source: trunk/src/uvmat.m @ 535

Last change on this file since 535 was 535, checked in by sommeria, 9 years ago

various bugs fixed, in particular patch projection with color images

File size: 207.2 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')
180UvData.OpenParam.PosColorbar=[0.805 0.022 0.019 0.445];
181UvData.OpenParam.PosSetObject=[-0.05 -0.03 0.3 0.7]; %position for set_object
182UvData.OpenParam.PosGeometryCalib=[0.95 -0.03 0.28 1 ];%position for geometry_calib (TO IMPROVE)
183% UvData.OpenParam.CalSize=[0.28 1];
184% UvData.PlotAxes=[];%initiate the record of plotted field
185% UvData.axes2=[];
186% UvData.axes1=[];
187AxeData.LimEditBox=1; %initialise AxeData
188set(handles.PlotAxes,'UserData',AxeData)
189
190%% set functions for the mouse and keyboard
191set(hObject,'KeyPressFcn',{'keyboard_callback',handles})%set keyboard action function
192set(hObject,'WindowButtonMotionFcn',{'mouse_motion',handles})%set mouse action functio
193set(hObject,'WindowButtonDownFcn',{'mouse_down'})%set mouse click action function
194set(hObject,'WindowButtonUpFcn',{'mouse_up',handles})
195set(hObject,'DeleteFcn',{@closefcn})%
196
197%% initialisation
198% set(handles.ListObject,'Value',1)% default: empty projection objectproj_field
199% set(handles.ListObject,'String',{''})
200% set(handles.ListObject_1,'Value',1)% default: empty projection objectproj_field
201% set(handles.ListObject_1,'String',{''})
202set(handles.FieldName,'Value',1)
203set(handles.FieldName,'string',{''})
204UvData.Object={[]};
205
206%% TRANSFORM menu: builtin fcts
207transform_menu={'';'sub_field';'phys';'phys_polar'};
208UvData.OpenParam.NbBuiltin=numel(transform_menu); %number of functions
209transform_path=fullfile(path_uvmat,'transform_field');
210path_list=cell(UvData.OpenParam.NbBuiltin,1);
211path_list{1}='';
212for ilist=2:UvData.OpenParam.NbBuiltin
213path_list{ilist}=transform_path; % set transform_path to the path_list
214end
215
216%% load the list of previously browsed files in menus Open, Open_1 and transform_fct
217 dir_perso=prefdir; % path to the directory .matlab for personal data
218 profil_perso=fullfile(dir_perso,'uvmat_perso.mat');% personal data file uvmauvmat_perso.mat' in .matlab
219 if exist(profil_perso,'file')
220     h=load (profil_perso);
221     if isfield(h,'MenuFile')% load the menu of previously opened files
222         for ifile=1:min(length(h.MenuFile),5)
223             eval(['set(handles.MenuFile_' num2str(ifile) ',''Label'',h.MenuFile{ifile});'])
224             eval(['set(handles.MenuFile_' num2str(ifile) '_1,''Label'',h.MenuFile{ifile});'])
225         end
226     end
227     if isfield(h,'transform_fct') && iscell(h.transform_fct) % load the menu of transform fct set by user
228         for ilist=1:length(h.transform_fct);
229             if exist(h.transform_fct{ilist},'file')
230                 [path,file]=fileparts(h.transform_fct{ilist});
231                 transform_menu=[transform_menu; {file}];
232                 path_list=[path_list; {path}];
233             end
234         end
235     end
236 end
237transform_menu=[transform_menu;{'more...'}];%append the option more.. to the menu
238set(handles.transform_fct,'String',transform_menu)% display the menu of transform fcts
239set(handles.transform_fct,'UserData',path_list)% store the corresponding list of path in UserData of uicontrol transform_fct
240set(handles.path_transform,'String','')
241set(handles.path_transform,'UserData',[])
242
243%% case of an input argument for uvmat
244testinputfield=0;
245inputfile=[];
246Field=[];
247if exist('input','var')
248    if ishandle(handles.UVMAT_title)
249        delete(handles.UVMAT_title)
250    end   
251    if isstruct(input)
252        if isfield(input,'InputFile')
253            inputfile=input.InputFile;
254        end
255        if isfield(input,'TimeIndex')
256            set(handles.i1,num2str(input.TimeIndex))
257        end
258        if isfield(input,'FieldsString')
259            UvData.FieldsString=input.FieldsString;
260        end
261    elseif ischar(input)% file name introduced as input
262           inputfile=input;
263    elseif isnumeric(input)%simple matrix introduced as input
264        sizinput=size(input);
265        if sizinput(1)<=1 || sizinput(2)<=1
266            msgbox_uvmat('ERROR','bad input for uvmat: file name, structure or numerical matrix accepted')
267            return
268        end
269        UvData.Field.ListVarName={'A','coord_y','coord_x'};
270        UvData.Field.VarDimName={{'coord_y','coord_x'},'cord_y','coord_x'};
271        UvData.Field.A=input;
272        UvData.Field.coord_x=[0.5 size(input,2)-0.5];
273        UvData.Field.coord_y=[size(input,1)-0.5 0.5];
274        testinputfield=1;
275    end
276else
277    %% check the path and date of modification of all functions in uvmat
278    path_to_uvmat=which ('uvmat');% check the path detected for source file uvmat
279    [infomsg,date_str,svn_info]=check_files;%check the path of the functions called by uvmat.m   
280    date_str=['last modification: ' date_str];
281    if ishandle(handles.UVMAT_title)
282        set(handles.UVMAT_title,'String',...
283            [{'Copyright  LEGI UMR 5519 /CNRS-UJF-Grenoble INP, 2010'};...
284            {'GNU General Public License'};...
285            {path_to_uvmat};...
286            {date_str};...
287            infomsg]);
288    end
289end
290set(handles.uvmat,'UserData',UvData)
291if ~isempty(inputfile)
292    %%%%% display the input field %%%%%%%
293    display_file_name(handles,inputfile)
294    %%%%%%%
295end
296
297set_vec_col_bar(handles) %update the display of color code for vectors
298
299%------------------------------------------------------------------------
300% --- Outputs from this function are returned to the command menuline.
301function varargout = uvmat_OutputFcn(hObject, eventdata, handles)
302varargout{1} = handles.output;% the only output argument is the handle to the GUI figure
303
304%------------------------------------------------------------------------
305% --- executed when closing uvmat: delete or desactivate the associated figures if exist
306function closefcn(gcbo,eventdata)
307%------------------------------------------------------------------------
308hh=findobj(allchild(0),'tag','view_field');
309if ~isempty(hh)
310    delete(hh)
311end
312hh=findobj(allchild(0),'tag','geometry_calib');
313if ~isempty(hh)
314    delete(hh)
315end
316hh=findobj(allchild(0),'tag','set_object');
317if ~isempty(hh)
318    hhh=findobj(hh,'tag','PLOT');
319    set(hhh,'enable','off')
320end
321
322%------------------------------------------------------------------------
323%------------------------------------------------------------------------
324%  II - FUNCTIONS FOR INTRODUCING THE INPUT FILES
325% automatically sets the global properties when the rootfile name is introduced
326% then activate the view-field action if selected
327% it is activated either by clicking on the RootPath window or by the
328% browser
329%------------------------------------------------------------------------
330%------------------------------------------------------------------------
331% --- Executes on the menu Open/Browse...
332% search the files, recognize their type according to their name and fill the rootfile input windows
333function MenuBrowse_Callback(hObject, eventdata, handles)
334[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
335%oldfile=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
336oldfile=fullfile(RootPath,SubDir);
337if isempty(oldfile)||isequal(oldfile,'') %loads the previously stored file name and set it as default in the file_input box
338         dir_perso=prefdir;
339         profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
340         if exist(profil_perso,'file')
341              h=load (profil_perso);
342             if isfield(h,'MenuFile_1')
343                  oldfile=h.MenuFile_1;
344             end
345         end
346end
347[FileName, PathName] = uigetfile({'*.*','All Files(*.*)'},'Pick a file',oldfile);
348if ~ischar(FileName),return,end %abandon if the browser is cancelled
349fileinput=[PathName FileName];%complete file name
350
351%% display the selected field and related information
352display_file_name( handles,fileinput)
353
354% -----------------------------------------------------------------------
355% --- Open again the file whose name has been recorded in MenuFile_1
356function MenuFile_1_Callback(hObject, eventdata, handles)
357%------------------------------------------------------------------------
358fileinput=get(handles.MenuFile_1,'Label');
359display_file_name( handles,fileinput)
360
361% -----------------------------------------------------------------------
362% --- Open again the file whose name has been recorded in MenuFile_2
363function MenuFile_2_Callback(hObject, eventdata, handles)
364%------------------------------------------------------------------------
365fileinput=get(handles.MenuFile_2,'Label');
366display_file_name(handles,fileinput)
367
368% -----------------------------------------------------------------------
369% --- Open again the file whose name has been recorded in MenuFile_3
370function MenuFile_3_Callback(hObject, eventdata, handles)
371%------------------------------------------------------------------------
372fileinput=get(handles.MenuFile_3,'Label');
373display_file_name(handles,fileinput)
374
375% -----------------------------------------------------------------------
376% --- Open again the file whose name has been recorded in MenuFile_4
377function MenuFile_4_Callback(hObject, eventdata, handles)
378%------------------------------------------------------------------------
379fileinput=get(handles.MenuFile_4,'Label');
380display_file_name(handles,fileinput)
381
382% -----------------------------------------------------------------------
383% --- Open again the file whose name has been recorded in MenuFile_5
384function MenuFile_5_Callback(hObject, eventdata, handles)
385%------------------------------------------------------------------------
386fileinput=get(handles.MenuFile_5,'Label');
387display_file_name(handles,fileinput)
388
389%------------------------------------------------------------------------
390% --- Executes on the menu Open/Browse_1 for the second input field,
391%     search the files, recognize their type according to their name and fill the rootfile input windows
392function MenuBrowse_1_Callback(hObject, eventdata, handles)
393%------------------------------------------------------------------------
394RootPath=get(handles.RootPath,'String');
395[FileName, PathName] = uigetfile({'*.*','All Files(*.*)'},'Pick a file',RootPath);
396if ~ischar(FileName),return,end %abandon if the browser is cancelled
397fileinput_1=[PathName FileName];%complete file name
398
399% refresh the current displayed field
400set(handles.SubField,'Value',1)
401display_file_name(handles,fileinput_1,2)
402
403%update list of recent files in the menubar
404MenuFile_1=fileinput_1;
405MenuFile_2=get(handles.MenuFile_1,'Label');
406MenuFile_3=get(handles.MenuFile_2,'Label');
407MenuFile_4=get(handles.MenuFile_3,'Label');
408MenuFile_5=get(handles.MenuFile_4,'Label');
409set(handles.MenuFile_1,'Label',MenuFile_1)
410set(handles.MenuFile_2,'Label',MenuFile_2)
411set(handles.MenuFile_3,'Label',MenuFile_3)
412set(handles.MenuFile_4,'Label',MenuFile_4)
413set(handles.MenuFile_5,'Label',MenuFile_5)
414set(handles.MenuFile_1_1,'Label',MenuFile_1)
415set(handles.MenuFile_2_1,'Label',MenuFile_2)
416set(handles.MenuFile_3_1,'Label',MenuFile_3)
417set(handles.MenuFile_4_1,'Label',MenuFile_4)
418set(handles.MenuFile_5_1,'Label',MenuFile_5)
419dir_perso=prefdir;
420profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
421if exist(profil_perso,'file')
422    save (profil_perso,'MenuFile_1','MenuFile_2','MenuFile_3','MenuFile_4', 'MenuFile_5','-append'); %store the file names for future opening of uvmat
423else
424    txt=ver('MATLAB');
425    Release=txt.Release;
426    relnumb=str2double(Release(3:4));
427    if relnumb >= 14
428        save (profil_perso,'MenuFile_1','MenuFile_2','MenuFile_3','MenuFile_4', 'MenuFile_5','-V6'); %store the file names for future opening of uvmat
429    else
430        save (profil_perso,'MenuFile_1','MenuFile_2','MenuFile_3','MenuFile_4', 'MenuFile_5'); %store the file names for future opening of uvmat
431    end
432end
433
434% -----------------------------------------------------------------------
435% --- Open again as second field the file whose name has been recorded in MenuFile_1
436function MenuFile_1_1_Callback(hObject, eventdata, handles)
437% -----------------------------------------------------------------------
438fileinput_1=get(handles.MenuFile_1_1,'Label');
439set(handles.SubField,'Value',1)
440display_file_name(handles,fileinput_1,2)
441
442% -----------------------------------------------------------------------
443% --- Open again as second field the file whose name has been recorded in MenuFile_2
444function MenuFile_2_1_Callback(hObject, eventdata, handles)
445% -----------------------------------------------------------------------
446fileinput_1=get(handles.MenuFile_2_1,'Label');
447set(handles.SubField,'Value',1)
448display_file_name(handles,fileinput_1,2)
449
450% -----------------------------------------------------------------------
451% --- Open again as second field the file whose name has been recorded in MenuFile_3
452function MenuFile_3_1_Callback(hObject, eventdata, handles)
453% -----------------------------------------------------------------------
454fileinput_1=get(handles.MenuFile_3_1,'Label');
455set(handles.SubField,'Value',1)
456display_file_name(handles,fileinput_1,2)
457
458% -----------------------------------------------------------------------
459% --- Open again as second field the file whose name has been recorded in MenuFile_4
460function MenuFile_4_1_Callback(hObject, eventdata, handles)
461% -----------------------------------------------------------------------
462fileinput_1=get(handles.MenuFile_4_1,'Label');
463set(handles.SubField,'Value',1)
464display_file_name(handles,fileinput_1,2)
465
466% -----------------------------------------------------------------------
467% --- Open again as second field the file whose name has been recorded in MenuFile_5
468function MenuFile_5_1_Callback(hObject, eventdata, handles)
469% -----------------------------------------------------------------------
470fileinput_1=get(handles.MenuFile_5_1,'Label');
471set(handles.SubField,'Value',1)
472display_file_name(handles,fileinput_1,2)
473
474%------------------------------------------------------------------------
475% --- Called by action in RootPath edit box
476function RootPath_Callback(hObject,eventdata,handles)
477%------------------------------------------------------------------------
478% read the current input file name:
479[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
480if ~exist(fullfile(RootPath,SubDir),'dir')
481    msgbox_uvmat('ERROR',['directory ' fullfile(RootPath,SubDir) ' does not exist'])
482    return
483end
484% detect the file type, get the movie object if relevant, and look for the corresponding file series:
485[RootPath,SubDir,RootFile,i1_series,i2_series,j1_series,j2_series,tild,FileType,MovieObject]=find_file_series(fullfile(RootPath,SubDir),[RootFile FileIndices FileExt]);
486% initiate the input file series and refresh the current field view:
487update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileType,MovieObject,1);
488
489%-----------------------------------------------------------------------
490% --- Called by action in RootPath_1 edit box
491function RootPath_1_Callback(hObject,eventdata,handles)
492% -----------------------------------------------------------------------
493% update_rootinfo_1(hObject,eventdata,handles)
494[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes_1(handles);
495if ~exist(fullfile(RootPath,SubDir),'dir')
496    msgbox_uvmat('ERROR',['directory ' fullfile(RootPath,SubDir) ' does not exist'])
497    return
498end
499% detect the file type, get the movie object if relevant, and look for the corresponding file series:
500[RootPath,SubDir,RootFile,i1_series,i2_series,j1_series,j2_series,tild,FileType,MovieObject]=find_file_series(fullfile(RootPath,SubDir),[RootFile FileIndices FileExt]);
501% initiate the input file series and refresh the current field view:
502update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileType,MovieObject,2);
503
504%------------------------------------------------------------------------
505% --- Called by action in RootFile edit box
506function SubDir_Callback(hObject, eventdata, handles)
507%------------------------------------------------------------------------
508%refresh the menu of input fieldname
509Fields_Callback(hObject, eventdata, handles);
510% refresh the current field view
511run0_Callback(hObject, eventdata, handles);
512
513%------------------------------------------------------------------------
514% --- Called by action in RootFile edit box
515function RootFile_Callback(hObject, eventdata, handles)
516%------------------------------------------------------------------------
517RootPath_Callback(hObject,eventdata,handles)
518
519%-----------------------------------------------------------------------
520% --- Called by action in RootFile_1 edit box
521function RootFile_1_Callback(hObject, eventdata, handles)
522% -----------------------------------------------------------------------
523RootPath_1_Callback(hObject,eventdata,handles)
524
525%------------------------------------------------------------------------
526% --- Called by action in FileIndex edit box
527function FileIndex_Callback(hObject, eventdata, handles)
528%------------------------------------------------------------------------
529[tild,tild,tild,i1,i2,j1,j2]=fileparts_uvmat(get(handles.FileIndex,'String'));
530set(handles.i1,'String',num2str(i1));
531set(handles.i2,'String',num2str(i2));
532set(handles.j1,'String',num2str(j1));
533set(handles.j2,'String',num2str(j2));
534
535% refresh the current field view
536run0_Callback(hObject, eventdata, handles)
537
538%------------------------------------------------------------------------
539% --- Called by action in FileIndex_1 edit box
540function FileIndex_1_Callback(hObject, eventdata, handles)
541%------------------------------------------------------------------------
542run0_Callback(hObject, eventdata, handles)
543
544%------------------------------------------------------------------------
545% --- Called by action in NomType edit box
546function NomType_Callback(hObject, eventdata, handles)
547%------------------------------------------------------------------------
548i1=str2num(get(handles.i1,'String'));
549i2=str2num(get(handles.i2,'String'));
550j1=str2num(get(handles.j1,'String'));
551j2=str2num(get(handles.j2,'String'));
552FileIndex=fullfile_uvmat('','','','',get(handles.NomType,'String'),i1,i2,j1,j2);
553set(handles.FileIndex,'String',FileIndex)
554% refresh the current settings and refresh the field view
555RootPath_Callback(hObject,eventdata,handles)
556
557%------------------------------------------------------------------------
558% --- Called by action in NomType edit box
559function NomType_1_Callback(hObject, eventdata, handles)
560%------------------------------------------------------------------------
561i1=str2num(get(handles.i1,'String'));
562i2=str2num(get(handles.i2,'String'));
563j1=str2num(get(handles.j1,'String'));
564j2=str2num(get(handles.j2,'String'));
565FileIndex=fullfile_uvmat('','','','',get(handles.NomType_1,'String'),i1,i2,j1,j2);
566set(handles.FileIndex_1,'String',FileIndex)
567% refresh the current settings and refresh the field view
568RootPath_1_Callback(hObject,eventdata,handles)
569
570%------------------------------------------------------------------------
571% --- Fills the edit boxes RootPath, RootFile,NomType...from an input file name 'fileinput'
572function display_file_name(handles,fileinput,index)
573%------------------------------------------------------------------------
574%% look for the input file existence
575if ~exist(fileinput,'file')
576    msgbox_uvmat('ERROR',['input file ' fileinput  ' does not exist'])
577    return
578end
579
580%% set the mouse pointer to 'watch'
581set(handles.uvmat,'Pointer','watch')
582set(handles.RootPath,'BackgroundColor',[1 1 0])
583drawnow
584
585%% define the relevant handles for the first field series (index=1) or the second file series (index=2)
586if ~exist('index','var')
587    index=1;
588end
589if index==1
590    handles_RootPath=handles.RootPath;
591    handles_SubDir=handles.SubDir;
592    handles_RootFile=handles.RootFile;
593    handles_FileIndex=handles.FileIndex;
594    handles_NomType=handles.NomType;
595    handles_FileExt=handles.FileExt;
596elseif index==2
597    handles_RootPath=handles.RootPath_1;
598    handles_SubDir=handles.SubDir_1;
599    handles_RootFile=handles.RootFile_1;
600    handles_FileIndex=handles.FileIndex_1;
601    handles_NomType=handles.NomType_1;
602    handles_FileExt=handles.FileExt_1;
603    set(handles.RootPath_1,'Visible','on')
604    set(handles.RootFile_1,'Visible','on')
605    set(handles.SubDir_1,'Visible','on');
606    set(handles.FileIndex_1,'Visible','on');
607    set(handles.FileExt_1,'Visible','on');
608    set(handles.NomType_1,'Visible','on');
609end
610
611%% detect root name, nomenclature and indices in the input file name:
612[FilePath,FileName,FileExt]=fileparts(fileinput);
613% detect the file type, get the movie object if relevant, and look for the corresponding file series:
614% the root name and indices may be corrected by including the first index i1 if a corresponding xml file exists
615[RootPath,SubDir,RootFile,i1_series,i2_series,j1_series,j2_series,NomType,FileType,MovieObject,i1,i2,j1,j2]=find_file_series(FilePath,[FileName FileExt]);
616
617%% open the file or fill the GUI uvmat according to the detected file type
618switch FileType
619    case ''
620        msgbox_uvmat('ERROR','invalid input file type')
621    case 'txt'
622        edit(fileinput)
623    case 'figure'                           %display matlab figure
624        hfig=open(fileinput);
625        set(hfig,'WindowButtonMotionFcn','mouse_motion')%set mouse action functio
626        set(hfig,'WindowButtonUpFcn','mouse_up')%set mouse click action function
627        set(hfig,'WindowButtonUpFcn','mouse_down')%set mouse click action function
628    case 'xml'                % edit xml files
629        t=xmltree(fileinput);
630        % the xml file marks a project or project link, open datatree_browser
631        if strcmp(get(t,1,'name'),'Project')&& exist(regexprep(fileinput,'.xml$',''),'dir')
632            datatree_browser(fileinput)
633        else % other xml file, open the xml editor
634            editxml(fileinput);
635        end
636    case 'xls'% Excel file opended by editxml
637        editxml(fileinput);
638    otherwise
639        set(handles_RootPath,'String',RootPath);
640        rootname=fullfile(RootPath,SubDir,RootFile);
641        set(handles_SubDir,'String',['/' SubDir]);
642        set(handles_RootFile,'String',['/' RootFile]); %display the separator
643        indices=fileinput(length(rootname)+1:end);
644        indices(end-length(FileExt)+1:end)=[]; %remove extension
645        set(handles_FileIndex,'String',indices);
646        set(handles_NomType,'String',NomType);
647        set(handles_FileExt,'String',FileExt);
648        if index==1
649            % fill file index counters if the first file series is opened
650            set(handles.i1,'String',num2str(i1));
651            set(handles.i2,'String',num2str(i2));
652            set(handles.j1,'String',num2stra(j1,NomType));
653            set(handles.j2,'String',num2stra(j2,NomType));
654        else %read the current field index to synchronise with the first series
655            i1_s=str2num(get(handles.i1,'String'));
656            i2_0=str2num(get(handles.i2,'String'));
657            if ~isempty(i2_0)
658                i2_s=i2_0;
659            else
660               i2_s=i2;
661            end
662            j1_0=stra2num(get(handles.j1,'String'));
663            if ~isempty(j1_0)
664                j1_s=j1_0;
665            else
666                j1_s=j1;
667            end
668            j2_0=stra2num(get(handles.j2,'String'));
669            if ~isempty(j2_0)
670                j2_s=j2_0;
671            else
672                j2_s=j2;
673            end
674        end
675       
676        % synchronise indices of the second  input file if it exists
677        if get(handles.SubField,'Value')==1% if the subfield button is activated, update the field numbers
678            Input=read_GUI(handles.InputFile);
679            if ~isfield(Input,'RootPath_1')||strcmp(Input.RootPath_1,'"')
680                Input.RootPath_1=Input.RootPath;
681            end
682            if ~isfield(Input,'SubDir_1')||strcmp(Input.SubDir_1,'"')
683                Input.SubDir_1=Input.SubDir;
684            end
685            if ~isfield(Input,'RootFile_1')||strcmp(Input.RootFile_1,'"')
686                Input.RootFile_1=Input.RootFile;
687            end
688            if ~isfield(Input,'FileExt_1')||strcmp(Input.FileExt_1,'"')
689                Input.FileExt_1=Input.FileExt;
690            end
691            if ~isfield(Input,'NomType_1')||strcmp(Input.NomType_1,'"')
692                Input.NomType_1=Input.NomType;
693            end
694            %updtate the indices of the second field series to correspond to the newly opened one
695            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);
696            if exist(FileName_1,'file')
697                FileIndex_1=fullfile_uvmat('','','','',Input.NomType_1,i1_s,i2_s,j1_s,j2_s);
698            else
699                FileIndex_1=fullfile_uvmat('','','','',Input.NomType_1,i1,i2,j1,j2);
700                msgbox_uvmat('WARNING','unable to synchronise the indices of the two series')
701            end
702            set(handles.FileIndex_1,'String',FileIndex_1)
703        end
704       
705        %enable other menus
706        set(handles.MenuOpen_1,'Enable','on')
707        set(handles.MenuFile_1_1,'Enable','on')
708        set(handles.MenuFile_2_1,'Enable','on')
709        set(handles.MenuFile_3_1,'Enable','on')
710        set(handles.MenuFile_4_1,'Enable','on')
711        set(handles.MenuFile_5_1,'Enable','on')
712        set(handles.MenuExport,'Enable','on')
713        set(handles.MenuExportFigure,'Enable','on')
714        set(handles.MenuExportMovie,'Enable','on')
715        set(handles.MenuTools,'Enable','on')
716
717        % initiate input file series and refresh the current field view:     
718        update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileType,MovieObject,index);
719
720end
721
722%% update list of recent files in the menubar and save it for future opening
723MenuFile=[{get(handles.MenuFile_1,'Label')};{get(handles.MenuFile_2,'Label')};...
