menus
4399create_object(data,handles)
4400
4401%------------------------------------------------------------------------
4402function Menurectangle_Callback(hObject, eventdata, handles)
4403%------------------------------------------------------------------------
4404data.Type='rectangle';
4405data.ProjMode='inside';%default
4406data.ProjModeMenu={};% do not restrict ProjMode menus
4407create_object(data,handles)
4408
4409%------------------------------------------------------------------------
4410function Menuellipse_Callback(hObject, eventdata, handles)
4411%------------------------------------------------------------------------
4412data.Type='ellipse';
4413data.ProjMode='inside';%default
4414data.ProjModeMenu={};% do not restrict ProjMode menus
4415create_object(data,handles)
4416
4417%------------------------------------------------------------------------
4418function MenuMaskObject_Callback(hObject, eventdata, handles)
4419%------------------------------------------------------------------------
4420data.Type='polygon';
4421data.TypeMenu={'polygon'};
4422data.ProjMode='mask_inside';%default
4423data.ProjModeMenu={'mask_inside';'mask_outside'};
4424create_object(data,handles)
4425
4426%------------------------------------------------------------------------
4427function Menuplane_Callback(hObject, eventdata, handles)
4428%------------------------------------------------------------------------
4429data.Type='plane';
4430data.ProjMode='projection';%default
4431data.ProjModeMenu={};% do not restrict ProjMode menus
4432create_object(data,handles)
4433
4434%------------------------------------------------------------------------
4435function Menuvolume_Callback(hObject, eventdata, handles)
4436%------------------------------------------------------------------------
4437data.Type='volume';
4438data.ProjMode='interp';%default
4439data.ProjModeMenu={};
4440% set(handles.create,'Visible','on')
4441% set(handles.create,'Value',1)
4442% VOLUME_Callback(hObject,eventdata,handles)data.ProjModeMenu={};
4443create_object(data,handles)
4444
4445%------------------------------------------------------------------------
4446% --- generic function used for the creation of a projection object
4447function create_object(data,handles)
4448%------------------------------------------------------------------------
4449% desactivate geometric calibration if opened
4450hgeometry_calib=findobj(allchild(0),'tag','geometry_calib');
4451if ishandle(hgeometry_calib)
4452    hhgeometry_calib=guidata(hgeometry_calib);
4453    set(hhgeometry_calib.edit_append,'Value',0)% desactivate mouse action in geometry_calib
4454    set(hhgeometry_calib.edit_append,'BackgroundColor',[0.7 0.7 0.7])
4455end
4456set(handles.edit_object,'Value',0); %suppress the object edit mode
4457set(handles.edit_object,'BackgroundColor',[0.7,0.7,0.7]) 
4458ListObject=get(handles.ListObject,'String');
4459if isempty(ListObject)
4460    ListObject={''};
4461end
4462if ~strcmp(ListObject{end},'')
4463    ListObject=[ListObject;{''}]; %append a blank to the list (if nort already done) to indicate the creation of a new object
4464    set(handles.ListObject,'String',ListObject)
4465end
4466IndexObj=length(ListObject);
4467set(handles.ListObject,'Value',IndexObj)
4468UvData=get(handles.uvmat,'UserData');
4469UvData.Object{IndexObj}=[]; %create a new empty object
4470UvData.Object{IndexObj}.DisplayHandle.uvmat=handles.PlotAxes; % axes for plot_object
4471UvData.Object{IndexObj}.DisplayHandle.view_field=[]; %no plot handle before plot_field operation
4472data.Name=data.Type;% default name=type
4473data.Coord=[0 0]; %default
4474if isfield(UvData,'Field')
4475    Field=UvData.Field;