724    {get(handles.MenuFile_3,'Label')};{get(handles.MenuFile_4,'Label')};{get(handles.MenuFile_5,'Label')}];
725str_find=strcmp(fileinput,MenuFile);
726if isempty(find(str_find,1))
727    MenuFile=[{fileinput};MenuFile];%insert the current file if not already in the list
728end
729for ifile=1:min(length(MenuFile),5)
730    eval(['set(handles.MenuFile_' num2str(ifile) ',''Label'',MenuFile{ifile});'])
731    eval(['set(handles.MenuFile_' num2str(ifile) '_1,''Label'',MenuFile{ifile});'])
732end
733dir_perso=prefdir;
734profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
735if exist(profil_perso,'file')
736    save (profil_perso,'MenuFile','-append'); %store the file names for future opening of uvmat
737else
738    save (profil_perso,'MenuFile','-V6'); %store the file names for future opening of uvmat
739end
740
741%% set back the mouse pointer to arrow
742set(handles.uvmat,'Pointer','arrow')
743
744
745%------------------------------------------------------------------------
746% --- Update information about a new field series (indices to scan, timing,
747%     calibration from an xml file, then refresh current plots
748
749function update_rootinfo(handles,i1_series,i2_series,j1_series,j2_series,FileType,VideoObject,index)
750%------------------------------------------------------------------------
751%% define the relevant handles depending on the index (1=first file series, 2= second file series)
752if ~exist('index','var')
753    index=1;
754end
755if index==1
756    handles_RootPath=handles.RootPath;
757    handles_Fields=handles.FieldName;
758elseif index==2
759    handles_RootPath=handles.RootPath_1;
760    handles_Fields=handles.FieldName_1;
761end
762
763set(handles_RootPath,'BackgroundColor',[1 1 0])
764drawnow
765set(handles.FieldName,'UserData',[])% reinialize data from uvmat opening
766UvData=get(handles.uvmat,'UserData');%huvmat=handles of the uvmat interface
767UvData.NewSeries=1; %flag for run0: begin a new series
768UvData.FileName_1='';% name of the current second field (used to detect a  constant field during file scanning)
769UvData.FileType{index}=FileType;
770UvData.i1_series{index}=i1_series;
771UvData.i2_series{index}=i2_series;
772UvData.j1_series{index}=j1_series;
773UvData.j2_series{index}=j2_series;
774set(handles.FixVelType,'Value',0); %desactivate fixed veltype
775if index==1
776    [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
777else
778    [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes_1(handles);
779end
780FileName=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
781FileBase=fullfile(RootPath,RootFile);
782if ~exist(FileName,'file')
783   msgbox_uvmat('ERROR',['input file ' FileName ' not found']);
784    return
785end
786
787%% read timing and total frame number from the current file (movie files) !! may be overrid by xml file
788XmlData.Time=[];%default
789XmlData.GeometryCalib=[];%default
790TimeUnit='';%default
791Time=[];
792testima=0; %test for image input
793imainfo=[];
794ColorType='falsecolor'; %default
795hhh=[];
796UvData.MovieObject{index}=VideoObject;
797if ~isempty(VideoObject)
798    imainfo=get(VideoObject);
799    testima=1;
800    TimeUnit='s';
801    if isempty(j1_series); %frame index along i
802        Time=(0:1/imainfo.FrameRate:(imainfo.NumberOfFrames)/imainfo.FrameRate)';
803    else
804    Time=ones(size(i1_series,1),1)*(0:1/imainfo.FrameRate:(imainfo.NumberOfFrames)/imainfo.FrameRate);
805    end
806    %nbfield=imainfo.NumberOfFrames;
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        RootFile=get(handles.RootFile,'String');
813        imainfo=imfinfo([fullfile(RootPath,SubDir,RootFile) FileIndices FileExt]);
814    else
815        imainfo=imfinfo([FileBase FileIndices FileExt]);
816    end
817    ColorType=imainfo.ColorType;%='truecolor' for color images
818    if length(imainfo) >1 %case of image with multiple frames
819       % nbfield=length(imainfo);
820       % nbfield_j=1;
821    end
822end
823if isfield(imainfo,'Width') && isfield(imainfo,'Height')
824    if length(imainfo)>1
825        set(handles.num_Npx,'String',num2str(imainfo(1).Width));%fills nbre of pixels x box
826        set(handles.num_Npy,'String',num2str(imainfo(1).Height));%fills nbre of pixels x box
827    else
828        set(handles.num_Npx,'String',num2str(imainfo.Width));%fills nbre of pixels x box
829        set(handles.num_Npy,'String',num2str(imainfo.Height));%fills nbre of pixels x box
830    end
831else
832    set(handles.num_Npx,'String','');%fills nbre of pixels x box
833    set(handles.num_Npy,'String','');%fills nbre of pixels x box
834end
835set(handles.CheckBW,'Value',strcmp(ColorType,'grayscale'))% select handles.CheckBW if grayscale image
836
837%% read parameters (time, geometric calibration..) from a documentation file (.xml advised)
838XmlFileName=find_imadoc(RootPath,SubDir,RootFile,FileExt);
839[tild,tild,DocExt]=fileparts(XmlFileName);
840warntext='';%default warning message
841NbSlice=1;%default
842set(handles.RootPath,'BackgroundColor',[1 1 1])
843if ~isempty(XmlFileName)
844    set(handles.view_xml,'Visible','on')
845    set(handles.view_xml,'BackgroundColor',[1 1 0])
846    set(handles.view_xml,'String','view .xml')
847    drawnow
848    [XmlDataRead,warntext]=imadoc2struct(XmlFileName);
849    if ~isempty(warntext)
850        msgbox_uvmat('WARNING',warntext)
851    end
852    if isempty(XmlDataRead)
853        set(handles.view_xml,'Visible','off')
854    else
855        set(handles.view_xml,'String',['view ' DocExt])   
856        XmlData=XmlDataRead;
857        if isfield(XmlData,'TimeUnit')
858            if isfield(XmlData,'TimeUnit')&& ~isempty(XmlData.TimeUnit)
859                TimeUnit=XmlData.TimeUnit;
860            end
861        end
862        set(handles.view_xml,'BackgroundColor',[1 1 1])
863        drawnow
864        if isfield(XmlData, 'GeometryCalib') && ~isempty(XmlData.GeometryCalib)
865            if isfield(XmlData.GeometryCalib,'VolumeScan') && isequal(XmlData.GeometryCalib.VolumeScan,'y')
866                set (handles.num_NbSlice,'String','volume')
867            end
868            hgeometry_calib=findobj('tag','geometry_calib');
869            if ~isempty(hgeometry_calib)
870                GUserData=get(hgeometry_calib,'UserData');
871                if ~(isfield(GUserData,'XmlInputFile') && strcmp(GUserData.XmlInputFile,XmlFileName))
872                    answer=msgbox_uvmat('INPUT_Y-N','replace the display of geometry_calib with the new input data?');
873                    if strcmp(answer,'Yes')
874                        geometry_calib(XmlFileName);%diplay the new calibration points and parameters in geometry_calib
875                    end
876                end
877            end
878        end
879    end
880end
881if ~(isfield(XmlData,'Time')&& ~isempty(XmlData.Time))
882    XmlData.Time=Time; %time set by video
883end
884
885%% store last index in handles.lat_i and .last_j
886nbfield=max(max(max(i2_series)));
887if isempty(nbfield)
888    nbfield=max(max(max(i1_series)));
889end
890nbfield_j=max(max(max(j2_series)));
891if isempty(nbfield_j)
892    nbfield_j=max(max(max(j2_series)));
893end
894if ~isempty(XmlData.Time)
895    %transform .Time to a column vector if it is a line vector the nomenclature uses a single index
896    if isequal(size(XmlData.Time,1),1)
897        NomType=get(handles.NomType,'String');
898        XmlData.Time=(XmlData.Time)';
899    end
900end
901last_i_cell=get(handles.last_i,'String');
902if isempty(nbfield)
903    last_i_cell{1}='';
904else
905    last_i_cell{1}=num2str(nbfield);
906end
907set(handles.last_i,'String',last_i_cell)
908last_j_cell=get(handles.last_j,'String');
909if isempty(nbfield_j)
910     last_j_cell{1}='';
911else
912     last_j_cell{1}=num2str(nbfield_j);
913end
914set(handles.last_j,'String',last_j_cell);
915
916%% store geometric calibration in UvData
917if isfield(XmlData,'GeometryCalib')
918    GeometryCalib=XmlData.GeometryCalib;
919    if isempty(GeometryCalib)
920        set(handles.pxcm,'String','')
921        set(handles.pycm,'String','')
922        set(handles.transform_fct,'Value',1); %  no transform by default
923    else
924        if (isfield(GeometryCalib,'R')&& ~isequal(GeometryCalib.R(2,1),0) && ~isequal(GeometryCalib.R(1,2),0)) ||...
925            (isfield(GeometryCalib,'kappa1')&& ~isequal(GeometryCalib.kappa1,0))
926            set(handles.pxcm,'String','var')
927            set(handles.pycm,'String','var')
928        elseif isfield(GeometryCalib,'fx_fy')
929            pixcmx=GeometryCalib.fx_fy(1);%*GeometryCalib.R(1,1)*GeometryCalib.sx/(GeometryCalib.Tz*GeometryCalib.dpx);
930            pixcmy=GeometryCalib.fx_fy(2);%*GeometryCalib.R(2,2)/(GeometryCalib.Tz*GeometryCalib.dpy);
931            set(handles.pxcm,'String',num2str(pixcmx))
932            set(handles.pycm,'String',num2str(pixcmy))
933        end
934        if ~get(handles.CheckFixLimits,'Value')
935            set(handles.transform_fct,'Value',3); % phys transform by default if fixedLimits is off
936        end
937        if isfield(GeometryCalib,'SliceCoord')           
938           siz=size(GeometryCalib.SliceCoord);
939           if siz(1)>1
940               NbSlice=siz(1);
941               set(handles.slices,'Visible','on')
942               set(handles.slices,'Value',1)
943           end
944           if isfield(GeometryCalib,'VolumeScan') && isequal(GeometryCalib.VolumeScan,'y')
945               set(handles.num_NbSlice,'String','volume')
946           else
947               set(handles.num_NbSlice,'String',num2str(NbSlice))
948           end
949           slices_Callback([],[], handles)
950        end           
951    end
952end
953
954%% update the data attached to the uvmat interface
955if ~isempty(TimeUnit)
956    set(handles.time_txt,'String',['time (' TimeUnit ')'])
957end
958UvData.TimeUnit=TimeUnit;
959UvData.XmlData{index}=XmlData;
960UvData.NewSeries=1;
961% UvData.MovieObject=MovieObject;
962
963%display warning message
964if ~isequal(warntext,'')
965    msgbox_uvmat('WARNING',warntext);
966end
967
968%% set default options in menu 'FieldName'
969switch FileType
970    case {'civx','civdata'}
971        [FieldList,ColorList]=calc_field;
972        set(handles_Fields,'String',[{'image'};FieldList;{'get_field...'}]);%standard menu for civx data
973        set(handles_Fields,'Value',2) % set menu to 'velocity
974        set(handles.ColorScalar,'Value',1)
975        set(handles.ColorScalar,'String',ColorList)
976        set(handles.Vectors,'Visible','on')
977        set(handles.Coord_x,'Value',1);
978        set(handles.Coord_x,'String',{'X'});
979        set(handles.Coord_y,'Value',1);
980        set(handles.Coord_y,'String',{'Y'});
981    case 'netcdf'
982        set(handles_Fields,'Value',1)
983        set(handles_Fields,'String',{'get_field...'})
984        hget_field=get_field(FileName);
985        hhget_field=guidata(hget_field);
986        get_field('RUN_Callback',hhget_field.RUN,[],hhget_field);
987    otherwise
988        set(handles_Fields,'Value',1) % set menu to 'image'
989        set(handles_Fields,'String',{'image'})
990        set(handles.Coord_x,'Value',1);
991        set(handles.Coord_x,'String',{'AX'});
992        set(handles.Coord_y,'Value',1);
993        set(handles.Coord_y,'String',{'AY'});
994end
995set(handles.uvmat,'UserData',UvData)
996
997%% set index navigation options and refresh plots
998scan_option='i';%default
999state_j='off'; %default
1000if index==2
1001    if get(handles.scan_j,'Value')
1002        scan_option='j'; %keep the scan option for the second file series
1003    end
1004    if strcmp(get(handles.j1,'Visible'),'on')
1005        state_j='on';
1006    end
1007end
1008[ref_j,ref_i]=find(squeeze(i1_series(1,:,:)));
1009if ~isempty(j1_series)
1010        state_j='on';
1011        if index==1
1012            if isequal(ref_i,ref_i(1)*ones(size(ref_j)))% if ref_i is always equal to its first value
1013                scan_option='j'; %scan j indext               
1014            end
1015        end
1016end
1017if isequal(scan_option,'i')
1018    diff_ref_i=diff(ref_i,1);
1019    if isempty(diff_ref_i)
1020        diff_ref_i=1;
1021    end
1022    if isequal (diff_ref_i,diff_ref_i(1)*ones(size(diff_ref_i)))
1023        set(handles.num_IndexIncrement,'String',num2str(diff_ref_i(1)))
1024    end
1025     set(handles.scan_i,'Value',1)
1026     scan_i_Callback([],[], handles);
1027else
1028    diff_ref_j=diff(ref_j);
1029    if isempty(diff_ref_j)
1030        diff_ref_j=1;
1031    end
1032    if isequal (diff_ref_j,diff_ref_j(1)*ones(size(diff_ref_j)))
1033        set(handles.num_IndexIncrement,'String',num2str(diff_ref_j(1)))
1034    end
1035     set(handles.scan_j,'Value',1)
1036     scan_j_Callback([],[], handles);
1037end
1038set(handles.scan_j,'Visible',state_j)
1039set(handles.j1,'Visible',state_j)
1040set(handles.j2,'Visible',state_j)
1041set(handles.last_j,'Visible',state_j);
1042set(handles.frame_j,'Visible',state_j);
1043set(handles.j_text,'Visible',state_j);
1044if ~isempty(i2_series)||~isempty(j2_series)
1045    set(handles.CheckFixPair,'Visible','on')
1046elseif index==1
1047    set(handles.CheckFixPair,'Visible','off')
1048end
1049
1050%% apply the effect of the transform fct and view the field 
1051transform=get(handles.path_transform,'UserData');
1052if index==2 && (~isa(transform,'function_handle')||nargin(transform)<3)
1053    set(handles.transform_fct,'value',2); % set transform to sub_field if the current fct doe not accept two input fields
1054end
1055transform_fct_Callback([],[],handles)
1056mask_test=get(handles.CheckMask,'value');
1057if mask_test
1058    MaskData=get(handles.CheckMask,'UserData');
1059    if isfield(MaskData,'maskhandle') && ishandle(MaskData.maskhandle)
1060          delete(MaskData.maskhandle)    %delete old mask
1061    end
1062    CheckMask_Callback([],[],handles)
1063end
1064
1065%------------------------------------------------------------------------
1066% --- switch file index scanning options scan_i and scan_j in an exclusive way
1067function scan_i_Callback(hObject, eventdata, handles)
1068%------------------------------------------------------------------------
1069if get(handles.scan_i,'Value')==1
1070    set(handles.scan_i,'BackgroundColor',[1 1 0])
1071    set(handles.scan_j,'Value',0)
1072else
1073    set(handles.scan_i,'BackgroundColor',[0.831 0.816 0.784])
1074    set(handles.scan_j,'Value',1)
1075end
1076scan_j_Callback(hObject, eventdata, handles)
1077
1078%------------------------------------------------------------------------
1079% --- switch file index scanning options scan_i and scan_j in an exclusive way
1080function scan_j_Callback(hObject, eventdata, handles)
1081%------------------------------------------------------------------------
1082if get(handles.scan_j,'Value')==1
1083    set(handles.scan_j,'BackgroundColor',[1 1 0])
1084    set(handles.scan_i,'Value',0)
1085    set(handles.scan_i,'BackgroundColor',[0.831 0.816 0.784])
1086%     NomType=get(handles.NomType,'String');
1087%     switch NomType
1088%     case {'_1_1-2','#_ab','%3dab'},% pair with j index
1089%         set(handles.CheckFixPair,'Visible','on')% option fixed pair on/off made visible (choice of avaible pair with buttons + and - if ='off')
1090%     otherwise
1091%         set(handles.CheckFixPair,'Visible','off')
1092%     end
1093else
1094    set(handles.scan_j,'BackgroundColor',[0.831 0.816 0.784])
1095    set(handles.scan_i,'Value',1)
1096    set(handles.scan_i,'BackgroundColor',[1 1 0])
1097    set(handles.CheckFixPair,'Visible','off')
1098end
1099
1100%------------------------------------------------------------------------
1101function i1_Callback(hObject, eventdata, handles)
1102%------------------------------------------------------------------------
1103update_ij(handles,1)
1104
1105%------------------------------------------------------------------------
1106function i2_Callback(hObject, eventdata, handles)
1107%------------------------------------------------------------------------
1108update_ij(handles,2)
1109
1110%------------------------------------------------------------------------
1111function j1_Callback(hObject, eventdata, handles)
1112%------------------------------------------------------------------------
1113update_ij(handles,3)
1114
1115%------------------------------------------------------------------------
1116function j2_Callback(hObject, eventdata, handles)
1117%------------------------------------------------------------------------
1118update_ij(handles,4)
1119
1120%------------------------------------------------------------------------
1121%--- update the index display after action on edit boxes i1, i2, j1 or j2
1122function update_ij(handles,index_rank)
1123NomType=get(handles.NomType,'String');
1124indices=get(handles.FileIndex,'String');
1125[tild,tild,tild,i1,i2,j1,j2]=fileparts_uvmat(indices);% the indices for the second series taken from FileIndex
1126switch index_rank
1127    case 1
1128        indices=fullfile_uvmat('','','','',NomType,stra2num(get(handles.i1,'String')),i2,j1,j2);
1129        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
1130    case 2
1131        indices=fullfile_uvmat('','','','',NomType,i1,stra2num(get(handles.i2,'String')),j1,j2);
1132        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
1133    case 3
1134        indices=fullfile_uvmat('','','','',NomType,i1,i2,stra2num(get(handles.j1,'String')),j2);
1135        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
1136    case 4
1137        indices=fullfile_uvmat('','','','',NomType,i1,i2,j1,stra2num(get(handles.j2,'String')));
1138        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
1139end
1140set(handles.FileIndex,'String',indices)
1141set(handles.FileIndex,'BackgroundColor',[0.7 0.7 0.7])% mark the edit box in grey, then RUN0 will mark it in white for confirmation
1142% update the second index if relevant
1143if strcmp(get(handles.FileIndex_1,'Visible'),'on')
1144    NomType_1=get(handles.NomType_1,'String');
1145    indices_1=get(handles.FileIndex_1,'String');
1146    [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
1147    switch index_rank
1148        case 1
1149            indices_1=fullfile_uvmat('','','','',NomType_1,stra2num(get(handles.i1,'String')),i2_1,j1_1,j2_1);
1150        case 2
1151            indices_1=fullfile_uvmat('','','','',NomType_1,i1_1,stra2num(get(handles.i2,'String')),j1_1,j2_1);
1152        case 3
1153            indices_1=fullfile_uvmat('','','','',NomType_1,i1_1,i2_1,stra2num(get(handles.j1,'String')),j2_1);
1154        case 4
1155            indices_1=fullfile_uvmat('','','','',NomType_1,i1_1,i2_1,j1_1,stra2num(get(handles.j2,'String')));
1156    end
1157    set(handles.FileIndex_1,'String',indices_1)
1158    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
1159end
1160   
1161%------------------------------------------------------------------------
1162
1163%------------------------------------------------------------------------
1164function slices_Callback(hObject, eventdata, handles)
1165%------------------------------------------------------------------------
1166if get(handles.slices,'Value')==1
1167    set(handles.slices,'BackgroundColor',[1 1 0])
1168    set(handles.num_NbSlice,'Visible','on')
1169    set(handles.z_text,'Visible','on')
1170    set(handles.z_index,'Visible','on')
1171    num_NbSlice_Callback(hObject, eventdata, handles)
1172else
1173    set(handles.num_NbSlice,'Visible','off')
1174    set(handles.slices,'BackgroundColor',[0.7 0.7 0.7])
1175    set(handles.z_text,'Visible','off')
1176    set(handles.z_index,'Visible','off')
1177    set(handles.masklevel,'Value',1)
1178    set(handles.masklevel,'String',{'1'})
1179end
1180
1181%------------------------------------------------------------------------
1182function num_NbSlice_Callback(hObject, eventdata, handles)
1183%------------------------------------------------------------------------
1184nb_slice_str=get(handles.num_NbSlice,'String');
1185if isequal(nb_slice_str,'volume')
1186    num=stra2num(get(handles.j1,'String'));
1187    last_j=get(handles.last_j,'String');
1188    nbslice=str2double(last_j{1});
1189else
1190    num=str2double(get(handles.i1,'String'));
1191    nbslice=str2double(get(handles.num_NbSlice,'String'));
1192end
1193z=mod(num-1,nbslice)+1;
1194set(handles.z_index,'String',num2str(z))
1195for ilist=1:nbslice
1196    list_index{ilist,1}=num2str(ilist);
1197end   
1198set(handles.masklevel,'String',list_index)
1199set(handles.masklevel,'Value',z)
1200
1201%------------------------------------------------------------------------
1202% --- Executes on button press in view_xml.
1203function view_xml_Callback(hObject, eventdata, handles)
1204%------------------------------------------------------------------------
1205%[FileName,RootPath,FileBase,FileIndices,FileExt]=read_file_boxes(handles);
1206 [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
1207FileBase=fullfile(RootPath,RootFile);
1208option=get(handles.view_xml,'String');
1209if isequal(option,'view .xml')
1210    FileXml=fullfile(RootPath,[SubDir '.xml']);
1211    if ~exist(FileXml,'file')% case of civ files , removes the extension for subdir
1212        FileXml=fullfile(RootPath,[regexprep(SubDir,'\..+$','') '.xml']);
1213    end
1214    heditxml=editxml(FileXml);
1215end
1216
1217%------------------------------------------------------------------------
1218% --- Executes on button press in CheckMask.
1219function CheckMask_Callback(hObject, eventdata, handles)
1220%------------------------------------------------------------------------
1221%case of view mask selection
1222if isequal(get(handles.CheckMask,'Value'),1)
1223     [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
1224     FileBase=fullfile(RootPath,RootFile);
1225    num_i1=stra2num(get(handles.i1,'String'));
1226    num_j1=stra2num(get(handles.j1,'String'));
1227    currentdir=pwd; 
1228    cd(RootPath);
1229    maskfiles=dir('*_*mask_*.png');%look for a mask file
1230    cd(currentdir);%come back to the working directory
1231    mdetect=0;
1232    if ~isempty(maskfiles)
1233        for ilist=1:length(maskfiles)
1234            maskname=maskfiles(ilist).name;% take the first mask file in the list
1235            [tild,tild,tild,tild,tild,tild,tild,MaskExt,Mask_NomType{ilist}]=fileparts_uvmat(maskname);
1236             [tild,Name]=fileparts(maskname);
1237            Namedouble=double(Name);
1238            val=(48>Namedouble)|(Namedouble>57);% select the non-numerical characters
1239            ind_mask=findstr('mask',Name);
1240            i=ind_mask-1;
1241            while val(i)==0 && i>0
1242                i=i-1;
1243            end
1244            nbmask_str=str2num(Name(i+1:ind_mask-1));
1245            if ~isempty(nbmask_str)
1246                nbslice(ilist)=nbmask_str; % number of different masks (slices)
1247            end
1248        end
1249        if isequal(min(nbslice),max(nbslice))
1250            nbslice=nbslice(1);
1251        else
1252            msgbox_uvmat('ERROR','several inconsistent mask sets coexist in the current image directory')
1253            return
1254        end
1255        if ~isempty(nbslice) && Name(i)=='_'
1256            Mask.Base=[FileBase Name(i:ind_mask+3)];
1257            Mask.NbSlice=nbslice;
1258            num_i1=mod(num_i1-1,nbslice)+1;
1259            Mask.NomType=regexprep(Mask_NomType{1},'0','');%remove '0' in nom type for masks
1260            [RootPath,RootFile]=fileparts(Mask.Base);
1261            maskname=fullfile_uvmat(RootPath,'',RootFile,'.png',Mask.NomType,num_i1,[],num_j1);
1262            %maskname=name_generator(Mask.Base,num_i1,num_j1,'.png',Mask.NomType);%
1263            mdetect=exist(maskname,'file');
1264            if mdetect
1265                set(handles.num_NbSlice,'String',Name(i+1:ind_mask-1));
1266                set(handles.num_NbSlice,'BackgroundColor',[1 1 0])
1267                set(handles.CheckMask,'UserData',Mask);
1268                set(handles.CheckMask,'BackgroundColor',[1 1 0])
1269                if nbslice > 1
1270                    set(handles.slices,'value',1)
1271                    slices_Callback(hObject, eventdata, handles)
1272                end
1273            end
1274        end
1275    end
1276    errormsg=[];%default
1277    if mdetect==0
1278        [FileName, PathName, filterindex] = uigetfile( ...
1279            {'*.png', ' (*.png)';
1280            '*.png',  '.png files '; ...
1281            '*.*', 'All Files (*.*)'}, ...
1282            'Pick a mask file *.png',FileBase);
1283        if ~ischar(FileName),return,end %abandon if the browser is cancelled
1284        maskname=fullfile(PathName,FileName);
1285        [RootDir,SubDir,RootFile,tild,tild,tild,tild,tild,Mask.NomType]=fileparts_uvmat(maskname);
1286        Mask.Base=fullfile(RootDir,SubDir,RootFile);
1287        Mask.NbSlice=1;
1288        set(handles.CheckMask,'UserData',Mask);
1289        set(handles.CheckMask,'BackgroundColor',[1 1 0])
1290    end
1291    if isempty(errormsg)
1292        errormsg=update_mask(handles,num_i1,num_j1);
1293    end
1294    if ~isempty(errormsg)
1295            set(handles.CheckMask,'Value',0)
1296            set(handles.CheckMask,'BackgroundColor',[0.7 0.7 0.7])
1297     end
1298else % desactivate mask display
1299    MaskData=get(handles.CheckMask,'UserData');
1300    if isfield(MaskData,'maskhandle') && ishandle(MaskData.maskhandle)
1301          delete(MaskData.maskhandle)   
1302    end
1303    set(handles.CheckMask,'UserData',[])   
1304    UvData=get(handles.uvmat,'UserData');
1305    if isfield(UvData,'MaskName')
1306        UvData=rmfield(UvData,'MaskName');
1307        set(handles.uvmat,'UserData',UvData)
1308    end
1309    set(handles.CheckMask,'BackgroundColor',[0.7 0.7 0.7])
1310end
1311
1312%------------------------------------------------------------------------
1313function errormsg=update_mask(handles,num_i1,num_j1)
1314%------------------------------------------------------------------------
1315errormsg=[];%default
1316MaskData=get(handles.CheckMask,'UserData');
1317if isfield(MaskData,'maskhandle')&& ishandle(MaskData.maskhandle)
1318    uistack(MaskData.maskhandle,'top');
1319end
1320num_i1_mask=mod(num_i1-1,MaskData.NbSlice)+1;
1321[RootPath,RootFile]=fileparts(MaskData.Base);
1322MaskName=fullfile_uvmat(RootPath,'',RootFile,'.png',MaskData.NomType,num_i1_mask,[],num_j1);
1323UvData=get(handles.uvmat,'UserData');
1324%update mask image if the mask is new
1325if ~ (isfield(UvData,'MaskName') && isequal(UvData.MaskName,MaskName))
1326    UvData.MaskName=MaskName; %update the recorded name on UvData
1327    set(handles.uvmat,'UserData',UvData);
1328    if ~exist(MaskName,'file')
1329        if isfield(MaskData,'maskhandle')&& ishandle(MaskData.maskhandle)
1330            delete(MaskData.maskhandle)   
1331        end
1332    else
1333        %read mask image
1334        Mask.AName='image';
1335        Mask.A=imread(MaskName);
1336        npxy=size(Mask.A);
1337        test_error=0;
1338        if length(npxy)>2
1339            errormsg=[MaskName ' is not a grey scale image'];
1340            return
1341        elseif ~isa(Mask.A,'uint8')
1342            errormsg=[MaskName ' is not a 8 bit grey level image'];
1343            return
1344        end
1345        Mask.AX=[0.5 npxy(2)-0.5];
1346        Mask.AY=[npxy(1)-0.5 0.5 ];
1347        Mask.CoordUnit='pixel';
1348        if isequal(get(handles.slices,'Value'),1)
1349           NbSlice=str2num(get(handles.num_NbSlice,'String'));
1350           num_i1=str2num(get(handles.i1,'String'));
1351           Mask.ZIndex=mod(num_i1-1,NbSlice)+1;
1352        end
1353        %px to phys or other transform on field
1354         menu_transform=get(handles.transform_fct,'String');
1355        choice_value=get(handles.transform_fct,'Value');
1356        transform_name=menu_transform{choice_value};%name of the transform fct  given by the menu 'transform_fct'
1357        transform_list=get(handles.transform_fct,'UserData');
1358        transform=transform_list{choice_value};
1359        if  ~isequal(transform_name,'') && ~isequal(transform_name,'px')
1360            if isfield(UvData,'XmlData') && isfield(UvData.XmlData{1},'GeometryCalib')%use geometry calib recorded from the ImaDoc xml file as first priority
1361                Calib=UvData.XmlData{1}.GeometryCalib;
1362                Mask=transform(Mask,UvData.XmlData{1});
1363            end
1364        end
1365        flagmask=Mask.A < 200;
1366       
1367        %make brown color image
1368        imflag(:,:,1)=0.9*flagmask;
1369        imflag(:,:,2)=0.7*flagmask;
1370        imflag(:,:,3)=zeros(size(flagmask));
1371       
1372        %update mask image
1373        hmask=[]; %default
1374        if isfield(MaskData,'maskhandle')&& ishandle(MaskData.maskhandle)
1375            hmask=MaskData.maskhandle;
1376        end
1377        if ~isempty(hmask)
1378            set(hmask,'CData',imflag)   
1379            set(hmask,'AlphaData',flagmask*0.6)
1380            set(hmask,'XData',Mask.AX);
1381            set(hmask,'YData',Mask.AY);
1382%             uistack(hmask,'top')
1383        else
1384            axes(handles.PlotAxes)
1385            hold on   
1386            size(flagmask)
1387           % MaskData.maskhandle=image(Mask.AX,Mask.AY,imflag,'Tag','mask','HitTest','off','AlphaData',0.6*flagmask);
1388            MaskData.maskhandle=image(Mask.AX,Mask.AY,imflag,'Tag','mask','HitTest','off','AlphaData',0.6*ones(size(flagmask)));
1389%             set(MaskData.maskhandle,'AlphaData',0.6*flagmask)
1390            set(handles.CheckMask,'UserData',MaskData)
1391        end
1392    end
1393end
1394
1395%------------------------------------------------------------------------
1396%------------------------------------------------------------------------
1397% III - MAIN REFRESH FUNCTIONS : 'FRAME PLOT'
1398%------------------------------------------------------------------------
1399
1400%------------------------------------------------------------------------
1401% --- Executes on button press in runplus: make one step forward and call
1402% --- run0. The step forward is along the fieldname series 1 or 2 depending on
1403% --- the scan_i and scan_j check box (exclusive each other)
1404function runplus_Callback(hObject, eventdata, handles)
1405%------------------------------------------------------------------------
1406set(handles.runplus,'BackgroundColor',[1 1 0])%paint the command button in yellow
1407drawnow
1408%TODO: introduce the option: increment ='*' to move to the next available view
1409increment=str2num(get(handles.num_IndexIncrement,'String')); %get the field increment d
1410% if isnan(increment)
1411%     set(handles.num_IndexIncrement,'String','1')%default value
1412%     increment=1;
1413% end
1414errormsg=runpm(hObject,eventdata,handles,increment);
1415if ~isempty(errormsg)
1416    msgbox_uvmat('ERROR',errormsg);
1417end
1418set(handles.runplus,'BackgroundColor',[1 0 0])%paint the command button back to red
1419
1420%------------------------------------------------------------------------
1421% --- Executes on button press in runmin: make one step backward and call
1422% --- run0. The step backward is along the fieldname series 1 or 2 depending on
1423% --- the scan_i and scan_j check box (exclusive each other)
1424function runmin_Callback(hObject, eventdata, handles)
1425%------------------------------------------------------------------------
1426set(handles.runmin,'BackgroundColor',[1 1 0])%paint the command button in yellow
1427drawnow
1428increment=-str2num(get(handles.num_IndexIncrement,'String')); %get the field increment d
1429% if isnan(increment)
1430%     set(handles.num_IndexIncrement,'String','1')%default value
1431%     increment=1;
1432% end
1433errormsg=runpm(hObject,eventdata,handles,increment);
1434if ~isempty(errormsg)
1435    msgbox_uvmat('ERROR',errormsg);
1436end
1437set(handles.runmin,'BackgroundColor',[1 0 0])%paint the command button back to red
1438
1439%------------------------------------------------------------------------
1440% -- Executes on button press in Movie: make a series of +> steps
1441function Movie_Callback(hObject, eventdata, handles)
1442%------------------------------------------------------------------------
1443set(handles.Movie,'BackgroundColor',[1 1 0])%paint the command button in yellow
1444drawnow
1445increment=str2num(get(handles.num_IndexIncrement,'String')); %get the field increment d
1446% if isnan(increment)
1447%     set(handles.num_IndexIncrement,'String','1')%default value
1448%     increment=1;
1449% end
1450set(handles.STOP,'Visible','on')
1451set(handles.speed,'Visible','on')
1452set(handles.speed_txt,'Visible','on')
1453set(handles.Movie,'BusyAction','queue')
1454UvData=get(handles.uvmat,'UserData');
1455
1456while get(handles.Movie,'Value')==1 && get(handles.speed,'Value')~=0 && isequal(get(handles.Movie,'BusyAction'),'queue') % enable STOP command
1457        errormsg=runpm(hObject,eventdata,handles,increment);
1458        if ~isempty(errormsg)
1459            set(handles.Movie,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1460            return
1461        end
1462        pause(1.02-get(handles.speed,'Value'))% wait for next image
1463end
1464if isfield(UvData,'aviobj') && ~isempty( UvData.aviobj),
1465    UvData.aviobj=close(UvData.aviobj);
1466   set(handles.uvmat,'UserData',UvData);
1467end
1468set(handles.Movie,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1469
1470%------------------------------------------------------------------------
1471% -- Executes on button press in Movie: make a series of <- steps
1472function MovieBackward_Callback(hObject, eventdata, handles)
1473%------------------------------------------------------------------------
1474set(handles.MovieBackward,'BackgroundColor',[1 1 0])%paint the command button in yellow
1475drawnow
1476increment=-str2num(get(handles.num_IndexIncrement,'String')); %get the field increment d
1477set(handles.STOP,'Visible','on')
1478set(handles.speed,'Visible','on')
1479set(handles.speed_txt,'Visible','on')
1480set(handles.MovieBackward,'BusyAction','queue')
1481UvData=get(handles.uvmat,'UserData');
1482
1483while get(handles.MovieBackward,'Value')==1 && get(handles.speed,'Value')~=0 && isequal(get(handles.MovieBackward,'BusyAction'),'queue') % enable STOP command
1484        errormsg=runpm(hObject,eventdata,handles,increment);
1485        if ~isempty(errormsg)
1486            set(handles.MovieBackward,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1487            return
1488        end
1489        pause(1.02-get(handles.speed,'Value'))% wait for next image
1490end
1491if isfield(UvData,'aviobj') && ~isempty( UvData.aviobj),
1492    UvData.aviobj=close(UvData.aviobj);
1493   set(handles.uvmat,'UserData',UvData);
1494end
1495set(handles.MovieBackward,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1496
1497%------------------------------------------------------------------------
1498function STOP_Callback(hObject, eventdata, handles)
1499%------------------------------------------------------------------------
1500set(handles.movie_pair,'BusyAction','Cancel')
1501set(handles.movie_pair,'value',0)
1502set(handles.Movie,'BusyAction','Cancel')
1503set(handles.MovieBackward,'BusyAction','Cancel')
1504set(handles.MenuExportMovie,'BusyAction','Cancel')
1505set(handles.movie_pair,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1506set(handles.Movie,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1507set(handles.MovieBackward,'BackgroundColor',[1 0 0])%paint the command buttonback to red
1508
1509%------------------------------------------------------------------------
1510% --- function activated by runplus and run minus
1511function errormsg=runpm(hObject,eventdata,handles,increment)
1512%------------------------------------------------------------------------
1513errormsg='';%default
1514%% check for movie pair status
1515movie_status=get(handles.movie_pair,'Value');
1516if isequal(movie_status,1)
1517    STOP_Callback(hObject, eventdata, handles)%interrupt movie pair if active
1518end
1519
1520%% read the current input file name(s) and field indices
1521InputFile=read_GUI(handles.InputFile);
1522InputFile.RootFile=regexprep(InputFile.RootFile,'^[\\/]|[\\/]$','');%suppress possible / or \ separator at the beginning or the end of the string
1523InputFile.SubDir=regexprep(InputFile.SubDir,'^[\\/]|[\\/]$','');%suppress possible / or \ separator at the beginning or the end of the string
1524FileExt=InputFile.FileExt;
1525NomType=get(handles.NomType,'String');
1526i1=str2num(get(handles.i1,'String'));%read the field indices (for movie, it is not given by the file name)
1527i2=[];%default
1528if strcmp(get(handles.i2,'Visible'),'on')
1529    i2=str2num(get(handles.i2,'String'));
1530end
1531j1=[];
1532if strcmp(get(handles.j1,'Visible'),'on')
1533    j1=stra2num(get(handles.j1,'String'));
1534end
1535j2=j1;
1536if strcmp(get(handles.j2,'Visible'),'on')
1537    j2=stra2num(get(handles.j2,'String'));
1538end
1539sub_value= get(handles.SubField,'Value');
1540if sub_value % a second input file has been entered
1541     [InputFile.RootPath_1,InputFile.SubDir_1,InputFile.RootFile_1,InputFile.FileIndex_1,InputFile.FileExt_1,InputFile.NomType_1]=read_file_boxes_1(handles);   
1542    [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
1543else
1544    filename_1=[];
1545end   
1546
1547%% increment (or decrement) the field indices and update the input filename(s)
1548if isempty(increment)
1549    set(handles.CheckFixPair,'Value',0)
1550end
1551CheckFixPair=get(handles.CheckFixPair,'Value')||(isempty(i2)&&isempty(j2));
1552
1553% the pair i1-i2 or j1-j2 is imposed (check box CheckFixPair selected)
1554if CheckFixPair
1555    if get(handles.scan_i,'Value')==1% case of scanning along index i
1556        i1=i1+increment;
1557        i2=i2+increment;
1558        if sub_value
1559            i1_1=i1_1+increment;
1560            i2_1=i2_1+increment;
1561        end
1562       
1563    else % case of scanning along index j (burst numbers)
1564        j1=j1+increment;
1565        j2=j2+increment;
1566        if sub_value
1567            j1_1=j1_1+increment;
1568            j2_1=j2_1+increment;
1569        end
1570    end
1571   
1572% the pair i1-i2 or j1-j2 is free (check box CheckFixPair not selected): the list of existing indices recorded in UvData is used
1573else
1574    UvData=get(handles.uvmat,'UserData');
1575    ref_i=i1;
1576    if ~isempty(i2)
1577        ref_i=floor((i1+i2)/2);% current reference index i
1578    end
1579    ref_j=1;
1580    if ~isempty(j1)
1581        ref_j=j1;
1582        if ~isempty(j2)
1583            ref_j=floor((j1+j2)/2);% current reference index j
1584        end
1585    end
1586    if ~isempty(increment)
1587        if get(handles.scan_i,'Value')==1% case of scanning along index i
1588            ref_i=ref_i+increment;% increment the current reference index i
1589        else % case of scanning along index j (burst numbers)
1590            ref_j=ref_j+increment;% increment the current reference index j if scan_j option is used
1591        end
1592    else % free increment
1593        runaction=get(gcbo,'tag');
1594        if strcmp(runaction,'runplus')||strcmp(runaction,'Movie')% if runplus or movie is activated
1595            step=1;
1596        else
1597            step=-1;
1598        end
1599        if get(handles.scan_i,'Value')==1% case of scanning along index i
1600            ref_i=ref_i+step;
1601            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
1602                ref_i=ref_i+step;
1603            end
1604        else % case of scanning along index j (burst numbers)
1605            ref_j=ref_j+step;
1606            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
1607                ref_j=ref_j+step;
1608            end
1609        end
1610    end
1611    if ref_i<0
1612        errormsg='minimum i index reached';
1613    elseif ref_j<0
1614        errormsg='minimum j index reached';
1615    elseif ref_i+1>size(UvData.i1_series{1},3)
1616        errormsg='maximum i index reached (reload the input file to update the index bound)';
1617    elseif ref_j+1>size(UvData.i1_series{1},2)
1618        errormsg='maximum j index reached (reload the input file to update the index bound)';
1619    end
1620    if ~isempty(errormsg),return,end
1621    siz=size(UvData.i1_series{1});
1622    ref_indices=ref_i*siz(1)*siz(2)+ref_j*siz(1)+1:ref_i*siz(1)*siz(2)+(ref_j+1)*siz(1);
1623    i1_subseries=UvData.i1_series{1}(ref_indices);
1624    ref_indices=ref_indices(i1_subseries>0);
1625    if isempty(ref_indices)% case of pairs (free index i)
1626        ref_indices=ref_i*siz(1)*siz(2)+1:(ref_i+1)*siz(1)*siz(2);
1627        i1_subseries=UvData.i1_series{1}(ref_indices);
1628        ref_indices=ref_indices(i1_subseries>0);
1629    end
1630    if isempty(ref_indices),errormsg='no next frame: set num_IndexIncrement =''*'' to reach the next existing file';return
1631    end
1632    i1=UvData.i1_series{1}(ref_indices(end));
1633    if ~isempty(UvData.i2_series{1})
1634        i2=UvData.i2_series{1}(ref_indices(end));
1635    end
1636    if ~isempty(UvData.j1_series{1})
1637        j1=UvData.j1_series{1}(ref_indices(end));
1638    end
1639    if ~isempty(UvData.j2_series{1})
1640        j2=UvData.j2_series{1}(ref_indices(end));
1641    end
1642   
1643    % case of a second file series
1644    if sub_value
1645        ref_i_1=i1_1;
1646        if ~isempty(i2_1)
1647            ref_i_1=floor((i1_1+i2_1)/2);% current reference index i
1648        end
1649        ref_j_1=1;
1650        if ~isempty(j1_1)
1651            ref_j_1=j1_1;
1652            if ~isempty(j2_1)
1653                ref_j_1=floor((j1_1+j2_1)/2);% current reference index j
1654            end
1655        end
1656        if ~isempty(increment)
1657            if get(handles.scan_i,'Value')==1% case of scanning along index i
1658                ref_i_1=ref_i_1+increment;% increment the current reference index i
1659            else % case of scanning along index j (burst numbers)
1660                ref_j_1=ref_j_1+increment;% increment the current reference index j if scan_j option is used
1661            end
1662        else % free increment, synchronise the ref indices with the first series
1663            ref_i_1=ref_i;
1664            ref_j_1=ref_j;
1665        end
1666        if numel(UvData.i1_series)==1
1667            UvData.i1_series{2}=UvData.i1_series{1};
1668            UvData.j1_series{2}=UvData.j1_series{1};
1669            UvData.i2_series{2}=UvData.i2_series{1};
1670            UvData.j2_series{2}=UvData.j2_series{1};
1671        end
1672        if ref_i_1<0
1673            errormsg='minimum i index reached';
1674        elseif ref_j_1<0
1675            errormsg='minimum j index reached';
1676        elseif ref_i_1+1>size(UvData.i1_series{2},3)
1677            errormsg='maximum i index reached for the second series (reload the input file to update the index bound)';
1678        elseif ref_j_1+1>size(UvData.i1_series{2},2)
1679            errormsg='maximum j index reached for the second series(reload the input file to update the index bound)';
1680        end
1681        if ~isempty(errormsg),return,end
1682        siz=size(UvData.i1_series{2});
1683        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);
1684        i1_subseries=UvData.i1_series{2}(ref_indices);
1685        ref_indices=ref_indices(i1_subseries>0);
1686        if isempty(ref_indices)% case of pairs (free index i)
1687            ref_indices=ref_i_1*siz(1)*siz(2)+1:(ref_i_1+1)*siz(1)*siz(2);
1688            i1_subseries=UvData.i1_series{2}(ref_indices);
1689            ref_indices=ref_indices(i1_subseries>0);
1690        end
1691        i1_1=UvData.i1_series{2}(ref_indices(end));
1692        if ~isempty(UvData.i2_series{2})
1693            i2_1=UvData.i2_series{2}(ref_indices(end));
1694        end
1695        if ~isempty(UvData.j1_series{2})
1696            j1_1=UvData.j1_series{2}(ref_indices(end));
1697        end
1698        if ~isempty(UvData.j2_series{2})
1699            j2_1=UvData.j2_series{1}(ref_indices(end));
1700        end   
1701    else% the second series (if needed) is the same file as the first
1702        i1_1=i1;
1703        i2_1=i2;
1704        j1_1=j1;
1705        j2_1=j2;
1706    end
1707end
1708filename=fullfile_uvmat(InputFile.RootPath,InputFile.SubDir,InputFile.RootFile,FileExt,NomType,i1,i2,j1,j2);
1709if sub_value
1710    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);
1711end
1712
1713%% refresh plots
1714errormsg=refresh_field(handles,filename,filename_1,i1,i2,j1,j2,i1_1,i2_1,j1_1,j2_1);
1715
1716%% update the index counters if the index move is successfull
1717if isempty(errormsg)
1718    set(handles.i1,'String',num2stra(i1,NomType,1));
1719    if isequal(i2,i1)
1720        set(handles.i2,'String','');
1721    else
1722        set(handles.i2,'String',num2stra(i2,NomType,1));
1723    end
1724    set(handles.j1,'String',num2stra(j1,NomType,2));
1725    if isequal(j2,j1)
1726        set(handles.j2,'String','');
1727    else
1728        set(handles.j2,'String',num2stra(j2,NomType,2));
1729    end
1730    indices=fullfile_uvmat('','','','',NomType,i1,i2,j1,j2);
1731    set(handles.FileIndex,'String',indices);
1732    if ~isempty(filename_1)
1733        indices_1=fullfile_uvmat('','','','',InputFile.NomType_1,i1_1,i2_1,j1_1,j2_1);
1734        set(handles.FileIndex_1,'String',indices_1);
1735    end
1736    if isequal(movie_status,1)
1737        set(handles.movie_pair,'Value',1)
1738        movie_pair_Callback(hObject, eventdata, handles); %reactivate moviepair if it was activated
1739    end
1740end
1741
1742%------------------------------------------------------------------------
1743% --- Executes on button press in movie_pair: create an alternating movie with two view
1744function movie_pair_Callback(hObject, eventdata, handles)
1745%------------------------------------------------------------------------
1746%% stop movie action if the movie_pair button is off
1747if ~get(handles.movie_pair,'value')
1748    set(handles.movie_pair,'BusyAction','Cancel')%stop movie pair if button is 'off'
1749    set(handles.i2,'String','')
1750    set(handles.j2,'String','')
1751    return
1752else
1753    set(handles.movie_pair,'BusyAction','queue')
1754end
1755
1756%% initialisation
1757set(handles.movie_pair,'BackgroundColor',[1 1 0])%paint the command button in yellow
1758drawnow
1759list_fields=get(handles.FieldName,'String');% list menu fields
1760index_fields=get(handles.FieldName,'Value');% selected string index
1761FieldName=list_fields{index_fields}; % selected field
1762UvData=get(handles.uvmat,'UserData');
1763if isequal(FieldName,'image')
1764    index=1;
1765    [RootPath,SubDir,RootFile,FileIndices,Ext]=read_file_boxes(handles);
1766    NomType=get(handles.NomType,'String');
1767else
1768    list_fields=get(handles.FieldName_1,'String');% list menu fields
1769    index_fields=get(handles.FieldName_1,'Value');% selected string index
1770    FieldName=list_fields{index_fields}; % selected field
1771    if isequal(FieldName,'image')
1772        index=2;
1773        [RootPath,tild,RootFile,FileIndex_1,Ext,NomType]=read_file_boxes_1(handles);
1774    else
1775        msgbox_uvmat('ERROR','an image or movie must be first introduced as input')
1776        set(handles.movie_pair,'BackgroundColor',[1 0 0])%paint the command button in red
1777        set(handles.movie_pair,'Value',0)
1778        return
1779    end
1780end
1781num_i1=str2num(get(handles.i1,'String'));
1782num_j1=stra2num(get(handles.j1,'String'));
1783num_i2=str2num(get(handles.i2,'String'));
1784num_j2=stra2num(get(handles.j2,'String'));
1785if isempty(num_j2)
1786    if isempty(num_i2)   
1787        msgbox_uvmat('ERROR', 'a second image index i2 or j2 is needed to show the pair as a movie')
1788        set(handles.movie_pair,'BackgroundColor',[1 0 0])%paint the command button in red
1789         set(handles.movie_pair,'Value',0)
1790        return
1791    else
1792        num_j2=num_j1;%repeat the index i1 by default
1793    end
1794end
1795if isempty(num_i2)
1796    num_i2=num_i1;%repeat the index i1 by default
1797end
1798imaname_1=fullfile_uvmat(RootPath,SubDir,RootFile,Ext,NomType,num_i2,[],num_j2);
1799if strcmp(NomType,'*')
1800    num_frame=num_i2;
1801else
1802    num_frame=num_j2;
1803end
1804if ~exist(imaname_1,'file')
1805      msgbox_uvmat('ERROR',['second input open (-)  ' imaname_1 ' not found']);
1806      set(handles.movie_pair,'BackgroundColor',[1 0 0])%paint the command button in red
1807       set(handles.movie_pair,'Value',0)
1808      return
1809end
1810
1811%% get the first image
1812%Field.AName='image';
1813if index==1
1814    Field_a=UvData.Field;% movie on the second field
1815else
1816    Field_a=UvData.Field_1;% movie on the first field
1817end
1818
1819%% read the second image
1820MovieObject=[];
1821if numel(UvData.MovieObject)>=index
1822    MovieObject=UvData.MovieObject{index};
1823end
1824[Field_b,ParamOut,errormsg] = read_field(imaname_1,UvData.FileType{index},MovieObject,num_frame)
1825% Field_b.AX=Field_a.AX;
1826% Field_b.AY=Field_a.AY;
1827% % z index
1828% nbslice=str2double(get(handles.num_NbSlice,'String'));
1829% if ~isempty(nbslice)
1830%     Field_b.ZIndex=mod(num_i2-1,nbslice)+1;
1831% end
1832% Field_b.CoordUnit='pixel';
1833%
1834% %% determine the input file type
1835% if (test_1 && isfield(UvData,'MovieObject')&& numel(UvData.MovieObject>=2))||(~test_1 && ~isempty(UvData.MovieObject{1}))
1836%     FileType='movie';
1837% elseif isequal(lower(Ext),'.avi')
1838%     FileType='avi';
1839% elseif isequal(lower(Ext),'.vol')
1840%     FileType='vol';
1841% else
1842%    form=imformats(Ext(2:end));
1843%    if ~isempty(form)% if the extension corresponds to an image format recognized by Matlab
1844%        if isequal(NomType,'*');
1845%            FileType='multimage';
1846%        else
1847%            FileType='image';
1848%        end
1849%    end
1850% end
1851% switch FileType
1852%         case 'movie'
1853%             if test_1
1854%                 Field_b.A=read(UvData.MovieObject{2},num_i2);
1855%             else
1856%                 Field_b.A=read(UvData.MovieObject{1},num_i2);
1857%             end
1858%         case 'avi'
1859%             mov=aviread(imaname_1,num_i2);
1860%             Field_b.A=frame2im(mov(1));
1861%         case 'vol'
1862%             Field_b.A=imread(imaname_1);
1863%         case 'multimage'
1864%             Field_b.A=imread(imaname_1,num_i2);
1865%         case 'image'
1866%             Field_b.A=imread(imaname_1);
1867% end
1868% if get(handles.slices,'Value')
1869%     Field.ZIndex=str2double(get(handles.z_index,'String'));
1870% end
1871
1872%px to phys or other transform on field
1873% menu_transform=get(handles.transform_fct,'String');
1874% choice_value=get(handles.transform_fct,'Value');
1875% transform_name=menu_transform{choice_value};%name of the transform fct  given by the menu 'transform_fct'
1876% transform_list=get(handles.transform_fct,'UserData');
1877transform=get(handles.path_transform,'UserData');
1878if  ~isempty(transform)
1879    if isfield(UvData,'XmlData') && numel(UvData.XmlData)>=index %use geometry calib recorded from the ImaDoc xml file as first priority
1880        if index==2
1881        Field_a=transform(Field_a,UvData.XmlData{index});%the first field has been stored without transform
1882        end
1883        Field_b=transform(Field_b,UvData.XmlData{index});
1884    end
1885end
1886
1887 % make movie until movie speed is set to 0 or STOP is activated
1888hima=findobj(handles.PlotAxes,'Tag','ima');% %handles.PlotAxes =main plotting window (A GENERALISER)
1889set(handles.STOP,'Visible','on')
1890set(handles.speed,'Visible','on')
1891set(handles.speed_txt,'Visible','on')
1892while get(handles.speed,'Value')~=0 && isequal(get(handles.movie_pair,'BusyAction'),'queue')%isequal(get(handles.run0,'BusyAction'),'queue'); % enable STOP command
1893    % read and plot the series of images in non erase mode
1894    set(hima,'CData',Field_b.A);
1895    pause(1.02-get(handles.speed,'Value'));% wait for next image
1896    set(hima,'CData',Field_a.A);
1897    pause(1.02-get(handles.speed,'Value'));% wait for next image
1898end
1899set(handles.movie_pair,'BackgroundColor',[1 0 0])%paint the command button in red
1900 set(handles.movie_pair,'Value',0)
1901
1902%------------------------------------------------------------------------
1903% --- Executes on button press in run0.
1904function run0_Callback(hObject, eventdata, handles)
1905%------------------------------------------------------------------------
1906set(handles.run0,'BackgroundColor',[1 1 0])%paint the command button in yellow
1907drawnow
1908[RootPath,SubDir,RootFile,FileIndex,FileExt]=read_file_boxes(handles);
1909filename=[fullfile(RootPath,SubDir,RootFile) FileIndex FileExt];
1910filename_1='';%default
1911FileIndex_1='';
1912if get(handles.SubField,'Value')
1913    [RootPath_1,SubDir_1,RootFile_1,FileIndex_1,FileExt_1]=read_file_boxes_1(handles);
1914    filename_1=[fullfile(RootPath_1,SubDir_1,RootFile_1) FileIndex_1 FileExt_1];
1915end
1916num_i1=stra2num(get(handles.i1,'String'));
1917num_i2=stra2num(get(handles.i2,'String'));
1918num_j1=stra2num(get(handles.j1,'String'));
1919num_j2=stra2num(get(handles.j2,'String'));
1920[tild,tild,tild,i1_1,i2_1,j1_1,j2_1]=fileparts_uvmat(FileIndex_1);
1921
1922errormsg=refresh_field(handles,filename,filename_1,num_i1,num_i2,num_j1,num_j2,i1_1,i2_1,j1_1,j2_1);
1923
1924if ~isempty(errormsg)
1925      msgbox_uvmat('ERROR',errormsg);
1926else
1927    set(handles.i1,'BackgroundColor',[1 1 1])
1928    set(handles.i2,'BackgroundColor',[1 1 1])
1929    set(handles.j1,'BackgroundColor',[1 1 1])
1930    set(handles.j2,'BackgroundColor',[1 1 1])
1931    set(handles.FileIndex,'BackgroundColor',[1 1 1])
1932    set(handles.FileIndex_1,'BackgroundColor',[1 1 1])
1933end   
1934set(handles.run0,'BackgroundColor',[1 0 0])
1935
1936
1937%------------------------------------------------------------------------
1938% --- read the input files and refresh all the plots, including projection.
1939% OUTPUT:
1940%  errormsg: error message char string  =[] by default
1941% INPUT:
1942% filename: first input file (=[] in the absence of input file)
1943% filename_1: second input file (=[] in the asbsenc of secodn input file)
1944% num_i1,num_i2,num_j1,num_j2; frame indices
1945% Field: structure describing an optional input field (then replace the input file)
1946
1947function errormsg=refresh_field(handles,FileName,FileName_1,num_i1,num_i2,num_j1,num_j2,i1_1,i2_1,j1_1,j2_1)
1948%------------------------------------------------------------------------
1949
1950%% initialisation
1951abstime=[];
1952abstime_1=[];
1953dt=[];
1954if ~exist('Field','var')
1955    Field={};
1956end
1957UvData=get(handles.uvmat,'UserData');
1958if ishandle(handles.UVMAT_title) %remove title panel on uvmat
1959    delete(handles.UVMAT_title)
1960end
1961
1962%% determine the main input file information for action
1963if ~exist(FileName,'file')
1964    errormsg=['input file ' FileName ' does not exist'];
1965    return
1966end
1967NomType=get(handles.NomType,'String');
1968NomType_1='';
1969if strcmp(get(handles.NomType_1,'Visible'),'on')
1970    NomType_1=get(handles.NomType_1,'String');
1971end
1972%update the z position index
1973nbslice_str=get(handles.num_NbSlice,'String');
1974if isequal(nbslice_str,'volume')%NOT USED
1975    z_index=num_j1;
1976    set(handles.z_index,'String',num2str(z_index))
1977else
1978    nbslice=str2num(nbslice_str);
1979    z_index=mod(num_i1-1,nbslice)+1;
1980    set(handles.z_index,'String',num2str(z_index))
1981end
1982% refresh menu for save_mask if relevant
1983masknumber=get(handles.masklevel,'String');
1984if length(masknumber)>=z_index
1985    set(handles.masklevel,'Value',z_index)
1986end
1987
1988%% test for need of tps
1989check_proj_tps=0;
1990if  (strcmp(UvData.FileType{1},'civdata')||strcmp(UvData.FileType{1},'civx'))
1991    for iobj=1:numel(UvData.Object)
1992        if isfield(UvData.Object{iobj},'ProjMode')&& strcmp(UvData.Object{iobj}.ProjMode,'filter')
1993            check_proj_tps=1;
1994            break
1995        end
1996    end
1997end
1998
1999%% read the first input field
2000ParamIn.ColorVar='';%default variable name for vector color
2001frame_index=1;%default
2002FieldName='';%default
2003VelType='';%default
2004switch UvData.FileType{1}
2005    case {'civx','civdata','netcdf'};
2006        list_fields=get(handles.FieldName,'String');% list menu fields
2007        FieldName= list_fields{get(handles.FieldName,'Value')}; % selected field
2008        if ~strcmp(FieldName,'get_field...')