4476    if isfield(UvData.Field,'Mesh')&&~isempty(UvData.Field.Mesh)
4477        data.RangeX=[UvData.Field.XMin UvData.Field.XMax];
4478        if strcmp(data.Type,'line')||strcmp(data.Type,'polyline')||strcmp(data.Type,'points')
4479            data.RangeY=UvData.Field.Mesh;
4480        else
4481            data.RangeY=[UvData.Field.YMin UvData.Field.YMax];
4482        end
4483        data.DX=UvData.Field.Mesh;
4484        data.DY=UvData.Field.Mesh;
4485    end
4486    if isfield(Field,'NbDim')&& isequal(Field.NbDim,3)
4487         data.Coord=[0 0 0]; %default
4488    end
4489    if isfield(Field,'CoordUnit')
4490        data.CoordUnit=Field.CoordUnit;
4491    end
4492end
4493if ishandle(handles.UVMAT_title)
4494    delete(handles.UVMAT_title)%delete the initial display of uvmat if no field has been entered
4495end
4496hset_object=set_object(data,handles);% call the set_object interface
4497hhset_object=guidata(hset_object);
4498hchild=get(hset_object,'children');
4499set(hchild,'enable','on')
4500set(handles.uvmat,'UserData',UvData)
4501set(handles.CheckZoom,'Value',0) %desactivate the zoom for object creation by the mouse
4502CheckZoom_Callback(handles.uvmat, [], handles)
4503set(handles.delete_object,'Visible','on')
4504
4505%------------------------------------------------------------------------
4506function MenuBrowseObject_Callback(hObject, eventdata, handles)
4507%------------------------------------------------------------------------
4508%get the object file
4509[FileName, PathName, filterindex] = uigetfile( ...
4510       {'*.xml;*.mat', ' (*.xml,*.mat)';
4511       '*.xml',  '.xml files '; ...
4512        '*.mat',  '.mat matlab files '}, ...
4513        'Pick an xml Object file',get(handles.RootPath,'String'));
4514fileinput=[PathName FileName];%complete file name
4515sizf=size(fileinput);
4516if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end
4517
4518%read the file
4519[data,heading]=xml2struct(fileinput);
4520if ~strcmp(heading,'ProjObject')
4521    msgbox_uvmat('WARNING','The xml file does not have the heading ProjObject for projection objects')
4522end
4523[tild,data.Name]=fileparts(FileName);% object name set as file name
4524ListObject=get(handles.ListObject,'String');
4525if ~strcmp(ListObject{end},'')
4526    ListObject=[ListObject;{''}]; %append a blank to the list (if not already done) to indicate the creation of a new object
4527    set(handles.ListObject,'String',ListObject)
4528end
4529IndexObj=length(ListObject);
4530
4531UvData=get(handles.uvmat,'UserData');
4532UvData.Object{IndexObj}=[]; %create a new empty object
4533UvData.Object{IndexObj}.DisplayHandle.uvmat=[]; %no plot handle before plot_field operation
4534UvData.Object{IndexObj}.DisplayHandle.view_field=[]; %no plot handle before plot_field operation
4535set(handles.uvmat,'UserData',UvData)
4536set(handles.ListObject,'Value',IndexObj)
4537hset_object=set_object(data);% call the set_object interface
4538set(get(hset_object,'children'),'enable','on')% enable edit action on elements on GUI set_object
4539set(handles.edit_object,'Value',0); %suppress the object edit mode
4540set(handles.edit_object,'BackgroundColor',[0.7,0.7,0.7]) 
4541set(handles.delete_object,'Visible','on')
4542
4543
4544%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
4545% MenuEdit Callbacks
4546%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
4547%------------------------------------------------------------------------
4548function MenuEditObject_Callback(hObject, eventdata, handles)
4549%------------------------------------------------------------------------
4550set(handles.edit_object,'Value',1)
4551edit_Callback(hObject, eventdata, handles)
4552