2009            if get(handles.FixVelType,'Value')
2010                VelTypeList=get(handles.VelType,'String');
2011                VelType=VelTypeList{get(handles.VelType,'Value')};
2012            end
2013        end
2014        if ~isempty(regexp(FieldName,'^vec('))
2015            list_code=get(handles.ColorCode,'String');% list menu fields
2016            index_code=get(handles.ColorCode,'Value');% selected string index
2017            if  ~strcmp(list_code{index_code},'black') &&  ~strcmp(list_code{index_code},'white')
2018                list_code=get(handles.ColorScalar,'String');% list menu fields
2019                index_code=get(handles.ColorScalar,'Value');% selected string index
2020                ParamIn.ColorVar= list_code{index_code}; % selected field
2021            end
2022        end
2023    case {'video','mmreader'}
2024        ParamIn=UvData.MovieObject{1};     
2025        if ~strcmp(NomType,'*')
2026            frame_index=num_j1;%frame index for movies or multimage
2027        else
2028            frame_index=num_i1;
2029        end
2030    case 'multimage'
2031        if ~strcmp(NomType,'*')
2032            frame_index=num_j1;%frame index for movies or multimage
2033        else
2034            frame_index=num_i1;
2035        end
2036    case 'vol' %TODO: update
2037        if isfield(UvData.XmlData,'Npy') && isfield(UvData.XmlData,'Npx')
2038            ParamIn.Npy=UvData.XmlData.Npy;
2039            ParamIn.Npx=UvData.XmlData.Npx;
2040        else           
2041            errormsg='Npx and Npy need to be defined in the xml file for volume images .vol';
2042            return
2043        end
2044end
2045if isstruct (ParamIn)
2046    ParamIn.FieldName=FieldName;
2047    ParamIn.VelType=VelType;
2048    XNameMenu=get(handles.Coord_x,'String');
2049    ParamIn.Coord_x=XNameMenu(get(handles.Coord_x,'Value'));
2050    YNameMenu=get(handles.Coord_y,'String');
2051    ParamIn.Coord_y=YNameMenu(get(handles.Coord_y,'Value'));
2052end
2053check_tps = 0;         
2054if strcmp(UvData.FileType{1},'civdata')&&~strcmp(ParamIn.FieldName,'velocity')&&~strcmp(ParamIn.FieldName,'get_field...')
2055       check_tps=1;%tps needed to get the requested field
2056end
2057[Field{1},ParamOut,errormsg] = read_field(FileName,UvData.FileType{1},ParamIn,frame_index);
2058if ~isempty(errormsg)
2059    errormsg=['uvmat / refresh_field / read_field( ' FileName ') / ' errormsg];
2060    return
2061end 
2062if isfield(ParamOut,'Npx')&& isfield(ParamOut,'Npy')
2063    set(handles.num_Npx,'String',num2str(ParamOut.Npx));% display image size on the interface
2064    set(handles.num_Npy,'String',num2str(ParamOut.Npy));
2065end
2066if isfield(ParamOut,'TimeIndex')% case of time obtained from get_field
2067    set(handles.i1,'String',num2str(ParamOut.TimeIndex))
2068end
2069if isfield(ParamOut,'TimeValue')
2070    Field{1}.Time=ParamOut.TimeValue;% case of time obtained from get_field
2071end
2072Field{1}.ZIndex=z_index; %used for multiplane 3D calibration
2073% end
2074
2075%% choose and read a second field FileName_1 if defined
2076VelType_1=[];%default
2077FieldName_1=[];
2078ParamIn_1=[];
2079ParamOut_1=[];
2080frame_index_1=1;
2081if ~isempty(FileName_1)
2082    if ~exist(FileName_1,'file')
2083        errormsg=['second file ' FileName_1 ' does not exist'];
2084        return
2085    end
2086    Name=FileName_1;
2087    switch UvData.FileType{2}
2088        case {'civx','civdata','netcdf'};
2089            list_fields=get(handles.FieldName_1,'String');% list menu fields
2090            if ischar(list_fields),list_fields={list_fields};end
2091            FieldName_1= list_fields{get(handles.FieldName_1,'Value')}; % selected field
2092            if ~strcmp(FieldName,'get_field...')
2093                if get(handles.FixVelType,'Value')
2094                    VelTypeList=get(handles.VelType_1,'String');
2095                    VelType_1=VelTypeList{get(handles.VelType_1,'Value')};% read the velocity type.
2096                end
2097            end
2098            if strcmp(FieldName_1,'velocity')&& strcmp(get(handles.ColorCode,'Visible'),'on')
2099                list_code=get(handles.ColorCode,'String');% list menu fields
2100                index_code=get(handles.ColorCode,'Value');% selected string index
2101                if  ~strcmp(list_code{index_code},'black') &&  ~strcmp(list_code{index_code},'white')
2102                    list_code=get(handles.ColorScalar,'String');% list menu fields
2103                    index_code=get(handles.ColorScalar,'Value');% selected string index
2104                    ParamIn_1.ColorVar= list_code{index_code}; % selected field for vector color display                 
2105                end
2106            end
2107        case {'video','mmreader'}
2108            ParamIn_1=UvData.MovieObject{2};
2109                        if ~strcmp(NomType_1,'*')
2110                frame_index_1=j1_1;%frame index for movies or multimage
2111            else
2112                frame_index_1=i1_1;
2113            end 
2114         case 'multimage'
2115            if ~strcmp(NomType_1,'*')
2116                frame_index_1=j1_1;%frame index for movies or multimage
2117            else
2118                frame_index_1=i1_1;
2119            end   
2120        case 'vol' %TODO: update
2121            if isfield(UvData.XmlData,'Npy') && isfield(UvData.XmlData,'Npx')
2122                ParamIn_1.Npy=UvData.XmlData.Npy;
2123                ParamIn_1.Npx=UvData.XmlData.Npx;
2124            else
2125                errormsg='Npx and Npy need to be defined in the xml file for volume images .vol';
2126                return
2127            end
2128    end
2129    if isequal(get(handles.NomType_1,'Visible'),'on')
2130    NomType_1=get(handles.NomType_1,'String');
2131    else
2132        NomType_1=get(handles.NomType,'String');
2133    end
2134    test_keepdata_1=0;% test for keeping the previous stored data if the input files are unchanged
2135    if ~isequal(NomType_1,'*')&& isfield(UvData,'FileName_1')
2136           test_keepdata_1= strcmp(FileName_1,UvData.FileName_1) ;%&& strcmp(FieldName_1,UvData.FieldName_1);
2137    end
2138    if test_keepdata_1
2139        Field{2}=UvData.Field_1;% keep the stored field
2140        ParamOut_1=UvData.ParamOut_1;
2141    else
2142        if isempty(ParamIn_1) || isstruct(ParamIn_1)
2143        ParamIn_1.FieldName=FieldName_1;
2144        ParamIn_1.VelType=VelType_1;
2145        ParamIn_1.GUIName='get_field_1';
2146        end 
2147        [Field{2},ParamOut_1,errormsg] = read_field(Name,UvData.FileType{2},ParamIn_1,frame_index_1);
2148        if ~isempty(errormsg)
2149            errormsg=['error in reading ' FieldName_1 ' in ' FileName_1 ': ' errormsg];
2150            return
2151        end
2152        if isstruct(ParamOut_1)&&~strcmp(ParamOut_1.FieldName,'get_field...')&& (strcmp(UvData.FileType{2},'civdata')||strcmp(UvData.FileType{2},'civx'))...
2153                &&~strcmp(ParamOut_1.FieldName,'velocity') && ~strcmp(ParamOut_1.FieldName,'get_field...')
2154            if ~check_proj_tps
2155             %   Field{2}=calc_field([{ParamOut_1.FieldName} {ParamOut_1.ColorVar}],Field{2});
2156            end
2157        end
2158    end
2159    Field{2}.ZIndex=z_index;%used for multi-plane 3D calibration
2160end
2161
2162%% update uvmat interface
2163if isfield(ParamOut,'Npx')
2164    set(handles.num_Npx,'String',num2str(ParamOut.Npx));% display image size on the interface
2165    set(handles.num_Npy,'String',num2str(ParamOut.Npy));
2166elseif isfield(ParamOut_1,'Npx')
2167    set(handles.num_Npx,'String',num2str(ParamOut_1.Npx));% display image size on the interface
2168    set(handles.num_Npy,'String',num2str(ParamOut_1.Npy));
2169end
2170
2171%% update the display menu for the first velocity type (first menuline)
2172test_veltype=0;
2173% if ~isequal(FileType,'netcdf')|| isequal(FieldName,'get_field...')
2174if (strcmp(UvData.FileType{1},'civx')||strcmp(UvData.FileType{1},'civdata'))&& ~strcmp(FieldName,'get_field...')
2175    test_veltype=1;
2176    set(handles.VelType,'Visible','on')
2177    set(handles.VelType_1,'Visible','on')
2178    set(handles.FixVelType,'Visible','on')
2179    menu=set_veltype_display(ParamOut.CivStage,UvData.FileType{1});
2180    index_menu=strcmp(ParamOut.VelType,menu);%look for VelType in  the menu
2181    index_val=find(index_menu,1);
2182    if isempty(index_val)
2183        index_val=1;
2184    end
2185    set(handles.VelType,'Value',index_val)
2186    if ~get(handles.SubField,'value')
2187        set(handles.VelType,'String',menu)
2188        set(handles.VelType_1,'Value',1)
2189        set(handles.VelType_1,'String',[{''};menu])
2190    end
2191else
2192    set(handles.VelType,'Visible','off')
2193end
2194% display the FieldName menu from the input file and pick the selected one:
2195% if isstruct(ParamOut)
2196%     field_index=strcmp(ParamOut.FieldName,ParamOut.FieldList);
2197%     set(handles.FieldName,'String',ParamOut.FieldList); %update the field menu
2198%     set(handles.FieldName,'Value',find(field_index,1))
2199% end
2200
2201%% update the display menu for the second velocity type (second menuline)
2202test_veltype_1=0;
2203if isempty(FileName_1)
2204%     set(handles.FieldName_1,'Value',1); %update the field menu
2205%     if isstruct(ParamOut)
2206%     set(handles.FieldName_1,'String',[{''};ParamOut.FieldList]); %update the field menu
2207%     end
2208elseif ~test_keepdata_1
2209    if (~strcmp(UvData.FileType{2},'netcdf')&&~strcmp(UvData.FileType{2},'civdata')&&~strcmp(UvData.FileType{2},'civx'))|| isequal(FieldName_1,'get_field...')
2210        set(handles.VelType_1,'Visible','off')
2211    else
2212        test_veltype_1=1;
2213        set(handles.VelType_1,'Visible','on')
2214        menu=set_veltype_display(ParamOut_1.CivStage,UvData.FileType{2});
2215        index_menu=strcmp(ParamOut_1.VelType,menu);
2216        set(handles.VelType_1,'Value',1+find(index_menu,1))
2217        set(handles.VelType_1,'String',[{''};menu])
2218    end
2219    % update the second field menu: the same quantity
2220    if isstruct(ParamOut_1)
2221    set(handles.FieldName_1,'String',[{''};ParamOut_1.FieldList]); %update the field menu
2222    % display the FieldName menu from the input file and pick the selected one:
2223    field_index=strcmp(ParamOut_1.FieldName,ParamOut_1.FieldList);
2224    set(handles.FieldName_1,'Value',find(field_index,1)+1) 
2225    end
2226   
2227end
2228if test_veltype||test_veltype_1
2229     set(handles.FixVelType,'Visible','on')
2230else
2231     set(handles.FixVelType,'Visible','off')
2232end
2233
2234% field_index=strcmp(ParamOut_1.FieldName,ParamOut_1.FieldList);
2235% set(handles.FieldName,'String',ParamOut.FieldList); %update the field menu
2236% set(handles.FieldName,'Value',find(field_index,1))
2237   
2238%% introduce w as background image by default for a new series (only for nbdim=2)
2239if ~isfield(UvData,'NewSeries')
2240    UvData.NewSeries=1;
2241end
2242%put W as background image by default if NbDim=2:
2243if  UvData.NewSeries && isequal(get(handles.SubField,'Value'),0) && isfield(Field{1},'W') && ~isempty(Field{1}.W) && ~isequal(Field{1}.NbDim,3);
2244        set(handles.SubField,'Value',1);
2245        set(handles.RootPath_1,'String','"')
2246        set(handles.RootFile_1,'String','"')
2247        set(handles.SubDir_1,'String','"');
2248         indices=fullfile_uvmat('','','','',NomType,num_i1,num_i2,num_j1,num_j2);
2249        set(handles.FileIndex_1,'String',indices)
2250        set(handles.FileExt_1,'String','"');
2251        set(handles.FieldName_1,'Visible','on');
2252        set(handles.FieldName_1,'Visible','on');
2253        set(handles.RootPath_1,'Visible','on')
2254        set(handles.RootFile_1,'Visible','on')
2255        set(handles.SubDir_1,'Visible','on');
2256        set(handles.FileIndex_1,'Visible','on');
2257        set(handles.FileExt_1,'Visible','on');
2258        set(handles.FieldName_1,'Visible','on');
2259        Field{1}.AName='w';
2260end           
2261
2262%% display time
2263testimedoc=0;
2264TimeUnit='';
2265if isfield(Field{1},'Time')
2266    abstime=Field{1}.Time;%time read from the netcdf input file
2267end
2268if numel(Field)==2 && isfield(Field{2},'Time')
2269    abstime_1=Field{2}.Time;%time read from the netcdf input file
2270end
2271if isfield(Field{1},'Dt')
2272    dt=Field{1}.Dt;%dt read from the netcdf input file
2273    if isfield(Field{1},'TimeUnit')
2274       TimeUnit=Field{1}.TimeUnit;
2275    end
2276elseif numel(Field)==2 && isfield(Field{2},'Dt')%dt obtained from the second field if not defined in the first
2277    dt=Field{2}.Dt;%dt read from the netcdf input file
2278    if isfield(Field{2},'TimeUnit')
2279       TimeUnit=Field{2}.TimeUnit;
2280    end
2281end
2282% time from xml file overset previous result
2283if isfield(UvData,'XmlData') && isfield(UvData.XmlData{1},'Time')
2284    if isempty(num_i2)||isnan(num_i2)
2285        num_i2=num_i1;
2286    end
2287    if isempty(num_j1)||isnan(num_j1)
2288        num_j1=1;
2289    end
2290    if isempty(num_j2)||isnan(num_j2)
2291        num_j2=num_j1;
2292    end
2293    siz=size(UvData.XmlData{1}.Time);
2294    if ~isempty(num_i1)&& ~isempty(num_i2)&&siz(1)>=max(num_i1,num_i2) && siz(2)>=max(num_j1,num_j2)
2295        abstime=(UvData.XmlData{1}.Time(num_i1,num_j1)+UvData.XmlData{1}.Time(num_i2,num_j2))/2;%overset the time read from files
2296        dt=(UvData.XmlData{1}.Time(num_i2,num_j2)-UvData.XmlData{1}.Time(num_i1,num_j1));
2297        Field{1}.Dt=dt;
2298        if isfield(UvData.XmlData{1},'TimeUnit')
2299            TimeUnit=UvData.XmlData{1}.TimeUnit;
2300        end
2301    end
2302    if numel(UvData.XmlData)==2
2303        if isempty(i2_1)
2304            i2_1=num_i1;
2305        end
2306        if isempty(j1_1)
2307            j1_1=1;
2308        end
2309        if isempty(j2_1)
2310            j2_1=j1_1;
2311        end
2312        siz=size(UvData.XmlData{2}.Time);
2313        if ~isempty(i1_1) && siz(1)>=max(i1_1,i2_1) && siz(2)>=max(j1_1,j2_1)
2314            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
2315            Field{2}.Dt=(UvData.XmlData{2}.Time(i2_1,j2_1)-UvData.XmlData{2}.Time(i1_1,j1_1));
2316        end
2317    end
2318end
2319if ~isequal(numel(abstime),1)
2320    abstime=[];
2321end
2322if ~isequal(numel(abstime_1),1)
2323      abstime_1=[];
2324end 
2325set(handles.abs_time,'String',num2str(abstime,5))
2326set(handles.abs_time_1,'String',num2str(abstime_1,5))
2327if isempty(dt)||isequal(dt,0)
2328    set(handles.Dt_txt,'String','')
2329else
2330    if  isempty(TimeUnit)
2331        set(handles.Dt_txt,'String',['Dt=' num2str(1000*dt,3) '  10^(-3)'] )
2332    else
2333        set(handles.Dt_txt,'String',['Dt=' num2str(1000*dt,3) '  m' TimeUnit] )
2334    end
2335end
2336
2337
2338%% store the current open names, fieldname and vel types in uvmat interface
2339UvData.FileName_1=FileName_1;
2340UvData.ParamOut_1=ParamOut_1;
2341if numel(Field)==2
2342UvData.Field_1=Field{2}; %store the second field for possible use at next RUN
2343end
2344
2345%% apply coordinate transform or other user fct
2346transform=get(handles.path_transform,'UserData');
2347if isempty(transform)
2348    UvData.Field=Field{1};
2349else
2350    XmlData=[];%default
2351    XmlData_1=[];%default
2352    if isfield(UvData,'XmlData')%use geometry calib recorded from the ImaDoc xml file as first priority
2353        XmlData=UvData.XmlData{1};
2354        if numel(UvData.XmlData)==2
2355            XmlData_1=UvData.XmlData{2};
2356        end
2357    end
2358    transform=get(handles.path_transform,'UserData');
2359    switch nargin(transform)
2360        case 4
2361            if length(Field)==2
2362                UvData.Field=transform(Field{1},XmlData,Field{2},XmlData_1);
2363            else
2364                UvData.Field=transform(Field{1},XmlData);
2365            end
2366        case 3
2367            if length(Field)==2
2368                UvData.Field=transform(Field{1},XmlData,Field{2});
2369            else
2370                UvData.Field=transform(Field{1},XmlData);
2371            end
2372        case 2
2373            UvData.Field=transform(Field{1},XmlData);
2374        case 1
2375            UvData.Field=transform(Field{1});
2376    end
2377end
2378
2379%% calculate tps coefficients if needed
2380UvData.Field=calc_tps(UvData.Field,check_proj_tps);
2381
2382%% analyse input field
2383%test_x=0;
2384%test_z=0;% test for unstructured z coordinate
2385%[errormsg,ListDimName,DimValue,VarDimIndex]=check_field_structure(UvData.Field);% check the input field structure
2386% if ~isempty(errormsg)
2387%     errormsg=['error in uvmat/refresh_field/check_field_structure: ' errormsg];% display error
2388%     return
2389% end
2390[CellInfo,NbDimArray,errormsg]=find_field_cells(UvData.Field);% analyse  the input field structure
2391if ~isempty(errormsg)
2392    errormsg=['uvmat /refresh_field / find_field_cells / ' errormsg];% display error
2393    return
2394end
2395
2396NbDim=max(NbDimArray);% spatial dimension of the input field
2397imax=find(NbDimArray==NbDim);% indices of field cells to consider
2398if isfield(UvData.Field,'NbDim')
2399    NbDim=double(UvData.Field.NbDim);% deal with plane fields containing z coordinates
2400end
2401
2402
2403%% get bounds and mesh (needed  to propose default options for projection objects)
2404if NbDim>1
2405    CoordMax=zeros(numel(imax),NbDim);
2406    CoordMin=zeros(numel(imax),NbDim);
2407    Mesh=zeros(numel(imax),NbDim);
2408    for ind=1:numel(imax)
2409        XName=UvData.Field.ListVarName{CellInfo{imax(ind)}.CoordIndex(end)};
2410        YName=UvData.Field.ListVarName{CellInfo{imax(ind)}.CoordIndex(end-1)};
2411        CoordMax(ind,NbDim)=max(max(UvData.Field.(XName)));
2412        CoordMin(ind,NbDim)=min(min(UvData.Field.(XName)));
2413        CoordMax(ind,NbDim-1)=max(max(UvData.Field.(YName)));
2414        CoordMin(ind,NbDim-1)=min(min(UvData.Field.(YName)));
2415        %         test_x=1;%test for unstructured coordinates
2416        if NbDim==3
2417            ZName=UvData.Field.ListVarName{CellInfo{imax(ind)}.CoordIndex(1)};
2418            CoordMax(imax(ind),1)=max(max(UvData.Field.(ZName)));
2419            CoordMin(ind,1)=min(min(UvData.Field.(ZName)));
2420        end
2421       
2422        switch CellInfo{imax(ind)}.CoordType
2423           
2424            case 'scattered' %unstructured coordinates
2425                NbPoints=CellInfo{imax(ind)}.CoordSize;% nbre of points
2426                Mesh(ind,:)=(prod(CoordMax(ind,:)-CoordMin(ind,:))/NbPoints)^(1/NbDim); %(volume or area per point)^(1/NbDim)
2427            case 'grid'%structured coordinate
2428                NbPoints=CellInfo{imax(ind)}.CoordSize;% nbre of points in each direction
2429                Mesh(ind,:)=min((CoordMax(ind,:)-CoordMin(ind,:))./(NbPoints-1));               
2430        end
2431    end
2432    UvData.Field.Mesh=min(Mesh);
2433    UvData.Field.XMax=max(CoordMax(ind,1));
2434    UvData.Field.XMin=min(CoordMin(ind,1));
2435    UvData.Field.YMax=max(CoordMax(ind,2));
2436    UvData.Field.YMin=max(CoordMin(ind,2));
2437    if NbDim==3
2438        UvData.Field.ZMax=max(CoordMax(ind,3));
2439        UvData.Field.ZMin=max(CoordMin(ind,3));
2440    end
2441    % adjust the mesh to a value 1, 2 , 5 *10^n
2442    ord=10^(floor(log10(UvData.Field.Mesh)));%order of magnitude
2443    if UvData.Field.Mesh/ord>=5
2444        UvData.Field.Mesh=5*ord;
2445    elseif UvData.Field.Mesh/ord>=2
2446        UvData.Field.Mesh=2*ord;
2447    else
2448        UvData.Field.Mesh=ord;
2449    end
2450    % default projection plane
2451    if isempty(UvData.Object{1})
2452        UvData.Object{1}.Type='plane';%main plotting plane
2453        UvData.Object{1}.ProjMode='projection';%main plotting plane
2454        UvData.Object{1}.DisplayHandle.uvmat=[]; %plane not visible in uvmat
2455        UvData.Object{1}.DisplayHandle.view_field=[]; %plane not visible in uvmat
2456    end
2457    %% 3D case (menuvolume)
2458    if NbDim==3% && UvData.NewSeries
2459        test_set_object=1;
2460        hset_object=findobj(allchild(0),'tag','set_object');% look for the set_object GUI
2461        ZBounds(1)=UvData.Field.ZMin; %minimum for the Z slider
2462        ZBounds(2)=UvData.Field.ZMax;%maximum for the Z slider
2463        if ~isempty(hset_object) %if set_object is detected
2464            delete(hset_object);% delete the GUI set_object if it does not fit
2465        end
2466        if test_set_object% reinitiate the GUI set_object
2467            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
2468            UvData.Object{1}.NbDim=NbDim;%test for 3D objects
2469            UvData.Object{1}.RangeZ=UvData.Field.Mesh;%main plotting plane
2470            UvData.Object{1}.Coord(1,3)=(UvData.Field.ZMin+UvData.Field.ZMax)/2;%section at a middle plane chosen
2471            UvData.Object{1}.Angle=[0 0 0];
2472            UvData.Object{1}.HandlesDisplay=plot(0,0,'Tag','proj_object');% A REVOIR
2473            UvData.Object{1}.Name='1-PLANE';
2474            UvData.Object{1}.enable_plot=1;
2475            set_object(UvData.Object{1},handles,ZBounds);
2476            set(handles.ListObject,'Value',1);
2477            set(handles.ListObject,'String',{'1-PLANE'});
2478            set(handles.edit_object,'Value',1)% put the plane in edit mode to enable the z cursor
2479            edit_object_Callback([],[], handles)
2480        end
2481        %multilevel case (single menuplane in a 3D space)
2482    elseif isfield(UvData,'Z')
2483        if isfield(UvData,'CoordType')&& isequal(UvData.CoordType,'phys') && isfield(UvData,'XmlData')
2484            XmlData=UvData.XmlData{1};
2485            if isfield(XmlData,'PlanePos')
2486                UvData.Object{1}.Coord=XmlData.PlanePos(UvData.ZIndex,:);
2487            end
2488            if isfield(XmlData,'PlaneAngle')
2489                siz=size(XmlData.PlaneAngle);
2490                indangle=min(siz(1),UvData.ZIndex);%take first angle if a single angle is defined (translating scanning)
2491                UvData.Object{1}.PlaneAngle=XmlData.PlaneAngle(indangle,:);
2492            end
2493        elseif isfield(UvData,'ZIndex')
2494            UvData.Object{1}.ZObject=UvData.ZIndex;
2495        end
2496    end
2497end
2498
2499testnewseries=UvData.NewSeries;
2500UvData.NewSeries=0;% put to 0 the test for a new field series (set by RootPath_callback)
2501set(handles.uvmat,'UserData',UvData)
2502
2503%% reset the min and max of scalar if only the mask is displayed(TODO: check the need)
2504% if isfield(UvData,'Mask')&& ~isfield(UvData,'A')
2505%     set(handles.num_MinA,'String','0')
2506%     set(handles.num_MaxA,'String','255')
2507% end
2508
2509%% usual 1D (x,y) plots
2510if NbDim<=1
2511    set(handles.Objects,'Visible','off')
2512    set(handles.ListObject_1_title,'Visible','off')
2513    set(handles.ListObject_1,'Visible','off')
2514    [PlotType,PlotParamOut]=plot_field(UvData.Field,handles.PlotAxes,read_GUI(handles.uvmat));
2515    write_plot_param(handles,PlotParamOut) %update the auto plot parameters
2516   
2517%% 2D or 3D fieldname are generally projected
2518else
2519    set(handles.Objects,'Visible','on')
2520    set(handles.ListObject_1_title,'Visible','on')
2521    set(handles.ListObject_1,'Visible','on')
2522   
2523    %% Plot the projections on the selected  projection objects
2524    % main projection object (uvmat display)
2525    list_object=get(handles.ListObject_1,'String');
2526    if isequal(list_object,{''})||isequal(list_object,' ')%refresh list of objects if the menu is empty
2527        set(handles.ListObject,'Value',1)
2528        set(handles.ListObject,'String',{'plane'})
2529        UvData.Object{1}.Type='plane';%main plotting plane
2530        UvData.Object{1}.ProjMode='projection';%main plotting plane
2531        UvData.Object{1}.DisplayHandle.uvmat=[]; %plane not visible in uvmat
2532        UvData.Object{1}.DisplayHandle.view_field=[]; %plane not visible in uvmat
2533        set(handles.ListObject_1,'Value',1)
2534        set(handles.ListObject_1,'String',{'plane'})
2535    end
2536    IndexObj(1)=get(handles.ListObject_1,'Value');%selected projection object for main view
2537    if IndexObj(1)> numel(UvData.Object)
2538        IndexObj(1)=1;%select the first object if the selected one does not exist
2539        set(handles.ListObject_1,'Value',1)
2540    end
2541    IndexObj(2)=get(handles.ListObject,'Value');%selected projection object for main view
2542    if isequal(IndexObj(2),IndexObj(1))
2543        IndexObj(2)=[];
2544    end
2545    plot_handles{1}=handles;
2546    if isfield(UvData,'plotaxes')%case of movies
2547        haxes(1)=UvData.plotaxes;
2548    else
2549        haxes(1)=handles.PlotAxes;
2550    end
2551    PlotParam{1}=read_GUI(handles.uvmat);
2552    %default settings if vectors not visible
2553    if ~isfield(PlotParam{1},'Vectors')
2554        PlotParam{1}.Vectors.MaxVec=1;
2555        PlotParam{1}.Vectors.MinVec=0;
2556        PlotParam{1}.Vectors.CheckFixVecColor=1;
2557        PlotParam{1}.Vectors.ColCode1=0.33;
2558        PlotParam{1}.Vectors.ColCode2=0.66;
2559        PlotParam{1}.Vectors.ColorScalar={''};
2560        PlotParam{1}.Vectors.ColorCode= {'rgb'};
2561    end
2562    PosColorbar{1}=UvData.OpenParam.PosColorbar;%prescribe the colorbar position on the uvmat interface
2563   
2564    %% second projection object (view_field display)
2565    if length( IndexObj)>=2