4553%------------------------------------------------------------------------
4554function MenuEditVectors_Callback(hObject, eventdata, handles)
4555%------------------------------------------------------------------------
4556set(handles.edit_vect,'Visible','on')
4557set(handles.edit_vect,'Value',1)
4558edit_vect_Callback(hObject, eventdata, handles)
4559
4560%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
4561% MenuTools Callbacks
4562%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
4563%------------------------------------------------------------------------
4564function MenuCalib_Callback(hObject, eventdata, handles)
4565%------------------------------------------------------------------------
4566
4567UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
4568
4569%suppress competing options
4570set(handles.CheckZoom,'Value',0)
4571set(handles.CheckZoom,'BackgroundColor',[0.7 0.7 0.7])
4572set(handles.ListObject,'Value',1)     
4573% initiate display of GUI geometry_calib
4574data=[]; %default
4575if isfield(UvData,'CoordType')
4576    data.CoordType=UvData.CoordType;
4577end
4578[RootPath,SubDir,RootFile,FileIndex,FileExt]=read_file_boxes(handles);
4579FileName=[fullfile(RootPath,SubDir,RootFile) FileIndex FileExt];
4580set(handles.view_xml,'Backgroundcolor',[1 1 0])%indicate the reading of the current xml file by geometry_calib
4581pos_uvmat=get(handles.uvmat,'Position');
4582pos_cal(1)=pos_uvmat(1)+UvData.OpenParam.PosGeometryCalib(1)*pos_uvmat(3);
4583pos_cal(2)=pos_uvmat(2)+UvData.OpenParam.PosGeometryCalib(2)*pos_uvmat(4);
4584pos_cal(3:4)=UvData.OpenParam.PosGeometryCalib(3:4).* pos_uvmat(3:4);
4585geometry_calib(FileName,pos_cal);% call the geometry_calib interface   
4586set(handles.view_xml,'Backgroundcolor',[1 1 1])%indicate the end of reading of the current xml file by geometry_calib
4587set(handles.MenuCalib,'checked','on')% indicate that MenuCalib is activated, test used by mouse action
4588
4589%------------------------------------------------------------------------
4590function MenuMask_Callback(hObject, eventdata, handles)
4591%------------------------------------------------------------------------
4592UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
4593ListObj=UvData.Object;
4594select=zeros(1,numel(ListObj));
4595for iobj=1:numel(ListObj);
4596    if strcmp(ListObj{iobj}.ProjMode,'mask_inside')||strcmp(ListObj{iobj}.ProjMode,'mask_outside')
4597        select(iobj)=1;
4598    end
4599end
4600val=find(select);
4601if isempty(val)
4602    msgbox_uvmat('ERROR','polygons must be first created by Projection object/mask polygon in the menu bar');
4603    return
4604else
4605    set(handles.ListObject,'Value',val);
4606    flag=1;
4607    npx=size(UvData.Field.A,2);
4608    npy=size(UvData.Field.A,1);
4609    xi=0.5:npx-0.5;
4610    yi=0.5:npy-0.5;
4611    [Xi,Yi]=meshgrid(xi,yi);
4612    if isfield(UvData,'Object')
4613        for iobj=1:length(UvData.Object)
4614            ObjectData=UvData.Object{iobj};
4615            if isfield(ObjectData,'ProjMode') &&(isequal(ObjectData.ProjMode,'mask_inside')||isequal(ObjectData.ProjMode,'mask_outside'));
4616                flagobj=1;
4617                testphys=0; %coordinates in pixels by default
4618                if isfield(ObjectData,'CoordUnit') && ~isequal(ObjectData.CoordUnit,'pixel')
4619                    if isfield(UvData,'XmlData')&& isfield(UvData.XmlData{1},'GeometryCalib')
4620                        Calib=UvData.XmlData{1}.GeometryCalib;
4621                        testphys=1;
4622                    end
4623                end
4624                if isfield(ObjectData,'Coord')&& isfield(ObjectData,'Type')