2566        view_field_handle=findobj(allchild(0),'tag','view_field');%handles of the view_field GUI
2567        if ~isempty(view_field_handle)
2568            plot_handles{2}=guidata(view_field_handle);
2569            haxes(2)=plot_handles{2}.PlotAxes;
2570            PlotParam{2}=read_GUI(handles.uvmat);%read plotting parameters on the uvmat interface
2571            PosColorbar{2}='*'; %TODO: deal with colorbar position on view_field
2572        end
2573    end
2574   
2575    %% loop on the projection objects: one or two
2576   
2577    for imap=1:numel(IndexObj)
2578        iobj=IndexObj(imap);
2579        [ObjectData,errormsg]=proj_field(UvData.Field,UvData.Object{iobj});% project field on the object
2580        if ~isempty(errormsg)
2581            return
2582        end
2583        if testnewseries
2584            PlotParam{imap}.Scalar.CheckBW=[]; %B/W option depends on the input field (image or scalar)
2585            if isfield(ObjectData,'CoordUnit')
2586                PlotParam{imap}.Coordinates.CheckFixAspectRatio=1;% set x and y scaling equal if CoordUnit is defined (common unit for x and y)
2587                PlotParam{imap}.Coordinates.AspectRatio=1; %set aspect ratio to 1
2588            end
2589        end
2590        %use of mask (TODO: check)
2591        if isfield(ObjectData,'NbDim') && isequal(ObjectData.NbDim,2) && isfield(ObjectData,'Mask') && isfield(ObjectData,'A')
2592            flag_mask=double(ObjectData.Mask>200);%=0 for masked regions
2593            AX=ObjectData.AX;%x coordiantes for the scalar field
2594            AY=ObjectData.AY;%y coordinates for the scalar field
2595            MaskX=ObjectData.MaskX;%x coordiantes for the mask
2596            MaskY=ObjectData.MaskY;%y coordiantes for the mask
2597            if ~isequal(MaskX,AX)||~isequal(MaskY,AY)
2598                nxy=size(flag_mask);
2599                sizpx=(ObjectData.MaskX(end)-ObjectData.MaskX(1))/(nxy(2)-1);%size of a mask pixel
2600                sizpy=(ObjectData.MaskY(1)-ObjectData.MaskY(end))/(nxy(1)-1);
2601                x_mask=ObjectData.MaskX(1):sizpx:ObjectData.MaskX(end); % pixel x coordinates for image display
2602                y_mask=ObjectData.MaskY(1):-sizpy:ObjectData.MaskY(end);% pixel x coordinates for image display
2603                %project on the positions of the scalar
2604                npxy=size(ObjectData.A);
2605                dxy(1)=(ObjectData.AY(end)-ObjectData.AY(1))/(npxy(1)-1);%grid mesh in y
2606                dxy(2)=(ObjectData.AX(end)-ObjectData.AX(1))/(npxy(2)-1);%grid mesh in x
2607                xi=ObjectData.AX(1):dxy(2):ObjectData.AX(end);
2608                yi=ObjectData.AY(1):dxy(1):ObjectData.AY(end);
2609                [XI,YI]=meshgrid(xi,yi);% creates the matrix of regular coordinates
2610                flag_mask = interp2(x_mask,y_mask,flag_mask,XI,YI);
2611            end
2612            AClass=class(ObjectData.A);
2613            ObjectData.A=flag_mask.*double(ObjectData.A);
2614            ObjectData.A=feval(AClass,ObjectData.A);
2615%             ind_off=[];
2616%             if isfield(ObjectData,'ListVarName')
2617%                 for ilist=1:length(ObjectData.ListVarName)
2618%                     if isequal(ObjectData.ListVarName{ilist},'Mask')||isequal(ObjectData.ListVarName{ilist},'MaskX')||isequal(ObjectData.ListVarName{ilist},'MaskY')
2619%                         ind_off=[ind_off ilist];
2620%                     end
2621%                 end
2622%                 ObjectData.ListVarName(ind_off)=[];
2623%                 VarDimIndex(ind_off)=[];
2624%                 ind_off=[];
2625%             
2626%             end
2627        end
2628        if ~isempty(ObjectData)
2629            PlotType='none'; %default
2630            if imap==2 && isempty(view_field_handle)
2631                view_field(ObjectData)
2632            else
2633                [PlotType,PlotParamOut]=plot_field(ObjectData,haxes(imap),PlotParam{imap},PosColorbar{imap});
2634                write_plot_param(plot_handles{imap},PlotParamOut) %update the auto plot parameters
2635                if isfield(Field,'Mesh')&&~isempty(Field.Mesh)
2636                    ObjectData.Mesh=Field.Mesh; % gives an estimated mesh size (useful for mouse action on the plot)
2637                end
2638            end
2639        end
2640    end
2641   
2642    %% update the mask
2643    if isequal(get(handles.CheckMask,'Value'),1)%if the mask option is on
2644        update_mask(handles,num_i1,num_i2);
2645    end
2646   
2647    %% prepare the menus of histograms and plot them (histogram of the whole volume in 3D case)
2648    menu_histo=(UvData.Field.ListVarName)';%list of field variables to be displayed for the menu of histogram display
2649    ind_skip=[];
2650    % nb_histo=1;
2651    Ustring='';
2652    Vstring='';
2653    % suppress coordinates from the histogram menu
2654    for ivar=1:numel(menu_histo)%l loop on field variables:
2655        if isfield(UvData.Field,'VarAttribute') && numel(UvData.Field.VarAttribute)>=ivar && isfield(UvData.Field.VarAttribute{ivar},'Role')
2656            Role=UvData.Field.VarAttribute{ivar}.Role;
2657            switch Role
2658                case {'coord_x','coord_y','coord_z','dimvar'}
2659                    ind_skip=[ind_skip ivar];
2660                case {'vector_x'}
2661                    Ustring=UvData.Field.ListVarName{ivar};
2662                    ind_skip=[ind_skip ivar];
2663                case {'vector_y'}
2664                    Vstring=UvData.Field.ListVarName{ivar};
2665                    ind_skip=[ind_skip ivar];
2666            end
2667        end
2668        DimCell=UvData.Field.VarDimName{ivar};
2669        DimName='';
2670        if ischar(DimCell)
2671            DimName=DimCell;
2672        elseif iscell(DimCell)&& numel(DimCell)==1
2673            DimName=DimCell{1};
2674        end
2675        if strcmp(DimName,menu_histo{ivar})
2676            ind_skip=[ind_skip ivar];
2677        end
2678    end
2679    menu_histo(ind_skip)=[];% remove skipped items
2680    if ~isempty(Ustring)
2681        menu_histo=[{[Ustring ',' Vstring]};menu_histo];% add U, V at the beginning if they exist
2682    end
2683   
2684    %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
2685    % display menus and plot histograms
2686    test_v=0;
2687    if ~isempty(menu_histo)
2688        set(handles.histo1_menu,'Value',1)
2689        set(handles.histo1_menu,'String',menu_histo)
2690        histo1_menu_Callback(handles.histo1_menu, [], handles)% plot first histogram
2691    end
2692end
2693
2694%------------------------------------------------------------------------
2695function histo1_menu_Callback(hObject, eventdata, handles)
2696%--------------------------------------------
2697histo_menu=get(handles.histo1_menu,'String');
2698histo_value=get(handles.histo1_menu,'Value');
2699FieldName=histo_menu{histo_value};
2700
2701UvData=get(handles.uvmat,'UserData');
2702Field=UvData.Field;
2703r=regexp(FieldName,'(?<var1>.*)(?<sep>,)(?<var2>.*)','names');
2704FieldName_2='';
2705if ~isempty(r)
2706    FieldName=r.var1;
2707    FieldName_2=r.var2;
2708end
2709if ~isfield(UvData.Field,FieldName)
2710    msgbox_uvmat('ERROR',['no field  ' FieldName ' for histogram'])
2711    return
2712end
2713FieldHisto=Field.(FieldName);
2714if isfield(Field,'FF') && ~isempty(Field.FF) && isequal(size(Field.FF),size(FieldHisto))
2715    indsel=find(Field.FF==0);%find values marked as false
2716    if ~isempty(indsel)
2717        FieldHisto=FieldHisto(indsel);
2718        if ~isempty(FieldName_2)
2719            FieldHisto(:,:,2)=Field.(FieldName_2)(indsel);
2720        end
2721    end
2722end
2723if isempty(Field)
2724    msgbox_uvmat('ERROR',['empty field ' FieldName])
2725else
2726    nxy=size(FieldHisto);
2727    Amin=double(min(min(min(FieldHisto))));%min of field value
2728    Amax=double(max(max(max(FieldHisto))));%max of field value
2729    if isequal(Amin,Amax)
2730        cla(handles.HistoAxes)
2731    else
2732        Histo.ListVarName={FieldName,'histo'};
2733        if isfield(Field,'NbDim') && isequal(Field.NbDim,3)
2734            Histo.VarDimName={FieldName,FieldName}; %dimensions for the histogram
2735        else
2736            if numel(nxy)==2
2737                Histo.VarDimName={FieldName,FieldName}; %dimensions for the histogram
2738            else
2739                Histo.VarDimName={FieldName,{FieldName,'component'}}; %dimensions for the histogram
2740            end
2741        end
2742        %unit
2743        units=[]; %default
2744        for ivar=1:numel(Field.ListVarName)
2745            if strcmp(Field.ListVarName{ivar},FieldName)
2746                if isfield(Field,'VarAttribute') && numel(Field.VarAttribute)>=ivar && isfield(Field.VarAttribute{ivar},'units')
2747                    units=Field.VarAttribute{ivar}.units;
2748                    break
2749                end
2750            end
2751        end
2752        if ~isempty(units)
2753            Histo.VarAttribute{1}.units=units;
2754        end
2755        eval(['Histo.' FieldName '=linspace(Amin,Amax,50);'])%absissa values for histo
2756        if isfield(Field,'NbDim') && isequal(Field.NbDim,3)
2757            C=reshape(double(FieldHisto),1,[]);% reshape in a vector
2758            Histo.histo(:,1)=hist(C, Histo.(FieldName));  %calculate histogram
2759        else
2760            for col=1:size(FieldHisto,3)
2761                B=FieldHisto(:,:,col);
2762                C=reshape(double(B),1,nxy(1)*nxy(2));% reshape in a vector
2763                Histo.histo(:,col)=hist(C, Histo.(FieldName));  %calculate histogram
2764            end
2765        end
2766        plot_field(Histo,handles.HistoAxes);
2767        hlegend=legend;
2768        if isempty(FieldName_2)
2769        set(hlegend,'String',FieldName)
2770        else
2771            set(hlegend,'String',{FieldName;FieldName_2})
2772        end
2773    end
2774end
2775
2776%-------------------------------------------------------------------
2777% --- translate coordinate to matrix index
2778%-------------------------------------------------------------------
2779function [indx,indy]=pos2ind(x0,rangx0,nxy)
2780indx=1+round((nxy(2)-1)*(x0-rangx0(1))/(rangx0(2)-rangx0(1)));% index x of pixel 
2781indy=1+round((nxy(1)-1)*(y12-rangy0(1))/(rangy0(2)-rangy0(1)));% index y of pixel
2782
2783
2784%-------------------------------------------------------------------
2785% --- Executes on button press in 'CheckZoom'.
2786%-------------------------------------------------------------------
2787function CheckZoom_Callback(hObject, eventdata, handles)
2788
2789if (get(handles.CheckZoom,'Value') == 1);
2790    set(handles.CheckZoom,'BackgroundColor',[1 1 0])
2791    set(handles.CheckFixLimits,'Value',1)% propose by default fixed limits for the plotting axes
2792    set(handles.CheckFixLimits,'BackgroundColor',[1 1 0])
2793else
2794    set(handles.CheckZoom,'BackgroundColor',[0.7 0.7 0.7])
2795end
2796
2797%-------------------------------------------------------------------
2798% --- Executes on button press in 'CheckFixLimits'.
2799%-------------------------------------------------------------------
2800function CheckFixLimits_Callback(hObject, eventdata, handles)
2801test=get(handles.CheckFixLimits,'Value');
2802if test
2803    set(handles.CheckFixLimits,'BackgroundColor',[1 1 0])
2804else
2805    set(handles.CheckFixLimits,'BackgroundColor',[0.7 0.7 0.7])
2806    update_plot(handles);
2807end
2808
2809%-------------------------------------------------------------------
2810% --- Executes on button press in CheckFixAspectRatio.
2811function CheckFixAspectRatio_Callback(hObject, eventdata, handles)
2812%-------------------------------------------------------------------
2813if get(handles.CheckFixAspectRatio,'Value')
2814    set(handles.CheckFixAspectRatio,'BackgroundColor',[1 1 0])
2815    update_plot(handles);
2816else
2817    set(handles.CheckFixAspectRatio,'BackgroundColor',[0.7 0.7 0.7])
2818    update_plot(handles);
2819end
2820
2821%-------------------------------------------------------------------
2822function num_AspectRatio_Callback(hObject, eventdata, handles)
2823%-------------------------------------------------------------------
2824set(handles.CheckFixAspectRatio,'Value',1)% select the fixed aspect ratio button
2825set(handles.CheckFixAspectRatio,'BackgroundColor',[1 1 0])% mark in yellow
2826update_plot(handles);
2827%-------------------------------------------------------------------
2828
2829%-------------------------------------------------------------------
2830
2831
2832
2833%-------------------------------------------------------------------
2834%----Executes on button press in 'record': records the current flags of manual correction.
2835%-------------------------------------------------------------------
2836function record_Callback(hObject, eventdata, handles)
2837% [filebase,num_i1,num_j1,num_i2,num_j2,Ext,NomType,SubDir]=read_input_file(handles);
2838[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
2839FileName=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
2840%FileName=read_file_boxes(handles);
2841[erread,message]=fileattrib(FileName);
2842if ~isempty(message) && ~isequal(message.UserWrite,1)
2843     msgbox_uvmat('ERROR',['no writting access to ' FileName])
2844     return
2845end
2846test_civ2=isequal(get(handles.civ2,'BackgroundColor'),[1 1 0]);
2847test_civ1=isequal(get(handles.VelType,'BackgroundColor'),[1 1 0]);
2848if ~test_civ2 && ~test_civ1
2849    msgbox_uvmat('ERROR','manual correction only possible for CIV1 or CIV2 velocity fields')
2850end
2851if test_civ2
2852    nbname='nb_vectors2';
2853   flagname='vec2_FixFlag';
2854   attrname='fix2';
2855end
2856if test_civ1
2857    nbname='nb_vectors';
2858   flagname='vec_FixFlag';
2859   attrname='fix';
2860end
2861%write fix flags in the netcdf file
2862UvData=get(handles.uvmat,'UserData');
2863hhh=which('netcdf.open');% look for built-in matlab netcdf library
2864if ~isequal(hhh,'')% case of new builtin Matlab netcdf library
2865    nc=netcdf.open(FileName,'NC_WRITE');
2866    netcdf.reDef(nc);
2867    netcdf.putAtt(nc,netcdf.getConstant('NC_GLOBAL'),attrname,1);
2868    dimid = netcdf.inqDimID(nc,nbname);
2869    try
2870        varid = netcdf.inqVarID(nc,flagname);% look for already existing fixflag variable
2871    catch
2872        varid=netcdf.defVar(nc,flagname,'double',dimid);%create fixflag variable if it does not exist
2873    end
2874    netcdf.endDef(nc);
2875    netcdf.putVar(nc,varid,UvData.PlotAxes.FF);
2876    netcdf.close(nc); 
2877else %old netcdf library
2878    netcdf_toolbox(FileName,AxeData,attrname,nbname,flagname)
2879end
2880
2881%-------------------------------------------------------------------
2882%----Correct the netcdf file, using toolbox (old versions of Matlab).
2883%-------------------------------------------------------------------
2884function netcdf_toolbox(FileName,AxeData,attrname,nbname,flagname)
2885nc=netcdf(FileName,'write'); %open netcdf file
2886result=redef(nc);
2887eval(['nc.' attrname '=1;']);
2888theDim=nc(nbname) ;% get the number of velocity vectors
2889nb_vectors=size(theDim);
2890var_FixFlag=ncvar(flagname,nc);% var_FixFlag will be written as the netcdf variable vec_FixFlag
2891var_FixFlag(1:nb_vectors)=AxeData.FF;%
2892fin=close(nc);
2893
2894%-------------------------------------------------------------------
2895% --- Executes on button press in SubField
2896function SubField_Callback(hObject, eventdata, handles)
2897%-------------------------------------------------------------------
2898UvData=get(handles.uvmat,'UserData');
2899if get(handles.SubField,'Value')==0% if the subfield button is desactivated   
2900    set(handles.RootPath_1,'String','')
2901    set(handles.RootFile_1,'String','')
2902    set(handles.SubDir_1,'String','');
2903    set(handles.FileIndex_1,'String','');
2904    set(handles.FileExt_1,'String','');
2905    set(handles.RootPath_1,'Visible','off')
2906    set(handles.RootFile_1,'Visible','off')
2907    set(handles.SubDir_1,'Visible','off');
2908    set(handles.NomType_1,'Visible','off');
2909    set(handles.abs_time_1,'Visible','off')
2910    set(handles.FileIndex_1,'Visible','off');
2911    set(handles.FileExt_1,'Visible','off');
2912    set(handles.FieldName_1,'Value',1);%set to blank state
2913    set(handles.VelType_1,'Value',1);%set to blank state
2914    set(handles.num_Opacity,'String','')% desactivate opacity setting
2915    if ~strcmp(get(handles.VelType,'Visible'),'on')
2916        set(handles.VelType_1,'Visible','off')
2917    end
2918    if isfield(UvData,'XmlData_1')
2919        UvData=rmfield(UvData,'XmlData_1');
2920    end
2921    set(handles.uvmat,'UserData',UvData);
2922    transform_fct_list=get(handles.transform_fct,'String');
2923    transform_fct=transform_fct_list(get(handles.transform_fct,'Value'));
2924    if strcmp(transform_fct,'sub_field')
2925        set(handles.transform_fct,'Value',1)%suppress the sub_field transform
2926        transform_fct_Callback(hObject, eventdata, handles);
2927    else
2928        run0_Callback(hObject, eventdata, handles)
2929    end 
2930else
2931    MenuBrowse_1_Callback(hObject, eventdata, handles)
2932end
2933
2934%------------------------------------------------------------------------
2935% --- read the data displayed for the input rootfile windows (new): TODO use read_GUI
2936
2937function [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles)
2938%------------------------------------------------------------------------
2939InputFile=read_GUI(handles.InputFile);
2940RootPath=InputFile.RootPath;
2941SubDir=regexprep(InputFile.SubDir,'/|\','');
2942RootFile=regexprep(InputFile.RootFile,'/|\','');
2943FileIndices=InputFile.FileIndex;
2944FileExt=InputFile.FileExt;
2945
2946
2947%------------------------------------------------------------------------
2948% ---- read the data displayed for the second input rootfile windows
2949function [RootPath_1,SubDir_1,RootFile_1,FileIndex_1,FileExt_1,NomType_1]=read_file_boxes_1(handles)
2950%------------------------------------------------------------------------
2951RootPath_1=get(handles.RootPath_1,'String'); % read the data from the file1_input window
2952if isequal(get(handles.RootPath_1,'Visible'),'off') || isequal(RootPath_1,'"')
2953    RootPath_1=get(handles.RootPath,'String');
2954end;
2955SubDir_1=get(handles.SubDir_1,'String');
2956if isequal(get(handles.SubDir_1,'Visible'),'off')|| isequal(SubDir_1,'"')
2957    SubDir_1=get(handles.SubDir,'String');
2958end
2959SubDir_1=regexprep(SubDir_1,'\<[\\/]|[\\/]\>','');%suppress possible / or \ separator at the beginning or the end of the string
2960RootFile_1=get(handles.RootFile_1,'String');
2961if isequal(get(handles.RootFile_1,'Visible'),'off') || isequal(RootFile_1,'"')
2962    RootFile_1=get(handles.RootFile,'String');
2963end
2964RootFile_1=regexprep(RootFile_1,'\<[\\/]|[\\/]\>','');%suppress possible / or \ separator at the beginning or the end of the string
2965FileIndex_1=get(handles.FileIndex_1,'String');
2966if isequal(get(handles.FileIndex_1,'Visible'),'off')|| isequal(FileIndex_1,'"')
2967    FileIndex_1=get(handles.FileIndex,'String');
2968end
2969FileExt_1=get(handles.FileExt_1,'String');
2970if isequal(get(handles.FileExt_1,'Visible'),'off') || isequal(FileExt_1,'"')
2971    FileExt_1=get(handles.FileExt,'String');%read FileExt by default
2972end
2973NomType_1=get(handles.NomType_1,'String');
2974if isequal(get(handles.NomType_1,'Visible'),'off') || isequal(NomType_1,'"')
2975    NomType_1=get(handles.NomType,'String');%read FileExt by default
2976end
2977%------------------------------------------------------------------------
2978% --- Executes on menu selection FieldName
2979function FieldName_Callback(hObject, eventdata, handles)
2980%------------------------------------------------------------------------
2981list_fields=get(handles.FieldName,'String');% list menu fields
2982index_fields=get(handles.FieldName,'Value');% selected string index
2983field= list_fields{index_fields(1)}; % selected string
2984if isequal(field,'get_field...')
2985    set(handles.FixVelType,'visible','off')
2986    set(handles.VelType,'visible','off')
2987    set(handles.VelType_1,'visible','off')
2988    [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
2989    FileName=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
2990    hget_field=findobj(allchild(0),'name','get_field');
2991    if ~isempty(hget_field)
2992        delete(hget_field)
2993    end
2994    get_field(FileName);
2995    return %no further action
2996end
2997
2998UvData=get(handles.uvmat,'UserData');
2999
3000%read the rootfile input display
3001[RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
3002FileName=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt];
3003[tild,tild,tild,i1,i2,j1,j2,tild,NomType]=fileparts_uvmat(['xxx' get(handles.FileIndex,'String') FileExt]);
3004if isequal(field,'image')
3005    if  isfield(UvData.Field,'Civ2_ImageA')%get the corresponding input image in the netcdf file
3006        imagename=UvData.Field.Civ2_ImageA;
3007    elseif isfield(UvData.Field,'Civ1_ImageA')%
3008        imagename=UvData.Field.Civ1_ImageA;
3009    else
3010        SubDirBase=regexprep(SubDir,'\..*','');%take the root part of SubDir, before the first dot '.'
3011        imagename=fullfile_uvmat(RootPath,SubDirBase,RootFile,'.png',NomType,i1,[],j1,[]);
3012    end
3013    if ~exist(imagename,'file')
3014        [FileName,PathName] = uigetfile( ...
3015            {'*.png;*.jpg;*.tif;*.avi;*.AVI;*.vol', ' (*.png, .tif, *.avi,*.vol)';
3016            '*.jpg',' jpeg image files'; ...
3017            '*.png','.png image files'; ...
3018            '*.tif','.tif image files'; ...
3019            '*.avi;*.AVI','.avi movie files'; ...
3020            '*.vol','.volume images (png)'; ...
3021            '*.*',  'All Files (*.*)'}, ...
3022            'Pick an image',imagename);
3023        if ~ischar(FileName),return,end %abandon if the browser is cancelled
3024        imagename=[PathName FileName];
3025    end
3026     % display the selected field and related information
3027    display_file_name(handles,imagename)%display the image
3028    return
3029else
3030    ext=get(handles.FileExt,'String');
3031    if ~isequal(ext,'.nc') %find the new NomType if the previous display was not already a netcdf file
3032        [FileName,PathName] = uigetfile( ...
3033            {'*.nc', ' (*.nc)';
3034            '*.nc',' netcdf files'; ...
3035            '*.*',  'All Files (*.*)'}, ...
3036            'Pick a netcdf file',FileBase);
3037        if ~ischar(FileName),return,end %abandon if the browser is cancelled
3038        FullFileName=[PathName FileName];
3039        % display the selected field and related information
3040        display_file_name( handles,FullFileName)
3041        return
3042    end
3043end
3044indices=fullfile_uvmat('','','','',NomType,i1,i2,j1,j2);
3045set(handles.FileIndex,'String',indices)
3046% set(handles.NomType,'String',NomType)
3047
3048%common to Fields_1_Callback
3049list_fields_1=get(handles.FieldName_1,'String');% list menu fields
3050field_1='';
3051if ~isempty(list_fields_1)
3052field_1= list_fields_1{get(handles.FieldName_1,'Value')}; % selected string
3053end
3054if isequal(field,'image')||isequal(field_1,'image')
3055    set(handles.TitleNpx,'Visible','on')% visible npx,pxcm... buttons
3056    set(handles.TitleNpy,'Visible','on')
3057    set(handles.num_Npx,'Visible','on')
3058    set(handles.num_Npy,'Visible','on')
3059else
3060    set(handles.TitleNpx,'Visible','off')% visible npx,pxcm... buttons
3061    set(handles.TitleNpy,'Visible','off')
3062    set(handles.num_Npx,'Visible','off')
3063    set(handles.num_Npy,'Visible','off')
3064end
3065if ~(isfield(UvData,'NewSeries')&&isequal(UvData.NewSeries,1))
3066    run0_Callback(hObject, eventdata, handles)
3067end
3068
3069%---------------------------------------------------
3070% --- Executes on menu selection FieldName
3071function FieldName_1_Callback(hObject, eventdata, handles)
3072%-------------------------------------------------
3073%% read input data
3074check_new=~get(handles.SubField,'Value'); %check_new=1 if a second field was not previously entered
3075UvData=get(handles.uvmat,'UserData');
3076if check_new && isfield(UvData,'XmlData')
3077    UvData.XmlData{2}=UvData.XmlData{1};
3078end
3079if isfield(UvData,'Field_1')
3080    UvData=rmfield(UvData,'Field_1');% remove the stored second field (a new one needs to be read)
3081end
3082UvData.FileName_1='';% desactivate the use of a constant second file
3083list_fields=get(handles.FieldName,'String');% list menu fields
3084field= list_fields{get(handles.FieldName,'Value')}; % selected string
3085list_fields=get(handles.FieldName_1,'String');% list menu fields
3086field_1= list_fields{get(handles.FieldName_1,'Value')}; % selected string for the second field
3087if isempty(field_1)%||(numel(UvData.FileType)>=2 && strcmp(UvData.FileType{2},'image'))
3088    set(handles.SubField,'Value',0)
3089    SubField_Callback(hObject, eventdata, handles)
3090    return
3091else
3092    set(handles.SubField,'Value',1)%state that a second field is now entered
3093end
3094
3095%% read the rootfile input display
3096[RootPath_1,SubDir_1,RootFile_1,FileIndex_1,FileExt_1]=read_file_boxes_1(handles);
3097FileName_1=[fullfile(RootPath_1,SubDir_1,RootFile_1) FileIndex_1 FileExt_1];
3098[tild,tild,tild,i1,i2,j1,j2]=fileparts_uvmat(get(handles.FileIndex,'String'));
3099switch field_1
3100    case 'get_field...'