4625                    if isequal(ObjectData.Type,'polygon')
4626                        X=ObjectData.Coord(:,1);
4627                        Y=ObjectData.Coord(:,2);
4628                        if testphys
4629                            pos=[X Y zeros(size(X))];
4630                            if isfield(Calib,'SliceCoord') && length(Calib.SliceCoord)>=3
4631                                if isfield(Calib,'SliceAngle')&&~isequal(Calib.SliceAngle,[0 0 0])
4632                                    om=norm(Calib.SliceAngle);%norm of rotation angle in radians
4633                                    OmAxis=Calib.SliceAngle/om; %unit vector marking the rotation axis
4634                                    cos_om=cos(pi*om/180);
4635                                    sin_om=sin(pi*om/180);
4636                                    pos=cos_om*pos+sin_om*cross(OmAxis,pos)+(1-cos_om)*(OmAxis*pos')*OmAxis;
4637                                end
4638                                pos(:,1)=pos(:,1)+Calib.SliceCoord(1);
4639                                pos(:,2)=pos(:,2)+Calib.SliceCoord(2);
4640                                pos(:,3)=pos(:,3)+Calib.SliceCoord(3);
4641                            end                           
4642                            [X,Y]=px_XYZ(Calib,pos(:,1),pos(:,2),pos(:,3));
4643                        end
4644                        flagobj=~inpolygon(Xi,Yi,X',Y');%=0 inside the polygon, 1 outside
4645                    elseif isequal(ObjectData.Type,'ellipse')
4646                        if testphys
4647                            %[X,Y]=px_XYZ(Calib,X,Y,0);% TODO:create a polygon boundary and transform to phys
4648                        end
4649                        RangeX=max(ObjectData.RangeX);
4650                        RangeY=max(ObjectData.RangeY);
4651                        X2Max=RangeX*RangeX;
4652                        Y2Max=RangeY*RangeY;
4653                        distX=(Xi-ObjectData.Coord(1,1));
4654                        distY=(Yi-ObjectData.Coord(1,2));
4655                        flagobj=(distX.*distX/X2Max+distY.*distY/Y2Max)>1;
4656                    elseif isequal(ObjectData.Type,'rectangle')
4657                        if testphys
4658                            %[X,Y]=px_XYZ(Calib,X,Y,0);% TODO:create a polygon boundary and transform to phys
4659                        end
4660                        distX=abs(Xi-ObjectData.Coord(1,1));
4661                        distY=abs(Yi-ObjectData.Coord(1,2));
4662                        flagobj=distX>max(ObjectData.RangeX) | distY>max(ObjectData.RangeY);
4663                    end
4664                    if isequal(ObjectData.ProjMode,'mask_outside')
4665                        flagobj=~flagobj;
4666                    end
4667                    flag=flag & flagobj;
4668                end
4669            end
4670        end
4671    end
4672    %mask name
4673    RootPath=get(handles.RootPath,'String');
4674    SubDir=get(handles.SubDir,'String');
4675    RootFile=get(handles.RootFile,'String');
4676    if ~isempty(RootFile)&&(isequal(RootFile(1),'/')|| isequal(RootFile(1),'\'))
4677        RootFile(1)=[];
4678    end
4679    list=get(handles.masklevel,'String');
4680    masknumber=num2str(length(list));
4681    maskindex=get(handles.masklevel,'Value');
4682   % mask_name=fullfile_uvmat(RootPath,'',[RootFile '_' masknumber 'mask'],'.png','_1',maskindex);
4683    mask_name=fullfile_uvmat(RootPath,[SubDir '.mask'],'mask','.png','_1',maskindex);
4684    imflag=uint8(255*(0.392+0.608*flag));% =100 for flag=0 (vectors not computed when 20<imflag<200)
4685    imflag=flipdim(imflag,1);
4686
4687    %display the mask
4688    hfigmask=figure;
4689    set(hfigmask,'Name','mask image')
4690    vec=linspace(0,1,256);%define a linear greyscale colormap
4691    map=[vec' vec' vec'];
4692    colormap(map)
4693    image(imflag);
4694    answer=msgbox_uvmat('INPUT_TXT','mask file name:', mask_name);
4695    if ~strcmp(answer,'Cancel')
4696        mask_dir=fileparts(answer);
4697        if ~exist(mask_dir,'dir')
4698            [xx,msg1]=mkdir(mask_dir);
4699            if ~strcmp(msg1,'')
4700                errormsg=['cannot create ' mask_dir ': ' msg1];%error message for directory creation
4701                return
4702            end
4703        end
4704        imwrite(imflag,answer,'BitDepth',8);
4705    end
4706    set(handles.ListObject,'Value',1)
4707end
4708
4709%------------------------------------------------------------------------
4710%-- open the GUI set_grid.fig to create grid
4711function MenuGrid_Callback(hObject, eventdata, handles)
4712%------------------------------------------------------------------------
4713%suppress the other options if grid is chosen
4714set(handles.edit_vect,'Value',0)
4715edit_vect_Callback(hObject, eventdata, handles)
4716set(handles.edit_object,'BackgroundColor',[0.7 0.7 0.7])
4717set(handles.ListObject,'Value',1)     
4718
4719%prepare display of the set_grid GUI
4720[RootPath,SubDir,RootFile,FileIndex,FileExt]=read_file_boxes(handles);
4721FileName=[fullfile(RootPath,SubDir,RootFile) FileIndex FileExt];
4722CoordList=get(handles.transform_fct,'String');
4723val=get(handles.transform_fct,'Value');
4724set_grid(FileName,CoordList{val});% call the set_object interface
4725
4726
4727%------------------------------------------------------------------------
4728function MenuRuler_Callback(hObject, eventdata, handles)
4729%------------------------------------------------------------------------
4730set(handles.CheckZoom,'Value',0)
4731CheckZoom_Callback(handles.uvmat, [], handles)
4732set(handles.MenuRuler,'checked','on')
4733UvData=get(handles.uvmat,'UserData');
4734UvData.MouseAction='ruler';
4735set(handles.uvmat,'UserData',UvData);
4736
4737%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
4738% MenuRun Callbacks
4739%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
4740
4741%------------------------------------------------------------------------
4742% open the GUI 'series'
4743function MenuSeries_Callback(hObject, eventdata, handles)
4744%------------------------------------------------------------------------
4745series; %first display of the GUI to fill waiting time
4746[RootPath,SubDir,RootFile,FileIndex,FileExt]=read_file_boxes(handles);
4747Param.FileName=[fullfile(RootPath,SubDir,RootFile) FileIndex FileExt];%first input file name
4748if isequal(get(handles.SubField,'Value'),1)
4749    [RootPath_1,SubDir_1,RootFile_1,FileIndex_1,FileExt_1]=read_file_boxes_1(handles);
4750    FileName_1=[fullfile(RootPath_1,SubDir_1,RootFile_1) FileIndex_1 FileExt_1];
4751    if ~isequal(FileName_1,Param.FileName)
4752        Param.FileName_1=FileName_1;%second input file name if relevant
4753    end
4754end
4755Param.NomType=get(handles.NomType,'String');
4756Param.NomType_1=get(handles.NomType_1,'String');
4757Param.CheckFixPair=get(handles.CheckFixPair,'Value');
4758UvData=get(handles.uvmat,'UserData');
4759if isfield(UvData,'XmlData')&& isfield(UvData.XmlData{1},'Time')
4760    Param.Time=UvData.XmlData{1}.Time;
4761end
4762if isequal(get(handles.scan_i,'Value'),1)
4763    Param.incr_i=str2num(get(handles.num_IndexIncrement,'String'));
4764elseif isequal(get(handles.scan_j,'Value'),1)
4765    Param.incr_j=str2num(get(handles.num_IndexIncrement,'String'));
4766end
4767
4768%% transfer fields and coordinate names