3101        set_veltype_display(0) % no veltype display
3102        hget_field=findobj(allchild(0),'name','get_field_1');
3103        if ~isempty(hget_field)
3104            delete(hget_field)
3105        end
3106        hget_field=get_field(FileName_1);
3107        set(hget_field,'name','get_field_1')
3108        hhget_field=guidata(hget_field);
3109        set(hhget_field.list_fig,'Value',1)
3110        set(hhget_field.list_fig,'String',{'uvmat'})
3111        if check_new
3112            UvData.FileType{2}=UvData.FileType{1};
3113            set(handles.FileIndex_1,'String',get(handles.FileIndex,'String'))
3114              set(handles.uvmat,'UserData',UvData)
3115        end
3116    case 'image'
3117        % get the image name corresponding to the current netcdf name (no unique correspondance)
3118        if  isfield(UvData.Field,'Civ2_ImageA')%get the corresponding input image in the netcdf file
3119            imagename=UvData.Field.Civ2_ImageA;
3120        elseif isfield(UvData.Field,'Civ1_ImageA')%
3121            imagename=UvData.Field.Civ1_ImageA;
3122        else
3123            SubDirBase=regexprep(SubDir_1,'\..*','');%take the root part of SubDir, before the first dot '.'
3124            imagename=fullfile_uvmat(RootPath_1,SubDirBase,RootFile_1,'.png',get(handles.NomType,'String'),i1,[],j1);
3125        end
3126        if ~exist(imagename,'file') % browse for images if it is not found
3127            [FileName,PathName] = uigetfile( ...
3128                {'*.png;*.jpg;*.tif;*.avi;*.AVI;*.vol', ' (*.png, .tif, *.avi,*.vol)';
3129                '*.jpg',' jpeg image files'; ...
3130                '*.png','.png image files'; ...
3131                '*.tif','.tif image files'; ...
3132                '*.avi;*.AVI','.avi movie files'; ...
3133                '*.vol','.volume images (png)'; ...
3134                '*.*',  'All Files (*.*)'}, ...
3135                'Pick an image',imagename);
3136            if ~ischar(FileName),return,end %abandon if the browser is cancelled
3137            imagename=[PathName FileName];
3138        end
3139        if ~ischar(imagename)% quit if the browser has  been closed
3140            set(handles.SubField,'Value',0)
3141        else %valid browser input:  display the selected image
3142            set(handles.TitleNpx,'Visible','on')% visible npx,pxcm... buttons
3143            set(handles.TitleNpy,'Visible','on')
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.TitleNpx,'Visible','off')% visible npx,pxcm... buttons
3156            set(handles.TitleNpy,'Visible','off')
3157            set(handles.num_Npx,'Visible','off')
3158            set(handles.num_Npy,'Visible','off')
3159        end
3160        set(handles.uvmat,'UserData',UvData)
3161        if ~(isfield(UvData,'NewSeries')&&isequal(UvData.NewSeries,1))
3162            run0_Callback(hObject, eventdata, handles)
3163        end
3164end
3165
3166%------------------------------------------------------------------------
3167% --- set the visibility of relevant velocity type menus:
3168function menu=set_veltype_display(Civ,FileType)
3169%------------------------------------------------------------------------
3170if ~exist('FileType','var')
3171    FileType='civx';
3172end
3173switch FileType
3174    case 'civx'
3175        menu={'civ1';'interp1';'filter1';'civ2';'interp2';'filter2'};
3176        if isequal(Civ,0)
3177            imax=0;
3178        elseif isequal(Civ,1) || isequal(Civ,2)
3179            imax=1;
3180        elseif isequal(Civ,3)
3181            imax=3;
3182        elseif isequal(Civ,4) || isequal(Civ,5)
3183            imax=4;
3184        elseif isequal(Civ,6) %patch2
3185            imax=6;
3186        end
3187    case 'civdata'
3188        menu={'civ1';'filter1';'civ2';'filter2'};
3189        if isequal(Civ,0)
3190            imax=0;
3191        elseif isequal(Civ,1) || isequal(Civ,2)
3192            imax=1;
3193        elseif isequal(Civ,3)
3194            imax=2;
3195        elseif isequal(Civ,4) || isequal(Civ,5)
3196            imax=3;
3197        elseif isequal(Civ,6) %patch2
3198            imax=4;
3199        end
3200end
3201menu=menu(1:imax);
3202
3203%------------------------------------------------------------------------
3204% --- Executes on button press in FixVelType.
3205function FixVelType_Callback(hObject, eventdata, handles)
3206%------------------------------------------------------------------------
3207% refresh the current plot if the fixed  veltype is unselected
3208if ~get(handles.FixVelType,'Value')
3209    run0_Callback(hObject, eventdata, handles)
3210end
3211
3212%------------------------------------------------------------------------
3213% --- Executes on button press in VelType.
3214function VelType_Callback(hObject, eventdata, handles)
3215%------------------------------------------------------------------------
3216set(handles.FixVelType,'Value',1)
3217run0_Callback(hObject, eventdata, handles)
3218
3219%------------------------------------------------------------------------
3220% --- Executes on choice selection in VelType_1.
3221function VelType_1_Callback(hObject, eventdata, handles)
3222%------------------------------------------------------------------------
3223set(handles.FixVelType,'Value',1)% the velocity type is now imposed by the GUI (not automatic)
3224UvData=get(handles.uvmat,'UserData');
3225set(handles.run0,'BackgroundColor',[1 1 0])%paint run0 button in yellow to indicate its activation
3226drawnow   
3227InputFile=read_GUI(handles.InputFile);% read the input file parameters
3228[RootPath,SubDir,RootFile,FileIndex,FileExt]=read_file_boxes(handles);
3229[RootPath_1,SubDir_1,RootFile_1,FileIndex_1,FileExt_1]=read_file_boxes_1(handles);
3230FileName=[fullfile(RootPath,SubDir,RootFile) FileIndex FileExt];% name of the first input file
3231
3232check_refresh=0;
3233if isempty(InputFile.VelType_1)
3234        FileName_1='';% we plot the first input field without the second field
3235        set(handles.SubField,'Value',0)
3236        SubField_Callback(hObject, eventdata, handles)% activate SubField_Callback and refresh current display, removing the second field
3237elseif get(handles.SubField,'Value')% if subfield is already 'on'
3238     FileName_1=[fullfile(RootPath_1,SubDir_1,RootFile_1) FileIndex_1 FileExt_1];% name of the second input file
3239     check_refresh=1;%will refresh the current display
3240else% we introduce the same file (with a different field) for the second series
3241     FileName_1=FileName;% we compare two fields in the same file
3242     UvData.FileType{2}=UvData.FileType{1};
3243     UvData.XmlData{2}= UvData.XmlData{1};
3244     set(handles.SubField,'Value',1)
3245     transform=get(handles.path_transform,'UserData');
3246     if (~isa(transform,'function_handle')||nargin(transform)<3)
3247        set(handles.transform_fct,'value',2); % set transform to sub_field if the current fct doe not accept two input fields
3248        transform_fct_Callback(hObject, eventdata, handles)% activate transform_fct_Callback and refresh current display
3249     else
3250         check_refresh=1;
3251     end 
3252end
3253
3254% refresh the current display if it has not been done previously
3255if check_refresh
3256    UvData.FileName_1='';% desactivate the use of a constant second file
3257    set(handles.uvmat,'UserData',UvData)
3258    num_i1=stra2num(get(handles.i1,'String'));
3259    num_i2=stra2num(get(handles.i2,'String'));
3260    num_j1=stra2num(get(handles.j1,'String'));
3261    num_j2=stra2num(get(handles.j2,'String'));
3262    [tild,tild,tild,i1_1,i2_1,j1_1,j2_1]=fileparts_uvmat(['xx' FileIndex_1]);
3263    errormsg=refresh_field(handles,FileName,FileName_1,num_i1,num_i2,num_j1,num_j2,i1_1,i2_1,j1_1,j2_1);
3264    if ~isempty(errormsg)
3265        msgbox_uvmat('ERROR',errormsg);
3266    else
3267        set(handles.i1,'BackgroundColor',[1 1 1])
3268        set(handles.i2,'BackgroundColor',[1 1 1])
3269        set(handles.j1,'BackgroundColor',[1 1 1])
3270        set(handles.j2,'BackgroundColor',[1 1 1])
3271        set(handles.FileIndex,'BackgroundColor',[1 1 1])
3272        set(handles.FileIndex_1,'BackgroundColor',[1 1 1])
3273    end
3274    set(handles.run0,'BackgroundColor',[1 0 0])
3275end
3276
3277%-----------------------------------------------
3278% --- reset civ buttons
3279function reset_vel_type(handles_civ0,handle1)
3280for ibutton=1:length(handles_civ0)
3281    set(handles_civ0(ibutton),'BackgroundColor',[0.831 0.816 0.784])
3282    set(handles_civ0(ibutton),'Value',0)
3283end
3284if exist('handle1','var')%handles of selected button
3285        set(handle1,'BackgroundColor',[1 1 0]) 
3286end
3287
3288%-------------------------------------------------------
3289% --- Executes on button press in MENUVOLUME.
3290%-------------------------------------------------------
3291function VOLUME_Callback(hObject, eventdata, handles)
3292%errordlg('command VOL not implemented yet')
3293if ishandle(handles.UVMAT_title)
3294    delete(handles.UVMAT_title)
3295end
3296UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
3297if isequal(get(handles.VOLUME,'Value'),1)
3298    set(handles.CheckZoom,'Value',0)
3299    set(handles.CheckZoom,'BackgroundColor',[0.7 0.7 0.7])
3300    set(handles.edit_vect,'Value',0)
3301    edit_vect_Callback(hObject, eventdata, handles)
3302    set(handles.edit_object,'Value',0)
3303    set(handles.edit_object,'BackgroundColor',[0.7 0.7 0.7])
3304%     set(handles.cal,'Value',0)
3305%     set(handles.cal,'BackgroundColor',[0 1 0])
3306    set(handles.edit_vect,'Value',0)
3307    edit_vect_Callback(hObject, eventdata, handles)
3308    %initiate set_object GUI
3309    data.Name='VOLUME';
3310    if isfield(UvData,'CoordType')
3311        data.CoordType=UvData.CoordType;
3312    end
3313    if isfield(UvData.Field,'Mesh')&~isempty(UvData.Field.Mesh)
3314        data.RangeX=[UvData.Field.XMin UvData.Field.XMax];
3315        data.RangeY=[UvData.Field.YMin UvData.Field.YMax];
3316        data.DX=UvData.Field.Mesh;
3317        data.DY=UvData.Field.Mesh;
3318    elseif isfield(UvData.Field,'AX')&isfield(UvData.Field,'AY')& isfield(UvData.Field,'A')%only image
3319        np=size(UvData.Field.A);
3320        meshx=(UvData.Field.AX(end)-UvData.Field.AX(1))/np(2);
3321        meshy=abs(UvData.Field.AY(end)-UvData.Field.AY(1))/np(1);
3322        data.RangeY=max(meshx,meshy);
3323        data.RangeX=max(meshx,meshy);
3324        data.DX=max(meshx,meshy);
3325    end
3326    data.ParentButton=handles.VOLUME;
3327    PlotHandles=get_plot_handles(handles);%get the handles of the interface elements setting the plotting parameters
3328    [hset_object,UvData.sethandles]=set_object(data,PlotHandles);% call the set_object interface with action on haxes,
3329                                                      % associate the set_object interface handle to the plotting axes
3330    set(hset_object,'Position',get(handles.uvmat,'Position')+UvData.OpenParam.PosSetObject)
3331    UvData.MouseAction='create_object';
3332else
3333    set(handles.VOLUME,'BackgroundColor',[0 1 0])
3334end
3335set(handles.uvmat,'UserData',UvData)
3336
3337%-------------------------------------------------------
3338function edit_vect_Callback(hObject, eventdata, handles)
3339%-------------------------------------------------------
3340%
3341% UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
3342if isequal(get(handles.edit_vect,'Value'),1)
3343    test_civ2=isequal(get(handles.civ2,'BackgroundColor'),[1 1 0]);
3344    test_civ1=isequal(get(handles.VelType,'BackgroundColor'),[1 1 0]);
3345    if ~test_civ2 && ~test_civ1
3346        msgbox_uvmat('ERROR','manual correction only possible for CIV1 or CIV2 velocity fields')
3347    end
3348    set(handles.record,'Visible','on')
3349    set(handles.edit_vect,'BackgroundColor',[1 1 0])
3350    set(handles.edit_object,'Value',0)
3351    set(handles.CheckZoom,'Value',0)
3352    set(handles.CheckZoom,'BackgroundColor',[0.7 0.7 0.7])
3353%     set(handles.create,'Value',0)
3354%     set(handles.create,'BackgroundColor',[0 1 0])
3355    set(handles.edit_object,'BackgroundColor',[0.7 0.7 0.7])
3356    set(gcf,'Pointer','arrow')
3357%     UvData.MouseAction='edit_vect';
3358else
3359    set(handles.record,'Visible','off')
3360    set(handles.edit_vect,'BackgroundColor',[0.7 0.7 0.7])
3361end
3362
3363%----------------------------------------------
3364function save_mask_Callback(hObject, eventdata, handles)
3365%-----------------------------------------------------------------------
3366UvData=get(handles.uvmat,'UserData');
3367
3368flag=1;
3369npx=size(UvData.Field.A,2);
3370npy=size(UvData.Field.A,1);
3371xi=0.5:npx-0.5;
3372yi=0.5:npy-0.5;
3373[Xi,Yi]=meshgrid(xi,yi);
3374if isfield(UvData,'Object')
3375    for iobj=1:length(UvData.Object)
3376        ObjectData=UvData.Object{iobj};
3377        if isfield(ObjectData,'ProjMode') &&(isequal(ObjectData.ProjMode,'mask_inside')||isequal(ObjectData.ProjMode,'mask_outside'));
3378            flagobj=1;
3379            testphys=0; %coordinates in pixels by default
3380            if isfield(ObjectData,'CoordType') && isequal(ObjectData.CoordType,'phys')
3381                if isfield(UvData,'XmlData')&& isfield(UvData.XmlData{1},'GeometryCalib')
3382                    Calib=UvData.XmlData{1}.GeometryCalib;
3383                    testphys=1;
3384                end
3385            end
3386            if isfield(ObjectData,'Coord')& isfield(ObjectData,'Style')
3387                if isequal(ObjectData.Type,'polygon')
3388                    X=ObjectData.Coord(:,1);
3389                    Y=ObjectData.Coord(:,2);
3390                    if testphys
3391                        [X,Y]=px_XYZ(Calib,X,Y,0);% to generalise with 3D cases
3392                    end
3393                    flagobj=~inpolygon(Xi,Yi,X',Y');%=0 inside the polygon, 1 outside                 
3394                elseif isequal(ObjectData.Type,'ellipse')
3395                    if testphys
3396                        %[X,Y]=px_XYZ(Calib,X,Y,0);% TODO:create a polygon boundary and transform to phys
3397                    end
3398                    RangeX=max(ObjectData.RangeX);
3399                    RangeY=max(ObjectData.RangeY);
3400                    X2Max=RangeX*RangeX;
3401                    Y2Max=RangeY*RangeY;
3402                    distX=(Xi-ObjectData.Coord(1,1));
3403                    distY=(Yi-ObjectData.Coord(1,2));
3404                    flagobj=(distX.*distX/X2Max+distY.*distY/Y2Max)>1;
3405                elseif isequal(ObjectData.Type,'rectangle')
3406                    if testphys
3407                        %[X,Y]=px_XYZ(Calib,X,Y,0);% TODO:create a polygon boundary and transform to phys
3408                    end
3409                    distX=abs(Xi-ObjectData.Coord(1,1));
3410                    distY=abs(Yi-ObjectData.Coord(1,2));
3411                    flagobj=distX>max(ObjectData.RangeX) | distY>max(ObjectData.RangeY);
3412                end
3413                if isequal(ObjectData.ProjMode,'mask_outside')
3414                    flagobj=~flagobj;
3415                end
3416                flag=flag & flagobj;
3417            end
3418        end
3419    end
3420end
3421% flag=~flag;
3422%mask name
3423RootPath=get(handles.RootPath,'String');
3424RootFile=get(handles.RootFile,'String');
3425RootFile=regexprep(RootFile,'\<[\\/]|[\\/]\>','');%suppress possible / or \ separator at the beginning or the end of the string
3426filebase=fullfile(RootPath,RootFile);
3427list=get(handles.masklevel,'String');
3428masknumber=num2str(length(list));
3429maskindex=get(handles.masklevel,'Value');
3430mask_name=fullfile_uvmat(RootPath,SubDir,[RootFile '_' masknumber 'mask'],'.png','_1',maskindex);
3431%mask_name=name_generator([filebase '_' masknumber 'mask'],maskindex,1,'.png','_i');
3432imflag=uint8(255*(0.392+0.608*flag));% =100 for flag=0 (vectors not computed when 20<imflag<200)
3433imflag=flipdim(imflag,1);
3434% imflag=uint8(255*flag);% =0 for flag=0 (vectors=0 when 20<imflag<200)
3435msgbox_uvmat('CONFIRMATION',[mask_name ' saved'])
3436imwrite(imflag,mask_name,'BitDepth',8);
3437
3438%display the mask
3439figure;
3440vec=linspace(0,1,256);%define a linear greyscale colormap
3441map=[vec' vec' vec'];
3442colormap(map)
3443
3444image(imflag);
3445
3446%-------------------------------------------------------------------
3447%-------------------------------------------------------------------
3448%  - FUNCTIONS FOR SETTING PLOTTING PARAMETERS
3449
3450%------------------------------------------------------------------
3451%-------------------------------------------------------------
3452% --- Executes on selection change in transform_fct.
3453
3454function transform_fct_Callback(hObject, eventdata, handles)
3455%-------------------------------------------------------------
3456UvData=get(handles.uvmat,'UserData');
3457menu=get(handles.transform_fct,'String');refresh
3458ichoice=get(handles.transform_fct,'Value');%item number in the menu
3459transform_name=menu{ichoice};% choice of the transform fct
3460list_path=get(handles.transform_fct,'UserData');
3461
3462%% add a new item to the menu if the option 'more...' has been selected
3463prev_path=fullfile(get(handles.path_transform,'String'));
3464if ~exist(prev_path,'dir')
3465    prev_path=fullfile(fileparts(which('uvmat')),'transform_field');
3466end
3467if strcmp(transform_name,'more...');
3468    [FileName, PathName] = uigetfile( ...
3469        {'*.m', ' (*.m)';
3470        '*.m',  '.m files '; ...
3471        '*.*', 'All Files (*.*)'}, ...
3472        'Pick the transform function', prev_path);
3473    if ~ischar(FileName),return,end %abandon if the browser is cancelled
3474    path_transform_fct =fullfile(PathName,FileName);
3475    if isempty(regexp(FileName,'.m$'))% detect file extension .m
3476        msgbox_uvmat('ERROR','a Matlab function .m must be introduced');
3477        return
3478    else
3479        transform_name=regexprep(FileName,'.m','');
3480    end
3481    ichoice=find(strcmp(transform_name,menu),1);%look for the selected fct in the existing menu
3482    if isempty(ichoice)% if the item is not found, add it to the menu (before 'more...' and select it)
3483        menu=[menu(1:end-1);{transform_name};{'more...'}];
3484        ichoice=numel(menu)-1;   
3485    end
3486    list_path{ichoice}=PathName;%update the list fo fct paths
3487    set(handles.transform_fct,'String',menu)
3488    set(handles.transform_fct,'Value',ichoice)
3489   
3490    % save the new menu in the personal file 'uvmat_perso.mat'
3491    dir_perso=prefdir;%personal Matalb directory
3492    profil_perso=fullfile(dir_perso,'uvmat_perso.mat');
3493    if exist(profil_perso,'file')
3494        nb_builtin=UvData.OpenParam.NbBuiltin;% number of 'builtin' (basic) transform fcts in uvmat
3495        if nb_builtin<numel(list_path)
3496        for ilist=nb_builtin+1:numel(list_path)
3497            transform_fct{ilist-nb_builtin}=[fullfile(list_path{ilist},menu{ilist}) '.m'];
3498        end
3499        save (profil_perso,'transform_fct','-append'); %store the root name for future opening of uvmat
3500        end
3501    end
3502end
3503
3504%% create the function handle of the selected fct
3505
3506if isempty(list_path{ichoice})% case of no selected fct
3507    transform_handle=[];
3508else
3509    if ~exist(list_path{ichoice},'dir')
3510        msgbox_uvmat('ERROR','invalid fct path: select the transform fct again with the option more...')
3511        return
3512    end
3513    current_dir=pwd;%current working dir
3514    cd(list_path{ichoice})
3515    transform_handle=str2func(transform_name);
3516    cd(current_dir)
3517end
3518set(handles.path_transform,'String',list_path{ichoice})
3519set(handles.path_transform,'UserData',transform_handle)
3520set(handles.transform_fct,'UserData',list_path)
3521
3522%% update the ToolTip string of the menu transform_fct with the first line of the selected fct file
3523if isempty(list_path{ichoice})% case of no selected fct
3524    set(handles.transform_fct,'ToolTipString','transform_fct:choose a transform function')
3525else
3526    try
3527        [fid,errormsg] =fopen([fullfile(list_path{ichoice},transform_name) '.m']);
3528        InputText=textscan(fid,'%s',1,'delimiter','\n');
3529        fclose(fid)
3530        set(handles.transform_fct,'ToolTipString',['transform_fct: ' InputText{1}{1}])% put the first line of the selected function as tooltip help
3531    end
3532end
3533
3534%% adapt the GUI to the input/output conditions of the selected transform fct
3535DataOut=[];
3536CoordUnit='';
3537CoordUnitPrev='';
3538if isfield(UvData,'Field')&&isfield(UvData.Field,'CoordUnit')
3539    CoordUnitPrev=UvData.Field.CoordUnit;
3540end
3541if ~isempty(list_path{ichoice})
3542    if nargin(transform_handle)>1 && isfield(UvData,'XmlData')&&~isempty(UvData.XmlData)
3543        XmlData=UvData.XmlData{1};
3544        DataOut=feval(transform_handle,'*',XmlData);
3545        if isfield(DataOut,'CoordUnit')
3546            CoordUnit=DataOut.CoordUnit;
3547        end
3548        if isfield(DataOut,'InputFieldType')
3549            UvData.InputFieldType=DataOut.InputFieldType;
3550        end
3551    else
3552        DataOut=feval(transform_handle,'*');
3553    end
3554end
3555
3556set(handles.CheckFixLimits,'Value',0)
3557set(handles.CheckFixLimits,'BackgroundColor',[0.7 0.7 0.7])
3558
3559%% delete drawn objects if the output CooordUnit is different from the previous one
3560if ~strcmp(CoordUnit,CoordUnitPrev)
3561    hother=findobj('Tag','proj_object');%find all the proj objects
3562    for iobj=1:length(hother)
3563        delete_object(hother(iobj))
3564    end
3565    hother=findobj('Tag','DeformPoint');%find all the proj objects
3566    for iobj=1:length(hother)
3567        delete_object(hother(iobj))
3568    end
3569    hh=findobj('Tag','calib_points');
3570    if ~isempty(hh)
3571        delete(hh)
3572    end
3573    hhh=findobj('Tag','calib_marker');
3574    if ~isempty(hhh)
3575        delete(hhh)
3576    end
3577%     if isfield(UvData,'Object')
3578%         UvData.Object=UvData.Object(1);
3579%     end
3580    set(handles.ListObject,'Value',1)
3581    set(handles.ListObject,'String',{''})
3582    set(handles.ListObject_1,'Value',1)
3583    set(handles.ListObject_1,'String',{''})
3584    set(handles.ViewObject,'value',0)
3585    ViewObject_Callback(hObject, eventdata, handles)
3586    set(handles.ViewField,'value',0)
3587    ViewField_Callback(hObject, eventdata, handles)
3588    set(handles.edit_object,'Value',0)
3589    edit_object_Callback(hObject, eventdata, handles)
3590    UvData.Object={[]};
3591end
3592set(handles.uvmat,'UserData',UvData)
3593
3594%% refresh the current plot
3595if isempty(list_path{ichoice}) || nargin(transform_handle)<3
3596    set(handles.SubField,'Value',0)
3597    SubField_Callback(hObject, eventdata, handles)
3598else
3599    run0_Callback(hObject, eventdata, handles)
3600end
3601
3602%------------------------------------------------
3603%CALLBACKS FOR PLOTTING PARAMETERS
3604%-------------------------------------------------
3605%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3606% Plot coordinates
3607%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3608%------------------------------------------------------------------------
3609function num_MinX_Callback(hObject, eventdata, handles)
3610%------------------------------------------------------------------------
3611set(handles.CheckFixLimits,'Value',1) %suppress auto mode
3612set(handles.CheckFixLimits,'BackgroundColor',[1 1 0])
3613update_plot(handles);
3614
3615%------------------------------------------------------------------------
3616function num_MaxX_Callback(hObject, eventdata, handles)
3617%------------------------------------------------------------------------
3618set(handles.CheckFixLimits,'Value',1) %suppress auto mode
3619set(handles.CheckFixLimits,'BackgroundColor',[1 1 0])
3620update_plot(handles);
3621
3622%------------------------------------------------------------------------
3623function num_MinY_Callback(hObject, eventdata, handles)
3624%------------------------------------------
3625set(handles.CheckFixLimits,'Value',1) %suppress auto mode
3626set(handles.CheckFixLimits,'BackgroundColor',[1 1 0])
3627update_plot(handles);
3628
3629%------------------------------------------------------------------------
3630function num_MaxY_Callback(hObject, eventdata, handles)
3631%------------------------------------------------------------------------
3632set(handles.CheckFixLimits,'Value',1) %suppress auto mode
3633set(handles.CheckFixLimits,'BackgroundColor',[1 1 0])
3634update_plot(handles);
3635
3636%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3637% Scalar or image representation
3638%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3639%------------------------------------------------------------------------
3640function num_MinA_Callback(hObject, eventdata, handles)
3641%------------------------------------------
3642set(handles.CheckFixScalar,'Value',1) %suppress auto mode
3643set(handles.CheckFixScalar,'BackgroundColor',[1 1 0])
3644MinA=str2double(get(handles.num_MinA,'String'));
3645MaxA=str2double(get(handles.num_MaxA,'String'));
3646if MinA>MaxA% switch minA and maxA in case of error
3647    MinA_old=MinA;
3648    MinA=MaxA;
3649    MaxA=MinA_old;
3650    set(handles.num_MinA,'String',num2str(MinA,5));
3651    set(handles.num_MaxA,'String',num2str(MaxA,5));
3652end
3653update_plot(handles);
3654
3655%------------------------------------------------------------------------
3656function num_MaxA_Callback(hObject, eventdata, handles)
3657%------------------------------------------------------------------------
3658set(handles.CheckFixScalar,'Value',1) %suppress auto mode
3659set(handles.CheckFixScalar,'BackgroundColor',[1 1 0])
3660MinA=str2double(get(handles.num_MinA,'String'));
3661MaxA=str2double(get(handles.num_MaxA,'String'));
3662if MinA>MaxA% switch minA and maxA in case of error
3663        MinA_old=MinA;
3664    MinA=MaxA;
3665    MaxA=MinA_old;
3666    set(handles.num_MinA,'String',num2str(MinA,5));
3667    set(handles.num_MaxA,'String',num2str(MaxA,5));
3668end
3669update_plot(handles);
3670
3671%------------------------------------------------------------------------
3672function CheckFixScalar_Callback(hObject, eventdata, handles)
3673%------------------------------------------------------------------------
3674test=get(handles.CheckFixScalar,'Value');
3675if test
3676    set(handles.CheckFixScalar,'BackgroundColor',[1 1 0])
3677else
3678    set(handles.CheckFixScalar,'BackgroundColor',[0.7 0.7 0.7])
3679    update_plot(handles);
3680end
3681
3682%-------------------------------------------------------------------
3683function CheckBW_Callback(hObject, eventdata, handles)
3684%-------------------------------------------------------------------
3685update_plot(handles);
3686
3687%-------------------------------------------------------------------
3688function num_Opacity_Callback(hObject, eventdata, handles)
3689update_plot(handles);
3690%-------------------------------------------------------------------
3691
3692%-------------------------------------------------------------------
3693function ListContour_Callback(hObject, eventdata, handles)
3694%-------------------------------------------------------------------
3695val=get(handles.ListContour,'Value');
3696if val==2
3697    set(handles.interval_txt,'Visible','on')
3698    set(handles.num_IncrA,'Visible','on')
3699else
3700    set(handles.interval_txt,'Visible','off')
3701    set(handles.num_IncrA,'Visible','off')
3702end
3703update_plot(handles);
3704
3705%-------------------------------------------------------------------
3706function num_IncrA_Callback(hObject, eventdata, handles)
3707%-------------------------------------------------------------------
3708update_plot(handles);
3709
3710
3711%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3712% Vector representation
3713%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
3714%-------------------------------------------------------------------
3715function CheckHideWarning_Callback(hObject, eventdata, handles)
3716%-------------------------------------------------------------------
3717update_plot(handles);
3718
3719%-------------------------------------------------------------------
3720function CheckHideFalse_Callback(hObject, eventdata, handles)
3721%-------------------------------------------------------------------
3722update_plot(handles);
3723
3724%-------------------------------------------------------------------
3725function num_VecScale_Callback(hObject, eventdata, handles)
3726%-------------------------------------------------------------------
3727set(handles.CheckFixVectors,'Value',1);
3728set(handles.CheckFixVectors,'BackgroundColor',[1 1 0])
3729update_plot(handles);
3730
3731%-------------------------------------------------------------------
3732function CheckFixVectors_Callback(hObject, eventdata, handles)
3733%-------------------------------------------------------------------
3734test=get(handles.CheckFixVectors,'Value');
3735if test
3736    set(handles.CheckFixVectors,'BackgroundColor',[1 1 0])
3737else
3738    update_plot(handles);
3739    %set(handles.num_VecScale,'String',num2str(ScalOut.num_VecScale,3))
3740    set(handles.CheckFixVectors,'BackgroundColor',[0.7 0.7 0.7])
3741end
3742
3743%------------------------------------------------------------------------
3744% --- Executes on selection change in CheckDecimate4 (nb_vec/4).
3745function CheckDecimate4_Callback(hObject, eventdata, handles)
3746%------------------------------------------------------------------------
3747update_plot(handles);
3748
3749%------------------------------------------------------------------------
3750% --- Executes on selection change in ColorCode menu
3751function ColorCode_Callback(hObject, eventdata, handles)
3752%------------------------------------------------------------------------
3753% edit the choice for color code
3754update_color_code_boxes(handles);
3755update_plot(handles);
3756
3757%------------------------------------------------------------------------
3758function update_color_code_boxes(handles)
3759%------------------------------------------------------------------------
3760list_code=get(handles.ColorCode,'String');% list menu fields
3761colcode= list_code{get(handles.ColorCode,'Value')}; % selected field
3762enable_slider='off';%default
3763enable_bounds='off';%default
3764enable_scalar='off';%default
3765switch colcode
3766    case {'rgb','bgr'}
3767        enable_slider='on';
3768        enable_bounds='on';
3769        enable_scalar='on';
3770    case '64 colors'
3771        enable_bounds='on';
3772        enable_scalar='on';
3773end
3774set(handles.Slider1,'Visible',enable_slider)
3775set(handles.Slider2,'Visible', enable_slider)
3776set(handles.num_ColCode1,'Visible',enable_slider)
3777set(handles.num_ColCode2,'Visible',enable_slider)
3778set(handles.TitleColCode1,'Visible',enable_slider)
3779set(handles.TitleColCode2,'Visible',enable_slider)
3780set(handles.CheckFixVecColor,'Visible',enable_bounds)
3781set(handles.num_MinVec,'Visible',enable_bounds)
3782set(handles.num_MaxVec,'Visible',enable_bounds)
3783set(handles.ColorScalar,'Visible',enable_scalar)
3784set_vec_col_bar(handles)
3785
3786%------------------------------------------------------------------
3787% --- Executes on selection change in ColorScalar: choice of the color code.
3788function ColorScalar_Callback(hObject, eventdata, handles)
3789%------------------------------------------------------------------
3790% edit the choice for color code
3791list_scalar=get(handles.ColorScalar,'String');% list menu fields
3792col_scalar= list_scalar{get(handles.ColorScalar,'Value')}; % selected field
3793if isequal(col_scalar,'ima_cor')
3794    set(handles.CheckFixVecColor,'Value',1)%fixed scale by default
3795    ColorCode='rgb';
3796    set(handles.num_MinVec,'String','0')
3797    set(handles.num_MaxVec,'String','1')
3798    set(handles.num_ColCode1,'String','0.333')
3799    set(handles.num_ColCode2,'String','0.666')
3800else
3801    set(handles.CheckFixVecColor,'Value',0)%auto scale between min,max by default
3802    ColorCode='64 colors';
3803end
3804ColorCodeList=get(handles.ColorCode,'String');
3805ichoice=find(strcmp(ColorCode,ColorCodeList),1);
3806set(handles.ColorCode,'Value',ichoice)% set color code in the menu
3807
3808update_color_code_boxes(handles);
3809%replot the current graph
3810run0_Callback(hObject, eventdata, handles)
3811
3812%----------------------------------------------------------------
3813% -- Executes on slider movement to set the color code
3814%
3815function Slider1_Callback(hObject, eventdata, handles)
3816%------------------------------------------------------------------
3817slider1=get(handles.Slider1,'Value');
3818min_val=str2num(get(handles.num_MinVec,'String'));
3819max_val=str2num(get(handles.num_MaxVec,'String'));
3820col=min_val+(max_val-min_val)*slider1;
3821set(handles.num_ColCode1,'String',num2str(col))
3822if(get(handles.Slider2,'Value') < col)%move also the second slider at the same value if needed
3823    set(handles.Slider2,'Value',col)
3824    set(handles.num_ColCode2,'String',num2str(col))
3825end
3826set_vec_col_bar(handles)
3827update_plot(handles);
3828
3829%----------------------------------------------------------------
3830% Executes on slider movement to set the color code
3831%----------------------------------------------------------------
3832function Slider2_Callback(hObject, eventdata, handles)
3833slider2=get(handles.Slider2,'Value');
3834min_val=str2num(get(handles.num_MinVec,'String'));
3835max_val=str2num(get(handles.num_MaxVec,'String'));
3836col=min_val+(max_val-min_val)*slider2;
3837set(handles.num_ColCode2,'String',num2str(col))
3838if(get(handles.Slider1,'Value') > col)%move also the first slider at the same value if needed
3839    set(handles.Slider1,'Value',col)
3840    set(handles.num_ColCode1,'String',num2str(col))
3841end
3842set_vec_col_bar(handles)
3843update_plot(handles);
3844
3845%----------------------------------------------------------------
3846% --- Execute on return carriage on the edit box corresponding to slider 1
3847%----------------------------------------------------------------
3848function num_ColCode1_Callback(hObject, eventdata, handles)
3849set_vec_col_bar(handles)
3850update_plot(handles);
3851
3852%----------------------------------------------------------------
3853% --- Execute on return carriage on the edit box corresponding to slider 2
3854%----------------------------------------------------------------
3855function num_ColCode2_Callback(hObject, eventdata, handles)
3856set_vec_col_bar(handles)
3857update_plot(handles);
3858%------------------------------------------------------------------------
3859%-------------------------------------------------------
3860% --- Executes on button press in CheckFixVecColor.
3861%-------------------------------------------------------
3862function VecColBar_Callback(hObject, eventdata, handles)
3863set_vec_col_bar(handles)
3864
3865%------------------------------------------------------------------------
3866% --- Executes on button press in CheckFixVecColor.
3867function CheckFixVecColor_Callback(hObject, eventdata, handles)
3868%------------------------------------------------------------------------
3869if ~get(handles.CheckFixVecColor,'Value')
3870    update_plot(handles);
3871end
3872
3873%------------------------------------------------------------------------
3874% --- Executes on selection change in num_MaxVec.
3875function num_MinVec_Callback(hObject, eventdata, handles)
3876%------------------------------------------------------------------------
3877max_vec_Callback(hObject, eventdata, handles)
3878
3879%------------------------------------------------------------------------
3880% --- Executes on selection change in num_MaxVec.
3881function num_MaxVec_Callback(hObject, eventdata, handles)
3882%------------------------------------------------------------------------
3883set(handles.CheckFixVecColor,'Value',1)
3884CheckFixVecColor_Callback(hObject, eventdata, handles)
3885min_val=str2num(get(handles.num_MinVec,'String'));
3886max_val=str2num(get(handles.num_MaxVec,'String'));
3887slider1=get(handles.Slider1,'Value');
3888slider2=get(handles.Slider2,'Value');
3889colcode1=min_val+(max_val-min_val)*slider1;
3890colcode2=min_val+(max_val-min_val)*slider2;
3891set(handles.num_ColCode1,'String',num2str(colcode1))
3892set(handles.num_ColCode2,'String',num2str(colcode2))
3893update_plot(handles);
3894
3895%------------------------------------------------------------------------
3896% --- update the display of color code for vectors (on vecColBar)
3897function set_vec_col_bar(handles)
3898%------------------------------------------------------------------------
3899%get the image of the color display button 'VecColBar' in pixels
3900set(handles.VecColBar,'Unit','pixel');
3901pos_vert=get(handles.VecColBar,'Position');
3902set(handles.VecColBar,'Unit','Normalized');
3903width=ceil(pos_vert(3));
3904height=ceil(pos_vert(4));
3905
3906%get slider indications
3907list=get(handles.ColorCode,'String');
3908ichoice=get(handles.ColorCode,'Value');
3909colcode.ColorCode=list{ichoice};
3910colcode.MinVec=str2num(get(handles.num_MinVec,'String'));
3911colcode.MaxVec=str2num(get(handles.num_MaxVec,'String'));
3912test3color=strcmp(colcode.ColorCode,'rgb') || strcmp(colcode.ColorCode,'bgr');
3913if test3color
3914    colcode.ColCode1=str2num(get(handles.num_ColCode1,'String'));
3915    colcode.ColCode2=str2num(get(handles.num_ColCode2,'String'));
3916end
3917vec_C=colcode.MinVec+(colcode.MaxVec-colcode.MinVec)*(0.5:width-0.5)/width;%sample of vec_C values from min to max
3918[colorlist,col_vec]=set_col_vec(colcode,vec_C);
3919oneheight=ones(1,height);
3920A1=colorlist(col_vec,1)*oneheight;
3921A2=colorlist(col_vec,2)*oneheight;
3922A3=colorlist(col_vec,3)*oneheight;
3923A(:,:,1)=A1';
3924A(:,:,2)=A2';
3925A(:,:,3)=A3';
3926set(handles.VecColBar,'Cdata',A)
3927
3928%-------------------------------------------------------------------
3929function update_plot(handles)
3930%-------------------------------------------------------------------
3931UvData=get(handles.uvmat,'UserData');
3932AxeData=UvData.PlotAxes;% retrieve the current plotted data
3933PlotParam=read_GUI(handles.uvmat);
3934[tild,PlotParamOut]= plot_field(AxeData,handles.PlotAxes,PlotParam);
3935write_plot_param(handles,PlotParamOut); %update the auto plot parameters
3936
3937%------------------------------------------------------------------------
3938%------------------------------------------------------------------------
3939%   SELECTION AND EDITION OF PROJECTION OBJECTS
3940%------------------------------------------------------------------------
3941%------------------------------------------------------------------------
3942
3943% --- Executes on selection change in ListObject_1.
3944function ListObject_1_Callback(hObject, eventdata, handles)
3945list_str=get(handles.ListObject,'String');
3946UvData=get(handles.uvmat,'UserData');
3947ObjectData=UvData.Object{get(handles.ListObject_1,'Value')};
3948
3949%% update the projection plot on uvmat
3950ProjData= proj_field(UvData.Field,ObjectData);%project the current input field on object ObjectData
3951plot_field(ProjData,handles.PlotAxes,read_GUI(handles.uvmat));% plot the projected field;
3952%replot all the objects within the new projected field
3953for IndexObj=1:numel(list_str)
3954        hobject=UvData.Object{IndexObj}.DisplayHandle.uvmat;
3955        if isempty(hobject) || ~ishandle(hobject)
3956            hobject=handles.PlotAxes;
3957        end
3958        if isequal(IndexObj,get(handles.ListObject,'Value'))
3959            objectcolor='m'; %paint in magenta the currently selected object in ListObject
3960        else
3961            objectcolor='b';
3962        end
3963        UvData.Object{IndexObj}.DisplayHandle.uvmat=plot_object(UvData.Object{IndexObj},ObjectData,hobject,objectcolor);%draw the object in uvmat     
3964end
3965set(handles.uvmat,'UserData',UvData)
3966
3967%% display the object parameters if the GUI set_object is already opened
3968if ~get(handles.ViewObject,'Value')
3969    ZBounds=0; % default
3970    if isfield(UvData.Field,'ZMin') && isfield(UvData.Field,'ZMax')
3971        ZBounds(1)=UvData.Field.ZMin; %minimum for the Z slider
3972        ZBounds(2)=UvData.Field.ZMax;%maximum for the Z slider
3973    end
3974    ObjectData.Name=list_str{get(handles.ListObject_1,'Value')};
3975    set_object(ObjectData,[],ZBounds);
3976    set(handles.ViewObject,'Value',1)% show that the selected object in ListObject_1 is currently visualised
3977end
3978
3979%  desactivate the edit object mode
3980set(handles.edit_object,'Value',0)
3981set(handles.edit_object,'BackgroundColor',[0.7,0.7,0.7])
3982
3983%------------------------------------------------------------------------
3984% --- Executes on selection change in ListObject.
3985function ListObject_Callback(hObject, eventdata, handles)
3986%------------------------------------------------------------------------
3987list_str=get(handles.ListObject,'String');
3988IndexObj=get(handles.ListObject,'Value');%present object selection
3989
3990%% The object  is displayed in set_object if this GUI is already opened
3991UvData=get(handles.uvmat,'UserData');
3992ObjectData=UvData.Object{IndexObj};
3993hset_object=findobj(allchild(0),'tag','set_object');
3994if ~isempty(hset_object)
3995    ZBounds=0; % default
3996    if isfield(UvData.Field,'ZMin') && isfield(UvData.Field,'ZMax')
3997        ZBounds(1)=UvData.Field.ZMin; %minimum for the Z slider
3998        ZBounds(2)=UvData.Field.ZMax;%maximum for the Z slider
3999    end
4000    ObjectData.Name=list_str{IndexObj};
4001    set_object(ObjectData,[],ZBounds);
4002    set(handles.ViewField,'Value',1)% show that the selected object in ListObject is currently visualised
4003end
4004
4005%%  desactivate the edit object mode
4006set(handles.edit_object,'Value',0)
4007set(handles.edit_object,'BackgroundColor',[0.7,0.7,0.7])
4008
4009%% update the  plot on view_field if view_field is already openened
4010hview_field=findobj(allchild(0),'tag','view_field');
4011if isempty(hview_field)
4012    hhview_field.PlotAxes=[];
4013else
4014    Data=get(hview_field,'UserData');
4015    hhview_field=guidata(hview_field);
4016    ProjData= proj_field(UvData.Field,ObjectData);%project the current interface field on ObjectData
4017    [PlotType,PlotParam]=plot_field(ProjData,hhview_field.PlotAxes,read_GUI(hview_field));%read plotting parameters on the uvmat interfachhview_fiel
4018    write_plot_param(hhview_field,PlotParam); %update the display of plotting parameters for the current object
4019    haxes=findobj(hview_field,'tag','axes3');
4020    pos=get(hview_field,'Position'); 
4021    if strcmp(get(haxes,'Visible'),'off')%sempty(PlotParam.Coordinates)% case of no plot display (pure text table)
4022        h_TableDisplay=findobj(hview_field,'tag','TableDisplay');
4023        pos_table=get(h_TableDisplay,'Position');
4024        set(hview_field,'Position',[pos(1)+pos(3)-pos_table(3) pos(2)+pos(4)-pos_table(4) pos_table(3) pos_table(4)])
4025        drawnow% needed to change position before the next command
4026        set(hview_field,'UserData',Data);% restore the previously stored GUI position after GUI resizing
4027    else
4028        set(hview_field,'Position',Data.GUISize)% return to the previously stored GUI position and size
4029    end
4030end
4031
4032%% update the color of the graphic object representation: the selected object in magenta, others in blue
4033update_object_color(handles.PlotAxes,hhview_field.PlotAxes,UvData.Object{IndexObj}.DisplayHandle.uvmat)
4034
4035%------------------------------------------------------------------------
4036%--- update the color representation of objects (indicating the selected ones)
4037function update_object_color(axes_uvmat,axes_view_field,DisplayHandle)
4038%------------------------------------------------------------------------
4039if isempty(axes_view_field)% case with no view_field plot
4040hother=[findobj(axes_uvmat,'Tag','proj_object');findobj(axes_uvmat,'Tag','DeformPoint')];%find all the proj object and deform point representations
4041else
4042hother=[findobj(axes_uvmat,'Tag','proj_object') ;findobj(axes_view_field,'Tag','proj_object');... %find all the proj object representations
4043findobj(axes_uvmat,'Tag','DeformPoint'); findobj(axes_view_field,'Tag','DeformPoint')];%find all the deform point representations
4044end
4045for iobj=1:length(hother)
4046    if isequal(get(hother(iobj),'Type'),'rectangle')||isequal(get(hother(iobj),'Type'),'patch')
4047        set(hother(iobj),'EdgeColor','b')
4048        if isequal(get(hother(iobj),'FaceColor'),'m')
4049            set(hother(iobj),'FaceColor','b')
4050        end
4051    elseif isequal(get(hother(iobj),'Type'),'image')
4052        Acolor=get(hother(iobj),'CData');
4053        Acolor(:,:,1)=zeros(size(Acolor,1),size(Acolor,2));
4054        set(hother(iobj),'CData',Acolor);
4055    else
4056        set(hother(iobj),'Color','b')
4057    end
4058    set(hother(iobj),'Selected','off')
4059end
4060if ishandle(DisplayHandle)
4061    linetype=get(DisplayHandle,'Type');
4062    if isequal(linetype,'line')
4063        set(DisplayHandle,'Color','m'); %set the selected object to magenta color
4064    elseif isequal(linetype,'rectangle')
4065        set(DisplayHandle,'EdgeColor','m'); %set the selected object to magenta color
4066    elseif isequal(linetype,'patch')
4067        set(DisplayHandle,'FaceColor','m'); %set the selected object to magenta color
4068    end
4069    SubObjectData=get(DisplayHandle,'UserData');
4070    if isfield(SubObjectData,'SubObject') & ishandle(SubObjectData.SubObject)
4071        for iobj=1:length(SubObjectData.SubObject)
4072            hsub=SubObjectData.SubObject(iobj);
4073            if isequal(get(hsub,'Type'),'rectangle')
4074                set(hsub,'EdgeColor','m'); %set the selected object to magenta color
4075            elseif isequal(get(hsub,'Type'),'image')
4076                Acolor=get(hsub,'CData');
4077                Acolor(:,:,1)=Acolor(:,:,3);
4078                set(hsub,'CData',Acolor);
4079            else
4080                set(hsub,'Color','m')
4081            end
4082        end
4083    end
4084    if isfield(SubObjectData,'DeformPoint') & ishandle(SubObjectData.DeformPoint)
4085        set(SubObjectData.DeformPoint,'Color','m')
4086    end
4087end
4088
4089%-------------------------------------------------------------------
4090% --- Executes on selection change in edit_object.
4091function edit_object_Callback(hObject, eventdata, handles)
4092%-------------------------------------------------------------------
4093UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
4094hset_object=findobj(allchild(0),'Tag','set_object');
4095if get(handles.edit_object,'Value')
4096    set(handles.edit_object,'BackgroundColor',[1,1,0]) 
4097    %suppress the other options
4098    set(handles.CheckZoom,'Value',0)
4099    CheckZoom_Callback(hObject, eventdata, handles)
4100    hgeometry_calib=findobj(allchild(0),'tag','geometry_calib');
4101    if ishandle(hgeometry_calib)
4102        hhgeometry_calib=guidata(hgeometry_calib);
4103        set(hhgeometry_calib.edit_append,'Value',0)% desactivate mouse action in geometry_calib
4104        set(hhgeometry_calib.edit_append,'BackgroundColor',[0.7 0.7 0.7])
4105    end
4106    set(handles.ViewObject,'value',1)
4107    ViewObject_Callback(hObject, eventdata, handles)
4108else % desctivate object edit mode
4109    set(handles.edit_object,'BackgroundColor',[0.7,0.7,0.7]) 
4110    if ~isempty(hset_object)% open the
4111        hhset_object=guidata(hset_object);
4112        set(hhset_object.PLOT,'enable','off');
4113        set(get(hset_object,'children'),'enable','inactive')
4114    end
4115end
4116
4117
4118%------------------------------------------------------------------------
4119% --- Executes on button press in ViewObject.
4120function ViewObject_Callback(hObject, eventdata, handles)
4121%------------------------------------------------------------------------
4122check_view=get(handles.ViewObject,'Value');
4123
4124if check_view %activate set_object   
4125    IndexObj=get(handles.ListObject,'Value');
4126    list_object=get(handles.ListObject,'String');
4127    UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
4128    UvData.Object{IndexObj}.Name=list_object{IndexObj};
4129    if numel(UvData.Object)<IndexObj;% error in UvData
4130        msgbox_uvmat('ERROR','invalid object list')
4131        return
4132    end
4133    ZBounds=0; % default
4134    if isfield(UvData.Field,'ZMin') && isfield(UvData.Field,'ZMax')
4135        ZBounds(1)=UvData.Field.ZMin; %minimum for the Z slider
4136        ZBounds(2)=UvData.Field.ZMax;%maximum for the Z slider
4137    end
4138%     set(handles.ListObject_1,'Value',IndexObj);%restore ListObject selection after set_object deletion
4139    data=UvData.Object{IndexObj};
4140    if ~isfield(data,'Type')% default plane
4141        data.Type='plane';
4142    end
4143%     if isfield(UvData,'Field')
4144%         Field=UvData.Field;
4145%         if isfield(UvData.Field,'Mesh')&&~isempty(UvData.Field.Mesh)
4146%             data.RangeX=[UvData.Field.XMin UvData.Field.XMax];
4147%             if strcmp(data.Type,'line')||strcmp(data.Type,'polyline')
4148%                 data.RangeY=UvData.Field.Mesh;
4149%             else
4150%                 data.RangeY=[UvData.Field.YMin UvData.Field.YMax];
4151%             end
4152%             data.DX=UvData.Field.Mesh;
4153%             data.DY=UvData.Field.Mesh;
4154%         end
4155%         if isfield(Field,'NbDim')&& isequal(Field.NbDim,3)
4156%             data.Coord=[0 0 0]; %default
4157%         end
4158%         if isfield(Field,'CoordUnit')
4159%             data.CoordUnit=Field.CoordUnit;
4160%         end
4161%     end
4162    hset_object=set_object(data,[],ZBounds);
4163    hhset_object=guidata(hset_object);
4164    if get(handles.edit_object,'Value')% edit mode
4165        set(hhset_object.PLOT,'Enable','on')
4166        set(get(hset_object,'children'),'enable','on')
4167    else
4168        set(hhset_object.PLOT,'Enable','off')
4169        set(get(hset_object,'children'),'enable','inactive')% deactivate the GUI except SAVE
4170        set(hhset_object.SAVE,'Enable','on')
4171    end
4172else
4173    hset_object=findobj(allchild(0),'tag','set_object');
4174    if ~isempty(hset_object)
4175        delete(hset_object)% delete existing version of set_object
4176    end
4177end
4178 
4179
4180%------------------------------------------------------------------------
4181% --- Executes on button press in ViewField.
4182function ViewField_Callback(hObject, eventdata, handles)
4183%------------------------------------------------------------------------
4184check_view=get(handles.ViewField,'Value');
4185
4186if check_view
4187    IndexObj=get(handles.ListObject,'Value');
4188    UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
4189    if numel(UvData.Object)<IndexObj(end);% error in UvData
4190        msgbox_uvmat('ERROR','invalid object list')
4191        return
4192    end
4193    ZBounds=0; % default
4194    if isfield(UvData.Field,'ZMin') && isfield(UvData.Field,'ZMax')
4195        ZBounds(1)=UvData.Field.ZMin; %minimum for the Z slider
4196        ZBounds(2)=UvData.Field.ZMax;%maximum for the Z slider
4197    end
4198    set(handles.ListObject,'Value',IndexObj);%restore ListObject selection after set_object deletion
4199    if ~isfield(UvData.Object{IndexObj(1)},'Type')% default plane
4200        UvData.Object{IndexObj(1)}.Type='plane';
4201    end
4202    list_object=get(handles.ListObject,'String');
4203    UvData.Object{IndexObj(end)}.Name=list_object{IndexObj(end)};
4204   
4205    %% show the projection of the selected object on view_field
4206    ProjData= proj_field(UvData.Field,UvData.Object{IndexObj});%project the current field on ObjectData
4207    hview_field=findobj(allchild(0),'tag','view_field');
4208    if isempty(hview_field)
4209        hview_field=view_field;
4210    end
4211    hhview_field=guidata(hview_field);
4212    [PlotType,PlotParam]=plot_field(ProjData,hhview_field.PlotAxes,read_GUI(hview_field));%read plotting parameters on the GUI view_field);
4213    write_plot_param(hhview_field,PlotParam); %update the display of plotting parameters for the current object
4214    haxes=findobj(hview_field,'tag','axes3');
4215    pos=get(hview_field,'Position');
4216    if strcmp(get(haxes,'Visible'),'off')%sempty(PlotParam.Coordinates)% case of no plot display (pure text table)
4217        h_TableDisplay=findobj(hview_field,'tag','TableDisplay');
4218        pos_table=get(h_TableDisplay,'Position');
4219        set(hview_field,'Position',[pos(1)+pos(3)-pos_table(3) pos(2)+pos(4)-pos_table(4) pos_table(3) pos_table(4)])
4220    else
4221        Data=get(hview_field,'UserData');
4222        set(hview_field,'Position',Data.GUISize)% restore the size of view_field for plots
4223    end
4224else
4225    hview_field=findobj(allchild(0),'tag','view_field');
4226    if ~isempty(hview_field)
4227        delete(hview_field)% delete existing version of set_object
4228    end
4229end
4230
4231
4232%------------------------------------------------------------------------
4233% --- Executes on button press in delete_object.
4234function delete_object_Callback(hObject, eventdata, handles)
4235%------------------------------------------------------------------------
4236IndexObj=get(handles.ListObject,'Value');%projection object selected for view_field
4237IndexObj_1=get(handles.ListObject_1,'Value');%projection object selected for uvmat plot
4238if IndexObj>1 && ~isequal(IndexObj,IndexObj_1) % do not delete the object used for the uvmat plot
4239    delete_object(IndexObj)
4240end
4241
4242%------------------------------------------------------------------------
4243%------------------------------------------------------------------------
4244%  II - TOOLS FROM THE UPPER MENU BAR
4245%------------------------------------------------------------------------
4246%------------------------------------------------------------------------
4247
4248%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
4249% Export  Menu Callbacks
4250%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
4251%------------------------------------------------------------------------
4252% --- Executes on button press in Menu/Export/field in workspace.