4769Param.list_fields=get(handles.FieldName,'String');% list menu fields
4770FieldName=Param.list_fields{get(handles.FieldName,'Value')};
4771ind_image=find(strcmp('image',Param.list_fields));
4772if ~isempty(ind_image) && numel(Param.list_fields)>1
4773    Param.list_fields(ind_image)=[]; %suppress  'image' option
4774end
4775Param.index_fields=find(strcmp(FieldName,Param.list_fields));% selected string index
4776Param.list_fields_1=get(handles.FieldName_1,'String');% list menu fields
4777if ischar(Param.list_fields_1),Param.list_fields_1={Param.list_fields_1};end
4778FieldName_1=Param.list_fields_1{get(handles.FieldName_1,'Value')};
4779ind_image=find(strcmp('image',Param.list_fields_1));
4780if ~isempty(ind_image) && numel(Param.list_fields_1)>1
4781    Param.list_fields_1(ind_image)=[]; %suppress  'image' option
4782end
4783Param.index_fields_1=find(strcmp(FieldName_1,Param.list_fields_1));% selected string index
4784Param.transform_str=get(handles.transform_fct,'String');
4785Param.transform_val=get(handles.transform_fct,'Value');
4786Param.Coord_x_str=get(handles.Coord_x,'String');
4787Param.Coord_x_val=get(handles.Coord_x,'Value');
4788Param.Coord_y_str=get(handles.Coord_y,'String');
4789Param.Coord_y_val=get(handles.Coord_y,'Value');
4790series(Param); %run the series interface
4791
4792%------------------------------------------------------------------------
4793% -- open the GUI civ.fig for PIV
4794function MenuPIV_Callback(hObject, eventdata, handles)
4795%------------------------------------------------------------------------
4796 [RootPath,SubDir,RootFile,FileIndex,FileExt]=read_file_boxes(handles);
4797 FileName=[fullfile(RootPath,SubDir,RootFile) FileIndex FileExt];
4798civ(FileName);% interface de civ(not in the uvmat file)
4799
4800% --------------------------------------------------------------------
4801function MenuHelp_Callback(hObject, eventdata, handles)
4802% --------------------------------------------------------------------
4803path_to_uvmat=which ('uvmat');% check the path of uvmat
4804pathelp=fileparts(path_to_uvmat);
4805helpfile=fullfile(pathelp,'uvmat_doc','uvmat_doc.html');
4806if isempty(dir(helpfile)), msgbox_uvmat('ERROR','Please put the help file uvmat_doc.html in the sub-directory /uvmat_doc of the UVMAT package')
4807else
4808    addpath (fullfile(pathelp,'uvmat_doc'))
4809    web(helpfile);
4810end
4811
4812
4813% --------------------------------------------------------------------
4814function MenuSetProject_Callback(hObject, eventdata, handles)
4815RootPath=get(handles.RootPath,'String');
4816ProjectDir = uigetdir(fileparts(fileparts(RootPath)), 'select the project source directory');
4817datatree_browser(ProjectDir)
4818
4819
4820% --------------------------------------------------------------------
4821function MenuBrowseProject_Callback(hObject, eventdata, handles)
4822RootPath=get(handles.RootPath,'String');
4823ProjectDir = uigetdir(fileparts(fileparts(RootPath)), 'select the project directory');
4824datatree_browser(ProjectDir)
4825
4826
4827% --- Executes on selection change in Coord_y.
4828function Coord_y_Callback(hObject, eventdata, handles)
4829
4830% --- Executes on selection change in Coord_x.
4831function Coord_x_Callback(hObject, eventdata, handles)
4832
4833
4834% --- Executes on button press in CheckColorBar.
4835function CheckColorBar_Callback(hObject, eventdata, handles)
4836% hObject    handle to CheckColorBar (see GCBO)
4837% eventdata  reserved - to be defined in a future version of MATLAB
4838% handles    structure with handles and user data (see GUIDATA)
4839
4840% Hint: get(hObject,'Value') returns toggle state of CheckColorBar
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