4253function MenuExportField_Callback(hObject, eventdata, handles)
4254%------------------------------------------------------------------------
4255global Data_uvmat
4256Data_uvmat=get(handles.uvmat,'UserData');
4257evalin('base','global Data_uvmat')%make CurData global in the workspace
4258display('current field :')
4259evalin('base','Data_uvmat') %display CurData in the workspace
4260commandwindow; %brings the Matlab command window to the front
4261
4262%------------------------------------------------------------------------
4263% --- Executes on button press in Menu/Export/extract figure.
4264function MenuExportFigure_Callback(hObject, eventdata, handles)
4265%------------------------------------------------------------------------
4266% huvmat=get(handles.MenuExport,'parent');
4267hfig=figure;
4268copyobj(handles.PlotAxes,hfig);
4269map=colormap(handles.PlotAxes);
4270colormap(map);%transmit the current colormap to the zoom fig
4271colorbar
4272
4273% --------------------------------------------------------------------
4274function MenuExportAxis_Callback(hObject, eventdata, handles)
4275answer=msgbox_uvmat('CONFIRMATION','select a figure/axis on which the current uvmat plot will be exported')
4276if strcmp(answer,'Yes')
4277hchild=get(handles.PlotAxes,'children');
4278copyobj(hchild,gca);
4279end
4280
4281%------------------------------------------------------------------------
4282% --------------------------------------------------------------------
4283function MenuExportMovie_Callback(hObject, eventdata, handles)
4284% --------------------------------------------------------------------
4285set(handles.MenuExportMovie,'BusyAction','queue')% activate the button
4286huvmat=get(handles.run0,'parent');
4287UvData=get(huvmat,'UserData');
4288%[xx,xx,FileBase]=read_file_boxes(handles);
4289[RootPath,SubDir,RootFile,FileIndex,FileExt]=read_file_boxes(handles);
4290FileBase=fullfile(RootPath,RootFile);
4291 %read the current input file name
4292prompt = {'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)'};
4293dlg_title = 'select properties of the output avi movie';
4294num_lines= 1;
4295def     = {[FileBase '_out.avi'];'10';'1';'[0.03 0.05 0.95 0.92]';'10'};
4296answer = inputdlg(prompt,dlg_title,num_lines,def,'on');
4297aviname=answer{1};
4298fps=str2double(answer{2});
4299% check for existing file with output name aviname
4300if exist(aviname,'file')
4301    backup=aviname;
4302    testexist=2;
4303    while testexist==2
4304        backup=[backup '~'];
4305        testexist=exist(backup,'file');     
4306    end
4307    [success,message]=copyfile(aviname,backup);%make backup of the existing file
4308    if isequal(success,1)
4309        delete(aviname)%delete existing file
4310    else
4311        msgbox_uvmat('ERROR',message)
4312        return
4313    end
4314end
4315%create avi open
4316aviobj=avifile(aviname,'Compression','None','fps',fps);
4317
4318%display first view for tests
4319newfig=figure;
4320newaxes=copyobj(handles.PlotAxes,newfig);%new plotting axes in the new figure
4321set(newaxes,'Tag','movieaxes')
4322nbpix=[512 384]*str2double(answer{3});
4323set(gcf,'Position',[1 1 nbpix])% resolution XVGA
4324set(newaxes,'Position',eval(answer{4}));
4325map=colormap(handles.PlotAxes);
4326colormap(map);%transmit the current colormap to the zoom fig
4327msgbox_uvmat('INPUT_Y-N',{['adjust figure ' num2str(newfig) ' with its matlab edit menu '] ;...
4328        ['then press OK to get the avi movie as a copy of figure ' num2str(newfig) ' display']});
4329UvData.plotaxes=newaxes;% the axis in the new figure becomes the current main plotting axes
4330set(huvmat,'UserData',UvData);
4331increment=str2num(get(handles.num_IndexIncrement,'String')); %get the field increment d
4332set(handles.STOP,'Visible','on')
4333set(handles.speed,'Visible','on')
4334set(handles.speed_txt,'Visible','on')
4335set(handles.Movie,'BusyAction','queue')
4336
4337%imin=str2double(get(handles.i1,'String'));
4338imax=str2double(answer{5});
4339% if isfield(UvData,'Time')
4340htitle=get(newaxes,'Title');
4341xlim=get(newaxes,'XLim');
4342ylim=get(newaxes,'YLim');
4343set(htitle,'Position',[xlim(2)+0.07*(xlim(2)-xlim(1)) ylim(2)-0.05*(ylim(2)-ylim(1)) 0])
4344time_str=get(handles.abs_time,'String');
4345set(htitle,'String',['t=' time_str])
4346set(handles.speed,'Value',1)
4347for i=1:imax
4348    if get(handles.speed,'Value')~=0 && isequal(get(handles.MenuExportMovie,'BusyAction'),'queue') % enable STOP command
4349            runpm(hObject,eventdata,handles,increment)% run plus
4350            drawnow
4351            time_str=get(handles.abs_time,'String');
4352            if ishandle(htitle)
4353             set(htitle,'String',['t=' time_str])
4354            end
4355            mov=getframe(newfig);
4356            aviobj=addframe(aviobj,mov);
4357    end
4358end
4359aviobj=close(aviobj);
4360UvData=rmfield(UvData,'plotaxes');
4361%UvData.Object{1}.plotaxes=handles.PlotAxes;
4362set(huvmat,'UserData',UvData);
4363msgbox_uvmat('CONFIRMATION',{['movie ' aviname ' created '];['with ' num2str(imax) ' frames']})
4364
4365
4366%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
4367% Projection Objects Menu Callbacks
4368%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
4369
4370% -----------------------------------------------------------------------
4371function Menupoints_Callback(hObject, eventdata, handles)
4372%------------------------------------------------------------------------
4373data.Type='points';
4374data.ProjMode='projection';%default
4375data.ProjModeMenu={};% do not restrict ProjMode menus
4376create_object(data,handles)
4377
4378% -----------------------------------------------------------------------
4379function Menuline_Callback(hObject, eventdata, handles)
4380%------------------------------------------------------------------------
4381data.Type='line';
4382data.ProjMode='projection';%default
4383data.ProjModeMenu={};% do not restrict ProjMode menus
4384create_object(data,handles)
4385
4386%------------------------------------------------------------------------
4387function Menupolyline_Callback(hObject, eventdata, handles)
4388%------------------------------------------------------------------------
4389data.Type='polyline';
4390data.ProjMode='projection';%default
4391data.ProjModeMenu={};% do not restrict ProjMode menus
4392create_object(data,handles)
4393
4394%------------------------------------------------------------------------
4395function Menupolygon_Callback(hObject, eventdata, handles)
4396%------------------------------------------------------------------------
4397data.Type='polygon';
4398data.ProjMode='inside';%default
4399data.ProjModeMenu={};% do not restrict ProjMode menus
4400create_object(data,handles)
4401
4402%------------------------------------------------------------------------
4403function Menurectangle_Callback(hObject, eventdata, handles)
4404%------------------------------------------------------------------------
4405data.Type='rectangle';
4406data.ProjMode='inside';%default
4407data.ProjModeMenu={};% do not restrict ProjMode menus
4408create_object(data,handles)
4409
4410%------------------------------------------------------------------------
4411function Menuellipse_Callback(hObject, eventdata, handles)
4412%------------------------------------------------------------------------
4413data.Type='ellipse';
4414data.ProjMode='inside';%default
4415data.ProjModeMenu={};% do not restrict ProjMode menus
4416create_object(data,handles)
4417
4418%------------------------------------------------------------------------
4419function MenuMaskObject_Callback(hObject, eventdata, handles)
4420%------------------------------------------------------------------------
4421data.Type='polygon';
4422data.TypeMenu={'polygon'};
4423data.ProjMode='mask_inside';%default
4424data.ProjModeMenu={'mask_inside';'mask_outside'};
4425create_object(data,handles)
4426
4427%------------------------------------------------------------------------
4428function Menuplane_Callback(hObject, eventdata, handles)
4429%------------------------------------------------------------------------
4430data.Type='plane';
4431data.ProjMode='projection';%default
4432data.ProjModeMenu={};% do not restrict ProjMode menus
4433create_object(data,handles)
4434
4435%------------------------------------------------------------------------
4436function Menuvolume_Callback(hObject, eventdata, handles)
4437%------------------------------------------------------------------------
4438data.Type='volume';
4439data.ProjMode='interp';%default
4440data.ProjModeMenu={};
4441% set(handles.create,'Visible','on')
4442% set(handles.create,'Value',1)
4443% VOLUME_Callback(hObject,eventdata,handles)data.ProjModeMenu={};
4444create_object(data,handles)
4445
4446%------------------------------------------------------------------------
4447% --- generic function used for the creation of a projection object
4448function create_object(data,handles)
4449%------------------------------------------------------------------------
4450% desactivate geometric calibration if opened
4451hgeometry_calib=findobj(allchild(0),'tag','geometry_calib');
4452if ishandle(hgeometry_calib)
4453    hhgeometry_calib=guidata(hgeometry_calib);
4454    set(hhgeometry_calib.edit_append,'Value',0)% desactivate mouse action in geometry_calib
4455    set(hhgeometry_calib.edit_append,'BackgroundColor',[0.7 0.7 0.7])
4456end
4457set(handles.edit_object,'Value',0); %suppress the object edit mode
4458set(handles.edit_object,'BackgroundColor',[0.7,0.7,0.7]) 
4459ListObject=get(handles.ListObject,'String');
4460if isempty(ListObject)
4461    ListObject={''};
4462end
4463if ~strcmp(ListObject{end},'')
4464    ListObject=[ListObject;{''}]; %append a blank to the list (if nort already done) to indicate the creation of a new object
4465    set(handles.ListObject,'String',ListObject)
4466end
4467IndexObj=length(ListObject);
4468set(handles.ListObject,'Value',IndexObj)
4469UvData=get(handles.uvmat,'UserData');
4470UvData.Object{IndexObj}=[]; %create a new empty object
4471UvData.Object{IndexObj}.DisplayHandle.uvmat=handles.PlotAxes; % axes for plot_object
4472UvData.Object{IndexObj}.DisplayHandle.view_field=[]; %no plot handle before plot_field operation
4473data.Name=data.Type;% default name=type
4474data.Coord=[0 0]; %default
4475if isfield(UvData,'Field')
4476    Field=UvData.Field;
4477    if isfield(UvData.Field,'Mesh')&&~isempty(UvData.Field.Mesh)
4478        data.RangeX=[UvData.Field.XMin UvData.Field.XMax];
4479        if strcmp(data.Type,'line')||strcmp(data.Type,'polyline')||strcmp(data.Type,'points')
4480            data.RangeY=UvData.Field.Mesh;
4481        else
4482            data.RangeY=[UvData.Field.YMin UvData.Field.YMax];
4483        end
4484        data.DX=UvData.Field.Mesh;
4485        data.DY=UvData.Field.Mesh;
4486    end
4487    if isfield(Field,'NbDim')&& isequal(Field.NbDim,3)
4488         data.Coord=[0 0 0]; %default
4489    end
4490    if isfield(Field,'CoordUnit')
4491        data.CoordUnit=Field.CoordUnit;
4492    end
4493end
4494if ishandle(handles.UVMAT_title)
4495    delete(handles.UVMAT_title)%delete the initial display of uvmat if no field has been entered
4496end
4497hset_object=set_object(data,handles);% call the set_object interface
4498hhset_object=guidata(hset_object);
4499hchild=get(hset_object,'children');
4500set(hchild,'enable','on')
4501set(handles.uvmat,'UserData',UvData)
4502set(handles.CheckZoom,'Value',0) %desactivate the zoom for object creation by the mouse
4503CheckZoom_Callback(handles.uvmat, [], handles)
4504set(handles.delete_object,'Visible','on')
4505
4506%------------------------------------------------------------------------
4507function MenuBrowseObject_Callback(hObject, eventdata, handles)
4508%------------------------------------------------------------------------
4509%get the object file
4510[FileName, PathName, filterindex] = uigetfile( ...
4511       {'*.xml;*.mat', ' (*.xml,*.mat)';
4512       '*.xml',  '.xml files '; ...
4513        '*.mat',  '.mat matlab files '}, ...
4514        'Pick an xml Object file',get(handles.RootPath,'String'));
4515fileinput=[PathName FileName];%complete file name
4516sizf=size(fileinput);
4517if (~ischar(fileinput)||~isequal(sizf(1),1)),return;end
4518
4519%read the file
4520[data,heading]=xml2struct(fileinput);
4521if ~strcmp(heading,'ProjObject')
4522    msgbox_uvmat('WARNING','The xml file does not have the heading ProjObject for projection objects')
4523end
4524[tild,data.Name]=fileparts(FileName);% object name set as file name
4525ListObject=get(handles.ListObject,'String');
4526if ~strcmp(ListObject{end},'')
4527    ListObject=[ListObject;{''}]; %append a blank to the list (if not already done) to indicate the creation of a new object
4528    set(handles.ListObject,'String',ListObject)
4529end
4530IndexObj=length(ListObject);
4531
4532UvData=get(handles.uvmat,'UserData');
4533UvData.Object{IndexObj}=[]; %create a new empty object
4534UvData.Object{IndexObj}.DisplayHandle.uvmat=[]; %no plot handle before plot_field operation
4535UvData.Object{IndexObj}.DisplayHandle.view_field=[]; %no plot handle before plot_field operation
4536set(handles.uvmat,'UserData',UvData)
4537set(handles.ListObject,'Value',IndexObj)
4538hset_object=set_object(data);% call the set_object interface
4539set(get(hset_object,'children'),'enable','on')% enable edit action on elements on GUI set_object
4540set(handles.edit_object,'Value',0); %suppress the object edit mode
4541set(handles.edit_object,'BackgroundColor',[0.7,0.7,0.7]) 
4542set(handles.delete_object,'Visible','on')
4543
4544
4545%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
4546% MenuEdit Callbacks
4547%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
4548%------------------------------------------------------------------------
4549function MenuEditObject_Callback(hObject, eventdata, handles)
4550%------------------------------------------------------------------------
4551set(handles.edit_object,'Value',1)
4552edit_Callback(hObject, eventdata, handles)
4553
4554%------------------------------------------------------------------------
4555function MenuEditVectors_Callback(hObject, eventdata, handles)
4556%------------------------------------------------------------------------
4557set(handles.edit_vect,'Visible','on')
4558set(handles.edit_vect,'Value',1)
4559edit_vect_Callback(hObject, eventdata, handles)
4560
4561%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
4562% MenuTools Callbacks
4563%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
4564%------------------------------------------------------------------------
4565function MenuCalib_Callback(hObject, eventdata, handles)
4566%------------------------------------------------------------------------
4567
4568UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
4569
4570%suppress competing options
4571set(handles.CheckZoom,'Value',0)
4572set(handles.CheckZoom,'BackgroundColor',[0.7 0.7 0.7])
4573set(handles.ListObject,'Value',1)     
4574% initiate display of GUI geometry_calib
4575data=[]; %default
4576if isfield(UvData,'CoordType')
4577    data.CoordType=UvData.CoordType;
4578end
4579[RootPath,SubDir,RootFile,FileIndex,FileExt]=read_file_boxes(handles);
4580FileName=[fullfile(RootPath,SubDir,RootFile) FileIndex FileExt];
4581set(handles.view_xml,'Backgroundcolor',[1 1 0])%indicate the reading of the current xml file by geometry_calib
4582pos_uvmat=get(handles.uvmat,'Position');
4583pos_cal(1)=pos_uvmat(1)+UvData.OpenParam.PosGeometryCalib(1)*pos_uvmat(3);
4584pos_cal(2)=pos_uvmat(2)+UvData.OpenParam.PosGeometryCalib(2)*pos_uvmat(4);
4585pos_cal(3:4)=UvData.OpenParam.PosGeometryCalib(3:4).* pos_uvmat(3:4);
4586geometry_calib(FileName,pos_cal);% call the geometry_calib interface   
4587set(handles.view_xml,'Backgroundcolor',[1 1 1])%indicate the end of reading of the current xml file by geometry_calib
4588set(handles.MenuCalib,'checked','on')% indicate that MenuCalib is activated, test used by mouse action
4589
4590%------------------------------------------------------------------------
4591function MenuMask_Callback(hObject, eventdata, handles)
4592%------------------------------------------------------------------------
4593UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface
4594ListObj=UvData.Object;
4595select=zeros(1,numel(ListObj));
4596for iobj=1:numel(ListObj);
4597    if strcmp(ListObj{iobj}.ProjMode,'mask_inside')||strcmp(ListObj{iobj}.ProjMode,'mask_outside')
4598        select(iobj)=1;
4599    end
4600end
4601val=find(select);
4602if isempty(val)
4603    msgbox_uvmat('ERROR','polygons must be first created by Projection object/mask polygon in the menu bar');
4604    return
4605else
4606%     set(handles.ListObject,'Max',2);%allow multiple selection
4607    set(handles.ListObject,'Value',val);
4608    flag=1;
4609    npx=size(UvData.Field.A,2);
4610    npy=size(UvData.Field.A,1);
4611    xi=0.5:npx-0.5;
4612    yi=0.5:npy-0.5;
4613    [Xi,Yi]=meshgrid(xi,yi);
4614    if isfield(UvData,'Object')
4615        for iobj=1:length(UvData.Object)
4616            ObjectData=UvData.Object{iobj};
4617            if isfield(ObjectData,'ProjMode') &&(isequal(ObjectData.ProjMode,'mask_inside')||isequal(ObjectData.ProjMode,'mask_outside'));
4618                flagobj=1;
4619                testphys=0; %coordinates in pixels by default
4620                if isfield(ObjectData,'CoordUnit') && ~isequal(ObjectData.CoordUnit,'pixel')
4621                    if isfield(UvData,'XmlData')&& isfield(UvData.XmlData{1},'GeometryCalib')
4622                        Calib=UvData.XmlData{1}.GeometryCalib;
4623                        testphys=1;
4624                    end
4625                end
4626                if isfield(ObjectData,'Coord')&& isfield(ObjectData,'Type')
4627                    if isequal(ObjectData.Type,'polygon')
4628                        X=ObjectData.Coord(:,1);
4629                        Y=ObjectData.Coord(:,2);
4630                        if testphys
4631                            [X,Y]=px_XYZ(Calib,X,Y,0);% to generalise with 3D cases
4632                        end
4633                        flagobj=~inpolygon(Xi,Yi,X',Y');%=0 inside the polygon, 1 outside
4634                    elseif isequal(ObjectData.Type,'ellipse')
4635                        if testphys
4636                            %[X,Y]=px_XYZ(Calib,X,Y,0);% TODO:create a polygon boundary and transform to phys
4637                        end
4638                        RangeX=max(ObjectData.RangeX);
4639                        RangeY=max(ObjectData.RangeY);
4640                        X2Max=RangeX*RangeX;
4641                        Y2Max=RangeY*RangeY;
4642                        distX=(Xi-ObjectData.Coord(1,1));
4643                        distY=(Yi-ObjectData.Coord(1,2));
4644                        flagobj=(distX.*distX/X2Max+distY.*distY/Y2Max)>1;
4645                    elseif isequal(ObjectData.Type,'rectangle')
4646                        if testphys
4647                            %[X,Y]=px_XYZ(Calib,X,Y,0);% TODO:create a polygon boundary and transform to phys
4648                        end
4649                        distX=abs(Xi-ObjectData.Coord(1,1));
4650                        distY=abs(Yi-ObjectData.Coord(1,2));
4651                        flagobj=distX>max(ObjectData.RangeX) | distY>max(ObjectData.RangeY);
4652                    end
4653                    if isequal(ObjectData.ProjMode,'mask_outside')
4654                        flagobj=~flagobj;
4655                    end
4656                    flag=flag & flagobj;
4657                end
4658            end
4659        end
4660    end
4661    %mask name
4662    RootPath=get(handles.RootPath,'String');
4663    SubDir=get(handles.SubDir,'String');
4664    RootFile=get(handles.RootFile,'String');
4665    if ~isempty(RootFile)&&(isequal(RootFile(1),'/')|| isequal(RootFile(1),'\'))
4666        RootFile(1)=[];
4667    end
4668   % filebase=fullfile(RootPath,RootFile);
4669    list=get(handles.masklevel,'String');
4670    masknumber=num2str(length(list));
4671    maskindex=get(handles.masklevel,'Value');
4672   % mask_name=fullfile_uvmat(RootPath,'',[RootFile '_' masknumber 'mask'],'.png','_1',maskindex);
4673    mask_name=fullfile_uvmat(RootPath,[SubDir '.mask'],'mask','.png','_1',maskindex);
4674    imflag=uint8(255*(0.392+0.608*flag));% =100 for flag=0 (vectors not computed when 20<imflag<200)
4675    imflag=flipdim(imflag,1);
4676
4677    %display the mask
4678    hfigmask=figure;
4679    set(hfigmask,'Name','mask image')
4680    vec=linspace(0,1,256);%define a linear greyscale colormap
4681    map=[vec' vec' vec'];
4682    colormap(map)
4683    image(imflag);
4684    answer=msgbox_uvmat('INPUT_TXT','mask file name:', mask_name);
4685    if ~strcmp(answer,'Cancel')
4686        mask_dir=fileparts(answer);
4687        if ~exist(mask_dir,'dir')
4688            [xx,msg1]=mkdir(mask_dir);
4689            if ~strcmp(msg1,'')
4690                errormsg=['cannot create ' mask_dir ': ' msg1];%error message for directory creation
4691                return
4692            end
4693        end
4694        imwrite(imflag,answer,'BitDepth',8);
4695    end
4696    set(handles.ListObject,'Value',1)
4697end
4698
4699%------------------------------------------------------------------------
4700%-- open the GUI set_grid.fig to create grid
4701function MenuGrid_Callback(hObject, eventdata, handles)
4702%------------------------------------------------------------------------
4703%suppress the other options if grid is chosen
4704set(handles.edit_vect,'Value',0)
4705edit_vect_Callback(hObject, eventdata, handles)
4706set(handles.edit_object,'BackgroundColor',[0.7 0.7 0.7])
4707set(handles.ListObject,'Value',1)     
4708
4709%prepare display of the set_grid GUI
4710[RootPath,SubDir,RootFile,FileIndex,FileExt]=read_file_boxes(handles);
4711FileName=[fullfile(RootPath,SubDir,RootFile) FileIndex FileExt];
4712CoordList=get(handles.transform_fct,'String');
4713val=get(handles.transform_fct,'Value');
4714set_grid(FileName,CoordList{val});% call the set_object interface
4715
4716
4717%------------------------------------------------------------------------
4718function MenuRuler_Callback(hObject, eventdata, handles)
4719%------------------------------------------------------------------------
4720set(handles.CheckZoom,'Value',0)
4721CheckZoom_Callback(handles.uvmat, [], handles)
4722set(handles.MenuRuler,'checked','on')
4723UvData=get(handles.uvmat,'UserData');
4724UvData.MouseAction='ruler';
4725set(handles.uvmat,'UserData',UvData);
4726
4727%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
4728% MenuRun Callbacks
4729%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
4730
4731%------------------------------------------------------------------------
4732% open the GUI 'series'
4733function MenuSeries_Callback(hObject, eventdata, handles)
4734%------------------------------------------------------------------------
4735series; %first display of the GUI to fill waiting time
4736[RootPath,SubDir,RootFile,FileIndex,FileExt]=read_file_boxes(handles);
4737Param.FileName=[fullfile(RootPath,SubDir,RootFile) FileIndex FileExt];%first input file name
4738if isequal(get(handles.SubField,'Value'),1)
4739    [RootPath_1,SubDir_1,RootFile_1,FileIndex_1,FileExt_1]=read_file_boxes_1(handles);
4740    FileName_1=[fullfile(RootPath_1,SubDir_1,RootFile_1) FileIndex_1 FileExt_1];
4741    if ~isequal(FileName_1,Param.FileName)
4742        Param.FileName_1=FileName_1;%second input file name if relevant
4743    end
4744end
4745Param.NomType=get(handles.NomType,'String');
4746Param.NomType_1=get(handles.NomType_1,'String');
4747Param.CheckFixPair=get(handles.CheckFixPair,'Value');
4748UvData=get(handles.uvmat,'UserData');
4749if isfield(UvData,'XmlData')&& isfield(UvData.XmlData{1},'Time')
4750    Param.Time=UvData.XmlData{1}.Time;
4751end
4752if isequal(get(handles.scan_i,'Value'),1)
4753    Param.incr_i=str2num(get(handles.num_IndexIncrement,'String'));
4754elseif isequal(get(handles.scan_j,'Value'),1)
4755    Param.incr_j=str2num(get(handles.num_IndexIncrement,'String'));
4756end
4757
4758%% transfer fields and coordinate names
4759Param.list_fields=get(handles.FieldName,'String');% list menu fields
4760FieldName=Param.list_fields{get(handles.FieldName,'Value')};
4761ind_image=find(strcmp('image',Param.list_fields));
4762if ~isempty(ind_image) && numel(Param.list_fields)>1
4763    Param.list_fields(ind_image)=[]; %suppress  'image' option
4764end
4765Param.index_fields=find(strcmp(FieldName,Param.list_fields));% selected string index
4766Param.list_fields_1=get(handles.FieldName_1,'String');% list menu fields
4767if ischar(Param.list_fields_1),Param.list_fields_1={Param.list_fields_1};end
4768FieldName_1=Param.list_fields_1{get(handles.FieldName_1,'Value')};
4769ind_image=find(strcmp('image',Param.list_fields_1));
4770if ~isempty(ind_image) && numel(Param.list_fields_1)>1
4771    Param.list_fields_1(ind_image)=[]; %suppress  'image' option
4772end
4773Param.index_fields_1=find(strcmp(FieldName_1,Param.list_fields_1));% selected string index
4774Param.transform_str=get(handles.transform_fct,'String');
4775Param.transform_val=get(handles.transform_fct,'Value');
4776Param.Coord_x_str=get(handles.Coord_x,'String');
4777Param.Coord_x_val=get(handles.Coord_x,'Value');
4778Param.Coord_y_str=get(handles.Coord_y,'String');
4779Param.Coord_y_val=get(handles.Coord_y,'Value');
4780series(Param); %run the series interface
4781
4782%------------------------------------------------------------------------
4783% -- open the GUI civ.fig for PIV
4784function MenuPIV_Callback(hObject, eventdata, handles)
4785%------------------------------------------------------------------------
4786 [RootPath,SubDir,RootFile,FileIndex,FileExt]=read_file_boxes(handles);
4787 FileName=[fullfile(RootPath,SubDir,RootFile) FileIndex FileExt];
4788civ(FileName);% interface de civ(not in the uvmat file)
4789
4790% --------------------------------------------------------------------
4791function MenuHelp_Callback(hObject, eventdata, handles)
4792% --------------------------------------------------------------------
4793path_to_uvmat=which ('uvmat');% check the path of uvmat
4794pathelp=fileparts(path_to_uvmat);
4795helpfile=fullfile(pathelp,'uvmat_doc','uvmat_doc.html');
4796if isempty(dir(helpfile)), msgbox_uvmat('ERROR','Please put the help file uvmat_doc.html in the sub-directory /uvmat_doc of the UVMAT package')
4797else
4798    addpath (fullfile(pathelp,'uvmat_doc'))
4799    web(helpfile);
4800end
4801
4802
4803% --------------------------------------------------------------------
4804function MenuSetProject_Callback(hObject, eventdata, handles)
4805RootPath=get(handles.RootPath,'String');
4806ProjectDir = uigetdir(fileparts(fileparts(RootPath)), 'select the project source directory');
4807datatree_browser(ProjectDir)
4808
4809
4810% --------------------------------------------------------------------
4811function MenuBrowseProject_Callback(hObject, eventdata, handles)
4812RootPath=get(handles.RootPath,'String');
4813ProjectDir = uigetdir(fileparts(fileparts(RootPath)), 'select the project directory');
4814datatree_browser(ProjectDir)
4815
4816
4817% --- Executes on selection change in Coord_y.
4818function Coord_y_Callback(hObject, eventdata, handles)
4819
4820% --- Executes on selection change in Coord_x.
4821function Coord_x_Callback(hObject, eventdata, handles)
Note: See TracBrowser for help on using the repository browser.